Structural, microstructural and vibrational analyses of the monoclinic tungstate BiLuWO6

NASA Astrophysics Data System (ADS)

Ait Ahsaine, H.; Taoufyq, A.; Patout, L.; Ezahri, M.; Benlhachemi, A.; Bakiz, B.; Villain, S.; Guinneton, F.; Gavarri, J.-R.

2014-10-01

The bismuth lutetium tungstate phase BiLuWO6 has been prepared using a solid state route with stoichiometric mixtures of oxide precursors. The obtained polycrystalline phase has been characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), and Raman spectroscopy. In the first step, the crystal structure has been refined using Rietveld method: the crystal cell was resolved using monoclinic system (parameters a, b, c, β) with space group A2/m. SEM images showed the presence of large crystallites with a constant local nominal composition (BiLuW). TEM analyses showed that the actual local structure could be better represented by a superlattice (a, 2b, c, β) associated with space groups P2 or P2/m. The Raman spectroscopy showed the presence of vibrational bands similar to those observed in the compounds BiREWO6 with RE=Y, Gd, Nd. However, these vibrational bands were characterized by large full width at half maximum, probably resulting from the long range Bi/Lu disorder and local WO6 octahedron distortions in the structure.

Pyrvinium pamoate changes alternative splicing of the serotonin receptor 2C by influencing its RNA structure

PubMed Central

Shen, Manli; Bellaousov, Stanislav; Hiller, Michael; de La Grange, Pierre; Creamer, Trevor P.; Malina, Orit; Sperling, Ruth; Mathews, David H.; Stoilov, Peter; Stamm, Stefan

2013-01-01

The serotonin receptor 2C plays a central role in mood and appetite control. It undergoes pre-mRNA editing as well as alternative splicing. The RNA editing suggests that the pre-mRNA forms a stable secondary structure in vivo. To identify substances that promote alternative exons inclusion, we set up a high-throughput screen and identified pyrvinium pamoate as a drug-promoting exon inclusion without editing. Circular dichroism spectroscopy indicates that pyrvinium pamoate binds directly to the pre-mRNA and changes its structure. SHAPE (selective 2′-hydroxyl acylation analysed by primer extension) assays show that part of the regulated 5′-splice site forms intramolecular base pairs that are removed by this structural change, which likely allows splice site recognition and exon inclusion. Genome-wide analyses show that pyrvinium pamoate regulates >300 alternative exons that form secondary structures enriched in A–U base pairs. Our data demonstrate that alternative splicing of structured pre-mRNAs can be regulated by small molecules that directly bind to the RNA, which is reminiscent to an RNA riboswitch. PMID:23393189

Percolation analyses of observed and simulated galaxy clustering

NASA Astrophysics Data System (ADS)

Bhavsar, S. P.; Barrow, J. D.

1983-11-01

A percolation cluster analysis is performed on equivalent regions of the CFA redshift survey of galaxies and the 4000 body simulations of gravitational clustering made by Aarseth, Gott and Turner (1979). The observed and simulated percolation properties are compared and, unlike correlation and multiplicity function analyses, favour high density (Omega = 1) models with n = - 1 initial data. The present results show that the three-dimensional data are consistent with the degree of filamentary structure present in isothermal models of galaxy formation at the level of percolation analysis. It is also found that the percolation structure of the CFA data is a function of depth. Percolation structure does not appear to be a sensitive probe of intrinsic filamentary structure.

Structural and seismic analyses of waste facility reinforced concrete storage vaults

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

Wang, C.Y.

1995-07-01

Facility 317 of Argonne National Laboratory consists of several reinforced concrete waste storage vaults designed and constructed in the late 1940`s through the early 1960`s. In this paper, structural analyses of these concrete vaults subjected to various natural hazards are described, emphasizing the northwest shallow vault. The natural phenomenon hazards considered include both earthquakes and tornados. Because these vaults are deeply embedded in the soil, the SASSI (System Analysis of Soil-Structure Interaction) code was utilized for the seismic calculations. The ultimate strength method was used to analyze the reinforced concrete structures. In all studies, moment and shear strengths at criticalmore » locations of the storage vaults were evaluated. Results of the structural analyses show that almost all the waste storage vaults meet the code requirements according to ACI 349--85. These vaults also satisfy the performance goal such that confinement of hazardous materials is maintained and functioning of the facility is not interrupted.« less

A Study of the Synchrotron Laue Method for Quantitative Crystal Structure Analysis

NASA Astrophysics Data System (ADS)

Gomez de Anderez, Dora M.

1990-01-01

Quantitative crystal structure analyses have been carried out on small molecule crystals using synchrotron radiation and the Laue method. A variety of single crystal structure determinations and associated refinements are used and compared with the monochromatic analyses. The new molecular structure of 7-amino-5-bromo -4-methyl-2-oxo-1,2,3,4 -tetrahidro-1,6 -naphthyridine-8-carbonitrile (C_{10 }H_9ON_4 BrcdotH_2O) has been determined, first using monochromatic Mo K alpha radiation and a four-circle diffractometer, then using synchrotron Laue diffraction photography. The structure refinements showed an R-factor of 4.97 and 14.0% for the Mo Kalpha and Laue data respectively. The molecular structure of (S)-2-chloro-2-fluoro-N-((S)-1-phenylethyl) ethanamide, (C_{10}H _{11}ClFNO), has been determined using the same crystal throughout for X-ray monochromatic analyses (Mo Kalpha and Cu K alpha) followed by synchrotron Laue data collection. The Laue and monochromatic data compare favourably. The R -factors (on F) were 6.23, 6.45 and 8.19% for the Mo K alpha, Cu Kalpha and Laue data sets respectively. The molecular structure of 3-(5-hydroxy-3-methyl-1-phenylpyrazol-4-yl)-1,3-diphenyl -prop-2-en-1-one, (C_{25}H _{20}N_2 O_2) has been determined using the synchrotron Laue method. The results compare very well with Mo Kalpha monochromatic data. The R-factors (on F) were 4.60 and 5.29% for Mo Kalpha and Laue analyses respectively. The Laue method is assessed in locating the 20 hydrogen atoms in this structure. The structure analyses of the benzil compound ((C_6H_5 OcdotCO_2)) is carried out using the synchrotron Laue method firstly at room temperature and secondly at low temperature. The structure shows an R-factor (on F) of 13.06% and 6.85% for each data set respectively. The synchrotron Laue method was used to collect data for ergocalciferol (Vitamin D_2). The same crystal was also used to record oscillation data with the synchrotron radiation monochromatic beam. A new molecular structure of (Dinitrato-(N,N ^'-dimethylethylene-diamine)copper(II)) has been determined using Mo Kalpha radiation on a four circle diffractometer. The refinement resulted in an R-factor (on F) of 4.06%.

Behavior of auxetic structures under compression and impact forces

NASA Astrophysics Data System (ADS)

Yang, Chulho; Vora, Hitesh D.; Chang, Young

2018-02-01

In recent years, various auxetic material structures have been designed and fabricated for diverse applications that utilize normal materials that follow Hooke’s law but still show the properties of negative Poisson’s ratios (NPR). One potential application is body protection pads that are comfortable to wear and effective in protecting body parts by reducing impact force and preventing injuries in high-risk individuals such as elderly people, industrial workers, law enforcement and military personnel, and athletes. This paper reports an integrated theoretical, computational, and experimental investigation conducted for typical auxetic materials that exhibit NPR properties. Parametric 3D CAD models of auxetic structures such as re-entrant hexagonal cells and arrowheads were developed. Then, key structural characteristics of protection pads were evaluated through static analyses of FEA models. Finally, impact analyses were conducted through dynamic simulations of FEA models to validate the results obtained from the static analyses. Efforts were also made to relate the individual and/or combined effect of auxetic structures and materials to the overall stiffness and shock-absorption performance of the protection pads. An advanced additive manufacturing (3D printing) technique was used to build prototypes of the auxetic structures. Three different materials typically used for fused deposition modeling technology, namely polylactic acid (PLA) and thermoplastic polyurethane material (NinjaFlex® and SemiFlex®), were used for different stiffness and shock-absorption properties. The 3D printed prototypes were then tested and the results were compared to the computational predictions. The results showed that the auxetic material could be effective in reducing the shock forces. Each structure and material combination demonstrated unique structural properties such as stiffness, Poisson’s ratio, and efficiency in shock absorption. Auxetic structures showed better shock absorption performance than non-auxetic ones. The mechanism for ideal input force distribution or shunting could be suggested for designing protectors using various shapes, thicknesses, and materials of auxetic materials to reduce the risk of injury.

Landscape patterns in rainforest phylogenetic signal: isolated islands of refugia or structured continental distributions?

PubMed

Kooyman, Robert M; Rossetto, Maurizio; Sauquet, Hervé; Laffan, Shawn W

2013-01-01

Identify patterns of change in species distributions, diversity, concentrations of evolutionary history, and assembly of Australian rainforests. We used the distribution records of all known rainforest woody species in Australia across their full continental extent. These were analysed using measures of species richness, phylogenetic diversity (PD), phylogenetic endemism (PE) and phylogenetic structure (net relatedness index; NRI). Phylogenetic structure was assessed using both continental and regional species pools. To test the influence of growth-form, freestanding and climbing plants were analysed independently, and in combination. Species richness decreased along two generally orthogonal continental axes, corresponding with wet to seasonally dry and tropical to temperate habitats. The PE analyses identified four main areas of substantially restricted phylogenetic diversity, including parts of Cape York, Wet Tropics, Border Ranges, and Tasmania. The continental pool NRI results showed evenness (species less related than expected by chance) in groups of grid cells in coastally aligned areas of species rich tropical and sub-tropical rainforest, and in low diversity moist forest areas in the south-east of the Great Dividing Range and in Tasmania. Monsoon and drier vine forests, and moist forests inland from upland refugia showed phylogenetic clustering, reflecting lower diversity and more relatedness. Signals for evenness in Tasmania and clustering in northern monsoon forests weakened in analyses using regional species pools. For climbing plants, values for NRI by grid cell showed strong spatial structuring, with high diversity and PE concentrated in moist tropical and subtropical regions. Concentrations of rainforest evolutionary history (phylo-diversity) were patchily distributed within a continuum of species distributions. Contrasting with previous concepts of rainforest community distribution, our findings of continuous distributions and continental connectivity have significant implications for interpreting rainforest evolutionary history and current day ecological processes, and for managing rainforest diversity in changing circumstances.

Relationships between physical properties and sequence in silkworm silks

PubMed Central

Malay, Ali D.; Sato, Ryota; Yazawa, Kenjiro; Watanabe, Hiroe; Ifuku, Nao; Masunaga, Hiroyasu; Hikima, Takaaki; Guan, Juan; Mandal, Biman B.; Damrongsakkul, Siriporn; Numata, Keiji

2016-01-01

Silk has attracted widespread attention due to its superlative material properties and promising applications. However, the determinants behind the variations in material properties among different types of silk are not well understood. We analysed the physical properties of silk samples from a variety of silkmoth cocoons, including domesticated Bombyx mori varieties and several species from Saturniidae. Tensile deformation tests, thermal analyses, and investigations on crystalline structure and orientation of the fibres were performed. The results showed that saturniid silks produce more highly-defined structural transitions compared to B. mori, as seen in the yielding and strain hardening events during tensile deformation and in the changes observed during thermal analyses. These observations were analysed in terms of the constituent fibroin sequences, which in B. mori are predicted to produce heterogeneous structures, whereas the strictly modular repeats of the saturniid sequences are hypothesized to produce structures that respond in a concerted manner. Within saturniid fibroins, thermal stability was found to correlate with the abundance of poly-alanine residues, whereas differences in fibre extensibility can be related to varying ratios of GGX motifs versus bulky hydrophobic residues in the amorphous phase. PMID:27279149

Relationships between physical properties and sequence in silkworm silks

NASA Astrophysics Data System (ADS)

Malay, Ali D.; Sato, Ryota; Yazawa, Kenjiro; Watanabe, Hiroe; Ifuku, Nao; Masunaga, Hiroyasu; Hikima, Takaaki; Guan, Juan; Mandal, Biman B.; Damrongsakkul, Siriporn; Numata, Keiji

2016-06-01

Silk has attracted widespread attention due to its superlative material properties and promising applications. However, the determinants behind the variations in material properties among different types of silk are not well understood. We analysed the physical properties of silk samples from a variety of silkmoth cocoons, including domesticated Bombyx mori varieties and several species from Saturniidae. Tensile deformation tests, thermal analyses, and investigations on crystalline structure and orientation of the fibres were performed. The results showed that saturniid silks produce more highly-defined structural transitions compared to B. mori, as seen in the yielding and strain hardening events during tensile deformation and in the changes observed during thermal analyses. These observations were analysed in terms of the constituent fibroin sequences, which in B. mori are predicted to produce heterogeneous structures, whereas the strictly modular repeats of the saturniid sequences are hypothesized to produce structures that respond in a concerted manner. Within saturniid fibroins, thermal stability was found to correlate with the abundance of poly-alanine residues, whereas differences in fibre extensibility can be related to varying ratios of GGX motifs versus bulky hydrophobic residues in the amorphous phase.

Structural dynamics of shroudless, hollow fan blades with composite in-lays

NASA Technical Reports Server (NTRS)

Aiello, R. A.; Hirschbein, M. S.; Chamis, C. C.

1982-01-01

Structural and dynamic analyses are presented for a shroudless, hollow titanium fan blade proposed for future use in aircraft turbine engines. The blade was modeled and analyzed using the composite blade structural analysis computer program (COBSTRAN); an integrated program consisting of mesh generators, composite mechanics codes, NASTRAN, and pre- and post-processors. Vibration and impact analyses are presented. The vibration analysis was conducted with COBSTRAN. Results show the effect of the centrifugal force field on frequencies, twist, and blade camber. Bird impact analysis was performed with the multi-mode blade impact computer program. This program uses the geometric model and modal analysis from the COBSTRAN vibration analysis to determine the gross impact response of the fan blades to bird strikes. The structural performance of this blade is also compared to a blade of similar design but with composite in-lays on the outer surface. Results show that the composite in-lays can be selected (designed) to substantially modify the mechanical performance of the shroudless, hollow fan blade.

Combining network analysis with Cognitive Work Analysis: insights into social organisational and cooperation analysis.

PubMed

Houghton, Robert J; Baber, Chris; Stanton, Neville A; Jenkins, Daniel P; Revell, Kirsten

2015-01-01

Cognitive Work Analysis (CWA) allows complex, sociotechnical systems to be explored in terms of their potential configurations. However, CWA does not explicitly analyse the manner in which person-to-person communication is performed in these configurations. Consequently, the combination of CWA with Social Network Analysis provides a means by which CWA output can be analysed to consider communication structure. The approach is illustrated through a case study of a military planning team. The case study shows how actor-to-actor and actor-to-function mapping can be analysed, in terms of centrality, to produce metrics of system structure under different operating conditions. In this paper, a technique for building social network diagrams from CWA is demonstrated.The approach allows analysts to appreciate the potential impact of organisational structure on a command system.

Nouvelles techniques pratiques pour la modelisation du comportement dynamique des systèmes eau-structure

NASA Astrophysics Data System (ADS)

Miquel, Benjamin

The dynamic or seismic behavior of hydraulic structures is, as for conventional structures, essential to assure protection of human lives. These types of analyses also aim at limiting structural damage caused by an earthquake to prevent rupture or collapse of the structure. The particularity of these hydraulic structures is that not only the internal displacements are caused by the earthquake, but also by the hydrodynamic loads resulting from fluid-structure interaction. This thesis reviews the existing complex and simplified methods to perform such dynamic analysis for hydraulic structures. For the complex existing methods, attention is placed on the difficulties arising from their use. Particularly, interest is given in this work on the use of transmitting boundary conditions to simulate the semi infinity of reservoirs. A procedure has been developed to estimate the error that these boundary conditions can introduce in finite element dynamic analysis. Depending on their formulation and location, we showed that they can considerably affect the response of such fluid-structure systems. For practical engineering applications, simplified procedures are still needed to evaluate the dynamic behavior of structures in contact with water. A review of the existing simplified procedures showed that these methods are based on numerous simplifications that can affect the prediction of the dynamic behavior of such systems. One of the main objectives of this thesis has been to develop new simplified methods that are more accurate than those existing. First, a new spectral analysis method has been proposed. Expressions for the fundamental frequency of fluid-structure systems, key parameter of spectral analysis, have been developed. We show that this new technique can easily be implemented in a spreadsheet or program, and that its calculation time is near instantaneous. When compared to more complex analytical or numerical method, this new procedure yields excellent prediction of the dynamic behavior of fluid-structure systems. Spectral analyses ignore the transient and oscillatory nature of vibrations. When such dynamic analyses show that some areas of the studied structure undergo excessive stresses, time history analyses allow a better estimate of the extent of these zones as well as a time notion of these excessive stresses. Furthermore, the existing spectral analyses methods for fluid-structure systems account only for the static effect of higher modes. Thought this can generally be sufficient for dams, for flexible structures the dynamic effect of these modes should be accounted for. New methods have been developed for fluid-structure systems to account for these observations as well as the flexibility of foundations. A first method was developed to study structures in contact with one or two finite or infinite water domains. This new technique includes flexibility of structures and foundations as well as the dynamic effect of higher vibration modes and variations of the levels of the water domains. Extension of this method was performed to study beam structures in contact with fluids. These new developments have also allowed extending existing analytical formulations of the dynamic properties of a dry beam to a new formulation that includes effect of fluid-structure interaction. The method yields a very good estimate of the dynamic behavior of beam-fluid systems or beam like structures in contact with fluid. Finally, a Modified Accelerogram Method (MAM) has been developed to modify the design earthquake into a new accelerogram that directly accounts for the effect of fluid-structure interaction. This new accelerogram can therefore be applied directly to the dry structure (i.e. without water) in order to calculate the dynamic response of the fluid-structure system. This original technique can include numerous parameters that influence the dynamic response of such systems and allows to treat analytically the fluid-structure interaction while keeping the advantages of finite element modeling.

Dynamics of representational change: entropy, action, and cognition.

PubMed

Stephen, Damian G; Dixon, James A; Isenhower, Robert W

2009-12-01

Explaining how the cognitive system can create new structures has been a major challenge for cognitive science. Self-organization from the theory of nonlinear dynamics offers an account of this remarkable phenomenon. Two studies provide an initial test of the hypothesis that the emergence of new cognitive structure follows the same universal principles as emergence in other domains (e.g., fluids, lasers). In both studies, participants initially solved gear-system problems by manually tracing the force across a system of gears. Subsequently, they discovered that the gears form an alternating sequence, thereby demonstrating a new cognitive structure. In both studies, dynamical analyses of action during problem solving predicted the spontaneous emergence of the new cognitive structure. Study 1 showed that a peak in entropy, followed by negentropy, key indicators of self-organization, predicted discovery of alternation. Study 2 replicated these effects, and showed that increasing environmental entropy accelerated discovery, a classic prediction from dynamics. Additional analyses based on the relationship between phase transitions and power-law behavior provide converging evidence. The studies provide an initial demonstration of the emergence of cognitive structure through self-organization.

Computational analysis of conserved RNA secondary structure in transcriptomes and genomes.

PubMed

Eddy, Sean R

2014-01-01

Transcriptomics experiments and computational predictions both enable systematic discovery of new functional RNAs. However, many putative noncoding transcripts arise instead from artifacts and biological noise, and current computational prediction methods have high false positive rates. I discuss prospects for improving computational methods for analyzing and identifying functional RNAs, with a focus on detecting signatures of conserved RNA secondary structure. An interesting new front is the application of chemical and enzymatic experiments that probe RNA structure on a transcriptome-wide scale. I review several proposed approaches for incorporating structure probing data into the computational prediction of RNA secondary structure. Using probabilistic inference formalisms, I show how all these approaches can be unified in a well-principled framework, which in turn allows RNA probing data to be easily integrated into a wide range of analyses that depend on RNA secondary structure inference. Such analyses include homology search and genome-wide detection of new structural RNAs.

Prediction and Biochemical Demonstration of a Catabolic Pathway for the Osmoprotectant Proline Betaine

PubMed Central

Kumar, Ritesh; Zhao, Suwen; Vetting, Matthew W.; Wood, B. McKay; Sakai, Ayano; Cho, Kyuil; Solbiati, José; Almo, Steven C.; Sweedler, Jonathan V.; Jacobson, Matthew P.; Gerlt, John A.; Cronan, John E.

2014-01-01

ABSTRACT Through the use of genetic, enzymatic, metabolomic, and structural analyses, we have discovered the catabolic pathway for proline betaine, an osmoprotectant, in Paracoccus denitrificans and Rhodobacter sphaeroides. Genetic and enzymatic analyses showed that several of the key enzymes of the hydroxyproline betaine degradation pathway also function in proline betaine degradation. Metabolomic analyses detected each of the metabolic intermediates of the pathway. The proline betaine catabolic pathway was repressed by osmotic stress and cold stress, and a regulatory transcription factor was identified. We also report crystal structure complexes of the P. denitrificans HpbD hydroxyproline betaine epimerase/proline betaine racemase with l-proline betaine and cis-hydroxyproline betaine. PMID:24520058

Readability and writing style analysis of selected allied health professional journals.

PubMed

Hedl, J J; Glazer-Waldman, H R; Parker, H J; Hopkins, K M

1991-01-01

Using US Department of Defense text sampling procedures, nine allied health journals were analyzed for readability and selected writing style indices via Right Writer, a commercial software program. Two indices of readability were computed for each journal as were several indices of writing style. The computed readability ranged from 13.0 to 15.4, depending upon the journal in question. Two journals showed the highest levels of readability (15.4) compared to the other seven journals. The writing style analyses indicated generally normal ranges for the descriptive and jargon indices, but seven journals showed below recommended strength indices. Sentence structure analyses indicated a need to reduce sentence structure complexity. Implications for journal editors and authors are discussed.

Structural basis for amino acid export by DMT superfamily transporter YddG.

PubMed

Tsuchiya, Hirotoshi; Doki, Shintaro; Takemoto, Mizuki; Ikuta, Tatsuya; Higuchi, Takashi; Fukui, Keita; Usuda, Yoshihiro; Tabuchi, Eri; Nagatoishi, Satoru; Tsumoto, Kouhei; Nishizawa, Tomohiro; Ito, Koichi; Dohmae, Naoshi; Ishitani, Ryuichiro; Nureki, Osamu

2016-06-16

The drug/metabolite transporter (DMT) superfamily is a large group of membrane transporters ubiquitously found in eukaryotes, bacteria and archaea, and includes exporters for a remarkably wide range of substrates, such as toxic compounds and metabolites. YddG is a bacterial DMT protein that expels aromatic amino acids and exogenous toxic compounds, thereby contributing to cellular homeostasis. Here we present structural and functional analyses of YddG. Using liposome-based analyses, we show that Escherichia coli and Starkeya novella YddG export various amino acids. The crystal structure of S. novella YddG at 2.4 Å resolution reveals a new membrane transporter topology, with ten transmembrane segments in an outward-facing state. The overall structure is basket-shaped, with a large substrate-binding cavity at the centre of the molecule, and is composed of inverted structural repeats related by two-fold pseudo-symmetry. On the basis of this intramolecular symmetry, we propose a structural model for the inward-facing state and a mechanism of the conformational change for substrate transport, which we confirmed by biochemical analyses. These findings provide a structural basis for the mechanism of transport of DMT superfamily proteins.

Molecular Clustering Interrelationships and Carbohydrate Conformation in Hull and Seeds Among Barley Cultivars

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

N Liu; P Yu

2011-12-31

The objective of this study was to use molecular spectral analyses with the diffuse reflectance Fourier transform infrared spectroscopy (DRIFT) bioanlytical technique to study carbohydrate conformation features, molecular clustering and interrelationships in hull and seed among six barley cultivars (AC Metcalfe, CDC Dolly, McLeod, CDC Helgason, CDC Trey, CDC Cowboy), which had different degradation kinetics in rumen. The molecular structure spectral analyses in both hull and seed involved the fingerprint regions of ca. 1536-1484 cm{sup -1} (attributed mainly to aromatic lignin semicircle ring stretch), ca. 1293-1212 cm{sup -1} (attributed mainly to cellulosic compounds in the hull), ca. 1269-1217 cm{sup -1}more » (attributed mainly to cellulosic compound in the seeds), and ca. 1180-800 cm{sup -1} (attributed mainly to total CHO C-O stretching vibrations) together with an agglomerative hierarchical cluster (AHCA) and principal component spectral analyses (PCA). The results showed that the DRIFT technique plus AHCA and PCA molecular analyses were able to reveal carbohydrate conformation features and identify carbohydrate molecular structure differences in both hull and seeds among the barley varieties. The carbohydrate molecular spectral analyses at the region of ca. 1185-800 cm{sup -1} together with the AHCA and PCA were able to show that the barley seed inherent structures exhibited distinguishable differences among the barley varieties. CDC Helgason had differences from AC Metcalfe, MeLeod, CDC Cowboy and CDC Dolly in carbohydrate conformation in the seed. Clear molecular cluster classes could be distinguished and identified in AHCA analysis and the separate ellipses could be grouped in PCA analysis. But CDC Helgason had no distinguished differences from CDC Trey in carbohydrate conformation. These carbohydrate conformation/structure difference could partially explain why the varieties were different in digestive behaviors in animals. The molecular spectroscopy technique used in this study could also be used for other plant-based feed and food structure studies.« less

Evolution of strigolactone receptors by gradual neo-functionalization of KAI2 paralogues.

PubMed

Bythell-Douglas, Rohan; Rothfels, Carl J; Stevenson, Dennis W D; Graham, Sean W; Wong, Gane Ka-Shu; Nelson, David C; Bennett, Tom

2017-06-29

Strigolactones (SLs) are a class of plant hormones that control many aspects of plant growth. The SL signalling mechanism is homologous to that of karrikins (KARs), smoke-derived compounds that stimulate seed germination. In angiosperms, the SL receptor is an α/β-hydrolase known as DWARF14 (D14); its close homologue, KARRIKIN INSENSITIVE2 (KAI2), functions as a KAR receptor and likely recognizes an uncharacterized, endogenous signal ('KL'). Previous phylogenetic analyses have suggested that the KAI2 lineage is ancestral in land plants, and that canonical D14-type SL receptors only arose in seed plants; this is paradoxical, however, as non-vascular plants synthesize and respond to SLs. We have used a combination of phylogenetic and structural approaches to re-assess the evolution of the D14/KAI2 family in land plants. We analysed 339 members of the D14/KAI2 family from land plants and charophyte algae. Our phylogenetic analyses show that the divergence between the eu-KAI2 lineage and the DDK (D14/DLK2/KAI2) lineage that includes D14 occurred very early in land plant evolution. We show that eu-KAI2 proteins are highly conserved, and have unique features not found in DDK proteins. Conversely, we show that DDK proteins show considerable sequence and structural variation to each other, and lack clearly definable characteristics. We use homology modelling to show that the earliest members of the DDK lineage structurally resemble KAI2 and that SL receptors in non-seed plants likely do not have D14-like structure. We also show that certain groups of DDK proteins lack the otherwise conserved MORE AXILLARY GROWTH2 (MAX2) interface, and may thus function independently of MAX2, which we show is highly conserved throughout land plant evolution. Our results suggest that D14-like structure is not required for SL perception, and that SL perception has relatively relaxed structural requirements compared to KAI2-mediated signalling. We suggest that SL perception gradually evolved by neo-functionalization within the DDK lineage, and that the transition from KAI2-like to D14-like protein may have been driven by interactions with protein partners, rather than being required for SL perception per se.

Up, Down, and All Around: Scale-Dependent Spatial Variation in Rocky-Shore Communities of Fildes Peninsula, King George Island, Antarctica

PubMed Central

Valdivia, Nelson; Díaz, María J.; Holtheuer, Jorge; Garrido, Ignacio; Huovinen, Pirjo; Gómez, Iván

2014-01-01

Understanding the variation of biodiversity along environmental gradients and multiple spatial scales is relevant for theoretical and management purposes. Hereby, we analysed the spatial variability in diversity and structure of intertidal and subtidal macrobenthic Antarctic communities along vertical environmental stress gradients and across multiple horizontal spatial scales. Since biotic interactions and local topographic features are likely major factors for coastal assemblages, we tested the hypothesis that fine-scale processes influence the effects of the vertical environmental stress gradients on the macrobenthic diversity and structure. We used nested sampling designs in the intertidal and subtidal habitats, including horizontal spatial scales ranging from few centimetres to 1000s of metres along the rocky shore of Fildes Peninsula, King George Island. In both intertidal and subtidal habitats, univariate and multivariate analyses showed a marked vertical zonation in taxon richness and community structure. These patterns depended on the horizontal spatial scale of observation, as all analyses showed a significant interaction between height (or depth) and the finer spatial scale analysed. Variance and pseudo-variance components supported our prediction for taxon richness, community structure, and the abundance of dominant species such as the filamentous green alga Urospora penicilliformis (intertidal), the herbivore Nacella concinna (intertidal), the large kelp-like Himantothallus grandifolius (subtidal), and the red crustose red alga Lithothamnion spp. (subtidal). We suggest that in coastal ecosystems strongly governed by physical factors, fine-scale processes (e.g. biotic interactions and refugia availability) are still relevant for the structuring and maintenance of the local communities. The spatial patterns found in this study serve as a necessary benchmark to understand the dynamics and adaptation of natural assemblages in response to observed and predicted environmental changes in Antarctica. PMID:24956114

Europium(III)-doped A2Hf2O7 (A = Y, Gd, Lu) nanoparticles: Influence of annealing temperature, europium(III) concentration and host cation on the luminescent properties

NASA Astrophysics Data System (ADS)

Papan, Jelena; Jovanović, Dragana J.; Vuković, Katarina; Smits, Krisjanis; Đorđević, Vesna; Dramićanin, Miroslav

2016-11-01

The detailed analyses of structure and luminescence of europium(III)-doped A2Hf2O7 (A = Y, Gd, Lu) nanoparticles is presented. Samples were prepared by time and cost effective combustion method that utilize polyethylene glycol both as a chelating agent and as a fuel, with different europium(III) concentrations (from 1 to 12 at.%), annealed at temperatures ranging from 800 to 1400 °C, and with alternating A3+ cation in the A2Hf2O7 host. Then, structural variations between materials were analysed by X-ray diffraction and structural refinement, while the changes in the luminescence were assessed from the Judd-Ofelt analyses of emission spectra. Nanoparticles prepared at the lowest temperature (800 °C) had the smallest particle size of ∼6 nm and showed the highest quantum efficiency when doped with 1 and 2 at.% of europium(III). Radiative transition rate and quantum efficiency of emission showed Lu2Hf2O7 > Gd2Hf2O7 > Y2Hf2O7 trend.

Diagnostic Comparison of Meteorological Analyses during the 2002 Antarctic Winter

NASA Technical Reports Server (NTRS)

Manney, Gloria L.; Allen, Douglas R.; Kruger, Kirstin; Naujokat, Barbara; Santee, Michelle L.; Sabutis, Joseph L.; Pawson, Steven; Swinbank, Richard; Randall, Cora E.; Simmons, Adrian J.;

The Self-Description Inventory+, Part 1: Factor Structure and Convergent Validity Analyses

DTIC Science & Technology

2013-07-01

measures 12 scales of personality. The current report examines the possibility of replacing the EQ with a Five Factor Model ( FFM ) measure of...Checklist. Our results show that the SDI + has scales that are intercorrelated in a manner consistent with the FFM (Experiment 1), a factor structure...met the criteria showing it to be an FFM instrument, we will conduct concurrent validity research to determine if the SDI+ has greater predictive

Zn(II) coordination polymers with flexible V-shaped dicarboxylate ligand: Syntheses, helical structures and properties

NASA Astrophysics Data System (ADS)

Li, Lin; Liu, Chong-Bo; Yang, Gao-Shan; Xiong, Zhi-Qiang; Liu, Hong; Wen, Hui-Liang

2015-11-01

Hydrothermal reactions of 2,2‧-[hexafluoroisopropylidenebis(p-phenyleneoxy)]diacetic acid (H2L) and zinc ions in the presence of N-donor ancillary ligands afford four novel coordination polymers, namely, [Zn2(μ2-OH)(μ4-O)0.5(L)]·0.5H2O (1), [Zn(L)(2,2‧-bipy)(H2O)] (2), [Zn3(L)3(phen)2]·H2O (3) and [Zn2(L)2(4,4‧-bipy)] (4) (2,2‧-bipy=2,2‧-bipyridine; 4,4‧-bipy=4,4‧-bipyridine; phen=1,10-phenanthroline). Their structures have been determined by single-crystal X-ray diffraction analyses, elemental analyses, IR spectra, powder X-ray diffraction (PXRD), and thermogravimetric (TG) analyses. Complex 1 shows a 3-D clover framework consisting of [Zn4(μ4-O)(μ2-OH)2]4+ clusters, and exhibits a novel (3,8)-connected topological net with the Schläfli symbol of {3·4·5}2{34·44·52·66·710·82}, and contains double-stranded and two kinds of meso-helices. 2 displays a helical chain structure, which is further extended via hydrogen bonds into a 3-D supramolecular structure with meso-helix chains. 3 displays a 2-D {44·62} parallelogram structure, which is further extended via hydrogen bonds into a 3-D supramolecular structure with single-stranded helical chains. 4 shows a 2-D {44·62} square structure with left- and right-handed helical chains. Moreover, the luminescent properties of 1-4 have been investigated.

Spatio-temporal analysis of wildfire ignitions in the St. Johns River Water Management District, Florida

Treesearch

Marc G. Genton; David T. Butry; Marcia L. Gumpertz; Jeffrey P. Prestemon

2006-01-01

We analyse the spatio-temporal structure of wildfire ignitions in the St. Johns River Water Management District in north-eastern Florida. We show, using tools to analyse point patterns (e.g. the L-function), that wildfire events occur in clusters. Clustering of these events correlates with irregular distribution of fire ignitions, including lightning...

Genetic variations in the serotonergic system contribute to amygdala volume in humans.

PubMed

Li, Jin; Chen, Chunhui; Wu, Karen; Zhang, Mingxia; Zhu, Bi; Chen, Chuansheng; Moyzis, Robert K; Dong, Qi

2015-01-01

The amygdala plays a critical role in emotion processing and psychiatric disorders associated with emotion dysfunction. Accumulating evidence suggests that amygdala structure is modulated by serotonin-related genes. However, there is a gap between the small contributions of single loci (less than 1%) and the reported 63-65% heritability of amygdala structure. To understand the "missing heritability," we systematically explored the contribution of serotonin genes on amygdala structure at the gene set level. The present study of 417 healthy Chinese volunteers examined 129 representative polymorphisms in genes from multiple biological mechanisms in the regulation of serotonin neurotransmission. A system-level approach using multiple regression analyses identified that nine SNPs collectively accounted for approximately 8% of the variance in amygdala volume. Permutation analyses showed that the probability of obtaining these findings by chance was low (p = 0.043, permuted for 1000 times). Findings showed that serotonin genes contribute moderately to individual differences in amygdala volume in a healthy Chinese sample. These results indicate that the system-level approach can help us to understand the genetic basis of a complex trait such as amygdala structure.

Preparation of γ-LiV2O5 from polyoxovanadate cluster Li7[V15O36(CO3)] as a high-performance cathode material and its reaction mechanism revealed by operando XAFS

NASA Astrophysics Data System (ADS)

Wang, Heng; Isobe, Jin; Shimizu, Takeshi; Matsumura, Daiju; Ina, Toshiaki; Yoshikawa, Hirofumi

2017-08-01

γ-phase LiV2O5, which shows superior electrochemical performance as cathode material in Li-ion batteries, was prepared by annealing the polyoxovanadate cluster Li7 [V15O36(CO3)]. The reaction mechanism was studied using operando X-ray absorption fine structure (XAFS), powder X-ray diffraction (PXRD), and X-ray photoelectron spectroscopy (XPS) analyses. The X-ray absorption near edge structure (XANES) and XPS results reveal that γ-LiV2O5 undergoes two-electron redox reaction per V2O5 pyramid unit, resulting in a large reversible capacity of 260 Ah/kg. The extended X-ray absorption fine structure (EXAFS) and PXRD analyses also suggest that the V-V distance slightly increases, due to the reduction of V5+ to V4+ during Li ion intercalation as the material structure is maintained. As a result, γ-LixV2O5 shows highly reversible electrochemical reaction with x = 0.1-1.9.

Differential structural and resting state connectivity between insular subdivisions and other pain-related brain regions.

PubMed

Wiech, K; Jbabdi, S; Lin, C S; Andersson, J; Tracey, I

2014-10-01

Functional neuroimaging studies suggest that the anterior, mid, and posterior division of the insula subserve different functions in the perception of pain. The anterior insula (AI) has predominantly been associated with cognitive-affective aspects of pain, while the mid and posterior divisions have been implicated in sensory-discriminative processing. We examined whether this functional segregation is paralleled by differences in (1) structural and (2) resting state connectivity and (3) in correlations with pain-relevant psychological traits. Analyses were restricted to the 3 insular subdivisions and other pain-related brain regions. Both type of analyses revealed largely overlapping results. The AI division was predominantly connected to the ventrolateral prefrontal cortex (structural and resting state connectivity) and orbitofrontal cortex (structural connectivity). In contrast, the posterior insula showed strong connections to the primary somatosensory cortex (SI; structural connectivity) and secondary somatosensory cortex (SII; structural and resting state connectivity). The mid insula displayed a hybrid connectivity pattern with strong connections with the ventrolateral prefrontal cortex, SII (structural and resting state connectivity) and SI (structural connectivity). Moreover, resting state connectivity revealed strong connectivity of all 3 subdivisions with the thalamus. On the behavioural level, AI structural connectivity was related to the individual degree of pain vigilance and awareness that showed a positive correlation with AI-amygdala connectivity and a negative correlation with AI-rostral anterior cingulate cortex connectivity. In sum, our findings show a differential structural and resting state connectivity for the anterior, mid, and posterior insula with other pain-relevant brain regions, which might at least partly explain their different functional profiles in pain processing. Copyright © 2014 The Authors. Published by Elsevier B.V. All rights reserved.

Ultrasonic-assisted synthesis of nano lead(II) coordination polymer as precursors for preparation of lead(II) oxide nano-structures: Thermal, optical properties and XRD studies.

PubMed

Ghavidelaghdam, Elham; Shahverdizadeh, Gholam Hossein; Motameni Tabatabai, Javad; Mirtamizdoust, Babak

2018-04-01

Nano structure of a lead (II) coordination polymer [Pb 2 (C 2 Cl 3 O 2 ) 2 (NO 3 ) 2 (C l2 H 8 N 2 ) 2 ] n (1), has been synthesized by a sonochemical method in different concentrations. The nano particles were characterized by scanning electron microscopy (SEM) X-ray powder diffraction (XRD), FT-IR spectroscopy and elemental analyses. The thermal stability of nano structure is closely investigated via thermal gravimetric (TGA), and compared with crystalline structure. The compounds are then heated to 600 °C to produce PbO nano particles. The resulting PbO is characterized through XRD and SEM analyses. Concentration of initial reagents effects on size and morphology of nano-structured compound 1 have been studied and show that low concentrations of initial reagents decreased particles size and leaded to uniform nano particles morphology. The photoluminescence properties of the prepared compound, as crystalline and as nanoparticles, have been investigated. The result showed a good correlation between the size and emission wavelength. Copyright © 2017. Published by Elsevier B.V.

Molecular ecology meets remote sensing: environmental drivers to population structure of humpback dolphins in the Western Indian Ocean.

PubMed

Mendez, M; Subramaniam, A; Collins, T; Minton, G; Baldwin, R; Berggren, P; Särnblad, A; Amir, O A; Peddemors, V M; Karczmarski, L; Guissamulo, A; Rosenbaum, H C

2011-10-01

Genetic analyses of population structure can be placed in explicit environmental contexts if appropriate environmental data are available. Here, we use high-coverage and high-resolution oceanographic and genetic sequence data to assess population structure patterns and their potential environmental influences for humpback dolphins in the Western Indian Ocean. We analyzed mitochondrial DNA data from 94 dolphins from the coasts of South Africa, Mozambique, Tanzania and Oman, employing frequency-based and maximum-likelihood algorithms to assess population structure and migration patterns. The genetic data were combined with 13 years of remote sensing oceanographic data of variables known to influence cetacean dispersal and population structure. Our analyses show strong and highly significant genetic structure between all putative populations, except for those in South Africa and Mozambique. Interestingly, the oceanographic data display marked environmental heterogeneity between all sampling areas and a degree of overlap between South Africa and Mozambique. Our combined analyses therefore suggest the occurrence of genetically isolated populations of humpback dolphins in areas that are environmentally distinct. This study highlights the utility of molecular tools in combination with high-resolution and high-coverage environmental data to address questions not only pertaining to genetic population structure, but also to relevant ecological processes in marine species.

Molecular ecology meets remote sensing: environmental drivers to population structure of humpback dolphins in the Western Indian Ocean

PubMed Central

Mendez, M; Subramaniam, A; Collins, T; Minton, G; Baldwin, R; Berggren, P; Särnblad, A; Amir, O A; Peddemors, V M; Karczmarski, L; Guissamulo, A; Rosenbaum, H C

2011-01-01

Genetic analyses of population structure can be placed in explicit environmental contexts if appropriate environmental data are available. Here, we use high-coverage and high-resolution oceanographic and genetic sequence data to assess population structure patterns and their potential environmental influences for humpback dolphins in the Western Indian Ocean. We analyzed mitochondrial DNA data from 94 dolphins from the coasts of South Africa, Mozambique, Tanzania and Oman, employing frequency-based and maximum-likelihood algorithms to assess population structure and migration patterns. The genetic data were combined with 13 years of remote sensing oceanographic data of variables known to influence cetacean dispersal and population structure. Our analyses show strong and highly significant genetic structure between all putative populations, except for those in South Africa and Mozambique. Interestingly, the oceanographic data display marked environmental heterogeneity between all sampling areas and a degree of overlap between South Africa and Mozambique. Our combined analyses therefore suggest the occurrence of genetically isolated populations of humpback dolphins in areas that are environmentally distinct. This study highlights the utility of molecular tools in combination with high-resolution and high-coverage environmental data to address questions not only pertaining to genetic population structure, but also to relevant ecological processes in marine species. PMID:21427750

Landscape Patterns in Rainforest Phylogenetic Signal: Isolated Islands of Refugia or Structured Continental Distributions?

PubMed Central

Kooyman, Robert M.; Rossetto, Maurizio; Sauquet, Hervé; Laffan, Shawn W.

2013-01-01

Objectives Identify patterns of change in species distributions, diversity, concentrations of evolutionary history, and assembly of Australian rainforests. Methods We used the distribution records of all known rainforest woody species in Australia across their full continental extent. These were analysed using measures of species richness, phylogenetic diversity (PD), phylogenetic endemism (PE) and phylogenetic structure (net relatedness index; NRI). Phylogenetic structure was assessed using both continental and regional species pools. To test the influence of growth-form, freestanding and climbing plants were analysed independently, and in combination. Results Species richness decreased along two generally orthogonal continental axes, corresponding with wet to seasonally dry and tropical to temperate habitats. The PE analyses identified four main areas of substantially restricted phylogenetic diversity, including parts of Cape York, Wet Tropics, Border Ranges, and Tasmania. The continental pool NRI results showed evenness (species less related than expected by chance) in groups of grid cells in coastally aligned areas of species rich tropical and sub-tropical rainforest, and in low diversity moist forest areas in the south-east of the Great Dividing Range and in Tasmania. Monsoon and drier vine forests, and moist forests inland from upland refugia showed phylogenetic clustering, reflecting lower diversity and more relatedness. Signals for evenness in Tasmania and clustering in northern monsoon forests weakened in analyses using regional species pools. For climbing plants, values for NRI by grid cell showed strong spatial structuring, with high diversity and PE concentrated in moist tropical and subtropical regions. Conclusions/Significance Concentrations of rainforest evolutionary history (phylo-diversity) were patchily distributed within a continuum of species distributions. Contrasting with previous concepts of rainforest community distribution, our findings of continuous distributions and continental connectivity have significant implications for interpreting rainforest evolutionary history and current day ecological processes, and for managing rainforest diversity in changing circumstances. PMID:24312493

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

Rodriguez, Mario E.

An area in earthquake risk reduction that needs an urgent examination is the selection of earthquake records for nonlinear dynamic analysis of structures. An often-mentioned shortcoming from results of nonlinear dynamic analyses of structures is that these results are limited to the type of records that these analyses use as input data. This paper proposes a procedure for selecting earthquake records for nonlinear dynamic analysis of structures. This procedure uses a seismic damage index evaluated using the hysteretic energy dissipated by a Single Degree of Freedom System (SDOF) representing a multi-degree-of freedom structure responding to an earthquake record, and themore » plastic work capacity of the system at collapse. The type of structural system is considered using simple parameters. The proposed method is based on the evaluation of the damage index for a suite of earthquake records and a selected type of structural system. A set of 10 strong ground motion records is analyzed to show an application of the proposed procedure for selecting earthquake records for structural design.« less

New metal-organic complexes based on bis(tetrazole) ligands: Synthesis, structures and properties

NASA Astrophysics Data System (ADS)

Du, Ceng-Ceng; Fan, Jian-Zhong; Wang, Xin-Fang; Zhou, Sheng-Bin; Wang, Duo-Zhi

2017-04-01

In this paper, a series of new complexes, [Zn2(HL1)2(H2O)4]·H2O (1), [Co2(HL1)2]·TEA (2), [Co3(HL1)2(H2L1)2(H2O)4]n (3), [Cu(HL1)(H2O)2]n (4), {[Cu5(HL2)2(OH)4(ClO4)2]·4H2O}n (5) and [Cu2(L3)]n (6) were successfully prepared by utilizing three bis(tetrazole) ligands [bis-(1H-tetrazol-5-ylmethyl)-amine (H3L1), bis-(1H-tetrazol-5-ylethyl)-amine (H3L2) and 1,5-bis(5-tetrazolo)-3-thiapentane (H2L3)], all of which have been characterized by elemental analyses, FT-IR spectroscopy, powder X-ray diffraction (PXRD), thermogravimetric analyses as well as single-crystal X-ray diffraction analyses showing different dimensionalities (0D, 1D and 3D). Complexes 1 and 2 are 0D structures, 1 shows a dinuclear structure, 2 displays two crystallographically different mononuclear structures, 1 and 2 are further assembled to form 3D supramolecular framework and 2D supramolecular network by hydrogen-bonding interactions, respectively. Complexes 3, 4 and 5 are 1D structures, 3 features a mononuclear unit and a 1D chain, which are arranged into 3D supramolecular architecture by hydrogen-bonding interactions, 4 presents a zigzag chain, 5 shows an infinite chain structure constructed from pentanuclear Cu(II) subunits and ClO4- anions. Complex 6 exhibits a 3D coordination framework based on cyclic [Cu4(L3)2] dimmer subunits as nodes possessing an 8-connected network topology with the point symbol {424·64}. Further, semiconductor behaviors, the solid-state luminescent properties of the complexes 1-3 and 6 were measured and studied seriously at room temperature.

Subsurface structure identification uses derivative analyses of the magnetic data in Candi Umbul-Telomoyo geothermal prospect area

NASA Astrophysics Data System (ADS)

Septyasari, U.; Niasari, S. W.; Maghfira, P. D.

2018-04-01

Telomoyo geothermal prospect area is located in Central Java, Indonesia. One of the manifestations around Telomoyo is a warm spring, called Candi Umbul. The hydrothermal fluids from the manifestation could be from the subsurface flowing up through geological structures. The previous research about 2D magnetic modeling in Candi Umbul showed that there was a normal fault with strike/dip N60°E/45° respectively. This research aims to know the distance boundary and the kind of the geological structure in the study area. We also compared the geological structure direction based on the geologic map and the derivative maps. We used derivative analyses of the magnetic data, i.e. First Horizontal Derivative (FHD) which is the rate of change of the horizontal gradient in the horizontal direction. FHD indicates the boundaries of the geological structure. We also used Second Vertical Derivative (SVD) which is the rate of change of the vertical gradient in the vertical direction. SVD can reveal normal fault or thrust fault. The FHD and SVD maps show that the geological structure boundary has the same direction with the north west-south east geological structure. The geological structure boundary is in 486 m of the local distance. Our result confirms that there is a normal fault in the study area.

Higher and Lower Order Factor Analyses of the Temperament in Middle Childhood Questionnaire.

PubMed

Kotelnikova, Yuliya; Olino, Thomas M; Klein, Daniel N; Mackrell, Sarah V M; Hayden, Elizabeth P

2017-12-01

The Temperament in Middle Childhood Questionnaire (TMCQ) is a widely used parent-report measure of temperament. However, neither its lower nor higher order structures has been tested via a bottom-up, empirically based approach. We conducted higher and lower order exploratory factor analyses (EFAs) of the TMCQ in a large ( N = 654) sample of 9-year-olds. Item-level EFAs identified 92 items as suitable (i.e., with loadings ≥.40) for constructing lower order factors, only half of which resembled a TMCQ scale posited by the measure's authors. Higher order EFAs of the lower order factors showed that a three-factor structure (Impulsivity/Negative Affectivity, Negative Affectivity, and Openness/Assertiveness) was the only admissible solution. Overall, many TMCQ items did not load well onto a lower order factor. In addition, only three factors, which did not show a clear resemblance to Rothbart's four-factor model of temperament in middle childhood, were needed to account for the higher order structure of the TMCQ.

An analysis of the AVE-SESAME I period using statistical structure and correlation functions. [Atmospheric Variability Experiment-Severe Environmental Storm and Mesoscale Experiment

NASA Technical Reports Server (NTRS)

Fuelberg, H. E.; Meyer, P. J.

1984-01-01

Structure and correlation functions are used to describe atmospheric variability during the 10-11 April day of AVE-SESAME 1979 that coincided with the Red River Valley tornado outbreak. The special mesoscale rawinsonde data are employed in calculations involving temperature, geopotential height, horizontal wind speed and mixing ratio. Functional analyses are performed in both the lower and upper troposphere for the composite 24 h experiment period and at individual 3 h observation times. Results show that mesoscale features are prominent during the composite period. Fields of mixing ratio and horizontal wind speed exhibit the greatest amounts of small-scale variance, whereas temperature and geopotential height contain the least. Results for the nine individual times show that small-scale variance is greatest during the convective outbreak. The functions also are used to estimate random errors in the rawinsonde data. Finally, sensitivity analyses are presented to quantify confidence limits of the structure functions.

Higher- and Lower-Order Factor Analyses of the Temperament in Middle Childhood Questionnaire

PubMed Central

Kotelnikova, Yuliya; Olino, Thomas M.; Klein, Daniel N.; Mackrell, Sarah V.M.; Hayden, Elizabeth P.

2017-01-01

The Temperament in Middle Childhood Questionnaire (TMCQ; Simonds & Rothbart, 2004) is a widely used parent-report measure of temperament. However, neither its lower- nor higher-order structures have been tested via a bottom-up, empirically based approach. We conducted higher- and lower-order exploratory factor analyses (EFAs) of the TMCQ in a large (N = 654) sample of 9-year-olds. Item-level EFAs identified 92 items as suitable (i.e., with loadings ≥.40) for constructing lower-order factors, only half of which resembled a TMCQ scale posited by the measure’s authors. Higher-order EFAs of the lower-order factors showed that a three-factor structure (Impulsivity/Negative Affectivity, Negative Affectivity, and Openness/Assertiveness) was the only admissible solution. Overall, many TMCQ items did not load well onto a lower-order factor. In addition, only three factors, which did not show a clear resemblance to Rothbart’s four-factor model of temperament in middle childhood, were needed to account for the higher-order structure of the TMCQ. PMID:27002124

Comparing efficacy of different taxonomic resolutions and surrogates in detecting changes in soft bottom assemblages due to coastal defence structures.

PubMed

Bertasi, Fabio; Colangelo, Marina Antonia; Colosio, Francesco; Gregorio, Gianni; Abbiati, Marco; Ceccherelli, Victor Ugo

2009-05-01

Sandy shores on the West coast of the North Adriatic Sea are extensively protected by different types of defence structures to prevent coastal erosion. Coastal defence schemes modify the hydrodynamic regime, the sediment structure and composition thus affecting the benthic assemblages. This study examines the effectiveness in detecting changes in soft bottom assemblages caused by coastal defence structures by using different levels of taxonomic resolution, polychaetes and/or bivalves as surrogates and different data transformations. A synoptic analyses of three datasets of subtidal benthic macrofauna used in studies aimed at assessing the impact of breakwaters along the North Adriatic coast has been done. Analyses of similarities and correlations between distance matrices were done using matrices with different levels of taxonomic resolution, and with polychaetes or bivalves data alone. Lentidium mediterraneum was the most abundant species in all datasets. Its abundance was not consistently related to the presence of defence structures. Moreover, distribution patterns of L. mediterraneum were masking the structure of the whole macrofaunal assemblages. Removal of L. mediterraneum from the datasets allowed the detection of changes in benthic assemblages due to coastal defences. Analyses on different levels of taxonomic resolution showed that the level of family maintained sufficient information to detect the impacts of coastal defence structures on benthic assemblages. Moreover, the outcomes depended on the transformation used. Patterns of distribution of bivalves, used as surrogates, showed low correlations with the patterns of the total macrofaunal species assemblages. Patterns of polychaetes, if identified to the species or genus level showed higher correlations with the whole dataset. However, the identification of polychaetes to species and genus level is as costly as the identification of all macrobenthic taxa at family level. This study provided additional evidences that taxonomic sufficiency is a useful tool in environmental monitoring, also in investigations on the impacts of coastal defence structures on subtidal macrofauna. The use of coarser taxonomic level, being time-efficient, would allow improving sampling designs of monitoring programs by increasing replication in space and time and by allowing long term monitoring studies.

Effects of Sample Selection Bias on the Accuracy of Population Structure and Ancestry Inference

PubMed Central

Shringarpure, Suyash; Xing, Eric P.

2014-01-01

Population stratification is an important task in genetic analyses. It provides information about the ancestry of individuals and can be an important confounder in genome-wide association studies. Public genotyping projects have made a large number of datasets available for study. However, practical constraints dictate that of a geographical/ethnic population, only a small number of individuals are genotyped. The resulting data are a sample from the entire population. If the distribution of sample sizes is not representative of the populations being sampled, the accuracy of population stratification analyses of the data could be affected. We attempt to understand the effect of biased sampling on the accuracy of population structure analysis and individual ancestry recovery. We examined two commonly used methods for analyses of such datasets, ADMIXTURE and EIGENSOFT, and found that the accuracy of recovery of population structure is affected to a large extent by the sample used for analysis and how representative it is of the underlying populations. Using simulated data and real genotype data from cattle, we show that sample selection bias can affect the results of population structure analyses. We develop a mathematical framework for sample selection bias in models for population structure and also proposed a correction for sample selection bias using auxiliary information about the sample. We demonstrate that such a correction is effective in practice using simulated and real data. PMID:24637351

Discriminative analysis of schizophrenia using support vector machine and recursive feature elimination on structural MRI images.

PubMed

Lu, Xiaobing; Yang, Yongzhe; Wu, Fengchun; Gao, Minjian; Xu, Yong; Zhang, Yue; Yao, Yongcheng; Du, Xin; Li, Chengwei; Wu, Lei; Zhong, Xiaomei; Zhou, Yanling; Fan, Ni; Zheng, Yingjun; Xiong, Dongsheng; Peng, Hongjun; Escudero, Javier; Huang, Biao; Li, Xiaobo; Ning, Yuping; Wu, Kai

2016-07-01

Structural abnormalities in schizophrenia (SZ) patients have been well documented with structural magnetic resonance imaging (MRI) data using voxel-based morphometry (VBM) and region of interest (ROI) analyses. However, these analyses can only detect group-wise differences and thus, have a poor predictive value for individuals. In the present study, we applied a machine learning method that combined support vector machine (SVM) with recursive feature elimination (RFE) to discriminate SZ patients from normal controls (NCs) using their structural MRI data. We first employed both VBM and ROI analyses to compare gray matter volume (GMV) and white matter volume (WMV) between 41 SZ patients and 42 age- and sex-matched NCs. The method of SVM combined with RFE was used to discriminate SZ patients from NCs using significant between-group differences in both GMV and WMV as input features. We found that SZ patients showed GM and WM abnormalities in several brain structures primarily involved in the emotion, memory, and visual systems. An SVM with a RFE classifier using the significant structural abnormalities identified by the VBM analysis as input features achieved the best performance (an accuracy of 88.4%, a sensitivity of 91.9%, and a specificity of 84.4%) in the discriminative analyses of SZ patients. These results suggested that distinct neuroanatomical profiles associated with SZ patients might provide a potential biomarker for disease diagnosis, and machine-learning methods can reveal neurobiological mechanisms in psychiatric diseases.

High-resolution structural and elemental analyses of calcium storage structures synthesized by the noble crayfish Astacus astacus.

PubMed

Luquet, Gilles; Salomé, Murielle; Ziegler, Andreas; Paris, Céline; Percot, Aline; Dauphin, Yannicke

2016-11-01

During premolt, crayfish develop deposits of calcium ions, called gastroliths, in their stomach wall. The stored calcium is used for the calcification of parts of the skeleton regularly renewed for allowing growth. Structural and molecular analyses of gastroliths have been primarily performed on three crayfish species, Orconectes virilis, Procambarus clarkii, and more recently, Cherax quadricarinatus. We have performed high-resolution analyses of gastroliths from the native noble crayfish, Astacus astacus, focusing on the microstructure, the mineralogical and elemental composition and distribution in a comparative perspective. Field emission scanning electron microscopy (FESEM) and atomic force microscopy (AFM) observations showed a classical layered microstructure composed of 200-nm diameter granules aligned along fibers. These granules are themselves composed of agglomerated nanogranules of 50nm-mean diameters. Denser regions of bigger fused granules are also present. Micro-Raman spectroscopy show that if A. astacus gastroliths, similarly to the other analyzed gastroliths, are mainly composed of amorphous calcium carbonate (ACC), they are also rich in amorphous calcium phosphate (ACP). The presence of a carotenoid pigment is also observed in A. astacus gastrolith contrary to C. quadricarinatus. Energy-dispersive X-ray spectroscopy (EDX) analyses demonstrate the presence of minor elements such as Mg, Sr, Si and P. The distribution of this last element is particularly heterogeneous. X-ray absorption near edge structure spectroscopy (XANES) reveals an alternation of layers more or less rich in phosphorus evidenced in the mineral phase as well as in the organic matrix in different molecular forms. Putative functions of the different P-comprising molecules are discussed. Copyright © 2016 Elsevier Inc. All rights reserved.

The Structure of Informal Social Networks of Persons with Profound Intellectual and Multiple Disabilities

ERIC Educational Resources Information Center

Kamstra, A.; van der Putten, A. A. J.; Vlaskamp, C.

2015-01-01

Background: Persons with less severe disabilities are able to express their needs and show initiatives in social contacts, persons with profound intellectual and multiple disabilities (PIMD), however, depend on others for this. This study analysed the structure of informal networks of persons with PIMD. Materials and Methods: Data concerning the…

Characteristic Analysis and Experiment of a Dynamic Flow Balance Valve

NASA Astrophysics Data System (ADS)

Bin, Li; Song, Guo; Xuyao, Mao; Chao, Wu; Deman, Zhang; Jin, Shang; Yinshui, Liu

2017-12-01

Comprehensive characteristics of a dynamic flow balance valve of water system were analysed. The flow balance valve can change the drag efficient automatically according to the condition of system, and the effective control flowrate is constant in the range of job pressure. The structure of the flow balance valve was introduced, and the theoretical calculation formula for the variable opening of the valve core was derived. A rated pressure of 20kPa to 200kPa and a rated flowrate of 10m3/h were offered in the numerical work. Static and fluent CFX analyses show good behaviours: through the valve core structure optimization and improve design of the compressive spring, the dynamic flow balance valve can stabilize the flowrate of system evidently. And experiments show that the flow control accuracy is within 5%.

Factorial validity of the Personality Adjective Checklist in a Dutch-speaking sample.

PubMed

Van den Broeck, Joke; Bastiaansen, Leen; Rossi, Gina; Dierckx, Eva; Mikolajczak-Degrauwe, Kalina; Hofmans, Joeri

2014-01-01

We examined the factorial structure of the Dutch version of the Personality Adjective Checklist (PACL-D) in a Belgian sample of 3,012 community-dwelling adults. Exploratory factor analyses revealed a 5-factor structure (Neurotic, Aggressive/Dominant, Introverted vs. Extraverted, Conscientious, and Cooperative), that showed considerable overlap with 3 of the Big Five factors (i.e., Neuroticism, Extraversion, and Conscientiousness). Moreover, the 5-factor structure closely resembled the structure found in the original American PACL and was equivalent across gender and age.

Analysis of the influence of the milling machine throw-out plate surfacing and structure design on throwing material

NASA Astrophysics Data System (ADS)

Fang, Yuanbin; Sha, Hongwei; Yu, Yunmin; Chen, Bing

2018-03-01

Material composition, hardness and wear properties of the throw-out plate improved are analysed on a road milling machine. At the same time, analyse the tissue and performance of Fe based alloy named Fe60 cladding layer using the plasma surfacing method. And the original and improved throw-out plates are analysed throwing material effect by the dynamic analysis. Then the throw-out plate samples are verified. The results show that Fe60 powder is selected as surface strengthening material. By the improved structure, the hardness of the throw-out plate increases from 14.6HRC to 57.5HRC, and the wear resistance increases from 0.452g-1 to 16.393g-1. At the same time, it increases from 3263 to 3433 to fall into the collecting material number of milling machine. It provides important guidance for structure design and process design of the milling machine throw-out plate.

Structural characterization and evaluation of the antioxidant activities of polysaccharides extracted from Qingzhuan brick tea.

PubMed

Yang, Xinhe; Huang, Mingjun; Qin, Caiqin; Lv, Bangyu; Mao, Qingli; Liu, Zhonghua

2017-08-01

The crude tea polysaccharides (CTPS) from Qingzhuan brick tea(QZBT) were extracted and fractionated to afford two fractions, namely TPS-1 and TPS-2. Analyses were conducted concerning the structural characterization and antioxidant activities of these samples. Component analysis revealed that the carbohydrate, uronic acid, protein and polyphenol contents of these samples differed significantly. Fourier transform infrared analysis showed that these samples showed similar characteristic absorption peaks for polysaccharides. Ultraviolet-visible spectroscopy, circular dichroism, scanning electron microscopy and thermogravimetric analyses indicated that there were considerable differences in the presence of protein, surface features, conformational characteristics and thermodynamic behaviors. For antioxidant activities in vitro, CTPS, TPS-1 and TPS-2 exhibited concentration-dependent antioxidant activities, with TPS-2 showing significantly higher antioxidant activity than CTPS and TPS-1. These results provide a scientific and strong foundation for the use of tea polysaccharides(TPS) from QZBT and further research towards the relationships between the characteristics and antioxidant activities of TPS. Copyright © 2017 Elsevier B.V. All rights reserved.

Demoralization Scale in Spanish-Speaking Palliative Care Patients.

PubMed

Rudilla, David; Galiana, Laura; Oliver, Amparo; Barreto, Pilar

2016-04-01

Among the approaches to the demoralization syndrome, the one proposed by Kissane et al. is prevalent in the literature. These authors developed the Demoralization Scale (DS) to assess emotional distress, conceived as demoralization. To present the Spanish adaptation of the Demoralization Scale in palliative care patients, with a new and more comprehensive approach to its factorial structure. A cross-sectional study was carried out in 226 Spanish palliative care patients in three different settings: hospital, home care unit, and continued care unit. Outcome measures included the DS and the Hospital Anxiety and Depression Scale. Analyses comprised confirmatory factor analyses to test the original, German, and Irish structure of the DS, exploratory structural equation modeling (ESEM), estimations of internal consistency, and multivariate analyses of variance for criterion-related validity. The confirmatory factor analyses showed inappropriate fit for the previous structures when studied in the Spanish version of the DS. With ESEM, the best fitting structure was the five-factor solution, without item 18. Reliability results offered good estimations of internal consistency for all the dimensions except for sense of failure. Cronbach alpha coefficients were appropriate for the dimensions of loss of meaning (0.86), helplessness (0.79), disheartenment (0.88), and dysphoria (0.80), but low reliability was found for sense of failure (0.62). Convergent and discriminant validity showed positive correlations between demoralization, anxiety, and depression. Patients with higher levels of anxiety had higher scores on every dimension of demoralization, and those with higher levels of depression had higher scores on loss of meaning, disheartenment, and sense of failure, but not on dysphoria or helplessness. The Spanish adaptation of the DS has shown appropriate psychometric properties. It has been useful to differentiate between depression and the demoralization syndrome, pointing to helplessness and dysphoria as unique characteristics of demoralized palliative care patients. Copyright © 2016. Published by Elsevier Inc.

A statistical study of magnetopause structures: Tangential versus rotational discontinuities

NASA Astrophysics Data System (ADS)

Chou, Y.-C.; Hau, L.-N.

2012-08-01

A statistical study of the structure of Earth's magnetopause is carried out by analyzing two-year AMPTE/IRM plasma and magnetic field data. The analyses are based on the minimum variance analysis (MVA), the deHoffmann-Teller (HT) frame analysis and the Walén relation. A total of 328 magnetopause crossings are identified and error estimates associated with MVA and HT frame analyses are performed for each case. In 142 out of 328 events both MVA and HT frame analyses yield high quality results which are classified as either tangential-discontinuity (TD) or rotational-discontinuity (RD) structures based only on the Walén relation: Events withSWA ≤ 0.4 (SWA ≥ 0.5) are classified as TD (RD), and rest (with 0.4 < SWA < 0.5) is classified as "uncertain," where SWA refers to the Walén slope. With this criterion, 84% of 142 events are TDs, 12% are RDs, and 4% are uncertain events. There are a large portion of TD events which exhibit a finite normal magnetic field component Bnbut have insignificant flow as compared to the Alfvén velocity in the HT frame. Two-dimensional Grad-Shafranov reconstruction of forty selected TD and RD events show that single or multiple X-line accompanied with magnetic islands are common feature of magnetopause current. A survey plot of the HT velocity associated with TD structures projected onto the magnetopause shows that the flow is diverted at the subsolar point and accelerated toward the dawn and dusk flanks.

"Aesthetic Emotion": An Ambiguous Concept in John Dewey's Aesthetics

ERIC Educational Resources Information Center

Hohr, H.

2010-01-01

This article analyses the concept of "aesthetic emotion" in John Dewey's "Art as experience". The analysis shows that Dewey's line of investigation offers valuable insights as to the role of emotion in experience: it shows emotion as an integral part and structuring force, as a cultural and historical category. However, the notion of aesthetic…

Validity of a brief workaholism scale.

PubMed

Del Líbano, Mario; Llorens, Susana; Salanova, Marisa; Schaufeli, Wilmar

2010-02-01

The current study contributes to our understanding of workaholism as a negative construct, and to its measurement by examining the psychometric properties of a short 10-item workaholism scale called DUWAS (Dutch Work Addiction Scale). Confirmatory factor analyses were carried out in a heterogeneous sample of 2,714 employees from the Netherlands (n= 2,164) and Spain (n= 550). The results confirmed the expected two-factor structure of workaholism: working excessively and working compulsively. Moreover, multi-group analyses showed that this two-factor structure was invariant across both countries. Lastly, negative correlations among workaholism and psychosocial well-being (i.e., perceived health and happiness) are indicators of the negative nature of workaholism.

Cloning, characterisation, and comparative quantitative expression analyses of receptor for advanced glycation end products (RAGE) transcript forms.

PubMed

Sterenczak, Katharina A; Willenbrock, Saskia; Barann, Matthias; Klemke, Markus; Soller, Jan T; Eberle, Nina; Nolte, Ingo; Bullerdiek, Jörn; Murua Escobar, Hugo

2009-04-01

RAGE is a member of the immunoglobulin superfamily of cell surface molecules playing key roles in pathophysiological processes, e.g. immune/inflammatory disorders, Alzheimer's disease, diabetic arteriosclerosis and tumourigenesis. In humans 19 naturally occurring RAGE splicing variants resulting in either N-terminally or C-terminally truncated proteins were identified and are lately discussed as mechanisms for receptor regulation. Accordingly, deregulation of sRAGE levels has been associated with several diseases e.g. Alzheimer's disease, Type 1 diabetes, and rheumatoid arthritis. Administration of recombinant sRAGE to animal models of cancer blocked tumour growth successfully. In spite of its obvious relationship to cancer and metastasis data focusing sRAGE deregulation and tumours is rare. In this study we screened a set of tumours, healthy tissues and various cancer cell lines for RAGE splicing variants and analysed their structure. Additionally, we analysed the ratio of the mainly found transcript variants using quantitative Real-Time PCR. In total we characterised 24 previously not described canine and 4 human RAGE splicing variants, analysed their structure, classified their characteristics, and derived their respective protein forms. Interestingly, the healthy and the neoplastic tissue samples showed in majority RAGE transcripts coding for the complete receptor and transcripts showing insertions of intron 1.

Ne matrix spectra of the sym-C6Br3F3+ radical cation

USGS Publications Warehouse

Bondybey, V.E.; Sears, T.J.; Miller, T.A.; Vaughn, C.; English, J.H.; Shiley, R.S.

1981-01-01

The electronic absorption and laser excited, wavelength resolved fluorescence spectra of the title cation have been observed in solid Ne matrix and vibrationally analysed. The vibrational structure of the excited B2A2??? state shows close similarity to the parent compound. The X2E??? ground state structure is strongly perturbed and irregular owing to a large Jahn-Teller distortion. The data are analysed in terms of a recently developed, sophisticated multimode Jahn-Teller theoretical model. We have generated the sym-C6Br3F3+ cations in solid Ne matrix and obtained their wavelength resolved emission and absorption spectra. T ground electronic X2E??? state exhibits an irregular and strongly perturbed vibrational structure, which can be successfully modeled using sophisticated multimode Jahn-Teller theory. ?? 1981.

Personality and the latent structure of PTSD comorbidity

PubMed Central

Miller, Mark W.; Wolf, Erika J.

2012-01-01

This study examined the structure of PTSD comorbidity and its relationship to personality in a sample of 214 veterans using data from diagnostic interviews and the Multidimensional Personality Questionnaire-Brief Form (MPQ-BF; Patrick, Curtin, & Tellegen, 2002). Confirmatory factor analyses supported a three factor model composed of Externalizing, Fear and Distress factors. Analyses that examined the location of borderline personality disorder revealed significant cross-loadings for this disorder on both Externalizing and Distress. Structural equation models showed trait negative emotionality to be significantly related to all three comorbidity factors whereas positive emotionality and constraint evidenced specific associations with Distress and Externalizing, respectively. These results shed new light on the location of borderline personality disorder within the internalizing/externalizing model and clarify the relative influence of broad dimensions of personality on patterns of comorbidity. PMID:22480716

Structural analyses of the JPL Mars Pathfinder impact

NASA Astrophysics Data System (ADS)

Gwinn, Kenneth W.

The purpose of this paper is to demonstrate that finite element analysis can be used in the design process for high performance fabric structures. These structures exhibit extreme geometric nonlinearity; specifically, the contact and interaction of fabric surfaces with the large deformation which necessarily results from membrane structures introduces great complexity to analyses of this type. All of these features are demonstrated here in the analysis of the Jet Propulsion Laboratory (JPL) Mars Pathfinder impact onto Mars. This lander system uses airbags to envelope the lander experiment package, protecting it with large deformation upon contact. Results from the analysis show the stress in the fabric airbags, forces in the internal tendon support system, forces in the latches and hinges which allow the lander to deploy after impact, and deceleration of the lander components. All of these results provide the JPL engineers with design guidance for the success of this novel lander system.

The genetic structure of Arabidopsis thaliana in the south-western Mediterranean range reveals a shared history between North Africa and southern Europe

PubMed Central

2014-01-01

Background Deciphering the genetic structure of Arabidopsis thaliana diversity across its geographic range provides the bases for elucidating the demographic history of this model plant. Despite the unique A. thaliana genomic resources currently available, its history in North Africa, the extreme southern limit in the biodiversity hotspot of the Mediterranean Basin, remains virtually unknown. Results To approach A. thaliana evolutionary history in North Africa, we have analysed the genetic diversity and structure of 151 individuals collected from 20 populations distributed across Morocco. Genotyping of 249 genome-wide SNPs indicated that Morocco contains substantially lower diversity than most analyzed world regions. However, IBD, STRUCTURE and PCA clustering analyses showed that genetic variation is strongly geographically structured. We also determined the genetic relationships between Morocco and the closest European region, the Iberian Peninsula, by analyses of 201 populations from both regions genotyped with the same SNPs. These analyses detected four genetic groups, but all Moroccan accessions belonged to a common Iberian/Moroccan cluster that appeared highly differentiated from the remaining groups. Thus, we identified a genetic lineage with an isolated demographic history in the south-western Mediterranean region. The existence of this lineage was further supported by the study of several flowering genes and traits, which also found Moroccan accessions similar to the same Iberian group. Nevertheless, genetic diversity for neutral SNPs and flowering genes was higher in Moroccan than in Iberian populations of this lineage. Furthermore, we analyzed the genetic relationships between Morocco and other world regions by joint analyses of a worldwide collection of 337 accessions, which detected an additional weak relationship between North Africa and Asia. Conclusions The patterns of genetic diversity and structure of A. thaliana in Morocco show that North Africa is part of the species native range and support the occurrence of a glacial refugium in the Atlas Mountains. In addition, the identification of a genetic lineage specific of Morocco and the Iberian Peninsula indicates that the Strait of Gibraltar has been an A. thaliana migration route between Europe and Africa. Finally, the genetic relationship between Morocco and Asia suggests another migration route connecting north-western Africa and Asia. PMID:24411008

Statistical analyses and computational prediction of helical kinks in membrane proteins

NASA Astrophysics Data System (ADS)

Huang, Y.-H.; Chen, C.-M.

2012-10-01

We have carried out statistical analyses and computer simulations of helical kinks for TM helices in the PDBTM database. About 59 % of 1562 TM helices showed a significant kink, and 38 % of these kinks are associated with prolines in a range of ±4 residues. Our analyses show that helical kinks are more populated in the central region of helices, particularly in the range of 1-3 residues away from the helix center. Among 1,053 helical kinks analyzed, 88 % of kinks are bends (change in helix axis without loss of helical character) and 12 % are disruptions (change in helix axis and loss of helical character). It is found that proline residues tend to cause larger kink angles in helical bends, while this effect is not observed in helical disruptions. A further analysis of these kinked helices suggests that a kinked helix usually has 1-2 broken backbone hydrogen bonds with the corresponding N-O distance in the range of 4.2-8.7 Å, whose distribution is sharply peaked at 4.9 Å followed by an exponential decay with increasing distance. Our main aims of this study are to understand the formation of helical kinks and to predict their structural features. Therefore we further performed molecular dynamics (MD) simulations under four simulation scenarios to investigate kink formation in 37 kinked TM helices and 5 unkinked TM helices. The representative models of these kinked helices are predicted by a clustering algorithm, SPICKER, from numerous decoy structures possessing the above generic features of kinked helices. Our results show an accuracy of 95 % in predicting the kink position of kinked TM helices and an error less than 10° in the angle prediction of 71.4 % kinked helices. For unkinked helices, based on various structure similarity tests, our predicted models are highly consistent with their crystal structure. These results provide strong supports for the validity of our method in predicting the structure of TM helices.

Public-Private Policy Change and Its Influence on the Linkage of Agricultural Research, Extension and Farmers in Iran

ERIC Educational Resources Information Center

Karamidehkordi, Esmail

2013-01-01

Purpose: This article aims to show the linkage of Iranian agricultural research centres with extension and farmers, using three case studies in 1999, 2005 and 2010. Design/methodology/approach: The data were collected through document analyses, structured and semi-structured interviews and observations. Findings: The 1999 and 2005 cases were…

Cybastacines A and B: Antibiotic Sesterterpenes from a Nostoc sp. Cyanobacterium.

PubMed

Cabanillas, Alfredo H; Tena Pérez, Víctor; Maderuelo Corral, Santiago; Rosero Valencia, Diego Fernando; Martel Quintana, Antera; Ortega Doménech, Montserrat; Rumbero Sánchez, Ángel

2018-02-23

Cybastacines A (1) and B (2) were discovered as a novel pentacyclic sesterterpenoid-alkaloid skeleton structure, with a guanidinium group. These molecules were isolated from a Nostoc sp. cyanobacterium collected in the Canary Islands. Their structures were elucidated primarily by a combination of spectroscopic analyses and X-ray diffraction. These compounds showed antibiotic activities against several clinically relevant bacterial strains.

Genetic variations in the serotonergic system contribute to amygdala volume in humans

PubMed Central

Li, Jin; Chen, Chunhui; Wu, Karen; Zhang, Mingxia; Zhu, Bi; Chen, Chuansheng; Moyzis, Robert K.; Dong, Qi

2015-01-01

The amygdala plays a critical role in emotion processing and psychiatric disorders associated with emotion dysfunction. Accumulating evidence suggests that amygdala structure is modulated by serotonin-related genes. However, there is a gap between the small contributions of single loci (less than 1%) and the reported 63–65% heritability of amygdala structure. To understand the “missing heritability,” we systematically explored the contribution of serotonin genes on amygdala structure at the gene set level. The present study of 417 healthy Chinese volunteers examined 129 representative polymorphisms in genes from multiple biological mechanisms in the regulation of serotonin neurotransmission. A system-level approach using multiple regression analyses identified that nine SNPs collectively accounted for approximately 8% of the variance in amygdala volume. Permutation analyses showed that the probability of obtaining these findings by chance was low (p = 0.043, permuted for 1000 times). Findings showed that serotonin genes contribute moderately to individual differences in amygdala volume in a healthy Chinese sample. These results indicate that the system-level approach can help us to understand the genetic basis of a complex trait such as amygdala structure. PMID:26500508

Analysis of variability in additive manufactured open cell porous structures.

