Solid-solution thermodynamics in Al-Li alloys

NASA Astrophysics Data System (ADS)

Alekseev, A. A.; Lukina, E. A.

2016-05-01

The relative equilibrium concentrations of lithium atoms distributed over different electron-structural states has been estimated. The possibility of the existence of various nonequilibrium electron-structural states of Li atoms in the solid solution in Al has been substantiated thermodynamically. Upon the decomposition of the supersaturated solid solution, the supersaturation on three electron-structural states of Li atoms that arises upon the quenching of the alloy can lead to the formation of lithium-containing phases in which the lithium atoms enter in one electron-structural state.

Insights into Penicillium roqueforti Morphological and Genetic Diversity

PubMed Central

Gillot, Guillaume; Jany, Jean-Luc; Coton, Monika; Le Floch, Gaétan; Debaets, Stella; Ropars, Jeanne; López-Villavicencio, Manuela; Dupont, Joëlle; Branca, Antoine; Giraud, Tatiana; Coton, Emmanuel

2015-01-01

Fungi exhibit substantial morphological and genetic diversity, often associated with cryptic species differing in ecological niches. Penicillium roqueforti is used as a starter culture for blue-veined cheeses, being responsible for their flavor and color, but is also a common spoilage organism in various foods. Different types of blue-veined cheeses are manufactured and consumed worldwide, displaying specific organoleptic properties. These features may be due to the different manufacturing methods and/or to the specific P. roqueforti strains used. Substantial morphological diversity exists within P. roqueforti and, although not taxonomically valid, several technological names have been used for strains on different cheeses (e.g., P. gorgonzolae, P. stilton). A worldwide P. roqueforti collection from 120 individual blue-veined cheeses and 21 other substrates was analyzed here to determine (i) whether P. roqueforti is a complex of cryptic species, by applying the Genealogical Concordance Phylogenetic Species Recognition criterion (GC-PSR), (ii) whether the population structure assessed using microsatellite markers correspond to blue cheese types, and (iii) whether the genetic clusters display different morphologies. GC-PSR multi-locus sequence analyses showed no evidence of cryptic species. The population structure analysis using microsatellites revealed the existence of highly differentiated populations, corresponding to blue cheese types and with contrasted morphologies. This suggests that the population structure has been shaped by different cheese-making processes or that different populations were recruited for different cheese types. Cheese-making fungi thus constitute good models for studying fungal diversification under recent selection. PMID:26091176

Second harmonic generation in resonant optical structures

DOEpatents

Eichenfield, Matt; Moore, Jeremy; Friedmann, Thomas A.; Olsson, Roy H.; Wiwi, Michael; Padilla, Camille; Douglas, James Kenneth; Hattar, Khalid Mikhiel

2018-01-09

An optical second-harmonic generator (or spontaneous parametric down-converter) includes a microresonator formed of a nonlinear optical medium. The microresonator supports at least two modes that can be phase matched at different frequencies so that light can be converted between them: A first resonant mode having substantially radial polarization and a second resonant mode having substantially vertical polarization. The first and second modes have the same radial order. The thickness of the nonlinear medium is less than one-half the pump wavelength within the medium.

An improved semi-implicit method for structural dynamics analysis

NASA Technical Reports Server (NTRS)

Park, K. C.

1982-01-01

A semi-implicit algorithm is presented for direct time integration of the structural dynamics equations. The algorithm avoids the factoring of the implicit difference solution matrix and mitigates the unacceptable accuracy losses which plagued previous semi-implicit algorithms. This substantial accuracy improvement is achieved by augmenting the solution matrix with two simple diagonal matrices of the order of the integration truncation error.

Structural Characterization of the Low-Molecular-Weight Heparin Dalteparin by Combining Different Analytical Strategies.

PubMed

Bisio, Antonella; Urso, Elena; Guerrini, Marco; de Wit, Pauline; Torri, Giangiacomo; Naggi, Annamaria

2017-06-24

A number of low molecular weight heparin (LMWH) products are available for clinical use and although all share a similar mechanism of action, they are classified as distinct drugs because of the different depolymerisation processes of the native heparin resulting in substantial pharmacokinetic and pharmacodynamics differences. While enoxaparin has been extensively investigated, little information is available regarding the LMWH dalteparin. The present study is focused on the detailed structural characterization of Fragmin ® by LC-MS and NMR applied both to the whole drug and to its enzymatic products. For a more in-depth approach, size homogeneous octasaccharide and decasaccharide components together with their fractions endowed with high or no affinity toward antithrombin were also isolated and their structural profiles characterized. The combination of different analytical strategies here described represents a useful tool for the assessment of batch-to-batch structural variability and for comparative evaluation of structural features of biosimilar products.

Ceramic honeycomb structures and the method thereof

NASA Technical Reports Server (NTRS)

Riccitiello, Salvatore R. (Inventor); Cagliostro, Domenick E. (Inventor)

1987-01-01

The subject invention pertains to a method of producing an improved composite-composite honeycomb structure for aircraft or aerospace use. Specifically, the subject invention relates to a method for the production of a lightweight ceramic-ceramic composite honeycomb structure, which method comprises: (1) pyrolyzing a loosely woven fabric/binder having a honeycomb shape and having a high char yield and geometric integrity after pyrolysis at between about 700 and 1,100 C; (2) substantially evenly depositing at least one layer of ceramic material on the pyrolyzed fabric/binder of step (1); (3) recovering the coated ceramic honeycomb structure; (4) removing the pyrolyzed fabric/binder of the structure of step (3) by slow pyrolysis at between 700 and 1000 C in between about a 2 to 5% by volume oxygen atmosphere for between about 0.5 and 5 hr.; and (5) substantially evenly depositing on and within the rigid hollow honeycomb structure at least one additional layer of the same or a different ceramic material by chemical vapor deposition and chemical vapor infiltration. The honeycomb shaped ceramic articles have enhanced physical properties and are useful in aircraft and aerospace uses.

A Comparative Analysis of the Wages of Hispanic, Black, and Anglo Men.

ERIC Educational Resources Information Center

Reimers, Cordelia

This paper details the factors contributing to the wage structure of Hispanic men and compares the wages of Black and Anglo men. The major finding is that controlling for differences in observable personal characteristics--such as education and work experience--substantially reduces the wage differences between Hispanics and Anglos. For example,…

What makes the difference in perovskite titanates?

NASA Astrophysics Data System (ADS)

Bussmann-Holder, Annette; Roleder, Krystian; Ko, Jae-Hyeon

2018-06-01

We have investigated in detail the lattice dynamics of five different perovskite titanates ATiO3 (A = Ca, Sr, Ba, Pb, Eu) where the A sites are occupied by +2 ions. In spite of the largely ionic character of these ions, the properties of these compounds differ substantially. They range from order/disorder like, to displacive ferroelectric, quantum paraelectric, and antiferromagnetic. All compounds crystallize in the cubic structure at high temperature and undergo structural phase transitions to tetragonal symmetry, partly followed by further transitions to lower symmetries. Since the TiO6 moiety is the essential electronic and structural unit, the question arises, what makes the significant difference between them. It is shown that the lattice dynamics of these compounds are very different, and that mode-mode coupling effects give rise to many distinct properties. In addition, the oxygen ion nonlinear polarizability plays a key role since it dominates the anharmonicity of these perovskites and determines the structural instability.

Error Tolerant Plan Recognition: An Empirical Investigation

DTIC Science & Technology

2015-05-01

structure can differ drastically in semantics. For instance, a plan to travel to a grocery store to buy milk might coincidentally be structurally...algorithm for its ability to tolerate input errors, and that storing and leveraging state information in its plan representation substantially...proposed a novel representation for storing and organizing plans in a plan library, based on action-state pairs and abstract states. It counts the

Effect of Barothermal Treatment on the Structure and the Mechanical Properties of a High-Strength Eutectic Al-Zn-Mg-Cu-Ni Aluminum Alloy

NASA Astrophysics Data System (ADS)

Akopyan, T. K.; Padalko, A. G.; Belov, N. A.; Karpova, Zh. A.

2017-11-01

The effect of barothermal treatment by hot isostatic pressing (HIP) on the structure and the properties of castings of a promising high-strength cast aluminum alloy, namely, nikalin ATs6N4 based on the Al‒Zn-Mg-Cu-Ni system, has been studied using two barothermal treatment regimes different in isothermal holding temperature. It is shown that the casting porosity substantially decreases after barothermal treatment; eutectic phase Al3Ni particles are additionally refined during exposure to the barothermal treatment temperature: the higher the HIP temperature, the more substantial the refinement. The improvement of the casting structure after HIP increases their mechanical properties. It is found, in particular, that the plasticity of the alloy in the state of the maximum hardening increases by a factor of more than 8 as compared to the initial state (from 0.82 to 6.9%).

Urea denatured state ensembles contain extensive secondary structure that is increased in hydrophobic proteins.

PubMed

Nick Pace, C; Huyghues-Despointes, Beatrice M P; Fu, Hailong; Takano, Kazufumi; Scholtz, J Martin; Grimsley, Gerald R

2010-05-01

The goal of this article is to gain a better understanding of the denatured state ensemble (DSE) of proteins through an experimental and computational study of their denaturation by urea. Proteins unfold to different extents in urea and the most hydrophobic proteins have the most compact DSE and contain almost as much secondary structure as folded proteins. Proteins that unfold to the greatest extent near pH 7 still contain substantial amounts of secondary structure. At low pH, the DSE expands due to charge-charge interactions and when the net charge per residue is high, most of the secondary structure is disrupted. The proteins in the DSE appear to contain substantial amounts of polyproline II conformation at high urea concentrations. In all cases considered, including staph nuclease, the extent of unfolding by urea can be accounted for using the data and approach developed in the laboratory of Wayne Bolen (Auton et al., Proc Natl Acad Sci 2007; 104:15317-15323).

Cultural differences in moral judgment and behavior, across and within societies.

PubMed

Graham, Jesse; Meindl, Peter; Beall, Erica; Johnson, Kate M; Zhang, Li

2016-04-01

We review contemporary work on cultural factors affecting moral judgments and values, and those affecting moral behaviors. In both cases, we highlight examples of within-societal cultural differences in morality, to show that these can be as substantial and important as cross-societal differences. Whether between or within nations and societies, cultures vary substantially in their promotion and transmission of a multitude of moral judgments and behaviors. Cultural factors contributing to this variation include religion, social ecology (weather, crop conditions, population density, pathogen prevalence, residential mobility), and regulatory social institutions such as kinship structures and economic markets. This variability raises questions for normative theories of morality, but also holds promise for future descriptive work on moral thought and behavior. Copyright © 2015 Elsevier Ltd. All rights reserved.

Hypothesis: spring-loaded boomerang mechanism of influenza hemagglutinin-mediated membrane fusion.

PubMed

Tamm, Lukas K

2003-07-11

Substantial progress has been made in recent years to augment the current understanding of structures and interactions that promote viral membrane fusion. This progress is reviewed with a particular emphasis on recently determined structures of viral fusion domains and their interactions with lipid membranes. The results from the different structural and thermodynamic experimental approaches are synthesized into a new proposed mechanism, termed the "spring-loaded boomerang" mechanism of membrane fusion, which is presented here as a hypothesis.

Structural studies of Saccharomyces cerevesiae mitochondrial NADP-dependent isocitrate dehydrogenase in different enzymatic states reveal substantial conformational changes during the catalytic reaction.

PubMed

Peng, Yingjie; Zhong, Chen; Huang, Wei; Ding, Jianping

2008-09-01

Isocitrate dehydrogenases (IDHs) catalyze oxidative decarboxylation of isocitrate (ICT) into alpha-ketoglutarate (AKG). We report here the crystal structures of Saccharomyces cerevesiae mitochondrial NADP-IDH Idp1p in binary complexes with coenzyme NADP, or substrate ICT, or product AKG, and in a quaternary complex with NADPH, AKG, and Ca(2+), which represent different enzymatic states during the catalytic reaction. Analyses of these structures identify key residues involved in the binding of these ligands. Comparisons among these structures and with the previously reported structures of other NADP-IDHs reveal that eukaryotic NADP-IDHs undergo substantial conformational changes during the catalytic reaction. Binding or release of the ligands can cause significant conformational changes of the structural elements composing the active site, leading to rotation of the large domain relative to the small and clasp domains along two hinge regions (residues 118-124 and residues 284-287) while maintaining the integrity of its secondary structural elements, and thus, formation of at least three distinct overall conformations. Specifically, the enzyme adopts an open conformation when bound to NADP, a quasi-closed conformation when bound to ICT or AKG, and a fully closed conformation when bound to NADP, ICT, and Ca(2+) in the pseudo-Michaelis complex or with NADPH, AKG, and Ca(2+) in the product state. The conformational changes of eukaryotic NADP-IDHs are quite different from those of Escherichia coli NADP-IDH, for which significant conformational changes are observed only between two forms of the apo enzyme, suggesting that the catalytic mechanism of eukaryotic NADP-IDHs is more complex than that of EcIDH, and involves more fine-tuned conformational changes.

Structural studies of Saccharomyces cerevesiae mitochondrial NADP-dependent isocitrate dehydrogenase in different enzymatic states reveal substantial conformational changes during the catalytic reaction

PubMed Central

Peng, Yingjie; Zhong, Chen; Huang, Wei; Ding, Jianping

2008-01-01

Isocitrate dehydrogenases (IDHs) catalyze oxidative decarboxylation of isocitrate (ICT) into α-ketoglutarate (AKG). We report here the crystal structures of Saccharomyces cerevesiae mitochondrial NADP-IDH Idp1p in binary complexes with coenzyme NADP, or substrate ICT, or product AKG, and in a quaternary complex with NADPH, AKG, and Ca2+, which represent different enzymatic states during the catalytic reaction. Analyses of these structures identify key residues involved in the binding of these ligands. Comparisons among these structures and with the previously reported structures of other NADP-IDHs reveal that eukaryotic NADP-IDHs undergo substantial conformational changes during the catalytic reaction. Binding or release of the ligands can cause significant conformational changes of the structural elements composing the active site, leading to rotation of the large domain relative to the small and clasp domains along two hinge regions (residues 118–124 and residues 284–287) while maintaining the integrity of its secondary structural elements, and thus, formation of at least three distinct overall conformations. Specifically, the enzyme adopts an open conformation when bound to NADP, a quasi-closed conformation when bound to ICT or AKG, and a fully closed conformation when bound to NADP, ICT, and Ca2+ in the pseudo-Michaelis complex or with NADPH, AKG, and Ca2+ in the product state. The conformational changes of eukaryotic NADP-IDHs are quite different from those of Escherichia coli NADP-IDH, for which significant conformational changes are observed only between two forms of the apo enzyme, suggesting that the catalytic mechanism of eukaryotic NADP-IDHs is more complex than that of EcIDH, and involves more fine-tuned conformational changes. PMID:18552125

Interdisciplinary Studies at a Crossroads

ERIC Educational Resources Information Center

Kleinberg, Ethan

2008-01-01

In today's competitive college market, "interdisciplinary studies" are a major selling point for colleges and universities. Yet, on closer examination, it is apparent that the academic structure and place of the majority of interdisciplinary programs, departments, and centers are not substantially different from the academic disciplines,…

More Than Filaments and Cores: Statistical Study of Structure Formation and Dynamics in Nearby Molecular Clouds

NASA Astrophysics Data System (ADS)

Chen, How-Huan; Goodman, Alyssa

2018-01-01

In the past decade, multiple attempts at understanding the connection between filaments and star forming cores have been made using observations across the entire epectrum. However, the filaments and the cores are usually treated as predefined--and well-defined--entities, instead of structures that often come at different sizes, shapes, with substantially different dynamics, and inter-connected at different scales. In my dissertation, I present an array of studies using different statistical methods, including the dendrogram and the probability distribution function (PDF), of structures at different size scales within nearby molecular clouds. These structures are identified using observations of different density tracers, and where possible, in the multi-dimensional parameter space of key dynamic properties--the LSR velocity, the velocity dispersion, and the column density. The goal is to give an overview of structure formation in nearby star-forming clouds, as well as of the dynamics in these structures. I find that the overall statistical properties of a larger structure is often the summation/superposition of sub-structures within, and that there could be significant variations due to local physical processes. I also find that the star formation process within molecular clouds could in fact take place in a non-monolithic manner, connecting potentially merging and/or transient structures, at different scales.

TaRh2B2 and NbRh2B2: Superconductors with a chiral noncentrosymmetric crystal structure.

PubMed

Carnicom, Elizabeth M; Xie, Weiwei; Klimczuk, Tomasz; Lin, Jingjing; Górnicka, Karolina; Sobczak, Zuzanna; Ong, Nai Phuan; Cava, Robert J

2018-05-01

It is a fundamental truth in solid compounds that the physical properties follow the symmetry of the crystal structure. Nowhere is the effect of symmetry more pronounced than in the electronic and magnetic properties of materials-even the projection of the bulk crystal symmetry onto different crystal faces is known to have a substantial impact on the surface electronic states. The effect of bulk crystal symmetry on the properties of superconductors is widely appreciated, although its study presents substantial challenges. The effect of a lack of a center of symmetry in a crystal structure, for example, has long been understood to necessitate that the wave function of the collective electron state that gives rise to superconductivity has to be more complex than usual. However, few nonhypothetical materials, if any, have actually been proven to display exotic superconducting properties as a result. We introduce two new superconductors that in addition to having noncentrosymmetric crystal structures also have chiral crystal structures. Because the wave function of electrons in solids is particularly sensitive to the host material's symmetry, crystal structure chirality is expected to have a substantial effect on their superconducting wave functions. Our two experimentally obtained chiral noncentrosymmetric superconducting materials have transition temperatures to superconductivity that are easily experimentally accessible, and our basic property characterization suggests that their superconducting properties may be unusual. We propose that their study may allow for a more in-depth understanding of how chirality influences the properties of superconductors and devices that incorporate them.

Composite theory applied to elastomers

NASA Technical Reports Server (NTRS)

Clark, S. K.

1986-01-01

Reinforced elastomers form the basis for most of the structural or load carrying applications of rubber products. Computer based structural analysis in the form of finite element codes was highly successful in refining structural design in both isotropic materials and rigid composites. This has lead the rubber industry to attempt to make use of such techniques in the design of structural cord-rubber composites. While such efforts appear promising, they were not easy to achieve for several reasons. Among these is a distinct lack of a clearly defined set of material property descriptors suitable for computer analysis. There are substantial differences between conventional steel, aluminum, or even rigid composites such as graphite-epoxy, and textile-cord reinforced rubber. These differences which are both conceptual and practical are discussed.

The impact of structural uncertainty on cost-effectiveness models for adjuvant endocrine breast cancer treatments: the need for disease-specific model standardization and improved guidance.

PubMed

Frederix, Gerardus W J; van Hasselt, Johan G C; Schellens, Jan H M; Hövels, Anke M; Raaijmakers, Jan A M; Huitema, Alwin D R; Severens, Johan L

2014-01-01

Structural uncertainty relates to differences in model structure and parameterization. For many published health economic analyses in oncology, substantial differences in model structure exist, leading to differences in analysis outcomes and potentially impacting decision-making processes. The objectives of this analysis were (1) to identify differences in model structure and parameterization for cost-effectiveness analyses (CEAs) comparing tamoxifen and anastrazole for adjuvant breast cancer (ABC) treatment; and (2) to quantify the impact of these differences on analysis outcome metrics. The analysis consisted of four steps: (1) review of the literature for identification of eligible CEAs; (2) definition and implementation of a base model structure, which included the core structural components for all identified CEAs; (3) definition and implementation of changes or additions in the base model structure or parameterization; and (4) quantification of the impact of changes in model structure or parameterizations on the analysis outcome metrics life-years gained (LYG), incremental costs (IC) and the incremental cost-effectiveness ratio (ICER). Eleven CEA analyses comparing anastrazole and tamoxifen as ABC treatment were identified. The base model consisted of the following health states: (1) on treatment; (2) off treatment; (3) local recurrence; (4) metastatic disease; (5) death due to breast cancer; and (6) death due to other causes. The base model estimates of anastrazole versus tamoxifen for the LYG, IC and ICER were 0.263 years, €3,647 and €13,868/LYG, respectively. In the published models that were evaluated, differences in model structure included the addition of different recurrence health states, and associated transition rates were identified. Differences in parameterization were related to the incidences of recurrence, local recurrence to metastatic disease, and metastatic disease to death. The separate impact of these model components on the LYG ranged from 0.207 to 0.356 years, while incremental costs ranged from €3,490 to €3,714 and ICERs ranged from €9,804/LYG to €17,966/LYG. When we re-analyzed the published CEAs in our framework by including their respective model properties, the LYG ranged from 0.207 to 0.383 years, IC ranged from €3,556 to €3,731 and ICERs ranged from €9,683/LYG to €17,570/LYG. Differences in model structure and parameterization lead to substantial differences in analysis outcome metrics. This analysis supports the need for more guidance regarding structural uncertainty and the use of standardized disease-specific models for health economic analyses of adjuvant endocrine breast cancer therapies. The developed approach in the current analysis could potentially serve as a template for further evaluations of structural uncertainty and development of disease-specific models.

Origami tubes assembled into stiff, yet reconfigurable structures and metamaterials.

PubMed

Filipov, Evgueni T; Tachi, Tomohiro; Paulino, Glaucio H

2015-10-06

Thin sheets have long been known to experience an increase in stiffness when they are bent, buckled, or assembled into smaller interlocking structures. We introduce a unique orientation for coupling rigidly foldable origami tubes in a "zipper" fashion that substantially increases the system stiffness and permits only one flexible deformation mode through which the structure can deploy. The flexible deployment of the tubular structures is permitted by localized bending of the origami along prescribed fold lines. All other deformation modes, such as global bending and twisting of the structural system, are substantially stiffer because the tubular assemblages are overconstrained and the thin sheets become engaged in tension and compression. The zipper-coupled tubes yield an unusually large eigenvalue bandgap that represents the unique difference in stiffness between deformation modes. Furthermore, we couple compatible origami tubes into a variety of cellular assemblages that can enhance mechanical characteristics and geometric versatility, leading to a potential design paradigm for structures and metamaterials that can be deployed, stiffened, and tuned. The enhanced mechanical properties, versatility, and adaptivity of these thin sheet systems can provide practical solutions of varying geometric scales in science and engineering.

Origami tubes assembled into stiff, yet reconfigurable structures and metamaterials

PubMed Central

Filipov, Evgueni T.; Tachi, Tomohiro; Paulino, Glaucio H.

2015-01-01

Thin sheets have long been known to experience an increase in stiffness when they are bent, buckled, or assembled into smaller interlocking structures. We introduce a unique orientation for coupling rigidly foldable origami tubes in a “zipper” fashion that substantially increases the system stiffness and permits only one flexible deformation mode through which the structure can deploy. The flexible deployment of the tubular structures is permitted by localized bending of the origami along prescribed fold lines. All other deformation modes, such as global bending and twisting of the structural system, are substantially stiffer because the tubular assemblages are overconstrained and the thin sheets become engaged in tension and compression. The zipper-coupled tubes yield an unusually large eigenvalue bandgap that represents the unique difference in stiffness between deformation modes. Furthermore, we couple compatible origami tubes into a variety of cellular assemblages that can enhance mechanical characteristics and geometric versatility, leading to a potential design paradigm for structures and metamaterials that can be deployed, stiffened, and tuned. The enhanced mechanical properties, versatility, and adaptivity of these thin sheet systems can provide practical solutions of varying geometric scales in science and engineering. PMID:26351693

Origami tubes assembled into stiff, yet reconfigurable structures and metamaterials

NASA Astrophysics Data System (ADS)

Filipov, Evgueni T.; Tachi, Tomohiro; Paulino, Glaucio H.

2015-10-01

Thin sheets have long been known to experience an increase in stiffness when they are bent, buckled, or assembled into smaller interlocking structures. We introduce a unique orientation for coupling rigidly foldable origami tubes in a "zipper" fashion that substantially increases the system stiffness and permits only one flexible deformation mode through which the structure can deploy. The flexible deployment of the tubular structures is permitted by localized bending of the origami along prescribed fold lines. All other deformation modes, such as global bending and twisting of the structural system, are substantially stiffer because the tubular assemblages are overconstrained and the thin sheets become engaged in tension and compression. The zipper-coupled tubes yield an unusually large eigenvalue bandgap that represents the unique difference in stiffness between deformation modes. Furthermore, we couple compatible origami tubes into a variety of cellular assemblages that can enhance mechanical characteristics and geometric versatility, leading to a potential design paradigm for structures and metamaterials that can be deployed, stiffened, and tuned. The enhanced mechanical properties, versatility, and adaptivity of these thin sheet systems can provide practical solutions of varying geometric scales in science and engineering.

MAISTAS: a tool for automatic structural evaluation of alternative splicing products.

PubMed

Floris, Matteo; Raimondo, Domenico; Leoni, Guido; Orsini, Massimiliano; Marcatili, Paolo; Tramontano, Anna

2011-06-15

Analysis of the human genome revealed that the amount of transcribed sequence is an order of magnitude greater than the number of predicted and well-characterized genes. A sizeable fraction of these transcripts is related to alternatively spliced forms of known protein coding genes. Inspection of the alternatively spliced transcripts identified in the pilot phase of the ENCODE project has clearly shown that often their structure might substantially differ from that of other isoforms of the same gene, and therefore that they might perform unrelated functions, or that they might even not correspond to a functional protein. Identifying these cases is obviously relevant for the functional assignment of gene products and for the interpretation of the effect of variations in the corresponding proteins. Here we describe a publicly available tool that, given a gene or a protein, retrieves and analyses all its annotated isoforms, provides users with three-dimensional models of the isoform(s) of his/her interest whenever possible and automatically assesses whether homology derived structural models correspond to plausible structures. This information is clearly relevant. When the homology model of some isoforms of a gene does not seem structurally plausible, the implications are that either they assume a structure unrelated to that of the other isoforms of the same gene with presumably significant functional differences, or do not correspond to functional products. We provide indications that the second hypothesis is likely to be true for a substantial fraction of the cases. http://maistas.bioinformatica.crs4.it/.

Technical Basis and Implementation Guidelines for a Technique for Human Event Analysis (ATHEANA)

DTIC Science & Technology

2000-05-01

posted at NRC’s Web site address www.nrc.gov/NRC/NUREGS/indexnum.html are updated regularly and may differ from the last printed version. Non-NRC...distinctly different in that it provides structured search schemes for finding such EFCs, by using and integrating knowledge and experience in...Learned from Serious Accidents The record of significant incidents in nuclear power plant NPP operations shows a substantially different picture of

Method for adhering a coating to a substrate structure

DOEpatents

Taxacher, Glenn Curtis; Crespo, Andres Garcia; Roberts, III, Herbert Chidsey

2015-02-17

A method for adhering a coating to a substrate structure comprises selecting a substrate structure having an outer surface oriented substantially parallel to a direction of radial stress, modifying the outer surface to provide a textured region having steps to adhere a coating thereto, and applying a coating to extend over at least a portion of the textured region, wherein the steps are oriented substantially perpendicular to the direction of radial stress to resist deformation of the coating relative to the substrate structure. A rotating component comprises a substrate structure having an outer surface oriented substantially parallel to a direction of radial stress. The outer surface defines a textured region having steps to adhere a coating thereto, and a coating extends over at least a portion of the textured region. The steps are oriented substantially perpendicular to the direction of radial stress to resist creep.

Method for fabricating high aspect ratio structures in perovskite material

DOEpatents

Karapetrov, Goran T.; Kwok, Wai-Kwong; Crabtree, George W.; Iavarone, Maria

2003-10-28

A method of fabricating high aspect ratio ceramic structures in which a selected portion of perovskite or perovskite-like crystalline material is exposed to a high energy ion beam for a time sufficient to cause the crystalline material contacted by the ion beam to have substantially parallel columnar defects. Then selected portions of the material having substantially parallel columnar defects are etched leaving material with and without substantially parallel columnar defects in a predetermined shape having high aspect ratios of not less than 2 to 1. Etching is accomplished by optical or PMMA lithography. There is also disclosed a structure of a ceramic which is superconducting at a temperature in the range of from about 10.degree. K. to about 90.degree. K. with substantially parallel columnar defects in which the smallest lateral dimension of the structure is less than about 5 microns, and the thickness of the structure is greater than 2 times the smallest lateral dimension of the structure.

Structure and performance of different DRG classification systems for neonatal medicine.

PubMed

Muldoon, J H

1999-01-01

There are a number of Diagnosis-Related Group (DRG) classification systems that have evolved over the past 2 decades, each with their own strengths and weaknesses. DRG systems are used for case-mix trending, utilization management and quality improvement, comparative reporting, prospective payment, and price negotiations. For any of these applications it is essential to know the accuracy with which the DRG system classifies patients, specifically for predicting resource use and also mortality. The objective of this study was to assess the adequacy of the three most commonly used DRG systems for neonatal patients-Medicare DRGs, All Patient Diagnosis-Related Groups (AP-DRGs), and All Patient Refined Diagnosis-Related Groups (APR-DRGs). A 2-part methodology is used to assess adequacy. The first part is a descriptive analysis that examines the structural characteristics of each system. This provides a framework for understanding the inherent strengths and weaknesses of each system and for interpreting their statistical performance. The second part examines the statistical performance of each system on a large nationally representative hospital database. The analysis identifies major differences in the structure and statistical performance of the three DRG systems for neonates. The Medicare DRGs are structurally the least developed and yield the poorest overall statistical performance (cost R2 = 0.292; mortality R2 = 0.083). The APR-DRGs are structurally the most developed and yield the best statistical performance (cost R2 = 0.627; mortality R2 = 0.416). The AP-DRGs are intermediate to Medicare DRGs and APR-DRGs, although closer to APR-DRGs (cost R2 = 0.507; mortality R2 = 0.304). An analysis of payment impacts and systematic effects identifies there are major systematic biases with the Medicare DRGs. At the patient level, there is substantial underpayment for surgical neonates, transferred-in neonates, neonates discharged to home health services, and neonates who die. In contrast, there is substantial overpayment for normal newborns. At the facility level, there is substantial underpayment for freestanding acute children's hospitals and major teaching general hospitals. There is overpayment for other urban general hospitals but this pattern varies by hospital size. There is very substantial overpayment for other rural hospitals. The AP-DRGs remove the majority of the systematic effects but significant biases remain. The APR-DRGs remove most of the systematic effects but some biases remain.

Probing the electronic and local structural changes across the pressure-induced insulator-to-metal transition in VO2

NASA Astrophysics Data System (ADS)

Marini, C.; Bendele, M.; Joseph, B.; Kantor, I.; Mitrano, M.; Mathon, O.; Baldini, M.; Malavasi, L.; Pascarelli, S.; Postorino, P.

2014-11-01

Local and electronic structures of vanadium in \\text{VO}2 are studied across the high-pressure insulator-to-metal (IMT) transition using V K-edge x-ray absorption spectroscopy. Unlike the temperature-induced IMT, pressure-induced metallization leads to only subtle changes in the V K-edge prepeak structure, indicating a different mechanism involving smaller electronic spectral weight transfer close to the chemical potential. Intriguingly, upon application of the hydrostatic pressure, the electronic structure begins to show substantial changes well before the occurrence of the IMT and the associated structural transition to an anisotropic compression of the monoclinic metallic phase.

Internal structure of shock waves in disparate mass mixtures

NASA Technical Reports Server (NTRS)

Chung, Chan-Hong; De Witt, Kenneth J.; Jeng, Duen-Ren; Penko, Paul F.

1992-01-01

The detailed flow structure of a normal shock wave for a gas mixture is investigated using the direct-simulation Monte Carlo method. A variable diameter hard-sphere (VDHS) model is employed to investigate the effect of different viscosity temperature exponents (VTE) for each species in a gas mixture. Special attention is paid to the irregular behavior in the density profiles which was previously observed in a helium-xenon experiment. It is shown that the VTE can have substantial effects in the prediction of the structure of shock waves. The variable hard-sphere model of Bird shows good agreement, but with some limitations, with the experimental data if a common VTE is chosen properly for each case. The VDHS model shows better agreement with the experimental data without adjusting the VTE. The irregular behavior of the light-gas component in shock waves of disparate mass mixtures is observed not only in the density profile, but also in the parallel temperature profile. The strength of the shock wave, the type of molecular interactions, and the mole fraction of heavy species have substantial effects on the existence and structure of the irregularities.

Structure of nickel-copper alloys subjected to high-pressure torsion to saturation stage

NASA Astrophysics Data System (ADS)

Popov, V. V.; Stolbovsky, A. V.; Popova, E. N.

2017-11-01

Transmission electron microscopy and microhardness measurements were used to study the structure of Ni-Cu alloys subjected to high-pressure torsion (to saturation state) at room-temperature using five revolutions. It was shown that, when passing from copper to nickel, the submicrocrystalline structure becomes substantially refined, and the microhardness increases by more than 1.5 times. This is related to differences in the melting temperature and stacking fault energy. The simultaneous effect of these two factors leads to the nonlinearity of the composition dependences of the crystallite size and microhardness.

Comparative Analysis of V-Akt Murine Thymoma Viral Oncogene Homolog 3 (AKT3) Gene between Cow and Buffalo Reveals Substantial Differences for Mastitis.

PubMed

Ullah, Farman; Bhattarai, Dinesh; Cheng, Zhangrui; Liang, Xianwei; Deng, Tingxian; Rehman, Zia Ur; Talpur, Hira Sajjad; Worku, Tesfaye; Brohi, Rahim Dad; Safdar, Muhammad; Ahmad, Muhammad Jamil; Salim, Mohammad; Khan, Momen; Ahmad, Hafiz Ishfaq; Zhang, Shujun

2018-01-01

AKT3 gene is a constituent of the serine/threonine protein kinase family and plays a crucial role in synthesis of milk fats and cholesterol by regulating activity of the sterol regulatory element binding protein (SREBP). AKT3 is highly conserved in mammals and its expression levels during the lactation periods of cattle are markedly increased. AKT3 is highly expressed in the intestine followed by mammary gland and it is also expressed in immune cells. It is involved in the TLR pathways as effectively as proinflammatory cytokines. The aims of this study were to investigate the sequences differences between buffalo and cow. Our results showed that there were substantial differences between buffalo and cow in some exons and noteworthy differences of the gene size in different regions. We also identified the important consensus sequence motifs, variation in 2000 upstream of ATG, substantial difference in the "3'UTR" region, and miRNA association in the buffalo sequences compared with the cow. In addition, genetic analyses, such as gene structure, phylogenetic tree, position of different motifs, and functional domains, were performed to establish their correlation with other species. This may indicate that a buffalo breed has potential resistance to disease, environment changes, and airborne microorganisms and some good production and reproductive traits.

Comparative Analysis of V-Akt Murine Thymoma Viral Oncogene Homolog 3 (AKT3) Gene between Cow and Buffalo Reveals Substantial Differences for Mastitis

PubMed Central

Bhattarai, Dinesh; Cheng, Zhangrui; Liang, Xianwei; Deng, Tingxian; Rehman, Zia Ur; Talpur, Hira Sajjad; Worku, Tesfaye; Brohi, Rahim Dad; Safdar, Muhammad; Ahmad, Muhammad Jamil; Salim, Mohammad; Khan, Momen; Ahmad, Hafiz Ishfaq

2018-01-01

AKT3 gene is a constituent of the serine/threonine protein kinase family and plays a crucial role in synthesis of milk fats and cholesterol by regulating activity of the sterol regulatory element binding protein (SREBP). AKT3 is highly conserved in mammals and its expression levels during the lactation periods of cattle are markedly increased. AKT3 is highly expressed in the intestine followed by mammary gland and it is also expressed in immune cells. It is involved in the TLR pathways as effectively as proinflammatory cytokines. The aims of this study were to investigate the sequences differences between buffalo and cow. Our results showed that there were substantial differences between buffalo and cow in some exons and noteworthy differences of the gene size in different regions. We also identified the important consensus sequence motifs, variation in 2000 upstream of ATG, substantial difference in the “3′UTR” region, and miRNA association in the buffalo sequences compared with the cow. In addition, genetic analyses, such as gene structure, phylogenetic tree, position of different motifs, and functional domains, were performed to establish their correlation with other species. This may indicate that a buffalo breed has potential resistance to disease, environment changes, and airborne microorganisms and some good production and reproductive traits. PMID:29862252

Power in methods: language to infants in structured and naturalistic contexts.

PubMed

Tamis-LeMonda, Catherine S; Kuchirko, Yana; Luo, Rufan; Escobar, Kelly; Bornstein, Marc H

2017-11-01

Methods can powerfully affect conclusions about infant experiences and learning. Data from naturalistic observations may paint a very different picture of learning and development from those based on structured tasks, as illustrated in studies of infant walking, object permanence, intention understanding, and so forth. Using language as a model system, we compared the speech of 40 mothers to their 13-month-old infants during structured play and naturalistic home routines. The contrasting methods yielded unique portrayals of infant language experiences, while simultaneously underscoring cross-situational correspondence at an individual level. Infants experienced substantially more total words and different words per minute during structured play than they did during naturalistic routines. Language input during structured play was consistently dense from minute to minute, whereas language during naturalistic routines showed striking fluctuations interspersed with silence. Despite these differences, infants' language experiences during structured play mirrored the peak language interactions infants experienced during naturalistic routines, and correlations between language inputs in the two conditions were strong. The implications of developmental methods for documenting the nature of experiences and individual differences are discussed. © 2017 John Wiley & Sons Ltd.

The lack of effect of market structure on hospice use.

PubMed

Iwashyna, Theodore J; Chang, Virginia W; Zhang, James X; Christakis, Nicholas A

2002-12-01

To describe the relative importance of health care market structure and county-level demographics in determining rates of hospice use. Medicare claims data for a cohort of elderly patients newly diagnosed with lung cancer, colon cancer, stroke, or heart attack in 1993, followed for up to five years, and linked to Census and Area Resource File data. Variation between markets in rates of hospice use by patients with serious illness was examined after taking into account differences in individual-level data using hierarchical linear models. The relative explanatory power of market-level structure and local demographic variables was compared. The cohort was defined within the Medicare hospital claims data using validated algorithms to detect incident cases of disease with a three-year lookback. Use of hospice was determined by linkage at an individual level to the Standard Analytic Files for Hospice through 1997. Individual-level data was linked to the Area Resource File using county identifiers present in the Medicare claims. There is substantial variation in hospice use across markets. This variation is not explained by differences in the major components of health care infrastructure: the availability of hospital, nursing home, or skilled nursing facilities, nor by the availability of HMOs, doctors, or generalists. Intercounty heterogeneity in hospice use is substantial, and may not be related to the set-up of the medical care system. The important local factors may be local preferences, differences in the particular mix of services provided by local hospices, or differences in community leadership on end of life-issues; many of these differences may be amenable to educational efforts.

Stability and change in adult personality over 6 years: findings from the Victoria Longitudinal Study.

PubMed

Small, Brent J; Hertzog, Christopher; Hultsch, David F; Dixon, Roger A

2003-05-01

Data from the Victoria Longitudinal Study were used to examine the 6-year longitudinal stability of personality in older adults. Personality was measured with the NEO Personality Inventory. The longitudinal sample consisted of 223 adults initially ranging from 55 to 85 years of age. Longitudinal confirmatory factor analyses were used to examine the stability of individual differences in change over time, and the stability of the longitudinal factor structure. The results indicated both substantial stability at the level of individual differences in change, as well as significant individual differences in change that were related to age and gender. Finally, the factor structure of personality was invariant over time but did not approximate simple structure for the five dimensions of personality. Our study of 6-year personality development provided both (a). a confirmation of early significant stability findings and (b). unique evidence for significant individual differences in late adulthood.

Cognitive Activities in Solving Mathematical Tasks: The Role of a Cognitive Obstacle

ERIC Educational Resources Information Center

Antonijevic, Radovan

2016-01-01

In the process of learning mathematics, students practice various forms of thinking activities aimed to substantially contribute to the development of their different cognitive structures. In this paper, the subject matter is a "cognitive obstacle", a phenomenon that occurs in the procedures of solving mathematical tasks. Each task in…

Surface characterization of insulin protofilaments and fibril polymorphs using tip-enhanced Raman spectroscopy (TERS).

PubMed

Kurouski, Dmitry; Deckert-Gaudig, Tanja; Deckert, Volker; Lednev, Igor K

2014-01-07

Amyloid fibrils are β-sheet-rich protein aggregates that are strongly associated with a variety of neurodegenerative maladies, such as Alzheimer's and Parkinson's diseases. Even if the secondary structure of such fibrils is well characterized, a thorough understanding of their surface organization still remains elusive. Tip-enhanced Raman spectroscopy (TERS) is one of a few techniques that allow the direct characterization of the amino acid composition and the protein secondary structure of the amyloid fibril surface. Herein, we investigated the surfaces of two insulin fibril polymorphs with flat (flat) and left-twisted (twisted) morphology. It was found that the two differ substantially in both amino acid composition and protein secondary structure. For example, the amounts of Tyr, Pro, and His differ, as does the number of carboxyl groups on the respective surfaces, whereas the amounts of Phe and of positively charged amino and imino groups remain similar. In addition, the surface of protofilaments, the precursors of the mature flat and twisted fibrils, was investigated using TERS. The results show substantial differences with respect to the mature fibrils. A correlation of amino acid frequencies and protein secondary structures on the surface of protofilaments and on flat and twisted fibrils allowed us to propose a hypothetical mechanism for the propagation to specific fibril polymorphs. This knowledge can shed a light on the toxicity of amyloids and define the key factors responsible for fibril polymorphism. Finally, this work demonstrates the potential of TERS for the surface characterization of amyloid fibril polymorphs. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Influence of fiber packing structure on permeability

NASA Technical Reports Server (NTRS)

Cai, Zhong; Berdichevsky, Alexander L.

1993-01-01

The study on the permeability of an aligned fiber bundle is the key building block in modeling the permeability of advanced woven and braided preforms. Available results on the permeability of fiber bundles in the literature show that a substantial difference exists between numerical and analytical calculations on idealized fiber packing structures, such as square and hexagonal packing, and experimental measurements on practical fiber bundles. The present study focuses on the variation of the permeability of a fiber bundle under practical process conditions. Fiber bundles are considered as containing openings and fiber clusters within the bundle. Numerical simulations on the influence of various openings on the permeability were conducted. Idealized packing structures are used, but with introduced openings distributed in different patterns. Both longitudinal and transverse flow are considered. The results show that openings within the fiber bundle have substantial effect on the permeability. In the longitudinal flow case, the openings become the dominant flow path. In the transverse flow case, the fiber clusters reduce the gap sizes among fibers. Therefore the permeability is greatly influenced by these openings and clusters, respectively. In addition to the porosity or fiber volume fraction, which is commonly used in the permeability expression, another fiber bundle status parameter, the ultimate fiber volume fraction, is introduced to capture the disturbance within a fiber bundle.

Methodological approach for substantiating disease freedom in a heterogeneous small population. Application to ovine scrapie, a disease with a strong genetic susceptibility.

PubMed

Martinez, Marie-José; Durand, Benoit; Calavas, Didier; Ducrot, Christian

2010-06-01

Demonstrating disease freedom is becoming important in different fields including animal disease control. Most methods consider sampling only from a homogeneous population in which each animal has the same probability of becoming infected. In this paper, we propose a new methodology to calculate the probability of detecting the disease if it is present in a heterogeneous population of small size with potentially different risk groups, differences in risk being defined using relative risks. To calculate this probability, for each possible arrangement of the infected animals in the different groups, the probability that all the animals tested are test-negative given this arrangement is multiplied by the probability that this arrangement occurs. The probability formula is developed using the assumption of a perfect test and hypergeometric sampling for finite small size populations. The methodology is applied to scrapie, a disease affecting small ruminants and characterized in sheep by a strong genetic susceptibility defining different risk groups. It illustrates that the genotypes of the tested animals influence heavily the confidence level of detecting scrapie. The results present the statistical power for substantiating disease freedom in a small heterogeneous population as a function of the design prevalence, the structure of the sample tested, the structure of the herd and the associated relative risks. (c) 2010 Elsevier B.V. All rights reserved.

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

Wołek, Karol; Cieplak, Marek, E-mail: mc@ifpan.edu.pl

In structure-based models of proteins, one often assumes that folding is accomplished when all contacts are established. This assumption may frequently lead to a conceptual problem that folding takes place in a temperature region of very low thermodynamic stability, especially when the contact map used is too sparse. We consider six different structure-based models and show that allowing for a small, but model-dependent, percentage of the native contacts not being established boosts the folding temperature substantially while affecting the time scales of folding only in a minor way. We also compare other properties of the six models. We show thatmore » the choice of the description of the backbone stiffness has a substantial effect on the values of characteristic temperatures that relate both to equilibrium and kinetic properties. Models without any backbone stiffness (like the self-organized polymer) are found to perform similar to those with the stiffness, including in the studies of stretching.« less

Radiation-modified natural zeolites for cleaning liquid nuclear waste (irradiation against radioactivity)

PubMed Central

Yeritsyan, Hrant; Sahakyan, Aram; Harutyunyan, Vachagan; Nikoghosyan, Sergey; Hakhverdyan, Eleonora; Grigoryan, Norair; Hovhannisyan, Aghasi; Atoyan, Vovik; Keheyan, Yeghis; Rhodes, Christopher

2013-01-01

There have been comparatively few investigations reported of radiation effects in zeolites, although it is known that these materials may be modified substantially by exposure to ionizing radiation. Thus, by exposure to γ-rays or high-energy particles, the charge states of atoms may be changed so to create, and accumulate, lattice point defects, and to form structurally disordered regions. Such a technique may permit the creation, in a controlled fashion, of additionally useful properties of the material while preserving its essential stoichiometry and structure. Accordingly, we present an application, in which the cation-exchange capacity of a natural zeolite (clinoptilolite) is substantially enhanced, for the treatment/decontamination of water contaminated with radionuclides e.g. 134Cs, 137Cs and 90Sr, by its exposure to high-energy (8 MeV) electrons, and to different total doses. PMID:24132177

Enhancing robustness and immunization in geographical networks

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

Huang Liang; Department of Physics, Lanzhou University, Lanzhou 730000; Yang Kongqing

2007-03-15

We find that different geographical structures of networks lead to varied percolation thresholds, although these networks may have similar abstract topological structures. Thus, strategies for enhancing robustness and immunization of a geographical network are proposed. Using the generating function formalism, we obtain an explicit form of the percolation threshold q{sub c} for networks containing arbitrary order cycles. For three-cycles, the dependence of q{sub c} on the clustering coefficients is ascertained. The analysis substantiates the validity of the strategies with analytical evidence.

The cost structure of routine infant immunization services: a systematic analysis of six countries

PubMed Central

Geng, Fangli; Suharlim, Christian; Brenzel, Logan; Resch, Stephen C; Menzies, Nicolas A

2017-01-01

Abstract Little information exists on the cost structure of routine infant immunization services in low- and middle-income settings. Using a unique dataset of routine infant immunization costs from six countries, we estimated how costs were distributed across budget categories and programmatic activities, and investigated how the cost structure of immunization sites varied by country and site characteristics. The EPIC study collected data on routine infant immunization costs from 319 sites in Benin, Ghana, Honduras, Moldova, Uganda, Zambia, using a standardized approach. For each country, we estimated the economic costs of infant immunization by administrative level, budget category, and programmatic activity from a programme perspective. We used regression models to describe how costs within each category were related to site operating characteristics and efficiency level. Site-level costs (incl. vaccines) represented 77–93% of national routine infant immunization costs. Labour and vaccine costs comprised 14–69% and 13–69% of site-level cost, respectively. The majority of site-level resources were devoted to service provision (facility-based or outreach), comprising 48–78% of site-level costs across the six countries. Based on the regression analyses, sites with the highest service volume had a greater proportion of costs devoted to vaccines, with vaccine costs per dose relatively unaffected by service volume but non-vaccine costs substantially lower with higher service volume. Across all countries, more efficient sites (compared with sites with similar characteristics) had a lower cost share devoted to labour. The cost structure of immunization services varied substantially between countries and across sites within each country, and was related to site characteristics. The substantial variation observed in this sample suggests differences in operating model for otherwise similar sites, and further understanding of these differences could reveal approaches to improve efficiency and performance of immunization sites. PMID:28575193

The cost structure of routine infant immunization services: a systematic analysis of six countries.

PubMed

Geng, Fangli; Suharlim, Christian; Brenzel, Logan; Resch, Stephen C; Menzies, Nicolas A

2017-10-01

Little information exists on the cost structure of routine infant immunization services in low- and middle-income settings. Using a unique dataset of routine infant immunization costs from six countries, we estimated how costs were distributed across budget categories and programmatic activities, and investigated how the cost structure of immunization sites varied by country and site characteristics. The EPIC study collected data on routine infant immunization costs from 319 sites in Benin, Ghana, Honduras, Moldova, Uganda, Zambia, using a standardized approach. For each country, we estimated the economic costs of infant immunization by administrative level, budget category, and programmatic activity from a programme perspective. We used regression models to describe how costs within each category were related to site operating characteristics and efficiency level. Site-level costs (incl. vaccines) represented 77-93% of national routine infant immunization costs. Labour and vaccine costs comprised 14-69% and 13-69% of site-level cost, respectively. The majority of site-level resources were devoted to service provision (facility-based or outreach), comprising 48-78% of site-level costs across the six countries. Based on the regression analyses, sites with the highest service volume had a greater proportion of costs devoted to vaccines, with vaccine costs per dose relatively unaffected by service volume but non-vaccine costs substantially lower with higher service volume. Across all countries, more efficient sites (compared with sites with similar characteristics) had a lower cost share devoted to labour. The cost structure of immunization services varied substantially between countries and across sites within each country, and was related to site characteristics. The substantial variation observed in this sample suggests differences in operating model for otherwise similar sites, and further understanding of these differences could reveal approaches to improve efficiency and performance of immunization sites. © The Author 2017. Published by Oxford University Press in association with The London School of Hygiene and Tropical Medicine.

Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome.

PubMed

Šponer, Jiří; Banáš, Pavel; Jurečka, Petr; Zgarbová, Marie; Kührová, Petra; Havrila, Marek; Krepl, Miroslav; Stadlbauer, Petr; Otyepka, Michal

2014-05-15

We present a brief overview of explicit solvent molecular dynamics (MD) simulations of nucleic acids. We explain physical chemistry limitations of the simulations, namely, the molecular mechanics (MM) force field (FF) approximation and limited time scale. Further, we discuss relations and differences between simulations and experiments, compare standard and enhanced sampling simulations, discuss the role of starting structures, comment on different versions of nucleic acid FFs, and relate MM computations with contemporary quantum chemistry. Despite its limitations, we show that MD is a powerful technique for studying the structural dynamics of nucleic acids with a fast growing potential that substantially complements experimental results and aids their interpretation.

Full genome sequence of Rocio virus reveal substantial variations from the prototype Rocio virus SPH 34675 sequence.

PubMed

Setoh, Yin Xiang; Amarilla, Alberto A; Peng, Nias Y; Slonchak, Andrii; Periasamy, Parthiban; Figueiredo, Luiz T M; Aquino, Victor H; Khromykh, Alexander A

2018-01-01

Rocio virus (ROCV) is an arbovirus belonging to the genus Flavivirus, family Flaviviridae. We present an updated sequence of ROCV strain SPH 34675 (GenBank: AY632542.4), the only available full genome sequence prior to this study. Using next-generation sequencing of the entire genome, we reveal substantial sequence variation from the prototype sequence, with 30 nucleotide differences amounting to 14 amino acid changes, as well as significant changes to predicted 3'UTR RNA structures. Our results present an updated and corrected sequence of a potential emerging human-virulent flavivirus uniquely indigenous to Brazil (GenBank: MF461639).

Epitaxial Al{sub x}Ga{sub 1–x}As:Mg alloys with different conductivity types

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

Seredin, P. V., E-mail: paul@phys.vsu.ru; Lenshin, A. S.; Arsentiev, I. N., E-mail: arsentyev@mail.ioffe.ru

The structural, optical, and energy properties of epitaxial Al{sub x}Ga{sub 1–x}As:Mg/GaAs(100) heterostructures at different levels of doping with Mg are studied by high-resolution X-ray diffraction analysis and Raman and photoluminescence spectroscopies. It is shown that, by choosing the technological conditions of Al{sub x}Ga{sub 1–x}As:Mg alloy production, it is possible to achieve not only different conductivity types, but also substantially different charge-carrier concentrations in an epitaxial film.

Advanced Containment System

DOEpatents

Kostelnik, Kevin M.; Kawamura, Hideki; Richardson, John G.; Noda, Masaru

2005-02-08

An advanced containment system for containing buried waste and associated leachate. The advanced containment system comprises a plurality of casing sections with each casing section interlocked to an adjacent casing section. Each casing section includes a complementary interlocking structure that interlocks with the complementary interlocking structure on an adjacent casing section. A barrier filler substantially fills the casing sections and may substantially fill the spaces of the complementary interlocking structure to form a substantially impermeable barrier. Some of the casing sections may include sensors so that the casing sections and the zone of interest may be remotely monitored after the casing sections are emplaced in the ground.

POD/MAC-Based Modal Basis Selection for a Reduced Order Nonlinear Response Analysis

NASA Technical Reports Server (NTRS)

Rizzi, Stephen A.; Przekop, Adam

2007-01-01

A feasibility study was conducted to explore the applicability of a POD/MAC basis selection technique to a nonlinear structural response analysis. For the case studied the application of the POD/MAC technique resulted in a substantial improvement of the reduced order simulation when compared to a classic approach utilizing only low frequency modes present in the excitation bandwidth. Further studies are aimed to expand application of the presented technique to more complex structures including non-planar and two-dimensional configurations. For non-planar structures the separation of different displacement components may not be necessary or desirable.

The controlled growth method - A tool for structural optimization

NASA Technical Reports Server (NTRS)

Hajela, P.; Sobieszczanski-Sobieski, J.

1981-01-01

An adaptive design variable linking scheme in a NLP based optimization algorithm is proposed and evaluated for feasibility of application. The present scheme, based on an intuitive effectiveness measure for each variable, differs from existing methodology in that a single dominant variable controls the growth of all others in a prescribed optimization cycle. The proposed method is implemented for truss assemblies and a wing box structure for stress, displacement and frequency constraints. Substantial reduction in computational time, even more so for structures under multiple load conditions, coupled with a minimal accompanying loss in accuracy, vindicates the algorithm.

Dopant type and/or concentration selective dry photochemical etching of semiconductor materials

DOEpatents

Ashby, Carol I. H.; Dishman, James L.

1987-01-01

A method of selectively photochemically dry etching a first semiconductor material of a given composition in the presence of a second semiconductor material which is of a composition different from said first material, said second material substantially not being etched during said method, comprises subjecting both materials to the same photon flux of an energy greater than their respective direct bandgaps and to the same gaseous chemical etchant under conditions where said etchant would be ineffective for chemical etching of either material were the photons not present, said conditions also being such that the resultant electronic structure of the first semiconductor material under said photon flux is sufficient for the first material to undergo substantial photochemical etching under said conditions and being such that the resultant electronic structure of the second semiconductor material under said photon flux is not sufficient for the second material to undergo substantial photochemical etching under said conditions. In a preferred mode, the materials are subjected to a bias voltage which suppresses etching in n- or p- type material but not in p- or n-type material, respectively; or suppresses etching in the more heavily doped of two n-type or two p-type materials.

Dopant type and/or concentration selective dry photochemical etching of semiconductor materials

DOEpatents

Ashby, C.R.H.; Dishman, J.L.

1985-10-11

Disclosed is a method of selectively photochemically dry etching a first semiconductor material of a given composition in the presence of a second semiconductor material which is of a composition different from said first material, said second material substantially not being etched during said method. The method comprises subjecting both materials to the same photon flux of an energy greater than their respective direct bandgaps and to the same gaseous chemical etchant under conditions where said etchant would be ineffective for chemical etching of either material were the photons not present, said conditions also being such that the resultant electronic structure of the first semiconductor material under said photon flux is sufficient for the first material to undergo substantial photochemical etching under said conditions and being such that the resultant electronic structure of the second semiconductor material under said photon flux is not sufficient for the second material to undergo substantial photochemical etching under said conditions. In a preferred mode, the materials are subjected to a bias voltage which suppresses etching in n- or p-type material but not in p- or n-type material, respectively; or suppresses etching in the more heavily doped of two n-type or two p-type materials.

Uncertainties in assessing tillage erosion - how appropriate are our measuring techniques?

NASA Astrophysics Data System (ADS)

Fiener, Peter; Deumlich, Detlef; Gómez, José A.; Guzmán, Gema; Hardy, Robert; Jague, Emilien A.; Quinton, John; Sommer, Michael; van Oost, Kristof; Wexler, Robert; Wilken, Florian

2017-04-01

In undulating arable landscapes tillage erosion is one of the dominant processes initiating lateral transfer of soil and soil constituents. Especially, in relatively dry regions, where tillage erosion can be much larger than water erosion, the associated changes in soil hydraulic properties might have substantial effects upon the sustainable use of soil resources. There have been some studies using different techniques to determine tillage erosion which build the basis for tillage erosion modelling approaches. However, tillage erosion is rather understudied compared to water erosion. The goal of this study was to bring together experts using different techniques to determine tillage erosion in an experimental set-up and to analyse the different results and assess the uncertainties associated with typical model inputs. Tillage erosion on a 50 x 10 m plot was determined after two phases of seven tillage passes performed within a week (simulating 10-14 yrs of tillage). As tracers, two different micro-tracers (magnetite mixed with soil and fluorescent sand) and one macro-tracer (passive Radio-Frequency Identification (RFID) transponders; dia. 3 mm, length 20 mm) were used. Moreover, tillage induced changes in topography were spatially determined for the entire plot with two different terrestrial laser scanners and an UAV-based structure by motion topography analysis. Topography changes were also evaluated at 12 points using buried concrete flagstones as reference. A preliminary analysis of tracer movement indicates substantial differences in tillage induced translocation depending on type of tracer. While the mean translocation of the RFIDs was 0.47 m per pass the mean movement of the micro-tracers was 0.70 m. Substantial differences were also found for the different techniques to determine changes in topography. Overall the experiment underlines the importance of tillage erosion for the lateral transfer of soil and soil constituents, but also shows the large discrepancies between measurements based on different techniques. The latter introduces substantial uncertainties in any existing tillage erosion modelling approach.

When structure affects function--the need for partial volume effect correction in functional and resting state magnetic resonance imaging studies.

PubMed

Dukart, Juergen; Bertolino, Alessandro

2014-01-01

Both functional and also more recently resting state magnetic resonance imaging have become established tools to investigate functional brain networks. Most studies use these tools to compare different populations without controlling for potential differences in underlying brain structure which might affect the functional measurements of interest. Here, we adapt a simulation approach combined with evaluation of real resting state magnetic resonance imaging data to investigate the potential impact of partial volume effects on established functional and resting state magnetic resonance imaging analyses. We demonstrate that differences in the underlying structure lead to a significant increase in detected functional differences in both types of analyses. Largest increases in functional differences are observed for highest signal-to-noise ratios and when signal with the lowest amount of partial volume effects is compared to any other partial volume effect constellation. In real data, structural information explains about 25% of within-subject variance observed in degree centrality--an established resting state connectivity measurement. Controlling this measurement for structural information can substantially alter correlational maps obtained in group analyses. Our results question current approaches of evaluating these measurements in diseased population with known structural changes without controlling for potential differences in these measurements.

Fine-scale spatial climate variation and drought mediate the likelihood of reburning

Treesearch

Sean A. Parks; Marc‐Andre Parisien; Carol Miller; Lisa M. Holsinger; Larry Scott Baggett

2018-01-01

In many forested ecosystems, it is increasingly recognized that the probability of burning is substantially reduced within the footprint of previously burned areas. This self‐limiting effect of wildland fire is considered a fundamental emergent property of ecosystems and is partly responsible for structuring landscape heterogeneity (i.e., mosaics of different age...

Beyond Black and White: How White, Male, College Students See Their Asian American Peers

ERIC Educational Resources Information Center

Cabrera, Nolan L.

2014-01-01

This research is a cross-site analysis of how white, male, college students see their Asian American peers. Semi-structured interviews with 43 white males were conducted at two universities that differed substantially in their representation of Asian American students. The interviews were theoretically framed by Critical Whiteness Studies and Bobo…

Tunnel junction multiple wavelength light-emitting diodes

DOEpatents

Olson, Jerry M.; Kurtz, Sarah R.

1992-01-01

A multiple wavelength LED having a monolithic cascade cell structure comprising at least two p-n junctions, wherein each of said at least two p-n junctions have substantially different band gaps, and electrical connector means by which said at least two p-n junctions may be collectively energized; and wherein said diode comprises a tunnel junction or interconnect.

A Healthy Sorting Machine? Social Inequality in the Transition to Upper Secondary Education in Germany

ERIC Educational Resources Information Center

Schneider, Silke L.; Tieben, Nicole

2011-01-01

The German secondary education system is highly stratified. However, the higher tracks have expanded vastly over the last decades, leading to substantial changes in the distribution of students across the different tracks. Following the German re-unification, the school structure itself has also changed to some degree. Furthermore, several smaller…

Stochasticity, succession, and environmental perturbations in a fluidic ecosystem.

PubMed

Zhou, Jizhong; Deng, Ye; Zhang, Ping; Xue, Kai; Liang, Yuting; Van Nostrand, Joy D; Yang, Yunfeng; He, Zhili; Wu, Liyou; Stahl, David A; Hazen, Terry C; Tiedje, James M; Arkin, Adam P

2014-03-04

Unraveling the drivers of community structure and succession in response to environmental change is a central goal in ecology. Although the mechanisms shaping community structure have been intensively examined, those controlling ecological succession remain elusive. To understand the relative importance of stochastic and deterministic processes in mediating microbial community succession, a unique framework composed of four different cases was developed for fluidic and nonfluidic ecosystems. The framework was then tested for one fluidic ecosystem: a groundwater system perturbed by adding emulsified vegetable oil (EVO) for uranium immobilization. Our results revealed that groundwater microbial community diverged substantially away from the initial community after EVO amendment and eventually converged to a new community state, which was closely clustered with its initial state. However, their composition and structure were significantly different from each other. Null model analysis indicated that both deterministic and stochastic processes played important roles in controlling the assembly and succession of the groundwater microbial community, but their relative importance was time dependent. Additionally, consistent with the proposed conceptual framework but contradictory to conventional wisdom, the community succession responding to EVO amendment was primarily controlled by stochastic rather than deterministic processes. During the middle phase of the succession, the roles of stochastic processes in controlling community composition increased substantially, ranging from 81.3% to 92.0%. Finally, there are limited successional studies available to support different cases in the conceptual framework, but further well-replicated explicit time-series experiments are needed to understand the relative importance of deterministic and stochastic processes in controlling community succession.

WAXS studies of the structural diversity of hemoglobin in solution.

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

Makowski, L.; Bardhan, J.; Gore, D.

2011-01-01

Specific ligation states of hemoglobin are, when crystallized, capable of taking on multiple quaternary structures. The relationship between these structures, captured in crystal lattices, and hemoglobin structure in solution remains uncertain. Wide-angle X-ray solution scattering (WAXS) is a sensitive probe of protein structure in solution that can distinguish among similar structures and has the potential to contribute to these issues. We used WAXS to assess the relationships among the structures of human and bovine hemoglobins in different liganded forms in solution. WAXS data readily distinguished among the various forms of hemoglobins. WAXS patterns confirm some of the relationships among hemoglobinmore » structures that have been defined through crystallography and NMR and extend others. For instance, methemoglobin A in solution is, as expected, nearly indistinguishable from HbCO A. Interestingly, for bovine hemoglobin, the differences between deoxy-Hb, methemoglobin and HbCO are smaller than the corresponding differences in human hemoglobin. WAXS data were also used to assess the spatial extent of structural fluctuations of various hemoglobins in solution. Dynamics has been implicated in allosteric control of hemoglobin, and increased dynamics has been associated with lowered oxygen affinity. Consistent with that notion, WAXS patterns indicate that deoxy-Hb A exhibits substantially larger structural fluctuations than HbCO A. Comparisons between the observed WAXS patterns and those predicted on the basis of atomic coordinate sets suggest that the structures of Hb in different liganded forms exhibit clear differences from known crystal structure.« less

Charting the neglected West: The social system of Guinea baboons.

PubMed

Fischer, Julia; Kopp, Gisela H; Dal Pesco, Federica; Goffe, Adeelia; Hammerschmidt, Kurt; Kalbitzer, Urs; Klapproth, Matthias; Maciej, Peter; Ndao, Ibrahima; Patzelt, Annika; Zinner, Dietmar

2017-01-01

Primate social systems are remarkably diverse, and thus play a central role in understanding social evolution, including the biological origin of human societies. Although baboons have been prominently featured in this context, historically little was known about the westernmost member of the genus, the Guinea baboon (Papio papio). Here, we summarize the findings from the first years of observations at the field site CRP Simenti in the Niokolo Koba National Park in Senegal. Guinea baboons reveal a nested multi-level social organization, with reproductive units comprising one "primary" male, one to several females, young, and occasionally "secondary" males at the base of the society. Three to five units form "parties," which team up with other parties to form a "gang." Different gangs have largely overlapping home ranges and agonistic interactions between different parties or gangs are rare. Some but not all strongly socially bonded males are highly related, and population genetic and behavioral evidence indicate female-biased dispersal. Females play an important role in intersexual bond formation and maintenance, and female tenure length varies between a few weeks to several years. While the social organization resembles that of hamadryas baboons (P. hamadryas), the social structure differs considerably, specifically in terms of low male aggressiveness and female freedom. Despite substantial differences in social organization and social structure, the acoustic structure of Guinea baboon vocalizations does not differ substantially from that of other baboon taxa. With its multi-level organization, stable bonds between males and females, as well as a high-degree of male-male cooperation and tolerance, Guinea baboons constitute an intriguing model for reconstructing human social evolution. © 2017 American Association of Physical Anthropologists.

The Ardipithecus ramidus skull and its implications for hominid origins.

PubMed

Suwa, Gen; Asfaw, Berhane; Kono, Reiko T; Kubo, Daisuke; Lovejoy, C Owen; White, Tim D

2009-10-02

The highly fragmented and distorted skull of the adult skeleton ARA-VP-6/500 includes most of the dentition and preserves substantial parts of the face, vault, and base. Anatomical comparisons and micro-computed tomography-based analysis of this and other remains reveal pre-Australopithecus hominid craniofacial morphology and structure. The Ardipithecus ramidus skull exhibits a small endocranial capacity (300 to 350 cubic centimeters), small cranial size relative to body size, considerable midfacial projection, and a lack of modern African ape-like extreme lower facial prognathism. Its short posterior cranial base differs from that of both Pan troglodytes and P. paniscus. Ar. ramidus lacks the broad, anteriorly situated zygomaxillary facial skeleton developed in later Australopithecus. This combination of features is apparently shared by Sahelanthropus, showing that the Mio-Pliocene hominid cranium differed substantially from those of both extant apes and Australopithecus.

Structural and Kinetic Basis for Substrate Selectivity in Populus tremuloides Sinapyl Alcohol Dehydrogenase

PubMed Central

Bomati, Erin K.; Noel, Joseph P.

2005-01-01

We describe the three-dimensional structure of sinapyl alcohol dehydrogenase (SAD) from Populus tremuloides (aspen), a member of the NADP(H)-dependent dehydrogenase family that catalyzes the last reductive step in the formation of monolignols. The active site topology revealed by the crystal structure substantiates kinetic results indicating that SAD maintains highest specificity for the substrate sinapaldehyde. We also report substantial substrate inhibition kinetics for the SAD-catalyzed reduction of hydroxycinnamaldehydes. Although SAD and classical cinnamyl alcohol dehydrogenases (CADs) catalyze the same reaction and share some sequence identity, the active site topology of SAD is strikingly different from that predicted for classical CADs. Kinetic analyses of wild-type SAD and several active site mutants demonstrate the complexity of defining determinants of substrate specificity in these enzymes. These results, along with a phylogenetic analysis, support the inclusion of SAD in a plant alcohol dehydrogenase subfamily that includes cinnamaldehyde and benzaldehyde dehydrogenases. We used the SAD three-dimensional structure to model several of these SAD-like enzymes, and although their active site topologies largely mirror that of SAD, we describe a correlation between substrate specificity and amino acid substitution patterns in their active sites. The SAD structure thus provides a framework for understanding substrate specificity in this family of enzymes and for engineering new enzyme specificities. PMID:15829607

Structural and kinetic basis for substrate selectivity in Populus tremuloides sinapyl alcohol dehydrogenase.

