Study of structural reliability of existing concrete structures

NASA Astrophysics Data System (ADS)

Druķis, P.; Gaile, L.; Valtere, K.; Pakrastiņš, L.; Goremikins, V.

2017-10-01

Structural reliability of buildings has become an important issue after the collapse of a shopping center in Riga 21.11.2013, caused the death of 54 people. The reliability of a building is the practice of designing, constructing, operating, maintaining and removing buildings in ways that ensure maintained health, ward suffered injuries or death due to use of the building. Evaluation and improvement of existing buildings is becoming more and more important. For a large part of existing buildings, the design life has been reached or will be reached in the near future. The structures of these buildings need to be reassessed in order to find out whether the safety requirements are met. The safety requirements provided by the Eurocodes are a starting point for the assessment of safety. However, it would be uneconomical to require all existing buildings and structures to comply fully with these new codes and corresponding safety levels, therefore the assessment of existing buildings differs with each design situation. This case study describes the simple and practical procedure of determination of minimal reliability index β of existing concrete structures designed by different codes than Eurocodes and allows to reassess the actual reliability level of different structural elements of existing buildings under design load.

Different Measures of Structural Similarity Tap Different Aspects of Visual Object Processing

PubMed Central

Gerlach, Christian

2017-01-01

The structural similarity of objects has been an important variable in explaining why some objects are easier to categorize at a superordinate level than to individuate, and also why some patients with brain injury have more difficulties in recognizing natural (structurally similar) objects than artifacts (structurally distinct objects). In spite of its merits as an explanatory variable, structural similarity is not a unitary construct, and it has been operationalized in different ways. Furthermore, even though measures of structural similarity have been successful in explaining task and category-effects, this has been based more on implication than on direct empirical demonstrations. Here, the direct influence of two different measures of structural similarity, contour overlap and within-item structural diversity, on object individuation (object decision) and superordinate categorization performance is examined. Both measures can account for performance differences across objects, but in different conditions. It is argued that this reflects differences between the measures in whether they tap: (i) global or local shape characteristics, and (ii) between- or within-category structural similarity. PMID:28861027

Quantifying similarity of pore-geometry in nanoporous materials

DOE PAGES

Lee, Yongjin; Barthel, Senja D.; Dłotko, Paweł; ...

2017-05-23

In most applications of nanoporous materials the pore structure is as important as the chemical composition as a determinant of performance. For example, one can alter performance in applications like carbon capture or methane storage by orders of magnitude by only modifying the pore structure. For these applications it is therefore important to identify the optimal pore geometry and use this information to find similar materials. But, the mathematical language and tools to identify materials with similar pore structures, but different composition, has been lacking. We develop a pore recognition approach to quantify similarity of pore structures and classify themmore » using topological data analysis. This then allows us to identify materials with similar pore geometries, and to screen for materials that are similar to given top-performing structures. Using methane storage as a case study, we also show that materials can be divided into topologically distinct classes requiring different optimization strategies.« less

A seismic analysis for masonry constructions: The different schematization methods of masonry walls

NASA Astrophysics Data System (ADS)

Olivito, Renato. S.; Codispoti, Rosamaria; Scuro, Carmelo

2017-11-01

Seismic analysis of masonry structures is usually analyzed through the use of structural calculation software based on equivalent frames method or to macro-elements method. In these approaches, the masonry walls are divided into vertical elements, masonry walls, and horizontal elements, so-called spandrel elements, interconnected by rigid nodes. The aim of this work is to make a critical comparison between different schematization methods of masonry wall underlining the structural importance of the spandrel elements. In order to implement the methods, two different structural calculation software were used and an existing masonry building has been examined.

Structural studies of Pseudomonas and Chromobacterium ω-aminotransferases provide insights into their differing substrate specificity

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

Sayer, Christopher; Isupov, Michail N.; Westlake, Aaron

2013-04-01

The X-ray structures of two ω-aminotransferases from P. aeruginosa and C. violaceum in complex with an inhibitor offer the first detailed insight into the structural basis of the substrate specificity of these industrially important enzymes. The crystal structures and inhibitor complexes of two industrially important ω-aminotransferase enzymes from Pseudomonas aeruginosa and Chromobacterium violaceum have been determined in order to understand the differences in their substrate specificity. The two enzymes share 30% sequence identity and use the same amino acceptor, pyruvate; however, the Pseudomonas enzyme shows activity towards the amino donor β-alanine, whilst the Chromobacterium enzyme does not. Both enzymes showmore » activity towards S-α-methylbenzylamine (MBA), with the Chromobacterium enzyme having a broader substrate range. The crystal structure of the P. aeruginosa enzyme has been solved in the holo form and with the inhibitor gabaculine bound. The C. violaceum enzyme has been solved in the apo and holo forms and with gabaculine bound. The structures of the holo forms of both enzymes are quite similar. There is little conformational difference observed between the inhibitor complex and the holoenzyme for the P. aeruginosa aminotransferase. In comparison, the crystal structure of the C. violaceum gabaculine complex shows significant structural rearrangements from the structures of both the apo and holo forms of the enzyme. It appears that the different rigidity of the protein scaffold contributes to the substrate specificity observed for the two ω-aminotransferases.« less

Moored offshore structures - evaluation of forces in elastic mooring lines

NASA Astrophysics Data System (ADS)

Crudu, L.; Obreja, D. C.; Marcu, O.

2016-08-01

In most situations, the high frequency motions of the floating structure induce important effects in the mooring lines which affect also the motions of the structure. The experience accumulated during systematic experimental tests and calculations, carried out for different moored floating structures, showed a complex influence of various parameters on the dynamic effects. Therefore, it was considered that a systematic investigation is necessary. Due to the complexity of hydrodynamics aspects of offshore structures behaviour, experimental tests are practically compulsory in order to be able to properly evaluate and then to validate their behaviour in real sea. Moreover the necessity to carry out hydrodynamic tests is often required by customers, classification societies and other regulatory bodies. Consequently, the correct simulation of physical properties of the complex scaled models becomes a very important issue. The paper is investigating such kind of problems identifying the possible simplification, generating different approaches. One of the bases of the evaluation has been found consideringtheresults of systematic experimental tests on the dynamic behaviour of a mooring chain reproduced at five different scales. Dynamic effects as well as the influences of the elasticity simulation for 5 different scales are evaluated together. The paper presents systematic diagrams and practical results for a typical moored floating structure operating as pipe layer based on motion evaluations and accelerations in waves.

Framework for Understanding Structural Errors (FUSE): A modular framework to diagnose differences between hydrological models

USGS Publications Warehouse

Clark, Martyn P.; Slater, Andrew G.; Rupp, David E.; Woods, Ross A.; Vrugt, Jasper A.; Gupta, Hoshin V.; Wagener, Thorsten; Hay, Lauren E.

2008-01-01

The problems of identifying the most appropriate model structure for a given problem and quantifying the uncertainty in model structure remain outstanding research challenges for the discipline of hydrology. Progress on these problems requires understanding of the nature of differences between models. This paper presents a methodology to diagnose differences in hydrological model structures: the Framework for Understanding Structural Errors (FUSE). FUSE was used to construct 79 unique model structures by combining components of 4 existing hydrological models. These new models were used to simulate streamflow in two of the basins used in the Model Parameter Estimation Experiment (MOPEX): the Guadalupe River (Texas) and the French Broad River (North Carolina). Results show that the new models produced simulations of streamflow that were at least as good as the simulations produced by the models that participated in the MOPEX experiment. Our initial application of the FUSE method for the Guadalupe River exposed relationships between model structure and model performance, suggesting that the choice of model structure is just as important as the choice of model parameters. However, further work is needed to evaluate model simulations using multiple criteria to diagnose the relative importance of model structural differences in various climate regimes and to assess the amount of independent information in each of the models. This work will be crucial to both identifying the most appropriate model structure for a given problem and quantifying the uncertainty in model structure. To facilitate research on these problems, the FORTRAN‐90 source code for FUSE is available upon request from the lead author.

Evolution of volcanic and tectonic features in caldera settings and their importance in the localization of ore deposits

USGS Publications Warehouse

Rytuba, J.J.

1994-01-01

Many calderas are located along regionally important fault zones that are intermittently active before and after the caldera cycle. In mineralized calderas, the ore deposits are controlled by structures developed during caldera formation and by regional faults which intersect and reactivate the caldera-related structures. The paper discusses the importance of the different stages of caldera formation in connection with the localization of ore deposits. -from Author

Interactive effects of live coral and structural complexity on the recruitment of reef fishes

NASA Astrophysics Data System (ADS)

Coker, D. J.; Graham, N. A. J.; Pratchett, M. S.

2012-12-01

Corals reefs are subjected to multiple disturbances that modify levels of coral cover and structural complexity of the reef matrix, and in turn influence the structure of associated fish communities. With disturbances predicted to increase, insight into how changes in substrate condition will influence the recruitment of many fishes is essential for understanding the recovery of reef fish populations following biological and physical disturbances. While studies have revealed that both live coral cover and structural complexity are important for many fishes, there is a lack of understanding regarding how a combination of these changes will impact the recruitment of fishes. This study used experimentally constructed patch reefs consisting of six different habitat treatments; three levels of live coral cover (high, medium, low) crossed with two levels of structural complexity (high, low), to test the independent and combined effects of live coral cover and structural complexity on the recruitment and recovery of fish communities. The abundance and species diversity of fishes varied significantly among the six habitat treatments, but differences were not clearly associated with either coral cover or structural complexity and varied through time. More striking, however, was a significant difference in the composition of fish assemblages among treatments, due mostly to disproportionate abundance of coral-dwelling fishes on high coral cover, high complexity reefs. Overall, it appears that coral cover had a more important influence than structural complexity, at least for the contrasting levels of structural complexity achieved on experimental patch reefs. Furthermore, we found that live coral cover is important for the recruitment of some non-coral-dependent fishes. This study confirms that live coral cover is critical for the maintenance of high biodiversity on tropical coral reefs, and that sustained and ongoing declines in coral cover will adversely affect recruitment for many different species of reef fishes.

A Decade of Experience in Creating and Maintaining Data Elements for Structured Clinical Documentation in EHRs

PubMed Central

Zhou, Li; Collins, Sarah; Morgan, Stephen J.; Zafar, Neelam; Gesner, Emily J.; Fehrenbach, Martin; Rocha, Roberto A.

2016-01-01

Structured clinical documentation is an important component of electronic health records (EHRs) and plays an important role in clinical care, administrative functions, and research activities. Clinical data elements serve as basic building blocks for composing the templates used for generating clinical documents (such as notes and forms). We present our experience in creating and maintaining data elements for three different EHRs (one home-grown and two commercial systems) across different clinical settings, using flowsheet data elements as examples in our case studies. We identified basic but important challenges (including naming convention, links to standard terminologies, and versioning and change management) and possible solutions to address them. We also discussed more complicated challenges regarding governance, documentation vs. structured data capture, pre-coordination vs. post-coordination, reference information models, as well as monitoring, communication and training. PMID:28269927

Impact of organizational structure on nurses' job satisfaction: a questionnaire survey.

PubMed

Willem, Annick; Buelens, Marc; De Jonghe, Ives

2007-08-01

Nurses' job satisfaction is an important issue because of its impact on the quality of the nursing job. Therefore, it receives a lot of attention in the international nursing literature but insight into the sources of nurses' job satisfaction is yet insufficient, in particular for sources related to organizational structure. We contribute by investigating the relationship between the organizational structure variables, formalization, centralization and specialization, and nurses' job satisfaction. This allows us to learn whether structural changes can help to improve satisfaction, and therefore nurses' work quality. Data were collected by questionnaires in a random sample of 764 non-managing nurses in three Belgian general care hospitals. We measured satisfaction by Stamps and Piedmont's work satisfaction index. Structure was also measured by an existing scale. The results support the negative effect of centralization and the clearly positive effects of specialization and formalization on nurses' job satisfaction. These effects differ according to the different dimensions of satisfaction. Furthermore, pay is the most important dimension of nurses job satisfaction but the dimension least influenced by organizational structure. The importance of the dimension pay in nurses' job satisfaction, which is not a function of organizational structure, is limiting hospitals in improving nurses' job satisfaction. However, organizational structure is related to the other dimensions of satisfaction. Especially, the fact that specialization and formalization are, contrary to our hypotheses, only positively related to satisfaction is important from a practice perspective and for further research. Furthermore, our data indicates that there is a need to refine one of the dimensions of Stamps and Piedmont index.

Comparing pristine and depleted ecosystems: The Sørfjord, Norway versus the Gulf of St. Lawrence, Canada. Effects of intense fisheries on marine ecosystems

NASA Astrophysics Data System (ADS)

Morissette, Lyne; Pedersen, Torstein; Nilsen, Marianne

2009-04-01

The Sørfjord, Norway, and the Gulf of St. Lawrence, Canada, are two sub-arctic ecosystems with similar trophic structure. However, in the Gulf of St. Lawrence, severe exploitation of groundfish stocks has lead to important shifts in the trophic structure. In the Sørfjord, the situation is different: fishing pressure is much lighter. Our hypothesis is that overexploitation leads to changes in the trophic structure and severely alters the resilience of ecosystems. Based on the same modelling approach ( Ecopath with Ecosim) the food web structure was compared, using different ecosystem indicators. Patterns of food web structure and trophodynamics were contrasted. Cod was the keystone species in both ecosystems, and forage fish were also important. Even after similar environmental changes in both ecosystems, and after a reduction of fishing pressure in the Gulf of St. Lawrence, there is no recovery of cod stocks in this ecosystem. In the Sørfjord, after different perturbations (but not from the fishery), the ecosystem seems to return to its equilibrium.

The Theory and Practice of Structural and Strategic Family Therapies: A Delphi Study.

ERIC Educational Resources Information Center

Fish, Linda Stone; Piercy, Fred P.

1987-01-01

Examined the similarities and differences in the theory and practice of structural and strategic family therapy. A national panel of structural and strategic therapists identified items they thought important to a profile of either structural or strategic family therapy. Mental Research Institute, Haley/Madanes, and Milan/Ackerman approaches to…

Connecting Structure-Property and Structure-Function Relationships across the Disciplines of Chemistry and Biology: Exploring Student Perceptions

ERIC Educational Resources Information Center

Kohn, Kathryn P.; Underwood, Sonia M.; Cooper, Melanie M.

2018-01-01

While many university students take science courses in multiple disciplines, little is known about how they perceive common concepts from different disciplinary perspectives. Structure-property and structure-function relationships have long been considered important explanatory concepts in the disciplines of chemistry and biology, respectively.…

The brain map of gait variability in aging, cognitive impairment and dementia. A systematic review

PubMed Central

Tian, Qu; Chastan, Nathalie; Bair, Woei-Nan; Resnick, Susan M.; Ferrucci, Luigi; Studenski, Stephanie A.

2017-01-01

While gait variability may reflect subtle changes due to aging or cognitive impairment (CI), associated brain characteristics remain unclear. We summarize structural and functional neuroimaging findings associated with gait variability in older adults with and without CI and dementia. We identified 17 eligible studies; all were cross-sectional; few examined multiple brain areas. In older adults, temporal gait variability was associated with structural differences in medial areas important for lower limb coordination and balance. Both temporal and spatial gait variability were associated with structural and functional differences in hippocampus and primary sensorimotor cortex and structural differences in anterior cingulate cortex, basal ganglia, association tracts, and posterior thalamic radiation. In CI or dementia, some associations were found in primary motor cortex, hippocampus, prefrontal cortex and basal ganglia. In older adults, gait variability may be associated with areas important for sensorimotor integration and coordination. To comprehend the neural basis of gait variability with aging and CI, longitudinal studies of multiple brain areas are needed. PMID:28115194

Structural similarities and differences between the human and the mouse pancreas

PubMed Central

Dolenšek, Jurij; Rupnik, Marjan Slak; Stožer, Andraž

2015-01-01

Mice remain the most studied animal model in pancreas research. Since the findings of this research are typically extrapolated to humans, it is important to understand both similarities and differences between the 2 species. Beside the apparent difference in size and macroscopic organization of the organ in the 2 species, there are a number of less evident and only recently described differences in organization of the acinar and ductal exocrine tissue, as well as in the distribution, composition, and architecture of the endocrine islets of Langerhans. Furthermore, the differences in arterial, venous, and lymphatic vessels, as well as innervation are potentially important. In this article, the structure of the human and the mouse pancreas, together with the similarities and differences between them are reviewed in detail in the light of conceivable repercussions for basic research and clinical application. PMID:26030186

The role of grain boundaries in hydrogen diffusion in metals at 25 C

NASA Technical Reports Server (NTRS)

Danford, M. D.

1993-01-01

The effect of grain size on hydrogen diffusion at 25 C was examined for 4340 steel (body-centered cubic) and for Inconel 718 (face-centered cubic). It was found that the effect of grain size is important for body-centered cubic structures, but plays a much less important role in face centered cubic structures. Accurate measurements of hydrogen desorption coefficients during hydrogen desorption show that these are not greatly different for both types of structures.

Hierarchical structures of correlations networks among Turkey’s exports and imports by currencies

NASA Astrophysics Data System (ADS)

Kocakaplan, Yusuf; Deviren, Bayram; Keskin, Mustafa

2012-12-01

We have examined the hierarchical structures of correlations networks among Turkey’s exports and imports by currencies for the 1996-2010 periods, using the concept of a minimal spanning tree (MST) and hierarchical tree (HT) which depend on the concept of ultrametricity. These trees are useful tools for understanding and detecting the global structure, taxonomy and hierarchy in financial markets. We derived a hierarchical organization and build the MSTs and HTs during the 1996-2001 and 2002-2010 periods. The reason for studying two different sub-periods, namely 1996-2001 and 2002-2010, is that the Euro (EUR) came into use in 2001, and some countries have made their exports and imports with Turkey via the EUR since 2002, and in order to test various time-windows and observe temporal evolution. We have carried out bootstrap analysis to associate a value of the statistical reliability to the links of the MSTs and HTs. We have also used the average linkage cluster analysis (ALCA) to observe the cluster structure more clearly. Moreover, we have obtained the bidimensional minimal spanning tree (BMST) due to economic trade being a bidimensional problem. From the structural topologies of these trees, we have identified different clusters of currencies according to their proximity and economic ties. Our results show that some currencies are more important within the network, due to a tighter connection with other currencies. We have also found that the obtained currencies play a key role for Turkey’s exports and imports and have important implications for the design of portfolio and investment strategies.

Variation in Soil Microbial Community Structure Associated with Different Legume Species Is Greater than that Associated with Different Grass Species

PubMed Central

Zhou, Yang; Zhu, Honghui; Fu, Shenglei; Yao, Qing

2017-01-01

Plants are the essential factors shaping soil microbial community (SMC) structure. When most studies focus on the difference in the SMC structure associated different plant species, the variation in the SMC structure associated with phylogenetically close species is less investigated. Legume (Fabaceae) and grass (Poaceae) are functionally important plant groups; however, their influences on the SMC structure are seldom compared, and the variation in the SMC structure among legume or grass species is largely unknown. In this study, we grew three legume species vs. three grass species in mesocosms, and monitored the soil chemical property, quantified the abundance of bacteria and fungi. The SMC structure was also characterized using PCR-DGGE and Miseq sequencing. Results showed that legume and grass differentially affected soil pH, dissolved organic C, total N content, and available P content, and that legume enriched fungi more greatly than grass. Both DGGE profiling and Miseq-sequencing indicated that the bacterial diversity associated with legume was higher than that associated with grass. When legume increased the abundance of Verrucomicrobia, grass decreased it, and furthermore, linear discriminant analysis identified some group-specific microbial taxa as potential biomarkers of legume or grass. These data suggest that legume and grass differentially select for the SMC. More importantly, clustering analysis based on both DGGE profiling and Miseq-sequencing demonstrated that the variation in the SMC structure associated with three legume species was greater than that associated with three grass species. PMID:28620371

Dispersal Ability Determines the Role of Environmental, Spatial and Temporal Drivers of Metacommunity Structure

PubMed Central

Padial, André A.; Ceschin, Fernanda; Declerck, Steven A. J.; De Meester, Luc; Bonecker, Cláudia C.; Lansac-Tôha, Fabio A.; Rodrigues, Liliana; Rodrigues, Luzia C.; Train, Sueli; Velho, Luiz F. M.; Bini, Luis M.

2014-01-01

Recently, community ecologists are focusing on the relative importance of local environmental factors and proxies to dispersal limitation to explain spatial variation in community structure. Albeit less explored, temporal processes may also be important in explaining species composition variation in metacommunities occupying dynamic systems. We aimed to evaluate the relative role of environmental, spatial and temporal variables on the metacommunity structure of different organism groups in the Upper Paraná River floodplain (Brazil). We used data on macrophytes, fish, benthic macroinvertebrates, zooplankton, periphyton, and phytoplankton collected in up to 36 habitats during a total of eight sampling campaigns over two years. According to variation partitioning results, the importance of predictors varied among biological groups. Spatial predictors were particularly important for organisms with comparatively lower dispersal ability, such as aquatic macrophytes and fish. On the other hand, environmental predictors were particularly important for organisms with high dispersal ability, such as microalgae, indicating the importance of species sorting processes in shaping the community structure of these organisms. The importance of watercourse distances increased when spatial variables were the main predictors of metacommunity structure. The contribution of temporal predictors was low. Our results emphasize the strength of a trait-based analysis and of better defining spatial variables. More importantly, they supported the view that “all-or- nothing” interpretations on the mechanisms structuring metacommunities are rather the exception than the rule. PMID:25340577

Structure Matters: The Role of Clique Hierarchy in the Relationship Between Adolescent Social Status and Aggression and Prosociality.

PubMed

Pattiselanno, Kim; Dijkstra, Jan Kornelis; Steglich, Christian; Vollebergh, Wilma; Veenstra, René

2015-12-01

Peer cliques form an important context for the social development of adolescents. Although clique members are often similar in social status, also within cliques, status differences exist. How differences in social status between clique members are related to behaviors of its individual members is rather unknown. This study examined to what extent the relationship of individual social status (i.e., perceived popularity) with aggression and prosocial behavior depends on the level of internal clique hierarchy. The sample consists of 2674 adolescents (49.8% boys), with a mean age of 14.02. We focused specifically on physical and relational aggression, and practical and emotional support, because these behaviors have shown to be of great importance for social relationships and social standing among adolescents. The internal status hierarchy of cliques was based on the variation in individual social status between clique members (i.e., clique hierarchization) and the structure of status scores within a clique (pyramid shape, inverted pyramid, or equal distribution of social status scores) (i.e., clique status structure). The results showed that differences in aggressive and prosocial behaviors were particularly moderated by clique status structure: aggression was stronger related to individual social status in (girls') cliques where the clique status structure reflected an inverted pyramid with relatively more high status adolescents within the clique than low status peers, and prosocial behavior showed a significant relationship with individual social status, again predominantly in inverted pyramid structured (boys' and girls') cliques. Furthermore, these effects differed by types of gender cliques: the associations were found in same gender but not mixed-gender cliques. The findings stress the importance of taking into account internal clique characteristics when studying adolescent social status in relationship to aggression and prosociality.

Different Interfacial Behaviors of Peptides Chemically Immobilized on Surfaces with Different Linker Lengths and via Different Termini

DTIC Science & Technology

2014-02-20

spectroscopy was applied to investigate such structures of peptides immobilized on self-assembled monolayers (SAMs). Here cysteine-modified antimicrobial ...modified antimicrobial peptide cecropin P1 (CP1) was chemically immobilized onto SAM with a maleimide terminal group. Two important characteristics...applied to investigate such structures of peptides immobilized on self-assembled monolayers (SAMs). Here cysteine-modified antimicrobial peptide cecropin

Supramolecular structure of methyl cellulose and lambda- and kappa-carrageenan in water: SAXS study using the string-of-beads model.