PubMed

Evans, Sam; Jones, Eric; Fox, Pete; Sutcliffe, Chris

2017-06-01

In this article, a novel method of analysing build consistency of additively manufactured open cell porous structures is presented. Conventionally, methods such as micro computed tomography or scanning electron microscopy imaging have been applied to the measurement of geometric properties of porous material; however, high costs and low speeds make them unsuitable for analysing high volumes of components. Recent advances in the image-based analysis of open cell structures have opened up the possibility of qualifying variation in manufacturing of porous material. Here, a photogrammetric method of measurement, employing image analysis to extract values for geometric properties, is used to investigate the variation between identically designed porous samples measuring changes in material thickness and pore size, both intra- and inter-build. Following the measurement of 125 samples, intra-build material thickness showed variation of ±12%, and pore size ±4% of the mean measured values across five builds. Inter-build material thickness and pore size showed mean ranges higher than those of intra-build, ±16% and ±6% of the mean material thickness and pore size, respectively. Acquired measurements created baseline variation values and demonstrated techniques suitable for tracking build deviation and inspecting additively manufactured porous structures to indicate unwanted process fluctuations.

Zn(II) coordination polymers with flexible V-shaped dicarboxylate ligand: Syntheses, helical structures and properties

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

Li, Lin; Liu, Chong-Bo, E-mail: cbliu@nchu.edu.cn; Yang, Gao-Shan

2015-11-15

Hydrothermal reactions of 2,2′-[hexafluoroisopropylidenebis(p-phenyleneoxy)]diacetic acid (H{sub 2}L) and zinc ions in the presence of N-donor ancillary ligands afford four novel coordination polymers, namely, [Zn{sub 2}(μ{sub 2}-OH)(μ{sub 4}-O){sub 0.5}(L)]·0.5H{sub 2}O (1), [Zn(L)(2,2′-bipy)(H{sub 2}O)] (2), [Zn{sub 3}(L){sub 3}(phen){sub 2}]·H{sub 2}O (3) and [Zn{sub 2}(L){sub 2}(4,4′-bipy)] (4) (2,2′-bipy=2,2′-bipyridine; 4,4′-bipy=4,4′-bipyridine; phen=1,10-phenanthroline). Their structures have been determined by single-crystal X-ray diffraction analyses, elemental analyses, IR spectra, powder X-ray diffraction (PXRD), and thermogravimetric (TG) analyses. Complex 1 shows a 3-D clover framework consisting of [Zn{sub 4}(µ{sub 4}-O)(µ{sub 2}-OH){sub 2}]{sup 4+} clusters, and exhibits a novel (3,8)-connected topological net with the Schläfli symbol of {3·4·5}{sub 2}{3"4·4"4·5"2·6"6·7"1"0·8"2}, andmore » contains double-stranded and two kinds of meso-helices. 2 displays a helical chain structure, which is further extended via hydrogen bonds into a 3-D supramolecular structure with meso-helix chains. 3 displays a 2-D {4"4·6"2} parallelogram structure, which is further extended via hydrogen bonds into a 3-D supramolecular structure with single-stranded helical chains. 4 shows a 2-D {4"4·6"2} square structure with left- and right-handed helical chains. Moreover, the luminescent properties of 1–4 have been investigated. - Graphical abstract: Four new Zn(II) coordination polymers with helical structures based on flexible V-shaped dicarboxylate ligand have been synthesized and structurally characterized. Photoluminescent properties have been investigated. - Highlights: • Four novel Zn(II) coordination polymers with V-shaped ligand were characterized. • Complexes 1–4 show diverse intriguing helical characters. • Fluorescence properties of complexes 1–4 were investigated.« less

The Work Role Functioning Questionnaire v2.0 Showed Consistent Factor Structure Across Six Working Samples.

PubMed

Abma, Femke I; Bültmann, Ute; Amick Iii, Benjamin C; Arends, Iris; Dorland, Heleen F; Flach, Peter A; van der Klink, Jac J L; van de Ven, Hardy A; Bjørner, Jakob Bue

2017-09-09

Objective The Work Role Functioning Questionnaire v2.0 (WRFQ) is an outcome measure linking a persons' health to the ability to meet work demands in the twenty-first century. We aimed to examine the construct validity of the WRFQ in a heterogeneous set of working samples in the Netherlands with mixed clinical conditions and job types to evaluate the comparability of the scale structure. Methods Confirmatory factor and multi-group analyses were conducted in six cross-sectional working samples (total N = 2433) to evaluate and compare a five-factor model structure of the WRFQ (work scheduling demands, output demands, physical demands, mental and social demands, and flexibility demands). Model fit indices were calculated based on RMSEA ≤ 0.08 and CFI ≥ 0.95. After fitting the five-factor model, the multidimensional structure of the instrument was evaluated across samples using a second order factor model. Results The factor structure was robust across samples and a multi-group model had adequate fit (RMSEA = 0.63, CFI = 0.972). In sample specific analyses, minor modifications were necessary in three samples (final RMSEA 0.055-0.080, final CFI between 0.955 and 0.989). Applying the previous first order specifications, a second order factor model had adequate fit in all samples. Conclusion A five-factor model of the WRFQ showed consistent structural validity across samples. A second order factor model showed adequate fit, but the second order factor loadings varied across samples. Therefore subscale scores are recommended to compare across different clinical and working samples.

Characterization of konjac glucomannan-gelatin IPN physical hydrogel scaffold

NASA Astrophysics Data System (ADS)

Chen, Xiliang; Chen, Qinghua; Yan, Tingting; Liu, Jinkun

2017-06-01

A novel IPN hydrogel scaffold is prepared by freeze-drying method, in which konjac galactomannan (KGM) and gelatin are physically crosslinked respectively. This scaffold is thermostable, and the structure of this scaffold is analysed by scanning electron microscope, Fourier transform infrared spectrum, and X-ray diffraction method. The FT-IR results show that hydrogen bonds are formed between KGM and gelatin molecules, which hinder the formation of their respective crosslinking. This is consistent with the XRD results that the crystallinity gets lower in the IPN gels compared with pure gelatin and KGM gels. The morphologies of freeze-dried hydrogels are observed by SEM and the mechanical properties of the scaffolds are tested to analyse the relationship between the structures and properties. Although this novel IPN hydrogel is physical gel, it shows rubber-like performance as chemical gels. And it is nontoxic, so it can be used as the scaffold for cartilage tissue engineering that embedded in human bodies.

Degradation of raw corn stover powder (RCSP) by an enriched microbial consortium and its community structure.

PubMed

Feng, Yujie; Yu, Yanling; Wang, Xin; Qu, Youpeng; Li, Dongmei; He, Weihua; Kim, Byung Hong

2011-01-01

A microbial consortium with a high cellulolytic activity was enriched to degrade raw corn stover powder (RCSP). This consortium degraded more than 51% of non-sterilized RCSP or 81% of non-sterilized filter paper within 8 days at 40°C under facultative anoxic conditions. Cellulosome-like structures were observed in scanning electron micrographs (SEM) of RCSP degradation residue. The high cellulolytic activity was maintained during 40 subcultures in a medium containing cellulosic substrate. Small ribosomal gene sequence analyses showed the consortium contains uncultured and cultured bacteria with or without cellulolytic activities. Among these bacteria, some are anaerobic others aerobic. Analyses of the culture filtrate showed a typical anoxic polysaccharide fermentation during the culturing process. Reducing sugar concentration increased at early stage followed by various fermentation products that were consumed at the late stage. Copyright © 2010 Elsevier Ltd. All rights reserved.

Multi-level structure in the large scale distribution of optically luminous galaxies

NASA Astrophysics Data System (ADS)

Deng, Xin-fa; Deng, Zu-gan; Liu, Yong-zhen

1992-04-01

Fractal dimensions in the large scale distribution of galaxies have been calculated with the method given by Wen et al. [1] Samples are taken from CfA redshift survey in northern and southern galactic [2] hemisphere in our analysis respectively. Results from these two regions are compared with each other. There are significant differences between the distributions in these two regions. However, our analyses do show some common features of the distributions in these two regions. All subsamples show multi-level fractal character distinctly. Combining it with the results from analyses of samples given by IRAS galaxies and results from samples given by redshift survey in pencil-beam fields, [3,4] we suggest that multi-level fractal structure is most likely to be a general and important character in the large scale distribution of galaxies. The possible implications of this character are discussed.

Comparison of fate profiles of PAHs in soil, sediments and mangrove leaves after oil spills by QSAR and QSPR.

PubMed

Tansel, Berrin; Lee, Mengshan; Tansel, Derya Z

2013-08-15

First order removal rates for 15 polyaromatic hydrocarbons (PAHs) in soil, sediments and mangrove leaves were compared in relation to the parameters used in fate transport analyses (i.e., octanol-water partition coefficient, organic carbon-water partition coefficient, solubility, diffusivity in water, HOMO-LUMO gap, molecular size, molecular aspect ratio). The quantitative structure activity relationships (QSAR) and quantitative structure property relationships (QSPR) showed that the rate of disappearance of PAHs is correlated with their diffusivities in water as well as molecular volumes in different media. Strong correlations for the rate of disappearance of PAHs in sediments could not be obtained in relation to most of the parameters evaluated. The analyses showed that the QSAR and QSPR correlations developed for removal rates of PAHs in soils would not be adequate for sediments and plant tissues. Copyright © 2013 Elsevier Ltd. All rights reserved.

Psychometric analysis of an eating behaviour questionnaire for an overweight and obese Chinese population in Singapore.

PubMed

Chong, Mary Foong-Fong; Ayob, M Na'im M; Chong, Kok Joon; Tai, E-Shyong; Khoo, Chin Meng; Leow, Melvin Khee-Shing; Lee, Yung Seng; Tham, Kwang Wei; Venkataraman, Kavita; Meaney, Michael J; Wee, Hwee Lin; Khoo, Eric Yin-Hao

2016-06-01

Previous studies reveal that the Three-Factor Eating Questionnaire (TFEQ), which assesses eating behaviour, performs differently across population groups and cultures. We aimed to identify the factor structure that is most appropriate to capture eating behaviour in an overweight and obese Chinese population in Singapore. TFEQ-51 was administered to 444 Chinese subjects pooled from four separate studies and scored according to various alternative versions of the TFEQ. Confirmatory factor analyses and goodness of fit indices were used to determine the most appropriate factor structure. Known-group validity analyses were conducted. Niemeier's Disinhibition Factors and the TFEQ-R18 factor structures were found to be the most applicable in our population based on goodness of fit indices, with a x(2)/df ratio of <3, RMSEA of ≤ 0.6 and a CFI value of >0.9 for both. Only two of three factors (Emotional Eating and Uncontrolled Eating) of the TFEQ-R18 showed good internal consistency, while none of Niemeier's Disinhibition Factors showed good internal consistency. Known-group validity showed that Emotional Eating and Internal Disinhibition were significantly associated with higher BMI. We found that the TFEQ-R18 factor structure is the most appropriate and practical for use in measuring eating behaviour in an overweight and obese Chinese population in Singapore. Copyright © 2016 Elsevier Ltd. All rights reserved.

Study of the glow curve structure of the minerals separated from black pepper (Piper nigrum L.)

NASA Astrophysics Data System (ADS)

Guzmán, S.; Ruiz Gurrola, B.; Cruz-Zaragoza, E.; Tufiño, A.; Furetta, C.; Favalli, A.; Brown, F.

2011-04-01

The inorganic mineral fraction extracted from black pepper (Piper nigrum L.) has been analysed using a thermoluminescence (TL) method, investigating the glow curve structure, including an evaluation of the kinetic parameters. Different grain sizes, i.e. 10, 74, and 149 μm, were selected from commercial black pepper. The X-ray diffraction of the inorganic fraction shows that quartz is the main mineral present in it. The samples were exposed to 1-25 kGy doses by gamma rays of 60Co in order to analyse the thermally stimulated luminescence response as a function of the delivered dose. The glow curves show a complex structure for different grain sizes of the pepper mineral samples. The fading of the TL signal at room temperature was obtained after irradiation, and it was observed that the maximum peaks of the glow curves shift towards higher values of the temperature when the elapsed time from irradiation increases. It seems that the fading characteristic may be related to a continuous trap distribution responsible for the complex structure of the glow curve. Similar glow curves structure behaviour was found under ultraviolet irradiation of the samples. The activation energy and the frequency factor were determined from the glow curves of different grain sizes using a deconvolution programme because of the evident complexity of the structure.

Genetic structure of Octopus vulgaris (Cephalopoda, Octopodidae) in the central Mediterranean Sea inferred from the mitochondrial COIII gene.

PubMed

Fadhlaoui-Zid, Karima; Knittweis, Leyla; Aurelle, Didier; Nafkha, Chaala; Ezzeddine, Soufia; Fiorentino, Fabio; Ghmati, Hisham; Ceriola, Luca; Jarboui, Othman; Maltagliati, Ferruccio

2012-01-01

The polymorphism of the mitochondrial gene cytochrome oxidase III was studied in the Mediterranean octopus, Octopus vulgaris Cuvier, 1797. A total of 202 specimens from seven sampling sites were analysed with the aim of elucidating patterns of genetic structure in the central Mediterranean Sea and to give an insight into the phylogeny of the Octopus genus. Phylogenetic analyses showed that individuals from the central Mediterranean belong to the O. vulgaris species whose limits should nevertheless be clarified. Concerning genetic structure, two high-frequency haplotypes were present in all locations. The overall genetic divergence (Φ(ST)=0.05, P<0.05) indicated a significant genetic structuring in the study area and an AMOVA highlighted a significant break between western and eastern Mediterranean basins (Φ(CT)=0.094, P<0.05). Possible explanations for the observed patterns of genetic structuring are discussed with reference to their relevance for fisheries management. Copyright © 2012. Published by Elsevier SAS.

Crystalline solution series and order-disorder within the natrolite mineral group

USGS Publications Warehouse

Ross, M.; Flohr, M.J.K.; Ross, D.R.

1992-01-01

Electron microprobe and X-ray analyses were made of natrolite, tetranatrolite, gonnardite, and thomsonite from the Magnet Cove alkaline igneous complex, Arkansas, and of selected specimens from the U.S. National Museum. This information and data from the literature indicate that natrolite, mesolite, scolecite, edingtonite, and tetraedingtonite show only small deviations from the ideal stoichiometry. In contrast, gonnardite, tetranatrolite, and thomsonite show large deviations from the ideal end-member compositions and compose three crystalline series. The structures of the natrolite minerals are defined by combining each of the three types of framework structures with various combinations of channel-occupying polyhedra. Various polysomatic series can be constructed by combining slices of two basic structures to form new hybrid structures. -from Authors

One-step nanoimprinted hybrid micro-/nano-structure for in situ protein detection of isolated cell array via localized surface plasmon resonance

NASA Astrophysics Data System (ADS)

Ali, Riyaz Ahmad Mohamed; Villariza Espulgar, Wilfred; Aoki, Wataru; Jiang, Shu; Saito, Masato; Ueda, Mitsuyoshi; Tamiya, Eiichi

2018-03-01

Nanoplasmonic biosensors show high potentials as label-free devices for continuous monitoring in biomolecular analyses. However, most current sensors comprise multiple-dedicated layers with complicated fabrication procedures, which increases production time and manufacturing costs. In this work, we report the synergistic integration of cell-trapping microwell structures with plasmonic sensing nanopillar structures in a single-layered substrate by one-step thermal nanoimprinting. Here, microwell arrays are used for isolating cells, wherein gold-capped nanostructures sense changes in local refractive index via localized surface plasmon resonance (LSPR). Hence, proteins secreted from trapped cells can be label-freely detected as peak shifts in absorbance spectra. The fabricated device showed a detection limit of 10 ng/µL anti-IgA. In Pichia pastoris cells trial analysis, a red shift of 6.9 nm was observed over 12 h, which is likely due to the protein secretion from the cells. This approach provides an inexpensive, rapid, and reproducible alternative for mass production of biosensors for continuous biomolecular analyses.

Further analysis of the structure and immunological activity of an RG-I type pectin from Panax ginseng.

PubMed

Zhang, Xu; Li, Shanshan; Sun, Lin; Ji, Li; Zhu, Jingjing; Fan, Yuying; Tai, Guihua; Zhou, Yifa

2012-06-20

In this paper, we further analysed the structure of a type I rhamnogalacturonan (RG-I) pectin (WGPA-2-RG) fractionated from ginseng polysaccharides. Methylation and periodate oxidation analyses showed that WGPA-2-RG has a backbone consisting of alternating rhamnose (Rha) and galacturonic acid (GalA) residues and side chains consisting of type II arabinogalactan (AG-II). Partial acidic hydrolysis for 6h completely removed arabinose (Ara), partial galactose (Gal), but little GalA and Rha. During partial hydrolysis, the molecular weight of WGPA-2-RG decreased smoothly, suggesting that the Ara and cleavable Gal residues exist on the surface of the molecule, while GalA and Rha residues exist in the core of the molecule. The bioactivity assay showed that the arabinogalactan side chains of WGPA-2-RG are essential structures for stimulating NO secretion and lymphocyte proliferation. However, removal of the Ara and Gal residues through hydrolysis did not appreciably affect the ability of WGPA-2-RG to enhance macrophage phagocytosis. Copyright © 2012 Elsevier Ltd. All rights reserved.

Multifractal analysis of a GCM climate

NASA Astrophysics Data System (ADS)

Carl, P.

2003-04-01

Multifractal analysis using the Wavelet Transform Modulus Maxima (WTMM) approach is being applied to the climate of a Mintz--Arakawa type, coarse resolution, two--layer AGCM. The model shows a backwards running period multiplication scenario throughout the northern summer, subsequent to a 'hard', subcritical Hopf bifurcation late in spring. This 'route out of chaos' (seen in cross sections of a toroidal phase space structure) is born in the planetary monsoon system which inflates the seasonal 'cycle' into these higher order structures and is blamed for the pronounced intraseasonal--to--centennial model climate variability. Previous analyses of the latter using advanced modal decompositions showed regularity based patterns in the time--frequency plane which are qualitatively similar to those obtained from the real world. The closer look here at the singularity structures, as a fundamental diagnostic supplement, aims at both more complete understanding (and quantification) of the model's qualitative dynamics and search for further tools of model intercomparison and verification in this respect. Analysing wavelet is the 10th derivative of the Gaussian which might suffice to suppress regular patterns in the data. Intraseasonal attractors, studied in time series of model precipitation over Central India, show shifting and braodening singularity spectra towards both more violent extreme events (premonsoon--monsoon transition) and weaker events (late summer to postmonsoon transition). Hints at a fractal basin boundary are found close to transition from period--2 to period--1 in the monsoon activity cycle. Interannual analyses are provided for runs with varied solar constants. To address the (in--)stationarity issue, first results are presented with a windowed multifractal analysis of longer--term runs ("singularity spectrogram").

Investigating Molecular Structures of Bio-Fuel and Bio-Oil Seeds as Predictors To Estimate Protein Bioavailability for Ruminants by Advanced Nondestructive Vibrational Molecular Spectroscopy.

PubMed

Ban, Yajing; L Prates, Luciana; Yu, Peiqiang

2017-10-18

This study was conducted to (1) determine protein and carbohydrate molecular structure profiles and (2) quantify the relationship between structural features and protein bioavailability of newly developed carinata and canola seeds for dairy cows by using Fourier transform infrared molecular spectroscopy. Results showed similarity in protein structural makeup within the entire protein structural region between carinata and canola seeds. The highest area ratios related to structural CHO, total CHO, and cellulosic compounds were obtained for carinata seeds. Carinata and canola seeds showed similar carbohydrate and protein molecular structures by multivariate analyses. Carbohydrate molecular structure profiles were highly correlated to protein rumen degradation and intestinal digestion characteristics. In conclusion, the molecular spectroscopy can detect inherent structural characteristics in carinata and canola seeds in which carbohydrate-relative structural features are related to protein metabolism and utilization. Protein and carbohydrate spectral profiles could be used as predictors of rumen protein bioavailability in cows.

Structural, microstructural and vibrational analyses of the monoclinic tungstate BiLuWO{sub 6}

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

Ait Ahsaine, H.; Taoufyq, A.; Institut Matériaux Microélectronique et Nanosciences de Provence, IM2NP, UMR CNRS 7334, Université de Toulon, BP 20132, 83957 La Garde Cedex

2014-10-15

The bismuth lutetium tungstate phase BiLuWO{sub 6} has been prepared using a solid state route with stoichiometric mixtures of oxide precursors. The obtained polycrystalline phase has been characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), and Raman spectroscopy. In the first step, the crystal structure has been refined using Rietveld method: the crystal cell was resolved using monoclinic system (parameters a, b, c, β) with space group A2/m. SEM images showed the presence of large crystallites with a constant local nominal composition (BiLuW). TEM analyses showed that the actual local structure could be better representedmore » by a superlattice (a, 2b, c, β) associated with space groups P2 or P2/m. The Raman spectroscopy showed the presence of vibrational bands similar to those observed in the compounds BiREWO{sub 6} with RE=Y, Gd, Nd. However, these vibrational bands were characterized by large full width at half maximum, probably resulting from the long range Bi/Lu disorder and local WO{sub 6} octahedron distortions in the structure. - Graphical abstract: The average structure of BiLuWO{sub 6} determined from X-ray diffraction data can be represented by A2/m space group. Experimental Electron Diffraction patterns along the [0vw] zone axes of the monoclinic structure and associated simulated patterns show the existence of a monoclinic superstructure with space group P2 or P2/m. - Highlights: • A new monoclinic BiLuWO{sub 6} phase has been elaborated from solid-state reaction. • The space group of the monoclinic disordered average structure should be A2/m. • Transmission electron microscopy leads to a superlattice with P2/m space group. • Raman spectroscopy suggests existence of local disorder.« less

Muscle structure and stiffness assessment after botulinum toxin type A injection. A systematic review.

PubMed

Mathevon, L; Michel, F; Decavel, P; Fernandez, B; Parratte, B; Calmels, P

2015-12-01

Botulinum toxin type A manages spasticity disorders in neurological central diseases. Some studies have reported that it might induce muscle changes. We present a literature review abiding by the PRISMA statement guidelines. The purpose was to explore the structural and passive biomechanical muscle properties after botulinum toxin type A injections in healthy and spastic limb muscles, on animals and humans, as well as methods for evaluating these properties. We searched the PubMed and Cochrane Library databases using the following keywords: "Botulinum toxin" AND ("muscle structure" OR "muscle atrophy") and, "Botulinum toxin" AND "muscle elasticity". From the 228 initially identified articles, 21 articles were included. Histological analyses were performed, especially on animals. A neurogenic atrophy systematically occurred. In humans, one year after a single injection, the histological recovery remained incomplete. Furthermore, 2D ultrasound analyses showed a reduction of the gastrocnemius thickness and pennation angle. MRI volumetric analysis evidenced muscular atrophy six months or one year after a single injection. Passive muscle stiffness depends on these structural changes. On the short term, the biomechanical analysis showed an elastic modulus increase in animals whereas no change was recorded in humans. On the short term, ultrasound elastography imaging showed a decreased elastic modulus. To date, few data are available, but all show a structural and mechanical muscle impact post injections, specifically muscle atrophy which can linger over time. Further studies are necessary to validate this element, and the possibility of change must be taken into account particularly with repeated injections. Thus, in clinical practice, 2D ultrasound and ultrasound elastography are two non-invasive techniques that will help physicians to develop an efficient long term monitoring. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

78 FR 51175 - Meeting of the National Commission on the Structure of the Air Force

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-20

..., and analyses to the full Commission. Meeting Accessibility: The building is fully handicap accessible. Visitors must show a picture I.D. and complete a security screening. Public parking is available within...

Factor Analyses and Score Validity of the Family Emotional Involvement and Criticism Scale in an Adolescent Sample

ERIC Educational Resources Information Center

Nelis, Sharon M.; Rae, Gordon; Liddell, Christine

2006-01-01

The factor structure of the Family Emotional Involvement and Criticism Scale (FEICS) is tested in a sample of Irish adolescents. Participants were 661 adolescents with a mean age of 15.9 years (SD = 1.26). Interpretation of both the exploratory and confirmatory factor analysis of the FEICS show support for the two-factor structure of the FEICS…

Understanding the Process of Radicalization: Review of the Empirical Literature

DTIC Science & Technology

2011-03-01

hypotheses. Analyses using structural equation modeling showed that glorification of the national group was positively associated with the use of...both) ought to be associated with an increased draw to conservative ideology, and an aversion to liberal views. The authors used structural ...with high levels of uncertainty—a two-way ANCOVA ( controlling for participant age) was conducted on the composite identification measure. Results of

Structural studies of the Sputnik virophage.

PubMed

Sun, Siyang; La Scola, Bernard; Bowman, Valorie D; Ryan, Christopher M; Whitelegge, Julian P; Raoult, Didier; Rossmann, Michael G

2010-01-01

The virophage Sputnik is a satellite virus of the giant mimivirus and is the only satellite virus reported to date whose propagation adversely affects its host virus' production. Genome sequence analysis showed that Sputnik has genes related to viruses infecting all three domains of life. Here, we report structural studies of Sputnik, which show that it is about 740 A in diameter, has a T=27 icosahedral capsid, and has a lipid membrane inside the protein shell. Structural analyses suggest that the major capsid protein of Sputnik is likely to have a double jelly-roll fold, although sequence alignments do not show any detectable similarity with other viral double jelly-roll capsid proteins. Hence, the origin of Sputnik's capsid might have been derived from other viruses prior to its association with mimivirus.

Structural Studies of the Sputnik Virophage▿

PubMed Central

Sun, Siyang; La Scola, Bernard; Bowman, Valorie D.; Ryan, Christopher M.; Whitelegge, Julian P.; Raoult, Didier; Rossmann, Michael G.

2010-01-01

The virophage Sputnik is a satellite virus of the giant mimivirus and is the only satellite virus reported to date whose propagation adversely affects its host virus' production. Genome sequence analysis showed that Sputnik has genes related to viruses infecting all three domains of life. Here, we report structural studies of Sputnik, which show that it is about 740 Å in diameter, has a T=27 icosahedral capsid, and has a lipid membrane inside the protein shell. Structural analyses suggest that the major capsid protein of Sputnik is likely to have a double jelly-roll fold, although sequence alignments do not show any detectable similarity with other viral double jelly-roll capsid proteins. Hence, the origin of Sputnik's capsid might have been derived from other viruses prior to its association with mimivirus. PMID:19889775

A new Keggin-type polyoxometalate catalyst for degradation of aqueous organic contaminants

NASA Astrophysics Data System (ADS)

Olgun, Asim; Çolak, Alper Tolga; Gübbük, İ. Hilal; Şahin, Onur; Kanar, Ebru

2017-04-01

In this study, a new polyoxometalate, K16[Ni(H2O)6]2[BW12O40]4·48H2O (1) was synthesized at room temperature and characterized by X-ray single crystal diffractions, elemental analyses, IR spectra, and thermo gravimetric analyses (TGA). Crystal structure analysis reveals that compound 1 exhibits a supramolecular structure containing one Keggin-type [BW12O40]4 heteropoly anion. The catalytic properties of this molecule for the degradation of Methyl red (MR), Rhodamine B (RhB), Methyl orange (MO) and Congo red (CR) were investigated. The results show that the compound 1 is a promising catalyst candidate for dye degradation.

Evaluation of a large capacity heat pump concept for active cooling of hypersonic aircraft structure

NASA Technical Reports Server (NTRS)

Pagel, L. L.; Herring, R. L.

1978-01-01

Results of engineering analyses assessing the conceptual feasibility of a large capacity heat pump for enhancing active cooling of hypersonic aircraft structure are presented. A unique heat pump arrangement which permits cooling the structure of a Mach 6 transport to aluminum temperatures without the aid of thermal shielding is described. The selected concept is compatible with the use of conventional refrigerants, with Freon R-11 selected as the preferred refrigerant. Condenser temperatures were limited to levels compatible with the use of conventional refrigerants by incorporating a unique multipass condenser design, which extracts mechanical energy from the hydrogen fuel, prior to each subsequent pass through the condenser. Results show that it is technically feasible to use a large capacity heat pump in lieu of external shielding. Additional analyses are required to optimally apply this concept.

Crystal Structure of Two V-shaped Ligands with N-Heterocycles

NASA Astrophysics Data System (ADS)

Wang, Gao-Feng; Sun, Shu-Wen; Zhang, Xiao; Sun, Shu-Gang

2017-12-01

Two V-shaped ligands with N-heterocycles, bis(4-(1 H-imidazol-1-yl) phenyl)methanone ( 1), and bis(4-(1 H-benzo[d]imidazol-1-yl)phenyl)methanone ( 2) have been synthesized and characterized by elemental analyses, IR and 1 H NMR spectroscopy. Crystal structures of 1 and 2 have been determined by X-ray diffraction. The crystal of 1 is monoclinic, sp. gr. P21/ c, Z = 4. The crystal of 2 is orthorhombic, sp. gr. Fdd2, Z = 8. X-ray diffraction analyses show that the V-shaped angles of 1 and 2 are 122.72(15)° and 120.7(4)°, respectively. Intermolecular C-H···O, C-H···N, C-H···π, and π···π interactions link the components into three-dimensional networks in the crystal structures.

Contemporary ultrasonic signal processing approaches for nondestructive evaluation of multilayered structures

NASA Astrophysics Data System (ADS)

Zhang, Guang-Ming; Harvey, David M.

2012-03-01

Various signal processing techniques have been used for the enhancement of defect detection and defect characterisation. Cross-correlation, filtering, autoregressive analysis, deconvolution, neural network, wavelet transform and sparse signal representations have all been applied in attempts to analyse ultrasonic signals. In ultrasonic nondestructive evaluation (NDE) applications, a large number of materials have multilayered structures. NDE of multilayered structures leads to some specific problems, such as penetration, echo overlap, high attenuation and low signal-to-noise ratio. The signals recorded from a multilayered structure are a class of very special signals comprised of limited echoes. Such signals can be assumed to have a sparse representation in a proper signal dictionary. Recently, a number of digital signal processing techniques have been developed by exploiting the sparse constraint. This paper presents a review of research to date, showing the up-to-date developments of signal processing techniques made in ultrasonic NDE. A few typical ultrasonic signal processing techniques used for NDE of multilayered structures are elaborated. The practical applications and limitations of different signal processing methods in ultrasonic NDE of multilayered structures are analysed.

Effect of tyrosinase-aided crosslinking on the IgE binding potential and conformational structure of shrimp (Metapenaeus ensis) tropomyosin.

PubMed

Ahmed, Ishfaq; Lv, Liangtao; Lin, Hong; Li, Zhenxing; Ma, Jiaju; Guanzhi, Chen; Sun, Lirui; Xu, Lili

2018-05-15

The present study was performed to determine crosslinking and oxidative reactions catalyzed by tyrosinase (Tyr), caffeic acid (CA) and their combination with respect to IgE binding potential and conformational structure of shrimp tropomyosin (TM). Cross-links and IgE binding potentials were analyzed by SDS-PAGE, western blot and indirect ELISA. While structural changes were characterized using surface hydrophobicity, ultraviolet (UV), fluorescence and circular dichroism (CD) spectroscopies. Maximum reduction in the IgG (37.19%) and IgE binding potentials (49.41%) were observed when treated with 2000 nkat/g Tyr + CA, as indicated by ELISA analyses. These findings correlated well with the denaturation of protein, as evident by slight blue shift and alterations in the ellipticities observed via structural analyses. The results demonstrated that addition of CA mediator with Tyr pronouncedly enhanced crosslinking, and altered the conformational structure, thereby mitigated allergenicity of TM, thus showing promise in developing novel food structures with reduced allergenic potential. Copyright © 2017 Elsevier Ltd. All rights reserved.

Static Structural Analysis of a Variable Span Morphing Wing for Unmanned Aerial Vehicle

NASA Astrophysics Data System (ADS)

Bashir, M.; Rajendran, P.

2018-05-01

While the primary reason to develop an adaptive wing is the aerodynamic benefits, the primary hindrance is the structural and vibrational considerations due to the unsteady nature of the airflow during the flight. Hence this study forms an important part of the morphable wing technology. In this paper, the design of a moderate aspect ratio variable span wing will be performed. The morphing wing is modeled structurally to observe the effect of spanwise load distribution on the wing structure. For the structural design and analysis of the unmanned aerial vehicle (UAV) under this study, commercial software Solidworks and Ansys/Static Structural/Modal are used. The static structural analyses of the wing are performed under different load conditions. The results of these analyses show that the designed structure is safe within the flight envelope. It is observed that the wing-root bending moment increases drastically due to an increase in the wingspan. Thus, the bending moment along the wingspan of the morphing wing is much larger than that of the conventional wing which results in an increase in the deflection of the free-end. The maximum stress for the un-extended wing configuration increases for the extended wing configuration.

Study on structural characteristics of pillared clay modified phosphate fertilizers and its increase efficiency mechanism*

PubMed Central

Wu, Ping-xiao; Liao, Zong-wen

2005-01-01

Three types of new high-efficiency phosphate fertilizers were made when pillared clays at certain proportions were added into ground phosphate rock. Chemical analyses showed that their soluble phosphorus content decreased more than that of superphosphate. Pot experiment showed that, under equal weights, the new fertilizers increased their efficiency by a large margin over that of superphosphate. Researches on their structures by means of XRD, IR and EPR spectrum revealed that their crystal structures changed considerably, improving their activity and preventing the fixation of available phosphorus in the soil, and consequently, greatly improved the bioavailability and became the main cause of the increase of biomass. PMID:15682504

Magnetic and neutron diffraction study on quaternary oxides MTeMoO6 (M = Mn and Zn)

NASA Astrophysics Data System (ADS)

Doi, Yoshihiro; Suzuki, Ryo; Hinatsu, Yukio; Ohoyama, Kenji

2009-01-01

Crystal structures and magnetic properties of quaternary oxides MTeMoO6 (M = Mn and Zn) were investigated. From the Rietveld analyses for the powder x-ray and neutron diffraction measurements, their detailed structures have been determined. Both compounds have orthorhombic structure with space group P 21212 and a charge configuration of M2+Te4+Mo6+O6. ZnTeMoO6 shows diamagnetic behavior. In this structure, M ions are arranged in a square-planar manner. The temperature dependence of the magnetic susceptibility for MnTeMoO6 shows a broad peak at ~33 K, which is due to a two-dimensional characteristic of the magnetic interaction. In addition, this compound shows an antiferromagnetic transition at 20 K. The magnetic structure was determined by the powder neutron diffraction measurement at 3.3 K. The magnetic moments of Mn2+ ions (4.45 μB) order in a collinear antiferromagnetic arrangement along the b axis.

Characterization of protein and carbohydrate mid-IR spectral features in crop residues

NASA Astrophysics Data System (ADS)

Xin, Hangshu; Zhang, Yonggen; Wang, Mingjun; Li, Zhongyu; Wang, Zhibo; Yu, Peiqiang

2014-08-01

To the best of our knowledge, a few studies have been conducted on inherent structure spectral traits related to biopolymers of crop residues. The objective of this study was to characterize protein and carbohydrate structure spectral features of three field crop residues (rice straw, wheat straw and millet straw) in comparison with two crop vines (peanut vine and pea vine) by using Fourier transform infrared spectroscopy (FTIR) technique with attenuated total reflectance (ATR). Also, multivariate analyses were performed on spectral data sets within the regions mainly related to protein and carbohydrate in this study. The results showed that spectral differences existed in mid-IR peak intensities that are mainly related to protein and carbohydrate among these crop residue samples. With regard to protein spectral profile, peanut vine showed the greatest mid-IR band intensities that are related to protein amide and protein secondary structures, followed by pea vine and the rest three field crop straws. The crop vines had 48-134% higher spectral band intensity than the grain straws in spectral features associated with protein. Similar trends were also found in the bands that are mainly related to structural carbohydrates (such as cellulosic compounds). However, the field crop residues had higher peak intensity in total carbohydrates region than the crop vines. Furthermore, spectral ratios varied among the residue samples, indicating that these five crop residues had different internal structural conformation. However, multivariate spectral analyses showed that structural similarities still exhibited among crop residues in the regions associated with protein biopolymers and carbohydrate. Further study is needed to find out whether there is any relationship between spectroscopic information and nutrition supply in various kinds of crop residue when fed to animals.

Characterization of protein and carbohydrate mid-IR spectral features in crop residues.

PubMed

Xin, Hangshu; Zhang, Yonggen; Wang, Mingjun; Li, Zhongyu; Wang, Zhibo; Yu, Peiqiang

2014-08-14

To the best of our knowledge, a few studies have been conducted on inherent structure spectral traits related to biopolymers of crop residues. The objective of this study was to characterize protein and carbohydrate structure spectral features of three field crop residues (rice straw, wheat straw and millet straw) in comparison with two crop vines (peanut vine and pea vine) by using Fourier transform infrared spectroscopy (FTIR) technique with attenuated total reflectance (ATR). Also, multivariate analyses were performed on spectral data sets within the regions mainly related to protein and carbohydrate in this study. The results showed that spectral differences existed in mid-IR peak intensities that are mainly related to protein and carbohydrate among these crop residue samples. With regard to protein spectral profile, peanut vine showed the greatest mid-IR band intensities that are related to protein amide and protein secondary structures, followed by pea vine and the rest three field crop straws. The crop vines had 48-134% higher spectral band intensity than the grain straws in spectral features associated with protein. Similar trends were also found in the bands that are mainly related to structural carbohydrates (such as cellulosic compounds). However, the field crop residues had higher peak intensity in total carbohydrates region than the crop vines. Furthermore, spectral ratios varied among the residue samples, indicating that these five crop residues had different internal structural conformation. However, multivariate spectral analyses showed that structural similarities still exhibited among crop residues in the regions associated with protein biopolymers and carbohydrate. Further study is needed to find out whether there is any relationship between spectroscopic information and nutrition supply in various kinds of crop residue when fed to animals. Copyright © 2014 Elsevier B.V. All rights reserved.

Analysing the magnetopause internal structure: new possibilities offered by MMS

NASA Astrophysics Data System (ADS)

Belmont, G.; Rezeau, L.; Manuzzo, R.; Aunai, N.; Dargent, J.

2017-12-01

We explore the structure of the magnetopause using a crossing observed by the MMS spacecraft on October 16th, 2015. Several methods (MVA, BV, CVA) are first applied to compute the normal to the magnetopause considered as a whole. The different results obtained are not identical and we show that the whole boundary is not stationary and not planar, so that basic assumptions of these methods are not well satisfied. We then analyse more finely the internal structure for investigating the departures from planarity. Using the basic mathematical definition of what is a one-dimensional physical problem, we introduce a new method, called LNA (Local Normal Analysis) for determining the varying normal, and we compare the results so obtained with those coming from the MDD tool developed by [Shi et al., 2005]. This method gives the dimensionality of the magnetic variations from multi-point measurements and allows estimating the direction of the local normal using the magnetic field. On the other hand, LNA is a single-spacecraft method which gives the local normal from the magnetic field and particle data. This study shows that the magnetopause does include approximate one-dimensional sub-structures but also two and three dimensional intervals. It also shows that the dimensionality of the magnetic variations can differ from the variations of the other fields so that, at some places, the magnetic field can have a 1D structure although all the plasma variations do not verify the properties of a global one-dimensional problem. Finally a generalisation and a systematic application of the MDD method to the physical quantities of interest is shown.

Identification, structural characterisation and expression analysis of a defensin gene from the tiger beetle Calomera littoralis (Coleoptera: Cicindelidae).

PubMed

Rodríguez-García, María Juliana; García-Reina, Andrés; Machado, Vilmar; Galián, José

2016-09-01

In this study, a defensin gene (Clit-Def) has been characterised in the tiger beetle Calomera littoralis for the first time. Bioinformatic analysis showed that the gene has an open reading frame of 246bp that contains a 46 amino acid mature peptide. The phylogenetic analysis showed a high variability in the coleopteran defensins analysed. The Clit-Def mature peptide has the features to be involved in the antimicrobial function: a predicted cationic isoelectric point of 8.94, six cysteine residues that form three disulfide bonds, and the typical cysteine-stabilized α-helix β-sheet (CSαβ) structural fold. Real time quantitative PCR analysis showed that Clit-Def was upregulated in the different body parts analysed after infection with lipopolysaccharides of Escherichia coli, and also indicated that has an expression peak at 12h post infection. The expression patterns of Clit-Def suggest that this gene plays important roles in the humoral system in the adephagan beetle Calomera littoralis. Copyright © 2016 Elsevier B.V. All rights reserved.

The dark side of technologies: technostress among users of information and communication technologies.

PubMed

Salanova, Marisa; Llorens, Susana; Cifre, Eva

2013-01-01

This paper tests the structure and the predictors of two psychological experiences of technostress associated with the use of information and communication technologies (ICT), i.e., technostrain (users report feelings of anxiety, fatigue, scepticism and inefficacy beliefs related to the use of technologies) and technoaddiction (users feel bad due to an excessive and compulsive use of these technologies). The study included a sample of 1072 ICT users (N = 675 nonintensive ICT users and N = 397 intensive ICT users). Results from multigroup confirmatory factor analyses among non-intensive and intensive ICT users showed, as expected, the four-factor structure of technostrain in both samples. Secondly, and also as expected, confirmatory factorial analyses revealed that technostress experiences are characterized not only by technostrain but also by an excessive and compulsive use of ICT. Moreover, multiple analyses of variance showed significant differences between non-intensive and intensive ICT users (1) in the dimensions of technostress and (2) in specific job demands and job/personal resources. Finally, linear multiple regression analyses revealed that technostrain is positively predicted by work overload, role ambiguity, emotional overload, mobbing and obstacles hindering ICT use, as well as by lack of autonomy, transformational leadership, social support, ICT use facilitators and mental competences. Work overload, role ambiguity and mobbing, as well as the lack of emotional competences, positively predict technoaddiction. Theoretical and practical implications, in addition to future research, are discussed.

Distribution pattern and genetic structure of Aedes zammitii (Diptera: Culicidae) along the Mediterranean and Aegean coasts of Turkey.

PubMed

Yavasoglu, Sare Ilknur; Simsek, Fatih Mehmet; Ulger, Celal

2016-06-01

The Mariae species complex, consisting of Aedes mariae, Aedes phoeniciae, and Aedes zammitii, has a limited distribution worldwide. All three species are found in rocky habitats on the coastal areas of Mediterranean countries. Aedes phoeniciae and Ae. zammitii are two members of the Mariae complex that exist in Turkey. The aim of this study was to determine the distribution pattern and genetic structure of Ae. zammitii along the Mediterranean and Aegean regions. For this purpose, larval and adult samples of Ae. zammitii were collected from 19 different rocky habitats along the coastal regions of Antalya, Muğla, Aydın, İzmir, Balıkesir, and Çanakkale provinces. DNA isolation was performed primarily from collected samples, and mitochondrial NADH dehydrogenase 4 (ND4) gene was amplified by polymerase chain reaction. Based on ND4 sequence analyses, 21 haplotypes were detected along the distribution range of the species. Analyses of molecular variance (AMOVA) and spatial analyses of molecular variance (SAMOVA) indicated six groups, and most of the variation was among groups, demonstrating the population structuring at group level. Isolation by distance analyses (IBD) showed a correlation between geographic and genetic distances. © 2016 The Society for Vector Ecology.

Stardust Interstellar Preliminary Examination V: XRF Analyses of Interstellar Dust Candidates at ESRF ID13

NASA Technical Reports Server (NTRS)

Brenker, Frank E.; Westphal, Andrew J.; Simionovici, Alexandre S.; Flynn, George J.; Gainsforth, Zack; Allen, Carlton C.; Sanford, Scott; Zolensky, Michael E.; Bastien, Ron K.; Frank, David R.

2014-01-01

Here, we report analyses by synchrotron X-ray fluorescence microscopy of the elemental composition of eight candidate impact features extracted from the Stardust Interstellar Dust Collector (SIDC). Six of the features were unambiguous tracks, and two were crater-like features. Five of the tracks are so-called midnight tracks that is, they had trajectories consistent with an origin either in the interstellar dust stream or as secondaries from impacts on the Sample Return Capsule (SRC). In a companion paper reporting synchrotron X-ray diffraction analyses of ISPE candidates, we show that two of these particles contain natural crystalline materials: the terminal particle of track 30contains olivine and spinel, and the terminal particle of track 34 contains olivine. Here, we show that the terminal particle of track 30, Orion, shows elemental abundances, normalized to Fe, that are close to CI values, and a complex, fine-grained structure. The terminal particle of track 34, Hylabrook, shows abundances that deviate strongly from CI, but shows little fine structure and is nearly homogenous. The terminal particles of other midnight tracks, 29 and 37, had heavy element abundances below detection threshold. A third, track28, showed a composition inconsistent with an extraterrestrial origin, but also inconsistent with known spacecraft materials. A sixth track, with a trajectory consistent with secondary ejecta from an impact on one of the spacecraft solar panels, contains abundant Ce and Zn. This is consistent with the known composition of the glass covering the solar panel. Neither crater-like feature is likely to be associated with extraterrestrial materials. We also analyzed blank aerogel samples to characterize background and variability between aerogel tiles. We found significant differences in contamination levels and compositions, emphasizing the need for local background subtraction for accurate quantification.

Students' Achievement Goal Orientations and Their Behavioral and Emotional Engagement: Co-Examining the Role of Perceived School Goal Structures and Parent Goals during Adolescence

ERIC Educational Resources Information Center

Gonida, Eleftheria N.; Voulala, Katerina; Kiosseoglou, Grigoris

2009-01-01

The role of perceived school goal structures and parent goals in predicting adolescents' goal orientations and their behavioral and emotional engagement in the classroom was examined in the present study. Surveys were given to a sample of 271 seventh- and ninth-grade students. Path analyses showed that (a) perceived school mastery goal structures…

Surface modification of EPDM rubber by plasma treatment.

PubMed

Grythe, Kai Frode; Hansen, Finn Knut

2006-07-04

The effect of argon, oxygen, and nitrogen plasma treatment of solvent cast EPDM rubber films has been investigated by means of atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), and surface energy measurements. Plasma treatment leads to changes in the surface energy from 25 to 70 mN/m. Treatment conditions influenced both the changes in surface energy and the stability, and it became more difficult to obtain good contact angle measurements after longer (> ca. 4 min) treatment times, probably because of an increasingly uneven surface structure. XPS analyses revealed that up to 20 at. % oxygen can be easily incorporated and that variations of approximately 5% can be controlled by the plasma conditions. Oxygen was mainly found in hydroxyl groups, but also as carbonyl and carboxyl. XPS analyses showed more stable surfaces than expected from contact angles, probably because XPS analysis is less surface sensitive than contact angle measurements. AFM measurements revealed different surface structures with the three gases. The surface roughness increased generally with treatment time, and dramatic changes could be observed at longer times. At short times, surface energy changes were much faster than the changes in surface structure, showing that plasma treatment conditions can be utilized to tailor both surface energies and surface structure of EPDM rubber.

Variability and genetic structure of the population of watermelon mosaic virus infecting melon in Spain.

PubMed

Moreno, I M; Malpica, J M; Díaz-Pendón, J A; Moriones, E; Fraile, A; García-Arenal, F

2004-01-05

The genetic structure of the population of Watermelon mosaic virus (WMV) in Spain was analysed by the biological and molecular characterisation of isolates sampled from its main host plant, melon. The population was a highly homogeneous one, built of a single pathotype, and comprising isolates closely related genetically. There was indication of temporal replacement of genotypes, but not of spatial structure of the population. Analyses of nucleotide sequences in three genomic regions, that is, in the cistrons for the P1, cylindrical inclusion (CI) and capsid (CP) proteins, showed lower similar values of nucleotide diversity for the P1 than for the CI or CP cistrons. The CI protein and the CP were under tighter evolutionary constraints than the P1 protein. Also, for the CI and CP cistrons, but not for the P1 cistron, two groups of sequences, defining two genetic strains, were apparent. Thus, different genomic regions of WMV show different evolutionary dynamics. Interestingly, for the CI and CP cistrons, sequences were clustered into two regions of the sequence space, defining the two strains above, and no intermediary sequences were identified. Recombinant isolates were found, accounting for at least 7% of the population. These recombinants presented two interesting features: (i) crossover points were detected between the analysed regions in the CI and CP cistrons, but not between those in the P1 and CI cistrons, (ii) crossover points were not observed within the analysed coding regions for the P1, CI or CP proteins. This indicates strong selection against isolates with recombinant proteins, even when originated from closely related strains. Hence, data indicate that genotypes of WMV, generated by mutation or recombination, outside of acceptable, discrete, regions in the evolutionary space, are eliminated from the virus population by negative selection.

A comprehensive visual rating scale of brain magnetic resonance imaging: application in elderly subjects with Alzheimer's disease, mild cognitive impairment, and normal cognition.

PubMed

Jang, Jae-Won; Park, So Young; Park, Young Ho; Baek, Min Jae; Lim, Jae-Sung; Youn, Young Chul; Kim, SangYun

2015-01-01

Brain magnetic resonance imaging (MRI) shows cerebral structural changes. However, a unified comprehensive visual rating scale (CVRS) has seldom been studied. Thus, we combined brain atrophy and small vessel disease scales and used an MRI template as a CVRS. The aims of this study were to design a simple and reliable CVRS, validate it by investigating cerebral structural changes in clinical groups, and made comparison to the volumetric measurements. Elderly subjects (n = 260) with normal cognition (NC, n = 65), mild cognitive impairment (MCI, n = 101), or Alzheimer's disease (AD, n = 94) were evaluated with brain MRI according to the CVRS of brain atrophy and small vessel disease. Validation of the CVRS with structural changes, neuropsychological tests, and volumetric analyses was performed. The CVRS revealed a high intra-rater and inter-rater agreement and it reflected the structural changes of subjects with NC, MCI, and AD better than volumetric measures (CVRS-coronal: F = 13.5, p < 0.001; CVRS-axial: F = 19.9, p < 0.001). The area under the receiver operation curve (aROC) of the CVRS showed higher accuracy than volumetric analyses. (NC versus MCI aROC: CVRS-coronal, 0.777; CVRS-axial, 0.773; MCI versus AD aROC: CVRS-coronal, 0.680; CVRS-axial, 0.681). The CVRS can be used clinically to conveniently measure structural changes of brain. It reflected cerebral structural changes of clinical groups and correlated with the age better than volumetric measures.

Posttest analysis of a 1:6-scale reinforced concrete reactor containment building

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

Weatherby, J.R.

In an experiment conducted at Sandia National Laboratories, 1:6-scale model of a reinforced concrete light water reactor containment building was pressurized with nitrogen gas to more than three times its design pressure. The pressurization produced one large tear and several smaller tears in the steel liner plate that functioned as the primary pneumatic seal for the structure. The data collected from the overpressurization test have been used to evaluate and further refine methods of structural analysis that can be used to predict the performance of containment buildings under conditions produced by a severe accident. This report describes posttest finite elementmore » analyses of the 1:6-scale model tests and compares pretest predictions of the structural response to the experimental results. Strain and displacements calculated in axisymmetric finite element analyses of the 1:6-scale model are compared to strains and displacement measured in the experiment. Detailed analyses of the liner plate are also described in the report. The region of the liner surrounding the large tear was analyzed using two different two-dimensional finite elements model. The results from these analyzed indicate that the primary mechanisms that initiated the tear can be captured in a two- dimensional finite element model. Furthermore, the analyses show that studs used to anchor the liner to the concrete wall, played an important role in initiating the liner tear. Three-dimensional finite element analyses of liner plates loaded by studs are also presented. Results from the three-dimensional analyses are compared to results from two-dimensional analyses of the same problems. 12 refs., 56 figs., 1 tab.« less

Assessing cognitive insight in nonpsychiatric individuals and outpatients with schizophrenia in Taiwan: an investigation using the Beck Cognitive Insight Scale

PubMed Central

2011-01-01

Background The Beck Cognitive Insight Scale (BCIS) was designed for the assessment of the cognitive processes involved in self-reflection and the ability to modify erroneous beliefs and misinterpretations. Studies investigating the factor structure of the BCIS have indicated a two-factor model in the psychotic population. The factor structure of the BCIS, however, has not received much consideration in the nonpsychiatric population. The present study examined the factor structure and validity of the BCIS and compared its scores between nonpsychiatric individuals and outpatients with psychosis. Method The Taiwanese version of the BCIS was administered to 507 nonpsychiatric individuals and 118 outpatients with schizophrenia. The psychometric properties of the BCIS were examined through the following analyses: exploratory and confirmatory factor analyses, reliability, correlation analyses, and discriminative validity. Results The BCIS showed adequate internal consistency and stability over time. Exploratory and confirmatory factor analyses on the 15-item measure indicated a two-factor solution that supported the two dimensions of the Taiwanese BCIS, which was also observed with the original BCIS. Following the construct validation, we obtained a composite index (self-reflectiveness minus self-certainty) of the Taiwanese BCIS that reflected cognitive insight. Consistent with previous studies, our results indicated that psychosis is associated with low self-reflectiveness and high self-certainty, which possibly reflect lower cognitive insight. Our results also showed that better cognitive insight is related to worse depression in patients with schizophrenia spectrum disorders, but not in nonpsychiatric individuals. The receiver operating characteristic (ROC) analyses revealed that the area under the curve (AUC) was 0.731. A composite index of 3 was a good limit, with a sensitivity of 87% and a specificity of 51%. Conclusion The BCIS proved to be useful for measuring cognitive insight in Taiwanese nonpsychiatric and psychotic populations. PMID:22018413

The structure of harassment and abuse in the workplace: a factorial comparison of two measures.

PubMed

Fendrich, Michael; Woodword, Paul; Richman, Judith A

2002-08-01

The structures of two measures examining negative experiences in the workplace, one focusing primarily on sexual harassment (SEQ) and one focusing on workplace abuse (GWA), were examined in detail. This article investigated whether the five subscales for the relatively unexplored measure (GWA) are reliably measured by a single underlying construct. It also investigated whether the two workplace-based measures are distinct but related constructs and the consistency of their factor structure across genders. Using a large and diverse organizational survey derived from a Midwestern university, analyses supported the distinctiveness of the two measures and showed that the factor structures for the two constructs were remarkably similar across genders. Analyses also suggested that indices of extreme behavior within each of the constructs were not reliably measured. The findings have important implications for data collection strategies in research focused on negative workplace experiences. This study provides considerable support for the continued use of both measures in research investigating the impact of adverse workplace environment on health.

Assessment of biofilm changes and concentration-depth profiles during arsenopyrite oxidation by Acidithiobacillus thiooxidans.

PubMed

Ramírez-Aldaba, Hugo; Vazquez-Arenas, Jorge; Sosa-Rodríguez, Fabiola S; Valdez-Pérez, Donato; Ruiz-Baca, Estela; García-Meza, Jessica Viridiana; Trejo-Córdova, Gabriel; Lara, René H

2017-08-01

Biofilm formation and evolution are key factors to consider to better understand the kinetics of arsenopyrite biooxidation. Chemical and surface analyses were carried out using Raman spectroscopy, scanning electron microscopy (SEM), confocal laser scanning microscopy (CLSM), glow discharge spectroscopy (GDS), and protein analysis (i.e., quantification) in order to evaluate the formation of intermediate secondary compounds and any significant changes arising in the biofilm structure of Acidithiobacillus thiooxidans during a 120-h period of biooxidation. Results show that the biofilm first evolves from a low cell density structure (1 to 12 h) into a formation of microcolonies (24 to 120 h) and then finally becomes enclosed by a secondary compound matrix that includes pyrite (FeS 2 )-like, S n 2- /S 0 , and As 2 S 3 compounds, as shown by Raman and SEM-EDS. GDS analyses (concentration-depth profiles, i.e., 12 h) indicate significant differences for depth speciation between abiotic control and biooxidized surfaces, thus providing a quantitative assessment of surface-bulk changes across samples (i.e. reactivity and /or structure-activity relationship). Respectively, quantitative protein analyses and CLSM analyses suggest variations in the type of extracellular protein expressed and changes in the biofilm structure from hydrophilic (i.e., exopolysaccharides) to hydrophobic (i.e., lipids) due to arsenopyrite and cell interactions during the 120-h period of biooxidation. We suggest feasible environmental and industrial implications for arsenopyrite biooxidation based on the findings of this study.

Influence of hyperbaric oxygen on biomechanics and structural bone matrix in type 1 diabetes mellitus rats.

PubMed

Limirio, Pedro Henrique Justino Oliveira; da Rocha Junior, Huberth Alexandre; Morais, Richarlisson Borges de; Hiraki, Karen Renata Nakamura; Balbi, Ana Paula Coelho; Soares, Priscilla Barbosa Ferreira; Dechichi, Paula

2018-01-01

The aim of this study was to evaluate the biomechanics and structural bone matrix in diabetic rats subjected to hyperbaric oxygen therapy (HBO). Twenty-four male rats were divided into the following groups: Control; Control + HBO; Diabetic, and Diabetic + HBO. Diabetes was induced with streptozotocin (STZ) in the diabetic Groups. After 30 days, HBO was performed every 48h in HBO groups and all animals were euthanized 60 days after diabetic induction. The femur was submitted to a biomechanical (maximum strength, energy-to-failure and stiffness) and Attenuated Total Reflectance Fourier transform infrared (ATR-FTIR) analyses (crosslink ratio, crystallinity index, matrix-to-mineral ratio: Amide I + II/Hydroxyapatite (M:MI) and Amide III + Collagen/HA (M:MIII)). In biomechanical analysis, diabetic animals showed lower values of maximum strength, energy and stiffness than non-diabetic animals. However, structural strength and stiffness were increased in groups with HBO compared with non-HBO. ATR-FTIR analysis showed decreased collagen maturity in the ratio of crosslink peaks in diabetic compared with the other groups. The bone from the diabetic groups showed decreased crystallinity compared with non-diabetic groups. M:MI showed no statistical difference between groups. However, M:MIII showed an increased matrix mineral ratio in diabetic+HBO and control+HBO compared with control and diabetic groups. Correlations between mechanical and ATR-FTIR analyses showed significant positive correlation between collagen maturity and stiffness. Diabetes decreased collagen maturation and the mineral deposition process, thus reducing biomechanical properties. Moreover, the study showed that HBO improved crosslink maturation and increased maximum strength and stiffness in the femur of T1DM animals.

Structural analyses of Legionella LepB reveal a new GAP fold that catalytically mimics eukaryotic RasGAP.

PubMed

Yu, Qin; Hu, Liyan; Yao, Qing; Zhu, Yongqun; Dong, Na; Wang, Da-Cheng; Shao, Feng

2013-06-01

Rab GTPases are emerging targets of diverse bacterial pathogens. Here, we perform biochemical and structural analyses of LepB, a Rab GTPase-activating protein (GAP) effector from Legionella pneumophila. We map LepB GAP domain to residues 313-618 and show that the GAP domain is Rab1 specific with a catalytic activity higher than the canonical eukaryotic TBC GAP and the newly identified VirA/EspG family of bacterial RabGAP effectors. Exhaustive mutation analyses identify Arg444 as the arginine finger, but no catalytically essential glutamine residues. Crystal structures of LepB313-618 alone and the GAP domain of Legionella drancourtii LepB in complex with Rab1-GDP-AlF3 support the catalytic role of Arg444, and also further reveal a 3D architecture and a GTPase-binding mode distinct from all known GAPs. Glu449, structurally equivalent to TBC RabGAP glutamine finger in apo-LepB, undergoes a drastic movement upon Rab1 binding, which induces Rab1 Gln70 side-chain flipping towards GDP-AlF3 through a strong ionic interaction. This conformationally rearranged Gln70 acts as the catalytic cis-glutamine, therefore uncovering an unexpected RasGAP-like catalytic mechanism for LepB. Our studies highlight an extraordinary structural and catalytic diversity of RabGAPs, particularly those from bacterial pathogens.

Analysis and Application of European Genetic Substructure Using 300 K SNP Information

PubMed Central

Tian, Chao; Plenge, Robert M; Ransom, Michael; Lee, Annette; Villoslada, Pablo; Selmi, Carlo; Klareskog, Lars; Pulver, Ann E; Qi, Lihong; Gregersen, Peter K; Seldin, Michael F

2008-01-01

European population genetic substructure was examined in a diverse set of >1,000 individuals of European descent, each genotyped with >300 K SNPs. Both STRUCTURE and principal component analyses (PCA) showed the largest division/principal component (PC) differentiated northern from southern European ancestry. A second PC further separated Italian, Spanish, and Greek individuals from those of Ashkenazi Jewish ancestry as well as distinguishing among northern European populations. In separate analyses of northern European participants other substructure relationships were discerned showing a west to east gradient. Application of this substructure information was critical in examining a real dataset in whole genome association (WGA) analyses for rheumatoid arthritis in European Americans to reduce false positive signals. In addition, two sets of European substructure ancestry informative markers (ESAIMs) were identified that provide substantial substructure information. The results provide further insight into European population genetic substructure and show that this information can be used for improving error rates in association testing of candidate genes and in replication studies of WGA scans. PMID:18208329

Constraints and spandrels of interareal connectomes

PubMed Central

Rubinov, Mikail

2016-01-01

Interareal connectomes are whole-brain wiring diagrams of white-matter pathways. Recent studies have identified modules, hubs, module hierarchies and rich clubs as structural hallmarks of these wiring diagrams. An influential current theory postulates that connectome modules are adequately explained by evolutionary pressures for wiring economy, but that the other hallmarks are not explained by such pressures and are therefore less trivial. Here, we use constraint network models to test these postulates in current gold-standard vertebrate and invertebrate interareal-connectome reconstructions. We show that empirical wiring-cost constraints inadequately explain connectome module organization, and that simultaneous module and hub constraints induce the structural byproducts of hierarchies and rich clubs. These byproducts, known as spandrels in evolutionary biology, include the structural substrate of the default-mode network. Our results imply that currently standard connectome characterizations are based on circular analyses or double dipping, and we emphasize an integrative approach to future connectome analyses for avoiding such pitfalls. PMID:27924867

Constraints and spandrels of interareal connectomes.

PubMed

Rubinov, Mikail

2016-12-07

Interareal connectomes are whole-brain wiring diagrams of white-matter pathways. Recent studies have identified modules, hubs, module hierarchies and rich clubs as structural hallmarks of these wiring diagrams. An influential current theory postulates that connectome modules are adequately explained by evolutionary pressures for wiring economy, but that the other hallmarks are not explained by such pressures and are therefore less trivial. Here, we use constraint network models to test these postulates in current gold-standard vertebrate and invertebrate interareal-connectome reconstructions. We show that empirical wiring-cost constraints inadequately explain connectome module organization, and that simultaneous module and hub constraints induce the structural byproducts of hierarchies and rich clubs. These byproducts, known as spandrels in evolutionary biology, include the structural substrate of the default-mode network. Our results imply that currently standard connectome characterizations are based on circular analyses or double dipping, and we emphasize an integrative approach to future connectome analyses for avoiding such pitfalls.

Structural investigation of re-deposited layers in JET

NASA Astrophysics Data System (ADS)

Likonen, J.; Vainonen-Ahlgren, E.; Khriachtchev, L.; Coad, J. P.; Rubel, M.; Renvall, T.; Arstila, K.; Hole, D. E.; Contributors to the EFDA-JET Work-programme

2008-07-01

JET Mk-II Gas Box divertor tiles exposed in 1998-2001 have been analysed with various ion beam techniques, secondary ion mass spectrometry (SIMS) and Raman spectroscopy. Inner divertor wall tiles removed in 2001 were covered with a duplex film. The inner layer was very rich in metallic impurities, with Be/C ˜ 1 and H-isotopes only present at low concentrations. The outer layer contained higher concentrations of D than normal for plasma-facing surfaces in JET (D/C ˜ 0.4), and Be/C ˜ 0.14. Raman and SIMS analyses show that the deposited films on inner divertor tiles are hydrogenated amorphous carbon with low sp 3 fractions. The deposits have polymeric structure and low density. Both Raman scattering and SIMS indicate that films on inner divertor wall Tiles 1 and 3, and on floor Tile 4 have some differences in the chemical structure of the deposited films

Structural and biochemical analyses of YvgN and YtbE from Bacillus subtilis

PubMed Central

Lei, Jian; Zhou, Yan-Feng; Li, Lan-Fen; Su, Xiao-Dong

2009-01-01

Bacillus subtilis is one of the most studied gram-positive bacteria. In this work, YvgN and YtbE from B. subtilis, assigned as AKR5G1 and AKR5G2 of aldo-keto reductase (AKR) superfamily. AKR catalyzes the NADPH-dependent reduction of aldehyde or aldose substrates to alcohols. YvgN and YtbE were studied by crystallographic and enzymatic analyses. The apo structures of these proteins were determined by molecular replacement, and the structure of holoenzyme YvgN with NADPH was also solved, revealing the conformational changes upon cofactor binding. Our biochemical data suggest both YvgN and YtbE have preferential specificity for derivatives of benzaldehyde, such as nitryl or halogen group substitution at the 2 or 4 positions. These proteins also showed broad catalytic activity on many standard substrates of AKR, such as glyoxal, dihydroxyacetone, and DL-glyceraldehyde, suggesting a possible role in bacterial detoxification. PMID:19585557

Analysis of Decomposition for Structure I Methane Hydrate by Molecular Dynamics Simulation

NASA Astrophysics Data System (ADS)

Wei, Na; Sun, Wan-Tong; Meng, Ying-Feng; Liu, An-Qi; Zhou, Shou-Wei; Guo, Ping; Fu, Qiang; Lv, Xin

2018-05-01

Under multi-nodes of temperatures and pressures, microscopic decomposition mechanisms of structure I methane hydrate in contact with bulk water molecules have been studied through LAMMPS software by molecular dynamics simulation. Simulation system consists of 482 methane molecules in hydrate and 3027 randomly distributed bulk water molecules. Through analyses of simulation results, decomposition number of hydrate cages, density of methane molecules, radial distribution function for oxygen atoms, mean square displacement and coefficient of diffusion of methane molecules have been studied. A significant result shows that structure I methane hydrate decomposes from hydrate-bulk water interface to hydrate interior. As temperature rises and pressure drops, the stabilization of hydrate will weaken, decomposition extent will go deep, and mean square displacement and coefficient of diffusion of methane molecules will increase. The studies can provide important meanings for the microscopic decomposition mechanisms analyses of methane hydrate.

Population genetic structure of critically endangered salamander (Hynobius amjiensis) in China: recommendations for conservation.

PubMed

Yang, J; Chen, C S; Chen, S H; Ding, P; Fan, Z Y; Lu, Y W; Yu, L P; Lin, H D

2016-06-10

Amji's salamander (Hynobius amjiensis) is a critically endangered species (IUCN Red List), which is endemic to mainland China. In the present study, five haplotypes were genotyped for the mtDNA cyt b gene in 45 specimens from three populations. Relatively low levels of haplotype diversity (h = 0.524) and nucleotide diversity (π = 0.00532) were detected. Analyses of the phylogenic structure of H. amjiensis showed no evidence of major geographic partitions or substantial barriers to historical gene flow throughout the species' range. Two major phylogenetic haplotype groups were revealed, and were estimated to have diverged about 1.262 million years ago. Mismatch distribution analysis, neutrality tests, and Bayesian skyline plots revealed no evidence of dramatic changes in the effective population size. According to the SAMOVA and STRUCTURE analyses, H. amjiensis should be regarded as two different management units.

a Study of the Synchrotron Laue Method for Quantitative Crystal Structure Analysis.

NASA Astrophysics Data System (ADS)

Gomez de Anderez, Dora M.

1990-01-01

Available from UMI in association with The British Library. Quantitative crystal structure analyses have been carried out on small molecule crystals using synchrotron radiation and the Laue method. A variety of single crystal structure determinations and associated refinements are used and compared with the monochromatic analyses. The new molecular structure of 7-amino-5-bromo -4-methyl-2-oxo-1,2,3,4-tetrahidro-1, 6 -naphthyridine-8-carbonitrile (C_{10 }H_9ON_4 Br.H_2O) has been determined, first using monochromatic Mo Kalpha radiation and a four-circle diffractometer, then using synchrotron Laue diffraction photography. The structure refinements showed a R-factor of 4.97 and 14.0% for the Mo Kalpha and Laue data respectively. The molecular structure of (S)-2-chloro-2-fluoro-N-((S)-1-phenylethyl) ethanamide, (C_{10}H _{11}ClFNO), has been determined using the same crystal throughout for X-ray monochromatic analyses (Mo Kalpha and Cu K alpha) followed by synchrotron Laue data collection. The Laue and monochromatic data compare favourably. The R -factors (on F) were 6.23, 6.45 and 8.19% for the Mo K alpha, Cu Kalpha and Laue data sets respectively. The molecular structure of 3-(5-hydroxy-3-methyl-1-phenylpyrazol-4-yl)-1,3-diphenyl -prop- 2-en-1-one, (C_{25 }H_{20}N _2O_2) has been determined using the synchrotron Laue method. The results compare very well with Mo Kalpha monochromatic data. The R-factors (on F) were 4.60 and 5.29% for Mo Kalpha and Laue analysis respectively. The Laue method is assessed in locating the 20 hydrogen atoms in this structure. The structure analysis of the benzil compound ((C_6H_5 O.CO_2)) is carried out using the synchrotron Laue method firstly at room temperature and secondly at low temperature -114 ^circC. The structure shows an R-factor (on F) of 13.06% and 6.85% for each data set respectively. The synchrotron Laue method was used to collect data for ergocalciferol (Vitamin D_2). The same crystal was also used to record oscillation data with the synchrotron radiation monochromatic beam. A new molecular structure of (Dinitrato-(N,N ^'-dimethylethylene-diamine)copper(II)) has been determined using Mo Kalpha radiation on a four circle diffractometer. The refinement resulted in an R-factor (on F) of 4.06%.

Sequence and structural analyses of nuclear export signals in the NESdb database

PubMed Central

Xu, Darui; Farmer, Alicia; Collett, Garen; Grishin, Nick V.; Chook, Yuh Min

2012-01-01

We compiled >200 nuclear export signal (NES)–containing CRM1 cargoes in a database named NESdb. We analyzed the sequences and three-dimensional structures of natural, experimentally identified NESs and of false-positive NESs that were generated from the database in order to identify properties that might distinguish the two groups of sequences. Analyses of amino acid frequencies, sequence logos, and agreement with existing NES consensus sequences revealed strong preferences for the Φ1-X3-Φ2-X2-Φ3-X-Φ4 pattern and for negatively charged amino acids in the nonhydrophobic positions of experimentally identified NESs but not of false positives. Strong preferences against certain hydrophobic amino acids in the hydrophobic positions were also revealed. These findings led to a new and more precise NES consensus. More important, three-dimensional structures are now available for 68 NESs within 56 different cargo proteins. Analyses of these structures showed that experimentally identified NESs are more likely than the false positives to adopt α-helical conformations that transition to loops at their C-termini and more likely to be surface accessible within their protein domains or be present in disordered or unobserved parts of the structures. Such distinguishing features for real NESs might be useful in future NES prediction efforts. Finally, we also tested CRM1-binding of 40 NESs that were found in the 56 structures. We found that 16 of the NES peptides did not bind CRM1, hence illustrating how NESs are easily misidentified. PMID:22833565

Asymmetric bias in user guided segmentations of brain structures

NASA Astrophysics Data System (ADS)

Styner, Martin; Smith, Rachel G.; Graves, Michael M.; Mosconi, Matthew W.; Peterson, Sarah; White, Scott; Blocher, Joe; El-Sayed, Mohammed; Hazlett, Heather C.

2007-03-01

Brain morphometric studies often incorporate comparative asymmetry analyses of left and right hemispheric brain structures. In this work we show evidence that common methods of user guided structural segmentation exhibit strong left-right asymmetric biases and thus fundamentally influence any left-right asymmetry analyses. We studied several structural segmentation methods with varying degree of user interaction from pure manual outlining to nearly fully automatic procedures. The methods were applied to MR images and their corresponding left-right mirrored images from an adult and a pediatric study. Several expert raters performed the segmentations of all structures. The asymmetric segmentation bias is assessed by comparing the left-right volumetric asymmetry in the original and mirrored datasets, as well as by testing each sides volumetric differences to a zero mean standard t-tests. The structural segmentations of caudate, putamen, globus pallidus, amygdala and hippocampus showed a highly significant asymmetric bias using methods with considerable manual outlining or landmark placement. Only the lateral ventricle segmentation revealed no asymmetric bias due to the high degree of automation and a high intensity contrast on its boundary. Our segmentation methods have been adapted in that they are applied to only one of the hemispheres in an image and its left-right mirrored image. Our work suggests that existing studies of hemispheric asymmetry without similar precautions should be interpreted in a new, skeptical light. Evidence of an asymmetric segmentation bias is novel and unknown to the imaging community. This result seems less surprising to the visual perception community and its likely cause is differences in perception of oppositely curved 3D structures.

Effects of autoclaving and high pressure on allergenicity of hazelnut proteins

PubMed Central

2012-01-01

Background Hazelnut is reported as a causative agent of allergic reactions. However it is also an edible nut with health benefits. The allergenic characteristics of hazelnut-samples after autoclaving (AC) and high-pressure (HHP) processing have been studied and are also presented here. Previous studies demonstrated that AC treatments were responsible for structural transformation of protein structure motifs. Thus, structural analyses of allergen proteins from hazelnut were carried out to observe what is occurring in relation to the specific-IgE recognition of the related allergenic proteins. The aims of this work are to evaluate the effect of AC and HHP processing on hazelnut in vitro allergenicity using human-sera and to analyse the complexity of hazelnut allergen-protein structures. Methods Hazelnut-samples were subjected to AC and HHP processing. The specific IgE- reactivity was studied in 15 allergic clinic-patients via western blotting analyses. A series of homology-based-bioinformatics 3D-models (Cora 1, Cora 8, Cora 9 and Cora 11) were generated for the antigens included in the study to analyse the co mplexity of their protein structure. This study is supported by the Declaration of Helsinki and subsequent ethical guidelines. Results A severe reduction in vitro in allergenicity to hazelnut after AC processing was observed in the allergic clinic-patients studied. The specific-IgE binding of some of the described immunoreactive hazelnut protein-bands: Cora 1 ~18KDa, Cora 8 ~9KDa, Cora 9 ~35-40KDa and Cora 11 ~47-48 KDa decreases. Furthermore a relevant glycosylation was assigned and visualized via structural analysis of proteins (3D-modelling) for the first time in the protein-allergen Cora 11 showing a new role which could open a new door for allergenicity-unravellings. Conclusion Hazelnut allergenicity-studies in vivo via Prick-Prick and other means using AC processing are crucial to verify the data we observed via in vitro analyses. Glycosylation studies provided us with clues to elucidate, in the near future, mechanisms of the structures that contribute to hazelnut allergenicity, which thus, in turn, help alleviate food allergens. PMID:22616776

Conceptual Design and Structural Analysis of an Open Rotor Hybrid Wing Body Aircraft

NASA Technical Reports Server (NTRS)

Gern, Frank H.

2013-01-01

Through a recent NASA contract, Boeing Research and Technology in Huntington Beach, CA developed and optimized a conceptual design of an open rotor hybrid wing body aircraft (HWB). Open rotor engines offer a significant potential for fuel burn savings over turbofan engines, while the HWB configuration potentially allows to offset noise penalties through possible engine shielding. Researchers at NASA Langley converted the Boeing design to a FLOPS model which will be used to develop take-off and landing trajectories for community noise analyses. The FLOPS model was calibrated using Boeing data and shows good agreement with the original Boeing design. To complement Boeing s detailed aerodynamics and propulsion airframe integration work, a newly developed and validated conceptual structural analysis and optimization tool was used for a conceptual loads analysis and structural weights estimate. Structural optimization and weight calculation are based on a Nastran finite element model of the primary HWB structure, featuring centerbody, mid section, outboard wing, and aft body. Results for flight loads, deformations, wing weight, and centerbody weight are presented and compared to Boeing and FLOPS analyses.

Genetic structure of Plasmodium falciparum populations across the Honduras-Nicaragua border.

PubMed

Larrañaga, Nerea; Mejía, Rosa E; Hormaza, José I; Montoya, Alberto; Soto, Aida; Fontecha, Gustavo A

2013-10-04

The Caribbean coast of Central America remains an area of malaria transmission caused by Plasmodium falciparum despite the fact that morbidity has been reduced in recent years. Parasite populations in that region show interesting characteristics such as chloroquine susceptibility and low mortality rates. Genetic structure and diversity of P. falciparum populations in the Honduras-Nicaragua border were analysed in this study. Seven neutral microsatellite loci were analysed in 110 P. falciparum isolates from endemic areas of Honduras (n = 77) and Nicaragua (n = 33), mostly from the border region called the Moskitia. Several analyses concerning the genetic diversity, linkage disequilibrium, population structure, molecular variance, and haplotype clustering were conducted. There was a low level of genetic diversity in P. falciparum populations from Honduras and Nicaragua. Expected heterozigosity (H(e)) results were similarly low for both populations. A moderate differentiation was revealed by the F(ST) index between both populations, and two putative clusters were defined through a structure analysis. The main cluster grouped most of samples from Honduras and Nicaragua, while the second cluster was smaller and included all the samples from the Siuna community in Nicaragua. This result could partially explain the stronger linkage disequilibrium (LD) in the parasite population from that country. These findings are congruent with the decreasing rates of malaria endemicity in Central America.