PubMed

Bomati, Erin K; Noel, Joseph P

2005-05-01

We describe the three-dimensional structure of sinapyl alcohol dehydrogenase (SAD) from Populus tremuloides (aspen), a member of the NADP(H)-dependent dehydrogenase family that catalyzes the last reductive step in the formation of monolignols. The active site topology revealed by the crystal structure substantiates kinetic results indicating that SAD maintains highest specificity for the substrate sinapaldehyde. We also report substantial substrate inhibition kinetics for the SAD-catalyzed reduction of hydroxycinnamaldehydes. Although SAD and classical cinnamyl alcohol dehydrogenases (CADs) catalyze the same reaction and share some sequence identity, the active site topology of SAD is strikingly different from that predicted for classical CADs. Kinetic analyses of wild-type SAD and several active site mutants demonstrate the complexity of defining determinants of substrate specificity in these enzymes. These results, along with a phylogenetic analysis, support the inclusion of SAD in a plant alcohol dehydrogenase subfamily that includes cinnamaldehyde and benzaldehyde dehydrogenases. We used the SAD three-dimensional structure to model several of these SAD-like enzymes, and although their active site topologies largely mirror that of SAD, we describe a correlation between substrate specificity and amino acid substitution patterns in their active sites. The SAD structure thus provides a framework for understanding substrate specificity in this family of enzymes and for engineering new enzyme specificities.

3D Printed Silicones with Shape Memory

DOE PAGES

Wu, Amanda S.; Small IV, Ward; Bryson, Taylor M.; ...

2017-07-05

Direct ink writing enables the layer-by-layer manufacture of ordered, porous structures whose mechanical behavior is driven by architecture and material properties. Here, we incorporate two different gas filled microsphere pore formers to evaluate the effect of shell stiffness and T g on compressive behavior and compression set in siloxane matrix printed structures. The lower T g microsphere structures exhibit substantial compression set when heated near and above T g, with full structural recovery upon reheating without constraint. By contrast, the higher T g microsphere structures exhibit reduced compression set with no recovery upon reheating. Aside from their role in tuningmore » the mechanical behavior of direct ink write structures, polymer microspheres are good candidates for shape memory elastomers requiring structural complexity, with potential applications toward tandem shape memory polymers.« less

3D Printed Silicones with Shape Memory

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

Wu, Amanda S.; Small IV, Ward; Bryson, Taylor M.

Direct ink writing enables the layer-by-layer manufacture of ordered, porous structures whose mechanical behavior is driven by architecture and material properties. Here, we incorporate two different gas filled microsphere pore formers to evaluate the effect of shell stiffness and T g on compressive behavior and compression set in siloxane matrix printed structures. The lower T g microsphere structures exhibit substantial compression set when heated near and above T g, with full structural recovery upon reheating without constraint. By contrast, the higher T g microsphere structures exhibit reduced compression set with no recovery upon reheating. Aside from their role in tuningmore » the mechanical behavior of direct ink write structures, polymer microspheres are good candidates for shape memory elastomers requiring structural complexity, with potential applications toward tandem shape memory polymers.« less

Structural characterization of viral epitopes recognized by broadly cross-reactive antibodies.

PubMed

Lee, Peter S; Wilson, Ian A

2015-01-01

Influenza hemagglutinin (HA) is the major surface glycoprotein on influenza viruses and mediates viral attachment and subsequent fusion with host cells. The HA is the major target of the immune response, but due to its high level of variability, as evidenced by substantial antigenic diversity, it had been historically considered to elicit only a narrow, strain-specific antibody response. However, a recent explosion in the discovery of broadly neutralizing antibodies (bnAbs) to influenza virus has identified two major supersites of vulnerability on the HA through structural characterization of HA-antibody complexes. These commonly targeted epitopes are involved with receptor binding as well as the fusion machinery and, hence, are functionally conserved and less prone to mutation. These bnAbs can neutralize viruses by blocking infection or the spread of infection by preventing progeny release. Structural analyses of these bnAbs show they exhibit striking similarities and trends in recognition of the HA and use recurring recognition motifs, despite substantial differences in their germline genes. This information can be utilized in design of novel therapeutics as well as in immunogens for improved vaccines with greater breadth and efficacy.

Tripolar electric field Structure in guide field magnetic reconnection

NASA Astrophysics Data System (ADS)

Fu, Song; Huang, Shiyong; Zhou, Meng; Ni, Binbin; Deng, Xiaohua

2018-03-01

It has been shown that the guide field substantially modifies the structure of the reconnection layer. For instance, the Hall magnetic and electric fields are distorted in guide field reconnection compared to reconnection without guide fields (i.e., anti-parallel reconnection). In this paper, we performed 2.5-D electromagnetic full particle simulation to study the electric field structures in magnetic reconnection under different initial guide fields (Bg). Once the amplitude of a guide field exceeds 0.3 times the asymptotic magnetic field B0, the traditional bipolar Hall electric field is clearly replaced by a tripolar electric field, which consists of a newly emerged electric field and the bipolar Hall electric field. The newly emerged electric field is a convective electric field about one ion inertial length away from the neutral sheet. It arises from the disappearance of the Hall electric field due to the substantial modification of the magnetic field and electric current by the imposed guide field. The peak magnitude of this new electric field increases linearly with the increment of guide field strength. Possible applications of these results to space observations are also discussed.

To the theory of mechanisms subfamilies

NASA Astrophysics Data System (ADS)

Fomin, A.; Dvornikov, L.; Paramonov, M.; Jahr, A.

2016-04-01

The principles of formation of mechanisms subfamilies based on the usage of different kinds of kinematic pairs within the families of mechanisms are substantiated in the current paper. The division of mechanisms into subfamilies allows defining not only fundamental differences in the structure of mechanisms, but also provides the necessary foundation for the synthesis of new structures. 57 subfamilies of mechanisms have been totally distinguished. Among them, 31 subfamilies - within the zero family, 15 subfamilies - within the first family, 7 subfamilies - within the second family, 3 subfamilies - within the third family and 1 subfamily-within the fourth family. There were separately viewed planar mechanisms of the third family with three general imposed constraints and spatial mechanisms of the second family with two general imposed constraints in terms of their subfamilies. New methods of kinematical and dynamical investigations of mechanisms might be developed according to their analytical equations describing structural organization of different subfamilies of mechanisms.

Genome-wide network analysis of Wnt signaling in three pediatric cancers

NASA Astrophysics Data System (ADS)

Bao, Ju; Lee, Ho-Jin; Zheng, Jie J.

2013-10-01

Genomic structural alteration is common in pediatric cancers, and analysis of data generated by the Pediatric Cancer Genome Project reveals such tumor-related alterations in many Wnt signaling-associated genes. Most pediatric cancers are thought to arise within developing tissues that undergo substantial expansion during early organ formation, growth and maturation, and Wnt signaling plays an important role in this development. We examined three pediatric tumors--medullobastoma, early T-cell precursor acute lymphoblastic leukemia, and retinoblastoma--that show multiple genomic structural variations within Wnt signaling pathways. We mathematically modeled this pathway to investigate the effects of cancer-related structural variations on Wnt signaling. Surprisingly, we found that an outcome measure of canonical Wnt signaling was consistently similar in matched cancer cells and normal cells, even in the context of different cancers, different mutations, and different Wnt-related genes. Our results suggest that the cancer cells maintain a normal level of Wnt signaling by developing multiple mutations.

The Preparation and Structural Characterization of Three Structural Types of Gallium Compounds Derived from Gallium (II) Chloride

NASA Technical Reports Server (NTRS)

Gordon, Edward M.; Hepp, Aloysius F.; Duraj. Stan A.; Habash, Tuhfeh S.; Fanwick, Phillip E.; Schupp, John D.; Eckles, William E.; Long, Shawn

1997-01-01

The three compounds Ga2Cl4(4-mepy)2 (1),[GaCl2(4-mepy)4]GaCl4x1/2(4-mepy); (2) and GaCl2(4-mepy)2(S2CNEt2); (3) (4-mepy= 4-methylpyridine) have been prepared from reactions of gallium (II) chloride in 4-methylpyridine and characterized by single-crystal X-ray analysis. Small variations in the reaction conditions for gallium(II) chloride can produce crystals with substantially different structural properties. The three compounds described here encompass a neutral gallium(II) dimer in which each gallium is four-coordinate, an ionic compound containing both anionic and cationic gallium complex ions with different coordination numbers and a neutral six-coordinate heteroleptic

Determinants of the spatiotemporal dynamics of the 2009 H1N1 pandemic in Europe: implications for real-time modelling.

PubMed

Merler, Stefano; Ajelli, Marco; Pugliese, Andrea; Ferguson, Neil M

2011-09-01

Influenza pandemics in the last century were characterized by successive waves and differences in impact and timing between different regions, for reasons not clearly understood. The 2009 H1N1 pandemic showed rapid global spread, but with substantial heterogeneity in timing within each hemisphere. Even within Europe substantial variation was observed, with the UK being unique in experiencing a major first wave of transmission in early summer and all other countries having a single major epidemic in the autumn/winter, with a West to East pattern of spread. Here we show that a microsimulation model, parameterised using data about H1N1pdm collected by the beginning of June 2009, explains the occurrence of two waves in UK and a single wave in the rest of Europe as a consequence of timing of H1N1pdm spread, fluxes of travels from US and Mexico, and timing of school vacations. The model provides a description of pandemic spread through Europe, depending on intra-European mobility patterns and socio-demographic structure of the European populations, which is in broad agreement with observed timing of the pandemic in different countries. Attack rates are predicted to depend on the socio-demographic structure, with age dependent attack rates broadly agreeing with available serological data. Results suggest that the observed heterogeneity can be partly explained by the between country differences in Europe: marked differences in school calendars, mobility patterns and sociodemographic structures. Moreover, higher susceptibility of children to infection played a key role in determining the epidemiology of the 2009 pandemic. Our work shows that it would have been possible to obtain a broad-brush prediction of timing of the European pandemic well before the autumn of 2009, much more difficult to achieve with simpler models or pre-pandemic parameterisation. This supports the use of models accounting for the structure of complex modern societies for giving insight to policy makers.

Measurements of the separated longitudinal structure function FL from hydrogen and deuterium targets at low Q2

NASA Astrophysics Data System (ADS)

Tvaskis, V.; Tvaskis, A.; Niculescu, I.; Abbott, D.; Adams, G. S.; Afanasev, A.; Ahmidouch, A.; Angelescu, T.; Arrington, J.; Asaturyan, R.; Avery, S.; Baker, O. K.; Benmouna, N.; Berman, B. L.; Biselli, A.; Blok, H. P.; Boeglin, W. U.; Bosted, P. E.; Brash, E.; Breuer, H.; Chang, G.; Chant, N.; Christy, M. E.; Connell, S. H.; Dalton, M. M.; Danagoulian, S.; Day, D.; Dodario, T.; Dunne, J. A.; Dutta, D.; El Khayari, N.; Ent, R.; Fenker, H. C.; Frolov, V. V.; Gaskell, D.; Garrow, K.; Gilman, R.; Gueye, P.; Hafidi, K.; Hinton, W.; Holt, R. J.; Horn, T.; Huber, G. M.; Jackson, H.; Jiang, X.; Jones, M. K.; Joo, K.; Kelly, J. J.; Keppel, C. E.; Kuhn, J.; Kinney, E.; Klein, A.; Kubarovsky, V.; Liang, Y.; Lolos, G.; Lung, A.; Mack, D.; Malace, S.; Markowitz, P.; Mbianda, G.; McGrath, E.; Mckee, D.; Meekins, D. G.; Mkrtchyan, H.; Napolitano, J.; Navasardyan, T.; Niculescu, G.; Nozar, M.; Ostapenko, T.; Papandreou, Z.; Potterveld, D.; Reimer, P. E.; Reinhold, J.; Roche, J.; Rock, S. E.; Schulte, E.; Segbefia, E.; Smith, C.; Smith, G. R.; Stoler, P.; Tadevosyan, V.; Tang, L.; Telfeyan, J.; Todor, L.; Ungaro, M.; Uzzle, A.; Vidakovic, S.; Villano, A.; Vulcan, W. F.; Warren, G.; Wesselmann, F.; Wojtsekhowski, B.; Wood, S. A.; Yan, C.; Zihlmann, B.

2018-04-01

Structure functions, as measured in lepton-nucleon scattering, have proven to be very useful in studying the partonic dynamics within the nucleon. However, it is experimentally difficult to separately determine the longitudinal and transverse structure functions, and consequently there are substantially less data available in particular for the longitudinal structure function. Here, we present separated structure functions for hydrogen and deuterium at low four-momentum transfer squared, Q2<1 GeV2 , and compare them with parton distribution parametrization and kT factorization approaches. While differences are found, the parametrizations generally agree with the data, even at the very low-Q2 scale of the data. The deuterium data show a smaller longitudinal structure function and a smaller ratio of longitudinal to transverse cross section, R , than the proton. This suggests either an unexpected difference in R for the proton and the neutron or a suppression of the gluonic distribution in nuclei.

Measurements of the separated longitudinal structure function F L from hydrogen and deuterium targets at low Q 2

DOE PAGES

Tvaskis, V.; Tvaskis, A.; Niculescu, I.; ...

2018-04-26

Structure functions, as measured in lepton-nucleon scattering, have proven to be very useful in studying the partonic dynamics within the nucleon. Furthermore, it is experimentally difficult to separately determine the longitudinal and transverse structure functions, and consequently there are substantially less data available in particular for the longitudinal structure function. Here, we present separated structure functions for hydrogen and deuterium at low four-momentum transfer squared, Q 2 < 1 GeV 2, and compare them with parton distribution parametrization and k T factorization approaches. While differences are found, the parametrizations generally agree with the data, even at the very low-Q 2more » scale of the data. The deuterium data show a smaller longitudinal structure function and a smaller ratio of longitudinal to transverse cross section, R, than the proton. This suggests either an unexpected difference in R for the proton and the neutron or a suppression of the gluonic distribution in nuclei.« less

Measurements of the separated longitudinal structure function F L from hydrogen and deuterium targets at low Q 2

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

Tvaskis, V.; Tvaskis, A.; Niculescu, I.

Structure functions, as measured in lepton-nucleon scattering, have proven to be very useful in studying the partonic dynamics within the nucleon. Furthermore, it is experimentally difficult to separately determine the longitudinal and transverse structure functions, and consequently there are substantially less data available in particular for the longitudinal structure function. Here, we present separated structure functions for hydrogen and deuterium at low four-momentum transfer squared, Q 2 < 1 GeV 2, and compare them with parton distribution parametrization and k T factorization approaches. While differences are found, the parametrizations generally agree with the data, even at the very low-Q 2more » scale of the data. The deuterium data show a smaller longitudinal structure function and a smaller ratio of longitudinal to transverse cross section, R, than the proton. This suggests either an unexpected difference in R for the proton and the neutron or a suppression of the gluonic distribution in nuclei.« less

Bacterial structures and ecosystem functions in glaciated floodplains: contemporary states and potential future shifts

PubMed Central

Freimann, Remo; Bürgmann, Helmut; Findlay, Stuart EG; Robinson, Christopher T

2013-01-01

Glaciated alpine floodplains are responding quickly to climate change through shrinking ice masses. Given the expected future changes in their physicochemical environment, we anticipated variable shifts in structure and ecosystem functioning of hyporheic microbial communities in proglacial alpine streams, depending on present community characteristics and landscape structures. We examined microbial structure and functioning during different hydrologic periods in glacial (kryal) streams and, as contrasting systems, groundwater-fed (krenal) streams. Three catchments were chosen to cover an array of landscape features, including interconnected lakes, differences in local geology and degree of deglaciation. Community structure was assessed by automated ribosomal intergenic spacer analysis and microbial function by potential enzyme activities. We found each catchment to contain a distinct bacterial community structure and different degrees of separation in structure and functioning that were linked to the physicochemical properties of the waters within each catchment. Bacterial communities showed high functional plasticity, although achieved by different strategies in each system. Typical kryal communities showed a strong linkage of structure and function that indicated a major prevalence of specialists, whereas krenal sediments were dominated by generalists. With the rapid retreat of glaciers and therefore altered ecohydrological characteristics, lotic microbial structure and functioning are likely to change substantially in proglacial floodplains in the future. The trajectory of these changes will vary depending on contemporary bacterial community characteristics and landscape structures that ultimately determine the sustainability of ecosystem functioning. PMID:23842653

Bacterial structures and ecosystem functions in glaciated floodplains: contemporary states and potential future shifts.

PubMed

Freimann, Remo; Bürgmann, Helmut; Findlay, Stuart E G; Robinson, Christopher T

2013-12-01

Glaciated alpine floodplains are responding quickly to climate change through shrinking ice masses. Given the expected future changes in their physicochemical environment, we anticipated variable shifts in structure and ecosystem functioning of hyporheic microbial communities in proglacial alpine streams, depending on present community characteristics and landscape structures. We examined microbial structure and functioning during different hydrologic periods in glacial (kryal) streams and, as contrasting systems, groundwater-fed (krenal) streams. Three catchments were chosen to cover an array of landscape features, including interconnected lakes, differences in local geology and degree of deglaciation. Community structure was assessed by automated ribosomal intergenic spacer analysis and microbial function by potential enzyme activities. We found each catchment to contain a distinct bacterial community structure and different degrees of separation in structure and functioning that were linked to the physicochemical properties of the waters within each catchment. Bacterial communities showed high functional plasticity, although achieved by different strategies in each system. Typical kryal communities showed a strong linkage of structure and function that indicated a major prevalence of specialists, whereas krenal sediments were dominated by generalists. With the rapid retreat of glaciers and therefore altered ecohydrological characteristics, lotic microbial structure and functioning are likely to change substantially in proglacial floodplains in the future. The trajectory of these changes will vary depending on contemporary bacterial community characteristics and landscape structures that ultimately determine the sustainability of ecosystem functioning.

THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures

PubMed Central

Theobald, Douglas L.; Wuttke, Deborah S.

2008-01-01

Summary THESEUS is a command line program for performing maximum likelihood (ML) superpositions and analysis of macromolecular structures. While conventional superpositioning methods use ordinary least-squares (LS) as the optimization criterion, ML superpositions provide substantially improved accuracy by down-weighting variable structural regions and by correcting for correlations among atoms. ML superpositioning is robust and insensitive to the specific atoms included in the analysis, and thus it does not require subjective pruning of selected variable atomic coordinates. Output includes both likelihood-based and frequentist statistics for accurate evaluation of the adequacy of a superposition and for reliable analysis of structural similarities and differences. THESEUS performs principal components analysis for analyzing the complex correlations found among atoms within a structural ensemble. PMID:16777907

Origins of the structural phase transitions in MoTe2 and WTe2

NASA Astrophysics Data System (ADS)

Kim, Hyun-Jung; Kang, Seoung-Hun; Hamada, Ikutaro; Son, Young-Woo

2017-05-01

Layered transition metal dichalcogenides MoTe2 and WTe2 share almost similar lattice constants as well as topological electronic properties except their structural phase transitions. While the former shows a first-order phase transition between monoclinic and orthorhombic structures, the latter does not. Using a recently proposed van der Waals density functional method, we investigate structural stability of the two materials and uncover that the disparate phase transitions originate from delicate differences between their interlayer bonding states near the Fermi energy. By exploiting the relation between the structural phase transitions and the low energy electronic properties, we show that a charge doping can control the transition substantially, thereby suggesting a way to stabilize or to eliminate their topological electronic energy bands.

Assessing agricultural management effects on structure related soil hydraulic properties by tension infiltrometry

NASA Astrophysics Data System (ADS)

Bodner, G.; Loiskandl, W.; Kaul, H.-P.

2009-04-01

Soil structure is a dynamic property subject to numerous natural and human influences. It is recognized as fundamental for sustainable functioning of soil. Therefore knowledge of management impacts on the sensitive structural states of soil is decisive in order to avoid soil degradation. The stabilization of the soil's (macro)pore system and eventually the improvement of its infiltrability are essential to avoid runoff and soil erosion, particularly in view of an increasing probability of intense rainfall events. However structure-related soil properties generally have a high natural spatiotemporal variability that interacts with the potential influence of agricultural land use. This complicates a clear determination of management vs. environmental effects and requires adequate measurement methods, allowing a sufficient spatiotemporal resolution to estimate the impact of the targeted management factors within the natural dynamics of soil structure. A common method to assess structure-related soil hydraulic properties is tension infiltrometry. A major advantage of tension infiltrometer measurements is that no or only minimum soil disturbance is necessary and several structure-controlled water transmission properties can readily be derived. The method is more time- and cost-efficient compared to laboratory measurements of soil hydraulic properties, thus enabling more replications. Furthermore in situ measurements of hydraulic properties generally allow a more accurate reproduction of field soil water dynamics. The present study analyses the impact of two common agricultural management options on structure related hydraulic properties based on tension infiltrometer measurements. Its focus is the identification of the role of management within the natural spatiotemporal variability, particularly in respect to seasonal temporal dynamics. Two management approaches are analysed, (i) cover cropping as a "plant-based" agro-environmental measure, and (ii) tillage with different intensities including conventional tillage with a mouldboard plough, reduced tillage with a chisel plough and no-tillage. The results showed that the plant-based management measure of cover cropping had only minor influence on near-saturated hydraulic conductivity (kh) and flow weighted mean pore radius (λm). Substantial over-winter changes were found with a significant increase in kh and a reduction in the pore radius. A spatial trend in soil texture along the cover cropped slope resulted in a higher kh at lower pressure heads at the summit with higher fractions of coarse particles, while kh tended to be highest at the toeslope towards saturation. Cover crop management accounted for a maximum of 9.7% of the total variability in kh, with a decreasing impact towards the unsaturated range. A substantial difference to bare soil in the cover cropped treatments could be identified in relation to a stabilization of macro-pores over winter. The different tillage treatments had a substantial impact on near-saturated kh and pore radius. Although conventional tillage showed the highest values in kh and λm, settling of the soil after the ploughing event tended to reduce differences over time compared to the other tillage methods. The long-term no-tillage (10 years) however had the lowest values of kh at all measurement dates. The high contents of silt and fine sand probably resulted in soil densification that was not counterbalanced sufficiently by biological structure forming agents. The study could show that soil structure related hydraulic properties are subject to a substantial seasonal variability. A comprehensive assessment of agricultural measures such as tillage or cover cropping requires an estimate of these temporal dynamics and their interaction with the management strategies. Particularly for plant-based management measures such as cover cropping, which represent a less intense intervention in the structural states of the soil compared to tillage, this was evident, as the main mechanism revealed for this measure was structure stabilization over time. While spatial variability is mostly controlled in designed experiments, the role of temporal variability is often underestimated. From our study we concluded that (i) a proper understanding of processes involved in management effects on soil structure must take into consideration the dynamic nature of the respective soil properties, (ii) experimental planning for studies regarding management impacts on soil structure should allow an estimation of temporal variability, and (iii) for this purpose tension infiltrometry provides an efficient measurement tool to assess structure related soil hydraulic properties.

Comparable contributions of structural-functional constraints and expression level to the rate of protein sequence evolution

PubMed Central

Wolf, Maxim Y; Wolf, Yuri I; Koonin, Eugene V

2008-01-01

Background Proteins show a broad range of evolutionary rates. Understanding the factors that are responsible for the characteristic rate of evolution of a given protein arguably is one of the major goals of evolutionary biology. A long-standing general assumption used to be that the evolution rate is, primarily, determined by the specific functional constraints that affect the given protein. These constrains were traditionally thought to depend both on the specific features of the protein's structure and its biological role. The advent of systems biology brought about new types of data, such as expression level and protein-protein interactions, and unexpectedly, a variety of correlations between protein evolution rate and these variables have been observed. The strongest connections by far were repeatedly seen between protein sequence evolution rate and the expression level of the respective gene. It has been hypothesized that this link is due to the selection for the robustness of the protein structure to mistranslation-induced misfolding that is particularly important for highly expressed proteins and is the dominant determinant of the sequence evolution rate. Results This work is an attempt to assess the relative contributions of protein domain structure and function, on the one hand, and expression level on the other hand, to the rate of sequence evolution. To this end, we performed a genome-wide analysis of the effect of the fusion of a pair of domains in multidomain proteins on the difference in the domain-specific evolutionary rates. The mistranslation-induced misfolding hypothesis would predict that, within multidomain proteins, fused domains, on average, should evolve at substantially closer rates than the same domains in different proteins because, within a mutlidomain protein, all domains are translated at the same rate. We performed a comprehensive comparison of the evolutionary rates of mammalian and plant protein domains that are either joined in multidomain proteins or contained in distinct proteins. Substantial homogenization of evolutionary rates in multidomain proteins was, indeed, observed in both animals and plants, although highly significant differences between domain-specific rates remained. The contributions of the translation rate, as determined by the effect of the fusion of a pair of domains within a multidomain protein, and intrinsic, domain-specific structural-functional constraints appear to be comparable in magnitude. Conclusion Fusion of domains in a multidomain protein results in substantial homogenization of the domain-specific evolutionary rates but significant differences between domain-specific evolution rates remain. Thus, the rate of translation and intrinsic structural-functional constraints both exert sizable and comparable effects on sequence evolution. Reviewers This article was reviewed by Sergei Maslov, Dennis Vitkup, Claus Wilke (nominated by Orly Alter), and Allan Drummond (nominated by Joel Bader). For the full reviews, please go to the Reviewers' Reports section. PMID:18840284

Agriculture and Climate Change in Global Scenarios: Why Don't the Models Agree

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

Nelson, Gerald; van der Mensbrugghe, Dominique; Ahammad, Helal

Agriculture is unique among economic sectors in the nature of impacts from climate change. The production activity that transforms inputs into agricultural outputs makes direct use of weather inputs. Previous studies of the impacts of climate change on agriculture have reported substantial differences in outcomes of key variables such as prices, production, and trade. These divergent outcomes arise from differences in model inputs and model specification. The goal of this paper is to review climate change results and underlying determinants from a model comparison exercise with 10 of the leading global economic models that include significant representation of agriculture. Bymore » providing common productivity drivers that include climate change effects, differences in model outcomes are reduced. All models show higher prices in 2050 because of negative productivity shocks from climate change. The magnitude of the price increases, and the adaptation responses, differ significantly across the various models. Substantial differences exist in the structural parameters affecting demand, area, and yield, and should be a topic for future research.« less

Pseudopotential plane-wave calculation of the structural properties of yttrium

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

Wang, Y.; Chou, M.Y.

1991-11-01

The structural properties of hexagonal-close-packed yttrium are studied by using the plane-wave basis within the pseudopotential method and local-density-functional approximation. By employing a soft'' pseudopotential proposed by Troullier and Martins, satisfactory convergence is achieved with a plane-wave energy cutoff of 30--40 Ry for this early-transition-metal element. The overall results for the structural properties are in good agreement with experiment. It is found that the charge overlap between core and valence electrons has a substantial effect on the accuracy of the calculated structural properties. Two different calculations are performed with and without the outer-core 4{ital p} orbital included as a valencemore » state. In addition, as found in some other local-density calculations, the uncertainty in the results due to different exchange-correlation energy functionals may not be negligible in transition metals.« less

MIS diode structure in As/+/ implanted CdS

NASA Technical Reports Server (NTRS)

Hutchby, J. A.

1977-01-01

Structure made by As implantation of carefully prepared high-conductivity CdS surfaces followed by Pt deposition and 450 C anneal display rectifying, although substantially different, I-V characteristics in the dark and during illumination with subband-gap light. Structures prepared in the same way on an unimplanted portion of the substrate have similar I-V characteristics, except that the forward turnover voltage for an illuminated unimplanted diode is much smaller than that for an implanted diode. It is suggested that the charge conduction in both structures is dominated by hole and/or electron tunneling through a metal-semiconductor potential barrier. The tunneling processes appear to be quite sensitive to subband-gap illumination, which causes the dramatic decreases of turnover voltages and apparent series resistances. The difference in turnover voltage appears to be caused by interface states between the Pt electrode and the implanted layer, which suggests a MIS model.

Network structure from rich but noisy data

NASA Astrophysics Data System (ADS)

Newman, M. E. J.

2018-06-01

Driven by growing interest across the sciences, a large number of empirical studies have been conducted in recent years of the structure of networks ranging from the Internet and the World Wide Web to biological networks and social networks. The data produced by these experiments are often rich and multimodal, yet at the same time they may contain substantial measurement error1-7. Accurate analysis and understanding of networked systems requires a way of estimating the true structure of networks from such rich but noisy data8-15. Here we describe a technique that allows us to make optimal estimates of network structure from complex data in arbitrary formats, including cases where there may be measurements of many different types, repeated observations, contradictory observations, annotations or metadata, or missing data. We give example applications to two different social networks, one derived from face-to-face interactions and one from self-reported friendships.

Structural genomics reveals EVE as a new ASCH/PUA-related domain

PubMed Central

Bertonati, Claudia; Punta, Marco; Fischer, Markus; Yachdav, Guy; Forouhar, Farhad; Zhou, Weihong; Kuzin, Alexander P.; Seetharaman, Jayaraman; Abashidze, Mariam; Ramelot, Theresa A.; Kennedy, Michael A.; Cort, John R.; Belachew, Adam; Hunt, John F.; Tong, Liang; Montelione, Gaetano T.; Rost, Burkhard

2014-01-01

Summary We report on several proteins recently solved by structural genomics consortia, in particular by the Northeast Structural Genomics consortium (NESG). The proteins considered in this study differ substantially in their sequences but they share a similar structural core, characterized by a pseudobarrel five-stranded beta sheet. This core corresponds to the PUA domain-like architecture in the SCOP database. By connecting sequence information with structural knowledge, we characterize a new subgroup of these proteins that we propose to be distinctly different from previously described PUA domain-like domains such as PUA proper or ASCH. We refer to these newly defined domains as EVE. Although EVE may have retained the ability of PUA domains to bind RNA, the available experimental and computational data suggests that both the details of its molecular function and its cellular function differ from those of other PUA domain-like domains. This study of EVE and its relatives illustrates how the combination of structure and genomics creates new insights by connecting a cornucopia of structures that map to the same evolutionary potential. Primary sequence information alone would have not been sufficient to reveal these evolutionary links. PMID:19191354

Structural Genomics Reveals EVE as a New ASCH/PUA-Related Domain

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

Bertonati, C.; Punta, M; Fischer, M

2008-01-01

We report on several proteins recently solved by structural genomics consortia, in particular by the Northeast Structural Genomics consortium (NESG). The proteins considered in this study differ substantially in their sequences but they share a similar structural core, characterized by a pseudobarrel five-stranded beta sheet. This core corresponds to the PUA domain-like architecture in the SCOP database. By connecting sequence information with structural knowledge, we characterize a new subgroup of these proteins that we propose to be distinctly different from previously described PUA domain-like domains such as PUA proper or ASCH. We refer to these newly defined domains as EVE.more » Although EVE may have retained the ability of PUA domains to bind RNA, the available experimental and computational data suggests that both the details of its molecular function and its cellular function differ from those of other PUA domain-like domains. This study of EVE and its relatives illustrates how the combination of structure and genomics creates new insights by connecting a cornucopia of structures that map to the same evolutionary potential. Primary sequence information alone would have not been sufficient to reveal these evolutionary links.« less

Structural insights into the difference in substrate recognition of two mannoside phosphorylases from two GH130 subfamilies.

PubMed

Ye, Yuxin; Saburi, Wataru; Odaka, Rei; Kato, Koji; Sakurai, Naofumi; Komoda, Keisuke; Nishimoto, Mamoru; Kitaoka, Motomitsu; Mori, Haruhide; Yao, Min

2016-03-01

In Ruminococcus albus, 4-O-β-D-mannosyl-D-glucose phosphorylase (RaMP1) and β-(1,4)-mannooligosaccharide phosphorylase (RaMP2) belong to two subfamilies of glycoside hydrolase family 130. The two enzymes phosphorolyze β-mannosidic linkages at the nonreducing ends of their substrates, and have substantially diverse substrate specificity. The differences in their mechanism of substrate binding have not yet been fully clarified. In the present study, we report the crystal structures of RaMP1 with/without 4-O-β-D-mannosyl-d-glucose and RaMP2 with/without β-(1→4)-mannobiose. The structures of the two enzymes differ at the +1 subsite of the substrate-binding pocket. Three loops are proposed to determine the different substrate specificities. One of these loops is contributed from the adjacent molecule of the oligomer structure. In RaMP1, His245 of loop 3 forms a hydrogen-bond network with the substrate through a water molecule, and is indispensible for substrate binding. © 2016 Federation of European Biochemical Societies.

Does the Type of Higher Education Affect Labor Market Outcomes? Evidence from Egypt and Jordan

ERIC Educational Resources Information Center

Assaad, Ragui; Krafft, Caroline; Salehi-Isfahani, Djavad

2018-01-01

In Egypt and Jordan, there is a substantial mismatch between the output of the higher education system and the needs of the labor market. Both demand and supply-side factors could be driving this mismatch. This paper tests a key supply-side issue, whether differences in the institutional structures and incentives in higher education affect the…

Tunnel junction multiple wavelength light-emitting diodes

DOEpatents

Olson, J.M.; Kurtz, S.R.

1992-11-24

A multiple wavelength LED having a monolithic cascade cell structure comprising at least two p-n junctions, wherein each of said at least two p-n junctions have substantially different band gaps, and electrical connector means by which said at least two p-n junctions may be collectively energized; and wherein said diode comprises a tunnel junction or interconnect. 5 figs.

Can forest management be used to sustain water-based ecosystem service in the face of climate change?

Treesearch

Chelcy Ford; Stephanie Laseter; Wayne Swank; James Vose

2011-01-01

Forested watersheds, an important provider of ecosystems services related to water supply, can have their structure, function, and resulting streamflow substantially altered by land use and land cover. Using a retrospective analysis and synthesis of long-term climate and streamflow data (75 years) from six watersheds differing in management histories we explored...

Child support and the postdivorce economic well-being of mothers, fathers, and children.

PubMed

Bartfeld, J

2000-05-01

This article provides national estimates of the current and potential impact of private child support transfers on the economic well-being of custodial and noncustodial families following marital dissolution. Mothers and children fare dramatically worse than fathers after marital dissolution; these differences, however, would be much more pronounced in the absence of private child support. Simulations of four existing child support guidelines show that substantial increases in economic well-being among mother-custody families are possible within the structure of the existing child support system, with minimal impact on poverty among nonresident fathers. Under all of these guidelines, however, custodial-mother families would continue to fare substantially worse than nonresident fathers.

Modified pectic polysaccharide from turmeric (Curcuma longa): A potent dietary component against gastric ulcer.

PubMed

Harsha, Mysore R; Chandra Prakash, Serkad V; Dharmesh, Shylaja M

2016-03-15

Native, intact (TrPP) and modified, low-molecular-weight (MTrPP) forms of pectic polysaccharides isolated from turmeric were evaluated for ulcer-preventive potentials in in vitro and in vivo models. Data indicated that MTrPP possessed significantly better ulcer-preventive property than TrPP; inhibiting ulcer scores up to 85%. Results were substantiated by effective muco-protection, H(+),K(+)-ATPase down-regulation, inhibition of H. pylori growth/adherence, higher antioxidant/cytoprotective mechanisms. Structural data indicated TrPP and MTrPP differ in their molecular weights and structural characteristics with different sugar compositions and side chain ratios. MTrPP was rich in galacturonic acid (687mg/g; TrPP-544mg/g) and galactose (52.9%; TrPP-21.7%). Results were substantiated by NMR/FTIR data indicating the presence of homogalacturonan and rhamnogalacturonam-I containing galactans. By virtue of binding to inflammatory marker (galectin-3), galactans may reduce inflammation induced ulcerations. The low molecular weight of MTrPP (155kDa; TrPP-13kDa) may increase its bioavailability than TrPP, thus MTrPP may possess higher antiulcer potential. Copyright © 2015 Elsevier Ltd. All rights reserved.

Developmental regulation of fear learning and anxiety behavior by endocannabinoids

PubMed Central

Lee, Tiffany T.-Y.; Hill, Matthew N.; Lee, Francis S.

2015-01-01

The developing brain undergoes substantial maturation into adulthood and the development of specific neural structures occurs on differing timelines. Transient imbalances between developmental trajectories of corticolimbic structures, which are known to contribute to regulation over fear learning and anxiety, can leave an individual susceptible to mental illness, particularly anxiety disorders. There is a substantial body of literature indicating that the endocannabinoid system critically regulates stress responsivity and emotional behavior throughout the life span, making this system a novel therapeutic target for stress- and anxiety-related disorders. During early life and adolescence, corticolimbic endocannabinoid signaling changes dynamically and coincides with different sensitive periods of fear learning, suggesting that endocannabinoid signaling underlies age-specific fear learning responses. Moreover, perturbations to these normative fluctuations in corticolimbic endocannabinoid signaling, such as stress or cannabinoid exposure, could serve as a neural substrate contributing to alterations to the normative developmental trajectory of neural structures governing emotional behavior and fear learning. In this review, we first introduce the components of the endocannabinoid system and discuss clinical and rodent models demonstrating endocannabinoid regulation of fear learning and anxiety in adulthood. Next, we highlight distinct fear learning and regulation profiles throughout development and discuss the ontogeny of the endocannabinoid system in the central nervous system, and models of pharmacological augmentation of endocannabinoid signaling during development in the context of fear learning and anxiety. PMID:26419643

Forecasting Influenza Outbreaks in Boroughs and Neighborhoods of New York City.

PubMed

Yang, Wan; Olson, Donald R; Shaman, Jeffrey

2016-11-01

The ideal spatial scale, or granularity, at which infectious disease incidence should be monitored and forecast has been little explored. By identifying the optimal granularity for a given disease and host population, and matching surveillance and prediction efforts to this scale, response to emergent and recurrent outbreaks can be improved. Here we explore how granularity and representation of spatial structure affect influenza forecast accuracy within New York City. We develop network models at the borough and neighborhood levels, and use them in conjunction with surveillance data and a data assimilation method to forecast influenza activity. These forecasts are compared to an alternate system that predicts influenza for each borough or neighborhood in isolation. At the borough scale, influenza epidemics are highly synchronous despite substantial differences in intensity, and inclusion of network connectivity among boroughs generally improves forecast accuracy. At the neighborhood scale, we observe much greater spatial heterogeneity among influenza outbreaks including substantial differences in local outbreak timing and structure; however, inclusion of the network model structure generally degrades forecast accuracy. One notable exception is that local outbreak onset, particularly when signal is modest, is better predicted with the network model. These findings suggest that observation and forecast at sub-municipal scales within New York City provides richer, more discriminant information on influenza incidence, particularly at the neighborhood scale where greater heterogeneity exists, and that the spatial spread of influenza among localities can be forecast.

Sex on the brain: Are gender-dependent structural and functional differences associated with behavior?

PubMed

Grabowska, Anna

2017-01-02

A substantial number of studies provide evidence documenting a variety of sex differences in the brain. It remains unclear whether sexual differentiation at the neural level is related to that observed in daily behavior, cognitive function, and the risk of developing certain psychiatric and neurological disorders. Some investigators have questioned whether the brain is truly sexually differentiated and support this view with several arguments including the following: (1) brain structural or functional differences are not necessarily reflected in appropriate differences at the behavioral level, which might suggest that these two phenomena are not linked to each other; and (2) sex-related differences in the brain are rather small and concern features that significantly overlap between males and females. This review polemicizes with those opinions and presents examples of sex-related local neural differences underpinning a variety of sex differences in behaviors, skills, and cognitive/emotional abilities. Although male/female brain differentiation may vary in pattern and scale, nonetheless, in some respects (e.g., relative local gray matter volumes) it can be substantial, taking the form of sexual dimorphism and involving large areas of the brain (the cortex in particular). A significant part of this review is devoted to arguing that some sex differences in the brain may serve to prevent (in the case where they are maladaptive), rather than to produce, differences at the behavioral/skill level. Specifically, some differences might result from compensatory mechanisms aimed at maintaining similar intellectual capacities across the sexes, despite the smaller average volume of the brain in females compared with males. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

The mitochondrial genomes of Campodea fragilis and C. lubbocki(Hexapoda: Diplura): high genetic divergence in a morphologically uniformtaxon

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

Podsiadlowski, L.; Carapelli, A.; Nardi, F.

2005-12-01

Mitochondrial genomes from two dipluran hexapods of the genus Campodea have been sequenced. Gene order is the same as in most other hexapods and crustaceans. Secondary structures of tRNAs reveal specific structural changes in tRNA-C, tRNA-R, tRNA-S1 and tRNA-S2. Comparative analyses of nucleotide and amino acid composition, as well as structural features of both ribosomal RNA subunits, reveal substantial differences among the analyzed taxa. Although the two Campodea species are morphologically highly uniform, genetic divergence is larger than expected, suggesting a long evolutionary history under stable ecological conditions.

Rough Set Approach to Incomplete Multiscale Information System

PubMed Central

Yang, Xibei; Qi, Yong; Yu, Dongjun; Yu, Hualong; Song, Xiaoning; Yang, Jingyu

2014-01-01

Multiscale information system is a new knowledge representation system for expressing the knowledge with different levels of granulations. In this paper, by considering the unknown values, which can be seen everywhere in real world applications, the incomplete multiscale information system is firstly investigated. The descriptor technique is employed to construct rough sets at different scales for analyzing the hierarchically structured data. The problem of unravelling decision rules at different scales is also addressed. Finally, the reduct descriptors are formulated to simplify decision rules, which can be derived from different scales. Some numerical examples are employed to substantiate the conceptual arguments. PMID:25276852

Dynamical origins of the community structure of an online multi-layer society

NASA Astrophysics Data System (ADS)

Klimek, Peter; Diakonova, Marina; Eguíluz, Víctor M.; San Miguel, Maxi; Thurner, Stefan

2016-08-01

Social structures emerge as a result of individuals managing a variety of different social relationships. Societies can be represented as highly structured dynamic multiplex networks. Here we study the dynamical origins of the specific community structures of a large-scale social multiplex network of a human society that interacts in a virtual world of a massive multiplayer online game. There we find substantial differences in the community structures of different social actions, represented by the various layers in the multiplex network. Community sizes distributions are either fat-tailed or appear to be centered around a size of 50 individuals. To understand these observations we propose a voter model that is built around the principle of triadic closure. It explicitly models the co-evolution of node- and link-dynamics across different layers of the multiplex network. Depending on link and node fluctuation probabilities, the model exhibits an anomalous shattered fragmentation transition, where one layer fragments from one large component into many small components. The observed community size distributions are in good agreement with the predicted fragmentation in the model. This suggests that several detailed features of the fragmentation in societies can be traced back to the triadic closure processes.

Method and apparatus for reducing spacecraft instrument induced jitter via multifrequency cancellation

NASA Technical Reports Server (NTRS)

Liu, Ketao (Inventor); Uetrecht, David S. (Inventor)

2002-01-01

A method, apparatus, article of manufacture, and a memory structure for compensating for instrument induced spacecraft jitter is disclosed. The apparatus comprises a spacecraft control processor for producing an actuator command signal, a signal generator, for producing a cancellation signal having at least one harmonic having a frequency and an amplitude substantially equal to that of a disturbance harmonic interacting with a spacecraft structural resonance and a phase substantially out of phase with the disturbance harmonic interacting with the spacecraft structural resonance, and at least one spacecraft control actuator, communicatively coupled to the spacecraft control processor and the signal generator for inducing satellite motion according to the actuator command signal and the cancellation signal. The method comprises the steps of generating a cancellation signal having at least one harmonic having a frequency and an amplitude substantially equal to that of a disturbance harmonic interacting with a spacecraft structural resonance and a phase substantially out of phase with the disturbance harmonic interacting with the spacecraft structural resonance, and providing the cancellation signal to a spacecraft control actuator. The apparatus comprises a storage device tangibly embodying the method steps described above.

UNICON: A Powerful and Easy-to-Use Compound Library Converter.

PubMed

Sommer, Kai; Friedrich, Nils-Ole; Bietz, Stefan; Hilbig, Matthias; Inhester, Therese; Rarey, Matthias

2016-06-27

The accurate handling of different chemical file formats and the consistent conversion between them play important roles for calculations in complex cheminformatics workflows. Working with different cheminformatic tools often makes the conversion between file formats a mandatory step. Such a conversion might become a difficult task in cases where the information content substantially differs. This paper describes UNICON, an easy-to-use software tool for this task. The functionality of UNICON ranges from file conversion between standard formats SDF, MOL2, SMILES, PDB, and PDBx/mmCIF via the generation of 2D structure coordinates and 3D structures to the enumeration of tautomeric forms, protonation states, and conformer ensembles. For this purpose, UNICON bundles the key elements of the previously described NAOMI library in a single, easy-to-use command line tool.

'They never talked to me about... ': Perspectives on aged care resident transfer to emergency departments.

PubMed

Arendts, Glenn; Popescu, Aurora; Howting, Denise; Quine, Susan; Howard, Kirsten

2015-06-01

To explore perspectives of three groups concerning transfers from aged care facilities to emergency departments. We sought to reveal factors influencing transfer decisions; how active each group was in making decisions; and to what extent groups ceded decision-making to others. Semi-structured interviews of 11 residents, 14 relatives and 17 staff with content analysis of interview transcripts. The three groups substantially differed in their involvement with initiating, and attitudes towards, transfer. Residents were least likely to be involved in the decision, yet most likely to support transfer. Staff felt conflicted between their desire to provide optimal treatment for one ill resident, and their obligations to other residents under care. Staff perspectives were largely consistent with published data, but we describe new results for other informant groups. Group expectations and preferences differ substantially. Service delivery to meet all preferences presents a challenge for health service design. © 2013 ACOTA.

Strengthening of certain types of arch dams at broad sites

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

Kaganov, G. M.; Volkov, V. I.; Uchevatkin, A. A.

2012-01-15

The problem of strengthening defective and damaged arch dams is formulated, and methodical calculations are performed to substantiate a set of structural and production measures permitting substantial improvement in the stress-strain state and an increase in the safety factor of the structure. Feasibility of practical implementation of the results is foreseen.

A Comparison of Solar p-Mode Parameters from MDI and Gong: Mode Frequencies and Structure Inversions

NASA Technical Reports Server (NTRS)

Basu, S.; Christensen-Dalsgaard, J.; Howe, R.; Schou, J.; Thompson, M. J.; Hill, F.; Komm, R.

2003-01-01

Helioseismic analysis of solar global oscillations allows investigation of the internal structure of the Sun. One important test of the reliability of the inferences from helioseismology is that the results from independent sets of contemporaneous data are consistent with one another. Here we compare mode frequencies from the Global Oscillation Network Group and Michelson Doppler Imager on board SOHO and resulting inversion results on the Sun's internal structure. The average relative differences between the data sets are typically less than 1 x 10(exp -5) substantially smaller than the formal errors in the differences; however, in some cases the frequency differences show a systematic behavior that might nonetheless influence the inversion results. We find that the differences in frequencies are not a result of instrumental effects but are almost entirely related to the data pipeline software. Inversion of the frequencies shows that their differences do not result in any significant effects on the resulting inferences on solar structure. We have also experimented with fitting asymmetric profiles to the oscillation power spectra and find that, compared with the symmetric fits, this causes no significant change in the inversion results.

Stochasticity, succession, and environmental perturbations in a fluidic ecosystem

PubMed Central

Zhou, Jizhong; Deng, Ye; Zhang, Ping; Xue, Kai; Liang, Yuting; Van Nostrand, Joy D.; Yang, Yunfeng; He, Zhili; Wu, Liyou; Stahl, David A.; Hazen, Terry C.; Tiedje, James M.; Arkin, Adam P.

2014-01-01

Unraveling the drivers of community structure and succession in response to environmental change is a central goal in ecology. Although the mechanisms shaping community structure have been intensively examined, those controlling ecological succession remain elusive. To understand the relative importance of stochastic and deterministic processes in mediating microbial community succession, a unique framework composed of four different cases was developed for fluidic and nonfluidic ecosystems. The framework was then tested for one fluidic ecosystem: a groundwater system perturbed by adding emulsified vegetable oil (EVO) for uranium immobilization. Our results revealed that groundwater microbial community diverged substantially away from the initial community after EVO amendment and eventually converged to a new community state, which was closely clustered with its initial state. However, their composition and structure were significantly different from each other. Null model analysis indicated that both deterministic and stochastic processes played important roles in controlling the assembly and succession of the groundwater microbial community, but their relative importance was time dependent. Additionally, consistent with the proposed conceptual framework but contradictory to conventional wisdom, the community succession responding to EVO amendment was primarily controlled by stochastic rather than deterministic processes. During the middle phase of the succession, the roles of stochastic processes in controlling community composition increased substantially, ranging from 81.3% to 92.0%. Finally, there are limited successional studies available to support different cases in the conceptual framework, but further well-replicated explicit time-series experiments are needed to understand the relative importance of deterministic and stochastic processes in controlling community succession. PMID:24550501

Taxonomies of networks from community structure

PubMed Central

Reid, Stephen; Porter, Mason A.; Mucha, Peter J.; Fricker, Mark D.; Jones, Nick S.

2014-01-01

The study of networks has become a substantial interdisciplinary endeavor that encompasses myriad disciplines in the natural, social, and information sciences. Here we introduce a framework for constructing taxonomies of networks based on their structural similarities. These networks can arise from any of numerous sources: they can be empirical or synthetic, they can arise from multiple realizations of a single process (either empirical or synthetic), they can represent entirely different systems in different disciplines, etc. Because mesoscopic properties of networks are hypothesized to be important for network function, we base our comparisons on summaries of network community structures. Although we use a specific method for uncovering network communities, much of the introduced framework is independent of that choice. After introducing the framework, we apply it to construct a taxonomy for 746 networks and demonstrate that our approach usefully identifies similar networks. We also construct taxonomies within individual categories of networks, and we thereby expose nontrivial structure. For example, we create taxonomies for similarity networks constructed from both political voting data and financial data. We also construct network taxonomies to compare the social structures of 100 Facebook networks and the growth structures produced by different types of fungi. PMID:23030977

Taxonomies of networks from community structure

NASA Astrophysics Data System (ADS)

Onnela, Jukka-Pekka; Fenn, Daniel J.; Reid, Stephen; Porter, Mason A.; Mucha, Peter J.; Fricker, Mark D.; Jones, Nick S.

2012-09-01

The study of networks has become a substantial interdisciplinary endeavor that encompasses myriad disciplines in the natural, social, and information sciences. Here we introduce a framework for constructing taxonomies of networks based on their structural similarities. These networks can arise from any of numerous sources: They can be empirical or synthetic, they can arise from multiple realizations of a single process (either empirical or synthetic), they can represent entirely different systems in different disciplines, etc. Because mesoscopic properties of networks are hypothesized to be important for network function, we base our comparisons on summaries of network community structures. Although we use a specific method for uncovering network communities, much of the introduced framework is independent of that choice. After introducing the framework, we apply it to construct a taxonomy for 746 networks and demonstrate that our approach usefully identifies similar networks. We also construct taxonomies within individual categories of networks, and we thereby expose nontrivial structure. For example, we create taxonomies for similarity networks constructed from both political voting data and financial data. We also construct network taxonomies to compare the social structures of 100 Facebook networks and the growth structures produced by different types of fungi.

Structural basis of respiratory syncytial virus subtype-dependent neutralization by an antibody targeting the fusion glycoprotein.

PubMed

Tian, Daiyin; Battles, Michael B; Moin, Syed M; Chen, Man; Modjarrad, Kayvon; Kumar, Azad; Kanekiyo, Masaru; Graepel, Kevin W; Taher, Noor M; Hotard, Anne L; Moore, Martin L; Zhao, Min; Zheng, Zi-Zheng; Xia, Ning-Shao; McLellan, Jason S; Graham, Barney S

2017-11-30

A licensed vaccine for respiratory syncytial virus (RSV) is unavailable, and passive prophylaxis with the antibody palivizumab is restricted to high-risk infants. Recently isolated antibodies 5C4 and D25 are substantially more potent than palivizumab, and a derivative of D25 is in clinical trials. Here we show that unlike D25, 5C4 preferentially neutralizes subtype A viruses. The crystal structure of 5C4 bound to the RSV fusion (F) protein reveals that the overall binding mode of 5C4 is similar to that of D25, but their angles of approach are substantially different. Mutagenesis and virological studies demonstrate that RSV F residue 201 is largely responsible for the subtype specificity of 5C4. These results improve our understanding of subtype-specific immunity and the neutralization breadth requirements of next-generation antibodies, and thereby contribute to the design of broadly protective RSV vaccines.

Substantial bulk photovoltaic effect enhancement via nanolayering

DOE PAGES

Wang, Fenggong; Young, Steve M.; Zheng, Fan; ...

2016-01-21

Spontaneous polarization and inversion symmetry breaking in ferroelectric materials lead to their use as photovoltaic devices. However, further advancement of their applications are hindered by the paucity of ways of reducing bandgaps and enhancing photocurrent. By unravelling the correlation between ferroelectric materials’ responses to solar irradiation and their local structure and electric polarization landscapes, here we show from first principles that substantial bulk photovoltaic effect enhancement can be achieved by nanolayering PbTiO 3 with nickel ions and oxygen vacancies ((PbNiO 2) x(PbTiO 3) 1–x). The enhancement of the total photocurrent for different spacings between the Ni-containing layers can be asmore » high as 43 times due to a smaller bandgap and photocurrent direction alignment for all absorption energies. This is due to the electrostatic effect that arises from nanolayering. Lastly, this opens up the possibility for control of the bulk photovoltaic effect in ferroelectric materials by nanoscale engineering of their structure and composition.« less

The HCUP SID Imputation Project: Improving Statistical Inferences for Health Disparities Research by Imputing Missing Race Data.

PubMed

Ma, Yan; Zhang, Wei; Lyman, Stephen; Huang, Yihe

2018-06-01

To identify the most appropriate imputation method for missing data in the HCUP State Inpatient Databases (SID) and assess the impact of different missing data methods on racial disparities research. HCUP SID. A novel simulation study compared four imputation methods (random draw, hot deck, joint multiple imputation [MI], conditional MI) for missing values for multiple variables, including race, gender, admission source, median household income, and total charges. The simulation was built on real data from the SID to retain their hierarchical data structures and missing data patterns. Additional predictive information from the U.S. Census and American Hospital Association (AHA) database was incorporated into the imputation. Conditional MI prediction was equivalent or superior to the best performing alternatives for all missing data structures and substantially outperformed each of the alternatives in various scenarios. Conditional MI substantially improved statistical inferences for racial health disparities research with the SID. © Health Research and Educational Trust.

Morphological Indicators of a Mascon Beneath Ceres's Largest Crater, Kerwan

NASA Astrophysics Data System (ADS)

Bland, M. T.; Ermakov, A. I.; Raymond, C. A.; Williams, D. A.; Bowling, T. J.; Preusker, F.; Park, R. S.; Marchi, S.; Castillo-Rogez, J. C.; Fu, R. R.; Russell, C. T.

2018-02-01

Gravity data of Ceres returned by the National Aeronautics and Space Administration's Dawn spacecraft is consistent with a lower density crust of variable thickness overlying a higher density mantle. Crustal thickness variations can affect the long-term, postimpact modification of impact craters on Ceres. Here we show that the unusual morphology of the 280 km diameter crater Kerwan may result from viscous relaxation in an outer layer that thins substantially beneath the crater floor. We propose that such a structure is consistent with either impact-induced uplift of the high-density mantle beneath the crater or from volatile loss during the impact event. In either case, the subsurface structure inferred from the crater morphology is superisostatic, and the mass excess would result in a positive Bouguer anomaly beneath the crater, consistent with the highest-degree gravity data from Dawn. Ceres joins the Moon, Mars, and Mercury in having basin-associated gravity anomalies, although their origin may differ substantially.

The effect of range changes on the functional turnover, structure and diversity of bird assemblages under future climate scenarios.

PubMed

Barbet-Massin, Morgane; Jetz, Walter

2015-08-01

Animal assemblages fulfill a critical set of ecological functions for ecosystems that may be altered substantially as climate change-induced distribution changes lead to community disaggregation and reassembly. We combine species and community perspectives to assess the consequences of projected geographic range changes for the diverse functional attributes of avian assemblages worldwide. Assemblage functional structure is projected to change highly unevenly across space. These differences arise from both changes in the number of species and changes in species' relative local functional redundancy or distinctness. They sometimes result in substantial losses of functional diversity that could have severe consequences for ecosystem health. Range expansions may counter functional losses in high-latitude regions, but offer little compensation in many tropical and subtropical biomes. Future management of local community function and ecosystem services thus relies on understanding the global dynamics of species distributions and multiscale approaches that include the biogeographic context of species traits. © 2015 John Wiley & Sons Ltd.

Morphological indicators of a mascon beneath Ceres' largest crater, Kerwan

USGS Publications Warehouse

Bland, Michael T.; Ermakov, Anton; Raymond, Carol A.; Williams, David A.; Bowling, Tim J.; Preusker, F.; Park, Ryan S.; Marchi, Simone; Castillo-Rogez, Julie C.; Fu, R.R.; Russell, Christopher T.

2018-01-01

Gravity data of Ceres returned by the National Aeronautics and Space Administration's Dawn spacecraft is consistent with a lower density crust of variable thickness overlying a higher density mantle. Crustal thickness variations can affect the long‐term, postimpact modification of impact craters on Ceres. Here we show that the unusual morphology of the 280 km diameter crater Kerwan may result from viscous relaxation in an outer layer that thins substantially beneath the crater floor. We propose that such a structure is consistent with either impact‐induced uplift of the high‐density mantle beneath the crater or from volatile loss during the impact event. In either case, the subsurface structure inferred from the crater morphology is superisostatic, and the mass excess would result in a positive Bouguer anomaly beneath the crater, consistent with the highest‐degree gravity data from Dawn. Ceres joins the Moon, Mars, and Mercury in having basin‐associated gravity anomalies, although their origin may differ substantially.

Community characteristics associated with child abuse in Iowa.

PubMed

Weissman, Alicia M; Jogerst, Gerald J; Dawson, Jeffrey D

2003-10-01

Various demographic and community characteristics are associated with child abuse rates in national and urban samples, but similar analyses have not been done within rural areas. This study analyzes the relationships between reported and substantiated rates of child abuse and county demographic, health care resource and social services factors in a predominantly rural state in the US. County-level data from Iowa between 1984-1993 were analyzed for associations between county characteristics and rates of child abuse using univariate correlations and multivariate stagewise regression analysis. Population-adjusted rates of reported and substantiated child abuse were correlated with rates of children in poverty, single-parent families, marriage and divorce, unemployment, high-school dropouts, median family income, elder abuse, birth and death rates, numbers of physicians and other healthcare providers, hospital, social workers, and number of caseworkers in the Department of Human Services. Rates of single-parent families, divorce and elder abuse were significantly associated with reported and substantiated child abuse in multivariate analysis, while economic and most health care factors were not. Reporting and substantiation rates differed across districts after adjustment for multiple factors including caseworker workload. In this rural state, family structure is more significantly associated with child abuse report and substantiation rates than are socioeconomic factors. The level of health care resources in a county does not appear to affect these rates.

Assessment of physical stability of an antibody drug conjugate by higher order structure analysis: impact of thiol- maleimide chemistry.

PubMed

Guo, Jianxin; Kumar, Sandeep; Prashad, Amarnauth; Starkey, Jason; Singh, Satish K

2014-07-01

To provide a systematic biophysical approach towards a better understanding of impact of conjugation chemistry on higher order structure and physical stability of an antibody drug conjugate (ADC). ADC was prepared using thiol-maleimide chemistry. Physical stabilities of ADC and its parent IgG1 mAb were compared using calorimetric, spectroscopic and molecular modeling techniques. ADC and mAb respond differently to thermal stress. Both the melting temperatures and heat capacities are substantially lower for the ADC. Spectroscopic experiments show that ADC and mAb have similar secondary and tertiary structures, but these are more easily destabilized by thermal stress on the ADC indicating reduced conformational stability. Molecular modeling calculations suggest a substantial decrease in the conformational energy of the mAb upon conjugation. The local surface around the conjugation sites also becomes more hydrophobic in the ADC, explaining the lower colloidal stability and greater tendency of the ADC to aggregate. Computational and biophysical analyses of an ADC and its parent mAb have provided insights into impact of conjugation on physical stability and pinpointed reasons behind lower structural stability and increased aggregation propensity of the ADC. This knowledge can be used to design appropriate formulations to stabilize the ADC.

Apparatus for integrating a rigid structure into a flexible wall of an inflatable structure

NASA Technical Reports Server (NTRS)

Johnson, Christopher J. (Inventor); Patterson, Ross M. (Inventor); Spexarth, Gary R. (Inventor)

2009-01-01

For an inflatable structure having a flexible outer shell or wall structure having a flexible restraint layer comprising interwoven, load-bearing straps, apparatus for integrating one or more substantially rigid members into the flexible shell. For each rigid member, a corresponding opening is formed through the flexible shell for receiving the rigid member. A plurality of connection devices are mounted on the rigid member for receiving respective ones of the load-bearing straps. In one embodiment, the connection devices comprise inner connecting mechanisms and outer connecting mechanisms, the inner and outer connecting mechanisms being mounted on the substantially rigid structure and spaced along a peripheral edge portion of the structure in an interleafed array in which respective outer connecting mechanisms are interposed between adjacent pairs of inner connecting mechanisms, the outer connecting mechanisms projecting outwardly from the peripheral edge portion of the substantially rigid structure beyond the adjacent inner connecting mechanisms to form a staggered array of connecting mechanisms extending along the panel structure edge portion. In one embodiment, the inner and outer connecting mechanisms form part of an integrated, structure rotatably mounted on the rigid member peripheral edge portion.

Experimental evidence of the role of pores on movement and distribution of bacteria in soil

NASA Astrophysics Data System (ADS)

Kravchenko, Alexandra N.; Rose, Joan B.; Marsh, Terence L.; Guber, Andrey K.

2014-05-01

It has been generally recognized that micro-scale heterogeneity in soil environments can have a substantial effect on movement, fate, and survival of soil microorganisms. However, only recently the development of tools for micro-scale soil analyses, including X-ray computed micro-tomography (μ-CT), enabled quantitative analyses of these effects. The long-term goal of our work is to explore how differences in micro-scale characteristics of pore structures influence movement, spatial distribution patterns, and activities of soil microorganisms. Using X-ray μ-CT we found that differences in land use and management practices lead to development of contrasting patterns in pore size-distributions within intact soil aggregates. Then our experiments with Escherichia coli added to intact soil aggregates demonstrated that the differences in pore structures can lead to substantial differences in bacteria redistribution and movement within the aggregates. Specifically, we observed more uniform E.coli redistribution in aggregates with homogeneously spread pores, while heterogeneous pore structures resulted in heterogeneous E.coli patterns. Water flow driven by capillary forces through intact aggregate pores appeared to be the main contributor to the movement patterns of the introduced bacteria. Influence of pore structure on E.coli distribution within the aggregates further continued after the aggregates were subjected to saturated water flow. E. coli's resumed movement with saturated water flow and subsequent redistribution within the soil matrix was influenced by porosity, abundance of medium and large pores, pore tortuosity, and flow rates, indicating that greater flow accompanied by less convoluted pores facilitated E. coli transport within the intra-aggregate space. We also found that intra-aggregate heterogeneity of pore structures can have an effect on spatial distribution patterns of indigenous microbial populations. Preliminary analysis showed that in aggregates from an organic agricultural system with cover crops, characterized by greater intra-aggregate pore heterogeneity, bacteria of Actinobacteria and Firmicutes groups were more abundant in presence of large as compared to small pores. In contrast, no differences were observed in the aggregates from conventionally managed soil, overall characterized by homogeneous intra-aggregate pore patterns. Further research efforts are being directed towards quantification of the pore structure effects on activities and community composition of soil microorganisms.

Visualizing global properties of a molecular dynamics trajectory.

PubMed

Zhou, Hao; Li, Shangyang; Makowski, Lee

2016-01-01

Molecular dynamics (MD) trajectories are very large data sets that contain substantial information about the dynamic behavior of a protein. Condensing these data into a form that can provide intuitively useful understanding of the molecular behavior during the trajectory is a substantial challenge that has received relatively little attention. Here, we introduce the sigma-r plot, a plot of the standard deviation of intermolecular distances as a function of that distance. This representation of global dynamics contains within a single, one-dimensional plot, the average range of motion between pairs of atoms within a macromolecule. Comparison of sigma-r plots calculated from 10 ns trajectories of proteins representing the four major SCOP fold classes indicates diversity of dynamic behaviors which are recognizably different among the four classes. Differences in domain structure and molecular weight also produce recognizable features in sigma-r plots, reflective of differences in global dynamics. Plots generated from trajectories with progressively increasing simulation time reflect the increased sampling of the structural ensemble as a function of time. Single amino acid replacements can give rise to changes in global dynamics detectable through comparison of sigma-r plots. Dynamic behavior of substructures can be monitored by careful choice of interatomic vectors included in the calculation. These examples provide demonstrations of the utility of the sigma-r plot to provide a simple measure of the global dynamics of a macromolecule. © 2015 Wiley Periodicals, Inc.

Temperature-driven topological quantum phase transitions in a phase-change material Ge2Sb2Te5.

PubMed

Eremeev, S V; Rusinov, I P; Echenique, P M; Chulkov, E V

2016-12-13

The Ge 2 Sb 2 Te 5 is a phase-change material widely used in optical memory devices and is a leading candidate for next generation non-volatile random access memory devices which are key elements of various electronics and portable systems. Despite the compound is under intense investigation its electronic structure is currently not fully understood. The present work sheds new light on the electronic structure of the Ge 2 Sb 2 Te 5 crystalline phases. We demonstrate by predicting from first-principles calculations that stable crystal structures of Ge 2 Sb 2 Te 5 possess different topological quantum phases: a topological insulator phase is realized in low-temperature structure and Weyl semimetal phase is a characteristic of the high-temperature structure. Since the structural phase transitions are caused by the temperature the switching between different topologically non-trivial phases can be driven by variation of the temperature. The obtained results reveal the rich physics of the Ge 2 Sb 2 Te 5 compound and open previously unexplored possibility for spintronics applications of this material, substantially expanding its application potential.

First iron and cobalt(II) hexabromoclathrochelates: structural, magnetic, redox, and electrocatalytic behavior.

PubMed

Dolganov, Alexander V; Belov, Alexander S; Novikov, Valentin V; Vologzhanina, Anna V; Romanenko, Galina V; Budnikova, Yulia G; Zelinskii, Genrikh E; Buzin, Michail I; Voloshin, Yan Z

2015-02-07

Template condensation of dibromoglyoxime with n-butylboronic acid on the corresponding metal ion as a matrix under vigorous reaction conditions afforded iron and cobalt(ii) hexabromoclathrochelates. The paramagnetic cobalt clathrochelate was found to be a low-spin complex at temperatures below 100 K, with a gradual increase in the effective magnetic moment at higher temperatures due to the temperature 1/2↔3/2 spin crossover and a gap caused by the structure phase transition. The multitemperature X-ray and DSC studies of this complex and its iron(ii)-containing analog also showed temperature structural transitions. The variation of an encapsulated metal ion's radius, electronic structure and spin state caused substantial differences in the geometry of its coordination polyhedron; these differences increase with the decrease in temperature due to Jahn-Teller distortion of the encapsulated cobalt(ii) ion with an electronic configuration d(7). As follows from CV and GC data, these cage iron and cobalt complexes undergo both oxidation and reduction quasireversibly, and showed an electrocatalytic activity for hydrogen production in different producing systems.