PubMed

Dogsa, Iztok; Cerar, Jure; Jamnik, Andrej; Tomšič, Matija

2017-09-15

A detailed data analysis utilizing the string-of-beads model was performed on experimental small-angle X-ray scattering (SAXS) curves in a targeted structural study of three, very important, industrial polysaccharides. The results demonstrate the quality of performance for this model on three polymers with quite different thermal structural behavior. Furthermore, they show the advantages of the model used by way of excellent fits in the ranges where the classic approach to the small-angle scattering data interpretation fails and an additional 3D visualization of the model's molecular conformations and anticipated polysaccharide supramolecular structure. The importance of this study is twofold: firstly, the methodology used and, secondly, the structural details of important biopolymers that are widely applicable in practice. Copyright © 2017 Elsevier Ltd. All rights reserved.

A Short Version of the Occupational Self-Efficacy Scale: Structural and Construct Validity across Five Countries

ERIC Educational Resources Information Center

Rigotti, Thomas; Schyns, Birgit; Mohr, Gisela

2008-01-01

Occupational self-efficacy is an important resource for individuals in organizations. To be able to compare the occupational self-efficacy of employees across different countries, equivalent versions of the standard instruments need to be made available in different languages. In this article, the authors report on the structural and construct…

Hippocampal Structure Predicts Statistical Learning and Associative Inference Abilities during Development.

PubMed

Schlichting, Margaret L; Guarino, Katharine F; Schapiro, Anna C; Turk-Browne, Nicholas B; Preston, Alison R

2017-01-01

Despite the importance of learning and remembering across the lifespan, little is known about how the episodic memory system develops to support the extraction of associative structure from the environment. Here, we relate individual differences in volumes along the hippocampal long axis to performance on statistical learning and associative inference tasks-both of which require encoding associations that span multiple episodes-in a developmental sample ranging from ages 6 to 30 years. Relating age to volume, we found dissociable patterns across the hippocampal long axis, with opposite nonlinear volume changes in the head and body. These structural differences were paralleled by performance gains across the age range on both tasks, suggesting improvements in the cross-episode binding ability from childhood to adulthood. Controlling for age, we also found that smaller hippocampal heads were associated with superior behavioral performance on both tasks, consistent with this region's hypothesized role in forming generalized codes spanning events. Collectively, these results highlight the importance of examining hippocampal development as a function of position along the hippocampal axis and suggest that the hippocampal head is particularly important in encoding associative structure across development.

Deterioration of concrete structures in coastal environment due to carbonation.

PubMed

Balaji, K V G D; Gopalaraju, S S S V; Trilochan, Jena

2010-07-01

Failure of existing concrete structures takes place due to lack of durability, and not due to less structural strength. One of the important aspects of durability is carbonation depth. The rate of carbonation in concrete is influenced by both its physical properties and exposure conditions. Rebar corrodes when carbonation reaches to a depth of concrete cover provided. In the present work, various concrete structures with different life periods and exposed to different weather conditions have been considered to study the carbonation effect. It is observed that the effect of carbonation is more in the structures located near to the sea coast and on windward face of the structure.

Experimental validation of a structural damage detection method based on marginal Hilbert spectrum

NASA Astrophysics Data System (ADS)

Banerji, Srishti; Roy, Timir B.; Sabamehr, Ardalan; Bagchi, Ashutosh

2017-04-01

Structural Health Monitoring (SHM) using dynamic characteristics of structures is crucial for early damage detection. Damage detection can be performed by capturing and assessing structural responses. Instrumented structures are monitored by analyzing the responses recorded by deployed sensors in the form of signals. Signal processing is an important tool for the processing of the collected data to diagnose anomalies in structural behavior. The vibration signature of the structure varies with damage. In order to attain effective damage detection, preservation of non-linear and non-stationary features of real structural responses is important. Decomposition of the signals into Intrinsic Mode Functions (IMF) by Empirical Mode Decomposition (EMD) and application of Hilbert-Huang Transform (HHT) addresses the time-varying instantaneous properties of the structural response. The energy distribution among different vibration modes of the intact and damaged structure depicted by Marginal Hilbert Spectrum (MHS) detects location and severity of the damage. The present work investigates damage detection analytically and experimentally by employing MHS. The testing of this methodology for different damage scenarios of a frame structure resulted in its accurate damage identification. The sensitivity of Hilbert Spectral Analysis (HSA) is assessed with varying frequencies and damage locations by means of calculating Damage Indices (DI) from the Hilbert spectrum curves of the undamaged and damaged structures.

Differential stemflow yield from European beech saplings: the role and respective importance of individual canopy structure metrics

NASA Astrophysics Data System (ADS)

Levia, Delphis; Michalzik, Beate

2013-04-01

Stemflow yield from individual trees varies as a function of both meteorological conditions and canopy structure. The importance and differential effects of various metrics of canopy structure in relation to stemflow yield is inadequately understood and the subject of debate among forest hydrologists. It is possible to evaluate the role and respective importance of individual canopy structure metrics by holding meteorological conditions constant. Twelve isolated experimental European beech (Fagus sylvatica L.) saplings in Jena, Germany were exposed to identical meteorological conditions to examine the effects of canopy structure on stemflow production during the 2012 growing season. The canopy structure metrics being evaluated include: trunk diameter, trunk lean, tree height, projected crown area, branch inclination angle, branch count, and biomass (foliar and woody). Principal components analysis and multiple regression are utilized to determine the relative importance of different canopy structure metrics on stemflow yield. Experimental results will provide insight as to which metrics of canopy structure most strongly govern stemflow production. Ultimately, with a more thorough understanding of the unique contributions of various canopy structural metrics to stemflow yield, a useful conceptual guide of stemflow generation can be formulated on the basis of canopy structure for management purposes. Sponsor note: This research was funded by the Alexander von Humboldt Foundation.

Demonstrating the Uneven Importance of Fine-Scale Forest Structure on Snow Distributions using High Resolution Modeling

NASA Astrophysics Data System (ADS)

Broxton, P. D.; Harpold, A. A.; van Leeuwen, W.; Biederman, J. A.

2016-12-01

Quantifying the amount of snow in forested mountainous environments, as well as how it may change due to warming and forest disturbance, is critical given its importance for water supply and ecosystem health. Forest canopies affect snow accumulation and ablation in ways that are difficult to observe and model. Furthermore, fine-scale forest structure can accentuate or diminish the effects of forest-snow interactions. Despite decades of research demonstrating the importance of fine-scale forest structure (e.g. canopy edges and gaps) on snow, we still lack a comprehensive understanding of where and when forest structure has the largest impact on snowpack mass and energy budgets. Here, we use a hyper-resolution (1 meter spatial resolution) mass and energy balance snow model called the Snow Physics and Laser Mapping (SnowPALM) model along with LIDAR-derived forest structure to determine where spatial variability of fine-scale forest structure has the largest influence on large scale mass and energy budgets. SnowPALM was set up and calibrated at sites representing diverse climates in New Mexico, Arizona, and California. Then, we compared simulations at different model resolutions (i.e. 1, 10, and 100 m) to elucidate the effects of including versus not including information about fine scale canopy structure. These experiments were repeated for different prescribed topographies (i.e. flat, 30% slope north, and south-facing) at each site. Higher resolution simulations had more snow at lower canopy cover, with the opposite being true at high canopy cover. Furthermore, there is considerable scatter, indicating that different canopy arrangements can lead to different amounts of snow, even when the overall canopy coverage is the same. This modeling is contributing to the development of a high resolution machine learning algorithm called the Snow Water Artificial Network (SWANN) model to generate predictions of snow distributions over much larger domains, which has implications for improving land surface models that do not currently resolve or parameterize fine-scale canopy structure. In addition, these findings have implications for understanding the potential of different forest management strategies (i.e. thinning) based on local topography and climate to maximize the amount and retention of snow.

Specific temperature-induced perturbations of secondary mRNA structures are associated with the cold-adapted temperature-sensitive phenotype of influenza A virus.

PubMed

Chursov, Andrey; Kopetzky, Sebastian J; Leshchiner, Ignaty; Kondofersky, Ivan; Theis, Fabian J; Frishman, Dmitrij; Shneider, Alexander

2012-10-01

For decades, cold-adapted, temperature-sensitive (ca/ts) strains of influenza A virus have been used as live attenuated vaccines. Due to their great public health importance it is crucial to understand the molecular mechanism(s) of cold adaptation and temperature sensitivity that are currently unknown. For instance, secondary RNA structures play important roles in influenza biology. Thus, we hypothesized that a relatively minor change in temperature (32-39°C) can lead to perturbations in influenza RNA structures and, that these structural perturbations may be different for mRNAs of the wild type (wt) and ca/ts strains. To test this hypothesis, we developed a novel in silico method that enables assessing whether two related RNA molecules would undergo (dis)similar structural perturbations upon temperature change. The proposed method allows identifying those areas within an RNA chain where dissimilarities of RNA secondary structures at two different temperatures are particularly pronounced, without knowing particular RNA shapes at either temperature. We identified such areas in the NS2, PA, PB2 and NP mRNAs. However, these areas are not identical for the wt and ca/ts mutants. Differences in temperature-induced structural changes of wt and ca/ts mRNA structures may constitute a yet unappreciated molecular mechanism of the cold adaptation/temperature sensitivity phenomena.

On the Parity of Structural Persistence in Language Production and Comprehension

PubMed Central

Tooley, Kristen M.; Bock, Kathryn

2014-01-01

Structural priming creates structural persistence. That is, differences in experience with syntax can change subsequent language performance, and the changes can be observed in both language production and comprehension. However, the effects in comprehension and production appear to differ. In comprehension, persistence is typically found when the verbs are the same in primes and targets; in production, persistence occurs without verb overlap. The contrast suggests a theoretically important hypothesis: parsing in comprehension is lexically driven while formulation in production is structurally driven. A major weakness in this hypothesis about comprehension-production differences is that its empirical motivation rests on the outcomes of experiments in which the priming manipulations differ, the primed sentence structures differ, and the measures of priming differ. To sharpen the comparison, we examined structural persistence with and without verb overlap in both reading comprehension and spoken production, using the same prime presentation procedure, the same syntactic structures, the same sentences, and the same participants. These methods yielded abstract sructural persistence in comprehension as well as production. A measure of the strength of persistence revealed significant effects of priming and verb overlap without significant comprehension—production differences. This argues for uniformity in the structural mechanisms of language processing. PMID:24803423

Remote sensing-based landscape indicators for the evaluation of threatened-bird habitats in a tropical forest.

PubMed

Singh, Minerva; Tokola, Timo; Hou, Zhengyang; Notarnicola, Claudia

2017-07-01

Avian species persistence in a forest patch is strongly related to the degree of isolation and size of a forest patch and the vegetation structure within a patch and its matrix are important predictors of bird habitat suitability. A combination of space-borne optical (Landsat), ALOS-PALSAR (radar), and airborne Light Detection and Ranging (LiDAR) data was used for assessing variation in forest structure across forest patches that had undergone different levels of forest degradation in a logged forest-agricultural landscape in Southern Laos. The efficacy of different remote sensing (RS) data sources in distinguishing forest patches that had different seizes, configurations, and vegetation structure was examined. These data were found to be sensitive to the varying levels of degradation of the different patch categories. Additionally, the role of local scale forest structure variables (characterized using the different RS data and patch area) and landscape variables (characterized by distance from different forest patches) in influencing habitat preferences of International Union for Conservation of Nature (IUCN) Red listed birds found in the study area was examined. A machine learning algorithm, MaxEnt, was used in conjunction with these data and field collected geographical locations of the avian species to identify the factors influencing habitat preference of the different bird species and their suitable habitats. Results show that distance from different forest patches played a more important role in influencing habitat suitability for the different avian species than local scale factors related to vegetation structure and health. In addition to distance from forest patches, LiDAR-derived forest structure and Landsat-derived spectral variables were important determinants of avian habitat preference. The models derived using MaxEnt were used to create an overall habitat suitability map (HSM) which mapped the most suitable habitat patches for sustaining all the avian species. This work also provides insight that retention of forest patches, including degraded and isolated forest patches in addition to large contiguous forest patches, can facilitate bird species retention within tropical agricultural landscapes. It also demonstrates the effective use of RS data in distinguishing between forests that have undergone varying levels of degradation and identifying the habitat preferences of different bird species. Practical conservation management planning endeavors can use such data for both landscape scale monitoring and habitat mapping.

The relative importance of different perceptual-cognitive skills during anticipation.

PubMed

North, Jamie S; Hope, Ed; Williams, A Mark

2016-10-01

We examined whether anticipation is underpinned by perceiving structured patterns or postural cues and whether the relative importance of these processes varied as a function of task constraints. Skilled and less-skilled soccer players completed anticipation paradigms in video-film and point light display (PLD) format. Skilled players anticipated more accurately regardless of display condition, indicating that both perception of structured patterns between players and postural cues contribute to anticipation. However, the Skill×Display interaction showed skilled players' advantage was enhanced in the video-film condition, suggesting that they make better use of postural cues when available during anticipation. We also examined anticipation as a function of proximity to the ball. When participants were near the ball, anticipation was more accurate for video-film than PLD clips, whereas when the ball was far away there was no difference between viewing conditions. Perceiving advance postural cues appears more important than structured patterns when the ball is closer to the observer, whereas the reverse is true when the ball is far away. Various perceptual-cognitive skills contribute to anticipation with the relative importance of perceiving structured patterns and advance postural cues being determined by task constraints and the availability of perceptual information. Copyright © 2016 Elsevier B.V. All rights reserved.

Effects of Social-Cognitive Processing Demands and Structural Importance on Narrative Recall: Differences between Children, Adolescents, and Adults

ERIC Educational Resources Information Center

Pavias, Marcella; van den Broek, Paul; Hickendorff, Marian; Beker, Katinka; Van Leijenhorst, Linda

2016-01-01

This study examined the contributions of developmental changes in social-cognitive ability throughout adolescence to the development of narrative comprehension. We measured the effects of sensitivity to the causal structure of narratives and of sensitivity to differences in social-cognitive processing demands on narrative recall by children (8-10…

Identification and Recall of Structurally Important Units in Prose by Mentally Retarded Learners.

ERIC Educational Resources Information Center

Luftig, Richard L.; Johnson, Ronald E.

The study investigated the ability of 80 mildly mentally retarded students (19 to 17 years old) to make accurate judgments of textual idea importance and to differentially and spontaneously remember important rather than unimportant ideas. Ss were assigned to one of six conditions which differed as a function of whether importance judgments were…

The logic of syntactic priming and acceptability judgments.

PubMed

Gaston, Phoebe; Huang, Nick; Phillips, Colin

2017-01-01

A critical flaw in Branigan & Pickering's (B&P's) advocacy of structural priming is the absence of a theory of priming. This undermines their claims about the value of priming as a methodology. In contrast, acceptability judgments enable clearer inferences about structure. It is important to engage thoroughly with the logic behind different structural diagnostics.

Virtual Learning and Instructional Tools: Perfecting the Weekly Roadmap

ERIC Educational Resources Information Center

Cicco, Gina

2015-01-01

This article will provide details on the importance of providing structure within an online graduate counseling course in the form of a weekly roadmap tool. There are various instructional tools that may be useful in providing students with differing levels of structure, to meet their learning style preferences for structural stimuli (Cicco,…

The War with Words: Structure and Transcendence. Approaches to Semiotics Series No. 12.

ERIC Educational Resources Information Center

Shands, Harley C.

Semiotic research increasingly reveals the basic importance of structure at all levels of genetic, linguistic, and social process. The paradox that structure not only liberates but also imprisons has been familiar to members of many different cultures, and the search for personal release in transcendent states of feeling contrapuntally illuminates…

Ordination of breeding birds in relation to environmental gradients in three southeastern United States floodplain forests

USGS Publications Warehouse

Wakeley, J.S.; Guilfoyle, M.P.; Antrobus, T.J.; Fischer, R.A.; Barrow, W.C.; Hamel, P.B.

2007-01-01

We used an ordination approach to identify factors important to the organization of breeding bird communities in three floodplains: Cache River, Arkansas (AR), Iatt Creek, Louisiana (LA), and the Coosawhatchie River, South Carolina (SC), USA. We used 5-min point counts to sample birds in each study area each spring from 1995 to 1998, and measured ground-surface elevations and a suite of other habitat variables to investigate bird distributions and community characteristics in relation to important environmental gradients. In both AR and SC, the average number of Neotropical migrant species detected was lowest in semipermanently flooded Nyssa aquatica Linnaeus habitats and greatest in the highest elevation floodplain zone. Melanerpes carolinus Linnaeus, Protonotaria citrea Boddaert, Quiscalus quiscula Linnaeus, and other species were more abundant in N. aquatica habitats, whereas Wilsonia citrina Boddaert, Oporornis formosus Wilson, Vireo griseus Boddaert, and others were more abundant in drier floodplain zones. In LA, there were no significant differences in community metrics or bird species abundances among forest types. Canonical correspondence analyses revealed that structural development of understory vegetation was the most important factor affecting bird distributions in all three study areas; however, potential causes of these structural gradients differed. In AR and SC, differences in habitat structure were related to the hydrologic gradient, as indexed by ground-surface elevation. In LA, structural variations were related mainly to the frequency of canopy gaps. Thus, bird communities in all three areas appeared to be organized primarily in response to repeated localized disturbance. Our results suggest that regular disturbance due to flooding plays an important role in structuring breeding bird communities in floodplains subject to prolonged inundation, whereas other agents of disturbance (e.g., canopy gaps) may be more important in headwater systems subject to only short-duration flooding. Management for avian community integrity in these systems should strive to maintain forest zonation and natural disturbance regimes. ?? 2007 Springer Science+Business Media B.V.

Variation in structure of proteins by adjusting reactive oxygen and nitrogen species generated from dielectric barrier discharge jet

NASA Astrophysics Data System (ADS)

Park, Ji Hoon; Kim, Minsup; Shiratani, Masaharu; Cho, Art. E.; Choi, Eun Ha; Attri, Pankaj

2016-10-01

Over the last few years, the variation in liquid chemistry due to the development of radicals generated by cold atmospheric plasma (CAP) has played an important role in plasma medicine. CAP direct treatment or CAP activated media treatment in cancer cells shows promising anticancer activity for both in vivo and in vitro studies. However, the anticancer activity or antimicrobial activity varies between plasma devices due to the different abilities among plasma devices to generate the reactive oxygen and nitrogen species (RONS) at different ratios and in different concentrations. While the generation of RONS depends on many factors, the feeding gas plays the most important role among the factors. Hence, in this study we used different compositions of feeding gas while fixing all other plasma characteristics. We used Ar, Ar-O2 (at different ratios), and Ar-N2 (at different ratios) as the working gases for CAP and investigated the structural changes in proteins (Hemoglobin (Hb) and Myoglobin (Mb)). We then analyzed the influence of RONS generated in liquid on the conformations of proteins. Additionally, to determine the influence of H2O2 on the Hb and Mb structures, we used molecular dynamic simulation.

Structural Color Tuning: Mixing Melanin-Like Particles with Different Diameters to Create Neutral Colors.

PubMed

Kawamura, Ayaka; Kohri, Michinari; Yoshioka, Shinya; Taniguchi, Tatsuo; Kishikawa, Keiki

2017-04-18

We present the ability to tune structural colors by mixing colloidal particles. To produce high-visibility structural colors, melanin-like core-shell particles composed of a polystyrene (PSt) core and a polydopamine (PDA) shell, were used as components. The results indicated that neutral structural colors could be successfully obtained by simply mixing two differently sized melanin-like PSt@PDA core-shell particles. In addition, the arrangements of the particles, which were important factors when forming structural colors, were investigated by mathematical processing using a 2D Fourier transform technique and Voronoi diagrams. These findings provide new insights for the development of structural color-based ink applications.

Conformational analysis of processivity clamps in solution demonstrates that tertiary structure does not correlate with protein dynamics.

PubMed

Fang, Jing; Nevin, Philip; Kairys, Visvaldas; Venclovas, Česlovas; Engen, John R; Beuning, Penny J

2014-04-08

The relationship between protein sequence, structure, and dynamics has been elusive. Here, we report a comprehensive analysis using an in-solution experimental approach to study how the conservation of tertiary structure correlates with protein dynamics. Hydrogen exchange measurements of eight processivity clamp proteins from different species revealed that, despite highly similar three-dimensional structures, clamp proteins display a wide range of dynamic behavior. Differences were apparent both for structurally similar domains within proteins and for corresponding domains of different proteins. Several of the clamps contained regions that underwent local unfolding with different half-lives. We also observed a conserved pattern of alternating dynamics of the α helices lining the inner pore of the clamps as well as a correlation between dynamics and the number of salt bridges in these α helices. Our observations reveal that tertiary structure and dynamics are not directly correlated and that primary structure plays an important role in dynamics. Copyright © 2014 Elsevier Ltd. All rights reserved.

Only-child and non-only-child exhibit differences in creativity and agreeableness: evidence from behavioral and anatomical structural studies.

PubMed

Yang, Junyi; Hou, Xin; Wei, Dongtao; Wang, Kangcheng; Li, Yadan; Qiu, Jiang

2017-04-01

Different family composition and size inevitably make only-children different from non-only-children. Previous studies have focused on the differences in behaviors, such as cognitive function and personality traits, between the only-child and the non-only-child. However, there are few studies that have focused on the topic of whether different family environments influence children's brain structural development and whether behavior differentially has its neural basis between only-child and non-only-child status. Thus, in the present study, we investigated the differences in cognition (e.g., intelligence and creativity) and personality and the anatomical structural differences of gray matter volume (GMV) using voxel-based morphometry (VBM) between only-children and non-only-children. The behavioral results revealed that only-children exhibited higher flexibility scores (a dimension of creativity) and lower agreeableness scores (a dimension of personality traits) than non-only-children. Most importantly, the GMV results revealed that there were significant differences in the GMV between only-children and non-only-children that occurred mainly in the brain regions of the supramarginal gyrus, which was positively correlated with flexibility scores; the medial prefrontal cortex (mPFC), which was positively correlated with agreeableness scores; and the parahippocampal gyrus. These findings may suggest that family environment (i.e., only-child vs. non-only-child), may play important roles in the development of the behavior and brain structure of individuals.

Structures composing protein domains.

PubMed

Kubrycht, Jaroslav; Sigler, Karel; Souček, Pavel; Hudeček, Jiří

2013-08-01

This review summarizes available data concerning intradomain structures (IS) such as functionally important amino acid residues, short linear motifs, conserved or disordered regions, peptide repeats, broadly occurring secondary structures or folds, etc. IS form structural features (units or elements) necessary for interactions with proteins or non-peptidic ligands, enzyme reactions and some structural properties of proteins. These features have often been related to a single structural level (e.g. primary structure) mostly requiring certain structural context of other levels (e.g. secondary structures or supersecondary folds) as follows also from some examples reported or demonstrated here. In addition, we deal with some functionally important dynamic properties of IS (e.g. flexibility and different forms of accessibility), and more special dynamic changes of IS during enzyme reactions and allosteric regulation. Selected notes concern also some experimental methods, still more necessary tools of bioinformatic processing and clinically interesting relationships. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

Impact of nitrogen concentration on validamycin A production and related gene transcription in fermentation of Streptomyces hygroscopicus 5008.

PubMed

Wei, Zhen-Hua; Bai, Linquan; Deng, Zixin; Zhong, Jian-Jiang

2012-09-01

Validamycin A (VAL-A) is an important and widely used agricultural antibiotic. In this study, statistical screening designs were applied to identify significant medium variables for VAL-A production and to find their optimal levels. The optimized medium caused 70% enhancement of VAL-A production. The difference between optimized medium and original medium suggested that low nitrogen source level might attribute to the enhancement of VAL-A production. The addition of different nitrogen sources to the optimized medium inhibited VAL-A production, which confirmed the importance of nitrogen concentration for VAL-A production. Furthermore, differences in structural gene transcription and enzyme activity between the two media were assayed. The results showed that lower nitrogen level in the optimized medium could regulate VAL-A production in gene transcriptional level. Our previous study indicated that the transcription of VAL-A structural genes could be enhanced at elevated temperature. In this work, the increased fermentation temperature from 37 to 42 °C with the optimized medium enhanced VAL-A production by 39%, which testified to the importance of structural gene transcription in VAL-A production. The information is useful for further VAL-A production enhancement.