Earthquake response of heavily damaged historical masonry mosques after restoration

NASA Astrophysics Data System (ADS)

Altunışık, Ahmet Can; Fuat Genç, Ali

2017-10-01

Restoration works have been accelerated substantially in Turkey in the last decade. Many historical buildings, mosques, minaret, bridges, towers and structures have been restored. With these restorations an important issue arises, namely how restoration work affects the structure. For this reason, we aimed to investigate the restoration effect on the earthquake response of a historical masonry mosque considering the openings on the masonry dome. For this purpose, we used the Hüsrev Pasha Mosque, which is located in the Ortakapı district in the old city of Van, Turkey. The region of Van is in an active seismic zone; therefore, earthquake analyses were performed in this study. Firstly a finite element model of the mosque was constructed considering the restoration drawings and 16 window openings on the dome. Then model was constructed with eight window openings. Structural analyses were performed under dead load and earthquake load, and the mode superposition method was used in analyses. Maximum displacements, maximum-minimum principal stresses and shear stresses are given with contours diagrams. The results are analyzed according to Turkish Earthquake Code (TEC, 2007) and compared between 8 and 16 window openings cases. The results show that reduction of the window openings affected the structural behavior of the mosque positively.

Factor structure of the Body Appreciation Scale among Malaysian women.

PubMed

Swami, Viren; Chamorro-Premuzic, Tomas

2008-12-01

The present study examined the factor structure of a Malay version of the Body Appreciation Scale (BAS), a recently developed scale for the assessment of positive body image that has been shown to have a unidimensional structure in Western settings. Results of exploratory and confirmatory factor analyses based on data from community sample of 591 women in Kuala Lumpur, Malaysia, failed to support a unidimensional structure for the Malay BAS. Results of a confirmatory factor analysis suggested two stable factors, which were labelled 'General Body Appreciation' and 'Body Image Investment'. Multi-group analysis showed that the two-factor structure was invariant for both Malaysian Malay and Chinese women, and that there were no significant ethnic differences on either factor. Results also showed that General Body Appreciation was significant negatively correlated with participants' body mass index. These results are discussed in relation to possible cross-cultural differences in positive body image.

Reinforcement and validation of the analyses and conclusions related to fishway evaluation data from Bunt et al.: ‘Performance of fish passage structures at upstream barriers to migration’

USGS Publications Warehouse

Bunt, C.M.; Castro-Santos, Theodore R.; Haro, Alexander

2016-01-01

Detailed re-examination of the datasets that were used for a meta-analysis of fishway attraction and passage revealed a number of errors that we addressed and corrected. We subsequently re-analysed the revised dataset, and results showed no significant changes in the primary conclusions of the original study; for most species, effective performance cannot be assured for any fishway type.

Steroidal saponins from fresh stems of Dracaena angustifolia

USDA-ARS?s Scientific Manuscript database

Six new steroidal saponins (1-6), angudracanosides A-F, were isolated from fresh stems of Dracaena angustifolia, together with eight known compounds. The structures of compounds 1-6 were determined by detailed spectroscopic analyses and chemical methods. Antifungal testing of all compounds showed th...

Reliability, Factor Structure, and Associations With Measures of Problem Relationship and Behavior of the Personality Inventory for DSM-5 in a Sample of Italian Community-Dwelling Adolescents.

PubMed

Somma, Antonella; Borroni, Serena; Maffei, Cesare; Giarolli, Laura E; Markon, Kristian E; Krueger, Robert F; Fossati, Andrea

2017-10-01

In order to assess the reliability, factorial validity, and criterion validity of the Personality Inventory for DSM-5 (PID-5) among adolescents, 1,264 Italian high school students were administered the PID-5. Participants were also administered the Questionnaire on Relationships and Substance Use as a criterion measure. In the full sample, McDonald's ω values were adequate for the PID-5 scales (median ω = .85, SD = .06), except for Suspiciousness. However, all PID-5 scales showed average inter-item correlation values in the .20-.55 range. Exploratory structural equation modeling analyses provided moderate support for the a priori model of PID-5 trait scales. Ordinal logistic regression analyses showed that selected PID-5 trait scales predicted a significant, albeit moderate (Cox & Snell R 2 values ranged from .08 to .15, all ps < .001) amount of variance in Questionnaire on Relationships and Substance Use variables.

Three reasons protein disorder analysis makes more sense in the light of collagen

PubMed Central

Oates, Matt E.; Tompa, Peter; Gough, Julian

2016-01-01

Abstract We have identified that the collagen helix has the potential to be disruptive to analyses of intrinsically disordered proteins. The collagen helix is an extended fibrous structure that is both promiscuous and repetitive. Whilst its sequence is predicted to be disordered, this type of protein structure is not typically considered as intrinsic disorder. Here, we show that collagen‐encoding proteins skew the distribution of exon lengths in genes. We find that previous results, demonstrating that exons encoding disordered regions are more likely to be symmetric, are due to the abundance of the collagen helix. Other related results, showing increased levels of alternative splicing in disorder‐encoding exons, still hold after considering collagen‐containing proteins. Aside from analyses of exons, we find that the set of proteins that contain collagen significantly alters the amino acid composition of regions predicted as disordered. We conclude that research in this area should be conducted in the light of the collagen helix. PMID:26941008

Mineral Types and Tree Species Determine the Functional and Taxonomic Structures of Forest Soil Bacterial Communities.

PubMed

Colin, Y; Nicolitch, O; Turpault, M-P; Uroz, S

2017-03-01

Although minerals represent important soil constituents, their impact on the diversity and structure of soil microbial communities remains poorly documented. In this study, pure mineral particles with various chemistries (i.e., obsidian, apatite, and calcite) were considered. Each mineral type was conditioned in mesh bags and incubated in soil below different tree stands (beech, coppice with standards, and Corsican pine) for 2.5 years to determine the relative impacts of mineralogy and mineral weatherability on the taxonomic and functional diversities of mineral-associated bacterial communities. After this incubation period, the minerals and the surrounding bulk soil were collected to determine mass loss and to perform soil analyses, enzymatic assays, and cultivation-dependent and -independent analyses. Notably, our 16S rRNA gene pyrosequencing analyses revealed that after the 2.5-year incubation period, the mineral-associated bacterial communities strongly differed from those of the surrounding bulk soil for all tree stands considered. When focusing only on minerals, our analyses showed that the bacterial communities associated with calcite, the less recalcitrant mineral type, significantly differed from those that colonized obsidian and apatite minerals. The cultivation-dependent analysis revealed significantly higher abundances of effective mineral-weathering bacteria on the most recalcitrant minerals (i.e., apatite and obsidian). Together, our data showed an enrichment of Betaproteobacteria and effective mineral-weathering bacteria related to the Burkholderia and Collimonas genera on the minerals, suggesting a key role for these taxa in mineral weathering and nutrient cycling in nutrient-poor forest ecosystems. IMPORTANCE Forests are usually developed on nutrient-poor and rocky soils, while nutrient-rich soils have been dedicated to agriculture. In this context, nutrient recycling and nutrient access are key processes in such environments. Deciphering how soil mineralogy influences the diversity, structure, and function of soil bacterial communities in relation to the soil conditions is crucial to better understanding the relative role of the soil bacterial communities in nutrient cycling and plant nutrition in nutrient-poor environments. The present study determined in detail the diversity and structure of bacterial communities associated with different mineral types incubated for 2.5 years in the soil under different tree species using cultivation-dependent and -independent analyses. Our data showed an enrichment of specific bacterial taxa on the minerals, specifically on the most weathered minerals, suggesting that they play key roles in mineral weathering and nutrient cycling in nutrient-poor forest ecosystems. Copyright © 2017 American Society for Microbiology.

Mineral Types and Tree Species Determine the Functional and Taxonomic Structures of Forest Soil Bacterial Communities

PubMed Central

Colin, Y.; Nicolitch, O.; Turpault, M.-P.

2016-01-01

ABSTRACT Although minerals represent important soil constituents, their impact on the diversity and structure of soil microbial communities remains poorly documented. In this study, pure mineral particles with various chemistries (i.e., obsidian, apatite, and calcite) were considered. Each mineral type was conditioned in mesh bags and incubated in soil below different tree stands (beech, coppice with standards, and Corsican pine) for 2.5 years to determine the relative impacts of mineralogy and mineral weatherability on the taxonomic and functional diversities of mineral-associated bacterial communities. After this incubation period, the minerals and the surrounding bulk soil were collected to determine mass loss and to perform soil analyses, enzymatic assays, and cultivation-dependent and -independent analyses. Notably, our 16S rRNA gene pyrosequencing analyses revealed that after the 2.5-year incubation period, the mineral-associated bacterial communities strongly differed from those of the surrounding bulk soil for all tree stands considered. When focusing only on minerals, our analyses showed that the bacterial communities associated with calcite, the less recalcitrant mineral type, significantly differed from those that colonized obsidian and apatite minerals. The cultivation-dependent analysis revealed significantly higher abundances of effective mineral-weathering bacteria on the most recalcitrant minerals (i.e., apatite and obsidian). Together, our data showed an enrichment of Betaproteobacteria and effective mineral-weathering bacteria related to the Burkholderia and Collimonas genera on the minerals, suggesting a key role for these taxa in mineral weathering and nutrient cycling in nutrient-poor forest ecosystems. IMPORTANCE Forests are usually developed on nutrient-poor and rocky soils, while nutrient-rich soils have been dedicated to agriculture. In this context, nutrient recycling and nutrient access are key processes in such environments. Deciphering how soil mineralogy influences the diversity, structure, and function of soil bacterial communities in relation to the soil conditions is crucial to better understanding the relative role of the soil bacterial communities in nutrient cycling and plant nutrition in nutrient-poor environments. The present study determined in detail the diversity and structure of bacterial communities associated with different mineral types incubated for 2.5 years in the soil under different tree species using cultivation-dependent and -independent analyses. Our data showed an enrichment of specific bacterial taxa on the minerals, specifically on the most weathered minerals, suggesting that they play key roles in mineral weathering and nutrient cycling in nutrient-poor forest ecosystems. PMID:28003192

The morphogenesis of feathers.

PubMed

Yu, Mingke; Wu, Ping; Widelitz, Randall B; Chuong, Cheng-Ming

2002-11-21

Feathers are highly ordered, hierarchical branched structures that confer birds with the ability of flight. Discoveries of fossilized dinosaurs in China bearing 'feather-like' structures have prompted interest in the origin and evolution of feathers. However, there is uncertainty about whether the irregularly branched integumentary fibres on dinosaurs such as Sinornithosaurus are truly feathers, and whether an integumentary appendage with a major central shaft and notched edges is a non-avian feather or a proto-feather. Here, we use a developmental approach to analyse molecular mechanisms in feather-branching morphogenesis. We have used the replication-competent avian sarcoma retrovirus to deliver exogenous genes to regenerating flight feather follicles of chickens. We show that the antagonistic balance between noggin and bone morphogenetic protein 4 (BMP4) has a critical role in feather branching, with BMP4 promoting rachis formation and barb fusion, and noggin enhancing rachis and barb branching. Furthermore, we show that sonic hedgehog (Shh) is essential for inducing apoptosis of the marginal plate epithelia, which results in spaces between barbs. Our analyses identify the molecular pathways underlying the topological transformation of feathers from cylindrical epithelia to the hierarchical branched structures, and provide insights on the possible developmental mechanisms in the evolution of feather forms.

Spatial and Alignment Analyses for a Field of Small Volcanic Vents South of Pavonis Mons and Implications for the Tharsis Province, Mars

NASA Technical Reports Server (NTRS)

Bleacher, Jacob E.; Glaze, Lori S.; Greeley, Ronald; Hauber, Ernst; Baloga, Stephen; Sakimoto, Susan E. H.; Williams, David A.; Glotch, Timothy D.

2009-01-01

A field of small volcanic vents south of Pavonis Mons was mapped with each vent assigned a two-dimensional data point. Nearest neighbor and two-point azimuth analyses were applied to the resulting location data. Nearest neighbor results show that vents within this field are spatially random in a Poisson sense, suggesting that the vents formed independently of each other without sharing a centralized magma source at shallow depth. Two-point azimuth results show that the vents display north-trending alignment relationships between one another. This trend corresponds to the trends of faults and fractures of the Noachian-aged Claritas Fossae, which might extend into our study area buried beneath more recently emplaced lava flows. However, individual elongate vent summit structures do not consistently display the same trend. The development of the volcanic field appears to display tectonic control from buried Noachian-aged structural patterns on small, ascending magma bodies while the surface orientations of the linear vents might reflect different, younger tectonic patterns. These results suggest a complex interaction between magma ascension through the crust, and multiple, older, buried Tharsis-related tectonic structures.

When mothers have serious mental health problems: parenting as a proximal mediator.

PubMed

Oyserman, Daphna; Bybee, Deborah; Mowbray, Carol; Hart-Johnson, Tamera

2005-08-01

Maternal mental health (MMH) problems are associated with lack of confidence in one's parenting, overly lax or too harsh discipline, and child academic underperformance. We asked if parenting mediates the effect of MMH problems on academic outcomes even among mothers with serious mental illness (n=164). Structural equation analyses show a significant association between MMH problems and permissive (lack of parenting confidence, lack of follow through) parenting and verbal hostility as well as worse academic outcomes (school recorded grades, teacher reported behaviour). Permissive parenting completely mediated the direct effect of MMH on academic outcomes. Further analyses showed that the mediation effect was attributed to a single component of permissive parenting-lack of parenting confidence.

Arc is a flexible modular protein capable of reversible self-oligomerization

PubMed Central

Myrum, Craig; Baumann, Anne; Bustad, Helene J.; Flydal, Marte Innselset; Mariaule, Vincent; Alvira, Sara; Cuéllar, Jorge; Haavik, Jan; Soulé, Jonathan; Valpuesta, José Maria; Márquez, José Antonio; Martinez, Aurora; Bramham, Clive R.

2015-01-01

The immediate early gene product Arc (activity-regulated cytoskeleton-associated protein) is posited as a master regulator of long-term synaptic plasticity and memory. However, the physicochemical and structural properties of Arc have not been elucidated. In the present study, we expressed and purified recombinant human Arc (hArc) and performed the first biochemical and biophysical analysis of hArc's structure and stability. Limited proteolysis assays and MS analysis indicate that hArc has two major domains on either side of a central more disordered linker region, consistent with in silico structure predictions. hArc's secondary structure was estimated using CD, and stability was analysed by CD-monitored thermal denaturation and differential scanning fluorimetry (DSF). Oligomerization states under different conditions were studied by dynamic light scattering (DLS) and visualized by AFM and EM. Biophysical analyses show that hArc is a modular protein with defined secondary structure and loose tertiary structure. hArc appears to be pyramid-shaped as a monomer and is capable of reversible self-association, forming large soluble oligomers. The N-terminal domain of hArc is highly basic, which may promote interaction with cytoskeletal structures or other polyanionic surfaces, whereas the C-terminal domain is acidic and stabilized by ionic conditions that promote oligomerization. Upon binding of presenilin-1 (PS1) peptide, hArc undergoes a large structural change. A non-synonymous genetic variant of hArc (V231G) showed properties similar to the wild-type (WT) protein. We conclude that hArc is a flexible multi-domain protein that exists in monomeric and oligomeric forms, compatible with a diverse, hub-like role in plasticity-related processes. PMID:25748042

Evolution of the Chos Malal and Agrio fold and thrust belts, Andes of Neuquén: Insights from structural analysis and apatite fission track dating

NASA Astrophysics Data System (ADS)

Rojas Vera, E. A.; Mescua, J.; Folguera, A.; Becker, T. P.; Sagripanti, L.; Fennell, L.; Orts, D.; Ramos, V. A.

2015-12-01

The Chos Malal and Agrio fold and thrust belts are located in the western part of the Neuquén basin, an Andean retroarc basin of central-western Argentina. Both belts show evidence of tectonic inversion at the western part during Late Cretaceous times. The eastern part is dominated by late Miocene deformation which also partially reactivated the western structures. This work focuses on the study of the regional structure and the deformational event that shaped the relief of this part of the Andes. Based on new field work and structural data and previously published works a detailed map of the central part of the Neuquén basin is presented. Three regional structural cross sections were surveyed and balanced using the 2d Move™ software. In order to define a more accurate uplift history, new apatite fission track analyses were carried on selected structures. These data was used for new thermal history modeling of the inner part of the Agrio and Chos Malal fold and thrust belts. The results of the fission track analyses improve the knowledge of how these fold and thrust belts have grown trough time. Two main deformational events are defined in Late Cretaceous to Paleocene and Late Miocene times. Based on this regional structural analysis and the fission track data the precise location of the orogenic front for the Late Cretaceous-Paleocene times is reconstructed and it is proposed a structural evolution of this segment of the Andes. This new exhumation data show how the Late Cretaceous to Paleocene event was a continuous and uninterrupted deformational event.

Microcephalia with mandibular and dental dysplasia in adult Zmpste24-deficient mice

PubMed Central

de Carlos, F; Varela, I; Germanà, A; Montalbano, G; Freije, J M P; Vega, J A; López-Otin, C; Cobo, J M

2008-01-01

ZMPSTE24 (also called FACE-1) is a zinc-metalloprotease involved in the post-translational processing of prelamin A to mature lamin A, a major component of the nuclear envelope. Mutations in the ZMPSTE24 gene or in that encoding its substrate prelamin A (LMNA) result in a series of human inherited diseases known collectively as laminopathies and showing regional or systemic manifestations (i.e. the Hutchinson–Gilford progeria syndrome). Typically, patients suffering some laminopathies show craniofacial or mandible anomalies, aberrant dentition or facial features characteristic of aged persons. To analyse whether Zmpste24−/– mice reproduce the cranial phenotype observed in humans due to mutations in ZMPSTE24or LMNA, we conducted a craniometric study based on micro-computer tomography (µCT) images. Furthermore, using simple radiology, µCT, µCT-densitometry and scanning electron microscopy, we analysed the mandible and the teeth from Zmpste24−/– mice. Finally, the structure of the lower incisor was investigated using an H&E technique. The results demonstrate that Zmpste24−/– mice are microcephalic and show mandibular and dental dysplasia affecting only the mandible teeth. In all cases, the lower incisor of mice lacking Zmpste24 was smaller than in control animals, showed cylindrical morphology and a transverse fissure at the incisal edge, and the pulpal cavity was severely reduced. Structurally, the dental layers were normally arranged but cellular layers were disorganized. The inferior molars showed a reduced cusp size. Taken together, these data strongly suggest that Zmpste24−/– mice represent a good model to analyse the craniofacial and teeth malformations characteristic of lamin-related pathologies, and might contribute to a better understanding of the molecular events underlying these diseases. PMID:19014358

Reduced Cortical Gray Matter Volume In Male Adolescents With Substance And Conduct Problems

PubMed Central

Dalwani, Manish; Sakai, Joseph T.; Mikulich-Gilbertson, Susan K.; Tanabe, Jody; Raymond, Kristen; McWilliams, Shannon K.; Thompson, Laetitia L.; Banich, Marie T.; Crowley, Thomas J.

2011-01-01

Boys with serious conduct and substance problems (“Antisocial Substance Dependence” (ASD)) repeatedly make impulsive and risky decisions in spite of possible negative consequences. Because prefrontal cortex (PFC) is involved in planning behavior in accord with prior rewards and punishments, structural abnormalities in PFC could contribute to a person's propensity to make risky decisions. Methods We acquired high-resolution structural images of 25 male ASD patients (ages 14–18 years) and 19 controls of similar ages using a 3T MR system. We conducted whole-brain voxel-based morphometric analysis (p<0.05, corrected for multiple comparisons at whole-brain cluster-level) using Statistical Parametric Mapping version-5 and tested group differences in regional gray matter (GM) volume with analyses of covariance, adjusting for total GM volume, age, and IQ; we further adjusted between-group analyses for ADHD and depression. As secondary analyses, we tested for negative associations between GM volume and impulsivity within groups and separately, GM volume and symptom severity within patients using whole-brain regression analyses. Results ASD boys had significantly lower GM volume than controls in left dorsolateral PFC (DLPFC), right lingual gyrus and bilateral cerebellum, and significantly higher GM volume in right precuneus. Left DLPFC GM volume showed negative association with impulsivity within controls and negative association with substance dependence severity within patients. Conclusions ASD boys show reduced GM volumes in several regions including DLPFC, a region highly relevant to impulsivity, disinhibition, and decision-making, and cerebellum, a region important for behavioral regulation, while they showed increased GM in precuneus, a region associated with self-referential and self-centered thinking. PMID:21592680

Effect of nutrient and selective inhibitor amendments on methane oxidation, nitrous oxide production, and key gene presence and expression in landfill cover soils: characterization of the role of methanotrophs, nitrifiers, and denitrifiers.

PubMed

Lee, Sung-Woo; Im, Jeongdae; Dispirito, Alan A; Bodrossy, Levente; Barcelona, Michael J; Semrau, Jeremy D

2009-11-01

Methane and nitrous oxide are both potent greenhouse gasses, with global warming potentials approximately 25 and 298 times that of carbon dioxide. A matrix of soil microcosms was constructed with landfill cover soils collected from the King Highway Landfill in Kalamazoo, Michigan and exposed to geochemical parameters known to affect methane consumption by methanotrophs while also examining their impact on biogenic nitrous oxide production. It was found that relatively dry soils (5% moisture content) along with 15 mg NH (4) (+) (kg soil)(-1) and 0.1 mg phenylacetylene(kg soil)(-1) provided the greatest stimulation of methane oxidation while minimizing nitrous oxide production. Microarray analyses of pmoA showed that the methanotrophic community structure was dominated by Type II organisms, but Type I genera were more evident with the addition of ammonia. When phenylacetylene was added in conjunction with ammonia, the methanotrophic community structure was more similar to that observed in the presence of no amendments. PCR analyses showed the presence of amoA from both ammonia-oxidizing bacteria and archaea, and that the presence of key genes associated with these cells was reduced with the addition of phenylacetylene. Messenger RNA analyses found transcripts of pmoA, but not of mmoX, nirK, norB, or amoA from either ammonia-oxidizing bacteria or archaea. Pure culture analyses showed that methanotrophs could produce significant amounts of nitrous oxide, particularly when expressing the particulate methane monooxygenase (pMMO). Collectively, these data suggest that methanotrophs expressing pMMO played a role in nitrous oxide production in these microcosms.

Crystal structure of simple metals at high pressures

NASA Astrophysics Data System (ADS)

Degtyareva, Olga

2010-09-01

The effects of pressure on the crystal structure of simple (or sp-) elements are analysed in terms of changes in coordination number, packing density, and interatomic distances, and general rules are established. In the polyvalent elements from groups 14-17, the covalently bonded structures tend to transform to metallic phases with a gradual increase in coordination number and packing density, a behaviour normally expected under pressure. Group 1 and 2 metallic elements, however, show a reverse trend towards structures with low packing density due to intricate changes in their electronic structure. Complex crystal structures such as host-guest and incommensurately modulated structures found in these elements are given special attention in this review in an attempt to determine their role in the observed phase-transition sequences.

Fine-scale genetic structure in populations of the Chagas' disease vector Triatoma infestans (Hemiptera, Reduvidae).

PubMed

Pérez de Rosas, Alicia R; Segura, Elsa L; Fusco, Octavio; Guiñazú, Adolfo L Bareiro; García, Beatriz A

2013-03-01

Fine scale patterns of genetic structure and dispersal in Triatoma infestans populations from Argentina was analysed. A total of 314 insects from 22 domestic and peridomestic sites from the locality of San Martín (Capayán department, Catamarca province) were typed for 10 polymorphic microsatellite loci. The results confirm subdivision of T. infestans populations with restricted dispersal among sampling sites and suggest inbreeding and/or stratification within the different domestic and peridomestic structures. Spatial correlation analysis showed that the scale of structuring is approximately of 400 m, indicating that active dispersal would occur within this distance range. It was detected difference in scale of structuring among sexes, with females dispersing over greater distances than males. This study suggests that insecticide treatment and surveillance should be extended within a radius of 400 m around the infested area, which would help to reduce the probability of reinfestation by covering an area of active dispersal. The inferences made from fine-scale spatial genetic structure analyses of T. infestans populations has demonstrated to be important for community-wide control programs, providing a complementary approach to help improve vector control strategies.

Microprobe studies of microtomed particles of white druse salts in shergottite EETA 79001

NASA Technical Reports Server (NTRS)

Lindstrom, D. J.

1991-01-01

The white druse material in Antarctic shergottite EETA 79001 has attracted much attention as a possible sample fo Martian aqueous deposits. Instrumental Neutron Activation Analysis (INAA) was used to determine trace element analyses of small particles of this material obtained by handpicking of likely grains from broken surfaces of the meteorite. Electron microprobe work was attempted on grain areas as large as 150x120 microns. Backscattered electron images show considerable variations in brightness, and botryoidal structures were observed. Microprobe analyses showed considerable variability both within single particles and between different particles. Microtomed surfaces of small selected particles were shown to be very useful in obtaining information on the texture and composition of rare lithologies like the white druse of EETA 79001. This material is clearly heterogeneous on all distance scales, so a large number of further analyses will be required to characterize it.

Chemical analysis applied to the radiation sterilization of solid ketoprofen

NASA Astrophysics Data System (ADS)

Colak, S.; Maquille, A.; Tilquin, B.

2006-01-01

The aim of this work is to investigate the feasibility of radiation sterilization of ketoprofen from a chemical point of view. Although irradiated ketoprofen has already been studied in the literature [Katusin-Razem et al., Radiat. Phys. Chem. 73 111-116 (2005)], new results, on the basis of electron spin resonance (ESR) measurements and the use of hyphenated techniques (GC-MS and LC-MS), are obtained. The ESR spectra of irradiated ketoprofen consists of four unresolved resonance peaks and the mean G-value of ketoprofen is found to be 4 +/- 0.9 nmoles/J, which is very small. HPLC-UV analyses indicate that no significant loss of ketoprofen is detected after irradiation. LC-MS-MS analyses show that the structures of the non-volatile final products are similar to ketoprofen. Benzaldehyde is detected in the irradiated samples after dynamic-extraction GC-MS. The analyses show that ketoprofen is radioresistant and therefore might be radiosterilized.

ACETOGENIC AND SULPHATE-REDUCING BACTERIA INHABITING THE RHIZOPLANE AND DEEP CORTEX CELLS OF THE SEAGRASS HALODULE WRIGHTII

EPA Science Inventory

Recent declines in sea grass distribution underscore the importance of understanding microbial community structure-function relationships in sea grass rhizosphere that might affect the viability of these plants. Phospholipid fatty acid analyses showed that sulfate-reducing bacter...

Measurement of replication structures at the nanometer scale using super-resolution light microscopy

PubMed Central

Baddeley, D.; Chagin, V. O.; Schermelleh, L.; Martin, S.; Pombo, A.; Carlton, P. M.; Gahl, A.; Domaing, P.; Birk, U.; Leonhardt, H.; Cremer, C.; Cardoso, M. C.

2010-01-01

DNA replication, similar to other cellular processes, occurs within dynamic macromolecular structures. Any comprehensive understanding ultimately requires quantitative data to establish and test models of genome duplication. We used two different super-resolution light microscopy techniques to directly measure and compare the size and numbers of replication foci in mammalian cells. This analysis showed that replication foci vary in size from 210 nm down to 40 nm. Remarkably, spatially modulated illumination (SMI) and 3D-structured illumination microscopy (3D-SIM) both showed an average size of 125 nm that was conserved throughout S-phase and independent of the labeling method, suggesting a basic unit of genome duplication. Interestingly, the improved optical 3D resolution identified 3- to 5-fold more distinct replication foci than previously reported. These results show that optical nanoscopy techniques enable accurate measurements of cellular structures at a level previously achieved only by electron microscopy and highlight the possibility of high-throughput, multispectral 3D analyses. PMID:19864256

Structural and Functional Analyses of a Glycoside Hydrolase Family 5 Enzyme with an Unexpected [beta]-Fucosidase Activity

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

Yoshida, Shosuke; Park, David S.; Bae, Brian

2012-02-15

We present characterization of PbFucA, a family 5 glycoside hydrolase (GH5) from Prevotella bryantii B{sub 1}4. While GH5 members typically are xylanases, PbFucA shows no activity toward xylan polysaccharides. A screen against a panel of p-nitrophenol coupled sugars identifies PbFucA as a {beta}-D-fucosidase. We also present the 2.2 {angstrom} resolution structure of PbFucA and use structure-based mutational analysis to confirm the role of catalytically essential residues. A comparison of the active sites of PbFucA with those of family 5 and 51 glycosidases reveals that while the essential catalytic framework is identical between these enzymes, the steric contours of the respectivemore » active site clefts are distinct and likely account for substrate discrimination. Our results show that members of this cluster of orthologous group (COG) 5520 have {beta}-D-fucosidase activities, despite showing an overall sequence and structural similarity to GH-5 xylanases.« less

Modeling and Analysis of Structural Dynamics for a One-Tenth Scale Model NGST Sunshield

NASA Technical Reports Server (NTRS)

Johnston, John; Lienard, Sebastien; Brodeur, Steve (Technical Monitor)

2001-01-01

New modeling and analysis techniques have been developed for predicting the dynamic behavior of the Next Generation Space Telescope (NGST) sunshield. The sunshield consists of multiple layers of pretensioned, thin-film membranes supported by deployable booms. Modeling the structural dynamic behavior of the sunshield is a challenging aspect of the problem due to the effects of membrane wrinkling. A finite element model of the sunshield was developed using an approximate engineering approach, the cable network method, to account for membrane wrinkling effects. Ground testing of a one-tenth scale model of the NGST sunshield were carried out to provide data for validating the analytical model. A series of analyses were performed to predict the behavior of the sunshield under the ground test conditions. Modal analyses were performed to predict the frequencies and mode shapes of the test article and transient response analyses were completed to simulate impulse excitation tests. Comparison was made between analytical predictions and test measurements for the dynamic behavior of the sunshield. In general, the results show good agreement with the analytical model correctly predicting the approximate frequency and mode shapes for the significant structural modes.

Subcortical volumetric changes across the adult lifespan: subregional thalamic atrophy accounts for age-related sensorimotor performance declines.

PubMed

Serbruyns, Leen; Leunissen, Inge; Huysmans, Toon; Cuypers, Koen; Meesen, Raf L; van Ruitenbeek, Peter; Sijbers, Jan; Swinnen, Stephan P

2015-04-01

Even though declines in sensorimotor performance during healthy aging have been documented extensively, its underlying neural mechanisms remain unclear. Here, we explored whether age-related subcortical atrophy plays a role in sensorimotor performance declines, and particularly during bimanual manipulative performance (Purdue Pegboard Test). The thalamus, putamen, caudate and pallidum of 91 participants across the adult lifespan (ages 20-79 years) were automatically segmented. In addition to studying age-related changes in the global volume of each subcortical structure, local deformations within these structures, indicative of subregional volume changes, were assessed by means of recently developed shape analyses. Results showed widespread age-related global and subregional atrophy, as well as some notable subregional expansion. Even though global atrophy failed to explain the observed performance declines with aging, shape analyses indicated that atrophy in left and right thalamic subregions, specifically subserving connectivity with the premotor, primary motor and somatosensory cortical areas, mediated the relation between aging and performance decline. It is concluded that subregional volume assessment by means of shape analyses offers a sensitive tool with high anatomical resolution in the search for specific age-related associations between brain structure and behavior. Copyright © 2015 Elsevier Ltd. All rights reserved.

kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity.

PubMed

Murray, Kevin D; Webers, Christfried; Ong, Cheng Soon; Borevitz, Justin; Warthmann, Norman

2017-09-01

Modern genomics techniques generate overwhelming quantities of data. Extracting population genetic variation demands computationally efficient methods to determine genetic relatedness between individuals (or "samples") in an unbiased manner, preferably de novo. Rapid estimation of genetic relatedness directly from sequencing data has the potential to overcome reference genome bias, and to verify that individuals belong to the correct genetic lineage before conclusions are drawn using mislabelled, or misidentified samples. We present the k-mer Weighted Inner Product (kWIP), an assembly-, and alignment-free estimator of genetic similarity. kWIP combines a probabilistic data structure with a novel metric, the weighted inner product (WIP), to efficiently calculate pairwise similarity between sequencing runs from their k-mer counts. It produces a distance matrix, which can then be further analysed and visualised. Our method does not require prior knowledge of the underlying genomes and applications include establishing sample identity and detecting mix-up, non-obvious genomic variation, and population structure. We show that kWIP can reconstruct the true relatedness between samples from simulated populations. By re-analysing several published datasets we show that our results are consistent with marker-based analyses. kWIP is written in C++, licensed under the GNU GPL, and is available from https://github.com/kdmurray91/kwip.

Canonical decomposition of magnetotelluric responses: Experiment on 1D anisotropic structures

NASA Astrophysics Data System (ADS)

Guo, Ze-qiu; Wei, Wen-bo; Ye, Gao-feng; Jin, Sheng; Jing, Jian-en

2015-08-01

Horizontal electrical heterogeneity of subsurface earth is mostly originated from structural complexity and electrical anisotropy, and local near-surface electrical heterogeneity will severely distort regional electromagnetic responses. Conventional distortion analyses for magnetotelluric soundings are primarily physical decomposition methods with respect to isotropic models, which mostly presume that the geoelectric distribution of geological structures is of local and regional patterns represented by 3D/2D models. Due to the widespread anisotropy of earth media, the confusion between 1D anisotropic responses and 2D isotropic responses, and the defects of physical decomposition methods, we propose to conduct modeling experiments with canonical decomposition in terms of 1D layered anisotropic models, and the method is one of the mathematical decomposition methods based on eigenstate analyses differentiated from distortion analyses, which can be used to recover electrical information such as strike directions, and maximum and minimum conductivity. We tested this method with numerical simulation experiments on several 1D synthetic models, which turned out that canonical decomposition is quite effective to reveal geological anisotropic information. Finally, for the background of anisotropy from previous study by geological and seismological methods, canonical decomposition is applied to real data acquired in North China Craton for 1D anisotropy analyses, and the result shows that, with effective modeling and cautious interpretation, canonical decomposition could be another good method to detect anisotropy of geological media.

Numerical investigation of flow structure and pressure pulsation in the Francis-99 turbine during startup

NASA Astrophysics Data System (ADS)

Minakov, A.; Sentyabov, A.; Platonov, D.

2017-01-01

We performed numerical simulation of flow in a laboratory model of a Francis hydroturbine at startup regimes. Numerical technique for calculating of low frequency pressure pulsations in a water turbine is based on the use of DES (k-ω Shear Stress Transport) turbulence model and the approach of “frozen rotor”. The structure of the flow behind the runner of turbine was analysed. Shows the effect of flow structure on the frequency and intensity of non-stationary processes in the flow path. Two version of the inlet boundary conditions were considered. The first one corresponded measured time dependence of the discharge. Comparison of the calculation results with the experimental data shows the considerable delay of the discharge in this calculation. Second version corresponded linear approximation of time dependence of the discharge. This calculation shows good agreement with experimental results.

Geo-Chip analysis reveals reduced functional diversity of the bacterial community at a dumping site for dredged Elbe sediment.

PubMed

Störmer, Rebecca; Wichels, Antje; Gerdts, Gunnar

2013-12-15

The dumping of dredged sediments represents a major stressor for coastal ecosystems. The impact on the ecosystem function is determined by its complexity not easy to assess. In the present study, we evaluated the potential of bacterial community analyses to act as ecological indicators in environmental monitoring programmes. We investigated the functional structure of bacterial communities, applying functional gene arrays (GeoChip4.2). The relationship between functional genes and environmental factors was analysed using distance-based multivariate multiple regression. Apparently, both the function and structure of the bacterial communities are impacted by dumping activities. The bacterial community at the dumping centre displayed a significant reduction of its entire functional diversity compared with that found at a reference site. DDX compounds separated bacterial communities of the dumping site from those of un-impacted sites. Thus, bacterial community analyses show great potential as ecological indicators in environmental monitoring. Copyright © 2013 Elsevier Ltd. All rights reserved.

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

Lawler, Keith V.; Childs, Bradley C.; Mast, Daniel S.

The molecular and electronic structures for the Group 7b heptoxides were investigated by computational methods as both isolated molecules and in the solid-state. The metal-oxygen-metal bending angle of the single molecule increased with increasing atomic number, with Re 2O 7 preferring a linear structure. Natural bond orbital and localized orbital bonding analyses indicate that there is a three-center covalent bond between the metal atoms and the bridging oxygen, and the increasing ionic character of the bonds favors larger bond angles. The calculations accurately reproduce the experimental crystal structures within a few percent. Analysis of the band structures and density ofmore » states shows similar bonding for all of the solid-state heptoxides, including the presence of the three-center covalent bond. DFT+U simulations show that PBE-D3 underpredicts the band gap by ~0.2 eV due to an under-correlation of the metal d conducting states. As a result, homologue and compression studies show that Re 2O 7 adopts a polymeric structure because the Re-oxide tetrahedra are easily distorted by packing stresses to form additional three-center covalent bonds.« less

Large scale analysis of the mutational landscape in β-glucuronidase: A major player of mucopolysaccharidosis type VII.

PubMed

Khan, Faez Iqbal; Shahbaaz, Mohd; Bisetty, Krishna; Waheed, Abdul; Sly, William S; Ahmad, Faizan; Hassan, Md Imtaiyaz

2016-01-15

The lysosomal storage disorders are a group of 50 unique inherited diseases characterized by unseemly lipid storage in lysosomes. These malfunctions arise due to genetic mutations that result in deficiency or reduced activities of the lysosomal enzymes, which are responsible for catabolism of biological macromolecules. Sly syndrome or mucopolysaccharidosis type VII is a lysosomal storage disorder associated with the deficiency of β-glucuronidase (EC 3.2.1.31) that catalyzes the hydrolysis of β-D-glucuronic acid residues from the non-reducing terminal of glycosaminoglycan. The effects of the disease causing mutations on the framework of the sequences and structure of β-glucuronidase (GUSBp) were analyzed utilizing a variety of bioinformatic tools. These analyses showed that 211 mutations may result in alteration of the biological activity of GUSBp, including previously experimentally validated mutations. Finally, we refined 90 disease causing mutations, which presumably cause a significant impact on the structure, function, and stability of GUSBp. Stability analyses showed that mutations p.Phe208Pro, p.Phe539Gly, p.Leu622Gly, p.Ile499Gly and p.Ile586Gly caused the highest impact on GUSBp stability and function because of destabilization of the protein structure. Furthermore, structures of wild type and mutant GUSBp were subjected to molecular dynamics simulation to examine the relative structural behaviors in the explicit conditions of water. In a broader view, the use of in silico approaches provided a useful understanding of the effect of single point mutations on the structure-function relationship of GUSBp. Copyright © 2015 Elsevier B.V. All rights reserved.

ns2np4 (n = 4, 5) lone pair triplets whirling in M*F2E3 (M* = Kr, Xe): Stereochemistry and ab initio analyses

NASA Astrophysics Data System (ADS)

Galy, Jean; Matar, Samir F.

2017-02-01

The stereochemistry of ns2np4 (n = 4, 5) lone pair LP characterizing noble gas Kr and Xe (labeled M*) in M*F2 difluorides is examined within coherent crystal chemistry and ab initio visualizations. M*2+ in such oxidation state brings three lone pairs (E) and difluorides are formulated M*F2E3. The analyses use electron localization function (ELF) obtained within density functional theory calculations showing the development of the LP triplets whirling {E3} quantified in the relevant chemical systems. Detailed ELF data analyses allowed showing that in α KrF2E3 and isostructural XeF2E3 difluorides the three E electronic clouds merge or hybridize into a torus and adopt a perfect gyration circle with an elliptical section, while in β KrF2 the network architecture deforms the whole torus into an ellipsoid shape. Original precise metrics are provided for the torus in the different compounds under study. In KrF2 the geometric changes upon β → α phase transition is schematized and mechanisms for the transformation with temperature or pressure are proposed. The results are further highlighted by electronic band structure calculations which show similar features of equal band gaps of 3 eV in both α and β KrF2 and a reorganization of frontier orbitals due to the different orientations of the F-Kr-F linear molecule in the two tetragonal structures.

Selection of Sphingomonadaceae at the base of Laccaria proxima and Russula exalbicans fruiting bodies.

PubMed

Boersma, F G Hidde; Warmink, Jan A; Andreote, Fernando A; van Elsas, Jan Dirk

2009-04-01

The dense hyphal network directly underneath the fruiting bodies of ectomycorrhizal fungi might exert strong influences on the bacterial community of soil. Such fruiting bodies might serve as hot spots for bacterial activity, for instance by providing nutrients and colonization sites in soil. Here, we assessed the putative selection of specific members of the Sphingomonadaceae family at the bases of the fruiting bodies of the ectomycorrhizal fungi Laccaria proxima and Russula exalbicans in comparison to the adjacent bulk soil. To do so, we used a previously designed Sphingomonadaceae-specific PCR-denaturing gradient gel electrophoresis (DGGE) system and complemented this with analyses of sequences from a Sphingomonadaceae-specific clone library. The analyses showed clear selective effects of the fruiting bodies of both fungi on the Sphingomonadaceae community structures. The effect was especially prevalent with R. exalbicans. Strikingly, similar fungi sampled approximately 100 m apart showed similar DGGE patterns, while corresponding bulk soil-derived patterns differed from each other. However, the mycospheres of L. proxima and R. exalbicans still revealed divergent community structures, indicating that different fungi select for different members of the Sphingomonadaceae family. Excision of specific bands from the DGGE patterns, as well as analyses of the clone libraries generated from both habitats, revealed fruiting body-specific Sphingomonadaceae types. It further showed that major groups from the mycospheres of R. exalbicans and L. proxima did not cluster with known bacteria from the database, indicating new groups within the family of Sphingomonadaceae present in these environments.

Microbial Community Structure in Lake and Wetland Sediments from a High Arctic Polar Desert Revealed by Targeted Transcriptomics

PubMed Central

Stoeva, Magdalena K.; Aris-Brosou, Stéphane; Chételat, John; Hintelmann, Holger; Pelletier, Philip; Poulain, Alexandre J.

2014-01-01

While microbial communities play a key role in the geochemical cycling of nutrients and contaminants in anaerobic freshwater sediments, their structure and activity in polar desert ecosystems are still poorly understood, both across heterogeneous freshwater environments such as lakes and wetlands, and across sediment depths. To address this question, we performed targeted environmental transcriptomics analyses and characterized microbial diversity across three depths from sediment cores collected in a lake and a wetland, located on Cornwallis Island, NU, Canada. Microbial communities were characterized based on 16S rRNA and two functional gene transcripts: mcrA, involved in archaeal methane cycling and glnA, a bacterial housekeeping gene implicated in nitrogen metabolism. We show that methane cycling and overall bacterial metabolic activity are the highest at the surface of lake sediments but deeper within wetland sediments. Bacterial communities are highly diverse and structured as a function of both environment and depth, being more diverse in the wetland and near the surface. Archaea are mostly methanogens, structured by environment and more diverse in the wetland. McrA transcript analyses show that active methane cycling in the lake and wetland corresponds to distinct communities with a higher potential for methane cycling in the wetland. Methanosarcina spp., Methanosaeta spp. and a group of uncultured Archaea are the dominant methanogens in the wetland while Methanoregula spp. predominate in the lake. PMID:24594936

Hydrogen bonding strength of diblock copolymers affects the self-assembled structures with octa-functionalized phenol POSS nanoparticles.

PubMed

Lu, Yi-Syuan; Yu, Chia-Yu; Lin, Yung-Chih; Kuo, Shiao-Wei

2016-02-28

In this study, the influence of the functional groups by the diblock copolymers of poly(styrene-b-4-vinylpyridine) (PS-b-P4VP), poly(styrene-b-2-vinylpyridine) (PS-b-P2VP), and poly(styrene-b-methyl methacrylate) (PS-b-PMMA) on their blends with octa-functionalized phenol polyhedral oligomeric silsesquioxane (OP-POSS) nanoparticles (NPs) was investigated. The relative hydrogen bonding strengths in these blends follow the order PS-b-P4VP/OP-POSS > PS-b-P2VP/OP-POSS > PS-b-PMMA/OP-POSS based on the Kwei equation from differential scanning calorimetry (DSC) and Fourier transform infrared spectroscopic analyses. Small-angle X-ray scattering and transmission electron microscopic analyses show that the morphologies of the self-assembly structures are strongly dependent on the hydrogen bonding strength at relatively higher OP-POSS content. The PS-b-P4VP/OP-POSS hybrid complex system with the strongest hydrogen bonds shows the order-order transition from lamellae to cylinders and finally to body-centered cubic spheres upon increasing OP-POSS content. However, PS-b-P2VP/OP-POSS and PS-b-PMMA/OP-POSS hybrid complex systems, having relatively weaker hydrogen bonds, transformed from lamellae to cylinder structures at lower OP-POSS content (<50 wt%), but formed disordered structures at relatively high OP-POSS contents (>50 wt%).

A cross-national study on the multidimensional characteristics of the five-item psychological demands scale of the Job Content Questionnaire.

PubMed

Choi, BongKyoo; Kawakami, Norito; Chang, SeiJin; Koh, SangBaek; Bjorner, Jakob; Punnett, Laura; Karasek, Robert

2008-01-01

The five-item psychological demands scale of the Job Content Questionnaire (JCQ) has been assumed to be one-dimensional in practice. To examine whether the scale has sufficient internal consistency and external validity to be treated as a single scale, using the cross-national JCQ datasets from the United States, Korea, and Japan. Exploratory factor analyses with 22 JCQ items, confirmatory factor analyses with the five psychological demands items, and correlations analyses with mental health indexes. Generally, exploratory factor analyses displayed the predicted demand/control/support structure with three and four factors extracted. However, at more detailed levels of exploratory and confirmatory factor analyses, the demands scale showed clear evidence of multi-factor structure. The correlations of items and subscales of the demands scale with mental health indexes were similar to those of the full scale in the Korean and Japanese datasets, but not in the U.S. data. In 4 out of 16 sub-samples of the U.S. data, several significant correlations of the components of the demands scale with job dissatisfaction and life dissatisfaction were obscured by the full scale. The multidimensionality of the psychological demands scale should be considered in psychometric analysis and interpretation, occupational epidemiologic studies, and future scale extension.

Dialogic Global Studies for Multicultural Technology Assessment

ERIC Educational Resources Information Center

Durakovic, Emina; Feigl, Britta Marion; Fischer, Bettina Marion; Fleck, Christopher; Galler, Lisa-Maria; Heinrich, Johannes; Kulmer, Karin; Kurzweil, Birgitta; Scholze, Markus; Sperl, Raphael Stefan; Unterkofler, Rene; Remele, Kurt; Matzenberger, Julian; Ahamer, Gilbert

2012-01-01

Purpose: The purpose of this paper is to show a practical case of dialogic web-based learning that has provided a set of questions analysing two complex technological projects in "southern" countries with effects on multicultural equity. Design/methodology/approach: Structured online review processes in multicultural and systems science…

Probabilistic Assessment of National Wind Tunnel

NASA Technical Reports Server (NTRS)

Shah, A. R.; Shiao, M.; Chamis, C. C.

1996-01-01

A preliminary probabilistic structural assessment of the critical section of National Wind Tunnel (NWT) is performed using NESSUS (Numerical Evaluation of Stochastic Structures Under Stress) computer code. Thereby, the capabilities of NESSUS code have been demonstrated to address reliability issues of the NWT. Uncertainties in the geometry, material properties, loads and stiffener location on the NWT are considered to perform the reliability assessment. Probabilistic stress, frequency, buckling, fatigue and proof load analyses are performed. These analyses cover the major global and some local design requirements. Based on the assumed uncertainties, the results reveal the assurance of minimum 0.999 reliability for the NWT. Preliminary life prediction analysis results show that the life of the NWT is governed by the fatigue of welds. Also, reliability based proof test assessment is performed.

Lidar-Based Rock-Fall Hazard Characterization of Cliffs

USGS Publications Warehouse

Collins, Brian D.; Greg M.Stock,

2017-01-01

Rock falls from cliffs and other steep slopes present numerous challenges for detailed geological characterization. In steep terrain, rock-fall source areas are both dangerous and difficult to access, severely limiting the ability to make detailed structural and volumetric measurements necessary for hazard assessment. Airborne and terrestrial lidar survey methods can provide high-resolution data needed for volumetric, structural, and deformation analyses of rock falls, potentially making these analyses straightforward and routine. However, specific methods to collect, process, and analyze lidar data of steep cliffs are needed to maximize analytical accuracy and efficiency. This paper presents observations showing how lidar data sets should be collected, filtered, registered, and georeferenced to tailor their use in rock fall characterization. Additional observations concerning surface model construction, volumetric calculations, and deformation analysis are also provided.

A Model for Simulating the Response of Aluminum Honeycomb Structure to Transverse Loading

NASA Technical Reports Server (NTRS)

Ratcliffe, James G.; Czabaj, Michael W.; Jackson, Wade C.

2012-01-01

A 1-dimensional material model was developed for simulating the transverse (thickness-direction) loading and unloading response of aluminum honeycomb structure. The model was implemented as a user-defined material subroutine (UMAT) in the commercial finite element analysis code, ABAQUS(Registered TradeMark)/Standard. The UMAT has been applied to analyses for simulating quasi-static indentation tests on aluminum honeycomb-based sandwich plates. Comparison of analysis results with data from these experiments shows overall good agreement. Specifically, analyses of quasi-static indentation tests yielded accurate global specimen responses. Predicted residual indentation was also in reasonable agreement with measured values. Overall, this simple model does not involve a significant computational burden, which makes it more tractable to simulate other damage mechanisms in the same analysis.

Rebelling for a Reason: Protein Structural “Outliers”

PubMed Central

Arumugam, Gandhimathi; Nair, Anu G.; Hariharaputran, Sridhar; Ramanathan, Sowdhamini

2013-01-01

Analysis of structural variation in domain superfamilies can reveal constraints in protein evolution which aids protein structure prediction and classification. Structure-based sequence alignment of distantly related proteins, organized in PASS2 database, provides clues about structurally conserved regions among different functional families. Some superfamily members show large structural differences which are functionally relevant. This paper analyses the impact of structural divergence on function for multi-member superfamilies, selected from the PASS2 superfamily alignment database. Functional annotations within superfamilies, with structural outliers or ‘rebels’, are discussed in the context of structural variations. Overall, these data reinforce the idea that functional similarities cannot be extrapolated from mere structural conservation. The implication for fold-function prediction is that the functional annotations can only be inherited with very careful consideration, especially at low sequence identities. PMID:24073209

A Flexible and Non-instrusive Approach for Computing Complex Structural Coverage Metrics

NASA Technical Reports Server (NTRS)

Whalen, Michael W.; Person, Suzette J.; Rungta, Neha; Staats, Matt; Grijincu, Daniela

2015-01-01

Software analysis tools and techniques often leverage structural code coverage information to reason about the dynamic behavior of software. Existing techniques instrument the code with the required structural obligations and then monitor the execution of the compiled code to report coverage. Instrumentation based approaches often incur considerable runtime overhead for complex structural coverage metrics such as Modified Condition/Decision (MC/DC). Code instrumentation, in general, has to be approached with great care to ensure it does not modify the behavior of the original code. Furthermore, instrumented code cannot be used in conjunction with other analyses that reason about the structure and semantics of the code under test. In this work, we introduce a non-intrusive preprocessing approach for computing structural coverage information. It uses a static partial evaluation of the decisions in the source code and a source-to-bytecode mapping to generate the information necessary to efficiently track structural coverage metrics during execution. Our technique is flexible; the results of the preprocessing can be used by a variety of coverage-driven software analysis tasks, including automated analyses that are not possible for instrumented code. Experimental results in the context of symbolic execution show the efficiency and flexibility of our nonintrusive approach for computing code coverage information

Cryo-EM near-atomic structure of a dsRNA fungal virus shows ancient structural motifs preserved in the dsRNA viral lineage

PubMed Central

Luque, Daniel; Gómez-Blanco, Josué; Garriga, Damiá; Brilot, Axel F.; González, José M.; Havens, Wendy M.; Carrascosa, José L.; Trus, Benes L.; Verdaguer, Nuria; Ghabrial, Said A.; Castón, José R.

2014-01-01

Viruses evolve so rapidly that sequence-based comparison is not suitable for detecting relatedness among distant viruses. Structure-based comparisons suggest that evolution led to a small number of viral classes or lineages that can be grouped by capsid protein (CP) folds. Here, we report that the CP structure of the fungal dsRNA Penicillium chrysogenum virus (PcV) shows the progenitor fold of the dsRNA virus lineage and suggests a relationship between lineages. Cryo-EM structure at near-atomic resolution showed that the 982-aa PcV CP is formed by a repeated α-helical core, indicative of gene duplication despite lack of sequence similarity between the two halves. Superimposition of secondary structure elements identified a single “hotspot” at which variation is introduced by insertion of peptide segments. Structural comparison of PcV and other distantly related dsRNA viruses detected preferential insertion sites at which the complexity of the conserved α-helical core, made up of ancestral structural motifs that have acted as a skeleton, might have increased, leading to evolution of the highly varied current structures. Analyses of structural motifs only apparent after systematic structural comparisons indicated that the hallmark fold preserved in the dsRNA virus lineage shares a long (spinal) α-helix tangential to the capsid surface with the head-tailed phage and herpesvirus viral lineage. PMID:24821769

Structural and functional hyperconnectivity within the sensorimotor system in xenomelia.

PubMed

Hänggi, Jürgen; Vitacco, Deborah A; Hilti, Leonie M; Luechinger, Roger; Kraemer, Bernd; Brugger, Peter

2017-03-01

Xenomelia is a rare condition characterized by the persistent and compulsive desire for the amputation of one or more physically healthy limbs. We highlight the neurological underpinnings of xenomelia by assessing structural and functional connectivity by means of whole-brain connectome and network analyses of regions previously implicated in empirical research in this condition. We compared structural and functional connectivity between 13 xenomelic men with matched controls using diffusion tensor imaging combined with fiber tractography and resting state functional magnetic resonance imaging. Altered connectivity in xenomelia within the sensorimotor system has been predicted. We found subnetworks showing structural and functional hyperconnectivity in xenomelia compared with controls. These subnetworks were lateralized to the right hemisphere and mainly comprised by nodes belonging to the sensorimotor system. In the connectome analyses, the paracentral lobule, supplementary motor area, postcentral gyrus, basal ganglia, and the cerebellum were hyperconnected to each other, whereas in the xenomelia-specific network analyses, hyperconnected nodes have been found in the superior parietal lobule, primary and secondary somatosensory cortex, premotor cortex, basal ganglia, thalamus, and insula. Our study provides empirical evidence of structural and functional hyperconnectivity within the sensorimotor system including those regions that are core for the reconstruction of a coherent body image. Aberrant connectivity is a common response to focal neurological damage. As exemplified here, it may affect different brain regions differentially. Due to the small sample size, our findings must be interpreted cautiously and future studies are needed to elucidate potential associations between hyperconnectivity and limb disownership reported in xenomelia.

An Integrated Approach for a Structural and Functional Evaluation of Biosimilars: Implications for Erythropoietin.

PubMed

Gianoncelli, Alessandra; Bonini, Sara A; Bertuzzi, Michela; Guarienti, Michela; Vezzoli, Sara; Kumar, Rajesh; Delbarba, Andrea; Mastinu, Andrea; Sigala, Sandra; Spano, Pierfranco; Pani, Luca; Pecorelli, Sergio; Memo, Maurizio

2015-08-01

Authorization to market a biosimilar product by the appropriate institutions is expected based on biosimilarity with its originator product. The analogy between the originator and its biosimilar(s) is assessed through safety, purity, and potency analyses. In this study, we proposed a useful quality control system for rapid and economic primary screening of potential biosimilar drugs. For this purpose, chemical and functional characterization of the originator rhEPO alfa and two of its biosimilars was discussed. Qualitative and quantitative analyses of the originator rhEPO alfa and its biosimilars were performed using reversed-phase high-performance liquid chromatography (RP-HPLC). The identification of proteins and the separation of isoforms were studied using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and two-dimensional gel electrophoresis (2D-PAGE), respectively. Furthermore, the biological activity of these drugs was measured both in vitro, evaluating the TF-1 cell proliferation rate, and in vivo, using the innovative experimental animal model of the zebrafish embryos. Chemical analyses showed that the quantitative concentrations of rhEPO alfa were in agreement with the labeled claims by the corresponding manufacturers. The qualitative analyses performed demonstrated that the three drugs were pure and that they had the same amino acid sequence. Chemical differences were found only at the level of isoforms containing N-glycosylation; however, functional in vitro and in vivo studies did not show any significant differences from a biosimilar point of view. These rapid and economic structural and functional analyses were effective in the evaluation of the biosimilarity between the originator rhEPO alfa and the biosimilars analyzed.

Impact Analyses and Tests of Metal Cask Considering Aircraft Engine Crash - 12308

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

Lee, Sanghoon; Choi, Woo-Seok; Kim, Ki-Young

2012-07-01

The structural integrity of a dual purpose metal cask currently under development by the Korea Radioactive Waste Management Cooperation (KRMC) is evaluated through analyses and tests under a high-speed missile impact considering the targeted aircraft crash conditions. The impact conditions were carefully chosen through a survey on accident cases and recommendations from the literature. The missile impact velocity was set at 150 m/s, and two impact orientations were considered. A simplified missile simulating a commercial aircraft engine is designed from an impact load history curve provided in the literature. In the analyses, the focus is on the evaluation of themore » containment boundary integrity of the metal cask. The analyses results are compared with the results of tests using a 1/3 scale model. The results show very good agreements, and the procedure and methodology adopted in the structural analyses are validated. While the integrity of the cask is maintained in one evaluation where the missile impacts the top side of the free standing cask, the containment boundary is breached in another case in which the missile impacts the center of the cask lid in a perpendicular orientation. A safety assessment using a numerical simulation of an aircraft engine crash into spent nuclear fuel storage systems is performed. A commercially available explicit finite element code is utilized for the dynamic simulation, and the strain rate effect is included in the modeling of the materials used in the target system and missile. The simulation results show very good agreement with the test results. It is noted that this is the first test considering an aircraft crash in Korea. (authors)« less

Deciphering the shape and deformation of secondary structures through local conformation analysis

PubMed Central

2011-01-01

Background Protein deformation has been extensively analysed through global methods based on RMSD, torsion angles and Principal Components Analysis calculations. Here we use a local approach, able to distinguish among the different backbone conformations within loops, α-helices and β-strands, to address the question of secondary structures' shape variation within proteins and deformation at interface upon complexation. Results Using a structural alphabet, we translated the 3 D structures of large sets of protein-protein complexes into sequences of structural letters. The shape of the secondary structures can be assessed by the structural letters that modeled them in the structural sequences. The distribution analysis of the structural letters in the three protein compartments (surface, core and interface) reveals that secondary structures tend to adopt preferential conformations that differ among the compartments. The local description of secondary structures highlights that curved conformations are preferred on the surface while straight ones are preferred in the core. Interfaces display a mixture of local conformations either preferred in core or surface. The analysis of the structural letters transition occurring between protein-bound and unbound conformations shows that the deformation of secondary structure is tightly linked to the compartment preference of the local conformations. Conclusion The conformation of secondary structures can be further analysed and detailed thanks to a structural alphabet which allows a better description of protein surface, core and interface in terms of secondary structures' shape and deformation. Induced-fit modification tendencies described here should be valuable information to identify and characterize regions under strong structural constraints for functional reasons. PMID:21284872

Deciphering the shape and deformation of secondary structures through local conformation analysis.

PubMed

Baussand, Julie; Camproux, Anne-Claude

2011-02-01

Protein deformation has been extensively analysed through global methods based on RMSD, torsion angles and Principal Components Analysis calculations. Here we use a local approach, able to distinguish among the different backbone conformations within loops, α-helices and β-strands, to address the question of secondary structures' shape variation within proteins and deformation at interface upon complexation. Using a structural alphabet, we translated the 3 D structures of large sets of protein-protein complexes into sequences of structural letters. The shape of the secondary structures can be assessed by the structural letters that modeled them in the structural sequences. The distribution analysis of the structural letters in the three protein compartments (surface, core and interface) reveals that secondary structures tend to adopt preferential conformations that differ among the compartments. The local description of secondary structures highlights that curved conformations are preferred on the surface while straight ones are preferred in the core. Interfaces display a mixture of local conformations either preferred in core or surface. The analysis of the structural letters transition occurring between protein-bound and unbound conformations shows that the deformation of secondary structure is tightly linked to the compartment preference of the local conformations. The conformation of secondary structures can be further analysed and detailed thanks to a structural alphabet which allows a better description of protein surface, core and interface in terms of secondary structures' shape and deformation. Induced-fit modification tendencies described here should be valuable information to identify and characterize regions under strong structural constraints for functional reasons.

[Morphometric analysis of lymphocyte nuclei in chronic lymphocytic leukemia].

PubMed

Ostapenko, V A; Kruchinskiĭ, N G; Smirnova, L A; Cherednik, A B; Nesterov, V N; Tepliakov, A I

1994-01-01

This work is dedicated to the study of use of quantitative analysis of cell nucleus structure for the analysis of peripheral blood lymphocytes in patients with chronic lymphocytic leukaemia. The structure of lymphocytic nuclei of healthy donors was evaluated by means of staining by toluidine blue purified cell suspensions smears. The preparations were analysed on the television measuring system "omnicon" with measurements of the following parameters: square of the nucleus, euchromatin, heterochromatin, and the ratio of heterochromatin and euchromatin squares. Actuarial analysis and nuclei classification of the previously mentioned parameters showed, that in peripheral blood of patients with chronic lymphocytic leukemia a large amount of atypical lymphocytes is present with reduced nucleus sizes. Atypical cells retain the ratio of structural components of chromatine, characteristic to normal cells, which show their low proliferative activity.

Molecular and electronic structures of M 2O 7 (M = Mn, Tc, Re)

DOE PAGES

Lawler, Keith V.; Childs, Bradley C.; Mast, Daniel S.; ...

2017-02-21

The molecular and electronic structures for the Group 7b heptoxides were investigated by computational methods as both isolated molecules and in the solid-state. The metal-oxygen-metal bending angle of the single molecule increased with increasing atomic number, with Re 2O 7 preferring a linear structure. Natural bond orbital and localized orbital bonding analyses indicate that there is a three-center covalent bond between the metal atoms and the bridging oxygen, and the increasing ionic character of the bonds favors larger bond angles. The calculations accurately reproduce the experimental crystal structures within a few percent. Analysis of the band structures and density ofmore » states shows similar bonding for all of the solid-state heptoxides, including the presence of the three-center covalent bond. DFT+U simulations show that PBE-D3 underpredicts the band gap by ~0.2 eV due to an under-correlation of the metal d conducting states. As a result, homologue and compression studies show that Re 2O 7 adopts a polymeric structure because the Re-oxide tetrahedra are easily distorted by packing stresses to form additional three-center covalent bonds.« less

In Search of Functional Advantages of Knots in Proteins.

PubMed

Dabrowski-Tumanski, Pawel; Stasiak, Andrzej; Sulkowska, Joanna I

2016-01-01

We analysed the structure of deeply knotted proteins representing three unrelated families of knotted proteins. We looked at the correlation between positions of knotted cores in these proteins and such local structural characteristics as the number of intra-chain contacts, structural stability and solvent accessibility. We observed that the knotted cores and especially their borders showed strong enrichment in the number of contacts. These regions showed also increased thermal stability, whereas their solvent accessibility was decreased. Interestingly, the active sites within these knotted proteins preferentially located in the regions with increased number of contacts that also have increased thermal stability and decreased solvent accessibility. Our results suggest that knotting of polypeptide chains provides a favourable environment for the active sites observed in knotted proteins. Some knotted proteins have homologues without a knot. Interestingly, these unknotted homologues form local entanglements that retain structural characteristics of the knotted cores.

Psychometric Evaluation of the Ford Insomnia Response to Stress Test (FIRST) in Early Pregnancy.

PubMed

Gelaye, Bizu; Zhong, Qiu-Yue; Barrios, Yasmin V; Redline, Susan; Drake, Christopher L; Williams, Michelle A

2016-04-15

To evaluate the construct validity and factor structure of the Spanish-language version of the Ford Insomnia Response to Stress Test questionnaire (FIRST-S) when used in early pregnancy. A cohort of 647 women were interviewed at ≤ 16 weeks of gestation to collect information regarding lifestyle, demographic, and sleep characteristics. The factorial structure of the FIRST-S was tested through exploratory and confirmatory factor analyses (EFA and CFA). Internal consistency and construct validity were also assessed by evaluating the association between the FIRST-S with symptoms of depression, anxiety, and sleep quality. Item response theory (IRT) analyses were conducted to complement classical test theory (CTT) analytic approaches. The mean score of the FIRST-S was 13.8 (range: 9-33). The results of the EFA showed that the FIRST-S contained a one-factor solution that accounted for 69.8% of the variance. The FIRST-S items showed good internal consistency (Cronbach α = 0.81). CFA results corroborated the one-factor structure finding from the EFA; and yielded measures indicating goodness of fit (comparative fit index of 0.902) and accuracy (root mean square error of approximation of 0.057). The FIRST-S had good construct validity as demonstrated by statistically significant associations of FIRST-S scores with sleep quality, antepartum depression and anxiety symptoms. Finally, results from IRT analyses suggested excellent item infit and outfit measures. The FIRST-S was found to have good construct validity and internal consistency for assessing vulnerability to insomnia during early pregnancy. © 2016 American Academy of Sleep Medicine.

Flutter suppression via piezoelectric actuation

NASA Technical Reports Server (NTRS)

Heeg, Jennifer

1991-01-01

Experimental flutter results obtained from wind tunnel tests of a two degree of freedom wind tunnel model are presented for the open and closed loop systems. The wind tunnel model is a two degree of freedom system which is actuated by piezoelectric plates configured as bimorphs. The model design was based on finite element structural analyses and flutter analyses. A control law was designed based on a discrete system model; gain feedback of strain measurements was utilized in the control task. The results show a 21 pct. increase in the flutter speed.

Analyses for Debonding of Stitched Composite Sandwich Structures Using Improved Constitutive Models

NASA Technical Reports Server (NTRS)

Glaessgen, E. H.; Sleight, D. W.; Krishnamurthy, T.; Raju, I. S.

2001-01-01

A fracture mechanics analysis based on strain energy release rates is used to study the effect of stitching in bonded sandwich beam configurations. Finite elements are used to model the configurations. The stitches were modeled as discrete nonlinear spring elements with a compliance determined by experiment. The constitutive models were developed using the results of flatwise tension tests from sandwich material rather than monolithic material. The analyses show that increasing stitch stiffness, stitch density and debond length decrease strain energy release rates for a fixed applied load.

F-12509A, a new sphingosine kinase inhibitor, produced by a discomycete.

PubMed

Kono, K; Tanaka, M; Ogita, T; Hosoya, T; Kohama, T

2000-05-01

In the course of our screening for inhibitors of sphingosine kinase, we found an active compound from a culture broth of a discomycete, Trichopezizella barbata SANK 25395. The structure of the compound, named F-12509A, was elucidated by a combination of spectroscopic analyses, to be a new sesquiterpene quinone consisting of a drimane moiety and a dihydroxybenzoquinone. Enzyme kinetic analyses showed that F-12509A inhibits sphingosine kinase activity in a competitive manner with respect to sphingosine, with a Ki value of 18 microM.

Non-destructive analysis of the conformational differences among feedstock sources and their corresponding co-products from bioethanol production with molecular spectroscopy.

PubMed

Gamage, I H; Jonker, A; Zhang, X; Yu, P

2014-01-24

The objective of this study was to determine the possibility of using molecular spectroscopy with multivariate technique as a fast method to detect the source effects among original feedstock sources of wheat and their corresponding co-products, wheat DDGS, from bioethanol production. Different sources of the bioethanol feedstock and their corresponding bioethanol co-products, three samples per source, were collected from the same newly-built bioethanol plant with current bioethanol processing technology. Multivariate molecular spectral analyses were carried out using agglomerative hierarchical cluster analysis (AHCA) and principal component analysis (PCA). The molecular spectral data of different feedstock sources and their corresponding co-products were compared at four different regions of ca. 1800-1725 cm(-1) (carbonyl CO ester, mainly related to lipid structure conformation), ca. 1725-1482 cm(-1) (amide I and amide II region mainly related to protein structure conformation), ca. 1482-1180 cm(-1) (mainly associated with structural carbohydrate) and ca. 1180-800 cm(-1) (mainly related to carbohydrates) in complex plant-based system. The results showed that the molecular spectroscopy with multivariate technique could reveal the structural differences among the bioethanol feedstock sources and among their corresponding co-products. The AHCA and PCA analyses were able to distinguish the molecular structure differences associated with chemical functional groups among the different sources of the feedstock and their corresponding co-products. The molecular spectral differences indicated the differences in functional, biomolecular and biopolymer groups which were confirmed by wet chemical analysis. These biomolecular and biopolymer structural differences were associated with chemical and nutrient profiles and nutrient utilization and availability. Molecular spectral analyses had the potential to identify molecular structure difference among bioethanol feedstock sources and their corresponding co-products. Copyright © 2013 Elsevier B.V. All rights reserved.

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.

Non-destructive analysis of the conformational differences among feedstock sources and their corresponding co-products from bioethanol production with molecular spectroscopy

NASA Astrophysics Data System (ADS)

Gamage, I. H.; Jonker, A.; Zhang, X.; Yu, P.

2014-01-01

The objective of this study was to determine the possibility of using molecular spectroscopy with multivariate technique as a fast method to detect the source effects among original feedstock sources of wheat and their corresponding co-products, wheat DDGS, from bioethanol production. Different sources of the bioethanol feedstock and their corresponding bioethanol co-products, three samples per source, were collected from the same newly-built bioethanol plant with current bioethanol processing technology. Multivariate molecular spectral analyses were carried out using agglomerative hierarchical cluster analysis (AHCA) and principal component analysis (PCA). The molecular spectral data of different feedstock sources and their corresponding co-products were compared at four different regions of ca. 1800-1725 cm-1 (carbonyl Cdbnd O ester, mainly related to lipid structure conformation), ca. 1725-1482 cm-1 (amide I and amide II region mainly related to protein structure conformation), ca. 1482-1180 cm-1 (mainly associated with structural carbohydrate) and ca. 1180-800 cm-1 (mainly related to carbohydrates) in complex plant-based system. The results showed that the molecular spectroscopy with multivariate technique could reveal the structural differences among the bioethanol feedstock sources and among their corresponding co-products. The AHCA and PCA analyses were able to distinguish the molecular structure differences associated with chemical functional groups among the different sources of the feedstock and their corresponding co-products. The molecular spectral differences indicated the differences in functional, biomolecular and biopolymer groups which were confirmed by wet chemical analysis. These biomolecular and biopolymer structural differences were associated with chemical and nutrient profiles and nutrient utilization and availability. Molecular spectral analyses had the potential to identify molecular structure difference among bioethanol feedstock sources and their corresponding co-products.

Genetic structure of Plasmodium falciparum populations across the Honduras-Nicaragua border

PubMed Central

2013-01-01

Background The Caribbean coast of Central America remains an area of malaria transmission caused by Plasmodium falciparum despite the fact that morbidity has been reduced in recent years. Parasite populations in that region show interesting characteristics such as chloroquine susceptibility and low mortality rates. Genetic structure and diversity of P. falciparum populations in the Honduras-Nicaragua border were analysed in this study. Methods Seven neutral microsatellite loci were analysed in 110 P. falciparum isolates from endemic areas of Honduras (n = 77) and Nicaragua (n = 33), mostly from the border region called the Moskitia. Several analyses concerning the genetic diversity, linkage disequilibrium, population structure, molecular variance, and haplotype clustering were conducted. Results There was a low level of genetic diversity in P. falciparum populations from Honduras and Nicaragua. Expected heterozigosity (He) results were similarly low for both populations. A moderate differentiation was revealed by the FST index between both populations, and two putative clusters were defined through a structure analysis. The main cluster grouped most of samples from Honduras and Nicaragua, while the second cluster was smaller and included all the samples from the Siuna community in Nicaragua. This result could partially explain the stronger linkage disequilibrium (LD) in the parasite population from that country. These findings are congruent with the decreasing rates of malaria endemicity in Central America. PMID:24093629

Wood digestion in Pselactus spadix Herbst--a weevil attacking marine timber structures.

PubMed

Oevering, Pascal; Pitman, Andrew J; Pandey, Krishna K

2003-04-01

Pselactus spadix tunnels timber structures in the marine environment. Recent studies reported a cosmopolitan distribution for this weevil, which is frequently found in harbour and port areas. P. spadix feeds on timber (hardwood and softwood) in immature and adult life stages, but its digestion of wood components had not been investigated. Using dry weight analyses of tunnel walls and frass produced, P. spadix adults consumed Scots pine with soft rot decay at a rate of 1.59 +/- 0.37 mg d-1 and the digestibility of this substrate was 57.96 +/- 5.89 (i.e. for 100 mg consumed SR-pine, 58 mg was digested). Using gravimetric analysis to quantify structural wood components in tunnel walls and frass, P. spadix adults were found to digest cellulose, lignin and hemicellulose with digestibility coefficients of 82.2, 41.2 and 14.5 respectively. Fourier Transform Infrared (FTIR) spectroscopy analyses of tunnel walls and frass of adults and larvae from soft rotted pine also indicated digestion of all structural components, with larvae digesting cellulose and lignin more efficiently than adults. When FTIR was employed to analyse adult tunnel walls and frass from undecayed pine, cellulose and hemicellulose were digested, but no evidence of lignin digestion was found. This study shows that adults digest lignin when soft rot is present and suggests a symbiotic function of wood degrading microorganisms.

Insights into the three-dimensional Lagrangian geometry of the Antarctic polar vortex

NASA Astrophysics Data System (ADS)

Curbelo, Jezabel; José García-Garrido, Víctor; Mechoso, Carlos Roberto; Mancho, Ana Maria; Wiggins, Stephen; Niang, Coumba

2017-07-01

In this paper we study the three-dimensional (3-D) Lagrangian structures in the stratospheric polar vortex (SPV) above Antarctica. We analyse and visualize these structures using Lagrangian descriptor function M. The procedure for calculation with reanalysis data is explained. Benchmarks are computed and analysed that allow us to compare 2-D and 3-D aspects of Lagrangian transport. Dynamical systems concepts appropriate to 3-D, such as normally hyperbolic invariant curves, are discussed and applied. In order to illustrate our approach we select an interval of time in which the SPV is relatively undisturbed (August 1979) and an interval of rapid SPV changes (October 1979). Our results provide new insights into the Lagrangian structure of the vertical extension of the stratospheric polar vortex and its evolution. Our results also show complex Lagrangian patterns indicative of strong mixing processes in the upper troposphere and lower stratosphere. Finally, during the transition to summer in the late spring, we illustrate the vertical structure of two counterrotating vortices, one the polar and the other an emerging one, and the invariant separatrix that divides them.

Cross-Validation of the Implementation Leadership Scale (ILS) in Child Welfare Service Organizations.

PubMed

Finn, Natalie K; Torres, Elisa M; Ehrhart, Mark G; Roesch, Scott C; Aarons, Gregory A

2016-08-01

The Implementation Leadership Scale (ILS) is a brief, pragmatic, and efficient measure that can be used for research or organizational development to assess leader behaviors and actions that actively support effective implementation of evidence-based practices (EBPs). The ILS was originally validated with mental health clinicians. This study validates the ILS factor structure with providers in community-based organizations (CBOs) providing child welfare services. Participants were 214 service providers working in 12 CBOs that provide child welfare services. All participants completed the ILS, reporting on their immediate supervisor. Confirmatory factor analyses were conducted to examine the factor structure of the ILS. Internal consistency reliability and measurement invariance were also examined. Confirmatory factor analyses showed acceptable fit to the hypothesized first- and second-order factor structure. Internal consistency reliability was strong and there was partial measurement invariance for the first-order factor structure when comparing child welfare and mental health samples. The results support the use of the ILS to assess leadership for implementation of EBPs in child welfare organizations. © The Author(s) 2016.

Examining gray matter structure associated with academic performance in a large sample of Chinese high school students.

PubMed

Wang, Song; Zhou, Ming; Chen, Taolin; Yang, Xun; Chen, Guangxiang; Wang, Meiyun; Gong, Qiyong

2017-04-18

Achievement in school is crucial for students to be able to pursue successful careers and lead happy lives in the future. Although many psychological attributes have been found to be associated with academic performance, the neural substrates of academic performance remain largely unknown. Here, we investigated the relationship between brain structure and academic performance in a large sample of high school students via structural magnetic resonance imaging (S-MRI) using voxel-based morphometry (VBM) approach. The whole-brain regression analyses showed that higher academic performance was related to greater regional gray matter density (rGMD) of the left dorsolateral prefrontal cortex (DLPFC), which is considered a neural center at the intersection of cognitive and non-cognitive functions. Furthermore, mediation analyses suggested that general intelligence partially mediated the impact of the left DLPFC density on academic performance. These results persisted even after adjusting for the effect of family socioeconomic status (SES). In short, our findings reveal a potential neuroanatomical marker for academic performance and highlight the role of general intelligence in explaining the relationship between brain structure and academic performance.

The interplay of the gap, the magnetic resonance, and the van Hove singularity

NASA Astrophysics Data System (ADS)

Levy, Giorgio; Berthod, Christophe; Fischer, Oystein

2007-03-01

The characteristic features of the tunneling spectra in the Bi-based HTS are a d-wave like gap structure, strong and often asymmetric coherence peaks, and an asymmetric dip-hump structure at higher energy. Hoogenboom et al. [1] analysed the spectra of the two-layer compound Bi2212 and showed that all of these properties can be understood assuming d-wave superconductivity, a band structure as measured by ARPES, and an interaction of the quasiparticles with the magnetic resonant mode. In particular the asymmetric dip-hump results in this model from the interplay of the gap, the mode and the van Hove singularity present in the band structure. Here we analyse new data for the three-layer compound Bi2223. Unlike in Ref. [1], we perform full unconstrained least-square fits in order to determine the various parameters of the model directly from the experimental data. This allows us to determine the doping dependence of the gap and of the magnetic resonance energy. [1] B. W. Hoogenboom, C. Berthod, M. Peter, ø. Fischer, and A. A. Kordyuk, Phys. Rev. B 67, 224502 (2003).