Cryo-Electron Microscopy of Viruses Infecting Bacterium

NASA Astrophysics Data System (ADS)

Chiu, Wah

2010-03-01

Single particle cryo-EM can yield structures of infectious bacterial viruses with and without imposed icosahedral symmetry at subnanometer resolution. Reconstructions of infectious and empty phage particles show substantial differences in the portal vertex protein complex at one of the 12 pentameric vertices in the icosahedral virus particle through which the viral genomes are packaged or released. In addition, electron cryo-tomography of viruses during infecting its bacterial host cell displayed multiple conformations of the tail fiber of the virus. Our structural observations by single particle and tomographic reconstructions suggest a mechanism whereby the viral tail fibers, upon binding to the host cell, induce a cascade of structural alterations of the portal vertex protein complex that triggers DNA release.

Protein Structure Classification and Loop Modeling Using Multiple Ramachandran Distributions.

PubMed

Najibi, Seyed Morteza; Maadooliat, Mehdi; Zhou, Lan; Huang, Jianhua Z; Gao, Xin

2017-01-01

Recently, the study of protein structures using angular representations has attracted much attention among structural biologists. The main challenge is how to efficiently model the continuous conformational space of the protein structures based on the differences and similarities between different Ramachandran plots. Despite the presence of statistical methods for modeling angular data of proteins, there is still a substantial need for more sophisticated and faster statistical tools to model the large-scale circular datasets. To address this need, we have developed a nonparametric method for collective estimation of multiple bivariate density functions for a collection of populations of protein backbone angles. The proposed method takes into account the circular nature of the angular data using trigonometric spline which is more efficient compared to existing methods. This collective density estimation approach is widely applicable when there is a need to estimate multiple density functions from different populations with common features. Moreover, the coefficients of adaptive basis expansion for the fitted densities provide a low-dimensional representation that is useful for visualization, clustering, and classification of the densities. The proposed method provides a novel and unique perspective to two important and challenging problems in protein structure research: structure-based protein classification and angular-sampling-based protein loop structure prediction.

Similarities and Differences between Silver Ions and Silver in Nanoforms as Antibacterial Agents

PubMed Central

Kędziora, Anna; Speruda, Mateusz; Rybka, Jacek; Łukowiak, Anna; Bugla-Płoskońska, Gabriela

2018-01-01

Silver is considered as antibacterial agent with well-known mode of action and bacterial resistance against it is well described. The development of nanotechnology provided different methods for the modification of the chemical and physical structure of silver, which may increase its antibacterial potential. The physico-chemical properties of silver nanoparticles and their interaction with living cells differs substantially from those of silver ions. Moreover, the variety of the forms and characteristics of various silver nanoparticles are also responsible for differences in their antibacterial mode of action and probably bacterial mechanism of resistance. The paper discusses in details the aforementioned aspects of silver activity. PMID:29393866

Carbon microtubes

DOEpatents

Peng, Huisheng [Shanghai, CN; Zhu, Yuntian Theodore [Cary, NC; Peterson, Dean E [Los Alamos, NM; Jia, Quanxi [Los Alamos, NM

2011-06-14

A carbon microtube comprising a hollow, substantially tubular structure having a porous wall, wherein the microtube has a diameter of from about 10 .mu.m to about 150 .mu.m, and a density of less than 20 mg/cm.sup.3. Also described is a carbon microtube, having a diameter of at least 10 .mu.m and comprising a hollow, substantially tubular structure having a porous wall, wherein the porous wall comprises a plurality of voids, said voids substantially parallel to the length of the microtube, and defined by an inner surface, an outer surface, and a shared surface separating two adjacent voids.

Nonlinear development of shocklike structure in the solar wind.

PubMed

Lee, E; Parks, G K; Wilber, M; Lin, N

2009-07-17

We report first in situ multispacecraft observations of nonlinear steepening of compressional pulses in the solar wind upstream of Earth's bow shock. The magnetic field of a compressional pulse formed at the upstream edge of density holes is shown to suddenly break and steepen into a shocklike structure. During the early phase of development thermalization of ions is insignificant. Substantial thermalization of ions occurs as gyrating ions are observed at the steepened edge. These observations indicate that the mechanisms causing the dissipation of magnetic fields (currents) and ions are different in the early phase of shock development.

Seismic Evaluation of A Historical Structure In Kastamonu - Turkey

NASA Astrophysics Data System (ADS)

Pınar, USTA; Işıl ÇARHOĞLU, Asuman; EVCİ, Ahmet

2018-01-01

The Kastomonu province is a seismically active zone. the city has many historical buildings made of stone-masonry. In case of any probable future earthquakes, existing buildings may suffer substantial or heavy damages. In the present study, one of the historical traditional house located in Kastamonu were structurally investigated through probabilistic seismic risk assessment methodology. In the study, the building was modeled by using the Finite Element Modeling (FEM) software, SAP2000. Time history analyses were carried out using 10 different ground motion data on the FEM models. Displacements were interpreted, and the results were displayed graphically and discussed.

Pluck or Luck: Does Trait Variation or Chance Drive Variation in Lifetime Reproductive Success?

PubMed

Snyder, Robin E; Ellner, Stephen P

2018-04-01

While there has been extensive interest in how intraspecific trait variation affects ecological processes, outcomes are highly variable even when individuals are identical: some are lucky, while others are not. Trait variation is therefore important only if it adds substantially to the variability produced by luck. We ask when trait variation has a substantial effect on variability in lifetime reproductive success (LRS), using two approaches: (1) we partition the variation in LRS into contributions from luck and trait variation and (2) we ask what can be inferred about an individual's traits and with what certainty, given their observed LRS. In theoretical stage- and size-structured models and two empirical case studies, we find that luck usually dominates the variance of LRS. Even when individuals differ substantially in ways that affect expected LRS, unless the effects of luck are substantially reduced (e.g., low variability in reproductive life span or annual fecundity), most variance in lifetime outcomes is due to luck, implying that departures from "null" models omitting trait variation will be hard to detect. Luck also obscures the relationship between realized LRS and individual traits. While trait variation may influence the fate of populations, luck often governs the lives of individuals.

Forecasting Influenza Outbreaks in Boroughs and Neighborhoods of New York City

PubMed Central

2016-01-01

The ideal spatial scale, or granularity, at which infectious disease incidence should be monitored and forecast has been little explored. By identifying the optimal granularity for a given disease and host population, and matching surveillance and prediction efforts to this scale, response to emergent and recurrent outbreaks can be improved. Here we explore how granularity and representation of spatial structure affect influenza forecast accuracy within New York City. We develop network models at the borough and neighborhood levels, and use them in conjunction with surveillance data and a data assimilation method to forecast influenza activity. These forecasts are compared to an alternate system that predicts influenza for each borough or neighborhood in isolation. At the borough scale, influenza epidemics are highly synchronous despite substantial differences in intensity, and inclusion of network connectivity among boroughs generally improves forecast accuracy. At the neighborhood scale, we observe much greater spatial heterogeneity among influenza outbreaks including substantial differences in local outbreak timing and structure; however, inclusion of the network model structure generally degrades forecast accuracy. One notable exception is that local outbreak onset, particularly when signal is modest, is better predicted with the network model. These findings suggest that observation and forecast at sub-municipal scales within New York City provides richer, more discriminant information on influenza incidence, particularly at the neighborhood scale where greater heterogeneity exists, and that the spatial spread of influenza among localities can be forecast. PMID:27855155

Developmental regulation of fear learning and anxiety behavior by endocannabinoids.

PubMed

Lee, T T-Y; Hill, M N; Lee, F S

2016-01-01

The developing brain undergoes substantial maturation into adulthood and the development of specific neural structures occurs on differing timelines. Transient imbalances between developmental trajectories of corticolimbic structures, which are known to contribute to regulation over fear learning and anxiety, can leave an individual susceptible to mental illness, particularly anxiety disorders. There is a substantial body of literature indicating that the endocannabinoid (eCB) system critically regulates stress responsivity and emotional behavior throughout the life span, making this system a novel therapeutic target for stress- and anxiety-related disorders. During early life and adolescence, corticolimbic eCB signaling changes dynamically and coincides with different sensitive periods of fear learning, suggesting that eCB signaling underlies age-specific fear learning responses. Moreover, perturbations to these normative fluctuations in corticolimbic eCB signaling, such as stress or cannabinoid exposure, could serve as a neural substrate contributing to alterations to the normative developmental trajectory of neural structures governing emotional behavior and fear learning. In this review, we first introduce the components of the eCB system and discuss clinical and rodent models showing eCB regulation of fear learning and anxiety in adulthood. Next, we highlight distinct fear learning and regulation profiles throughout development and discuss the ontogeny of the eCB system in the central nervous system, and models of pharmacological augmentation of eCB signaling during development in the context of fear learning and anxiety. © 2015 John Wiley & Sons Ltd and International Behavioural and Neural Genetics Society.

Characteristics of middle and upper tropospheric clouds as deduced from rawinsonde data

NASA Technical Reports Server (NTRS)

Starr, D. D. O.; Cox, S. K.

1982-01-01

The static environment of middle and upper tropospheric clouds is characterized. Computed relative humidity with respect to ice is used to diagnose the presence of cloud layer. The deduced seasonal mean cloud cover estimates based on this technique are shown to be reasonable. The cases are stratified by season and pressure thickness, and the dry static stability, vertical wind speed shear, and Richardson number are computed for three layers for each case. Mean values for each parameter are presented for each stratification and layer. The relative frequency of occurrence of various structures is presented for each stratification. The observed values of each parameter and the observed structure of each parameter are quite variable. Structures corresponding to any of a number of different conceptual models may be found. Moist adiabatic conditions are not commonly observed and the stratification based on thickness yields substantially different results for each group.

Tunable Thermosetting Epoxies Based on Fractionated and Well-Characterized Lignins.

PubMed

Gioia, Claudio; Lo Re, Giada; Lawoko, Martin; Berglund, Lars

2018-03-21

Here we report the synthesis of thermosetting resins from low molar mass Kraft lignin fractions of high functionality, refined by solvent extraction. Such fractions were fully characterized by 31 P NMR, 2D-HSQC NMR, SEC, and DSC in order to obtain a detailed description of the structures. Reactive oxirane moieties were introduced on the lignin backbone under mild reaction conditions and quantified by simple 1 H NMR analysis. The modified fractions were chemically cross-linked with a flexible polyether diamine ( M n ≈ 2000), in order to obtain epoxy thermosets. Epoxies from different lignin fractions, studied by DSC, DMA, tensile tests, and SEM, demonstrated substantial differences in terms of thermo-mechanical properties. For the first time, strong relationships between lignin structures and epoxy properties could be demonstrated. The suggested approach provides unprecedented possibilities to tune network structure and properties of thermosets based on real lignin fractions, rather than model compounds.

Distinct hippocampal functional networks revealed by tractography-based parcellation.

PubMed

Adnan, Areeba; Barnett, Alexander; Moayedi, Massieh; McCormick, Cornelia; Cohn, Melanie; McAndrews, Mary Pat

2016-07-01

Recent research suggests the anterior and posterior hippocampus form part of two distinct functional neural networks. Here we investigate the structural underpinnings of this functional connectivity difference using diffusion-weighted imaging-based parcellation. Using this technique, we substantiated that the hippocampus can be parcellated into distinct anterior and posterior segments. These structurally defined segments did indeed show different patterns of resting state functional connectivity, in that the anterior segment showed greater connectivity with temporal and orbitofrontal cortex, whereas the posterior segment was more highly connected to medial and lateral parietal cortex. Furthermore, we showed that the posterior hippocampal connectivity to memory processing regions, including the dorsolateral prefrontal cortex, parahippocampal, inferior temporal and fusiform gyri and the precuneus, predicted interindividual relational memory performance. These findings provide important support for the integration of structural and functional connectivity in understanding the brain networks underlying episodic memory.

Subcortical Correlates of Individual Differences in Aptitude

PubMed Central

Jung, Rex E.; Ryman, Sephira G.; Vakhtin, Andrei A.; Carrasco, Jessica; Wertz, Chris; Flores, Ranee A.

2014-01-01

The study of individual differences encompasses broad constructs including intelligence, creativity, and personality. However, substantially less research is devoted to the study of specific aptitudes in spite of their importance to educational, occupational, and avocational success. We sought to determine subcortical brain structural correlates of several broad aptitudes including Math, Vocabulary, Foresight, Paper Folding, and Inductive Reasoning in a large (N = 107), healthy, young (age range  = 16–29) cohort. Subcortical volumes were measured using an automated technique (FreeSurfer) across structures including bilateral caudate, putamen, globus pallidus, thalamus, nucleus accumbens, hippocampus, amygdala, and five equal regions of the corpus callosum. We found that performance on measures of each aptitude was predicted by different subcortical structures: Math – higher right nucleus accumbens volume; Vocabulary – higher left hippocampus volume; Paper Folding – higher right thalamus volume; Foresight – lower right thalamus and higher mid anterior corpus callosum volume; Inductive Reasoning – higher mid anterior corpus callosum volume. Our results support general findings, within the cognitive neurosciences, showing lateralization of structure-function relationships, as well as more specific relationships between individual structures (e.g., left hippocampus) and functions relevant to particular aptitudes (e.g., Vocabulary). PMID:24586770

N-body simulations with a cosmic vector for dark energy

NASA Astrophysics Data System (ADS)

Carlesi, Edoardo; Knebe, Alexander; Yepes, Gustavo; Gottlöber, Stefan; Jiménez, Jose Beltrán.; Maroto, Antonio L.

2012-07-01

We present the results of a series of cosmological N-body simulations of a vector dark energy (VDE) model, performed using a suitably modified version of the publicly available GADGET-2 code. The set-ups of our simulations were calibrated pursuing a twofold aim: (1) to analyse the large-scale distribution of massive objects and (2) to determine the properties of halo structure in this different framework. We observe that structure formation is enhanced in VDE, since the mass function at high redshift is boosted up to a factor of 10 with respect to Λ cold dark matter (ΛCDM), possibly alleviating tensions with the observations of massive clusters at high redshifts and early reionization epoch. Significant differences can also be found for the value of the growth factor, which in VDE shows a completely different behaviour, and in the distribution of voids, which in this cosmology are on average smaller and less abundant. We further studied the structure of dark matter haloes more massive than 5 × 1013 h-1 M⊙, finding that no substantial difference emerges when comparing spin parameter, shape, triaxiality and profiles of structures evolved under different cosmological pictures. Nevertheless, minor differences can be found in the concentration-mass relation and the two-point correlation function, both showing different amplitudes and steeper slopes. Using an additional series of simulations of a ΛCDM scenario with the same ? and σ8 used in the VDE cosmology, we have been able to establish whether the modifications induced in the new cosmological picture were due to the particular nature of the dynamical dark energy or a straightforward consequence of the cosmological parameters. On large scales, the dynamical effects of the cosmic vector field can be seen in the peculiar evolution of the cluster number density function with redshift, in the shape of the mass function, in the distribution of voids and on the characteristic form of the growth index γ(z). On smaller scales, internal properties of haloes are almost unaffected by the change of cosmology, since no statistical difference can be observed in the characteristics of halo profiles, spin parameters, shapes and triaxialities. Only halo masses and concentrations show a substantial increase, which can, however, be attributed to the change in the cosmological parameters.

The Purpose of Generating Fatigue Crack Growth Threshold Data

NASA Technical Reports Server (NTRS)

Forth, Scott

2006-01-01

Test data shows that different width and thickness C(T), M(T) and ESE(T) specimens generate different thresholds Structures designed for "infinite life" are being re-evaluated: a) Threshold changes from 6 to 3 ksi in(sup 1/2); b) Computational life changes from infinite to 4 missions. Multi-million dollar test programs required to substantiate operation. Using ASTM E647 as standard guidance to generate threshold data is not practical. A threshold test approach needs to be standardized that will provide positive margin for high cycle fatigue applications.

Large-Eddy Simulation in Planetary Boundary-Layer Research

NASA Technical Reports Server (NTRS)

Wyngaard, J. C.

1985-01-01

The structure and dynamics of the convective boundary layer are discussed. The vertical transport of a conservative, passive scalar was simulated. Also studied were the statistics by top-down and bottom-up scalar fields. Substantial differences were found between them due, presumably, to the asymmetry in the convective boundary layer. A generalization of mixed-layer scaling was developed which allows one to include the effects of top-down diffusion.

Optical fiber having wave-guiding rings

DOEpatents

Messerly, Michael J [Danville, CA; Dawson, Jay W [Livermore, CA; Beach, Raymond J [Livermore, CA; Barty, Christopher P. J. [Hayward, CA

2011-03-15

A waveguide includes a cladding region that has a refractive index that is substantially uniform and surrounds a wave-guiding region that has an average index that is close to the index of the cladding. The wave-guiding region also contains a thin ring or series of rings that have an index or indices that differ significantly from the index of the cladding. The ring or rings enable the structure to guide light.

Isolation and characterization of mammalian eumelanins from hair and irides.

PubMed

Novellino, L; Napolitano, A; Prota, G

2000-07-26

A new enzymatic procedure was developed for isolation of eumelanin from black human hair which might provide a substantially intact pigment for structural characterization. Sequential digestion with protease, proteinase K and papaine in the presence of dithiothreitol afforded a pigment with a 6% w/w protein content. HPLC analysis of pyrrole acids resulting from alkaline H(2)O(2) degradation, carboxyl content determination, and ferricyanide titration showed that the isolated pigment is made up of 5,6-dihydroxyindole (DHI)- and 5, 6-dihydroxyindole-2-carboxylic acid (DHICA)-derived units at a 6:1 ratio, exhibiting a significant degree of oxidative degradation. For comparison, a different eumelanin isolated from black bovine irides by a similar enzymatic procedure was analyzed. Matrix-assisted laser desorption ionization (MALDI) mass spectrometry of the final pigment provided evidence for homologous series of DHICA oligomers, while chemical analysis allowed an estimate of 2:1 DHICA/DHI-derived units in the polymer, with a substantial proportion of intact o-diphenolic functions. Iris melanin proved able to promote the Fenton oxidation of deoxyribose while hair melanin was ineffective. Overall, these results provide, for the first time, unambiguous evidence for marked structural differences of mammalian eumelanins which may be directly related to the diversity of the sites of biosynthesis and storage, as well as to functional role of these pigments.

Structure of D-tagatose 3-epimerase-like protein from Methanocaldococcus jannaschii.

PubMed

Uechi, Keiko; Takata, Goro; Yoneda, Kazunari; Ohshima, Toshihisa; Sakuraba, Haruhiko

2014-07-01

The crystal structure of a D-tagatose 3-epimerase-like protein (MJ1311p) encoded by a hypothetical open reading frame, MJ1311, in the genome of the hyperthermophilic archaeon Methanocaldococcus jannaschii was determined at a resolution of 2.64 Å. The asymmetric unit contained two homologous subunits, and the dimer was generated by twofold symmetry. The overall fold of the subunit proved to be similar to those of the D-tagatose 3-epimerase from Pseudomonas cichorii and the D-psicose 3-epimerases from Agrobacterium tumefaciens and Clostridium cellulolyticum. However, the situation at the subunit-subunit interface differed substantially from that in D-tagatose 3-epimerase family enzymes. In MJ1311p, Glu125, Leu126 and Trp127 from one subunit were found to be located over the metal-ion-binding site of the other subunit and appeared to contribute to the active site, narrowing the substrate-binding cleft. Moreover, the nine residues comprising a trinuclear zinc centre in endonuclease IV were found to be strictly conserved in MJ1311p, although a distinct groove involved in DNA binding was not present. These findings indicate that the active-site architecture of MJ1311p is quite unique and is substantially different from those of D-tagatose 3-epimerase family enzymes and endonuclease IV.

Structure of d-tagatose 3-epimerase-like protein from Methanocaldococcus jannaschii

PubMed Central

Uechi, Keiko; Takata, Goro; Yoneda, Kazunari; Ohshima, Toshihisa; Sakuraba, Haruhiko

2014-01-01

The crystal structure of a d-tagatose 3-epimerase-like protein (MJ1311p) encoded by a hypothetical open reading frame, MJ1311, in the genome of the hyperthermophilic archaeon Methanocaldococcus jannaschii was determined at a resolution of 2.64 Å. The asymmetric unit contained two homologous subunits, and the dimer was generated by twofold symmetry. The overall fold of the subunit proved to be similar to those of the d-tagatose 3-epimerase from Pseudomonas cichorii and the d-psicose 3-epimerases from Agrobacterium tumefaciens and Clostridium cellulolyticum. However, the situation at the subunit–subunit interface differed substantially from that in d-tagatose 3-epimerase family enzymes. In MJ1311p, Glu125, Leu126 and Trp127 from one subunit were found to be located over the metal-ion-binding site of the other subunit and appeared to contribute to the active site, narrowing the substrate-binding cleft. Moreover, the nine residues comprising a trinuclear zinc centre in endonuclease IV were found to be strictly conserved in MJ1311p, although a distinct groove involved in DNA binding was not present. These findings indicate that the active-site architecture of MJ1311p is quite unique and is substantially different from those of d-tagatose 3-epimerase family enzymes and endonuclease IV. PMID:25005083

Frequency selective infrared sensors

DOEpatents

Davids, Paul; Peters, David W

2014-11-25

A frequency selective infrared (IR) photodetector having a predetermined frequency band. The exemplary frequency selective photodetector includes: a dielectric IR absorber having a first surface and a second surface substantially parallel to the first surface; an electrode electrically coupled to the first surface of the dielectric IR absorber; and a frequency selective surface plasmonic (FSSP) structure formed on the second surface of the dielectric IR absorber. The FSSP structure is designed to selectively transmit radiation in the predetermined frequency band that is incident on the FSSP structure substantially independent of the angle of incidence of the incident radiation on the FSSP structure.

Frequency selective infrared sensors

DOEpatents

Davids, Paul; Peters, David W

2013-05-28

A frequency selective infrared (IR) photodetector having a predetermined frequency band. The exemplary frequency selective photodetector includes: a dielectric IR absorber having a first surface and a second surface substantially parallel to the first surface; an electrode electrically coupled to the first surface of the dielectric IR absorber; and a frequency selective surface plasmonic (FSSP) structure formed on the second surface of the dielectric IR absorber. The FSSP structure is designed to selectively transmit radiation in the predetermined frequency band that is incident on the FSSP structure substantially independent of the angle of incidence of the incident radiation on the FSSP structure.

Structural studies of series HIV-1 nonnucleoside reverse transcriptase inhibitors 1-(2,6-difluorobenzyl)-2-(2,6-difluorophenyl)-benzimidazoles with different 4-substituents

NASA Astrophysics Data System (ADS)

Ziółkowska, Natasza E.; Michejda, Christopher J.; Bujacz, Grzegorz D.

2010-03-01

Over the past 10 years, several anti-viral drugs have become available to fight the HIV infection. Antiretroviral treatment reduces the mortality of AIDS. Nonnucleoside inhibitors of HIV-1 reverse transcriptase are specific and potentially nontoxic drugs against AIDS. The crystal structures of five nonnucleoside inhibitors of HIV-1 reverse transcriptase are presented here. The structural parameters, especially those describing the angular orientation of the π-electron systems and influencing biological activity, were determined for all of the investigated inhibitors. The chemical character and orientation of the substituent at C4 position of the benzimidazole moiety substantially influences the anti-viral activity. The structural data of the investigated inhibitors is a good basis for modeling enzyme-inhibitor interactions for structure-assisted drug design.

T cell receptor cross-reactivity directed by antigen-dependent tuning of peptide-MHC molecular flexibility

PubMed Central

Borbulevych, Oleg Y.; Piepenbrink, Kurt H.; Gloor, Brian E.; Scott, Daniel R.; Sommese, Ruth F.; Cole, David K.; Sewell, Andrew K.; Baker, Brian M.

2011-01-01

Summary Tell mediated immunity requires T cell receptor (TCR) cross-reactivity, the mechanisms behind which remain incompletely elucidated. The αβ TCR A6 recognizes both the Tax (LLFGYPVYV) and Tel1p (MLWGYLQYV) peptides presented by the human class I MHC molecule HLA-A2. Here we found that although the two ligands are ideal structural mimics, they form substantially different interfaces with A6, with conformational differences in the peptide, the TCR, and unexpectedly, the MHC molecule. The differences between the Tax and Tel1p ternary complexes could not be predicted from the free peptide-MHC structures and are inconsistent with a traditional induced-fit mechanism. Instead, the differences were attributable to peptide and MHC molecular motion present in Tel1p-HLA-A2 but absent in Tax-HLA-A2. Differential “tuning” of the dynamic properties of HLA-A2 by the Tax and Tel1p peptides thus facilitates cross-recognition and impacts how structural diversity can be presented to and accommodated by receptors of the immune system. PMID:20064447

African Savanna-Forest Boundary Dynamics: A 20-Year Study

PubMed Central

Cuni-Sanchez, Aida; White, Lee J. T.; Calders, Kim; Jeffery, Kathryn J.; Abernethy, Katharine; Burt, Andrew; Disney, Mathias; Gilpin, Martin; Gomez-Dans, Jose L.; Lewis, Simon L.

2016-01-01

Recent studies show widespread encroachment of forest into savannas with important consequences for the global carbon cycle and land-atmosphere interactions. However, little research has focused on in situ measurements of the successional sequence of savanna to forest in Africa. Using long-term inventory plots we quantify changes in vegetation structure, above-ground biomass (AGB) and biodiversity of trees ≥10 cm diameter over 20 years for five vegetation types: savanna; colonising forest (F1), monodominant Okoume forest (F2); young Marantaceae forest (F3); and mixed Marantaceae forest (F4) in Lopé National Park, central Gabon, plus novel 3D terrestrial laser scanning (TLS) measurements to assess forest structure differences. Over 20 years no plot changed to a new stage in the putative succession, but F1 forests strongly moved towards the structure, AGB and diversity of F2 forests. Overall, savanna plots showed no detectable change in structure, AGB or diversity using this method, with zero trees ≥10 cm diameter in 1993 and 2013. F1 and F2 forests increased in AGB, mainly as a result of adding recruited stems (F1) and increased Basal Area (F2), whereas F3 and F4 forests did not change substantially in structure, AGB or diversity. Critically, the stability of the F3 stage implies that this stage may be maintained for long periods. Soil carbon was low, and did not show a successional gradient as for AGB and diversity. TLS vertical plant profiles showed distinctive differences amongst the vegetation types, indicating that this technique can improve ecological understanding. We highlight two points: (i) as forest colonises, changes in biodiversity are much slower than changes in forest structure or AGB; and (ii) all forest types store substantial quantities of carbon. Multi-decadal monitoring is likely to be required to assess the speed of transition between vegetation types. PMID:27336632

African Savanna-Forest Boundary Dynamics: A 20-Year Study.

PubMed

Cuni-Sanchez, Aida; White, Lee J T; Calders, Kim; Jeffery, Kathryn J; Abernethy, Katharine; Burt, Andrew; Disney, Mathias; Gilpin, Martin; Gomez-Dans, Jose L; Lewis, Simon L

2016-01-01

Recent studies show widespread encroachment of forest into savannas with important consequences for the global carbon cycle and land-atmosphere interactions. However, little research has focused on in situ measurements of the successional sequence of savanna to forest in Africa. Using long-term inventory plots we quantify changes in vegetation structure, above-ground biomass (AGB) and biodiversity of trees ≥10 cm diameter over 20 years for five vegetation types: savanna; colonising forest (F1), monodominant Okoume forest (F2); young Marantaceae forest (F3); and mixed Marantaceae forest (F4) in Lopé National Park, central Gabon, plus novel 3D terrestrial laser scanning (TLS) measurements to assess forest structure differences. Over 20 years no plot changed to a new stage in the putative succession, but F1 forests strongly moved towards the structure, AGB and diversity of F2 forests. Overall, savanna plots showed no detectable change in structure, AGB or diversity using this method, with zero trees ≥10 cm diameter in 1993 and 2013. F1 and F2 forests increased in AGB, mainly as a result of adding recruited stems (F1) and increased Basal Area (F2), whereas F3 and F4 forests did not change substantially in structure, AGB or diversity. Critically, the stability of the F3 stage implies that this stage may be maintained for long periods. Soil carbon was low, and did not show a successional gradient as for AGB and diversity. TLS vertical plant profiles showed distinctive differences amongst the vegetation types, indicating that this technique can improve ecological understanding. We highlight two points: (i) as forest colonises, changes in biodiversity are much slower than changes in forest structure or AGB; and (ii) all forest types store substantial quantities of carbon. Multi-decadal monitoring is likely to be required to assess the speed of transition between vegetation types.

Aminotryptophan-containing barstar: structure--function tradeoff in protein design and engineering with an expanded genetic code.

PubMed

Rubini, Marina; Lepthien, Sandra; Golbik, Ralph; Budisa, Nediljko

2006-07-01

The indole ring of the canonical amino acid tryptophan (Trp) possesses distinguished features, such as sterical bulk, hydrophobicity and the nitrogen atom which is capable of acting as a hydrogen bond donor. The introduction of an amino group into the indole moiety of Trp yields the structural analogs 4-aminotryptophan ((4-NH(2))Trp) and 5-aminotryptophan ((5-NH(2))Trp). Their hydrophobicity and spectral properties are substantially different when compared to those of Trp. They resemble the purine bases of DNA and share their capacity for pH-sensitive intramolecular charge transfer. The Trp --> aminotryptophan substitution in proteins during ribosomal translation is expected to result in related protein variants that acquire these features. These expectations have been fulfilled by incorporating (4-NH(2))Trp and (5-NH(2))Trp into barstar, an intracellular inhibitor of the ribonuclease barnase from Bacillus amyloliquefaciens. The crystal structure of (4-NH(2))Trp-barstar is similar to that of the parent protein, whereas its spectral and thermodynamic behavior is found to be remarkably different. The T(m) value of (4-NH(2))Trp- and (5-NH(2))Trp-barstar is lowered by about 20 degrees Celsius, and they exhibit a strongly reduced unfolding cooperativity and substantial loss of free energy in folding. Furthermore, folding kinetic study of (4-NH(2))Trp-barstar revealed that the denatured state is even preferred over native one. The combination of structural and thermodynamic analyses clearly shows how structures of substituted barstar display a typical structure-function tradeoff: the acquirement of unique pH-sensitive charge transfer as a novel function is achieved at the expense of protein stability. These findings provide a new insight into the evolution of the amino acid repertoire of the universal genetic code and highlight possible problems regarding protein engineering and design by using an expanded genetic code.

The impact of family formation change on the cognitive, social, and emotional well-being of the next generation.

PubMed

Amato, Paul R

2005-01-01

How have recent changes in U.S. family structure affected the cognitive, social, and emotional well-being of the nation's children? Paul Amato examines the effects of family formation on children and evaluates whether current marriage-promotion programs are likely to meet children's needs. Amato begins by investigating how children in households with both biological parents differ from children in households with only one biological parent. He shows that children growing up with two continuously married parents are less likely to experience a wide range of cognitive, emotional, and social problems, not only during childhood but also in adulthood. Although it is not possible to demonstrate that family structure causes these differences, studies using a variety of sophisticated statistical methods suggest that this is the case. Amato then asks what accounts for the differences between these two groups of children. He shows that compared with other children, those who grow up in stable, two-parent families have a higher standard of living, receive more effective parenting, experience more cooperative co-parenting, are emotionally closer to both parents, and are subjected to fewer stressful events and circumstances. Finally, Amato assesses how current marriage-promotion policies will affect the well-being of children. He finds that interventions that increase the share of children who grow up with both parents would improve the overall well-being of U.S. children only modestly, because children's social or emotional problems have many causes, of which family structure is but one. But interventions that lower only modestly the overall share of U.S. children experiencing various problems could nevertheless lower substantially the number of children experiencing them. Even a small decline in percentages, when multiplied by the many children in the population, is a substantial social benefit.

Differences in Intertidal Microbial Assemblages on Urban Structures and Natural Rocky Reef

PubMed Central

Tan, Elisa L.-Y.; Mayer-Pinto, Mariana; Johnston, Emma L.; Dafforn, Katherine A.

2015-01-01

Global seascapes are increasingly modified to support high levels of human activity in the coastal zone. Modifications include the addition of defense structures and boating infrastructure, such as seawalls and marinas that replace natural habitats. Artificial structures support different macrofaunal communities to those found on natural rocky shores; however, little is known about differences in microbial community structure or function in urban seascapes. Understanding how artificial constructions in marine environments influence microbial communities is important as these assemblages contribute to many basic ecological processes. In this study, the bacterial communities of intertidal biofilms were compared between artificial structures (seawalls) and natural habitats (rocky shores) within Sydney Harbour. Plots were cleared on each type of habitat at eight locations. After 3 weeks the newly formed biofilm was sampled and the 16S rRNA gene sequenced using the Illumina Miseq platform. To account for differences in orientation and substrate material between seawalls and rocky shores that might have influenced our survey, we also deployed recruitment blocks next to the habitats at all locations for 3 weeks and then sampled and sequenced their microbial communities. Intertidal bacterial community structure sampled from plots differed between seawalls and rocky shores, but when substrate material, age and orientation were kept constant (with recruitment blocks) then bacterial communities were similar in composition and structure among habitats. This suggests that changes in bacterial communities on seawalls are not related to environmental differences between locations, but may be related to other intrinsic factors that differ between the habitats such as orientation, complexity, or predation. This is one of the first comparisons of intertidal microbial communities on natural and artificial surfaces and illustrates substantial ecological differences with potential consequences for biofilm function and the recruitment of macrofauna. PMID:26635747

Theoretical prediction of low-density hexagonal ZnO hollow structures

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

Tuoc, Vu Ngoc, E-mail: tuoc.vungoc@hust.edu.vn; Huan, Tran Doan; Thao, Nguyen Thi

2016-10-14

Along with wurtzite and zinc blende, zinc oxide (ZnO) has been found in a large number of polymorphs with substantially different properties and, hence, applications. Therefore, predicting and synthesizing new classes of ZnO polymorphs are of great significance and have been gaining considerable interest. Herein, we perform a density functional theory based tight-binding study, predicting several new series of ZnO hollow structures using the bottom-up approach. The geometry of the building blocks allows for obtaining a variety of hexagonal, low-density nanoporous, and flexible ZnO hollow structures. Their stability is discussed by means of the free energy computed within the lattice-dynamicsmore » approach. Our calculations also indicate that all the reported hollow structures are wide band gap semiconductors in the same fashion with bulk ZnO. The electronic band structures of the ZnO hollow structures are finally examined in detail.« less

Neighborhood-Level Social Processes and Substantiated Cases of Child Maltreatment

PubMed Central

Molnar, Beth E.; Goerge, Robert M.; Gilsanz, Paola; Hill, Andrea; Subramanian, SV; Holton, John K.; Duncan, Dustin T.; Beatriz, Elizabeth D.; Beardslee, William R.

2015-01-01

Child maltreatment is a preventable public health problem. Research has demonstrated that neighborhood structural factors (e.g. poverty, crime) can influence the proportion of a neighborhood’s children who are victims of maltreatment. A newer strategy is the identification of potentially modifiable social processes at the neighborhood level that can also influence maltreatment. Toward this end, this study examines neighborhood-level data (maltreatment cases substantiated by Illinois’ child protection agency, 1995–2005, social processes measured by the Project on Human Development in Chicago Neighborhoods, U.S. Census data, proportions of neighborhoods on public assistance, and crime data) that were linked across clusters of contiguous, relatively homogenous Chicago, IL census tracts with respect to racial/ethnic and socioeconomic composition. Our analysis—an ecological-level, repeated cross-sectional design utilizing random-intercept logit models— with a sensitivity analysis using spatial models to control for spatial autocorrelation – revealed consistent associations between neighborhood social processes and maltreatment. Neighborhoods higher in collective efficacy, intergenerational closure, and social networks, and lower in disorder had lower proportions of neglect, physical abuse, and sexual abuse substantiated cases, controlling for differences in structural factors. Higher collective efficacy and social network size also predicted a lower proportion of substance-exposed infants. This research indicates that strategies to mobilize neighborhood-level protective factors may decrease child maltreatment more effectively than individual and family-focused efforts alone. PMID:26684963

Neighborhood-level social processes and substantiated cases of child maltreatment.

PubMed

Molnar, Beth E; Goerge, Robert M; Gilsanz, Paola; Hill, Andrea; Subramanian, S V; Holton, John K; Duncan, Dustin T; Beatriz, Elizabeth D; Beardslee, William R

2016-01-01

Child maltreatment is a preventable public health problem. Research has demonstrated that neighborhood structural factors (e.g. poverty, crime) can influence the proportion of a neighborhood's children who are victims of maltreatment. A newer strategy is the identification of potentially modifiable social processes at the neighborhood level that can also influence maltreatment. Toward this end, this study examines neighborhood-level data (maltreatment cases substantiated by Illinois' child protection agency, 1995-2005, social processes measured by the Project on Human Development in Chicago Neighborhoods, U.S. Census data, proportions of neighborhoods on public assistance, and crime data) that were linked across clusters of contiguous, relatively homogenous Chicago, IL census tracts with respect to racial/ethnic and socioeconomic composition. Our analysis-an ecological-level, repeated cross-sectional design utilizing random-intercept logit models-with a sensitivity analysis using spatial models to control for spatial autocorrelation-revealed consistent associations between neighborhood social processes and maltreatment. Neighborhoods higher in collective efficacy, intergenerational closure, and social networks, and lower in disorder had lower proportions of neglect, physical abuse, and sexual abuse substantiated cases, controlling for differences in structural factors. Higher collective efficacy and social network size also predicted a lower proportion of substance-exposed infants. This research indicates that strategies to mobilize neighborhood-level protective factors may decrease child maltreatment more effectively than individual and family-focused efforts alone. Copyright © 2015 Elsevier Ltd. All rights reserved.

Mesh fixation in laparoscopic incisional hernia repair: glue fixation provides attachment strength similar to absorbable tacks but differs substantially in different meshes.

PubMed

Rieder, Erwin; Stoiber, Martin; Scheikl, Verena; Poglitsch, Marcus; Dal Borgo, Andrea; Prager, Gerhard; Schima, Heinrich

2011-01-01

Laparoscopic ventral hernia repair has gained popularity among minimally invasive surgeons. However, mesh fixation remains a matter of discussion. This study was designed to compare noninvasive fibrin-glue attachment with tack fixation of meshes developed primarily for intra-abdominal use. It was hypothesized that particular mesh structures would substantially influence detachment force. For initial evaluation, specimens of laminated polypropylene/polydioxanone meshes were anchored to porcine abdominal walls by either helical titanium tacks or absorbable tacks in vitro. A universal tensile-testing machine was used to measure tangential detachment forces (TF). For subsequent experiments of glue fixation, polypropylene/polydioxanone mesh and 4 additional meshes with diverse particular mesh structure, ie, polyvinylidene fluoride/polypropylene mesh, a titanium-coated polypropylene mesh, a polyester mesh bonded with a resorbable collagen, and a macroporous condensed PTFE mesh were evaluated. TF tests revealed that fibrin-glue attachment was not substantially different from that achieved with absorbable tacks (median TF 7.8 Newton [N], range 1.3 to 15.8 N), but only when certain open porous meshes (polyvinylidene fluoride/polypropylene mesh: median 6.2 N, range 3.4 to 10.3 N; titanium-coated polypropylene mesh: median 5.2 N, range 2.1 to 11.7 N) were used. Meshes coated by an anti-adhesive barrier (polypropylene/polydioxanone mesh: median 3.1 N, range 1.7 to 5.8 N; polyester mesh bonded with a resorbable collagen: median 1.3 N, range 0.5 to 1.9 N), or the condensed PTFE mesh (median 3.1 N, range 2.1 to 7.0 N) provided a significantly lower TF (p < 0.01). Fibrin glue appears to be an appealing noninvasive option for mesh fixation in laparoscopic ventral hernia repair, but only if appropriate meshes are used. Glue can also serve as an adjunct to mechanical fixation to reduce the number of invasive tacks. Copyright © 2010 American College of Surgeons. Published by Elsevier Inc. All rights reserved.

Network-based statistical comparison of citation topology of bibliographic databases

PubMed Central

Šubelj, Lovro; Fiala, Dalibor; Bajec, Marko

2014-01-01

Modern bibliographic databases provide the basis for scientific research and its evaluation. While their content and structure differ substantially, there exist only informal notions on their reliability. Here we compare the topological consistency of citation networks extracted from six popular bibliographic databases including Web of Science, CiteSeer and arXiv.org. The networks are assessed through a rich set of local and global graph statistics. We first reveal statistically significant inconsistencies between some of the databases with respect to individual statistics. For example, the introduced field bow-tie decomposition of DBLP Computer Science Bibliography substantially differs from the rest due to the coverage of the database, while the citation information within arXiv.org is the most exhaustive. Finally, we compare the databases over multiple graph statistics using the critical difference diagram. The citation topology of DBLP Computer Science Bibliography is the least consistent with the rest, while, not surprisingly, Web of Science is significantly more reliable from the perspective of consistency. This work can serve either as a reference for scholars in bibliometrics and scientometrics or a scientific evaluation guideline for governments and research agencies. PMID:25263231

Land use planning and wildfire: development policies influence future probability of housing loss

USGS Publications Warehouse

Syphard, Alexandra D.; Massada, Avi Bar; Butsic, Van; Keeley, Jon E.

2013-01-01

Increasing numbers of homes are being destroyed by wildfire in the wildland-urban interface. With projections of climate change and housing growth potentially exacerbating the threat of wildfire to homes and property, effective fire-risk reduction alternatives are needed as part of a comprehensive fire management plan. Land use planning represents a shift in traditional thinking from trying to eliminate wildfires, or even increasing resilience to them, toward avoiding exposure to them through the informed placement of new residential structures. For land use planning to be effective, it needs to be based on solid understanding of where and how to locate and arrange new homes. We simulated three scenarios of future residential development and projected landscape-level wildfire risk to residential structures in a rapidly urbanizing, fire-prone region in southern California. We based all future development on an econometric subdivision model, but we varied the emphasis of subdivision decision-making based on three broad and common growth types: infill, expansion, and leapfrog. Simulation results showed that decision-making based on these growth types, when applied locally for subdivision of individual parcels, produced substantial landscape-level differences in pattern, location, and extent of development. These differences in development, in turn, affected the area and proportion of structures at risk from burning in wildfires. Scenarios with lower housing density and larger numbers of small, isolated clusters of development, i.e., resulting from leapfrog development, were generally predicted to have the highest predicted fire risk to the largest proportion of structures in the study area, and infill development was predicted to have the lowest risk. These results suggest that land use planning should be considered an important component to fire risk management and that consistently applied policies based on residential pattern may provide substantial benefits for future risk reduction.

Relationship between global structural parameters and Enzyme Commission hierarchy: implications for function prediction.

PubMed

Boareto, Marcelo; Yamagishi, Michel E B; Caticha, Nestor; Leite, Vitor B P

2012-10-01

In protein databases there is a substantial number of proteins structurally determined but without function annotation. Understanding the relationship between function and structure can be useful to predict function on a large scale. We have analyzed the similarities in global physicochemical parameters for a set of enzymes which were classified according to the four Enzyme Commission (EC) hierarchical levels. Using relevance theory we introduced a distance between proteins in the space of physicochemical characteristics. This was done by minimizing a cost function of the metric tensor built to reflect the EC classification system. Using an unsupervised clustering method on a set of 1025 enzymes, we obtained no relevant clustering formation compatible with EC classification. The distance distributions between enzymes from the same EC group and from different EC groups were compared by histograms. Such analysis was also performed using sequence alignment similarity as a distance. Our results suggest that global structure parameters are not sufficient to segregate enzymes according to EC hierarchy. This indicates that features essential for function are rather local than global. Consequently, methods for predicting function based on global attributes should not obtain high accuracy in main EC classes prediction without relying on similarities between enzymes from training and validation datasets. Furthermore, these results are consistent with a substantial number of studies suggesting that function evolves fundamentally by recruitment, i.e., a same protein motif or fold can be used to perform different enzymatic functions and a few specific amino acids (AAs) are actually responsible for enzyme activity. These essential amino acids should belong to active sites and an effective method for predicting function should be able to recognize them. Copyright © 2012 Elsevier Ltd. All rights reserved.

Structure of the Rift Valley fever virus nucleocapsid protein reveals another architecture for RNA encapsidation

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

Raymond, Donald D.; Piper, Mary E.; Gerrard, Sonja R.

2010-07-13

Rift Valley fever virus (RVFV) is a negative-sense RNA virus (genus Phlebovirus, family Bunyaviridae) that infects livestock and humans and is endemic to sub-Saharan Africa. Like all negative-sense viruses, the segmented RNA genome of RVFV is encapsidated by a nucleocapsid protein (N). The 1.93-{angstrom} crystal structure of RVFV N and electron micrographs of ribonucleoprotein (RNP) reveal an encapsidated genome of substantially different organization than in other negative-sense RNA virus families. The RNP polymer, viewed in electron micrographs of both virus RNP and RNP reconstituted from purified N with a defined RNA, has an extended structure without helical symmetry. N-RNA speciesmore » of {approx}100-kDa apparent molecular weight and heterogeneous composition were obtained by exhaustive ribonuclease treatment of virus RNP, by recombinant expression of N, and by reconstitution from purified N and an RNA oligomer. RNA-free N, obtained by denaturation and refolding, has a novel all-helical fold that is compact and well ordered at both the N and C termini. Unlike N of other negative-sense RNA viruses, RVFV N has no positively charged surface cleft for RNA binding and no protruding termini or loops to stabilize a defined N-RNA oligomer or RNP helix. A potential protein interaction site was identified in a conserved hydrophobic pocket. The nonhelical appearance of phlebovirus RNP, the heterogeneous {approx}100-kDa N-RNA multimer, and the N fold differ substantially from the RNP and N of other negative-sense RNA virus families and provide valuable insights into the structure of the encapsidated phlebovirus genome.« less

Magnitude and nature of carbohydrate-aromatic interactions in fucose-phenol and fucose-indole complexes: CCSD(T) level interaction energy calculations.

PubMed

Tsuzuki, Seiji; Uchimaru, Tadafumi; Mikami, Masuhiro

2011-10-20

The CH/π contact structures of the fucose-phenol and fucose-indole complexes and the stabilization energies by formation of the complexes (E(form)) were studied by ab initio molecular orbital calculations. The three types of interactions (CH/π and OH/π interactions and OH/O hydrogen bonds) were compared and evaluated in a single molecular system and at the same level of theory. The E(form) calculated for the most stable CH/π contact structure of the fucose-phenol complex at the CCSD(T) level (-4.9 kcal/mol) is close to that for the most stable CH/π contact structure of the fucose-benzene complex (-4.5 kcal/mol). On the other hand the most stable CH/π contact structure of the fucose-indole complex has substantially larger E(form) (-6.5 kcal/mol). The dispersion interaction is the major source of the attraction in the CH/π contact structures of the fucose-phenol and fucose-indole complexes as in the case of the fucose-benzene complex. The electrostatic interactions in the CH/π contact structures are small (less than 1.5 kcal/mol). The nature of the interactions between the nonpolar surface of the carbohydrate and aromatic rings is completely different from that of the conventional hydrogen bonds where the electrostatic interaction is the major source of the attraction. The distributed multipole analysis and DFT-SATP analysis show that the dispersion interactions in the CH/π contact structure of fucose-indole complex are substantially larger than those in the CH/π contact structures of fucose-benzene and fucose-phenol complexes. The large dispersion interactions are responsible for the large E(form) for the fucose-indole complex.

Dissecting cross-impact on stock markets: an empirical analysis

NASA Astrophysics Data System (ADS)

Benzaquen, M.; Mastromatteo, I.; Eisler, Z.; Bouchaud, J.-P.

2017-02-01

The vast majority of market impact studies assess each product individually, and the interactions between the different order flows are disregarded. This strong approximation may lead to an underestimation of trading costs and possible contagion effects. Transactions in fact mediate a significant part of the correlation between different instruments. In turn, liquidity shares the sectorial structure of market correlations, which can be encoded as a set of eigenvalues and eigenvectors. We introduce a multivariate linear propagator model that successfully describes such a structure, and accounts for a significant fraction of the covariance of stock returns. We dissect the various dynamical mechanisms that contribute to the joint dynamics of assets. We also define two simplified models with substantially less parameters in order to reduce overfitting, and show that they have superior out-of-sample performance.

Bone matrix structure in different seasons of cervid antlerogenesis and gestation

NASA Astrophysics Data System (ADS)

Silvennoinen, Raimo V. J.; Nygren, Kaarlo; Rouvinen, Juha; Petrova, Valentina V.

1994-05-01

During the antlerogenesis and gestation, substantial amounts of mineral compounds are removed from the skeleton and transferred to the growing antler or foetus. We have used holographic nondestructive testing for sorting out biomechanically aberrant radioulnar bones of European moose and radiological methods to study, whether observed aberrations are due to changes of the structure of the long bones (radius). In males, these changes were studied in three phases of antler cycle: antlerless season, antler growing and mature antler. In females, the studies were made with samples of adult individuals in and after gestation period. We studied x-ray diffraction responses of the bones before and after compression up to saturation level. Our results are indicating that compact and spongy part of the bones are giving seasonally different biomechanical responses.

Mixing in a T-shaped micromixer at moderate Reynolds numbers

NASA Astrophysics Data System (ADS)

Minakov, A. V.; Rudyak, V. Ya.; Gavrilov, A. A.; Dekterev, A. A.

2012-09-01

In the present work, the regimes of the flow and mixing of fluids in a T-shaped micromixer in the range of the Reynolds numbers from 1 to 1000 are investigated systematically with the aid of numerical modeling. The flow and mixing regimes are shown to alter substantially with increasing Reynolds numbers. Five different flow regimes have been identified in the total. The dependencies of the friction coefficient and mixing efficiency on the Reynolds number are obtained. A sharp increase in the mixing efficiency at a flow transition from the symmetric to asymmetric steady regime is shown. On the other hand, the mixing efficiency slightly drops in the laminar-turbulent transition region. A substantial influence of the slip presence on walls on flow structure in the channel and mixing efficiency has been revealed.

Phenotypic and Genetic Divergence among Poison Frog Populations in a Mimetic Radiation

PubMed Central

Twomey, Evan; Yeager, Justin; Brown, Jason Lee; Morales, Victor; Cummings, Molly; Summers, Kyle

2013-01-01

The evolution of Müllerian mimicry is, paradoxically, associated with high levels of diversity in color and pattern. In a mimetic radiation, different populations of a species evolve to resemble different models, which can lead to speciation. Yet there are circumstances under which initial selection for divergence under mimicry may be reversed. Here we provide evidence for the evolution of extensive phenotypic divergence in a mimetic radiation in Ranitomeya imitator, the mimic poison frog, in Peru. Analyses of color hue (spectral reflectance) and pattern reveal substantial divergence between morphs. However, we also report that there is a “transition-zone” with mixed phenotypes. Analyses of genetic structure using microsatellite variation reveals some differentiation between populations, but this does not strictly correspond to color pattern divergence. Analyses of gene flow between populations suggest that, while historical levels of gene flow were low, recent levels are high in some cases, including substantial gene flow between some color pattern morphs. We discuss possible explanations for these observations. PMID:23405150

Explosive bulk charge

DOEpatents

Miller, Jacob Lee

2015-04-21

An explosive bulk charge, including: a first contact surface configured to be selectively disposed substantially adjacent to a structure or material; a second end surface configured to selectively receive a detonator; and a curvilinear side surface joining the first contact surface and the second end surface. The first contact surface, the second end surface, and the curvilinear side surface form a bi-truncated hemispherical structure. The first contact surface, the second end surface, and the curvilinear side surface are formed from an explosive material. Optionally, the first contact surface and the second end surface each have a substantially circular shape. Optionally, the first contact surface and the second end surface consist of planar structures that are aligned substantially parallel or slightly tilted with respect to one another. The curvilinear side surface has one of a smooth curved geometry, an elliptical geometry, and a parabolic geometry.

Bacterial Diversity and Biogeochemistry of Two Marine Shallow-Water Hydrothermal Systems off Dominica (Lesser Antilles).

PubMed

Pop Ristova, Petra; Pichler, Thomas; Friedrich, Michael W; Bühring, Solveig I

2017-01-01

Shallow-water hydrothermal systems represent extreme environments with unique biogeochemistry and high biological productivity, at which autotrophic microorganisms use both light and chemical energy for the production of biomass. Microbial communities of these ecosystems are metabolically diverse and possess the capacity to transform a large range of chemical compounds. Yet, little is known about their diversity or factors shaping their structure or how they compare to coastal sediments not impacted by hydrothermalism. To this end, we have used automated ribosomal intergenic spacer analysis (ARISA) and high-throughput Illumina sequencing combined with porewater geochemical analysis to investigate microbial communities along geochemical gradients in two shallow-water hydrothermal systems off the island of Dominica (Lesser Antilles). At both sites, venting of hydrothermal fluids substantially altered the porewater geochemistry by enriching it with silica, iron and dissolved inorganic carbon, resulting in island-like habitats with distinct biogeochemistry. The magnitude of fluid flow and difference in sediment grain size, which impedes mixing of the fluids with seawater, were correlated with the observed differences in the porewater geochemistry between the two sites. Concomitantly, individual sites harbored microbial communities with a significantly different community structure. These differences could be statistically linked to variations in the porewater geochemistry and the hydrothermal fluids. The two shallow-water hydrothermal systems of Dominica harbored bacterial communities with high taxonomical and metabolic diversity, predominated by heterotrophic microorganisms associated with the Gammaproteobacterial genera Pseudomonas and Pseudoalteromonas , indicating the importance of heterotrophic processes. Overall, this study shows that shallow-water hydrothermal systems contribute substantially to the biogeochemical heterogeneity and bacterial diversity of coastal sediments.

Bacterial Diversity and Biogeochemistry of Two Marine Shallow-Water Hydrothermal Systems off Dominica (Lesser Antilles)

PubMed Central

Pop Ristova, Petra; Pichler, Thomas; Friedrich, Michael W.; Bühring, Solveig I.

2017-01-01

Shallow-water hydrothermal systems represent extreme environments with unique biogeochemistry and high biological productivity, at which autotrophic microorganisms use both light and chemical energy for the production of biomass. Microbial communities of these ecosystems are metabolically diverse and possess the capacity to transform a large range of chemical compounds. Yet, little is known about their diversity or factors shaping their structure or how they compare to coastal sediments not impacted by hydrothermalism. To this end, we have used automated ribosomal intergenic spacer analysis (ARISA) and high-throughput Illumina sequencing combined with porewater geochemical analysis to investigate microbial communities along geochemical gradients in two shallow-water hydrothermal systems off the island of Dominica (Lesser Antilles). At both sites, venting of hydrothermal fluids substantially altered the porewater geochemistry by enriching it with silica, iron and dissolved inorganic carbon, resulting in island-like habitats with distinct biogeochemistry. The magnitude of fluid flow and difference in sediment grain size, which impedes mixing of the fluids with seawater, were correlated with the observed differences in the porewater geochemistry between the two sites. Concomitantly, individual sites harbored microbial communities with a significantly different community structure. These differences could be statistically linked to variations in the porewater geochemistry and the hydrothermal fluids. The two shallow-water hydrothermal systems of Dominica harbored bacterial communities with high taxonomical and metabolic diversity, predominated by heterotrophic microorganisms associated with the Gammaproteobacterial genera Pseudomonas and Pseudoalteromonas, indicating the importance of heterotrophic processes. Overall, this study shows that shallow-water hydrothermal systems contribute substantially to the biogeochemical heterogeneity and bacterial diversity of coastal sediments. PMID:29255454

Self-assembled ordered structures in thin films of HAT5 discotic liquid crystal.

PubMed

Morales, Piero; Lagerwall, Jan; Vacca, Paolo; Laschat, Sabine; Scalia, Giusy

2010-05-20

Thin films of the discotic liquid crystal hexapentyloxytriphenylene (HAT5), prepared from solution via casting or spin-coating, were investigated by atomic force microscopy and polarizing optical microscopy, revealing large-scale ordered structures substantially different from those typically observed in standard samples of the same material. Thin and very long fibrils of planar-aligned liquid crystal were found, possibly formed as a result of an intermediate lyotropic nematic state arising during the solvent evaporation process. Moreover, in sufficiently thin films the crystallization seems to be suppressed, extending the uniform order of the liquid crystal phase down to room temperature. This should be compared to the bulk situation, where the same material crystallizes into a polymorphic structure at 68 °C.

High-Temperature Carbon Deposition on Oxide Surfaces by CO Disproportionation

PubMed Central

2016-01-01

Carbon deposition due to the inverse Boudouard reaction (2CO → CO2 + C) has been studied on yttria-stabilized zirconia (YSZ), Y2O3, and ZrO2 in comparison to CH4 by a variety of different chemical, structural, and spectroscopic characterization techniques, including electrochemical impedance spectroscopy (EIS), Fourier-transform infrared (FT-IR) spectroscopy and imaging, Raman spectroscopy, and electron microscopy. Consentaneously, all experimental methods prove the formation of a more or less conducting carbon layer (depending on the used oxide) of disordered nanocrystalline graphite covering the individual grains of the respective pure oxides after treatment in flowing CO at temperatures above ∼1023 K. All measurements show that during carbon deposition, a more or less substantial surface reduction of the oxides takes place. These results, therefore, reveal that the studied pure oxides can act as efficient nonmetallic substrates for CO-induced growth of highly distorted graphitic carbon with possible important technological implications especially with respect to treatment in pure CO or CO-rich syngas mixtures. Compared to CH4, more carbon is generally deposited in CO under otherwise similar experimental conditions. Although Raman and electron microscopy measurements do not show substantial differences in the structure of the deposited carbon layers, in particular, electrochemical impedance measurements reveal major differences in the dynamic growth process of the carbon layer, eventually leading to less percolated islands and suppressed metallic conductivity in comparison to CH4-induced graphite. PMID:26877828

A general mixture equation of state for double bonding carboxylic acids with ≥2 association sites

NASA Astrophysics Data System (ADS)

Marshall, Bennett D.

2018-05-01

In this paper, we obtain the first general multi-component solution to Wertheim's thermodynamic perturbation theory for the case that molecules can participate in cyclic double bonds. In contrast to previous authors, we do not restrict double bonding molecules to a 2-site association scheme. Each molecule in a multi-component mixture can have an arbitrary number of donor and acceptor association sites. The one restriction on the theory is that molecules can have at most one pair of double bonding sites. We also incorporate the effect of hydrogen bond cooperativity in cyclic double bonds. We then apply this new association theory to 2-site and 3-site models for carboxylic acids within the polar perturbed chain statistical associating fluid theory equation of state. We demonstrate the accuracy of the approach by comparison to both pure and multi-component phase equilibria data. It is demonstrated that the 3-site association model gives substantially a different hydrogen bonding structure than a 2-site approach. We also demonstrate that inclusion of hydrogen bond cooperativity has a substantial effect on a liquid phase hydrogen bonding structure.

Method of repairing discontinuity in fiberglass structures

NASA Technical Reports Server (NTRS)

Gelb, L. L.; Helbert, W. B., Jr.; Enie, R. B.; Mulliken, R. F. (Inventor)

1974-01-01

Damaged fiberglass structures are repaired by substantially filling the irregular surfaced damaged area with a liquid, self-curing resin, preferably an epoxy resin mixed with chopped fiberglass, and then applying to the resin surface the first of several woven fiberglass swatches which has stitching in a zig-zag pattern parallel to each of its edges and a fringe of warp and fill glass fibers about the edges outward of the stitching. The method is especially applicable to repair of fiberglass rocket engine casings and is particularly advantageous since it restores the repaired fiberglass structure to substantially its original strength without any significant changes in the geometry or mass of the structure.

Conventionalism about what? Where Duhem and Poincaré part ways.

PubMed

Ivanova, Milena

2015-12-01

This paper examines whether, and in what contexts, Duhem's and Poincaré's views can be regarded as conventionalist or structural realist. After analysing the three different contexts in which conventionalism is attributed to them-in the context of the aim of science, the underdetermination problem and the epistemological status of certain principles-I show that neither Duhem's nor Poincaré's arguments can be regarded as conventionalist. I argue that Duhem and Poincaré offer different solutions to the problem of theory choice, differ in their stances towards scientific knowledge and the status of scientific principles, making their epistemological claims substantially different. Copyright © 2015 Elsevier Ltd. All rights reserved.

Critical Features of Fragment Libraries for Protein Structure Prediction

PubMed Central

dos Santos, Karina Baptista

2017-01-01

The use of fragment libraries is a popular approach among protein structure prediction methods and has proven to substantially improve the quality of predicted structures. However, some vital aspects of a fragment library that influence the accuracy of modeling a native structure remain to be determined. This study investigates some of these features. Particularly, we analyze the effect of using secondary structure prediction guiding fragments selection, different fragments sizes and the effect of structural clustering of fragments within libraries. To have a clearer view of how these factors affect protein structure prediction, we isolated the process of model building by fragment assembly from some common limitations associated with prediction methods, e.g., imprecise energy functions and optimization algorithms, by employing an exact structure-based objective function under a greedy algorithm. Our results indicate that shorter fragments reproduce the native structure more accurately than the longer. Libraries composed of multiple fragment lengths generate even better structures, where longer fragments show to be more useful at the beginning of the simulations. The use of many different fragment sizes shows little improvement when compared to predictions carried out with libraries that comprise only three different fragment sizes. Models obtained from libraries built using only sequence similarity are, on average, better than those built with a secondary structure prediction bias. However, we found that the use of secondary structure prediction allows greater reduction of the search space, which is invaluable for prediction methods. The results of this study can be critical guidelines for the use of fragment libraries in protein structure prediction. PMID:28085928

Critical Features of Fragment Libraries for Protein Structure Prediction.

PubMed

Trevizani, Raphael; Custódio, Fábio Lima; Dos Santos, Karina Baptista; Dardenne, Laurent Emmanuel

2017-01-01

The use of fragment libraries is a popular approach among protein structure prediction methods and has proven to substantially improve the quality of predicted structures. However, some vital aspects of a fragment library that influence the accuracy of modeling a native structure remain to be determined. This study investigates some of these features. Particularly, we analyze the effect of using secondary structure prediction guiding fragments selection, different fragments sizes and the effect of structural clustering of fragments within libraries. To have a clearer view of how these factors affect protein structure prediction, we isolated the process of model building by fragment assembly from some common limitations associated with prediction methods, e.g., imprecise energy functions and optimization algorithms, by employing an exact structure-based objective function under a greedy algorithm. Our results indicate that shorter fragments reproduce the native structure more accurately than the longer. Libraries composed of multiple fragment lengths generate even better structures, where longer fragments show to be more useful at the beginning of the simulations. The use of many different fragment sizes shows little improvement when compared to predictions carried out with libraries that comprise only three different fragment sizes. Models obtained from libraries built using only sequence similarity are, on average, better than those built with a secondary structure prediction bias. However, we found that the use of secondary structure prediction allows greater reduction of the search space, which is invaluable for prediction methods. The results of this study can be critical guidelines for the use of fragment libraries in protein structure prediction.

THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures.

PubMed

Theobald, Douglas L; Wuttke, Deborah S

2006-09-01

THESEUS is a command line program for performing maximum likelihood (ML) superpositions and analysis of macromolecular structures. While conventional superpositioning methods use ordinary least-squares (LS) as the optimization criterion, ML superpositions provide substantially improved accuracy by down-weighting variable structural regions and by correcting for correlations among atoms. ML superpositioning is robust and insensitive to the specific atoms included in the analysis, and thus it does not require subjective pruning of selected variable atomic coordinates. Output includes both likelihood-based and frequentist statistics for accurate evaluation of the adequacy of a superposition and for reliable analysis of structural similarities and differences. THESEUS performs principal components analysis for analyzing the complex correlations found among atoms within a structural ensemble. ANSI C source code and selected binaries for various computing platforms are available under the GNU open source license from http://monkshood.colorado.edu/theseus/ or http://www.theseus3d.org.

The preparation and structure of salty ice VII under pressure

NASA Astrophysics Data System (ADS)

Klotz, Stefan; Bove, Livia E.; Strässle, Thierry; Hansen, Thomas C.; Saitta, Antonino M.

2009-05-01

It is widely accepted that ice, no matter what phase, is unable to incorporate large amounts of salt into its structure. This conclusion is based on the observation that on freezing of salt water, ice expels the salt almost entirely as brine. Here, we show that this behaviour is not an intrinsic physico-chemical property of ice phases. We demonstrate by neutron diffraction that substantial amounts of dissolved LiCl can be built homogeneously into the ice VII structure if it is produced by recrystallization of its glassy (amorphous) state under pressure. Such `alloyed' ice VII has significantly different structural properties compared with pure ice VII, such as an 8% larger unit cell volume, 5 times larger displacement factors, an absence of a transition to an ordered ice VIII structure and plasticity. Our study suggests that there could be a whole new class of `salty' high-pressure ice forms.

The preparation and structure of salty ice VII under pressure.

PubMed

Klotz, Stefan; Bove, Livia E; Strässle, Thierry; Hansen, Thomas C; Saitta, Antonino M

2009-05-01

It is widely accepted that ice, no matter what phase, is unable to incorporate large amounts of salt into its structure. This conclusion is based on the observation that on freezing of salt water, ice expels the salt almost entirely as brine. Here, we show that this behaviour is not an intrinsic physico-chemical property of ice phases. We demonstrate by neutron diffraction that substantial amounts of dissolved LiCl can be built homogeneously into the ice VII structure if it is produced by recrystallization of its glassy (amorphous) state under pressure. Such 'alloyed' ice VII has significantly different structural properties compared with pure ice VII, such as an 8% larger unit cell volume, 5 times larger displacement factors, an absence of a transition to an ordered ice VIII structure and plasticity. Our study suggests that there could be a whole new class of 'salty' high-pressure ice forms.

Vibration suppression and slewing control of a flexible structure

NASA Technical Reports Server (NTRS)

Inman, Daniel J.; Garcia, Ephrahim; Pokines, Brett

1991-01-01

Examined here are the effects of motor dynamics and secondary piezoceramic actuators on vibration suppression during the slewing of flexible structures. The approach focuses on the interaction between the structure, the actuators, and the choice of control law. The results presented here are all simulated, but are based on experimentally determined parameters for the motor, structure, piezoceramic actuators, and piezofilm sensors. The simulation results clearly illustrate that the choice of motor inertia relative to beam inertia makes a critical difference in the performance of the system. In addition, the use of secondary piezoelectric actuators reduces the load requirements on the motor and also reduces the overshoot of the tip deflection. The structures considered here are a beam and a frame. The majority of results are based on a Euler Bernoulli beam model. The slewing frame introduces substantial torsional modes and a more realistic model. The slewing frame results are incomplete and represent work in progress.

Topological distribution of four-alpha-helix bundles.

PubMed Central

Presnell, S R; Cohen, F E

1989-01-01

The four-alpha-helix bundle, a common structural motif in globular proteins, provides an excellent forum for the examination of predictive constraints for protein backbone topology. An exhaustive examination of the Brookhaven Crystallographic Protein Data Bank and other literature sources has lead to the discovery of 20 putative four-alpha-helix bundles. Application of an analytical method that examines the difference between solvent-accessible surface areas in packed and partially unpacked bundles reduced the number of structures to 16. Angular requirements further reduced the list of bundles to 13. In 12 of these bundles, all pairs of neighboring helices were oriented in an anti-parallel fashion. This distribution is in accordance with structure types expected if the helix macro dipole effect makes a substantial contribution to the stability of the native structure. The characterizations and classifications made in this study prompt a reevaluation of constraints used in structure prediction efforts. Images PMID:2771946

Ab initio study on structural stability of uranium carbide

NASA Astrophysics Data System (ADS)

Sahoo, B. D.; Joshi, K. D.; Gupta, Satish C.