Uridine Nucleoside Thiation: Gas-Phase Structures and Energetics

NASA Astrophysics Data System (ADS)

Hamlow, Lucas; Lee, Justin; Rodgers, M. T.; Berden, Giel; Oomens, Jos

2016-06-01

The naturally occurring thiated uridine nucleosides, 4-thiouridine (s4Urd) and 2-thiouridine (s2Urd), play important roles in the function and analysis of a variety of RNAs. 2-Thiouridine and its C5 modified analogues are commonly found in tRNAs and are believed to play an important role in codon recognition possibly due to their different structure, which has been shown by NMR to be predominantly C3'-endo. 2-Thiouridine may also play an important role in facilitating nonenzymatic RNA replication and transcription. 4-Thiouridine is a commonly used photoactivatable crosslinker that is often used to study RNA-RNA and RNA-protein cross-linking behavior. Differences in the base pairing between uracil and 4-thiouracil with adenine and guanine are an important factor in their role as a cross linker. The photoactivity of s4Urd may also aid in preventing near-UV lethality in cells. An understanding of their intrinsic structure in the gas-phase may help further elucidate the roles these modified nucleosides play in the regulation of RNAs. In this work, infrared multiple photon dissociation (IRMPD) action spectra of the protonated forms of s2Urd and s4Urd were collected in the IR fingerprint region. Structural information is determined by comparison with theoretical linear IR spectra generated from density functional theory calculations using molecular modeling to generate low-energy candidate structures. Present results are compared with analogous results for the protonated forms of uridine and 2'-deoxyuridine as well as solution phase NMR data and crystal structures.

Thermal response of novel shape memory polymer-shape memory alloy hybrids

NASA Astrophysics Data System (ADS)

Rossiter, Jonathan; Takashima, Kazuto; Mukai, Toshiharu

2014-03-01

Shape memory polymers (SMP) and shape memory alloys (SMA) have both been proven important smart materials in their own fields. Shape memory polymers can be formed into complex three-dimensional structures and can undergo shape programming and large strain recovery. These are especially important for deployable structures including those for space applications and micro-structures such as stents. Shape memory alloys on the other hand are readily exploitable in a range of applications where simple, silent, light-weight and low-cost repeatable actuation is required. These include servos, valves and mobile robotic artificial muscles. Despite their differences, one important commonality between SMPs and SMAs is that they are both typically activated by thermal energy. Given this common characteristic it is important to consider how these two will behave when in close environmental proximity, and hence exposed to the same thermal stimulus, and when they are incorporated into a hybrid SMA-SMP structure. In this paper we propose and examine the operation of SMA-SMP hybrids. The relationship between the two temperatures Tg, the glass transition temperature of the polymer, and Ta, the nominal austenite to martensite transition temperature of the alloy is considered. We examine how the choice of these two temperatures affects the thermal response of the hybrid. Electrical stimulation of the SMA is also considered as a method not only of actuating the SMA but also of inducing heating in the surrounding polymer, with consequent effects on actuator behaviour. Likewise by varying the rate and degree of thermal stimulation of the SMA significantly different actuation and structural stiffness can be achieved. Novel SMP-SMA hybrid actuators and structures have many ready applications in deployable structures, robotics and tuneable engineering systems.

Schaffer Collateral Inputs to CA1 Excitatory and Inhibitory Neurons Follow Different Connectivity Rules.

PubMed

Kwon, Osung; Feng, Linqing; Druckmann, Shaul; Kim, Jinhyun

2018-05-30

Neural circuits, governed by a complex interplay between excitatory and inhibitory neurons, are the substrate for information processing, and the organization of synaptic connectivity in neural network is an important determinant of circuit function. Here, we analyzed the fine structure of connectivity in hippocampal CA1 excitatory and inhibitory neurons innervated by Schaffer collaterals (SCs) using mGRASP in male mice. Our previous study revealed spatially structured synaptic connectivity between CA3 and CA1 pyramidal cells (PCs). Surprisingly, parvalbumin-positive interneurons (PVs) showed a significantly more random pattern spatial structure. Notably, application of Peters' rule for synapse prediction by random overlap between axons and dendrites enhanced structured connectivity in PCs, but, by contrast, made the connectivity pattern in PVs more random. In addition, PCs in a deep sublayer of striatum pyramidale appeared more highly structured than PCs in superficial layers, and little or no sublayer specificity was found in PVs. Our results show that CA1 excitatory PCs and inhibitory PVs innervated by the same SC inputs follow different connectivity rules. The different organizations of fine scale structured connectivity in hippocampal excitatory and inhibitory neurons provide important insights into the development and functions of neural networks. SIGNIFICANCE STATEMENT Understanding how neural circuits generate behavior is one of the central goals of neuroscience. An important component of this endeavor is the mapping of fine-scale connection patterns that underlie, and help us infer, signal processing in the brain. Here, using our recently developed synapse detection technology (mGRASP and neuTube), we provide detailed profiles of synaptic connectivity in excitatory (CA1 pyramidal) and inhibitory (CA1 parvalbumin-positive) neurons innervated by the same presynaptic inputs (CA3 Schaffer collaterals). Our results reveal that these two types of CA1 neurons follow different connectivity patterns. Our new evidence for differently structured connectivity at a fine scale in hippocampal excitatory and inhibitory neurons provides a better understanding of hippocampal networks and will guide theoretical and experimental studies. Copyright © 2018 the authors 0270-6474/18/385140-13$15.00/0.

Color constancy influenced by unnatural spatial structure.

PubMed

Mizokami, Yoko; Yaguchi, Hirohisa

2014-04-01

The recognition of spatial structures is important for color constancy because we cannot identify an object's color under different illuminations without knowing which space it is in and how that space is illuminated. To show the importance of the natural structure of environments on color constancy, we investigated the way in which color appearance was affected by unnatural viewing conditions in which a spatial structure was distorted. Observers judged the color of a test patch placed in the center of a small room illuminated by white or reddish lights, as well as two rooms illuminated by white and reddish light, respectively. In the natural viewing condition, an observer saw the room(s) through a viewing window, whereas in an unnatural viewing condition, the scene structure was scrambled by a kaleidoscope-type viewing box. Results of single room condition with one illuminant color showed little difference in color constancy between the two viewing conditions. However, it decreased in the two-rooms condition with a more complex arrangement of space and illumination. The patch's appearance under the unnatural viewing condition was more influenced by simultaneous contrast than its appearance under the natural viewing condition. It also appears that color appearance under white illumination is more stable compared to that under reddish illumination. These findings suggest that natural spatial structure plays an important role for color constancy in a complex environment.

Correlation Between Chain Architecture and Hydration Water Structure in Polysaccharides.

PubMed

Grossutti, Michael; Dutcher, John R

2016-03-14

The physical properties of confined water can differ dramatically from those of bulk water. Hydration water associated with polysaccharides provides a particularly interesting example of confined water, because differences in polysaccharide structure provide different spatially confined environments for water sorption. We have used attenuated total reflection infrared (ATR-IR) spectroscopy to investigate the structure of hydration water in films of three different polysaccharides under controlled relative humidity (RH) conditions. We compare the results obtained for films of highly branched, dendrimer-like phytoglycogen nanoparticles to those obtained for two unbranched polysaccharides, hyaluronic acid (HA), and chitosan. We find similarities between the water structuring in the two linear polysaccharides and significant differences for phytoglycogen. In particular, the results suggest that the high degree of branching in phytoglycogen leads to a much more well-ordered water structure (low density, high connectivity network water), indicating the strong influence of chain architecture on the structuring of water. These measurements provide unique insight into the relationship between the structure and hydration of polysaccharides, which is important for understanding and exploiting these sustainable nanomaterials in a wide range of applications.

Modeled structure of trypanothione reductase of Leishmania infantum.

PubMed

Singh, Bishal K; Sarkar, Nandini; Jagannadham, M V; Dubey, Vikash K

2008-06-30

Trypanothione reductase is an important target enzyme for structure-based drug design against Leishmania. We used homology modeling to construct a three-dimensional structure of the trypanothione reductase (TR) of Leishmania infantum. The structure shows acceptable Ramachandran statistics and a remarkably different active site from glutathione reductase(GR). Thus, a specific inhibitor against TR can be designed without interfering with host (human) GR activity.

Structural constraints on the three-dimensional geometry of simple viruses: case studies of a new predictive tool

PubMed Central

Keef, Thomas; Wardman, Jessica P.; Ranson, Neil A.; Stockley, Peter G.; Twarock, Reidun

2013-01-01

Understanding the fundamental principles of virus architecture is one of the most important challenges in biology and medicine. Crick and Watson were the first to propose that viruses exhibit symmetry in the organization of their protein containers for reasons of genetic economy. Based on this, Caspar and Klug introduced quasi-equivalence theory to predict the relative locations of the coat proteins within these containers and classified virus structure in terms of T-numbers. Here it is shown that quasi-equivalence is part of a wider set of structural constraints on virus structure. These constraints can be formulated using an extension of the underlying symmetry group and this is demonstrated with a number of case studies. This new concept in virus biology provides for the first time predictive information on the structural constraints on coat protein and genome topography, and reveals a previously unrecognized structural interdependence of the shapes and sizes of different viral components. It opens up the possibility of distinguishing the structures of different viruses with the same T-number, suggesting a refined viral structure classification scheme. It can moreover be used as a basis for models of virus function, e.g. to characterize the start and end configurations of a structural transition important for infection. PMID:23403965

Structural constraints on the three-dimensional geometry of simple viruses: case studies of a new predictive tool.

PubMed

Keef, Thomas; Wardman, Jessica P; Ranson, Neil A; Stockley, Peter G; Twarock, Reidun

2013-03-01

Understanding the fundamental principles of virus architecture is one of the most important challenges in biology and medicine. Crick and Watson were the first to propose that viruses exhibit symmetry in the organization of their protein containers for reasons of genetic economy. Based on this, Caspar and Klug introduced quasi-equivalence theory to predict the relative locations of the coat proteins within these containers and classified virus structure in terms of T-numbers. Here it is shown that quasi-equivalence is part of a wider set of structural constraints on virus structure. These constraints can be formulated using an extension of the underlying symmetry group and this is demonstrated with a number of case studies. This new concept in virus biology provides for the first time predictive information on the structural constraints on coat protein and genome topography, and reveals a previously unrecognized structural interdependence of the shapes and sizes of different viral components. It opens up the possibility of distinguishing the structures of different viruses with the same T-number, suggesting a refined viral structure classification scheme. It can moreover be used as a basis for models of virus function, e.g. to characterize the start and end configurations of a structural transition important for infection.

Is there a reliable factorial structure in the 20-item Toronto Alexithymia Scale? A comparison of factor models in clinical and normal adult samples.

PubMed

Müller, Jochen; Bühner, Markus; Ellgring, Heiner

2003-12-01

The 20-item Toronto Alexithymia Scale (TAS-20) is the most widely used instrument for measuring alexithymia. However, different studies did not always yield identical factor structures of this scale. The present study aims at clarifying some discrepant results. Maximum likelihood confirmatory factor analyses of a German version of the TAS-20 were conducted on data from a clinical sample (N=204) and a sample of normal adults (N=224). Five different models with one to four factors were compared. A four-factor model with factors (F1) "Difficulty identifying feelings" (F2), "Difficulty describing feelings" (F3), "Low importance of emotion" and (F4) "Pragmatic thinking" and a three-factor model with the combined factor "Difficulties in identifying and describing feelings" described the data best. Factors related to "externally oriented thinking" provided no acceptable level of reliability. Results from the present and other studies indicate that the factorial structure of the TAS-20 may vary across samples. Whether factor structures different from the common three-factor structure are an exception in some mainly clinical populations or a common phenomenon outside student populations has still to be determined. For a further exploration of the factor structure of the TAS-20 in different populations, it would be important not only to test the fit of the common three-factor model, but also to consider other competing solutions like the models of the present study.

Introduction to fatty acids and lipids.

PubMed

Burdge, Graham C; Calder, Philip C

2015-01-01

The purpose of this article is to describe the structure, function and metabolism of fatty acids and lipids that are of particular importance in the context of parenteral nutrition. Lipids are a heterogeneous group of molecules that share the common property of hydrophobicity. Lipids range in structure from simple short hydrocarbon chains to more complex molecules, including triacylglycerols, phospholipids and sterols and their esters. Lipids within each class may differ structurally. Fatty acids are common components of complex lipids, and these differ according to chain length and the presence, number and position of double bonds in the hydrocarbon chain. Structural variation among complex lipids and among fatty acids gives rise to functional differences that result in different impacts upon metabolism and upon cell and tissue responses. Fatty acids and complex lipids exhibit a variety of structural variations that influence their metabolism and their functional effects. © 2015 S. Karger AG, Basel.

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

Simulating Food Web Dynamics along a Gradient: Quantifying Human Influence

PubMed Central

Jordán, Ferenc; Gjata, Nerta; Mei, Shu; Yule, Catherine M.

2012-01-01

Realistically parameterized and dynamically simulated food-webs are useful tool to explore the importance of the functional diversity of ecosystems, and in particular relations between the dynamics of species and the whole community. We present a stochastic dynamical food web simulation for the Kelian River (Borneo). The food web was constructed for six different locations, arrayed along a gradient of increasing human perturbation (mostly resulting from gold mining activities) along the river. Along the river, the relative importance of grazers, filterers and shredders decreases with increasing disturbance downstream, while predators become more dominant in governing eco-dynamics. Human activity led to increased turbidity and sedimentation which adversely impacts primary productivity. Since the main difference between the study sites was not the composition of the food webs (structure is quite similar) but the strengths of interactions and the abundance of the trophic groups, a dynamical simulation approach seemed to be useful to better explain human influence. In the pristine river (study site 1), when comparing a structural version of our model with the dynamical model we found that structurally central groups such as omnivores and carnivores were not the most important ones dynamically. Instead, primary consumers such as invertebrate grazers and shredders generated a greater dynamical response. Based on the dynamically most important groups, bottom-up control is replaced by the predominant top-down control regime as distance downstream and human disturbance increased. An important finding, potentially explaining the poor structure to dynamics relationship, is that indirect effects are at least as important as direct ones during the simulations. We suggest that our approach and this simulation framework could serve systems-based conservation efforts. Quantitative indicators on the relative importance of trophic groups and the mechanistic modeling of eco-dynamics could greatly contribute to understanding various aspects of functional diversity. PMID:22768346

Hippocampal structure predicts statistical learning and associative inference abilities during development

PubMed Central

Schlichting, Margaret L.; Guarino, Katharine F.; Schapiro, Anna C.; Turk-Browne, Nicholas B.; Preston, Alison R.

2016-01-01

Despite the importance of learning and remembering across the lifespan, little is known about how the episodic memory system develops to support the extraction of associative structure from the environment. Here, we relate individual differences in volumes along the hippocampal long axis to performance on statistical learning and associative inference tasks—both of which require encoding associations that span multiple episodes—in a developmental sample ranging from ages 6–30 years. Relating age to volume, we found dissociable patterns across the hippocampal long axis, with opposite nonlinear volume changes in the head and body. These structural differences were paralleled by performance gains across the age range on both tasks, suggesting improvements in the cross-episode binding ability from childhood to adulthood. Controlling for age, we also found that smaller hippocampal heads were associated with superior behavioral performance on both tasks, consistent with this region’s hypothesized role in forming generalized codes spanning events. Collectively, these results highlight the importance of examining hippocampal development as a function of position along the hippocampal axis and suggest that the hippocampal head is particularly important in encoding associative structure across development. PMID:27575916

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.

Canopy structure on forest lands in western Oregon: differences among forest types and stand ages

Treesearch

Anne C.S. McIntosh; Andrew N. Gray; Steven L. Garman

2009-01-01

Canopy structure is an important attribute affecting economic and ecological values of forests in the Pacific Northwest. However, canopy cover and vertical layering are rarely measured directly; they are usually inferred from other forest measurements. In this study, we quantified and compared vertical and horizontal patterns of tree canopy structure and understory...

Ludic Elicitation: Using Games for Knowledge Elicitation

ERIC Educational Resources Information Center

Cao, Yan

2014-01-01

Knowledge elicitation from human beings is important for many fields, such as decision support systems, risk communication, and customer preference studying. Traditional approaches include observations, questionnaires, structured and semi-structured interviews, and group discussions. Many publications have been studying different techniques for a…

Application of Solid-State NMR to Reveal Structural Differences in Cefazolin Sodium Pentahydrate from Different Manufacturing Processes

NASA Astrophysics Data System (ADS)

Tian, Ye; Wang, Wei D.; Zou, Wen-Bo; Qian, Jian-Qin; Hu, Chang-Qin

2018-04-01

The solid form of an active pharmaceutical ingredient is important when developing a new chemical entity. A solid understanding of the crystal structure and morphology that affect the mechanical and physical characteristics of pharmaceutical powders determines the manufacturing process. Solid-state NMR, thermogravimetric analysis, X-ray diffraction, and Fourier-transform infrared spectroscopy were combined with theoretical calculation to investigate different crystal packings of α-cefazolin sodium from three different vendors and conformational polymorphism was identified to exist in the α-cefazolin sodium. Marginal differences observed among CEZ-Na pentahydrate 1, 2, and 3 were speculated as the proportion of conformation 2. Understanding the differences in the polymorphic structure of α-cefazolin sodium may help with making modifications to incorporate new knowledge with a product’s development.

Wasp waist or beer belly? Modeling food web structure and energetic control in Alaskan marine ecosystems, with implications for fishing and environmental forcing

NASA Astrophysics Data System (ADS)

Gaichas, Sarah; Aydin, Kerim; Francis, Robert C.

2015-11-01

The Eastern Bering Sea (EBS) and Gulf of Alaska (GOA) continental shelf ecosystems show some similar and some distinctive groundfish biomass dynamics. Given that similar species occupy these regions and fisheries management is also comparable, similarities might be expected, but to what can we attribute the differences? Different types of ecosystem structure and control (e.g. top-down, bottom-up, mixed) can imply different ecosystem dynamics and climate interactions. Further, the structural type identified for a given ecosystem may suggest optimal management for sustainable fishing. Here, we use information on the current system state derived from food web models of both the EBS and the GOA combined with dynamic ecosystem models incorporating uncertainty to classify each ecosystem by its structural type. We then suggest how this structure might be generally related to dynamics and predictability. We find that the EBS and GOA have fundamentally different food web structures both overall, and when viewed from the perspective of the same commercially and ecologically important species in each system, walleye pollock (Gadus chalcogrammus). EBS food web structure centers on a large mass of pollock, which appears to contribute to relative system stability and predictability. In contrast, GOA food web structure features high predator biomass, which contributes to a more dynamic, less predictable ecosystem. Mechanisms for climate influence on pollock production in the EBS are increasingly understood, while climate forcing mechanisms contributing to the potentially destabilizing high predator biomass in the GOA remain enigmatic. We present results of identical pollock fishing and climate-driven pollock recruitment simulations in the EBS and GOA which show different system responses, again with less predictable response in the GOA. Overall, our results suggest that identifying structural properties of fished food webs is as important for sustainable fisheries management as attempting to predict climate and fisheries effects within each ecosystem.

Evolving knowledge of sex differences in brain structure, function, and chemistry.

PubMed

Cosgrove, Kelly P; Mazure, Carolyn M; Staley, Julie K

2007-10-15

Clinical and epidemiologic evidence demonstrates sex differences in the prevalence and course of various psychiatric disorders. Understanding sex-specific brain differences in healthy individuals is a critical first step toward understanding sex-specific expression of psychiatric disorders. Here, we evaluate evidence on sex differences in brain structure, chemistry, and function using imaging methodologies, including functional magnetic resonance imaging (fMRI), positron emission tomography (PET), single photon emission computed tomography (SPECT), and structural magnetic resonance imaging (MRI) in mentally healthy individuals. MEDLINE searches of English-language literature (1980-November 2006) using the terms sex, gender, PET, SPECT, MRI, fMRI, morphometry, neurochemistry, and neurotransmission were performed to extract relevant sources. The literature suggests that while there are many similarities in brain structure, function, and neurotransmission in healthy men and women, there are important differences that distinguish the male from the female brain. Overall, brain volume is greater in men than women; yet, when controlling for total volume, women have a higher percentage of gray matter and men a higher percentage of white matter. Regional volume differences are less consistent. Global cerebral blood flow is higher in women than in men. Sex-specific differences in dopaminergic, serotonergic, and gamma-aminobutyric acid (GABA)ergic markers indicate that male and female brains are neurochemically distinct. Insight into the etiology of sex differences in the normal living human brain provides an important foundation to delineate the pathophysiological mechanisms underlying sex differences in neuropsychiatric disorders and to guide the development of sex-specific treatments for these devastating brain disorders.

A Visual Evaluation Study of Graph Sampling Techniques

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

Zhang, Fangyan; Zhang, Song; Wong, Pak C.

2017-01-29

We evaluate a dozen prevailing graph-sampling techniques with an ultimate goal to better visualize and understand big and complex graphs that exhibit different properties and structures. The evaluation uses eight benchmark datasets with four different graph types collected from Stanford Network Analysis Platform and NetworkX to give a comprehensive comparison of various types of graphs. The study provides a practical guideline for visualizing big graphs of different sizes and structures. The paper discusses results and important observations from the study.

Characterization and Quantification of the Pore Structures of the Shale Oil Reservoir Formations in Multiscale

NASA Astrophysics Data System (ADS)

Liu, K.; Ostadhassan, M.

2016-12-01

Due to the fast development of hydraulic fracturing and horizontal drilling, shale formations now are one important resource of energy in North America. Characterizing the pore structure of these shale formations is of critical importance in understanding the original oil/gas in place and also the flow properties of the rock matrix. Pore with different properties such as pore size and pore shape can impact the physical, mechanical and chemical properties including strength, elastic modulus, permeability and conductivity. Nowadays, image analysis has been a robust method to quantify the pore information from the porous medium.SEM has been one of the most useful tools to study the pore microstructures due to its high depth of focus which can provide detailed topographical information about the surface. The suitable difference between solid matrix and pores due to the different gray level pixels can be used to study the pore structures.In this paper, we characterized and quantified the pore structures of rock samples from Middle Bakken Formation which is a typical unconventional reservoir in North America. High resolution SEM images of five samples we chose based on the gamma logs were derived after sample preparation. After determining the threshold of the images, we extracted the pore spaces. Then we analyzed the pore structures properties such as pore size distributions and pore shape distributions of the five samples and compared based on their mineral compositions. After that, we analyzed their heterogeneity and isotropy properties which have been identified as an important factor affecting reservoir productivity. Finally, we studied the impact of scale effect on the pore structures characterization.

The track structure in condensed matter

NASA Astrophysics Data System (ADS)

Kaplan, I. G.

1995-11-01

The physical stage of track formation in a condensed phase is discussed. For interaction of charged particles with condensed molecular media its most important specific features are: (a) the continuous oscillator strength distribution with the broak peak in the energy range 21-22 eV attributed to the collective plasmon-type state; (b) the lowering of ionization potential compared to a gas phase. These specific features must be taken into account for simulation of track structures. The great difference in mass and charge for a electron and heavy ions cause a qualitative difference in their track structures. We analyse the structure of heavy ion tracks and prove the impossibility to use the LET as a universal characteristic for the radiation action of different ions.