Thermal-distortion analysis of an antenna strongback for geostationary high-frequency microwave applications

NASA Technical Reports Server (NTRS)

Farmer, Jeffrey T.; Wahls, Deborah M.; Wright, Robert L.

1990-01-01

The global change technology initiative calls for a geostationary platform for Earth science monitoring. One of the major science instruments is the high frequency microwave sounder (HFMS) which uses a large diameter, high resolution, high frequency microwave antenna. This antenna's size and required accuracy dictates the need for a segmented reflector. On-orbit disturbances may be a significant factor in its design. A study was performed to examine the effects of the geosynchronous thermal environment on the performance of the strongback structure for a proposed antenna concept for this application. The study included definition of the strongback and a corresponding numerical model to be used in the thermal and structural analyses definition of the thermal environment, determination of structural element temperature throughout potential orbits, estimation of resulting thermal distortions, and assessment of the structure's capability to meet surface accuracy requirements. Analyses show that shadows produced by the antenna reflector surface play a major role in increasing thermal distortions. Through customization of surface coating and element expansion characteristics, the segmented reflector concept can meet the tight surface accuracy requirements.

A multilevel approach to the relationship between birth order and intelligence.

PubMed

Wichman, Aaron L; Rodgers, Joseph Lee; MacCallum, Robert C

2006-01-01

Many studies show relationships between birth order and intelligence but use cross-sectional designs or manifest other threats to internal validity. Multilevel analyses with a control variable show that when these threats are removed, two major results emerge: (a) birth order has no significant influence on children's intelligence and (b) earlier reported birth order effects on intelligence are attributable to factors that vary between, not within, families. Analyses on 7- to 8 - and 13- to 14-year-old children from the National Longitudinal Survey of Youth support these conclusions. When hierarchical data structures, age variance of children, and within-family versus between-family variance sources are taken into account, previous research is seen in a new light.

Assessment of Simulated Ground Motions in Earthquake Engineering Practice: A Case Study for Duzce (Turkey)

NASA Astrophysics Data System (ADS)

Karimzadeh, Shaghayegh; Askan, Aysegul; Yakut, Ahmet

2017-09-01

Simulated ground motions can be used in structural and earthquake engineering practice as an alternative to or to augment the real ground motion data sets. Common engineering applications of simulated motions are linear and nonlinear time history analyses of building structures, where full acceleration records are necessary. Before using simulated ground motions in such applications, it is important to assess those in terms of their frequency and amplitude content as well as their match with the corresponding real records. In this study, a framework is outlined for assessment of simulated ground motions in terms of their use in structural engineering. Misfit criteria are determined for both ground motion parameters and structural response by comparing the simulated values against the corresponding real values. For this purpose, as a case study, the 12 November 1999 Duzce earthquake is simulated using stochastic finite-fault methodology. Simulated records are employed for time history analyses of frame models of typical residential buildings. Next, the relationships between ground motion misfits and structural response misfits are studied. Results show that the seismological misfits around the fundamental period of selected buildings determine the accuracy of the simulated responses in terms of their agreement with the observed responses.

A Model Structure for the Heterodimer apoA-IMilano–apoA-II Supports Its Peculiar Susceptibility to Proteolysis

PubMed Central

Rocco, Alessandro Guerini; Mollica, Luca; Gianazza, Elisabetta; Calabresi, Laura; Franceschini, Guido; Sirtori, Cesare R.; Eberini, Ivano

2006-01-01

In this study, we propose a structure for the heterodimer between apolipoprotein A-IMilano and apolipoprotein A-II (apoA-IM–apoA-II) in a synthetic high-density lipoprotein (HDL) containing L-α-palmitoyloleoyl phosphatidylcholine. We applied bioinformatics/computational tools and procedures, such as molecular docking, molecular and essential dynamics, starting from published crystal structures for apolipoprotein A-I and apolipoprotein A-II. Structural and energetic analyses onto the simulated system showed that the molecular dynamics produced a stabilized synthetic HDL. The essential dynamic analysis showed a deviation from the starting belt structure. Our structural results were validated by limited proteolysis experiments on HDL from apoA-IM carriers in comparison with control HDL. The high sensitivity of apoA-IM–apoA-II to proteases was in agreement with the high root mean-square fluctuation values and the reduction in secondary structure content from molecular dynamics data. Circular dichroism on synthetic HDL containing apoA-IM–apoA-II was consistent with the α-helix content computed on the proposed model. PMID:16891368

Theoretical Investigation of Dual Tuning of Solitonic Processes in Multiferroic Structures

NASA Astrophysics Data System (ADS)

Cherkasskii, M. A.; Nikitin, A. A.; Ustinov, A. B.; Stashkevich, A.; Kalinikos, B. A.

2016-11-01

. The solitonic wave processes in a multiferroic structure based on ferroelectric and ferrite layers are studied. The influence of external electric and magnetic fields on frequency and wave-number ranges, where bright and dark solitons can exist, are analysed. The investigation was carried out with the nonlinear Schrodinger equation. Results show that an increase of the electric field shifts the boundary between bright and dark solitons to long-wave region. An increase in magnetic field results in the opposite effect.

Multi-peak electromagnetically induced transparency (EIT)-like transmission from bull's-eye-shaped metamaterial.

PubMed

Kim, Jaeyoun; Soref, Richard; Buchwald, Walter R

2010-08-16

We investigate the electromagnetic response of the concentric multi-ring, or the bull's eye, structure as an extension of the dual-ring metamaterial which exhibits electromagnetically-induced transparency (EIT)-like transmission characteristics. Our results show that adding inner rings produces additional EIT-like peaks, and widens the metamaterial's spectral range of operation. Analyses of the dispersion characteristics and induced current distribution further confirmed the peak's EIT-like nature. Impacts of structural and dielectric parameters are also investigated.

Improving the Factor Structure of Psychological Scales

PubMed Central

Zhang, Xijuan; Savalei, Victoria

2015-01-01

Many psychological scales written in the Likert format include reverse worded (RW) items in order to control acquiescence bias. However, studies have shown that RW items often contaminate the factor structure of the scale by creating one or more method factors. The present study examines an alternative scale format, called the Expanded format, which replaces each response option in the Likert scale with a full sentence. We hypothesized that this format would result in a cleaner factor structure as compared with the Likert format. We tested this hypothesis on three popular psychological scales: the Rosenberg Self-Esteem scale, the Conscientiousness subscale of the Big Five Inventory, and the Beck Depression Inventory II. Scales in both formats showed comparable reliabilities. However, scales in the Expanded format had better (i.e., lower and more theoretically defensible) dimensionalities than scales in the Likert format, as assessed by both exploratory factor analyses and confirmatory factor analyses. We encourage further study and wider use of the Expanded format, particularly when a scale’s dimensionality is of theoretical interest. PMID:27182074

An exact arithmetic toolbox for a consistent and reproducible structural analysis of metabolic network models

PubMed Central

Chindelevitch, Leonid; Trigg, Jason; Regev, Aviv; Berger, Bonnie

2014-01-01

Constraint-based models are currently the only methodology that allows the study of metabolism at the whole-genome scale. Flux balance analysis is commonly used to analyse constraint-based models. Curiously, the results of this analysis vary with the software being run, a situation that we show can be remedied by using exact rather than floating-point arithmetic. Here we introduce MONGOOSE, a toolbox for analysing the structure of constraint-based metabolic models in exact arithmetic. We apply MONGOOSE to the analysis of 98 existing metabolic network models and find that the biomass reaction is surprisingly blocked (unable to sustain non-zero flux) in nearly half of them. We propose a principled approach for unblocking these reactions and extend it to the problems of identifying essential and synthetic lethal reactions and minimal media. Our structural insights enable a systematic study of constraint-based metabolic models, yielding a deeper understanding of their possibilities and limitations. PMID:25291352

Structural characterization of humic-like substances with conventional and surface-enhanced spectroscopic techniques

NASA Astrophysics Data System (ADS)

Carletti, Paolo; Roldán, Maria Lorena; Francioso, Ornella; Nardi, Serenella; Sanchez-Cortes, Santiago

2010-10-01

Emission-excitation, synchronous fluorescence spectroscopy and surface-enhanced Raman scattering (SERS) combined with surface-enhanced fluorescence (SEF) were applied to aqueous solutions of a humic-like substance (HLS) extracted from earthworm faeces. All measurements were acquired in a wide range of pH (4-12) and analysed by the linear regression analysis. Diffuse Reflectance Infrared Fourier Transform (DRIFT) spectra were also acquired to assist in the structural characterization of this HLS. The emission and excitation spectra allowed the identification of two main fluorophores in the analysed sample. Moreover, a close correlation between fluorescence intensities of each fluorophore with pH variation was observed. SERS and SEF, in agreement with the fluorescence spectroscopy, showed that the HLS at low pH values exists in an aggregated and coiled molecular structure while it is dispersed and uncoiled at alkaline conditions. The obtained spectra also evidenced that different conditions modify the functional groups exposed to the surrounding aqueous environment.

Association between smoking status and the parameters of vascular structure and function in adults: results from the EVIDENT study.

PubMed

Recio-Rodriguez, Jose I; Gomez-Marcos, Manuel A; Patino Alonso, Maria C; Martin-Cantera, Carlos; Ibañez-Jalon, Elisa; Melguizo-Bejar, Amor; Garcia-Ortiz, Luis

2013-12-01

The present study analyses the relation between smoking status and the parameters used to assess vascular structure and function. This cross-sectional, multi-centre study involved a random sample of 1553 participants from the EVIDENT study. The smoking status, peripheral augmentation index and ankle-brachial index were measured in all participants. In a small subset of the main population (265 participants), the carotid intima-media thickness and pulse wave velocity were also measured. After controlling for the effect of age, sex and other risk factors, present smokers have higher values of carotid intima-media thickness (p = 0.011). Along the same lines, current smokers have higher values of pulse wave velocity and lower mean values of ankle-brachial index but without statistical significance in both cases. Among the parameters of vascular structure and function analysed, only the IMT shows association with the smoking status, after adjusting for confounders.

Association between smoking status and the parameters of vascular structure and function in adults: results from the EVIDENT study

PubMed Central

2013-01-01

Background The present study analyses the relation between smoking status and the parameters used to assess vascular structure and function. Methods This cross-sectional, multi-centre study involved a random sample of 1553 participants from the EVIDENT study. Measurements: The smoking status, peripheral augmentation index and ankle-brachial index were measured in all participants. In a small subset of the main population (265 participants), the carotid intima-media thickness and pulse wave velocity were also measured. Results After controlling for the effect of age, sex and other risk factors, present smokers have higher values of carotid intima-media thickness (p = 0.011). Along the same lines, current smokers have higher values of pulse wave velocity and lower mean values of ankle-brachial index but without statistical significance in both cases. Conclusions Among the parameters of vascular structure and function analysed, only the IMT shows association with the smoking status, after adjusting for confounders. PMID:24289208

Genetic relationships among American donkey populations: insights into the process of colonization.

PubMed

Jordana, J; Ferrando, A; Miró, J; Goyache, F; Loarca, A; Martínez López, O R; Canelón, J L; Stemmer, A; Aguirre, L; Lara, M A C; Álvarez, L A; Llambí, S; Gómez, N; Gama, L T; Nóvoa, M F; Martínez, R D; Pérez, E; Sierra, A; Contreras, M A; Guastella, A M; Marletta, D; Arsenos, G; Curik, I; Landi, V; Martínez, A; Delgado, J V

2016-04-01

This study presents the first insights into the genetic diversity and structure of the American donkey metapopulation. The primary objectives were to detect the main structural features underlying variability among American donkey populations, identify boundaries between differentiated gene pools, and draw the main colonization pathways since the introduction of donkeys into America in the 15th century. A panel of 14 microsatellite markers was applied for genotyping 350 American donkeys from 13 countries. The genetic structure of this metapopulation was analysed using descriptive statistics and Bayesian model-based methods. These populations were then compared to a database containing information on 476 individuals from 11 European breeds to identify the most likely ancestral donor populations. Results showed the presence of two distinct genetic pools, with confluence of the two in Colombia. The southern pool showed a unique genetic signature subsequent to an older founder event, but lacked any significant influence of modern gene flow from Europe. The northern pool, conversely, may have retained more ancestral polymorphisms and/or have experienced modern gene flow from Spanish breeds. The Andalusian and, to a lesser extent, the Catalan breeds have left a more pronounced footprint in some of the American donkey populations analysed. © 2015 Blackwell Verlag GmbH.

Emotional intelligence in older adults: psychometric properties of the TMMS-24 and relationship with psychological well-being and life satisfaction.

PubMed

Delhom, I; Gutierrez, M; Lucas-Molina, B; Meléndez, J C

2017-08-01

Aging is a process during which important changes occur in different areas of development and emotional intelligence plays an essential role. The objective of this study was twofold: first, to validate the TMMS-24 in an older population; and second, to examine the mediating role of life satisfaction in the relationship between emotional intelligence and psychological well-being. The sample consisted of 215 older adults (60.15% women) with a mean age of 69.56 (SD = 6.42), without cognitive impairment. Data on emotional intelligence, satisfaction with life, and psychological well-being were obtained through the TMMS-24, the SWLS, and Ryff's psychological well-being scales, respectively. Confirmatory factor analyses and structural equation modeling were conducted. Confirmatory factor analyses confirmed the three-dimensional structure of the TMMS-24. The total scale showed an internal consistency of 0.90, ranging from 0.84 to 0.85 for the subscales. Structural equation modeling indicated that emotional intelligence exerted an influence on psychological well-being both directly and indirectly through life satisfaction. These findings show that the TMMS-24 has adequate psychometric properties for assessing emotional intelligence in elderly participants, and they indicate that emotional intelligence influences cognitive and affective judgments of life satisfaction, with these judgments of life satisfaction predicting psychological well-being.

Influence of Soil Properties on Soldierless Termite Distribution.

PubMed

Bourguignon, Thomas; Drouet, Thomas; Šobotník, Jan; Hanus, Robert; Roisin, Yves

2015-01-01

In tropical rainforests, termites constitute an important part of the soil fauna biomass, and as for other soil arthropods, variations in soil composition create opportunities for niche partitioning. The aim of this study was twofold: first, we tested whether soil-feeding termite species differ in the foraging substrate; second, we investigated whether soil-feeding termites select their foraging sites to enhance nutrients intake. To do so, we collected termites and analysed the composition and structure of their feeding substrates. Although Anoplotermes-group members are all considered soil-feeders, our results show that some species specifically feed on abandoned termite nests and very rotten wood, and that this substrate selection is correlated with previous stable isotope analyses, suggesting that one component of niche differentiation among species is substrate selection. Our results show that the composition and structure of bare soils on which different termite species foraged do not differ, suggesting that there is no species specialization for a particular type of bare soil. Finally, the bare soil on which termites forage does not differ from random soil samples. Overall, our results suggest that few species of the Anoplotermes-group are specialized toward substrates rich in organic matter, but that the vast majority forage on soil independently of its structural and chemical composition, being ecologically equivalent for this factor.

Evidence of liquid phase during laser-induced periodic surface structures formation induced by accumulative ultraviolet picosecond laser beam

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

Huynh, T. T. D.; Petit, A.; Semmar, N., E-mail: nadjib.semmar@univ-orleans.fr

2015-11-09

Laser-induced periodic surface structures (LIPSS) were formed on Cu/Si or Cu/glass thin films using Nd:YAG laser beam (40 ps, 10 Hz, and 30 mJ/cm{sup 2}). The study of ablation threshold is always achieved over melting when the variation of the number of pulses increases from 1 to 1000. But the incubation effect is leading to reduce the threshold of melting as increasing the number of laser pulse. Also, real time reflectivity signals exhibit typical behavior to stress the formation of a liquid phase during the laser-processing regime and helps to determine the threshold of soft ablation. Atomic Force Microscopy (AFM) analyses have shownmore » the topology of the micro-crater containing regular spikes with different height. Transmission Electron Microscopy (TEM) allows finally to show three distinguished zones in the close region of isolated protrusions. The central zone is a typical crystallized area of few nanometers surrounded by a mixed poly-crystalline and amorphous area. Finally, in the region far from the protrusion zone, Cu film shows an amorphous structure. The real time reflectivity, AFM, and HR-TEM analyses evidence the formation of a liquid phase during the LIPSS formation in the picosecond regime.« less

Multifactorial genetic divergence processes drive the onset of speciation in an Amazonian fish

PubMed Central

Torrente-Vilara, Gislene; Quilodran, Claudio; Rodrigues da Costa Doria, Carolina; Montoya-Burgos, Juan I.

2017-01-01

Understanding the processes that drive population genetic divergence in the Amazon is challenging because of the vast scale, the environmental richness and the outstanding biodiversity of the region. We addressed this issue by determining the genetic structure of the widespread Amazonian common sardine fish Triportheus albus (Characidae). We then examined the influence, on this species, of all previously proposed population-structuring factors, including isolation-by-distance, isolation-by-barrier (the Teotônio Falls) and isolation-by-environment using variables that describe floodplain and water characteristics. The population genetics analyses revealed an unusually strong structure with three geographical groups: Negro/Tapajós rivers, Lower Madeira/Central Amazon, and Upper Madeira. Distance-based redundancy analyses showed that the optimal model for explaining the extreme genetic structure contains all proposed structuring factors and accounts for up to 70% of the genetic structure. We further quantified the contribution of each factor via a variance-partitioning analysis. Our results demonstrate that multiple factors, often proposed as individual drivers of population divergence, have acted in conjunction to divide T. albus into three genetic lineages. Because the conjunction of multiple long-standing population-structuring processes may lead to population reproductive isolation, that is, the onset of speciation, we suggest that the multifactorial population-structuring processes highlighted in this study could account for the high speciation rate characterising the Amazon Basin. PMID:29261722

Electron microscopy analyses and electrical properties of the layered Bi{sub 2}WO{sub 6} phase

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

Taoufyq, A.; Laboratoire Matériaux et Environnement LME, Faculté des Sciences, Université Ibn Zohr, BP 8106, Cité Dakhla, Agadir, Maroc; Département d‘Études des Réacteurs, Laboratoire Dosimétrie Capteurs Instrumentation, CEA Cadarache

2013-07-15

The bismuth tungstate Bi{sub 2}WO{sub 6} was synthesized using a classical coprecipitation method followed by a calcination process at different temperatures. The samples were characterized by X-ray diffraction, simultaneous thermogravimetry and differential thermal analysis (TGA/DTA), scanning and transmission electron microscopy (SEM, TEM) analyses. The Rietveld analysis and electron diffraction clearly confirmed the Pca2{sub 1} non centrosymmetric space group previously proposed for this phase. The layers Bi{sub 2}O{sub 2}{sup 2+} and WO{sub 4}{sup 2−} have been directly evidenced from the HRTEM images. The electrical properties of Bi{sub 2}WO{sub 6} compacted pellets systems were determined from electrical impedance spectrometry (EIS) and directmore » current (DC) analyses, under air and argon, between 350 and 700 °C. The direct current analyses showed that the conduction observed from EIS analyses was mainly ionic in this temperature range, with a small electronic contribution. Electrical change above the transition temperature of 660 °C is observed under air and argon atmospheres. The strong conductivity increase observed under argon is interpreted in terms of formation of additional oxygen vacancies coupled with electron conduction. - Graphical abstract: High resolution transmission electron microscopy: inverse fast Fourier transform giving the layered structure of the Bi{sub 2}WO{sub 6} phase, with a representation of the cell dimensions (b and c vectors). The Bi{sub 2}O{sub 2}{sup 2+} and WO{sub 4}{sup 2−} sandwiches are visible in the IFFT image. - Highlights: • Using transmission electron microscopy, we visualize the layered structure of Bi{sub 2}WO{sub 6}. • Electrical analyses under argon gas show some increase in conductivity. • The phase transition at 660 °C is evidenced from electrical modification.« less

Widespread increase of tree mortality rates in the western United States

Treesearch

Phillip J. van Mantgem; Nathan L. Stephenson; John C. Byrne; Lori D. Daniels; Jerry F. Franklin; Peter Z. Fule; Mark E. Harmon; Andrew J. Larson; Jeremy M. Smith; Alan H. Taylor; Thomas T. Veblen

2009-01-01

Persistent changes in tree mortality rates can alter forest structure, composition, and ecosystem services such as carbon sequestration. Our analyses of longitudinal data from unmanaged old forests in the western United States showed that background (noncatastrophic) mortality rates have increased rapidly in recent decades, with doubling periods ranging from 17 to 29...

Reliability and Validity of the Chinese Version of the Solution-Focused Inventory in College Students

ERIC Educational Resources Information Center

Yang, Hongfei; Hai, Tang

2015-01-01

The psychometrics of the Chinese Solution-Focused Inventory (CSFI) was studied in Chinese college students. Confirmatory factor analysis confirmed the 3-factor structure. All subscales showed good reliability and convergent and incremental validity. Results of hierarchical regression analyses indicated that the 3 subscales accounted for additional…

Factorial Validity of the Vocational Interest Scales of the Holland Vocational Preference Inventory for Australian High School Students.

ERIC Educational Resources Information Center

Athanasou, James A.; And Others

1981-01-01

The structure of the six vocational interests measured by the Holland Vocational Preference Inventory was identified. Results of two separate analyses showed that a general factor accounted for much of the total variance. Remaining bipolar factors supported previous classifications of interests. (Author/GK)

The W22 genome: a foundation for maize functional genomics and transposon biology

USDA-ARS?s Scientific Manuscript database

The maize W22 inbred has served as a platform for maize genetics since the mid twentieth century. To streamline maize genome analyses, we have sequenced and de novo assembled a W22 reference genome using small-read sequencing technologies. We show that significant structural heterogeneity exists in ...

Secondary School Teachers' Classroom Activities and Their Perceptions on Effectiveness of the Activity

ERIC Educational Resources Information Center

Guvenc, Hulya

2017-01-01

In the present research, effective and ineffective activities that secondary school teachers used and their perceptions on the effectiveness of the activities are investigated. The data were collected from 20 teachers using semi-structured interviews. Data were analysed using open coding and directed content analysis. Research findings showed that…

When Mothers Have Serious Mental Health Problems: Parenting as a Proximal Mediator

ERIC Educational Resources Information Center

Oyserman, D.; Bybee, D.; Mowbray, C.; Hart-Johnson, T.

2005-01-01

Maternal mental health (MMH) problems are associated with lack of confidence in one's parenting, overly lax or too harsh discipline, and child academic underperformance. We asked if parenting mediates the effect of MMH problems on academic outcomes even among mothers with serious mental illness (n=164). Structural equation analyses show a…

Dramatic Change in Jupiter's Great Red Spot

NASA Technical Reports Server (NTRS)

Simon, A. A.; Wong, M. H.; Rogers, J. H.; Orton, G. S.; de Pater, I.; Asay-Davis, X.; Carlson, R. W.; Marcus, P. S.

2015-01-01

Jupiter's Great Red Spot (GRS) is one of its most distinct and enduring features, having been continuously observed since the 1800's. It currently spans the smallest latitude and longitude size ever recorded. Here we show analyses of 2014 Hubble spectral imaging data to study the color, structure and internal dynamics of this long-live storm.

CFD Analyses and Jet-Noise Predictions of Chevron Nozzles with Vortex Stabilization

NASA Technical Reports Server (NTRS)

Dippold, Vance

2008-01-01

The wind computational fluid dynamics code was used to perform a series of analyses on a single-flow plug nozzle with chevrons. Air was injected from tubes tangent to the nozzle outer surface at three different points along the chevron at the nozzle exit: near the chevron notch, at the chevron mid-point, and near the chevron tip. Three injection pressures were used for each injection tube location--10, 30, and 50 psig-giving injection mass flow rates of 0.1, 0.2, and 0.3 percent of the nozzle mass flow. The results showed subtle changes in the jet plume s turbulence and vorticity structure in the region immediately downstream of the nozzle exit. Distinctive patterns in the plume structure emerged from each injection location, and these became more pronounced as the injection pressure was increased. However, no significant changes in centerline velocity decay or turbulent kinetic energy were observed in the jet plume as a result of flow injection. Furthermore, computational acoustics calculations performed with the JeNo code showed no real reduction in jet noise relative to the baseline chevron nozzle.

Concurrent validation of CHIRP, a new instrument for measuring healthcare student attitudes towards interdisciplinary teamwork.

PubMed

Hollar, David; Hobgood, Cherri; Foster, Beverly; Aleman, Marco; Sawning, Susan

2012-01-01

Positive attitudes towards teamwork among health care professionals are critical to patient safety. The purpose of this study is to describe the development and concurrent validation of a new instrument to measure attitudes towards healthcare teamwork that is generalizable across various populations of healthcare students. The Collaborative Healthcare Interdisciplinary Planning (CHIRP) scale was validated against the Readiness for Inter-Professional Learning Scale (RIPLS). Analyses included student (n = 266) demographics, ANOVA, internal consistency, factor analysis, and Rasch analysis. The two instruments correlated at r = .582. The CHIRP showed a multifactorial structure having excellent internal consistency (alpha = .850), with 25 of the 36 scale items loading onto a single Teamwork Attitudes factor. The RIPLS likewise had strong internal consistency (alpha = .796) and a three-factor structure, supporting previous studies of the instrument. However, Rasch analyses showed 14 (38.9%) of the 36 CHIRP items, but only four (21.1%) of the 19 RIPLS items remaining within the satisfactory standardized OUTFIT zone of 2.0 standard deviation units. We propose the 14 fitting items as a new, validated teamwork attitudes scale.

New insights into replication origin characteristics in metazoans

PubMed Central

Puy, Aurore; Rialle, Stéphanie; Kaplan, Noam; Segal, Eran

2012-01-01

We recently reported the identification and characterization of DNA replication origins (Oris) in metazoan cell lines. Here, we describe additional bioinformatic analyses showing that the previously identified GC-rich sequence elements form origin G-rich repeated elements (OGREs) that are present in 67% to 90% of the DNA replication origins from Drosophila to human cells, respectively. Our analyses also show that initiation of DNA synthesis takes place precisely at 160 bp (Drosophila) and 280 bp (mouse) from the OGRE. We also found that in most CpG islands, an OGRE is positioned in opposite orientation on each of the two DNA strands and detected two sites of initiation of DNA synthesis upstream or downstream of each OGRE. Conversely, Oris not associated with CpG islands have a single initiation site. OGRE density along chromosomes correlated with previously published replication timing data. Ori sequences centered on the OGRE are also predicted to have high intrinsic nucleosome occupancy. Finally, OGREs predict G-quadruplex structures at Oris that might be structural elements controlling the choice or activation of replication origins. PMID:22373526

Functional and structural neural alterations in Internet gaming disorder: A systematic review and meta-analysis.

PubMed

Yao, Yuan-Wei; Liu, Lu; Ma, Shan-Shan; Shi, Xin-Hui; Zhou, Nan; Zhang, Jin-Tao; Potenza, Marc N

2017-12-01

This meta-analytic study aimed to identify the common and specific neural alterations in Internet gaming disorder (IGD) across different domains and modalities. Two separate meta-analyses for functional neural activation and gray-matter volume were conducted. Sub-meta-analyses for the domains of reward, cold-executive, and hot-executive functions were also performed, respectively. IGD subjects, compared with healthy controls, showed: (1) hyperactivation in the anterior and posterior cingulate cortices, caudate, posterior inferior frontal gyrus (IFG), which were mainly associated with studies measuring reward and cold-executive functions; and, (2) hypoactivation in the anterior IFG in relation to hot-executive function, the posterior insula, somatomotor and somatosensory cortices in relation to reward function. Furthermore, IGD subjects showed reduced gray-matter volume in the anterior cingulate, orbitofrontal, dorsolateral prefrontal, and premotor cortices. These findings suggest that IGD is associated with both functional and structural neural alterations in fronto-striatal and fronto-cingulate regions. Moreover, multi-domain assessments capture different aspects of neural alterations in IGD, which may be helpful for developing effective interventions targeting specific functions. Copyright © 2017 Elsevier Ltd. All rights reserved.

Role of Altered Sialylation of the I-Like Domain of β1 Integrin in the Binding of Fibronectin to β1 Integrin: Thermodynamics and Conformational Analyses

PubMed Central

Pan, Di; Song, Yuhua

2010-01-01

Abstract N-glycosylation of the I-like domain of β1 integrin plays an essential role in integrin structure and function, and the altered sialylation of β1 integrin regulates β1 integrin binding to fibronectin. However, the structural basis underlying the effect of altered sialylation of the β1 I-like domain on β1 integrin binding to fibronectin remains largely unknown. In this study, we used a combination of molecular dynamics simulations and binding free energy analyses to investigate changes in binding thermodynamics and in conformation of the glycosylated β1 I-like domain-FN-III9-10 complex caused by altered sialylation of the β1 I-like domain. Binding free energy analyses showed that desialylation of β1 I-like domain increased β1 integrin binding to fibronectin, consistent with experimental results. Interaction analyses showed that altered sialylation of the β1 I-like domain resulted in significant changes in the interaction of the N-glycans of the I-like domain with both the I-like domain and fibronectin, and these changes could directly affect the allosteric regulation of the interaction between the I-like domain and fibronectin. Altered sialylation of the β1 I-like domain caused significant conformational changes in key functional sites of both the β1 I-like domain and fibronectin. In addition, altered sialylation of the β1 I-like domain resulted in changes in the degree of correlated motions between residues in the I-like domain and residues in fibronectin, and in the degree of motion changes in fibronectin, which could affect β1 integrin binding to fibronectin. We believe results from this study provide thermodynamic and structural evidence for a role of altered sialylation of β1 integrin in regulating β1 integrin binding to fibronectin and it's induced cellular activities. PMID:20655849

Characterization of structures of the Nankai Trough accretionary prism from integrated analyses of LWD log response, resistivity images and clay mineralogy of cuttings: Expedition 338 Site C0002

NASA Astrophysics Data System (ADS)

Jurado, Maria Jose; Schleicher, Anja

2014-05-01

The objective of our research is a detailed characterization of structures on the basis of LWD oriented images and logs,and clay mineralogy of cuttings from Hole C0002F of the Nankai Trough accretionary prism. Our results show an integrated interpretation of structures derived from borehole images, petrophysical characterization on LWD logs and cuttings mineralogy. The geometry of the structure intersected at Hole C0002F has been characterized by the interpretation of oriented borehole resistivity images acquired during IODP Expedition 338. The characterization of structural features, faults and fracture zones is based on a detailed post-cruise interpretation of bedding and fractures on borehole images and also on the analysis of Logging While Drilling (LWD) log response (gamma radioactivity, resistivity and sonic logs). The interpretation and complete characterization of structures (fractures, fracture zones, fault zones, folds) was achieved after detailed shorebased reprocessing of resistivity images, which allowed to enhance bedding and fracture's imaging for geometry and orientation interpretation. In order to characterize distinctive petrophysical properties based on LWD log response, it could be compared with compositional changes derived from cuttings analyses. Cuttings analyses were used to calibrate and to characterize log response and to verify interpretations in terms of changes in composition and texture at fractures and fault zones defined on borehole images. Cuttings were taken routinely every 5 m during Expedition 338, indicating a clay-dominated lithology of silty claystone with interbeds of weakly consolidated, fine sandstones. The main mineralogical components are clay minerals, quartz, feldspar and calcite. Selected cuttings were taken from areas of interest as defined on LWD logs and images. The clay mineralogy was investigated on the <2 micron clay-size fraction, with special focus on smectite and illite minerals. Based on X-ray diffraction analysis measured at room temperature and a relative humidity of ~30%, we compared the shape and size of illite and smectite, as well as their water content and their polytypes. The comparison of cuttings mineralogy with logging while drilling (LWD) data allowed us to characterize structural, petrophysical and mineralogical properties at fracture and fault zones. We also analyzed the relationship between deformation structures and compositional and mineralogical changes. We established a correlation between observed results on clay mineralogy and log responses in relation with the structures and trends characterized on logging data. In general, the log data provide a good correlation with the actual mineralogy and the relative abundance of clay. In particular we analyzed trends characterized by smectite water layers as indication of compaction. These trends were correlated with log response (on sonic velocity) within Unit IV. Our results show the integration of logging data and cutting sample analyses as a valuable tool for characterization of petrophysical and mineralogical changes of the structures of the Nankai accretionary prism.

Multilevel Factor Structure and Concurrent Validity of the Teacher Version of the Authoritative School Climate Survey.

PubMed

Huang, Francis L; Cornell, Dewey G; Konold, Timothy; Meyer, Joseph P; Lacey, Anna; Nekvasil, Erin K; Heilbrun, Anna; Shukla, Kathan D

2015-12-01

School climate is well recognized as an important influence on student behavior and adjustment to school, but there is a need for theory-guided measures that make use of teacher perspectives. Authoritative school climate theory hypothesizes that a positive school climate is characterized by high levels of disciplinary structure and student support. A teacher version of the Authoritative School Climate Survey (ASCS) was administered to a statewide sample of 9099 7th- and 8th-grade teachers from 366 schools. The study used exploratory and multilevel confirmatory factor analyses (MCFA) that accounted for the nested data structure and allowed for the modeling of the factor structures at 2 levels. Multilevel confirmatory factor analyses conducted on both an exploratory (N = 4422) and a confirmatory sample (N = 4677) showed good support for the factor structures investigated. Factor correlations at 2 levels indicated that schools with greater levels of disciplinary structure and student support had higher student engagement, less teasing and bullying, and lower student aggression toward teachers. The teacher version of the ASCS can be used to assess 2 key domains of school climate and associated measures of student engagement and aggression toward peers and teachers. © 2015, American School Health Association.

Genetic Structure of Bluefin Tuna in the Mediterranean Sea Correlates with Environmental Variables

PubMed Central

Riccioni, Giulia; Stagioni, Marco; Landi, Monica; Ferrara, Giorgia; Barbujani, Guido; Tinti, Fausto

2013-01-01

Background Atlantic Bluefin Tuna (ABFT) shows complex demography and ecological variation in the Mediterranean Sea. Genetic surveys have detected significant, although weak, signals of population structuring; catch series analyses and tagging programs identified complex ABFT spatial dynamics and migration patterns. Here, we tested the hypothesis that the genetic structure of the ABFT in the Mediterranean is correlated with mean surface temperature and salinity. Methodology We used six samples collected from Western and Central Mediterranean integrated with a new sample collected from the recently identified easternmost reproductive area of Levantine Sea. To assess population structure in the Mediterranean we used a multidisciplinary framework combining classical population genetics, spatial and Bayesian clustering methods and a multivariate approach based on factor analysis. Conclusions FST analysis and Bayesian clustering methods detected several subpopulations in the Mediterranean, a result also supported by multivariate analyses. In addition, we identified significant correlations of genetic diversity with mean salinity and surface temperature values revealing that ABFT is genetically structured along two environmental gradients. These results suggest that a preference for some spawning habitat conditions could contribute to shape ABFT genetic structuring in the Mediterranean. However, further studies should be performed to assess to what extent ABFT spawning behaviour in the Mediterranean Sea can be affected by environmental variation. PMID:24260341

The inner formal structure of the H-T-P drawings: an exploratory study.

PubMed

Vass, Z

1998-08-01

The study describes some interrelated patterns of traits of the House-Tree-Person (H-T-P) drawings with the instruments of hierarchical cluster analysis. First, according to the literature 1 7 formal or structural aspects of the projective drawings were collected, after which a detailed manual for coding was compiled. Second, the interrater reliability and the consistency of this manual was tested. Third, the hierarchical cluster structure of the reliable and consistent formal aspects was analysed. Results are: (a) a psychometrically tested coding manual of the investigated formal-structural aspects, each of them illustrated with drawings that showed the highest interrater agreement; and (b) the hierarchic cluster structure of the formal aspects of the H-T-P drawings of "normal" adults.

Determining crystal structures through crowdsourcing and coursework

NASA Astrophysics Data System (ADS)

Horowitz, Scott; Koepnick, Brian; Martin, Raoul; Tymieniecki, Agnes; Winburn, Amanda A.; Cooper, Seth; Flatten, Jeff; Rogawski, David S.; Koropatkin, Nicole M.; Hailu, Tsinatkeab T.; Jain, Neha; Koldewey, Philipp; Ahlstrom, Logan S.; Chapman, Matthew R.; Sikkema, Andrew P.; Skiba, Meredith A.; Maloney, Finn P.; Beinlich, Felix R. M.; Caglar, Ahmet; Coral, Alan; Jensen, Alice Elizabeth; Lubow, Allen; Boitano, Amanda; Lisle, Amy Elizabeth; Maxwell, Andrew T.; Failer, Barb; Kaszubowski, Bartosz; Hrytsiv, Bohdan; Vincenzo, Brancaccio; de Melo Cruz, Breno Renan; McManus, Brian Joseph; Kestemont, Bruno; Vardeman, Carl; Comisky, Casey; Neilson, Catherine; Landers, Catherine R.; Ince, Christopher; Buske, Daniel Jon; Totonjian, Daniel; Copeland, David Marshall; Murray, David; Jagieła, Dawid; Janz, Dietmar; Wheeler, Douglas C.; Cali, Elie; Croze, Emmanuel; Rezae, Farah; Martin, Floyd Orville; Beecher, Gil; de Jong, Guido Alexander; Ykman, Guy; Feldmann, Harald; Chan, Hugo Paul Perez; Kovanecz, Istvan; Vasilchenko, Ivan; Connellan, James C.; Borman, Jami Lynne; Norrgard, Jane; Kanfer, Jebbie; Canfield, Jeffrey M.; Slone, Jesse David; Oh, Jimmy; Mitchell, Joanne; Bishop, John; Kroeger, John Douglas; Schinkler, Jonas; McLaughlin, Joseph; Brownlee, June M.; Bell, Justin; Fellbaum, Karl Willem; Harper, Kathleen; Abbey, Kirk J.; Isaksson, Lennart E.; Wei, Linda; Cummins, Lisa N.; Miller, Lori Anne; Bain, Lyn; Carpenter, Lynn; Desnouck, Maarten; Sharma, Manasa G.; Belcastro, Marcus; Szew, Martin; Szew, Martin; Britton, Matthew; Gaebel, Matthias; Power, Max; Cassidy, Michael; Pfützenreuter, Michael; Minett, Michele; Wesselingh, Michiel; Yi, Minjune; Cameron, Neil Haydn Tormey; Bolibruch, Nicholas I.; Benevides, Noah; Kathleen Kerr, Norah; Barlow, Nova; Crevits, Nykole Krystyne; Dunn, Paul; Silveira Belo Nascimento Roque, Paulo Sergio; Riber, Peter; Pikkanen, Petri; Shehzad, Raafay; Viosca, Randy; James Fraser, Robert; Leduc, Robert; Madala, Roman; Shnider, Scott; de Boisblanc, Sharon; Butkovich, Slava; Bliven, Spencer; Hettler, Stephen; Telehany, Stephen; Schwegmann, Steven A.; Parkes, Steven; Kleinfelter, Susan C.; Michael Holst, Sven; van der Laan, T. J. A.; Bausewein, Thomas; Simon, Vera; Pulley, Warwick; Hull, William; Kim, Annes Yukyung; Lawton, Alexis; Ruesch, Amanda; Sundar, Anjali; Lawrence, Anna-Lisa; Afrin, Antara; Maheshwer, Bhargavi; Turfe, Bilal; Huebner, Christian; Killeen, Courtney Elizabeth; Antebi-Lerrman, Dalia; Luan, Danny; Wolfe, Derek; Pham, Duc; Michewicz, Elaina; Hull, Elizabeth; Pardington, Emily; Galal, Galal Osama; Sun, Grace; Chen, Grace; Anderson, Halie E.; Chang, Jane; Hewlett, Jeffrey Thomas; Sterbenz, Jennifer; Lim, Jiho; Morof, Joshua; Lee, Junho; Inn, Juyoung Samuel; Hahm, Kaitlin; Roth, Kaitlin; Nair, Karun; Markin, Katherine; Schramm, Katie; Toni Eid, Kevin; Gam, Kristina; Murphy, Lisha; Yuan, Lucy; Kana, Lulia; Daboul, Lynn; Shammas, Mario Karam; Chason, Max; Sinan, Moaz; Andrew Tooley, Nicholas; Korakavi, Nisha; Comer, Patrick; Magur, Pragya; Savliwala, Quresh; Davison, Reid Michael; Sankaran, Roshun Rajiv; Lewe, Sam; Tamkus, Saule; Chen, Shirley; Harvey, Sho; Hwang, Sin Ye; Vatsia, Sohrab; Withrow, Stefan; Luther, Tahra K.; Manett, Taylor; Johnson, Thomas James; Ryan Brash, Timothy; Kuhlman, Wyatt; Park, Yeonjung; Popović, Zoran; Baker, David; Khatib, Firas; Bardwell, James C. A.

2016-09-01

We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit players achieved the most accurate structure. Analysing the target protein of the competition, YPL067C, uncovered a new family of histidine triad proteins apparently involved in the prevention of amyloid toxicity. From this study, we conclude that crystallographers can utilize crowdsourcing to interpret electron density information and to produce structure solutions of the highest quality.

Determining crystal structures through crowdsourcing and coursework.

PubMed

Horowitz, Scott; Koepnick, Brian; Martin, Raoul; Tymieniecki, Agnes; Winburn, Amanda A; Cooper, Seth; Flatten, Jeff; Rogawski, David S; Koropatkin, Nicole M; Hailu, Tsinatkeab T; Jain, Neha; Koldewey, Philipp; Ahlstrom, Logan S; Chapman, Matthew R; Sikkema, Andrew P; Skiba, Meredith A; Maloney, Finn P; Beinlich, Felix R M; Popović, Zoran; Baker, David; Khatib, Firas; Bardwell, James C A

2016-09-16

We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit players achieved the most accurate structure. Analysing the target protein of the competition, YPL067C, uncovered a new family of histidine triad proteins apparently involved in the prevention of amyloid toxicity. From this study, we conclude that crystallographers can utilize crowdsourcing to interpret electron density information and to produce structure solutions of the highest quality.

Finite element analysis of structural engineering problems using a viscoplastic model incorporating two back stresses

NASA Technical Reports Server (NTRS)

Arya, Vinod K.; Halford, Gary R.

1993-01-01

The feasibility of a viscoplastic model incorporating two back stresses and a drag strength is investigated for performing nonlinear finite element analyses of structural engineering problems. To demonstrate suitability for nonlinear structural analyses, the model is implemented into a finite element program and analyses for several uniaxial and multiaxial problems are performed. Good agreement is shown between the results obtained using the finite element implementation and those obtained experimentally. The advantages of using advanced viscoplastic models for performing nonlinear finite element analyses of structural components are indicated.

Molecular modeling of the human sperm associated antigen 11 B (SPAG11B) proteins.

PubMed

Narmadha, Ganapathy; Yenugu, Suresh

2015-04-01

Antimicrobial proteins and peptides are ubiquitous in nature with diverse structural and biological properties. Among them, the human beta-defensins are known to contribute to the innate immune response. Besides the defensins, a number of defensin-like proteins and peptides are expressed in many organ systems including the male reproductive system. Some of the protein isoforms encoded by the sperm associated antigen 11B (SPAG11) gene in humans are beta-defensin-like and exhibit structure dependent and salt tolerant antimicrobial activity, besides contributing to sperm maturation. Though some of the functional roles of these proteins are reported, the structural and molecular features that contribute to their antimicrobial activity is not yet reported. In this study, using in silico tools, we report the three dimensional structure of the human SPAG11B proteins and their C-terminal peptides. web-based hydropathy, amphipathicity, and topology (WHAT) analyses and grand average of hydropathy (GRAVY) indices show that these proteins and peptides are amphipathic and highly hydrophilic. Self-optimized prediction method with alignment (SOPMA) analyses and circular dichroism data suggest that the secondary structure of these proteins and peptides primarily contain beta-sheet and random coil structure and alpha-helix to a lesser extent. Ramachandran plots show that majority of the amino acids in these proteins and peptides fall in the permissible regions, thus indicating stable structures. The secondary structure of SPAG11B isoforms and their peptides were not perturbed with increasing NaCl concentration (0-300 mM) and at different pH (3, 7, and 10), thus reinforcing our previously reported observation that their antimicrobial activity is salt tolerant. To the best of our knowledge, for the first time, results of our study provide vital information on the structural features of SPAG11B protein isoforms and their contribution to antimicrobial activity.

Outlier analyses to test for local adaptation to breeding grounds in a migratory arctic seabird.

PubMed

Tigano, Anna; Shultz, Allison J; Edwards, Scott V; Robertson, Gregory J; Friesen, Vicki L

2017-04-01

Investigating the extent (or the existence) of local adaptation is crucial to understanding how populations adapt. When experiments or fitness measurements are difficult or impossible to perform in natural populations, genomic techniques allow us to investigate local adaptation through the comparison of allele frequencies and outlier loci along environmental clines. The thick-billed murre ( Uria lomvia ) is a highly philopatric colonial arctic seabird that occupies a significant environmental gradient, shows marked phenotypic differences among colonies, and has large effective population sizes. To test whether thick-billed murres from five colonies along the eastern Canadian Arctic coast show genomic signatures of local adaptation to their breeding grounds, we analyzed geographic variation in genome-wide markers mapped to a newly assembled thick-billed murre reference genome. We used outlier analyses to detect loci putatively under selection, and clustering analyses to investigate patterns of differentiation based on 2220 genomewide single nucleotide polymorphisms (SNPs) and 137 outlier SNPs. We found no evidence of population structure among colonies using all loci but found population structure based on outliers only, where birds from the two northernmost colonies (Minarets and Prince Leopold) grouped with birds from the southernmost colony (Gannet), and birds from Coats and Akpatok were distinct from all other colonies. Although results from our analyses did not support local adaptation along the latitudinal cline of breeding colonies, outlier loci grouped birds from different colonies according to their non-breeding distributions, suggesting that outliers may be informative about adaptation and/or demographic connectivity associated with their migration patterns or nonbreeding grounds.

Voltage- and ATP-dependent structural rearrangements of the P2X2 receptor associated with the gating of the pore

PubMed Central

Keceli, Batu; Kubo, Yoshihiro

2014-01-01

P2X2 is an extracellular ATP-gated cation channel which has a voltage-dependent gating property even though it lacks a canonical voltage sensor. It is a trimer in which each subunit has two transmembrane helices and a large extracellular domain. The three inter-subunit ATP binding sites are linked to the pore forming transmembrane (TM) domains by β-strands. We analysed structural rearrangements of the linker strands between the ATP binding site and TM domains upon ligand binding and voltage change, electrophysiologically in Xenopus oocytes, using mutants carrying engineered thiol-modifiable cysteine residues. (1) We demonstrated that the double mutant D315C&I67C (at β-14 and β-1, respectively) shows a 2- to 4-fold increase in current amplitude after treatment with a reducing reagent, dithiothreitol (DTT). Application of the thiol-reactive metal Cd2+ induced current decline due to bond formation between D315C and I67C. This effect was not observed in wild type (WT) or in single point mutants. (2) Cd2+-induced current decline was analysed in hyperpolarized and depolarized conditions with different pulse protocols, and also in the presence and absence of ATP. (3) Current decline induced by Cd2+ could be clearly observed in the presence of ATP, but was not clear in the absence of ATP, showing a state-dependent modification. (4) In the presence of ATP, Cd2+ modification was significantly faster in hyperpolarized than in depolarized conditions, showing voltage-dependent structural rearrangements of the linker strands. (5) Experiments using tandem trimeric constructs (TTCs) with controlled number and position of mutations in the trimer showed that the bridging by Cd2+ between 315 and 67 was not intra- but inter-subunit. (6) Finally, we performed similar analyses of a pore mutant T339S, which makes the channel activation voltage insensitive. Cd2+ modification rates of T339S were similar in hyperpolarized and depolarized conditions. Taking these results together, we demonstrated that structural rearrangements of the linker region of the P2X2 receptor channel are induced not only by ligand binding but also by membrane potential change. PMID:25172943

Structural Analyses of Phase Stability in Amorphous and Partially Crystallized Ge-Rich GeTe Films Prepared by Atomic Layer Deposition.

PubMed

Gwon, Taehong; Mohamed, Ahmed Yousef; Yoo, Chanyoung; Park, Eui-Sang; Kim, Sanggyun; Yoo, Sijung; Lee, Han-Koo; Cho, Deok-Yong; Hwang, Cheol Seong

2017-11-29

The local bonding structures of Ge x Te 1-x (x = 0.5, 0.6, and 0.7) films prepared through atomic layer deposition (ALD) with Ge(N(Si(CH 3 ) 3 ) 2 ) 2 and ((CH 3 ) 3 Si) 2 Te precursors were investigated using Ge K-edge X-ray absorption spectroscopy (XAS). The results of the X-ray absorption fine structure analyses show that for all of the compositions, the as-grown films were amorphous with a tetrahedral Ge coordination of a mixture of Ge-Te and Ge-Ge bonds but without any signature of Ge-GeTe decomposition. The compositional evolution in the valence band electronic structures probed through X-ray photoelectron spectroscopy suggests a substantial chemical influence of additional Ge on the nonstoichiometric GeTe. This implies that the ALD process can stabilize Ge-abundant bonding networks like -Te-Ge-Ge-Te- in amorphous GeTe. Meanwhile, the XAS results on the Ge-rich films that had undergone post-deposition annealing at 350 °C show that the parts of the crystalline Ge-rich GeTe became separated into Ge crystallites and rhombohedral GeTe in accordance with the bulk phase diagram, whereas the disordered GeTe domains still remained, consistent with the observations of transmission electron microscopy and Raman spectroscopy. Therefore, amorphousness in GeTe may be essential for the nonsegregated Ge-rich phases and the low growth temperature of the ALD enables the achievement of the structurally metastable phases.

Secretory Structure, Histochemistry and Phytochemistry Analyses of Stimulant Plant

NASA Astrophysics Data System (ADS)

Umah, C.; Dorly; Sulistyaningsih, Y. C.

2017-03-01

Plants that are used as stimulant supposed to contains various metabolit compounds that are produced or secreted by secretory structures. This study aimed to identify the secretory structure of plant used as stimulant and chemical compounds accumulated in it. The secretory structure and its histochemistry were observed on plant material that are used as herbal ingredient. Phytochemical content was analyzed by using a qualitative test. The result showed that the idioblast cells and secretory cavities were found in the leaves of Decaspermum fruticosum, and Polyalthia rumphii. Most idioblast cells contained lipophilic substances and terpenoids or alkaloids, while secretory cavity contained alkaloid. Phytochemical analysis for D. fruticosum, and P. rumphii contain terpenoids, phenols, steroids, and flavonoids

An asset-based approach to vulnerability: the case of small-scale fishing areas in Cameroon and Nigeria.

PubMed

Chiwaula, Levison S; Witt, Rudolf; Waibel, Hermann

2011-01-01

This paper analyses vulnerability to poverty of rural small-scale fishing communities using cross-section data from 295 households in Cameroon and 267 in Nigeria. We propose a vulnerability measure that incorporates the idea of asset poverty into the concept of expected poverty, which allows decomposing expected poverty into expected structural-chronic, structural-transient, and stochastic-transient poverty. The findings show that most households in our study areas are expected to be structurally-chronic and structurally-transient poor. This underlines the importance of asset formation for long-term poverty reduction strategies. Further refinements are possible with longitudinal data and information about future states of nature.

Crystal structure of simple metals at high pressures

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

Degtyareva, Olga

2010-10-22

The effects of pressure on the crystal structure of simple (or sp-) elements are analysed in terms of changes in coordination number, packing density, and interatomic distances, and general rules are established. In the polyvalent elements from groups 14-17, the covalently bonded structures tend to transform to metallic phases with a gradual increase in coordination number and packing density, a behaviour normally expected under pressure. Group 1 and 2 metallic elements, however, show a reverse trend towards structures with low packing density due to intricate changes in their electronic structure. Complex crystal structures such as host-guest and incommensurately modulated structuresmore » found in these elements are given special attention in this review in an attempt to determine their role in the observed phase-transition sequences.« less

LC-MS guided isolation of diterpenoids from Sapium insigne with α-glucosidase inhibitory activities.

PubMed

Yan, De-Xiu; Geng, Chang-An; Yang, Tong-Hua; Huang, Xiao-Yan; Li, Tian-Ze; Gao, Zhen; Ma, Yun-Bao; Peng, Hua; Zhang, Xue-Mei; Chen, Ji-Jun

2018-04-08

Ten new (1-10) and ten known (11-20) diterpenoids involving ent-atisane, ent-seco-atisane, ent-kaurane and ent-seco-kaurane types were isolated from Sapium insigne under the guidance of LCMS-IT-TOF analyses. Their structures were characterized by extensive spectroscopic analyses (HRESIMS, UV, IR, 1D and 2D NMR). A putative biosynthetic pathway was proposed for ent-seco-atisane diterpenoids. Their inhibitory activities on α-glucosidase in vitro were tested for the first time. Compound 4 showed moderate inhibitory effect on α-glucosidase with an IC 50 value of 0.34 mM via a noncompetitive inhibition mechanism (K i  = 0.27 mM). The preliminary structure-activity relationships of the ent-atisane diterpenoids inhibiting α-glucosidase were discussed. Copyright © 2018 Elsevier B.V. All rights reserved.

Transition to motherhood and the self: measurement, stability, and change.

PubMed

Ruble, D N; Brooks-Gunn, J; Fleming, A S; Fitzmaurice, G; Stangor, C; Deutsch, F

1990-03-01

Different ways of conceptualizing and measuring change in attitudes during transition to motherhood are examined. A series of analyses was performed on data from a cross-sectional sample (N = 667) and a smaller longitudinal sample (n = 48) to demonstrate sound psychometric properties for 2 new scales and to show construct comparability across different phases of childbearing. For Childbearing Attitudes Questionnaire, results demonstrated equality of covariance for 16 scales and comparability of structure and meaning of 4 higher order factors--identification with motherhood, social orientation, self-confidence, and negative aspects of giving birth. For Mothering Self-Definition Questionnaire, results demonstrated equality of covariance of 5 scales and comparability of structure and meaning of a single higher order factor, interpreted as reflecting positive feelings about one's mothering characteristics. Analyses of correlations and mean differences identified areas of change and stability.

Effects of social support and self-esteem on depressive symptoms in Japanese middle-aged and elderly people.

PubMed

Fukukawa, Y; Tsuboi, S; Niino, N; Ando, F; Kosugi, S; Shimokata, H

2000-04-01

We examined the relationship among social support, self-esteem, and depression. The subjects were 1,116 Japanese community-dwelling adults aged between 40-79, who were the first wave participants of the National Institute for Longevity Sciences--Longitudinal Study of Aging (NILS-LSA). Exploratory and confirmatory factor analyses were performed on the Rosenberg's self-esteem scale that supported the superiority of the bi-dimensional structure of the scale marked by self-confidence and self-deprecation subscales. The subsequent causal analyses, using structural equation modeling, demonstrated that social support reduced depressed affect through an increase in self-confidence and a decrease in self-deprecation. By contrast, social support did not show a direct effect on depressed affect. The findings suggest the importance of esteem-improving elements of social support in reducing depressive symptoms.

Development of methodology for identification the nature of the polyphenolic extracts by FTIR associated with multivariate analysis

NASA Astrophysics Data System (ADS)

Grasel, Fábio dos Santos; Ferrão, Marco Flôres; Wolf, Carlos Rodolfo

2016-01-01

Tannins are polyphenolic compounds of complex structures formed by secondary metabolism in several plants. These polyphenolic compounds have different applications, such as drugs, anti-corrosion agents, flocculants, and tanning agents. This study analyses six different type of polyphenolic extracts by Fourier transform infrared spectroscopy (FTIR) combined with multivariate analysis. Through both principal component analysis (PCA) and hierarchical cluster analysis (HCA), we observed well-defined separation between condensed (quebracho and black wattle) and hydrolysable (valonea, chestnut, myrobalan, and tara) tannins. For hydrolysable tannins, it was also possible to observe the formation of two different subgroups between samples of chestnut and valonea and between samples of tara and myrobalan. Among all samples analysed, the chestnut and valonea showed the greatest similarity, indicating that these extracts contain equivalent chemical compositions and structure and, therefore, similar properties.

Dynamic regulation of GDP binding to G proteins revealed by magnetic field-dependent NMR relaxation analyses

PubMed Central

Toyama, Yuki; Kano, Hanaho; Mase, Yoko; Yokogawa, Mariko; Osawa, Masanori; Shimada, Ichio

2017-01-01

Heterotrimeric guanine-nucleotide-binding proteins (G proteins) serve as molecular switches in signalling pathways, by coupling the activation of cell surface receptors to intracellular responses. Mutations in the G protein α-subunit (Gα) that accelerate guanosine diphosphate (GDP) dissociation cause hyperactivation of the downstream effector proteins, leading to oncogenesis. However, the structural mechanism of the accelerated GDP dissociation has remained unclear. Here, we use magnetic field-dependent nuclear magnetic resonance relaxation analyses to investigate the structural and dynamic properties of GDP bound Gα on a microsecond timescale. We show that Gα rapidly exchanges between a ground-state conformation, which tightly binds to GDP and an excited conformation with reduced GDP affinity. The oncogenic D150N mutation accelerates GDP dissociation by shifting the equilibrium towards the excited conformation. PMID:28223697

Dynamic regulation of GDP binding to G proteins revealed by magnetic field-dependent NMR relaxation analyses.

PubMed

Toyama, Yuki; Kano, Hanaho; Mase, Yoko; Yokogawa, Mariko; Osawa, Masanori; Shimada, Ichio

2017-02-22

Heterotrimeric guanine-nucleotide-binding proteins (G proteins) serve as molecular switches in signalling pathways, by coupling the activation of cell surface receptors to intracellular responses. Mutations in the G protein α-subunit (Gα) that accelerate guanosine diphosphate (GDP) dissociation cause hyperactivation of the downstream effector proteins, leading to oncogenesis. However, the structural mechanism of the accelerated GDP dissociation has remained unclear. Here, we use magnetic field-dependent nuclear magnetic resonance relaxation analyses to investigate the structural and dynamic properties of GDP bound Gα on a microsecond timescale. We show that Gα rapidly exchanges between a ground-state conformation, which tightly binds to GDP and an excited conformation with reduced GDP affinity. The oncogenic D150N mutation accelerates GDP dissociation by shifting the equilibrium towards the excited conformation.

Structural distortions due to missense mutations in human formylglycine-generating enzyme leading to multiple sulfatase deficiency.

PubMed

Meshach Paul, D; Chadah, Tania; Senthilkumar, B; Sethumadhavan, Rao; Rajasekaran, R

2017-11-03

The major candidate for multiple sulfatase deficiency is a defective formylglycine-generating enzyme (FGE). Though adequately produced, mutations in FGE stall the activation of sulfatases and prevent their activity. Missense mutations, viz. E130D, S155P, A177P, W179S, C218Y, R224W, N259I, P266L, A279V, C336R, R345C, A348P, R349Q and R349W associated with multiple sulfatase deficiency are yet to be computationally studied. Aforementioned mutants were initially screened through ws-SNPs&GO 3D program. Mutant R345C acquired the highest score, and hence was studied in detail. Discrete molecular dynamics explored structural distortions due to amino acid substitution. Therein, comparative analyses of wild type and mutant were carried out. Changes in structural contours were observed between wild type and mutant. Mutant had low conformational fluctuation, high atomic mobility and more compactness than wild type. Moreover, free energy landscape showed mutant to vary in terms of its conformational space as compared to wild type. Subsequently, wild type and mutant were subjected to single-model analyses. Mutant had lesser intra molecular interactions than wild type suggesting variations pertaining to its secondary structure. Furthermore, simulated thermal denaturation showed dissimilar pattern of hydrogen bond dilution. Effects of these variations were observed as changes in elements of secondary structure. Docking studies of mutant revealed less favourable binding energy towards its substrate as compared to wild type. Therefore, theoretical explanations for structural distortions of mutant R345C leading to multiple sulfatase deficiency were revealed. The protocol of the study could be useful to examine the effectiveness of pharmacological chaperones prior to experimental studies.

Alterations of white matter structural networks in patients with non-neuropsychiatric systemic lupus erythematosus identified by probabilistic tractography and connectivity-based analyses.

PubMed

Xu, Man; Tan, Xiangliang; Zhang, Xinyuan; Guo, Yihao; Mei, Yingjie; Feng, Qianjin; Xu, Yikai; Feng, Yanqiu

2017-01-01

Systemic lupus erythematosus (SLE) is a chronic inflammatory female-predominant autoimmune disease that can affect the central nervous system and exhibit neuropsychiatric symptoms. In SLE patients without neuropsychiatric symptoms (non-NPSLE), recent diffusion tensor imaging studies showed white matter abnormalities in their brains. The present study investigated the entire brain white matter structural connectivity in non-NPSLE patients by using probabilistic tractography and connectivity-based analyses. Whole-brain structural networks of 29 non-NPSLE patients and 29 healthy controls (HCs) were examined. The structural networks were constructed with interregional probabilistic connectivity. Graph theory analysis was performed to investigate the topological properties, and network-based statistic was employed to assess the alterations of the interregional connections among non-NPSLE patients and controls. Compared with HCs, non-NPSLE patients demonstrated significantly decreased global and local network efficiencies and showed increased characteristic path length. This finding suggests that the global integration and local specialization were impaired. Moreover, the regional properties (nodal efficiency and degree) in the frontal, occipital, and cingulum regions of the non-NPSLE patients were significantly changed and negatively correlated with the disease activity index. The distribution pattern of the hubs measured by nodal degree was altered in the patient group. Finally, the non-NPSLE group exhibited decreased structural connectivity in the left median cingulate-centered component and increased connectivity in the left precuneus-centered component and right middle temporal lobe-centered component. This study reveals an altered topological organization of white matter networks in non-NPSLE patients. Furthermore, this research provides new insights into the structural disruptions underlying the functional and neurocognitive deficits in non-NPSLE patients.

Structural Brain Abnormalities of Attention-Deficit/Hyperactivity Disorder With Oppositional Defiant Disorder.

PubMed

Noordermeer, Siri D S; Luman, Marjolein; Greven, Corina U; Veroude, Kim; Faraone, Stephen V; Hartman, Catharina A; Hoekstra, Pieter J; Franke, Barbara; Buitelaar, Jan K; Heslenfeld, Dirk J; Oosterlaan, Jaap

2017-11-01

Attention-deficit/hyperactivity disorder (ADHD) is associated with structural abnormalities in total gray matter, basal ganglia, and cerebellum. Findings of structural abnormalities in frontal and temporal lobes, amygdala, and insula are less consistent. Remarkably, the impact of comorbid oppositional defiant disorder (ODD) (comorbidity rates up to 60%) on these neuroanatomical differences is scarcely studied, while ODD (in combination with conduct disorder) has been associated with structural abnormalities of the frontal lobe, amygdala, and insula. The aim of this study was to investigate the effect of comorbid ODD on cerebral volume and cortical thickness in ADHD. Three groups, 16 ± 3.5 years of age (mean ± SD; range 7-29 years), were studied on volumetric and cortical thickness characteristics using structural magnetic resonance imaging (surface-based morphometry): ADHD+ODD (n = 67), ADHD-only (n = 243), and control subjects (n = 233). Analyses included the moderators age, gender, IQ, and scan site. ADHD+ODD and ADHD-only showed volumetric reductions in total gray matter and (mainly) frontal brain areas. Stepwise volumetric reductions (ADHD+ODD < ADHD-only < control subjects) were found for mainly frontal regions, and ADHD+ODD was uniquely associated with reductions in several structures (e.g., the precuneus). In general, findings remained significant after accounting for ADHD symptom severity. There were no group differences in cortical thickness. Exploratory voxelwise analyses showed no group differences. ADHD+ODD and ADHD-only were associated with volumetric reductions in brain areas crucial for attention, (working) memory, and decision-making. Volumetric reductions of frontal lobes were largest in the ADHD+ODD group, possibly underlying observed larger impairments in neurocognitive functions. Previously reported striatal abnormalities in ADHD may be caused by comorbid conduct disorder rather than ODD. Copyright © 2017 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

WASH and WAVE actin regulators of the Wiskott-Aldrich syndrome protein (WASP) family are controlled by analogous structurally related complexes.

PubMed

Jia, Da; Gomez, Timothy S; Metlagel, Zoltan; Umetani, Junko; Otwinowski, Zbyszek; Rosen, Michael K; Billadeau, Daniel D

2010-06-08

We recently showed that the Wiskott-Aldrich syndrome protein (WASP) family member, WASH, localizes to endosomal subdomains and regulates endocytic vesicle scission in an Arp2/3-dependent manner. Mechanisms regulating WASH activity are unknown. Here we show that WASH functions in cells within a 500 kDa core complex containing Strumpellin, FAM21, KIAA1033 (SWIP), and CCDC53. Although recombinant WASH is constitutively active toward the Arp2/3 complex, the reconstituted core assembly is inhibited, suggesting that it functions in cells to regulate actin dynamics through WASH. FAM21 interacts directly with CAPZ and inhibits its actin-capping activity. Four of the five core components show distant (approximately 15% amino acid sequence identify) but significant structural homology to components of a complex that negatively regulates the WASP family member, WAVE. Moreover, biochemical and electron microscopic analyses show that the WASH and WAVE complexes are structurally similar. Thus, these two distantly related WASP family members are controlled by analogous structurally related mechanisms. Strumpellin is mutated in the human disease hereditary spastic paraplegia, and its link to WASH suggests that misregulation of actin dynamics on endosomes may play a role in this disorder.

Structural characterization of ferric hemoglobins from three antarctic fish species of the suborder notothenioidei.

PubMed

Vergara, Alessandro; Franzese, Marisa; Merlino, Antonello; Vitagliano, Luigi; Verde, Cinzia; di Prisco, Guido; Lee, H Caroline; Peisach, Jack; Mazzarella, Lelio

2007-10-15

Spontaneous autoxidation of tetrameric Hbs leads to the formation of Fe (III) forms, whose physiological role is not fully understood. Here we report structural characterization by EPR of the oxidized states of tetrameric Hbs isolated from the Antarctic fish species Trematomus bernacchii, Trematomus newnesi, and Gymnodraco acuticeps, as well as the x-ray crystal structure of oxidized Trematomus bernacchii Hb, redetermined at high resolution. The oxidation of these Hbs leads to formation of states that were not usually detected in previous analyses of tetrameric Hbs. In addition to the commonly found aquo-met and hydroxy-met species, EPR analyses show that two distinct hemichromes coexist at physiological pH, referred to as hemichromes I and II, respectively. Together with the high-resolution crystal structure (1.5 A) of T. bernacchii and a survey of data available for other heme proteins, hemichrome I was assigned by x-ray crystallography and by EPR as a bis-His complex with a distorted geometry, whereas hemichrome II is a less constrained (cytochrome b5-like) bis-His complex. In four of the five Antartic fish Hbs examined, hemichrome I is the major form. EPR shows that for HbCTn, the amount of hemichrome I is substantially reduced. In addition, the concomitant presence of a penta-coordinated high-spin Fe (III) species, to our knowledge never reported before for a wild-type tetrameric Hb, was detected. A molecular modeling investigation demonstrates that the presence of the bulkier Ile in position 67beta in HbCTn in place of Val as in the other four Hbs impairs the formation of hemichrome I, thus favoring the formation of the ferric penta-coordinated species. Altogether the data show that ferric states commonly associated with monomeric and dimeric Hbs are also found in tetrameric Hbs.

Comparison of nitrogen adsorption and transmission electron microscopy analyses for structural characterization of carbon nanotubes

NASA Astrophysics Data System (ADS)

Abbaslou, Reza Malek; Vosoughi, Vahid; Dalai, Ajay K.

2017-10-01

Carbon nanotubes (CNTs) are different from other porous substrates such as activated carbon due to their high external surfaces. This structural feature can lead in some uncertainties in the results of nitrogen adsorption analysis for characterization of CNTs. In this paper, the results of microscopic analyses and nitrogen adsorption method for characterization of carbon nanotubes were compared. Five different types of CNTs with different structures were either synthesized or purchased. The CNT samples were characterized by high resolution transmission electron microscopy (HRTEM), scanning electron microscopy (SEM) and N2 adsorption analysis. The comparisons between the results from the microscopic analyses and N2 adsorption showed that the total pore volume and BET surface measurements include the internal and external porosity of CNTs. Therefore, the interpretation of N2 adsorption data required accurate TEM analysis. In addition, the evaluation of pore size distribution curves from all CNT samples in this study and several instances in the literature revealed the presence of a common peak in the range of 2-5 nm. This peak does not explain the inner pore size distribution. The presence of this common peak can be attributed to the strong adsorption of N2 on the junction of touched and crossed nanotubes.

Host Resistance, Population Structure and the Long-Term Persistence of Bubonic Plague: Contributions of a Modelling Approach in the Malagasy Focus

PubMed Central

Gascuel, Fanny; Choisy, Marc; Duplantier, Jean-Marc; Débarre, Florence; Brouat, Carine

2013-01-01

Although bubonic plague is an endemic zoonosis in many countries around the world, the factors responsible for the persistence of this highly virulent disease remain poorly known. Classically, the endemic persistence of plague is suspected to be due to the coexistence of plague resistant and plague susceptible rodents in natural foci, and/or to a metapopulation structure of reservoirs. Here, we test separately the effect of each of these factors on the long-term persistence of plague. We analyse the dynamics and equilibria of a model of plague propagation, consistent with plague ecology in Madagascar, a major focus where this disease is endemic since the 1920s in central highlands. By combining deterministic and stochastic analyses of this model, and including sensitivity analyses, we show that (i) endemicity is favoured by intermediate host population sizes, (ii) in large host populations, the presence of resistant rats is sufficient to explain long-term persistence of plague, and (iii) the metapopulation structure of susceptible host populations alone can also account for plague endemicity, thanks to both subdivision and the subsequent reduction in the size of subpopulations, and extinction-recolonization dynamics of the disease. In the light of these results, we suggest scenarios to explain the localized presence of plague in Madagascar. PMID:23675291

Host resistance, population structure and the long-term persistence of bubonic plague: contributions of a modelling approach in the Malagasy focus.

PubMed

Gascuel, Fanny; Choisy, Marc; Duplantier, Jean-Marc; Débarre, Florence; Brouat, Carine

2013-01-01

Although bubonic plague is an endemic zoonosis in many countries around the world, the factors responsible for the persistence of this highly virulent disease remain poorly known. Classically, the endemic persistence of plague is suspected to be due to the coexistence of plague resistant and plague susceptible rodents in natural foci, and/or to a metapopulation structure of reservoirs. Here, we test separately the effect of each of these factors on the long-term persistence of plague. We analyse the dynamics and equilibria of a model of plague propagation, consistent with plague ecology in Madagascar, a major focus where this disease is endemic since the 1920s in central highlands. By combining deterministic and stochastic analyses of this model, and including sensitivity analyses, we show that (i) endemicity is favoured by intermediate host population sizes, (ii) in large host populations, the presence of resistant rats is sufficient to explain long-term persistence of plague, and (iii) the metapopulation structure of susceptible host populations alone can also account for plague endemicity, thanks to both subdivision and the subsequent reduction in the size of subpopulations, and extinction-recolonization dynamics of the disease. In the light of these results, we suggest scenarios to explain the localized presence of plague in Madagascar.

What Types of Pornography Do People Find Arousing and Do They Cluster? Assessing Types and Categories of Pornography in a Large-Scale Online Sample.

PubMed

Hald, Gert Martin; Štulhofer, Aleksandar

2016-09-01

Previous research on exposure to different types of pornography has primarily relied on analyses of millions of search terms and histories or on user exposure patterns within a given time period rather than the self-reported frequency of consumption. Further, previous research has almost exclusively relied on theoretical or ad hoc overarching categorizations of different types of pornography, when investigating patterns of pornography exposure, rather than latent structure analyses of these exposure patterns. In contrast, using a large sample of 18- to 40-year-old heterosexual and nonheterosexual Croatian men and women, this study investigated the self-reported frequency of using 27 different types of pornography and statistically explored their latent structures. The results showed substantial differences in consumption patterns across gender and sexual orientation. However, latent structure analyses of the 27 different types of pornography assessed suggested that although several categories of consumption were gender and sexual orientation specific, common categories across the different types of pornography could be established. Based on this finding, a five-item scale was proposed to indicate the use of nonmainstream (paraphilic) pornographic content, as this type of pornography has often been targeted in previous research. To the best of our knowledge, no similar measurement tool has been proposed before.

A comparative study of cold- and warm-adapted Endonucleases A using sequence analyses and molecular dynamics simulations.

PubMed

Michetti, Davide; Brandsdal, Bjørn Olav; Bon, Davide; Isaksen, Geir Villy; Tiberti, Matteo; Papaleo, Elena

2017-01-01

The psychrophilic and mesophilic endonucleases A (EndA) from Aliivibrio salmonicida (VsEndA) and Vibrio cholera (VcEndA) have been studied experimentally in terms of the biophysical properties related to thermal adaptation. The analyses of their static X-ray structures was no sufficient to rationalize the determinants of their adaptive traits at the molecular level. Thus, we used Molecular Dynamics (MD) simulations to compare the two proteins and unveil their structural and dynamical differences. Our simulations did not show a substantial increase in flexibility in the cold-adapted variant on the nanosecond time scale. The only exception is a more rigid C-terminal region in VcEndA, which is ascribable to a cluster of electrostatic interactions and hydrogen bonds, as also supported by MD simulations of the VsEndA mutant variant where the cluster of interactions was introduced. Moreover, we identified three additional amino acidic substitutions through multiple sequence alignment and the analyses of MD-based protein structure networks. In particular, T120V occurs in the proximity of the catalytic residue H80 and alters the interaction with the residue Y43, which belongs to the second coordination sphere of the Mg2+ ion. This makes T120V an amenable candidate for future experimental mutagenesis.

Multilocus Patterns of Nucleotide Diversity, Population Structure and Linkage Disequilibrium in Boechera stricta, a Wild Relative of Arabidopsis

PubMed Central

Song, Bao-Hua; Windsor, Aaron J.; Schmid, Karl J.; Ramos-Onsins, Sebastian; Schranz, M. Eric; Heidel, Andrew J.; Mitchell-Olds, Thomas

2009-01-01

Information about polymorphism, population structure, and linkage disequilibrium (LD) is crucial for association studies of complex trait variation. However, most genomewide studies have focused on model systems, with very few analyses of undisturbed natural populations. Here, we sequenced 86 mapped nuclear loci for a sample of 46 genotypes of Boechera stricta and two individuals of B. holboellii, both wild relatives of Arabidopsis. Isolation by distance was significant across the species range of B. stricta, and three geographic groups were identified by structure analysis, principal coordinates analysis, and distance-based phylogeny analyses. The allele frequency spectrum indicated a genomewide deviation from an equilibrium neutral model, with silent nucleotide diversity averaging 0.004. LD decayed rapidly, declining to background levels in ∼10 kb or less. For tightly linked SNPs separated by <1 kb, LD was dependent on the reference population. LD was lower in the specieswide sample than within populations, suggesting that low levels of LD found in inbreeding species such as B. stricta, Arabidopsis thaliana, and barley may result from broad geographic sampling that spans heterogeneous genetic groups. Finally, analyses also showed that inbreeding B. stricta and A. thaliana have ∼45% higher recombination per kilobase than outcrossing A. lyrata. PMID:19104077

Genetic and structural analyses of cytochrome P450 hydroxylases in sex hormone biosynthesis: Sequential origin and subsequent coevolution.

PubMed

Goldstone, Jared V; Sundaramoorthy, Munirathinam; Zhao, Bin; Waterman, Michael R; Stegeman, John J; Lamb, David C

2016-01-01

Biosynthesis of steroid hormones in vertebrates involves three cytochrome P450 hydroxylases, CYP11A1, CYP17A1 and CYP19A1, which catalyze sequential steps in steroidogenesis. These enzymes are conserved in the vertebrates, but their origin and existence in other chordate subphyla (Tunicata and Cephalochordata) have not been clearly established. In this study, selected protein sequences of CYP11A1, CYP17A1 and CYP19A1 were compiled and analyzed using multiple sequence alignment and phylogenetic analysis. Our analyses show that cephalochordates have sequences orthologous to vertebrate CYP11A1, CYP17A1 or CYP19A1, and that echinoderms and hemichordates possess CYP11-like but not CYP19 genes. While the cephalochordate sequences have low identity with the vertebrate sequences, reflecting evolutionary distance, the data show apparent origin of CYP11 prior to the evolution of CYP19 and possibly CYP17, thus indicating a sequential origin of these functionally related steroidogenic CYPs. Co-occurrence of the three CYPs in early chordates suggests that the three genes may have coevolved thereafter, and that functional conservation should be reflected in functionally important residues in the proteins. CYP19A1 has the largest number of conserved residues while CYP11A1 sequences are less conserved. Structural analyses of human CYP11A1, CYP17A1 and CYP19A1 show that critical substrate binding site residues are highly conserved in each enzyme family. The results emphasize that the steroidogenic pathways producing glucocorticoids and reproductive steroids are several hundred million years old and that the catalytic structural elements of the enzymes have been conserved over the same period of time. Analysis of these elements may help to identify when precursor functions linked to these enzymes first arose. Copyright © 2015 Elsevier Inc. All rights reserved.

Socket augmentation using a commercial collagen-based product--an animal study in pigs.