2013-06-01

First principles calculations have been performed using plane wave pseudopotential and full potential linearized augmented plane wave (FP-LAPW) methods to analyze structural, elastic and dynamic stability of UC under hydrostatic compression. Our calculations within pseudopotential method suggest that the rocksalt (B1) structure will transform to body centered orthorhombic (bco) structure at ˜21.5 GPa. The FP-LAPW calculations put this transition at 23 GPa. The transition pressures determined from our calculations though agree reasonably with the experimental value of 27 GPa, the high pressure bco structure suggested by theory differs slightly from the experimentally reported pseudo bco phase. The elastic stability analysis of B1 phase suggests that the B1 to bco transition is driven by the failure of C44 modulus. This finding is further substantiated by the lattice dynamic calculations which demonstrate that the B1 phase becomes dynamically unstable around the transition pressure and the instability is of long wavelength nature.

Economic efficiency of application of innovative materials and structures in high-rise construction

NASA Astrophysics Data System (ADS)

Golov, Roman; Dikareva, Varvara; Gorshkov, Roman; Agarkov, Anatoly

2018-03-01

The article is devoted to the analysis of technical and economic efficiency of application of tube confined concrete structures in high-rise construction. The study of comparative costs of materials with the use of different supporting columns was carried out. The main design, operational, technological and economic advantages of the tube confined concrete technology were evaluated, conclusions were drawn about the high strength and deformation properties of axial compression of steel tubes filled with high-strength concrete. The efficiency of the tube confined concrete use is substantiated, which depends mainly on the scale factor and percentage of reinforcement affecting its load-bearing capacity.

Between-Site Differences in the Scale of Dispersal and Gene Flow in Red Oak

PubMed Central

Moran, Emily V.; Clark, James S.

2012-01-01

Background Nut-bearing trees, including oaks (Quercus spp.), are considered to be highly dispersal limited, leading to concerns about their ability to colonize new sites or migrate in response to climate change. However, estimating seed dispersal is challenging in species that are secondarily dispersed by animals, and differences in disperser abundance or behavior could lead to large spatio-temporal variation in dispersal ability. Parentage and dispersal analyses combining genetic and ecological data provide accurate estimates of current dispersal, while spatial genetic structure (SGS) can shed light on past patterns of dispersal and establishment. Methodology and Principal Findings In this study, we estimate seed and pollen dispersal and parentage for two mixed-species red oak populations using a hierarchical Bayesian approach. We compare these results to those of a genetic ML parentage model. We also test whether observed patterns of SGS in three size cohorts are consistent with known site history and current dispersal patterns. We find that, while pollen dispersal is extensive at both sites, the scale of seed dispersal differs substantially. Parentage results differ between models due to additional data included in Bayesian model and differing genotyping error assumptions, but both indicate between-site dispersal differences. Patterns of SGS in large adults, small adults, and seedlings are consistent with known site history (farmed vs. selectively harvested), and with long-term differences in seed dispersal. This difference is consistent with predator/disperser satiation due to higher acorn production at the low-dispersal site. While this site-to-site variation results in substantial differences in asymptotic spread rates, dispersal for both sites is substantially lower than required to track latitudinal temperature shifts. Conclusions Animal-dispersed trees can exhibit considerable spatial variation in seed dispersal, although patterns may be surprisingly constant over time. However, even under favorable conditions, migration in heavy-seeded species is likely to lag contemporary climate change. PMID:22563504

Ab initio structure determination and quantitative disorder analysis on nanoparticles by electron diffraction tomography.

PubMed

Krysiak, Yaşar; Barton, Bastian; Marler, Bernd; Neder, Reinhard B; Kolb, Ute

2018-03-01

Nanoscaled porous materials such as zeolites have attracted substantial attention in industry due to their catalytic activity, and their performance in sorption and separation processes. In order to understand the properties of such materials, current research focuses increasingly on the determination of structural features beyond the averaged crystal structure. Small particle sizes, various types of disorder and intergrown structures render the description of structures at atomic level by standard crystallographic methods difficult. This paper reports the characterization of a strongly disordered zeolite structure, using a combination of electron exit-wave reconstruction, automated diffraction tomography (ADT), crystal disorder modelling and electron diffraction simulations. Zeolite beta was chosen for a proof-of-principle study of the techniques, because it consists of two different intergrown polymorphs that are built from identical layer types but with different stacking sequences. Imaging of the projected inner Coulomb potential of zeolite beta crystals shows the intergrowth of the polymorphs BEA and BEB. The structures of BEA as well as BEB could be extracted from one single ADT data set using direct methods. A ratio for BEA/BEB = 48:52 was determined by comparison of the reconstructed reciprocal space based on ADT data with simulated electron diffraction data for virtual nanocrystals, built with different ratios of BEA/BEB. In this way, it is demonstrated that this smart interplay of the above-mentioned techniques allows the elaboration of the real structures of functional materials in detail - even if they possess a severely disordered structure.

UV absorption spectrum and photodissociation channels of the simplest Criegee intermediate (CH2OO).

PubMed

Dawes, Richard; Jiang, Bin; Guo, Hua

2015-01-14

The lowest-lying singlet states of the simplest Criegee intermediate (CH2OO) have been characterized along the O-O dissociation coordinate using explicitly correlated MRCI-F12 electronic structure theory and large active spaces. It is found that a high-level treatment of dynamic electron-correlation is essential to accurately describe these states. A significant well on the B-state is identified at the MRCI-F12 level with an equilibrium structure that differs substantially from that of the ground X-state. This well is presumably responsible for the apparent vibrational structure in some experimental UV absorption spectra, analogous to the structured Huggins band of the iso-electronic ozone. The B-state potential in the Franck-Condon region is sufficiently accurate that an absorption spectrum calculated with a one-dimensional model agrees remarkably well with experiment.

On the influence of ion exchange on the local structure of the titanosilicate ETS-10.

PubMed

Pavel, Claudiu C; Zibrowius, Bodo; Löffler, Elke; Schmidt, Wolfgang

2007-07-14

The effect of ion exchange with different monovalent cations (NH(4)(+), K(+), Na(+) and Cs(+)) on the local structure of the titanosilicate ETS-10 has been studied by (29)Si MAS NMR and Raman spectroscopy. Although X-ray diffraction shows no significant influence of ion exchange on the long range order, ammonium exchange is found to result in substantial damage to the local structure. Ion exchange experiments with alkali cations under significantly more acidic conditions clearly show that the structural damage brought about by ammonium exchange is not caused by the low pH of the exchange solution. The exchange with potassium and caesium ions also leads to significant changes in the (29)Si NMR and Raman spectra. However, these changes can largely be reversed by sodium back-exchange.

Structural and Functional Differences Between Porcine Aorta and Vena Cava.

PubMed

Mattson, Jeffrey M; Zhang, Yanhang

2017-07-01

Elastin and collagen fibers are the major load-bearing extracellular matrix (ECM) constituents of the vascular wall. Arteries function differently than veins in the circulatory system; however as a result from several treatment options, veins are subjected to sudden elevated arterial pressure. It is thus important to recognize the fundamental structure and function differences between a vein and an artery. Our research compared the relationship between biaxial mechanical function and ECM structure of porcine thoracic aorta and inferior vena cava. Our study suggests that aorta contains slightly more elastin than collagen due to the cyclical extensibility, but vena cava contains almost four times more collagen than elastin to maintain integrity. Furthermore, multiphoton imaging of vena cava showed longitudinally oriented elastin and circumferentially oriented collagen that is recruited at supraphysiologic stress, but low levels of strain. However in aorta, elastin is distributed uniformly, and the primarily circumferentially oriented collagen is recruited at higher levels of strain than vena cava. These structural observations support the functional finding that vena cava is highly anisotropic with the longitude being more compliant and the circumference stiffening substantially at low levels of strain. Overall, our research demonstrates that fiber distributions and recruitment should be considered in addition to relative collagen and elastin contents. Also, the importance of accounting for the structural and functional differences between arteries and veins should be taken into account when considering disease treatment options.

Multiscale Computer Simulation of Failure in Aerogels

NASA Technical Reports Server (NTRS)

Good, Brian S.

2008-01-01

Aerogels have been of interest to the aerospace community primarily for their thermal properties, notably their low thermal conductivities. While such gels are typically fragile, recent advances in the application of conformal polymer layers to these gels has made them potentially useful as lightweight structural materials as well. We have previously performed computer simulations of aerogel thermal conductivity and tensile and compressive failure, with results that are in qualitative, and sometimes quantitative, agreement with experiment. However, recent experiments in our laboratory suggest that gels having similar densities may exhibit substantially different properties. In this work, we extend our original diffusion limited cluster aggregation (DLCA) model for gel structure to incorporate additional variation in DLCA simulation parameters, with the aim of producing DLCA clusters of similar densities that nevertheless have different fractal dimension and secondary particle coordination. We perform particle statics simulations of gel strain on these clusters, and consider the effects of differing DLCA simulation conditions, and the resultant differences in fractal dimension and coordination, on gel strain properties.

Fabricating fiber-reinforced composite posts.

PubMed

Manhart, Jürgen

2011-03-01

Endodontic posts do not increase the strength of the remaining tooth structure in endodontically treated teeth. On the contrary, depending on the post design employed (tapered versus parallel-sided), the root can be weakened relative to the amount of tooth removed during preparation. In many cases, if there has been a high degree of damage to the clinical crown, conservative preparation for an anatomic tapered (biomimetic) post with the incorporation of a ferrule on solid tooth structure is necessary to protect the reaming root structure as well as for the long-term retention of the composite resin core and the definitive restoration. Adhesively luted endodontic posts reinforced with glass or quartz fiber lead to better homogeneous tension distribution when loaded than rigid metal or zirconium oxide ceramic posts. Fiber-reinforced posts also possess advantageous optical properties over metal or metal oxide post systems. The clinician should realize that there are admittedly substantial differences in the mechanical loading capacity of the different fiber-reinforced endodontic posts and should be aware of such differences in order to research and select a suitable post system for use.

Quantitative cardiac SPECT reconstruction with reduced image degradation due to patient anatomy

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

Tsui, B.M.W.; Zhao, X.D.; Gregoriou, G.K.

1994-12-01

Patient anatomy has complicated effects on cardiac SPECT images. The authors investigated reconstruction methods which substantially reduced these effects for improved image quality. A 3D mathematical cardiac-torso (MCAT) phantom which models the anatomical structures in the thorax region were used in the study. The phantom was modified to simulate variations in patient anatomy including regions of natural thinning along the myocardium, body size, diaphragmatic shape, gender, and size and shape of breasts for female patients. Distributions of attenuation coefficients and Tl-201 uptake in different organs in a normal patient were also simulated. Emission projection data were generated from the phantomsmore » including effects of attenuation and detector response. The authors have observed the attenuation-induced artifacts caused by patient anatomy in the conventional FBP reconstructed images. Accurate attenuation compensation using iterative reconstruction algorithms and attenuation maps substantially reduced the image artifacts and improved quantitative accuracy. They conclude that reconstruction methods which accurately compensate for non-uniform attenuation can substantially reduce image degradation caused by variations in patient anatomy in cardiac SPECT.« less

Deciduous and evergreen trees differ in juvenile biomass allometries because of differences in allocation to root storage.

PubMed

Tomlinson, Kyle W; van Langevelde, Frank; Ward, David; Bongers, Frans; da Silva, Dulce Alves; Prins, Herbert H T; de Bie, Steven; Sterck, Frank J

2013-08-01

Biomass partitioning for resource conservation might affect plant allometry, accounting for a substantial amount of unexplained variation in existing plant allometry models. One means of resource conservation is through direct allocation to storage in particular organs. In this study, storage allocation and biomass allometry of deciduous and evergreen tree species from seasonal environments were considered. It was expected that deciduous species would have greater allocation to storage in roots to support leaf regrowth in subsequent growing seasons, and consequently have lower scaling exponents for leaf to root and stem to root partitioning, than evergreen species. It was further expected that changes to root carbohydrate storage and biomass allometry under different soil nutrient supply conditions would be greater for deciduous species than for evergreen species. Root carbohydrate storage and organ biomass allometries were compared for juveniles of 20 savanna tree species of different leaf habit (nine evergreen, 11 deciduous) grown in two nutrient treatments for periods of 5 and 20 weeks (total dry mass of individual plants ranged from 0·003 to 258·724 g). Deciduous species had greater root non-structural carbohydrate than evergreen species, and lower scaling exponents for leaf to root and stem to root partitioning than evergreen species. Across species, leaf to stem scaling was positively related, and stem to root scaling was negatively related to root carbohydrate concentration. Under lower nutrient supply, trees displayed increased partitioning to non-structural carbohydrate, and to roots and leaves over stems with increasing plant size, but this change did not differ between leaf habits. Substantial unexplained variation in biomass allometry of woody species may be related to selection for resource conservation against environmental stresses, such as resource seasonality. Further differences in plant allometry could arise due to selection for different types of biomass allocation in response to different environmental stressors (e.g. fire vs. herbivory).

Macroscopic Crosslinked Neat Carbon Nanotube Materials and CNT/Carbon Fiber Hybrid Composites: Supermolecular Structure and New Failure Mode Study

DTIC Science & Technology

2015-10-01

Materials; CRC Press, 1997. (70) Zhang, Y.; Zheng, L.; Sun , G.; Zhan, Z.; Liao, K. Failure Mechanisms of Carbon Nanotube Fibers under Different...Buehler, M. J. Mesoscale Modeling of Mechanics of Carbon Nanotubes: Self-Assembly, Self-Folding, and Fracture . J. Mater. Res. 2006, 21 (11), 2855–2869...close surface contact between CNTs to substantially improve the load transfer and mechanical properties. We also revealed that extremely low

Nitrogen Incorporation Effects On Site-Controlled Quantum Dots

NASA Astrophysics Data System (ADS)

Juska, G.; Dimastrodonato, V.; Mereni, L. O.; Pelucchi, E.

2011-12-01

We report here on the optical properties of site-controlled diluted nitride In0.25Ga0.75As1-xNx quantum dots grown by metalorganic vapour phase epitaxy (MOVPE). We show photoluminescence energy shift as a function of nitrogen precursor U-dimethylhydrazine, with a maximum value of 35 meV achieved. Optical features, substantially different from the counterpart nitrogen-free dots, are presented: an antibinding biexciton, a large distribution of lifetimes, significantly reduced fine structure splitting.

Deconstructing white matter connectivity of human amygdala nuclei with thalamus and cortex subdivisions in vivo.

PubMed

Abivardi, Aslan; Bach, Dominik R

2017-08-01

Structural alterations in long-range amygdala connections are proposed to crucially underlie several neuropsychiatric disorders. While progress has been made in elucidating the function of these connections, our understanding of their structure in humans remains sparse and non-systematic. Harnessing diffusion-weighted imaging and probabilistic tractography in humans, we investigate connections between two main amygdala nucleus groups, thalamic nuclei, and cortex. We first parcellated amygdala into deep (basolateral) and superficial (centrocortical) nucleus groups, and thalamus into six subregions, using previously established protocols based on connectivity. Cortex was parcellated based on T1-weighted images. We found substantial amygdala connections to thalamus, with different patterns for the two amygdala nuclei. Crucially, we describe direct subcortical connections between amygdala and paraventricular thalamus. Different from rodents but similar to non-human primates, these are more pronounced for basolateral than centrocortical amygdala. Substantial white-matter connectivity between amygdala and visual pulvinar is also more pronounced for basolateral amygdala. Furthermore, we establish detailed connectivity profiles for basolateral and centrocortical amygdala to cortical regions. These exhibit cascadic connections with sensory cortices as suggested previously based on tracer methods in non-human animals. We propose that the quantitative connectivity profiles provided here may guide future work on normal and pathological function of human amygdala. Hum Brain Mapp 38:3927-3940, 2017. © 2017 Wiley Periodicals, Inc. © 2017 The Authors Human Brain Mapping Published by Wiley Periodicals, Inc.

Deconstructing white matter connectivity of human amygdala nuclei with thalamus and cortex subdivisions in vivo

PubMed Central

2017-01-01

Abstract Structural alterations in long‐range amygdala connections are proposed to crucially underlie several neuropsychiatric disorders. While progress has been made in elucidating the function of these connections, our understanding of their structure in humans remains sparse and non‐systematic. Harnessing diffusion‐weighted imaging and probabilistic tractography in humans, we investigate connections between two main amygdala nucleus groups, thalamic nuclei, and cortex. We first parcellated amygdala into deep (basolateral) and superficial (centrocortical) nucleus groups, and thalamus into six subregions, using previously established protocols based on connectivity. Cortex was parcellated based on T1‐weighted images. We found substantial amygdala connections to thalamus, with different patterns for the two amygdala nuclei. Crucially, we describe direct subcortical connections between amygdala and paraventricular thalamus. Different from rodents but similar to non‐human primates, these are more pronounced for basolateral than centrocortical amygdala. Substantial white‐matter connectivity between amygdala and visual pulvinar is also more pronounced for basolateral amygdala. Furthermore, we establish detailed connectivity profiles for basolateral and centrocortical amygdala to cortical regions. These exhibit cascadic connections with sensory cortices as suggested previously based on tracer methods in non‐human animals. We propose that the quantitative connectivity profiles provided here may guide future work on normal and pathological function of human amygdala. Hum Brain Mapp 38:3927–3940, 2017. © 2017 Wiley Periodicals, Inc. PMID:28512761

Bacterial diversity across a highly stratified ecosystem: A salt-wedge Mediterranean estuary.

PubMed

Korlević, M; Šupraha, L; Ljubešić, Z; Henderiks, J; Ciglenečki, I; Dautović, J; Orlić, S

2016-09-01

Highly stratified Mediterranean estuaries are unique environments where the tidal range is low and the tidal currents are almost negligible. The main characteristics of these environments are strong salinity gradients and other environmental parameters. In this study, 454 pyrosequencing of the 16S rRNA gene in combination with catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) was used to estimate the bacterial diversity across the Krka estuary in February and July 2013. The comparison of the data derived from these two techniques resulted in a significant but weak positive correlation (R=0.28) indicating a substantial difference in the bacterial community structure, depending on the applied method. The phytoplankton bloom observed in February was identified as one of the main factors shaping the bacterial community structure between the two environmentally contrasting sampling months. Roseobacter, Bacteroidetes and Gammaproteobacteria differed substantially between February and July. Typical freshwater bacterial classes (Actinobacteria and Betaproteobacteria) showed strong vertical distribution patterns depending on the salinity gradient. Cyanobacteria decreased in abundance in February due to competition with phytoplankton, while the SAR11 clade increased its abundance in July as a result of a better adaptation toward more oligotrophic conditions. The results provided the first detailed insight into the bacterial diversity in a highly stratified Mediterranean karstic estuary. Copyright © 2016 Elsevier GmbH. All rights reserved.

Transforming growth factor alpha, Shope fibroma growth factor, and vaccinia growth factor can replace myxoma growth factor in the induction of myxomatosis in rabbits.

PubMed

Opgenorth, A; Nation, N; Graham, K; McFadden, G

1993-02-01

The epidermal growth factor (EGF) homologues encoded by vaccinia virus, myxoma virus, and malignant rabbit fibroma virus have been shown to contribute to the pathogenicity of virus infection upon inoculation of susceptible hosts. However, since the primary structures of these growth factors and the disease profiles induced by different poxvirus genera vary substantially, the degree to which the various EGF homologues perform similar roles in viral pathogenesis remains unclear. In order to determine whether different EGF-like growth factors can perform qualitatively similar functions in the induction of myxomatosis in rabbits, we created recombinant myxoma virus variants in which the native growth factor, myxoma growth factor (MGF), was disrupted and replaced with either vaccinia virus growth factor, Shope fibroma growth factor, or rat transforming growth factor alpha. Unlike the control virus containing an inactivated MGF gene, which caused marked attenuation of the disease syndrome and substantially less proliferation of the epithelial cell layers in the conjunctiva and respiratory tract, the recombinant myxoma virus strains expressing heterologous growth factors produced infections which were both clinically and histopathologically indistinguishable from wild-type myxomatosis. We conclude that these poxviral and cellular EGF-like growth factors, which are diverse with respect to primary structure and origin, have similar biological functions in the context of myxoma virus pathogenesis and are mitogenic for the same target cells.

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.

Consensus between Pipelines in Structural Brain Networks

PubMed Central

Parker, Christopher S.; Deligianni, Fani; Cardoso, M. Jorge; Daga, Pankaj; Modat, Marc; Dayan, Michael; Clark, Chris A.

2014-01-01

Structural brain networks may be reconstructed from diffusion MRI tractography data and have great potential to further our understanding of the topological organisation of brain structure in health and disease. Network reconstruction is complex and involves a series of processesing methods including anatomical parcellation, registration, fiber orientation estimation and whole-brain fiber tractography. Methodological choices at each stage can affect the anatomical accuracy and graph theoretical properties of the reconstructed networks, meaning applying different combinations in a network reconstruction pipeline may produce substantially different networks. Furthermore, the choice of which connections are considered important is unclear. In this study, we assessed the similarity between structural networks obtained using two independent state-of-the-art reconstruction pipelines. We aimed to quantify network similarity and identify the core connections emerging most robustly in both pipelines. Similarity of network connections was compared between pipelines employing different atlases by merging parcels to a common and equivalent node scale. We found a high agreement between the networks across a range of fiber density thresholds. In addition, we identified a robust core of highly connected regions coinciding with a peak in similarity across network density thresholds, and replicated these results with atlases at different node scales. The binary network properties of these core connections were similar between pipelines but showed some differences in atlases across node scales. This study demonstrates the utility of applying multiple structural network reconstrution pipelines to diffusion data in order to identify the most important connections for further study. PMID:25356977

Structurally compliant microbearing devices and methods thereof

NASA Technical Reports Server (NTRS)

Boedo, Stephen (Inventor); Grande, William (Inventor)

2011-01-01

A microbearing device includes at least one inner bearing structure, at least one outer bearing structure, and one or more fasteners. Each of the one or more fasteners is connected between the inner bearing structure and the outer bearing structure and the inner bearing structure is substantially elastic.

Using the structure of social networks to map inter-agency relationships in public health services.

PubMed

West, Robert M; House, Allan O; Keen, Justin; Ward, Vicky L

2015-11-01

This article investigates network governance in the context of health and wellbeing services in England, focussing on relationships between managers in a range of services. There are three aims, namely to investigate, (i) the configurations of networks, (ii) the stability of network relationships over time and, (iii) the balance between formal and informal ties that underpin inter-agency relationships. Latent position cluster network models were used to characterise relationships. Managers were asked two questions, both designed to characterise informal relationships. The resulting networks differed substantially from one another in membership. Managers described networks of relationships that spanned organisational boundaries, and that changed substantially over time. The findings suggest that inter-agency co-ordination depends more on informal than on formal relationships. Copyright © 2015 Elsevier Ltd. All rights reserved.

Sequence and Structure Dependent DNA-DNA Interactions

NASA Astrophysics Data System (ADS)

Kopchick, Benjamin; Qiu, Xiangyun

Molecular forces between dsDNA strands are largely dominated by electrostatics and have been extensively studied. Quantitative knowledge has been accumulated on how DNA-DNA interactions are modulated by varied biological constituents such as ions, cationic ligands, and proteins. Despite its central role in biology, the sequence of DNA has not received substantial attention and ``random'' DNA sequences are typically used in biophysical studies. However, ~50% of human genome is composed of non-random-sequence DNAs, particularly repetitive sequences. Furthermore, covalent modifications of DNA such as methylation play key roles in gene functions. Such DNAs with specific sequences or modifications often take on structures other than the canonical B-form. Here we present series of quantitative measurements of the DNA-DNA forces with the osmotic stress method on different DNA sequences, from short repeats to the most frequent sequences in genome, and to modifications such as bromination and methylation. We observe peculiar behaviors that appear to be strongly correlated with the incurred structural changes. We speculate the causalities in terms of the differences in hydration shell and DNA surface structures.

Molecular And Structural Basis of Cytokine Receptor Pleiotropy in the Interleukin-4/13 System

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

LaPorte, S.L.; Juo, Z.S.; Vaclavikova, J.

2009-05-20

Interleukin-4 and Interleukin-13 are cytokines critical to the development of T cell-mediated humoral immune responses, which are associated with allergy and asthma, and exert their actions through three different combinations of shared receptors. Here we present the crystal structures of the complete set of type I (IL-4R{alpha}/{gamma}{sub c}/IL-4) and type II (IL-4R/IL-13R{alpha}1/IL-4, IL-4R{alpha}/IL-13R{alpha}1/IL-13) ternary signaling complexes. The type I complex reveals a structural basis for {gamma}{sub c}'s ability to recognize six different {gamma}{sub c}-cytokines. The two type II complexes utilize an unusual top-mounted Ig-like domain on IL-13R{alpha}1 for a novel mode of cytokine engagement that contributes to a reversal inmore » the IL-4 versus IL-13 ternary complex assembly sequences, which are mediated through substantially different recognition chemistries. We also show that the type II receptor heterodimer signals with different potencies in response to IL-4 versus IL-13 and suggest that the extracellular cytokine-receptor interactions are modulating intracellular membrane-proximal signaling events.« less

Density Functional Theory (DFT) study of β-Hairpins in Antiparallel β-Sheets, A New Classification Based upon H-bond Topology

PubMed Central

Roy, Dipankar; Pohl, Gabor; Ali-Torres, Jorge; Marianski, Mateusz; Dannenberg, J. J.

2012-01-01

We present a new classification of β-turns specific to antiparallel β-sheets based upon the topology of H-bond formation. This classification results from ONIOM calculations using B3LYP/D95** DFT and AM1 semiempirical calculations as the high and low levels respectively. We chose acetyl(Ala)6NH2 as a model system as it is the simplest all alanine system that can form all the H-bonds required for a β-turn in a sheet. Of the ten different conformation we have found, the most stable structures have C7 cyclic H-bonds in place of the C10 interactions specified in the classic definition. Also, the chiralities specified for the i+1st and i+2nd residues in the classic definition disappear when the structures are optimized using our techniques, as the energetic differences between the four diastereomers of each structure are not substantial for eight of the ten conformations. PMID:22731966

Validation of the World Health Organization's Quality of Life Questionnaire with parents of children with autistic disorder.

PubMed

Dardas, Latefa A; Ahmad, Muayyad M

2014-09-01

The World Health Organization's Quality of Life Questionnaire-BREF (WHOQOL-BREF) has been used in many studies that target parents of children with Autistic Disorder. However, the measure has yet to be validated and adapted to this sample group whose daily experiences are considered substantially different from those of parents of children with typical development and parents of children with other disabilities. Therefore, this study was designed to examine the psychometric properties and the theoretical structure of the WHOQOL-BREF with a sample of 184 parents of children with Autistic Disorder. The factor structure for the WHOQOL-BREF was examined using exploratory and confirmatory factor analyses. Our analyses provided no evidence of a better model than the original 4-domain model. Nevertheless, some items in the measure were re-distributed to different domains based on theoretical meanings and/or clean loading criteria. The new model structure gained the measure's required validity with parents of children with Autistic Disorder.

Density functional theory study of β-hairpins in antiparallel β-sheets, a new classification based upon H-bond topology.

PubMed

Roy, Dipankar; Pohl, Gabor; Ali-Torres, Jorge; Marianski, Mateusz; Dannenberg, J J

2012-07-10

We present a new classification of β-turns specific to antiparallel β-sheets based upon the topology of H-bond formation. This classification results from ONIOM calculations using B3LYP/D95** density functional theory and AM1 semiempirical calculations as the high and low levels, respectively. We chose acetyl(Ala)(6)NH(2) as a model system as it is the simplest all-alanine system that can form all the H-bonds required for a β-turn in a sheet. Of the 10 different conformations we have found, the most stable structures have C(7) cyclic H-bonds in place of the C(10) interactions specified in the classic definition. Also, the chiralities specified for residues i + 1 and i + 2 in the classic definition disappear when the structures are optimized using our techniques, as the energetic differences among the four diastereomers of each structure are not substantial for 8 of the 10 conformations.

Reconceptualizing the classification of PNAS articles

PubMed Central

Airoldi, Edoardo M.; Erosheva, Elena A.; Fienberg, Stephen E.; Joutard, Cyrille; Love, Tanzy; Shringarpure, Suyash

2010-01-01

PNAS article classification is rooted in long-standing disciplinary divisions that do not necessarily reflect the structure of modern scientific research. We reevaluate that structure using latent pattern models from statistical machine learning, also known as mixed-membership models, that identify semantic structure in co-occurrence of words in the abstracts and references. Our findings suggest that the latent dimensionality of patterns underlying PNAS research articles in the Biological Sciences is only slightly larger than the number of categories currently in use, but it differs substantially in the content of the categories. Further, the number of articles that are listed under multiple categories is only a small fraction of what it should be. These findings together with the sensitivity analyses suggest ways to reconceptualize the organization of papers published in PNAS. PMID:21078953

Local self-uniformity in photonic networks.

PubMed

Sellers, Steven R; Man, Weining; Sahba, Shervin; Florescu, Marian

2017-02-17

The interaction of a material with light is intimately related to its wavelength-scale structure. Simple connections between structure and optical response empower us with essential intuition to engineer complex optical functionalities. Here we develop local self-uniformity (LSU) as a measure of a random network's internal structural similarity, ranking networks on a continuous scale from crystalline, through glassy intermediate states, to chaotic configurations. We demonstrate that complete photonic bandgap structures possess substantial LSU and validate LSU's importance in gap formation through design of amorphous gyroid structures. Amorphous gyroid samples are fabricated via three-dimensional ceramic printing and the bandgaps experimentally verified. We explore also the wing-scale structuring in the butterfly Pseudolycaena marsyas and show that it possesses substantial amorphous gyroid character, demonstrating the subtle order achieved by evolutionary optimization and the possibility of an amorphous gyroid's self-assembly.

Local self-uniformity in photonic networks

NASA Astrophysics Data System (ADS)

Sellers, Steven R.; Man, Weining; Sahba, Shervin; Florescu, Marian

2017-02-01

The interaction of a material with light is intimately related to its wavelength-scale structure. Simple connections between structure and optical response empower us with essential intuition to engineer complex optical functionalities. Here we develop local self-uniformity (LSU) as a measure of a random network's internal structural similarity, ranking networks on a continuous scale from crystalline, through glassy intermediate states, to chaotic configurations. We demonstrate that complete photonic bandgap structures possess substantial LSU and validate LSU's importance in gap formation through design of amorphous gyroid structures. Amorphous gyroid samples are fabricated via three-dimensional ceramic printing and the bandgaps experimentally verified. We explore also the wing-scale structuring in the butterfly Pseudolycaena marsyas and show that it possesses substantial amorphous gyroid character, demonstrating the subtle order achieved by evolutionary optimization and the possibility of an amorphous gyroid's self-assembly.

Lightweight composite reflectors for space optics

NASA Astrophysics Data System (ADS)

Williams, Brian E.; McNeal, Shawn R.; Ono, Russell M.

1998-01-01

The primary goal of this work was to advance the state of the art in lightweight, high optical quality reflectors for space- and Earth-based telescopes. This was accomplished through the combination of a precision silicon carbide (SiC) reflector surface and a high specific strength, low-mass SiC structural support. Reducing the mass of components launched into space can lead to substantial cost savings, but an even greater benefit of lightweight reflectors for both space- and Earth-based optics applications is the fact that they require far less complex and less expensive positioning systems. While Ultramet is not the first company to produce SiC by chemical vapor deposition (CVD) for reflector surfaces, it is the first to propose and demonstrate a lightweight, open-cell SiC structural foam that can support a thin layer of the highly desirable polished SiC reflector material. SiC foam provides a substantial structural and mass advantage over conventional honeycomb supports and alternative finned structures. The result is a reflector component that meets or exceeds the optical properties of current high-quality glass, ceramic, and metal reflectors while maintaining a substantially lower areal density.

Evaluation of Denoising Strategies to Address Motion-Correlated Artifacts in Resting-State Functional Magnetic Resonance Imaging Data from the Human Connectome Project

PubMed Central

Kandala, Sridhar; Nolan, Dan; Laumann, Timothy O.; Power, Jonathan D.; Adeyemo, Babatunde; Harms, Michael P.; Petersen, Steven E.; Barch, Deanna M.

2016-01-01

Abstract Like all resting-state functional connectivity data, the data from the Human Connectome Project (HCP) are adversely affected by structured noise artifacts arising from head motion and physiological processes. Functional connectivity estimates (Pearson's correlation coefficients) were inflated for high-motion time points and for high-motion participants. This inflation occurred across the brain, suggesting the presence of globally distributed artifacts. The degree of inflation was further increased for connections between nearby regions compared with distant regions, suggesting the presence of distance-dependent spatially specific artifacts. We evaluated several denoising methods: censoring high-motion time points, motion regression, the FMRIB independent component analysis-based X-noiseifier (FIX), and mean grayordinate time series regression (MGTR; as a proxy for global signal regression). The results suggest that FIX denoising reduced both types of artifacts, but left substantial global artifacts behind. MGTR significantly reduced global artifacts, but left substantial spatially specific artifacts behind. Censoring high-motion time points resulted in a small reduction of distance-dependent and global artifacts, eliminating neither type. All denoising strategies left differences between high- and low-motion participants, but only MGTR substantially reduced those differences. Ultimately, functional connectivity estimates from HCP data showed spatially specific and globally distributed artifacts, and the most effective approach to address both types of motion-correlated artifacts was a combination of FIX and MGTR. PMID:27571276

Developmental plasticity of mating calls enables acoustic communication in diverse environments

PubMed Central

Beckers, Oliver M; Schul, Johannes

2008-01-01

Male calls of the katydid Neoconocephalus triops exhibit substantial developmental plasticity in two parameters: (i) calls of winter males are continuous and lack the verse structure of summer calls and (ii) at equal temperatures, summer males produce calls with a substantially higher pulse rate than winter males. We raised female N. triops under conditions that reliably induced either summer or winter phenotype and tested their preferences for the call parameters that differ between summer and winter males. Neither generation was selective for the presence of verses, but females had strong preferences for pulse rates: only a narrow range of pulse rates was attractive. The attractive ranges did not differ between summer and winter females. Both male pulse rate and female preference for pulse rate changed with ambient temperature, but female preference changed more than the male calls. As a result, the summer call was attractive only at 25°C, whereas the slower winter call was attractive only at 20°C. Thus, developmental plasticity of male calls compensates for differences in temperature dependency between calls and preferences and enables the communication system to function in heterogeneous environments. The potential role of call plasticity during the invasion of new habitats is discussed. PMID:18302998

The sequential structure of brain activation predicts skill.

PubMed

Anderson, John R; Bothell, Daniel; Fincham, Jon M; Moon, Jungaa

2016-01-29

In an fMRI study, participants were trained to play a complex video game. They were scanned early and then again after substantial practice. While better players showed greater activation in one region (right dorsal striatum) their relative skill was better diagnosed by considering the sequential structure of whole brain activation. Using a cognitive model that played this game, we extracted a characterization of the mental states that are involved in playing a game and the statistical structure of the transitions among these states. There was a strong correspondence between this measure of sequential structure and the skill of different players. Using multi-voxel pattern analysis, it was possible to recognize, with relatively high accuracy, the cognitive states participants were in during particular scans. We used the sequential structure of these activation-recognized states to predict the skill of individual players. These findings indicate that important features about information-processing strategies can be identified from a model-based analysis of the sequential structure of brain activation. Copyright © 2015 Elsevier Ltd. All rights reserved.

Genetic structure of the crown-of-thorns seastar in the Pacific Ocean, with focus on Guam.

PubMed

Tusso, Sergio; Morcinek, Kerstin; Vogler, Catherine; Schupp, Peter J; Caballes, Ciemon F; Vargas, Sergio; Wörheide, Gert

2016-01-01

Population outbreaks of the corallivorous crown-of-thorns seastar (COTS), Acanthaster 'planci' L., are among the most important biological disturbances of tropical coral reefs. Over the past 50 years, several devastating outbreaks have been documented around Guam, an island in the western Pacific Ocean. Previous analyses have shown that in the Pacific Ocean, COTS larval dispersal may be geographically restricted to certain regions. Here, we assess the genetic structure of Pacific COTS populations and compared samples from around Guam with a number of distant localities in the Pacific Ocean, and focused on determining the degree of genetic structure among populations previously considered to be isolated. Using microsatellites, we document substantial genetic structure between 14 localities from different geographical regions in the Pacific Ocean. Populations from the 14 locations sampled were found to be structured in three significantly differentiated groups: (1) all locations immediately around Guam, as well as Kingman Reef and Swains Island; (2) Japan, Philippines, GBR and Vanuatu; and (3) Johnston Atoll, which was significantly different from all other localities. The lack of genetic differentiation between Guam and extremely distant populations from Kingman Reef and Swains Island suggests potential long-distance dispersal of COTS in the Pacific.

Origin of structural analogies and differences between the atomic structures of GeSe4 and GeS4 glasses: A first principles study.

PubMed

Bouzid, Assil; Le Roux, Sébastien; Ori, Guido; Boero, Mauro; Massobrio, Carlo

2015-07-21

First-principles molecular dynamics simulations based on density functional theory are employed for a comparative study of structural and bonding properties of two stoichiometrically identical chalcogenide glasses, GeSe4 and GeS4. Two periodic cells of 120 and 480 atoms are adopted. Both glasses feature a coexistence of Ge-centered tetrahedra and Se(S) homopolar connections. Results obtained for N = 480 indicate substantial differences at the level of the Se(S) environment, since Ge-Se-Se connections are more frequent than the corresponding Ge-S-S ones. The presence of a more prominent first sharp diffraction peak in the total neutron structure factor of glassy GeS4 is rationalized in terms of a higher number of large size rings, accounting for extended Ge-Se correlations. Both the electronic density of states and appropriate electronic localization tools provide evidence of a higher ionic character of Ge-S bonds when compared to Ge-Se bonds. An interesting byproduct of these investigations is the occurrence of discernible size effects that affect structural motifs involving next nearest neighbor distances, when 120 or 480 atoms are used.

The assemblage composition and structure of swimming crabs (Portunoidea) in continental shelf waters of southeastern Brazil

NASA Astrophysics Data System (ADS)

Andrade, L. S.; Frameschi, I. F.; Costa, R. C.; Castilho, A. L.; Fransozo, A.

2015-02-01

Three regions along the Brazilian coast characterized by the occurrence of contrasting natural phenomena, such as upwellings and continental input, were surveyed to determine the composition and structure of the assemblage of swimming crabs. Twelve monthly collections were undertaken (July 2010 to June 2011) in Macaé, Rio de Janeiro (MAC); Ubatuba, São Paulo (UBA); and São Francisco do Sul, Santa Catarina (SFS). The lowest values ​​of the phi sediment grain size measure, bottom temperature and the highest values of organic matter and salinity were measured in MAC. In all, 10,686 individuals were collected, belonging to six species of Portunoidea: Arenaeus cribrarius, Callinectes danae, Callinectes ornatus, Callinectes sapidus, Achelous spinicarpus and Achelous spinimanus. A Multiple Response Permutation Procedure (MRPP) test indicated that the species composition differed significantly among the sampling sites, showing substantial heterogeneity in the composition and abundance of species among regions. The results suggest that C. danae was more abundant in waters with lower salinity and lower organic matter content. In contrast, A. spinimanus is positively correlated with these factors, showing a greater abundance under the opposite conditions. Callinectes ornatus appeared not to show strong selectivity for particular habitat characteristics. We conclude from these findings that areas affected by different phenomena produce changes in the composition and abundance of the assemblage of Portunoidea. Although the strength of eutrophication differs between UBA and MAC, the substantial continental inflow affecting SFS favors the development of species that complete their life cycle in the estuary.

Assessing hippocampal development and language in early childhood: Evidence from a new application of the Automatic Segmentation Adapter Tool.

PubMed

Lee, Joshua K; Nordahl, Christine W; Amaral, David G; Lee, Aaron; Solomon, Marjorie; Ghetti, Simona

2015-11-01

Volumetric assessments of the hippocampus and other brain structures during childhood provide useful indices of brain development and correlates of cognitive functioning in typically and atypically developing children. Automated methods such as FreeSurfer promise efficient and replicable segmentation, but may include errors which are avoided by trained manual tracers. A recently devised automated correction tool that uses a machine learning algorithm to remove systematic errors, the Automatic Segmentation Adapter Tool (ASAT), was capable of substantially improving the accuracy of FreeSurfer segmentations in an adult sample [Wang et al., 2011], but the utility of ASAT has not been examined in pediatric samples. In Study 1, the validity of FreeSurfer and ASAT corrected hippocampal segmentations were examined in 20 typically developing children and 20 children with autism spectrum disorder aged 2 and 3 years. We showed that while neither FreeSurfer nor ASAT accuracy differed by disorder or age, the accuracy of ASAT corrected segmentations were substantially better than FreeSurfer segmentations in every case, using as few as 10 training examples. In Study 2, we applied ASAT to 89 typically developing children aged 2 to 4 years to examine relations between hippocampal volume, age, sex, and expressive language. Girls had smaller hippocampi overall, and in left hippocampus this difference was larger in older than younger girls. Expressive language ability was greater in older children, and this difference was larger in those with larger hippocampi, bilaterally. Overall, this research shows that ASAT is highly reliable and useful to examinations relating behavior to hippocampal structure. © 2015 Wiley Periodicals, Inc.

How does conversion of natural tropical rainforest ecosystems affect soil bacterial and fungal communities in the Nile river watershed of Uganda?

PubMed

Alele, Peter O; Sheil, Douglas; Surget-Groba, Yann; Lingling, Shi; Cannon, Charles H

2014-01-01

Uganda's forests are globally important for their conservation values but are under pressure from increasing human population and consumption. In this study, we examine how conversion of natural forest affects soil bacterial and fungal communities. Comparisons in paired natural forest and human-converted sites among four locations indicated that natural forest soils consistently had higher pH, organic carbon, nitrogen, and calcium, although variation among sites was large. Despite these differences, no effect on the diversity of dominant taxa for either bacterial or fungal communities was detected, using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). Composition of fungal communities did generally appear different in converted sites, but surprisingly, we did not observe a consistent pattern among sites. The spatial distribution of some taxa and community composition was associated with soil pH, organic carbon, phosphorus and sodium, suggesting that changes in soil communities were nuanced and require more robust metagenomic methods to understand the various components of the community. Given the close geographic proximity of the paired sampling sites, the similarity between natural and converted sites might be due to continued dispersal between treatments. Fungal communities showed greater environmental differentiation than bacterial communities, particularly according to soil pH. We detected biotic homogenization in converted ecosystems and substantial contribution of β-diversity to total diversity, indicating considerable geographic structure in soil biota in these forest communities. Overall, our results suggest that soil microbial communities are relatively resilient to forest conversion and despite a substantial and consistent change in the soil environment, the effects of conversion differed widely among sites. The substantial difference in soil chemistry, with generally lower nutrient quantity in converted sites, does bring into question, how long this resilience will last.

How Does Conversion of Natural Tropical Rainforest Ecosystems Affect Soil Bacterial and Fungal Communities in the Nile River Watershed of Uganda?

PubMed Central

Alele, Peter O.; Sheil, Douglas; Surget-Groba, Yann; Lingling, Shi; Cannon, Charles H.

2014-01-01

Uganda's forests are globally important for their conservation values but are under pressure from increasing human population and consumption. In this study, we examine how conversion of natural forest affects soil bacterial and fungal communities. Comparisons in paired natural forest and human-converted sites among four locations indicated that natural forest soils consistently had higher pH, organic carbon, nitrogen, and calcium, although variation among sites was large. Despite these differences, no effect on the diversity of dominant taxa for either bacterial or fungal communities was detected, using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). Composition of fungal communities did generally appear different in converted sites, but surprisingly, we did not observe a consistent pattern among sites. The spatial distribution of some taxa and community composition was associated with soil pH, organic carbon, phosphorus and sodium, suggesting that changes in soil communities were nuanced and require more robust metagenomic methods to understand the various components of the community. Given the close geographic proximity of the paired sampling sites, the similarity between natural and converted sites might be due to continued dispersal between treatments. Fungal communities showed greater environmental differentiation than bacterial communities, particularly according to soil pH. We detected biotic homogenization in converted ecosystems and substantial contribution of β-diversity to total diversity, indicating considerable geographic structure in soil biota in these forest communities. Overall, our results suggest that soil microbial communities are relatively resilient to forest conversion and despite a substantial and consistent change in the soil environment, the effects of conversion differed widely among sites. The substantial difference in soil chemistry, with generally lower nutrient quantity in converted sites, does bring into question, how long this resilience will last. PMID:25118069

Assembly, maturation and three-dimensional helical structure of the teratogenic rubella virus

PubMed Central

Mangala Prasad, Vidya

2017-01-01

Viral infections during pregnancy are a significant cause of infant morbidity and mortality. Of these, rubella virus infection is a well-substantiated example that leads to miscarriages or severe fetal defects. However, structural information about the rubella virus has been lacking due to the pleomorphic nature of the virions. Here we report a helical structure of rubella virions using cryo-electron tomography. Sub-tomogram averaging of the surface spikes established the relative positions of the viral glycoproteins, which differed from the earlier icosahedral models of the virus. Tomographic analyses of in vitro assembled nucleocapsids and virions provide a template for viral assembly. Comparisons of immature and mature virions show large rearrangements in the glycoproteins that may be essential for forming the infectious virions. These results present the first known example of a helical membrane-enveloped virus, while also providing a structural basis for its assembly and maturation pathway. PMID:28575072

Assembly, maturation and three-dimensional helical structure of the teratogenic rubella virus.

PubMed

Mangala Prasad, Vidya; Klose, Thomas; Rossmann, Michael G

2017-06-01

Viral infections during pregnancy are a significant cause of infant morbidity and mortality. Of these, rubella virus infection is a well-substantiated example that leads to miscarriages or severe fetal defects. However, structural information about the rubella virus has been lacking due to the pleomorphic nature of the virions. Here we report a helical structure of rubella virions using cryo-electron tomography. Sub-tomogram averaging of the surface spikes established the relative positions of the viral glycoproteins, which differed from the earlier icosahedral models of the virus. Tomographic analyses of in vitro assembled nucleocapsids and virions provide a template for viral assembly. Comparisons of immature and mature virions show large rearrangements in the glycoproteins that may be essential for forming the infectious virions. These results present the first known example of a helical membrane-enveloped virus, while also providing a structural basis for its assembly and maturation pathway.

The statistical geometry of transcriptome divergence in cell-type evolution and cancer.

PubMed

Liang, Cong; Forrest, Alistair R R; Wagner, Günter P

2015-01-14

In evolution, body plan complexity increases due to an increase in the number of individualized cell types. Yet, there is very little understanding of the mechanisms that produce this form of organismal complexity. One model for the origin of novel cell types is the sister cell-type model. According to this model, each cell type arises together with a sister cell type through specialization from an ancestral cell type. A key prediction of the sister cell-type model is that gene expression profiles of cell types exhibit tree structure. Here we present a statistical model for detecting tree structure in transcriptomic data and apply it to transcriptomes from ENCODE and FANTOM5. We show that transcriptomes of normal cells harbour substantial amounts of hierarchical structure. In contrast, cancer cell lines have less tree structure, suggesting that the emergence of cancer cells follows different principles from that of evolutionary cell-type origination.

Response measurements for two building structures excited by noise from a large horizontal axis wind turbine generator

NASA Technical Reports Server (NTRS)

Hubbard, H. H.; Shepherd, K. P.

1984-01-01

Window and wall acceleration measurements and interior noise measurements ere made for two different building structures during excitation by noise from the WTS-4 horizontal axis wind turbine generator operating in a normal power generation mode. With turbine noise input pulses resulted in acceleration pulses for the wall and window elements of the two tests buildings. Response spectra suggest that natural vibration modes of the structures are excited. Responses of a house trailer were substantially greater than those for a building of sturdier construction. Peak acceleration values correlate well with similar data for houses excited by flyover noise from commercial and military airplanes and helicopters, and sonic booms from supersonic aircraft. Interior noise spectra have peaks at frequencies corresponding to structural vibration modes and room standing waves; and the levels for particular frequencies and locations can be higher than the outside levels.

A computational prediction of structure and function of novel homologue of Arabidopsis thaliana Vps51/Vps67 subunit in Corchorus olitorius.

PubMed

Zaman, Aubhishek; Fancy, Nurun Nahar

2012-12-01

Vps mediated vesicular transport is important for transferring macromolecules trapped inside a vesicle. Although highly abundant, Vps shows tremendous sequence variation among diverse array of species. However, this difference in sequence, which seems to also translate into substantial functional variation, is hardly characterized in Corchorus spp. Here, our computational study investigates structural and functional features of one of the Vps subunit namely Vps51/Vps67 in C. olitorius. Broad scale structural characterization revealed novel information about the overall Vps structure and binding sites. Moreover, functional analyses indicate interaction partners which were unexplored to date. Since membrane trafficking is essentially associated with nutrient uptake and chemical de-toxification, characterization of the Vps subunit can well provide us with better insight into important agronomic traits such as stress response, immune response and phytoremediation capacity.

Child protection decisions to substantiate hospital child protection teams' reports of suspected maltreatment.

PubMed

Jedwab, Merav; Benbenishty, Rami; Chen, Wendy; Glasser, Saralee; Siegal, Gil; Lerner-Geva, Liat

2015-02-01

The present study focuses on the way child protection officers (CPOs) in Israel assess suspected abuse and neglect (SCAN) reports made by hospital child protection teams (CPTs), to determine whether the alleged maltreatment is substantiated. The study was conducted in six medical centers and included 358 reports investigated by CPOs for SCAN. A structured questionnaire was completed by hospital CPTs to capture all relevant information on each child referred to the CPTs. Structured phone interviews were conducted with each of the CPOs who received a CPT report. Bivariate associations and multivariate logistic regressions were conducted to estimate the substantiation rate of cases reported by CPTs and the types of maltreatment substantiated, as well as to identify case characteristics of the child and the family that were associated with the CPOs' substantiation decision. CPO follow-up investigations revealed a substantiation rate of 53.5%. The maltreatment type most commonly substantiated was neglect. The case characteristics associated with substantiation included socio-demographic background, parents' health and functioning, previous contact with social services, characteristics of the hospital referral, medical findings and an assessment of the parents' behaviors. The findings of the study highlighted the importance of cooperation between the health and welfare services and the policy makers. This cooperation is essential for identifying early signs of maltreatment. Enhanced cooperation and effective information transfer between various professionals would help prevent or at least reduce the recurrence of maltreatment and would ensure that the children and their families are treated appropriately. Copyright © 2014 Elsevier Ltd. All rights reserved.

Periodic permanent magnet focused klystron

DOEpatents

Ferguson, Patrick; Read, Michael; Ives, R Lawrence

2015-04-21

A periodic permanent magnet (PPM) klystron has beam transport structures and RF cavity structures, each of which has permanent magnets placed substantially equidistant from a beam tunnel formed about the central axis, and which are also outside the extent of a cooling chamber. The RF cavity sections also have permanent magnets which are placed substantially equidistant from the beam tunnel, but which include an RF cavity coupling to the beam tunnel for enhancement of RF carried by an electron beam in the beam tunnel.

Structural-functional diversity of the natural oligopeptides.

PubMed

Zamyatnin, Alexander A

2018-03-01

Natural oligopeptides may regulate nearly all vital processes. To date, the chemical structures of many oligopeptides have been identified from >2000 organisms representing all the biological kingdoms. We have considered a number of mathematical (sequence length), chemical, physical, and biological features of an array of natural oligopeptides on the basis of the oligopeptide EROP-Moscow database (http://erop.inbi.ras.ru, 15,351 entries) data. There is the substantial difference of these substances from polypeptide molecules of proteins according to their physicochemical characteristics. These characteristics may be critical for understanding the molecular mechanisms of the action of oligopeptides that lead to the development of physiological effects. Copyright © 2017 Elsevier Ltd. All rights reserved.

Benthic Crustacea from tropical and temperate reef locations: differences in assemblages and their relationship with habitat structure

NASA Astrophysics Data System (ADS)

Kramer, Michael J.; Bellwood, David R.; Taylor, Richard B.; Bellwood, Orpha

2017-09-01

Tropical and temperate marine habitats have long been recognised as fundamentally different system, yet comparative studies are rare, particularly for small organisms such as Crustacea. This study investigates the ecological attributes (abundance, biomass and estimated productivity) of benthic Crustacea in selected microhabitats from a tropical and a temperate location, revealing marked differences in the crustacean assemblages. In general, microhabitats from the tropical location (dead coral, the epilithic algal matrix [algal turfs] and sand) supported high abundances of small individuals (mean length = 0.53 mm vs. 0.96 mm in temperate microhabitats), while temperate microhabitats (the brown seaweed Carpophyllum sp., coralline turf and sand) had substantially greater biomasses of crustaceans and higher estimated productivity rates. In both locations, the most important microhabitats for crustaceans (per unit area) were complex structures: tropical dead coral and temperate Carpophyllum sp. It appears that the differences between microhabitats are largely driven by the size and relative abundance of key crustacean groups. Temperate microhabitats have a higher proportion of relatively large Peracarida (Amphipoda and Isopoda), whereas tropical microhabitats are dominated by small detrital- and microalgal-feeding crustaceans (harpacticoid copepods and ostracods). These differences highlight the vulnerability of tropical and temperate systems to the loss of complex benthic structures and their associated crustacean assemblages.

Advanced Organic Solid States Materials. Volume 173. Materials Research Society Symposium Proceedings

DTIC Science & Technology

1990-08-08

for their collaboration in synthetic study. We also thank Prof. N. Kasai and Dr. Y. Kai for their collaboration in X - ray crystallographic study. We...substantially with the increasing amount of doping as monitored by the powder x - ray diffraction. After doping the sample was kept for at least one day...physical properties at different oxidation states in solution and in the solid state of tEDTB complexed with TCNQF4. The X ray crystal structure of

Coherent structures and dynamical systems

NASA Technical Reports Server (NTRS)

Jimenez, Javier

1987-01-01

Any flow of a viscous fluid has a finite number of degrees of freedom, and can therefore be seen as a dynamical system. A coherent structure can be thought of as a lower dimensional manifold in whose neighborhood the dynamical system spends a substantial fraction of its time. If such a manifold exists, and if its dimensionality is substantially lower that that of the full flow, it is conceivable that the flow could be described in terms of the reduced set of degrees of freedom, and that such a description would be simpler than one in which the existence of structure was not recognized. Several examples are briefly summarized.

Method of determining the extent to which a nickel structure has been attached by a fluorine-containing gas

DOEpatents

Brusie, James P.

2004-07-13

The method of determining the extent to which a nickel structure has been attacked by a halogen containing gas to which it has been exposed which comprises preparing a quantity of water substantially free from dissolved oxygen, passing ammonia gas through a cuprammonium solution to produce ammonia substantially free from oxygen, dissolving said oxygen-free ammonia in said water to produce a saturated aqueous ammonia solution free from uncombined oxygen, treating at least a portion of said nickel structure of predetermined weight with said solution to dissolve nickel compounds from the surface of said structure without dissolving an appreciable amount of said nickel and analyzing the resulting solution to determine the quantity of said nickel compounds that was associated with said said portion of said structure to determine the proportion of combined nickel in said nickel structure.

Population Structure of the Coral-eating Fireworm Hermodice carunculata in the Wider Caribbean, Atlantic and Mediterranean Sea

NASA Astrophysics Data System (ADS)

Cruz, M.; Schizas, N. V.

2016-02-01

The bearded fireworm Hermodice carunculata is an important benthic invertebrate scavenger distributed in reefs worldwide. Fireworms are facultative corallivores and have been shown to transfer pathogenic agents between coral colonies. The effects of predation on coral species can be substantial. There is limited data on the genetic population structure of H. carunculata because of its cryptic nature and past studies resulted in ambiguous findings. Both morphological and molecular data suggest the presence of multiple fireworm sibling species but the morphological differences do not reflect the phylogeographic patterns of the species complex. Hermodice carunculata is an ideal species to use for genetic analysis to infer patterns of population structure and gene flow because of its biphasic life style with planktonic larvae and benthic adults. We collected 412 H. carunculata samples from over 20 locations in the Caribbean, Mediterranean Sea, Gulf of Mexico, Western and Eastern Atlantic Ocean. We sequenced two mitochondrial markers: Cytochrome C Oxidase subunit I (COI) and Cytochrome b (Cytb) from each specimen to examine the genetic diversity of H. carunculata. There is substantial genetic diversity within H. carunculata and preliminary evidence suggests the presence of at least two cryptic species in multiple locations. The presence of multiple species in bearded fireworms indicates our incomplete knowledge in one of the most important invertebrate scavengers in tropical and subtropical reefs.

Hexavalent chromium reduction under fermentative conditions with lactate stimulated native microbial communities.

PubMed

Somenahally, Anil C; Mosher, Jennifer J; Yuan, Tong; Podar, Mircea; Phelps, Tommy J; Brown, Steven D; Yang, Zamin K; Hazen, Terry C; Arkin, Adam P; Palumbo, Anthony V; Van Nostrand, Joy D; Zhou, Jizhong; Elias, Dwayne A

2013-01-01

Microbial reduction of toxic hexavalent chromium (Cr(VI)) in-situ is a plausible bioremediation strategy in electron-acceptor limited environments. However, higher [Cr(VI)] may impose stress on syntrophic communities and impact community structure and function. The study objectives were to understand the impacts of Cr(VI) concentrations on community structure and on the Cr(VI)-reduction potential of groundwater communities at Hanford, WA. Steady state continuous flow bioreactors were used to grow native communities enriched with lactate (30 mM) and continuously amended with Cr(VI) at 0.0 (No-Cr), 0.1 (Low-Cr) and 3.0 (High-Cr) mg/L. Microbial growth, metabolites, Cr(VI), 16S rRNA gene sequences and GeoChip based functional gene composition were monitored for 15 weeks. Temporal trends and differences in growth, metabolite profiles, and community composition were observed, largely between Low-Cr and High-Cr bioreactors. In both High-Cr and Low-Cr bioreactors, Cr(VI) levels were below detection from week 1 until week 15. With lactate enrichment, native bacterial diversity substantially decreased as Pelosinus spp., and Sporotalea spp., became the dominant groups, but did not significantly differ between Cr concentrations. The Archaea diversity also substantially decreased after lactate enrichment from Methanosaeta (35%), Methanosarcina (17%) and others, to mostly Methanosarcina spp. (95%). Methane production was lower in High-Cr reactors suggesting some inhibition of methanogens. Several key functional genes were distinct in Low-Cr bioreactors compared to High-Cr. Among the Cr resistant microbes, Burkholderia vietnamiensis, Comamonas testosterone and Ralstonia pickettii proliferated in Cr amended bioreactors. In-situ fermentative conditions facilitated Cr(VI) reduction, and as a result 3.0 mg/L Cr(VI) did not impact the overall bacterial community structure.

An original model of the northern Gulf of Mexico using Ecopath with Ecosim and its implications for the effects of fishing on ecosystem structure and maturity

NASA Astrophysics Data System (ADS)

Geers, T. M.; Pikitch, E. K.; Frisk, M. G.

2016-07-01

The Gulf of Mexico (GoM) is a valuable ecosystem both socially and economically, and fisheries contribute substantially to this value. Gulf menhaden, Brevoortia patronus, support the largest fishery in the Gulf (by weight) and provide forage for marine mammals, seabirds and commercially and recreationally important fish species. Understanding the complex interactions among multiple fisheries and myriad unfished species requires tools different from those used in traditional single-species management. One such tool, Ecopath with Ecosim (EwE) is increasingly being used to construct food web models of aquatic ecosystems and to evaluate fisheries management options within a broader, ecosystem context. Here, an EwE model was developed to examine the impact of Gulf fisheries on ecosystem structure and maturity. This model builds on previously published EwE models of the GoM, and is tailored to the range and habitat of Gulf menhaden. The model presented here consists of 47 functional groups, including 4 seabird groups, 1 marine mammal group, 3 elasmobranch groups, 26 bony fish groups, 9 invertebrate groups, 3 primary producer groups and 1 detritus group. A number of different management scenarios for Gulf fisheries were modeled and the results were evaluated in terms of impacts on ecosystem maturity and development. The results of the model simulations indicated that the northern Gulf of Mexico is in an immature state (sensuOdum, 1969). Management scenarios that increased fishing pressure over time consistently resulted in a decrease in the maturity indices. In particular, we found that Gulf menhaden, as a key forage fish in the ecosystem, plays a substantial role in the structure and functioning of the ecosystem.

Empathizing, systemizing, and autistic traits: latent structure in individuals with autism, their parents, and general population controls.

PubMed

Grove, Rachel; Baillie, Andrew; Allison, Carrie; Baron-Cohen, Simon; Hoekstra, Rosa A

2013-05-01

The search for genes involved in autism spectrum conditions (ASC) may have been hindered by the assumption that the different symptoms that define the condition can be attributed to the same causal mechanism. Instead the social and nonsocial aspects of ASC may have distinct causes at genetic, cognitive, and neural levels. It has been posited that the core features of ASC can be explained by a deficit in empathizing alongside intact or superior systemizing; the drive to understand and derive rules about a system. First-degree relatives also show some mild manifestations that parallel the defining features of ASC, termed the broader autism phenotype. Factor analyses were conducted to assess whether the latent structure of empathizing, systemizing, and autistic traits differs across samples with a high (individuals on the spectrum), medium (first-degree relatives) or low (general population controls) genetic vulnerability to autism. Results highlighted a two-factor model, confirming an empathizing and a systemizing factor. The relationship between these two factors was significantly stronger in first-degree relatives and the autism group compared with controls. The same model provided the best fit among the three groups, suggesting a similar latent structure irrespective of genetic vulnerability. However, results also suggest that although these traits are relatively independent in the general population, they are substantially correlated in individuals with ASC and their parents. This implies that there is substantially more overlap between systemizing and empathizing among individuals with an increased genetic liability to autism. This has potential implications for the genetic, environmental, and cognitive explanations of autism spectrum conditions. © 2013 American Psychological Association

Understanding sexual harassment using aggregate construct models.

PubMed

Nye, Christopher D; Brummel, Bradley J; Drasgow, Fritz

2014-11-01

Sexual harassment has received a substantial amount of empirical attention over the past few decades, and this research has consistently shown that experiencing these behaviors has a detrimental effect on employees' well-being, job attitudes, and behaviors at work. However, these findings, and the conclusions that are drawn from them, make the implicit assumption that the empirical models used to examine sexual harassment are properly specified. This article presents evidence that properly specified aggregate construct models are more consistent with theoretical structures and definitions of sexual harassment and can result in different conclusions about the nomological network of harassment. Results from 3 large samples, 2 military and 1 from a civilian population, are used to illustrate the differences between aggregate construct and reflective indicator models of sexual harassment. These analyses suggested that the factor structure and the nomological network of sexual harassment differ when modeling harassment as an aggregate construct. The implications of these results for the continued study of sexual harassment are discussed. (PsycINFO Database Record (c) 2014 APA, all rights reserved).

Structural Basis of Immune Evasion at the Site of CD4 Attachment on HIV-1 gp120

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

Chen, Lei; Kwon, Young Do; Zhou, Tongqing

2010-01-13

The site on HIV-1 gp120 that binds to the CD4 receptor is vulnerable to antibodies. However, most antibodies that interact with this site cannot neutralize HIV-1. To understand the basis of this resistance, we determined co-crystal structures for two poorly neutralizing, CD4-binding site (CD4BS) antibodies, F105 and b13, in complexes with gp120. Both antibodies exhibited approach angles to gp120 similar to those of CD4 and a rare, broadly neutralizing CD4BS antibody, b12. Slight differences in recognition, however, resulted in substantial differences in F105- and b13-bound conformations relative to b12-bound gp120. Modeling and binding experiments revealed these conformations to be poorlymore » compatible with the viral spike. This incompatibility, the consequence of slight differences in CD4BS recognition, renders HIV-1 resistant to all but the most accurately targeted antibodies.« less

Microlensing of Relativistic Knots in the Quasar HE 1104-1805 AB

NASA Astrophysics Data System (ADS)

Schechter, Paul L.; Udalski, A.; Szymański, M.; Kubiak, M.; Pietrzyński, G.; Soszyński, I.; Woźniak, P.; Żebruń, K.; Szewczyk, O.; Wyrzykowski, Ł.

2003-02-01

We present 3 years of photometry of the ``Double Hamburger'' lensed quasar, HE 1104-1805 AB, obtained on 102 separate nights using the Optical Gravitational Lensing Experiment 1.3 m telescope. Both the A and B images show variations, but with substantial differences in the light curves at all time delays. At the 310 day delay reported by Wisotzki and collaborators, the difference light curve has an rms amplitude of 0.060 mag. The structure functions for the A and B images are quite different, with image A more than twice as variable as image B (a factor of 4 in structure function) on timescales of less than a month. Adopting microlensing as a working hypothesis for the uncorrelated variability, the short timescale argues for the relativistic motion of one or more components of the source. We argue that the small amplitude of the fluctuations is due to the finite size of the source with respect to the microlenses.

Role of passive deformation on propulsion through a lumped torsional flexibility model

NASA Astrophysics Data System (ADS)

Arora, Nipun; Gupta, Amit

2016-11-01

Scientists and biologists have been affianced in a deeper examination of insect flight to develop an improved understanding of the role of flexibility on aerodynamic performance. Here, we mimic a flapping wing through a fluid-structure interaction framework based upon a lumped torsional flexibility model. The developed fluid and structural solvers together determine the aerodynamic forces and wing deformation, respectively. An analytical solution to the simplified single-spring structural dynamics equation is established to substantiate simulations. It is revealed that the dynamics of structural deformation is governed by the balance between inertia, stiffness and aerodynamics, where the former two oscillate at the plunging frequency and the latter oscillates at twice the plunging frequency. We demonstrate that an induced phase difference between plunging and passive pitching is responsible for a higher thrust coefficient. This phase difference is also shown to be dependent on aerodynamics to inertia and natural to plunging frequency ratios. For inertia dominated flows, pitching and plunging always remain in phase. As the aerodynamics dominates, a large phase difference is induced which is accountable for a large passive deformation and higher thrust. Authors acknowledge the financial support received from the Aeronautics Research and Development Board (ARDB) under SIGMA Project No. 1705 and thank the IIT Delhi HPC facility for computational resources.

Fixation of slightly beneficial mutations: effects of life history.

PubMed

Vindenes, Yngvild; Lee, Aline Magdalena; Engen, Steinar; Saether, Bernt-Erik

2010-04-01

Recent studies of rates of evolution have revealed large systematic differences among organisms with different life histories, both within and among taxa. Here, we consider how life history may affect the rate of evolution via its influence on the fixation probability of slightly beneficial mutations. Our approach is based on diffusion modeling for a finite, stage-structured population with stochastic population dynamics. The results, which are verified by computer simulations, demonstrate that even with complex population structure just two demographic parameters are sufficient to give an accurate approximation of the fixation probability of a slightly beneficial mutation. These are the reproductive value of the stage in which the mutation first occurs and the demographic variance of the population. The demographic variance also determines what influence population size has on the fixation probability. This model represents a substantial generalization of earlier models, covering a large range of life histories.

Local structure and charge distribution in the UO(2)-U(4)O(9) system.

PubMed

Conradson, Steven D; Manara, Dario; Wastin, Franck; Clark, David L; Lander, Gerard H; Morales, Luis A; Rebizant, Jean; Rondinella, Vincenzo V

2004-11-01

Analysis of X-ray absorption fine structure spectra of UO(2+x) for x = 0-0.20 (UO(2)--U(4)O(9)) reveals that the adventitious O atoms are incorporated as oxo groups with U--O distances of 1.74 A, most likely associated with U(VI), that occur in clusters so that the UO(2) fraction of the material largely remains intact. In addition to the formation of some additional longer U--O bonds, the U sublattice consists of an ordered portion that displays the original U--U distance and a spectroscopically silent, glassy part. This is very different from previous models derived from neutron diffraction that maintained long U--O distances and high U--O coordination numbers. UO(2+x) also differs from PuO(2+x) in its substantially shorter An-oxo distances and no sign of stable coordination with H(2)O and its hydrolysis products.

Spatial Patterns of Carbonate Biomineralization in Biofilms

PubMed Central

Li, Xiaobao; Chopp, David L.; Russin, William A.; Brannon, Paul T.; Parsek, Matthew R.