Bacterial community and arsenic functional genes diversity in arsenic contaminated soils from different geographic locations

PubMed Central

Gu, Yunfu; D. Van Nostrand, Joy; Wu, Liyou; He, Zhili; Qin, Yujia; Zhao, Fang-Jie; Zhou, Jizhong

2017-01-01

To understand how soil microbial communities and arsenic (As) functional genes respond to soil arsenic (As) contamination, five soils contaminated with As at different levels were collected from diverse geographic locations, incubated for 54 days under flooded conditions, and examined by both MiSeq sequencing of 16S rRNA gene amplicons and functional gene microarray (GeoChip 4.0). The results showed that both bacterial community structure and As functional gene structure differed among geographical locations. The diversity of As functional genes correlated positively with the diversity of 16S rRNA genes (P< 0.05). Higher diversities of As functional genes and 16S rRNA genes were observed in the soils with higher available As. Soil pH, phosphate-extractable As, and amorphous Fe content were the most important factors in shaping the bacterial community structure and As transformation functional genes. Geographic location was also important in controlling both the bacterial community and As transformation functional potential. These findings provide insights into the variation of As transformation functional genes in soils contaminated with different levels of As at different geographic locations, and the impact of environmental As contamination on the soil bacterial community. PMID:28475654

Structure and Mechanism of a Eukaryotic FMN Adenylyltransferase

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

Huerta, Carlos; Borek, Dominika; Machius, Mischa

2009-12-01

Flavin mononucleotide adenylyltransferase (FMNAT) catalyzes the formation of the essential flavocoenzyme flavin adenine dinucleotide (FAD) and plays an important role in flavocoenzyme homeostasis regulation. By sequence comparison, bacterial and eukaryotic FMNAT enzymes belong to two different protein superfamilies and apparently utilize different sets of active-site residues to accomplish the same chemistry. Here we report the first structural characterization of a eukaryotic FMNAT from the pathogenic yeast Candida glabrata. Four crystal structures of C. glabrata FMNAT in different complexed forms were determined at 1.20-1.95 A resolutions, capturing the enzyme active-site states prior to and after catalysis. These structures reveal a novelmore » flavin-binding mode and a unique enzyme-bound FAD conformation. Comparison of the bacterial and eukaryotic FMNATs provides a structural basis for understanding the convergent evolution of the same FMNAT activity from different protein ancestors. Structure-based investigation of the kinetic properties of FMNAT should offer insights into the regulatory mechanisms of FAD homeostasis by FMNAT in eukaryotic organisms.« less

Native fat globules of different sizes selected from raw milk: thermal and structural behavior.

PubMed

Michalski, Marie-Caroline; Ollivon, Michel; Briard, Valérie; Leconte, Nadine; Lopez, Christelle

2004-12-01

The aim of this study was to characterize differences in the thermal and structural behavior between different sized native milk fat globules. A novel microfiltration process permits the selection of native small fat globules (SFG, 1-3 microm) and large fat globules (LFG, >5 microm) in raw milk, that were analyzed by X-ray diffraction (XRD) coupled to differential scanning calorimetry (DSC). There were no major differences in triglyceride crystalline structures between SFG and LFG, after eliminating thermal history and the influence of cooling rates. The three main 3L and 2L crystalline structures appearing under slow cooling existed regardless of globule size. The supercooling increased for the SFG, mainly due to heterogeneous nucleation in winter milk, and also to compositional variations in spring milk. Differences appeared regarding stabilized crystalline forms at 20 degrees C and subsequent cooling: the SFG contained less 2L triglyceride structures than the LFG. These results can be important in dairy manufactures using tempering periods.

Correlation Between Chain Architecture and Hydration Water Structure in Polysaccharides

NASA Astrophysics Data System (ADS)

Grossutti, Michael; Dutcher, John

The physical properties of confined water can differ dramatically from those of bulk water. Hydration water associated with polysaccharides provides a particularly important example of confined water, with differences in polysaccharide structure providing different spatially confined environments for water adsorption. We have used attenuated total reflection infrared (ATR-IR) spectroscopy to investigate the structure of hydration water in films of three different polysaccharides under controlled relative humidity (RH) conditions. We compare the results obtained for films of highly branched, monodisperse phytoglycogen nanoparticles to those obtained for two unbranched polysaccharides, hyaluronic acid (HA) and chitosan. We find similarities between water structuring in the two linear polysaccharides, and significant differences for phytoglycogen. In particular, the phytoglycogen nanoparticles exhibited high network water connectivity, and a large increase in the fraction of multimer water clusters with increasing RH, whereas the water structure for HA and chitosan was found to be insensitive to changes in RH. These measurements provide unique insight into the relationship between the chain architecture and hydration of polysaccharides.

Peroxisome protein import: a complex journey.

PubMed

Baker, Alison; Lanyon-Hogg, Thomas; Warriner, Stuart L

2016-06-15

The import of proteins into peroxisomes possesses many unusual features such as the ability to import folded proteins, and a surprising diversity of targeting signals with differing affinities that can be recognized by the same receptor. As understanding of the structure and function of many components of the protein import machinery has grown, an increasingly complex network of factors affecting each step of the import pathway has emerged. Structural studies have revealed the presence of additional interactions between cargo proteins and the PEX5 receptor that affect import potential, with a subtle network of cargo-induced conformational changes in PEX5 being involved in the import process. Biochemical studies have also indicated an interdependence of receptor-cargo import with release of unloaded receptor from the peroxisome. Here, we provide an update on recent literature concerning mechanisms of protein import into peroxisomes. © 2016 The Author(s).

Divergent Synthesis of Chondroitin Sulfate Disaccharides and Identification of Sulfate Motifs that Inhibit Triple Negative Breast Cancer

NASA Astrophysics Data System (ADS)

Wei Poh, Zhong; Heng Gan, Chin; Lee, Eric J.; Guo, Suxian; Yip, George W.; Lam, Yulin

2015-09-01

Glycosaminoglycans (GAGs) regulate many important physiological processes. A pertinent issue to address is whether GAGs encode important functional information via introduction of position specific sulfate groups in the GAG structure. However, procurement of pure, homogenous GAG motifs to probe the “sulfation code” is a challenging task due to isolation difficulty and structural complexity. To this end, we devised a versatile synthetic strategy to obtain all the 16 theoretically possible sulfation patterns in the chondroitin sulfate (CS) repeating unit; these include rare but potentially important sulfated motifs which have not been isolated earlier. Biological evaluation indicated that CS sulfation patterns had differing effects for different breast cancer cell types, and the greatest inhibitory effect was observed for the most aggressive, triple negative breast cancer cell line MDA-MB-231.

Superimposition of protein structures with dynamically weighted RMSD.

PubMed

Wu, Di; Wu, Zhijun

2010-02-01

In protein modeling, one often needs to superimpose a group of structures for a protein. A common way to do this is to translate and rotate the structures so that the square root of the sum of squares of coordinate differences of the atoms in the structures, called the root-mean-square deviation (RMSD) of the structures, is minimized. While it has provided a general way of aligning a group of structures, this approach has not taken into account the fact that different atoms may have different properties and they should be compared differently. For this reason, when superimposed with RMSD, the coordinate differences of different atoms should be evaluated with different weights. The resulting RMSD is called the weighted RMSD (wRMSD). Here we investigate the use of a special wRMSD for superimposing a group of structures with weights assigned to the atoms according to certain thermal motions of the atoms. We call such an RMSD the dynamically weighted RMSD (dRMSD). We show that the thermal motions of the atoms can be obtained from several sources such as the mean-square fluctuations that can be estimated by Gaussian network model analysis. We show that the superimposition of structures with dRMSD can successfully identify protein domains and protein motions, and that it has important implications in practice, e.g., in aligning the ensemble of structures determined by nuclear magnetic resonance.

Detecting brain dynamics during resting state: a tensor based evolutionary clustering approach

NASA Astrophysics Data System (ADS)

Al-sharoa, Esraa; Al-khassaweneh, Mahmood; Aviyente, Selin

2017-08-01

Human brain is a complex network with connections across different regions. Understanding the functional connectivity (FC) of the brain is important both during resting state and task; as disruptions in connectivity patterns are indicators of different psychopathological and neurological diseases. In this work, we study the resting state functional connectivity networks (FCNs) of the brain from fMRI BOLD signals. Recent studies have shown that FCNs are dynamic even during resting state and understanding the temporal dynamics of FCNs is important for differentiating between different conditions. Therefore, it is important to develop algorithms to track the dynamic formation and dissociation of FCNs of the brain during resting state. In this paper, we propose a two step tensor based community detection algorithm to identify and track the brain network community structure across time. First, we introduce an information-theoretic function to reduce the dynamic FCN and identify the time points that are similar topologically to combine them into a tensor. These time points will be used to identify the different FC states. Second, a tensor based spectral clustering approach is developed to identify the community structure of the constructed tensors. The proposed algorithm applies Tucker decomposition to the constructed tensors and extract the orthogonal factor matrices along the connectivity mode to determine the common subspace within each FC state. The detected community structure is summarized and described as FC states. The results illustrate the dynamic structure of resting state networks (RSNs), including the default mode network, somatomotor network, subcortical network and visual network.

Shining light on the differences in molecular structural chemical makeup and the cause of distinct degradation behavior between malting- and feed-type barley using synchrotron FTIR microspectroscopy: a novel approach.

PubMed

Yu, Peiqiang; Doiron, Kevin; Liu, Dasen

2008-05-14

The objective of this study was to use advanced synchrotron-sourced FTIR microspectroscopy (SFTIRM) as a novel approach to identify the differences in protein and carbohydrate molecular structure (chemical makeup) between these two varieties of barley and illustrate the exact causes for their significantly different degradation kinetics. Items assessed included (1) molecular structural differences in protein amide I to amide II intensities and their ratio within cellular dimensions, (2) molecular structural differences in protein secondary structure profile and their ratios, and (3) molecular structural differences in carbohydrate component peak profile. Our hypothesis was that molecular structure (chemical makeup) affects barley quality, fermentation, and degradation behavior in both humans and animals. Using SFTIRM, the protein and carbohydrate molecular structural chemical makeup of barley was revealed and identified. The protein molecular structural chemical makeup differed significantly between the two varieties of barleys. No difference in carbohydrate molecular structural chemical makeup was detected. Harrington was lower than Valier in protein amide I, amide II, and protein amide I to amide II ratio, while Harrington was relatively higher in model-fitted protein alpha-helix and beta-sheet, but lower in the others (beta-turn and random coil). These results indicated that it is the molecular structure of protein (chemical makeup) that may play a major role in the different degradation kinetics between the two varieties of barleys (not the molecular structure of carbohydrate). It is believed that use of the advanced synchrotron technology will make a significant step and an important contribution to research in examining the molecular structure (chemical makeup) of plant, feed, and seeds.

Probing disorder in isometric pyrochlore and related complex oxides

NASA Astrophysics Data System (ADS)

Shamblin, Jacob; Feygenson, Mikhail; Neuefeind, Joerg; Tracy, Cameron L.; Zhang, Fuxiang; Finkeldei, Sarah; Bosbach, Dirk; Zhou, Haidong; Ewing, Rodney C.; Lang, Maik

2016-05-01

There has been an increased focus on understanding the energetics of structures with unconventional ordering (for example, correlated disorder that is heterogeneous across different length scales). In particular, compounds with the isometric pyrochlore structure, A2B2O7, can adopt a disordered, isometric fluorite-type structure, (A, B)4O7, under extreme conditions. Despite the importance of the disordering process there exists only a limited understanding of the role of local ordering on the energy landscape. We have used neutron total scattering to show that disordered fluorite (induced intrinsically by composition/stoichiometry or at far-from-equilibrium conditions produced by high-energy radiation) consists of a local orthorhombic structural unit that is repeated by a pseudo-translational symmetry, such that orthorhombic and isometric arrays coexist at different length scales. We also show that inversion in isometric spinel occurs by a similar process. This insight provides a new basis for understanding order-to-disorder transformations important for applications such as plutonium immobilization, fast ion conduction, and thermal barrier coatings.

Structural Elucidation of Enzymatically Synthesized Galacto-oligosaccharides Using Ion-Mobility Spectrometry-Tandem Mass Spectrometry.

PubMed

Carević, Milica; Bezbradica, Dejan; Banjanac, Katarina; Milivojević, Ana; Fanuel, Mathieu; Rogniaux, Hélène; Ropartz, David; Veličković, Dušan

2016-05-11

Galacto-oligosaccharides (GOS) represent a diverse group of well-characterized prebiotic ingredients derived from lactose in a reaction catalyzed with β-galactosidases. Enzymatic transgalactosylation results in a mixture of compounds of various degrees of polymerization and types of linkages. Because structure plays an important role in terms of prebiotic activity, it is of crucial importance to provide an insight into the mechanism of transgalactosylation reaction and occurrence of different types of β-linkages during GOS synthesis. Our study proved that a novel one-step method, based on ion-mobility spectrometry-tandem mass spectrometry (IMS-MS/MS), enables complete elucidation of GOS structure. It has been shown that β-galactosidase from Aspergillus oryzae has the highest affinity toward formation of β-(1→3) or β-(1→6) linkages. Additionally, it was observed that the occurrence of different linkages varies during the reaction course, indicating that tailoring favorable GOS structures with improved prebiotic activity can be achieved by adequate control of enzymatic synthesis.

Crystal Structural Effect of AuCu Alloy Nanoparticles on Catalytic CO Oxidation

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

Zhan, Wangcheng; Wang, Jinglin; Wang, Haifeng

2017-06-07

Controlling the physical and chemical properties of alloy nanoparticles (NPs) is an important approach to optimize NP catalysis. Unlike other tuning knobs, such as size, shape, and composition, crystal structure has received limited attention and not been well understood for its role in catalysis. This deficiency is mainly due to the difficulty in synthesis and fine-tuning of the NPs’ crystal structure. Here, Exemplifying by AuCu alloy NPs with face centered cubic (fcc) and face centered tetragonal (fct) structure, we demonstrate a remarkable difference in phase segregation and catalytic performance depending on the crystal structure. During the thermal treatment in air,more » the Cu component in fcc-AuCu alloy NPs segregates more easily onto the alloy surface as compared to that in fct-AuCu alloy NPs. As a result, after annealing at 250 °C in air for 1 h, the fcc- and fct-AuCu alloy NPs are phase transferred into Au/CuO and AuCu/CuO core/shell structures, respectively. More importantly, this variation in heterostructures introduces a significant difference in CO adsorption on two catalysts, leading to a largely enhanced catalytic activity of AuCu/CuO NP catalyst for CO oxidation. Furthermore, the same concept can be extended to other alloy NPs, making it possible to fine-tune NP catalysis for many different chemical reactions.« less

Modal Response of Trapezoidal Wing Structures Using Second Order Shape Sensitivities

NASA Technical Reports Server (NTRS)

Liu, Youhua; Kapania, Rakesh K.

2000-01-01

The modal response of wing structures is very important for assessing their dynamic response including dynamic aeroelastic instabilities. Moreover, in a recent study an efficient structural optimization approach was developed using structural modes to represent the static aeroelastic wing response (both displacement and stress). In this paper, the modal response of general trapezoidal wing structures is approximated using shape sensitivities up to the 2nd order. Also different approaches of computing the derivatives are investigated.

Large-scale biochemical profiling of the Candida albicans biofilm matrix: new compositional, structural, and functional insights.

PubMed

Lopez-Ribot, Jose L

2014-09-09

Among pathogenic fungi, Candida albicans is most frequently associated with biofilm formation, a lifestyle that is entirely different from the planktonic state. One of the distinguishing features of these biofilms is the presence of extracellular material, commonly referred to as the "biofilm matrix." The fungal biofilm matrix embeds sessile cells within these communities and plays important structural and physiological functions, including antifungal drug resistance with important clinical repercussions. This matrix is mostly self-produced by the fungal cells themselves and is composed of different types of biopolymers. In C. albicans, the main components of the biofilm matrix are carbohydrates, proteins, lipids, and DNA, but many of them remain unidentified and/or poorly characterized. In their recent article, Zarnowski et al. [mBio 5(4):e01333-14, 2014, doi:10.1128/mBio.01333-14] used a variety of biochemical and state-of-the-art "omic" approaches (glycomics, proteomics, and lipidomics) to identify and characterize unique biopolymers present in the C. albicans biofilm matrix. Besides generating a true "encyclopedic" catalog of individual moieties from each of the different macromolecular categories, results also provide important insights into structural and functional aspects of the fungal biofilm matrix, particularly the interaction between different components and the contribution of multiple matrix constituents to biofilm antifungal drug resistance. Copyright © 2014 Lopez-Ribot.

The evolutionary and ecological consequences of animal social networks: emerging issues.

PubMed

Kurvers, Ralf H J M; Krause, Jens; Croft, Darren P; Wilson, Alexander D M; Wolf, Max

2014-06-01

The first generation of research on animal social networks was primarily aimed at introducing the concept of social networks to the fields of animal behaviour and behavioural ecology. More recently, a diverse body of evidence has shown that social fine structure matters on a broader scale than initially expected, affecting many key ecological and evolutionary processes. Here, we review this development. We discuss the effects of social network structure on evolutionary dynamics (genetic drift, fixation probabilities, and frequency-dependent selection) and social evolution (cooperation and between-individual behavioural differences). We discuss how social network structure can affect important coevolutionary processes (host-pathogen interactions and mutualisms) and population stability. We also discuss the potentially important, but poorly studied, role of social network structure on dispersal and invasion. Throughout, we highlight important areas for future research. Copyright © 2014 Elsevier Ltd. All rights reserved.

Charitable giving and reflexive individuals: How personal reflexivity mediates between structure and agency

PubMed Central

Sanghera, Balihar

2016-01-01

This article examines how individuals are reflexive beings who interpret the world in relation to things that matter to them, and how charitable acts are evaluated and embedded in their lives with different degrees of meaning and importance. Rather than framing the discussion of charitable practices in terms of an altruism/egoism binary or imputing motivations and values to social structures, the article explains how reflexivity is an important and neglected dimension of social practices, and how it interacts with sympathy, sentiments and discourses to shape giving. The study also shows that there are different modes of reflexivity, which have varied effects on charity and volunteering. PMID:28232772

The unfoldomics decade: an update on intrinsically disordered proteins.

PubMed

Dunker, A Keith; Oldfield, Christopher J; Meng, Jingwei; Romero, Pedro; Yang, Jack Y; Chen, Jessica Walton; Vacic, Vladimir; Obradovic, Zoran; Uversky, Vladimir N

2008-09-16

Our first predictor of protein disorder was published just over a decade ago in the Proceedings of the IEEE International Conference on Neural Networks (Romero P, Obradovic Z, Kissinger C, Villafranca JE, Dunker AK (1997) Identifying disordered regions in proteins from amino acid sequence. Proceedings of the IEEE International Conference on Neural Networks, 1: 90-95). By now more than twenty other laboratory groups have joined the efforts to improve the prediction of protein disorder. While the various prediction methodologies used for protein intrinsic disorder resemble those methodologies used for secondary structure prediction, the two types of structures are entirely different. For example, the two structural classes have very different dynamic properties, with the irregular secondary structure class being much less mobile than the disorder class. The prediction of secondary structure has been useful. On the other hand, the prediction of intrinsic disorder has been revolutionary, leading to major modifications of the more than 100 year-old views relating protein structure and function. Experimentalists have been providing evidence over many decades that some proteins lack fixed structure or are disordered (or unfolded) under physiological conditions. In addition, experimentalists are also showing that, for many proteins, their functions depend on the unstructured rather than structured state; such results are in marked contrast to the greater than hundred year old views such as the lock and key hypothesis. Despite extensive data on many important examples, including disease-associated proteins, the importance of disorder for protein function has been largely ignored. Indeed, to our knowledge, current biochemistry books don't present even one acknowledged example of a disorder-dependent function, even though some reports of disorder-dependent functions are more than 50 years old. The results from genome-wide predictions of intrinsic disorder and the results from other bioinformatics studies of intrinsic disorder are demanding attention for these proteins. Disorder prediction has been important for showing that the relatively few experimentally characterized examples are members of a very large collection of related disordered proteins that are wide-spread over all three domains of life. Many significant biological functions are now known to depend directly on, or are importantly associated with, the unfolded or partially folded state. Here our goal is to review the key discoveries and to weave these discoveries together to support novel approaches for understanding sequence-function relationships. Intrinsically disordered protein is common across the three domains of life, but especially common among the eukaryotic proteomes. Signaling sequences and sites of posttranslational modifications are frequently, or very likely most often, located within regions of intrinsic disorder. Disorder-to-order transitions are coupled with the adoption of different structures with different partners. Also, the flexibility of intrinsic disorder helps different disordered regions to bind to a common binding site on a common partner. Such capacity for binding diversity plays important roles in both protein-protein interaction networks and likely also in gene regulation networks. Such disorder-based signaling is further modulated in multicellular eukaryotes by alternative splicing, for which such splicing events map to regions of disorder much more often than to regions of structure. Associating alternative splicing with disorder rather than structure alleviates theoretical and experimentally observed problems associated with the folding of different length, isomeric amino acid sequences. The combination of disorder and alternative splicing is proposed to provide a mechanism for easily "trying out" different signaling pathways, thereby providing the mechanism for generating signaling diversity and enabling the evolution of cell differentiation and multicellularity. Finally, several recent small molecules of interest as potential drugs have been shown to act by blocking protein-protein interactions based on intrinsic disorder of one of the partners. Study of these examples has led to a new approach for drug discovery, and bioinformatics analysis of the human proteome suggests that various disease-associated proteins are very rich in such disorder-based drug discovery targets.

Bacterial Enzymes and Antibiotic Resistance- Oral Presentation

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

Maltz, Lauren

By using protein crystallography and X-ray diffraction, structures of bacterial enzymes were solved to gain a better understanding of how enzymatic modification acts as an antibacterial resistance mechanism. Aminoglycoside phosphotransferases (APHs) are one of three aminoglycoside modifying enzymes that confer resistance to the aminoglycoside antibiotics via enzymatic modification, rendering many drugs obsolete. Specifically, the APH(2”) family vary in their substrate specificities and also in their preference for the phosphate donor (ADP versus GDP). By solving the structures of members of the APH(2”) family of enzymes, we can see how domain movements are important to their substrate specificity. Our structure ofmore » the ternary complex of APH(2”)-IIIa with GDP and kanamycin, when compared to the known structures of APH(2”)-IVa, reveals that there are real physical differences between these two enzymes, a structural finding that explains why the two enzymes differ in their preferences for certain aminoglycosides. Another important group of bacterial resistance enzymes are the Class D β-lactamases. Oxacillinase carbapenemases (OXAs) are part of this enzyme class and have begun to confer resistance to ‘last resort’ drugs, most notably carbapenems. Our structure of OXA-143 shows that the conformational flexibility of a conserved hydrophobic residue in the active site (Val130) serves to control the entry of a transient water molecule responsible for a key step in the enzyme’s mechanism. Our results provide insight into the structural mechanisms of these two different enzymes.« less

Relevance, structure and analysis of ferulic acid in maize cell walls.

PubMed

Bento-Silva, Andreia; Vaz Patto, Maria Carlota; do Rosário Bronze, Maria

2018-04-25

Phenolic compounds in foods have been widely studied due to their health benefits. In cereals, phenolic compounds are extensively linked to cell wall polysaccharides, mainly arabinoxylans, which cross-link with each other and with other cell wall components. In maize, ferulic acid is the phenolic acid present in the highest concentration, forming ferulic acid dehydrodimers, trimers and tetramers. The cross-linking of polysaccharides is important for the cell wall structure and growth, and may protect against pathogen invasion. In addition to the importance for maize physiology, ferulic acid has been recognized as an important chemical structure with a wide range of health benefits when consumed in a diet rich in fibre. This review paper presents the different ways ferulic acid can be present in maize, the importance of ferulic acid derivatives and the methodologies that can be used for their analysis. Copyright © 2017 Elsevier Ltd. All rights reserved.

The impact of domain knowledge on structured data collection and templated note design.