PubMed

Kunert-Keil, Christiane; Gredes, Tomasz; Heinemann, Friedhelm; Dominiak, Marzena; Botzenhart, Ute; Gedrange, Tomasz

2015-01-01

The aim of the present study was to identify properties of pure collagen for augmentation techniques and compare to a proved xenogenic material and natural bone regeneration. For that the osteogenesis of extraction alveoli after augmentation with a collagen cone covered with an absorbable collagen membrane in a single product (PARASORB Sombrero®, Resorba) was evaluated in a pig model. Extraction alveoli were treated with the collagen cone and the collagen membrane in a single product (test group; n=7) or demineralized bovine bone mineral and a collagen membrane (two separate products; positive control; n=7). Untreated alveoli were used (n=6) as negative controls.(1) Bone specimens were extracted 1 and 3 months after teeth extraction. Serial longitudinal sections were stained with Masson Goldner trichrome. Furthermore, bone specimens were examined using X-ray analyses. Significant differences of bone atrophy were detected 12 weeks after material insertion using X-ray analyses. The bone atrophy was reduced by approximately 32% after insertion of the positive control (P=0.046). Bone atrophy reached 37.6% of those from untreated alveoli (P=0.002) using the test group. After 4 weeks, bone formation was noticeable in most sites, whereas after 12 weeks of healing, specimens of all groups exhibited nearly complete osseous organization of the former defected area. The mandibulary bone texture showed typical spongious bone structures. Histomorphometric analyses revealed after 4 and 12 weeks significant higher levels of bone marrow in test and negative control than in positive control. Quantification of bone tissue and osteoid does not show any significant difference. The present study confirms reduced bone resorption following socket augmentation with an absorbable collagen membrane with collagen cone while the resulting bone structure is similar to natural bone regeneration. Pure collagen can be used for bone augmentation, and shows over other xenogenic materials, a clear advantage with respect to the bone density and structure. Copyright © 2014 Elsevier B.V. All rights reserved.

Significant population genetic structure detected in the rock bream Oplegnathus fasciatus (Temminck & Schlegel, 1844) inferred from fluorescent-AFLP analysis

NASA Astrophysics Data System (ADS)

Xiao, Yongshuang; Ma, Daoyuan; Xu, Shihong; Liu, Qinghua; Wang, Yanfeng; Xiao, Zhizhong; Li, Jun

2016-05-01

Oplegnathus fasciatus (rock bream) is a commercial rocky reef fish species in East Asia that has been considered for aquaculture. We estimated the population genetic diversity and population structure of the species along the coastal waters of China using fluorescent-amplified fragment length polymorphisms technology. Using 53 individuals from three populations and four pairs of selective primers, we amplified 1 264 bands, 98.73% of which were polymorphic. The Zhoushan population showed the highest Nei's genetic diversity and Shannon genetic diversity. The results of analysis of molecular variance (AMOVA) showed that 59.55% of genetic variation existed among populations and 40.45% occurred within populations, which indicated that a significant population genetic structure existed in the species. The pairwise fixation index F st ranged from 0.20 to 0.63 and were significant after sequential Bonferroni correction. The topology of an unweighted pair group method with arithmetic mean tree showed two significant genealogical branches corresponding to the sampling locations of North and South China. The AMOVA and STRUCTURE analyses suggested that the O. fasciatus populations examined should comprise two stocks.

Social Network Analysis and Nutritional Behavior: An Integrated Modeling Approach

PubMed Central

Senior, Alistair M.; Lihoreau, Mathieu; Buhl, Jerome; Raubenheimer, David; Simpson, Stephen J.

2016-01-01

Animals have evolved complex foraging strategies to obtain a nutritionally balanced diet and associated fitness benefits. Recent research combining state-space models of nutritional geometry with agent-based models (ABMs), show how nutrient targeted foraging behavior can also influence animal social interactions, ultimately affecting collective dynamics and group structures. Here we demonstrate how social network analyses can be integrated into such a modeling framework and provide a practical analytical tool to compare experimental results with theory. We illustrate our approach by examining the case of nutritionally mediated dominance hierarchies. First we show how nutritionally explicit ABMs that simulate the emergence of dominance hierarchies can be used to generate social networks. Importantly the structural properties of our simulated networks bear similarities to dominance networks of real animals (where conflicts are not always directly related to nutrition). Finally, we demonstrate how metrics from social network analyses can be used to predict the fitness of agents in these simulated competitive environments. Our results highlight the potential importance of nutritional mechanisms in shaping dominance interactions in a wide range of social and ecological contexts. Nutrition likely influences social interactions in many species, and yet a theoretical framework for exploring these effects is currently lacking. Combining social network analyses with computational models from nutritional ecology may bridge this divide, representing a pragmatic approach for generating theoretical predictions for nutritional experiments. PMID:26858671

Fractal and multifractal analyses of bipartite networks

NASA Astrophysics Data System (ADS)

Liu, Jin-Long; Wang, Jian; Yu, Zu-Guo; Xie, Xian-Hua

2017-03-01

Bipartite networks have attracted considerable interest in various fields. Fractality and multifractality of unipartite (classical) networks have been studied in recent years, but there is no work to study these properties of bipartite networks. In this paper, we try to unfold the self-similarity structure of bipartite networks by performing the fractal and multifractal analyses for a variety of real-world bipartite network data sets and models. First, we find the fractality in some bipartite networks, including the CiteULike, Netflix, MovieLens (ml-20m), Delicious data sets and (u, v)-flower model. Meanwhile, we observe the shifted power-law or exponential behavior in other several networks. We then focus on the multifractal properties of bipartite networks. Our results indicate that the multifractality exists in those bipartite networks possessing fractality. To capture the inherent attribute of bipartite network with two types different nodes, we give the different weights for the nodes of different classes, and show the existence of multifractality in these node-weighted bipartite networks. In addition, for the data sets with ratings, we modify the two existing algorithms for fractal and multifractal analyses of edge-weighted unipartite networks to study the self-similarity of the corresponding edge-weighted bipartite networks. The results show that our modified algorithms are feasible and can effectively uncover the self-similarity structure of these edge-weighted bipartite networks and their corresponding node-weighted versions.

Fractal and multifractal analyses of bipartite networks.

PubMed

Liu, Jin-Long; Wang, Jian; Yu, Zu-Guo; Xie, Xian-Hua

2017-03-31

Bipartite networks have attracted considerable interest in various fields. Fractality and multifractality of unipartite (classical) networks have been studied in recent years, but there is no work to study these properties of bipartite networks. In this paper, we try to unfold the self-similarity structure of bipartite networks by performing the fractal and multifractal analyses for a variety of real-world bipartite network data sets and models. First, we find the fractality in some bipartite networks, including the CiteULike, Netflix, MovieLens (ml-20m), Delicious data sets and (u, v)-flower model. Meanwhile, we observe the shifted power-law or exponential behavior in other several networks. We then focus on the multifractal properties of bipartite networks. Our results indicate that the multifractality exists in those bipartite networks possessing fractality. To capture the inherent attribute of bipartite network with two types different nodes, we give the different weights for the nodes of different classes, and show the existence of multifractality in these node-weighted bipartite networks. In addition, for the data sets with ratings, we modify the two existing algorithms for fractal and multifractal analyses of edge-weighted unipartite networks to study the self-similarity of the corresponding edge-weighted bipartite networks. The results show that our modified algorithms are feasible and can effectively uncover the self-similarity structure of these edge-weighted bipartite networks and their corresponding node-weighted versions.

Fractal and multifractal analyses of bipartite networks

PubMed Central

Liu, Jin-Long; Wang, Jian; Yu, Zu-Guo; Xie, Xian-Hua

2017-01-01

Bipartite networks have attracted considerable interest in various fields. Fractality and multifractality of unipartite (classical) networks have been studied in recent years, but there is no work to study these properties of bipartite networks. In this paper, we try to unfold the self-similarity structure of bipartite networks by performing the fractal and multifractal analyses for a variety of real-world bipartite network data sets and models. First, we find the fractality in some bipartite networks, including the CiteULike, Netflix, MovieLens (ml-20m), Delicious data sets and (u, v)-flower model. Meanwhile, we observe the shifted power-law or exponential behavior in other several networks. We then focus on the multifractal properties of bipartite networks. Our results indicate that the multifractality exists in those bipartite networks possessing fractality. To capture the inherent attribute of bipartite network with two types different nodes, we give the different weights for the nodes of different classes, and show the existence of multifractality in these node-weighted bipartite networks. In addition, for the data sets with ratings, we modify the two existing algorithms for fractal and multifractal analyses of edge-weighted unipartite networks to study the self-similarity of the corresponding edge-weighted bipartite networks. The results show that our modified algorithms are feasible and can effectively uncover the self-similarity structure of these edge-weighted bipartite networks and their corresponding node-weighted versions. PMID:28361962

Fracture Mechanics Analyses of the Slip-Side Joggle Regions of Wing-Leading Edge Panels

NASA Technical Reports Server (NTRS)

Raju, Ivatury S.; Knight, Norman F., Jr.; Song, Kyongchan; Phillips, Dawn R.

2010-01-01

The Space Shuttle Orbiter wing comprises of 22 leading edge panels on each side of the wing. These panels are part of the thermal protection system that protects the Orbiter wings from extreme heating that take place on the reentry in to the earth atmosphere. On some panels that experience extreme heating, liberation of silicon carbon (SiC) coating was observed on the slip side regions of the panels. Global structural and local fracture mechanics analyses were performed on these panels as a part of the root cause investigation of this coating liberation anomaly. The wing-leading-edge reinforced carbon-carbon (RCC) panels, Panel 9, T-seal 10, and Panel 10, are shown in Figure 1 and the progression of the stress analysis models is presented in Figure 2. The global structural analyses showed minimal interaction between adjacent panels and the T-seal that bridges the gap between the panels. A bounding uniform temperature is applied to a representative panel and the resulting stress distribution is examined. For this loading condition, the interlaminar normal stresses showed negligible variation in the chord direction and increased values in the vicinity of the slip-side joggle shoulder. As such, a representative span wise slice on the panel can be taken and the cross section can be analyzed using plane strain analysis.

Shifts in soil chemical properties and bacterial communities responding to biotransformed dry olive residue used as organic amendment.

PubMed

Siles, José A; Cajthaml, Tomas; Hernández, Paola; Pérez-Mendoza, Daniel; García-Romera, Inmaculada; Sampedro, Inmaculada

2015-07-01

Dry olive residue (DOR) is a waste product derived from olive oil extraction and has been proposed as an organic amendment. However, it has been demonstrated that a pre-treatment, such as its transformation by saprophytic fungi, is required before DOR soil application. A greenhouse experiment was designed where 0 and 50 g kg(-1) of raw DOR (DOR), Coriolopsis floccosa-transformed DOR (CORDOR) and Fusarium oxysporum-transformed DOR (FUSDOR) were added to soil. Analyses of the soil chemical properties as well as the structure and relative abundance of bacterial and actinobacterial communities were conducted after 0, 30 and 60 days following amendment. The different amendments produced a slight decrease in soil pH and significant increases in carbon fractions, C/N ratios, phenols and K, with these increases being more significant after DOR application. Quantitative PCR assays of the 16S rRNA gene and PLFA analyses showed that all amendments favoured bacterial growth at 30 and 60 days, although actinobacterial proliferation was more evident after CORDOR and FUSDOR application at 60 days. Bacterial and actinobacterial DGGE multivariate analyses showed that the amendments produced structural changes in both communities, especially after 60 days of amendment. PLFA data analysis identified changes in soil microbial communities according to the amendment considered, with FUSDOR and CORDOR being less disruptive than DOR. Finally, integrated analysis of all data monitored in the present study enabled us to conclude that the greatest impact on soil properties was caused by DOR at 30 days and that soil showed some degree of resilience after this time.

Dispersal, mating events and fine-scale genetic structure in the lesser flat-headed bats.

PubMed

Hua, Panyu; Zhang, Libiao; Guo, Tingting; Flanders, Jon; Zhang, Shuyi

2013-01-01

Population genetic structure has important consequences in evolutionary processes and conservation genetics in animals. Fine-scale population genetic structure depends on the pattern of landscape, the permanent movement of individuals, and the dispersal of their genes during temporary mating events. The lesser flat-headed bat (Tylonycteris pachypus) is a nonmigratory Asian bat species that roosts in small groups within the internodes of bamboo stems and the habitats are fragmented. Our previous parentage analyses revealed considerable extra-group mating in this species. To assess the spatial limits and sex-biased nature of gene flow in the same population, we used 20 microsatellite loci and mtDNA sequencing of the ND2 gene to quantify genetic structure among 54 groups of adult flat-headed bats, at nine localities in South China. AMOVA and F(ST) estimates revealed significant genetic differentiation among localities. Alternatively, the pairwise F(ST) values among roosting groups appeared to be related to the incidence of associated extra-group breeding, suggesting the impact of mating events on fine-scale genetic structure. Global spatial autocorrelation analyses showed positive genetic correlation for up to 3 km, indicating the role of fragmented habitat and the specialized social organization as a barrier in the movement of individuals among bamboo forests. The male-biased dispersal pattern resulted in weaker spatial genetic structure between localities among males than among females, and fine-scale analyses supported that relatedness levels within internodes were higher among females than among males. Finally, only females were more related to their same sex roost mates than to individuals from neighbouring roosts, suggestive of natal philopatry in females.

Identification of Naegleria fowleri in warm ground water aquifers.

PubMed

Laseke, Ian; Korte, Jill; Lamendella, Regina; Kaneshiro, Edna S; Marciano-Cabral, Francine; Oerther, Daniel B

2010-01-01

The free-living amoeba Naegleria fowleri was identified as the etiological agent of primary amoebic meningoencephalitis that caused the deaths of two children in Peoria, Arizona, in autumn of 2002. It was suspected that the source of N. fowleri was the domestic water supply, which originates from ground water sources. In this study, ground water from the greater Phoenix Metropolitan area was tested for the presence of N. fowleri using a nested polymerase chain reaction approach. Phylogenetic analyses of 16S rRNA sequences of bacterial populations in the ground water were performed to examine the potential link between the presence of N. fowleri and bacterial groups inhabiting water wells. The results showed the presence of N. fowleri in five out of six wells sampled and in 26.6% of all ground water samples tested. Phylogenetic analyses showed that beta- and gamma-proteobacteria were the dominant bacterial populations present in the ground water. Bacterial community analyses revealed a very diverse community structure in ground water samples testing positive for N. fowleri.

Contrasting effects of geographical separation on the genetic population structure of sympatric species of mites in avocado orchards.

PubMed

Guzman-Valencia, S; Santillán-Galicia, M T; Guzmán-Franco, A W; González-Hernández, H; Carrillo-Benítez, M G; Suárez-Espinoza, J

2014-10-01

Oligonychus punicae and Oligonychus perseae (Acari: Tetranychidae) are the most important mite species affecting avocado orchards in Mexico. Here we used nucleotide sequence data from segments of the nuclear ribosomal internal transcribed spacers (ITS1 and ITS2) and mitochondrial cytochrome oxidase subunit I (COI) genes to assess the phylogenetic relationships between both sympatric mite species and, using only ITS sequence data, examine genetic variation and population structure in both species, to test the hypothesis that, although both species co-occur, their genetic population structures are different in both Michoacan state (main producer) and Mexico state. Phylogenetic analysis showed a clear separation between both species using ITS and COI sequence information. Haplotype network analysis done on 24 samples of O. punicae revealed low genetic diversity with only three haplotypes found but a significant geographical population structure confirmed by analysis of molecular variance (AMOVA) and Kimura-2-parameter (K2P) analyses. In addition, a Mantel test revealed that geographical isolation was a factor responsible for the genetic differentiation. In contrast, analyses of 22 samples of O. perseae revealed high genetic diversity with 15 haplotypes found but no geographical structure confirmed by the AMOVA, K2P and Mantel test analyses. We have suggested that geographical separation is one of the most important factors driving genetic variation, but that it affected each species differently. The role of the ecology of these species on our results, and the importance of our findings in the development of monitoring and control strategies are discussed.

A Deep Analysis of Center Displacement in An Idealized Tropical Cyclone with Low-wavenumber Asymmetries

NASA Astrophysics Data System (ADS)

Zhao, C.; Song, J.; Leng, H.

2017-12-01

The Tropical Cyclone(TC) center-finding technique plays an important role when diagnostic analyses of TC structure are performed, especially when dealing with low-wavenumber asymmetries. Previous works have already established that structure of TCs can vary greatly depending on the displacement induced by center-finding techniques. As it is difficult to define a true TC center in the real world, this work seeks to explore how low-wavenumber azimuthal Fourier analyses can vary with center displacement using idealized, parametric TC-like vortices with different perturbation structures. It is shown that the errors is sensitive to the location and radial structure of the adding perturbation. In the case of adding azimuthal wavenumber 1 and 3 asymmetries, the increasing radial shear of initial asymmetries will enhance the corresponding spectral energy around radius of maximum wind(RMW) significantly, and they also have a great effect on spectral energy of wavenumber 2. On the contrary, the wavenumber 2 cases show a reduction from 1RMW to outer radius when shear is increasing and has little effect on spectral energy of wavenumber 1 or 2. Pervious findings indicated that the aliasing is dependent on the placement of center relative to the location of the asymmetries, which is also valid in these shearing situations. Moreover, it is found that this aliasing caused by phase displacement is less sensitive with the radial shear in wavenumber 2 and 3 cases, while it shows an significant amplification and deformation when wavenumber 1 asymmetry is added.

Structure and Correlates of Self-Reported Empathy in Schizophrenia

PubMed Central

Horan, William P.; Reise, Steven P.; Kern, Robert S.; Lee, Junghee; Penn, David L.; Green, Michael F.

2015-01-01

Research on empathy in schizophrenia has relied on dated self-report scales that do not conform to contemporary social neuroscience models of empathy. The current study evaluated the structure and correlates of the recently-developed Questionnaire of Cognitive and Affective Empathy (QCAE) in schizophrenia. This measure, whose structure and validity was established in healthy individuals, includes separate scales to assess the two main components of empathy: Cognitive Empathy (assessed by two subscales) and Affective Empathy (assessed by three subscales). Stable outpatients with schizophrenia (n=145) and healthy individuals (n= 45) completed the QCAE, alternative measures of empathy, and assessments of clinical symptoms, neurocognition, and functional outcome. Exploratory and confirmatory factor analyses provided consistent support for a two-factor solution in the schizophrenia group, justifying the use of separate cognitive and affective empathy scales in this population. However, one of the three Affective Empathy subscales was not psychometrically sound and was excluded from further analyses. Patients reported significantly lower Cognitive Empathy but higher Affective Empathy than controls. Among patients, the QCAE scales showed significant correlations with an alternative self-report empathy scale, but not with performance on an empathic accuracy task. The QCAE Cognitive Empathy subscales also showed significant, though modest, correlations with negative symptoms and functional outcome. These findings indicate that structure of self-reported empathy is similar in people with schizophrenia and healthy subjects, and can be meaningfully compared between groups. They also contribute to emerging evidence that some aspects of empathy may be intact or hyper-responsive in schizophrenia. PMID:25985922

Structural diversity of domain superfamilies in the CATH database.

PubMed

Reeves, Gabrielle A; Dallman, Timothy J; Redfern, Oliver C; Akpor, Adrian; Orengo, Christine A

2006-07-14

The CATH database of domain structures has been used to explore the structural variation of homologous domains in 294 well populated domain structure superfamilies, each containing at least three sequence diverse relatives. Our analyses confirm some previously detected trends relating sequence divergence to structural variation but for a much larger dataset and in some superfamilies the new data reveal exceptional structural variation. Use of a new algorithm (2DSEC) to analyse variability in secondary structure compositions across a superfamily sheds new light on how structures evolve. 2DSEC detects inserted secondary structures that embellish the core of conserved secondary structures found throughout the superfamily. Analysis showed that for 56% of highly populated superfamilies (>9 sequence diverse relatives), there are twofold or more increases in the numbers of secondary structures in some relatives. In some families fivefold increases occur, sometimes modifying the fold of the domain. Manual inspection of secondary structure insertions or embellishments in 48 particularly variable superfamilies revealed that although these insertions were usually discontiguous in the sequence they were often co-located in 3D resulting in a larger structural motif that often modified the geometry of the active site or the surface conformation promoting diverse domain partnerships and protein interactions. These observations, supported by automatic analysis of all well populated CATH families, suggest that accretion of small secondary structure insertions may provide a simple mechanism for evolving new functions in diverse relatives. Some layered domain architectures (e.g. mainly-beta and alpha-beta sandwiches) that recur highly in the genomes more frequently exploit these types of embellishments to modify function. In these architectures, aggregation occurs most often at the edges, top or bottom of the beta-sheets. Information on structural variability across domain superfamilies has been made available through the CATH Dictionary of Homologous Structures (DHS).

The effect of geographical indices on left ventricular structure in healthy Han Chinese population

NASA Astrophysics Data System (ADS)

Cen, Minyi; Ge, Miao; Liu, Yonglin; Wang, Congxia; Yang, Shaofang

2017-02-01

The left ventricular posterior wall thickness (LVPWT) and interventricular septum thickness (IVST) are generally regarded as the functional parts of the left ventricular (LV) structure. This paper aims to examine the effects of geographical indices on healthy Han adults' LV structural indices and to offer a scientific basis for developing a unified standard for the reference values of adults' LV structural indices in China. Fifteen terrain, climate, and soil indices were examined as geographical explanatory variables. Statistical analysis was performed using correlation analysis. Moreover, a back propagation neural network (BPNN) and a support vector regression (SVR) were applied to developing models to predict the values of two indices. After the prediction models were built, distribution maps were produced. The results show that LV structural indices are characteristically associated with latitude, longitude, altitude, average temperature, average wind velocity, topsoil sand fraction, topsoil silt fraction, topsoil organic carbon, and topsoil sodicity. The model test analyses show the BPNN model possesses better simulative and predictive ability in comparison with the SVR model. The distribution maps of the LV structural indices show that, in China, the values are higher in the west and lower in the east. These results demonstrate that the reference values of the adults' LV structural indices will be different affected by different geographical environment. The reference values of LV structural indices in one region can be calculated by setting up a BPNN, which showed better applicability in this study. The distribution of the reference values of the LV structural indices can be seen clearly on the geographical distribution map.

The effect of geographical indices on left ventricular structure in healthy Han Chinese population.

PubMed

Cen, Minyi; Ge, Miao; Liu, Yonglin; Wang, Congxia; Yang, Shaofang

2017-02-01

The left ventricular posterior wall thickness (LVPWT) and interventricular septum thickness (IVST) are generally regarded as the functional parts of the left ventricular (LV) structure. This paper aims to examine the effects of geographical indices on healthy Han adults' LV structural indices and to offer a scientific basis for developing a unified standard for the reference values of adults' LV structural indices in China. Fifteen terrain, climate, and soil indices were examined as geographical explanatory variables. Statistical analysis was performed using correlation analysis. Moreover, a back propagation neural network (BPNN) and a support vector regression (SVR) were applied to developing models to predict the values of two indices. After the prediction models were built, distribution maps were produced. The results show that LV structural indices are characteristically associated with latitude, longitude, altitude, average temperature, average wind velocity, topsoil sand fraction, topsoil silt fraction, topsoil organic carbon, and topsoil sodicity. The model test analyses show the BPNN model possesses better simulative and predictive ability in comparison with the SVR model. The distribution maps of the LV structural indices show that, in China, the values are higher in the west and lower in the east. These results demonstrate that the reference values of the adults' LV structural indices will be different affected by different geographical environment. The reference values of LV structural indices in one region can be calculated by setting up a BPNN, which showed better applicability in this study. The distribution of the reference values of the LV structural indices can be seen clearly on the geographical distribution map.

Genome-wide Analyses of the Structural Gene Families Involved in the Legume-specific 5-Deoxyisoflavonoid Biosynthesis of Lotus japonicus

PubMed Central

Shimada, Norimoto; Sato, Shusei; Akashi, Tomoyoshi; Nakamura, Yasukazu; Tabata, Satoshi; Ayabe, Shin-ichi; Aoki, Toshio

2007-01-01

Abstract A model legume Lotus japonicus (Regel) K. Larsen is one of the subjects of genome sequencing and functional genomics programs. In the course of targeted approaches to the legume genomics, we analyzed the genes encoding enzymes involved in the biosynthesis of the legume-specific 5-deoxyisoflavonoid of L. japonicus, which produces isoflavan phytoalexins on elicitor treatment. The paralogous biosynthetic genes were assigned as comprehensively as possible by biochemical experiments, similarity searches, comparison of the gene structures, and phylogenetic analyses. Among the 10 biosynthetic genes investigated, six comprise multigene families, and in many cases they form gene clusters in the chromosomes. Semi-quantitative reverse transcriptase–PCR analyses showed coordinate up-regulation of most of the genes during phytoalexin induction and complex accumulation patterns of the transcripts in different organs. Some paralogous genes exhibited similar expression specificities, suggesting their genetic redundancy. The molecular evolution of the biosynthetic genes is discussed. The results presented here provide reliable annotations of the genes and genetic markers for comparative and functional genomics of leguminous plants. PMID:17452423

Femtosecond laser ablation of cemented carbides: properties and tribological applications

NASA Astrophysics Data System (ADS)

Dumitru, G.; Romano, V.; Weber, H. P.; Gerbig, Y.; Haefke, H.; Bruneau, S.; Hermann, J.; Sentis, M.

Laser ablation with fs laser pulses was performed in air on cobalt cemented tungsten carbide by means of a Ti : sapphire laser (800 nm, 100 fs). Small and moderate fluences (2, 5, 10 J/cm2) and up to 5×104 pulses per irradiated spot were used to drill holes with aspect ratios up to 10. Cross-section cuts from laser-irradiated samples were produced and they were analysed with optical microscopy and SEM. EDX analyses were carried out on selected zones. Quasi-cylindrical holes were found for 2 J/cm2, whereas for 5 and 10 J/cm2 irregular shapes (lobes, bottoms wider than hole entrances) were found to occur after a given number of incident pulses. Layers with modified structure were evidenced at pore walls. SEM revealed a denser structure, while EDX analyses showed uniform and almost similar contents of W, C, and Co in these layers. As a direct application, patterning of coated WC-Co was carried out with 2 J/cm2 and 100 pulses per pore. The resulted surfaces were tribologically tested and these tests revealed an improved friction and wear behaviour.

Characterization, antioxidant and immunomodulatory activities of polysaccharides from Prunella vulgaris Linn.

PubMed

Li, Chao; Huang, Qiang; Fu, Xiong; Yue, Xiu-Jie; Liu, Rui Hai; You, Li-Jun

2015-04-01

Water-soluble polysaccharides from Prunella vulgaris Linn (P. vulgaris) were fractionated using DEAE-Sepharose fast-flow column to obtain several eluents of water (PV-P1), 0.1M NaCl (PV-P2) and 0.2M NaCl (PV-P3). Structural analyses showed that PV-P1 had a higher molecular weight and degree of branching as compared to PV-P2 and PV-P3. Tertiary structure analyses indicated that PV-P1, PV-P2 and PV-P3 did not have triple-helical conformation. PV-P2 and PV-P3 showed stronger antioxidant activities than PV-P1, as measured radical scavenging capacities. PV-P1 showed stronger immunomodulatory activities than PV-P2 and PV-P3 in term of stimulation of the production of pro-inflammatory cytokines, including nitric oxide (NO), tumor necrosis factor-α (TNF-α), and interleukin-6 (IL-6) in murine macrophage RAW 264.7 cells. PV-P1, PV-P2 and PV-P3 did not exhibit cytotoxicities against RAW 264.7 at the concentrations tested. These results suggest that P. vulgaris polysaccharides could be explored as potential antioxidant and immunomodulatory agents for the complementary medicine or functional foods. Copyright © 2015 Elsevier B.V. All rights reserved.

Chronic indeterminate phase of Chagas' disease: mitochondrial involvement in infection with two strains.

PubMed

Báez, Alejandra Lidia; Lo Presti, María Silvina; Fretes, Ricardo; Díaz, Cintia; Pons, Patricia; Bazán, Paola Carolina; Strauss, Mariana; Rivarola, Héctor Walter; Paglini-Oliva, Patricia

2013-03-01

Chagasic cardiopathy has become one of the most frequent causes of heart failure and sudden death, as well as one of the most common causes of cardio-embolic stroke in Latin America. The myocyte response to oxidative stress involves the progression of cellular changes, primarily targeting the mitochondria and modifying therefore the energy supply. In this paper we analysed the effect of the infection of mice with 2 different strains of Trypanosoma cruzi (Tulahuen and SGO Z12) in the chronic indeterminate stage (75 days post-infection), upon the structure and function of cardiac mitochondria. The structural results showed that 83% of the mitochondria from the Tulahuen-infected mice presented an increase in their matrix and 91% of the mitochondria from the SGO Z12-infected group showed a reduction in their diameter (P < 0.05). When the Krebs cycle and mitochondrial respiratory chain functionality was analysed through the measurement of the citrate synthase and complexes I to IV activity, it showed that their activity was altered in all cases in a similar manner in both infected groups. In this paper we have demonstrated that the chronic indeterminate phase is not 'silent' and that cardiac mitochondria are clearly involved in the genesis and progression to the chronic chagasic cardiopathy when different factors alter the host-parasite equilibrium.

Health effects of sulfur-related environmental air pollution. V. Lung structure.

PubMed

Takenaka, S; Godleski, J J; Heini, A; Karg, E; Kreyling, W G; Ritter, B; Schulz, H; Ziesenis, A; Heyder, J

1999-05-01

The lungs of 8 male beagle dogs were examined morphologically and morphometrically after exposure for 13 mo to a respirable sulfur(IV) aerosol at a mass concentration of 1.53 mg m(-3) (16.5 h/day), and to an acidic sulfate aerosol carrying 15.2 micromol m(-3) hydrogen ions into the lungs (6 h/day). An additional eight dogs served as unexposed controls. Standard morphometric analyses of both the surface epithelia of the conducting airways and the alveolar region were performed. These analyses showed no difference between the exposure group and control group. However, there was a tendency to an increase in the volume density of bronchial glands in the exposure group. Five of eight exposed animals showed thickened ridges (knob-like structures) at the entrance to alveoli in the alveolar duct and alveolar sac. Transmission electron microscopy revealed that the thickening was mainly due to type II cell proliferation. As the previous experiment using sulfite aerosol only showed no alterations in the proximal alveolar regions, the changes observed may be considered as effects of acidic sulfate aerosol alone or in combination with sulfite. These findings suggest that sulfur aerosols have the potential to induce epithelial alterations in the proximal alveolar region, which is a primary target for air pollutants.

Computational analysis of histidine mutations on the structural stability of human tyrosinases leading to albinism insurgence.

PubMed

Hassan, Mubashir; Abbas, Qamar; Raza, Hussain; Moustafa, Ahmed A; Seo, Sung-Yum

2017-07-25

Misfolding and structural alteration in proteins lead to serious malfunctions and cause various diseases in humans. Mutations at the active binding site in tyrosinase impair structural stability and cause lethal albinism by abolishing copper binding. To evaluate the histidine mutational effect, all mutated structures were built using homology modelling. The protein sequence was retrieved from the UniProt database, and 3D models of original and mutated human tyrosinase sequences were predicted by changing the residual positions within the target sequence separately. Structural and mutational analyses were performed to interpret the significance of mutated residues (N 180 , R 202 , Q 202 , R 211 , Y 363 , R 367 , Y 367 and D 390 ) at the active binding site of tyrosinases. CSpritz analysis depicted that 23.25% residues actively participate in the instability of tyrosinase. The accuracy of predicted models was confirmed through online servers ProSA-web, ERRAT score and VERIFY 3D values. The theoretical pI and GRAVY generated results also showed the accuracy of the predicted models. The CCA negative correlation results depicted that the replacement of mutated residues at His within the active binding site disturbs the structural stability of tyrosinases. The predicted CCA scores of Tyr 367 (-0.079) and Q/R 202 (0.032) revealed that both mutations have more potential to disturb the structural stability. MD simulation analyses of all predicted models justified that Gln 202 , Arg 202 , Tyr 367 and D 390 replacement made the protein structures more susceptible to destabilization. Mutational results showed that the replacement of His with Q/R 202 and Y/R 363 has a lethal effect and may cause melanin associated diseases such as OCA1. Taken together, our computational analysis depicts that the mutated residues such as Q/R 202 and Y/R 363 actively participate in instability and misfolding of tyrosinases, which may govern OCA1 through disturbing the melanin biosynthetic pathway.

Measuring variations in bicultural identity across U.S. ethnic and generational groups: Development and validation of the Bicultural Identity Integration Scale-Version 2 (BIIS-2).

PubMed

Huynh, Que-Lam; Benet-Martínez, Verònica; Nguyen, Angela-MinhTu D

2018-06-14

Bicultural Identity Integration (BII) is an individual difference construct that captures variations in the experience of biculturalism. Using multiple samples in a series of steps, we refined BII measurement and then tested the construct in a diverse sample of bicultural individuals. Specifically, we wrote new BII items based on qualitative data ( n = 108), examined the quality of the new measure using subject-matter experts ( n = 23) and bicultural individuals ( n = 5), and then collected validation data from bicultural college students ( n = 1049). We used exploratory factor analyses to select items and explore BIIS-2 structure with a random subset of the larger sample ( n = 600), confirmatory factor analyses to show that the factor structure fit the data well ( n = 449), and multigroup confirmatory factor analyses to demonstrate measurement invariance in two ethnic and two generational groups. Results showed that the Bicultural Identity Integration Scale-Version 2 (BIIS-2) yielded reliable and stable scores. The data also revealed interesting and important patterns of associations with theoretically relevant constructs: personality, acculturation, and psychological well-being. Additionally, structural equation models confirmed that in general, personality and acculturation variables influence individuals' experiences with their dual cultural identities, which in turn influence adjustment, but there were interesting and important generational differences in how these variables were related. These findings lend support for the validity of BIIS-2 score interpretations; add to our understanding of the sociocultural, personality, and adjustment correlates of the bicultural experience; and have important implications for understanding the well-being of bicultural individuals. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Behavioural Regulation in Exercise Questionnaire in people with schizophrenia: construct validity of the Portuguese versions.

PubMed

Costa, Raquel; Probst, Michel; Bastos, Tânia; Vilhena, Estela; Seabra, André; Corredeira, Rui

2017-06-22

People with schizophrenia have low physical activity levels that can be explained by the restriction in motivation. The Behavioural Regulation in Exercise Questionnaire-2 is a 19-item scale commonly used to assess five different motivational subtypes for physical activity. However, there are limited psychometric analyses of this version in the schizophrenia context. Moreover, there is a lack of information related to the psychometric properties of version 3 of this questionnaire, with 24 items and six different motivational subtypes. The aim of this study was to examine the construct validity of both Portuguese versions in people with schizophrenia. A total of 118 persons with schizophrenia were included (30 women). Cronbach's alpha was used for internal consistency, Pearson's correlation for the retained motivation-types, confirmatory factor analysis for the structural validity of version 2 and exploratory factor analysis for the factor structure of version 3. Analyses of version 2 provided an adequate fit index for the structure of the five factors. Exploratory analyses suggested retaining 2 factors of version 3. The results of this study suggest that version 3 was an appropriate measure to assess controlled and autonomous motivation for physical activity in people with schizophrenia and support its use in clinical practice and research. Implications for Rehabilitation This study supports the need to identify the reasons why people with schizophrenia practice physical activity. For that purpose, it is important to use valid and cost-effective instruments. The Portuguese version of BREQ-2 confirmed a 5-factor model and showed adequate fit for the application in people with schizophrenia. However, the incremental indices values were lower than expected. The Portuguese version of BREQ-3 showed acceptable psychometric properties to assess controlled and autonomous motivation for physical activity in people with schizophrenia.

Monitoring of Students' Interaction in Online Learning Settings by Structural Network Analysis and Indicators.

PubMed

Ammenwerth, Elske; Hackl, Werner O

2017-01-01

Learning as a constructive process works best in interaction with other learners. Support of social interaction processes is a particular challenge within online learning settings due to the spatial and temporal distribution of participants. It should thus be carefully monitored. We present structural network analysis and related indicators to analyse and visualize interaction patterns of participants in online learning settings. We validate this approach in two online courses and show how the visualization helps to monitor interaction and to identify activity profiles of learners. Structural network analysis is a feasible approach for an analysis of the intensity and direction of interaction in online learning settings.

Evaluating Measurement of Dynamic Constructs: Defining a Measurement Model of Derivatives

PubMed Central

Estabrook, Ryne

2015-01-01

While measurement evaluation has been embraced as an important step in psychological research, evaluating measurement structures with longitudinal data is fraught with limitations. This paper defines and tests a measurement model of derivatives (MMOD), which is designed to assess the measurement structure of latent constructs both for analyses of between-person differences and for the analysis of change. Simulation results indicate that MMOD outperforms existing models for multivariate analysis and provides equivalent fit to data generation models. Additional simulations show MMOD capable of detecting differences in between-person and within-person factor structures. Model features, applications and future directions are discussed. PMID:24364383

Structural Insights into the Phospholipid Binding Specificity of Human Evectin-2

NASA Astrophysics Data System (ADS)

Okazaki, Seiji; Kato, Ryuichi; Wakatsuki, Soichi; Uchida, Yasunori; Taguchi, Tomohiko; Arai, Hiroyuki

Evectin-2 is a recycling endosomal protein and plays an essential role in retrograde transport from recycling endosomes to the trans-Golgi network. The pleckstrin homology (PH) domain of Evectin-2 can specifically binds to phosphatidylserine (PS), which is enriched in recycling endosomes. To elucidate the molecular mechanism how it specifically binds to PS, we solved the crystal structures of human Evectin-2 PH domain for apo and O-phospho-L-serine complexed forms at 1.75 and 1.00 Å resolution, respectively. These structural analyses clearly show that PS-induced conformational change of Evectin-2 PH domain effectively explains the strict phospholipid binding specificity.

Relative Displacement Method for Track-Structure Interaction

PubMed Central

Ramos, Óscar Ramón; Pantaleón, Marcos J.

2014-01-01

The track-structure interaction effects are usually analysed with conventional FEM programs, where it is difficult to implement the complex track-structure connection behaviour, which is nonlinear, elastic-plastic and depends on the vertical load. The authors developed an alternative analysis method, which they call the relative displacement method. It is based on the calculation of deformation states in single DOF element models that satisfy the boundary conditions. For its solution, an iterative optimisation algorithm is used. This method can be implemented in any programming language or analysis software. A comparison with ABAQUS calculations shows a very good result correlation and compliance with the standard's specifications. PMID:24634610

High power, 1060-nm diode laser with an asymmetric hetero-waveguide

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

Li, T; Zhang, Yu; Hao, E

2015-07-31

By introducing an asymmetric hetero-waveguide into the epitaxial structure of a diode laser, a 6.21-W output is achieved at a wavelength of 1060 nm. A different design in p- and n-confinement, based on optimisation of energy bands, is used to reduce voltage loss and meet the requirement of high power and high wall-plug efficiency. A 1060-nm diode laser with a single quantum well and asymmetric hetero-structure waveguide is fabricated and analysed. Measurement results show that the asymmetric hetero-structure waveguide can be efficiently used for reducing voltage loss and improving the confinement of injection carriers and wall-plug efficiency. (lasers)

Genetic patterns of habitat fragmentation and past climate-change effects in the Mediterranean high-mountain plant Armeria caespitosa (Plumbaginaceae).

PubMed

García-Fernández, Alfredo; Iriondo, Jose M; Escudero, Adrián; Aguilar, Javier Fuertes; Feliner, Gonzalo Nieto

2013-08-01

Mountain plants are among the species most vulnerable to global warming, because of their isolation, narrow geographic distribution, and limited geographic range shifts. Stochastic and selective processes can act on the genome, modulating genetic structure and diversity. Fragmentation and historical processes also have a great influence on current genetic patterns, but the spatial and temporal contexts of these processes are poorly known. We aimed to evaluate the microevolutionary processes that may have taken place in Mediterranean high-mountain plants in response to changing historical environmental conditions. Genetic structure, diversity, and loci under selection were analyzed using AFLP markers in 17 populations distributed over the whole geographic range of Armeria caespitosa, an endemic plant that inhabits isolated mountains (Sierra de Guadarrama, Spain). Differences in altitude, geographic location, and climate conditions were considered in the analyses, because they may play an important role in selective and stochastic processes. Bayesian clustering approaches identified nine genetic groups, although some discrepancies in assignment were found between alternative analyses. Spatially explicit analyses showed a weak relationship between genetic parameters and spatial or environmental distances. However, a large proportion of outlier loci were detected, and some outliers were related to environmental variables. A. caespitosa populations exhibit spatial patterns of genetic structure that cannot be explained by the isolation-by-distance model. Shifts along the altitude gradient in response to Pleistocene climatic oscillations and environmentally mediated selective forces might explain the resulting structure and genetic diversity values found.

A Systems Biology Approach for Identifying Hepatotoxicant Groups Based on Similarity in Mechanisms of Action and Chemical Structure.

PubMed

Hebels, Dennie G A J; Rasche, Axel; Herwig, Ralf; van Westen, Gerard J P; Jennen, Danyel G J; Kleinjans, Jos C S

2016-01-01

When evaluating compound similarity, addressing multiple sources of information to reach conclusions about common pharmaceutical and/or toxicological mechanisms of action is a crucial strategy. In this chapter, we describe a systems biology approach that incorporates analyses of hepatotoxicant data for 33 compounds from three different sources: a chemical structure similarity analysis based on the 3D Tanimoto coefficient, a chemical structure-based protein target prediction analysis, and a cross-study/cross-platform meta-analysis of in vitro and in vivo human and rat transcriptomics data derived from public resources (i.e., the diXa data warehouse). Hierarchical clustering of the outcome scores of the separate analyses did not result in a satisfactory grouping of compounds considering their known toxic mechanism as described in literature. However, a combined analysis of multiple data types may hypothetically compensate for missing or unreliable information in any of the single data types. We therefore performed an integrated clustering analysis of all three data sets using the R-based tool iClusterPlus. This indeed improved the grouping results. The compound clusters that were formed by means of iClusterPlus represent groups that show similar gene expression while simultaneously integrating a similarity in structure and protein targets, which corresponds much better with the known mechanism of action of these toxicants. Using an integrative systems biology approach may thus overcome the limitations of the separate analyses when grouping liver toxicants sharing a similar mechanism of toxicity.

Approach for Structurally Clearing an Adaptive Compliant Trailing Edge Flap for Flight

NASA Technical Reports Server (NTRS)

Miller, Eric J.; Lokos, William A.; Cruz, Josue; Crampton, Glen; Stephens, Craig A.; Kota, Sridhar; Ervin, Gregory; Flick, Pete

2015-01-01

The Adaptive Compliant Trailing Edge (ACTE) flap was flown on the National Aeronautics and Space Administration (NASA) Gulfstream GIII testbed at the NASA Armstrong Flight Research Center. This smoothly curving flap replaced the existing Fowler flaps creating a seamless control surface. This compliant structure, developed by FlexSys Inc. in partnership with the Air Force Research Laboratory, supported NASA objectives for airframe structural noise reduction, aerodynamic efficiency, and wing weight reduction through gust load alleviation. A thorough structures airworthiness approach was developed to move this project safely to flight. A combination of industry and NASA standard practice require various structural analyses, ground testing, and health monitoring techniques for showing an airworthy structure. This paper provides an overview of compliant structures design, the structural ground testing leading up to flight, and the flight envelope expansion and monitoring strategy. Flight data will be presented, and lessons learned along the way will be highlighted.

Sensitivity to musical structure in the human brain

PubMed Central

McDermott, Josh H.; Norman-Haignere, Sam; Kanwisher, Nancy

2012-01-01

Evidence from brain-damaged patients suggests that regions in the temporal lobes, distinct from those engaged in lower-level auditory analysis, process the pitch and rhythmic structure in music. In contrast, neuroimaging studies targeting the representation of music structure have primarily implicated regions in the inferior frontal cortices. Combining individual-subject fMRI analyses with a scrambling method that manipulated musical structure, we provide evidence of brain regions sensitive to musical structure bilaterally in the temporal lobes, thus reconciling the neuroimaging and patient findings. We further show that these regions are sensitive to the scrambling of both pitch and rhythmic structure but are insensitive to high-level linguistic structure. Our results suggest the existence of brain regions with representations of musical structure that are distinct from high-level linguistic representations and lower-level acoustic representations. These regions provide targets for future research investigating possible neural specialization for music or its associated mental processes. PMID:23019005

Personality Inventory for DSM-5-Short Form (PID-5-SF): Reliability, Factorial Structure, and Relationship With Functional Impairment in Dual Diagnosis Patients.

PubMed

Díaz-Batanero, Carmen; Ramírez-López, Juan; Domínguez-Salas, Sara; Fernández-Calderón, Fermín; Lozano, Óscar M

2017-11-01

Section III of the Diagnostic and Statistical Manual of Mental Disorders-Fifth edition ( DSM-5) has generated a personality paradigm consisting of 25 personality facets identified in five domains. The developed assessment instrument Personality Inventory for DSM-5 (PID-5) has showed good psychometric properties, but the potential for certain improvements still remain. In this article, a sample of 282 dual diagnosis patients is used to provide evidence of the psychometric properties of the PID-5-Short Form. The mean value of Cronbach's alpha coefficients reached .73 on the facets and .84 for domains and test-retest values ranged between .57 to .83 for facets and .70 to .87 for the domains. Confirmatory factor analyses conducted showed good fit on both models tested: the five correlated factor structure and hierarchical structure of personality traits. The WHODAS 2.0 domains of understanding and communicating, and participating in society, appear to show the strongest relationship with personality facets. In general, the PID-5-Short Form shows adequate psychometric properties for use in dual diagnosis patients.

Divergent structural brain abnormalities between different genetic subtypes of children with Prader-Willi syndrome.

PubMed

Lukoshe, Akvile; White, Tonya; Schmidt, Marcus N; van der Lugt, Aad; Hokken-Koelega, Anita C

2013-10-22

Prader-Willi syndrome (PWS) is a complex neurogenetic disorder with symptoms that indicate not only hypothalamic, but also a global, central nervous system (CNS) dysfunction. However, little is known about developmental differences in brain structure in children with PWS. Thus, our aim was to investigate global brain morphology in children with PWS, including the comparison between different genetic subtypes of PWS. In addition, we performed exploratory cortical and subcortical focal analyses. High resolution structural magnetic resonance images were acquired in 20 children with genetically confirmed PWS (11 children carrying a deletion (DEL), 9 children with maternal uniparental disomy (mUPD)), and compared with 11 age- and gender-matched typically developing siblings as controls. Brain morphology measures were obtained using the FreeSurfer software suite. Both children with DEL and mUPD showed smaller brainstem volume, and a trend towards smaller cortical surface area and white matter volume. Children with mUPD had enlarged lateral ventricles and larger cortical cerebrospinal fluid (CSF) volume. Further, a trend towards increased cortical thickness was found in children with mUPD. Children with DEL had a smaller cerebellum, and smaller cortical and subcortical grey matter volumes. Focal analyses revealed smaller white matter volumes in left superior and bilateral inferior frontal gyri, right cingulate cortex, and bilateral precuneus areas associated with the default mode network (DMN) in children with mUPD. Children with PWS show signs of impaired brain growth. Those with mUPD show signs of early brain atrophy. In contrast, children with DEL show signs of fundamentally arrested, although not deviant brain development and presented few signs of cortical atrophy. Our results of global brain measurements suggest divergent neurodevelopmental patterns in children with DEL and mUPD.

Divergent structural brain abnormalities between different genetic subtypes of children with Prader–Willi syndrome

PubMed Central

2013-01-01

Background Prader–Willi syndrome (PWS) is a complex neurogenetic disorder with symptoms that indicate not only hypothalamic, but also a global, central nervous system (CNS) dysfunction. However, little is known about developmental differences in brain structure in children with PWS. Thus, our aim was to investigate global brain morphology in children with PWS, including the comparison between different genetic subtypes of PWS. In addition, we performed exploratory cortical and subcortical focal analyses. Methods High resolution structural magnetic resonance images were acquired in 20 children with genetically confirmed PWS (11 children carrying a deletion (DEL), 9 children with maternal uniparental disomy (mUPD)), and compared with 11 age- and gender-matched typically developing siblings as controls. Brain morphology measures were obtained using the FreeSurfer software suite. Results Both children with DEL and mUPD showed smaller brainstem volume, and a trend towards smaller cortical surface area and white matter volume. Children with mUPD had enlarged lateral ventricles and larger cortical cerebrospinal fluid (CSF) volume. Further, a trend towards increased cortical thickness was found in children with mUPD. Children with DEL had a smaller cerebellum, and smaller cortical and subcortical grey matter volumes. Focal analyses revealed smaller white matter volumes in left superior and bilateral inferior frontal gyri, right cingulate cortex, and bilateral precuneus areas associated with the default mode network (DMN) in children with mUPD. Conclusions Children with PWS show signs of impaired brain growth. Those with mUPD show signs of early brain atrophy. In contrast, children with DEL show signs of fundamentally arrested, although not deviant brain development and presented few signs of cortical atrophy. Our results of global brain measurements suggest divergent neurodevelopmental patterns in children with DEL and mUPD. PMID:24144356

[X-ray semiotics of the morphological and functional changes in chronic bronchitis].

PubMed

Khomenko, A G; Dmitrieva, L I; Polak, J; Gapon'ko, G A; Starilova, I P

1985-01-01

The authors analysed structural disorders of a pulmonary pattern in patients with non-obstructive, obstructive and purulent bronchitis. Characteristic x-ray symptom-complexes were singled out for each clinical variant of the disease. In addition to roentgenomorphological changes functional disorders showing changes of biomechanics in patients with chronic bronchitis were revealed at roentgenopneumopolygraphy.

Mapping Trade-Offs in Teachers' Integration of Technology-Supported Inquiry in High School Science Classes

ERIC Educational Resources Information Center

Sandoval, William A.; Daniszewski, Kenneth

2004-01-01

This paper explores how two teachers concurrently enacting the same technology-based inquiry unit on evolution structured activity and discourse in their classrooms to connect students' computer-based investigations to formal domain theories. Our analyses show that the teachers' interactions with their students during inquiry were quite similar,…

Students' Silent Messages: Can Teacher Verbal and Nonverbal Immediacy Moderate Student Use of Text Messaging in Class?

ERIC Educational Resources Information Center

Wei, Fang-Yi Flora; Wang, Y. Ken

2010-01-01

This study investigated the relationship between teacher immediacy and college students' use of text messaging in class. Using a cross-sectional survey sample (N=228), structural equation model analyses showed that students' learning motivation does not mediate the potential effects of teacher immediacy and students' use of text messaging in…

Argentinean Students' and Teachers' Conceptions of Day and Night: An Analysis in Relation to Astronomical Reference Systems

ERIC Educational Resources Information Center

Galperin, D.; Raviolo, A.

2015-01-01

This work analysed the evolution of day/night cycle conceptions held by students of different ages and teachers in the Patagonian region of Argentina. The research was based on drawings, written explanations and semi-structured individual interviews. The results showed that both teachers and students had significant comprehension problems. These…

The Validity of the Psychopathic Personality Inventory-Revised in a Community Sample

ERIC Educational Resources Information Center

Uzieblo, Katarzyna; Verschuere, Bruno; Van den Bussche, Eva; Crombez, Geert

2010-01-01

Research on the Psychopathic Personality Inventory-Revised (PPI-R) has revealed two factors: Fearless Dominance, and Self-Centered Impulsivity. This study examined the validity of these PPI-R factors in a community sample (N = 675). First, confirmatory factor analyses did not support the two-factor structure. Second, the PPI-R factors showed good…

Parenting Styles and Bullying at School: The Mediating Role of Locus of Control

ERIC Educational Resources Information Center

Georgiou, Stelios N.; Ioannou, Myria; Stavrinides, Panayiotis

2017-01-01

The current study examined the mediating role of children's locus of control in the relation between parenting styles and bully-victim experiences at school. Participants were 447 students aged 10 and 11 years old from 13 different elementary, urban, and rural schools in Cyprus. Analyses using structural equation modeling showed that parenting…

Association between structural and functional brain alterations in drug-free patients with schizophrenia: a multimodal meta-analysis

PubMed

Gao, Xin; Zhang, Wenjing; Yao, Li; Xiao, Yuan; Liu, Lu; Liu, Jieke; Li, Siyi; Tao, Bo; Shah, Chandan; Gong, Qiyong; Sweeney, John; Lui, Su

2017-12-05

Neuroimaging studies have shown both structural and functional abnormalities in patients with schizophrenia. Recently, studies have begun to explore the association between structural and functional grey matter abnormalities. By conducting a meta­-analysis on morphometric and functional imaging studies of grey matter alterations in drug-free patients, the present study aims to examine the degree of overlap between brain regions with anatomic and functional changes in patients with schizophrenia. We performed a systematic search of PubMed, Embase, Web of Science and the Cochrane Library to identify relevant publications. A multimodal analysis was then conducted using Seed-based d Mapping software. Exploratory analyses included jackknife, subgroup and meta-regression analyses. We included 15 structural MRI studies comprising 486 drug-free patients and 485 healthy controls, and 16 functional MRI studies comprising 403 drug-free patients and 428 controls in our meta-analysis. Drug-free patients were examined to reduce pharmacological effects on the imaging data. Multimodal analysis showed considerable overlap between anatomic and functional changes, mainly in frontotemporal regions, bilateral medial posterior cingulate/paracingulate gyrus, bilateral insula, basal ganglia and left cerebellum. There were also brain regions showing only anatomic changes in the right superior frontal gyrus, left supramarginal gyrus, right lingual gyrus and functional alternations involving the right angular ­gyrus. The methodological aspects, patient characteristics and clinical variables of the included studies were heterogeneous, and we cannot exclude medication effects. The present study showed overlapping anatomic and functional brain abnormalities mainly in the default mode (DMN) and auditory networks (AN) in drug-free patients with schizophrenia. However, the pattern of changes differed in these networks. Decreased grey matter was associated with decreased activation within the DMN, whereas it was associated with increased activation within the AN. These discrete patterns suggest different pathophysiological changes impacting structural and functional associations within different neural networks in patients with schizophrenia. 2017 Joule Inc., or its licensors

Association between structural and functional brain alterations in drug-free patients with schizophrenia: a multimodal meta-analysis.

PubMed

Gao, Xin; Zhang, Wenjing; Yao, Li; Xiao, Yuan; Liu, Lu; Liu, Jieke; Li, Siyi; Tao, Bo; Shah, Chandan; Gong, Qiyong; Sweeney, John A; Lui, Su

2018-03-01

Neuroimaging studies have shown both structural and functional abnormalities in patients with schizophrenia. Recently, studies have begun to explore the association between structural and functional grey matter abnormalities. By conducting a meta-analysis on morphometric and functional imaging studies of grey matter alterations in drug-free patients, the present study aims to examine the degree of overlap between brain regions with anatomic and functional changes in patients with schizophrenia. We performed a systematic search of PubMed, Embase, Web of Science and the Cochrane Library to identify relevant publications. A multimodal analysis was then conducted using Seed-based d Mapping software. Exploratory analyses included jackknife, subgroup and meta-regression analyses. We included 15 structural MRI studies comprising 486 drug-free patients and 485 healthy controls, and 16 functional MRI studies comprising 403 drug-free patients and 428 controls in our meta-analysis. Drug-free patients were examined to reduce pharmacological effects on the imaging data. Multimodal analysis showed considerable overlap between anatomic and functional changes, mainly in frontotemporal regions, bilateral medial posterior cingulate/paracingulate gyrus, bilateral insula, basal ganglia and left cerebellum. There were also brain regions showing only anatomic changes in the right superior frontal gyrus, left supramarginal gyrus, right lingual gyrus and functional alternations involving the right angular gyrus. The methodological aspects, patient characteristics and clinical variables of the included studies were heterogeneous, and we cannot exclude medication effects. The present study showed overlapping anatomic and functional brain abnormalities mainly in the default mode (DMN) and auditory networks (AN) in drug-free patients with schizophrenia. However, the pattern of changes differed in these networks. Decreased grey matter was associated with decreased activation within the DMN, whereas it was associated with increased activation within the AN. These discrete patterns suggest different pathophysiological changes impacting structural and functional associations within different neural networks in patients with schizophrenia.

Association between structural and functional brain alterations in drug-free patients with schizophrenia: a multimodal meta-analysis.

PubMed

Gao, Xin; Zhang, Wenjing; Yao, Li; Xiao, Yuan; Liu, Lu; Liu, Jieke; Li, Siyi; Tao, Bo; Shah, Chandan; Gong, Qiyong; Sweeney, John A; Lui, Su

2017-12-15

Neuroimaging studies have shown both structural and functional abnormalities in patients with schizophrenia. Recently, studies have begun to explore the association between structural and functional grey matter abnormalities. By conducting a meta-analysis on morphometric and functional imaging studies of grey matter alterations in drug-free patients, the present study aims to examine the degree of overlap between brain regions with anatomic and functional changes in patients with schizophrenia. We performed a systematic search of PubMed, Embase, Web of Science and the Cochrane Library to identify relevant publications. A multimodal analysis was then conducted using Seed-based d Mapping software. Exploratory analyses included jackknife, subgroup and meta-regression analyses. We included 15 structural MRI studies comprising 486 drug-free patients and 485 healthy controls, and 16 functional MRI studies comprising 403 drug-free patients and 428 controls in our meta-analysis. Drug-free patients were examined to reduce pharmacological effects on the imaging data. Multimodal analysis showed considerable overlap between anatomic and functional changes, mainly in frontotemporal regions, bilateral medial posterior cingulate/paracingulate gyrus, bilateral insula, basal ganglia and left cerebellum. There were also brain regions showing only anatomic changes in the right superior frontal gyrus, left supramarginal gyrus, right lingual gyrus and functional alternations involving the right angular gyrus. The methodological aspects, patient characteristics and clinical variables of the included studies were heterogeneous, and we cannot exclude medication effects. The present study showed overlapping anatomic and functional brain abnormalities mainly in the default mode (DMN) and auditory networks (AN) in drug-free patients with schizophrenia. However, the pattern of changes differed in these networks. Decreased grey matter was associated with decreased activation within the DMN, whereas it was associated with increased activation within the AN. These discrete patterns suggest different pathophysiological changes impacting structural and functional associations within different neural networks in patients with schizophrenia.

Structural Covariance Networks in Children with Autism or ADHD

PubMed Central

Romero-Garcia, R.; Mak, E.; Bullmore, E. T.; Baron-Cohen, S.

2017-01-01

Abstract Background While autism and attention-deficit/hyperactivity disorder (ADHD) are considered distinct conditions from a diagnostic perspective, clinically they share some phenotypic features and have high comorbidity. Regardless, most studies have focused on only one condition, with considerable heterogeneity in their results. Taking a dual-condition approach might help elucidate shared and distinct neural characteristics. Method Graph theory was used to analyse topological properties of structural covariance networks across both conditions and relative to a neurotypical (NT; n = 87) group using data from the ABIDE (autism; n = 62) and ADHD-200 datasets (ADHD; n = 69). Regional cortical thickness was used to construct the structural covariance networks. This was analysed in a theoretical framework examining potential differences in long and short-range connectivity, with a specific focus on relation between central graph measures and cortical thickness. Results We found convergence between autism and ADHD, where both conditions show an overall decrease in CT covariance with increased Euclidean distance between centroids compared with a NT population. The 2 conditions also show divergence. Namely, there is less modular overlap between the 2 conditions than there is between each condition and the NT group. The ADHD group also showed reduced cortical thickness and lower degree in hub regions than the autism group. Lastly, the ADHD group also showed reduced wiring costs compared with the autism groups. Conclusions Our results indicate a need for taking an integrated approach when considering highly comorbid conditions such as autism and ADHD. Furthermore, autism and ADHD both showed alterations in the relation between inter-regional covariance and centroid distance, where both groups show a steeper decline in covariance as a function of distance. The 2 groups also diverge on modular organization, cortical thickness of hub regions and wiring cost of the covariance network. Thus, on some network features the groups are distinct, yet on others there is convergence. PMID:28633299

Structural Covariance Networks in Children with Autism or ADHD.

PubMed

Bethlehem, R A I; Romero-Garcia, R; Mak, E; Bullmore, E T; Baron-Cohen, S

2017-08-01

While autism and attention-deficit/hyperactivity disorder (ADHD) are considered distinct conditions from a diagnostic perspective, clinically they share some phenotypic features and have high comorbidity. Regardless, most studies have focused on only one condition, with considerable heterogeneity in their results. Taking a dual-condition approach might help elucidate shared and distinct neural characteristics. Graph theory was used to analyse topological properties of structural covariance networks across both conditions and relative to a neurotypical (NT; n = 87) group using data from the ABIDE (autism; n = 62) and ADHD-200 datasets (ADHD; n = 69). Regional cortical thickness was used to construct the structural covariance networks. This was analysed in a theoretical framework examining potential differences in long and short-range connectivity, with a specific focus on relation between central graph measures and cortical thickness. We found convergence between autism and ADHD, where both conditions show an overall decrease in CT covariance with increased Euclidean distance between centroids compared with a NT population. The 2 conditions also show divergence. Namely, there is less modular overlap between the 2 conditions than there is between each condition and the NT group. The ADHD group also showed reduced cortical thickness and lower degree in hub regions than the autism group. Lastly, the ADHD group also showed reduced wiring costs compared with the autism groups. Our results indicate a need for taking an integrated approach when considering highly comorbid conditions such as autism and ADHD. Furthermore, autism and ADHD both showed alterations in the relation between inter-regional covariance and centroid distance, where both groups show a steeper decline in covariance as a function of distance. The 2 groups also diverge on modular organization, cortical thickness of hub regions and wiring cost of the covariance network. Thus, on some network features the groups are distinct, yet on others there is convergence. © The Author 2017. Published by Oxford University Press.

Determining crystal structures through crowdsourcing and coursework

PubMed Central

Horowitz, Scott; Koepnick, Brian; Martin, Raoul; Tymieniecki, Agnes; Winburn, Amanda A.; Cooper, Seth; Flatten, Jeff; Rogawski, David S.; Koropatkin, Nicole M.; Hailu, Tsinatkeab T.; Jain, Neha; Koldewey, Philipp; Ahlstrom, Logan S.; Chapman, Matthew R.; Sikkema, Andrew P.; Skiba, Meredith A.; Maloney, Finn P.; Beinlich, Felix R. M.; Caglar, Ahmet; Coral, Alan; Jensen, Alice Elizabeth; Lubow, Allen; Boitano, Amanda; Lisle, Amy Elizabeth; Maxwell, Andrew T.; Failer, Barb; Kaszubowski, Bartosz; Hrytsiv, Bohdan; Vincenzo, Brancaccio; de Melo Cruz, Breno Renan; McManus, Brian Joseph; Kestemont, Bruno; Vardeman, Carl; Comisky, Casey; Neilson, Catherine; Landers, Catherine R.; Ince, Christopher; Buske, Daniel Jon; Totonjian, Daniel; Copeland, David Marshall; Murray, David; Jagieła, Dawid; Janz, Dietmar; Wheeler, Douglas C.; Cali, Elie; Croze, Emmanuel; Rezae, Farah; Martin, Floyd Orville; Beecher, Gil; de Jong, Guido Alexander; Ykman, Guy; Feldmann, Harald; Chan, Hugo Paul Perez; Kovanecz, Istvan; Vasilchenko, Ivan; Connellan, James C.; Borman, Jami Lynne; Norrgard, Jane; Kanfer, Jebbie; Canfield, Jeffrey M.; Slone, Jesse David; Oh, Jimmy; Mitchell, Joanne; Bishop, John; Kroeger, John Douglas; Schinkler, Jonas; McLaughlin, Joseph; Brownlee, June M.; Bell, Justin; Fellbaum, Karl Willem; Harper, Kathleen; Abbey, Kirk J.; Isaksson, Lennart E.; Wei, Linda; Cummins, Lisa N.; Miller, Lori Anne; Bain, Lyn; Carpenter, Lynn; Desnouck, Maarten; Sharma, Manasa G.; Belcastro, Marcus; Szew, Martin; Szew, Martin; Britton, Matthew; Gaebel, Matthias; Power, Max; Cassidy, Michael; Pfützenreuter, Michael; Minett, Michele; Wesselingh, Michiel; Yi, Minjune; Cameron, Neil Haydn Tormey; Bolibruch, Nicholas I.; Benevides, Noah; Kathleen Kerr, Norah; Barlow, Nova; Crevits, Nykole Krystyne; Dunn, Paul; Roque, Paulo Sergio Silveira Belo Nascimento; Riber, Peter; Pikkanen, Petri; Shehzad, Raafay; Viosca, Randy; James Fraser, Robert; Leduc, Robert; Madala, Roman; Shnider, Scott; de Boisblanc, Sharon; Butkovich, Slava; Bliven, Spencer; Hettler, Stephen; Telehany, Stephen; Schwegmann, Steven A.; Parkes, Steven; Kleinfelter, Susan C.; Michael Holst, Sven; van der Laan, T. J. A.; Bausewein, Thomas; Simon, Vera; Pulley, Warwick; Hull, William; Kim, Annes Yukyung; Lawton, Alexis; Ruesch, Amanda; Sundar, Anjali; Lawrence, Anna-Lisa; Afrin, Antara; Maheshwer, Bhargavi; Turfe, Bilal; Huebner, Christian; Killeen, Courtney Elizabeth; Antebi-Lerrman, Dalia; Luan, Danny; Wolfe, Derek; Pham, Duc; Michewicz, Elaina; Hull, Elizabeth; Pardington, Emily; Galal, Galal Osama; Sun, Grace; Chen, Grace; Anderson, Halie E.; Chang, Jane; Hewlett, Jeffrey Thomas; Sterbenz, Jennifer; Lim, Jiho; Morof, Joshua; Lee, Junho; Inn, Juyoung Samuel; Hahm, Kaitlin; Roth, Kaitlin; Nair, Karun; Markin, Katherine; Schramm, Katie; Toni Eid, Kevin; Gam, Kristina; Murphy, Lisha; Yuan, Lucy; Kana, Lulia; Daboul, Lynn; Shammas, Mario Karam; Chason, Max; Sinan, Moaz; Andrew Tooley, Nicholas; Korakavi, Nisha; Comer, Patrick; Magur, Pragya; Savliwala, Quresh; Davison, Reid Michael; Sankaran, Roshun Rajiv; Lewe, Sam; Tamkus, Saule; Chen, Shirley; Harvey, Sho; Hwang, Sin Ye; Vatsia, Sohrab; Withrow, Stefan; Luther, Tahra K; Manett, Taylor; Johnson, Thomas James; Ryan Brash, Timothy; Kuhlman, Wyatt; Park, Yeonjung; Popović, Zoran; Baker, David; Khatib, Firas; Bardwell, James C. A.

2016-01-01

We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit players achieved the most accurate structure. Analysing the target protein of the competition, YPL067C, uncovered a new family of histidine triad proteins apparently involved in the prevention of amyloid toxicity. From this study, we conclude that crystallographers can utilize crowdsourcing to interpret electron density information and to produce structure solutions of the highest quality. PMID:27633552

Psychometric properties of the Brief Symptom Inventory-18 in a Spanish breast cancer sample.

PubMed

Galdón, Ma José; Durá, Estrella; Andreu, Yolanda; Ferrando, Maite; Murgui, Sergio; Pérez, Sandra; Ibañez, Elena

2008-12-01

The objective of this work was to study the psychometric and structural properties of the Brief Symptom Inventory-18 (BSI-18) in a sample of breast cancer patients (N=175). Confirmatory factor analyses were conducted. Two models were tested: the theoretical model with the original structure (three-dimensional), and the empirical model (a four-factor structure) obtained through exploratory factor analysis initially performed by the authors of the BSI-18. The eligible structure was the original proposal consisting of three dimensions: somatization, depression, and anxiety scores. These measures also showed good internal consistency. The results of this study support the reliability and structural validity of the BSI-18 as a standardized instrument for screening purposes in breast cancer patients, with the added benefits of simplicity and ease of application.

A feast of visualization

NASA Astrophysics Data System (ADS)

2008-12-01

Strength through structure The visualization and assessment of inner human bone structures can provide better predictions of fracture risk due to osteoporosis. Using micro-computed tomography (µCT), Christoph Räth from the Max Planck Institute for Extraterrestrial Physics and colleagues based in Munich, Vienna and Salzburg have shown how complex lattice-shaped bone structures can be visualized. The structures were quantified by calculating certain "texture measures" that yield new information about the stability of the bone. A 3D visualization showing the variation with orientation of one of the texture measures for four different bone specimens (from left to right) is shown above. Such analyses may help us to improve our understanding of disease and drug-induced changes in bone structure (C Räth et al. 2008 New J. Phys. 10 125010).

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

Yang, Hao; Lee, H. S.; Sarahan, M. C.

Grain boundaries (GBs) in complex oxides such as perovskites have been shown to readily accommodate nonstoichiometry changing the electrostatic potential at the boundary plane and effectively controlling material properties such as capacitance, magnetoresistance and superconductivity. Understanding and quantifying exactly how variations in atomic scale nonstoichiometry at the boundary plane extend to the practical mesoscale operating length of the system is therefore critical for improving the overall properties. Bicrystals of SrTiO 3 were fabricated to provide the model GB model structures that are analysed in this paper. We show that statistical analysis of aberration-corrected scanning transmission electron microscope images acquired frommore » a large area of GB is an effective routine to understanding the variation in boundary structure that occurs to accommodate nonstoichiometry. In the case of the SrTiO 3 22.6° Σ13 (510)/[100] GB analysed here, the symmetric atomic structures observed from a micron-long GB can be categorized as two different competing structural arrangements, with and without a rigid-body translation along the boundary plane. How this quantified experimental approach can provide direct insights into the GB energetics is further confirmed from the first principles density functional theory, and the effect of nonstoichiometry in determining the GB energies is quantified.« less

Neptune Aerocapture Systems Analysis

NASA Technical Reports Server (NTRS)

Lockwood, Mary Kae

2004-01-01

A Neptune Aerocapture Systems Analysis is completed to determine the feasibility, benefit and risk of an aeroshell aerocapture system for Neptune and to identify technology gaps and technology performance goals. The high fidelity systems analysis is completed by a five center NASA team and includes the following disciplines and analyses: science; mission design; aeroshell configuration screening and definition; interplanetary navigation analyses; atmosphere modeling; computational fluid dynamics for aerodynamic performance and database definition; initial stability analyses; guidance development; atmospheric flight simulation; computational fluid dynamics and radiation analyses for aeroheating environment definition; thermal protection system design, concepts and sizing; mass properties; structures; spacecraft design and packaging; and mass sensitivities. Results show that aerocapture can deliver 1.4 times more mass to Neptune orbit than an all-propulsive system for the same launch vehicle. In addition aerocapture results in a 3-4 year reduction in trip time compared to all-propulsive systems. Aerocapture is feasible and performance is adequate for the Neptune aerocapture mission. Monte Carlo simulation results show 100% successful capture for all cases including conservative assumptions on atmosphere and navigation. Enabling technologies for this mission include TPS manufacturing; and aerothermodynamic methods and validation for determining coupled 3-D convection, radiation and ablation aeroheating rates and loads, and the effects on surface recession.

Evolutionary relationship and structural characterization of the EPF/EPFL gene family.

PubMed

Takata, Naoki; Yokota, Kiyonobu; Ohki, Shinya; Mori, Masashi; Taniguchi, Toru; Kurita, Manabu

2013-01-01

EPF1-EPF2 and EPFL9/Stomagen act antagonistically in regulating leaf stomatal density. The aim of this study was to elucidate the evolutionary functional divergence of EPF/EPFL family genes. Phylogenetic analyses showed that AtEPFL9/Stomagen-like genes are conserved only in vascular plants and are closely related to AtEPF1/EPF2-like genes. Modeling showed that EPF/EPFL peptides share a common 3D structure that is constituted of a scaffold and loop. Molecular dynamics simulation suggested that AtEPF1/EPF2-like peptides form an additional disulfide bond in their loop regions and show greater flexibility in these regions than AtEPFL9/Stomagen-like peptides. This study uncovered the evolutionary relationship and the conformational divergence of proteins encoded by the EPF/EPFL family genes.

Evolutionary Relationship and Structural Characterization of the EPF/EPFL Gene Family

PubMed Central

Takata, Naoki; Yokota, Kiyonobu; Ohki, Shinya; Mori, Masashi; Taniguchi, Toru; Kurita, Manabu

2013-01-01

EPF1-EPF2 and EPFL9/Stomagen act antagonistically in regulating leaf stomatal density. The aim of this study was to elucidate the evolutionary functional divergence of EPF/EPFL family genes. Phylogenetic analyses showed that AtEPFL9/Stomagen-like genes are conserved only in vascular plants and are closely related to AtEPF1/EPF2-like genes. Modeling showed that EPF/EPFL peptides share a common 3D structure that is constituted of a scaffold and loop. Molecular dynamics simulation suggested that AtEPF1/EPF2-like peptides form an additional disulfide bond in their loop regions and show greater flexibility in these regions than AtEPFL9/Stomagen-like peptides. This study uncovered the evolutionary relationship and the conformational divergence of proteins encoded by the EPF/EPFL family genes. PMID:23755192

Structural and mechanical study of concrete made from cementitious materials of low environmental impact

NASA Astrophysics Data System (ADS)

González, A. K.; Montaño, A. M.; González, C. P.; Santos, A.

2017-12-01

This work shows the results obtained by replacing Type I Portland®, by cementitious geopolymers materials, derived from minerals, in concrete mixtures. Synthesis of both geopolymers through alkaline activation of two alluminosilicates: Bentonite and Pumice with sodium silicate (Na2SiO3). XRD, SEM and XRDE are used to structural study of new geopolymers. Concrete mixtures with replacement of Portland have 10% and 30% of geopolymer. Finally, concrete mortars formed were mechanically analysed according to ICONTEC 220 at 7, 14, 28, 41, 90 and 120 days of cure. Results shows that compressive strength of concrete from Bentonite and Pumice are almost the same for the standard concrete at 28 days of cure. At 90 days of cure, compression resistance of concrete from Pumice at 10% is even higher than those that standard concrete shows.

Short loop length and high thermal stability determine genomic instability induced by G-quadruplex-forming minisatellites

PubMed Central

Piazza, Aurèle; Adrian, Michael; Samazan, Frédéric; Heddi, Brahim; Hamon, Florian; Serero, Alexandre; Lopes, Judith; Teulade-Fichou, Marie-Paule; Phan, Anh Tuân; Nicolas, Alain

2015-01-01

G-quadruplexes (G4) are polymorphic four-stranded structures formed by certain G-rich nucleic acids, with various biological roles. However, structural features dictating their formation and/or functionin vivo are unknown. InS. cerevisiae, the pathological persistency of G4 within the CEB1 minisatellite induces its rearrangement during leading-strand replication. We now show that several other G4-forming sequences remain stable. Extensive mutagenesis of the CEB25 minisatellite motif reveals that only variants with very short (≤ 4 nt) G4 loops preferentially containing pyrimidine bases trigger genomic instability. Parallel biophysical analyses demonstrate that shortening loop length does not change the monomorphic G4 structure of CEB25 variants but drastically increases its thermal stability, in correlation with thein vivo instability. Finally, bioinformatics analyses reveal that the threat for genomic stability posed by G4 bearing short pyrimidine loops is conserved inC. elegans and humans. This work provides a framework explanation for the heterogeneous instability behavior of G4-forming sequencesin vivo, highlights the importance of structure thermal stability, and questions the prevailing assumption that G4 structures with short or longer loops are as likely to formin vivo. PMID:25956747

Structural and Biochemical Consequences of Disease-Causing Mutations in the Ankyrin Repeat Domain of the Human TRPV4 Channel

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

Inada, Hitoshi; Procko, Erik; Sotomayor, Marcos

2012-10-23

The TRPV4 calcium-permeable cation channel plays important physiological roles in osmosensation, mechanosensation, cell barrier formation, and bone homeostasis. Recent studies reported that mutations in TRPV4, including some in its ankyrin repeat domain (ARD), are associated with human inherited diseases, including neuropathies and skeletal dysplasias, probably because of the increased constitutive activity of the channel. TRPV4 activity is regulated by the binding of calmodulin and small molecules such as ATP to the ARD at its cytoplasmic N-terminus. We determined structures of ATP-free and -bound forms of human TRPV4-ARD and compared them with available TRPV-ARD structures. The third inter-repeat loop region (Fingermore » 3 loop) is flexible and may act as a switch to regulate channel activity. Comparisons of TRPV-ARD structures also suggest an evolutionary link between ARD structure and ATP binding ability. Thermal stability analyses and molecular dynamics simulations suggest that ATP increases stability in TRPV-ARDs that can bind ATP. Biochemical analyses of a large panel of TRPV4-ARD mutations associated with human inherited diseases showed that some impaired thermal stability while others weakened ATP binding ability, suggesting molecular mechanisms for the diseases.« less

Mega-pockmarks surrounding IODP Site U1414: Insights from the CRISP 3D seismic survey

NASA Astrophysics Data System (ADS)

Nale, S. M.; Kluesner, J. W.; Silver, E. A.; Bangs, N. L.; McIntosh, K. D.; Ranero, C. R.

2013-12-01

Visualization of neural network meta-attribute analyses reveals fluid migration pathways associated with mega-pockmarks within the CRISP 3D seismic volume offshore southern Costa Rica, near site U1414 of IODP Expedition 344. A 245km2 field of mega-pockmarks was imaged on the Cocos Ridge using EM122 multibeam bathymetry, backscatter and 3D seismic reflection aboard R/V Marcus G. Langseth during the 2011 CRISP seismic survey. We utilize the OpendTect software package to calculate supervised neural network meta-attributes within the 3D seismic volume, in order to detect and visualize probable faults and fluid-migration pathways within the sedimentary section of the incoming Cocos plate [see Kluesner et al., this meeting]. Pockmarks imaged within the 3D volume near the trench commonly show a two-tier structure with upper pockmarks located above the steep walls of deeper, older pockmarks. The latter appear to truncate surrounding strata, including widespread high-amplitude reverse polarity reflectors (RPRs), interpreted as trapping horizons. In addition, RPRs are also truncated by positive polarity crosscutting reflections (CCRs), most of which form the base and sides of lens-like structures below the RPRs that are frequently located next to imaged pockmarks. Site U1414 intersects one of these lens-like structures and this appears to correlate to a sharp density and porosity swing observed at ~255 mbsf. In addition, preliminary geochemical analyses from site U1414 show evidence of lateral fluid flow through sediments below the RPR [Expedition 344 Scientists, 2013]. Thus, we interpret the 3D lens-like structures to be pockets of trapped gas and/or over-pressured fluid. Based on 3D imaging we propose a 3-stage pockmark evolution: (1) Overpressure and blowout along RPRs, resulting in pockmark formation, (2) sustained seepage along pockmark walls, resulting in preferential deposition near the center of the pockmark, and (3) rapid burial as pockmarks near the trench axis. On the seafloor, small high-backscatter mounds are found near the walls of a subset of pockmarks, suggesting recent or active seafloor seepage. Further geochemical analyses are needed to determine the source of fluid/gas migration associated with the pockmark structures.