2015-01-01

Microbially catalyzed precipitation of carbonate minerals is an important process in diverse biological, geological, and engineered systems. However, the processes that regulate carbonate biomineralization and their impacts on biofilms are largely unexplored, mainly because of the inability of current methods to directly observe biomineralization within biofilms. Here, we present a method for in situ, real-time imaging of biomineralization in biofilms and use it to show that Pseudomonas aeruginosa biofilms produce morphologically distinct carbonate deposits that substantially modify biofilm structures. The patterns of carbonate biomineralization produced in situ were substantially different from those caused by accumulation of particles produced by abiotic precipitation. Contrary to the common expectation that mineral precipitation should occur at the biofilm surface, we found that biomineralization started at the base of the biofilm. The carbonate deposits grew over time, detaching biofilm-resident cells and deforming the biofilm morphology. These findings indicate that biomineralization is a general regulator of biofilm architecture and properties. PMID:26276112

Method for quantitative determination and separation of trace amounts of chemical elements in the presence of large quantities of other elements having the same atomic mass

DOEpatents

Miller, C.M.; Nogar, N.S.

1982-09-02

Photoionization via autoionizing atomic levels combined with conventional mass spectroscopy provides a technique for quantitative analysis of trace quantities of chemical elements in the presence of much larger amounts of other elements with substantially the same atomic mass. Ytterbium samples smaller than 10 ng have been detected using an ArF* excimer laser which provides the atomic ions for a time-of-flight mass spectrometer. Elemental selectivity of greater than 5:1 with respect to lutetium impurity has been obtained. Autoionization via a single photon process permits greater photon utilization efficiency because of its greater absorption cross section than bound-free transitions, while maintaining sufficient spectroscopic structure to allow significant photoionization selectivity between different atomic species. Separation of atomic species from others of substantially the same atomic mass is also described.

Hetero-junction photovoltaic device and method of fabricating the device

DOEpatents

Aytug, Tolga; Christen, David K; Paranthaman, Mariappan Parans; Polat, Ozgur

2014-02-10

A hetero-junction device and fabrication method in which phase-separated n-type and p-type semiconductor pillars define vertically-oriented p-n junctions extending above a substrate. Semiconductor materials are selected for the p-type and n-type pillars that are thermodynamically stable and substantially insoluble in one another. An epitaxial deposition process is employed to form the pillars on a nucleation layer and the mutual insolubility drives phase separation of the materials. During the epitaxial deposition process, the orientation is such that the nucleation layer initiates propagation of vertical columns resulting in a substantially ordered, three-dimensional structure throughout the deposited material. An oxidation state of at least a portion of one of the p-type or the n-type semiconductor materials is altered relative to the other, such that the band-gap energy of the semiconductor materials differ with respect to stoichiometric compositions and the device preferentially absorbs particular selected bands of radiation.

Shifts in bacterial community structure during succession in a glacier foreland of the High Arctic.

PubMed

Kim, Mincheol; Jung, Ji Young; Laffly, Dominique; Kwon, Hye Young; Lee, Yoo Kyung

2017-01-01

Primary succession after glacier retreat has been widely studied in plant communities, but bacterial succession is still poorly understood. In particular, few studies of microbial succession have been performed in the Arctic. We investigated the shifts in bacterial community structure and soil physicochemical properties along a successional gradient in a 100-year glacier foreland of the High Arctic. Multivariate analyses revealed that time after glacier retreat played a key role in associated bacterial community structure during succession. However, environmental filtering (i.e. pH and soil temperature) also accounted for a different, but substantial, proportion of the bacterial community structure. Using the functional trait-based approach, we found that average rRNA operon (rrn) copy number of bacterial communities is high in earlier successional stages and decreased over time. This suggests that soil bacterial taxa with higher rrn copy number have a selective advantage in early successional stages due to their ability of rapidly responding to nutrient inputs in newly exposed soils after glacier retreat. Taken together, our results demonstrate that both deglaciation time and environmental filters play key roles in structuring bacterial communities and soil bacterial groups with different ecological strategies occur in different stages of succession in this glacier foreland. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Tectonic stratification and seismicity of the accretionary prism of the Azerbaijani part of Greater Caucasus

NASA Astrophysics Data System (ADS)

Alizade, Akif; Kangarli, Talat; Aliyev, Fuad

2013-04-01

The Greater Caucasus has formed during last stage of the tectogenesis in a geodynamic condition of the lateral compression, peculiar to the zone pseudo-subduction interaction zone between Northern and Southern Caucasian continental microplates. Its present day structure formed as a result of horizontal movements of the different phases and sub-phases of Alpine tectogenesis (from late Cimmerian to Valakhian), and is generally regarded as zone where, along Zangi deformation, the insular arc formations of the Northern edge of South Caucasian microplate thrust under the Meso-Cenozoic substantial complex contained in the facials of marginal sea of Greater Caucasus. The last, in its turn, has been pushed beneath the North-Caucasus continental margin of the Scythian plate along Main Caucasus Thrust fault. Data collected from the territory of Azerbaijan and its' sector of the Caspian area stands for pseudo-subduction interaction of microplates which resulted in the tectonic stratification of the continental slope of Alpine formations, marginal sea and insular arc into different scale plates of south vergent combined into napping complexes. In the orogeny's present structure, tectonically stratified Alpine substantial complex of the marginal sea of Greater Caucasus bordered by Main Caucasus and Zangi thrusts, is represented by allochthonous south vergent accretionary prism in the front of first deformation with its' root buried under the southern border of Scythian plate. Allocated beneath mentioned prism, the autochthonous bedding is presented by Meso-Cenosoic complex of the Northern flank of the South-Caucasian miroplate, which is in its' turn crushed and lensed into southward shifted tectonic microplates gently overlapping the northern flank of Kura flexure along Ganykh-Ayrichay-Alyat thrust. Data of real-time GPS measurement of regional geodynamics indicates that pseudo-subduction of South Caucasian microplate under the North Caucasian microplate still continues during present stage of alpine tectogenesis. Among others, ongoing pseudo-subduction is indicated by data of regional seismicity which is irregularly distributed by depth (foci levels 2-6; 8-12; 17-22; 25-45 km). Horizontal and vertical seismic zoning is explained by Earth crust's block divisibility and tectonic stratification, within the structure of which the earthquake focuses are mainly confined to the crossing nodes of differently oriented ruptures, or to the planes of deep tectonic disruptions and lateral displacements along unstable contacts of the substantial complexes with various degree of competence. At present stage of tectogenesis, seismically most active are the structures of the northern flank of South Caucasian microplate, controlled by Ganyx-Ayrichay-Alyat deep thrust with "General Caucasus" spread in the west, and sub-meridian right-lateral strike slip zone of the Western Caspian fault in the east of Azerbaijani part of Greater Caucasus.

Facial Structure Predicts Sexual Orientation in Both Men and Women.

PubMed

Skorska, Malvina N; Geniole, Shawn N; Vrysen, Brandon M; McCormick, Cheryl M; Bogaert, Anthony F

2015-07-01

Biological models have typically framed sexual orientation in terms of effects of variation in fetal androgen signaling on sexual differentiation, although other biological models exist. Despite marked sex differences in facial structure, the relationship between sexual orientation and facial structure is understudied. A total of 52 lesbian women, 134 heterosexual women, 77 gay men, and 127 heterosexual men were recruited at a Canadian campus and various Canadian Pride and sexuality events. We found that facial structure differed depending on sexual orientation; substantial variation in sexual orientation was predicted using facial metrics computed by a facial modelling program from photographs of White faces. At the univariate level, lesbian and heterosexual women differed in 17 facial features (out of 63) and four were unique multivariate predictors in logistic regression. Gay and heterosexual men differed in 11 facial features at the univariate level, of which three were unique multivariate predictors. Some, but not all, of the facial metrics differed between the sexes. Lesbian women had noses that were more turned up (also more turned up in heterosexual men), mouths that were more puckered, smaller foreheads, and marginally more masculine face shapes (also in heterosexual men) than heterosexual women. Gay men had more convex cheeks, shorter noses (also in heterosexual women), and foreheads that were more tilted back relative to heterosexual men. Principal components analysis and discriminant functions analysis generally corroborated these results. The mechanisms underlying variation in craniofacial structure--both related and unrelated to sexual differentiation--may thus be important in understanding the development of sexual orientation.

Hydrogen atoms in protein structures: high-resolution X-ray diffraction structure of the DFPase

PubMed Central

2013-01-01

Background Hydrogen atoms represent about half of the total number of atoms in proteins and are often involved in substrate recognition and catalysis. Unfortunately, X-ray protein crystallography at usual resolution fails to access directly their positioning, mainly because light atoms display weak contributions to diffraction. However, sub-Ångstrom diffraction data, careful modeling and a proper refinement strategy can allow the positioning of a significant part of hydrogen atoms. Results A comprehensive study on the X-ray structure of the diisopropyl-fluorophosphatase (DFPase) was performed, and the hydrogen atoms were modeled, including those of solvent molecules. This model was compared to the available neutron structure of DFPase, and differences in the protein and the active site solvation were noticed. Conclusions A further examination of the DFPase X-ray structure provides substantial evidence about the presence of an activated water molecule that may constitute an interesting piece of information as regard to the enzymatic hydrolysis mechanism. PMID:23915572

Acoustic Analysis of a Sandwich Non Metallic Panel for Roofs by FEM and Experimental Validation

NASA Astrophysics Data System (ADS)

Nieto, P. J. García; del Coz Díaz, J. J.; Vilán, J. A. Vilán; Rabanal, F. P. Alvarez

2007-12-01

In this paper we have studied the acoustic behavior of a sandwich non metallic panel for roofs by the finite element method (FEM). This new field of analysis is the fully coupled solution of fluid flows with structural interactions, commonly referred to as fluid-structure interaction (FSI). It is the natural next step to take in the simulation of mechanical systems. The finite element analysis of acoustic-fluid/structure interactions using potential-based or displacement-based Lagrangian formulations is now well established. The non-linearity is due to the `fluid-structure interaction' (FSI) that governs the problem. In a very considerable range of problems the fluid displacement remains small while interaction is substantial. In this category falls our problem, in which the structural motion influence and react with the generation of pressures in two reverberation rooms. The characteristic of acoustic insulation of the panel is calculated basing on the pressures for different frequencies and points in the transmission rooms. Finally the conclusions reached are shown.

Structural Basis of Wee Kinases Functionality and Inactivation by Diverse Small Molecule Inhibitors.

PubMed

Zhu, Jin-Yi; Cuellar, Rebecca A; Berndt, Norbert; Lee, Hee Eun; Olesen, Sanne H; Martin, Mathew P; Jensen, Jeffrey T; Georg, Gunda I; Schönbrunn, Ernst

2017-09-28

Members of the Wee family of kinases negatively regulate the cell cycle via phosphorylation of CDK1 and are considered potential drug targets. Herein, we investigated the structure-function relationship of human Wee1, Wee2, and Myt1 (PKMYT1). Purified recombinant full-length proteins and kinase domain constructs differed substantially in phosphorylation states and catalytic competency, suggesting complex mechanisms of activation. A series of crystal structures reveal unique features that distinguish Wee1 and Wee2 from Myt1 and establish the structural basis of differential inhibition by the widely used Wee1 inhibitor MK-1775. Kinome profiling and cellular studies demonstrate that, in addition to Wee1 and Wee2, MK-1775 is an equally potent inhibitor of the polo-like kinase PLK1. Several previously unrecognized inhibitors of Wee kinases were discovered and characterized. Combined, the data provide a comprehensive view on the catalytic and structural properties of Wee kinases and a framework for the rational design of novel inhibitors thereof.

Land Use Planning and Wildfire: Development Policies Influence Future Probability of Housing Loss

PubMed Central

Syphard, Alexandra D.; Bar Massada, Avi; Butsic, Van; Keeley, Jon E.

2013-01-01

Increasing numbers of homes are being destroyed by wildfire in the wildland-urban interface. With projections of climate change and housing growth potentially exacerbating the threat of wildfire to homes and property, effective fire-risk reduction alternatives are needed as part of a comprehensive fire management plan. Land use planning represents a shift in traditional thinking from trying to eliminate wildfires, or even increasing resilience to them, toward avoiding exposure to them through the informed placement of new residential structures. For land use planning to be effective, it needs to be based on solid understanding of where and how to locate and arrange new homes. We simulated three scenarios of future residential development and projected landscape-level wildfire risk to residential structures in a rapidly urbanizing, fire-prone region in southern California. We based all future development on an econometric subdivision model, but we varied the emphasis of subdivision decision-making based on three broad and common growth types: infill, expansion, and leapfrog. Simulation results showed that decision-making based on these growth types, when applied locally for subdivision of individual parcels, produced substantial landscape-level differences in pattern, location, and extent of development. These differences in development, in turn, affected the area and proportion of structures at risk from burning in wildfires. Scenarios with lower housing density and larger numbers of small, isolated clusters of development, i.e., resulting from leapfrog development, were generally predicted to have the highest predicted fire risk to the largest proportion of structures in the study area, and infill development was predicted to have the lowest risk. These results suggest that land use planning should be considered an important component to fire risk management and that consistently applied policies based on residential pattern may provide substantial benefits for future risk reduction. PMID:23977120

Life extension of Structural Repairs – A statistical approach towards efficiency improvement

NASA Astrophysics Data System (ADS)

Deepashri, N. V.; Kalaiyappan, Mohan

2018-05-01

The life extension program of aircraft is taken up whenever aircraft’s intended life reaches close to its DSG (Design Service Goal). The Extended Service Goal (ESG) of an aircraft, in general, and structural repairs, in particular, is arrived at on the basis of F&DT (Fatigue & Damage Tolerance) analysis. Life extension program of aircraft consists of assessment of remaining life of all parts of the aircrafts including structural, mechanical, and electrical and avionics equipment and structural repairs. For life extension of stringer repair, as an example, it is required to re-assess the fatigue life of stringer in the presence of coupling under modified load spectrum. This is achieved by assessing the fatigue life of Web and Outer Flange (OF) part of stringers separately as per F&DT justification philosophy. Assessment of the fatigue life requires determination of stress concentration factor (Kt) for different combination of width, pitch, stringer thickness, coupling thickness and pad-up thickness of all stringer profiles available in different sections of fuselage. Determination of stress concentration factor for Web and Outer Flange of stringer profile covering entire ranges involves substantial number of Finite Element (FE) analysis. In order to optimise the number of FE runs, stress concentration factor is determined under worst repair factors combination (max. plate width; max. thickness; max. pitch; min. rivet dia.; and min. No. of rivets) resulting in conservative value. A parametric study of Web and Outer Flange data across stringer profiles were carried out and proven statistical techniques were used to find the optimal equation to predict stress concentration factor. This in turn reduced number of FE runs substantially for a given range of width, pitch, stringer thickness and so on. The use of optimal equation obtained through regression analysis is able to predict Kt within reasonable accuracy for a given range of inputs.

Pressure effects on structural, electronic, elastic and lattice dynamical properties of XSi2 (X = Cr, Mo, W) from first principles

NASA Astrophysics Data System (ADS)

Zhu, Haiyan; Shi, Liwei; Li, Shuaiqi; Zhang, Shaobo; Xia, Wangsuo

2018-04-01

First-principles calculations have been performed to study the structure, elastic and lattice dynamical properties of C40 XSi2 (X=Cr, Mo, W) under hydrostatic pressure. The obtained structural parameters are in line with existing experimental and theoretical data. The evolutions of fundamental bandgap energies, elastic moduli, IR absorption spectra with pressure have been investigated in detail. Our results indicate that the energy gaps of XSi2 (X=Cr, Mo, W) show different trends as the pressure increases. Larger BH/GH ratio and Poisson’s ratio are achieved with pressure, suggesting an improved ductility for XSi2 (X=Cr, Mo, W). Moreover, a large elastic anisotropy under pressure is exhibited in Young’s anisotropic factors. The infrared-active phonon frequencies exhibit substantial blueshifts under pressure.

Spatial and spectral characteristics of the distribution post-filamentation zone of femtosecond laser pulses

NASA Astrophysics Data System (ADS)

Apeksimov, D. V.; Zemlyanov, A. A.; Iglakova, A. N.; Kabanov, A. M.; Kuchinskaya, O. I.; Matvienko, G. G.; Oshlakov, V. K.; Petrov, A. V.

2017-11-01

The transverse structure formation processes of a laser beam after multiple filamentation were investigated. It is shown that the spectra of post-filamentation light channels (PFC), rings and beam differ substantially. The spectrum of PFC has a significant and symmetrical spectral broadening and covers a range of 600-1100 nm. The broadening of the spectrum of the rings is asymmetric and is directed mainly to the short-wavelength region of the spectrum. The broadening data are stable and do not change when moving away from the multiple filamentation zone. The annular structure of radiation in the cross section of the beam is formed around individual filaments within the region of multiple filamentation, and at a distance of tens of meters from it begins to form a common ring structure surrounding postfilamentation channels.

Anisotropic Dirac Fermions in BaMnBi2 and BaZnBi2

NASA Astrophysics Data System (ADS)

Ryu, Hyejin; Park, Se Young; Li, Lijun; Ren, Weijun; Petrovic, Cedomir; Hwang, Choonkyu; Mo, Sung-Kwan

We report electronic structures of BaMnBi2 and BaZnBi2 sharing similar structural properties but having different valence configuration of the Mn/Zn-Bi complex. Our angle-resolved photoemission measurements found a strong anisotropic Dirac dispersion in BaMnBi2 and a complete departure from the Dirac dispersion in BaZnBi2. Our findings, substantiated by the first principle calculations, allow us to understand role of Mn/Zn-Bi tetrahedra in the changes of the electronic structures as well as the effect of varying band filling of Bi-square net. Work at BNL was supported by the U.S. Dept of Energy-BES, Division of Materials Science and Engineering, under Contract No. DE-SC0012704 and Chinese Academy of Sciences under Grant No. KJZD-EW-M05.

Black grandmothers in multigenerational households: diversity in family structure and parenting involvement in the Woodlawn community.

PubMed

Pearson, J L; Hunter, A G; Ensminger, M E; Kellam, S G

1990-04-01

We report here the frequency of black grandmothers' coresidence in households with first-grade children, their patterns of involvement in parenting, and the degree to which family structure and employment affected the grandmothers' parenting involvement in a 1966/1967 community-defined population. Coresidence between grandmothers and their target first-grade grandchildren was found in 10% of the households. The 130 grandmothers' parenting involvement was substantial, second only to mother involvement, and was characterized by 2 parenting activity patterns: control and punishment, and support and punishment. The degree of grandmothers' parenting involvement differed by family structure, with grandmothers in mother-absent homes most likely to be involved. Grandmothers' employment did not moderate their engagement in parenting behaviors. These findings are consistent with previous reports of significant parenting involvement by black extended family members.

A two-dimensional analytical modeling for channel potential and threshold voltage of short channel triple material symmetrical gate Stack (TMGS) DG-MOSFET

NASA Astrophysics Data System (ADS)

Tripathi, Shweta

2016-10-01

In the present work, a two-dimensional (2D) analytical framework of triple material symmetrical gate stack (TMGS) DG-MOSFET is presented in order to subdue the short channel effects. A lightly doped channel along with triple material gate having different work functions and symmetrical gate stack structure, showcases substantial betterment in quashing short channel effects to a good extent. The device functioning amends in terms of improved exemption to threshold voltage roll-off, thereby suppressing the short channel effects. The encroachments of respective device arguments on the threshold voltage of the proposed structure are examined in detail. The significant outcomes are compared with the numerical simulation data obtained by using 2D ATLAS™ device simulator to affirm and formalize the proposed device structure.

Syntactic structure building in the anterior temporal lobe during natural story listening.

PubMed

Brennan, Jonathan; Nir, Yuval; Hasson, Uri; Malach, Rafael; Heeger, David J; Pylkkänen, Liina

2012-02-01

The neural basis of syntax is a matter of substantial debate. In particular, the inferior frontal gyrus (IFG), or Broca's area, has been prominently linked to syntactic processing, but the anterior temporal lobe has been reported to be activated instead of IFG when manipulating the presence of syntactic structure. These findings are difficult to reconcile because they rely on different laboratory tasks which tap into distinct computations, and may only indirectly relate to natural sentence processing. Here we assessed neural correlates of syntactic structure building in natural language comprehension, free from artificial task demands. Subjects passively listened to Alice in Wonderland during functional magnetic resonance imaging and we correlated brain activity with a word-by-word measure of the amount syntactic structure analyzed. Syntactic structure building correlated with activity in the left anterior temporal lobe, but there was no evidence for a correlation between syntactic structure building and activity in inferior frontal areas. Our results suggest that the anterior temporal lobe computes syntactic structure under natural conditions. Copyright © 2010 Elsevier Inc. All rights reserved.

Numerical Simulation of Galvanic Corrosion Caused by Shaft Grounding Systems in Steel Ship Hulls

DTIC Science & Technology

2005-01-01

ship hull on paint holidays because of the substantial difference of the electric potentials between the steel ship hull and the nickel-aluminum...steel ship hull on paint holidays because of the substantial difference of the electric potentials between the steel ship hull and the nickel...substantial difference of the electric potentials between the steel ship hull and the nickel-aluminum bronze propellers. There are concerns on the

Multi-point laser ignition device

DOEpatents

McIntyre, Dustin L.; Woodruff, Steven D.

2017-01-17

A multi-point laser device comprising a plurality of optical pumping sources. Each optical pumping source is configured to create pumping excitation energy along a corresponding optical path directed through a high-reflectivity mirror and into substantially different locations within the laser media thereby producing atomic optical emissions at substantially different locations within the laser media and directed along a corresponding optical path of the optical pumping source. An output coupler and one or more output lenses are configured to produce a plurality of lasing events at substantially different times, locations or a combination thereof from the multiple atomic optical emissions produced at substantially different locations within the laser media. The laser media is a single continuous media, preferably grown on a single substrate.

Nanoscopy for nanoscience: how super-resolution microscopy extends imaging for nanotechnology.

PubMed

Johnson, Sam A

2015-01-01

Imaging methods have presented scientists with powerful means of investigation for centuries. The ability to resolve structures using light microscopes is though limited to around 200 nm. Fluorescence-based super-resolution light microscopy techniques of several principles and methods have emerged in recent years and offer great potential to extend the capabilities of microscopy. This resolution improvement is especially promising for nanoscience where the imaging of nanoscale structures is inherently restricted by the resolution limit of standard forms of light microscopy. Resolution can be improved by several distinct approaches including structured illumination microscopy, stimulated emission depletion, and single-molecule positioning methods such as photoactivated localization microscopy and stochastic optical reconstruction microscopy and several derivative variations of each of these. These methods involve substantial differences in the resolutions achievable in the different axes, speed of acquisition, compatibility with different labels, ease of use, hardware complexity, and compatibility with live biological samples. The field of super-resolution imaging and its application to nanotechnology is relatively new and still rapidly developing. An overview of how these methods may be used with nanomaterials is presented with some examples of pioneering uses of these approaches. © 2014 Wiley Periodicals, Inc.

Method of making an air electrode material having controlled sinterability

DOEpatents

Vasilow, Theodore R.; Kuo, Lewis J. H.; Ruka, Roswell J.

1994-01-01

A tubular, porous ceramic electrode structure (3) is made from the sintered admixture of doped lanthanum manganite and an additive containing cerium where a solid electrolyte (4), substantially surrounds the air electrode, and a porous outer fuel electrode (7) substantially surrounds the electrolyte, to form a fuel cell (1).

Method of making an air electrode material having controlled sinterability

DOEpatents

Vasilow, T.R.; Kuo, L.J.H.; Ruka, R.J.

1994-08-30

A tubular, porous ceramic electrode structure is made from the sintered admixture of doped lanthanum manganite and an additive containing cerium where a solid electrolyte, substantially surrounds the air electrode, and a porous outer fuel electrode substantially surrounds the electrolyte, to form a fuel cell. 2 figs.

Neural Bases of Recovery after Brain Injury

ERIC Educational Resources Information Center

Nudo, Randolph J.

2011-01-01

Substantial data have accumulated over the past decade indicating that the adult brain is capable of substantial structural and functional reorganization after stroke. While some limited recovery is known to occur spontaneously, especially within the first month post-stroke, there is currently significant optimism that new interventions based on…

Knowledge of the human body: a distinct semantic domain.

PubMed

Coslett, H Branch; Saffran, Eleanor M; Schwoebel, John

2002-08-13

Patients with selective deficits in the naming and comprehension of animals, plants, and artifacts have been reported. These descriptions of specific semantic category deficits have contributed substantially to the understanding of the architecture of semantic representations. This study sought to further understanding of the organization of the semantic system by demonstrating that another semantic category, knowledge of the human body, may be selectively preserved. The performance of a patient with semantic dementia was compared with the performance of healthy controls on a variety of tasks assessing distinct types of body representations, including the body schema, body image, and body structural description. Despite substantial deficits on tasks involving language and knowledge of the world generally, the patient performed normally on all tests of body knowledge except body part naming; even in this naming task, however, her performance with body parts was significantly better than on artifacts. The demonstration that body knowledge may be preserved despite substantial semantic deficits involving other types of semantic information argues that body knowledge is a distinct and dissociable semantic category. These data are interpreted as support for a model of semantics that proposes that knowledge is distributed across different cortical regions reflecting the manner in which the information was acquired.

The structural basis of secondary active transport mechanisms.

PubMed

Forrest, Lucy R; Krämer, Reinhard; Ziegler, Christine

2011-02-01

Secondary active transporters couple the free energy of the electrochemical potential of one solute to the transmembrane movement of another. As a basic mechanistic explanation for their transport function the model of alternating access was put forward more than 40 years ago, and has been supported by numerous kinetic, biochemical and biophysical studies. According to this model, the transporter exposes its substrate binding site(s) to one side of the membrane or the other during transport catalysis, requiring a substantial conformational change of the carrier protein. In the light of recent structural data for a number of secondary transport proteins, we analyze the model of alternating access in more detail, and correlate it with specific structural and chemical properties of the transporters, such as their assignment to different functional states in the catalytic cycle of the respective transporter, the definition of substrate binding sites, the type of movement of the central part of the carrier harboring the substrate binding site, as well as the impact of symmetry on fold-specific conformational changes. Besides mediating the transmembrane movement of solutes, the mechanism of secondary carriers inherently involves a mechanistic coupling of substrate flux to the electrochemical potential of co-substrate ions or solutes. Mainly because of limitations in resolution of available transporter structures, this important aspect of secondary transport cannot yet be substantiated by structural data to the same extent as the conformational change aspect. We summarize the concepts of coupling in secondary transport and discuss them in the context of the available evidence for ion binding to specific sites and the impact of the ions on the conformational state of the carrier protein, which together lead to mechanistic models for coupling. Copyright © 2010 Elsevier B.V. All rights reserved.

Developmental models for estimating ecological responses to environmental variability: structural, parametric, and experimental issues.

PubMed

Moore, Julia L; Remais, Justin V

2014-03-01

Developmental models that account for the metabolic effect of temperature variability on poikilotherms, such as degree-day models, have been widely used to study organism emergence, range and development, particularly in agricultural and vector-borne disease contexts. Though simple and easy to use, structural and parametric issues can influence the outputs of such models, often substantially. Because the underlying assumptions and limitations of these models have rarely been considered, this paper reviews the structural, parametric, and experimental issues that arise when using degree-day models, including the implications of particular structural or parametric choices, as well as assumptions that underlie commonly used models. Linear and non-linear developmental functions are compared, as are common methods used to incorporate temperature thresholds and calculate daily degree-days. Substantial differences in predicted emergence time arose when using linear versus non-linear developmental functions to model the emergence time in a model organism. The optimal method for calculating degree-days depends upon where key temperature threshold parameters fall relative to the daily minimum and maximum temperatures, as well as the shape of the daily temperature curve. No method is shown to be universally superior, though one commonly used method, the daily average method, consistently provides accurate results. The sensitivity of model projections to these methodological issues highlights the need to make structural and parametric selections based on a careful consideration of the specific biological response of the organism under study, and the specific temperature conditions of the geographic regions of interest. When degree-day model limitations are considered and model assumptions met, the models can be a powerful tool for studying temperature-dependent development.

The Epidemiology of Observed Temperament: Factor Structure and Demographic Group Differences

PubMed Central

Willoughby, Michael T.; Stifter, Cynthia A.; Gottfredson, Nisha C.

2015-01-01

This study investigated the factor structure of observational indicators of children’s temperament that were collected across the first three years of life in the Family Life Project (N = 1205) sample. A four-factor model (activity level, fear, anger, regulation), which corresponded broadly to Rothbart’s distinction between reactivity and regulation, provided an acceptable fit the observed data. Tests of measurement invariance demonstrated that a majority of the observational indicators exhibited comparable measurement properties for male vs. female, black vs. white, and poor vs. not-poor children, which improved the generalizability of these results. Unadjusted demographic group comparisons revealed small to moderate sized differences (Cohen ds = |.23 – .42|) in temperamental reactivity and moderate to large sized differences (Cohen ds = −.64 – −.97) in regulation. Collectively, demographic variables explained more of the variation in regulation (R2 = .25) than in reactivity (R2 = .02 – .06). Follow-up analyses demonstrated that race differences were substantially diminished in magnitude and better accounted for by poverty. These results help to validate the distinction between temperamental reactivity and regulation using observational indicators. PMID:25733489

Regulation of podocalyxin trafficking by Rab small GTPases in 2D and 3D epithelial cell cultures

PubMed Central

Mrozowska, Paulina S.

2016-01-01

MDCK II cells, a widely used model of polarized epithelia, develop into different structures depending on culture conditions: two-dimensional (2D) monolayers when grown on synthetic supports or three-dimensional (3D) cysts when surrounded by an extracellular matrix. The establishment of epithelial polarity is accompanied by transcytosis of the apical marker podocalyxin from the outer plasma membrane to the newly formed apical domain, but its exact route and regulation remain poorly understood. Here, through comprehensive colocalization and knockdown screenings, we identified the Rab GTPases mediating podocalyxin transcytosis and showed that different sets of Rabs coordinate its transport during cell polarization in 2D and 3D structures. Moreover, we demonstrated that different Rab35 effectors regulate podocalyxin trafficking in 2D and 3D environments; trafficking is mediated by OCRL in 2D monolayers and ACAP2 in 3D cysts. Our results give substantial insight into regulation of the transcytosis of this apical marker and highlight differences between trafficking mechanisms in 2D and 3D cell cultures. PMID:27138252

Photocatalytic Activity of Nanotubular TiO2 Films Obtained by Anodic Oxidation: A Comparison in Gas and Liquid Phase

PubMed Central

Sanabria Arenas, Beatriz Eugenia; Schiavi, Luca; Russo, Valeria; Pedeferri, MariaPia

2018-01-01

The availability of immobilized nanostructured photocatalysts is of great importance in the purification of both polluted air and liquids (e.g., industrial wastewaters). Metal-supported titanium dioxide films with nanotubular morphology and good photocatalytic efficiency in both environments can be produced by anodic oxidation, which avoids release of nanoscale materials in the environment. Here we evaluate the effect of different anodizing procedures on the photocatalytic activity of TiO2 nanostructures in gas and liquid phases, in order to identify the most efficient and robust technique for the production of TiO2 layers with different morphologies and high photocatalytic activity in both phases. Rhodamine B and toluene were used as model pollutants in the two media, respectively. It was found that the role of the anodizing electrolyte is particularly crucial, as it provides substantial differences in the oxide specific surface area: nanotubular structures show remarkably different activities, especially in gas phase degradation reactions, and within nanotubular structures, those produced by organic electrolytes lead to better photocatalytic activity in both conditions tested. PMID:29587360

The Relationship Between Social Support and Subjective Well-Being Across Age

PubMed Central

Salthouse, Timothy A.; Oishi, Shigehiro; Jeswani, Sheena

2014-01-01

The relationships among types of social support and different facets of subjective well-being (i.e., life satisfaction, positive affect, and negative affect) were examined in a sample of 1,111 individuals between the ages of 18 and 95. Using structural equation modeling we found that life satisfaction was predicted by enacted and perceived support, positive affect was predicted by family embeddedness and provided support, and negative affect was predicted by perceived support. When personality variables were included in a subsequent model, the influence of the social support variables were generally reduced. Invariance analyses conducted across age groups indicated that there were no substantial differences in predictors of the different types of subjective well-being across age. PMID:25045200

New Insights on Neurobiological Mechanisms underlying Alcohol Addiction

PubMed Central

Cui, Changhai; Noronha, Antonio; Morikawa, Hitoshi; Alvarez, Veronica A.; Stuber, Garret D.; Szumlinski, Karen K.; Kash, Thomas L.; Roberto, Marisa; Wilcox, Mark V.

2012-01-01

Alcohol dependence/addiction is mediated by complex neural mechanisms that involve multiple brain circuits and neuroadaptive changes in a variety of neurotransmitter and neuropeptide systems. Although recent studies have provided substantial information on the neurobiological mechanisms that drive alcohol drinking behavior, significant challenges remain in understanding how alcohol-induced neuroadaptations occur and how different neurocircuits and pathways cross-talk. This review article highlights recent progress in understanding neural mechanisms of alcohol addiction from the perspectives of the development and maintenance of alcohol dependence. It provides insights on cross talks of different mechanisms and reviews the latest studies on metaplasticity, structural plasticity, interface of reward and stress pathways, and cross-talk of different neural signaling systems involved in binge-like drinking and alcohol dependence. PMID:23159531

Air Structures. Educational Facilities Review Series Number 23.

ERIC Educational Resources Information Center

Finne, Mary Lou

Air structures can be erected quickly, cover large areas, cost substantially less than conventional buildings, and use less natural resources. Air structures are economically utilized for many facilities, such as athletic fields, swimming pools, high schools, day care centers, and college campuses. The literature on air structures covered in this…

Preparation of highly oxidized RBa.sub.2 Cu.sub.4 O.sub.8 superconductors

DOEpatents

Morris, Donald E.

1991-01-01

Novel superconducting materials in the form of compounds, structures or phases are formed by performing otherwise known syntheses in a highly oxidizing atmosphere rather than that created by molecular oxygen at atmospheric pressure or below. This leads to the successful synthesis of novel superconducting compounds which are thermodynamically stable at the conditions under which they are formed. The compounds and structures thus formed are substantially nonsusceptible to variations in their oxygen content when subjected to changing temperatures, thereby forming a temperature-stable substantially single phase crystal.

Automated NMR structure determination of stereo-array isotope labeled ubiquitin from minimal sets of spectra using the SAIL-FLYA system.

PubMed

Ikeya, Teppei; Takeda, Mitsuhiro; Yoshida, Hitoshi; Terauchi, Tsutomu; Jee, Jun-Goo; Kainosho, Masatsune; Güntert, Peter

2009-08-01

Stereo-array isotope labeling (SAIL) has been combined with the fully automated NMR structure determination algorithm FLYA to determine the three-dimensional structure of the protein ubiquitin from different sets of input NMR spectra. SAIL provides a complete stereo- and regio-specific pattern of stable isotopes that results in sharper resonance lines and reduced signal overlap, without information loss. Here we show that as a result of the superior quality of the SAIL NMR spectra, reliable, fully automated analyses of the NMR spectra and structure calculations are possible using fewer input spectra than with conventional uniformly 13C/15N-labeled proteins. FLYA calculations with SAIL ubiquitin, using a single three-dimensional "through-bond" spectrum (and 2D HSQC spectra) in addition to the 13C-edited and 15N-edited NOESY spectra for conformational restraints, yielded structures with an accuracy of 0.83-1.15 A for the backbone RMSD to the conventionally determined solution structure of SAIL ubiquitin. NMR structures can thus be determined almost exclusively from the NOESY spectra that yield the conformational restraints, without the need to record many spectra only for determining intermediate, auxiliary data of the chemical shift assignments. The FLYA calculations for this report resulted in 252 ubiquitin structure bundles, obtained with different input data but identical structure calculation and refinement methods. These structures cover the entire range from highly accurate structures to seriously, but not trivially, wrong structures, and thus constitute a valuable database for the substantiation of structure validation methods.

Patterns of coordinated cortical remodeling during adolescence and their associations with functional specialization and evolutionary expansion.

PubMed

Sotiras, Aristeidis; Toledo, Jon B; Gur, Raquel E; Gur, Ruben C; Satterthwaite, Theodore D; Davatzikos, Christos

2017-03-28

During adolescence, the human cortex undergoes substantial remodeling to support a rapid expansion of behavioral repertoire. Accurately quantifying these changes is a prerequisite for understanding normal brain development, as well as the neuropsychiatric disorders that emerge in this vulnerable period. Past accounts have demonstrated substantial regional heterogeneity in patterns of brain development, but frequently have been limited by small samples and analytics that do not evaluate complex multivariate imaging patterns. Capitalizing on recent advances in multivariate analysis methods, we used nonnegative matrix factorization (NMF) to uncover coordinated patterns of cortical development in a sample of 934 youths ages 8-20, who completed structural neuroimaging as part of the Philadelphia Neurodevelopmental Cohort. Patterns of structural covariance (PSCs) derived by NMF were highly reproducible over a range of resolutions, and differed markedly from common gyral-based structural atlases. Moreover, PSCs were largely symmetric and showed correspondence to specific large-scale functional networks. The level of correspondence was ordered according to their functional role and position in the evolutionary hierarchy, being high in lower-order visual and somatomotor networks and diminishing in higher-order association cortex. Furthermore, PSCs showed divergent developmental associations, with PSCs in higher-order association cortex networks showing greater changes with age than primary somatomotor and visual networks. Critically, such developmental changes within PSCs were significantly associated with the degree of evolutionary cortical expansion. Together, our findings delineate a set of structural brain networks that undergo coordinated cortical thinning during adolescence, which is in part governed by evolutionary novelty and functional specialization.

Mounting Systems for Structural Members, Fastening Assemblies Thereof, and Vibration Isolation Systems Including the Same

NASA Technical Reports Server (NTRS)

Young, Ken (Inventor); Hindle, Timothy (Inventor); Barber, Tim Daniel (Inventor)

2016-01-01

Mounting systems for structural members, fastening assemblies thereof, and vibration isolation systems including the same are provided. Mounting systems comprise a pair of mounting brackets, each clamped against a fastening assembly forming a mounting assembly. Fastening assemblies comprise a spherical rod end comprising a spherical member having a through opening and an integrally threaded shaft, first and second seating members on opposite sides of the spherical member and each having a through opening that is substantially coaxial with the spherical member through opening, and a partially threaded fastener that threadably engages each mounting bracket forming the mounting assembly. Structural members have axial end portions, each releasably coupled to a mounting bracket by the integrally threaded shaft. Axial end portions are threaded in opposite directions for permitting structural member rotation to adjust a length thereof to a substantially zero strain position. Structural members may be vibration isolator struts in vibration isolation systems.

Comparison of modal identification techniques using a hybrid-data approach

NASA Technical Reports Server (NTRS)

Pappa, Richard S.

1986-01-01

Modal identification of seemingly simple structures, such as the generic truss is often surprisingly difficult in practice due to high modal density, nonlinearities, and other nonideal factors. Under these circumstances, different data analysis techniques can generate substantially different results. The initial application of a new hybrid-data method for studying the performance characteristics of various identification techniques with such data is summarized. This approach offers new pieces of information for the system identification researcher. First, it allows actual experimental data to be used in the studies, while maintaining the traditional advantage of using simulated data. That is, the identification technique under study is forced to cope with the complexities of real data, yet the performance can be measured unquestionably for the artificial modes because their true parameters are known. Secondly, the accuracy achieved for the true structural modes in the data can be estimated from the accuracy achieved for the artificial modes if the results show similar characteristics. This similarity occurred in the study, for example, for a weak structural mode near 56 Hz. It may even be possible--eventually--to use the error information from the artificial modes to improve the identification accuracy for the structural modes.

Nucleosome Positioning and NDR Structure at RNA Polymerase III Promoters

NASA Astrophysics Data System (ADS)

Helbo, Alexandra Søgaard; Lay, Fides D.; Jones, Peter A.; Liang, Gangning; Grønbæk, Kirsten

2017-02-01

Chromatin is structurally involved in the transcriptional regulation of all genes. While the nucleosome positioning at RNA polymerase II (pol II) promoters has been extensively studied, less is known about the chromatin structure at pol III promoters in human cells. We use a high-resolution analysis to show substantial differences in chromatin structure of pol II and pol III promoters, and between subtypes of pol III genes. Notably, the nucleosome depleted region at the transcription start site of pol III genes extends past the termination sequences, resulting in nucleosome free gene bodies. The +1 nucleosome is located further downstream than at pol II genes and furthermore displays weak positioning. The variable position of the +1 location is seen not only within individual cell populations and between cell types, but also between different pol III promoter subtypes, suggesting that the +1 nucleosome may be involved in the transcriptional regulation of pol III genes. We find that expression and DNA methylation patterns correlate with distinct accessibility patterns, where DNA methylation associates with the silencing and inaccessibility at promoters. Taken together, this study provides the first high-resolution map of nucleosome positioning and occupancy at human pol III promoters at specific loci and genome wide.

14 CFR 25.629 - Aeroelastic stability requirements.

Code of Federal Regulations, 2012 CFR

2012-01-01

... weights are used, their effectiveness and strength, including supporting structure, must be substantiated... of any single element of the structure supporting any engine, independently mounted propeller shaft... dynamic forces, any single failure of the engine structure that would reduce the rigidity of the...

14 CFR 25.629 - Aeroelastic stability requirements.

Code of Federal Regulations, 2014 CFR

2014-01-01

... weights are used, their effectiveness and strength, including supporting structure, must be substantiated... of any single element of the structure supporting any engine, independently mounted propeller shaft... dynamic forces, any single failure of the engine structure that would reduce the rigidity of the...

14 CFR 25.629 - Aeroelastic stability requirements.

Code of Federal Regulations, 2011 CFR

2011-01-01

... weights are used, their effectiveness and strength, including supporting structure, must be substantiated... of any single element of the structure supporting any engine, independently mounted propeller shaft... dynamic forces, any single failure of the engine structure that would reduce the rigidity of the...

14 CFR 25.629 - Aeroelastic stability requirements.

Code of Federal Regulations, 2013 CFR

2013-01-01

... weights are used, their effectiveness and strength, including supporting structure, must be substantiated... of any single element of the structure supporting any engine, independently mounted propeller shaft... dynamic forces, any single failure of the engine structure that would reduce the rigidity of the...

Structural and functional photoacoustic molecular tomography aided by emerging contrast agents

PubMed Central

Nie, Liming

2015-01-01

Photoacoustic tomography (PAT) can offer structural, functional and molecular contrasts at scalable observation level. By ultrasonically overcoming the strong optical scattering, this imaging technology can reach centimeters penetration depth while retaining high spatial resolution in biological tissue. Recent extensive research has been focused on developing new contrast agents to improve the imaging sensitivity, specificity and efficiency. These emerging materials have substantially accelerated PAT applications in signal sensing, functional imaging, biomarker labeling and therapy monitoring etc. Here, the potentials of different optical probes as PAT contrast agents were elucidated. We first describe the instrumental embodiments and the measured functional parameters, then focus on emerging contrast agent-based PAT applications, and finally discuss the challenges and prospects. PMID:24967718

Is the Kapuskasing structure the site of a cryptic suture

NASA Technical Reports Server (NTRS)

Burke, K.

1983-01-01

The demonstration that the Kapuskasing structure involves substantial thrusting of deep continental crustal rocks over shallower continental rocks calls into question an earlier suggestion (by Wilson) that the Circum-Ungaua suture zone continued through the Kapuskasing to join the Penokean fold belt (implying that the Kapuskasing marked the site of what has since come to be called a cryptic suture). Problems are discussed which arose in attempting to reconcile Wilson's idea with data from more recent studies: whether the Kapuskasing and the Thompson belt both mark sutures of about 1700 Ma age; why there is no age difference across the Kapuskasing if it does mark the site of continental collision, and why there is no offset of Superior subprovinces across the Kapuskasing.

Harnessing of radio frequency discharge for production of biologically compatible coatings for ophthalmology

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

Abdullin, I.Sh.; Bragin, V.E.; Bykanov, A.N.

Gas discharge plasma modification of polymer materials and metals is one of the known physical approaches for improving of materials biocompatibility in ophthalmology and surgery. The surface treatment in RF discharges can be effectively realized in the discharge afterglow and in the discharge region itself too. This modification method is more convenient and produces more uniform surfaces in comparison with other discharge types. The carried out experiments and published up to now results show that interaction of UV radiation, fluxes of ions, electrons and metastable particles with material`s surface changes chemical composition and surface structure. The exerting of these agentsmore » on the sample surface produces the following effects. There are processes of physical and plasma-chemical surface etching producing effective surface cleaning of different types of contaminations. It may be surface contaminations by hydrocarbons because of preliminary surface contacts with biological or physical bodies. It may be surface contaminations caused by characteristic properties of chemical technology too. There is a surface layer with thickness from some angstroms up to few hundreds of angstroms. The chemical content and structure of this layer is distinguished from the bulk polymer properties. The presence of such {open_quotes}technological{close_quotes} contaminations produces the layer of material substantially differing from the base polymer. The basic layer physical and chemical properties for example, gas permeation rate may substantially differ from the base polymer. Attempts to clean the surface from these contaminations by chemical methods (solutions) have not been successful and produced contaminations of more deep polymer layers. So the plasma cleaning is the most profitable method of polymer treatment for removing the surface contaminations. The improving of wettability occurs during this stage of treatment.« less

Direct collapse to supermassive black hole seeds: comparing the AMR and SPH approaches.

PubMed

Luo, Yang; Nagamine, Kentaro; Shlosman, Isaac

2016-07-01

We provide detailed comparison between the adaptive mesh refinement (AMR) code enzo-2.4 and the smoothed particle hydrodynamics (SPH)/ N -body code gadget-3 in the context of isolated or cosmological direct baryonic collapse within dark matter (DM) haloes to form supermassive black holes. Gas flow is examined by following evolution of basic parameters of accretion flows. Both codes show an overall agreement in the general features of the collapse; however, many subtle differences exist. For isolated models, the codes increase their spatial and mass resolutions at different pace, which leads to substantially earlier collapse in SPH than in AMR cases due to higher gravitational resolution in gadget-3. In cosmological runs, the AMR develops a slightly higher baryonic resolution than SPH during halo growth via cold accretion permeated by mergers. Still, both codes agree in the build-up of DM and baryonic structures. However, with the onset of collapse, this difference in mass and spatial resolution is amplified, so evolution of SPH models begins to lag behind. Such a delay can have effect on formation/destruction rate of H 2 due to UV background, and on basic properties of host haloes. Finally, isolated non-cosmological models in spinning haloes, with spin parameter λ ∼ 0.01-0.07, show delayed collapse for greater λ, but pace of this increase is faster for AMR. Within our simulation set-up, gadget-3 requires significantly larger computational resources than enzo-2.4 during collapse, and needs similar resources, during the pre-collapse, cosmological structure formation phase. Yet it benefits from substantially higher gravitational force and hydrodynamic resolutions, except at the end of collapse.

Direct collapse to supermassive black hole seeds: comparing the AMR and SPH approaches

NASA Astrophysics Data System (ADS)

Luo, Yang; Nagamine, Kentaro; Shlosman, Isaac

2016-07-01

We provide detailed comparison between the adaptive mesh refinement (AMR) code ENZO-2.4 and the smoothed particle hydrodynamics (SPH)/N-body code GADGET-3 in the context of isolated or cosmological direct baryonic collapse within dark matter (DM) haloes to form supermassive black holes. Gas flow is examined by following evolution of basic parameters of accretion flows. Both codes show an overall agreement in the general features of the collapse; however, many subtle differences exist. For isolated models, the codes increase their spatial and mass resolutions at different pace, which leads to substantially earlier collapse in SPH than in AMR cases due to higher gravitational resolution in GADGET-3. In cosmological runs, the AMR develops a slightly higher baryonic resolution than SPH during halo growth via cold accretion permeated by mergers. Still, both codes agree in the build-up of DM and baryonic structures. However, with the onset of collapse, this difference in mass and spatial resolution is amplified, so evolution of SPH models begins to lag behind. Such a delay can have effect on formation/destruction rate of H2 due to UV background, and on basic properties of host haloes. Finally, isolated non-cosmological models in spinning haloes, with spin parameter λ ˜ 0.01-0.07, show delayed collapse for greater λ, but pace of this increase is faster for AMR. Within our simulation set-up, GADGET-3 requires significantly larger computational resources than ENZO-2.4 during collapse, and needs similar resources, during the pre-collapse, cosmological structure formation phase. Yet it benefits from substantially higher gravitational force and hydrodynamic resolutions, except at the end of collapse.

Variations in the structure of nexuses in the myocardium of the golden hamster Mesocricetus auratus.

PubMed Central

Skepper, J N; Navaratnam, V

1986-01-01

The structure of nexuses in the atrioventricular node of the golden hamster was studied with the transmission electron microscope, using thin sections and freeze-fracture replicas, and was compared with that of nexuses in the working myocardium of the right ventricular wall. Whereas ventricular myocardium contained macular nexuses only, nodal tissue contained annular and linear configurations as well as maculae of varying size. The significance of such variations in nexus pattern is not clear although several hypotheses are discussed in the literature. Measurements made on electron micrographs, after allowing for tilt of the specimen, yielded a particle diameter of 10.59 nm for nodal myocardium and 10.95 nm for ventricular myocardium, both measurements being substantially higher than figures generally cited in the literature. In each area the measurements had a normal distribution suggesting a single type of particle. The small but significant difference in particle size between the two areas is more likely to be caused by dissimilarities in packing arrangement rather than by differences in intrinsic structure or in functional state. Images Fig. 1 Fig. 3 PMID:3693102

Conserved structures formed by heterogeneous RNA sequences drive silencing of an inflammation responsive post-transcriptional operon

PubMed Central

Basu, Abhijit; Jain, Niyati; Tolbert, Blanton S.; Komar, Anton A.

2017-01-01

Abstract RNA–protein interactions with physiological outcomes usually rely on conserved sequences within the RNA element. By contrast, activity of the diverse gamma-interferon-activated inhibitor of translation (GAIT)-elements relies on the conserved RNA folding motifs rather than the conserved sequence motifs. These elements drive the translational silencing of a group of chemokine (CC/CXC) and chemokine receptor (CCR) mRNAs, thereby helping to resolve physiological inflammation. Despite sequence dissimilarity, these RNA elements adopt common secondary structures (as revealed by 2D-1H NMR spectroscopy), providing a basis for their interaction with the RNA-binding GAIT complex. However, many of these elements (e.g. those derived from CCL22, CXCL13, CCR4 and ceruloplasmin (Cp) mRNAs) have substantially different affinities for GAIT complex binding. Toeprinting analysis shows that different positions within the overall conserved GAIT element structure contribute to differential affinities of the GAIT protein complex towards the elements. Thus, heterogeneity of GAIT elements may provide hierarchical fine-tuning of the resolution of inflammation. PMID:29069516

Genetic structure of the crown-of-thorns seastar in the Pacific Ocean, with focus on Guam

PubMed Central

Tusso, Sergio; Morcinek, Kerstin; Vogler, Catherine; Schupp, Peter J.; Caballes, Ciemon F.; Vargas, Sergio

2016-01-01

Population outbreaks of the corallivorous crown-of-thorns seastar (COTS), Acanthaster ‘planci’ L., are among the most important biological disturbances of tropical coral reefs. Over the past 50 years, several devastating outbreaks have been documented around Guam, an island in the western Pacific Ocean. Previous analyses have shown that in the Pacific Ocean, COTS larval dispersal may be geographically restricted to certain regions. Here, we assess the genetic structure of Pacific COTS populations and compared samples from around Guam with a number of distant localities in the Pacific Ocean, and focused on determining the degree of genetic structure among populations previously considered to be isolated. Using microsatellites, we document substantial genetic structure between 14 localities from different geographical regions in the Pacific Ocean. Populations from the 14 locations sampled were found to be structured in three significantly differentiated groups: (1) all locations immediately around Guam, as well as Kingman Reef and Swains Island; (2) Japan, Philippines, GBR and Vanuatu; and (3) Johnston Atoll, which was significantly different from all other localities. The lack of genetic differentiation between Guam and extremely distant populations from Kingman Reef and Swains Island suggests potential long-distance dispersal of COTS in the Pacific. PMID:27168979

Effect of regional slopes on local structure and exploration of tilted paleo-highs

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

Nazarov, D.A.; Chernobrov, B.S.

1986-06-01

Prospects for discovering local highs in old petroleum-producing regions have by now been substantially exhausted. Hence it is of great importance at this stage to seek non-anticlinal accumulations of hydrocarbons, including those in traps genetically associated with tilted paleo-highs, often represented in the modern structural plan by structural noses and terraces. Appropriate exploration for such types of deposits may soon become important in Ciscaucasia and other old petroleum-producing regions. Consequently, problems of the scientific basis for prospecting paleo-highs tilted in the modern structural plan, and developing procedures both for revealing and also for assessing their expression in the structural planmore » during different stages of geological history, and establishing the time and depth of changes in aspect, will become extremely topical. In order to discover possible local highs and to study their features within the margins of the platformal basins and the platformal edges of the marginal troughs, the authors use the method of removing the effect of the regional slope on the local structural plan. This paper describes this method. 13 references.« less

Visuomotor learning in cerebellar patients.

PubMed

Timmann, D; Shimansky, Y; Larson, P S; Wunderlich, D A; Stelmach, G E; Bloedel, J R

1996-11-01

The aim of the present study was to demonstrate that patients with pathology affecting substantial regions of the cerebellum can improve their performance in a series of two-dimensional tracing tasks, thus supporting the view that this type of motor behavior can be acquired even when the integrity of this structure is compromised. Eight patients with chronic, isolated cerebellar lesions and eight age- and sex-matched healthy controls were tested. Three patients had mild, five had moderate upper limb ataxia. The experiment was divided into two parts. In the first, subjects traced an irregularly shaped outline over 20 consecutive trials ('Trace 1' task). Next, subjects were asked to redraw the object without any underlying template as a guide ('Memory 1' task). In the second part of the study, subjects were asked to trace a different, irregularly shaped outline over 20 consecutive trials ('Trace 2' task). Next, they were required to redraw it by memory with its axis rotated 90 degrees ('Memory 2' task). In each of the memory tasks the template was placed over the drawn image after each trial and shown to the subjects. The error of performance was determined by calculating three different measurements, each focused on different aspects of the task. Based on these measurements, the cerebellar patients showed improvement in both memory tasks. In the 'Memory 1' task the calculated error decreased significantly for the patients with mild ataxia. In the 'Memory 2' task all cerebellar patients improved their performance substantially enough to reduce significantly the magnitude of all three error measurements. The experiments demonstrate that patients with cerebellar lesions are capable of improving substantially their performance of a complex motor task involving the recall of memorized shapes and the visuomotor control of a tracing movement.

Population Genetic Structure of Apple Scab (Venturia inaequalis (Cooke) G. Winter) in Iran

PubMed Central

Ebrahimi, Leila; Fotuhifar, Khalil-Berdi; Javan Nikkhah, Mohammad; Naghavi, Mohammad-Reza; Baisakh, Niranjan

2016-01-01

The population genetic structure of 278 Venturia inaequalis isolates, collected from different apple cultivars of eighteen different provinces in Iran, was investigated using 22 polymorphic microsatellite markers. Analysis of molecular variation, Bayesian clustering and Nei's genetic distance analyses based on 88 microsatellite alleles indicated substantial levels of gene flow among the collection sites. Ninety three percent of the variation was observed among the individuals within the populations and only 7% variation was observed among the populations. Structure analysis grouped the isolates into two populations. Maximum number of pathogen genotypes (44) was observed in the North of Iran that grows various different apple cultivars. Investigation on the variation of the pathogen on different cultivars in the North of Iran suggested a significant differentiation of the pathogen populations between wild apple and commercial cultivars. During sampling, varying ranges of scab infection were observed on various apple cultivars in forests, monoculture and mix orchards. Wild type apple (Malus orientalis) along the Caspian Sea Coast had the most infection in comparison with the Iranian endemic and commercial cultivars. Based on the genetic analysis and host tracking scenario of the pathogen, it was presumed that Iran could potentially be the center of origin of V. inaequalis, which requires further detailed studies with isolates collected from different parts of central Asia and world for confirmation. PMID:27631622

Biochemical and Structural Analysis of an Eis Family Aminoglycoside Acetyltransferase from Bacillus anthracis

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

Green, Keith D.; Biswas, Tapan; Chang, Changsoo

Proteins from the enhanced intracellular survival (Eis) family are versatile acetyltransferases that acetylate amines at multiple positions of several aminoglycosides (AGs). Their upregulation confers drug resistance. Homologues of Eis are present in diverse bacteria, including many pathogens. Eis from Mycobacterium tuberculosis (Eis_Mtb) has been well characterized. In this study, we explored the AG specificity and catalytic efficiency of the Eis family protein from Bacillus anthracis (Eis_Ban). Kinetic analysis of specificity and catalytic efficiency of acetylation of six AGs indicates that Eis_Ban displays significant differences from Eis_Mtb in both substrate binding and catalytic efficiency. The number of acetylated amines was alsomore » different for several AGs, indicating a distinct regiospecificity of Eis_Ban. Furthermore, most recently identified inhibitors of Eis_Mtb did not inhibit Eis_Ban, underscoring the differences between these two enzymes. To explain these differences, we determined an Eis_Ban crystal structure. The comparison of the crystal structures of Eis_Ban and Eis_Mtb demonstrates that critical residues lining their respective substrate binding pockets differ substantially, explaining their distinct specificities. Our results suggest that acetyltransferases of the Eis family evolved divergently to garner distinct specificities while conserving catalytic efficiency, possibly to counter distinct chemical challenges. The unique specificity features of these enzymes can be utilized as tools for developing AGs with novel modifications and help guide specific AG treatments to avoid Eis-mediated resistance.« less

A Grammar Library for Information Structure

ERIC Educational Resources Information Center

Song, Sanghoun

2014-01-01

This dissertation makes substantial contributions to both the theoretical and computational treatment of information structure, with an eye toward creating natural language processing applications such as multilingual machine translation systems. The aim of the present dissertation is to create a grammar library of information structure for the…

Characterization of the highly branched glycogen from the thermoacidophilic red microalga Galdieria sulphuraria and comparison with other glycogens.

PubMed

Martinez-Garcia, Marta; Stuart, Marc C A; van der Maarel, Marc J E C

2016-08-01

The thermoacidophilic red microalga Galdieria sulphuraria synthesizes glycogen when growing under heterotrophic conditions. Structural characterization revealed that G. sulphuraria glycogen is the most highly branched glycogen described to date, with 18% of α-(1→6) linkages. Moreover, it differs from other glycogens because it is composed of short chains only and has a substantially smaller molecular weight and particle size. The physiological role of this highly branched glycogen in G. sulphuraria is discussed. Copyright © 2016 Elsevier B.V. All rights reserved.

Fluorescent lamp unit with magnetic field generating means

DOEpatents

Grossman, Mark W.; George, William A.

1989-01-01

A fluorescent lamp unit having a magnetic field generating means for improving the performance of the fluorescent lamp is disclosed. In a preferred embodiment the fluorescent lamp comprises four longitudinally extending leg portions disposed in substantially quadrangular columnar array and joined by three generally U-shaped portions disposed in different planes. In another embodiment of the invention the magnetic field generating means comprises a plurality of permanent magnets secured together to form a single columnar structure disposed within a centrally located region defined by the shape of lamp envelope.

Fluorescent lamp unit with magnetic field generating means

DOEpatents

Grossman, M.W.; George, W.A.

1989-08-08

A fluorescent lamp unit having a magnetic field generating means for improving the performance of the fluorescent lamp is disclosed. In a preferred embodiment the fluorescent lamp comprises four longitudinally extending leg portions disposed in substantially quadrangular columnar array and joined by three generally U-shaped portions disposed in different planes. In another embodiment of the invention the magnetic field generating means comprises a plurality of permanent magnets secured together to form a single columnar structure disposed within a centrally located region defined by the shape of lamp envelope. 4 figs.

Method of fabricating a scalable nanoporous membrane filter

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

Tringe, Joseph W; Balhorn, Rodney L; Zaidi, Saleem

A method of fabricating a nanoporous membrane filter having a uniform array of nanopores etch-formed in a thin film structure (e.g. (100)-oriented single crystal silicon) having a predetermined thickness, by (a) using interferometric lithography to create an etch pattern comprising a plurality array of unit patterns having a predetermined width/diameter, (b) using the etch pattern to etch frustum-shaped cavities or pits in the thin film structure such that the dimension of the frustum floors of the cavities are substantially equal to a desired pore size based on the predetermined thickness of the thin film structure and the predetermined width/diameter ofmore » the unit patterns, and (c) removing the frustum floors at a boundary plane of the thin film structure to expose, open, and thereby create the nanopores substantially having the desired pore size.« less

The dimensionality of between-person differences in white matter microstructure in old age.

PubMed

Lövdén, Martin; Laukka, Erika Jonsson; Rieckmann, Anna; Kalpouzos, Grégoria; Li, Tie-Qiang; Jonsson, Tomas; Wahlund, Lars-Olof; Fratiglioni, Laura; Bäckman, Lars

2013-06-01

Between-person differences in white matter microstructure may partly generalize across the brain and partly play out differently for distinct tracts. We used diffusion-tensor imaging and structural equation modeling to investigate this issue in a sample of 260 adults aged 60-87 years. Mean fractional anisotropy and mean diffusivity of seven white matter tracts in each hemisphere were quantified. Results showed good fit of a model positing that individual differences in white matter microstructure are structured according to tracts. A general factor, although accounting for variance in the measures, did not adequately represent the individual differences. This indicates the presence of a substantial amount of tract-specific individual differences in white matter microstructure. In addition, individual differences are to a varying degree shared between tracts, indicating that general factors also affect white matter microstructure. Age-related differences in white matter microstructure were present for all tracts. Correlations among tract factors did not generally increase as a function of age, suggesting that aging is not a process with homogenous effects on white matter microstructure across the brain. These findings highlight the need for future research to examine whether relations between white matter microstructure and diverse outcomes are specific or general. Copyright © 2011 Wiley Periodicals, Inc.

Structural correlates of psychopathological symptom dimensions in schizophrenia: a voxel-based morphometric study.

PubMed

Koutsouleris, Nikolaos; Gaser, Christian; Jäger, Markus; Bottlender, Ronald; Frodl, Thomas; Holzinger, Silvia; Schmitt, Gisela J E; Zetzsche, Thomas; Burgermeister, Bernhard; Scheuerecker, Johanna; Born, Christine; Reiser, Maximilian; Möller, Hans-Jürgen; Meisenzahl, Eva M

2008-02-15

Structural neuroimaging has substantially advanced the neurobiological research of schizophrenia by describing a range of focal brain alterations as possible neuroanatomical underpinnings of the disease. Despite this progress, a considerable heterogeneity of structural findings persists that may reflect the phenomenological diversity of schizophrenia. It is unclear whether the range of possible clinical disease manifestations relates to a core structural brain deficit or to distinct structural correlates. Therefore, gray matter density (GMD) differences between 175 schizophrenic patients (SZ) and 177 matched healthy control subjects (HC) were examined in a three-step approach using cross-sectional and conjunctional voxel-based morphometry (VBM): (1) analysis of structural alterations irrespective of symptomatology; (2) subdivision of the patient sample according to a three-dimensional factor model of the PANSS and investigation of structural differences between these subsamples and healthy controls; (3) analysis of a common pattern of structural alterations present in all patient subsamples compared to healthy controls. Significant GMD reductions in patients compared to controls were identified within the prefrontal, limbic, paralimbic, temporal and thalamic regions. The disorganized symptom dimension was associated with bilateral alterations in temporal, insular and medial prefrontal cortices. Positive symptoms were associated with left-pronounced alterations in perisylvian regions and extended thalamic GMD losses. Negative symptoms were linked to the most extended alterations within orbitofrontal, medial prefrontal, lateral prefrontal and temporal cortices as well as limbic and subcortical structures. Thus, structural heterogeneity in schizophrenia may relate to specific patterns of GMD reductions that possibly share a common prefrontal-perisylvian pattern of structural brain alterations.

HIV Treatment as Prevention: Systematic Comparison of Mathematical Models of the Potential Impact of Antiretroviral Therapy on HIV Incidence in South Africa

PubMed Central

Eaton, Jeffrey W.; Johnson, Leigh F.; Salomon, Joshua A.; Bärnighausen, Till; Bendavid, Eran; Bershteyn, Anna; Bloom, David E.; Cambiano, Valentina; Fraser, Christophe; Hontelez, Jan A. C.; Humair, Salal; Klein, Daniel J.; Long, Elisa F.; Phillips, Andrew N.; Pretorius, Carel; Stover, John; Wenger, Edward A.; Williams, Brian G.; Hallett, Timothy B.

2012-01-01

Background Many mathematical models have investigated the impact of expanding access to antiretroviral therapy (ART) on new HIV infections. Comparing results and conclusions across models is challenging because models have addressed slightly different questions and have reported different outcome metrics. This study compares the predictions of several mathematical models simulating the same ART intervention programmes to determine the extent to which models agree about the epidemiological impact of expanded ART. Methods and Findings Twelve independent mathematical models evaluated a set of standardised ART intervention scenarios in South Africa and reported a common set of outputs. Intervention scenarios systematically varied the CD4 count threshold for treatment eligibility, access to treatment, and programme retention. For a scenario in which 80% of HIV-infected individuals start treatment on average 1 y after their CD4 count drops below 350 cells/µl and 85% remain on treatment after 3 y, the models projected that HIV incidence would be 35% to 54% lower 8 y after the introduction of ART, compared to a counterfactual scenario in which there is no ART. More variation existed in the estimated long-term (38 y) reductions in incidence. The impact of optimistic interventions including immediate ART initiation varied widely across models, maintaining substantial uncertainty about the theoretical prospect for elimination of HIV from the population using ART alone over the next four decades. The number of person-years of ART per infection averted over 8 y ranged between 5.8 and 18.7. Considering the actual scale-up of ART in South Africa, seven models estimated that current HIV incidence is 17% to 32% lower than it would have been in the absence of ART. Differences between model assumptions about CD4 decline and HIV transmissibility over the course of infection explained only a modest amount of the variation in model results. Conclusions Mathematical models evaluating the impact of ART vary substantially in structure, complexity, and parameter choices, but all suggest that ART, at high levels of access and with high adherence, has the potential to substantially reduce new HIV infections. There was broad agreement regarding the short-term epidemiologic impact of ambitious treatment scale-up, but more variation in longer term projections and in the efficiency with which treatment can reduce new infections. Differences between model predictions could not be explained by differences in model structure or parameterization that were hypothesized to affect intervention impact. Please see later in the article for the Editors' Summary PMID:22802730

Structural, Optical, and Vibrational Properties of ZnO Microrods Deposited on Silicon Substrate

NASA Astrophysics Data System (ADS)

Lahlouh, Bashar I.; Ikhmayies, Shadia J.; Juwhari, Hassan K.

2018-03-01

Zinc oxide (ZnO) microrod films deposited by spray pyrolysis on silicon substrate at 350 ± 5°C have been studied and evaluated, and compared with thin films deposited by electron beam to confirm the identity of the studied samples. The films were characterized using different techniques. The microrod structure was studied and confirmed by scanning electron microscopy. Fourier-transform infrared (FTIR) spectroscopy and x-ray diffraction analysis confirmed successful deposition of ZnO thin films with the expected wurtzite structure. Reflectance data showed a substantial drop across the whole studied wavelength range. The photoluminescence (PL) spectra of the studied samples showed a peak at ˜ 360 nm, representing a signature of ZnO. The shift in the PL peak position is due to defects and other species present in the films, as confirmed by FTIR and energy-dispersive x-ray spectroscopy results.