PubMed

Windle, T; McClay, J C; Windle, J R

2013-01-01

The objective of this case report is to evaluate the importance of specialized domain knowledge when designing and using structured templated notes in a clinical environment. To analyze the impact of specialization on structured note generation we compared notes generated for three scenarios: 1) We compared the templated history of present illness (HPI) for patients presenting with a dermatology concern to the dermatologist versus the emergency department. 2) We compared the evaluation of chest pain by ED physicians versus cardiologists. 3) Finally, we compared the data elements asked for in the evaluation of the gastrointestinal system between cardiologists and the liver transplant service (LTS). We used the SNOMED CT representation via BioPortal to evaluate specificity and grouping between data elements and specialized physician groups. We found few similarities in structured data elements designed by and for the specific physician groups. The distinctness represented both differences in granularity as well as fundamental differences in data elements requested. When compared to ED physicians, dermatologists had different and more granular elements while cardiologists requested much more granular data. Comparing cardiologists and LTS, there were differences in the data elements requested. This case study supports the importance of domain knowledge in EHR design and implementation. That different specialities should want and use different information is well supported by cognitive science literature. Despite this, it is rare for domain knowledge to be considered in EHR implementation. Physicians with correct domain knowledge should be involved in the design process of templated notes.

In silico quantitative structure-toxicity relationship study of aromatic nitro compounds.

PubMed

Pasha, Farhan Ahmad; Neaz, Mohammad Morshed; Cho, Seung Joo; Ansari, Mohiuddin; Mishra, Sunil Kumar; Tiwari, Sharvan

2009-05-01

Small molecules often have toxicities that are a function of molecular structural features. Minor variations in structural features can make large difference in such toxicity. Consequently, in silico techniques may be used to correlate such molecular toxicities with their structural features. Relative to nine different sets of aromatic nitro compounds having known observed toxicities against different targets, we developed ligand-based 2D quantitative structure-toxicity relationship models using 20 selected topological descriptors. The topological descriptors have several advantages such as conformational independency, facile and less time-consuming computation to yield good results. Multiple linear regression analysis was used to correlate variations of toxicity with molecular properties. The information index on molecular size, lopping centric index and Kier flexibility index were identified as fundamental descriptors for different kinds of toxicity, and further showed that molecular size, branching and molecular flexibility might be particularly important factors in quantitative structure-toxicity relationship analysis. This study revealed that topological descriptor-guided quantitative structure-toxicity relationship provided a very useful, cost and time-efficient, in silico tool for describing small-molecule toxicities.

Effects of Vegetation Structure on the Location of Lion Kill Sites in African Thicket.

PubMed

Davies, Andrew B; Tambling, Craig J; Kerley, Graham I H; Asner, Gregory P

2016-01-01

Predator-prey relationships are integral to ecosystem stability and functioning. These relationships are, however, difficult to maintain in protected areas where large predators are increasingly being reintroduced and confined. Where predators make kills has a profound influence on their role in ecosystems, but the relative importance of environmental variables in determining kill sites, and how these might vary across ecosystems is poorly known. We investigated kill sites for lions in South Africa's thicket biome, testing the importance of vegetation structure for kill site locations compared to other environmental variables. Kill sites were located over four years using GPS telemetry and compared to non-kill sites that had been occupied by lions, as well as to random sites within lion ranges. Measurements of 3D vegetation structure obtained from Light Detection and Ranging (LiDAR) were used to calculate the visible area (viewshed) around each site and, along with wind and moonlight data, used to compare kill sites between lion sexes, prey species and prey sexes. Viewshed area was the most important predictor of kill sites (sites in dense vegetation were twice as likely to be kill sites compared to open areas), followed by wind speed and, less so, moonlight. Kill sites for different prey species varied with vegetation structure, and male prey were killed when wind speeds were higher compared to female prey of the same species. Our results demonstrate that vegetation structure is an important component of predator-prey interactions, with varying effects across ecosystems. Such differences require consideration in terms of the ecological roles performed by predators, and in predator and prey conservation.

Season-modulated responses of Neotropical bats to forest fragmentation.

PubMed

Ferreira, Diogo F; Rocha, Ricardo; López-Baucells, Adrià; Farneda, Fábio Z; Carreiras, João M B; Palmeirim, Jorge M; Meyer, Christoph F J

2017-06-01

Seasonality causes fluctuations in resource availability, affecting the presence and abundance of animal species. The impacts of these oscillations on wildlife populations can be exacerbated by habitat fragmentation. We assessed differences in bat species abundance between the wet and dry season in a fragmented landscape in the Central Amazon characterized by primary forest fragments embedded in a secondary forest matrix. We also evaluated whether the relative importance of local vegetation structure versus landscape characteristics (composition and configuration) in shaping bat abundance patterns varied between seasons. Our working hypotheses were that abundance responses are species as well as season specific, and that in the wet season, local vegetation structure is a stronger determinant of bat abundance than landscape-scale attributes. Generalized linear mixed-effects models in combination with hierarchical partitioning revealed that relationships between species abundances and local vegetation structure and landscape characteristics were both season specific and scale dependent. Overall, landscape characteristics were more important than local vegetation characteristics, suggesting that landscape structure is likely to play an even more important role in landscapes with higher fragment-matrix contrast. Responses varied between frugivores and animalivores. In the dry season, frugivores responded more to compositional metrics, whereas during the wet season, local and configurational metrics were more important. Animalivores showed similar patterns in both seasons, responding to the same group of metrics in both seasons. Differences in responses likely reflect seasonal differences in the phenology of flowering and fruiting between primary and secondary forests, which affected the foraging behavior and habitat use of bats. Management actions should encompass multiscale approaches to account for the idiosyncratic responses of species to seasonal variation in resource abundance and consequently to local and landscape scale attributes.

Physical-chemical and microbiological changes in Cerrado Soil under differing sugarcane harvest management systems

PubMed Central

2012-01-01

Background Sugarcane cultivation plays an important role in Brazilian economy, and it is expanding fast, mainly due to the increasing demand for ethanol production. In order to understand the impact of sugarcane cultivation and management, we studied sugarcane under different management regimes (pre-harvest burn and mechanical, unburnt harvest, or green cane), next to a control treatment with native vegetation. The soil bacterial community structure (including an evaluation of the diversity of the ammonia oxidizing (amoA) and denitrifying (nirK) genes), greenhouse gas flow and several soil physicochemical properties were evaluated. Results Our results indicate that sugarcane cultivation in this region resulted in changes in several soil properties. Moreover, such changes are reflected in the soil microbiota. No significant influence of soil management on greenhouse gas fluxes was found. However, we did find a relationship between the biological changes and the dynamics of soil nutrients. In particular, the burnt cane and green cane treatments had distinct modifications. There were significant differences in the structure of the total bacterial, the ammonia oxidizing and the denitrifying bacterial communities, being that these groups responded differently to the changes in the soil. A combination of physical and chemical factors was correlated to the changes in the structures of the total bacterial communities of the soil. The changes in the structures of the functional groups follow a different pattern than the physicochemical variables. The latter might indicate a strong influence of interactions among different bacterial groups in the N cycle, emphasizing the importance of biological factors in the structuring of these communities. Conclusion Sugarcane land use significantly impacted the structure of total selected soil bacterial communities and ammonia oxidizing and denitrifier gene diversities in a Cerrado field site in Central Brazil. A high impact of land use was observed in soil under the common burnt cane management. The green cane soil also presented different profiles compared to the control soil, but to at a lesser degree. PMID:22873209

Structure of Importin-α from a Filamentous Fungus in Complex with a Classical Nuclear Localization Signal.

PubMed

Bernardes, Natalia E; Takeda, Agnes A S; Dreyer, Thiago R; Freitas, Fernanda Z; Bertolini, Maria Célia; Fontes, Marcos R M

2015-01-01

Neurospora crassa is a filamentous fungus that has been extensively studied as a model organism for eukaryotic biology, providing fundamental insights into cellular processes such as cell signaling, growth and differentiation. To advance in the study of this multicellular organism, an understanding of the specific mechanisms for protein transport into the cell nucleus is essential. Importin-α (Imp-α) is the receptor for cargo proteins that contain specific nuclear localization signals (NLSs) that play a key role in the classical nuclear import pathway. Structures of Imp-α from different organisms (yeast, rice, mouse, and human) have been determined, revealing that this receptor possesses a conserved structural scaffold. However, recent studies have demonstrated that the Impα mechanism of action may vary significantly for different organisms or for different isoforms from the same organism. Therefore, structural, functional, and biophysical characterization of different Impα proteins is necessary to understand the selectivity of nuclear transport. Here, we determined the first crystal structure of an Impα from a filamentous fungus which is also the highest resolution Impα structure already solved to date (1.75 Å). In addition, we performed calorimetric analysis to determine the affinity and thermodynamic parameters of the interaction between Imp-α and the classical SV40 NLS peptide. The comparison of these data with previous studies on Impα proteins led us to demonstrate that N. crassa Imp-α possess specific features that are distinct from mammalian Imp-α but exhibit important similarities to rice Imp-α, particularly at the minor NLS binding site.

Structural Studies of Bacterial Enzymes and their Relation to Antibiotic Resistance Mechanisms - Final Paper

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

Maltz, Lauren

By using protein crystallography and X-ray diffraction, structures of bacterial enzymes were solved to gain a better understanding of how enzymatic modification acts as an antibacterial resistance mechanism. Aminoglycoside phosphotransferases (APHs) are one of three aminoglycoside modifying enzymes that confer resistance to the aminoglycoside antibiotics via enzymatic modification, rendering many drugs obsolete. Specifically, the APH(2”) family vary in their substrate specificities and also in their preference for the phosphate donor (ADP versus GDP). By solving the structures of members of the APH(2”) family of enzymes, we can see how domain movements are important to their substrate specificity. Our structure ofmore » the ternary complex of APH(2”)-IIIa with GDP and kanamycin, when compared to the known structures of APH(2”)-IVa, reveals that there are real physical differences between these two enzymes, a structural finding that explains why the two enzymes differ in their preferences for certain aminoglycosides. Another important group of bacterial resistance enzymes are the Class D β- lactamases. Oxacillinase carbapenemases (OXAs) are part of this enzyme class and have begun to confer resistance to ‘last resort’ drugs, most notably carbapenems. Our structure of OXA-143 shows that the conformational flexibility of a conserved hydrophobic residue in the active site (Val130) serves to control the entry of a transient water molecule responsible for a key step in the enzyme’s mechanism. Our results provide insight into the structural mechanisms of these two different enzymes« less

Sodium Peroxide Dihydrate or Sodium Superoxide: The Importance of the Cell Configuration for Sodium-Oxygen Batteries

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

Bi, Xuanxuan; Wang, Rongyue; Ma, Lu

In sodium–oxygen (Na–O2) batteries, multiple discharge products have been observed by different research groups. Given the fact that different materials, gas supplies, and cell configurations are used by different groups, it is a great challenge to draw a clear conclusion on the formation of the different products. Here, two different cell setups are used to investigate the cell chemistries of Na–O2 batteries. With the same materials and gas supplies, a peroxide-based product is observed in a glass chamber cell and a superoxide-based product is observed in a stainless-steel cell. Ex situ high-energy X-ray diffraction (HEXRD) and Raman spectroscopy are performedmore » to investigate the structure and composition of the product. In addition, in situ XRD is used to investigate the structure evolution of the peroxide-based product. The findings highlight the importance of the cell design and emphasize the critical environment of the formation of the discharge products of Na–O2 batteries.« less

Relation between native ensembles and experimental structures of proteins

PubMed Central

Best, Robert B.; Lindorff-Larsen, Kresten; DePristo, Mark A.; Vendruscolo, Michele

2006-01-01

Different experimental structures of the same protein or of proteins with high sequence similarity contain many small variations. Here we construct ensembles of “high-sequence similarity Protein Data Bank” (HSP) structures and consider the extent to which such ensembles represent the structural heterogeneity of the native state in solution. We find that different NMR measurements probing structure and dynamics of given proteins in solution, including order parameters, scalar couplings, and residual dipolar couplings, are remarkably well reproduced by their respective high-sequence similarity Protein Data Bank ensembles; moreover, we show that the effects of uncertainties in structure determination are insufficient to explain the results. These results highlight the importance of accounting for native-state protein dynamics in making comparisons with ensemble-averaged experimental data and suggest that even a modest number of structures of a protein determined under different conditions, or with small variations in sequence, capture a representative subset of the true native-state ensemble. PMID:16829580

A comparison of the capital structures of nonprofit and proprietary health care organizations.

PubMed

Trussel, John

2012-01-01

The relative amount of debt used by an organization is an important determination of the organization's likelihood of financial problems and its cost of capital. This study addresses whether or not there are any differences between proprietary and nonprofit health care organizations in terms of capital structure. Controlling for profitability, risk, growth, and size, analysis of covariance is used to determine whether or not proprietary and nonprofit health care organizations use the same amount of leverage in their capital structures. The results indicate that there is no difference in the amount of leverage between the two institutional types. Although nonprofit and proprietary organizations have unique financing mechanisms, these differences do not impact the relative amount of debt and equity in their capital structures.

Prosody Production and Perception with Conversational Speech

ERIC Educational Resources Information Center

Mo, Yoonsook

2010-01-01

Speech utterances are more than the linear concatenation of individual phonemes or words. They are organized by prosodic structures comprising phonological units of different sizes (e.g., syllable, foot, word, and phrase) and the prominence relations among them. As the linguistic structure of spoken languages, prosody serves an important function…

Structure, and culture of the gut microbiome of the Mormon cricket Anabrus simplex

USDA-ARS?s Scientific Manuscript database

The gut microbiome of insects plays an important role in their ecology and evolution, participating in nutrient acquisition, immunity, and behavior. Microbial community structure within the gut is heavily influenced by differences among gut regions in morphology and physiology, which determine the n...

Typography, Color, and Information Structure.

ERIC Educational Resources Information Center

Keyes, Elizabeth

1993-01-01

Focuses on how typography and color complement and differ from each other in signaling an underlying content structure; the synergism between typography, color, and page layout (use of white space) that aids audience understanding and use; and the characteristics of typography and of color that are most important in these contexts. (SR)

LIBP-Pred: web server for lipid binding proteins using structural network parameters; PDB mining of human cancer biomarkers and drug targets in parasites and bacteria.

PubMed

González-Díaz, Humberto; Munteanu, Cristian R; Postelnicu, Lucian; Prado-Prado, Francisco; Gestal, Marcos; Pazos, Alejandro

2012-03-01

Lipid-Binding Proteins (LIBPs) or Fatty Acid-Binding Proteins (FABPs) play an important role in many diseases such as different types of cancer, kidney injury, atherosclerosis, diabetes, intestinal ischemia and parasitic infections. Thus, the computational methods that can predict LIBPs based on 3D structure parameters became a goal of major importance for drug-target discovery, vaccine design and biomarker selection. In addition, the Protein Data Bank (PDB) contains 3000+ protein 3D structures with unknown function. This list, as well as new experimental outcomes in proteomics research, is a very interesting source to discover relevant proteins, including LIBPs. However, to the best of our knowledge, there are no general models to predict new LIBPs based on 3D structures. We developed new Quantitative Structure-Activity Relationship (QSAR) models based on 3D electrostatic parameters of 1801 different proteins, including 801 LIBPs. We calculated these electrostatic parameters with the MARCH-INSIDE software and they correspond to the entire protein or to specific protein regions named core, inner, middle, and surface. We used these parameters as inputs to develop a simple Linear Discriminant Analysis (LDA) classifier to discriminate 3D structure of LIBPs from other proteins. We implemented this predictor in the web server named LIBP-Pred, freely available at , along with other important web servers of the Bio-AIMS portal. The users can carry out an automatic retrieval of protein structures from PDB or upload their custom protein structural models from their disk created with LOMETS server. We demonstrated the PDB mining option performing a predictive study of 2000+ proteins with unknown function. Interesting results regarding the discovery of new Cancer Biomarkers in humans or drug targets in parasites have been discussed here in this sense.

Social structure of Facebook networks

NASA Astrophysics Data System (ADS)

Traud, Amanda L.; Mucha, Peter J.; Porter, Mason A.

2012-08-01

We study the social structure of Facebook “friendship” networks at one hundred American colleges and universities at a single point in time, and we examine the roles of user attributes-gender, class year, major, high school, and residence-at these institutions. We investigate the influence of common attributes at the dyad level in terms of assortativity coefficients and regression models. We then examine larger-scale groupings by detecting communities algorithmically and comparing them to network partitions based on user characteristics. We thereby examine the relative importance of different characteristics at different institutions, finding for example that common high school is more important to the social organization of large institutions and that the importance of common major varies significantly between institutions. Our calculations illustrate how microscopic and macroscopic perspectives give complementary insights on the social organization at universities and suggest future studies to investigate such phenomena further.

Spatial variability in fish species assemblage and community structure in four subtropical lagoons of the Okavango Delta, Botswana

NASA Astrophysics Data System (ADS)

Mosepele, K.; Mosepele, B.; Bokhutlo, T.; Amutenya, K.

The species assemblage and community structure of four lagoons was assessed through time series data collected between 2001 and 2005 in the Okavango Delta. The main aim of this study was to evaluate the importance of lagoons as fish habitats in the Delta. Therefore, this study assessed the importance of these habitats through determining fish species diversity, composition, relative abundance, and community structure between the lagoons. Forty six species belonging to 11 families and five orders were collected over the study period. Main results showed that Cichlidae was the most important family and had the highest species richness in the lagoons. Significant differences ( p < 0.05) were observed in species richness, faunal composition, and diversity among some of the lagoons. Moreover, there were also variations in species composition, and also significant differences in mean length and weight of some selected fish species in the four lagoons. This study showed that lagoons are important repositories of food fish to local communities. Moreover, a management of the fish stocks based on restricting fishing in some lagoons as protected areas is not feasible because of these significant differences in species assemblages between lagoons. Furthermore, lagoons are subject to multiple where most of the lodges are constructed, which makes subsequently makes them vulnerable to pollution. Therefore, the integrity of lagoon habitats needs to be maintained so that their ecosystem functioning (i.e. fish repositories) is maintained.

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.

Modelling and enhanced molecular dynamics to steer structure-based drug discovery.

PubMed

Kalyaanamoorthy, Subha; Chen, Yi-Ping Phoebe

2014-05-01

The ever-increasing gap between the availabilities of the genome sequences and the crystal structures of proteins remains one of the significant challenges to the modern drug discovery efforts. The knowledge of structure-dynamics-functionalities of proteins is important in order to understand several key aspects of structure-based drug discovery, such as drug-protein interactions, drug binding and unbinding mechanisms and protein-protein interactions. This review presents a brief overview on the different state of the art computational approaches that are applied for protein structure modelling and molecular dynamics simulations of biological systems. We give an essence of how different enhanced sampling molecular dynamics approaches, together with regular molecular dynamics methods, assist in steering the structure based drug discovery processes. Copyright © 2013 Elsevier Ltd. All rights reserved.

Describing content in middle school science curricula

NASA Astrophysics Data System (ADS)

Schwarz-Ballard, Jennifer A.

As researchers and designers, we intuitively recognize differences between curricula and describe them in terms of design strategy: project-based, laboratory-based, modular, traditional, and textbook, among others. We assume that practitioners recognize the differences in how each requires that students use knowledge, however these intuitive differences have not been captured or systematically described by the existing languages for describing learning goals. In this dissertation I argue that we need new ways of capturing relationships among elements of content, and propose a theory that describes some of the important differences in how students reason in differently designed curricula and activities. Educational researchers and curriculum designers have taken a variety of approaches to laying out learning goals for science. Through an analysis of existing descriptions of learning goals I argue that to describe differences in the understanding students come away with, they need to (1) be specific about the form of knowledge, (2) incorporate both the processes through which knowledge is used and its form, and (3) capture content development across a curriculum. To show the value of inquiry curricula, learning goals need to incorporate distinctions among the variety of ways we ask students to use knowledge. Here I propose the Epistemic Structures Framework as one way to describe differences in students reasoning that are not captured by existing descriptions of learning goals. The usefulness of the Epistemic Structures framework is demonstrated in the four curriculum case study examples in Part II of this work. The curricula in the case studies represent a range of content coverage, curriculum structure, and design rationale. They serve both to illustrate the Epistemic Structures analysis process and make the case that it does in fact describe learning goals in a way that captures important differences in students reasoning in differently designed curricula. Describing learning goals in terms of Epistemic Structures provides one way to define what we mean when we talk about "project-based" curricula and demonstrate its "value added" to educators, administrators and policy makers.

Evaluation of Structure, Chaperone-Like Activity and Allergenicity of Reduced Glycated Adduct of Bovine β-casein.

PubMed

Yousefi, Reza; Ferdowsi, Leila; Tavaf, Zohreh; Sadeghian, Tanaz; Tamaddon, Ali M; Moghtaderi, Mozhgan; Pourpak, Zahra

2017-01-01

Milk has a potent reducing environment with an important quantity of sugar levels. In the current study β-casein was glycated in the presence of D-glucose and sodium cyanoborohydride as a reducing agent. Then, the reduced glucitol adduct of β-casein was used for the structural and functional analyses using different spectroscopic techniques. The results of fluorescence and far ultraviolet circular dichroism assessments suggest important structural alteration upon non-enzymatic glycation of β-casein. In addition, the chaperone activity, micellization properties and antioxidant activity of this protein were altered upon glucose modification. Also, as a result of reduced glycation, the allergenicity profile of this protein remained largely unchanged. Additional to its energetic and nutritional values, β-casein has important functional properties. The native structure of this protein is important to perform accurately its biological functions. Non-enzymatic glycation under reducing state was capable to alter both structural and functional aspects of β-casein. Due to effective reducing environment and significant quantity of reducing sugar of human milk, similar structural and functional alterations are most likely to occur upon reducing glycation of β-casein in vivo. Also, these changes might be even intensified during chronic hyperglycemia in diabetic mothers. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Impact load-induced micro-structural damage and micro-structure associated mechanical response of concrete made with different surface roughness and porosity aggregates

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

Erdem, Savas, E-mail: evxse1@nottingham.ac.uk; Dawson, Andrew Robert; Thom, Nicholas Howard

2012-02-15

The relationship between the nature of micro damage under impact loading and changes in mechanical behavior associated with different microstructures is studied for concretes made with two different coarse aggregates having significant differences mainly in roughness and porosity - sintered fly ash and uncrushed gravel. A range of techniques including X-ray diffraction, digital image analysis, mercury porosimetry, X-ray computed tomography, laser surface profilometry and scanning electron microscopy were used to characterize the aggregates and micro-structures. The concrete prepared with lightweight aggregates was stronger in compression than the gravel aggregate concrete due to enhanced hydration as a result of internal curing.more » In the lightweight concrete, it was deduced that an inhomogeneous micro-structure led to strain incompatibilities and consequent localized stress concentrations in the mix, leading to accelerated failure. The pore structure, compressibility, and surface texture of the aggregates are of paramount importance for the micro-cracking growth.« less

Interactions of Multimodal Ligands with Proteins: Insights into Selectivity Using Molecular Dynamics Simulations.

PubMed

Parimal, Siddharth; Garde, Shekhar; Cramer, Steven M

2015-07-14

Fundamental understanding of protein-ligand interactions is important to the development of efficient bioseparations in multimodal chromatography. Here we employ molecular dynamics (MD) simulations to investigate the interactions of three different proteins--ubiquitin, cytochrome C, and α-chymotrypsinogen A, sampling a range of charge from +1e to +9e--with two multimodal chromatographic ligands containing similar chemical moieties--aromatic, carboxyl, and amide--in different structural arrangements. We use a spherical harmonic expansion to analyze ligand and individual moiety density profiles around the proteins. We find that the Capto MMC ligand, which contains an additional aliphatic group, displays stronger interactions than Nuvia CPrime ligand with all three proteins. Studying the ligand densities at the moiety level suggests that hydrophobic interactions play a major role in determining the locations of high ligand densities. Finally, the greater structural flexibility of the Capto MMC ligand compared to that of the Nuvia cPrime ligand allows for stronger structural complementarity and enables stronger hydrophobic interactions. These subtle and not-so-subtle differences in binding affinities and modalities for multimodal ligands can result in significantly different binding behavior towards proteins with important implications for bioprocessing.