Stationarity is undead: Uncertainty dominates the distribution of extremes

NASA Astrophysics Data System (ADS)

Serinaldi, Francesco; Kilsby, Chris G.

2015-03-01

The increasing effort to develop and apply nonstationary models in hydrologic frequency analyses under changing environmental conditions can be frustrated when the additional uncertainty related to the model complexity is accounted for along with the sampling uncertainty. In order to show the practical implications and possible problems of using nonstationary models and provide critical guidelines, in this study we review the main tools developed in this field (such as nonstationary distribution functions, return periods, and risk of failure) highlighting advantages and disadvantages. The discussion is supported by three case studies that revise three illustrative examples reported in the scientific and technical literature referring to the Little Sugar Creek (at Charlotte, North Carolina), Red River of the North (North Dakota/Minnesota), and the Assunpink Creek (at Trenton, New Jersey). The uncertainty of the results is assessed by complementing point estimates with confidence intervals (CIs) and emphasizing critical aspects such as the subjectivity affecting the choice of the models' structure. Our results show that (1) nonstationary frequency analyses should not only be based on at-site time series but require additional information and detailed exploratory data analyses (EDA); (2) as nonstationary models imply that the time-varying model structure holds true for the entire future design life period, an appropriate modeling strategy requires that EDA identifies a well-defined deterministic mechanism leading the examined process; (3) when the model structure cannot be inferred in a deductive manner and nonstationary models are fitted by inductive inference, model structure introduces an additional source of uncertainty so that the resulting nonstationary models can provide no practical enhancement of the credibility and accuracy of the predicted extreme quantiles, whereas possible model misspecification can easily lead to physically inconsistent results; (4) when the model structure is uncertain, stationary models and a suitable assessment of the uncertainty accounting for possible temporal persistence should be retained as more theoretically coherent and reliable options for practical applications in real-world design and management problems; (5) a clear understanding of the actual probabilistic meaning of stationary and nonstationary return periods and risk of failure is required for a correct risk assessment and communication.

Psychometric evaluation of the Forensic Inpatient Observation Scale (FIOS) in youngsters with a judicial measure

PubMed Central

2011-01-01

Background In this article, the psychometric properties of the Forensic Inpatient Observation Scale (FIOS) were examined. This instrument was developed to observe behavioral functioning of forensic psychiatric patients. Up till now, it has only been used among adult forensic psychiatric patients and this is the first study in which the FIOS is used with youngsters. Methods Data were gathered of 133 patients. The FIOS was routinely used to assess the psychiatric condition of youngsters at fixed intervals with a three-month time period between each measurement. Ward staff working in close contact with the patient conducted the assessments. Of these 133 patients, an YSR/ASR questionnaire was available for 96 of them and a TRF for 110 of the 133 patients. For the descriptive, reliability and validity analyses, SPSS version 16.0 was used. Factor analyses were performed by means of Mplus Version 5.2. Results A series of confirmatory and exploratory factor analyses revealed a five-factor structure for the FIOS. The five-factor structure consisted of the following scales: self-care, social behavior, oppositional behavior, verbal skills and distress. The insight scale of the original factor structure could not be replicated in the youth sample. Cronbach's alpha's of the five scales ranged from .70 to .85. The self-care, verbal skills and oppositional behavior scales of the FIOS showed no relation with emotional and behavior problems reported by the patients themselves or their teachers. The distress scale of the FIOS did show a relation with the emotional problems reported by patients themselves and the social behavior scale with behavioral problems as reported by teachers. Conclusions The internal consistency of the FIOS was sufficient and the factor structure in the present sample of youngsters was in general comparable to the original factor structure in an adult sample. Its value lies in the focus on behavioral functioning of youngsters with judicial measures. What remains to be seen is whether this instrument is sensitive enough to register all aspects of behavioral changes, whether the interrater reliability is sufficient, and whether it has predictive validity to relapse and recidivism. PMID:21951650

Detection of stable community structures within gut microbiota co-occurrence networks from different human populations.

PubMed

Jackson, Matthew A; Bonder, Marc Jan; Kuncheva, Zhana; Zierer, Jonas; Fu, Jingyuan; Kurilshikov, Alexander; Wijmenga, Cisca; Zhernakova, Alexandra; Bell, Jordana T; Spector, Tim D; Steves, Claire J

2018-01-01

Microbes in the gut microbiome form sub-communities based on shared niche specialisations and specific interactions between individual taxa. The inter-microbial relationships that define these communities can be inferred from the co-occurrence of taxa across multiple samples. Here, we present an approach to identify comparable communities within different gut microbiota co-occurrence networks, and demonstrate its use by comparing the gut microbiota community structures of three geographically diverse populations. We combine gut microbiota profiles from 2,764 British, 1,023 Dutch, and 639 Israeli individuals, derive co-occurrence networks between their operational taxonomic units, and detect comparable communities within them. Comparing populations we find that community structure is significantly more similar between datasets than expected by chance. Mapping communities across the datasets, we also show that communities can have similar associations to host phenotypes in different populations. This study shows that the community structure within the gut microbiota is stable across populations, and describes a novel approach that facilitates comparative community-centric microbiome analyses.

Structural and catalytic roles of amino acid residues located at substrate-binding pocket in Fibrobacter succinogenes 1,3-1,4-beta-D-glucanase.

PubMed

Chen, Je-Hsin; Tsai, Li-Chu; Huang, Hsiao-Chuan; Shyur, Lie-Fen

2010-10-01

We created 12 mutant enzymes (E11L, F40I, Y42L, N44L, N44Q, E47I, L62G, K64A, K64M, R137M, R137Q, and N139A) from the truncated Fibrobacter succinogenes 1,3-1,4-beta-D-glucanase (TF-glucanase). The enzymes were used to investigate the structural and catalytic roles of specific amino acid residues located at the catalytic pocket and having direct interactions with glucose subsites of the product beta-1,3-1,4-cellotriose (CLTR). Fluorescence spectrometry showed no discernible changes in secondary structures among purified TF-glucanase and the mutants. Kinetic analyses showed E11L, F40I, Y42L, R137M, and R137Q with a >10-fold decrease of specific activity (11.2- to 67.4-fold), and E11L, N44Q, E47I, K64M, R137M, R137Q, and N139A with a 2.17- to 4.3-fold increase of K(m) value when compared with TF-glucanase. Notably, E11L, R137Q, R137M, F40I, and N139A showed the most significant decrease in catalytic efficiency relative to TF-glucanase, by 2155-, 84.9-, 48.5-, 41.1-, and 19.1-fold, respectively; the five mutants showed the greatest changes in comparative energy DeltaDeltaG(b), with values of 1.94 to 4.92 kcal/mol. Combined with results from kinetic and structure modeling analyses of all mutant enzymes and X-ray crystallography of F40I, we elucidate that Glu11, Phe40, Arg137, and Asn139 play a crucial role in the catalysis of TF-glucanase owing to their local and direct interaction through hydrogen bonds or van der Waals stacking interaction by aromatic rings onto the glucose subsites -3, -2, and -1 of CLTR/substrate. The overall globular structures in the wild-type and mutant F40I enzymes do not differ. 2010 Wiley-Liss, Inc.

Revealing the hidden language of complex networks.

PubMed

Yaveroğlu, Ömer Nebil; Malod-Dognin, Noël; Davis, Darren; Levnajic, Zoran; Janjic, Vuk; Karapandza, Rasa; Stojmirovic, Aleksandar; Pržulj, Nataša

2014-04-01

Sophisticated methods for analysing complex networks promise to be of great benefit to almost all scientific disciplines, yet they elude us. In this work, we make fundamental methodological advances to rectify this. We discover that the interaction between a small number of roles, played by nodes in a network, can characterize a network's structure and also provide a clear real-world interpretation. Given this insight, we develop a framework for analysing and comparing networks, which outperforms all existing ones. We demonstrate its strength by uncovering novel relationships between seemingly unrelated networks, such as Facebook, metabolic, and protein structure networks. We also use it to track the dynamics of the world trade network, showing that a country's role of a broker between non-trading countries indicates economic prosperity, whereas peripheral roles are associated with poverty. This result, though intuitive, has escaped all existing frameworks. Finally, our approach translates network topology into everyday language, bringing network analysis closer to domain scientists.

Measuring subjective resilience despite adversity due to family, peers and teachers.

PubMed

Alonso-Tapia, Jesús; Nieto, Carmen; Ruíz, Miguel A

2013-01-01

The objective of this study is to develop and validate a scale of subjective resilience for students 12-17 years old. Items covered adverse situations due to parents', peers' and teachers' actions. The validation process included the analysis on the generalizability of the factor structure and of relationships of resilience scores with different kinds of protective and vulnerability factors -goal orientations and learning-oriented classroom motivational climate (CMC)-. A total of 471 students answered four questionnaires. Confirmatory factor analyses, reliability analysis and correlation and regression analyses were carried out. Results showed: (a) that factor structure was well defined; (b) that resilience scale had good reliability; (c) that scores correlated as expected with protective-vulnerability factors such as goal orientations and CMC defined by teachers' teaching-patterns, and (d) that students' attribution of perceived change in resilience to teachers' work depended on the degree in which CMC was learning oriented. Theoretical and practical implications are discussed.

Development of methodology for identification the nature of the polyphenolic extracts by FTIR associated with multivariate analysis.

PubMed

Grasel, Fábio dos Santos; Ferrão, Marco Flôres; Wolf, Carlos Rodolfo

2016-01-15

Tannins are polyphenolic compounds of complex structures formed by secondary metabolism in several plants. These polyphenolic compounds have different applications, such as drugs, anti-corrosion agents, flocculants, and tanning agents. This study analyses six different type of polyphenolic extracts by Fourier transform infrared spectroscopy (FTIR) combined with multivariate analysis. Through both principal component analysis (PCA) and hierarchical cluster analysis (HCA), we observed well-defined separation between condensed (quebracho and black wattle) and hydrolysable (valonea, chestnut, myrobalan, and tara) tannins. For hydrolysable tannins, it was also possible to observe the formation of two different subgroups between samples of chestnut and valonea and between samples of tara and myrobalan. Among all samples analysed, the chestnut and valonea showed the greatest similarity, indicating that these extracts contain equivalent chemical compositions and structure and, therefore, similar properties. Copyright © 2015 Elsevier B.V. All rights reserved.

Aromatic compounds produced by Periconia atropurpurea, an endophytic fungus associated with Xylopia aromatica.

PubMed

Teles, Helder Lopes; Sordi, Renata; Silva, Geraldo Humberto; Castro-Gamboa, Ian; Bolzani, Vanderlan da Silva; Pfenning, Ludwig Heinrich; de Abreu, Lucas Magalhães; Costa-Neto, Claudio Miguel; Young, Maria Claudia Marx; Araújo, Angela Regina

2006-12-01

6,8-Dimethoxy-3-(2'-oxo-propyl)-coumarin (1) and 2,4-dihydroxy-6-[(1'E,3'E)-penta-1',3'-dienyl]-benzaldehyde (2), in addition to the known compound periconicin B (3), were isolated from the ethyl acetate extract of Periconia atropurpurea, an endophytic fungus obtained from the leaves of Xylopia aromatica, a native plant of the Brazilian Cerrado. Their chemical structures were assigned based on analyses of MS, 1D and 2D-NMR spectroscopic experiments. Biological analyses were performed using two mammalian cell lines, human cervix carcinoma (HeLa) and Chinese hamster ovary (CHO). The results showed that compound 1 had no effect when compared to the control group, which was treated with the vehicle (DMSO). Compound 2 was able to induce a slight increase in cell proliferation of HeLa (37% of increase) and CHO (38% of increase) cell lines. Analysis of compound 3 showed that it has potent cytotoxic activity against both cell lines, with an IC50 of 8.0 microM. Biological analyses using the phytopathogenic fungi Cladosporium sphaerospermum and C. cladosporioides revealed that also 2 showed potent antifungal activity compared to nystatin.

Structural Changes Associated with Transthyretin Misfolding and Amyloid Formation Revealed by Solution and Solid-State NMR

DOE PAGES

Lim, Kwang Hun; Dasari, Anvesh K. R.; Hung, Ivan; ...

2016-03-21

Elucidation of structural changes involved in protein misfolding and amyloid formation is crucial for unraveling the molecular basis of amyloid formation. We report structural analyses of the amyloidogenic intermediate and amyloid aggregates of transthyretin using solution and solid-state nuclear magnetic resonance (NMR) spectroscopy. These NMR solution results show that one of the two main β-sheet structures (CBEF β-sheet) is maintained in the aggregation-competent intermediate, while the other DAGH β-sheet is more flexible on millisecond time scales. Magic-angle-spinning solid-state NMR revealed that AB loop regions interacting with strand A in the DAGH β-sheet undergo conformational changes, leading to the destabilized DAGHmore » β-sheet.« less

Syntheses, structures and photoluminescence properties of three M(II)-coordination polymers (M dbnd Zn(II), Mn(II)) based on a pyridine N-oxide bridging ligand

NASA Astrophysics Data System (ADS)

Ren, Xiu-Hui; Wang, Peng; Cheng, Jun-Yan; Dong, Yu-Bin

2018-06-01

Three M(II)-coordination polymers (M dbnd Zn(II), Mn(II)) were synthesized based on a pyridine N-oxide bridging ligand 3,5-bis(4-carboxylphenyl)-pyridine N-oxide (L1). Compounds 1-3 all have novel complicated structures. Compound 1 (Zn(L1)2(H2O)2) and 2 (Zn2(L1)2(H2O)2) are two single crystals obtained in "one pot" and 1 features 1D double chains motif and 2 features 3D network structure. Compound 3 shows 3D network structure with triangular tunnels. The thermogravimetric analyses and photoluminescence properties were also used to investigate the title compounds.

Micromechanical analysis on anisotropy of structured magneto-rheological elastomer

NASA Astrophysics Data System (ADS)

Li, R.; Zhang, Z.; Chen, S. W.; Wang, X. J.

2015-07-01

This paper investigates the equivalent elastic modulus of structured magneto-rheological elastomer (MRE) in the absence of magnetic field. We assume that both matrix and ferromagnetic particles are linear elastic materials, and ferromagnetic particles are embedded in matrix with layer-like structure. The structured composite could be divided into matrix layer and reinforced layer, in which the reinforced layer is composed of matrix and the homogenously distributed ferromagnetic particles in matrix. The equivalent elastic modulus of reinforced layer is analysed by the Mori-Tanaka method. Finite Element Method (FEM) is also carried out to illustrate the relationship between the elastic modulus and the volume fraction of ferromagnetic particles. The results show that the anisotropy of elastic modulus becomes noticeable, as the volume fraction of particles increases.

Global Distribution of Polaromonas Phylotypes - Evidence for a Highly Successful Dispersal Capacity

PubMed Central

Darcy, John L.; Lynch, Ryan C.; King, Andrew J.; Robeson, Michael S.; Schmidt, Steven K.

2011-01-01

Bacteria from the genus Polaromonas are dominant phylotypes in clone libraries and culture collections from polar and high-elevation environments. Although Polaromonas has been found on six continents, we do not know if the same phylotypes exist in all locations or if they exhibit genetic isolation by distance patterns. To examine their biogeographic distribution, we analyzed all available, long-read 16S rRNA gene sequences of Polaromonas phylotypes from glacial and periglacial environments across the globe. Using genetic isolation by geographic distance analyses, including Mantel tests and Mantel correlograms, we found that Polaromonas phylotypes are globally distributed showing weak isolation by distance patterns at global scales. More focused analyses using discrete, equally sampled distances classes, revealed that only two distance classes (out of 12 total) showed significant spatial structuring. Overall, our analyses show that most Polaromonas phylotypes are truly globally distributed, but that some, as yet unknown, environmental variable may be selecting for unique phylotypes at a minority of our global sites. Analyses of aerobiological and genomic data suggest that Polaromonas phylotypes are globally distributed as dormant cells through high-elevation air currents; Polaromonas phylotypes are common in air and snow samples from high altitudes, and a glacial-ice metagenome and the two sequenced Polaromonas genomes contain the gene hipA, suggesting that Polaromonas can form dormant cells. PMID:21897856

Application of Sub-Bottom Profiler to Study Riverbed Structure and Sediment Density

NASA Astrophysics Data System (ADS)

Rui, Wang; Changzheng, Li; Xiaofei, Yan

2018-03-01

In this pater, we present a study on the riverbed structure and sediment density in-situ test by using sub-bottom profiler. Compared with traditional direct observation methods, the sub-bottom profiler method based on sonar technology is non-contact, low-disturbance and high-efficient. We finish the investigation of several sections in Sanmenxia and Xiaolangdi reservoirs, which located on the main channel of lower reaches of Yellow River. Collected data show a detailed layered structure of the riverbed sediment which believed caused by sedimentary processes in different periods. Further more, we analyse the reflection coefficient of water-sediment interface and inverse the sediment density data from the raw wave record. The inversion method is based on the effective density fluid model and Kozeny-Carman formula. The comparison of the inversion results and sample tests shows that the in-situ test is reliable and useable.

Deconstructing Temperature Gradients across Fluid Interfaces: The Structural Origin of the Thermal Resistance of Liquid-Vapor Interfaces

NASA Astrophysics Data System (ADS)

Muscatello, Jordan; Chacón, Enrique; Tarazona, Pedro; Bresme, Fernando

2017-07-01

The interfacial thermal resistance determines condensation-evaporation processes and thermal transport across material-fluid interfaces. Despite its importance in transport processes, the interfacial structure responsible for the thermal resistance is still unknown. By combining nonequilibrium molecular dynamics simulations and interfacial analyses that remove the interfacial thermal fluctuations we show that the thermal resistance of liquid-vapor interfaces is connected to a low density fluid layer that is adsorbed at the liquid surface. This thermal resistance layer (TRL) defines the boundary where the thermal transport mechanism changes from that of gases (ballistic) to that characteristic of dense liquids, dominated by frequent particle collisions involving very short mean free paths. We show that the thermal conductance is proportional to the number of atoms adsorbed in the TRL, and hence we explain the structural origin of the thermal resistance in liquid-vapor interfaces.

Safety Evaluation of Enterocin Producer Enterococcus sp. Strains Isolated from Traditional Turkish Cheeses.

PubMed

Avcı, Mine; Özden Tuncer, Banu

2017-07-06

The purpose of this study was to determine the antimicrobial activity and occurrence of bacteriocin structural genes in Enterococcus spp. isolated from different cheeses and also investigate some of their virulence factors. Enterococcus strains were isolated from 33 different cheeses. Enterococcus faecium (6 strains) and Enterococcus faecalis (5 strains) enterocin-producing strains were identified by 16S rDNA analyses. Structural genes entA, entB, entP and entX were detected in some isolates. Multiple enterocin structural genes were found in 7 strains. None of the tested enterococci demonstrated anyβ-haemolytic activity and only one strain had gelatinase activity. Six strains showed multiple antibiotic resistance patterns and in addition, vanA and several virulence genes were detected in many strains. Only E. faecalis MBE1-9 showed tyrosine decarboxylase activity and tdc gene was detected only in this strain.

Structure and permeation mechanism of a mammalian urea transporter

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

Levin, Elena J.; Cao, Yu; Enkavi, Giray

2012-09-17

As an adaptation to infrequent access to water, terrestrial mammals produce urine that is hyperosmotic to plasma. To prevent osmotic diuresis by the large quantity of urea generated by protein catabolism, the kidney epithelia contain facilitative urea transporters (UTs) that allow rapid equilibration between the urinary space and the hyperosmotic interstitium. Here we report the first X-ray crystal structure of a mammalian UT, UT-B, at a resolution of 2.36 {angstrom}. UT-B is a homotrimer and each protomer contains a urea conduction pore with a narrow selectivity filter. Structural analyses and molecular dynamics simulations showed that the selectivity filter has twomore » urea binding sites separated by an approximately 5.0 kcal/mol energy barrier. Functional studies showed that the rate of urea conduction in UT-B is increased by hypoosmotic stress, and that the site of osmoregulation coincides with the location of the energy barrier.« less

Solar Coronal Loop Dynamics Near the Null Point Above Active Region NOAA 2666

NASA Astrophysics Data System (ADS)

Filippov, B.

2018-06-01

We analyse observations of a saddle-like structure in the corona above the western limb of the Sun on 2017 July 18. The structure was clearly outlined by coronal loops with typical coronal temperature no more than 1 MK. The dynamics of loops showed convergence towards the centre of the saddle in the vertical direction and divergence in the horizontal direction. The event is a clear example of smooth coronal magnetic field reconnection. No heating manifestations in the reconnection region or magnetically connected areas were observed. Potential magnetic field calculations, which use as the boundary condition the SDO/HMI magnetogram taken on July 14, showed the presence of a null point at the height of 122 arcsec above the photosphere just at the centre of the saddle structure. The shape of field lines fits the fan-spine magnetic configuration above NOAA 2666.

Opening Furan for Tailoring Properties of Bio-based Poly(Furfuryl Alcohol) Thermoset.

PubMed

Falco, Guillaume; Guigo, Nathanael; Vincent, Luc; Sbirrazzuoli, Nicolas

2018-06-11

This work shows how furan ring-opening reactions were controlled by polymerization conditions to tune the cross-link density in bio-based poly(furfuryl alcohol) (PFA). The influence of water and isopropyl alcohol (IPA) on the polymerization of furfuryl alcohol, and particularly on furan ring-opening, was investigated by means of 13 C NMR and FT-IR spectroscopy. Results indicated that formation of open structures were favored in the presence of solvents, thus leading to modification of the thermo-mechanical properties compared to PFA cross-linked without solvent. Dynamic mechanical analyses showed that when slightly more open structures were present in PFA it resulted in an important decrease of the cross-link density. Despite lower glass-transition temperature and lower elastic modulus for PFA polymerized with solvent, the thermal stability remains very high (>350 °C) even with more open structures in PFA. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structure and permeation mechanism of a mammalian urea transporter

PubMed Central

Levin, Elena J.; Cao, Yu; Enkavi, Giray; Quick, Matthias; Pan, Yaping; Tajkhorshid, Emad; Zhou, Ming

2012-01-01

As an adaptation to infrequent access to water, terrestrial mammals produce urine that is hyperosmotic to plasma. To prevent osmotic diuresis by the large quantity of urea generated by protein catabolism, the kidney epithelia contain facilitative urea transporters (UTs) that allow rapid equilibration between the urinary space and the hyperosmotic interstitium. Here we report the first X-ray crystal structure of a mammalian UT, UT-B, at a resolution of 2.36 Å. UT-B is a homotrimer and each protomer contains a urea conduction pore with a narrow selectivity filter. Structural analyses and molecular dynamics simulations showed that the selectivity filter has two urea binding sites separated by an approximately 5.0 kcal/mol energy barrier. Functional studies showed that the rate of urea conduction in UT-B is increased by hypoosmotic stress, and that the site of osmoregulation coincides with the location of the energy barrier. PMID:22733730

In silico identification and analysis of phytoene synthase genes in plants.

PubMed

Han, Y; Zheng, Q S; Wei, Y P; Chen, J; Liu, R; Wan, H J

2015-08-14

In this study, we examined phytoene synthetase (PSY), the first key limiting enzyme in the synthesis of carotenoids and catalyzing the formation of geranylgeranyl pyrophosphate in terpenoid biosynthesis. We used known amino acid sequences of the PSY gene in tomato plants to conduct a genome-wide search and identify putative candidates in 34 sequenced plants. A total of 101 homologous genes were identified. Phylogenetic analysis revealed that PSY evolved independently in algae as well as monocotyledonous and dicotyledonous plants. Our results showed that the amino acid structures exhibited 5 motifs (motifs 1 to 5) in algae and those in higher plants were highly conserved. The PSY gene structures showed that the number of intron in algae varied widely, while the number of introns in higher plants was 4 to 5. Identification of PSY genes in plants and the analysis of the gene structure may provide a theoretical basis for studying evolutionary relationships in future analyses.

Physical-chemical characterization and biological assessment of simple and lithium-doped biological-derived hydroxyapatite thin films for a new generation of metallic implants

NASA Astrophysics Data System (ADS)

Popescu, A. C.; Florian, P. E.; Stan, G. E.; Popescu-Pelin, G.; Zgura, I.; Enculescu, M.; Oktar, F. N.; Trusca, R.; Sima, L. E.; Roseanu, A.; Duta, L.

2018-05-01

We report on the synthesis by PLD of simple and lithium-doped biological-origin hydroxyapatite (HA) films. The role of doping reagents (Li2CO3, Li3PO4) on the morphology, structure, chemical composition, bonding strength and cytocompatibility of the films was investigated. SEM investigations of the films evidenced a surface morphology consisting of particles with mean diameters of (5-7) μm. GIXRD analyses demonstrated that the synthesized structures consisted of HA phase only, with different degrees of crystallinity, mainly influenced by the doping reagent type. After only three days of immersion in simulated body fluid, FTIR spectra showed a remarkable growth of a biomimetic apatitic film, indicative of a high biomineralization capacity of the coatings. EDS analyses revealed a quasi-stoichiometric target-to-substrate transfer, the values inferred for the Ca/P ratio corresponding to a biological apatite. All synthesized structures displayed a hydrophilic behavior, suitable for attachment of osteoblast cells. In vitro cell viability tests showed that the presence of Li2CO3 and Li3PO4 as doping reagents promoted the hMSC growth on film surfaces. Taking into consideration these enhanced characteristics, corroborated with a low fabrication cost generated by sustainable resources, one should consider the lithium-doped biological-derived materials as promising prospective solutions for a next generation of coated implants with rapid osteointegration.

Structure and phylogeography of two tropical predators, spinner (Stenella longirostris) and pantropical spotted (S. attenuata) dolphins, from SNP data

PubMed Central

Morin, Phillip A.

2018-01-01

Little is known about global patterns of genetic connectivity in pelagic dolphins, including how circumtropical pelagic dolphins spread globally following the rapid and recent radiation of the subfamily delphininae. In this study, we tested phylogeographic hypotheses for two circumtropical species, the spinner dolphin (Stenella longirostris) and the pantropical spotted dolphin (Stenella attenuata), using more than 3000 nuclear DNA single nucleotide polymorphisms (SNPs) in each species. Analyses for population structure indicated significant genetic differentiation between almost all subspecies and populations in both species. Bayesian phylogeographic analyses of spinner dolphins showed deep divergence between Indo-Pacific, Atlantic and eastern tropical Pacific Ocean (ETP) lineages. Despite high morphological variation, our results show very close relationships between endemic ETP spinner subspecies in relation to global diversity. The dwarf spinner dolphin is a monophyletic subspecies nested within a major clade of pantropical spinner dolphins from the Indian and western Pacific Ocean populations. Population-level division among the dwarf spinner dolphins was detected—with the northern Australia population being very different from that in Indonesia. In contrast to spinner dolphins, the major boundary for spotted dolphins is between offshore and coastal habitats in the ETP, supporting the current subspecies-level taxonomy. Comparing these species underscores the different scale at which population structure can arise, even in species that are similar in habitat (i.e. pelagic) and distribution. PMID:29765639

Roles of silica and lignin in horsetail (Equisetum hyemale), with special reference to mechanical properties

NASA Astrophysics Data System (ADS)

Yamanaka, Shigeru; Sato, Kanna; Ito, Fuyu; Komatsubara, Satoshi; Ohata, Hiroshi; Yoshino, Katsumi

2012-02-01

This research deals with detailed analyses of silica and lignin distribution in horsetail with special reference to mechanical strength. Scanning electron images of a cross-section of an internode showed silica deposited densely only around the outer epidermis. Detailed histochemical analyses of lignin showed no lignin deposition in the silica-rich outer internodes of horsetail, while a characteristic lignin deposition was noticed in the vascular bundle in inner side of internodes. To analyze the structure of horsetail from a mechanical viewpoint, we calculated the response of a model structure of horsetail to a mechanical force applied perpendicularly to the long axis by a finite element method. We found that silica distributed in the outer epidermis may play the major structural role, with lignin's role being limited ensuring that the vascular bundle keep waterproof. These results were in contrast to more modern tall trees like gymnosperms, for which lignin provides mechanical strength. Lignin has the advantage of sticking to cellulose, hemicellulose, and other materials. Such properties make it possible for plants containing lignin to branch. Branching of tree stems aids in competing for light and other atmospheric resources. This type of branching was impossible for ancient horsetails, which relied on the physical properties of silica. From the evolutional view points, over millennia in trees with high lignin content, true branching, and many chlorophyll-containing leaves developed.

Coherent emission from integrated Talbot-cavity quantum cascade lasers.

PubMed

Meng, Bo; Qiang, Bo; Rodriguez, Etienne; Hu, Xiao Nan; Liang, Guozhen; Wang, Qi Jie

2017-02-20

We report experimental realization of phase-locked quantum cascade laser (QCL) array using a monolithically integrated Talbot cavity. An array with six laser elements at a wavelength of ~4.8 μm shows a maximum peak power of ~4 W which is more than 5 times higher than that of a single ridge laser element and a slope efficiency of 1 W/A at room temperature. Operation of in-phase coherent supermode has been achieved over the whole dynamic range of the Talbot-cavity QCL. The structure was analysed using a straightforward theoretical model, showing quantitatively good agreement with the experimental results. The reduced thermal resistance makes the structure an attractive approach to achieve high beam quality continuous wave QCLs.

Population genetics of the westernmost distribution of the glaciations-surviving black truffle Tuber melanosporum.

PubMed

García-Cunchillos, Iván; Sánchez, Sergio; Barriuso, Juan José; Pérez-Collazos, Ernesto

2014-04-01

The black truffle (Tuber melanosporum Vittad.) is an important natural resource due to its relevance as a delicacy in gastronomy. Different aspects of this hypogeous fungus species have been studied, including population genetics of French and Italian distribution ranges. Although those studies include some Spanish populations, this is the first time that the genetic diversity and genetic structure of the wide geographical range of the natural Spanish populations have been analysed. To achieve this goal, 23 natural populations were sampled across the Spanish geographical distribution. ISSR technique demonstrated its reliability and capability to detect high levels of polymorphism in the species. Studied populations showed high levels of genetic diversity (h N  = 0.393, h S  = 0.678, Hs = 0.418), indicating a non threatened genetic conservation status. These high levels may be a consequence of the wide distribution range of the species, of its spore dispersion by animals, and by its evolutionary history. AMOVA analysis showed a high degree of genetic structure among populations (47.89%) and other partitions as geographical ranges. Bayesian genetic structure analyses differentiated two main Spanish groups separated by the Iberian Mountain System, and showed the genetic uniqueness of some populations. Our results suggest the survival of some of these populations during the last glaciation, the Spanish southern distribution range perhaps surviving as had occurred in France and Italy, but it is also likely that specific northern areas may have acted as a refugia for the later dispersion to other calcareous areas in the Iberian Peninsula and probably France.

Geographical structuring of Trypanosoma cruzi populations from Chilean Triatoma infestans triatomines and their genetic relationship with other Latino American counterparts

PubMed Central

Venegas, J; Rojas, T; DÍaz, F; Miranda, S; Jercic, M I; González, C; Coñoepán, W; Pichuantes, S; RodrÍguez, J; Gajardo, M; Sánchez, G

2011-01-01

In order to obtain more information about the population structure of Chilean Trypanosoma cruzi, and their genetic relationship with other Latino American counterparts, we performed the study of T. cruzi samples detected in the midgut content of Triatoma infestans insects from three endemic regions of Chile. The genetic characteristics of these samples were analysed using microsatellite markers and PCR conditions that allow the detection of predominant T. cruzi clones directly in triatomine midgut content. Population genetic analyses using the Fisher’s exact method, analysis of molecular variance (AMOVA) and the determination of FST showed that the northern T. cruzi population sample was genetically differentiated from the two southern population counterparts. Further analysis showed that the cause of this genetic differentiation was the asymmetrical distribution of TcIII T. cruzi predominant clones. Considering all triatomines from the three regions, the most frequent predominant lineages were TcIII (38%), followed by TcI (34%) and hybrid (8%). No TcII lineage was observed along the predominant T. cruzi clones. The best phylogenetic reconstruction using the shared allelic genetic distance was concordant with the population genetic analysis and tree topology previously described studying foreign samples. The correlation studies showed that the lineage TcIII from the III region was genetically differentiated from the other two, and this differentiation was correlated with geographical distance including Chilean and mainly Brazilian samples. It will be interesting to investigate whether this geographical structure may be related with different clinical manifestation of Chagas disease. PMID:22325822

Child Behavior Checklist—Mania Scale (CBCL-MS): Development and Evaluation of a Population-Based Screening Scale for Bipolar Disorder

PubMed Central

Papachristou, Efstathios; Ormel, Johan; Oldehinkel, Albertine J.; Kyriakopoulos, Marinos; Reinares, María; Reichenberg, Abraham; Frangou, Sophia

2013-01-01

Context Early identification of Bipolar Disorder (BD) remains poor despite the high levels of disability associated with the disorder. Objective We developed and evaluated a new DSM orientated scale for the identification of young people at risk for BD based on the Child Behavior Checklist (CBCL) and compared its performance against the CBCL-Pediatric Bipolar Disorder (CBCL-PBD) and the CBCL-Externalizing Scale, the two most widely used scales. Methods The new scale, CBCL-Mania Scale (CBCL-MS), comprises 19 CBCL items that directly correspond to operational criteria for mania. We tested the reliability, longitudinal stability and diagnostic accuracy of the CBCL-MS on data from the TRacking Adolescents' Individual Lives Survey (TRAILS), a prospective epidemiological cohort study of 2230 Dutch youths assessed with the CBCL at ages 11, 13 and 16. At age 19 lifetime psychiatric diagnoses were ascertained with the Composite International Diagnostic Interview. We compared the predictive ability of the CBCL-MS against the CBCL-Externalising Scale and the CBCL-PBD in the TRAILS sample. Results The CBCL-MS had high internal consistency and satisfactory accuracy (area under the curve = 0.64) in this general population sample. Principal Component Analyses, followed by parallel analyses and confirmatory factor analyses, identified four factors corresponding to distractibility/disinhibition, psychosis, increased libido and disrupted sleep. This factor structure remained stable across all assessment ages. Logistic regression analyses showed that the CBCL-MS had significantly higher predictive ability than both the other scales. Conclusions Our data demonstrate that the CBCL-MS is a promising screening instrument for BD. The factor structure of the CBCL-MS showed remarkable temporal stability between late childhood and early adulthood suggesting that it maps on to meaningful developmental dimensions of liability to BD. PMID:23967059

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

Segmentation of 3d Models for Cultural Heritage Structural Analysis - Some Critical Issues

NASA Astrophysics Data System (ADS)

Gonizzi Barsanti, S.; Guidi, G.; De Luca, L.

2017-08-01

Cultural Heritage documentation and preservation has become a fundamental concern in this historical period. 3D modelling offers a perfect aid to record ancient buildings and artefacts and can be used as a valid starting point for restoration, conservation and structural analysis, which can be performed by using Finite Element Methods (FEA). The models derived from reality-based techniques, made up of the exterior surfaces of the objects captured at high resolution, are - for this reason - made of millions of polygons. Such meshes are not directly usable in structural analysis packages and need to be properly pre-processed in order to be transformed in volumetric meshes suitable for FEA. In addition, dealing with ancient objects, a proper segmentation of 3D volumetric models is needed to analyse the behaviour of the structure with the most suitable level of detail for the different sections of the structure under analysis. Segmentation of 3D models is still an open issue, especially when dealing with ancient, complicated and geometrically complex objects that imply the presence of anomalies and gaps, due to environmental agents such as earthquakes, pollution, wind and rain, or human factors. The aims of this paper is to critically analyse some of the different methodologies and algorithms available to segment a 3D point cloud or a mesh, identifying difficulties and problems by showing examples on different structures.

Striatal and Hippocampal Atrophy in Idiopathic Parkinson's Disease Patients without Dementia: A Morphometric Analysis.

PubMed

Tanner, Jared J; McFarland, Nikolaus R; Price, Catherine C

2017-01-01

Analyses of subcortical gray structure volumes in non-demented idiopathic Parkinson's disease (PD) often, but not always, show volume loss of the putamen, caudate nucleus, nucleus accumbens, and hippocampus. There is building evidence that structure morphometry might be more sensitive to disease-related processes than volume. To assess morphometric differences of subcortical structures (putamen, caudate nucleus, thalamus, globus pallidus, nucleus accumbens, and amygdala) as well as the hippocampus in non-demented individuals with PD relative to age and education matched non-PD peers. Prospective recruitment of idiopathic no-dementia PD and non-PD peers as part of a federally funded investigation. T1-weighted isovoxel metrics acquired via 3-T Siemens Verio for all individuals [PD n  = 72 (left side onset n  = 27, right side onset n  = 45); non-PD n  = 48]. FIRST (FMRIB Software Library) applications provided volumetric and vertex analyses on group differences for structure size and morphometry. Group volume differences were observed only for putamen and hippocampi (PD < non-PD) with hippocampal volume significantly associating with disease duration. Group shape differences were observed for bilateral putamen, caudate nucleus, and hippocampus with greater striatal atrophy contralateral to side of motor symptom onset. Hippocampal shape differences disappeared when removing the effects of volume. The putamen was the primary structure to show both volume and shape differences in PD, indicating that the putamen is the predominant site of basal ganglia atrophy in early- to mid-stage PD. Side of PD symptom onset associates with contralateral striatal atrophy. Left-onset PD might experience more extensive striatal atrophy than right-onset PD. Hippocampus morphometric results suggest possible primary atrophy of CA3/4 and dentate gyrus.

Analysis/test correlation using VAWT-SDS on a step-relaxation test for the rotating Sandia 34 m test bed

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

Argueello, J.G.; Dohrmann, C.R.; Carne, T.G.

The combined analysis/test effort described in this paper compares predictions with measured data from a step-relaxation test in the absence of significant wind-driven aerodynamic loading. The process described here is intended to illustrate a method for validation of time domain codes for structural analysis of wind turbine structures. Preliminary analyses were performed to investigate the transient dynamic response that the rotating Sandia 34 m Vertical Axis Wind Turbine (VAWT) would undergo when one of the two blades was excited by step-relaxation. The calculations served two purposes. The first was for pretest planning to evaluate the relative importance of the variousmore » forces that would be acting on the structure during the test and to determine if the applied force in the step-relaxation would be sufficient to produce an excitation that was distinguishable from that produced by the aerodynamic loads. The second was to provide predictions that could subsequently be compared to the data from the test. The test was carried out specifically to help in the validation of the time-domain structural dynamics code, VAWT-SDS, which predicts the dynamic response of VAWTs subject to transient events. Post-test comparisons with the data were performed and showed a qualitative agreement between pretest predictions and measured response. However, they also showed that there was significantly more damping in the measurements than included in the predictions. Efforts to resolve this difference, including post-test analyses, were undertaken and are reported herein. The overall effort described in this paper represents a major step in the process of arriving at a validated structural dynamics code.« less

Small-scale disturbances in the stratigraphy of the NEEM ice core: observations and numerical model simulations

NASA Astrophysics Data System (ADS)

Jansen, D.; Llorens, M.-G.; Westhoff, J.; Steinbach, F.; Kipfstuhl, S.; Bons, P. D.; Griera, A.; Weikusat, I.

2016-02-01

Disturbances on the centimetre scale in the stratigraphy of the North Greenland Eemian Ice Drilling (NEEM) ice core (North Greenland) can be mapped by an optical line scanner as long as the ice has visual layering, such as, for example, cloudy bands. Different focal depths allow, to a certain extent, a three-dimensional view of the structures. In this study we present a detailed analysis of the visible folds, discuss their characteristics and frequency, and present examples of typical fold structures. We also analyse the structures with regard to the deformation boundary conditions under which they formed. The structures evolve from gentle waves at about 1500 m to overturned z folds with increasing depth. Occasionally, the folding causes significant thickening of layers. Their similar fold shape indicates that they are passive features and are probably not initiated by rheology differences between alternating layers. Layering is heavily disturbed and tracing of single layers is no longer possible below a depth of 2160 m. C axes orientation distributions for the corresponding core sections were analysed, where available, in addition to visual stratigraphy. The data show axial-plane parallel strings of grains with c axis orientations that deviate from that of the matrix, which shows a single maximum fabric at the depth where the folding occurs. Numerical modelling of crystal viscoplastic deformation and dynamic recrystallisation was used to improve the understanding of the formation of the observed structures during deformation. The modelling reproduces the development of bands of grains with a tilted-lattice orientation relative to the single maximum fabric of the matrix, and also the associated local deformation. We conclude from these results that the observed folding can be explained by formation of these tilted-lattice bands.

Validating the cross-cultural factor structure and invariance property of the Insomnia Severity Index: evidence based on ordinal EFA and CFA.

PubMed

Chen, Po-Yi; Yang, Chien-Ming; Morin, Charles M

2015-05-01

The purpose of this study is to examine the factor structure of the Insomnia Severity Index (ISI) across samples recruited from different countries. We tried to identify the most appropriate factor model for the ISI and further examined the measurement invariance property of the ISI across samples from different countries. Our analyses included one data set collected from a Taiwanese sample and two data sets obtained from samples in Hong Kong and Canada. The data set collected in Taiwan was analyzed with ordinal exploratory factor analysis (EFA) to obtain the appropriate factor model for the ISI. After that, we conducted a series of confirmatory factor analyses (CFAs), which is a special case of the structural equation model (SEM) that concerns the parameters in the measurement model, to the statistics collected in Canada and Hong Kong. The purposes of these CFA were to cross-validate the result obtained from EFA and further examine the cross-cultural measurement invariance of the ISI. The three-factor model outperforms other models in terms of global fit indices in Taiwan's population. Its external validity is also supported by confirmatory factor analyses. Furthermore, the measurement invariance analyses show that the strong invariance property between the samples from different cultures holds, providing evidence that the ISI results obtained in different cultures are comparable. The factorial validity of the ISI is stable in different populations. More importantly, its invariance property across cultures suggests that the ISI is a valid measure of the insomnia severity construct across countries. Copyright © 2014 Elsevier B.V. All rights reserved.

Abnormalities in Structural Covariance of Cortical Gyrification in Parkinson's Disease.

PubMed

Xu, Jinping; Zhang, Jiuquan; Zhang, Jinlei; Wang, Yue; Zhang, Yanling; Wang, Jian; Li, Guanglin; Hu, Qingmao; Zhang, Yuanchao

2017-01-01

Although abnormal cortical morphology and connectivity between brain regions (structural covariance) have been reported in Parkinson's disease (PD), the topological organizations of large-scale structural brain networks are still poorly understood. In this study, we investigated large-scale structural brain networks in a sample of 37 PD patients and 34 healthy controls (HC) by assessing the structural covariance of cortical gyrification with local gyrification index (lGI). We demonstrated prominent small-world properties of the structural brain networks for both groups. Compared with the HC group, PD patients showed significantly increased integrated characteristic path length and integrated clustering coefficient, as well as decreased integrated global efficiency in structural brain networks. Distinct distributions of hub regions were identified between the two groups, showing more hub regions in the frontal cortex in PD patients. Moreover, the modular analyses revealed significantly decreased integrated regional efficiency in lateral Fronto-Insula-Temporal module, and increased integrated regional efficiency in Parieto-Temporal module in the PD group as compared to the HC group. In summary, our study demonstrated altered topological properties of structural networks at a global, regional and modular level in PD patients. These findings suggests that the structural networks of PD patients have a suboptimal topological organization, resulting in less effective integration of information between brain regions.

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.

[Family and school violence: the mediator role of self-esteem and attitudes towards institutional authority].

PubMed

Cava, María Jesús; Musitu, Gonzalo; Murgui, Sergio

2006-08-01

This study analyses the influence of family communication and parental valuation of school on adolescent violent behaviour at school. By means of a structural equation model, both its direct and indirect influence through school and family self-esteem of the adolescent and his attitude towards school authority are analysed. The sample is composed of 665 adolescents whose ages range from 12 to 16 years old. The results confirm the existence of an indirect relationship but not direct influence of the family on school violence. The attitude of the adolescent towards school authority is the mediator variable which shows the strongest direct effect on school violence. Also, the two dimensions of self-esteem considered are significant intermediate variables. These results and their implications are analysed.

On mining complex sequential data by means of FCA and pattern structures

NASA Astrophysics Data System (ADS)

Buzmakov, Aleksey; Egho, Elias; Jay, Nicolas; Kuznetsov, Sergei O.; Napoli, Amedeo; Raïssi, Chedy

2016-02-01

Nowadays data-sets are available in very complex and heterogeneous ways. Mining of such data collections is essential to support many real-world applications ranging from healthcare to marketing. In this work, we focus on the analysis of "complex" sequential data by means of interesting sequential patterns. We approach the problem using the elegant mathematical framework of formal concept analysis and its extension based on "pattern structures". Pattern structures are used for mining complex data (such as sequences or graphs) and are based on a subsumption operation, which in our case is defined with respect to the partial order on sequences. We show how pattern structures along with projections (i.e. a data reduction of sequential structures) are able to enumerate more meaningful patterns and increase the computing efficiency of the approach. Finally, we show the applicability of the presented method for discovering and analysing interesting patient patterns from a French healthcare data-set on cancer. The quantitative and qualitative results (with annotations and analysis from a physician) are reported in this use-case which is the main motivation for this work.

Nucleic and Amino Acid Sequences Support Structure-Based Viral Classification.

PubMed

Sinclair, Robert M; Ravantti, Janne J; Bamford, Dennis H

2017-04-15

Viral capsids ensure viral genome integrity by protecting the enclosed nucleic acids. Interactions between the genome and capsid and between individual capsid proteins (i.e., capsid architecture) are intimate and are expected to be characterized by strong evolutionary conservation. For this reason, a capsid structure-based viral classification has been proposed as a way to bring order to the viral universe. The seeming lack of sufficient sequence similarity to reproduce this classification has made it difficult to reject structural convergence as the basis for the classification. We reinvestigate whether the structure-based classification for viral coat proteins making icosahedral virus capsids is in fact supported by previously undetected sequence similarity. Since codon choices can influence nascent protein folding cotranslationally, we searched for both amino acid and nucleotide sequence similarity. To demonstrate the sensitivity of the approach, we identify a candidate gene for the pandoravirus capsid protein. We show that the structure-based classification is strongly supported by amino acid and also nucleotide sequence similarities, suggesting that the similarities are due to common descent. The correspondence between structure-based and sequence-based analyses of the same proteins shown here allow them to be used in future analyses of the relationship between linear sequence information and macromolecular function, as well as between linear sequence and protein folds. IMPORTANCE Viral capsids protect nucleic acid genomes, which in turn encode capsid proteins. This tight coupling of protein shell and nucleic acids, together with strong functional constraints on capsid protein folding and architecture, leads to the hypothesis that capsid protein-coding nucleotide sequences may retain signatures of ancient viral evolution. We have been able to show that this is indeed the case, using the major capsid proteins of viruses forming icosahedral capsids. Importantly, we detected similarity at the nucleotide level between capsid protein-coding regions from viruses infecting cells belonging to all three domains of life, reproducing a previously established structure-based classification of icosahedral viral capsids. Copyright © 2017 Sinclair et al.

Nucleic and Amino Acid Sequences Support Structure-Based Viral Classification

PubMed Central

Sinclair, Robert M.; Ravantti, Janne J.

2017-01-01

ABSTRACT Viral capsids ensure viral genome integrity by protecting the enclosed nucleic acids. Interactions between the genome and capsid and between individual capsid proteins (i.e., capsid architecture) are intimate and are expected to be characterized by strong evolutionary conservation. For this reason, a capsid structure-based viral classification has been proposed as a way to bring order to the viral universe. The seeming lack of sufficient sequence similarity to reproduce this classification has made it difficult to reject structural convergence as the basis for the classification. We reinvestigate whether the structure-based classification for viral coat proteins making icosahedral virus capsids is in fact supported by previously undetected sequence similarity. Since codon choices can influence nascent protein folding cotranslationally, we searched for both amino acid and nucleotide sequence similarity. To demonstrate the sensitivity of the approach, we identify a candidate gene for the pandoravirus capsid protein. We show that the structure-based classification is strongly supported by amino acid and also nucleotide sequence similarities, suggesting that the similarities are due to common descent. The correspondence between structure-based and sequence-based analyses of the same proteins shown here allow them to be used in future analyses of the relationship between linear sequence information and macromolecular function, as well as between linear sequence and protein folds. IMPORTANCE Viral capsids protect nucleic acid genomes, which in turn encode capsid proteins. This tight coupling of protein shell and nucleic acids, together with strong functional constraints on capsid protein folding and architecture, leads to the hypothesis that capsid protein-coding nucleotide sequences may retain signatures of ancient viral evolution. We have been able to show that this is indeed the case, using the major capsid proteins of viruses forming icosahedral capsids. Importantly, we detected similarity at the nucleotide level between capsid protein-coding regions from viruses infecting cells belonging to all three domains of life, reproducing a previously established structure-based classification of icosahedral viral capsids. PMID:28122979

Parallel computation of genome-scale RNA secondary structure to detect structural constraints on human genome.

PubMed

Kawaguchi, Risa; Kiryu, Hisanori

2016-05-06

RNA secondary structure around splice sites is known to assist normal splicing by promoting spliceosome recognition. However, analyzing the structural properties of entire intronic regions or pre-mRNA sequences has been difficult hitherto, owing to serious experimental and computational limitations, such as low read coverage and numerical problems. Our novel software, "ParasoR", is designed to run on a computer cluster and enables the exact computation of various structural features of long RNA sequences under the constraint of maximal base-pairing distance. ParasoR divides dynamic programming (DP) matrices into smaller pieces, such that each piece can be computed by a separate computer node without losing the connectivity information between the pieces. ParasoR directly computes the ratios of DP variables to avoid the reduction of numerical precision caused by the cancellation of a large number of Boltzmann factors. The structural preferences of mRNAs computed by ParasoR shows a high concordance with those determined by high-throughput sequencing analyses. Using ParasoR, we investigated the global structural preferences of transcribed regions in the human genome. A genome-wide folding simulation indicated that transcribed regions are significantly more structural than intergenic regions after removing repeat sequences and k-mer frequency bias. In particular, we observed a highly significant preference for base pairing over entire intronic regions as compared to their antisense sequences, as well as to intergenic regions. A comparison between pre-mRNAs and mRNAs showed that coding regions become more accessible after splicing, indicating constraints for translational efficiency. Such changes are correlated with gene expression levels, as well as GC content, and are enriched among genes associated with cytoskeleton and kinase functions. We have shown that ParasoR is very useful for analyzing the structural properties of long RNA sequences such as mRNAs, pre-mRNAs, and long non-coding RNAs whose lengths can be more than a million bases in the human genome. In our analyses, transcribed regions including introns are indicated to be subject to various types of structural constraints that cannot be explained from simple sequence composition biases. ParasoR is freely available at https://github.com/carushi/ParasoR .

Atlantic Tropical Cyclogenetic Processes during SOP-3 NAMMA in the GEOS-5 Global Data Assimilation and Forecast System

NASA Technical Reports Server (NTRS)

Reale, Oreste; Lau, William K.; Kim, Kyu-Myong; Brin, Eugenia

2009-01-01

This article investigates the role of the Saharan Air Layer (SAL) in tropical cyclogenetic processes associated with a non-developing and a developing African easterly wave observed during the Special Observation Period (SOP-3) phase of the 2006 NASA African Monsoon Multidisciplinary Analyses (NAMMA). The two waves are chosen because both interact heavily with Saharan air. A global data assimilation and forecast system, the NASA GEOS-5, is being run to produce a set of high-quality global analyses, inclusive of all observations used operationally but with denser satellite information. In particular, following previous works by the same Authors, the quality-controlled data from the Atmospheric Infrared Sounder (AIRS) used to produce these analyses have a better coverage than the one adopted by operational centers. From these improved analyses, two sets of 31 5-day high resolution forecasts, at horizontal resolutions of both half and quarter degrees, are produced. Results show that very steep moisture gradients are associated with the SAL in forecasts and analyses even at great distance from the Sahara. In addition, a thermal dipole (warm above, cool below) is present in the non-developing case. Moderate Resolution Imaging Spectroradiometer (MODIS) show that aerosol optical thickness is higher in the non-developing case. Altogether, results suggest that radiative effect of dust may play some role in producing a thermal structure less favorable to cyclogenesis. Results also indicate that only global horizontal resolutions on the order of 20-30 kilometers can capture the large-scale transport and the fine thermal structure of the SAL, inclusive of the sharp moisture gradients, reproducing the effect of tropical cyclone suppression which has been hypothesized by previous authors from observational and regional modeling perspectives. These effects cannot be fully represented at lower resolutions. Global resolution of a quarter of a degree is a minimum critical threshold to investigate Atlantic tropical cyclogenesis from a global modeling perspective.

Characteristics of hierarchical micro/nano surface structure formation generated by picosecond laser processing in water and air

NASA Astrophysics Data System (ADS)

Rajab, Fatema H.; Whitehead, David; Liu, Zhu; Li, Lin

2017-12-01

Laser surface texturing or micro/nano surface structuring in the air has been extensively studied. However, until now, there are very few studies on the characteristics of laser-textured surfaces in water, and there was no reported work on picosecond laser surface micro/nano-structuring in water. In this work, the surface properties of picosecond laser surface texturing in water and air were analysed and compared. 316L stainless steel substrates were textured using a picosecond laser. The surface morphology and the chemical composition were characterised using Philips XL30 FEG-SEM, EDX and confocal laser microscopy. The wettability of the textured surfaces was determined using a contact angle analyser FTA 188. Results showed that a variety of hierarchical micro/nano surface patterns could be controlled by a suitable adjustment of laser parameters. Not only surface morphology but also remarkable differences in wettability, optical reflectivity and surface oxygen content were observed for different types of surface textures produced by laser surface texture in water and air. The possible mechanisms of the changes in the behaviour of laser-textured surfaces are discussed.

Thermostructural Analysis of Unconventional Wing Structures of a Hyper-X Hypersonic Flight Research Vehicle for the Mach 7 Mission

NASA Technical Reports Server (NTRS)

Ko, William L.; Gong, Leslie

2001-01-01

Heat transfer, thermal stresses, and thermal buckling analyses were performed on the unconventional wing structures of a Hyper-X hypersonic flight research vehicle (designated as X-43) subjected to nominal Mach 7 aerodynamic heating. A wing midspan cross section was selected for the heat transfer and thermal stress analyses. Thermal buckling analysis was performed on three regions of the wing skin (lower or upper); 1) a fore wing panel, 2) an aft wing panel, and 3) a unit panel at the middle of the aft wing panel. A fourth thermal buckling analysis was performed on a midspan wing segment. The unit panel region is identified as the potential thermal buckling initiation zone. Therefore, thermal buckling analysis of the Hyper-X wing panels could be reduced to the thermal buckling analysis of that unit panel. "Buckling temperature magnification factors" were established. Structural temperature-time histories are presented. The results show that the concerns of shear failure at wing and spar welded sites, and of thermal buckling of Hyper-X wing panels, may not arise under Mach 7 conditions.

A Model of the Chicxulub Impact Basin Based on Evaluation of Geophysical Data, Well Logs, and Drill Core Samples

NASA Technical Reports Server (NTRS)

Sharpton, Virgil L.; Marin, Luis E.; Carney, John D.; Lee, Scott; Ryder, Graham; Schuraytz, Benjamin C.; Sikora, Paul; Spudis, Paul D.

1996-01-01

Abundant evidence now shows that the buried Chicxulub structure in northern Yucatan, Mexico, is indeed the intensely sought-after source of the ejecta found world-wide at the Cretaceous-Tertiary (K/T) boundary. In addition to large-scale concentric patterns in gravity and magnetic data over the structure, recent analyses of drill-core samples reveal a lithological assemblage similar to that observed at other terrestrial craters. This assemblage comprises suevite breccias, ejecta deposit breccias (Bunte Breccia equivalents), fine-grained impact melt rocks, and melt-matrix breccias. All these impact-produced lithologies contain diagnostic evidence of shock metamorphism, including planar deformation features in quartz, feldspar, and zircons; diaplectic glasses of quartz and feldspar; and fused mineral melts and whole-rock melts. In addition, elevated concentrations of Ir, Re, and Os, in meteoritic relative proportions, have been detected in some melt-rock samples from the center of the structure. Isotopic analyses, magnetization of melt-rock samples, and local stratigraphic constraints identify this crater as the source of K/T boundary deposits.

Assessing the role of spatial correlations during collective cell spreading

PubMed Central

Treloar, Katrina K.; Simpson, Matthew J.; Binder, Benjamin J.; McElwain, D. L. Sean; Baker, Ruth E.

2014-01-01

Spreading cell fronts are essential features of development, repair and disease processes. Many mathematical models used to describe the motion of cell fronts, such as Fisher's equation, invoke a mean–field assumption which implies that there is no spatial structure, such as cell clustering, present. Here, we examine the presence of spatial structure using a combination of in vitro circular barrier assays, discrete random walk simulations and pair correlation functions. In particular, we analyse discrete simulation data using pair correlation functions to show that spatial structure can form in a spreading population of cells either through sufficiently strong cell–to–cell adhesion or sufficiently rapid cell proliferation. We analyse images from a circular barrier assay describing the spreading of a population of MM127 melanoma cells using the same pair correlation functions. Our results indicate that the spreading melanoma cell populations remain very close to spatially uniform, suggesting that the strength of cell–to–cell adhesion and the rate of cell proliferation are both sufficiently small so as not to induce any spatial patterning in the spreading populations. PMID:25026987

Quasi-Rayleigh waves in butt-welded thick steel plate

NASA Astrophysics Data System (ADS)

Kamas, Tuncay; Giurgiutiu, Victor; Lin, Bin

2015-03-01

This paper discusses theoretical and experimental analyses of weld guided surface acoustic waves (SAW) through the guided wave propagation (GWP) analyses. The GWP analyses have been carried out by utilizing piezoelectric wafer active sensors (PWAS) for in situ structural inspection of a thick steel plate with butt weld as the weld bead is ground flush. Ultrasonic techniques are commonly used for validation of welded structures in many in-situ monitoring applications, e.g. in off-shore structures, in nuclear and pressure vessel industries and in a range of naval applications. PWAS is recently employed in such ultrasonic applications as a resonator as well as a transducer. Quasi-Rayleigh waves a.k.a. SAW can be generated in relatively thick isotropic elastic plate having the same phase velocity as Rayleigh waves whereas Rayleigh waves are a high frequency approximation of the first symmetric (S0) and anti-symmetric (A0) Lamb wave modes. As the frequency becomes very high the S0 and the A0 wave speeds coalesce, and both have the same value. This value is exactly the Rayleigh wave speed and becomes constant along the frequency i.e. Rayleigh waves are non-dispersive guided surface acoustic waves. The study is followed with weld-GWP tests through the pitch-catch method along the butt weld line. The tuning curves of quasi-Rayleigh wave are determined to show the tuning and trapping effect of the weld bead that has higher thickness than the adjacent plates on producing a dominant quasi-Rayleigh wave mode. The significant usage of the weld tuned and guided quasi-Rayleigh wave mode is essentially discussed for the applications in the in-situ inspection of relatively thick structures with butt weld such as naval offshore structures. The paper ends with summary, conclusions and suggestions for future work.

PDBsum: Structural summaries of PDB entries.

PubMed

Laskowski, Roman A; Jabłońska, Jagoda; Pravda, Lukáš; Vařeková, Radka Svobodová; Thornton, Janet M

2018-01-01

PDBsum is a web server providing structural information on the entries in the Protein Data Bank (PDB). The analyses are primarily image-based and include protein secondary structure, protein-ligand and protein-DNA interactions, PROCHECK analyses of structural quality, and many others. The 3D structures can be viewed interactively in RasMol, PyMOL, and a JavaScript viewer called 3Dmol.js. Users can upload their own PDB files and obtain a set of password-protected PDBsum analyses for each. The server is freely accessible to all at: http://www.ebi.ac.uk/pdbsum. © 2017 The Protein Society.

Comparison of the structure, crystallography and composition of eggshells of the guinea fowl and graylag goose.

PubMed

Pérez-Huerta, Alberto; Dauphin, Yannicke

2016-02-01

The structure and composition of the eggshells of two commercial species (guinea fowl and greylag goose) have been studied. Thin sections and scanning electron microcopy show the similarity of the overall structure, but the relative thickness of the layers differs in these two taxa. Atomic force microscopy shows that the different layers are composed of rounded, heterogeneous granules, the diameter of which is between 50 and 100 nm, with a thin cortex. Infrared data and thermogravimetric analyses show that both eggshells are made of calcite, but differing on the quality and quantity when the organic component is considered. Chemical maps show that chemical element distribution is not uniform within a sample, and differs between the species, but with low magnesium content. Electron back scattered diffraction confirms the eggshells are calcite, but the microtexture strongly differs between the two species. Based on the chemical-structural differences, a species-specific biological control on the biomineralization is found, despite the rapid formation of an eggshell. Overall results indicate that to estimate the quality of eggshells, such as resistance to breakage, is not a straightforward process because of the high complexity of avian eggshell biomineralization. Copyright © 2015 Elsevier GmbH. All rights reserved.

Transition metal coordination polymers based on tetrabromoterephthalic and bis(imidazole) ligands: Syntheses, structures, topological analysis and photoluminescence properties

NASA Astrophysics Data System (ADS)

Zhang, Xiaowei; Xing, Peiqi; Geng, Xiujuan; Sun, Daofeng; Xiao, Zhenyu; Wang, Lei

2015-09-01

Eight new coordination polymers (CPs), namely, [Zn(1,2-mbix)(tbtpa)]n (1), [Co(1,2-mbix)(tbtpa)]n (2), [CdCl(1,2-mbix)(tbtpa)0.5]n (3), {[Cd(1,2-bix)(tbtpa)]·H2O}n (4), {[Cd0.5(1,2-bix)(tbtpa)0.5]·H2O}n (5), {[Co0.5(1,2-bix)(tbtpa)0.5]·2H2O}n (6), {[Co(1,2-bix)(tbtpa)]·H2O}n (7) and {[Co(1,2-bix)(tbtpa)]·Diox·2H2O}n (8), were synthesized under solvothermal conditions based on mix-ligand strategy (H2tbtpa=tetrabromoterephthalic acid and 1,2-mbix=1,2-bis((2-methyl-1H-imidazol-1-yl)methyl)benzene, 1,2-bix=1,2-bis(imidazol-1-ylmethyl)benzene). All of the CPs have been structurally characterized by single-crystal X-ray diffraction analyses and further characterized by elemental analyses, IR spectroscopy, powder X-ray diffraction (PXRD), and thermogravimetric analyses (TGA). X-ray diffraction analyses show that 1 and 2 are isotypics which have 2D highly undulated networks with (4,4)-sql topology with the existence of C-H ⋯Br interactions; for 3, it has a 2D planar network with (4,4)-sql topology with the occurrence of C-H ⋯Cl interactions other than C-H ⋯Br interactions; 4 shows a 3D 2-fold interpenetrated nets with rare 65·8-mok topology which has a self-catention property. As the same case as 1 and 2, 5 and 6 are also isostructural with planar layers with 44-sql topology which further assembled into 3D supramolecular structure through the interdigitated stacking fashion and the C-Br ⋯Cph interactions. As for 7, it has a 2D slightly undulated networks with (4,4)-sql topology which has one dimension channel. While 8 has a 2-fold interpenetrated networks with (3,4)-connect jeb topology with point symbol {63}{65·8}. And their structures can be tuned by conformations of bis(imidazol) ligands and solvent mixture. Besides, the TGA properties for all compounds and the luminescent properties for 1, 3, 4, 5 are discussed in detail.

Personality Traits' Effects on Self-Efficacy and Outcome Expectations for High School Major Choice

ERIC Educational Resources Information Center

Brown, Dikla; Cinamon, Rachel Gali

2016-01-01

The current study focuses on the contribution of the Big Five personality traits to the development of self-efficacy and outcome expectations regarding selection of a high school major among 368 Israeli adolescents (Mage = 16.07, SD = 0.41). Structural equation analyses showed that higher levels of conscientiousness and extraversion and lower…

A Multidimensional Model of School Dropout from an 8-Year Longitudinal Study in a General High School Population

ERIC Educational Resources Information Center

Fortin, Laurier; Marcotte, Diane; Diallo, Thierno; Potvin, Pierre; Royer, Egide

2013-01-01

This study tests an empirical multidimensional model of school dropout, using data collected in the first year of an 8-year longitudinal study, with first year high school students aged 12-13 years. Structural equation modeling analyses show that five personal, family, and school latent factors together contribute to school dropout identified at…

Parenting and Neighborhood Predictors of Youth Problem Behaviors within Hispanic Families: The Moderating Role of Family Structure

ERIC Educational Resources Information Center

Gayles, Jochebed G.; Coatsworth, J. Douglas; Pantin, Hilda M.; Szapocznik, Jose

2009-01-01

This study examined the influence of family and neighborhood contexts on Hispanic youth problem behavior. The effects of parents' perceptions of neighborhood context and parenting practices on problem behavior were examined in 167 one-parent (n = 75) and two-parent (n = 92) families. Results from multigroup path analyses showed significant main…

Catalyst-Free Growth of Large Scale Ga2O3 Nanowires

DTIC Science & Technology

2001-11-01

XRD and TEM analyses indicate that the Ga 20 3 nanowires exhibit a monoclinic structure. PL characteristic of the Ga2O3 nanowires shows a UV emission...using Ga metal and N2 / H 20 reactants. The Ga2O3 nanowires, which have diameters ranging from 60 to 150 nm and lengths of several micrometers, are 133

The Contributions of Intrinsic and Extrinsic Reading Motivation to the Development of Reading Competence over Summer Vacation

ERIC Educational Resources Information Center

Schaffner, Ellen; Schiefele, Ulrich

2016-01-01

This study addressed the role of reading motivation as a potential determinant of losses or gains in reading competence over six weeks of summer vacation (SV). Based on a sample of 223 third-grade elementary students, structural equation analyses showed that intrinsic reading motivation before SV contributed positively to both word and sentence…

The Factorial Invariance of the CES-D during Adolescence: Are Symptom Profiles for Depression Stable across Gender and Time?

ERIC Educational Resources Information Center

Verhoeven, Marjolein; Sawyer, Michael G.; Spence, Susan H.

2013-01-01

This study examined the factorial invariance of the Center for Epidemiologic Studies of Depression Scale (CES-D) across gender and time during adolescence. The factor structure of the CES-D was compared at four annual measurement waves in a community sample of 2650 Australian adolescents. Confirmatory factor analyses showed that the factor…

Structural Modulation from 1D Chain to 3D Framework: Improved Thermostability, Insensitivity, and Energies of Two Nitrogen-Rich Energetic Coordination Polymers.

PubMed

Guo, Zhaoqi; Wu, Yunlong; Deng, Chongqing; Yang, Guoping; Zhang, Jiangong; Sun, Zhihua; Ma, Haixia; Gao, Chao; An, Zhongwei

2016-11-07

Two new energetic coordination polymers (CPs) [Pb(BT)(H 2 O) 3 ] n (1) and [Pb 3 (DOBT) 3 (H 2 O) 2 ] n ·(4H 2 O) n (2) with 1D and 3D structures were synthesized by employing two rational designed ligands, 1H,1'H-5,5'-bitetrazole (H 2 BT) and 1H,1'H-[5,5'-bitetrazole]-1,1'-diol ligands (DHBT), respectively. Thermal analyses and sensitivity tests show that the 3D architecture reinforces the network of 2 which has higher thermal stability and lower sensitivity than that of 1. Through oxygen-bomb combustion calorimetry the molar enthalpy of formation of 2 is derived to be much higher than that of 1 as well as the reported CPs. Herein, more importantly, the heats of detonation (ΔH det ) were calculated according to the decomposition products of TG-DSC-MS-FTIR simultaneous analyses for the first time. The calculated results show that ΔH det of 2 is 23% higher than that of 1. This research demonstrates that 3D energetic CP with outstanding energetic properties can be obtained through efficient and reasonable design.

Detection of bio-signature by microscopy and mass spectrometry

NASA Astrophysics Data System (ADS)

Tulej, M.; Wiesendanger, R.; Neuland, M., B.; Meyer, S.; Wurz, P.; Neubeck, A.; Ivarsson, M.; Riedo, V.; Moreno-Garcia, P.; Riedo, A.; Knopp, G.

2017-09-01

We demonstrate detection of micro-sized fossilized bacteria by means of microscopy and mass spectrometry. The characteristic structures of lifelike forms are visualized with a micrometre spatial resolution and mass spectrometric analyses deliver elemental and isotope composition of host and fossilized materials. Our studies show that high selectivity in isolation of fossilized material from host phase can be achieved while applying a microscope visualization (location), a laser ablation ion source with sufficiently small laser spot size and applying depth profiling method. Our investigations shows that fossilized features can be well isolated from host phase. The mass spectrometric measurements can be conducted with sufficiently high accuracy and precision yielding quantitative elemental and isotope composition of micro-sized objects. The current performance of the instrument allows the measurement of the isotope fractionation in per mill level and yield exclusively definition of the origin of the investigated species by combining optical visualization of investigated samples (morphology and texture), chemical characterization of host and embedded in the host micro-sized structure. Our isotope analyses involved bio-relevant B, C, S, and Ni isotopes which could be measured with sufficiently accuracy to conclude about the nature of the micro-sized objects.

Indications of marine bioinvasion from network theory. An analysis of the global cargo ship network

NASA Astrophysics Data System (ADS)

Kölzsch, A.; Blasius, B.

2011-12-01

The transport of huge amounts of small aquatic organisms in the ballast tanks and at the hull of large cargo ships leads to ever increasing rates of marine bioinvasion. In this study, we apply a network theoretic approach to examine the introduction of invasive species into new ports by global shipping. This is the first stage of the invasion process where it is still possible to intervene with regulating measures. We compile a selection of widely used and newly developed network properties and apply these to analyse the structure and spread characteristics of the directed and weighted global cargo ship network (GCSN). Our results reveal that the GCSN is highly efficient, shows small world characteristics and is positive assortative, indicating that quick spread of invasive organisms between ports is likely. The GCSN shows strong community structure and contains two large communities, the Atlantic and Pacific trading groups. Ports that appear as connector hubs and are of high centralities are the Suez and Panama Canal, Singapore and Shanghai. Furthermore, from robustness analyses and the network's percolation behaviour, we evaluate differences of onboard and in-port ballast water treatment, set them into context with previous studies and advise bioinvasion management strategies.

Encapsulation of CO2 into amorphous alpha-cyclodextrin powder at different moisture contents - Part 2: Characterization of complexed powders and determination of crystalline structure.

PubMed

Ho, Thao M; Howes, Tony; Jack, Kevin S; Bhandari, Bhesh R

2016-09-01

This study aims to characterize CO2-α-cyclodextrin (α-CD) inclusion complexes produced from amorphous α-CD powder at moisture contents (MC) close to or higher than the critical level of crystallization (e.g. 13, 15 and 17% MC on wet basis, w.b.) at 0.4 and 1.6MPa pressure for 72h. The results of (13)C NMR, SEM, DSC and X-ray analyses showed that these MC levels were high enough to induce crystallization of CO2-α-CD complexed powders during encapsulation, by which amount of CO2 encapsulated by amorphous α-CD powder was significantly increased. The formation of inclusion complexes were well confirmed by results of FTIR and (13)C NMR analyses through an appearance of a peak associated with CO2 on the FTIR (2334cm(-1)) and NMR (125.3ppm) spectra. Determination of crystal packing patterns of CO2-α-CD complexed powders showed that during crystallization, α-CD molecules were arranged in cage-type structure in which CO2 molecules were entrapped in isolated cavities. Copyright © 2016 Elsevier Ltd. All rights reserved.

A genotype network reveals homoplastic cycles of convergent evolution in influenza A (H3N2) haemagglutinin.

PubMed

Wagner, Andreas

2014-07-07

Networks of evolving genotypes can be constructed from the worldwide time-resolved genotyping of pathogens like influenza viruses. Such genotype networks are graphs where neighbouring vertices (viral strains) differ in a single nucleotide or amino acid. A rich trove of network analysis methods can help understand the evolutionary dynamics reflected in the structure of these networks. Here, I analyse a genotype network comprising hundreds of influenza A (H3N2) haemagglutinin genes. The network is rife with cycles that reflect non-random parallel or convergent (homoplastic) evolution. These cycles also show patterns of sequence change characteristic for strong and local evolutionary constraints, positive selection and mutation-limited evolution. Such cycles would not be visible on a phylogenetic tree, illustrating that genotype network analysis can complement phylogenetic analyses. The network also shows a distinct modular or community structure that reflects temporal more than spatial proximity of viral strains, where lowly connected bridge strains connect different modules. These and other organizational patterns illustrate that genotype networks can help us study evolution in action at an unprecedented level of resolution. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Temperature-controlled two new Co(II) compounds with distinct topological networks: Syntheses, crystal structures and catalytic properties

NASA Astrophysics Data System (ADS)

Meng, Qing-Hua; Long, Xu; Liu, Jing-Li; Zhang, Shuan; Zhang, Guang-Hui

2018-04-01

Two new Co(II) coordination compounds, namely [Co2(bptc)(bpp)2]n (1) and [Co(bptc)0.5(bpp)]n (2) (H4bptc = biphenyl-3,3‧,5,5‧-tetracarboxylic acid, bpp = 1,3-di(4-pyridyl)propane), have been hydrothermally synthesized from the same reactants via tuning the reaction temperature. Single crystal X-ray diffraction analyses revealed that both 1 and 2 feature 2D sheet motifs. Topological analyses revealed that compounds 1 and 2 show distinct topological networks. Under the weak Van der Waals interactions, the 2D sheet motifs of compounds 1 and 2 are further packed into 2D→3D interdigitated supramolecular frameworks. Moreover, the two Co(II) compounds show high catalytic activities for degradation of methyl orange (MO) in a Fenten-like process.

Amino acid pair- and triplet-wise groupings in the interior of α-helical segments in proteins.

PubMed

de Sousa, Miguel M; Munteanu, Cristian R; Pazos, Alejandro; Fonseca, Nuno A; Camacho, Rui; Magalhães, A L

2011-02-21

A statistical approach has been applied to analyse primary structure patterns at inner positions of α-helices in proteins. A systematic survey was carried out in a recent sample of non-redundant proteins selected from the Protein Data Bank, which were used to analyse α-helix structures for amino acid pairing patterns. Only residues more than three positions apart from both termini of the α-helix were considered as inner. Amino acid pairings i, i+k (k=1, 2, 3, 4, 5), were analysed and the corresponding 20×20 matrices of relative global propensities were constructed. An analysis of (i, i+4, i+8) and (i, i+3, i+4) triplet patterns was also performed. These analysis yielded information on a series of amino acid patterns (pairings and triplets) showing either high or low preference for α-helical motifs and suggested a novel approach to protein alphabet reduction. In addition, it has been shown that the individual amino acid propensities are not enough to define the statistical distribution of these patterns. Global pair propensities also depend on the type of pattern, its composition and orientation in the protein sequence. The data presented should prove useful to obtain and refine useful predictive rules which can further the development and fine-tuning of protein structure prediction algorithms and tools. Copyright © 2010 Elsevier Ltd. All rights reserved.

Gene flow connects coastal populations of a habitat specialist, the Clapper Rail Rallus crepitans

USGS Publications Warehouse

Coster, Stephanie S.; Welsh, Amy B.; Costanzo, Gary R.; Harding, Sergio R.; Anderson, James T.; Katzner, Todd

2018-01-01

Examining population genetic structure can reveal patterns of reproductive isolation or population mixing and inform conservation management. Some avian species are predicted to exhibit minimal genetic differentiation among populations as a result of the species high mobility, with habitat specialists tending to show greater fine‐scale genetic structure. To explore the relationship between habitat specialization and gene flow, we investigated the genetic structure of a saltmarsh specialist with high potential mobility across a wide geographic range of fragmented habitat. Little variation among mitochondrial sequences (620 bp from ND2) was observed among 149 individual Clapper Rails Rallus crepitans sampled along the Atlantic coast of North America, with the majority of individuals at all sampling sites sharing a single haplotype. Genotyping of nine microsatellite loci across 136 individuals revealed moderate genetic diversity, no evidence of bottlenecks, and a weak pattern of genetic differentiation that increased with geographic distance. Multivariate analyses, Bayesian clustering and an AMOVA all suggested a lack of genetic structuring across the North American Atlantic coast, with all individuals grouped into a single interbreeding population. Spatial autocorrelation analyses showed evidence of weak female philopatry and a lack of male philopatry. We conclude that high gene flow connecting populations of this habitat specialist may result from the interaction of ecological and behavioral factors that promote dispersal and limit natal philopatry and breeding‐site fidelity. As climate change threatens saltmarshes, the genetic diversity and population connectivity of Clapper Rails may promote resilience of their populations. This finding helps inform about potential fates of other similarly behaving saltmarsh specialists on the Atlantic coast.