Crystal structure, spectrum character and explosive property of a new cocrystal CL-20/DNT

NASA Astrophysics Data System (ADS)

Liu, Ke; Zhang, Gao; Luan, Jieyu; Chen, Zhiqun; Su, Pengfei; Shu, Yuanjie

2016-04-01

A new cocrystal explosive of 2,4,6,8,10,12-hexanitrohexaazaiso-wurtzitane(CL-20) and 2,5-dinitrotoluene(DNT) in a molar ratio of 1:2 has been prepared by slow solvent evaporation method. Crystal structure of the cocrystal characterized by single crystal X-ray diffraction (SXRD) reveals that the cocrystal is formed by intermolecular hydrogen bond interactions and belongs to the triclinic system with P-1 group. Moreover, the obivious differences of powder X-ray diffraction (PXRD) patterns, infrared spectroscopy and Raman spectroscopy confirm that the intermolecular interactions have great influence for the crystal structure and formation of cocrystal. The cocrystal exhibits a lower impact height of 44 cm, suggesting a substantial reduction of sensitivity in comparison with CL-20. And thermal test results showed cocrystal obtains a lower melting point than DNT, which means huge advantages in blasting engineering.

Symmetry and asymmetry in the human brain

NASA Astrophysics Data System (ADS)

Hugdahl, Kenneth

2005-10-01

Structural and functional asymmetry in the human brain and nervous system is reviewed in a historical perspective, focusing on the pioneering work of Broca, Wernicke, Sperry, and Geschwind. Structural and functional asymmetry is exemplified from work done in our laboratory on auditory laterality using an empirical procedure called dichotic listening. This also involves different ways of validating the dichotic listening procedure against both invasive and non-invasive techniques, including PET and fMRI blood flow recordings. A major argument is that the human brain shows a substantial interaction between structurally, or "bottom-up" asymmetry and cognitively, or "top-down" modulation, through a focus of attention to the right or left side in auditory space. These results open up a more dynamic and interactive view of functional brain asymmetry than the traditional static view that the brain is lateralized, or asymmetric, only for specific stimuli and stimulus properties.

Bacterial Polysaccharide Co-Polymerases Share a Common Framework for Control of Polymer Length

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

Tocilj,A.; Munger, C.; Proteau, A.

2008-01-01

The chain length distribution of complex polysaccharides present on the bacterial surface is determined by polysaccharide co-polymerases (PCPs) anchored in the inner membrane. We report crystal structures of the periplasmic domains of three PCPs that impart substantially different chain length distributions to surface polysaccharides. Despite very low sequence similarities, they have a common protomer structure with a long central alpha-helix extending 100 Angstroms into the periplasm. The protomers self-assemble into bell-shaped oligomers of variable sizes, with a large internal cavity. Electron microscopy shows that one of the full-length PCPs has a similar organization as that observed in the crystal formore » its periplasmic domain alone. Functional studies suggest that the top of the PCP oligomers is an important region for determining polysaccharide modal length. These structures provide a detailed view of components of the bacterial polysaccharide assembly machinery.« less

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.

Seismotectonic zoning of Azerbaijan territory

NASA Astrophysics Data System (ADS)

Kangarli, Talat; Aliyev, Ali; Aliyev, Fuad; Rahimov, Fuad

2017-04-01

Studying of the space-time correlation and consequences effect between tectonic events and other geological processes that have created modern earth structure still remains as one of the most important problems in geology. This problem is especially important for the East Caucasus-South Caspian geodynamic zone. Being situated at the eastern part of the Caucasian strait, this zone refers to a center of Alpine-Himalayan active folded belt, and is known as a complex tectonic unit with jointing heterogeneous structural-substantial complexes arising from different branches of the belt (Doburja-Caucasus-Kopetdag from the north and Pyrenean-Alborz from the south with Kura and South Caspian zone). According to GPS and precise leveling data, activity of regional geodynamic processes shows intensive horizontal and vertical movements of the Earth's crust as conditioned by collision of the Arabian and Eurasian continental plates continuing since the end of Miocene. So far studies related to the regional of geology-geophysical data, periodically used for the geological and tectonic modeling of the environment mainly based on the fixing ideology. There still remains a number of uncertainties in solution of issues related to regional geology, tectonics and magmatism, structure and interrelation of different structural zones, space-time interrelations between onshore and offshore complexes, etc. At the same time large dataset produced by surface geological surveys, deep geological mapping of on- and offshore areas with the use of seismic and electrical reconnaissance and geophysical field zoning methods, deep well drilling and remote sensing activities. Conducted new studies produced results including differentiation of formerly unknown nappe complexes of the different ages and scales within the structure of mountain-fold zones, identification of new zones containing ophiolites in their section, outlining of currently active faulting areas, geophysical interpretation of the deep structure of Greater and Lesser Caucasus, detailed description of the deep structure of Caspian zone, Kur and Caspian megadepressions, identification of nappe-folded structure of the Absheron Peninsula and the Absheron threshold at the border of Middle and South Caspian, justification of the possible hydrocarbon concentration at the tectonically stratified substantial complexes of mountain and foothill areas, etc. Based on the outcomes of implemented researches, some general conclusions and schemes were drawn for some parts of the project region within the plate tectonics conceptual frameworks, to include the territories of Lesser Caucasus and South Caspian. Analysis and comparison of these data with macroseismic and instrumental data allowed us to conduct seismotectonic studies in a region and develop a new scheme of seismotectonic map with outlined recent and forecasted seismic activity. There also correlated foci zones of earthquakes with subhorizontal and subvertical borders in earth crust, which shows their structure-dynamic relationship. In the one hand, the earthquake foci zones belong to the faults of the basement which extend to sedimentary cover and their intersection knots. On the other hand, there appearing inner-block seismogenic levels, namely, in seismic generation acts all the earth crust: tectonic stress results on movements along fault zones, as well as lateral displacements along non-stable contacts of the structure-substance complexes of different competency.

Zero torque gear head wrench

NASA Technical Reports Server (NTRS)

Mcdougal, A. R.; Norman, R. M. (Inventor)

1976-01-01

A gear head wrench particularly suited for use in applying torque to bolts without transferring torsional stress to bolt-receiving structures is introduced. The wrench is characterized by a coupling including a socket, for connecting a bolt head with a torque multiplying gear train, provided within a housing having an annulus concentrically related to the socket and adapted to be coupled with a spacer interposed between the bolt head and the juxtaposed surface of the bolt-receiving structure for applying a balancing counter-torque to the spacer as torque is applied to the bolt head whereby the bolt-receiving structure is substantially isolated from torsional stress. As a result of the foregoing, the operator of the wrench is substantially isolated from any forces which may be imposed.

Ditch network sustains functional connectivity and influences patterns of gene flow in an intensive agricultural landscape

PubMed Central

Favre-Bac, L; Mony, C; Ernoult, A; Burel, F; Arnaud, J-F

2016-01-01

In intensive agricultural landscapes, plant species previously relying on semi-natural habitats may persist as metapopulations within landscape linear elements. Maintenance of populations' connectivity through pollen and seed dispersal is a key factor in species persistence in the face of substantial habitat loss. The goals of this study were to investigate the potential corridor role of ditches and to identify the landscape components that significantly impact patterns of gene flow among remnant populations. Using microsatellite loci, we explored the spatial genetic structure of two hydrochorous wetland plants exhibiting contrasting local abundance and different habitat requirements: the rare and regionally protected Oenanthe aquatica and the more commonly distributed Lycopus europaeus, in an 83 km2 agricultural lowland located in northern France. Both species exhibited a significant spatial genetic structure, along with substantial levels of genetic differentiation, especially for L. europaeus, which also expressed high levels of inbreeding. Isolation-by-distance analysis revealed enhanced gene flow along ditches, indicating their key role in effective seed and pollen dispersal. Our data also suggested that the configuration of the ditch network and the landscape elements significantly affected population genetic structure, with (i) species-specific scale effects on the genetic neighborhood and (ii) detrimental impact of human ditch management on genetic diversity, especially for O. aquatica. Altogether, these findings highlighted the key role of ditches in the maintenance of plant biodiversity in intensive agricultural landscapes with few remnant wetland habitats. PMID:26486611

Hidden relationships between metalloproteins unveiled by structural comparison of their metal sites

NASA Astrophysics Data System (ADS)

Valasatava, Yana; Andreini, Claudia; Rosato, Antonio

2015-03-01

Metalloproteins account for a substantial fraction of all proteins. They incorporate metal atoms, which are required for their structure and/or function. Here we describe a new computational protocol to systematically compare and classify metal-binding sites on the basis of their structural similarity. These sites are extracted from the MetalPDB database of minimal functional sites (MFSs) in metal-binding biological macromolecules. Structural similarity is measured by the scoring function of the available MetalS2 program. Hierarchical clustering was used to organize MFSs into clusters, for each of which a representative MFS was identified. The comparison of all representative MFSs provided a thorough structure-based classification of the sites analyzed. As examples, the application of the proposed computational protocol to all heme-binding proteins and zinc-binding proteins of known structure highlighted the existence of structural subtypes, validated known evolutionary links and shed new light on the occurrence of similar sites in systems at different evolutionary distances. The present approach thus makes available an innovative viewpoint on metalloproteins, where the functionally crucial metal sites effectively lead the discovery of structural and functional relationships in a largely protein-independent manner.

42 CFR 422.254 - Submission of bids.

Code of Federal Regulations, 2011 CFR

2011-10-01

... part or may choose not to renew the contract. (4) Substantial differences between bids. An MA organization's bid submissions must reflect differences in benefit packages or plan costs that CMS determines to represent substantial differences relative to a sponsor's other bid submissions. (5) CMS may...

42 CFR 422.254 - Submission of bids.

Code of Federal Regulations, 2012 CFR

2012-10-01

... this part or may choose not to renew the contract. (4) Substantial differences between bids. An MA organization's bid submissions must reflect differences in benefit packages or plan costs that CMS determines to represent substantial differences relative to a sponsor's other bid submissions. (5) CMS may...

42 CFR 422.254 - Submission of bids.

Code of Federal Regulations, 2013 CFR

2013-10-01

... this part or may choose not to renew the contract. (4) Substantial differences between bids. An MA organization's bid submissions must reflect differences in benefit packages or plan costs that CMS determines to represent substantial differences relative to a sponsor's other bid submissions. (5) CMS may...

The Changing Family Structure.

ERIC Educational Resources Information Center

Bernard van Leer Foundation Newsletter, 1993

1993-01-01

This newsletter issue contains feature articles and short reports on how and why family structures are undergoing substantial change in many parts of the world. These articles include: (1) "The Changing Family Structure," a review of how families are changing and why; (2) "Peru: Families in the Andes"; (3) "Thailand:…

GraDeR: Membrane Protein Complex Preparation for Single-Particle Cryo-EM.

PubMed

Hauer, Florian; Gerle, Christoph; Fischer, Niels; Oshima, Atsunori; Shinzawa-Itoh, Kyoko; Shimada, Satoru; Yokoyama, Ken; Fujiyoshi, Yoshinori; Stark, Holger

2015-09-01

We developed a method, named GraDeR, which substantially improves the preparation of membrane protein complexes for structure determination by single-particle cryo-electron microscopy (cryo-EM). In GraDeR, glycerol gradient centrifugation is used for the mild removal of free detergent monomers and micelles from lauryl maltose-neopentyl glycol detergent stabilized membrane complexes, resulting in monodisperse and stable complexes to which standard processes for water-soluble complexes can be applied. We demonstrate the applicability of the method on three different membrane complexes, including the mammalian FoF1 ATP synthase. For this highly dynamic and fragile rotary motor, we show that GraDeR allows visualizing the asymmetry of the F1 domain, which matches the ground state structure of the isolated domain. Therefore, the present cryo-EM structure of FoF1 ATP synthase provides direct structural evidence for Boyer's binding change mechanism in the context of the intact enzyme. Copyright © 2015 Elsevier Ltd. All rights reserved.

Synchrotron Protein Footprinting Supports Substrate Translocation by ClpA via ATP-Induced Movements of the D2 Loop

PubMed Central

Bohon, Jen; Jennings, Laura D.; Phillips, Christine M.; Licht, Stuart; Chance, Mark R.

2010-01-01

SUMMARY Synchrotron x-ray protein footprinting is used to study structural changes upon formation of the ClpA hexamer. Comparative solvent accessibilities between ClpA monomer and ClpA hexamer samples are in agreement throughout most of the sequence with calculations based on two previously proposed hexameric models. The data differ substantially from the proposed models in two parts of the structure: the D1 sensor 1 domain and the D2 loop region. The results suggest that these two regions can access alternate conformations in which their solvent protection is greater than in the structural models based on crystallographic data. In combination with previously reported structural data, the footprinting data provide support for a revised model in which the D2 loop contacts the D1 sensor 1 domain in the ATP-bound form of the complex. These data provide the first direct experimental support for the nucleotide-dependent D2 loop conformational change previously proposed to mediate substrate translocation. PMID:18682217

The effect of boron concentration on the structure and elastic properties of Ru-Ir alloys: first-principles calculations

NASA Astrophysics Data System (ADS)

Li, Xiaolong; Zhou, Zhaobo; Hu, Riming; Zhou, Xiaolong; Yu, Jie; Liu, Manmen

2018-04-01

The Phase stability, electronic structure, elastic properties and hardness of Ru-Ir alloys with different B concentration were investigated by first principles calculations. The calculated formation enthaplies and cohesive energies show that these compounds are all thermodynamically stable. Information on electronic structure indicates that they possess metallic characteristic and Ru-Ir-B alloys were composed of the Ru-B and Ir-B covalent bond. The elastic properties were calculated, which included bulk modulus, shear modulus, Young’s modulus, Poisson’s ratio and hardness. The calculated results reveal that the plastic of Ru-Ir-B alloys increase with the increase of the content of B atoms, but the hardness of Ru-Ir-B alloys have no substantial progress with the increase of the content of B atoms. However, it is interesting that the hardness of the Ru-Ir-B compound was improved obviously as the B content was higher than 18 atoms because of a phase structure transition.

Differences in self-rated health by employment contract and household structure among Japanese employees: a nationwide cross-sectional study.

PubMed

Kachi, Yuko; Inoue, Mariko; Nishikitani, Mariko; Yano, Eiji

2014-01-01

The aim of this study was to examine whether the association between employment contract and self-rated health differs by household structure in a representative sample of employees in Japan. The participants were 81,441 male and 64,471 female employees aged 18-59 years who had participated in the 2010 Comprehensive Survey of Living Conditions. We assessed the interactive effect of employment contract (permanent or precarious) and household structure (couple only, couple with children, single parent, single person, or other multi-person) on fair/poor health, adjusting for covariates by using logistic regression. We then calculated the relative poverty rate by employment contract and household structure. The interaction effect was significant for women (p<0.001) but not for men (p=0.413). A higher percentage of female precarious workers who lived in single-parent households (20.2%) reported fair/poor health compared with those in other types of households (10.4-13.2%), although the prevalence of fair/poor health did not differ substantially by household structure among female permanent workers. The relative poverty rates of female precarious workers who lived in single-parent households were higher compared with those of other female workers. Our results suggest that female precarious workers are not a homogeneous group and that those living in single-parent households suffer from poor health due to low income and insufficient coverage by insurance firms and family-based safety nets.

Ontogenetic variation of heritability and maternal effects in yellow-bellied marmot alarm calls.

PubMed

Blumstein, Daniel T; Nguyen, Kathy T; Martin, Julien G A

2013-05-07

Individuals of many species produce distinctive vocalizations that may relay potential information about the signaller. The alarm calls of some species have been reported to be individually specific, and this distinctiveness may allow individuals to access the reliability or kinship of callers. While not much is known generally about the heritability of mammalian vocalizations, if alarm calls were individually distinctive to permit kinship assessment, then call structure should be heritable. Here, we show conclusively for the first time that alarm call structure is heritable. We studied yellow-bellied marmots (Marmota flaviventris) and made nine quantitative measurements of their alarm calls. With a known genealogy, we used the animal model (a statistical technique) to estimate alarm call heritability. In juveniles, only one of the measured variables had heritability significantly different from zero; however, most variables had significant maternal environmental effects. By contrast, yearlings and adults had no significant maternal environmental effects, but the heritability of nearly all measured variables was significantly different from zero. Some, but not all of these heritable effects were significantly different across age classes. The presence of significantly non-zero maternal environmental effects in juveniles could reflect the impact of maternal environmental stresses on call structure. Regardless of this mechanism, maternal environmental effects could permit kinship recognition in juveniles. In older animals, the substantial genetic basis of alarm call structure suggests that calls could be used to assess kinship and, paradoxically, might also suggest a role of learning in call structure.

Ontogenetic variation of heritability and maternal effects in yellow-bellied marmot alarm calls

PubMed Central

Blumstein, Daniel T.; Nguyen, Kathy T.; Martin, Julien G. A.

2013-01-01

Individuals of many species produce distinctive vocalizations that may relay potential information about the signaller. The alarm calls of some species have been reported to be individually specific, and this distinctiveness may allow individuals to access the reliability or kinship of callers. While not much is known generally about the heritability of mammalian vocalizations, if alarm calls were individually distinctive to permit kinship assessment, then call structure should be heritable. Here, we show conclusively for the first time that alarm call structure is heritable. We studied yellow-bellied marmots (Marmota flaviventris) and made nine quantitative measurements of their alarm calls. With a known genealogy, we used the animal model (a statistical technique) to estimate alarm call heritability. In juveniles, only one of the measured variables had heritability significantly different from zero; however, most variables had significant maternal environmental effects. By contrast, yearlings and adults had no significant maternal environmental effects, but the heritability of nearly all measured variables was significantly different from zero. Some, but not all of these heritable effects were significantly different across age classes. The presence of significantly non-zero maternal environmental effects in juveniles could reflect the impact of maternal environmental stresses on call structure. Regardless of this mechanism, maternal environmental effects could permit kinship recognition in juveniles. In older animals, the substantial genetic basis of alarm call structure suggests that calls could be used to assess kinship and, paradoxically, might also suggest a role of learning in call structure. PMID:23466987

Silicon-integrated thin-film structure for electro-optic applications

DOEpatents

McKee, Rodney A.; Walker, Frederick Joseph

2000-01-01

A crystalline thin-film structure suited for use in any of an number of electro-optic applications, such as a phase modulator or a component of an interferometer, includes a semiconductor substrate of silicon and a ferroelectric, optically-clear thin film of the perovskite BaTiO.sub.3 overlying the surface of the silicon substrate. The BaTiO.sub.3 thin film is characterized in that substantially all of the dipole moments associated with the ferroelectric film are arranged substantially parallel to the surface of the substrate to enhance the electro-optic qualities of the film.

Spatial structure and distribution of small pelagic fish in the northwestern Mediterranean Sea.

PubMed

Saraux, Claire; Fromentin, Jean-Marc; Bigot, Jean-Louis; Bourdeix, Jean-Hervé; Morfin, Marie; Roos, David; Van Beveren, Elisabeth; Bez, Nicolas

2014-01-01

Understanding the ecological and anthropogenic drivers of population dynamics requires detailed studies on habitat selection and spatial distribution. Although small pelagic fish aggregate in large shoals and usually exhibit important spatial structure, their dynamics in time and space remain unpredictable and challenging. In the Gulf of Lions (north-western Mediterranean), sardine and anchovy biomasses have declined over the past 5 years causing an important fishery crisis while sprat abundance rose. Applying geostatistical tools on scientific acoustic surveys conducted in the Gulf of Lions, we investigated anchovy, sardine and sprat spatial distributions and structures over 10 years. Our results show that sardines and sprats were more coastal than anchovies. The spatial structure of the three species was fairly stable over time according to variogram outputs, while year-to-year variations in kriged maps highlighted substantial changes in their location. Support for the McCall's basin hypothesis (covariation of both population density and presence area with biomass) was found only in sprats, the most variable of the three species. An innovative method to investigate species collocation at different scales revealed that globally the three species strongly overlap. Although species often co-occurred in terms of presence/absence, their biomass density differed at local scale, suggesting potential interspecific avoidance or different sensitivity to local environmental characteristics. Persistent favourable areas were finally detected, but their environmental characteristics remain to be determined.

Effects of age on navigation strategy.

PubMed

Rodgers, M Kirk; Sindone, Joseph A; Moffat, Scott D

2012-01-01

Age differences in navigation strategies have been demonstrated in animals, with aged animals more likely to prefer an egocentric (route) strategy and younger animals more likely to prefer an allocentric (place) strategy. Using a novel virtual Y-maze strategy assessment (vYSA), the present study demonstrated substantial age differences in strategy preference in humans. Older adults overwhelmingly preferred an egocentric strategy, while younger adults were equally distributed between egocentric and allocentric preference. A preference for allocentric strategy on the Y-maze strategy assessment was found to benefit performance on an independent assessment (virtual Morris water task) only in younger adults. These results establish baseline age differences in spatial strategies and suggest this may impact performance on other spatial navigation assessments. The results are interpreted within the framework of age differences in hippocampal structure and function. Copyright © 2012 Elsevier Inc. All rights reserved.

Differing rates of antibody acquisition to merozoite antigens in malaria: implications for immunity and surveillance.

PubMed

McCallum, Fiona J; Persson, Kristina E M; Fowkes, Freya J I; Reiling, Linda; Mugyenyi, Cleopatra K; Richards, Jack S; Simpson, Julie A; Williams, Thomas N; Gilson, Paul R; Hodder, Anthony N; Sanders, Paul R; Anders, Robin F; Narum, David L; Chitnis, Chetan; Crabb, Brendan S; Marsh, Kevin; Beeson, James G

2017-04-01

Antibodies play a key role in acquired human immunity to Plasmodium falciparum (Pf) malaria and target merozoites to reduce or prevent blood-stage replication and the development of disease. Merozoites present a complex array of antigens to the immune system, and currently, there is only a partial understanding of the targets of protective antibodies and how responses to different antigens are acquired and boosted. We hypothesized that there would be differences in the rate of acquisition of antibodies to different antigens and how well they are boosted by infection, which impacts the acquisition of immunity. We examined responses to a range of merozoite antigens in 2 different cohorts of children and adults with different age structures and levels of malaria exposure. Overall, antibodies were associated with age, exposure, and active infection, and the repertoire of responses increased with age and active infection. However, rates of antibody acquisition varied between antigens and different regions within an antigen following exposure to malaria, supporting our hypothesis. Antigen-specific responses could be broadly classified into early response types in which antibodies were acquired early in childhood exposure and late response types that appear to require substantially more exposure for the development of substantial levels. We identified antigen-specific responses that were effectively boosted after recent infection, whereas other responses were not. These findings advance our understanding of the acquisition of human immunity to malaria and are relevant to the development of malaria vaccines targeting merozoite antigens and the selection of antigens for use in malaria surveillance. © Society for Leukocyte Biology.

User costs as one of main advantages of precast concrete application in highway construction

NASA Astrophysics Data System (ADS)

Tomek, Radan

2017-09-01

Road user cost primarily refer to the monetized components of road (re)construction impacts, such as the user delay costs, vehicle operating costs, crash costs and emission costs. Objective of this paper is to analyze and appraise the advantages and benefits of the innovative prefabrication approach in contrast to traditional cast-in-place construction method. The goal is to reduce these additional costs borne by motorists and the community at-large as a result of road construction activity to their minimum through application of the prefabrication. Assessing two basic possible approaches to highway infrastructure construction - casting the road pavements and structures either in place or precast off the site - it can be concluded that the initial capital investment costs do not vary much. Substantial differences can be recognized when comparing their life-cycle costs and an extent to which their construction process affects the public, environment and the local economy. Prefabrication of any structure component off-site offers major construction time and user cost savings in comparison with the traditional cast-in-place methods of construction. Precast prestressed road pavements’ technology and precasting bridges’ parts and elements offers dramatic increase in durability, while it also substantially decreases construction time and resulting user costs.

A pilot prospective feasibility study of organ-at-risk definition using Target Contour Testing/Instructional Computer Software (TaCTICS), a training and evaluation platform for radiotherapy target delineation.

PubMed

Kalpathy-Cramer, Jayashree; Bedrick, Steven D; Boccia, Kelly; Fuller, Clifton D

2011-01-01

Target volume delineation is a critical, but time-consuming step in the creation of radiation therapy plans used in the treatment of many types of cancer. However, variability in target volume definitions can introduce substantial differences in resulting doses to tumors and critical structures. We developed TaCTICS, a web-based educational training software application targeted towards non-expert users. We report on a small, prospective study to evaluate the utility of this online tool in improving conformance of regions-of-interest (ROIs) with a reference set. Eight residents contoured a set of structures for a head-and-neck cancer case. Subsequently, they were provided access to TaCTICS as well as contouring atlases to allow evaluation of their contours in reference to other users as well as reference ROIs. The residents then contoured a second case using these resources. Volume overlap metrics between the users showed a substantial improvement following the intervention. Additionally, 66% of users reported that they found TaCTICS to be a useful educational tool and all participants reported they would like to use TaCTICS to track their contouring skills over the course of their residency.

Substantial Expansion of Detectable Size Range in Ionic Current Sensing through Pores by Using a Microfluidic Bridge Circuit.

PubMed

Yasaki, Hirotoshi; Yasui, Takao; Yanagida, Takeshi; Kaji, Noritada; Kanai, Masaki; Nagashima, Kazuki; Kawai, Tomoji; Baba, Yoshinobu

2017-10-11

Measuring ionic currents passing through nano- or micropores has shown great promise for the electrical discrimination of various biomolecules, cells, bacteria, and viruses. However, conventional measurements have shown there is an inherent limitation to the detectable particle volume (1% of the pore volume), which critically hinders applications to real mixtures of biomolecule samples with a wide size range of suspended particles. Here we propose a rational methodology that can detect samples with the detectable particle volume of 0.01% of the pore volume by measuring a transient current generated from the potential differences in a microfluidic bridge circuit. Our method substantially suppresses the background ionic current from the μA level to the pA level, which essentially lowers the detectable particle volume limit even for relatively large pore structures. Indeed, utilizing a microscale long pore structure (volume of 5.6 × 10 4 aL; height and width of 2.0 × 2.0 μm; length of 14 μm), we successfully detected various samples including polystyrene nanoparticles (volume: 4 aL), bacteria, cancer cells, and DNA molecules. Our method will expand the applicability of ionic current sensing systems for various mixed biomolecule samples with a wide size range, which have been difficult to measure by previously existing pore technologies.

A comparison between the dynamics of horizontal and vertical axis offshore floating wind turbines.

PubMed

Borg, M; Collu, M

2015-02-28

The need to further exploit offshore wind resources in deeper waters has led to a re-emerging interest in vertical axis wind turbines (VAWTs) for floating foundation applications. However, there has been little effort to systematically compare VAWTs to the more conventional horizontal axis wind turbine (HAWT). This article initiates this comparison based on prime principles, focusing on the turbine aerodynamic forces and their impact on the floating wind turbine static and dynamic responses. VAWTs generate substantially different aerodynamic forces on the support structure, in particular, a potentially lower inclining moment and a substantially higher torque than HAWTs. Considering the static stability requirements, the advantages of a lower inclining moment, a lower wind turbine mass and a lower centre of gravity are illustrated, all of which are exploitable to have a less costly support structure. Floating VAWTs experience increased motion in the frequency range surrounding the turbine [number of blades]×[rotational speed] frequency. For very large VAWTs with slower rotational speeds, this frequency range may significantly overlap with the range of wave excitation forces. Quantitative considerations are undertaken comparing the reference NREL 5 MW HAWT with the NOVA 5 MW VAWT. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

A new registration method with voxel-matching technique for temporal subtraction images

NASA Astrophysics Data System (ADS)

Itai, Yoshinori; Kim, Hyoungseop; Ishikawa, Seiji; Katsuragawa, Shigehiko; Doi, Kunio

2008-03-01

A temporal subtraction image, which is obtained by subtraction of a previous image from a current one, can be used for enhancing interval changes on medical images by removing most of normal structures. One of the important problems in temporal subtraction is that subtraction images commonly include artifacts created by slight differences in the size, shape, and/or location of anatomical structures. In this paper, we developed a new registration method with voxel-matching technique for substantially removing the subtraction artifacts on the temporal subtraction image obtained from multiple-detector computed tomography (MDCT). With this technique, the voxel value in a warped (or non-warped) previous image is replaced by a voxel value within a kernel, such as a small cube centered at a given location, which would be closest (identical or nearly equal) to the voxel value in the corresponding location in the current image. Our new method was examined on 16 clinical cases with MDCT images. Preliminary results indicated that interval changes on the subtraction images were enhanced considerably, with a substantial reduction of misregistration artifacts. The temporal subtraction images obtained by use of the voxel-matching technique would be very useful for radiologists in the detection of interval changes on MDCT images.

Surprisingly little population genetic structure in a fungus-associated beetle despite its exploitation of multiple hosts

PubMed Central

Wood, Corlett W; Donald, Hannah M; Formica, Vincent A; Brodie, Edmund D

2013-01-01

In heterogeneous environments, landscape features directly affect the structure of genetic variation among populations by functioning as barriers to gene flow. Resource-associated population genetic structure, in which populations that use different resources (e.g., host plants) are genetically distinct, is a well-studied example of how environmental heterogeneity structures populations. However, the pattern that emerges in a given landscape should depend on its particular combination of resources. If resources constitute barriers to gene flow, population differentiation should be lowest in homogeneous landscapes, and highest where resources exist in equal proportions. In this study, we tested whether host community diversity affects population genetic structure in a beetle (Bolitotherus cornutus) that exploits three sympatric host fungi. We collected B. cornutus from plots containing the three host fungi in different proportions and quantified population genetic structure in each plot using a panel of microsatellite loci. We found no relationship between host community diversity and population differentiation in this species; however, we also found no evidence of resource-associated differentiation, suggesting that host fungi are not substantial barriers to gene flow. Moreover, we detected no genetic differentiation among B. cornutus populations separated by several kilometers, even though a previous study demonstrated moderate genetic structure on the scale of a few hundred meters. Although we found no effect of community diversity on population genetic structure in this study, the role of host communities in the structuring of genetic variation in heterogeneous landscapes should be further explored in a species that exhibits resource-associated population genetic structure. PMID:23789061

Lessons Learned in the Selection and Development of Test Cases for the Aeroelastic Prediction Workshop: Rectangular Supercritical Wing

NASA Technical Reports Server (NTRS)

Heeg, Jennifer; Chwalowski, Pawel; Wieseman, Carol D.; Florance, Jennifer P.; Schuster, David M.

2013-01-01

The Aeroelastic Prediction Workshop brought together an international community of computational fluid dynamicists as a step in defining the state of the art in computational aeroelasticity. The Rectangular Supercritical Wing (RSW) was chosen as the first configuration to study due to its geometric simplicity, perceived simple flow field at transonic conditions and availability of an experimental data set containing forced oscillation response data. Six teams performed analyses of the RSW; they used Reynolds-Averaged Navier-Stokes flow solvers exercised assuming that the wing had a rigid structure. Both steady-state and forced oscillation computations were performed by each team. The results of these calculations were compared with each other and with the experimental data. The steady-state results from the computations capture many of the flow features of a classical supercritical airfoil pressure distribution. The most dominant feature of the oscillatory results is the upper surface shock dynamics. Substantial variations were observed among the computational solutions as well as differences relative to the experimental data. Contributing issues to these differences include substantial wind tunnel wall effects and diverse choices in the analysis parameters.

Probing the structure of Leishmania major DHFR TS and structure based virtual screening of peptide library for the identification of anti-leishmanial leads.

PubMed

Rajasekaran, Rajalakshmi; Chen, Yi-Ping Phoebe

2012-09-01

Leishmaniasis, a multi-faceted ethereal disease is considered to be one of the World's major communicable diseases that demands exhaustive research and control measures. The substantial data on these protozoan parasites has not been utilized completely to develop potential therapeutic strategies against Leishmaniasis. Dihydrofolate reductase thymidylate synthase (DHFR-TS) plays a major role in the infective state of the parasite and hence the DHFR-TS based drugs remains of much interest to researchers working on Leishmaniasis. Although, crystal structures of DHFR-TS from different species including Plasmodium falciparum and Trypanosoma cruzi are available, the experimentally determined structure of the Leishmania major DHFR-TS has not yet been reported in the Protein Data Bank. A high quality three dimensional structure of L.major DHFR-TS has been modeled through the homology modeling approach. Carefully refined and the energy minimized structure of the modeled protein was validated using a number of structure validation programs to confirm its structure quality. The modeled protein structure was used in the process of structure based virtual screening to figure out a potential lead structure against DHFR TS. The lead molecule identified has a binding affinity of 0.51 nM and clearly follows drug like properties.

Framing Health Equity: US Health Disparities in Comparative Perspective.

PubMed

Lynch, Julia F; Perera, Isabel M

2017-10-01

In this article we explore systematically the different conceptions of health equity in key national health policy documents in the United States, the United Kingdom, and France. We find substantial differences across the three countries in the characterization of group differences (by SES, race/ethnicity, or territory), and the theorized causes of health inequalities (socioeconomic structures versus health care system features). In all three countries, reports throughout the period alluded at least minimally to inequalities in social determinants as the underlying cause of health inequalities. However, even in the reports with the strongest attachment to this causal model, the authors stop well short of advocating the redistribution of power and resources that would likely be necessary to redress these inequalities. Copyright © 2017 by Duke University Press.

Chemistry of acetylene on platinum (111) and (100) surfaces

PubMed Central

Muetterties, E. L.; Tasi, M.-C.; Kelemen, S. R.

1981-01-01

An ultra-high vacuum experimental study of acetylene chemisorption on Pt(111) and Pt(100) and of the reaction of hydrogen with the acetylene adsorbate has established distinguishing features of carbon-hydrogen bond breaking and making processes as a function of pressure, temperature, and surface crystallography. The rates for both processes are substantially higher on the Pt(100) surface. Net acetylene-hydrogen processes, in the temperature range of 20°C to ≈130°C, are distinctly different on the two surfaces: on Pt(100) the net reaction is hydrogen exchange (1H-2H exchange) and on Pt(111) the only detectable reaction is hydrogenation. Stereochemical differences in the acetylene adsorbate structure are considered to be a contributing factor to the differences in acetylene chemistry on these two surfaces. Images PMID:16593110

Identification, definition and mapping of terrestrial ecosystems in interior Alaska

NASA Technical Reports Server (NTRS)

Anderson, J. H. (Principal Investigator)

1973-01-01

The author has identified the following significant results. Two new, as yet unfinished vegetation maps are presented. These tend further to substantiate the belief that ERTS-1 imagery is a valuable mapping tool. Newly selected scenes show that vegetation interpretations can be refined through use of non-growing season imagery, particularly through the different spectral characteristics of vegetation lacking foliage and through the effect of vegetation structure on apparent snow cover. Scenes now are available for all test area north of the Alaska Range except Mt. McKinley National Park. No support was obtained for the hypothesis that similar interband ratios, from two areas apparently different spectrally because of different sun angles, would indicate similar surface features. However, attempts to test this hypothesis have so far been casual.

Structure of Particle Networks in Capillary Suspensions with Wetting and Nonwetting Fluids

PubMed Central

2016-01-01

The mechanical properties of a suspension can be dramatically altered by adding a small amount of a secondary fluid that is immiscible with the bulk phase. The substantial changes in the strength of these capillary suspensions arise due to the capillary force inducing a percolating particle network. Spatial information on the structure of the particle networks is obtained using confocal microscopy. It is possible, for the first time, to visualize the different types of percolating structures of capillary suspensions in situ. These capillary networks are unique from other types of particulate networks due to the nature of the capillary attraction. We investigate the influence of the three-phase contact angle on the structure of an oil-based capillary suspension with silica microspheres. Contact angles smaller than 90° lead to pendular networks of particles connected with single capillary bridges or clusters comparable to the funicular state in wet granular matter, whereas a different clustered structure, the capillary state, forms for angles larger than 90°. Particle pair distribution functions are obtained by image analysis, which demonstrate differences in the network microstructures. When porous particles are used, the pendular conformation also appears for apparent contact angles larger than 90°. The complex shear modulus can be correlated to these microstructural changes. When the percolating structure is formed, the complex shear modulus increases by nearly three decades. Pendular bridges lead to stronger networks than the capillary state network conformations, but the capillary state clusters are nevertheless much stronger than pure suspensions without the added liquid. PMID:26807651

The mammalian Cretaceous cochlear revolution.

PubMed

Manley, Geoffrey A

2017-09-01

The hearing organs of amniote vertebrates show large differences in their size and structure between the species' groups. In spite of this, their performance in terms of hearing sensitivity and the frequency selectivity of auditory-nerve units shows unexpectedly small differences. The only substantial difference is that therian, defined as live-bearing, mammalian groups are able to hear ultrasonic frequencies (above 15-20 kHz), whereas in contrast monotreme (egg laying) mammals and all non-mammalian amniotes cannot. This review compares the structure and physiology of the cochleae of the main groups and asks the question as to why the many structural differences seen in therian mammals arose, yet did not result in greater differences in physiology. The likely answers to this question are found in the history of the mammals during the Cretaceous period that ended 65 million years ago. During that period, the therian cochlea lost its lagenar macula, leading to a fall in endolymph calcium levels. This likely resulted in a small revolution and an auditory crisis that was compensated for by a subsequent series of structural and physiological adaptations. The end result was a system of equivalent performance to that independently evolved in other amniotes but with the additional - and of course "unforeseen" - advantage that ultrasonic-frequency responses became an available option. That option was not always availed of, but in most groups of therian mammals it did evolve and is used for communication and orientation based on improved sound localization, with micro-bats and toothed whales relying on it for prey capture. Copyright © 2016 Elsevier B.V. All rights reserved.

Clumpak: a program for identifying clustering modes and packaging population structure inferences across K.

PubMed

Kopelman, Naama M; Mayzel, Jonathan; Jakobsson, Mattias; Rosenberg, Noah A; Mayrose, Itay

2015-09-01

The identification of the genetic structure of populations from multilocus genotype data has become a central component of modern population-genetic data analysis. Application of model-based clustering programs often entails a number of steps, in which the user considers different modelling assumptions, compares results across different predetermined values of the number of assumed clusters (a parameter typically denoted K), examines multiple independent runs for each fixed value of K, and distinguishes among runs belonging to substantially distinct clustering solutions. Here, we present Clumpak (Cluster Markov Packager Across K), a method that automates the postprocessing of results of model-based population structure analyses. For analysing multiple independent runs at a single K value, Clumpak identifies sets of highly similar runs, separating distinct groups of runs that represent distinct modes in the space of possible solutions. This procedure, which generates a consensus solution for each distinct mode, is performed by the use of a Markov clustering algorithm that relies on a similarity matrix between replicate runs, as computed by the software Clumpp. Next, Clumpak identifies an optimal alignment of inferred clusters across different values of K, extending a similar approach implemented for a fixed K in Clumpp and simplifying the comparison of clustering results across different K values. Clumpak incorporates additional features, such as implementations of methods for choosing K and comparing solutions obtained by different programs, models, or data subsets. Clumpak, available at http://clumpak.tau.ac.il, simplifies the use of model-based analyses of population structure in population genetics and molecular ecology. © 2015 John Wiley & Sons Ltd.

Current density distributions and sputter marks in electron cyclotron resonance ion sources

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

Panitzsch, Lauri; Peleikis, Thies; Boettcher, Stephan

2013-01-15

Most electron cyclotron resonance ion sources use hexapolar magnetic fields for the radial confinement of the plasma. The geometry of this magnetic structure is then-induced by charged particles-mapped onto the inner side of the plasma electrode via sputtering and deposition. The resulting structures usually show two different patterns: a sharp triangular one in the central region which in some cases is even sputtered deep into the material (referred to as thin groove or sharp structure), and a blurred but still triangular-like one in the surroundings (referred to as broad halo). Therefore, both patterns seem to have different sources. To investigatemore » their origins we replaced the standard plasma electrode by a custom-built plasma electrode acting as a planar, multi-segment current-detector. For different biased disc voltages, detector positions, and source biases (referred to the detector) we measured the electrical current density distributions in the plane of the plasma electrode. The results show a strong and sharply confined electron population with triangular shape surrounded by less intense and spatially less confined ions. Observed sputter- and deposition marks are related to the analysis of the results. Our measurements suggest that the two different patterns (thin and broad) indeed originate from different particle populations. The thin structures seem to be caused by the hot electron population while the broad marks seem to stem from the medium to highly charged ions. In this paper we present our measurements together with theoretical considerations and substantiate the conclusions drawn above. The validity of these results is also discussed.« less

Black liquor and the hangover effect: fish assemblage recovery dynamics following a pulse disturbance

PubMed Central

Piller, Kyle R; Geheber, Aaron D

2015-01-01

Anthropogenic perturbations impact aquatic systems causing wide-ranging responses, from assemblage restructuring to assemblage recovery. Previous studies indicate the duration and intensity of disturbances play a role in the dynamics of assemblage recovery. In August 2011, the Pearl River, United States, was subjected to a weak black liquor spill from a paper mill which resulted in substantial loss of fish in a large stretch of the main channel. We quantified resilience and recovery of fish assemblage structure in the impacted area following the event. We compared downstream (impacted) assemblages to upstream (unimpacted) assemblages to determine initial impacts on structure. Additionally, we incorporated historic fish collections (1988–2011) to examine impacts on assemblage structure across broad temporal scales. Based on NMDS, upstream and downstream sites generally showed similar assemblage structure across sample periods with the exception of the 2 months postdischarge, where upstream and downstream sites visually differed. Multivariate analysis of variance (PERMANOVA) indicated significant seasonal variation among samples, but found no significant interaction between impacted and unimpacted assemblages following the discharge event. However, multivariate dispersion (MVDISP) showed greater variance among assemblage structure following the discharge event. These results suggest that 2 months following the disturbance represent a time period of stochasticity in regard to assemblage structure dynamics, and this was followed by rapid recovery. We term this dynamic the “hangover effect” as it represents the time frame from the cessation of the perturbation to the assemblage's return to predisturbance conditions. The availability and proximity of tributaries and upstream refugia, which were not affected by the disturbance, as well as the rapid recovery of abiotic parameters likely played a substantial role in assemblage recovery. This study not only demonstrates rapid recovery in an aquatic system, but further demonstrates the value of continuous, long-term, data collections which enhance our understanding of assemblage dynamics. PMID:26120432

Comminution process to produce engineered wood particles of uniform size and shape with disrupted grain structure from veneer

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

Dooley, James H; Lanning, David N

Comminution process of wood veneer to produce wood particles, by feeding wood veneer in a direction of travel substantially normal to grain through a counter rotating pair of intermeshing arrays of cutting discs arrayed axially perpendicular to the direction of veneer travel, wherein the cutting discs have a uniform thickness (Td), to produce wood particles characterized by a length dimension (L) substantially equal to the Td and aligned substantially parallel to grain, a width dimension (W) normal to L and aligned cross grain, and a height dimension (H) substantially equal to the veneer thickness (Tv) and aligned normal to Wmore » and L, wherein the W.times.H dimensions define a pair of substantially parallel end surfaces with end checking between crosscut fibers.« less

Pseudoscorpion mitochondria show rearranged genes and genome-wide reductions of RNA gene sizes and inferred structures, yet typical nucleotide composition bias

PubMed Central

2012-01-01

Background Pseudoscorpions are chelicerates and have historically been viewed as being most closely related to solifuges, harvestmen, and scorpions. No mitochondrial genomes of pseudoscorpions have been published, but the mitochondrial genomes of some lineages of Chelicerata possess unusual features, including short rRNA genes and tRNA genes that lack sequence to encode arms of the canonical cloverleaf-shaped tRNA. Additionally, some chelicerates possess an atypical guanine-thymine nucleotide bias on the major coding strand of their mitochondrial genomes. Results We sequenced the mitochondrial genomes of two divergent taxa from the chelicerate order Pseudoscorpiones. We find that these genomes possess unusually short tRNA genes that do not encode cloverleaf-shaped tRNA structures. Indeed, in one genome, all 22 tRNA genes lack sequence to encode canonical cloverleaf structures. We also find that the large ribosomal RNA genes are substantially shorter than those of most arthropods. We inferred secondary structures of the LSU rRNAs from both pseudoscorpions, and find that they have lost multiple helices. Based on comparisons with the crystal structure of the bacterial ribosome, two of these helices were likely contact points with tRNA T-arms or D-arms as they pass through the ribosome during protein synthesis. The mitochondrial gene arrangements of both pseudoscorpions differ from the ancestral chelicerate gene arrangement. One genome is rearranged with respect to the location of protein-coding genes, the small rRNA gene, and at least 8 tRNA genes. The other genome contains 6 tRNA genes in novel locations. Most chelicerates with rearranged mitochondrial genes show a genome-wide reversal of the CA nucleotide bias typical for arthropods on their major coding strand, and instead possess a GT bias. Yet despite their extensive rearrangement, these pseudoscorpion mitochondrial genomes possess a CA bias on the major coding strand. Phylogenetic analyses of all 13 mitochondrial protein-coding gene sequences consistently yield trees that place pseudoscorpions as sister to acariform mites. Conclusion The well-supported phylogenetic placement of pseudoscorpions as sister to Acariformes differs from some previous analyses based on morphology. However, these two lineages share multiple molecular evolutionary traits, including substantial mitochondrial genome rearrangements, extensive nucleotide substitution, and loss of helices in their inferred tRNA and rRNA structures. PMID:22409411

Predicting the performance of fingerprint similarity searching.

PubMed

Vogt, Martin; Bajorath, Jürgen

2011-01-01

Fingerprints are bit string representations of molecular structure that typically encode structural fragments, topological features, or pharmacophore patterns. Various fingerprint designs are utilized in virtual screening and their search performance essentially depends on three parameters: the nature of the fingerprint, the active compounds serving as reference molecules, and the composition of the screening database. It is of considerable interest and practical relevance to predict the performance of fingerprint similarity searching. A quantitative assessment of the potential that a fingerprint search might successfully retrieve active compounds, if available in the screening database, would substantially help to select the type of fingerprint most suitable for a given search problem. The method presented herein utilizes concepts from information theory to relate the fingerprint feature distributions of reference compounds to screening libraries. If these feature distributions do not sufficiently differ, active database compounds that are similar to reference molecules cannot be retrieved because they disappear in the "background." By quantifying the difference in feature distribution using the Kullback-Leibler divergence and relating the divergence to compound recovery rates obtained for different benchmark classes, fingerprint search performance can be quantitatively predicted.

Convergent immunological solutions to Argentine hemorrhagic fever virus neutralization.

PubMed

Zeltina, Antra; Krumm, Stefanie A; Sahin, Mehmet; Struwe, Weston B; Harlos, Karl; Nunberg, Jack H; Crispin, Max; Pinschewer, Daniel D; Doores, Katie J; Bowden, Thomas A

2017-07-03

Transmission of hemorrhagic fever New World arenaviruses from their rodent reservoirs to human populations poses substantial public health and economic dangers. These zoonotic events are enabled by the specific interaction between the New World arenaviral attachment glycoprotein, GP1, and cell surface human transferrin receptor (hTfR1). Here, we present the structural basis for how a mouse-derived neutralizing antibody (nAb), OD01, disrupts this interaction by targeting the receptor-binding surface of the GP1 glycoprotein from Junín virus (JUNV), a hemorrhagic fever arenavirus endemic in central Argentina. Comparison of our structure with that of a previously reported nAb complex (JUNV GP1-GD01) reveals largely overlapping epitopes but highly distinct antibody-binding modes. Despite differences in GP1 recognition, we find that both antibodies present a key tyrosine residue, albeit on different chains, that inserts into a central pocket on JUNV GP1 and effectively mimics the contacts made by the host TfR1. These data provide a molecular-level description of how antibodies derived from different germline origins arrive at equivalent immunological solutions to virus neutralization.

Influence of modulation periods on the tribological behavior of Si/a-C: H multilayer film

NASA Astrophysics Data System (ADS)

Zhu, Linan; Wu, Yanxia; Zhang, Shujiao; Yu, Shengwang; Tang, Bin; Liu, Ying; Zhou, Bing; Shen, Yanyan

2018-01-01

A series of Si/a-C: H multilayer films with different modulation periods were fabricated on stainless steel and silicon substrates by radio-frequency magnetron sputtering. The influence of the modulation period on the structure, morphology, mechanical properties and tribological behaviors in different environments (air, simulated acid rain, and NaCl solution) was investigated. The results show that the content of the sp2 hybrid carbon, surface roughness and hardness of the multilayer film increased firstly and then decreased with the decreased modulation period. Furthermore, the combination of the sublayer agrees well with the formation of the SiC crystal at the interface. Interestingly, the films show quite substantially different tribological properties in various test environments. The lowest friction coefficient is 0.2 for the S1 film in air. However, the lowest friction coefficient can reach 0.13 in solution. Importantly, the tribological behavior of the multilayer film is mainly determined by its hardness, as well as surface roughness in air while it is closely related with modulation period and interface structure in solution.

Misoriented grain boundaries vicinal to the (1 1 1) <1 1¯0> twin in nickel Part I: Thermodynamics & temperature-dependent structure

DOE PAGES

O’Brien, Christopher J.; Medlin, Douglas L.; Foiles, Stephen M.

2016-03-30

Here, grain boundary-engineered materials are of immense interest for their corrosion resistance, fracture resistance and microstructural stability. This work contributes to a larger goal of understanding both the structure and thermodynamic properties of grain boundaries vicinal (within ±30°) to the Σ3(1 1 1) <1 1¯0> (coherent twin) boundary which is found in grain boundary-engineered materials. The misoriented boundaries vicinal to the twin show structural changes at elevated temperatures. In the case of nickel, this transition temperature is substantially below the melting point and at temperatures commonly reached during processing, making the existence of such boundaries very likely in applications. Thus,more » the thermodynamic stability of such features is thoroughly investigated in order to predict and fully understand the structure of boundaries vicinal to twins. Low misorientation angle grain boundaries (|θ| ≲ 16°) show distinct ±1/3(1 1 1) disconnections which accommodate misorientation in opposite senses. The two types of disconnection have differing low-temperature structures which show different temperature-dependent behaviours with one type undergoing a structural transition at approximately 600 K. At misorientation angles greater than approximately ±16°, the discrete disconnection nature is lost as the disconnections merge into one another. Free energy calculations demonstrate that these high-angle boundaries, which exhibit a transition from a planar to a faceted structure, are thermodynamically more stable in the faceted configuration.« less

Adsorption-Induced Changes in Ribonuclease A Structure and Enzymatic Activity on Solid Surfaces

PubMed Central

2015-01-01

Ribonuclease A (RNase A) is a small globular enzyme that lyses RNA. The remarkable solution stability of its structure and enzymatic activity has led to its investigation to develop a new class of drugs for cancer chemotherapeutics. However, the successful clinical application of RNase A has been reported to be limited by insufficient stability and loss of enzymatic activity when it was coupled with a biomaterial carrier for drug delivery. The objective of this study was to characterize the structural stability and enzymatic activity of RNase A when it was adsorbed on different surface chemistries (represented by fused silica glass, high-density polyethylene, and poly(methyl-methacrylate)). Changes in protein structure were measured by circular dichroism, amino acid labeling with mass spectrometry, and in vitro assays of its enzymatic activity. Our results indicated that the process of adsorption caused RNase A to undergo a substantial degree of unfolding with significant differences in its adsorbed structure on each material surface. Adsorption caused RNase A to lose about 60% of its native-state enzymatic activity independent of the material on which it was adsorbed. These results indicate that the native-state structure of RNase A is greatly altered when it is adsorbed on a wide range of surface chemistries, especially at the catalytic site. Therefore, drug delivery systems must focus on retaining the native structure of RNase A in order to maintain a high level of enzymatic activity for applications such as antitumor chemotherapy. PMID:25420087

Structure of Leishmania major Methionyl-tRNA Synthetase in Complex with Intermediate Products Methionyladenylate and Pyrophosphate

PubMed Central

Larson, Eric T.; Kim, Jessica E.; Zucker, Frank H.; Kelley, Angela; Mueller, Natascha; Napuli, Alberto J.; Verlinde, Christophe L.M.J.; Fan, Erkang; Buckner, Frederick S.; Van Voorhis, Wesley C.; Merritt, Ethan A.; Hol, Wim G.J.

2011-01-01

Leishmania parasites cause two million new cases of leishmaniasis each year with several hundreds of millions people at risk. Due to the paucity and shortcomings of available drugs, we have undertaken the crystal structure determination of a key enzyme from Leishmania major in hopes of creating a platform for the rational design of new therapeutics. Crystals of the catalytic core of methionyl-tRNA synthetase from L. major (LmMetRS) were obtained with the substrates MgATP and methionine present in the crystallization medium. These crystals yielded the 2.0 Å resolution structure of LmMetRS in complex with two products, methionyladenylate and pyrophosphate, along with a Mg2+ ion that bridges them. This is the first class I aminoacyl-tRNA synthetase (aaRS) structure with pyrophosphate bound. The residues of the class I aaRS signature sequence motifs, KISKS and HIGH, make numerous contacts with the pyrophosphate. Substantial differences between the LmMetRS structure and previously reported complexes of E. coli MetRS (EcMetRS) with analogs of the methionyladenylate intermediate product are observed, even though one of these analogs only differs by one atom from the intermediate. The source of these structural differences is attributed to the presence of the product pyrophosphate in LmMetRS. Analysis of the LmMetRS structure in light of the Aquifex aeolicus MetRS-tRNAMet complex shows that major rearrangements of multiple structural elements of enzyme and/or tRNA are required to allow the CCA acceptor triplet to reach the methionyladenylate intermediate in the active site. Comparison with sequences of human cytosolic and mitochondrial MetRS reveals interesting differences near the ATP- and methionine-binding regions of LmMetRS, suggesting that it should be possible to obtain compounds that selectively inhibit the parasite enzyme. PMID:21144880

Thermionic converter

DOEpatents

Fitzpatrick, G.O.

1987-05-19

A thermionic converter is set forth which includes an envelope having an electron collector structure attached adjacent to a wall. An electron emitter structure is positioned adjacent the collector structure and spaced apart from opposite wall. The emitter and collector structures are in a common chamber. The emitter structure is heated substantially only by thermal radiation. Very small interelectrode gaps can be maintained utilizing the thermionic converter whereby increased efficiency results. 10 figs.

Structural basis for immunization with postfusion respiratory syncytial virus fusion F glycoprotein (RSV F) to elicit high neutralizing antibody titers

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

Swanson, Kurt A.; Settembre, Ethan C.; Shaw, Christine A.

2012-02-07

Respiratory syncytial virus (RSV), the main cause of infant bronchiolitis, remains a major unmet vaccine need despite more than 40 years of vaccine research. Vaccine candidates based on a chief RSV neutralization antigen, the fusion (F) glycoprotein, have foundered due to problems with stability, purity, reproducibility, and potency. Crystal structures of related parainfluenza F glycoproteins have revealed a large conformational change between the prefusion and postfusion states, suggesting that postfusion F antigens might not efficiently elicit neutralizing antibodies. We have generated a homogeneous, stable, and reproducible postfusion RSV F immunogen that elicits high titers of neutralizing antibodies in immunized animals.more » The 3.2-{angstrom} X-ray crystal structure of this substantially complete RSV F reveals important differences from homology-based structural models. Specifically, the RSV F crystal structure demonstrates the exposure of key neutralizing antibody binding sites on the surface of the postfusion RSV F trimer. This unanticipated structural feature explains the engineered RSV F antigen's efficiency as an immunogen. This work illustrates how structural-based antigen design can guide the rational optimization of candidate vaccine antigens.« less

A Fast Surrogate-facilitated Data-driven Bayesian Approach to Uncertainty Quantification of a Regional Groundwater Flow Model with Structural Error

NASA Astrophysics Data System (ADS)

Xu, T.; Valocchi, A. J.; Ye, M.; Liang, F.

2016-12-01

Due to simplification and/or misrepresentation of the real aquifer system, numerical groundwater flow and solute transport models are usually subject to model structural error. During model calibration, the hydrogeological parameters may be overly adjusted to compensate for unknown structural error. This may result in biased predictions when models are used to forecast aquifer response to new forcing. In this study, we extend a fully Bayesian method [Xu and Valocchi, 2015] to calibrate a real-world, regional groundwater flow model. The method uses a data-driven error model to describe model structural error and jointly infers model parameters and structural error. In this study, Bayesian inference is facilitated using high performance computing and fast surrogate models. The surrogate models are constructed using machine learning techniques to emulate the response simulated by the computationally expensive groundwater model. We demonstrate in the real-world case study that explicitly accounting for model structural error yields parameter posterior distributions that are substantially different from those derived by the classical Bayesian calibration that does not account for model structural error. In addition, the Bayesian with error model method gives significantly more accurate prediction along with reasonable credible intervals.

Lactate Dehydrogenase Undergoes a Substantial Structural Change to Bind its Substrate

PubMed Central

Qiu, Linlin; Gulotta, Miriam; Callender, Robert

2007-01-01

Employing temperature-jump relaxation spectroscopy, we investigate the kinetics and thermodynamics of the formation of a very early ternary binding intermediate formed when lactate dehydrogenase (LDH) binds a substrate mimic on its way to forming the productive LDH/NADH·substrate Michaelis complex. Temperature-jump scans show two distinct submillisecond processes are involved in the formation of this ternary binding intermediate, called the encounter complex here. The on-rate of the formation of the encounter complex from LDH/NADH with oxamate (a substrate mimic) is determined as a function of temperature and in the presence of small concentrations of a protein destabilizer (urea) and protein stabilizer (TMAO). It shows a strong temperature dependence with inverse Arrhenius behavior and a temperature-dependent enthalpy (heat capacity of 610 ± 84 cal/Mol K), is slowed in the presence of TMAO and speeded up in the presence of urea. These results suggest that LDH/NADH occupies a range of conformations, some competent to bind substrate (open structure; a minority population) and others noncompetent (closed), in fast equilibrium with each other in accord with a select fit model of binding. From the thermodynamic results, the two species differ in the rearrangement of low energy hydrogen bonds as would arise from changes in internal hydrogen bonding and/or increases in the solvation of the protein structure. The binding-competent species can bind ligand at or very near diffusion-limited speeds, suggesting that the binding pocket is substantially exposed to solvent in these species. This would be in contrast to the putative closed structure where the binding pocket resides deep within the protein interior. PMID:17483169

Crystal Structure of Cockroach Allergen Bla g 2, an Unusual Zinc Binding Aspartic Protease with a Novel Mode of Self-inhibition

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

Gustchina, Alla; Li, Mi; Wunschmann, Sabina

2010-07-19

The crystal structure of Bla g 2 was solved in order to investigate the structural basis for the allergenic properties of this unusual protein. This is the first structure of an aspartic protease in which conserved glycine residues, in two canonical DTG triads, are substituted by different amino acid residues. Another unprecedented feature revealed by the structure is the single phenylalanine residue insertion on the tip of the flap, with the side-chain occupying the S1 binding pocket. This and other important amino acid substitutions in the active site region of Bla g 2 modify the interactions in the vicinity ofmore » the catalytic aspartate residues, increasing the distance between them to {approx}4 {angstrom} and establishing unique direct contacts between the flap and the catalytic residues. We attribute the absence of substantial catalytic activity in Bla g 2 to these unusual features of the active site. Five disulfide bridges and a Zn-binding site confer stability to the protein, which may contribute to sensitization at lower levels of exposure than other allergens.« less

An Unusual Hydrophobic Core Confers Extreme Flexibility to HEAT Repeat Proteins

PubMed Central

Kappel, Christian; Zachariae, Ulrich; Dölker, Nicole; Grubmüller, Helmut

2010-01-01

Alpha-solenoid proteins are suggested to constitute highly flexible macromolecules, whose structural variability and large surface area is instrumental in many important protein-protein binding processes. By equilibrium and nonequilibrium molecular dynamics simulations, we show that importin-β, an archetypical α-solenoid, displays unprecedentedly large and fully reversible elasticity. Our stretching molecular dynamics simulations reveal full elasticity over up to twofold end-to-end extensions compared to its bound state. Despite the absence of any long-range intramolecular contacts, the protein can return to its equilibrium structure to within 3 Å backbone RMSD after the release of mechanical stress. We find that this extreme degree of flexibility is based on an unusually flexible hydrophobic core that differs substantially from that of structurally similar but more rigid globular proteins. In that respect, the core of importin-β resembles molten globules. The elastic behavior is dominated by nonpolar interactions between HEAT repeats, combined with conformational entropic effects. Our results suggest that α-solenoid structures such as importin-β may bridge the molecular gap between completely structured and intrinsically disordered proteins. PMID:20816072

A study of fluid-structure problems

NASA Astrophysics Data System (ADS)

Lam, Dennis Kang-Por

The stability of structures with and without fluid load is investigated. A method is developed for determining the fluid load in terms of added structural mass. Finite element methods are employed to study the buckling of a cylindrical shell under axial compression and liquid storage tanks under hydrodynamic load. Both linear and nonlinear analyses are performed. Diamond modes are found to be the possible postbuckling shapes of the cylindrical shell. Local buckling including elephant-foot buckle and diamond buckle are found for the liquid storage tank models. Comparison between the linear and nonlinear results indicates a substantial difference in buckling mode shapes, though the buckling loads are close to each other. The method for determining the hydrodynamic mass is applied to the impeller stage of a centrifugal pump. The method is based on a linear perturbation technique which assumes that the disturbance in the flow boundaries and velocities caused by the motion of the structure is small. A potential method is used to estimate the velocity flow field. The hydrodynamic mass is then obtained by calculating the total force which results from the pressure induced by a perturbation of the structure.

Changing Nuclear Landscape and Unique PML Structures During Early Epigenetic Transitions of Human Embryonic Stem Cells

PubMed Central

Butler, John T.; Hall, Lisa L.; Smith, Kelly P.; Lawrence, Jeanne B.

2010-01-01

The complex nuclear structure of somatic cells is important to epigenomic regulation, yet little is known about nuclear organization of human embryonic stem cells (hESC). Here we surveyed several nuclear structures in pluripotent and transitioning hESC. Observations of centromeres, telomeres, SC35 speckles, Cajal Bodies, lamin A/C and emerin, nuclear shape and size demonstrate a very different “nuclear landscape” in hESC. This landscape is remodeled during a brief transitional window, concomitant with or just prior to differentiation onset. Notably, hESC initially contain abundant signal for spliceosome assembly factor, SC35, but lack discrete SC35 domains; these form as cells begin to specialize, likely reflecting cell-type specific genomic organization. Concomitantly, nuclear size increases and shape changes as lamin A/C and emerin incorporate into the lamina. During this brief window, hESC exhibit dramatically different PML-defined structures, which in somatic cells are linked to gene regulation and cancer. Unlike the numerous, spherical somatic PML bodies, hES cells often display ~1–3 large PML structures of two morphological types: long linear “rods” or elaborate “rosettes”, which lack substantial SUMO-1, Daxx, and Sp100.These occur primarily between Day 0–2 of differentiation and become rare thereafter. PML rods may be “taut” between other structures, such as centromeres, but clearly show some relationship with the lamina, where PML often abuts or fills a “gap” in early lamin A/C staining. Findings demonstrate that pluripotent hES cells have a markedly different overall nuclear architecture, remodeling of which is linked to early epigenomic programming and involves formation of unique PML-defined structures. PMID:19449340

The Relationship between the Morphology and Structure and the Quality of Fruits of Two Pear Cultivars (Pyrus communis L.) during Their Development and Maturation

PubMed Central

2013-01-01

The flavour and nutritional values of pears are appreciated by consumers worldwide, who, however, demand specific fruit quality, that is, attractive appearance, firmness and flavour, and health safety as well as long-term shelf life and storability. Pear cultivars differ in terms of the above-mentioned traits; therefore, we undertook investigations to demonstrate the differences in structure of fruits of two pear cultivars that determine fruit quality in its broadest sense. The micromorphology, anatomy, and ultrastructure of “Clapp's Favourite” and “Conference” fruits in the fruit set stage and in the harvest maturity stage were investigated under light microscope and scanning and transmission electron microscopes. The fruits of “Clapp's Favourite” and “Conference” in the fruit set stage exhibited distinct differences in the values of anatomical parameters only. Substantial differences in fruit structure were observed in the harvest maturity stage. The analyses indicate that firmness and durability of pear fruits are largely influenced by the presence of russeting, the proportion of closed lenticels and number of stone cells, and the content of starch grains and tannin compounds. The thickness of the cuticle and presence of epicuticular waxes as well as the number of lenticels and the number and depth of microcracks play a minor role. PMID:24327806

Colony social structure in native and invasive populations of the social wasp Vespula pensylvanica

USGS Publications Warehouse

Hanna, Cause; Cook, Erin D.; Thompson, Ariel R.; Dare, Lyndzey E.; Palaski, Amanda L.; Foote, David; Goodisman, Michael A. D.

2014-01-01

Social insects rank among the most invasive of terrestrial species. The success of invasive social insects stems, in part, from the flexibility derived from their social behaviors. We used genetic markers to investigate if the social system of the invasive wasp, Vespula pensylvanica, differed in its introduced and native habitats in order to better understand variation in social phenotype in invasive social species. We found that (1) nestmate workers showed lower levels of relatedness in introduced populations than native populations, (2) introduced colonies contained workers produced by multiple queens whereas native colonies contained workers produced by only a single queen, (3) queen mate number did not differ significantly between introduced and native colonies, and (4) workers from introduced colonies were frequently produced by queens that originated from foreign nests. Thus, overall, native and introduced colonies differed substantially in social phenotype because introduced colonies more frequently contained workers produced by multiple, foreign queens. In addition, the similarity in levels of genetic variation in introduced and native habitats, as well as observed variation in colony social phenotype in native populations, suggest that colony structure in invasive populations may be partially associated with social plasticity. Overall, the differences in social structure observed in invasive V. pensylvanica parallel those in other, distantly related invasive social insects, suggesting that insect societies often develop similar social phenotypes upon introduction into new habitats.

Market structures, socioeconomics, and tobacco usage patterns in Madagascar.

PubMed

Blecher, Evan; Liber, Alex C; Chaussard, Martine; Fedewa, Stacey

2014-01-01

The isolated island nation of Madagascar has substantial prevalence of both smoking and smokeless tobacco use, although not of dual use. Madagascar's tobacco market, much like its historical and cultural underpinnings, appears to have both Asian and African influences. Additionally, it has a unique market structure that plays an important role in influencing patterns of tobacco use. This study analyzes the determinants of smoking and smokeless tobacco use in Madagascar. We used the 2008 Madagascar Demographic and Health Survey to analyze both smoking tobacco and smokeless tobacco use, stratified by gender. Multivariate log binomial models were used to evaluate the relationship between tobacco use and age, residence (urban/rural), province, marital status, and education. Our analysis indicates that two distinctly different groups of people use two distinctly different tobacco products. Smoking is almost exclusively used by men and does not appear to be related to socioeconomic status. Conversely, smokeless tobacco is consumed by large proportions of both men and women, who are less educated and live in rural areas of the country. This disparate pattern in consumption is a reflection of the different market structures for smokeless tobacco (a cottage industry) and smoking tobacco (a near monopoly). Distinct market-based, geographic, and socioeconomic disparities in tobacco use are explored in order to begin the classification of Madagascar's tobacco epidemic as more African, more Asian, or as a distinctly different environment.

Effect of Nitrooxy Compounds with Different Molecular Structures on the Rumen Methanogenesis, Metabolic Profile, and Methanogenic Community.

PubMed

Jin, Wei; Meng, Zhenxiang; Wang, Jing; Cheng, Yanfen; Zhu, Weiyun

2017-08-01

Rumen in vitro fermentation was used to evaluate the capacity of nitrooxy compounds to mitigate rumen methane production. The following three nitrooxy compounds, each with different molecular structures, were evaluated: 2,2-dimethyl-3-(nitrooxy) propanoic (DNP), N-[2-(Nitrooxy)ethyl]-3-pyridinecarboxamide (NPD), and nitroglycerin (NG). All three compounds substantially decreased the total gas production, methane production, and the acetate:propionate ratio, while increasing hydrogen production. The growth of methanogens was specifically inhibited by all three compounds, without affecting the abundance of bacteria, anaerobic fungi, or protozoa. However, inhibition of methanogenesis required a much higher dose of DNP when compared to NPD or NG. Further investigations were conducted on NG to determine its effects on the methanogenic community. NG reduced the relative abundance of Methanomassiliicoccales, while increasing the relative abundance of Methanobrevibacter and Methanosphaera. Overall, the results suggested that all three of these nitrooxy compounds could specifically inhibit rumen methanogenesis, but NPD and NG were much more efficient than DNP at rumen methane mitigation.