Do Individual Differences in Children's Curiosity Relate to Their Inquiry-Based Learning?

ERIC Educational Resources Information Center

van Schijndel, Tessa J. P.; Jansen, Brenda R. J.; Raijmakers, Maartje E. J.

2018-01-01

This study investigates how individual differences in 7- to 9-year-olds' curiosity relate to the inquiry-learning process and outcomes in environments differing in structure. The focus on curiosity as individual differences variable was motivated by the importance of curiosity in science education, and uncertainty being central to both the…

High resolution structure of cleaved Serpin 42 Da from Drosophila melanogaster.

PubMed

Ellisdon, Andrew M; Zhang, Qingwei; Henstridge, Michelle A; Johnson, Travis K; Warr, Coral G; Law, Ruby Hp; Whisstock, James C

2014-04-24

The Drosophila melanogaster Serpin 42 Da gene (previously Serpin 4) encodes a serine protease inhibitor that is capable of remarkable functional diversity through the alternative splicing of four different reactive centre loop exons. Eight protein isoforms of Serpin 42 Da have been identified to date, targeting the protease inhibitor to both different proteases and cellular locations. Biochemical and genetic studies suggest that Serpin 42 Da inhibits target proteases through the classical serpin 'suicide' inhibition mechanism, however the crystal structure of a representative Serpin 42 Da isoform remains to be determined. We report two high-resolution crystal structures of Serpin 42 Da representing the A/B isoforms in the cleaved conformation, belonging to two different space-groups and diffracting to 1.7 Å and 1.8 Å. Structural analysis reveals the archetypal serpin fold, with the major elements of secondary structure displaying significant homology to the vertebrate serpin, neuroserpin. Key residues known to have central roles in the serpin inhibitory mechanism are conserved in both the hinge and shutter regions of Serpin 42 Da. Furthermore, these structures identify important conserved interactions that appear to be of crucial importance in allowing the Serpin 42 Da fold to act as a versatile template for multiple reactive centre loops that have different sequences and protease specificities. In combination with previous biochemical and genetic studies, these structures confirm for the first time that the Serpin 42 Da isoforms are typical inhibitory serpin family members with the conserved serpin fold and inhibitory mechanism. Additionally, these data reveal the remarkable structural plasticity of serpins, whereby the basic fold is harnessed as a template for inhibition of a large spectrum of proteases by reactive centre loop exon 'switching'. This is the first structure of a Drosophila serpin reported to date, and will provide a platform for future mutational studies in Drosophila to ascertain the functional role of each of the Serpin 42 Da isoforms.

DSSPcont: continuous secondary structure assignments for proteins

PubMed Central

Carter, Phil; Andersen, Claus A. F.; Rost, Burkhard

2003-01-01

The DSSP program automatically assigns the secondary structure for each residue from the three-dimensional co-ordinates of a protein structure to one of eight states. However, discrete assignments are incomplete in that they cannot capture the continuum of thermal fluctuations. Therefore, DSSPcont (http://cubic.bioc.columbia.edu/services/DSSPcont) introduces a continuous assignment of secondary structure that replaces ‘static’ by ‘dynamic’ states. Technically, the continuum results from calculating weighted averages over 10 discrete DSSP assignments with different hydrogen bond thresholds. A DSSPcont assignment for a particular residue is a percentage likelihood of eight secondary structure states, derived from a weighted average of the ten DSSP assignments. The continuous assignments have two important features: (i) they reflect the structural variations due to thermal fluctuations as detected by NMR spectroscopy; and (ii) they reproduce the structural variation between many NMR models from one single model. Therefore, functionally important variation can be extracted from a single X-ray structure using the continuous assignment procedure. PMID:12824310

Surface relief model for photopolymers without cover plating.

PubMed

Gallego, S; Márquez, A; Ortuño, M; Francés, J; Marini, S; Beléndez, A; Pascual, I

2011-05-23

Relief surface changes provide interesting possibilities for storing diffractive optical elements on photopolymers and are an important source of information to characterize and understand the material behaviour. In this paper we present a 3-dimensional model based on direct measurements of parameters to predict the relief structures generated on the material. This model is successfully applied to different photopolymers with different values of monomer diffusion. The importance of monomer diffusion in depth is also discussed.

Roles of glutamates and metal ions in a rationally designed nitric oxide reductase based on myoglobin

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

Lin, Y.W.; Robinson, H.; Yeung, N.

2010-05-11

A structural and functional model of bacterial nitric oxide reductase (NOR) has been designed by introducing two glutamates (Glu) and three histidines (His) in sperm whale myoglobin. X-ray structural data indicate that the three His and one Glu (V68E) residues bind iron, mimicking the putative FeB site in NOR, while the second Glu (I107E) interacts with a water molecule and forms a hydrogen bonding network in the designed protein. Unlike the first Glu (V68E), which lowered the heme reduction potential by {approx}110 mV, the second Glu has little effect on the heme potential, suggesting that the negatively charged Glu hasmore » a different role in redox tuning. More importantly, introducing the second Glu resulted in a {approx}100% increase in NOR activity, suggesting the importance of a hydrogen bonding network in facilitating proton delivery during NOR reactivity. In addition, EPR and X-ray structural studies indicate that the designed protein binds iron, copper, or zinc in the FeB site, each with different effects on the structures and NOR activities, suggesting that both redox activity and an intermediate five-coordinate heme-NO species are important for high NOR activity. The designed protein offers an excellent model for NOR and demonstrates the power of using designed proteins as a simpler and more well-defined system to address important chemical and biological issues.« less

Roles of Glutamates and Metal ions in a Rationally Designed Nitric Oxide Reductase Based on Myoglobin

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

Y Lin; N Yeung; Y Gao

2011-12-31

A structural and functional model of bacterial nitric oxide reductase (NOR) has been designed by introducing two glutamates (Glu) and three histidines (His) in sperm whale myoglobin. X-ray structural data indicate that the three His and one Glu (V68E) residues bind iron, mimicking the putative FeB site in NOR, while the second Glu (I107E) interacts with a water molecule and forms a hydrogen bonding network in the designed protein. Unlike the first Glu (V68E), which lowered the heme reduction potential by {approx}110 mV, the second Glu has little effect on the heme potential, suggesting that the negatively charged Glu hasmore » a different role in redox tuning. More importantly, introducing the second Glu resulted in a {approx}100% increase in NOR activity, suggesting the importance of a hydrogen bonding network in facilitating proton delivery during NOR reactivity. In addition, EPR and X-ray structural studies indicate that the designed protein binds iron, copper, or zinc in the FeB site, each with different effects on the structures and NOR activities, suggesting that both redox activity and an intermediate five-coordinate heme-NO species are important for high NOR activity. The designed protein offers an excellent model for NOR and demonstrates the power of using designed proteins as a simpler and more well-defined system to address important chemical and biological issues.« less

Identification of kin structure among Guam rail founders: a comparison of pedigrees and DNA profiles

USGS Publications Warehouse

Haig, Susan M.; Ballou, J.D.; Casna, N.J.

1994-01-01

Kin structure among founders can have a significant effect on subsequent population structure. Here we use the correlation between DNA profile similarity and relatedness calculated from pedigrees to test hypotheses regarding kin structure among founders to the captive Guam rail (Rallus owstoni) population. Five different pedigrees were generated under the following hypotheses: (i) founders are unrelated; (ii) founders are unrelated except for same-nest chicks; (iii) founders from the same major site are siblings; (iv) founders from the same local site are siblings; and (v) founders are related as defined by a UPGMA cluster analysis of DNA similarity data. Relatedness values from pedigrees 1, 2 and 5 had the highest correlation with DNA similarity but the correlation between relatedness and similarity were not significantly different among pedigrees. Pedigree 5 resulted in the highest correlation overall when using only relatedness values that changed as a result of different founder hypotheses. Thus, founders were assigned relatedness based on pedigree 5 because it had the highest correlations with DNA similarity, was the most conservative approach, and incorporated all field data. The analyses indicated that estimating relatedness using DNA profiles remains problematic, therefore we compared mean kinship, a measure of genetic importance, with mean DNA profile similarity to determine if genetic importance among individuals could be determined via use of DNA profiles alone. The significant correlation suggests this method may provide more information about population structure than was previously thought. Thus, DNA profiles can provide a reasonable explanation for founder relatedness and mean DNA profile similarity may be helpful in determining relative genetic importance of individuals when detailed pedigrees are absent.

A fine structure genetic analysis evaluating ecoregional adaptability of a Bos taurus breed (Hereford)

PubMed Central

Krehbiel, B.; Ericsson, S. A.; Wilson, C.; Caetano, A. R.; Paiva, S. R.

2017-01-01

Ecoregional differences contribute to genetic environmental interactions and impact animal performance. These differences may become more important under climate change scenarios. Utilizing genetic diversity within a species to address such problems has not been fully explored. In this study Hereford cattle were genotyped with 50K Bead Chip or 770K Bovine Bead Chip to test the existence of genetic structure in five U.S. ecoregions characterized by precipitation, temperature and humidity and designated: cool arid (CA), cool humid (CH), transition zone (TZ), warm arid (WA), and warm humid (WH). SNP data were analyzed in three sequential analyses. Broad genetic structure was evaluated with STRUCTURE, and ADMIXTURE software using 14,312 SNPs after passing quality control variables. The second analysis was performed using principal coordinate analysis with 66 Tag SNPs associated in the literature with various aspects of environmental stressors (e.g., heat tolerance) or production (e.g., milk production). In the third analysis TreeSelect was used with the 66 SNPs to evaluate if ecoregional allelic frequencies deviated from a central frequency and by so doing are indicative of directional selection. The three analyses suggested subpopulation structures associated with ecoregions from where animals were derived. ADMIXTURE and PCA results illustrated the importance of temperature and humidity and confirm subpopulation assignments. Comparisons of allele frequencies with TreeSelect showed ecoregion differences, in particular the divergence between arid and humid regions. Patterns of genetic variability obtained by medium and high density SNP chips can be used to acclimatize a temperately derived breed to various ecoregions. As climate change becomes an important factor in cattle production, this study should be used as a proof of concept to review future breeding and conservation schemes aimed at adaptation to climatic events. PMID:28459870

Small differences in amylopectin fine structure may explain large functional differences of starch.

PubMed

Bertoft, Eric; Annor, George A; Shen, Xinyu; Rumpagaporn, Pinthip; Seetharaman, Koushik; Hamaker, Bruce R

2016-04-20

Four amylose-free waxy rice starches were found to give rise to gels with clearly different morphology after storage for seven days at 4°C. The thermal and rheological properties of these gels were also different. This was remarkable in light of the subtle differences in the molecular structure of the amylopectin in the samples. Addition of iodine to the amylopectin samples suggested that not only external chains, but also the internal chains of amylopectin, could form helical inclusion complexes. It is suggested that these internal helical segments participate in the retrogradation of amylopectin, thereby stabilising the gels through double helical structures with external chains of adjacent molecules. Albeit few in number, such interactions appear to have important influences on starch functional properties. Copyright © 2015 Elsevier Ltd. All rights reserved.

Comparison of genetic diversity and population structure between two Schistosoma japonicum isolates--the field and the laboratory.

PubMed

Bian, Chao-Rong; Gao, Yu-Meng; Lamberton, Poppy H L; Lu, Da-Bing

2015-06-01

Schistosomiasis japonicum is one of the most important human parasitic diseases, and a number of studies have recently elucidated the difference in biological characteristics of S. japonicum among different parasite isolates, for example, between the field and the laboratory isolates. Therefore, the understanding of underlying genetic mechanism is of both theoretical and practical importance. In this study, we used six microsatellite markers to assess genetic diversity, population structure, and the bottleneck effect (a sharp reduction in population size) of two parasite populations, one field and one laboratory. A total of 136 S. japonicum cercariae from the field and 86 from the laboratory, which were genetically unique within single snails, were analyzed. The results showed bigger numbers of alleles and higher allelic richness in the field parasite population than in the laboratory indicating lower genetic diversity in the laboratory parasites. A bottleneck effect was detected in the laboratory population. When the field and laboratory isolates were combined, there was a clear distinction between two parasite populations using the software Structure. These genetic differences may partially explain the previously observed contrasted biological traits.

Biodiversity in canopy-forming algae: Structure and spatial variability of the Mediterranean Cystoseira assemblages

NASA Astrophysics Data System (ADS)

Piazzi, L.; Bonaviri, C.; Castelli, A.; Ceccherelli, G.; Costa, G.; Curini-Galletti, M.; Langeneck, J.; Manconi, R.; Montefalcone, M.; Pipitone, C.; Rosso, A.; Pinna, S.

2018-07-01

In the Mediterranean Sea, Cystoseira species are the most important canopy-forming algae in shallow rocky bottoms, hosting high biodiverse sessile and mobile communities. A large-scale study has been carried out to investigate the structure of the Cystoseira-dominated assemblages at different spatial scales and to test the hypotheses that alpha and beta diversity of the assemblages, the abundance and the structure of epiphytic macroalgae, epilithic macroalgae, sessile macroinvertebrates and mobile macroinvertebrates associated to Cystoseira beds changed among scales. A hierarchical sampling design in a total of five sites across the Mediterranean Sea (Croatia, Montenegro, Sardinia, Tuscany and Balearic Islands) was used. A total of 597 taxa associated to Cystoseira beds were identified with a mean number per sample ranging between 141.1 ± 6.6 (Tuscany) and 173.9 ± 8.5(Sardinia). A high variability at small (among samples) and large (among sites) scale was generally highlighted, but the studied assemblages showed different patterns of spatial variability. The relative importance of the different scales of spatial variability should be considered to optimize sampling designs and propose monitoring plans of this habitat.

Identifying protein β-turns with vibrational Raman optical activity.

PubMed

Weymuth, Thomas; Jacob, Christoph R; Reiher, Markus

2011-04-18

β-turns belong to the most important secondary structure elements in proteins. On the basis of density functional calculations, vibrational Raman optical activity signatures of different types of β-turns are established and compared as well as related to other signatures proposed in the literature earlier. Our findings indicate that there are much more characteristic ROA signals of β-turns than have been hitherto suggested. These suggested signatures are, however, found to be valid for the most important type of β-turns. Moreover, we compare the influence of different amino acid side chains on these signatures and investigate the discrimination of β-turns from other secondary structure elements, namely α- and 3(10)-helices. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quantification of network structural dissimilarities.

PubMed

Schieber, Tiago A; Carpi, Laura; Díaz-Guilera, Albert; Pardalos, Panos M; Masoller, Cristina; Ravetti, Martín G

2017-01-09

Identifying and quantifying dissimilarities among graphs is a fundamental and challenging problem of practical importance in many fields of science. Current methods of network comparison are limited to extract only partial information or are computationally very demanding. Here we propose an efficient and precise measure for network comparison, which is based on quantifying differences among distance probability distributions extracted from the networks. Extensive experiments on synthetic and real-world networks show that this measure returns non-zero values only when the graphs are non-isomorphic. Most importantly, the measure proposed here can identify and quantify structural topological differences that have a practical impact on the information flow through the network, such as the presence or absence of critical links that connect or disconnect connected components.

Strategies of offspring investment and dispersal in a spatially structured environment: a theoretical study using ants.

PubMed

Cronin, Adam L; Loeuille, Nicolas; Monnin, Thibaud

2016-02-05

Offspring investment strategies vary markedly between and within taxa, and much of this variation is thought to stem from the trade-off between offspring size and number. While producing larger offspring can increase their competitive ability, this often comes at a cost to their colonization ability. This competition-colonization trade-off (CCTO) is thought to be an important mechanism supporting coexistence of alternative strategies in a wide range of taxa. However, the relative importance of an alternative and possibly synergistic mechanism-spatial structuring of the environment-remains the topic of some debate. In this study, we explore the influence of these mechanisms on metacommunity structure using an agent-based model built around variable life-history traits. Our model combines explicit resource competition and spatial dynamics, allowing us to tease-apart the influence of, and explore the interaction between, the CCTO and the spatial structure of the environment. We test our model using two reproductive strategies which represent extremes of the CCTO and are common in ants. Our simulations show that colonisers outperform competitors in environments subject to higher temporal and spatial heterogeneity and are favoured when agents mature late and invest heavily in reproduction, whereas competitors dominate in low-disturbance, high resource environments and when maintenance costs are low. Varying life-history parameters has a marked influence on coexistence conditions and yields evolutionary stable strategies for both modes of reproduction. Nonetheless, we show that these strategies can coexist over a wide range of life-history and environmental parameter values, and that coexistence can in most cases be explained by a CCTO. By explicitly considering space, we are also able to demonstrate the importance of the interaction between dispersal and landscape structure. The CCTO permits species employing different reproductive strategies to coexist over a wide range of life-history and environmental parameters, and is likely to be an important factor in structuring ant communities. Our consideration of space highlights the importance of dispersal, which can limit the success of low-dispersers through kin competition, and enhance coexistence conditions for different strategies in spatially structured environments.

Water dynamics in glass ionomer cements

NASA Astrophysics Data System (ADS)

Berg, M. C.; Jacobsen, J.; Momsen, N. C. R.; Benetti, A. R.; Telling, M. T. F.; Seydel, T.; Bordallo, H. N.

2016-07-01

Glass ionomer cements (GIC) are an alternative for preventive dentistry. However, these dental cements are complex systems where important motions related to the different states of the hydrogen atoms evolve in a confined porous structure. In this paper, we studied the water dynamics of two different liquids used to prepare either conventional or resin-modified glass ionomer cement. By combining thermal analysis with neutron scattering data we were able to relate the water structure in the liquids to the materials properties.

A Mössbauer spectroscopic study of an industrial catalyst for dehydrogenation of etylbenzene to styrene

NASA Astrophysics Data System (ADS)

Jiang, K. Y.; Fan, Q.; Zhao, Z. J.; Mao, L. S.; Yang, X. L.

2006-01-01

Iron oxide catalyst with spinel structure used for dehydrogenation of ethylbenzene is one kind of important catalyst in petrochemical industry. In this work several series of industrial catalyst were prepared with different components and different manufacturing processes. Mössbauer Spectroscopy has been used to determine the optimal components and the better manufacturing process for spinel structure formation. The results may prove useful for producing the industrial dehydrogenation catalyst with better catalytic property.

The Role of the β5-α11 Loop in the Active-Site Dynamics of Acylated Penicillin-Binding Protein A from Mycobacterium tuberculosis

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

Fedarovich, Alena; Nicholas, Robert A.; Davies, Christopher

Penicillin-binding protein A (PBPA) is a class B penicillin-binding protein that is important for cell division in Mycobacterium tuberculosis. We have determined a second crystal structure of PBPA in apo form and compared it with an earlier structure of apoenzyme. Significant structural differences in the active site region are apparent, including increased ordering of a β-hairpin loop and a shift of the SxN active site motif such that it now occupies a position that appears catalytically competent. Using two assays, including one that uses the intrinsic fluorescence of a tryptophan residue, we have also measured the second-order acylation rate constantsmore » for the antibiotics imipenem, penicillin G, and ceftriaxone. Of these, imipenem, which has demonstrable anti-tubercular activity, shows the highest acylation efficiency. Crystal structures of PBPA in complex with the same antibiotics were also determined, and all show conformational differences in the β5–α11 loop near the active site, but these differ for each β-lactam and also for each of the two molecules in the crystallographic asymmetric unit. Overall, these data reveal the β5–α11 loop of PBPA as a flexible region that appears important for acylation and provide further evidence that penicillin-binding proteins in apo form can occupy different conformational states.« less

Characterisation of different polymorphs of tris(8-hydroxyquinolinato)aluminium(III) using solid-state NMR and DFT calculations

PubMed Central

Goswami, Mithun; Nayak, Pabitra K; Periasamy, N; Madhu, PK

2009-01-01

Background Organic light emitting devices (OLED) are becoming important and characterisation of them, in terms of structure, charge distribution, and intermolecular interactions, is important. Tris(8-hydroxyquinolinato)-aluminium(III), known as Alq3, an organomettalic complex has become a reference material of great importance in OLED. It is important to elucidate the structural details of Alq3 in its various isomeric and solvated forms. Solid-state nuclear magnetic resonance (NMR) is a useful tool for this which can also complement the information obtained with X-ray diffraction studies. Results We report here 27Al one-dimensional (1D) and two-dimensional (2D) multiple-quantum magic-angle spinning (MQMAS) NMR studies of the meridional (α-phase) and the facial (δ-phase) isomeric forms of Alq3. Quadrupolar parameters are estimated from the 1D spectra under MAS and anisotropic slices of the 2D spectra and also calculated using DFT (density functional theory) quantum-chemical calculations. We have also studied solvated phase of Alq3 containing ethanol in its lattice. We show that both the XRD patterns and the quadrupolar parameters of the solvated phase are different from both the α-phase and the δ-phase, although the fluorescence emission shows no substantial difference between the α-phase and the solvated phase. Moreover, we have shown that after the removal of ethanol from the matrix the solvated Alq3 has similar XRD patterns and quadrupolar parameters to that of the α-phase. Conclusion The 2D MQMAS experiments have shown that all the different modifications of Alq3 have 27Al in single unique crystallographic site. The quadrupolar parameters predicted using the DFT calculation under the isodensity polarisable continuum model resemble closely the experimentally obtained values. The solvated phase of Alq3 containing ethanol has structural difference from the α-phase of Alq3 (containing meridional isomer) from the solid-state NMR studies. Solid-state NMR can hence be used as an effective complementary tool to XRD for characterisation and structural elucidation. PMID:19900275

Characterisation of different polymorphs of tris(8-hydroxyquinolinato)aluminium(III) using solid-state NMR and DFT calculations.

PubMed

Goswami, Mithun; Nayak, Pabitra K; Periasamy, N; Madhu, P K

2009-11-09

Organic light emitting devices (OLED) are becoming important and characterisation of them, in terms of structure, charge distribution, and intermolecular interactions, is important. Tris(8-hydroxyquinolinato)-aluminium(III), known as Alq3, an organomettalic complex has become a reference material of great importance in OLED. It is important to elucidate the structural details of Alq3 in its various isomeric and solvated forms. Solid-state nuclear magnetic resonance (NMR) is a useful tool for this which can also complement the information obtained with X-ray diffraction studies. We report here 27Al one-dimensional (1D) and two-dimensional (2D) multiple-quantum magic-angle spinning (MQMAS) NMR studies of the meridional (alpha-phase) and the facial (delta-phase) isomeric forms of Alq3. Quadrupolar parameters are estimated from the 1D spectra under MAS and anisotropic slices of the 2D spectra and also calculated using DFT (density functional theory) quantum-chemical calculations. We have also studied solvated phase of Alq3 containing ethanol in its lattice. We show that both the XRD patterns and the quadrupolar parameters of the solvated phase are different from both the alpha-phase and the delta-phase, although the fluorescence emission shows no substantial difference between the alpha-phase and the solvated phase. Moreover, we have shown that after the removal of ethanol from the matrix the solvated Alq3 has similar XRD patterns and quadrupolar parameters to that of the alpha-phase. The 2D MQMAS experiments have shown that all the different modifications of Alq3 have 27Al in single unique crystallographic site. The quadrupolar parameters predicted using the DFT calculation under the isodensity polarisable continuum model resemble closely the experimentally obtained values. The solvated phase of Alq3 containing ethanol has structural difference from the alpha-phase of Alq3 (containing meridional isomer) from the solid-state NMR studies. Solid-state NMR can hence be used as an effective complementary tool to XRD for characterisation and structural elucidation.

Topology-aware illumination design for volume rendering.