Investigating the Genetic Diversity, Population Differentiation and Population Dynamics of Cycas segmentifida (Cycadaceae) Endemic to Southwest China by Multiple Molecular Markers

PubMed Central

Feng, Xiuyan; Liu, Jian; Chiang, Yu-Chung; Gong, Xun

2017-01-01

Climate change, species dispersal ability and habitat fragmentation are major factors influencing species distribution and genetic diversity, especially for the range-restricted and threatened taxa. Here, using four sequences of chloroplast DNAs (cpDNAs), three nuclear genes (nDNAs) and 12 nuclear microsatellites (SSRs), we investigated the genetic diversity, genetic structure, divergence time and population dynamics of Cycas segmentifida D. Y. Wang and C. Y. Deng, a threatened cycad species endemic to Southwest China. High levels of genetic diversity and genetic differentiation were revealed in C. segmentifida. Haplotypes of networks showed two evolutionary units in C. segmentifida, with the exception of the nuclear gene GTP network. Meanwhile, the UPGMA tree, structure and PCoA analyses suggested that 14 populations of C. segmentifida were divided into two clades. There was significant effect of isolation by distance (IBD) in this species. However, this species did not display a significant phylogeographic structure. The divergence time estimation suggested that its haplotypes diverged during the Middle Pleistocene. Additionally, the population dynamics inferred from different DNA sequences analyses were discordant. Bottleneck analysis showed that populations of C. segmentifida did not experience any recent bottleneck effect, but rather pointed to a contraction of its effective population size over time. Furthermore, our results suggested that the population BM which held an intact population structure and occupied undisturbed habitat was at the Hardy–Weinberg equilibrium, implying that this population is a free-mating system. These genetic features provide important information for the sustainable management of C. segmentifida. PMID:28580005

The structure of stereotyped calls reflects kinship and social affiliation in resident killer whales (Orcinus orca).

PubMed

Deecke, Volker B; Barrett-Lennard, Lance G; Spong, Paul; Ford, John K B

2010-05-01

A few species of mammals produce group-specific vocalisations that are passed on by learning, but the function of learned vocal variation remains poorly understood. Resident killer whales live in stable matrilineal groups with repertoires of seven to 17 stereotyped call types. Some types are shared among matrilines, but their structure typically shows matriline-specific differences. Our objective was to analyse calls of nine killer whale matrilines in British Columbia to test whether call similarity primarily reflects social or genetic relationships. Recordings were made in 1985-1995 in the presence of focal matrilines that were either alone or with groups with non-overlapping repertoires. We used neural network discrimination performance to measure the similarity of call types produced by different matrilines and determined matriline association rates from 757 encounters with one or more focal matrilines. Relatedness was measured by comparing variation at 11 microsatellite loci for the oldest female in each group. Call similarity was positively correlated with association rates for two of the three call types analysed. Similarity of the N4 call type was also correlated with matriarch relatedness. No relationship between relatedness and association frequency was detected. These results show that call structure reflects relatedness and social affiliation, but not because related groups spend more time together. Instead, call structure appears to play a role in kin recognition and shapes the association behaviour of killer whale groups. Our results therefore support the hypothesis that increasing social complexity plays a role in the evolution of learned vocalisations in some mammalian species.

The structure of stereotyped calls reflects kinship and social affiliation in resident killer whales ( Orcinus orca)

NASA Astrophysics Data System (ADS)

Deecke, Volker B.; Barrett-Lennard, Lance G.; Spong, Paul; Ford, John K. B.

2010-05-01

A few species of mammals produce group-specific vocalisations that are passed on by learning, but the function of learned vocal variation remains poorly understood. Resident killer whales live in stable matrilineal groups with repertoires of seven to 17 stereotyped call types. Some types are shared among matrilines, but their structure typically shows matriline-specific differences. Our objective was to analyse calls of nine killer whale matrilines in British Columbia to test whether call similarity primarily reflects social or genetic relationships. Recordings were made in 1985-1995 in the presence of focal matrilines that were either alone or with groups with non-overlapping repertoires. We used neural network discrimination performance to measure the similarity of call types produced by different matrilines and determined matriline association rates from 757 encounters with one or more focal matrilines. Relatedness was measured by comparing variation at 11 microsatellite loci for the oldest female in each group. Call similarity was positively correlated with association rates for two of the three call types analysed. Similarity of the N4 call type was also correlated with matriarch relatedness. No relationship between relatedness and association frequency was detected. These results show that call structure reflects relatedness and social affiliation, but not because related groups spend more time together. Instead, call structure appears to play a role in kin recognition and shapes the association behaviour of killer whale groups. Our results therefore support the hypothesis that increasing social complexity plays a role in the evolution of learned vocalisations in some mammalian species.

Brain cortical thickness in male adolescents with serious substance use and conduct problems.

PubMed

Chumachenko, Serhiy Y; Sakai, Joseph T; Dalwani, Manish S; Mikulich-Gilbertson, Susan K; Dunn, Robin; Tanabe, Jody; Young, Susan; McWilliams, Shannon K; Banich, Marie T; Crowley, Thomas J

2015-01-01

Adolescents with substance use disorder (SUD) and conduct problems exhibit high levels of impulsivity and poor self-control. Limited work to date tests for brain cortical thickness differences in these youths. To investigate differences in cortical thickness between adolescents with substance use and conduct problems and controls. We recruited 25 male adolescents with SUD, and 19 male adolescent controls, and completed structural 3T magnetic resonance brain imaging. Using the surface-based morphometry software FreeSurfer, we completed region-of-interest (ROI) analyses for group cortical thickness differences in left, and separately right, inferior frontal gyrus (IFG), orbitofrontal cortex (OFC) and insula. Using FreeSurfer, we completed whole-cerebrum analyses of group differences in cortical thickness. Versus controls, the SUD group showed no cortical thickness differences in ROI analyses. Controlling for age and IQ, no regions with cortical thickness differences were found using whole-cerebrum analyses (though secondary analyses co-varying IQ and whole-cerebrum cortical thickness yielded a between-group cortical thickness difference in the left posterior cingulate/precuneus). Secondary findings showed that the SUD group, relative to controls, demonstrated significantly less right > left asymmetry in IFG, had weaker insular-to-whole-cerebrum cortical thickness correlations, and showed a positive association between conduct disorder symptom count and cortical thickness in a superior temporal gyrus cluster. Functional group differences may reflect a more nuanced cortical morphometric difference than ROI cortical thickness. Further investigation of morphometric differences is needed. If replicable findings can be established, they may aid in developing improved diagnostic or more targeted treatment approaches.

Brain cortical thickness in male adolescents with serious substance use and conduct problems

PubMed Central

Chumachenko, Serhiy Y.; Sakai, Joseph T.; Dalwani, Manish S.; Mikulich-Gilbertson, Susan K.; Dunn, Robin; Tanabe, Jody; Young, Susan; McWilliams, Shannon K.; Banich, Marie T.; Crowley, Thomas J.

2016-01-01

Background Adolescents with substance use disorder (SUD) and conduct problems exhibit high levels of impulsivity and poor self-control. Limited work to date tests for brain cortical thickness differences in these youths. Objectives To investigate differences in cortical thickness between adolescents with substance use and conduct problems and controls. Methods We recruited 25 male adolescents with SUD, and 19 male adolescent controls, and completed structural 3T magnetic resonance brain imaging. Using the surface-based morphometry software FreeSurfer, we completed region-of-interest (ROI) analyses for group cortical thickness differences in left, and separately right, inferior frontal gyrus (IFG), orbitofrontal cortex (OFC) and insula. Using FreeSurfer, we completed whole-cerebrum analyses of group differences in cortical thickness. Results Versus controls, the SUD group showed no cortical thickness differences in ROI analyses. Controlling for age and IQ, no regions with cortical thickness differences were found using whole-cerebrum analyses (though secondary analyses co-varying IQ and whole-cerebrum cortical thickness yielded a between-group cortical thickness difference in the left posterior cingulate/precuneus). Secondary findings showed that the SUD group, relative to controls, demonstrated significantly less right>left asymmetry in IFG, had weaker insular-to-whole-cerebrum cortical thickness correlations, and showed a positive association between conduct disorder symptom count and cortical thickness in a superior temporal gyrus cluster. Conclusion Functional group differences may reflect a more nuanced cortical morphometric difference than ROI cortical thickness. Further investigation of morphometric differences is needed. If replicable findings can be established, they may aid in developing improved diagnostic or more targeted treatment approaches. PMID:26337200

Collisional excitation of CH2 rotational/fine-structure levels by helium

NASA Astrophysics Data System (ADS)

Dagdigian, P. J.; Lique, F.

2018-02-01

Accurate determination of the abundance of CH2 in interstellar media relies on both radiative and collisional rate coefficients. We investigate here the rotational/fine-structure excitation of CH2 induced by collisions with He. We employ a recoupling technique to generate fine-structure-resolved cross-sections and rate coefficients from close coupling spin-free scattering calculations. The calculations are based on a recent, high-accuracy CH2-He potential energy surface computed at the coupled clusters level of theory. The collisional cross-section calculations are performed for all fine-structure transitions among the first 22 and 24 energy levels of ortho- and para-CH2, respectively, and for temperatures up to 300 K. As a first application, we simulate the excitation of CH2 in typical molecular clouds. The excitation temperatures of the CH2 lines are found to be small at typical densities of molecular clouds, showing that the non-local thermodynamic equilibrium approach has to be used to analyse interstellar spectra. We also found that the fine-structure lines connected with the 404 - 313 and 505 - 414 rotational transitions show possible maser emissions so that they can be easily seen in emission. These calculations show that CH2 may have to be detected mainly through absorption spectra.

Structural empowerment, job stress and burnout of nurses in China.

PubMed

Guo, Jiajia; Chen, Juan; Fu, Jie; Ge, Xinling; Chen, Min; Liu, Yanhui

2016-08-01

To investigate the status of structural empowerment, job stress and burnout in China, and to explore the relationships among them. The questionnaires of CWEQ-II, job stressors and MBI were used to investigate 1002 nurses working at tertiary-level hospitals. The average score of CWEQ-II was 2.23±0.59. The score of EE of MBI was 29.75±13.94, PA was 27.40±11.21, both of them showed a high level of exhaustion, DP was 8.07±5.82 and showed a middle level of exhaustion. The findings showed that workload and time pressure were the most frequently encountered job stress among staff nurses, the score was 3.23±0.95; There was a significantly correlation among structural empowerment, job stressors and the level of burnout(p<0.05). Hierarchical regression analysis showed that structural empowerment had significant influence on the every factors of job stressors (p<0.05) and burnout, job stressors had significant influence on the every factors of burnout (p<0.05). Structural equation modeling analyses revealed a good fit to the data based on various fit indices (χ(2)/df=2.29, GFI=0.945, CFI=0.965, IFI=0.966, RMSEA=0.061). Staff nurses felt that structural empowerment in their workplace resulted in lower levels of job stress which in turn strongly influenced Burnout. These results provide initial support for an expanded model of structural empowerment, and offer a broader understanding of the empowerment process. Copyright © 2016 Elsevier Inc. All rights reserved.

Genetic structure of nomadic Bedouin from Kuwait

PubMed Central

Mohammad, T.; Xue, Yali; Evison, M.; Tyler-Smith, Chris

2009-01-01

Bedouin are traditionally nomadic inhabitants of the Persian Gulf who claim descent from two male lineages: Adnani and Qahtani. We have investigated whether or not this tradition is reflected in the current genetic structure of a sample of 153 Bedouin males from six Kuwaiti tribes, including three tribes from each traditional lineage. Volunteers were genotyped using a panel of autosomal and Y-STRs, and Y-SNPs. The samples clustered with their geographical neighbours in both the autosomal and Y-chromosomal analyses, and showed strong evidence of genetic isolation and drift. Whilst there was no evidence of segregation into the two male lineages, other aspects of genetic structure were in accord with tradition. PMID:19639002

3D quantitative comparative analysis of long bone diaphysis variations in microanatomy and cross-sectional geometry.

PubMed

Houssaye, Alexandra; Taverne, Maxime; Cornette, Raphaël

2018-05-01

Long bone inner structure and cross-sectional geometry display a strong functional signal, leading to convergences, and are widely analyzed in comparative anatomy at small and large taxonomic scales. Long bone microanatomical studies have essentially been conducted on transverse sections but also on a few longitudinal ones. Recent studies highlighted the interest in analyzing variations of the inner structure along the diaphysis using a qualitative as well as a quantitative approach. With the development of microtomography, it has become possible to study three-dimensional (3D) bone microanatomy and, in more detail, the form-function relationships of these features. This study focused on the selection of quantitative parameters to describe in detail the cross-sectional shape changes and distribution of the osseous tissue along the diaphysis. Two-dimensional (2D) virtual transverse sections were also performed in the two usual reference planes and results were compared with those obtained based on the whole diaphysis analysis. The sample consisted in 14 humeri and 14 femora of various mammalian taxa that are essentially terrestrial. Comparative quantitative analyses between different datasets made it possible to highlight the parameters that are strongly impacted by size and phylogeny and the redundant ones, and thus to estimate their relevance for use in form-function analyses. The analysis illustrated that results based on 2D transverse sections are similar for both sectional planes; thus if a strong bias exists when mixing sections from the two reference planes in the same analysis, it would not problematic to use either one plane or the other in comparative studies. However, this may no longer hold for taxa showing a much stronger variation in bone microstructure along the diaphysis. Finally, the analysis demonstrated the significant contribution of the parameters describing variations along the diaphysis, and thus the interest in performing 3D analyses; this should be even more fruitful for heterogeneous diaphyses. In addition, covariation analyses showed that there is a strong interest in removing the size effect to access the differences in the microstructure of the humerus and femur. This methodological study provides a reference for future quantitative analyses on long bone inner structure and should make it possible, through a detailed knowledge of each descriptive parameter, to better interpret results from the multivariate analyses associated with these studies. This will have direct implications for studies in vertebrate anatomy, but also in paleontology and anthropology. © 2018 Anatomical Society.

PDBe: improved accessibility of macromolecular structure data from PDB and EMDB

PubMed Central

Velankar, Sameer; van Ginkel, Glen; Alhroub, Younes; Battle, Gary M.; Berrisford, John M.; Conroy, Matthew J.; Dana, Jose M.; Gore, Swanand P.; Gutmanas, Aleksandras; Haslam, Pauline; Hendrickx, Pieter M. S.; Lagerstedt, Ingvar; Mir, Saqib; Fernandez Montecelo, Manuel A.; Mukhopadhyay, Abhik; Oldfield, Thomas J.; Patwardhan, Ardan; Sanz-García, Eduardo; Sen, Sanchayita; Slowley, Robert A.; Wainwright, Michael E.; Deshpande, Mandar S.; Iudin, Andrii; Sahni, Gaurav; Salavert Torres, Jose; Hirshberg, Miriam; Mak, Lora; Nadzirin, Nurul; Armstrong, David R.; Clark, Alice R.; Smart, Oliver S.; Korir, Paul K.; Kleywegt, Gerard J.

2016-01-01

The Protein Data Bank in Europe (http://pdbe.org) accepts and annotates depositions of macromolecular structure data in the PDB and EMDB archives and enriches, integrates and disseminates structural information in a variety of ways. The PDBe website has been redesigned based on an analysis of user requirements, and now offers intuitive access to improved and value-added macromolecular structure information. Unique value-added information includes lists of reviews and research articles that cite or mention PDB entries as well as access to figures and legends from full-text open-access publications that describe PDB entries. A powerful new query system not only shows all the PDB entries that match a given query, but also shows the ‘best structures’ for a given macromolecule, ligand complex or sequence family using data-quality information from the wwPDB validation reports. A PDBe RESTful API has been developed to provide unified access to macromolecular structure data available in the PDB and EMDB archives as well as value-added annotations, e.g. regarding structure quality and up-to-date cross-reference information from the SIFTS resource. Taken together, these new developments facilitate unified access to macromolecular structure data in an intuitive way for non-expert users and support expert users in analysing macromolecular structure data. PMID:26476444

SAD phasing of a structure based on cocrystallized iodides using an in-house Cu Kalpha X-ray source: effects of data redundancy and completeness on structure solution.

PubMed

Yogavel, Manickam; Gill, Jasmita; Mishra, Prakash Chandra; Sharma, Amit

2007-08-01

Superoxide dismutase (SOD) from Potentilla atrosanguinea (Wall. ex. Lehm.) was crystallized using 20% PEG 3350 and 0.2 M ammonium iodide and diffraction data were collected to 2.36 A resolution using an in-house Cu Kalpha X-ray source. Analyses show that data with a redundancy of 3.2 were sufficient to determine the structure by the SAD technique using the iodine anomalous signal. This redundancy is lower than that in previous cases in which protein structures were determined using iodines for phasing and in-house copper X-ray sources. Cocrystallization of proteins with halide salts such as ammonium iodide in combination with copper-anode X-ray radiation can therefore serve as a powerful and easy avenue for structure solution.

Synchrotron FTIR micro-spectroscopy for structural analysis of Lewy bodies in the brain of Parkinson’s disease patients

NASA Astrophysics Data System (ADS)

Araki, Katsuya; Yagi, Naoto; Ikemoto, Yuka; Yagi, Hisashi; Choong, Chi-Jing; Hayakawa, Hideki; Beck, Goichi; Sumi, Hisae; Fujimura, Harutoshi; Moriwaki, Taro; Nagai, Yoshitaka; Goto, Yuji; Mochizuki, Hideki

2015-12-01

Lewy bodies (LBs), which mainly consist of α-synuclein (α-syn), are neuropathological hallmarks of patients with Parkinson’s disease (PD). The fine structure of LBs is unknown, and LBs cannot be made artificially. Nevertheless, many studies have described fibrillisation using recombinant α-syn purified from E. coli. An extremely fundamental problem is whether the structure of LBs is the same as that of recombinant amyloid fibrils. Thus, we used synchrotron Fourier transform infrared micro-spectroscopy (FTIRM) to analyse the fine structure of LBs in the brain of PD patients. Our results showed a shift in the infrared spectrum that indicates abundance of a β-sheet-rich structure in LBs. Also, 2D infrared mapping of LBs revealed that the content of the β-sheet structure is higher in the halo than in the core, and the core contains a large amount of proteins and lipids.

Characteristics of amorphous kerogens fractionated from terrigenous sedimentary rocks

NASA Astrophysics Data System (ADS)

Suzuki, Noriyuki

1984-02-01

A preliminary attempt to fractionate amorphous kerogens from terrigenous bulk kerogen by a benzene-water two phase partition method under acidic condition was made. Microscopic observation revealed that amorphous kerogens and structured kerogens were fractionated effectively by this method. Characteristics of the amorphous and structured kerogens fractionated by this method were examined by some chemical analyses and compared with those of the bulk kerogen and humic acid isolated from the same rock sample (Haizume Formation, Pleistocene, Japan). The elemental and infrared (IR) analyses showed that the amorphous kerogen fraction had the highest atomic H/C ratio and the lowest atomic N/C ratio and was the richest in aliphatic structures and carbonyl and carboxyl functional groups. Quantities of fatty acids from the saponification products of each geopolymer were in agreement with the results of elemental and IR analyses. Distribution of the fatty acids was suggestive that more animal lipids participate in the formation of amorphous kerogens because of the abundance of relatively lower molecular weight fatty acids (such as C 16 and C 18 acids) in saponification products of amorphous kerogens. On the other hand, although the amorphous kerogen fraction tends to be rich in aliphatic structures compared with bulk kerogen of the same rock samples, van Krevelen plots of elemental compositions of kerogens from the core samples (Nishiyama Oil Field, Tertiary, Japan) reveal that the amorphous kerogen fraction is not necessarily characterized by markedly high atomic H/C ratio. This was attributed to the oxic environment of deposition and the abundance of biodegraded terrestrial amorphous organic matter in the amorphous kerogen fraction used in this work.

Testing the equivalence of modern human cranial covariance structure: Implications for bioarchaeological applications.

PubMed

von Cramon-Taubadel, Noreen; Schroeder, Lauren

2016-10-01

Estimation of the variance-covariance (V/CV) structure of fragmentary bioarchaeological populations requires the use of proxy extant V/CV parameters. However, it is currently unclear whether extant human populations exhibit equivalent V/CV structures. Random skewers (RS) and hierarchical analyses of common principal components (CPC) were applied to a modern human cranial dataset. Cranial V/CV similarity was assessed globally for samples of individual populations (jackknifed method) and for pairwise population sample contrasts. The results were examined in light of potential explanatory factors for covariance difference, such as geographic region, among-group distance, and sample size. RS analyses showed that population samples exhibited highly correlated multivariate responses to selection, and that differences in RS results were primarily a consequence of differences in sample size. The CPC method yielded mixed results, depending upon the statistical criterion used to evaluate the hierarchy. The hypothesis-testing (step-up) approach was deemed problematic due to sensitivity to low statistical power and elevated Type I errors. In contrast, the model-fitting (lowest AIC) approach suggested that V/CV matrices were proportional and/or shared a large number of CPCs. Pairwise population sample CPC results were correlated with cranial distance, suggesting that population history explains some of the variability in V/CV structure among groups. The results indicate that patterns of covariance in human craniometric samples are broadly similar but not identical. These findings have important implications for choosing extant covariance matrices to use as proxy V/CV parameters in evolutionary analyses of past populations. © 2016 Wiley Periodicals, Inc.

Vertebral microanatomy in squamates: structure, growth and ecological correlates

PubMed Central

Houssaye, Alexandra; Mazurier, Arnaud; Herrel, Anthony; Volpato, Virginie; Tafforeau, Paul; Boistel, Renaud; de Buffrénil, Vivian

2010-01-01

The histological study of vertebrae in extant squamates shows that the internal vertebral structure in this group differs from that of other tetrapods. Squamate vertebrae are lightly built and basically composed of two roughly concentric osseous tubes – one surrounding the neural canal and the other constituting the peripheral cortex of the vertebra – connected by few thin trabeculae. This structure, which characteristically evokes that of a tubular bone, results from a peculiar remodelling process characterised by an imbalance between local bone resorption and redeposition; in both periosteal and endosteo-endochondral territories, bone is extensively resorbed but not reconstructed in the same proportion by secondary deposits. This process is particularly intense in the deep region of the centrum, where originally compact cortices are made cancellous, and where the endochondral spongiosa is very loose. This remodelling process starts at an early stage of development and remains active throughout subsequent growth. The growth of squamate centra is also strongly asymmetrical, with the posterior (condylar) part growing much faster than the anterior (cotylar) part. Preliminary analyses testing for associations between vertebral structure and habitat use suggest that vertebrae of fossorial taxa are denser than those of terrestrial taxa, those in aquatic taxa being of intermediate density. However, phylogenetically informed analyses do not corroborate these findings, thus suggesting a strong phylogenetic signal in the data. As our analyses demonstrate that vertebrae in snakes are generally denser than those of lizards sensu stricto, this may drive the presence of a phylogenetic signal in the data. More comprehensive sampling of fossorial and aquatic lizards is clearly needed to more rigorously evaluate these patterns. PMID:21039477

Genetic structure characterization of Chileans reflects historical immigration patterns.

PubMed

Eyheramendy, Susana; Martinez, Felipe I; Manevy, Federico; Vial, Cecilia; Repetto, Gabriela M

2015-03-17

Identifying the ancestral components of genomes of admixed individuals helps uncovering the genetic basis of diseases and understanding the demographic history of populations. We estimate local ancestry on 313 Chileans and assess the contribution from three continental populations. The distribution of ancestry block-length suggests an average admixing time around 10 generations ago. Sex-chromosome analyses confirm imbalanced contribution of European men and Native-American women. Previously known genes under selection contain SNPs showing large difference in allele frequencies. Furthermore, we show that assessing ancestry is harder at SNPs with higher recombination rates and easier at SNPs with large difference in allele frequencies at the ancestral populations. Two observations, that African ancestry proportions systematically decrease from North to South, and that European ancestry proportions are highest in central regions, show that the genetic structure of Chileans is under the influence of a diffusion process leading to an ancestry gradient related to geography.

Genetic structure characterization of Chileans reflects historical immigration patterns

PubMed Central

Eyheramendy, Susana; Martinez, Felipe I.; Manevy, Federico; Vial, Cecilia; Repetto, Gabriela M.

2015-01-01

Identifying the ancestral components of genomes of admixed individuals helps uncovering the genetic basis of diseases and understanding the demographic history of populations. We estimate local ancestry on 313 Chileans and assess the contribution from three continental populations. The distribution of ancestry block-length suggests an average admixing time around 10 generations ago. Sex-chromosome analyses confirm imbalanced contribution of European men and Native-American women. Previously known genes under selection contain SNPs showing large difference in allele frequencies. Furthermore, we show that assessing ancestry is harder at SNPs with higher recombination rates and easier at SNPs with large difference in allele frequencies at the ancestral populations. Two observations, that African ancestry proportions systematically decrease from North to South, and that European ancestry proportions are highest in central regions, show that the genetic structure of Chileans is under the influence of a diffusion process leading to an ancestry gradient related to geography. PMID:25778948

NASA/FAA general aviation crash dynamics program

NASA Technical Reports Server (NTRS)

Thomson, R. G.; Hayduk, R. J.; Carden, H. D.

1981-01-01

The program involves controlled full scale crash testing, nonlinear structural analyses to predict large deflection elastoplastic response, and load attenuating concepts for use in improved seat and subfloor structure. Both analytical and experimental methods are used to develop expertise in these areas. Analyses include simplified procedures for estimating energy dissipating capabilities and comprehensive computerized procedures for predicting airframe response. These analyses are developed to provide designers with methods for predicting accelerations, loads, and displacements on collapsing structure. Tests on typical full scale aircraft and on full and subscale structural components are performed to verify the analyses and to demonstrate load attenuating concepts. A special apparatus was built to test emergency locator transmitters when attached to representative aircraft structure. The apparatus is shown to provide a good simulation of the longitudinal crash pulse observed in full scale aircraft crash tests.

Bmp signaling mediates endoderm pouch morphogenesis by regulating Fgf signaling in zebrafish.

PubMed

Lovely, C Ben; Swartz, Mary E; McCarthy, Neil; Norrie, Jacqueline L; Eberhart, Johann K

2016-06-01

The endodermal pouches are a series of reiterated structures that segment the pharyngeal arches and help pattern the vertebrate face. Multiple pathways regulate the complex process of endodermal development, including the Bone morphogenetic protein (Bmp) pathway. However, the role of Bmp signaling in pouch morphogenesis is poorly understood. Using genetic and chemical inhibitor approaches, we show that pouch morphogenesis requires Bmp signaling from 10-18 h post-fertilization, immediately following gastrulation. Blocking Bmp signaling during this window results in morphological defects to the pouches and craniofacial skeleton. Using genetic chimeras we show that Bmp signals directly to the endoderm for proper morphogenesis. Time-lapse imaging and analysis of reporter transgenics show that Bmp signaling is necessary for pouch outpocketing via the Fibroblast growth factor (Fgf) pathway. Double loss-of-function analyses demonstrate that Bmp and Fgf signaling interact synergistically in craniofacial development. Collectively, our analyses shed light on the tissue and signaling interactions that regulate development of the vertebrate face. © 2016. Published by The Company of Biologists Ltd.

Treatment of type 1 diabetes with adipose tissue-derived stem cells expressing pancreatic duodenal homeobox 1.

PubMed

Lin, Guiting; Wang, Guifang; Liu, Gang; Yang, Li-Jun; Chang, Lung-Ji; Lue, Tom F; Lin, Ching-Shwun

2009-12-01

Due to the limited supply of donor pancreas, it is imperative that we identify alternative cell sources that can be used to treat diabetes mellitus (DM). Multipotent adipose tissue-derived stem cells (ADSC) can be abundantly and safely isolated for autologous transplantation and therefore are an ideal candidate. Here, we report the derivation of insulin-producing cells from human or rat ADSC by transduction with the pancreatic duodenal homeobox 1 (Pdx1) gene. RT-PCR analyses showed that native ADSC expressed insulin, glucagon, and NeuroD genes that were up-regulated following Pdx1 transduction. ELISA analyses showed that the transduced cells secreted increasing amount of insulin in response to increasing concentration of glucose. Transplantation of these cells under the renal capsule of streptozotocin-induced diabetic rats resulted in lowered blood glucose, higher glucose tolerance, smoother fur, and less cataract. Histological examination showed that the transplanted cells formed tissue-like structures and expressed insulin. Thus, ADSC-expressing Pdx1 appear to be suitable for treatment of DM.

The landscape context of cereal aphid–parasitoid interactions

PubMed Central

Thies, Carsten; Roschewitz, Indra; Tscharntke, Teja

2005-01-01

Analyses at multiple spatial scales may show how important ecosystem services such as biological control are determined by processes acting on the landscape scale. We examined cereal aphid–parasitoid interactions in wheat fields in agricultural landscapes differing in structural complexity (32–100% arable land). Complex landscapes were associated with increased aphid mortality resulting from parasitism, but also with higher aphid colonization, thereby counterbalancing possible biological control by parasitoids and lastly resulting in similar aphid densities across landscapes. Thus, undisturbed perennial habitats appeared to enhance both pests and natural enemies. Analyses at multiple spatial scales (landscape sectors of 0.5–6 km diameter) showed that correlations between parasitism and percentage of arable land were significant at scales of 0.5–2 km, whereas aphid densities responded to percentage of arable land at scales of 1–6 km diameter. Hence, the higher trophic level populations appeared to be determined by smaller landscape sectors owing to dispersal limitation, showing the ‘functional spatial scale’ for species-specific landscape management. PMID:15695212

Bmp signaling mediates endoderm pouch morphogenesis by regulating Fgf signaling in zebrafish

PubMed Central

Swartz, Mary E.; McCarthy, Neil; Norrie, Jacqueline L.; Eberhart, Johann K.

2016-01-01

The endodermal pouches are a series of reiterated structures that segment the pharyngeal arches and help pattern the vertebrate face. Multiple pathways regulate the complex process of endodermal development, including the Bone morphogenetic protein (Bmp) pathway. However, the role of Bmp signaling in pouch morphogenesis is poorly understood. Using genetic and chemical inhibitor approaches, we show that pouch morphogenesis requires Bmp signaling from 10-18 h post-fertilization, immediately following gastrulation. Blocking Bmp signaling during this window results in morphological defects to the pouches and craniofacial skeleton. Using genetic chimeras we show that Bmp signals directly to the endoderm for proper morphogenesis. Time-lapse imaging and analysis of reporter transgenics show that Bmp signaling is necessary for pouch outpocketing via the Fibroblast growth factor (Fgf) pathway. Double loss-of-function analyses demonstrate that Bmp and Fgf signaling interact synergistically in craniofacial development. Collectively, our analyses shed light on the tissue and signaling interactions that regulate development of the vertebrate face. PMID:27122171

Long-distance travel behaviours accelerate and aggravate the large-scale spatial spreading of infectious diseases.

PubMed

Xu, Zhijing; Zu, Zhenghu; Zheng, Tao; Zhang, Wendou; Xu, Qing; Liu, Jinjie

2014-01-01

The study analyses the role of long-distance travel behaviours on the large-scale spatial spreading of directly transmitted infectious diseases, focusing on two different travel types in terms of the travellers travelling to a specific group or not. For this purpose, we have formulated and analysed a metapopulation model in which the individuals in each subpopulation are organised into a scale-free contact network. The long-distance travellers between the subpopulations will temporarily change the network structure of the destination subpopulation through the "merging effects (MEs)," which indicates that the travellers will be regarded as either connected components or isolated nodes in the contact network. The results show that the presence of the MEs has constantly accelerated the transmission of the diseases and aggravated the outbreaks compared to the scenario in which the diversity of the long-distance travel types is arbitrarily discarded. Sensitivity analyses show that these results are relatively constant regarding a wide range variation of several model parameters. Our study has highlighted several important causes which could significantly affect the spatiotemporal disease dynamics neglected by the present studies.

Functional Evolution in Orthologous Cell-encoded RNA-dependent RNA Polymerases.

PubMed

Qian, Xinlei; Hamid, Fursham M; El Sahili, Abbas; Darwis, Dina Amallia; Wong, Yee Hwa; Bhushan, Shashi; Makeyev, Eugene V; Lescar, Julien

2016-04-22

Many eukaryotic organisms encode more than one RNA-dependent RNA polymerase (RdRP) that probably emerged as a result of gene duplication. Such RdRP paralogs often participate in distinct RNA silencing pathways and show characteristic repertoires of enzymatic activities in vitro However, to what extent members of individual paralogous groups can undergo functional changes during speciation remains an open question. We show that orthologs of QDE-1, an RdRP component of the quelling pathway in Neurospora crassa, have rapidly diverged in evolution at the amino acid sequence level. Analyses of purified QDE-1 polymerases from N. crassa (QDE-1(Ncr)) and related fungi, Thielavia terrestris (QDE-1(Tte)) and Myceliophthora thermophila (QDE-1(Mth)), show that all three enzymes can synthesize RNA, but the precise modes of their action differ considerably. Unlike their QDE-1(Ncr) counterpart favoring processive RNA synthesis, QDE-1(Tte) and QDE-1(Mth) produce predominantly short RNA copies via primer-independent initiation. Surprisingly, a 3.19 Å resolution crystal structure of QDE-1(Tte) reveals a quasisymmetric dimer similar to QDE-1(Ncr) Further electron microscopy analyses confirm that QDE-1(Tte) occurs as a dimer in solution and retains this status upon interaction with a template. We conclude that divergence of orthologous RdRPs can result in functional innovation while retaining overall protein fold and quaternary structure. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Functional Evolution in Orthologous Cell-encoded RNA-dependent RNA Polymerases*

PubMed Central

Qian, Xinlei; Hamid, Fursham M.; El Sahili, Abbas; Darwis, Dina Amallia; Wong, Yee Hwa; Bhushan, Shashi; Makeyev, Eugene V.; Lescar, Julien

2016-01-01

Many eukaryotic organisms encode more than one RNA-dependent RNA polymerase (RdRP) that probably emerged as a result of gene duplication. Such RdRP paralogs often participate in distinct RNA silencing pathways and show characteristic repertoires of enzymatic activities in vitro. However, to what extent members of individual paralogous groups can undergo functional changes during speciation remains an open question. We show that orthologs of QDE-1, an RdRP component of the quelling pathway in Neurospora crassa, have rapidly diverged in evolution at the amino acid sequence level. Analyses of purified QDE-1 polymerases from N. crassa (QDE-1Ncr) and related fungi, Thielavia terrestris (QDE-1Tte) and Myceliophthora thermophila (QDE-1Mth), show that all three enzymes can synthesize RNA, but the precise modes of their action differ considerably. Unlike their QDE-1Ncr counterpart favoring processive RNA synthesis, QDE-1Tte and QDE-1Mth produce predominantly short RNA copies via primer-independent initiation. Surprisingly, a 3.19 Å resolution crystal structure of QDE-1Tte reveals a quasisymmetric dimer similar to QDE-1Ncr. Further electron microscopy analyses confirm that QDE-1Tte occurs as a dimer in solution and retains this status upon interaction with a template. We conclude that divergence of orthologous RdRPs can result in functional innovation while retaining overall protein fold and quaternary structure. PMID:26907693

Kinematics and subpopulations' structure definition of blue fox (Alopex lagopus) sperm motility using the ISAS® V1 CASA system.

PubMed

Soler, C; García, A; Contell, J; Segervall, J; Sancho, M

2014-08-01

Over recent years, technological advances have brought innovation in assisted reproduction to the agriculture. Fox species are of great economical interest in some countries, but their semen characteristics have not been studied enough. To advance the knowledge of function of fox spermatozoa, five samples were obtained by masturbation, in the breeding season. Kinetic analysis was performed using ISAS® v1 system. Usual kinematic parameters (VCL, VSL, VAP, LIN, STR, WOB, ALH and BCF) were considered. To establish the standardization for the analysis of samples, the minimum number of cells to analyse and the minimum number of fields to capture were defined. In the second step, the presence of subpopulations in blue fox semen was analysed. The minimum number of cells to test was 30, because kinematic parameters remained constant along the groups of analysis. Also, the effectiveness of ISAS® D4C20 counting chamber was studied, showing that the first five squares presented equivalent results, while in the squares six and seven, the kinematic parameters showed a reduction in all of them, but not in the concentration or motility percentage. Kinematic variables were grouped into two principal components (PC). A linear movement characterized PC1, while PC2 showed an oscillatory movement. Three subpopulations were found, varying in structure among different animals. © 2014 Blackwell Verlag GmbH.

Analyses of the NAC transcription factor gene family in Gossypium raimondii Ulbr.: chromosomal location, structure, phylogeny, and expression patterns.

PubMed

Shang, Haihong; Li, Wei; Zou, Changsong; Yuan, Youlu

2013-07-01

NAC domain proteins are plant-specific transcription factors known to play diverse roles in various plant developmental processes. In the present study, we performed the first comprehensive study of the NAC gene family in Gossypium raimondii Ulbr., incorporating phylogenetic, chromosomal location, gene structure, conserved motif, and expression profiling analyses. We identified 145 NAC transcription factor (NAC-TF) genes that were phylogenetically clustered into 18 distinct subfamilies. Of these, 127 NAC-TF genes were distributed across the 13 chromosomes, 80 (55%) were preferentially retained duplicates located in both duplicated regions and six were located in triplicated chromosomal regions. The majority of NAC-TF genes showed temporal-, spatial-, and tissue-specific expression patterns based on transcriptomic and qRT-PCR analyses. However, the expression patterns of several duplicate genes were partially redundant, suggesting the occurrence of sub-functionalization during their evolution. Based on their genomic organization, we concluded that genomic duplications contributed significantly to the expansion of the NAC-TF gene family in G. raimondii. Comprehensive analysis of their expression profiles could provide novel insights into the functional divergence among members of the NAC gene family in G. raimondii. © 2013 Institute of Botany, Chinese Academy of Sciences.

Evidence for a large expansion and subfunctionalisation of globin genes in sea anemones.

PubMed

Smith, Hayden L; Pavasovic, Ana; Surm, Joachim M; Phillips, Matthew J; Prentis, Peter J

2018-06-27

The globin gene superfamily has been well-characterised in vertebrates, however, there has been limited research in early-diverging lineages, such as phylum Cnidaria. This study aimed to identify globin genes in multiple cnidarian lineages, and use bioinformatic approaches to characterise the evolution, structure and expression of these genes. Phylogenetic analyses and in silico protein predictions showed that all cnidarians have undergone an expansion of globin genes, which likely have a hexacoordinate protein structure. Our protein modelling has also revealed the possibility of a single pentacoordinate globin lineage in anthozoan species. Some cnidarian globin genes displayed tissue and development specific expression with very few orthologous genes similarly expressed across species. Our phylogenetic analyses also revealed that eumetazoan globin genes form a polyphyletic relationship with vertebrate globin genes. Overall, our analyses suggest that a Ngb-like and GbX-like gene were most likely present in the globin gene repertoire for the last common ancestor of eumetazoans. The identification of a large-scale expansion and subfunctionalisation of globin genes in actiniarians provides an excellent starting point to further our understanding of the evolution and function of the globin gene superfamily in early-diverging lineages.

On the nature of motivational orientations: implications of assessed goals and gender differences for motivational goal theory.

PubMed

Alonso-Tapia, Jesús; Huertas, Juan A; Ruiz, Miguel A

2010-05-01

In a historical revision of the achievement goal construct, Elliot (2005) recognized that there is little consensus on whether the term "goal" in "achievement goal orientations" (GO) is best represented as an "aim", as an overarching orientation encompassing several "aims", or as a combination of aims and other processes -self-regulation, etc.-. Elliot pointed also that goal theory research provides evidence for different models of GO. As there were no consensus on these issues, we decided to get evidence about the nature and structure of GO, about the role of gender differences in the configuration of such structure, and about relations between GO, expectancies, volitional processes and achievement. A total of 382 university students from different faculties of two public universities of Madrid (Spain) that voluntarily accepted to fill in a questionnaire that assessed different goals, expectancies and self-regulatory processes participated in the study. Scales reliability, confirmatory factor analyses, multiple-group analyses, and correlation and regression analyses were carried out. Results support the trichotomous model of GO, the consideration of GO as a combination of aims and other psychological processes, showed some gender differences and favour the adoption of a multiple goal perspective for explaining students' motivation.

Structural Analysis of Composite Flywheels: an Integrated NDE and FEM Approach

NASA Technical Reports Server (NTRS)

Abdul-Aziz, Ali; Baaklini, George; Trudell, Jeffrey

2001-01-01

A structural assessment by integrating finite-element methods (FEM) and a nondestructive evaluation (NDE) of two flywheel rotor assemblies is presented. Composite rotor A is pancake-like with a solid hub design, and composite rotor B is cylindrical with a hollow hub design. Detailed analyses under combined centrifugal and interference-fit loading are performed. Two- and three-dimensional stress analyses and two-dimensional fracture mechanics analyses are conducted. A comparison of the structural analysis results obtained with those extracted via NDE findings is reported. Contact effects due to press-fit conditions are evaluated. Stress results generated from the finite-element analyses were corroborated with the analytical solution. Cracks due to rotational loading up to 48,000 rpm for rotor A and 34,000 rpm for rotor B were successfully imaged with NDE and predicted with FEM and fracture mechanics analyses. A procedure that extends current structural analysis to a life prediction tool is also defined.

Liquid level sensor based on fiber ring laser with single-mode-offset coreless-single-mode fiber structure

NASA Astrophysics Data System (ADS)

Wang, Zixiao; Tan, Zhongwei; Xing, Rui; Liang, Linjun; Qi, Yanhui; Jian, Shuisheng

2016-10-01

A novel reflective liquid level sensor based on single-mode-offset coreless-single-mode (SOCS) fiber structure is proposed and experimentally demonstrated. Theory analyses and experimental results indicate that offset fusion can remarkably enhance the sensitivity of sensor. Ending-reflecting structure makes the sensor compact and easy to deploy. Meanwhile, we propose a laser sensing system, and the SOCS structure is used as sensing head and laser filter simultaneously. Experimental results show that laser spectra with high optical signal-to-noise ratio (-30 dB) and narrow 3-dB bandwidth (<0.15 nm) are achieved. Various liquids with different indices are used for liquid level sensing, besides, the refractive index sensitivity is also investigated. In measurement range, the sensing system presents steady laser output.

High-Resolution Mapping of Chromatin Conformation in Cardiac Myocytes Reveals Structural Remodeling of the Epigenome in Heart Failure

PubMed Central

Rosa-Garrido, Manuel; Chapski, Douglas J.; Schmitt, Anthony D.; Kimball, Todd H.; Karbassi, Elaheh; Monte, Emma; Balderas, Enrique; Pellegrini, Matteo; Shih, Tsai-Ting; Soehalim, Elizabeth; Liem, David; Ping, Peipei; Galjart, Niels J.; Ren, Shuxun; Wang, Yibin; Ren, Bing

2017-01-01

Background: Cardiovascular disease is associated with epigenomic changes in the heart; however, the endogenous structure of cardiac myocyte chromatin has never been determined. Methods: To investigate the mechanisms of epigenomic function in the heart, genome-wide chromatin conformation capture (Hi-C) and DNA sequencing were performed in adult cardiac myocytes following development of pressure overload–induced hypertrophy. Mice with cardiac-specific deletion of CTCF (a ubiquitous chromatin structural protein) were generated to explore the role of this protein in chromatin structure and cardiac phenotype. Transcriptome analyses by RNA-seq were conducted as a functional readout of the epigenomic structural changes. Results: Depletion of CTCF was sufficient to induce heart failure in mice, and human patients with heart failure receiving mechanical unloading via left ventricular assist devices show increased CTCF abundance. Chromatin structural analyses revealed interactions within the cardiac myocyte genome at 5-kb resolution, enabling examination of intra- and interchromosomal events, and providing a resource for future cardiac epigenomic investigations. Pressure overload or CTCF depletion selectively altered boundary strength between topologically associating domains and A/B compartmentalization, measurements of genome accessibility. Heart failure involved decreased stability of chromatin interactions around disease-causing genes. In addition, pressure overload or CTCF depletion remodeled long-range interactions of cardiac enhancers, resulting in a significant decrease in local chromatin interactions around these functional elements. Conclusions: These findings provide a high-resolution chromatin architecture resource for cardiac epigenomic investigations and demonstrate that global structural remodeling of chromatin underpins heart failure. The newly identified principles of endogenous chromatin structure have key implications for epigenetic therapy. PMID:28802249

High-Resolution Mapping of Chromatin Conformation in Cardiac Myocytes Reveals Structural Remodeling of the Epigenome in Heart Failure.

PubMed

Rosa-Garrido, Manuel; Chapski, Douglas J; Schmitt, Anthony D; Kimball, Todd H; Karbassi, Elaheh; Monte, Emma; Balderas, Enrique; Pellegrini, Matteo; Shih, Tsai-Ting; Soehalim, Elizabeth; Liem, David; Ping, Peipei; Galjart, Niels J; Ren, Shuxun; Wang, Yibin; Ren, Bing; Vondriska, Thomas M

2017-10-24

Cardiovascular disease is associated with epigenomic changes in the heart; however, the endogenous structure of cardiac myocyte chromatin has never been determined. To investigate the mechanisms of epigenomic function in the heart, genome-wide chromatin conformation capture (Hi-C) and DNA sequencing were performed in adult cardiac myocytes following development of pressure overload-induced hypertrophy. Mice with cardiac-specific deletion of CTCF (a ubiquitous chromatin structural protein) were generated to explore the role of this protein in chromatin structure and cardiac phenotype. Transcriptome analyses by RNA-seq were conducted as a functional readout of the epigenomic structural changes. Depletion of CTCF was sufficient to induce heart failure in mice, and human patients with heart failure receiving mechanical unloading via left ventricular assist devices show increased CTCF abundance. Chromatin structural analyses revealed interactions within the cardiac myocyte genome at 5-kb resolution, enabling examination of intra- and interchromosomal events, and providing a resource for future cardiac epigenomic investigations. Pressure overload or CTCF depletion selectively altered boundary strength between topologically associating domains and A/B compartmentalization, measurements of genome accessibility. Heart failure involved decreased stability of chromatin interactions around disease-causing genes. In addition, pressure overload or CTCF depletion remodeled long-range interactions of cardiac enhancers, resulting in a significant decrease in local chromatin interactions around these functional elements. These findings provide a high-resolution chromatin architecture resource for cardiac epigenomic investigations and demonstrate that global structural remodeling of chromatin underpins heart failure. The newly identified principles of endogenous chromatin structure have key implications for epigenetic therapy. © 2017 The Authors.

Synthesis and physical characterization of γ-Fe2O3 and (α+γ)-Fe2O3 nanoparticles

NASA Astrophysics Data System (ADS)

Bhavani, P.; Reddy, N. Ramamanohar; Reddy, I. Venkata Subba

2017-01-01

Magnetic nanoparticles were synthesized at different hydrothermal temperatures (HT; 100, 130, 160 and 190 °C) by using a facile hydrothermal route combined with a subsequent calcination process. The calcined materials were analyzed for phase, microstructure, and magnetic and dielectric properties through different characterization techniques. The structural analyses revealed that the material prepared at a HT of 100 °C and sequentially calcined at 300 °C for 3 h showed a high degree of the maghemite structure. On the other hand calcined materials showed a small additional peak belonging to the hematite structure. FESEM micrographs of the materials calcined at HT, of 100 °C and 190 °C showed spherical-like nanoparticles with diameters in range 30 - 54 nm. Materials prepared at a HT of 160 °C followed by calcination at 300 °C for 3 h exhibited the highest saturation magnetization, Ms = 67 emu/g, with a lower coercivity; all materials were in a single domain state. A high dielectric constant (105.54) was observed for the calcined material that had been prepared at a HT of 130 °C. The dielectric properties of synthesized materials showed an almost frequency-independent behavior.

Self-Assembled Multi-Component Catenanes: Structural Insights into an Adaptable Class of Molecular Receptors and [2]-Catenanes

DTIC Science & Technology

2012-06-11

V fragmentor setting, the targeted MS1 ion was the singly charged ion [1b2 F22 + H] + (m/z = 1626.7100). For DSA reaction mixtures containing F4b and...the basis of its high abundance under the electrospray conditions. Both analyses showed two tetrameric daughter ions ([1b3 F21 + H] + and [1b2 F22 ...dimeric daughter ion [ F22 + H] + (Scheme 2), which only occurs in the non-alternating [1b2 F22 ] structure, was observed in both cases, but with only

The relationship between motivational structure, sense of control, intrinsic motivation and university students' alcohol consumption.

PubMed

Shamloo, Zohreh Sepehri; Cox, W Miles

2010-02-01

The aim of this study was to determine how sense of control and intrinsic motivation are related to university students' motivational structure and alcohol consumption. Participants were 94 university students who completed the Personal Concerns Inventory, Shapiro Control Inventory, Helplessness Questionnaire, Intrinsic-Extrinsic Aspirations Scale, and Alcohol Use Questionnaire. Results showed that sense of control and intrinsic motivation were positively correlated with adaptive motivation and negatively correlated with alcohol consumption. Mediational analyses indicated that adaptive motivation fully mediated the relationship between sense of control/intrinsic motivation and alcohol consumption.

Hospital cost-containment strategies that earn the respect of rating agencies.

PubMed

Dopoulos, Jason

2016-01-01

To confirm that hospitals have the necessary structures and strategies in place to reduce costs and secure future market share, credit rating agencies analyze a variety of quantitative and qualitative criteria, including: Salaries and benefits, bad debt, age of plant and depreciation, and other line items that may point to inefficiencies in a hospital's expense structure. Cost-benefit analyses, strategic plans, and leadership qualities that show the long-term value of expense cuts, capital investments, and mergers and acquisitions. Cost-effective and clinically appropriate shifts in a hospital's outpatient-to-inpatient ratio. Liquidity and market share.

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

Kelly, R.F.; Kravchenko, I.I.; Kuharik, J.C.

Widespread use of chromated copper arsenate (CCA) as a wood preservative has led to increasing public concern regarding possible toxic contamination of areas surrounding CCA-treated structures, e.g., decks, playground equipment, etc. Appreciable leaching of arsenic, chromium, and copper into soils adjacent to such structures has been demonstrated via standard techniques of analytical chemistry. The advantages of PIXE [rapid analysis, quick sample turnover, possible lower cost] suggest its application to this area of interest. PIXE studies in our laboratory of CCA-contaminated soil samples show good agreement with previous analyses of As, Cu, Cr, and other heavy-elemental content, with some variability inmore » diffusion rates.« less

The dynamics, structure, and conformational free energy of proline-containing antifreeze glycoprotein.

PubMed Central

Nguyen, Dat H; Colvin, Michael E; Yeh, Yin; Feeney, Robert E; Fink, William H

2002-01-01

Recent NMR studies of the solution structure of the 14-amino acid antifreeze glycoprotein AFGP-8 have concluded that the molecule lacks long-range order. The implication that an apparently unstructured molecule can still have a very precise function as a freezing inhibitor seems startling at first consideration. To gain insight into the nature of conformations and motions in AFGP-8, we have undertaken molecular dynamics simulations augmented with free energy calculations using a continuum solvation model. Starting from 10 different NMR structures, 20 ns of dynamics of AFGP were explored. The dynamics show that AFGP structure is composed of four segments, joined by very flexible pivots positioned at alanine 5, 8, and 11. The dynamics also show that the presence of prolines in this small AFGP structure facilitates the adoption of the poly-proline II structure as its overall conformation, although AFGP does adopt other conformations during the course of dynamics as well. The free energies calculated using a continuum solvation model show that the lowest free energy conformations, while being energetically equal, are drastically different in conformations. In other words, this AFGP molecule has many structurally distinct and energetically equal minima in its energy landscape. In addition, conformational, energetic, and hydrogen bond analyses suggest that the intramolecular hydrogen bonds between the N-acetyl group and the protein backbone are an important integral part of the overall stability of the AFGP molecule. The relevance of these findings to the mechanism of freezing inhibition is discussed. PMID:12023212

The dynamics, structure, and conformational free energy of proline-containing antifreeze glycoprotein.

PubMed

Nguyen, Dat H; Colvin, Michael E; Yeh, Yin; Feeney, Robert E; Fink, William H

2002-06-01

Recent NMR studies of the solution structure of the 14-amino acid antifreeze glycoprotein AFGP-8 have concluded that the molecule lacks long-range order. The implication that an apparently unstructured molecule can still have a very precise function as a freezing inhibitor seems startling at first consideration. To gain insight into the nature of conformations and motions in AFGP-8, we have undertaken molecular dynamics simulations augmented with free energy calculations using a continuum solvation model. Starting from 10 different NMR structures, 20 ns of dynamics of AFGP were explored. The dynamics show that AFGP structure is composed of four segments, joined by very flexible pivots positioned at alanine 5, 8, and 11. The dynamics also show that the presence of prolines in this small AFGP structure facilitates the adoption of the poly-proline II structure as its overall conformation, although AFGP does adopt other conformations during the course of dynamics as well. The free energies calculated using a continuum solvation model show that the lowest free energy conformations, while being energetically equal, are drastically different in conformations. In other words, this AFGP molecule has many structurally distinct and energetically equal minima in its energy landscape. In addition, conformational, energetic, and hydrogen bond analyses suggest that the intramolecular hydrogen bonds between the N-acetyl group and the protein backbone are an important integral part of the overall stability of the AFGP molecule. The relevance of these findings to the mechanism of freezing inhibition is discussed.

Aeroelastic Modeling of a Nozzle Startup Transient

NASA Technical Reports Server (NTRS)

Wang, Ten-See; Zhao, Xiang; Zhang, Sijun; Chen, Yen-Sen

2014-01-01

Lateral nozzle forces are known to cause severe structural damage to any new rocket engine in development during test. While three-dimensional, transient, turbulent, chemically reacting computational fluid dynamics methodology has been demonstrated to capture major side load physics with rigid nozzles, hot-fire tests often show nozzle structure deformation during major side load events, leading to structural damages if structural strengthening measures were not taken. The modeling picture is incomplete without the capability to address the two-way responses between the structure and fluid. The objective of this study is to develop a tightly coupled aeroelastic modeling algorithm by implementing the necessary structural dynamics component into an anchored computational fluid dynamics methodology. The computational fluid dynamics component is based on an unstructured-grid, pressure-based computational fluid dynamics formulation, while the computational structural dynamics component is developed under the framework of modal analysis. Transient aeroelastic nozzle startup analyses at sea level were performed, and the computed transient nozzle fluid-structure interaction physics presented,

Structural Anomalies Detected in Ceramic Matrix Composites Using Combined Nondestructive Evaluation and Finite Element Analysis (NDE and FEA)

NASA Technical Reports Server (NTRS)

Abdul-Aziz, Ali; Baaklini, George Y.; Bhatt, Ramakrishna T.

2003-01-01

Most reverse engineering approaches involve imaging or digitizing an object and then creating a computerized reconstruction that can be integrated, in three dimensions, into a particular design environment. The rapid prototyping technique builds high-quality physical prototypes directly from computer-aided design files. This fundamental technique for interpreting and interacting with large data sets is being used here via Velocity2 (an integrated image-processing software, ref. 1) using computed tomography (CT) data to produce a prototype three-dimensional test specimen model for analyses. A study at the NASA Glenn Research Center proposes to use these capabilities to conduct a combined nondestructive evaluation (NDE) and finite element analysis (FEA) to screen pretest and posttest structural anomalies in structural components. A tensile specimen made of silicon nitrite (Si3N4) ceramic matrix composite was considered to evaluate structural durability and deformity. Ceramic matrix composites are being sought as candidate materials to replace nickel-base superalloys for turbine engine applications. They have the unique characteristics of being able to withstand higher operating temperatures and harsh combustion environments. In addition, their low densities relative to metals help reduce component mass (ref. 2). Detailed three-dimensional volume rendering of the tensile test specimen was successfully carried out with Velocity2 (ref. 1) using two-dimensional images that were generated via computed tomography. Subsequent, three-dimensional finite element analyses were performed, and the results obtained were compared with those predicted by NDE-based calculations and experimental tests. It was shown that Velocity2 software can be used to render a three-dimensional object from a series of CT scan images with a minimum level of complexity. The analytical results (ref. 3) show that the high-stress regions correlated well with the damage sites identified by the CT scans and the experimental data. Furthermore, modeling of the voids collected via NDE offered an analytical advantage that resulted in more accurate assessments of the material s structural strength. The top figure shows a CT scan image of the specimen test section illustrating various hidden structural entities in the material and an optical image of the test specimen considered in this study. The bottom figure represents the stress response predicted from the finite element analyses (ref .3 ) for a selected CT slice where it clearly illustrates the correspondence of the high stress risers due to voids in the material with those predicted by the NDE. This study is continuing, and efforts are concentrated on improving the modeling capabilities to imitate the structural anomalies as detected.

SOLEIL shining on the solution-state structure of biomacromolecules by synchrotron X-ray footprinting at the Metrology beamline.

PubMed

Baud, A; Aymé, L; Gonnet, F; Salard, I; Gohon, Y; Jolivet, P; Brodolin, K; Da Silva, P; Giuliani, A; Sclavi, B; Chardot, T; Mercère, P; Roblin, P; Daniel, R

2017-05-01

Synchrotron X-ray footprinting complements the techniques commonly used to define the structure of molecules such as crystallography, small-angle X-ray scattering and nuclear magnetic resonance. It is remarkably useful in probing the structure and interactions of proteins with lipids, nucleic acids or with other proteins in solution, often better reflecting the in vivo state dynamics. To date, most X-ray footprinting studies have been carried out at the National Synchrotron Light Source, USA, and at the European Synchrotron Radiation Facility in Grenoble, France. This work presents X-ray footprinting of biomolecules performed for the first time at the X-ray Metrology beamline at the SOLEIL synchrotron radiation source. The installation at this beamline of a stopped-flow apparatus for sample delivery, an irradiation capillary and an automatic sample collector enabled the X-ray footprinting study of the structure of the soluble protein factor H (FH) from the human complement system as well as of the lipid-associated hydrophobic protein S3 oleosin from plant seed. Mass spectrometry analysis showed that the structural integrity of both proteins was not affected by the short exposition to the oxygen radicals produced during the irradiation. Irradiated molecules were subsequently analysed using high-resolution mass spectrometry to identify and locate oxidized amino acids. Moreover, the analyses of FH in its free state and in complex with complement C3b protein have allowed us to create a map of reactive solvent-exposed residues on the surface of FH and to observe the changes in oxidation of FH residues upon C3b binding. Studies of the solvent accessibility of the S3 oleosin show that X-ray footprinting offers also a unique approach to studying the structure of proteins embedded within membranes or lipid bodies. All the biomolecular applications reported herein demonstrate that the Metrology beamline at SOLEIL can be successfully used for synchrotron X-ray footprinting of biomolecules.

Retrospective and Prospective Decomposition Analysis of Chinese Manufacturing Energy Use, 1995-2020

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

Hasanbeigi, Ali; Price, Lynn; Fino-Chen, Cecilia

In 2010, China was responsible for nearly 20 percent of global energy use and 25 percent of energy-related carbon dioxide (CO 2) emissions. Unlike most countries, China’s energy consumption pattern is unique because the industrial sector dominates the country’s total energy consumption, accounting for about 70 percent of energy use and 72 percent of CO 2 emissions in 2010. For this reason, the development path of China’s industrial sector will greatly affect future energy demand and dynamics of not only China, but the entire world. A number of analyses of historical trends have been conducted, but careful projections of themore » key factors affecting China’s industry sector energy use over the next decade are scarce. This study analyzes industrial energy use and the economic structure of the Chinese manufacturing sector in detail. First, the study analyzes the energy use of and output from 18 industry sub-sectors. Then, retrospective (1995-2010) and prospective (2010-2020) decomposition analyses are conducted for these industrial sectors in order to show how different factors (production growth, structural change, and energy intensity change) influenced industrial energy use trends in China over the last 15 years and how they will do so over the next 10 years. The results of this study will allow policy makers to quantitatively compare the level of structural change in the past and in the years to come and adjust their policies if needed to move towards the target of less energy-intensive industries. The scenario analysis shows the structural change achieved through different paths and helps to understand the consequences of supporting or limiting the growth of certain manufacturing subsectors from the point of view of energy use and structural change. The results point out the industries that have the largest influence in such structural change« less

Isolation by environmental distance in mobile marine species: molecular ecology of franciscana dolphins at their southern range.

PubMed

Mendez, Martin; Rosenbaum, Howard C; Subramaniam, Ajit; Yackulic, Charles; Bordino, Pablo

2010-06-01

The assessment of population structure is a valuable tool for studying the ecology of endangered species and drafting conservation strategies. As we enhance our understanding about the structuring of natural populations, it becomes important that we also understand the processes behind these patterns. However, there are few rigorous assessments of the influence of environmental factors on genetic patterns in mobile marine species. Given their dispersal capabilities and localized habitat preferences, coastal cetaceans are adequate study species for evaluating environmental effects on marine population structure. The franciscana dolphin, a rare coastal cetacean endemic to the Western South Atlantic, was studied to examine these issues. We analysed genetic data from the mitochondrial DNA and 12 microsatellite markers for 275 franciscana samples utilizing frequency-based, maximum-likelihood and Bayesian algorithms to assess population structure and migration patterns. This information was combined with 10 years of remote sensing environmental data (chlorophyll concentration, water turbidity and surface temperature). Our analyses show the occurrence of genetically isolated populations within Argentina, in areas that are environmentally distinct. Combined evidence of genetic and environmental structure suggests that isolation by distance and a process here termed isolation by environmental distance can explain the observed correlations. Our approach elucidated important ecological and conservation aspects of franciscana dolphins, and has the potential to increase our understanding of ecological processes influencing genetic patterns in other marine species.

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

The determinants of bond angle variability in protein/peptide backbones: A comprehensive statistical/quantum mechanics analysis.

PubMed

Improta, Roberto; Vitagliano, Luigi; Esposito, Luciana

2015-11-01

The elucidation of the mutual influence between peptide bond geometry and local conformation has important implications for protein structure refinement, validation, and prediction. To gain insights into the structural determinants and the energetic contributions associated with protein/peptide backbone plasticity, we here report an extensive analysis of the variability of the peptide bond angles by combining statistical analyses of protein structures and quantum mechanics calculations on small model peptide systems. Our analyses demonstrate that all the backbone bond angles strongly depend on the peptide conformation and unveil the existence of regular trends as function of ψ and/or φ. The excellent agreement of the quantum mechanics calculations with the statistical surveys of protein structures validates the computational scheme here employed and demonstrates that the valence geometry of protein/peptide backbone is primarily dictated by local interactions. Notably, for the first time we show that the position of the H(α) hydrogen atom, which is an important parameter in NMR structural studies, is also dependent on the local conformation. Most of the trends observed may be satisfactorily explained by invoking steric repulsive interactions; in some specific cases the valence bond variability is also influenced by hydrogen-bond like interactions. Moreover, we can provide a reliable estimate of the energies involved in the interplay between geometry and conformations. © 2015 Wiley Periodicals, Inc.

Isolation of 8-hydroxyglycitein and 6-hydroxydaidzein from soybean miso.

PubMed

Hirota, Akira; Inaba, Miyuki; Chen, Yu-Chi; Abe, Naoki; Taki, Shoji; Yano, Masamichi; Kawaii, Satoru

2004-06-01

We isolated from soybean miso 8-hydroxyglycitein and 6-hydroxydaidzein as DPPH-radical scavengers, and elucidated their chemical structures by mass spectrometric, and (1)H- and (13)C-NMR spectrosopic analyses. These compounds showed DPPH-radical scavenging activity as high as that of alpha-tocopherol, 8-hydroxygenistein and 8-hydroxydaidzein. This is the first report of the isolation of 8-hydroxyglycitein from a natural source.

Community microrespirometry and molecular analyses reveal a diverse energy economy in Great Boiling Spring and Sandy's Spring West in the U.S. Great Basin.

PubMed

Murphy, Caitlin N; Dodsworth, Jeremy A; Babbitt, Aaron B; Hedlund, Brian P

2013-05-01

Microrespirometry showed that several organic and inorganic electron donors stimulated oxygen consumption in two ∼80°C springs. Sediment and planktonic communities were structurally and functionally distinct, and quantitative PCR revealed catabolically distinct subpopulations of Thermocrinis. This study suggests that a variety of chemolithotrophic metabolisms operate simultaneously in these springs.

Associations between DSM-5 section III personality traits and the Minnesota Multiphasic Personality Inventory 2-Restructured Form (MMPI-2-RF) scales in a psychiatric patient sample.

PubMed

Anderson, Jaime L; Sellbom, Martin; Ayearst, Lindsay; Quilty, Lena C; Chmielewski, Michael; Bagby, R Michael

2015-09-01

Our aim in the current study was to evaluate the convergence between Diagnostic and Statistical Manual of Mental Disorders, fifth edition (DSM-5) Section III dimensional personality traits, as operationalized via the Personality Inventory for DSM-5 (PID-5), and Minnesota Multiphasic Personality Inventory 2-Restructured Form (MMPI-2-RF) scale scores in a psychiatric patient sample. We used a sample of 346 (171 men, 175 women) patients who were recruited through a university-affiliated psychiatric facility in Toronto, Canada. We estimated zero-order correlations between the PID-5 and MMPI-2-RF substantive scale scores, as well as a series of exploratory structural equation modeling (ESEM) analyses to examine how these scales converged in multivariate latent space. Results generally showed empirical convergence between the scales of these two measures that were thematically meaningful and in accordance with conceptual expectations. Correlation analyses showed significant associations between conceptually expected scales, and the highest associations tended to be between scales that were theoretically related. ESEM analyses generated evidence for distinct internalizing, externalizing, and psychoticism factors across all analyses. These findings indicate convergence between these two measures and help further elucidate the associations between dysfunctional personality traits and general psychopathology. (c) 2015 APA, all rights reserved.

A new high-resolution 3-D quantitative method for analysing small morphological features: an example using a Cambrian trilobite.

PubMed

Esteve, Jorge; Zhao, Yuan-Long; Maté-González, Miguel Ángel; Gómez-Heras, Miguel; Peng, Jin

2018-02-12

Taphonomic processes play an important role in the preservation of small morphological features such as granulation or pits. However, the assessment of these features may face the issue of the small size of the specimens and, sometimes, the destructiveness of these analyses, which makes impossible carrying them out in singular specimen, such as holotypes or lectotypes. This paper takes a new approach to analysing small-morphological features, by using an optical surface roughness (OSR) meter to create a high-resolution three-dimensional digital-elevation model (DEM). This non-destructive technique allows analysing quantitatively the DEM using geometric morphometric methods (GMM). We created a number of DEMs from three populations putatively belonging to the same species of trilobite (Oryctocephalus indicus) that present the same cranidial outline, but differ in the presence or absence of the second and third transglabellar furrows. Profile analysis of the DEMs demonstrate that all three populations show similar preservation variation in the glabellar furrows and lobes. The GMM shows that all populations exhibit the same range of variation. Differences in preservation are a consequence of different degrees of cementation and rates of dissolution. Fast cementation enhances the preservation of glabellar furrows and lobes, while fast dissolution hampers preservation of the same structures.

Nematode communities in sediments of the Kermadec Trench, Southwest Pacific Ocean

NASA Astrophysics Data System (ADS)

Leduc, Daniel; Rowden, Ashley A.

2018-04-01

Hadal trenches are characterized by environmental conditions not found in any other deep-sea environment, such as steep topography and periodic disturbance by turbidity flows, which are likely responsible for the distinct nature of benthic communities of hadal trenches relative to those of the abyssal plain. Nematodes are the most abundant metazoans in the deep-sea benthos, but it is not yet clear if different trenches host distinct nematode communities, and no data are yet available on the communities of most trenches, including the Kermadec Trench in the Southwest Pacific. Quantitative core samples from the seafloor of the Kermadec Trench were recently obtained from four sites at 6000-9000 m depth which allowed for analyses of meiofauna, and nematodes in particular, for the first time. Nematode community and trophic structure was also compared with other trenches using published data. There was a bathymetric gradient in meiofauna abundance, biomass, and community structure within the Kermadec Trench, but patterns for species richness were ambiguous depending on which metric was used. There was a change in community structure from shallow to deep sites, as well as a consistent change in community structure from the upper sediment layers to the deeper sediment layers across the four sites. These patterns are most likely explained by variation in food availability within the trench, and related to trench topography. Together, deposit and microbial feeders represented 48-92% of total nematode abundance in the samples, which suggests that fine organic detritus and bacteria are major food sources. The relatively high abundance of epigrowth feeders at the 6000 and 9000 m sites (38% and 31%, respectively) indicates that relatively freshly settled microalgal cells represent another important food source at these sites. We found a significant difference in species community structure between the Kermadec and Tonga trenches, which was due to both the presence/absence of species as well as differences in relative abundances of shared species. The cluster and SIMPROF analyses of nematode genus community data across Pacific and Atlantic trenches identified two statistically significant natural groupings: the first group comprised all three Puerto Rico Trench samples, and the second comprised all remaining trenches (South Sandwich, Atacama, Tonga, and Kermadec). Our analyses show that differences in nematode between the adjacent Kermadec and Tonga trenches are observable when analyses are conducted with species-level identifications, but genera-based and trophic structure analyses revealed only limited heterogeneity among trenches. The present study contributes to the growing amount of information on hadal trench environments, which ultimately will build a greater understanding of these rarely sampled deep-sea habitats.

Cognitive aging on latent constructs for visual processing capacity: a novel structural equation modeling framework with causal assumptions based on a theory of visual attention.

PubMed

Nielsen, Simon; Wilms, L Inge

2014-01-01

We examined the effects of normal aging on visual cognition in a sample of 112 healthy adults aged 60-75. A testbattery was designed to capture high-level measures of visual working memory and low-level measures of visuospatial attention and memory. To answer questions of how cognitive aging affects specific aspects of visual processing capacity, we used confirmatory factor analyses in Structural Equation Modeling (SEM; Model 2), informed by functional structures that were modeled with path analyses in SEM (Model 1). The results show that aging effects were selective to measures of visual processing speed compared to visual short-term memory (VSTM) capacity (Model 2). These results are consistent with some studies reporting selective aging effects on processing speed, and inconsistent with other studies reporting aging effects on both processing speed and VSTM capacity. In the discussion we argue that this discrepancy may be mediated by differences in age ranges, and variables of demography. The study demonstrates that SEM is a sensitive method to detect cognitive aging effects even within a narrow age-range, and a useful approach to structure the relationships between measured variables, and the cognitive functional foundation they supposedly represent.

The disciplinary and epistemological structure of paleoanthropology: one hundred and fifty years of development.

PubMed

Delisle, Richard G

2012-01-01

This paper aims to provide a reflection on the nature of the several disciplines that contribute to the field of human evolution or paleoanthropology. An historical approach is adopted on the grounds that the nature of their relationship is perhaps more clearly seen if a dynamic perspective is adopted; that is, if paleoanthropology is analysed as an historical entity in constant flux from 1860 to today. By following the debates over human phylogeny and various scenarios of hominization separately, I will show that paleoanthropology was in the early decades of its development only very loosely organized around a host of disciplines, disciplines that went through a unification process as the twentieth century progressed under a rapidly improving empirical basis. Interestingly, to analyse the disciplinary structure of paleoanthropology from an historical approach is also to reveal its epistemological structure as both are intimately intertwined. It will be suggested that paleoanthropology's disciplinary and epistemological structure can be understood as a multi-level organization comprising at least four distinct explanatory levels characterized by unidirectional and/or bidirectional flows of information, depending on the specific circumstances: (1) a meta-theoretical foundation; (2) a level concerned with phylogeny building; (3) a level which takes up evolutionary theories and models; and (4) a level devoted to scenarios of hominization.

The persuasion network is modulated by drug-use risk and predicts anti-drug message effectiveness

PubMed Central

Mangus, J Michael; Turner, Benjamin O

2017-01-01

Abstract While a persuasion network has been proposed, little is known about how network connections between brain regions contribute to attitude change. Two possible mechanisms have been advanced. One hypothesis predicts that attitude change results from increased connectivity between structures implicated in affective and executive processing in response to increases in argument strength. A second functional perspective suggests that highly arousing messages reduce connectivity between structures implicated in the encoding of sensory information, which disrupts message processing and thereby inhibits attitude change. However, persuasion is a multi-determined construct that results from both message features and audience characteristics. Therefore, persuasive messages should lead to specific functional connectivity patterns among a priori defined structures within the persuasion network. The present study exposed 28 subjects to anti-drug public service announcements where arousal, argument strength, and subject drug-use risk were systematically varied. Psychophysiological interaction analyses provide support for the affective-executive hypothesis but not for the encoding-disruption hypothesis. Secondary analyses show that video-level connectivity patterns among structures within the persuasion network predict audience responses in independent samples (one college-aged, one nationally representative). We propose that persuasion neuroscience research is best advanced by considering network-level effects while accounting for interactions between message features and target audience characteristics. PMID:29140500

DNA G-Wire Formation Using an Artificial Peptide is Controlled by Protease Activity.

PubMed

Usui, Kenji; Okada, Arisa; Sakashita, Shungo; Shimooka, Masayuki; Tsuruoka, Takaaki; Nakano, Shu-Ichi; Miyoshi, Daisuke; Mashima, Tsukasa; Katahira, Masato; Hamada, Yoshio

2017-11-16

The development of a switching system for guanine nanowire (G-wire) formation by external signals is important for nanobiotechnological applications. Here, we demonstrate a DNA nanostructural switch (G-wire <--> particles) using a designed peptide and a protease. The peptide consists of a PNA sequence for inducing DNA to form DNA-PNA hybrid G-quadruplex structures, and a protease substrate sequence acting as a switching module that is dependent on the activity of a particular protease. Micro-scale analyses via TEM and AFM showed that G-rich DNA alone forms G-wires in the presence of Ca 2+ , and that the peptide disrupted this formation, resulting in the formation of particles. The addition of the protease and digestion of the peptide regenerated the G-wires. Macro-scale analyses by DLS, zeta potential, CD, and gel filtration were in agreement with the microscopic observations. These results imply that the secondary structure change (DNA G-quadruplex <--> DNA/PNA hybrid structure) induces a change in the well-formed nanostructure (G-wire <--> particles). Our findings demonstrate a control system for forming DNA G-wire structures dependent on protease activity using designed peptides. Such systems hold promise for regulating the formation of nanowire for various applications, including electronic circuits for use in nanobiotechnologies.

Structural neurobiological correlates of Mayer-Salovery-Caruso Emotional Intelligence Test performance in early course schizophrenia.

PubMed

Wojtalik, Jessica A; Eack, Shaun M; Keshavan, Matcheri S

2013-01-10

The Mayer-Salovey-Caruso Emotional Intelligence Test (MSCEIT) is a key measure of social cognition in schizophrenia that has good psychometric properties and is recommended by the MATRICS committee. As a way to further investigate the validity of the MSCEIT, this study sought to examine the neurobiological correlates of MSCEIT performance in patients with early course schizophrenia. A total of 51 patients diagnosed with early course, stabilized schizophrenia or schizoaffective disorder completed structural magnetic resonance imaging (MRI) scans and the MSCEIT. Investigation of the associations between MSCEIT performance and gray matter morphology was examined by conducting voxel-based morphometry (VBM) analyses across hypothesized social-cognitive regions of interest using automated anatomical labeling in Statistical Parametric Mapping Software, version 5 (SPM5). All VBM analyses utilized general linear models examining gray matter density partitioned images, adjusting for demographic and illness-related confounds. VBM results were then followed up with confirmatory volumetric analyses. Patients with poorer overall and Facilitating, Understanding, and Managing Emotions subscale performances on the MSCEIT showed significantly reduced gray matter density in the left parahippocampal gyrus. Additionally, attenuated performance on the Facilitating and Managing Emotions subscales was significantly associated with reduced right posterior cingulate gray matter density. All associations observed between MSCEIT performance and gray matter density were supported with confirmatory gray matter volumetric analyses, with the exception of the association between the right posterior cingulate and the facilitation of emotions. These findings provide additional evidence for the MSCEIT as a valid social-cognitive measure by elucidating its correlates with neurobiological structures commonly implicated in emotion processing. These findings provide additional biological evidence supporting the use of the MSCEIT in cognitive enhancing clinical trials in schizophrenia. Copyright © 2012 Elsevier Inc. All rights reserved.

Chemical Characterization and Determination of the Anti-Oxidant Capacity of Two Brown Algae with Respect to Sampling Season and Morphological Structures Using Infrared Spectroscopy and Multivariate Analyses.

PubMed

Beratto, Angelo; Agurto, Cristian; Freer, Juanita; Peña-Farfal, Carlos; Troncoso, Nicolás; Agurto, Andrés; Castillo, Rosario Del P

2017-10-01

Brown algae biomass has been shown to be a highly important industrial source for the production of alginates and different nutraceutical products. The characterization of this biomass is necessary in order to allocate its use to specific applications according to the chemical and biological characteristics of this highly variable resource. The methods commonly used for algae characterization require a long time for the analysis and rigorous pretreatments of samples. In this work, nondestructive and fast analyses of different morphological structures from Lessonia spicata and Macrocystis pyrifera, which were collected during different seasons, were performed using Fourier transform infrared (FT-IR) techniques in combination with chemometric methods. Mid-infrared (IR) and near-infrared (NIR) spectral ranges were tested to evaluate the spectral differences between the species, seasons, and morphological structures of algae using a principal component analysis (PCA). Quantitative analyses of the polyphenol and alginate contents and the anti-oxidant capacity of the samples were performed using partial least squares (PLS) with both spectral ranges in order to build a predictive model for the rapid quantification of these parameters with industrial purposes. The PCA mainly showed differences in the samples based on seasonal sampling, where changes were observed in the bands corresponding to polysaccharides, proteins, and lipids. The obtained PLS models had high correlation coefficients (r) for the polyphenol content and anti-oxidant capacity (r > 0.9) and lower values for the alginate determination (0.7 < r < 0.8). Fourier transform infrared-based techniques were suitable tools for the rapid characterization of algae biomass, in which high variability in the samples was incorporated for the qualitative and quantitative analyses, and have the potential to be used on an industrial scale.