Temperature structure and emergent flux of the Jovian planets

NASA Technical Reports Server (NTRS)

Silvaggio, P.; Sagan, C.

1978-01-01

Long path, low temperature, moderate resolution spectra of methane and ammonia, broadened by hydrogen and helium, are used to calculate non-gray model atmospheres for the four Jovian planets. The fundamental and first overtone of hydrogen contributes enough absorption to create a thermal inversion for each of the planets. The suite of emergent spectral fluxes and representative limb darkenings and brightenings are calculated for comparison with the Voyager infrared spectra. The temperature differences between Jovian belts and zones corresponds to a difference in the ammonia cirrus particle radii (1 to 3 micron in zones; 10 micron in belts). The Jovian tropopause is approximately at the 0.1 bar level. A thin ammonia cirrus haze should be distributed throughout the Saturnian troposphere; and NH3 gas must be slightly supersaturated or ammonia ice particles are carried upwards convectively in the upper troposphere of Saturn. Substantial methane clouds exist on both Uranus and Neptune. There is some evidence for almost isothermal structures in the deep atmospheres of these two planets.

Validating Female Psychopathy Subtypes: Differences in Personality, Antisocial and Violent Behavior, Substance Abuse, Trauma, and Mental Health

PubMed Central

Hicks, Brian M.; Vaidyanathan, Uma; Patrick, Christopher J.

2010-01-01

Recent empirical investigations utilizing male prisoners have begun to validate clinical conceptualizations of primary and secondary psychopathy subtypes. We extended this literature by identifying similar psychopathic subtypes in female prisoners on the basis of personality structure using model-based cluster analysis. Secondary psychopaths (n = 39) were characterized by personality traits of negative emotionality and low behavioral constraint, an early onset of antisocial and criminal behavior, greater substance use and abuse, more violent behavior and institutional misconduct, and more mental health problems including symptoms of post-traumatic stress disorder and suicide attempts. Primary psychopaths (n = 31) exhibited few distinguishing personality features but were prolific criminals especially in regards to non-violent crime, and exhibited relatively few mental health problems despite substantial exposure to traumatic events. The results support alternative etiological pathways to antisocial and criminal behavior that are evident in personality structure as well as gender similarities and differences in the manifestation of psychopathic personalities. PMID:20582155

Synthesis of substantially monodispersed colloids

NASA Technical Reports Server (NTRS)

Stoeva, Savka (Inventor); Klabunde, Kenneth J. (Inventor); Sorensen, Christopher (Inventor)

2003-01-01

A method of forming ligated nanoparticles of the formula Y(Z).sub.x where Y is a nanoparticle selected from the group consisting of elemental metals having atomic numbers ranging from 21-34, 39-52, 57-83 and 89-102, all inclusive, the halides, oxides and sulfides of such metals, and the alkali metal and alkaline earth metal halides, and Z represents ligand moieties such as the alkyl thiols. In the method, a first colloidal dispersion is formed made up of nanoparticles solvated in a molar excess of a first solvent (preferably a ketone such as acetone), a second solvent different than the first solvent (preferably an organic aryl solvent such as toluene) and a quantity of ligand moieties; the first solvent is then removed under vacuum and the ligand moieties ligate to the nanoparticles to give a second colloidal dispersion of the ligated nanoparticles solvated in the second solvent. If substantially monodispersed nanoparticles are desired, the second dispersion is subjected to a digestive ripening process. Upon drying, the ligated nanoparticles may form a three-dimensional superlattice structure.

Carbon nanotube-based sensor and method for detection of crack growth in a structure

NASA Technical Reports Server (NTRS)

Smits, Jan M. (Inventor); Moore, Thomas C. (Inventor); Kite, Marlen T. (Inventor); Wincheski, Russell A. (Inventor); Ingram, JoAnne L. (Inventor); Watkins, Anthony N. (Inventor); Williams, Phillip A. (Inventor)

2007-01-01

A sensor has a plurality of carbon nanotube (CNT)-based conductors operatively positioned on a substrate. The conductors are arranged side-by-side, such as in a substantially parallel relationship to one another. At least one pair of spaced-apart electrodes is coupled to opposing ends of the conductors. A portion of each of the conductors spanning between each pair of electrodes comprises a plurality of carbon nanotubes arranged end-to-end and substantially aligned along an axis. Because a direct correlation exists between the resistance of a carbon nanotube and its strain, changes experienced by the portion of the structure to which the sensor is coupled induce a corresponding change in the electrical properties of the conductors, thereby enabling detection of crack growth in the structure.

Substrate structures for InP-based devices

DOEpatents

Wanlass, Mark W.; Sheldon, Peter

1990-01-01

A substrate structure for an InP-based semiconductor device having an InP based film is disclosed. The substrate structure includes a substrate region having a lightweight bulk substrate and an upper GaAs layer. An interconnecting region is disposed between the substrate region and the InP-based device. The interconnecting region includes a compositionally graded intermediate layer substantially lattice-matched at one end to the GaAs layer and substantially lattice-matched at the opposite end to the InP-based film. The interconnecting region further includes a dislocation mechanism disposed between the GaAs layer and the InP-based film in cooperation with the graded intermediate layer, the buffer mechanism blocking and inhibiting propagation of threading dislocations between the substrate region, and the InP-based device.

Abbreviated neuropsychological assessment in schizophrenia

PubMed Central

Harvey, Philip D.; Keefe, Richard S. E.; Patterson, Thomas L.; Heaton, Robert K.; Bowie, Christopher R.

2008-01-01

The aim of this study was to identify the best subset of neuropsychological tests for prediction of several different aspects of functioning in a large (n = 236) sample of older people with schizophrenia. While the validity of abbreviated assessment methods has been examined before, there has never been a comparative study of the prediction of different elements of cognitive impairment, real-world outcomes, and performance-based measures of functional capacity. Scores on 10 different tests from a neuropsychological assessment battery were used to predict global neuropsychological (NP) performance (indexed with averaged scores or calculated general deficit scores), performance-based indices of everyday-living skills and social competence, and case-manager ratings of real-world functioning. Forward entry stepwise regression analyses were used to identify the best predictors for each of the outcomes measures. Then, the analyses were adjusted for estimated premorbid IQ, which reduced the magnitude, but not the structure, of the correlations. Substantial amounts (over 70%) of the variance in overall NP performance were accounted for by a limited number of NP tests. Considerable variance in measures of functional capacity was also accounted for by a limited number of tests. Different tests constituted the best predictor set for each outcome measure. A substantial proportion of the variance in several different NP and functional outcomes can be accounted for by a small number of NP tests that can be completed in a few minutes, although there is considerable unexplained variance. However, the abbreviated assessments that best predict different outcomes vary across outcomes. Future studies should determine whether responses to pharmacological and remediation treatments can be captured with brief assessments as well. PMID:18720182

Effects of a large wildfire on vegetation structure in a variable fire mosaic.

PubMed

Foster, C N; Barton, P S; Robinson, N M; MacGregor, C I; Lindenmayer, D B

2017-12-01

Management guidelines for many fire-prone ecosystems highlight the importance of maintaining a variable mosaic of fire histories for biodiversity conservation. Managers are encouraged to aim for fire mosaics that are temporally and spatially dynamic, include all successional states of vegetation, and also include variation in the underlying "invisible mosaic" of past fire frequencies, severities, and fire return intervals. However, establishing and maintaining variable mosaics in contemporary landscapes is subject to many challenges, one of which is deciding how the fire mosaic should be managed following the occurrence of large, unplanned wildfires. A key consideration for this decision is the extent to which the effects of previous fire history on vegetation and habitats persist after major wildfires, but this topic has rarely been investigated empirically. In this study, we tested to what extent a large wildfire interacted with previous fire history to affect the structure of forest, woodland, and heath vegetation in Booderee National Park in southeastern Australia. In 2003, a summer wildfire burned 49.5% of the park, increasing the extent of recently burned vegetation (<10 yr post-fire) to more than 72% of the park area. We tracked the recovery of vegetation structure for nine years following the wildfire and found that the strength and persistence of fire effects differed substantially between vegetation types. Vegetation structure was modified by wildfire in forest, woodland, and heath vegetation, but among-site variability in vegetation structure was reduced only by severe fire in woodland vegetation. There also were persistent legacy effects of the previous fire regime on some attributes of vegetation structure including forest ground and understorey cover, and woodland midstorey and overstorey cover. For example, woodland midstorey cover was greater on sites with higher fire frequency, irrespective of the severity of the 2003 wildfire. Our results show that even after a large, severe wildfire, underlying fire histories can contribute substantially to variation in vegetation structure. This highlights the importance of ensuring that efforts to reinstate variation in vegetation fire age after large wildfires do not inadvertently reduce variation in vegetation structure generated by the underlying invisible mosaic. © 2017 by the Ecological Society of America.

Experimental insights into the importance of aquatic bacterial community composition to the degradation of dissolved organic matter

PubMed Central

Logue, Jürg B; Stedmon, Colin A; Kellerman, Anne M; Nielsen, Nikoline J; Andersson, Anders F; Laudon, Hjalmar; Lindström, Eva S; Kritzberg, Emma S

2016-01-01

Bacteria play a central role in the cycling of carbon, yet our understanding of the relationship between the taxonomic composition and the degradation of dissolved organic matter (DOM) is still poor. In this experimental study, we were able to demonstrate a direct link between community composition and ecosystem functioning in that differently structured aquatic bacterial communities differed in their degradation of terrestrially derived DOM. Although the same amount of carbon was processed, both the temporal pattern of degradation and the compounds degraded differed among communities. We, moreover, uncovered that low-molecular-weight carbon was available to all communities for utilisation, whereas the ability to degrade carbon of greater molecular weight was a trait less widely distributed. Finally, whereas the degradation of either low- or high-molecular-weight carbon was not restricted to a single phylogenetic clade, our results illustrate that bacterial taxa of similar phylogenetic classification differed substantially in their association with the degradation of DOM compounds. Applying techniques that capture the diversity and complexity of both bacterial communities and DOM, our study provides new insight into how the structure of bacterial communities may affect processes of biogeochemical significance. PMID:26296065

Substantial population structure of Plasmodium vivax in Thailand facilitates identification of the sources of residual transmission.

PubMed

Kittichai, Veerayuth; Koepfli, Cristian; Nguitragool, Wang; Sattabongkot, Jetsumon; Cui, Liwang

2017-10-01

Plasmodium vivax transmission in Thailand has been substantially reduced over the past 10 years, yet it remains highly endemic along international borders. Understanding the genetic relationship of residual parasite populations can help track the origins of the parasites that are reintroduced into malaria-free regions within the country. A total of 127 P. vivax isolates were genotyped from two western provinces (Tak and Kanchanaburi) and one eastern province (Ubon Ratchathani) of Thailand using 10 microsatellite markers. Genetic diversity was high, but recent clonal expansion was detected in all three provinces. Substantial population structure and genetic differentiation of parasites among provinces suggest limited gene flow among these sites. There was no haplotype sharing among the three sites, and a reduced panel of four microsatellite markers was sufficient to assign the parasites to their provincial origins. Significant parasite genetic differentiation between provinces shows successful interruption of parasite spread within Thailand, but high diversity along international borders implies a substantial parasite population size in these regions. The provincial origin of P. vivax cases can be reliably determined by genotyping four microsatellite markers, which should be useful for monitoring parasite reintroduction after malaria elimination.

26 CFR 1.6043-4 - Information returns relating to certain acquisitions of control and changes in capital structure.

Code of Federal Regulations, 2010 CFR

2010-04-01

.... Information Returns,” and 1099-CAP, “Changes in Corporate Control and Capital Structure,” with respect to each... acquisitions of control and changes in capital structure. 1.6043-4 Section 1.6043-4 Internal Revenue INTERNAL... structure. (a) Information returns for an acquisition of control or a substantial change in capital...

HCV IRES domain IIb affects the configuration of coding RNA in the 40S subunit's decoding groove

PubMed Central

Filbin, Megan E.; Kieft, Jeffrey S.

2011-01-01

Hepatitis C virus (HCV) uses a structured internal ribosome entry site (IRES) RNA to recruit the translation machinery to the viral RNA and begin protein synthesis without the ribosomal scanning process required for canonical translation initiation. Different IRES structural domains are used in this process, which begins with direct binding of the 40S ribosomal subunit to the IRES RNA and involves specific manipulation of the translational machinery. We have found that upon initial 40S subunit binding, the stem–loop domain of the IRES that contains the start codon unwinds and adopts a stable configuration within the subunit's decoding groove. This configuration depends on the sequence and structure of a different stem–loop domain (domain IIb) located far from the start codon in sequence, but spatially proximal in the IRES•40S complex. Mutation of domain IIb results in misconfiguration of the HCV RNA in the decoding groove that includes changes in the placement of the AUG start codon, and a substantial decrease in the ability of the IRES to initiate translation. Our results show that two distal regions of the IRES are structurally communicating at the initial step of 40S subunit binding and suggest that this is an important step in driving protein synthesis. PMID:21606179

HCV IRES domain IIb affects the configuration of coding RNA in the 40S subunit's decoding groove.

PubMed

Filbin, Megan E; Kieft, Jeffrey S

2011-07-01

Hepatitis C virus (HCV) uses a structured internal ribosome entry site (IRES) RNA to recruit the translation machinery to the viral RNA and begin protein synthesis without the ribosomal scanning process required for canonical translation initiation. Different IRES structural domains are used in this process, which begins with direct binding of the 40S ribosomal subunit to the IRES RNA and involves specific manipulation of the translational machinery. We have found that upon initial 40S subunit binding, the stem-loop domain of the IRES that contains the start codon unwinds and adopts a stable configuration within the subunit's decoding groove. This configuration depends on the sequence and structure of a different stem-loop domain (domain IIb) located far from the start codon in sequence, but spatially proximal in the IRES•40S complex. Mutation of domain IIb results in misconfiguration of the HCV RNA in the decoding groove that includes changes in the placement of the AUG start codon, and a substantial decrease in the ability of the IRES to initiate translation. Our results show that two distal regions of the IRES are structurally communicating at the initial step of 40S subunit binding and suggest that this is an important step in driving protein synthesis.

Social and place-focused communities in location-based online social networks

NASA Astrophysics Data System (ADS)

Brown, Chloë; Nicosia, Vincenzo; Scellato, Salvatore; Noulas, Anastasios; Mascolo, Cecilia

2013-06-01

Thanks to widely available, cheap Internet access and the ubiquity of smartphones, millions of people around the world now use online location-based social networking services. Understanding the structural properties of these systems and their dependence upon users' habits and mobility has many potential applications, including resource recommendation and link prediction. Here, we construct and characterise social and place-focused graphs by using longitudinal information about declared social relationships and about users' visits to physical places collected from a popular online location-based social service. We show that although the social and place-focused graphs are constructed from the same data set, they have quite different structural properties. We find that the social and location-focused graphs have different global and meso-scale structure, and in particular that social and place-focused communities have negligible overlap. Consequently, group inference based on community detection performed on the social graph alone fails to isolate place-focused groups, even though these do exist in the network. By studying the evolution of tie structure within communities, we show that the time period over which location data are aggregated has a substantial impact on the stability of place-focused communities, and that information about place-based groups may be more useful for user-centric applications than that obtained from the analysis of social communities alone.

Local Wave Propagation and Crustal Structure Tomography in Northern Mississippi Embayment

NASA Astrophysics Data System (ADS)

Yang, Y.; Langston, C. A.

2016-12-01

Several datasets in the vicinity of the New Madrid Seismic Zone (NMSZ) are used to study local wave propagation and crustal structure in this region, including data collected for the Northern Embayment Lithosphere Experiment (NELE) project, Transportable Array, New Madrid Cooperative Network and Embayment Seismic Excitation Experiment (ESEE). Focal mechanisms and focal depths are determined with the help of synthetic seismograms for earthquakes with magnitude larger than 3. The thick unconsolidated sediment complicates waveforms inside the Mississippi Embayment by producing large converted PS, SP phases and reverberations that mask important near-source depth phases. Modeling events with well-constrained focal mechanisms using synthetic seismograms reveals a variety of waveguide propagation effects including P and S sediment reverberations as well as leaky mode P wave trains. Substantial differences in the travel time of the mid-crustal reflection are observed for waves traveling in different directions. The travel time of the mid-crustal reflection waves and direct waves are then used in a tomography for the crustal structure. The result reveals that there is a significant southwest dip to the top of the mid-crust in the vicinity of the NMSZ. Resulting image and the determined source parameters are essential for full waveform inversion to determine high-resolution crustal structure of the Northern Mississippi Embayment.

Turbulent kinetic energy equation and free mixing

NASA Technical Reports Server (NTRS)

Morel, T.; Torda, T. P.; Bradshaw, P.

1973-01-01

Calculation of free shear flows was carried out to investigate the usefulness of several concepts which were previously successfully applied to wall flows. The method belongs to the class of differential approaches. The turbulence is taken into account by the introduction of one additional partial differential equation, the transport equation for the turbulent shear stress. The structure of turbulence is modeled after Bradshaw et al. This model was used successfully in boundary layers and its applicability to other flows is demonstrated. The work reported differs substantially from that of an earlier attempt to use this approach for calculation of free flows. The most important difference is that the region around the center line is treated by invoking the interaction hypothesis (concerning the structure of turbulence in the regions separated by the velocity extrema). The compressibility effects on shear layer spreading at low and moderate Mach numbers were investigated. In the absence of detailed experiments in free flows, the evidence from boundary layers that at low Mach numbers the structure of turbulence is unaffected by the compressibility was relied on. The present model was tested over a range of self-preserving and developing flows including pressure gradients using identical empirical input. The dependence of the structure of turbulence on the spreading rate of the shear layer was established.

Lessons in molecular recognition. 2. Assessing and improving cross-docking accuracy.

PubMed

Sutherland, Jeffrey J; Nandigam, Ravi K; Erickson, Jon A; Vieth, Michal

2007-01-01

Docking methods are used to predict the manner in which a ligand binds to a protein receptor. Many studies have assessed the success rate of programs in self-docking tests, whereby a ligand is docked into the protein structure from which it was extracted. Cross-docking, or using a protein structure from a complex containing a different ligand, provides a more realistic assessment of a docking program's ability to reproduce X-ray results. In this work, cross-docking was performed with CDocker, Fred, and Rocs using multiple X-ray structures for eight proteins (two kinases, one nuclear hormone receptor, one serine protease, two metalloproteases, and two phosphodiesterases). While average cross-docking accuracy is not encouraging, it is shown that using the protein structure from the complex that contains the bound ligand most similar to the docked ligand increases docking accuracy for all methods ("similarity selection"). Identifying the most successful protein conformer ("best selection") and similarity selection substantially reduce the difference between self-docking and average cross-docking accuracy. We identify universal predictors of docking accuracy (i.e., showing consistent behavior across most protein-method combinations), and show that models for predicting docking accuracy built using these parameters can be used to select the most appropriate docking method.

26 CFR 1.593-11 - Qualifying real property loan and nonqualifying loan defined.

Code of Federal Regulations, 2014 CFR

2014-04-01

... consisting of a structure or structures containing, in the aggregate, no more than four family units..., apartment house, office building, hospital, shopping center, warehouse, garage, or other similar permanent structure), provided that the value of such building is substantial in relation to the value of such land...

26 CFR 1.593-11 - Qualifying real property loan and nonqualifying loan defined.

Code of Federal Regulations, 2013 CFR

2013-04-01

... consisting of a structure or structures containing, in the aggregate, no more than four family units..., apartment house, office building, hospital, shopping center, warehouse, garage, or other similar permanent structure), provided that the value of such building is substantial in relation to the value of such land...

26 CFR 1.593-11 - Qualifying real property loan and nonqualifying loan defined.

Code of Federal Regulations, 2011 CFR

2011-04-01

... consisting of a structure or structures containing, in the aggregate, no more than four family units..., apartment house, office building, hospital, shopping center, warehouse, garage, or other similar permanent structure), provided that the value of such building is substantial in relation to the value of such land...

26 CFR 1.593-11 - Qualifying real property loan and nonqualifying loan defined.

Code of Federal Regulations, 2010 CFR

2010-04-01

... consisting of a structure or structures containing, in the aggregate, no more than four family units..., apartment house, office building, hospital, shopping center, warehouse, garage, or other similar permanent structure), provided that the value of such building is substantial in relation to the value of such land...

26 CFR 1.593-11 - Qualifying real property loan and nonqualifying loan defined.

Code of Federal Regulations, 2012 CFR

2012-04-01

... consisting of a structure or structures containing, in the aggregate, no more than four family units..., apartment house, office building, hospital, shopping center, warehouse, garage, or other similar permanent structure), provided that the value of such building is substantial in relation to the value of such land...

14 CFR 77.15 - Construction or alteration not requiring notice.

Code of Federal Regulations, 2011 CFR

2011-01-01

... be shielded by existing structures of a permanent and substantial character or by natural terrain or..., or settlement where it is evident beyond all reasonable doubt that the structure so shielded will not adversely affect safety in air navigation. (b) Any antenna structure of 20 feet or less in height except one...

Permanent magnet design for high-speed superconducting bearings

DOEpatents

Hull, John R.; Uherka, Kenneth L.; Abdoud, Robert G.

1996-01-01

A high temperature superconducting bearing including a permanent magnet rotor levitated by a high temperature superconducting structure. The rotor preferably includes one or more concentric permanent magnet rings coupled to permanent magnet ring structures having substantially triangular and quadrangular cross-sections. Both alternating and single direction polarity magnet structures can be used in the bearing.

14 CFR 77.15 - Construction or alteration not requiring notice.

Code of Federal Regulations, 2010 CFR

2010-01-01

... existing structures of a permanent and substantial character or by natural terrain or topographic features... where it is evident beyond all reasonable doubt that the structure so shielded will not adversely affect safety in air navigation. (b) Any antenna structure of 20 feet or less in height except one that would...

Predictors of Global Quality in Family Child Care Homes: Structural and Belief Characteristics

ERIC Educational Resources Information Center

Hughes-Belding, Kere; Hegland, Susan; Stein, Amanda; Sideris, John; Bryant, Donna

2012-01-01

Research Findings: With a substantial number of young children receiving care in family child care settings, an examination of the characteristics, both structural and attitudinal, that predict program quality is warranted. The current study examines gaps in the research by examining both structural characteristics and provider beliefs that…

Krill population dynamics in the Scotia Sea: variability in growth and mortality within a single population

NASA Astrophysics Data System (ADS)

Reid, K.; Murphy, E. J.; Loeb, V.; Hewitt, R. P.

2002-07-01

Understanding the demographics of Antarctic krill over large scales may be complicated by regional differences in the processes that govern population structure. The influence of regional differences in growth and mortality on population size structure was examined using data on the length-frequency distribution of krill in the Scotia Sea using samples from the South Shetland Islands and South Georgia collected annually from 1991 to 2000. A correction function, which took account of the higher growth rate at South Georgia, produced a consistent similarity in the position of the modal size classes that was not present in the raw data. Optimising the mortality rate, to minimise the differences in the growth corrected length-frequency distribution, suggested a higher mortality rate at South Georgia that the South Shetlands. The intra-specific variations in growth and mortality rates are consistent with published values and with other Euphausiids species. Having accounted for the demographic plasticity, it is apparent that strong recruitment of the smallest size class of krill is represented in both populations simultaneously. It appears that first-year krill are advected into different regions of the Scotia Sea where the resultant population size structure is determined by regional differences in growth and mortality. The majority of the commercial harvest of krill in the Antarctic occurs in a relatively small number of regional fisheries within the Scotia Sea and is managed using population models based on a single set of demographic parameters. Where substantial differences in these parameters exist between fishing areas, the calculation of catch limits should take these differences into account.

Effect of enzymatic hydrolysis on native starch granule structure.

PubMed

Blazek, Jaroslav; Gilbert, Elliot Paul

2010-12-13

Enzymatic digestion of six starches of different botanical origin was studied in real time by in situ time-resolved small-angle neutron scattering (SANS) and complemented by the analysis of native and digested material by X-ray diffraction, differential scanning calorimetry, small-angle X-ray scattering, and scanning electron microscopy with the aim of following changes in starch granule nanostructure during enzymatic digestion. This range of techniques enables coverage over five orders of length-scale, as is necessary for this hierarchically structured material. Starches studied varied in their digestibility and displayed structural differences in the course of enzymatic digestion. The use of time-resolved SANS showed that solvent-drying of digested residues does not induce any structural artifacts on the length scale followed by small-angle scattering. In the course of digestion, the lamellar peak intensity gradually decreased and low-q scattering increased. These trends were more substantial for A-type than for B-type starches. These observations were explained by preferential digestion of the amorphous growth rings. Hydrolysis of the semicrystalline growth rings was explained on the basis of a liquid-crystalline model for starch considering differences between A-type and B-type starches in the length and rigidity of amylopectin spacers and branches. As evidenced by differing morphologies of enzymatic attack among varieties, the existence of granular pores and channels and physical penetrability of the amorphous growth ring affect the accessibility of the enzyme to the substrate. The combined effects of the granule microstructure and the nanostructure of the growth rings influence the opportunity of the enzyme to access its substrate; as a consequence, these structures determine the enzymatic digestibility of granular starches more than the absolute physical densities of the amorphous growth rings and amorphous and crystalline regions of the semicrystalline growth rings.

Stark absorption spectroscopy on the carotenoids bound to B800-820 and B800-850 type LH2 complexes from a purple photosynthetic bacterium, Phaeospirillum molischianum strain DSM120.

PubMed

Horibe, Tomoko; Qian, Pu; Hunter, C Neil; Hashimoto, Hideki

2015-04-15

Stark absorption spectroscopy was applied to clarify the structural differences between carotenoids bound to the B800-820 and B800-850 LH2 complexes from a purple photosynthetic bacterium Phaeospirillum (Phs.) molischianum DSM120. The former complex is produced when the bacteria are grown under stressed conditions of low temperature and dim light. These two LH2 complexes bind carotenoids with similar composition, 10% lycopene and 80% rhodopin, each with the same number of conjugated CC double bonds (n=11). Quantitative classical and semi-quantum chemical analyses of Stark absorption spectra recorded in the carotenoid absorption region reveal that the absolute values of the difference dipole moments |Δμ| have substantial differences (2 [D/f]) for carotenoids bound to either B800-820 or B800-850 complexes. The origin of this striking difference in the |Δμ| values was analyzed using the X-ray crystal structure of the B800-850 LH2 complex from Phs. molischianum DSM119. Semi-empirical molecular orbital calculations predict structural deformations of the major carotenoid, rhodopin, bound within the B800-820 complex. We propose that simultaneous rotations around neighboring CC and CC bonds account for the differences in the 2 [D/f] of the |Δμ| value. The plausible position of the rotation is postulated to be located around C21-C24 bonds of rhodopin. Copyright © 2014 Elsevier Inc. All rights reserved.

Comparison of high-speed rail and maglev systems

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

Najafi, F.T.; Nassar, F.E.

1996-07-01

European and Japanese high-speed rail (HSR) and magnetically levitated (maglev) systems were each developed to respond to specific transportation needs within local economic, social, and political constraints. Not only is maglev technology substantially different from that of HSR, but also HSR and maglev systems differ in trainset design, track characteristics, cost structure, and cost sensitivity to design changes. This paper attempts to go beyond the traditional technology comparison table and focuses on the characteristics and conditions for which existing European and Japanese systems were developed. The technologies considered are the French train a grand vitesse (TGV), the Swedish X2000, themore » German Intercity Express (ICE) and Transrapid, and the Japanese Shinkansen, MLU, and high-speed surface train (HSST).« less

Effects of cation stoichiometry on electronic and structural properties of LaNiO{sub 3}

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

Smith, Cole R.; Lang, Andrew C.; Taheri, Mitra L.

2015-07-15

LaNiO{sub 3} films with varying La:Ni ratios were deposited onto SrTiO{sub 3} (001) substrates via molecular beam epitaxy to elucidate the effects of cation off-stoichiometry. The physical properties of La-deficient films are found to differ substantially from those of Ni-deficient films, with La-deficient films exhibiting lower electrical resistivities and smaller c-axis parameters than Ni-deficient films. No evidence of secondary phases is observed; however, transmission electron microscopy reveals an abundance of defects, the nature of which differs in lanthanum- and nickel-deficient films. This work illustrates the nontrivial role that cation stoichiometry can play on the functional properties of complex oxides.

The Profile of Memory Function in Children With Autism

PubMed Central

Williams, Diane L.; Goldstein, Gerald; Minshew, Nancy J.

2007-01-01

A clinical memory test was administered to 38 high-functioning children with autism and 38 individually matched normal controls, 8–16 years of age. The resulting profile of memory abilities in the children with autism was characterized by relatively poor memory for complex visual and verbal information and spatial working memory with relatively intact associative learning ability, verbal working memory, and recognition memory. A stepwise discriminant function analysis of the subtests found that the Finger Windows subtest, a measure of spatial working memory, discriminated most accurately between the autism and normal control groups. A principal components analysis indicated that the factor structure of the subtests differed substantially between the children with autism and controls, suggesting differing organizations of memory ability. PMID:16460219

Analysis of dependent scattering mechanism in hard-sphere Yukawa random media

NASA Astrophysics Data System (ADS)

Wang, B. X.; Zhao, C. Y.

2018-06-01

The structural correlations in the microscopic structures of random media can induce the dependent scattering mechanism and thus influence the optical scattering properties. Based on our recent theory on the dependent scattering mechanism in random media composed of discrete dipolar scatterers [B. X. Wang and C. Y. Zhao, Phys. Rev. A 97, 023836 (2018)], in this paper, we study the hard-sphere Yukawa random media, in order to further elucidate the role of structural correlations in the dependent scattering mechanism and hence optical scattering properties. Here, we consider charged colloidal suspensions, whose effective pair interaction between colloids is described by a screened Coulomb (Yukawa) potential. By means of adding salt ions, the pair interaction between the charged particles can be flexibly tailored and therefore the structural correlations are modified. It is shown that this strategy can affect the optical properties significantly. For colloidal TiO2 suspensions, the modification of electric and magnetic dipole excitations induced by the structural correlations can substantially influence the optical scattering properties, in addition to the far-field interference effect described by the structure factor. However, this modification is only slightly altered by different salt concentrations and is mainly because of the packing-density-dependent screening effect. On the other hand, for low refractive index colloidal polystyrene suspensions, the dependent scattering mechanism mainly involves the far-field interference effect, and the effective exciting field amplitude for the electric dipole almost remains unchanged under different structural correlations. The present study has profound implications for understanding the role of structural correlations in the dependent scattering mechanism.

Large herbivores maintain termite-caused differences in herbaceous species diversity patterns.

PubMed

Okullo, Paul; Moe, Stein R

2012-09-01

Termites and large herbivores affect African savanna plant communities. Both functional groups are also important for nutrient redistribution across the landscape. We conducted an experiment to study how termites and large herbivores, alone and in combination, affect herbaceous species diversity patterns in an African savanna. Herbaceous vegetation on large vegetated Macrotermes mounds (with and without large herbivores) and on adjacent savanna areas (with and without large herbivores) was monitored over three years in Lake Mburo National Park, Uganda. We found substantial differences in species richness, alpha diversity, evenness, and stability between termite mound herbaceous vegetation and adjacent savanna vegetation. Within months of fencing, levels of species richness, evenness, and stability were no longer significantly different between savanna and mounds. However, fencing reduced the cumulative number of species, particularly for forbs, of which 48% of the species were lost. Fencing increased the beta diversity (dissimilarity among plots) on the resource-poor (in terms of both nutrients and soil moisture) savanna areas, while it did not significantly affect beta diversity on the resource-rich termite mounds. While termites cause substantial heterogeneity in savanna vegetation, large herbivores further amplify these differences by reducing beta diversity on the savanna areas. Large herbivores are, however, responsible for the maintenance of a large number of forbs at the landscape level. These findings suggest that the mechanisms underlying the effects of termites and large herbivores on savanna plant communities scale up to shape community structure and dynamics at a landscape level.

Phillips CO-oxidation catalyts for long-lived CO2 lasers: Activity and initial characterization studies

NASA Technical Reports Server (NTRS)

Kolts, J. H.; Elliott, D. J.; Pennella, F.

1990-01-01

Four different catalysts have been developed specifically for use in sealed carbon dioxide lasers. The catalysts have been designed to be low dusting, stable to shock and vibration, have high activity at low temperatures and have long active lifetimes. Measured global CO oxidation rates range from 1.4 to 2.2 cc CO converted per minute per gram of catalyst at ambient temperature. The catalysts also retain substantial activity at temperatures as low as -35 C. The Phillips laser catalysts are prepared in a variety of different shapes to meet the different pressure drop and gas flow profiles present in the many different styles of lasers. Each catalyst has been tested in sealed TEA lasers and has been shown to substantially increase the sealed life of the laser. Activity measurements made on the precious metal catalysts which were prepared with and without activity promoters showed that the promoter materials increase catalyst CO oxidation activity at least an order of magnitude at ambient temperature. Initial studies using H2 and CO chemisorption, X ray diffraction (XRD) and X ray photoelectron spectroscopy (XPS) have shown that the activity promoters do not significantly affect the precious metal crystallite size or the electronic structure around the precious metal. In addition, the formation or lack of formation of solid solutions between the precious metal and promoters has also been shown not to affect the activity of the promoted catalyst.

Two alternative solar energy scenarios for Western Europe

NASA Astrophysics Data System (ADS)

Nakicenovic, N.

1982-11-01

Two limiting scenarios that lead to a sustainable energy system in Western Europe toward the end of the next century are described. The scenarios consider exclusively solar energy futures: one based on centralized solar technologies (hard scenario) and the other on decentralized user-oriented technologies (soft scenario). While both scenarios eliminate Western Europe's dependence on domestic and foreign fossil energy sources, the hard solar scenario requires substantial imports of solar produced hydrogen. Fundamental but different changes of the whole energy system, economic structure and lifestyles are necessary in order to achieve sustainable solar energy futures in the scenarios.

Boundary formulations for sensitivity analysis without matrix derivatives

NASA Technical Reports Server (NTRS)

Kane, J. H.; Guru Prasad, K.

1993-01-01

A new hybrid approach to continuum structural shape sensitivity analysis employing boundary element analysis (BEA) is presented. The approach uses iterative reanalysis to obviate the need to factor perturbed matrices in the determination of surface displacement and traction sensitivities via a univariate perturbation/finite difference (UPFD) step. The UPFD approach makes it possible to immediately reuse existing subroutines for computation of BEA matrix coefficients in the design sensitivity analysis process. The reanalysis technique computes economical response of univariately perturbed models without factoring perturbed matrices. The approach provides substantial computational economy without the burden of a large-scale reprogramming effort.

Phylogenetic trees and Euclidean embeddings.

PubMed

Layer, Mark; Rhodes, John A

2017-01-01

It was recently observed by de Vienne et al. (Syst Biol 60(6):826-832, 2011) that a simple square root transformation of distances between taxa on a phylogenetic tree allowed for an embedding of the taxa into Euclidean space. While the justification for this was based on a diffusion model of continuous character evolution along the tree, here we give a direct and elementary explanation for it that provides substantial additional insight. We use this embedding to reinterpret the differences between the NJ and BIONJ tree building algorithms, providing one illustration of how this embedding reflects tree structures in data.

Measurement of SIFT operating system overhead

NASA Technical Reports Server (NTRS)

Palumbo, D. L.; Butler, R. W.

1985-01-01

The overhead of the software implemented fault tolerance (SIFT) operating system was measured. Several versions of the operating system evolved. Each version represents different strategies employed to improve the measured performance. Three of these versions are analyzed. The internal data structures of the operating systems are discussed. The overhead of the SIFT operating system was found to be of two types: vote overhead and executive task overhead. Both types of overhead were found to be significant in all versions of the system. Improvements substantially reduced this overhead; even with these improvements, the operating system consumed well over 50% of the available processing time.

Structure of adenovirus bound to cellular receptor car

DOEpatents

Freimuth, Paul I.

2007-01-02

Disclosed is a mutant CAR-DI-binding adenovirus which has a genome comprising one or more mutations in sequences which encode the fiber protein knob domain wherein the mutation causes the encoded viral particle to have a significantly weakened binding affinity for CAR-DI relative to wild-type adenovirus. Such mutations may be in sequences which encode either the AB loop, or the HI loop of the fiber protein knob domain. Specific residues and mutations are described. Also disclosed is a method for generating a mutant adenovirus which is characterized by a receptor binding affinity or specificity which differs substantially from wild type.

Markets for hospital services in Zambia.

PubMed

Nakamba, Pamela; Hanson, Kara; McPake, Barbara

2002-01-01

Hospital reforms involving the introduction of measures to increase competition in hospital markets are being implemented in a range of low and middle-income countries. However, little is understood about the operation of hospital markets outside the USA and the UK. This paper assesses the degree of competition for hospital services in two hospital markets in Zambia (Copperbelt and Midlands), and the implications for prices, quality and efficiency. We found substantial differences among different hospital types in prices, costs and quality, suggesting that the hospital service market is a segmented market. The two markets differ significantly in their degree of competition, with the high cost inpatient services market in Copperbelt relatively more competitive than that in the Midlands market. The implications of these differences are discussed in terms of the potential for competition to improve hospital performance, the impact of market structure on equity of access, and how the government should address the problem of the mine hospitals.

Neuro-cognitive foundations of word stress processing - evidence from fMRI

PubMed Central

2011-01-01

Background To date, the neural correlates of phonological word stress processing are largely unknown. Methods In the present study, we investigated the processing of word stress and vowel quality using an identity matching task with pseudowords. Results In line with previous studies, a bilateral fronto-temporal network comprising the superior temporal gyri extending into the sulci as well as the inferior frontal gyri was observed for word stress processing. Moreover, we found differences in the superior temporal gyrus and the superior temporal sulcus, bilaterally, for the processing of different stress patterns. For vowel quality processing, our data reveal a substantial contribution of the left intraparietal cortex. All activations were modulated by task demands, yielding different patterns for same and different pairs of stimuli. Conclusions Our results suggest that the left superior temporal gyrus represents a basic system underlying stress processing to which additional structures including the homologous cortex site are recruited with increasing difficulty. PMID:21575209

Pressurizer tank upper support

DOEpatents

Baker, Tod H.; Ott, Howard L.

1994-01-01

A pressurizer tank in a pressurized water nuclear reactor is mounted between structural walls of the reactor on a substructure of the reactor, the tank extending upwardly from the substructure. For bearing lateral loads such as seismic shocks, a girder substantially encircles the pressurizer tank at a space above the substructure and is coupled to the structural walls via opposed sway struts. Each sway strut is attached at one end to the girder and at an opposite end to one of the structural walls, and the sway struts are oriented substantially horizontally in pairs aligned substantially along tangents to the wall of the circular tank. Preferably, eight sway struts attach to the girder at 90.degree. intervals. A compartment encloses the pressurizer tank and forms the structural wall. The sway struts attach to corners of the compartment for maximum stiffness and load bearing capacity. A valve support frame carrying the relief/discharge piping and valves of an automatic depressurization arrangement is fixed to the girder, whereby lateral loads on the relief/discharge piping are coupled directly to the compartment rather than through any portion of the pressurizer tank. Thermal insulation for the valve support frame prevents thermal loading of the piping and valves. The girder is shimmed to define a gap for reducing thermal transfer, and the girder is free to move vertically relative to the compartment walls, for accommodating dimensional variation of the pressurizer tank with changes in temperature and pressure.

High Redundancy as well as Complementary Prey Choice Characterize Generalist Predator Food Webs in Agroecosystems.

PubMed

Roubinet, Eve; Jonsson, Tomas; Malsher, Gerard; Staudacher, Karin; Traugott, Michael; Ekbom, Barbara; Jonsson, Mattias

2018-05-23

Food web structure influences ecosystem functioning and the strength and stability of associated ecosystem services. With their broad diet, generalist predators represent key nodes in the structure of many food webs and they contribute substantially to ecosystem services such as biological pest control. However, until recently it has been difficult to empirically assess food web structure with generalist predators. We utilized DNA-based molecular gut-content analyses to assess the prey use of a set of generalist invertebrate predator species common in temperate agricultural fields. We investigated the degree of specialization of predator-prey food webs at two key stages of the cropping season and analysed the link temperature of different trophic links, to identify non-random predation. We found a low level of specialization in our food webs, and identified warm and cool links which may result from active prey choice or avoidance. We also found a within-season variation in interaction strength between predators and aphid pests which differed among predator species. Our results show a high time-specific functional redundancy of the predator community, but also suggest temporally complementary prey choice due to within-season succession of some predator species.

Graphene-based two-dimensional Janus materials

NASA Astrophysics Data System (ADS)

Ng, Sze-Wing; Noor, Nuruzzaman; Zheng, Zijian

2018-04-01

Two-dimensional (2D) Janus materials with opposing components and properties on two sides have recently attracted fevered attention from various research fields for use as, for example, oil/water separating membranes, interfacial layers for mass transfer, 2D sensors and actuators. The Janus structure allows for a unidirectional transportation system and programmed response to certain stimuli to be achieved. Graphene, the 2D honeycomb network formed from one atomic layer of carbon atoms, has also received substantial research interest because of its intriguing structure and fascinating properties. The high mechanical strength, flexibility and optical transparency make graphene a unique candidate as a building block of 2D Janus materials through asymmetric modification with different functional groups on the graphene surfaces. This article reviews graphene-based 2D Janus materials, starting with a theoretical understanding of the behavior of Janus graphene. Then, different strategies for fabricating Janus graphene and its derivatives are reviewed in detail according to the chemical strategies of the modification methods. The applications of graphene-based Janus materials are discussed with a specific focus on the Janus structures that lead to bandgap engineering, as well as the construction of a responsive system on graphene.

K-Ras Populates Conformational States Differently from Its Isoform H-Ras and Oncogenic Mutant K-RasG12D.

PubMed

Parker, Jillian A; Volmar, Alicia Y; Pavlopoulos, Spiro; Mattos, Carla

2018-06-05

Structures of wild-type K-Ras from crystals obtained in the presence of guanosine triphosphate (GTP) or its analogs have remained elusive. Of the K-Ras mutants, only K-RasG12D and K-RasQ61H are available in the PDB representing the activated form of the GTPase not in complex with other proteins. We present the crystal structure of wild-type K-Ras bound to the GTP analog GppCH 2 p, with K-Ras in the state 1 conformation. Signatures of conformational states obtained by one-dimensional proton NMR confirm that K-Ras has a more substantial population of state 1 in solution than H-Ras, which predominantly favors state 2. The oncogenic mutant K-RasG12D favors state 2, changing the balance of conformational states in favor of interactions with effector proteins. Differences in the population of conformational states between K-Ras and H-Ras, as well as between K-Ras and its mutants, can provide a structural basis for focused targeting of the K-Ras isoform in cancer-specific strategies. Copyright © 2018 Elsevier Ltd. All rights reserved.

Vibroacoustic Model Validation for a Curved Honeycomb Composite Panel

NASA Technical Reports Server (NTRS)

Buehrle, Ralph D.; Robinson, Jay H.; Grosveld, Ferdinand W.

2001-01-01

Finite element and boundary element models are developed to investigate the vibroacoustic response of a curved honeycomb composite sidewall panel. Results from vibroacoustic tests conducted in the NASA Langley Structural Acoustic Loads and Transmission facility are used to validate the numerical predictions. The sidewall panel is constructed from a flexible honeycomb core sandwiched between carbon fiber reinforced composite laminate face sheets. This type of construction is being used in the development of an all-composite aircraft fuselage. In contrast to conventional rib-stiffened aircraft fuselage structures, the composite panel has nominally uniform thickness resulting in a uniform distribution of mass and stiffness. Due to differences in the mass and stiffness distribution, the noise transmission mechanisms for the composite panel are expected to be substantially different from those of a conventional rib-stiffened structure. The development of accurate vibroacoustic models will aide in the understanding of the dominant noise transmission mechanisms and enable optimization studies to be performed that will determine the most beneficial noise control treatments. Finite element and boundary element models of the sidewall panel are described. Vibroacoustic response predictions are presented for forced vibration input and the results are compared with experimental data.

Tetrahedrality and hydrogen bonds in water

NASA Astrophysics Data System (ADS)

Székely, Eszter; Varga, Imre K.; Baranyai, András

2016-06-01

We carried out extensive calculations of liquid water at different temperatures and pressures using the BK3 model suggested recently [P. T. Kiss and A. Baranyai, J. Chem. Phys. 138, 204507 (2013)]. In particular, we were interested in undercooled regions to observe the propensity of water to form tetrahedral coordination of closest neighbors around a central molecule. We compared the found tetrahedral order with the number of hydrogen bonds and with the partial pair correlation functions unfolded as distributions of the closest, the second closest, etc. neighbors. We found that contrary to the number of hydrogen bonds, tetrahedrality changes substantially with state variables. Not only the number of tetrahedral arrangements increases with lowering the pressure, the density, and the temperature but the domain size of connecting tetrahedral structures as well. The difference in tetrahedrality is very pronounced between the two sides of the Widom line and even more so between the low density amorphous (LDA) and high density amorphous (HDA) phases. We observed that in liquid water and in HDA, the 5th water molecule, contrary to ice and LDA, is positioned between the first and the second coordination shell. We found no convincing evidence of structural heterogeneity or regions referring to structural transition.

Sex differences in structural brain asymmetry predict overt aggression in early adolescents.

PubMed

Visser, Troy A W; Ohan, Jeneva L; Whittle, Sarah; Yücel, Murat; Simmons, Julian G; Allen, Nicholas B

2014-04-01

The devastating social, emotional and economic consequences of human aggression are laid bare nightly on newscasts around the world. Aggression is principally mediated by neural circuitry comprising multiple areas of the prefrontal cortex and limbic system, including the orbitofrontal cortex (OFC), anterior cingulate cortex (ACC), amygdala and hippocampus. A striking characteristic of these regions is their structural asymmetry about the midline (i.e. left vs right hemisphere). Variations in these asymmetries have been linked to clinical disorders characterized by aggression and the rate of aggressive behavior in psychiatric patients. Here, we show for the first time that structural asymmetries in prefrontal cortical areas are also linked to aggression in a normal population of early adolescents. Our findings indicate a relationship between parent reports of aggressive behavior in adolescents and structural asymmetries in the limbic and paralimbic ACC and OFC, and moreover, that this relationship varies by sex. Furthermore, while there was no relationship between aggression and structural asymmetries in the amygdala or hippocampus, hippocampal volumes did predict aggression in females. Taken together, the results suggest that structural asymmetries in the prefrontal cortex may influence human aggression, and that the anatomical basis of aggression varies substantially by sex.

Discovery, genotyping and characterization of structural variation and novel sequence at single nucleotide resolution from de novo genome assemblies on a population scale.

PubMed

Liu, Siyang; Huang, Shujia; Rao, Junhua; Ye, Weijian; Krogh, Anders; Wang, Jun

2015-01-01

Comprehensive recognition of genomic variation in one individual is important for understanding disease and developing personalized medication and treatment. Many tools based on DNA re-sequencing exist for identification of single nucleotide polymorphisms, small insertions and deletions (indels) as well as large deletions. However, these approaches consistently display a substantial bias against the recovery of complex structural variants and novel sequence in individual genomes and do not provide interpretation information such as the annotation of ancestral state and formation mechanism. We present a novel approach implemented in a single software package, AsmVar, to discover, genotype and characterize different forms of structural variation and novel sequence from population-scale de novo genome assemblies up to nucleotide resolution. Application of AsmVar to several human de novo genome assemblies captures a wide spectrum of structural variants and novel sequences present in the human population in high sensitivity and specificity. Our method provides a direct solution for investigating structural variants and novel sequences from de novo genome assemblies, facilitating the construction of population-scale pan-genomes. Our study also highlights the usefulness of the de novo assembly strategy for definition of genome structure.

Length-independent structural similarities enrich the antibody CDR canonical class model.

PubMed

Nowak, Jaroslaw; Baker, Terry; Georges, Guy; Kelm, Sebastian; Klostermann, Stefan; Shi, Jiye; Sridharan, Sudharsan; Deane, Charlotte M

2016-01-01

Complementarity-determining regions (CDRs) are antibody loops that make up the antigen binding site. Here, we show that all CDR types have structurally similar loops of different lengths. Based on these findings, we created length-independent canonical classes for the non-H3 CDRs. Our length variable structural clusters show strong sequence patterns suggesting either that they evolved from the same original structure or result from some form of convergence. We find that our length-independent method not only clusters a larger number of CDRs, but also predicts canonical class from sequence better than the standard length-dependent approach. To demonstrate the usefulness of our findings, we predicted cluster membership of CDR-L3 sequences from 3 next-generation sequencing datasets of the antibody repertoire (over 1,000,000 sequences). Using the length-independent clusters, we can structurally classify an additional 135,000 sequences, which represents a ∼20% improvement over the standard approach. This suggests that our length-independent canonical classes might be a highly prevalent feature of antibody space, and could substantially improve our ability to accurately predict the structure of novel CDRs identified by next-generation sequencing.

Electronic structure of germanium selenide investigated using ultra-violet photo-electron spectroscopy

NASA Astrophysics Data System (ADS)

Mishra, P.; Lohani, H.; Kundu, A. K.; Patel, R.; Solanki, G. K.; Menon, Krishnakumar S. R.; Sekhar, B. R.

2015-07-01

The valence band electronic structure of GeSe single crystals has been investigated using angle resolved photoemission spectroscopy (ARPES) and x-ray photoelectron spectroscopy. The experimentally observed bands from ARPES, match qualitatively with our LDA-based band structure calculations along the Γ-Z, Γ-Y and Γ-T symmetry directions. The valence band maximum occurs nearly midway along the Γ-Z direction, at a binding energy of -0.5 eV, substantiating the indirect band gap of GeSe. Non-dispersive features associated with surface states and indirect transitions have been observed. The difference in hybridization of Se and Ge 4p orbitals leads to the variation of dispersion along the three symmetry directions. The predominance of the Se 4pz orbitals, evidenced from theoretical calculations, may be the cause for highly dispersive bands along the Γ-T direction. Detailed electronic structure analysis reveals the significance of the cation-anion 4p orbitals hybridization in the valence band dispersion of IV-VI semiconductors. This is the first comprehensive report of the electronic structure of a GeSe single crystal using ARPES in conjugation with theoretical band structure analysis.

Estimating 4D CBCT from prior information and extremely limited angle projections using structural PCA and weighted free-form deformation for lung radiotherapy

PubMed Central

Harris, Wendy; Zhang, You; Yin, Fang-Fang; Ren, Lei

2017-01-01

Purpose To investigate the feasibility of using structural-based principal component analysis (PCA) motion-modeling and weighted free-form deformation to estimate on-board 4D-CBCT using prior information and extremely limited angle projections for potential 4D target verification of lung radiotherapy. Methods A technique for lung 4D-CBCT reconstruction has been previously developed using a deformation field map (DFM)-based strategy. In the previous method, each phase of the 4D-CBCT was generated by deforming a prior CT volume. The DFM was solved by a motion-model extracted by global PCA and free-form deformation (GMM-FD) technique, using a data fidelity constraint and deformation energy minimization. In this study, a new structural-PCA method was developed to build a structural motion-model (SMM) by accounting for potential relative motion pattern changes between different anatomical structures from simulation to treatment. The motion model extracted from planning 4DCT was divided into two structures: tumor and body excluding tumor, and the parameters of both structures were optimized together. Weighted free-form deformation (WFD) was employed afterwards to introduce flexibility in adjusting the weightings of different structures in the data fidelity constraint based on clinical interests. XCAT (computerized patient model) simulation with a 30 mm diameter lesion was simulated with various anatomical and respirational changes from planning 4D-CT to onboard volume to evaluate the method. The estimation accuracy was evaluated by the Volume-Percent-Difference (VPD)/Center-of-Mass-Shift (COMS) between lesions in the estimated and “ground-truth” on board 4D-CBCT. Different onboard projection acquisition scenarios and projection noise levels were simulated to investigate their effects on the estimation accuracy. The method was also evaluated against 3 lung patients. Results The SMM-WFD method achieved substantially better accuracy than the GMM-FD method for CBCT estimation using extremely small scan angles or projections. Using orthogonal 15° scanning angles, the VPD/COMS were 3.47±2.94% and 0.23±0.22mm for SMM-WFD and 25.23±19.01% and 2.58±2.54mm for GMM-FD among all 8 XCAT scenarios. Compared to GMM-FD, SMM-WFD was more robust against reduction of the scanning angles down to orthogonal 10° with VPD/COMS of 6.21±5.61% and 0.39±0.49mm, and more robust against reduction of projection numbers down to only 8 projections in total for both orthogonal-view 30° and orthogonal-view 15° scan angles. SMM-WFD method was also more robust than the GMM-FD method against increasing levels of noise in the projection images. Additionally, the SMM-WFD technique provided better tumor estimation for all three lung patients compared to the GMM-FD technique. Conclusion Compared to the GMM-FD technique, the SMM-WFD technique can substantially improve the 4D-CBCT estimation accuracy using extremely small scan angles and low number of projections to provide fast low dose 4D target verification. PMID:28079267

Taxonomic and compositional differences of ground-dwelling arthropods in riparian habitats in Glen Canyon, Arizona, USA

USGS Publications Warehouse

Ralston, Barbara; Cobb, Neil S.; Brantley, Sandra L.; Higgins, Jacob; Yackulic, Charles B.

2017-01-01

The disturbance history, plant species composition, productivity, and structural complexity of a site can exert bottom-up controls on arthropod diversity, abundance, and trophic structure. Regulation alters the hydrology and disturbance regimes of rivers and affects riparian habitats by changing plant quality parameters. Fifty years of regulation along the Colorado River downstream of Glen Canyon Dam has created a no-analog, postdam “lower” riparian zone close to the water's edge that includes tamarisk (Tamarix sp.), a nonnative riparian shrub. At the same time, the predam “upper” facultative riparian zone has persisted several meters above the current flood stage. In summer 2009, we used pitfall traps within these 2 riparian zones that differ in plant composition, productivity, and disturbance frequency to test for differences in arthropod community (Hymenoptera, Arachnida, and Coleoptera) structure. Arthropod community structure differed substantially between the 2 zones. Arthropod abundance and species richness was highest in the predam upper riparian zone, even though there was a greater amount of standing plant biomass in the postdam lower riparian zone. Omnivore abundance was proportionately greater in the upper riparian zone and was associated with lower estimated productivity values. Predators and detritivores were proportionately greater in the postdam lower riparian zone. In this case, river regulation may create habitats that support species of spiders and carabid beetles, but few other species that are exclusive to this zone. The combined richness found in both zones suggests a small increase in total richness and functional diversity for the Glen Canyon reach of the Colorado River.

Quantitative analysis of structural variations in corpus callosum in adults with multiple system atrophy (MSA)

NASA Astrophysics Data System (ADS)

Bhattacharya, Debanjali; Sinha, Neelam; Saini, Jitender

2017-03-01

Multiple system atrophy (MSA) is a rare, non-curable, progressive neurodegenerative disorder that affects nervous system and movement, poses a considerable diagnostic challenge to medical researchers. Corpus callosum (CC) being the largest white matter structure in brain, enabling inter-hemispheric communication, quantification of callosal atrophy may provide vital information at the earliest possible stages. The main objective is to identify the differences in CC structure for this disease, based on quantitative analysis on the pattern of callosal atrophy. We report results of quantification of structural changes in regional anatomical thickness, area and length of CC between patient-groups with MSA with respect to healthy controls. The method utilizes isolating and parcellating the mid-sagittal CC into 100 segments along the length - measuring the width of each segment. It also measures areas within geometrically defined five callosal compartments of the well-known Witelson, and Hofer-Frahma schemes. For quantification, statistical tests are performed on these different callosal measurements. From the statistical analysis, it is concluded that compared to healthy controls, width is reduced drastically throughout CC for MSA group and as well as changes in area and length are also significant for MSA. The study is further extended to check if any significant difference in thickness is found between the two variations of MSA, Parkinsonian MSA and Cerebellar MSA group, using the same methodology. However area and length of this two sub-MSA group, no substantial difference is obtained. The study is performed on twenty subjects for each control and MSA group, who had T1-weighted MRI.

A new statistical framework to assess structural alignment quality using information compression

PubMed Central

Collier, James H.; Allison, Lloyd; Lesk, Arthur M.; Garcia de la Banda, Maria; Konagurthu, Arun S.

2014-01-01

Motivation: Progress in protein biology depends on the reliability of results from a handful of computational techniques, structural alignments being one. Recent reviews have highlighted substantial inconsistencies and differences between alignment results generated by the ever-growing stock of structural alignment programs. The lack of consensus on how the quality of structural alignments must be assessed has been identified as the main cause for the observed differences. Current methods assess structural alignment quality by constructing a scoring function that attempts to balance conflicting criteria, mainly alignment coverage and fidelity of structures under superposition. This traditional approach to measuring alignment quality, the subject of considerable literature, has failed to solve the problem. Further development along the same lines is unlikely to rectify the current deficiencies in the field. Results: This paper proposes a new statistical framework to assess structural alignment quality and significance based on lossless information compression. This is a radical departure from the traditional approach of formulating scoring functions. It links the structural alignment problem to the general class of statistical inductive inference problems, solved using the information-theoretic criterion of minimum message length. Based on this, we developed an efficient and reliable measure of structural alignment quality, I-value. The performance of I-value is demonstrated in comparison with a number of popular scoring functions, on a large collection of competing alignments. Our analysis shows that I-value provides a rigorous and reliable quantification of structural alignment quality, addressing a major gap in the field. Availability: http://lcb.infotech.monash.edu.au/I-value Contact: arun.konagurthu@monash.edu Supplementary information: Online supplementary data are available at http://lcb.infotech.monash.edu.au/I-value/suppl.html PMID:25161241

Behavior of wet precast beam column connections under progressive collapse scenario: an experimental study

NASA Astrophysics Data System (ADS)

Nimse, Rohit B.; Joshi, Digesh D.; Patel, Paresh V.

2014-12-01

Progressive collapse denotes a failure of a major portion of a structure that has been initiated by failure of a relatively small part of the structure such as failure of any vertical load carrying element (typically columns). Failure of large part of any structure will results into substantial loss of human lives and natural resources. Therefore, it is important to prevent progressive collapse which is also known as disproportionate collapse. Nowadays, there is an increasing trend toward construction of buildings using precast concrete. In precast concrete construction, all the components of structures are produced in controlled environment and they are being transported to the site. At site such individual components are connected appropriately. Connections are the most critical elements of any precast structure, because in past major collapse of precast structure took place because of connection failure. In this study, behavior of three different 1/3rd scaled wet precast beam column connections under progressive collapse scenario are studied and its performance is compared with monolithic connection. Precast connections are constructed by adopting different connection detailing at the junction by considering reinforced concrete corbel for two specimens and steel billet for one specimen. Performance of specimen is evaluated on the basis of ultimate load carrying capacity, maximum deflection and deflection measured along the span of the beam. From the results, it is observed that load carrying capacity and ductility of precast connections considered in this study are more than that of monolithic connections.

Human insulin analogues modified at the B26 site reveal a hormone conformation that is undetected in the receptor complex

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

Žáková, Lenka; Kletvíková, Emília; Lepšík, Martin

[AsnB26]- and [GlyB26]-insulin mutants attain a B26-turn like fold without assistance of chemical modifications. Their structures match the insulin receptor interface and expand the spectrum of insulin conformations. The structural characterization of the insulin–insulin receptor (IR) interaction still lacks the conformation of the crucial B21–B30 insulin region, which must be different from that in its storage forms to ensure effective receptor binding. Here, it is shown that insulin analogues modified by natural amino acids at the TyrB26 site can represent an active form of this hormone. In particular, [AsnB26]-insulin and [GlyB26]-insulin attain a B26-turn-like conformation that differs from that inmore » all known structures of the native hormone. It also matches the receptor interface, avoiding substantial steric clashes. This indicates that insulin may attain a B26-turn-like conformation upon IR binding. Moreover, there is an unexpected, but significant, binding specificity of the AsnB26 mutant for predominantly the metabolic B isoform of the receptor. As it is correlated with the B26 bend of the B-chain of the hormone, the structures of AsnB26 analogues may provide the first structural insight into the structural origins of differential insulin signalling through insulin receptor A and B isoforms.« less

Structure and function of methanotrophic communities in a landfill-cover soil.

PubMed

Henneberger, Ruth; Lüke, Claudia; Mosberger, Lona; Schroth, Martin H

2012-07-01

In landfill-cover soils, aerobic methane-oxidizing bacteria (MOB) convert CH(4) to CO(2), mitigating emissions of the greenhouse gas CH(4) to the atmosphere. We investigated overall MOB community structure and assessed spatial differences in MOB diversity, abundance and activity in a Swiss landfill-cover soil. Molecular cloning, terminal restriction-fragment length polymorphism (T-RFLP) and quantitative PCR of pmoA genes were applied to soil collected from 16 locations at three different depths to study MOB community structure, diversity and abundance; MOB activity was measured in the field using gas push-pull tests. The MOB community was highly diverse but dominated by Type Ia MOB, with novel pmoA sequences present. Type II MOB were detected mainly in deeper soil with lower nutrient and higher CH(4) concentrations. Substantial differences in MOB community structure were observed between one high- and one low-activity location. MOB abundance was highly variable across the site [4.0 × 10(4) to 1.1 × 10(7) (g soil dry weight)(-1)]. Potential CH(4) oxidation rates were high [1.8-58.2 mmol CH(4) (L soil air)(-1) day(-1) ] but showed significant lateral variation and were positively correlated with mean CH(4) concentrations (P < 0.01), MOB abundance (P < 0.05) and MOB diversity (weak correlation, P < 0.17). Our findings indicate that Methylosarcina and closely related MOB are key players and that MOB abundance and community structure are driving factors in CH(4) oxidation at this landfill. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Recalibration of blood analytes over 25 years in the Atherosclerosis Risk in Communities Study: The impact of recalibration on chronic kidney disease prevalence and incidence

PubMed Central

Parrinello, Christina M.; Grams, Morgan E.; Couper, David; Ballantyne, Christie M.; Hoogeveen, Ron C.; Eckfeldt, John H.; Selvin, Elizabeth; Coresh, Josef

2016-01-01

Background Equivalence of laboratory tests over time is important for longitudinal studies. Even a small systematic difference (bias) can result in substantial misclassification. Methods We selected 200 Atherosclerosis Risk in Communities Study participants attending all 5 study visits over 25 years. Eight analytes were re-measured in 2011–13 from stored blood samples from multiple visits: creatinine, uric acid, glucose, total cholesterol, HDL-cholesterol, LDL-cholesterol, triglycerides, and high-sensitivity C-reactive protein. Original values were recalibrated to re-measured values using Deming regression. Differences >10% were considered to reflect substantial bias, and correction equations were applied to affected analytes in the total study population. We examined trends in chronic kidney disease (CKD) pre- and post-recalibration. Results Repeat measures were highly correlated with original values (Pearson’s r>0.85 after removing outliers [median 4.5% of paired measurements]), but 2 of 8 analytes (creatinine and uric acid) had differences >10%. Original values of creatinine and uric acid were recalibrated to current values using correction equations. CKD prevalence differed substantially after recalibration of creatinine (visits 1, 2, 4 and 5 pre-recalibration: 21.7%, 36.1%, 3.5%, 29.4%; post-recalibration: 1.3%, 2.2%, 6.4%, 29.4%). For HDL-cholesterol, the current direct enzymatic method differed substantially from magnesium dextran precipitation used during visits 1–4. Conclusions Analytes re-measured in samples stored for ~25 years were highly correlated with original values, but two of the 8 analytes showed substantial bias at multiple visits. Laboratory recalibration improved reproducibility of test results across visits and resulted in substantial differences in CKD prevalence. We demonstrate the importance of consistent recalibration of laboratory assays in a cohort study. PMID:25952043

Sputter coating of microspherical substrates by levitation

DOEpatents

Lowe, A.T.; Hosford, C.D.

Microspheres are substantially uniformly coated with metals or nonmetals by simltaneously levitating them and sputter coating them at total chamber pressures less than 1 torr. A collimated hole structure comprising a parallel array of upwardly projecting individual gas outlets is machined out to form a dimple. Glass microballoons,, which are particularly useful in laser fusion applications, can be substantially uniformly coated using the coating method and apparatus.

Effects of sensorineural hearing loss on temporal coding of narrowband and broadband signals in the auditory periphery

PubMed Central

Henry, Kenneth S.; Heinz, Michael G.

2013-01-01

People with sensorineural hearing loss have substantial difficulty understanding speech under degraded listening conditions. Behavioral studies suggest that this difficulty may be caused by changes in auditory processing of the rapidly-varying temporal fine structure (TFS) of acoustic signals. In this paper, we review the presently known effects of sensorineural hearing loss on processing of TFS and slower envelope modulations in the peripheral auditory system of mammals. Cochlear damage has relatively subtle effects on phase locking by auditory-nerve fibers to the temporal structure of narrowband signals under quiet conditions. In background noise, however, sensorineural loss does substantially reduce phase locking to the TFS of pure-tone stimuli. For auditory processing of broadband stimuli, sensorineural hearing loss has been shown to severely alter the neural representation of temporal information along the tonotopic axis of the cochlea. Notably, auditory-nerve fibers innervating the high-frequency part of the cochlea grow increasingly responsive to low-frequency TFS information and less responsive to temporal information near their characteristic frequency (CF). Cochlear damage also increases the correlation of the response to TFS across fibers of varying CF, decreases the traveling-wave delay between TFS responses of fibers with different CFs, and can increase the range of temporal modulation frequencies encoded in the periphery for broadband sounds. Weaker neural coding of temporal structure in background noise and degraded coding of broadband signals along the tonotopic axis of the cochlea are expected to contribute considerably to speech perception problems in people with sensorineural hearing loss. PMID:23376018

An in vitro comparison of subjective image quality of panoramic views acquired via 2D or 3D imaging.

PubMed

Pittayapat, P; Galiti, D; Huang, Y; Dreesen, K; Schreurs, M; Souza, P Couto; Rubira-Bullen, I R F; Westphalen, F H; Pauwels, R; Kalema, G; Willems, G; Jacobs, R

2013-01-01

The objective of this study is to compare subjective image quality and diagnostic validity of cone-beam CT (CBCT) panoramic reformatting with digital panoramic radiographs. Four dry human skulls and two formalin-fixed human heads were scanned using nine different CBCTs, one multi-slice CT (MSCT) and one standard digital panoramic device. Panoramic views were generated from CBCTs in four slice thicknesses. Seven observers scored image quality and visibility of 14 anatomical structures. Four observers repeated the observation after 4 weeks. Digital panoramic radiographs showed significantly better visualization of anatomical structures except for the condyle. Statistical analysis of image quality showed that the 3D imaging modalities (CBCTs and MSCT) were 7.3 times more likely to receive poor scores than the 2D modality. Yet, image quality from NewTom VGi® and 3D Accuitomo 170® was almost equivalent to that of digital panoramic radiographs with respective odds ratio estimates of 1.2 and 1.6 at 95% Wald confidence limits. A substantial overall agreement amongst observers was found. Intra-observer agreement was moderate to substantial. While 2D-panoramic images are significantly better for subjective diagnosis, 2/3 of the 3D-reformatted panoramic images are moderate or good for diagnostic purposes. Panoramic reformattings from particular CBCTs are comparable to digital panoramic images concerning the overall image quality and visualization of anatomical structures. This clinically implies that a 3D-derived panoramic view can be generated for diagnosis with a recommended 20-mm slice thickness, if CBCT data is a priori available for other purposes.

Uncertainty in the fate of soil organic carbon: A comparison of three conceptually different soil decomposition models

USGS Publications Warehouse

He, Yujie; Yang, Jinyan; Zhuang, Qianlai; McGuire, A. David; Zhu, Qing; Liu, Yaling; Teskey, Robert O.