PubMed

Zhou, Jianlong; Wang, Xiuying; Cui, Hui; Gong, Peng; Miao, Xianglin; Miao, Yalin; Xiao, Chun; Chen, Fang; Feng, Dagan

2016-08-19

Direct volume rendering is one of flexible and effective approaches to inspect large volumetric data such as medical and biological images. In conventional volume rendering, it is often time consuming to set up a meaningful illumination environment. Moreover, conventional illumination approaches usually assign same values of variables of an illumination model to different structures manually and thus neglect the important illumination variations due to structure differences. We introduce a novel illumination design paradigm for volume rendering on the basis of topology to automate illumination parameter definitions meaningfully. The topological features are extracted from the contour tree of an input volumetric data. The automation of illumination design is achieved based on four aspects of attenuation, distance, saliency, and contrast perception. To better distinguish structures and maximize illuminance perception differences of structures, a two-phase topology-aware illuminance perception contrast model is proposed based on the psychological concept of Just-Noticeable-Difference. The proposed approach allows meaningful and efficient automatic generations of illumination in volume rendering. Our results showed that our approach is more effective in depth and shape depiction, as well as providing higher perceptual differences between structures.

Air-gun signature modelling considering the influence of mechanical structure factors

NASA Astrophysics Data System (ADS)

Li, Guofa; Liu, Zhao; Wang, Jianhua; Cao, Mingqiang

2014-04-01

In marine seismic prospecting, as the air-gun array is usually composed of different types of air-guns, the signature modelling of different air-guns is particularly important to the array design. Different types of air-guns have different mechanical structures, which directly or indirectly affect the signatures. In order to simulate the influence of the mechanical structure, five parameters—the throttling constant, throttling power law exponent, mass release efficiency, fluid viscosity and heat transfer coefficient—are used in signature modelling. Through minimizing the energy relative error between the simulated and the measured signatures by the simulated annealing method, the five optimal parameters can be estimated. The method is tested in a field experiment, and the consistency between the simulated and the measured signatures is improved with the optimal parameters.

Effect of edge pruning on structural controllability and observability of complex networks

PubMed Central

Mengiste, Simachew Abebe; Aertsen, Ad; Kumar, Arvind

2015-01-01

Controllability and observability of complex systems are vital concepts in many fields of science. The network structure of the system plays a crucial role in determining its controllability and observability. Because most naturally occurring complex systems show dynamic changes in their network connectivity, it is important to understand how perturbations in the connectivity affect the controllability of the system. To this end, we studied the control structure of different types of artificial, social and biological neuronal networks (BNN) as their connections were progressively pruned using four different pruning strategies. We show that the BNNs are more similar to scale-free networks than to small-world networks, when comparing the robustness of their control structure to structural perturbations. We introduce a new graph descriptor, ‘the cardinality curve’, to quantify the robustness of the control structure of a network to progressive edge pruning. Knowing the susceptibility of control structures to different pruning methods could help design strategies to destroy the control structures of dangerous networks such as epidemic networks. On the other hand, it could help make useful networks more resistant to edge attacks. PMID:26674854

Characterising protein, salt and water interactions with combined vibrational spectroscopic techniques.

PubMed

Perisic, Nebojsa; Afseth, Nils Kristian; Ofstad, Ragni; Hassani, Sahar; Kohler, Achim

2013-05-01

In this paper a combination of NIR spectroscopy and FTIR and Raman microspectroscopy was used to elucidate the effects of different salts (NaCl, KCl and MgSO(4)) on structural proteins and their hydration in muscle tissue. Multivariate multi-block technique Consensus Principal Component Analysis enabled integration of different vibrational spectroscopic techniques: macroscopic information obtained by NIR spectroscopy is directly related to microscopic information obtained by FTIR and Raman microspectroscopy. Changes in protein secondary structure observed at different concentrations of salts were linked to changes in protein hydration affinity. The evidence for this was given by connecting the underlying FTIR bands of the amide I region (1700-1600 cm(-1)) and the water region (3500-3000 cm(-1)) with water vibrations obtained by NIR spectroscopy. In addition, Raman microspectroscopy demonstrated that different cations affected structures of aromatic amino acid residues differently, which indicates that cation-π interactions play an important role in determination of the final structure of protein molecules. Copyright © 2012 Elsevier Ltd. All rights reserved.

Reef flattening effects on total richness and species responses in the Caribbean.

PubMed

Newman, Steven P; Meesters, Erik H; Dryden, Charlie S; Williams, Stacey M; Sanchez, Cristina; Mumby, Peter J; Polunin, Nicholas V C

2015-11-01

There has been ongoing flattening of Caribbean coral reefs with the loss of habitat having severe implications for these systems. Complexity and its structural components are important to fish species richness and community composition, but little is known about its role for other taxa or species-specific responses. This study reveals the importance of reef habitat complexity and structural components to different taxa of macrofauna, total species richness, and individual coral and fish species in the Caribbean. Species presence and richness of different taxa were visually quantified in one hundred 25-m(2) plots in three marine reserves in the Caribbean. Sampling was evenly distributed across five levels of visually estimated reef complexity, with five structural components also recorded: the number of corals, number of large corals, slope angle, maximum sponge and maximum octocoral height. Taking advantage of natural heterogeneity in structural complexity within a particular coral reef habitat (Orbicella reefs) and discrete environmental envelope, thus minimizing other sources of variability, the relative importance of reef complexity and structural components was quantified for different taxa and individual fish and coral species on Caribbean coral reefs using boosted regression trees (BRTs). Boosted regression tree models performed very well when explaining variability in total (82·3%), coral (80·6%) and fish species richness (77·3%), for which the greatest declines in richness occurred below intermediate reef complexity levels. Complexity accounted for very little of the variability in octocorals, sponges, arthropods, annelids or anemones. BRTs revealed species-specific variability and importance for reef complexity and structural components. Coral and fish species occupancy generally declined at low complexity levels, with the exception of two coral species (Pseudodiploria strigosa and Porites divaricata) and four fish species (Halichoeres bivittatus, H. maculipinna, Malacoctenus triangulatus and Stegastes partitus) more common at lower reef complexity levels. A significant interaction between country and reef complexity revealed a non-additive decline in species richness in areas of low complexity and the reserve in Puerto Rico. Flattening of Caribbean coral reefs will result in substantial species losses, with few winners. Individual structural components have considerable value to different species, and their loss may have profound impacts on population responses of coral and fish due to identity effects of key species, which underpin population richness and resilience and may affect essential ecosystem processes and services. © 2015 The Authors. Journal of Animal Ecology © 2015 British Ecological Society.

Molecular dynamics simulations and structure-based network analysis reveal structural and functional aspects of G-protein coupled receptor dimer interactions.

PubMed

Baltoumas, Fotis A; Theodoropoulou, Margarita C; Hamodrakas, Stavros J

2016-06-01

A significant amount of experimental evidence suggests that G-protein coupled receptors (GPCRs) do not act exclusively as monomers but also form biologically relevant dimers and oligomers. However, the structural determinants, stoichiometry and functional importance of GPCR oligomerization remain topics of intense speculation. In this study we attempted to evaluate the nature and dynamics of GPCR oligomeric interactions. A representative set of GPCR homodimers were studied through Coarse-Grained Molecular Dynamics simulations, combined with interface analysis and concepts from network theory for the construction and analysis of dynamic structural networks. Our results highlight important structural determinants that seem to govern receptor dimer interactions. A conserved dynamic behavior was observed among different GPCRs, including receptors belonging in different GPCR classes. Specific GPCR regions were highlighted as the core of the interfaces. Finally, correlations of motion were observed between parts of the dimer interface and GPCR segments participating in ligand binding and receptor activation, suggesting the existence of mechanisms through which dimer formation may affect GPCR function. The results of this study can be used to drive experiments aimed at exploring GPCR oligomerization, as well as in the study of transmembrane protein-protein interactions in general.

Molecular dynamics simulations and structure-based network analysis reveal structural and functional aspects of G-protein coupled receptor dimer interactions

NASA Astrophysics Data System (ADS)

Baltoumas, Fotis A.; Theodoropoulou, Margarita C.; Hamodrakas, Stavros J.

2016-06-01

A significant amount of experimental evidence suggests that G-protein coupled receptors (GPCRs) do not act exclusively as monomers but also form biologically relevant dimers and oligomers. However, the structural determinants, stoichiometry and functional importance of GPCR oligomerization remain topics of intense speculation. In this study we attempted to evaluate the nature and dynamics of GPCR oligomeric interactions. A representative set of GPCR homodimers were studied through Coarse-Grained Molecular Dynamics simulations, combined with interface analysis and concepts from network theory for the construction and analysis of dynamic structural networks. Our results highlight important structural determinants that seem to govern receptor dimer interactions. A conserved dynamic behavior was observed among different GPCRs, including receptors belonging in different GPCR classes. Specific GPCR regions were highlighted as the core of the interfaces. Finally, correlations of motion were observed between parts of the dimer interface and GPCR segments participating in ligand binding and receptor activation, suggesting the existence of mechanisms through which dimer formation may affect GPCR function. The results of this study can be used to drive experiments aimed at exploring GPCR oligomerization, as well as in the study of transmembrane protein-protein interactions in general.

Crystal structures of ricin toxin's enzymatic subunit (RTA) in complex with neutralizing and non-neutralizing single-chain antibodies.

PubMed

Rudolph, Michael J; Vance, David J; Cheung, Jonah; Franklin, Matthew C; Burshteyn, Fiana; Cassidy, Michael S; Gary, Ebony N; Herrera, Cristina; Shoemaker, Charles B; Mantis, Nicholas J

2014-08-26

Ricin is a select agent toxin and a member of the RNA N-glycosidase family of medically important plant and bacterial ribosome-inactivating proteins. In this study, we determined X-ray crystal structures of the enzymatic subunit of ricin (RTA) in complex with the antigen binding domains (VHH) of five unique single-chain monoclonal antibodies that differ in their respective toxin-neutralizing activities. None of the VHHs made direct contact with residues involved in RTA's RNA N-glycosidase activity or induced notable allosteric changes in the toxin's subunit. Rather, the five VHHs had overlapping structural epitopes on the surface of the toxin and differed in the degree to which they made contact with prominent structural elements in two folding domains of the RTA. In general, RTA interactions were influenced most by the VHH CDR3 (CDR, complementarity-determining region) elements, with the most potent neutralizing antibody having the shortest and most conformationally constrained CDR3. These structures provide unique insights into the mechanisms underlying toxin neutralization and provide critically important information required for the rational design of ricin toxin subunit vaccines. Copyright © 2014 Elsevier Ltd. All rights reserved.

RNA secondary structure prediction using soft computing.

PubMed

Ray, Shubhra Sankar; Pal, Sankar K

2013-01-01

Prediction of RNA structure is invaluable in creating new drugs and understanding genetic diseases. Several deterministic algorithms and soft computing-based techniques have been developed for more than a decade to determine the structure from a known RNA sequence. Soft computing gained importance with the need to get approximate solutions for RNA sequences by considering the issues related with kinetic effects, cotranscriptional folding, and estimation of certain energy parameters. A brief description of some of the soft computing-based techniques, developed for RNA secondary structure prediction, is presented along with their relevance. The basic concepts of RNA and its different structural elements like helix, bulge, hairpin loop, internal loop, and multiloop are described. These are followed by different methodologies, employing genetic algorithms, artificial neural networks, and fuzzy logic. The role of various metaheuristics, like simulated annealing, particle swarm optimization, ant colony optimization, and tabu search is also discussed. A relative comparison among different techniques, in predicting 12 known RNA secondary structures, is presented, as an example. Future challenging issues are then mentioned.

Experimental Study on the Fire Properties of Nitrocellulose with Different Structures

PubMed Central

Wei, Ruichao; He, Yaping; Liu, Jiahao; He, Yu; Mi, Wenzhong; Yuen, Richard; Wang, Jian

2017-01-01

In order to ensure the safety of inflammable and explosive chemical substance such as nitrocellulose (NC) mixtures in the process of handing, storage, and usage, it is necessary to obtain the fire properties of NC with different exterior structures. In present study, fire properties of two commonly used nitrocelluloses with soft fiber structure and white chip structure were investigated by scanning electron microscope (SEM) and the ISO 5660 cone calorimeter. Experimental findings revealed that the most important fire properties such as ignition time, mass loss rate and ash content exhibited significant differences between the two structures of NC. Compared with the soft fiber NC, chip NC possesses a lower fire hazard, and its heat release rate intensity (HRRI) is mainly affected by the sample mass. In addition, oxygen consumption (OC) calorimetry method was compared with thermal chemistry (TC) method based on stoichiometry for HRRI calculation. HRRI results of NC with two structures obtained by these two methods showed a good consistency. PMID:28772675

Structural comparison of nickel electrodes and precursor phases

NASA Technical Reports Server (NTRS)

Cornilsen, Bahne C.; Shan, Xiaoyin; Loyselle, Patricia

1989-01-01

A summary of previous Raman spectroscopic results and a discussion of important structural differences in the various phases of active mass and active mass precurors are presented. Raman spectra provide unique signatures for these phases, and allow one to distinguish each phase, even when the compound is amorphous to X-rays (i.e., does not scatter X-rays because of a lack of order and/or small particle size). The structural changes incurred during formation, charge and discharge, cobalt addition, and aging will be discussed and related to electrode properties. Important structural differences include NiO2 layer stacking, nonstoichiometry (especially cation-deficit nonstoichiometry), disorder, dopant content, and water content. The results indicate that optimal nickel active mass is non-close packed and nonstoichiometric. The formation process transforms precursor phases into this structure. Therefore, the precursor disorder, or lack thereof, influences this final active mass structure and the rate of formation. Aging processes induce structural change which is believed to be detrimental. The role of cobalt addition can be appreciated in terms of structures favored or stabilized by the dopant. In recent work, the in situ Raman technique to characterize the critical structural parameters was developed. An in situ method relates structure, electrochemistry, and preparation. In situ Raman spectra of cells during charge and discharge, either during cyclic voltammetry or under constant current conditions were collected. With the structure-preparation knowledge and the in situ Raman tool, it will be possible to define the structure-property-preparation relations in more detail. This instrumentation has application to a variety of electrode systems.

Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments.

PubMed

Shen, Rong; Han, Wei; Fiorin, Giacomo; Islam, Shahidul M; Schulten, Klaus; Roux, Benoît

2015-10-01

The knowledge of multiple conformational states is a prerequisite to understand the function of membrane transport proteins. Unfortunately, the determination of detailed atomic structures for all these functionally important conformational states with conventional high-resolution approaches is often difficult and unsuccessful. In some cases, biophysical and biochemical approaches can provide important complementary structural information that can be exploited with the help of advanced computational methods to derive structural models of specific conformational states. In particular, functional and spectroscopic measurements in combination with site-directed mutations constitute one important source of information to obtain these mixed-resolution structural models. A very common problem with this strategy, however, is the difficulty to simultaneously integrate all the information from multiple independent experiments involving different mutations or chemical labels to derive a unique structural model consistent with the data. To resolve this issue, a novel restrained molecular dynamics structural refinement method is developed to simultaneously incorporate multiple experimentally determined constraints (e.g., engineered metal bridges or spin-labels), each treated as an individual molecular fragment with all atomic details. The internal structure of each of the molecular fragments is treated realistically, while there is no interaction between different molecular fragments to avoid unphysical steric clashes. The information from all the molecular fragments is exploited simultaneously to constrain the backbone to refine a three-dimensional model of the conformational state of the protein. The method is illustrated by refining the structure of the voltage-sensing domain (VSD) of the Kv1.2 potassium channel in the resting state and by exploring the distance histograms between spin-labels attached to T4 lysozyme. The resulting VSD structures are in good agreement with the consensus model of the resting state VSD and the spin-spin distance histograms from ESR/DEER experiments on T4 lysozyme are accurately reproduced.

Phytophthora community structure analyses in Oregon nurseries inform systems approaches to disease management

Treesearch

J.L. Parke; B.J. Knaus; V.J. Fieland; C. Lewis; N.J. Grünwald

2014-01-01

Nursery plants are important vectors for plant pathogens. Understanding what pathogens occur in nurseries in different production stages can be useful to the development of integrated systems approaches. Four horticultural nurseries in Oregon were sampled every 2 months for 4 years to determine the identity and community structure of Phytophthora...

Spatial structure of the Mormon cricket gut microbiome and its predicted contribution to nutrition and immune function

USDA-ARS?s Scientific Manuscript database

The gut microbiome of insects plays an important role in their ecology and evolution, participating in nutrient acquisition, immunity, and behavior. Microbial community structure within the gut is heavily influenced by differences among gut regions in morphology and physiology, which determine the n...

Olfactory receptor neuron profiling using sandalwood odorants.

PubMed

Bieri, Stephan; Monastyrskaia, Katherine; Schilling, Boris

2004-07-01

The mammalian olfactory system can discriminate between volatile molecules with subtle differences in their molecular structures. Efforts in synthetic chemistry have delivered a myriad of smelling compounds of different qualities as well as many molecules with very similar olfactive properties. One important class of molecules in the fragrance industry are sandalwood odorants. Sandalwood oil and four synthetic sandalwood molecules were selected to study the activation profile of endogenous olfactory receptors when exposed to compounds from the same odorant family. Dissociated rat olfactory receptor neurons were exposed to the sandalwood molecules and the receptor activation studied by monitoring fluxes in the internal calcium concentration. Olfactory receptor neurons were identified that were specifically stimulated by sandalwood compounds. These neurons expressed olfactory receptors that can discriminate between sandalwood odorants with slight differences in their molecular structures. This is the first study in which an important class of perfume compounds was analyzed for its ability to activate endogenous olfactory receptors in olfactory receptor neurons.

Locating structures and evolution pathways of reconstructed rutile TiO2(011) using genetic algorithm aided density functional theory calculations.

PubMed

Ding, Pan; Gong, Xue-Qing

2016-05-01

Titanium dioxide (TiO2) is an important metal oxide that has been used in many different applications. TiO2 has also been widely employed as a model system to study basic processes and reactions in surface chemistry and heterogeneous catalysis. In this work, we investigated the (011) surface of rutile TiO2 by focusing on its reconstruction. Density functional theory calculations aided by a genetic algorithm based optimization scheme were performed to extensively sample the potential energy surfaces of reconstructed rutile TiO2 structures that obey (2 × 1) periodicity. A lot of stable surface configurations were located, including the global-minimum configuration that was proposed previously. The wide variety of surface structures determined through the calculations performed in this work provide insight into the relationship between the atomic configuration of a surface and its stability. More importantly, several analytical schemes were proposed and tested to gauge the differences and similarities among various surface structures, aiding the construction of the complete pathway for the reconstruction process.

Do we Underestimate the Importance of Leaf Size in Plant Economics? Disproportional Scaling of Support Costs Within the Spectrum of Leaf Physiognomy

PubMed Central

Niinemets, Ülo; Portsmuth, Angelika; Tena, David; Tobias, Mari; Matesanz, Silvia; Valladares, Fernando

2007-01-01

Background Broad scaling relationships between leaf size and function do not take into account that leaves of different size may contain different fractions of support in petiole and mid-rib. Methods The fractions of leaf biomass in petiole, mid-rib and lamina, and the differences in chemistry and structure among mid-ribs, petioles and laminas were investigated in 122 species of contrasting leaf size, life form and climatic distribution to determine the extent to which differences in support modify whole-lamina and whole-leaf structural and chemical characteristics, and the extent to which size-dependent support investments are affected by plant life form and site climate. Key Results For the entire data set, leaf fresh mass varied over five orders of magnitude. The percentage of dry mass in mid-rib increased strongly with lamina size, reaching more than 40 % in the largest laminas. The whole-leaf percentage of mid-rib and petiole increased with leaf size, and the overall support investment was more than 60 % in the largest leaves. Fractional support investments were generally larger in herbaceous than in woody species and tended to be lower in Mediterranean than in cool temperate and tropical plants. Mid-ribs and petioles had lower N and C percentages, and lower dry to fresh mass ratio, but greater density (mass per unit volume) than laminas. N percentage of lamina without mid-rib was up to 40 % higher in the largest leaves than the total-lamina (lamina and mid-rib) N percentage, and up to 60 % higher than whole-leaf N percentage, while lamina density calculated without mid-rib was up to 80 % less than that with the mid-rib. For all leaf compartments, N percentage was negatively associated with density and dry to fresh mass ratio, while C percentage was positively linked to these characteristics, reflecting the overall inverse scaling between structural and physiological characteristics. However, the correlations between N and C percentages and structural characteristics differed among mid-ribs, petioles and laminas, implying that the mass-weighted average leaf N and C percentage, density, and dry to fresh mass ratio can have different functional values depending on the importance of within-leaf support investments. Conclusions These data demonstrate that variation in leaf size is associated with major changes in within-leaf support investments and in large modifications in integrated leaf chemical and structural characteristics. These size-dependent alterations can importantly affect general leaf structure vs. function scaling relationships. These data further demonstrate important life-form effects on and climatic differentiation in foliage support costs. PMID:17586597

Effects of Vegetation Structure on the Location of Lion Kill Sites in African Thicket

PubMed Central

Davies, Andrew B.; Tambling, Craig J.; Kerley, Graham I. H.; Asner, Gregory P.

2016-01-01

Predator-prey relationships are integral to ecosystem stability and functioning. These relationships are, however, difficult to maintain in protected areas where large predators are increasingly being reintroduced and confined. Where predators make kills has a profound influence on their role in ecosystems, but the relative importance of environmental variables in determining kill sites, and how these might vary across ecosystems is poorly known. We investigated kill sites for lions in South Africa’s thicket biome, testing the importance of vegetation structure for kill site locations compared to other environmental variables. Kill sites were located over four years using GPS telemetry and compared to non-kill sites that had been occupied by lions, as well as to random sites within lion ranges. Measurements of 3D vegetation structure obtained from Light Detection and Ranging (LiDAR) were used to calculate the visible area (viewshed) around each site and, along with wind and moonlight data, used to compare kill sites between lion sexes, prey species and prey sexes. Viewshed area was the most important predictor of kill sites (sites in dense vegetation were twice as likely to be kill sites compared to open areas), followed by wind speed and, less so, moonlight. Kill sites for different prey species varied with vegetation structure, and male prey were killed when wind speeds were higher compared to female prey of the same species. Our results demonstrate that vegetation structure is an important component of predator-prey interactions, with varying effects across ecosystems. Such differences require consideration in terms of the ecological roles performed by predators, and in predator and prey conservation. PMID:26910832

Exploration of enzyme-ligand interactions in CYP2D6 & 3A4 homology models and crystal structures using a novel computational approach.

PubMed

Kjellander, Britta; Masimirembwa, Collen M; Zamora, Ismael

2007-01-01

New crystal structures of human CYP2D6 and CYP3A4 have recently been reported, and in this study, we wanted to compare them with previously used homology models with respect to predictions of site of metabolism and ligand-enzyme interactions. The data set consisted of a family of synthetic opioid analgesics with the aim to cover both CYP2D6 and CYP3A4, as most of these compounds are metabolized by both isoforms. The program MetaSite was used for the site of metabolism predictions, and the results were validated by experimental assessment of the major metabolites formed with recombinant CYP450s. This was made on a selection of 14 compounds in the data set. The prediction rates for MetaSite were 79-100% except for the CYP3A4 homology model, which picked the correct site in half of the cases. Despite differences in orientation of some important amino acids in the active sites, the MetaSite-predicted sites were the same for the different structures, with the exception of the CYP3A4 homology model. Further exploration of interactions with ligands was done by docking substrates/inhibitors in the different structures with the docking program GLUE. To address the challenge in interpreting patterns of enzyme-ligand interactions for the large number of different docking poses, a new computational tool to handle the results from the dockings was developed, in which the output highlights the relative importance of amino acids in CYP450-substrate/inhibitor interactions. The method is based on calculations of the interaction energies for each pose with the surrounding amino acids. For the CYP3A4 structures, this method was compared with consensus principal component analysis (CPCA), a commonly used method for structural comparison to evaluate the usefulness of the new method. The results from the two methods were comparable with each other, and the highlighted amino acids resemble those that were identified to have a different orientation in the compared structures. The new method has clear advantages over CPCA in that it is far simpler to interpret and there is no need for protein alignment. The methodology enables structural comparison but also gives insights on important amino acid substrate/inhibitor interactions and can therefore be very useful when suggesting modifications of new chemical entities to improve their metabolic profiles.