[Dimensions of Empathy in Ex-Combatants of the Colombian Armed Conflict Using a Standardized Scale].

PubMed

Pineda, David A; Aguirre-Acevedo, Daniel Camilo; Trujillo, Natalia; Valencia, Ana María; Pareja, Ángela; Tobón, Carlos; Velilla, Lina; Ibáñez, Agustín

2013-03-01

Empathy is one of the main concepts of in social neurosciences. It is defined as a trait with multiple dimensions allowing individuals to place themselves in the emotional states of others. Colombia has an irregular, internal and long-lasting armed conflict which has been increasing its cruelty levels. to assess the empathy dimensions of 285 ex-combatants from the internal Colombian conflict, using the Interpersonal Reactivity Index(IRI) in Spanish. METHODOLOGY AND SUBJECTS: a sample of 285 male ex-combatants, 241 (84, 6%) males: 85,3% paramilitaries, and 14,7% guerillas. The 28 Item IRI questionnaires were administered. 3 exploratory factor analyses (EFA) were performed. Confirmatory factor analyses (CFA) were developed using structural equation procedures. The first EFA obtained 9 factors (KMO=0,74, variance 54,7% and internal consistency (IC): 0,22 - 0,63). The second EFA produced 20 items with burdens above 0,4 and showed a 6-factor structure (KMO=0,70, variance 50,3%, IC: 0,37 - 0,63). The third EFA forced the 4 original IRI dimensions (KMO=0,74, variance 33,77, IC: 0,44 - 0,77. CFAs showed goodness of adjustment indexes adequate for the three models. The 4-factor model obtained the lowest value, while the 6-factor model obtained the highest. The 4- factor model showed the best IC. The Spanish IRI administered to ex-combatants of the Colombian conflict has possible structures of 4, 6 and 9 factors. The best adjustment was for the 6-fctor. The 4-factor model exhibited the best IC. Copyright © 2013 Asociación Colombiana de Psiquiatría. Publicado por Elsevier España. All rights reserved.

Whole Proteome Analyses on Ruminiclostridium cellulolyticum Show a Modulation of the Cellulolysis Machinery in Response to Cellulosic Materials with Subtle Differences in Chemical and Structural Properties

PubMed Central

Badalato, Nelly; Guillot, Alain; Sabarly, Victor; Dubois, Marc; Pourette, Nina; Pontoire, Bruno; Robert, Paul; Bridier, Arnaud; Monnet, Véronique; Sousa, Diana Z.; Durand, Sylvie; Mazéas, Laurent; Buléon, Alain; Bouchez, Théodore; Mortha, Gérard

2017-01-01

Lignocellulosic materials from municipal solid waste emerge as attractive resources for anaerobic digestion biorefinery. To increase the knowledge required for establishing efficient bioprocesses, dynamics of batch fermentation by the cellulolytic bacterium Ruminiclostridium cellulolyticum were compared using three cellulosic materials, paper handkerchief, cotton discs and Whatman filter paper. Fermentation of paper handkerchief occurred the fastest and resulted in a specific metabolic profile: it resulted in the lowest acetate-to-lactate and acetate-to-ethanol ratios. By shotgun proteomic analyses of paper handkerchief and Whatman paper incubations, 151 proteins with significantly different levels were detected, including 20 of the 65 cellulosomal components, 8 non-cellulosomal CAZymes and 44 distinct extracytoplasmic proteins. Consistent with the specific metabolic profile observed, many enzymes from the central carbon catabolic pathways had higher levels in paper handkerchief incubations. Among the quantified CAZymes and cellulosomal components, 10 endoglucanases mainly from the GH9 families and 7 other cellulosomal subunits had lower levels in paper handkerchief incubations. An in-depth characterization of the materials used showed that the lower levels of endoglucanases in paper handkerchief incubations could hypothetically result from its lower crystallinity index (50%) and degree of polymerization (970). By contrast, the higher hemicellulose rate in paper handkerchief (13.87%) did not result in the enhanced expression of enzyme with xylanase as primary activity, including enzymes from the “xyl-doc” cluster. It suggests the absence, in this material, of molecular structures that specifically lead to xylanase induction. The integrated approach developed in this work shows that subtle differences among cellulosic materials regarding chemical and structural characteristics have significant effects on expressed bacterial functions, in particular the cellulolysis machinery, resulting in different metabolic patterns and degradation dynamics. PMID:28114419

Basketball Teams as Strategic Networks

PubMed Central

Fewell, Jennifer H.; Armbruster, Dieter; Ingraham, John; Petersen, Alexander; Waters, James S.

2012-01-01

We asked how team dynamics can be captured in relation to function by considering games in the first round of the NBA 2010 play-offs as networks. Defining players as nodes and ball movements as links, we analyzed the network properties of degree centrality, clustering, entropy and flow centrality across teams and positions, to characterize the game from a network perspective and to determine whether we can assess differences in team offensive strategy by their network properties. The compiled network structure across teams reflected a fundamental attribute of basketball strategy. They primarily showed a centralized ball distribution pattern with the point guard in a leadership role. However, individual play-off teams showed variation in their relative involvement of other players/positions in ball distribution, reflected quantitatively by differences in clustering and degree centrality. We also characterized two potential alternate offensive strategies by associated variation in network structure: (1) whether teams consistently moved the ball towards their shooting specialists, measured as “uphill/downhill” flux, and (2) whether they distributed the ball in a way that reduced predictability, measured as team entropy. These network metrics quantified different aspects of team strategy, with no single metric wholly predictive of success. However, in the context of the 2010 play-offs, the values of clustering (connectedness across players) and network entropy (unpredictability of ball movement) had the most consistent association with team advancement. Our analyses demonstrate the utility of network approaches in quantifying team strategy and show that testable hypotheses can be evaluated using this approach. These analyses also highlight the richness of basketball networks as a dataset for exploring the relationships between network structure and dynamics with team organization and effectiveness. PMID:23139744

Basketball teams as strategic networks.

PubMed

Fewell, Jennifer H; Armbruster, Dieter; Ingraham, John; Petersen, Alexander; Waters, James S

2012-01-01

We asked how team dynamics can be captured in relation to function by considering games in the first round of the NBA 2010 play-offs as networks. Defining players as nodes and ball movements as links, we analyzed the network properties of degree centrality, clustering, entropy and flow centrality across teams and positions, to characterize the game from a network perspective and to determine whether we can assess differences in team offensive strategy by their network properties. The compiled network structure across teams reflected a fundamental attribute of basketball strategy. They primarily showed a centralized ball distribution pattern with the point guard in a leadership role. However, individual play-off teams showed variation in their relative involvement of other players/positions in ball distribution, reflected quantitatively by differences in clustering and degree centrality. We also characterized two potential alternate offensive strategies by associated variation in network structure: (1) whether teams consistently moved the ball towards their shooting specialists, measured as "uphill/downhill" flux, and (2) whether they distributed the ball in a way that reduced predictability, measured as team entropy. These network metrics quantified different aspects of team strategy, with no single metric wholly predictive of success. However, in the context of the 2010 play-offs, the values of clustering (connectedness across players) and network entropy (unpredictability of ball movement) had the most consistent association with team advancement. Our analyses demonstrate the utility of network approaches in quantifying team strategy and show that testable hypotheses can be evaluated using this approach. These analyses also highlight the richness of basketball networks as a dataset for exploring the relationships between network structure and dynamics with team organization and effectiveness.

Eating Behaviour in the General Population: An Analysis of the Factor Structure of the German Version of the Three-Factor-Eating-Questionnaire (TFEQ) and Its Association with the Body Mass Index

PubMed Central

Löffler, Antje; Luck, Tobias; Then, Francisca S.; Sikorski, Claudia; Kovacs, Peter; Böttcher, Yvonne; Breitfeld, Jana; Tönjes, Anke; Horstmann, Annette; Löffler, Markus; Engel, Christoph; Thiery, Joachim; Villringer, Arno; Stumvoll, Michael; Riedel-Heller, Steffi G.

2015-01-01

The Three-Factor-Eating-Questionnaire (TFEQ) is an established instrument to assess eating behaviour. Analysis of the TFEQ-factor structure was based on selected, convenient and clinical samples so far. Aims of this study were (I) to analyse the factor structure of the German version of the TFEQ and (II)—based on the refined factor structure—to examine the association between eating behaviour and the body mass index (BMI) in a general population sample of 3,144 middle-aged and older participants (40–79 years) of the ongoing population based cohort study of the Leipzig Research Center for Civilization Diseases (LIFE Health Study). The factor structure was examined in a split-half analysis with both explorative and confirmatory factor analysis. Associations between TFEQ-scores and BMI values were tested with multiple regression analyses controlled for age, gender, and education. We found a three factor solution for the TFEQ with an ‘uncontrolled eating’, a ‘cognitive restraint’ and an ‘emotional eating’ domain including 29 of the original 51 TFEQ-items. Scores of the ‘uncontrolled eating domain’ showed the strongest correlation with BMI values (partial r = 0.26). Subjects with scores above the median in both ‘uncontrolled eating’ and ‘emotional eating’ showed the highest BMI values (mean = 29.41 kg/m²), subjects with scores below the median in all three domains showed the lowest BMI values (mean = 25.68 kg/m²; F = 72.074, p<0.001). Our findings suggest that the TFEQ is suitable to identify subjects with specific patterns of eating behaviour that are associated with higher BMI values. Such information may help health care professionals to develop and implement more tailored interventions for overweight and obese individuals. PMID:26230264

Structural Characterization of Ferric Hemoglobins from Three Antarctic Fish Species of the Suborder Notothenioidei

PubMed Central

Vergara, Alessandro; Franzese, Marisa; Merlino, Antonello; Vitagliano, Luigi; Verde, Cinzia; di Prisco, Guido; Lee, H. Caroline; Peisach, Jack; Mazzarella, Lelio

2007-01-01

Spontaneous autoxidation of tetrameric Hbs leads to the formation of Fe (III) forms, whose physiological role is not fully understood. Here we report structural characterization by EPR of the oxidized states of tetrameric Hbs isolated from the Antarctic fish species Trematomus bernacchii, Trematomus newnesi, and Gymnodraco acuticeps, as well as the x-ray crystal structure of oxidized Trematomus bernacchii Hb, redetermined at high resolution. The oxidation of these Hbs leads to formation of states that were not usually detected in previous analyses of tetrameric Hbs. In addition to the commonly found aquo-met and hydroxy-met species, EPR analyses show that two distinct hemichromes coexist at physiological pH, referred to as hemichromes I and II, respectively. Together with the high-resolution crystal structure (1.5 Å) of T. bernacchii and a survey of data available for other heme proteins, hemichrome I was assigned by x-ray crystallography and by EPR as a bis-His complex with a distorted geometry, whereas hemichrome II is a less constrained (cytochrome b5-like) bis-His complex. In four of the five Antartic fish Hbs examined, hemichrome I is the major form. EPR shows that for HbCTn, the amount of hemichrome I is substantially reduced. In addition, the concomitant presence of a penta-coordinated high-spin Fe (III) species, to our knowledge never reported before for a wild-type tetrameric Hb, was detected. A molecular modeling investigation demonstrates that the presence of the bulkier Ile in position 67β in HbCTn in place of Val as in the other four Hbs impairs the formation of hemichrome I, thus favoring the formation of the ferric penta-coordinated species. Altogether the data show that ferric states commonly associated with monomeric and dimeric Hbs are also found in tetrameric Hbs. PMID:17545238

Temperament and Character in the Child and Adolescent Twin Study in Sweden (CATSS): Comparison to the General Population, and Genetic Structure Analysis

PubMed Central

Garcia, Danilo; Lundström, Sebastian; Brändström, Sven; Råstam, Maria; Cloninger, C. Robert; Kerekes, Nóra; Nilsson, Thomas; Anckarsäter, Henrik

2013-01-01

Background The Child and Adolescent Twin Study in Sweden (CATSS) is an on-going, large population-based longitudinal twin study. We aimed (1) to investigate the reliability of two different versions (125-items and 238-items) of Cloninger's Temperament and Character Inventory (TCI) used in the CATSS and the validity of extracting the short version from the long version, (2) to compare these personality dimensions between twins and adolescents from the general population, and (3) to investigate the genetic structure of Cloninger's model. Method Reliability and correlation analyses were conducted for both TCI versions, 2,714 CATSS-twins were compared to 631 adolescents from the general population, and the genetic structure was investigated through univariate genetic analyses, using a model-fitting approach with structural equation-modeling techniques based on same-sex twin pairs from the CATSS (423 monozygotic and 408 dizygotic pairs). Results The TCI scores from the short and long versions showed comparable reliability coefficients and were strongly correlated. Twins scored about half a standard deviation higher in the character scales. Three of the four temperament dimensions (Novelty Seeking, Harm Avoidance, and Persistence) had strong genetic and non-shared environmental effects, while Reward Dependence and the three character dimensions had moderate genetic effects, and both shared and non-shared environmental effects. Conclusions Twins showed higher scores in character dimensions compared to adolescents from the general population. At least among adolescents there is a shared environmental influence for all of the character dimensions, but only for one of the temperament dimensions (i.e., Reward Dependence). This specific finding regarding the existence of shared environmental factors behind the character dimensions in adolescence, together with earlier findings showing a small shared environmental effects on character among young adults and no shared environmental effects on character among adults, suggest that there is a shift in type of environmental influence from adolescence to adulthood regarding character. PMID:23940581

An objective isobaric/isentropic technique for upper air analysis

NASA Technical Reports Server (NTRS)

Mancuso, R. L.; Endlich, R. M.; Ehernberger, L. J.

1981-01-01

An objective meteorological analysis technique is presented whereby both horizontal and vertical upper air analyses are performed. The process used to interpolate grid-point values from the upper-air station data is the same as for grid points on both an isobaric surface and a vertical cross-sectional plane. The nearby data surrounding each grid point are used in the interpolation by means of an anisotropic weighting scheme, which is described. The interpolation for a grid-point potential temperature is performed isobarically; whereas wind, mixing-ratio, and pressure height values are interpolated from data that lie on the isentropic surface that passes through the grid point. Two versions (A and B) of the technique are evaluated by qualitatively comparing computer analyses with subjective handdrawn analyses. The objective products of version A generally have fair correspondence with the subjective analyses and with the station data, and depicted the structure of the upper fronts, tropopauses, and jet streams fairly well. The version B objective products correspond more closely to the subjective analyses, and show the same strong gradients across the upper front with only minor smoothing.

Spatial variation in the bacterial and denitrifying bacterial community in a biofilter treating subsurface agricultural drainage.

PubMed

Andrus, J Malia; Porter, Matthew D; Rodríguez, Luis F; Kuehlhorn, Timothy; Cooke, Richard A C; Zhang, Yuanhui; Kent, Angela D; Zilles, Julie L

2014-02-01

Denitrifying biofilters can remove agricultural nitrates from subsurface drainage, reducing nitrate pollution that contributes to coastal hypoxic zones. The performance and reliability of natural and engineered systems dependent upon microbially mediated processes, such as the denitrifying biofilters, can be affected by the spatial structure of their microbial communities. Furthermore, our understanding of the relationship between microbial community composition and function is influenced by the spatial distribution of samples.In this study we characterized the spatial structure of bacterial communities in a denitrifying biofilter in central Illinois. Bacterial communities were assessed using automated ribosomal intergenic spacer analysis for bacteria and terminal restriction fragment length polymorphism of nosZ for denitrifying bacteria.Non-metric multidimensional scaling and analysis of similarity (ANOSIM) analyses indicated that bacteria showed statistically significant spatial structure by depth and transect,while denitrifying bacteria did not exhibit significant spatial structure. For determination of spatial patterns, we developed a package of automated functions for the R statistical environment that allows directional analysis of microbial community composition data using either ANOSIM or Mantel statistics.Applying this package to the biofilter data, the flow path correlation range for the bacterial community was 6.4 m at the shallower, periodically in undated depth and 10.7 m at the deeper, continually submerged depth. These spatial structures suggest a strong influence of hydrology on the microbial community composition in these denitrifying biofilters. Understanding such spatial structure can also guide optimal sample collection strategies for microbial community analyses.

Stable genetic structure and connectivity in pollution-adapted and nearby pollution-sensitive populations of Fundulus heteroclitus

PubMed Central

Biancani, Leann M.; Flight, Patrick A.; Nacci, Diane E.; Rand, David M.; Crawford, Douglas L.; Oleksiak, Marjorie F.

2018-01-01

Populations of the non-migratory estuarine fish Fundulus heteroclitus inhabiting the heavily polluted New Bedford Harbour (NBH) estuary have shown inherited tolerance to local pollutants introduced to their habitats in the past 100 years. Here we examine two questions: (i) Is there pollution-driven selection on the mitochondrial genome across a fine geographical scale? and (ii) What is the pattern of migration among sites spanning a strong pollution gradient? Whole mitochondrial genomes were analysed for 133 F. heteroclitus from seven nearby collection sites: four sites along the NBH pollution cline (approx. 5 km distance), which had pollution-adapted fish, as well as one site adjacent to the pollution cline and two relatively unpolluted sites about 30 km away, which had pollution-sensitive fish. Additionally, we used microsatellite analyses to quantify genetic variation over three F. heteroclitus generations in both pollution-adapted and sensitive individuals collected from two sites at two different time points (1999/2000 and 2007/2008). Our results show no evidence for a selective sweep of mtDNA in the polluted sites. Moreover, mtDNA analyses revealed that both pollution-adapted and sensitive populations harbour similar levels of genetic diversity. We observed a high level of non-synonymous mutations in the most polluted site. This is probably associated with a reduction in Ne and concomitant weakening of purifying selection, a demographic expansion following a pollution-related bottleneck or increased mutation rates. Our demographic analyses suggest that isolation by distance influences the distribution of mtDNA genetic variation between the pollution cline and the clean populations at broad spatial scales. At finer scales, population structure is patchy, and neither spatial distance, pollution concentration or pollution tolerance is a good predictor of mtDNA variation. Lastly, microsatellite analyses revealed stable population structure over the last decade. PMID:29892357

The effects of the therapist's disengaged feelings on the in-session process in psychodynamic psychotherapy.

PubMed

Ulberg, Randi; Amlo, Svein; Hersoug, Anne Grete; Dahl, Hanne-Sofie Johnsen; Høglend, Per

2014-05-01

The primary aim of this article was to explore the effects of the therapist's disengaged feelings (i.e., bored, tired of, sleepy, indifferent, aloof) in psychodynamic therapy. The Transference Work Scale was used in combination with the Defense Mechanism Rating Scales and Structural Analyses of Social Behavior to explore the in-session process in 2 therapies with female patients with interpersonal problems. Analyses showed differences in in-session processes (i.e., defense mechanisms; transference work; degree of affiliation and interdependence in the dialogue) and treatment outcome between therapies characterized by a low versus a higher degree of disengaged feelings. Compared to the case with the engaged therapist, the disengaged therapist showed poorer interaction and less response to transference and defense interpretation. When aware of their disengaged feelings, therapists are advised to encourage their patients to discuss the patient-therapist interaction. © 2014 Wiley Periodicals, Inc.

Stress analysis for structures with surface cracks

NASA Technical Reports Server (NTRS)

Bell, J. C.

1978-01-01

Two basic forms of analysis, one treating stresses around arbitrarily loaded circular cracks, the other treating stresses due to loads arbitrarily distributed on the surface of a half space, are united by a boundary-point least squares method to obtain analyses for stresses from surface cracks in places or bars. Calculations were for enough cases to show how effects from the crack vary with the depth-to-length ratio, the fractional penetration ratio, the obliquity of the load, and to some extent the fractional span ratio. The results include plots showing stress intensity factors, stress component distributions near the crack, and crack opening displacement patterns. Favorable comparisons are shown with two kinds of independent experiments, but the main method for confirming the results is by wide checking of overall satisfaction of boundary conditions, so that external confirmation is not essential. Principles involved in designing analyses which promote dependability of the results are proposed and illustrated.

Psychometric properties of the Liebowitz Social Anxiety Scale (LSAS) in a longitudinal study of African Americans with anxiety disorders.

PubMed

Beard, Courtney; Rodriguez, Benjamin F; Moitra, Ethan; Sibrava, Nicholas J; Bjornsson, Andri; Weisberg, Risa B; Keller, Martin B

2011-06-01

The Liebowitz Social Anxiety Scale (LSAS) is a widely used measure of social anxiety. However, no study has examined the psychometric properties of the LSAS in an African American sample. The current study examined the LSAS characteristics in 97 African Americans diagnosed with an anxiety disorder. Overall, the original LSAS subscales showed excellent internal consistency and temporal stability. Similar to previous reports, fear and avoidance subscales were so highly correlated that they yielded redundant information. Confirmatory factor analyses for three previously proposed models failed to demonstrate an excellent fit to our data. However, a four-factor model showed minimally acceptable fit. Overall, the LSAS performed similarly in our African American sample as in previous European American samples. Exploratory factor analyses are warranted to determine whether a better factor structure exists for African Americans. Copyright © 2011 Elsevier Ltd. All rights reserved.

PDBe: improved accessibility of macromolecular structure data from PDB and EMDB.

PubMed

Velankar, Sameer; van Ginkel, Glen; Alhroub, Younes; Battle, Gary M; Berrisford, John M; Conroy, Matthew J; Dana, Jose M; Gore, Swanand P; Gutmanas, Aleksandras; Haslam, Pauline; Hendrickx, Pieter M S; Lagerstedt, Ingvar; Mir, Saqib; Fernandez Montecelo, Manuel A; Mukhopadhyay, Abhik; Oldfield, Thomas J; Patwardhan, Ardan; Sanz-García, Eduardo; Sen, Sanchayita; Slowley, Robert A; Wainwright, Michael E; Deshpande, Mandar S; Iudin, Andrii; Sahni, Gaurav; Salavert Torres, Jose; Hirshberg, Miriam; Mak, Lora; Nadzirin, Nurul; Armstrong, David R; Clark, Alice R; Smart, Oliver S; Korir, Paul K; Kleywegt, Gerard J

2016-01-04

The Protein Data Bank in Europe (http://pdbe.org) accepts and annotates depositions of macromolecular structure data in the PDB and EMDB archives and enriches, integrates and disseminates structural information in a variety of ways. The PDBe website has been redesigned based on an analysis of user requirements, and now offers intuitive access to improved and value-added macromolecular structure information. Unique value-added information includes lists of reviews and research articles that cite or mention PDB entries as well as access to figures and legends from full-text open-access publications that describe PDB entries. A powerful new query system not only shows all the PDB entries that match a given query, but also shows the 'best structures' for a given macromolecule, ligand complex or sequence family using data-quality information from the wwPDB validation reports. A PDBe RESTful API has been developed to provide unified access to macromolecular structure data available in the PDB and EMDB archives as well as value-added annotations, e.g. regarding structure quality and up-to-date cross-reference information from the SIFTS resource. Taken together, these new developments facilitate unified access to macromolecular structure data in an intuitive way for non-expert users and support expert users in analysing macromolecular structure data. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Cytophotometric and biochemical analyses of DNA in pentaploid and diploid Agave species.

PubMed

Cavallini, A; Natali, L; Cionini, G; Castorena-Sanchez, I

1996-04-01

Nuclear DNA content, chromatin structure, and DNA composition were investigated in four Agave species: two diploid, Agave tequilana Weber and Agave angustifolia Haworth var. marginata Hort., and two pentaploid, Agave fourcroydes Lemaire and Agave sisalana Perrine. It was determined that the genome size of pentaploid species is nearly 2.5 times that of diploid ones. Cytophotometric analyses of chromatin structure were performed following Feulgen or DAPI staining to determine optical density profiles of interphase nuclei. Pentaploid species showed higher frequencies of condensed chromatin (heterochromatin) than diploid species. On the other hand, a lower frequency of A-T rich (DAPI stained) heterochromatin was found in pentaploid species than in diploid ones, indicating that heterochromatin in pentaploid species is made up of sequences with base compositions different from those of diploid species. Since thermal denaturation profiles of extracted DNA showed minor variations in the base composition of the genomes of the four species, it is supposed that, in pentaploid species, the large heterochromatin content is not due to an overrepresentation of G-C repetitive sequences but rather to the condensation of nonrepetitive sequences, such as, for example, redundant gene copies switched off in the polyploid complement. It is suggested that speciation in the genus Agave occurs through point mutations and minor DNA rearrangements, as is also indicated by the relative stability of the karyotype of this genus. Key words : Agave, DNA cytophotometry, DNA melting profiles, chromatin structure, genome size.

Structural, vibrational and luminescence properties of the (1−x)CaWO{sub 4}−xCdWO{sub 4} system

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

Taoufyq, A.; Laboratoire Matériaux et Environnement LME, Faculté des Sciences, Université Ibn Zohr, BP 8106, Cité Dakhla, Agadir, Maroc; CEA/DEN, Département d’Études des Réacteurs, Laboratoire Dosimétrie Capteurs Instrumentation, CEA Cadarache, 13108, Saint-Paul-lez-Durance

2014-11-15

In the present work, we investigate the structural, microstructural, vibrational and luminescence properties of the system (1−x)CaWO{sub 4}−xCdWO{sub 4} with x ranging between 0 and 1. Polycrystalline samples were elaborated using a coprecipitation technique followed by thermal treatment at 1000 °C. The samples were then characterized using X-ray diffraction, scanning electron microscopy, Raman spectroscopy and luminescence analyses. X-ray diffraction profile analyses using Rietveld method showed that two kinds of solid solutions Ca{sub 1−x}Cd{sub x}WO{sub 4} having scheelite and wolframite structures, with respectively tetragonal and monoclinic crystal cells, were observed, with a biphasic system for compositions x=0.6 and 0.7. The scanningmore » electron microscopy experiments showed a complex evolution of morphologies and crystallite sizes as x increased. The vibration modes of Raman spectra were characteristic of composition-dependent disordered solid solutions with decreasing wavenumbers as x increased. Luminescence experiments were performed under UV-laser light irradiation. The energies of emission bands increased linearly with cadmium composition x. The integrated intensity of luminescence reached a maximum value for the substituted wolframite phase with composition x=0.8. - Graphical abstract: Luminescence on UV excitation (364.5 nm) of (1−x)CaWO{sub 4−x}CdWO{sub 4} system, elaborated from coprecipitation technique at 1000 °C, with 0« less

Analyses of Dynein Heavy Chain Mutations Reveal Complex Interactions Between Dynein Motor Domains and Cellular Dynein Functions

PubMed Central

Sivagurunathan, Senthilkumar; Schnittker, Robert R.; Razafsky, David S.; Nandini, Swaran; Plamann, Michael D.; King, Stephen J.

2012-01-01

Cytoplasmic dynein transports cargoes for a variety of crucial cellular functions. However, since dynein is essential in most eukaryotic organisms, the in-depth study of the cellular function of dynein via genetic analysis of dynein mutations has not been practical. Here, we identify and characterize 34 different dynein heavy chain mutations using a genetic screen of the ascomycete fungus Neurospora crassa, in which dynein is nonessential. Interestingly, our studies show that these mutations segregate into five different classes based on the in vivo localization of the mutated dynein motors. Furthermore, we have determined that the different classes of dynein mutations alter vesicle trafficking, microtubule organization, and nuclear distribution in distinct ways and require dynactin to different extents. In addition, biochemical analyses of dynein from one mutant strain show a strong correlation between its in vitro biochemical properties and the aberrant intracellular function of that altered dynein. When the mutations were mapped to the published dynein crystal structure, we found that the three-dimensional structural locations of the heavy chain mutations were linked to particular classes of altered dynein functions observed in cells. Together, our data indicate that the five classes of dynein mutations represent the entrapment of dynein at five separate points in the dynein mechanochemical and transport cycles. We have developed N. crassa as a model system where we can dissect the complexities of dynein structure, function, and interaction with other proteins with genetic, biochemical, and cell biological studies. PMID:22649085

Zero-gravity atmospheric Cloud Physics Experiment Laboratory; Programmatics report

NASA Technical Reports Server (NTRS)

1974-01-01

The programmatics effort included comprehensive analyses in four major areas: (1) work breakdown structure, (2) schedules, (3) costs, and (4) supporting research and technology. These analyses are discussed in detail in the following sections which identify and define the laboratory project development schedule, cost estimates, funding distributions and supporting research and technology requirements. All programmatics analyses are correlated among themselves and with the technical analyses by means of the work breakdown structure which serves as a common framework for program definition. In addition, the programmatic analyses reflect the results of analyses and plans for reliability, safety, test, and maintenance and refurbishment.

Kinetic analysis of pre-ribosome structure in vivo

PubMed Central

Swiatkowska, Agata; Wlotzka, Wiebke; Tuck, Alex; Barrass, J. David; Beggs, Jean D.; Tollervey, David

2012-01-01

Pre-ribosomal particles undergo numerous structural changes during maturation, but their high complexity and short lifetimes make these changes very difficult to follow in vivo. In consequence, pre-ribosome structure and composition have largely been inferred from purified particles and analyzed in vitro. Here we describe techniques for kinetic analyses of the changes in pre-ribosome structure in living cells of Saccharomyces cerevisiae. To allow this, in vivo structure probing by DMS modification was combined with affinity purification of newly synthesized 20S pre-rRNA over a time course of metabolic labeling with 4-thiouracil. To demonstrate that this approach is generally applicable, we initially analyzed the accessibility of the region surrounding cleavage site D site at the 3′ end of the mature 18S rRNA region of the pre-rRNA. This revealed a remarkably flexible structure throughout 40S subunit biogenesis, with little stable RNA–protein interaction apparent. Analysis of folding in the region of the 18S central pseudoknot was consistent with previous data showing U3 snoRNA–18S rRNA interactions. Dynamic changes in the structure of the hinge between helix 28 (H28) and H44 of pre-18S rRNA were consistent with recently reported interactions with the 3′ guide region of U3 snoRNA. Finally, analysis of the H18 region indicates that the RNA structure matures early, but additional protection appears subsequently, presumably reflecting protein binding. The structural analyses described here were performed on total, affinity-purified, newly synthesized RNA, so many classes of RNA and RNA–protein complex are potentially amenable to this approach. PMID:23093724

Au Nanoparticle Sub-Monolayers Sandwiched between Sol-Gel Oxide Thin Films

PubMed Central

Della Gaspera, Enrico; Menin, Enrico; Sada, Cinzia

2018-01-01

Sub-monolayers of monodisperse Au colloids with different surface coverage have been embedded in between two different metal oxide thin films, combining sol-gel depositions and proper substrates functionalization processes. The synthetized films were TiO2, ZnO, and NiO. X-ray diffraction shows the crystallinity of all the oxides and verifies the nominal surface coverage of Au colloids. The surface plasmon resonance (SPR) of the metal nanoparticles is affected by both bottom and top oxides: in fact, the SPR peak of Au that is sandwiched between two different oxides is centered between the SPR frequencies of Au sub-monolayers covered with only one oxide, suggesting that Au colloids effectively lay in between the two oxide layers. The desired organization of Au nanoparticles and the morphological structure of the prepared multi-layered structures has been confirmed by Rutherford backscattering spectrometry (RBS), Secondary Ion Mass Spectrometry (SIMS), and Scanning Electron Microscopy (SEM) analyses that show a high quality sandwich structure. The multi-layered structures have been also tested as optical gas sensors. PMID:29538338

Design of a biomimetic robotic octopus arm.

PubMed

Laschi, C; Mazzolai, B; Mattoli, V; Cianchetti, M; Dario, P

2009-03-01

This paper reports the rationale and design of a robotic arm, as inspired by an octopus arm. The octopus arm shows peculiar features, such as the ability to bend in all directions, to produce fast elongations, and to vary its stiffness. The octopus achieves these unique motor skills, thanks to its peculiar muscular structure, named muscular hydrostat. Different muscles arranged on orthogonal planes generate an antagonistic action on each other in the muscular hydrostat, which does not change its volume during muscle contractions, and allow bending and elongation of the arm and stiffness variation. By drawing inspiration from natural skills of octopus, and by analysing the geometry and mechanics of the muscular structure of its arm, we propose the design of a robot arm consisting of an artificial muscular hydrostat structure, which is completely soft and compliant, but also able to stiffen. In this paper, we discuss the design criteria of the robotic arm and how this design and the special arrangement of its muscular structure may bring the building of a robotic arm into being, by showing the results obtained by mathematical models and prototypical mock-ups.

[Validity and internal consistency of the Maslach Burnout Inventory in Dental Students from Cartagena, Colombia].

PubMed

Simancas-Pallares, Miguel Angel; Fortich Mesa, Natalia; González Martínez, Farith Damián

To determine the internal consistency and content validity of the Maslach Burnout Inventory-Student Survey (MBI-SS) in dental students from Cartagena, Colombia. Scale validation study in 886 dental students from Cartagena, Colombia. Factor structure was determined through exploratory factor analysis (EFA) and confirmatory factor analysis (CFA). Internal consistency was measured using the Cronbach's alpha coefficient. Analyses were performed using the Stata v.13.2 for Windows (Statacorp., USA) and Mplus v.7.31 for Windows (Muthén & Muthén, USA) software. Internal consistency was α=.806. The factor structure showed three that accounted for the 56.6% of the variance. CFA revealed: χ 2 =926.036; df=85; RMSEA=.106 (90%CI, .100-.112); CFI=.947; TLI=.934. The MBI showed an adequate internal consistency and a factor structure being consistent with the original proposed structure with a poor fit, which does not reflect adequate content validity in this sample. Copyright © 2016 Asociación Colombiana de Psiquiatría. Publicado por Elsevier España. All rights reserved.

Structural analysis of zwitterionic liquids vs. homologous ionic liquids

NASA Astrophysics Data System (ADS)

Wu, Boning; Kuroda, Kosuke; Takahashi, Kenji; Castner, Edward W.

2018-05-01

Zwitterionic liquids (Zw-ILs) have been developed that are homologous to monovalent ionic liquids (ILs) and show great promise for controlled dissolution of cellulosic biomass. Using both high energy X-ray scattering and atomistic molecular simulations, this article compares the bulk liquid structural properties for novel Zw-ILs with their homologous ILs. It is shown that the significant localization of the charges on Zw-ILs leads to charge ordering similar to that observed for conventional ionic liquids with monovalent anions and cations. A low-intensity first sharp diffraction peak in the liquid structure factor S(q) is observed for both the Zw-IL and the IL. This is unexpected since both the Zw-IL and IL have a 2-(2-methoxyethoxy)ethyl (diether) functional group on the cationic imidazolium ring and ether functional groups are known to suppress this peak. Detailed analyses show that this intermediate range order in the liquid structure arises for slightly different reasons in the Zw-IL vs. the IL. For the Zw-IL, the ether tails in the liquid are shown to aggregate into nanoscale domains.

First-principles calculations on slip system activation in the rock salt structure: electronic origin of ductility in silver chloride

NASA Astrophysics Data System (ADS)

Nakamura, Atsutomo; Ukita, Masaya; Shimoda, Naofumi; Furushima, Yuho; Toyoura, Kazuaki; Matsunaga, Katsuyuki

2017-06-01

First principles calculations were performed to understand an electronic origin of high ductility in silver chloride (AgCl) with the rock salt structure. From calculations of generalised stacking fault energies for different slip systems, it was found that only the {1 1 0}? slip system is favourably activated in sodium chloride (NaCl) with the same rock salt structure, whereas AgCl shows three kinds of possible slip systems along the ? direction on the {0 0 1}, {1 1 0}, and {1 1 1} planes, which is in excellent agreement with experiment. Detailed analyses of the electronic structures across slip planes showed that the more covalent character of bonding of Ag-Cl than Na-Cl tends to make the slip motion energetically favourable. It was also surprising to find out that strong Ag-Ag covalent bonds across the slip plane are formed in the {0 0 1}〈1 1 0〉 slip system in AgCl, which makes it possible to activate the multiple slip systems in AgCl.

Impacts of Long-Term Irrigation of Domestic Treated Wastewater on Soil Biogeochemistry and Bacterial Community Structure

PubMed Central

Wafula, Denis; White, John R.; Canion, Andy; Jagoe, Charles; Pathak, Ashish

2015-01-01

Freshwater scarcity and regulations on wastewater disposal have necessitated the reuse of treated wastewater (TWW) for soil irrigation, which has several environmental and economic benefits. However, TWW irrigation can cause nutrient loading to the receiving environments. We assessed bacterial community structure and associated biogeochemical changes in soil plots irrigated with nitrate-rich TWW (referred to as pivots) for periods ranging from 13 to 30 years. Soil cores (0 to 40 cm) were collected in summer and winter from five irrigated pivots and three adjacently located nonirrigated plots. Total bacterial and denitrifier gene abundances were estimated by quantitative PCR (qPCR), and community structure was assessed by 454 massively parallel tag sequencing (MPTS) of small-subunit (SSU) rRNA genes along with terminal restriction fragment length polymorphism (T-RFLP) analysis of nirK, nirS, and nosZ functional genes responsible for denitrification of the TWW-associated nitrate. Soil physicochemical analyses showed that, regardless of the seasons, pH and moisture contents (MC) were higher in the irrigated (IR) pivots than in the nonirrigated (NIR) plots; organic matter (OM) and microbial biomass carbon (MBC) were higher as a function of season but not of irrigation treatment. MPTS analysis showed that TWW loading resulted in the following: (i) an increase in the relative abundance of Proteobacteria, especially Betaproteobacteria and Gammaproteobacteria; (ii) a decrease in the relative abundance of Actinobacteria; (iii) shifts in the communities of acidobacterial groups, along with a shift in the nirK and nirS denitrifier guilds as shown by T-RFLP analysis. Additionally, bacterial biomass estimated by genus/group-specific real-time qPCR analyses revealed that higher numbers of total bacteria, Acidobacteria, Actinobacteria, Alphaproteobacteria, and the nirS denitrifier guilds were present in the IR pivots than in the NIR plots. Identification of the nirK-containing microbiota as a proxy for the denitrifier community indicated that bacteria belonged to alphaproteobacteria from the Rhizobiaceae family within the agroecosystem studied. Multivariate statistical analyses further confirmed some of the above soil physicochemical and bacterial community structure changes as a function of long-term TWW application within this agroecosystem. PMID:26253672

Structural diversity and photocatalytic properties of Cd(II) coordination polymers constructed by a flexible V-shaped bipyridyl benzene ligand and dicarboxylate derivatives.

PubMed

Liu, Lei-Lei; Yu, Cai-Xia; Ma, Feng-Ji; Li, Ya-Ru; Han, Jing-Jing; Lin, Lu; Ma, Lu-Fang

2015-01-28

Hydrothermal reactions of Cd(OAc)2·2H2O with a flexible V-shaped bipyridyl benzene ligand and five benzenedicarboxylic acid derivatives gave rise to five new coordination polymers i.e., [Cd(1,4-BDC)(bpmb)(H2O)]n (1), {[Cd(1,3-BDC)(bpmb)]·0.125H2O}n (2), [Cd2(5-Me-1,3-BDC)2(bpmb)2]n (3), [Cd(5-NO2-1,3-BDC)(bpmb)(H2O)]n (4) and [Cd(5-OH-1,3-BDC)(bpmb)(H2O)]n (5) (bpmb = 1,3-bis(pyridine-3-ylmethoxy)benzene, 1,4-H2BDC = 1,4-benzenedicarboxylic acid, 1,3-H2BDC = 1,3-benzenedicarboxylic acid, 5-Me-1,3-H2BDC = 5-methyl-1,3-benzenedicarboxylic acid, 5-NO2-1,3-H2BDC = 5-nitro-1,3-benzenedicarboxylic acid, 5-OH-1,3-H2BDC = 5-hydroxy-1,3-benzenedicarboxylic acid). Their structures have been determined by single-crystal X-ray diffraction analyses, elemental analyses, IR spectra, powder X-ray diffraction (PXRD) and thermogravimetric analyses (TGA). Compound 1 is a two-fold interpenetrating network showing the coexistence of polyrotaxane and polycatenane characters. Compounds 2 and 3 exhibit similar 2D (3,5)-connected (4(2)·6(7)·8)(4(2)·6) nets in which the bpmb ligands work as lockers in interlocking 1D [Cd(1,3-BDC/5-Me-1,3-BDC)]n chains. Compound 4 shows a 2D 4-connected (6(6)) sandwich-like structure with differently oriented [Cd(5-NO2-1,3-BDC)]n chains. Compound 5 is a 3D supramolecular pcu net based on a 1D ladder-shaped chain. These results suggest that the substituted positions of carboxylate groups and changes in substituted R groups in the 5-position of BDC ligands have significant effect on the final structures. These compounds exhibited relatively good photocatalytic activity towards the degradation of methylene blue (MB) in aqueous solution under UV irradiation. Moreover, solid-state photoluminescence properties of 1-5 were also investigated.

Crystal structure, biochemical and genetic characterization of yeast and E. cuniculi TAF(II)5 N-terminal domain: implications for TFIID assembly.

PubMed

Romier, Christophe; James, Nicole; Birck, Catherine; Cavarelli, Jean; Vivarès, Christian; Collart, Martine A; Moras, Dino

2007-05-18

General transcription factor TFIID plays an essential role in transcription initiation by RNA polymerase II at numerous promoters. However, understanding of the assembly and a full structural characterization of this large 15 subunit complex is lacking. TFIID subunit TAF(II)5 has been shown to be present twice in this complex and to be critical for the function and assembly of TFIID. Especially, the TAF(II)5 N-terminal domain is required for its incorporation within TFIID and immuno-labelling experiments carried out by electron microscopy at low resolution have suggested that this domain might homodimerize, possibly explaining the three-lobed architecture of TFIID. However, the resolution at which the electron microscopy (EM) analyses were conducted is not sufficient to determine whether homodimerization occurs or whether a more intricate assembly implying other subunits is required. Here we report the X-ray structures of the fully evolutionary conserved C-terminal sub-domain of the TAF(II)5 N terminus, from yeast and the mammalian parasite Encephalitozoon cuniculi. This sub-domain displays a novel fold with specific surfaces having conserved physico-chemical properties that can form protein-protein interactions. Although a crystallographic dimer implying one of these surfaces is present in one of the crystal forms, several biochemical analyses show that this sub-domain is monomeric in solution, even at various salt conditions and in presence of different divalent cations. Consequently, the N-terminal sub-domain of the TAF(II)5 N terminus, which is homologous to a dimerization motif but has not been fully conserved during evolution, was studied by analytical ultracentrifugation and yeast genetics. Our results show that this sub-domain dimerizes at very high concentration but is neither required for yeast viability, nor for incorporation of two TAF(II)5 molecules within TFIID and for the assembly of this complex. Altogether, although our results do not argue in favour of a homodimerization of the TAF(II)5 N-terminal domain, our structural analyses suggest a role for this domain in assembly of TFIID and its related complexes SAGA, STAGA, TFTC and PCAF.

Reliability and Validity of Assessing User Satisfaction With Web-Based Health Interventions

PubMed Central

Lehr, Dirk; Reis, Dorota; Vis, Christiaan; Riper, Heleen; Berking, Matthias; Ebert, David Daniel

2016-01-01

Background The perspective of users should be taken into account in the evaluation of Web-based health interventions. Assessing the users’ satisfaction with the intervention they receive could enhance the evidence for the intervention effects. Thus, there is a need for valid and reliable measures to assess satisfaction with Web-based health interventions. Objective The objective of this study was to analyze the reliability, factorial structure, and construct validity of the Client Satisfaction Questionnaire adapted to Internet-based interventions (CSQ-I). Methods The psychometric quality of the CSQ-I was analyzed in user samples from 2 separate randomized controlled trials evaluating Web-based health interventions, one from a depression prevention intervention (sample 1, N=174) and the other from a stress management intervention (sample 2, N=111). At first, the underlying measurement model of the CSQ-I was analyzed to determine the internal consistency. The factorial structure of the scale and the measurement invariance across groups were tested by multigroup confirmatory factor analyses. Additionally, the construct validity of the scale was examined by comparing satisfaction scores with the primary clinical outcome. Results Multigroup confirmatory analyses on the scale yielded a one-factorial structure with a good fit (root-mean-square error of approximation =.09, comparative fit index =.96, standardized root-mean-square residual =.05) that showed partial strong invariance across the 2 samples. The scale showed very good reliability, indicated by McDonald omegas of .95 in sample 1 and .93 in sample 2. Significant correlations with change in depressive symptoms (r=−.35, P<.001) and perceived stress (r=−.48, P<.001) demonstrated the construct validity of the scale. Conclusions The proven internal consistency, factorial structure, and construct validity of the CSQ-I indicate a good overall psychometric quality of the measure to assess the user’s general satisfaction with Web-based interventions for depression and stress management. Multigroup analyses indicate its robustness across different samples. Thus, the CSQ-I seems to be a suitable measure to consider the user’s perspective in the overall evaluation of Web-based health interventions. PMID:27582341

Reliability and Validity of Assessing User Satisfaction With Web-Based Health Interventions.

PubMed

Boß, Leif; Lehr, Dirk; Reis, Dorota; Vis, Christiaan; Riper, Heleen; Berking, Matthias; Ebert, David Daniel

2016-08-31

The perspective of users should be taken into account in the evaluation of Web-based health interventions. Assessing the users' satisfaction with the intervention they receive could enhance the evidence for the intervention effects. Thus, there is a need for valid and reliable measures to assess satisfaction with Web-based health interventions. The objective of this study was to analyze the reliability, factorial structure, and construct validity of the Client Satisfaction Questionnaire adapted to Internet-based interventions (CSQ-I). The psychometric quality of the CSQ-I was analyzed in user samples from 2 separate randomized controlled trials evaluating Web-based health interventions, one from a depression prevention intervention (sample 1, N=174) and the other from a stress management intervention (sample 2, N=111). At first, the underlying measurement model of the CSQ-I was analyzed to determine the internal consistency. The factorial structure of the scale and the measurement invariance across groups were tested by multigroup confirmatory factor analyses. Additionally, the construct validity of the scale was examined by comparing satisfaction scores with the primary clinical outcome. Multigroup confirmatory analyses on the scale yielded a one-factorial structure with a good fit (root-mean-square error of approximation =.09, comparative fit index =.96, standardized root-mean-square residual =.05) that showed partial strong invariance across the 2 samples. The scale showed very good reliability, indicated by McDonald omegas of .95 in sample 1 and .93 in sample 2. Significant correlations with change in depressive symptoms (r=-.35, P<.001) and perceived stress (r=-.48, P<.001) demonstrated the construct validity of the scale. The proven internal consistency, factorial structure, and construct validity of the CSQ-I indicate a good overall psychometric quality of the measure to assess the user's general satisfaction with Web-based interventions for depression and stress management. Multigroup analyses indicate its robustness across different samples. Thus, the CSQ-I seems to be a suitable measure to consider the user's perspective in the overall evaluation of Web-based health interventions.

Chapter C. The Loma Prieta, California, Earthquake of October 17, 1989 - Building Structures

USGS Publications Warehouse

Çelebi, Mehmet

1998-01-01

Several approaches are used to assess the performance of the built environment following an earthquake -- preliminary damage surveys conducted by professionals, detailed studies of individual structures, and statistical analyses of groups of structures. Reports of damage that are issued by many organizations immediately following an earthquake play a key role in directing subsequent detailed investigations. Detailed studies of individual structures and statistical analyses of groups of structures may be motivated by particularly good or bad performance during an earthquake. Beyond this, practicing engineers typically perform stress analyses to assess the performance of a particular structure to vibrational levels experienced during an earthquake. The levels may be determined from recorded or estimated ground motions; actual levels usually differ from design levels. If a structure has seismic instrumentation to record response data, the estimated and recorded response and behavior of the structure can be compared.

Ways of looking ahead: hierarchical planning in language production.

PubMed

Lee, Eun-Kyung; Brown-Schmidt, Sarah; Watson, Duane G

2013-12-01

It is generally assumed that language production proceeds incrementally, with chunks of linguistic structure planned ahead of speech. Extensive research has examined the scope of language production and suggests that the size of planned chunks varies across contexts (Ferreira & Swets, 2002; Wagner & Jescheniak, 2010). By contrast, relatively little is known about the structure of advance planning, specifically whether planning proceeds incrementally according to the surface structure of the utterance, or whether speakers plan according to the hierarchical relationships between utterance elements. In two experiments, we examine the structure and scope of lexical planning in language production using a picture description task. Analyses of speech onset times and word durations show that speakers engage in hierarchical planning such that structurally dependent lexical items are planned together and that hierarchical planning occurs for both direct and indirect dependencies. Copyright © 2013 Elsevier B.V. All rights reserved.

Evaluating structural connectomics in relation to different Q-space sampling techniques.

PubMed

Rodrigues, Paulo; Prats-Galino, Alberto; Gallardo-Pujol, David; Villoslada, Pablo; Falcon, Carles; Prckovska, Vesna

2013-01-01

Brain networks are becoming forefront research in neuroscience. Network-based analysis on the functional and structural connectomes can lead to powerful imaging markers for brain diseases. However, constructing the structural connectome can be based upon different acquisition and reconstruction techniques whose information content and mutual differences has not yet been properly studied in a unified framework. The variations of the structural connectome if not properly understood can lead to dangerous conclusions when performing these type of studies. In this work we present evaluation of the structural connectome by analysing and comparing graph-based measures on real data acquired by the three most important Diffusion Weighted Imaging techniques: DTI, HARDI and DSI. We thus come to several important conclusions demonstrating that even though the different techniques demonstrate differences in the anatomy of the reconstructed fibers the respective connectomes show variations of 20%.

Dynamical compensation and structural identifiability of biological models: Analysis, implications, and reconciliation.

PubMed

Villaverde, Alejandro F; Banga, Julio R

2017-11-01

The concept of dynamical compensation has been recently introduced to describe the ability of a biological system to keep its output dynamics unchanged in the face of varying parameters. However, the original definition of dynamical compensation amounts to lack of structural identifiability. This is relevant if model parameters need to be estimated, as is often the case in biological modelling. Care should we taken when using an unidentifiable model to extract biological insight: the estimated values of structurally unidentifiable parameters are meaningless, and model predictions about unmeasured state variables can be wrong. Taking this into account, we explore alternative definitions of dynamical compensation that do not necessarily imply structural unidentifiability. Accordingly, we show different ways in which a model can be made identifiable while exhibiting dynamical compensation. Our analyses enable the use of the new concept of dynamical compensation in the context of parameter identification, and reconcile it with the desirable property of structural identifiability.

Stress Analysis for the Formation of En Echelon Veins and Vortex Structures: a Lesson Plan with a Brief Illumination

NASA Astrophysics Data System (ADS)

Zeng, Z.; Birnbaum, S.

2006-12-01

An English lesson plan exploring stress analysis of En Echelon veins and vortex structures used in the bilingual course in Structural Geology at the National Science Training Base of China is described. Two mechanical models are introduced in class and both mathematical and mechanical analyses are conducted. Samples, pictures and case studies are selected from Britain, Switzerland, and China. These case studies are augmented from the previous research results of the first author. Students are guided through the entire thought process, including methods and procedures used in the stress analysis of geologic structures. The teaching procedures are also illustrated. The method showed is effective to help students to get the initial knowledge of quantitative analysis for the formation of geological structures. This work is supported by the Ministry of Education of China, the Education Bureau of Hubei Province of China and China University of Geosciences (Wuhan).

Pestalols A-E, new alkenyl phenol and benzaldehyde derivatives from endophytic fungus Pestalotiopsis sp. AcBC2 isolated from the Chinese mangrove plant Aegiceras corniculatum.

PubMed

Sun, Jian-Fan; Lin, Xiuping; Zhou, Xue-Feng; Wan, Junting; Zhang, Tianyu; Yang, Bin; Yang, Xian-Wen; Tu, Zhengchao; Liu, Yonghong

2014-06-01

Five alkenyl phenol and benzaldehyde derivatives, pestalols A-E (1-5), as well as seven known compounds (6-12), were isolated from endophytic fungus Pestalotiopsis sp. AcBC2 derived from the Chinese mangrove plant Aegiceras corniculatum. Their structures were determined by spectroscopic analyses. Compounds 2 and 3 showed cytotoxicity against a panel of 10 tumor cell lines. Compounds 1-5, 8, 9, 11, and 12 showed inhibitory activities against Influenza A virus subtype (H3N2) and Swine Flu (H1N1) viruses. Compound 2 also showed inhibitory activity against tuberculosis.

Patterns of Gray Matter Abnormalities in Schizophrenia Based on an International Mega-analysis.

PubMed

Gupta, Cota Navin; Calhoun, Vince D; Rachakonda, Srinivas; Chen, Jiayu; Patel, Veena; Liu, Jingyu; Segall, Judith; Franke, Barbara; Zwiers, Marcel P; Arias-Vasquez, Alejandro; Buitelaar, Jan; Fisher, Simon E; Fernandez, Guillen; van Erp, Theo G M; Potkin, Steven; Ford, Judith; Mathalon, Daniel; McEwen, Sarah; Lee, Hyo Jong; Mueller, Bryon A; Greve, Douglas N; Andreassen, Ole; Agartz, Ingrid; Gollub, Randy L; Sponheim, Scott R; Ehrlich, Stefan; Wang, Lei; Pearlson, Godfrey; Glahn, David C; Sprooten, Emma; Mayer, Andrew R; Stephen, Julia; Jung, Rex E; Canive, Jose; Bustillo, Juan; Turner, Jessica A

2015-09-01

Analyses of gray matter concentration (GMC) deficits in patients with schizophrenia (Sz) have identified robust changes throughout the cortex. We assessed the relationships between diagnosis, overall symptom severity, and patterns of gray matter in the largest aggregated structural imaging dataset to date. We performed both source-based morphometry (SBM) and voxel-based morphometry (VBM) analyses on GMC images from 784 Sz and 936 controls (Ct) across 23 scanning sites in Europe and the United States. After correcting for age, gender, site, and diagnosis by site interactions, SBM analyses showed 9 patterns of diagnostic differences. They comprised separate cortical, subcortical, and cerebellar regions. Seven patterns showed greater GMC in Ct than Sz, while 2 (brainstem and cerebellum) showed greater GMC for Sz. The greatest GMC deficit was in a single pattern comprising regions in the superior temporal gyrus, inferior frontal gyrus, and medial frontal cortex, which replicated over analyses of data subsets. VBM analyses identified overall cortical GMC loss and one small cluster of increased GMC in Sz, which overlapped with the SBM brainstem component. We found no significant association between the component loadings and symptom severity in either analysis. This mega-analysis confirms that the commonly found GMC loss in Sz in the anterior temporal lobe, insula, and medial frontal lobe form a single, consistent spatial pattern even in such a diverse dataset. The separation of GMC loss into robust, repeatable spatial patterns across multiple datasets paves the way for the application of these methods to identify subtle genetic and clinical cohort effects. © The Author 2014. Published by Oxford University Press on behalf of the Maryland Psychiatric Research Center. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Inverse Analysis of Cavitation Impact Phenomena on Structures

DTIC Science & Technology

2007-07-02

can occur within different types of dynamic water environments of structures. Case study analyses using experimental data are used to demonstrate the...cavitation impact phenomena, and ultimately, with cavitation erosion of structures within turbulent water environments. 02-07-2007 Memorandum Report...of dynamic water environments of structures. Case study analyses using experimental data are used to demonstrate the fundamentals of various aspects

Thermo-selective Tm(x)Ti(1-x)O(2-x/2) nanoparticles: from Tm-doped anatase TiO2 to a rutile/pyrochlore Tm2Ti2O7 mixture. An experimental and theoretical study with a photocatalytic application.

PubMed

Navas, Javier; Sánchez-Coronilla, Antonio; Aguilar, Teresa; De los Santos, Desireé M; Hernández, Norge C; Alcántara, Rodrigo; Fernández-Lorenzo, Concha; Martín-Calleja, Joaquín

2014-11-07

This is an experimental and theoretical study of thulium doped TiO2 nanoparticles. From an experimental perspective, a method was used to synthesize thulium-doped TiO2 nanoparticles in which Tm(3+) replaces Ti(4+) in the lattice, which to our knowledge has neither been reported nor studied theoretically so far. Different proportions of anatase and rutile phases were obtained at different annealing temperatures, and XRD and Raman spectroscopy also revealed the presence of a pyrochlore phase (Tm2Ti2O7) at 1173 K. Thus, the structure of the Tm-doped nanoparticles was thermally-controlled. Furthermore, XPS showed the presence of Tm(3+) in the samples synthesized, which produces oxygen vacancies to maintain the local neutrality in the lattice. The presence of Tm(3+) in the samples led to changes in the UV-Vis absorption spectra, so they showed photoluminescence properties and new states in the band gap, which produce a new lower energy electronic transition than the main TiO2 one. Periodic DFT calculations were performed to understand the experimentally produced structures. The production of oxygen vacancies was analysed and the changes generated in the structure were fully detailed. The DOS and PDOS analyses confirmed the experimental results obtained using UV-Vis spectroscopy, and showed that the new electronic states in the band gap are due to interactions of the f state of Tm and the p state of O. Likewise, the charge study and the ELF analysis indicate that when Tm is introduced into the TiO2 structure, the Ti-O bond around the oxygen vacancy is strengthened. Finally, an example of a photocatalytic application was developed to show the high efficiency of the samples due to the heterojunction in the interfaces of the phases in the samples, which improved the charge separation and the good charge carrier mobility due to the presence of the pyrochlore phase, as was also shown theoretically.

Consensuses and discrepancies of basin-scale ocean heat content changes in different ocean analyses

NASA Astrophysics Data System (ADS)

Wang, Gongjie; Cheng, Lijing; Abraham, John; Li, Chongyin

2018-04-01

Inconsistent global/basin ocean heat content (OHC) changes were found in different ocean subsurface temperature analyses, especially in recent studies related to the slowdown in global surface temperature rise. This finding challenges the reliability of the ocean subsurface temperature analyses and motivates a more comprehensive inter-comparison between the analyses. Here we compare the OHC changes in three ocean analyses (Ishii, EN4 and IAP) to investigate the uncertainty in OHC in four major ocean basins from decadal to multi-decadal scales. First, all products show an increase of OHC since 1970 in each ocean basin revealing a robust warming, although the warming rates are not identical. The geographical patterns, the key modes and the vertical structure of OHC changes are consistent among the three datasets, implying that the main OHC variabilities can be robustly represented. However, large discrepancies are found in the percentage of basinal ocean heating related to the global ocean, with the largest differences in the Pacific and Southern Ocean. Meanwhile, we find a large discrepancy of ocean heat storage in different layers, especially within 300-700 m in the Pacific and Southern Oceans. Furthermore, the near surface analysis of Ishii and IAP are consistent with sea surface temperature (SST) products, but EN4 is found to underestimate the long-term trend. Compared with ocean heat storage derived from the atmospheric budget equation, all products show consistent seasonal cycles of OHC in the upper 1500 m especially during 2008 to 2012. Overall, our analyses further the understanding of the observed OHC variations, and we recommend a careful quantification of errors in the ocean analyses.

Empirical analyses on the development trend of non-ferrous metal industry under China’s new normal

NASA Astrophysics Data System (ADS)

Li, C. X.; Liu, C. X.; Zhang, Q. L.

2017-08-01

The CGE model of Yunnan’s macro economy was constructed based on the input-output data of Yunnan in 2012, and the development trend of the non-ferrous metals industry (NMI) under the China’s new normal was simulated. In view of this, according to different expected economic growth, and optimized economic structure, the impact on development of Yunnan NMI was simulated. The results show that the NMI growth rate is expected to decline when the economic growth show a downward trend, but the change of the proportion is relatively small. Moreover, the structure in proportion was adjusted to realize the economic structure optimization, while the proportion of NMI in GDP will decline. In contrast, the biggest influence on the NMI is the change of economic structure. From the statistics of last two years, we can see that NMI is growing, and at the same time, its proportion is declining, which is consistent with the results of simulation. But the adjustment of economic structure will take a long time. It is need to improve the proportion of deep-processing industry, extend the industrial chain, enhance the value chain, so as to be made good use of resource advantage.

Investigating the Structural Compaction of Biomolecules Upon Transition to the Gas-Phase Using ESI-TWIMS-MS.

PubMed

Devine, Paul W A; Fisher, Henry C; Calabrese, Antonio N; Whelan, Fiona; Higazi, Daniel R; Potts, Jennifer R; Lowe, David C; Radford, Sheena E; Ashcroft, Alison E

2017-09-01

Collision cross-section (CCS) measurements obtained from ion mobility spectrometry-mass spectrometry (IMS-MS) analyses often provide useful information concerning a protein's size and shape and can be complemented by modeling procedures. However, there have been some concerns about the extent to which certain proteins maintain a native-like conformation during the gas-phase analysis, especially proteins with dynamic or extended regions. Here we have measured the CCSs of a range of biomolecules including non-globular proteins and RNAs of different sequence, size, and stability. Using traveling wave IMS-MS, we show that for the proteins studied, the measured CCS deviates significantly from predicted CCS values based upon currently available structures. The results presented indicate that these proteins collapse to different extents varying on their elongated structures upon transition into the gas-phase. Comparing two RNAs of similar mass but different solution structures, we show that these biomolecules may also be susceptible to gas-phase compaction. Together, the results suggest that caution is needed when predicting structural models based on CCS data for RNAs as well as proteins with non-globular folds. Graphical Abstract ᅟ.

Ultrastructural and Functional Analyses of Recombinant Influenza Virus Ribonucleoproteins Suggest Dimerization of Nucleoprotein during Virus Amplification

PubMed Central

Ortega, Joaquín; Martín-Benito, Jaime; Zürcher, Thomas; Valpuesta, José M.; Carrascosa, José L.; Ortín, Juan

2000-01-01

Influenza virus ribonucleoproteins (RNPs) were reconstituted in vivo from cloned cDNAs expressing the three polymerase subunits, the nucleoprotein (NP), and short template RNAs. The structure of purified RNPs was studied by electron microscopy and image processing. Circular and elliptic structures were obtained in which the NP and the polymerase complex could be defined. Comparison of the structure of RNPs of various lengths indicated that each NP monomer interacts with approximately 24 nucleotides. The analysis of the amplification of RNPs with different lengths showed that those with the highest replication efficiency contained an even number of NP monomers, suggesting that the NP is incorporated as dimers into newly synthesized RNPs. PMID:10590102

Turbulent flow structures and aeolian sediment transport over a barchan sand dune

NASA Astrophysics Data System (ADS)

Wiggs, G. F. S.; Weaver, C. M.

2012-03-01

The turbulent structure of airflow over a barchan sand dune is determined using quadrant analysis of wind velocity data derived from sonic anemometers. Results indicate an increased frequency of ejection and sweep events in the toe region of the dune, characteristic of the turbulent bursting process. In contrast, at the crest there was a significant increase in the occurrence of outward interactions. Combined with high frequency saltation data our analyses show that turbulent structures characterised by a positive streamwise fluctuating velocity (+u‧ sweeps at the toe and outward interactions at the crest) have a dominant influence on sand transport on the dune, together accounting for up to 83% and 95% of transporting events at the toe and crest respectively.

Micromechanics of Sea Urchin spines.

PubMed

Tsafnat, Naomi; Fitz Gerald, John D; Le, Hai N; Stachurski, Zbigniew H

2012-01-01

The endoskeletal structure of the Sea Urchin, Centrostephanus rodgersii, has numerous long spines whose known functions include locomotion, sensing, and protection against predators. These spines have a remarkable internal microstructure and are made of single-crystal calcite. A finite-element model of the spine's unique porous structure, based on micro-computed tomography (microCT) and incorporating anisotropic material properties, was developed to study its response to mechanical loading. Simulations show that high stress concentrations occur at certain points in the spine's architecture; brittle cracking would likely initiate in these regions. These analyses demonstrate that the organization of single-crystal calcite in the unique, intricate morphology of the sea urchin spine results in a strong, stiff and lightweight structure that enhances its strength despite the brittleness of its constituent material.

Development of an Aeroelastic Modeling Capability for Transient Nozzle Side Load Analysis

NASA Technical Reports Server (NTRS)

Wang, Ten-See; Zhao, Xiang; Zhang, Sijun; Chen, Yen-Sen

2013-01-01

Lateral nozzle forces are known to cause severe structural damage to any new rocket engine in development during test. While three-dimensional, transient, turbulent, chemically reacting computational fluid dynamics methodology has been demonstrated to capture major side load physics with rigid nozzles, hot-fire tests often show nozzle structure deformation during major side load events, leading to structural damages if structural strengthening measures were not taken. The modeling picture is incomplete without the capability to address the two-way responses between the structure and fluid. The objective of this study is to develop a coupled aeroelastic modeling capability by implementing the necessary structural dynamics component into an anchored computational fluid dynamics methodology. The computational fluid dynamics component is based on an unstructured-grid, pressure-based computational fluid dynamics formulation, while the computational structural dynamics component is developed in the framework of modal analysis. Transient aeroelastic nozzle startup analyses of the Block I Space Shuttle Main Engine at sea level were performed. The computed results from the aeroelastic nozzle modeling are presented.

Ares I-X Upper Stage Simulator Structural Analyses Supporting the NESC Critical Initial Flaw Size Assessment

NASA Technical Reports Server (NTRS)

Knight, Norman F., Jr.; Phillips, Dawn R.; Raju, Ivatury S.

2008-01-01

The structural analyses described in the present report were performed in support of the NASA Engineering and Safety Center (NESC) Critical Initial Flaw Size (CIFS) assessment for the ARES I-X Upper Stage Simulator (USS) common shell segment. The structural analysis effort for the NESC assessment had three thrusts: shell buckling analyses, detailed stress analyses of the single-bolt joint test; and stress analyses of two-segment 10 degree-wedge models for the peak axial tensile running load. Elasto-plastic, large-deformation simulations were performed. Stress analysis results indicated that the stress levels were well below the material yield stress for the bounding axial tensile design load. This report also summarizes the analyses and results from parametric studies on modeling the shell-to-gusset weld, flange-surface mismatch, bolt preload, and washer-bearing-surface modeling. These analyses models were used to generate the stress levels specified for the fatigue crack growth assessment using the design load with a factor of safety.

75 FR 16202 - Office of New Reactors; Interim Staff Guidance on Ensuring Hazard-Consistent Seismic Input for...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-31

... Staff Guidance on Ensuring Hazard-Consistent Seismic Input for Site Response and Soil Structure...-Consistent Seismic Input for Site Response and Soil Structure Interaction Analyses,'' (Agencywide Documents... Soil Structure Interaction Analyses,'' (ADAMS Accession No. ML092230455) to solicit public and industry...

Top Down Tandem Mass Spectrometric Analysis of a Chemically Modified Rough-Type Lipopolysaccharide Vaccine Candidate.

PubMed

Oyler, Benjamin L; Khan, Mohd M; Smith, Donald F; Harberts, Erin M; Kilgour, David P A; Ernst, Robert K; Cross, Alan S; Goodlett, David R

2018-06-01

Recent advances in lipopolysaccharide (LPS) biology have led to its use in drug discovery pipelines, including vaccine and vaccine adjuvant discovery. Desirable characteristics for LPS vaccine candidates include both the ability to produce a specific antibody titer in patients and a minimal host inflammatory response directed by the innate immune system. However, in-depth chemical characterization of most LPS extracts has not been performed; hence, biological activities of these extracts are unpredictable. Additionally, the most widely adopted workflow for LPS structure elucidation includes nonspecific chemical decomposition steps before analyses, making structures inferred and not necessarily biologically relevant. In this work, several different mass spectrometry workflows that have not been previously explored were employed to show proof-of-principle for top down LPS primary structure elucidation, specifically for a rough-type mutant (J5) E. coli-derived LPS component of a vaccine candidate. First, ion mobility filtered precursor ions were subjected to collision induced dissociation (CID) to define differences in native J5 LPS v. chemically detoxified J5 LPS (dLPS). Next, ultra-high mass resolving power, accurate mass spectrometry was employed for unequivocal precursor and product ion empirical formulae generation. Finally, MS 3 analyses in an ion trap instrument showed that previous knowledge about dissociation of LPS components can be used to reconstruct and sequence LPS in a top down fashion. A structural rationale is also explained for differential inflammatory dose-response curves, in vitro, when HEK-Blue hTLR4 cells were administered increasing concentrations of native J5 LPS v. dLPS, which will be useful in future drug discovery efforts. Graphical Abstract ᅟ.

An extensive spectroscopic time series of three Wolf-Rayet stars - I. The lifetime of large-scale structures in the wind of WR 134

NASA Astrophysics Data System (ADS)

Aldoretta, E. J.; St-Louis, N.; Richardson, N. D.; Moffat, A. F. J.; Eversberg, T.; Hill, G. M.; Shenar, T.; Artigau, É.; Gauza, B.; Knapen, J. H.; Kubát, J.; Kubátová, B.; Maltais-Tariant, R.; Muñoz, M.; Pablo, H.; Ramiaramanantsoa, T.; Richard-Laferrière, A.; Sablowski, D. P.; Simón-Díaz, S.; St-Jean, L.; Bolduan, F.; Dias, F. M.; Dubreuil, P.; Fuchs, D.; Garrel, T.; Grutzeck, G.; Hunger, T.; Küsters, D.; Langenbrink, M.; Leadbeater, R.; Li, D.; Lopez, A.; Mauclaire, B.; Moldenhawer, T.; Potter, M.; dos Santos, E. M.; Schanne, L.; Schmidt, J.; Sieske, H.; Strachan, J.; Stinner, E.; Stinner, P.; Stober, B.; Strandbaek, K.; Syder, T.; Verilhac, D.; Waldschläger, U.; Weiss, D.; Wendt, A.

2016-08-01

During the summer of 2013, a 4-month spectroscopic campaign took place to observe the variabilities in three Wolf-Rayet stars. The spectroscopic data have been analysed for WR 134 (WN6b), to better understand its behaviour and long-term periodicity, which we interpret as arising from corotating interaction regions (CIRs) in the wind. By analysing the variability of the He II λ5411 emission line, the previously identified period was refined to P = 2.255 ± 0.008 (s.d.) d. The coherency time of the variability, which we associate with the lifetime of the CIRs in the wind, was deduced to be 40 ± 6 d, or ˜18 cycles, by cross-correlating the variability patterns as a function of time. When comparing the phased observational grey-scale difference images with theoretical grey-scales previously calculated from models including CIRs in an optically thin stellar wind, we find that two CIRs were likely present. A separation in longitude of Δφ ≃ 90° was determined between the two CIRs and we suggest that the different maximum velocities that they reach indicate that they emerge from different latitudes. We have also been able to detect observational signatures of the CIRs in other spectral lines (C IV λλ5802,5812 and He I λ5876). Furthermore, a DAC was found to be present simultaneously with the CIR signatures detected in the He I λ5876 emission line which is consistent with the proposed geometry of the large-scale structures in the wind. Small-scale structures also show a presence in the wind, simultaneously with the larger scale structures, showing that they do in fact co-exist.

Top Down Tandem Mass Spectrometric Analysis of a Chemically Modified Rough-Type Lipopolysaccharide Vaccine Candidate

NASA Astrophysics Data System (ADS)

Oyler, Benjamin L.; Khan, Mohd M.; Smith, Donald F.; Harberts, Erin M.; Kilgour, David P. A.; Ernst, Robert K.; Cross, Alan S.; Goodlett, David R.

2018-02-01

Recent advances in lipopolysaccharide (LPS) biology have led to its use in drug discovery pipelines, including vaccine and vaccine adjuvant discovery. Desirable characteristics for LPS vaccine candidates include both the ability to produce a specific antibody titer in patients and a minimal host inflammatory response directed by the innate immune system. However, in-depth chemical characterization of most LPS extracts has not been performed; hence, biological activities of these extracts are unpredictable. Additionally, the most widely adopted workflow for LPS structure elucidation includes nonspecific chemical decomposition steps before analyses, making structures inferred and not necessarily biologically relevant. In this work, several different mass spectrometry workflows that have not been previously explored were employed to show proof-of-principle for top down LPS primary structure elucidation, specifically for a rough-type mutant (J5) E. coli-derived LPS component of a vaccine candidate. First, ion mobility filtered precursor ions were subjected to collision induced dissociation (CID) to define differences in native J5 LPS v. chemically detoxified J5 LPS (dLPS). Next, ultra-high mass resolving power, accurate mass spectrometry was employed for unequivocal precursor and product ion empirical formulae generation. Finally, MS3 analyses in an ion trap instrument showed that previous knowledge about dissociation of LPS components can be used to reconstruct and sequence LPS in a top down fashion. A structural rationale is also explained for differential inflammatory dose-response curves, in vitro, when HEK-Blue hTLR4 cells were administered increasing concentrations of native J5 LPS v. dLPS, which will be useful in future drug discovery efforts. [Figure not available: see fulltext.

Comparative Mitogenomic Analysis of Species Representing Six Subfamilies in the Family Tenebrionidae

PubMed Central

Zhang, Hong-Li; Liu, Bing-Bing; Wang, Xiao-Yang; Han, Zhi-Ping; Zhang, Dong-Xu; Su, Cai-Na

2016-01-01

To better understand the architecture and evolution of the mitochondrial genome (mitogenome), mitogenomes of ten specimens representing six subfamilies in Tenebrionidae were selected, and comparative analysis of these mitogenomes was carried out in this study. Ten mitogenomes in this family share a similar gene composition, gene order, nucleotide composition, and codon usage. In addition, our results show that nucleotide bias was strongly influenced by the preference of codon usage for A/T rich codons which significantly correlated with the G + C content of protein coding genes (PCGs). Evolutionary rate analyses reveal that all PCGs have been subjected to a purifying selection, whereas 13 PCGs displayed different evolution rates, among which ATPase subunit 8 (ATP8) showed the highest evolutionary rate. We inferred the secondary structure for all RNA genes of Tenebrio molitor (Te2) and used this as the basis for comparison with the same genes from other Tenebrionidae mitogenomes. Some conserved helices (stems) and loops of RNA structures were found in different domains of ribosomal RNAs (rRNAs) and the cloverleaf structure of transfer RNAs (tRNAs). With regard to the AT-rich region, we analyzed tandem repeat sequences located in this region and identified some essential elements including T stretches, the consensus motif at the flanking regions of T stretch, and the secondary structure formed by the motif at the 3′ end of T stretch in major strand, which are highly conserved in these species. Furthermore, phylogenetic analyses using mitogenomic data strongly support the relationships among six subfamilies: ((Tenebrionidae incertae sedis + (Diaperinae + Tenebrioninae)) + (Pimeliinae + Lagriinae)), which is consistent with phylogenetic results based on morphological traits. PMID:27258256

Phylogeography, phylogeny and hybridization in trichechid sirenians: Implications for manatee conservation

USGS Publications Warehouse

Vianna, J.A.; Bonde, R.K.; Caballero, S.; Giraldo, J.P.; Lima, R.P.; Clark, A.; Marmontel, M.; Morales-Vela, B.; De Souza, M. J.; Parr, L.; Rodriguez-Lopez, M.A.; Mignucci-Giannoni, A. A.; Powell, J.A.; Santos, F.R.

2006-01-01

The three living species of manatees, West Indian (Trichechus manatus), Amazonian (Trichechus inunguis) and West African (Trichechus senegalensis), are distributed across the shallow tropical and subtropical waters of America and the western coast of Africa. We have sequenced the mitochondrial DNA control region in 330 Trichechus to compare their phylogeographic patterns. In T. manatus we observed a marked population structure with the identification of three haplotype clusters showing a distinct spatial distribution. A geographic barrier represented by the continuity of the Lesser Antilles to Trinidad Island, near the mouth of the Orinoco River in Venezuela, appears to have restricted the gene flow historically in T. manatus. However, for T. inunguis we observed a single expanding population cluster, with a high diversity of very closely related haplotypes. A marked geographic population structure is likely present in T. senegalensis with at least two distinct clusters. Phylogenetic analyses with the mtDNA cytochrome b gene suggest a clade of the marine Trichechus species, with T. inunguis as the most basal trichechid. This is in agreement with previous morphological analyses. Mitochondrial DNA, autosomal microsatellites and cytogenetic analyses revealed the presence of hybrids between the T. manatus and T. inunguis species at the mouth of the Amazon River in Brazil, extending to the Guyanas and probably as far as the mouth of the Orinoco River. Future conservation strategies should consider the distinct population structure of manatee species, as well as the historical barriers to gene flow and the likely occurrence of interspecific hybridization. ?? 2006 Blackwell Publishing Ltd.

Study of the electrochemical oxidation and reduction of C.I. Reactive Orange 4 in sodium sulphate alkaline solutions.

PubMed

del Río, A I; Molina, J; Bonastre, J; Cases, F

2009-12-15

Synthetic solutions of hydrolysed C.I. Reactive Orange 4, a monoazo textile dye commercially named Procion Orange MX-2R (PMX2R) and colour index number C.I. 18260, was exposed to electrochemical treatment under galvanostatic conditions and Na2SO4 as electrolyte. The influence of the electrochemical process as well as the applied current density was evaluated. Ti/SnO2-Sb-Pt and stainless steel electrodes were used as anode and cathode, respectively, and the intermediates generated on the cathode during electrochemical reduction were investigated. Aliquots of the solutions treated were analysed by UV-visible and FTIR-ATR spectroscopy confirming the presence of aromatic structures in solution when an electro-reduction was carried out. Electro-oxidation degraded both the azo group and aromatic structures. HPLC measures revealed that all processes followed pseudo-first order kinetics and decolourisation rates showed a considerable dependency on the applied current density. CV experiments and XPS analyses were carried out to study the behaviour of both PMX2R and intermediates and to analyse the state of the cathode after the electrochemical reduction, respectively. It was observed the presence of a main intermediate in solution after an electrochemical reduction whose chemical structure is similar to 2-amino-1,5-naphthalenedisulphonic acid. Moreover, the analysis of the cathode surface after electrochemical reduction reveals the presence of a coating layer with organic nature.