2014-01-01

Conventional Q10 soil organic matter decomposition models and more complex microbial models are available for making projections of future soil carbon dynamics. However, it is unclear (1) how well the conceptually different approaches can simulate observed decomposition and (2) to what extent the trajectories of long-term simulations differ when using the different approaches. In this study, we compared three structurally different soil carbon (C) decomposition models (one Q10 and two microbial models of different complexity), each with a one- and two-horizon version. The models were calibrated and validated using 4 years of measurements of heterotrophic soil CO2 efflux from trenched plots in a Dahurian larch (Larix gmelinii Rupr.) plantation. All models reproduced the observed heterotrophic component of soil CO2 efflux, but the trajectories of soil carbon dynamics differed substantially in 100 year simulations with and without warming and increased litterfall input, with microbial models that produced better agreement with observed changes in soil organic C in long-term warming experiments. Our results also suggest that both constant and varying carbon use efficiency are plausible when modeling future decomposition dynamics and that the use of a short-term (e.g., a few years) period of measurement is insufficient to adequately constrain model parameters that represent long-term responses of microbial thermal adaption. These results highlight the need to reframe the representation of decomposition models and to constrain parameters with long-term observations and multiple data streams. We urge caution in interpreting future soil carbon responses derived from existing decomposition models because both conceptual and parameter uncertainties are substantial.

Co-extinction in a host-parasite network: identifying key hosts for network stability.

PubMed

Dallas, Tad; Cornelius, Emily

2015-08-17

Parasites comprise a substantial portion of total biodiversity. Ultimately, this means that host extinction could result in many secondary extinctions of obligate parasites and potentially alter host-parasite network structure. Here, we examined a highly resolved fish-parasite network to determine key hosts responsible for maintaining parasite diversity and network structure (quantified here as nestedness and modularity). We evaluated four possible host extinction orders and compared the resulting co-extinction dynamics to random extinction simulations; including host removal based on estimated extinction risk, parasite species richness and host level contributions to nestedness and modularity. We found that all extinction orders, except the one based on realistic extinction risk, resulted in faster declines in parasite diversity and network structure relative to random biodiversity loss. Further, we determined species-level contributions to network structure were best predicted by parasite species richness and host family. Taken together, we demonstrate that a small proportion of hosts contribute substantially to network structure and that removal of these hosts results in rapid declines in parasite diversity and network structure. As network stability can potentially be inferred through measures of network structure, our findings may provide insight into species traits that confer stability.

Exploring sex differences in autistic traits: A factor analytic study of adults with autism.

PubMed

Grove, Rachel; Hoekstra, Rosa A; Wierda, Marlies; Begeer, Sander

2017-08-01

Research has highlighted potential differences in the phenotypic and clinical presentation of autism spectrum conditions across sex. Furthermore, the measures utilised to evaluate autism spectrum conditions may be biased towards the male autism phenotype. It is important to determine whether these instruments measure the autism phenotype consistently in autistic men and women. This study evaluated the factor structure of the Autism Spectrum Quotient Short Form in a large sample of autistic adults. It also systematically explored specific sex differences at the item level, to determine whether the scale assesses the autism phenotype equivalently across males and females. Factor analyses were conducted among 265 males and 285 females. A two-factor structure consisting of a social behaviour and numbers and patterns factor was consistent across groups, indicating that the latent autism phenotype is similar among both autistic men and women. Subtle differences were observed on two social behaviour item thresholds of the Autism Spectrum Quotient Short Form, with women reporting scores more in line with the scores expected in autism on these items than men. However, these differences were not substantial. This study showed that the Autism Spectrum Quotient Short Form detects autistic traits equivalently in males and females and is not biased towards the male autism phenotype.

Wind Variability of B Supergiants. No. 2; The Two-component Stellar Wind of gamma Arae

NASA Technical Reports Server (NTRS)

Prinja, R. K.; Massa, D.; Fullerton, A. W.; Howarth, I. D.; Pontefract, M.

1996-01-01

The stellar wind of the rapidly rotating early-B supergiant, gamma Ara, is studied using time series, high-resolution IUE spectroscopy secured over approx. 6 days in 1993 March. Results are presented based on an analysis of several line species, including N(N), C(IV), Si(IV), Si(III), C(II), and Al(III). The wind of this star is grossly structured, with evidence for latitude-dependent mass loss which reflects the role of rapid rotation. Independent, co-existing time variable features are identified at low-velocity (redward of approx. -750 km/s) and at higher-speeds extending to approx. -1500 km/s. The interface between these structures is 'defined' by the appearance of a discrete absorption component which is extremely sharp (in velocity space). The central velocity of this 'Super DAC' changes only gradually, over several days, between approx. -400 and -750 km/s in most of the ions. However, its location is shifted redward by almost 400 km/s in Al(III) and C(II), indicating that the physical structure giving rise to this feature has a substantial velocity and ionization jump. Constraints on the relative ionization properties of the wind structures are discussed, together with results based on SEI line-profile-fitting methods. The overall wind activity in gamma Ara exhibits a clear ion dependence, such that low-speed features are promoted in low-ionization species, including Al(III), C(II), and Si(III). We also highlight that - in contrast to most OB stars - there are substantial differences in the epoch-to-epoch time-averaged wind profiles of gamma Ara. We interpret the results in terms of a two-component wind model for gamma Ara, with an equatorially compressed low ionization region, and a high speed, higher-ionization polar outflow. This picture is discussed in the context of the predicted bi-stability mechanism for line-driven winds in rapidly rotating early-B type stars, and the formation of compressed wind regions in rapidly rotating hot stars. The apparent absence of a substantial shift in the wind ionization mixture of gamma Ara, and the normal nature of its photospheric spectrum, suggests wind-compression as the likely dominant cause for the observed equatorial density enhancements.

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

Turner, Terry D.; Bingham, Dennis N.; Benefiel, Bradley C.

Reactors for carrying out a chemical reaction, as well as related components, systems and methods are provided. In accordance with one embodiment, a reactor is provided that includes a furnace and a crucible positioned for heating by the furnace. A downtube is disposed at least partially within the interior crucible along an axis. At least one structure is coupled with the downtube and extends substantially across the cross-sectional area of the interior volume taken in a direction substantially perpendicular to the axis. A plurality of holes is formed in the structure enabling fluid flow therethrough. The structure coupled with themore » downtube may include a lower body portion and an upper body portion coupled with the lower body portion, wherein the plurality of holes is formed in the lower body portion adjacent to, and radially outward from, a periphery of the upper body portion.« less

An integrated catch-and-hold mechanism activates nicotinic acetylcholine receptors.

PubMed

Jadey, Snehal; Auerbach, Anthony

2012-07-01

In neuromuscular acetylcholine (ACh) receptor channels (AChRs), agonist molecules bind with a low affinity (LA) to two sites that can switch to high affinity (HA) and increase the probability of channel opening. We measured (by using single-channel kinetic analysis) the rate and equilibrium constants for LA binding and channel gating for several different agonists of adult-type mouse AChRs. Almost all of the variation in the equilibrium constants for LA binding was from differences in the association rate constants. These were consistently below the limit set by diffusion and were substantially different even though the agonists had similar sizes and the same charge. This suggests that binding to resting receptors is not by diffusion alone and, hence, that each binding site can undergo two conformational changes ("catch" and "hold") that connect three different structures (apo-, LA-bound, and HA-bound). Analyses of ACh-binding protein structures suggest that this binding site, too, may adopt three discrete structures having different degrees of loop C displacement ("capping"). For the agonists we tested, the logarithms of the equilibrium constants for LA binding and LA↔HA gating were correlated. Although agonist binding and channel gating have long been considered to be separate processes in the activation of ligand-gated ion channels, this correlation implies that the catch-and-hold conformational changes are energetically linked and together comprise an integrated process having a common structural basis. We propose that loop C capping mainly reflects agonist binding, with its two stages corresponding to the formation of the LA and HA complexes. The catch-and-hold reaction coordinate is discussed in terms of preopening states and thermodynamic cycles of activation.

An integrated catch-and-hold mechanism activates nicotinic acetylcholine receptors

PubMed Central

Jadey, Snehal

2012-01-01

In neuromuscular acetylcholine (ACh) receptor channels (AChRs), agonist molecules bind with a low affinity (LA) to two sites that can switch to high affinity (HA) and increase the probability of channel opening. We measured (by using single-channel kinetic analysis) the rate and equilibrium constants for LA binding and channel gating for several different agonists of adult-type mouse AChRs. Almost all of the variation in the equilibrium constants for LA binding was from differences in the association rate constants. These were consistently below the limit set by diffusion and were substantially different even though the agonists had similar sizes and the same charge. This suggests that binding to resting receptors is not by diffusion alone and, hence, that each binding site can undergo two conformational changes (“catch” and “hold”) that connect three different structures (apo-, LA-bound, and HA-bound). Analyses of ACh-binding protein structures suggest that this binding site, too, may adopt three discrete structures having different degrees of loop C displacement (“capping”). For the agonists we tested, the logarithms of the equilibrium constants for LA binding and LA↔HA gating were correlated. Although agonist binding and channel gating have long been considered to be separate processes in the activation of ligand-gated ion channels, this correlation implies that the catch-and-hold conformational changes are energetically linked and together comprise an integrated process having a common structural basis. We propose that loop C capping mainly reflects agonist binding, with its two stages corresponding to the formation of the LA and HA complexes. The catch-and-hold reaction coordinate is discussed in terms of preopening states and thermodynamic cycles of activation. PMID:22732309

First Comparative Analysis of the Community Structures and Carbon Metabolic Pathways of the Bacteria Associated with Alvinocaris longirostris in a Hydrothermal Vent of Okinawa Trough.

PubMed

Sun, Qing-Lei; Zeng, Zhi-Gang; Chen, Shuai; Sun, Li

2016-01-01

Alvinocaris longirostris is a species of shrimp existing in the hydrothermal fields of Okinawa Trough. To date the structure and function of the microbial community associated with A. longirostris are essentially unknown. In this study, by employment of the techniques of high through-put sequencing and clone library construction and analysis, we compared for the first time the community structures and metabolic profiles of microbes associated with the gill and gut of A. longirostris in a hydrothermal field of Okinawa Trough. Fourteen phyla were detected in the gill and gut communities, of which 11 phyla were shared by both tissues. Proteobacteria made up a substantial proportion in both tissues, while Firmicutes was abundant only in gut. Although gill and gut communities were similar in bacterial diversities, the bacterial community structures in these two tissues were significantly different. Further, we discovered for the first time the existence in the gill and gut communities of A. longirostris the genes (cbbM and aclB) encoding the key enzymes of Calvin-Benson-Bassham (CBB) cycle and the reductive tricarboxylic acid (rTCA) cycle, and that both cbbM and aclB were significantly more abundant in gill than in gut. Taken together, these results provide the first evidence that at least two carbon fixation pathways are present in both the gill and the gut communities of A. longirostris, and that the communities in different tissues likely differ in autotrophic productivity.

A cross-ocean comparison of responses to settlement cues in reef-building corals

PubMed Central

Meyer, Eli; Guermond, Sarah M.; Matz, Mikhail V.

2014-01-01

Caribbean coral reefs have deteriorated substantially over the past 30 years, which is broadly attributable to the effects of global climate change. In the same time, Indo-Pacific reefs maintain higher coral cover and typically recover rapidly after disturbances. This difference in reef resilience is largely due to much higher coral recruitment rates in the Pacific. We hypothesized that the lack of Caribbean recruitment might be explained by diminishing quality of settlement cues and/or impaired sensitivity of Caribbean coral larvae to those cues, relative to the Pacific. To evaluate this hypothesis, we assembled a collection of bulk samples of reef encrusting communities, mostly consisting of crustose coralline algae (CCA), from various reefs around the world and tested them as settlement cues for several coral species originating from different ocean provinces. Cue samples were meta-barcoded to evaluate their taxonomic diversity. We observed no systematic differences either in cue potency or in strength of larval responses depending on the ocean province, and no preference of coral larvae towards cues from the same ocean. Instead, we detected significant differences in cue preferences among coral species, even for corals originating from the same reef. We conclude that the region-wide disruption of the settlement process is unlikely to be the major cause of Caribbean reef loss. However, due to their high sensitivity to the effects of climate change, shifts in the composition of CCA-associated communities, combined with pronounced differences in cue preferences among coral species, could substantially influence future coral community structure. PMID:24765568

40 CFR 191.12 - Definitions.

Code of Federal Regulations, 2011 CFR

2011-07-01

... TRANSURANIC RADIOACTIVE WASTES Environmental Standards for Disposal § 191.12 Definitions. Unless otherwise... environment. For example, a barrier may be a geologic structure, a canister, a waste form with physical and... over and around waste, provided that the material or structure substantially delays movement of water...

Understanding Longitudinal Wood Fiber Ultra-structure for Producing Cellulose Nanofibrils Using Disk Milling with Diluted Acid Prehydrolysis

NASA Astrophysics Data System (ADS)

Qin, Yanlin; Qiu, Xueqing; Zhu, J. Y.

2016-10-01

Here we used dilute oxalic acid to pretreat a kraft bleached Eucalyptus pulp (BEP) fibers to facilitate mechanical fibrillation in producing cellulose nanofibrils using disk milling with substantial mechanical energy savings. We successfully applied a reaction kinetics based combined hydrolysis factor (CHFX) as a severity factor to quantitatively control xylan dissolution and BEP fibril deploymerization. More importantly, we were able to accurately predict the degree of polymerization (DP) of disk-milled fibrils using CHFX and milling time or milling energy consumption. Experimentally determined ratio of fibril DP and number mean fibril height (diameter d), DP/d, an aspect ratio measurer, were independent of the processing conditions. Therefore, we hypothesize that cellulose have a longitudinal hierarchical structure as in the lateral direction. Acid hydrolysis and milling did not substantially cut the “natural” chain length of cellulose fibrils. This cellulose longitudinal hierarchical model provides support for using weak acid hydrolysis in the production of cellulose nanofibrils with substantially reduced energy input without negatively affecting fibril mechanical strength.

Vibration and noise characteristics of an elevated box girder paved with different track structures

NASA Astrophysics Data System (ADS)

Li, Xiaozhen; Liang, Lin; Wang, Dangxiong

2018-07-01

The vibration and noise of elevated concrete box girders (ECBGs) are now among the most concerned issues in the field of urban rail transit (URT) systems. The track structure, belonging to critical load-transfer components, directly affects the characteristics of loading transmission into bridge, as well as the noise radiation from such system, which further determines the reduction of vibration and noise in ECBGs significantly. In order to investigate the influence of different track structures on the vibration and structure-borne noise of ECBGs, a frequency-domain theoretical model of vehicle-track coupled system, taking into account the effect of multiple wheels, is firstly established in the present work. The analysis of track structures focuses on embedded sleepers, trapezoidal sleepers, and steel-spring floating slabs (SSFS). Next, a vibration and noise field test was performed, with regard to a 30 m simple supported ECBG (with the embedded-sleeper track structure) of an URT system. Based on the tested results, two numerical models, involving a finite element model for the vibration analysis, as well as a statistical energy analysis (SEA) model for the prediction of the noise radiation, are established and validated. The results of the numerical simulations and the field tests are well matched, which offers opportunities to predict the vibration and structure-borne noise of ECBGs by the proposed modelling methodology. From the comparison between the different types of track structures, the spatial distribution and reduction effect of vibration and noise are lastly studied. The force applied on ECBG is substantially determined by both the wheel-rail force (external factor) and the transmission rate of track structure (internal factor). The SSFS track is the most effective for vibration and noise reduction of ECBGs, followed in descending order by the trapezoidal-sleeper and embedded-sleeper tracks. The above result provides a theoretical basis for the vibration and noise reduction design of urban rail transit systems.

Genome Pool Strategy for Structural Coverage of Protein Families

PubMed Central

Jaroszewski, Lukasz; Slabinski, Lukasz; Wooley, John; Deacon, Ashley M.; Lesley, Scott A.; Wilson, Ian. A.; Godzik, Adam

2010-01-01

As noticed by generations of structural biologists, closely homologous proteins may have substantially different crystallization properties and propensities. These observations can be used to systematically introduce additional dimensionality into crystallization trials by targeting homologous proteins from multiple genomes in a “genome pool” strategy. Through extensive use of our recently introduced “crystallization feasibility score” (Slabinski et al., 2007a), we can explain that the genome pool strategy works well because the crystallization feasibility scores are surprisingly broad within families of homologous proteins, with most families containing a range of optimal to very difficult targets. We also show that some families can be regarded as relatively “easy”, where a significant number of proteins are predicted to have optimal crystallization features, and others are “very difficult”, where almost none are predicted to result in a crystal structure. Thus, the outcome of such variable distributions of such crystallizability' preferences leads to uneven structural coverage of known families, with “easier” or “optimal” families having several times more solved structures than “very difficult” ones. Nevertheless, this latter category can be successfully targeted by increasing the number of genomes that are used to select targets from a given family. On average, adding 10 new genomes to the “genome pool” provides more promising targets for 7 “very difficult” families. In contrast, our crystallization feasibility score does not indicate that any specific microbial genomes can be readily classified as “easier” or “very difficult” with respect to providing suitable candidates for crystallization and structure determination. Finally, our analyses show that specific physicochemical properties of the protein sequence favor successful outcomes for structure determination and, hence, the group of proteins with known 3D structures is systematically different from the general pool of known proteins. We, therefore, assess the structural consequences of these differences in protein sequence and protein biophysical properties. PMID:19000818

Permanent magnet design for high-speed superconducting bearings

DOEpatents

Hull, J.R.; Uherka, K.L.; Abdoud, R.G.

1996-09-10

A high temperature superconducting bearing including a permanent magnet rotor levitated by a high temperature superconducting structure is disclosed. The rotor preferably includes one or more concentric permanent magnet rings coupled to permanent magnet ring structures having substantially triangular and quadrangular cross-sections. Both alternating and single direction polarity magnet structures can be used in the bearing. 9 figs.

Comminution process to produce wood particles of uniform size and shape with disrupted grain structure from veneer

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

Dooley, James H.; Lanning, David N.

Comminution process of wood veneer to produce wood particles, by feeding wood veneer in a direction of travel substantially normal to grain through a counter rotating pair of intermeshing arrays of cutting discs arrayed axially perpendicular to the direction of wood veneer travel, wherein the cutting discs have a uniform thickness (Td), to produce wood particles characterized by a length dimension (L) substantially equal to the Td and aligned substantially parallel to grain, a width dimension (W) normal to L and aligned cross grain, and a height dimension (H) aligned normal to W and L, wherein the W.times.H dimensions definemore » a pair of substantially parallel end surfaces with end checking between crosscut fibers.« less

Meta-metallic coils and resonators: Methods for high Q-value resonant geometries

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

Mett, R. R.; Department of Physics and Chemistry, Milwaukee School of Engineering, Milwaukee, Wisconsin 53202; Sidabras, J. W.

A novel method of decreasing ohmic losses and increasing Q-value in metallic resonators at high frequencies is presented. The method overcomes the skin-depth limitation of rf current flow cross section. The method uses layers of conductive foil of thickness less than a skin depth and capacitive gaps between layers. The capacitive gaps can substantially equalize the rf current flowing in each layer, resulting in a total cross-sectional dimension for rf current flow many times larger than a skin depth. Analytic theory and finite-element simulations indicate that, for a variety of structures, the Q-value enhancement over a single thick conductor approachesmore » the ratio of total conductor thickness to skin depth if the total number of layers is greater than one-third the square of the ratio of total conductor thickness to skin depth. The layer number requirement is due to counter-currents in each foil layer caused by the surrounding rf magnetic fields. We call structures that exhibit this type of Q-enhancement “meta-metallic.” In addition, end effects due to rf magnetic fields wrapping around the ends of the foils can substantially reduce the Q-value for some classes of structures. Foil structures with Q-values that are substantially influenced by such end effects are discussed as are five classes of structures that are not. We focus particularly on 400 MHz, which is the resonant frequency of protons at 9.4 T. Simulations at 400 MHz are shown with comparison to measurements on fabricated structures. The methods and geometries described here are general for magnetic resonance and can be used at frequencies much higher than 400 MHz.« less

Meta-metallic coils and resonators: Methods for high Q-value resonant geometries

PubMed Central

Mett, R. R.; Hyde, J. S.

2016-01-01

A novel method of decreasing ohmic losses and increasing Q-value in metallic resonators at high frequencies is presented. The method overcomes the skin-depth limitation of rf current flow cross section. The method uses layers of conductive foil of thickness less than a skin depth and capacitive gaps between layers. The capacitive gaps can substantially equalize the rf current flowing in each layer, resulting in a total cross-sectional dimension for rf current flow many times larger than a skin depth. Analytic theory and finite-element simulations indicate that, for a variety of structures, the Q-value enhancement over a single thick conductor approaches the ratio of total conductor thickness to skin depth if the total number of layers is greater than one-third the square of the ratio of total conductor thickness to skin depth. The layer number requirement is due to counter-currents in each foil layer caused by the surrounding rf magnetic fields. We call structures that exhibit this type of Q-enhancement “meta-metallic.” In addition, end effects due to rf magnetic fields wrapping around the ends of the foils can substantially reduce the Q-value for some classes of structures. Foil structures with Q-values that are substantially influenced by such end effects are discussed as are five classes of structures that are not. We focus particularly on 400 MHz, which is the resonant frequency of protons at 9.4 T. Simulations at 400 MHz are shown with comparison to measurements on fabricated structures. The methods and geometries described here are general for magnetic resonance and can be used at frequencies much higher than 400 MHz. PMID:27587143

Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery.

PubMed

Chu, Derrick M; Ma, Jun; Prince, Amanda L; Antony, Kathleen M; Seferovic, Maxim D; Aagaard, Kjersti M

2017-03-01

Human microbial communities are characterized by their taxonomic, metagenomic and metabolic diversity, which varies by distinct body sites and influences human physiology. However, when and how microbial communities within each body niche acquire unique taxonomical and functional signatures in early life remains underexplored. We thus sought to determine the taxonomic composition and potential metabolic function of the neonatal and early infant microbiota across multiple body sites and assess the effect of the mode of delivery and its potential confounders or modifiers. A cohort of pregnant women in their early third trimester (n = 81) were prospectively enrolled for longitudinal sampling through 6 weeks after delivery, and a second matched cross-sectional cohort (n = 81) was additionally recruited for sampling once at the time of delivery. Samples across multiple body sites, including stool, oral gingiva, nares, skin and vagina were collected for each maternal-infant dyad. Whole-genome shotgun sequencing and sequencing analysis of the gene encoding the 16S rRNA were performed to interrogate the composition and function of the neonatal and maternal microbiota. We found that the neonatal microbiota and its associated functional pathways were relatively homogeneous across all body sites at delivery, with the notable exception of the neonatal meconium. However, by 6 weeks after delivery, the infant microbiota structure and function had substantially expanded and diversified, with the body site serving as the primary determinant of the composition of the bacterial community and its functional capacity. Although minor variations in the neonatal (immediately at birth) microbiota community structure were associated with the cesarean mode of delivery in some body sites (oral gingiva, nares and skin; R 2 = 0.038), this was not true for neonatal stool (meconium; Mann-Whitney P > 0.05), and there was no observable difference in community function regardless of delivery mode. For infants at 6 weeks of age, the microbiota structure and function had expanded and diversified with demonstrable body site specificity (P < 0.001, R 2 = 0.189) but without discernable differences in community structure or function between infants delivered vaginally or by cesarean surgery (P = 0.057, R 2 = 0.007). We conclude that within the first 6 weeks of life, the infant microbiota undergoes substantial reorganization, which is primarily driven by body site and not by mode of delivery.

Gene order and recombination rate in homologous chromosome regions of the chicken and a passerine bird.

PubMed

Dawson, Deborah A; Akesson, Mikael; Burke, Terry; Pemberton, Josephine M; Slate, Jon; Hansson, Bengt

2007-07-01

Genome structure has been found to be highly conserved between distantly related birds and recent data for a limited part of the genome suggest that this is true also for the gene order (synteny) within chromosomes. Here, we confirm that synteny is maintained for large chromosomal regions in chicken and a passerine bird, the great reed warbler Acrocephalus arundinaceus, with few rearrangements, but in contrast show that the recombination-based linkage map distances differ substantially between these species. We assigned a chromosomal location based on sequence similarity to the chicken genome sequence to a set of microsatellite loci mapped in a pedigree of great reed warblers. We detected homologous loci on 14 different chromosomes corresponding to chicken chromosomes Gga1-5, 7-9, 13, 19, 20, 24, 25, and Z. It is known that 2 passerine macrochromosomes correspond to the chicken chromosome Gga1. Homology of 2 different great reed warbler linkage groups (LG13 and LG5) to Gga1 allowed us to locate the split to a position between 20.8 and 84.8 Mb on Gga1. Data from the 5 chromosomal regions (on Gga1, 2, 3, 5, and Z) with 3 or more homologous loci showed that synteny was conserved with the exception of 2 large previously unreported inversions on Gga1/LG5 and Gga2/LG3, respectively. Recombination data from the 9 chromosomal regions in which we identified 2 or more homologous loci (accounting for the inversions) showed that the linkage map distances in great reed warblers were only 6.3% and 13.3% of those in chickens for males and females, respectively. This is likely to reflect the true interspecific difference in recombination rate because our markers were not located in potentially low-recombining regions: several linkage groups covered a substantial part of their corresponding chicken chromosomes and were not restricted to centromeres. We conclude that recombination rates may differ strongly between bird species with highly conserved genome structure and synteny and that the chicken linkage map may not be suitable, in terms of genetic distances, as a model for all bird species.

Inbreeding avoidance under different null models of random mating in the great tit.

PubMed

Szulkin, Marta; Zelazowski, Przemyslaw; Nicholson, George; Sheldon, Ben C

2009-07-01

1. In populations where inbreeding causes a substantial decrease in fitness, selection is expected to favour the evolution of inbreeding avoidance behaviours. Elsewhere we have documented substantial inbreeding depression and the importance of dispersal in avoiding inbreeding in a long-term population study of the great tit Parus major in Wytham (UK). In this study, we ask whether individuals from this population actively avoid mating with kin. 2. We generated four contrasting models of random mate choice that assumed varying levels of mate availability in each year of the data set. This allowed us to compare observed and simulated distributions and frequencies of inbreeding coefficients from 41 years of breeding data. 3. We found no evidence that birds avoid mating with related partners. Our results show that birds breed more often with relatives than expected under null models of mate choice that lack population structure, but not when compared to scenarios where birds were mated with their nearest neighbours. Pedigree-derived F(IS) values were positive for all scenarios of random mating, confirming the lack of inbreeding avoidance in this population. 4. These results imply the existence of spatial genetic structure where related individuals occur closer together than nonrelated individuals while breeding, and suggest that the relatedness between breeding individuals of the opposite sex decreases with distance. Thus, while dispersal from the natal site decreases the number of relatives around an individual, it does not completely homogenize genetic structure. 5. We show that brother-sister pairs are observed more often than under any scenario of random mating, suggesting that not only birds do not avoid mating with kin, but also that the apparently maladaptive choice of mating with a sibling is made more often than expected. 6. Our results provide no evidence to suggest that individuals actively avoid kin. In fact, some types of inbreeding occur more often than expected, despite the substantial fitness costs. The observed lack of inbreeding avoidance is in agreement with other studies of non-cooperatively breeding passerine birds, although the higher than expected frequency of sibling mating remains a puzzling result.

Factor Structure of Scores from the Conners’ Rating Scales–Revised Among Nepali Children

PubMed Central

Pendergast, Laura L.; Vandiver, Beverly J.; Schaefer, Barbara A.; Cole, Pamela M.; Murray-Kolb, Laura M.; Christian, Parul

2014-01-01

This study used exploratory and confirmatory factor analyses to examine the structures of scores from the Conners’ Teacher and Parent Rating Scales–Revised (CTRS-R and CPRS-R, respectively; Conners, 1997). The scales were administered to 1,835 parents and 1,387 teachers of children in Nepal's Sarlahi district – a region where no other measures of child psychopathology have been studied. With a Nepali sample, the findings indicate that reduced two factor models for the Conners’ scales are superior to the models identified in the scale development research. The hyperactivity and inattention factors were comparable to what has been identified in prior research, while other factors (e.g., social problems) differed substantially. Implications for use of the Conners’ scales in Nepal and cross cultural issues in the assessment of ADHD symptoms are discussed. PMID:25574454

Biochemical Effects of six Ti02 and four Ce02 Nanomaterials ...

EPA Pesticide Factsheets

Abstract The potential mammalian hepatotoxicity of nanomaterials were explored in dose-response and structure-activity studies with human hepatic HepG2 cells exposed to between 10 and 1000 ug/ml of six different TiO2 and four CeO2 nanomaterials for 3 days. Various biochemical parameters were then evaluated to study cytotoxicity, cell growth, hepatic function and oxidative stress. Few indications of cytotoxicity were observed between 10 and 100 ug/ml. In the 300 to 1000 ug/ml exposure range a moderate to substantial degree of cytotoxicity was observed. The percent of lactic dehydrogenase released from cells was the most sensitive cytotoxicity parameter. There were four major biochemical effects observed. By far decreased activities of glucose 6-phosphate dehydrogenase was the major finding of this enzymatic study with some significant decreases observed at 10 ug/ml. In the range of 100 to 1000 ug/ml, the activities of superoxide dismutase, glutathione reductase and glutathione peroxidase were decreased by many nanomaterials. There are six factors that contribute to substantial oxidative stress in cultured hepatocytes (decreased GSH content, and reduced G6PDH, GRD, GPX, SOD and altered catalase activities). Cytotoxicity per se did not seem to fully explain the patterns of biological responses observed. With respect to structure-activity, nanomaterials of CeO2 were more effective than TiO2 in reducing glutathione reductase and SOD activ

Visualization of air flow around soccer ball using a particle image velocimetry

PubMed Central

Hong, Sungchan; Asai, Takeshi; Seo, Kazuya

2015-01-01

A traditional soccer ball is constructed using 32 pentagonal and hexagonal panels. In recent years, however, the likes of the Teamgeist and Jabulani balls, constructed from 14 and 8 panels, respectively, have entered the field, marking a significant departure from conventionality in terms of shape and design. Moreover, the recently introduced Brazuca ball features a new 6-panel design and has already been adopted by many soccer leagues. However, the shapes of the constituent panels of these balls differ substantially from those of conventional balls. Therefore, this study set out to investigate the flight and aerodynamic characteristics of different orientations of the soccer ball, which is constructed from panels of different shapes. A wind tunnel test showed substantial differences in the aerodynamic forces acting on the ball, depending on its orientation. Substantial differences were also observed in the aerodynamic forces acting on the ball in different directions, corresponding to its orientation and rotation. Moreover, two-dimensional particle image velocimetry (2D-PIV) measurements showed that the boundary separation varies depending on the orientation of the ball. Based on these results, we can conclude that the shape of the panels of a soccer ball substantially affects its flight trajectory. PMID:26446616

Visualization of air flow around soccer ball using a particle image velocimetry

NASA Astrophysics Data System (ADS)

Hong, Sungchan; Asai, Takeshi; Seo, Kazuya

2015-10-01

A traditional soccer ball is constructed using 32 pentagonal and hexagonal panels. In recent years, however, the likes of the Teamgeist and Jabulani balls, constructed from 14 and 8 panels, respectively, have entered the field, marking a significant departure from conventionality in terms of shape and design. Moreover, the recently introduced Brazuca ball features a new 6-panel design and has already been adopted by many soccer leagues. However, the shapes of the constituent panels of these balls differ substantially from those of conventional balls. Therefore, this study set out to investigate the flight and aerodynamic characteristics of different orientations of the soccer ball, which is constructed from panels of different shapes. A wind tunnel test showed substantial differences in the aerodynamic forces acting on the ball, depending on its orientation. Substantial differences were also observed in the aerodynamic forces acting on the ball in different directions, corresponding to its orientation and rotation. Moreover, two-dimensional particle image velocimetry (2D-PIV) measurements showed that the boundary separation varies depending on the orientation of the ball. Based on these results, we can conclude that the shape of the panels of a soccer ball substantially affects its flight trajectory.

20 CFR 404.1574a - When and how we will average your earnings.

Code of Federal Regulations, 2011 CFR

2011-04-01

... has been no change in the substantial gainful activity earnings levels, we will average your earnings... time during which the substantial gainful activity earnings levels change, we will average your earnings separately for each period in which a different substantial gainful activity earnings level...

20 CFR 404.1574a - When and how we will average your earnings.

Code of Federal Regulations, 2010 CFR

2010-04-01

... has been no change in the substantial gainful activity earnings levels, we will average your earnings... time during which the substantial gainful activity earnings levels change, we will average your earnings separately for each period in which a different substantial gainful activity earnings level...

Engineered plant biomass feedstock particles

DOEpatents

Dooley, James H [Federal Way, WA; Lanning, David N [Federal Way, WA; Broderick, Thomas F [Lake Forest Park, WA

2011-10-11

A novel class of flowable biomass feedstock particles with unusually large surface areas that can be manufactured in remarkably uniform sizes using low-energy comminution techniques. The feedstock particles are roughly parallelepiped in shape and characterized by a length dimension (L) aligned substantially with the grain direction and defining a substantially uniform distance along the grain, a width dimension (W) normal to L and aligned cross grain, and a height dimension (H) normal to W and L. The particles exhibit a disrupted grain structure with prominent end and surface checks that greatly enhances their skeletal surface area as compared to their envelope surface area. The L.times.H dimensions define a pair of substantially parallel side surfaces characterized by substantially intact longitudinally arrayed fibers. The W.times.H dimensions define a pair of substantially parallel end surfaces characterized by crosscut fibers and end checking between fibers. The L.times.W dimensions define a pair of substantially parallel top surfaces characterized by some surface checking between longitudinally arrayed fibers. The feedstock particles are manufactured from a variety of plant biomass materials including wood, crop residues, plantation grasses, hemp, bagasse, and bamboo.

Re-Organizing Universities for the Information Age

ERIC Educational Resources Information Center

Annand, David

2007-01-01

University education is still generally conducted within pre-Industrial Age organizational structures. As a result of their inability to evolve the predominant cohort-based classroom structure to more cost-effectively meet the aspirations of burgeoning worldwide populations for higher education, universities may see substantial organizational…

NEUTRONIC REACTOR CORE

DOEpatents

Thomson, W.B.; Corbin, A. Jr.

1961-07-18

An improved core for a gas-cooled power reactor which admits gas coolant at high temperatures while affording strong integral supporting structure and efficient moderation of neutrons is described. The multiplicities of fuel elements constituting the critical amassment of fissionable material are supported and confined by a matrix of metallic structure which is interspersed therebetween. Thermal insulation is interposed between substantially all of the metallic matrix and the fuel elements; the insulation then defines the principal conduit system for conducting the coolant gas in heat-transfer relationship with the fuel elements. The metallic matrix itseif comprises a system of ducts through which an externally-cooled hydrogeneous liquid, such as water, is circulated to serve as the principal neutron moderant for the core and conjointly as the principal coolant for the insulated metallic structure. In this way, use of substantially neutron transparent metals, such as aluminum, becomes possible for the supporting structure, despite the high temperatures of the proximate gas. The Aircraft Nuclear Propulsion program's "R-1" reactor design is a preferred embodiment.

Effect of Yeast Cell Morphology, Cell Wall Physical Structure and Chemical Composition on Patulin Adsorption

PubMed Central

Luo, Ying; Wang, Jianguo; Liu, Bin; Wang, Zhouli; Yuan, Yahong; Yue, Tianli

2015-01-01

The capability of yeast to adsorb patulin in fruit juice can aid in substantially reducing the patulin toxic effect on human health. This study aimed to investigate the capability of yeast cell morphology and cell wall internal structure and composition to adsorb patulin. To compare different yeast cell morphologies, cell wall internal structure and composition, scanning electron microscope, transmission electron microscope and ion chromatography were used. The results indicated that patulin adsorption capability of yeast was influenced by cell surface areas, volume, and cell wall thickness, as well as 1,3-β-glucan content. Among these factors, cell wall thickness and 1,3-β-glucan content serve significant functions. The investigation revealed that patulin adsorption capability was mainly affected by the three-dimensional network structure of the cell wall composed of 1,3-β-glucan. Finally, patulin adsorption in commercial kiwi fruit juice was investigated, and the results indicated that yeast cells could adsorb patulin from commercial kiwi fruit juice efficiently. This study can potentially simulate in vitro cell walls to enhance patulin adsorption capability and successfully apply to fruit juice industry. PMID:26295574

Effect of Yeast Cell Morphology, Cell Wall Physical Structure and Chemical Composition on Patulin Adsorption.

PubMed

Luo, Ying; Wang, Jianguo; Liu, Bin; Wang, Zhouli; Yuan, Yahong; Yue, Tianli

2015-01-01

The capability of yeast to adsorb patulin in fruit juice can aid in substantially reducing the patulin toxic effect on human health. This study aimed to investigate the capability of yeast cell morphology and cell wall internal structure and composition to adsorb patulin. To compare different yeast cell morphologies, cell wall internal structure and composition, scanning electron microscope, transmission electron microscope and ion chromatography were used. The results indicated that patulin adsorption capability of yeast was influenced by cell surface areas, volume, and cell wall thickness, as well as 1,3-β-glucan content. Among these factors, cell wall thickness and 1,3-β-glucan content serve significant functions. The investigation revealed that patulin adsorption capability was mainly affected by the three-dimensional network structure of the cell wall composed of 1,3-β-glucan. Finally, patulin adsorption in commercial kiwi fruit juice was investigated, and the results indicated that yeast cells could adsorb patulin from commercial kiwi fruit juice efficiently. This study can potentially simulate in vitro cell walls to enhance patulin adsorption capability and successfully apply to fruit juice industry.

Structure of the hexameric HerA ATPase reveals a mechanism of translocation-coupled DNA-end processing in archaea.

PubMed

Rzechorzek, Neil J; Blackwood, John K; Bray, Sian M; Maman, Joseph D; Pellegrini, Luca; Robinson, Nicholas P

2014-11-25

The HerA ATPase cooperates with the NurA nuclease and the Mre11-Rad50 complex for the repair of double-strand DNA breaks in thermophilic archaea. Here we extend our structural knowledge of this minimal end-resection apparatus by presenting the first crystal structure of hexameric HerA. The full-length structure visualizes at atomic resolution the N-terminal HerA-ATP synthase domain and a conserved C-terminal extension, which acts as a physical brace between adjacent protomers. The brace also interacts in trans with nucleotide-binding residues of the neighbouring subunit. Our observations support a model in which the coaxial interaction of the HerA ring with the toroidal NurA dimer generates a continuous channel traversing the complex. HerA-driven translocation would propel the DNA towards the narrow annulus of NurA, leading to duplex melting and nucleolytic digestion. This system differs substantially from the bacterial end-resection paradigms. Our findings suggest a novel mode of DNA-end processing by this integrated archaeal helicase-nuclease machine.

The special features of the crystal structure and properties of oxides with mixed conductivity based on lanthanum gallate

NASA Astrophysics Data System (ADS)

Politova, E. D.; Ivanov, S. A.; Kaleva, G. M.; Mosunov, A. V.; Rusakov, V. S.

2008-10-01

The paper presents a review of works on the synthesis, structural composition effects, phase transitions, and electrical conductivity properties of multicomponent solid solutions based on heterosubstituted lanthanum gallate (La,A)(Ga,M)O3 - y . High-temperature phase transitions and structural and charge ordering effects were studied. The presence of iron cations in different valence states was proved; the relative contents of these cations depended on the x parameter and nonstoichiometry parameter y of the base composition. For M = Fe, antiferromagnetic ordering was observed; its temperature interval was determined by the concentration of iron cations in the high-spin state. The total conductivity was found to increase as the concentration of transition metal cations grew because of an increase in the electronic conductivity component. The data on structural parameters and dc and ac conductivity substantiated the conclusion that the highest ionic conductivity and permeability to oxygen were characteristic of iron-containing oxides. The results obtained are evidence that crystal chemical factors play a determining role in the formation of the ion-conducting properties of anion-deficient perovskite-like oxides.

A model of the complex between human {beta}-microseminoprotein and CRISP-3 based on NMR data

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

Ghasriani, Houman; Fernlund, Per; Udby, Lene

2009-01-09

{beta}-Microseminoprotein (MSP), a 10 kDa seminal plasma protein, forms a tight complex with cysteine-rich secretory protein 3 (CRISP-3) from granulocytes. The 3D structure of human MSP has been determined but there is as yet no 3D structure for CRISP-3. We have now studied the complex between human MSP and CRISP-3 with multidimensional NMR. {sup 15}N-HSQC spectra show substantial differences between free and complexed hMSP. Using several 3D-NMR spectra of triply labeled hMSP in complex with a recombinant N-terminal domain of CRISP-3, most of the backbone of hMSP could be assigned. The data show that only one side of hMSP, comprisingmore » {beta}-strands 1, 4, 5, and 8 are affected by the complex formation, indicating that {beta}-strands 1 and 8 form the main binding surface. Based on this we present a tentative structure for the hMSP-CRISP-3 complex using the known crystal structure of triflin as a model of CRISP-3.« less

Fifty years of herbicide research: comparing the discovery of trifluralin and halauxifen-methyl.

PubMed

Epp, Jeffrey B; Schmitzer, Paul R; Crouse, Gary D

2018-01-01

Fifty years separate the commercialization of the herbicides trifluralin and halauxifen-methyl. Despite the vast degree of technological change that occurred over that time frame, some aspects of their discovery stories are remarkably similar. For example, both herbicides were prepared very early in the iterative discovery process and both were developed from known lead compound structures by hypothesis-driven research efforts without the use of in vitro assays or computer-aided molecular design. However, there are aspects of the halauxifen-methyl and trifluralin discovery stories that are substantially different. For example, the chemical technology required for the cost-effective production of halauxifen-methyl simply did not exist just two decades prior to its commercial launch. By contrast, the chemical technology required for the cost-effective production of trifluralin was reported in the chemical literature more than two decades prior to its commercial launch. In addition, changes in regulatory environment since the early 1960s ensured that their respective discovery to commercial launch stories would also differ in substantial ways. Ultimately, the time and cost required to develop and register halauxifen-methyl demanded a global initial business case while the lower registration hurdles that trifluralin cleared enabled a narrow initial business case mainly focused on the USA. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Modeling economic implications of alternative treatment strategies for acute bacterial skin and skin structure infections.

PubMed

Revankar, Nikhil; Ward, Alexandra J; Pelligra, Christopher G; Kongnakorn, Thitima; Fan, Weihong; LaPensee, Kenneth T

2014-10-01

The economic implications from the US Medicare perspective of adopting alternative treatment strategies for acute bacterial skin and skin structure infections (ABSSSIs) are substantial. The objective of this study is to describe a modeling framework that explores the impact of decisions related to both the location of care and switching to different antibiotics at discharge. A discrete event simulation (DES) was developed to model the treatment pathway of each patient through various locations (emergency department [ED], inpatient, and outpatient) and the treatments prescribed (empiric antibiotic, switching to a different antibiotic at discharge, or a second antibiotic). Costs are reported in 2012 USD. The mean number of days on antibiotic in a cohort assigned to a full course of vancomycin was 11.2 days, with 64% of the treatment course being administered in the outpatient setting. Mean total costs per patient were $8671, with inpatient care accounting for 58% of the costs accrued. The majority of outpatient costs were associated with parenteral administration rather than drug acquisition or monitoring. Scenarios modifying the treatment pathway to increase the proportion of patients receiving the first dose in the ED, and then managing them in the outpatient setting or prescribing an oral antibiotic at discharge to avoid the cost associated with administering parenteral therapy, therefore have a major impact and lower the typical cost per patient by 11-20%. Since vancomycin is commonly used as empiric therapy in clinical practice, based on these analyses, a shift in treatment practice could result in substantial savings from the Medicare perspective. The choice of antibiotic and location of care influence the costs and resource use associated with the management of ABSSSIs. The DES framework presented here can provide insight into the potential economic implications of decisions that modify the treatment pathway.

Structure, Process, and Culture of Intensive Care Units Treating Patients with Severe Traumatic Brain Injury: Survey of Centers Participating in the American College of Surgeons Trauma Quality Improvement Program.

PubMed

Alali, Aziz S; McCredie, Victoria A; Mainprize, Todd G; Gomez, David; Nathens, Avery B

2017-10-01

Outcome after severe traumatic brain injury (TBI) differs substantially between hospitals. Explaining this variation begins with understanding the differences in structures and processes of care, particularly at intensive care units (ICUs) where acute TBI care takes place. We invited trauma medical directors (TMDs) from 187 centers participating in the American College of Surgeons Trauma Quality Improvement Program (ACS TQIP) to complete a survey. The survey domains included ICU model, type, availability of specialized units, staff, training programs, standard protocols and order sets, approach to withdrawal of life support, and perceived level of neurosurgeons' engagement in the ICU management of TBI. One hundred forty-two TMDs (76%) completed the survey. Severe TBI patients are admitted to dedicated neurocritical care units in 52 hospitals (37%), trauma ICUs in 44 hospitals (31%), general ICUs in 34 hospitals (24%), and surgical ICUs in 11 hospitals (8%). Fifty-seven percent are closed units. Board-certified intensivists directed 89% of ICUs, whereas 17% were led by neurointensivists. Sixty percent of ICU directors were general surgeons. Thirty-nine percent of hospitals had critical care fellowships and 11% had neurocritical care fellowships. Fifty-nine percent of ICUs had standard order sets and 61% had standard protocols specific for TBI, with the most common protocol relating to intracranial pressure management (53%). Only 43% of TMDs were satisfied with the current level of neurosurgeons' engagement in the ICU management of TBI; 46% believed that neurosurgeons should be more engaged; 11% believed they should be less engaged. In the largest survey of North American ICUs caring for TBI patients, there is substantial variation in the current approaches to ICU care for TBI, highlighting multiple opportunities for comparative effectiveness research.

Measurement invariance of big-five factors over the life span: ESEM tests of gender, age, plasticity, maturity, and la dolce vita effects.

PubMed

Marsh, Herbert W; Nagengast, Benjamin; Morin, Alexandre J S

2013-06-01

This substantive-methodological synergy applies evolving approaches to factor analysis to substantively important developmental issues of how five-factor-approach (FFA) personality measures vary with gender, age, and their interaction. Confirmatory factor analyses (CFAs) conducted at the item level often do not support a priori FFA structures, due in part to the overly restrictive assumptions of CFA models. Here we demonstrate that exploratory structural equation modeling (ESEM), an integration of CFA and exploratory factor analysis, overcomes these problems with the 15-item Big Five Inventory administered as part of the nationally representative British Household Panel Study (N = 14,021; age: 15-99 years, Mage = 47.1). ESEM fitted the data substantially better and resulted in much more differentiated (less correlated) factors than did CFA. Methodologically, we extended ESEM (introducing ESEM-within-CFA models and a hybrid of multiple groups and multiple indicators multiple causes models), evaluating full measurement invariance and latent mean differences over age, gender, and their interaction. Substantively the results showed that women had higher latent scores for all Big Five factors except for Openness and that these gender differences were consistent over the entire life span. Substantial nonlinear age effects led to the rejection of the plaster hypothesis and the maturity principle but did support a newly proposed la dolce vita effect in old age. In later years, individuals become happier (more agreeable and less neurotic), more self-content and self-centered (less extroverted and open), more laid back and satisfied with what they have (less conscientious, open, outgoing and extroverted), and less preoccupied with productivity. PsycINFO Database Record (c) 2013 APA, all rights reserved

Simplified and refined structural modeling for economical flutter analysis and design

NASA Technical Reports Server (NTRS)

Ricketts, R. H.; Sobieszczanski, J.

1977-01-01

A coordinated use of two finite-element models of different levels of refinement is presented to reduce the computer cost of the repetitive flutter analysis commonly encountered in structural resizing to meet flutter requirements. One model, termed a refined model (RM), represents a high degree of detail needed for strength-sizing and flutter analysis of an airframe. The other model, called a simplified model (SM), has a relatively much smaller number of elements and degrees-of-freedom. A systematic method of deriving an SM from a given RM is described. The method consists of judgmental and numerical operations to make the stiffness and mass of the SM elements equivalent to the corresponding substructures of RM. The structural data are automatically transferred between the two models. The bulk of analysis is performed on the SM with periodical verifications carried out by analysis of the RM. In a numerical example of a supersonic cruise aircraft with an arrow wing, this approach permitted substantial savings in computer costs and acceleration of the job turn-around.

Structural Characterization of the Boca/Mesd Maturation Factors for LDL-Receptor-Type beta Propeller Domains

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

M Collins; W Hendrickson

2011-12-31

Folding and trafficking of low-density lipoprotein receptor (LDLR) family members, which play essential roles in development and homeostasis, are mediated by specific chaperones. The Boca/Mesd chaperone family specifically promotes folding and trafficking of the YWTD {beta} propeller-EGF domain pair found in the ectodomain of all LDLR members. Limited proteolysis, NMR spectroscopy, analytical ultracentrifugation, and X-ray crystallography were used to define a conserved core composed of a structured domain that is preceded by a disordered N-terminal region. High-resolution structures of the ordered domain were determined for homologous proteins from three metazoans. Seven independent protomers reveal a novel ferrodoxin-like superfamily fold withmore » two distinct {beta} sheet topologies. A conserved hydrophobic surface forms a dimer interface in each crystal, but these differ substantially at the atomic level, indicative of nonspecific hydrophobic interactions that may play a role in the chaperone activity of the Boca/Mesd family.« less

Guano-Derived Nutrient Subsidies Drive Food Web Structure in Coastal Ponds.

PubMed

Vizzini, Salvatrice; Signa, Geraldina; Mazzola, Antonio

2016-01-01

A stable isotope study was carried out seasonally in three coastal ponds (Marinello system, Italy) affected by different gull guano input to investigate the effect of nutrient subsidies on food web structure and dynamics. A marked 15N enrichment occurred in the pond receiving the highest guano input, indicating that gull-derived fertilization (guanotrophication) had a strong localised effect and flowed across trophic levels. The main food web response to guanotrophication was an overall erosion of the benthic pathway in favour of the planktonic. Subsidized primary consumers, mostly deposit feeders, switched their diet according to organic matter source availability. Secondary consumers and, in particular, fish from the guanotrophic pond, acted as couplers of planktonic and benthic pathways and showed an omnivorous trophic behaviour. Food web structure showed substantial variability among ponds and a marked seasonality in the subsidized one: an overall simplification was evident only in summer when guano input maximises its trophic effects, while higher trophic diversity and complexity resulted when guano input was low to moderate.

Guano-Derived Nutrient Subsidies Drive Food Web Structure in Coastal Ponds

PubMed Central

Vizzini, Salvatrice; Signa, Geraldina; Mazzola, Antonio

2016-01-01

A stable isotope study was carried out seasonally in three coastal ponds (Marinello system, Italy) affected by different gull guano input to investigate the effect of nutrient subsidies on food web structure and dynamics. A marked 15N enrichment occurred in the pond receiving the highest guano input, indicating that gull-derived fertilization (guanotrophication) had a strong localised effect and flowed across trophic levels. The main food web response to guanotrophication was an overall erosion of the benthic pathway in favour of the planktonic. Subsidized primary consumers, mostly deposit feeders, switched their diet according to organic matter source availability. Secondary consumers and, in particular, fish from the guanotrophic pond, acted as couplers of planktonic and benthic pathways and showed an omnivorous trophic behaviour. Food web structure showed substantial variability among ponds and a marked seasonality in the subsidized one: an overall simplification was evident only in summer when guano input maximises its trophic effects, while higher trophic diversity and complexity resulted when guano input was low to moderate. PMID:26953794

H-fractal seismic metamaterial with broadband low-frequency bandgaps

NASA Astrophysics Data System (ADS)

Du, Qiujiao; Zeng, Yi; Xu, Yang; Yang, Hongwu; Zeng, Zuoxun

2018-03-01

The application of metamaterial in civil engineering to achieve isolation of a building by controlling the propagation of seismic waves is a substantial challenge because seismic waves, a superposition of longitudinal and shear waves, are more complex than electromagnetic and acoustic waves. In this paper, we design a broadband seismic metamaterial based on H-shaped fractal pillars and report numerical simulation of band structures for seismic surface waves propagating. Comparative study on the band structures of H-fractal seismic metamaterials with different levels shows that a new level of fractal structure creates new band gap, widens the total band gaps and shifts the same band gap towards lower frequencies. Moreover, the vibration modes for H-fractal seismic metamaterials are computed and analyzed to clarify the mechanism of widening band gaps. A numerical investigation of seismic surface waves propagation on a 2D array of fractal unit cells on the surface of semi-infinite substrate is proposed to show the efficiency of earthquake shielding in multiple complete band gaps.

Structural basis of receptor sulfotyrosine recognition by a CC chemokine: the N-terminal region of CCR3 bound to CCL11/eotaxin-1.

PubMed

Millard, Christopher J; Ludeman, Justin P; Canals, Meritxell; Bridgford, Jessica L; Hinds, Mark G; Clayton, Daniel J; Christopoulos, Arthur; Payne, Richard J; Stone, Martin J

2014-11-04

Trafficking of leukocytes in immune surveillance and inflammatory responses is activated by chemokines engaging their receptors. Sulfation of tyrosine residues in peptides derived from the eosinophil chemokine receptor CCR3 dramatically enhances binding to cognate chemokines. We report the structural basis of this recognition and affinity enhancement. We describe the structure of a CC chemokine (CCL11/eotaxin-1) bound to a fragment of a chemokine receptor: residues 8–23 of CCR3, including two sulfotyrosine residues. We also show that intact CCR3 is sulfated and sulfation enhances receptor activity. The CCR3 sulfotyrosine residues form hydrophobic, salt bridge and cation-p interactions with residues that are highly conserved in CC chemokines. However, the orientation of the chemokine relative to the receptor N terminus differs substantially from those observed for two CXC chemokines, suggesting that initial binding of the receptor sulfotyrosine residues guides subsequent steps in receptor activation, thereby influencing the receptor conformational changes and signaling.

Trimeric HIV-1-Env Structures Define Glycan Shields from Clades A, B and G

PubMed Central

Stewart-Jones, Guillaume B. E.; Soto, Cinque; Lemmin, Thomas; Chuang, Gwo-Yu; Druz, Aliaksandr; Kong, Rui; Thomas, Paul V.; Wagh, Kshitij; Zhou, Tongqing; Behrens, Anna-Janina; Bylund, Tatsiana; Choi, Chang W.; Davison, Jack R.; Georgiev, Ivelin S.; Joyce, M. Gordon; Do Kwon, Young; Pancera, Marie; Taft, Justin; Yang, Yongping; Zhang, Baoshan; Shivatare, Sachin S.; Shivatare, Vidya S.; Lee, Chang-Chun D.; Wu, Chung-Yi; Bewley, Carole A.; Burton, Dennis R.; Koff, Wayne C.; Connors, Mark; Crispin, Max; Baxa, Ulrich; Korber, Bette T.; Wong, Chi-Huey; Mascola, John R.; Kwong, Peter D.

2017-01-01

The HIV-1-envelope (Env) trimer is covered by a glycan shield of ~90 N-linked oligosaccharides, which comprises roughly half its mass and is a key component of HIV evasion from humoral immunity. To understand how antibodies can overcome the barriers imposed by the glycan shield, we crystallized fully glycosylated Env trimers from clades A, B and G, visualizing the shield at 3.4-3.7 Å resolution. These structures reveal the HIV-1-glycan shield to comprise a network of interlocking oligosaccharides, substantially ordered by glycan crowding, which encase the protein component of Env and enable HIV-1 to avoid most antibody-mediated neutralization. The revealed features delineate a taxonomy of N-linked glycan-glycan interactions. Crowded and dispersed glycans are differently ordered, conserved, processed and recognized by antibody. The structures, along with glycan-array binding and molecular dynamics, reveal a diversity in oligosaccharide affinity and a requirement for accommodating glycans amongst known broadly neutralizing antibodies that target the glycan-shielded trimer. PMID:27114034

Structural and Mechanistic Insight into the Listeria monocytogenes Two-enzyme Lipoteichoic Acid Synthesis System*

PubMed Central

Campeotto, Ivan; Percy, Matthew G.; MacDonald, James T.; Förster, Andreas; Freemont, Paul S.; Gründling, Angelika

2014-01-01

Lipoteichoic acid (LTA) is an important cell wall component required for proper cell growth in many Gram-positive bacteria. In Listeria monocytogenes, two enzymes are required for the synthesis of this polyglycerolphosphate polymer. The LTA primase LtaPLm initiates LTA synthesis by transferring the first glycerolphosphate (GroP) subunit onto the glycolipid anchor and the LTA synthase LtaSLm extends the polymer by the repeated addition of GroP subunits to the tip of the growing chain. Here, we present the crystal structures of the enzymatic domains of LtaPLm and LtaSLm. Although the enzymes share the same fold, substantial differences in the cavity of the catalytic site and surface charge distribution contribute to enzyme specialization. The eLtaSLm structure was also determined in complex with GroP revealing a second GroP binding site. Mutational analysis confirmed an essential function for this binding site and allowed us to propose a model for the binding of the growing chain. PMID:25128528

Synthesis, Structure and bonding Analysis of the Polar Intermetallic Phase Ca2Pt2Cd

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

Samal, Saroj L.; Corbett, John D.

The polar intermetallic phase Ca2Pt2Cd was discovered during explorations of the Ca-Pt-Cd system. The compound was synthesized by high temperature reactions, and its structure refined by single-crystal X-ray diffraction as orthorhombic, Immm, a = 4.4514(5), b = 5.8415(6), c = 8.5976(9) Å, Z = 2. The structure formally contains infinite, planar networks of [Pt2Cd]4– along the ab plane, which can be described as tessellation of six and four-member rings of the anions, with cations stuffed between the anion layers. The infinite condensed platinum chains show a substantial long–short distortion of 0.52 Å, an appreciable difference between Ca2Pt2Cd (26 valence electrons)more » and the isotypic but regular Ca2Cu2Ga (29 VE). The relatively large cation proportion diminishes the usual dominance of polar (Pt–Cd) and 5d–5d (Pt–Pt) contributions to the total Hamilton populations.« less

The increasing unemployment gap between the low and high educated in West Germany. Structural or cyclical crowding-out?

PubMed

Klein, Markus

2015-03-01

This paper addresses trends in education-specific unemployment risks at labor market entry in West Germany from the mid-1970s to the present. In line with previous research it shows that vocationally qualified school-leavers have relatively lower unemployment risks than school-leavers with general education. Over time, the gap in unemployment risks between the low-educated and medium- and highly educated labor market entrants substantially widened for both sexes. The literature identifies two different mechanisms for this trend: structural or cyclical crowding out. While in the former scenario low-educated become increasingly unemployed due to an oversupply of tertiary graduates and displacement from above, in the latter their relative unemployment risk varies with the business cycle. The results provide evidence for cyclical rather than structural crowding-out in West Germany. Since macroeconomic conditions became generally worse over time, this strongly explains the widening unemployment gap between the low-educated and all other education groups. Copyright © 2014 Elsevier Inc. All rights reserved.

Acicular photomultiplier photocathode structure

DOEpatents

Craig, Richard A.; Bliss, Mary

2003-09-30

A method and apparatus for increasing the quantum efficiency of a photomultiplier tube by providing a photocathode with an increased surface-to-volume ratio. The photocathode includes a transparent substrate, upon one major side of which is formed one or more large aspect-ratio structures, such as needles, cones, fibers, prisms, or pyramids. The large aspect-ratio structures are at least partially composed of a photoelectron emitting material, i.e., a material that emits a photoelectron upon absorption of an optical photon. The large aspect-ratio structures may be substantially composed of the photoelectron emitting material (i.e., formed as such upon the surface of a relatively flat substrate) or be only partially composed of a photoelectron emitting material (i.e., the photoelectron emitting material is coated over large aspect-ratio structures formed from the substrate material itself.) The large aspect-ratio nature of the photocathode surface allows for an effective increase in the thickness of the photocathode relative the absorption of optical photons, thereby increasing the absorption rate of incident photons, without substantially increasing the effective thickness of the photocathode relative the escape incidence of the photoelectrons.

Ultrasonic influence on evolution of disordered dislocation structures

NASA Astrophysics Data System (ADS)

Bachurin, D. V.; Murzaev, R. T.; Nazarov, A. A.

2017-12-01

Evolution of disordered dislocation structures under ultrasonic influence is studied in a model two-dimensional grain within the discrete-dislocation approach. Non-equilibrium grain boundary state is mimicked by a mesodefect located at the corners of the grain, stress field of which is described by that of a wedge junction disclination quadrupole. Significant rearrangement related to gliding of lattice dislocations towards the grain boundaries is found, which results in a noticeable reduction of internal stress fields and cancel of disclination quadrupole. The process of dislocation structure evolution passes through two stages: rapid and slow. The main dislocation rearrangement occurs during the first stage. Reduction of internal stress fields is associated with the number of dislocations entered into the grain boundaries. The change of misorientation angle due to lattice dislocations absorbed by the grain boundaries is evaluated. Amplitude of ultrasonic treatment significantly influences the relaxation of dislocation structure. Preliminary elastic relaxation of dislocation structure does not affect substantially the results of the following ultrasonic treatment. Substantial grain size dependence of relaxation of disordered dislocation systems is found. Simulation results are consistent with experimental data.

A pediatric brain structure atlas from T1-weighted MR images

NASA Astrophysics Data System (ADS)

Shan, Zuyao Y.; Parra, Carlos; Ji, Qing; Ogg, Robert J.; Zhang, Yong; Laningham, Fred H.; Reddick, Wilburn E.

2006-03-01

In this paper, we have developed a digital atlas of the pediatric human brain. Human brain atlases, used to visualize spatially complex structures of the brain, are indispensable tools in model-based segmentation and quantitative analysis of brain structures. However, adult brain atlases do not adequately represent the normal maturational patterns of the pediatric brain, and the use of an adult model in pediatric studies may introduce substantial bias. Therefore, we proposed to develop a digital atlas of the pediatric human brain in this study. The atlas was constructed from T1 weighted MR data set of a 9 year old, right-handed girl. Furthermore, we extracted and simplified boundary surfaces of 25 manually defined brain structures (cortical and subcortical) based on surface curvature. Higher curvature surfaces were simplified with more reference points; lower curvature surfaces, with fewer. We constructed a 3D triangular mesh model for each structure by triangulation of the structure's reference points. Kappa statistics (cortical, 0.97; subcortical, 0.91) indicated substantial similarities between the mesh-defined and the original volumes. Our brain atlas and structural mesh models (www.stjude.org/BrainAtlas) can be used to plan treatment, to conduct knowledge and modeldriven segmentation, and to analyze the shapes of brain structures in pediatric patients.

Sputter coating of microspherical substrates by levitation

DOEpatents

Lowe, Arthur T.; Hosford, Charles D.

1981-01-01

Microspheres are substantially uniformly coated with metals or nonmetals by simultaneously levitating them and sputter coating them at total chamber pressures less than 1 torr. A collimated hole structure 12 comprising a parallel array of upwardly projecting individual gas outlets 16 is machined out to form a dimple 11. Glass microballoons, which are particularly useful in laser fusion applications, can be substantially uniformly coated using the coating method and apparatus.

High average power pockels cell

DOEpatents

Daly, Thomas P.

1991-01-01

A high average power pockels cell is disclosed which reduces the effect of thermally induced strains in high average power laser technology. The pockels cell includes an elongated, substantially rectangular crystalline structure formed from a KDP-type material to eliminate shear strains. The X- and Y-axes are oriented substantially perpendicular to the edges of the crystal cross-section and to the C-axis direction of propagation to eliminate shear strains.

42 CFR 423.265 - Submission of bids and related information.

Code of Federal Regulations, 2010 CFR

2010-10-01

... calendar year. (2) Substantial differences between bids. Potential Part D sponsors' bid submissions must reflect differences in benefit packages or plan costs that CMS determines to represent substantial...) General. Not later than the first Monday in June, each potential Part D sponsor must submit bids and...

42 CFR 423.265 - Submission of bids and related information.

Code of Federal Regulations, 2011 CFR

2011-10-01

... calendar year. (2) Substantial differences between bids. Potential Part D sponsors' bid submissions must reflect differences in benefit packages or plan costs that CMS determines to represent substantial...) General. Not later than the first Monday in June, each potential Part D sponsor must submit bids and...

ANALYSIS OF GLYCANS DERIVED FROM GLYCOCONJUGATES BY CAPILLARY ELECTROPHORESIS-MASS SPECTROMETRY

PubMed Central

Mechref, Yehia

2012-01-01

The high structural variation of glycan derived from glycoconjugates, which substantially increases with the molecular size of a protein, contributes to the complexity of glycosylation patterns commonly associated with glycoconjugates. In the case of glycoproteins, such variation originates from the multiple glycosylation sites of proteins and the number of glycan structures associated with each site (microheterogeneity). The ability to comprehensively characterize highly complex mixture of glycans has been analytically stimulating and challenging. Although the most powerful mass spectrometric (MS) and tandem MS techniques are capable of providing a wealth of structural information, they are still not able to readily identify isomeric glycan structures without high order tandem MS (MSn). The analysis of isomeric glycan structures has been attained using several separation methods, including high-pH anion exchange chromatography (HPAEC), hydrophilic interaction chromatography (HILIC) and gas chromatography (GC). However, capillary electrophoresis (CE) and microfluidics capillary electrophoresis (MCE) offer high separation efficiency and resolutions, allowing the separation of closely related glycan structures. Therefore, interfacing CE and MCE to MS is a powerful analytical approach, allowing potentially comprehensive and sensitive analysis of complex glycan samples. This review describes and discusses the utility of different CE and MCE approaches in the structural characterization of glycoproteins and the feasibility of interfacing these approaches to mass spectrometry. PMID:22180203

Thermionic converter

DOEpatents

Fitzpatrick, Gary O.

1987-05-19

A thermionic converter (10) is set forth which includes an envelope (12) having an electron collector structure (22) attached adjacent to a wall (16). An electron emitter structure (24) is positioned adjacent the collector structure (22) and spaced apart from opposite wall (14). The emitter (24) and collector (22) structures are in a common chamber (20). The emitter structure (24) is heated substantially only by thermal radiation. Very small interelectrode gaps (28) can be maintained utilizing the thermionic converter (10) whereby increased efficiency results.

Profile of the genes expressed in the human peripheral retina, macula, and retinal pigment epithelium determined through serial analysis of gene expression (SAGE)

PubMed Central

Sharon, Dror; Blackshaw, Seth; Cepko, Constance L.; Dryja, Thaddeus P.

2002-01-01

We used the serial analysis of gene expression (SAGE) technique to catalogue and measure the relative levels of expression of the genes expressed in the human peripheral retina, macula, and retinal pigment epithelium (RPE) from one or both of two humans, aged 88 and 44 years. The cone photoreceptor contribution to all transcription in the retina was found to be similar in the macula versus the retinal periphery, whereas the rod contribution was greater in the periphery versus the macula. Genes encoding structural proteins for axons were found to be expressed at higher levels in the macula versus the retinal periphery, probably reflecting the large proportion of ganglion cells in the central retina. In comparison with the younger eye, the peripheral retina of the older eye had a substantially higher proportion of mRNAs from genes encoding proteins involved in iron metabolism or protection against oxidative damage and a substantially lower proportion of mRNAs from genes encoding proteins involved in rod phototransduction. These differences may reflect the difference in age between the two donors or merely interindividual variation. The RPE library had numerous previously unencountered tags, suggesting that this cell type has a large, idiosyncratic repertoire of expressed genes. Comparison of these libraries with 100 reported nonocular SAGE libraries revealed 89 retina-specific or enriched genes expressed at substantial levels, of which 14 are known to cause a retinal disease and 53 are RPE-specific genes. We expect that these libraries will serve as a resource for understanding the relative expression levels of genes in the retina and the RPE and for identifying additional disease genes. PMID:11756676