Agonistic reciprocity is associated with reduced male reproductive success within haremic social networks

PubMed Central

Solomon-Lane, Tessa K.; Pradhan, Devaleena S.; Willis, Madelyne C.; Grober, Matthew S.

2015-01-01

While individual variation in social behaviour is ubiquitous and causes social groups to differ in structure, how these structural differences affect fitness remains largely unknown. We used social network analysis of replicate bluebanded goby (Lythrypnus dalli) harems to identify the reproductive correlates of social network structure. In stable groups, we quantified agonistic behaviour, reproduction and steroid hormones, which can both affect and respond to social/reproductive cues. We identified distinct, optimal social structures associated with different reproductive measures. Male hatching success (HS) was negatively associated with agonistic reciprocity, a network structure that describes whether subordinates ‘reciprocated’ agonism received from dominants. Egg laying was associated with the individual network positions of the male and dominant female. Thus, males face a trade-off between promoting structures that facilitate egg laying versus HS. Whether this reproductive conflict is avoidable remains to be determined. We also identified different social and/or reproductive roles for 11-ketotestosterone, 17β-oestradiol and cortisol, suggesting that specific neuroendocrine mechanisms may underlie connections between network structure and fitness. This is one of the first investigations of the reproductive and neuroendocrine correlates of social behaviour and network structure in replicate, naturalistic social groups and supports network structure as an important target for natural selection. PMID:26156769

Disentangling environmental and spatial effects on phylogenetic structure of angiosperm tree communities in China.

PubMed

Qian, Hong; Chen, Shengbin; Zhang, Jin-Long

2017-07-17

Niche-based and neutrality-based theories are two major classes of theories explaining the assembly mechanisms of local communities. Both theories have been frequently used to explain species diversity and composition in local communities but their relative importance remains unclear. Here, we analyzed 57 assemblages of angiosperm trees in 0.1-ha forest plots across China to examine the effects of environmental heterogeneity (relevant to niche-based processes) and spatial contingency (relevant to neutrality-based processes) on phylogenetic structure of angiosperm tree assemblages distributed across a wide range of environment and space. Phylogenetic structure was quantified with six phylogenetic metrics (i.e., phylogenetic diversity, mean pairwise distance, mean nearest taxon distance, and the standardized effect sizes of these three metrics), which emphasize on different depths of evolutionary histories and account for different degrees of species richness effects. Our results showed that the variation in phylogenetic metrics explained independently by environmental variables was on average much greater than that explained independently by spatial structure, and the vast majority of the variation in phylogenetic metrics was explained by spatially structured environmental variables. We conclude that niche-based processes have played a more important role than neutrality-based processes in driving phylogenetic structure of angiosperm tree species in forest communities in China.

Tuning structural motifs and alloying of bulk immiscible Mo-Cu bimetallic nanoparticles by gas-phase synthesis

NASA Astrophysics Data System (ADS)

Krishnan, Gopi; Verheijen, Marcel A.; Ten Brink, Gert H.; Palasantzas, George; Kooi, Bart J.

2013-05-01

Nowadays bimetallic nanoparticles (NPs) have emerged as key materials for important modern applications in nanoplasmonics, catalysis, biodiagnostics, and nanomagnetics. Consequently the control of bimetallic structural motifs with specific shapes provides increasing functionality and selectivity for related applications. However, producing bimetallic NPs with well controlled structural motifs still remains a formidable challenge. Hence, we present here a general methodology for gas phase synthesis of bimetallic NPs with distinctively different structural motifs ranging at a single particle level from a fully mixed alloy to core-shell, to onion (multi-shell), and finally to a Janus/dumbbell, with the same overall particle composition. These concepts are illustrated for Mo-Cu NPs, where the precise control of the bimetallic NPs with various degrees of chemical ordering, including different shapes from spherical to cube, is achieved by tailoring the energy and thermal environment that the NPs experience during their production. The initial state of NP growth, either in the liquid or in the solid state phase, has important implications for the different structural motifs and shapes of synthesized NPs. Finally we demonstrate that we are able to tune the alloying regime, for the otherwise bulk immiscible Mo-Cu, by achieving an increase of the critical size, below which alloying occurs, closely up to an order of magnitude. It is discovered that the critical size of the NP alloy is not only affected by controlled tuning of the alloying temperature but also by the particle shape.Nowadays bimetallic nanoparticles (NPs) have emerged as key materials for important modern applications in nanoplasmonics, catalysis, biodiagnostics, and nanomagnetics. Consequently the control of bimetallic structural motifs with specific shapes provides increasing functionality and selectivity for related applications. However, producing bimetallic NPs with well controlled structural motifs still remains a formidable challenge. Hence, we present here a general methodology for gas phase synthesis of bimetallic NPs with distinctively different structural motifs ranging at a single particle level from a fully mixed alloy to core-shell, to onion (multi-shell), and finally to a Janus/dumbbell, with the same overall particle composition. These concepts are illustrated for Mo-Cu NPs, where the precise control of the bimetallic NPs with various degrees of chemical ordering, including different shapes from spherical to cube, is achieved by tailoring the energy and thermal environment that the NPs experience during their production. The initial state of NP growth, either in the liquid or in the solid state phase, has important implications for the different structural motifs and shapes of synthesized NPs. Finally we demonstrate that we are able to tune the alloying regime, for the otherwise bulk immiscible Mo-Cu, by achieving an increase of the critical size, below which alloying occurs, closely up to an order of magnitude. It is discovered that the critical size of the NP alloy is not only affected by controlled tuning of the alloying temperature but also by the particle shape. Electronic supplementary information (ESI) available: Experimental details including schematics of the gas phase synthesis set up, target arrangement, synthesis condition for various structures, and TEM images of alloy, core-shell and Mo-Cu-Mo onion nanoparticles. See DOI: 10.1039/c3nr00565h

Structural studies of Pseudomonas and Chromobacterium ω-aminotransferases provide insights into their differing substrate specificity.

PubMed

Sayer, Christopher; Isupov, Michail N; Westlake, Aaron; Littlechild, Jennifer A

2013-04-01

The crystal structures and inhibitor complexes of two industrially important ω-aminotransferase enzymes from Pseudomonas aeruginosa and Chromobacterium violaceum have been determined in order to understand the differences in their substrate specificity. The two enzymes share 30% sequence identity and use the same amino acceptor, pyruvate; however, the Pseudomonas enzyme shows activity towards the amino donor β-alanine, whilst the Chromobacterium enzyme does not. Both enzymes show activity towards S-α-methylbenzylamine (MBA), with the Chromobacterium enzyme having a broader substrate range. The crystal structure of the P. aeruginosa enzyme has been solved in the holo form and with the inhibitor gabaculine bound. The C. violaceum enzyme has been solved in the apo and holo forms and with gabaculine bound. The structures of the holo forms of both enzymes are quite similar. There is little conformational difference observed between the inhibitor complex and the holoenzyme for the P. aeruginosa aminotransferase. In comparison, the crystal structure of the C. violaceum gabaculine complex shows significant structural rearrangements from the structures of both the apo and holo forms of the enzyme. It appears that the different rigidity of the protein scaffold contributes to the substrate specificity observed for the two ω-aminotransferases.

[Purification and structural identification of herbicides from Botrytis cinerea].

PubMed

Zheng, Meng; Xu, Kuo; Dong, Jingao

2008-10-01

Toxin produced by phytopathogenic fungi is one of the important microbial herbicides. We found a new compound with herbicidal activity. Five different ultraviolet absorption components were isolated from the filtrate of Botrytis cinerea isolate 7-3 culture. Of the five components, one showed strong inhibitory to Digitaria sanguinalis. The pure fraction with high herbicidal activity was obtained by HPLC purification. Its structure was identified as 10-syn-dihydrobotrydial by Ultraviolet and Visible Spectroscopy, Infrared Spectrum, Nuclear Magnetic Resonance Spectroscopy analysis. The findings are important for future preparation and application of the herbicide.

Comparative analyses of structural features and scaffold diversity for purchasable compound libraries.

PubMed

Shang, Jun; Sun, Huiyong; Liu, Hui; Chen, Fu; Tian, Sheng; Pan, Peichen; Li, Dan; Kong, Dexin; Hou, Tingjun

2017-04-21

Large purchasable screening libraries of small molecules afforded by commercial vendors are indispensable sources for virtual screening (VS). Selecting an optimal screening library for a specific VS campaign is quite important to improve the success rates and avoid wasting resources in later experimental phases. Analysis of the structural features and molecular diversity for different screening libraries can provide valuable information to the decision making process when selecting screening libraries for VS. In this study, the structural features and scaffold diversity of eleven purchasable screening libraries and Traditional Chinese Medicine Compound Database (TCMCD) were analyzed and compared. Their scaffold diversity represented by the Murcko frameworks and Level 1 scaffolds was characterized by the scaffold counts and cumulative scaffold frequency plots, and visualized by Tree Maps and SAR Maps. The analysis demonstrates that, based on the standardized subsets with similar molecular weight distributions, Chembridge, ChemicalBlock, Mucle, TCMCD and VitasM are more structurally diverse than the others. Compared with all purchasable screening libraries, TCMCD has the highest structural complexity indeed but more conservative molecular scaffolds. Moreover, we found that some representative scaffolds were important components of drug candidates against different drug targets, such as kinases and guanosine-binding protein coupled receptors, and therefore the molecules containing pharmacologically important scaffolds found in screening libraries might be potential inhibitors against the relevant targets. This study may provide valuable perspective on which purchasable compound libraries are better for you to screen. Graphical abstract Selecting diverse compound libraries with scaffold analyses.

Cell Wall Structure of Coccoid Green Algae as an Important Trade-Off Between Biotic Interference Mechanisms and Multidimensional Cell Growth.

PubMed

Dunker, Susanne; Wilhelm, Christian

2018-01-01

Coccoid green algae can be divided in two groups based on their cell wall structure. One group has a highly chemical resistant cell wall (HR-cell wall) containing algaenan. The other group is more susceptible to chemicals (LR-cell wall - Low resistant cell wall). Algaenan is considered as important molecule to explain cell wall resistance. Interestingly, cell wall types (LR- and HR-cell wall) are not in accordance with the taxonomic classes Chlorophyceae and Trebouxiophyceae, which makes it even more interesting to consider the ecological function. It was already shown that algaenan helps to protect against virus, bacterial and fungal attack, but in this study we show for the first time that green algae with different cell wall properties show different sensitivity against interference competition with the cyanobacterium Microcystis aeruginosa . Based on previous work with co-cultures of M. aeruginosa and two green algae ( Acutodesmus obliquus and Oocystis marssonii ) differing in their cell wall structure, it was shown that M. aeruginosa could impair only the growth of the green algae if they belong to the LR-cell wall type. In this study it was shown that the sensitivity to biotic interference mechanism shows a more general pattern within coccoid green algae species depending on cell wall structure.

Molecular Structure and Regulation of P2X Receptors With a Special Emphasis on the Role of P2X2 in the Auditory System.

PubMed

Mittal, Rahul; Chan, Brandon; Grati, M'hamed; Mittal, Jeenu; Patel, Kunal; Debs, Luca H; Patel, Amit P; Yan, Denise; Chapagain, Prem; Liu, Xue Zhong

2016-08-01

The P2X purinergic receptors are cation-selective channels gated by extracellular adenosine 5'-triphosphate (ATP). These purinergic receptors are found in virtually all mammalian cell types and facilitate a number of important physiological processes. Within the past few years, the characterization of crystal structures of the zebrafish P2X4 receptor in its closed and open states has provided critical insights into the mechanisms of ligand binding and channel activation. Understanding of this gating mechanism has facilitated to design and interpret new modeling and structure-function experiments to better elucidate how different agonists and antagonists can affect the receptor with differing levels of potency. This review summarizes the current knowledge on the structure, activation, allosteric modulators, function, and location of the different P2X receptors. Moreover, an emphasis on the P2X2 receptors has been placed in respect to its role in the auditory system. In particular, the discovery of three missense mutations in P2X2 receptors could become important areas of study in the field of gene therapy to treat progressive and noise-induced hearing loss. J. Cell. Physiol. 231: 1656-1670, 2016. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

Structure-preserving model reduction of large-scale logistics networks. Applications for supply chains

NASA Astrophysics Data System (ADS)

Scholz-Reiter, B.; Wirth, F.; Dashkovskiy, S.; Makuschewitz, T.; Schönlein, M.; Kosmykov, M.

2011-12-01

We investigate the problem of model reduction with a view to large-scale logistics networks, specifically supply chains. Such networks are modeled by means of graphs, which describe the structure of material flow. An aim of the proposed model reduction procedure is to preserve important features within the network. As a new methodology we introduce the LogRank as a measure for the importance of locations, which is based on the structure of the flows within the network. We argue that these properties reflect relative importance of locations. Based on the LogRank we identify subgraphs of the network that can be neglected or aggregated. The effect of this is discussed for a few motifs. Using this approach we present a meta algorithm for structure-preserving model reduction that can be adapted to different mathematical modeling frameworks. The capabilities of the approach are demonstrated with a test case, where a logistics network is modeled as a Jackson network, i.e., a particular type of queueing network.

The development of episodic memory: items, contexts, and relations.

PubMed

Yim, Hyungwook; Dennis, Simon J; Sloutsky, Vladimir M

2013-11-01

Episodic memory involves the formation of relational structures that bind information about the stimuli people experience to the contexts in which they experience them. The ability to form and retain such structures may be at the core of the development of episodic memory. In the first experiment reported here, 4- and 7-year-olds were presented with paired-associate learning tasks requiring memory structures of different complexity. A multinomial-processing tree model was applied to estimate the use of different structures in the two age groups. The use of two-way list-context-to-target structures and three-way structures was found to increase between the ages of 4 and 7. Experiment 2 demonstrated that the ability to form increasingly complex relational memory structures develops between the ages of 4 and 7 years and that this development extends well into adulthood. These results have important implications for theories of memory development.

Forest Attributes from Radar Interferometric Structure and its Fusion with Optical Remote Sensing

NASA Technical Reports Server (NTRS)

Treuhaft, Robert N.; Law, Beverly E.; Asner, Gregory P.

2004-01-01

The possibility of global, three-dimensional remote sensing of forest structure with interferometric synthetic aperture radar (InSAR) bears on important forest ecological processes, particularly the carbon cycle. InSAR supplements two-dimensional remote sensing with information in the vertical dimension. Its strengths in potential for global coverage complement those of lidar (light detecting and ranging), which has the potential for high-accuracy vertical profiles over small areas. InSAR derives its sensitivity to forest vertical structure from the differences in signals received by two, spatially separate radar receivers. Estimation of parameters describing vertical structure requires multiple-polarization, multiple-frequency, or multiple-baseline InSAR. Combining InSAR with complementary remote sensing techniques, such as hyperspectral optical imaging and lidar, can enhance vertical-structure estimates and consequent biophysical quantities of importance to ecologists, such as biomass. Future InSAR experiments will supplement recent airborne and spaceborne demonstrations, and together with inputs from ecologists regarding structure, they will suggest designs for future spaceborne strategies for measuring global vegetation structure.

Effects of system size and cooling rate on the structure and properties of sodium borosilicate glasses from molecular dynamics simulations.

PubMed

Deng, Lu; Du, Jincheng

2018-01-14

Borosilicate glasses form an important glass forming system in both glass science and technologies. The structure and property changes of borosilicate glasses as a function of thermal history in terms of cooling rate during glass formation and simulation system sizes used in classical molecular dynamics (MD) simulation were investigated with recently developed composition dependent partial charge potentials. Short and medium range structural features such as boron coordination, Si and B Q n distributions, and ring size distributions were analyzed to elucidate the effects of cooling rate and simulation system size on these structure features and selected glass properties such as glass transition temperature, vibration density of states, and mechanical properties. Neutron structure factors, neutron broadened pair distribution functions, and vibrational density of states were calculated and compared with results from experiments as well as ab initio calculations to validate the structure models. The results clearly indicate that both cooling rate and system size play an important role on the structures of these glasses, mainly by affecting the 3 B and 4 B distributions and consequently properties of the glasses. It was also found that different structure features and properties converge at different sizes or cooling rates; thus convergence tests are needed in simulations of the borosilicate glasses depending on the targeted properties. The results also shed light on the complex thermal history dependence on structure and properties in borosilicate glasses and the protocols in MD simulations of these and other glass materials.

Effects of system size and cooling rate on the structure and properties of sodium borosilicate glasses from molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Deng, Lu; Du, Jincheng

2018-01-01

Borosilicate glasses form an important glass forming system in both glass science and technologies. The structure and property changes of borosilicate glasses as a function of thermal history in terms of cooling rate during glass formation and simulation system sizes used in classical molecular dynamics (MD) simulation were investigated with recently developed composition dependent partial charge potentials. Short and medium range structural features such as boron coordination, Si and B Qn distributions, and ring size distributions were analyzed to elucidate the effects of cooling rate and simulation system size on these structure features and selected glass properties such as glass transition temperature, vibration density of states, and mechanical properties. Neutron structure factors, neutron broadened pair distribution functions, and vibrational density of states were calculated and compared with results from experiments as well as ab initio calculations to validate the structure models. The results clearly indicate that both cooling rate and system size play an important role on the structures of these glasses, mainly by affecting the 3B and 4B distributions and consequently properties of the glasses. It was also found that different structure features and properties converge at different sizes or cooling rates; thus convergence tests are needed in simulations of the borosilicate glasses depending on the targeted properties. The results also shed light on the complex thermal history dependence on structure and properties in borosilicate glasses and the protocols in MD simulations of these and other glass materials.

Modeling activated states of GPCRs: the rhodopsin template.

PubMed

Niv, Masha Y; Skrabanek, Lucy; Filizola, Marta; Weinstein, Harel

2006-01-01

Activation of G Protein-Coupled Receptors (GPCRs) is an allosteric mechanism triggered by ligand binding and resulting in conformational changes transduced by the transmembrane domain. Models of the activated forms of GPCRs have become increasingly necessary for the development of a clear understanding of signal propagation into the cell. Experimental evidence points to a multiplicity of conformations related to the activation of the receptor, rendered important physiologically by the suggestion that different conformations may be responsible for coupling to different signaling pathways. In contrast to the inactive state of rhodopsin (RHO) for which several high quality X-ray structures are available, the structure-related information for the active states of rhodopsin and all other GPCRs is indirect. We have collected and stored such information in a repository we maintain for activation-specific structural data available for rhodopsin-like GPCRs, http://www.physiology.med.cornell.edu/GPCRactivation/gpcrindex.html . Using these data as structural constraints, we have applied Simulated Annealing Molecular Dynamics to construct a number of different active state models of RHO starting from the known inactive structure. The common features of the models indicate that TM3 and TM5 play an important role in activation, in addition to the well-established rearrangement of TM6. Some of the structural changes observed in these models occur in regions that were not involved in the constraints, and have not been previously tested experimentally; they emerge as interesting candidates for further experimental exploration of the conformational space of activated GPCRs. We show that none of the normal modes calculated from the inactive structure has a dominant contribution along the path of conformational rearrangement from inactive to the active forms of RHO in the models. This result may differentiate rhodopsin from other GPCRs, and the reasons for this difference are discussed in the context of the structural properties and the physiological function of the protein.

Hyaluronic acid: its role in voice.

PubMed

Ward, P Daniel; Thibeault, Susan L; Gray, Steven D

2002-09-01

The extracellular matrix (ECM), once regarded simply as a structural scaffold, is now recognized as an important modulator of cellular behavior and function. One component that plays a prominent role in this process is hyaluronic acid (HA)--a molecule found in many different tissues. Research into the roles of HA indicates that it plays a key role in tissue viscosity, shock absorption, and space filling. Specifically, research into the role of HA in laryngology indicates that it has profound effects on the structure and viscosity of vocal folds. This article provides an introduction to the structure and biological functions of HA and its importance in voice. In addition, an overview of the pharmaceutical applications of HA is discussed.

Evolutionary Design of Controlled Structures

NASA Technical Reports Server (NTRS)

Masters, Brett P.; Crawley, Edward F.

1997-01-01

Basic physical concepts of structural delay and transmissibility are provided for simple rod and beam structures. Investigations show the sensitivity of these concepts to differing controlled-structures variables, and to rational system modeling effects. An evolutionary controls/structures design method is developed. The basis of the method is an accurate model formulation for dynamic compensator optimization and Genetic Algorithm based updating of sensor/actuator placement and structural attributes. One and three dimensional examples from the literature are used to validate the method. Frequency domain interpretation of these controlled structure systems provide physical insight as to how the objective is optimized and consequently what is important in the objective. Several disturbance rejection type controls-structures systems are optimized for a stellar interferometer spacecraft application. The interferometric designs include closed loop tracking optics. Designs are generated for differing structural aspect ratios, differing disturbance attributes, and differing sensor selections. Physical limitations in achieving performance are given in terms of average system transfer function gains and system phase loss. A spacecraft-like optical interferometry system is investigated experimentally over several different optimized controlled structures configurations. Configurations represent common and not-so-common approaches to mitigating pathlength errors induced by disturbances of two different spectra. Results show that an optimized controlled structure for low frequency broadband disturbances achieves modest performance gains over a mass equivalent regular structure, while an optimized structure for high frequency narrow band disturbances is four times better in terms of root-mean-square pathlength. These results are predictable given the nature of the physical system and the optimization design variables. Fundamental limits on controlled performance are discussed based on the measured and fit average system transfer function gains and system phase loss.

Studies of the structure-activity relationships of peptides and proteins involved in growth and development based on their three-dimensional structures.

PubMed

Nagata, Koji

2010-01-01

Peptides and proteins with similar amino acid sequences can have different biological functions. Knowledge of their three-dimensional molecular structures is critically important in identifying their functional determinants. In this review, I describe the results of our and other groups' structure-based functional characterization of insect insulin-like peptides, a crustacean hyperglycemic hormone-family peptide, a mammalian epidermal growth factor-family protein, and an intracellular signaling domain that recognizes proline-rich sequence.

Atomic-resolution 3D structure of amyloid β fibrils: The Osaka mutation

DOE PAGES

Schutz, Anne K.; Wall, Joseph; Vagt, Toni; ...

2014-11-13

Despite its central importance for understanding the molecular basis of Alzheimer's disease (AD), high-resolution structural information on amyloid β-peptide (Aβ) fibrils, which are intimately linked with AD, is scarce. We report an atomic-resolution fibril structure of the Aβ 1-40 peptide with the Osaka mutation (E22Δ), associated with early-onset AD. The structure, which differs substantially from all previously proposed models, is based on a large number of unambiguous intra- and intermolecular solid-state NMR distance restraints

Importance of wetland landscape structure to shorebirds wintering in an agricultural valley

USGS Publications Warehouse

Taft, Oriane W.; Haig, Susan M.

2006-01-01

Only recently has the influence of landscape structure on habitat use been a research focus in wetland systems. During non-breeding periods when food can be locally limited, wetland spatial pattern across a landscape may be of great importance in determining wetland use. We studied the influence of landscape structure on abundances of wintering Dunlin (Calidris alpina) and Killdeer (Charadrius vociferus) observed on wetlands in the agricultural Willamette Valley of Oregon, USA, during two winters (1999a??2000, 2000a??2001) of differing rainfall. We examined (1) shorebird use within a sample of 100 km2 regions differing in landscape structure (hectares of shorebird habitat [wet, unvegetated]) and (2) use of sites differing in landscape context (area of shorebird habitat within a species-defined radius). For use of sites, we also assessed the influence of two local characteristics: percent of soil exposed and area of wet habitat. We analyzed data using linear regression and information-theoretic modeling. During the dry winter (2000a??2001), Dunlin were attracted to regions with more wetland habitat and their abundances at sites increased with greater area of shorebird habitat within both the site and the surrounding landscape. In contrast, Dunlin abundances at sites were related to availability of habitat at only a local scale during the wet winter (1999a??2000). Regional habitat availability was of little importance in predicting Killdeer distributions, and Killdeer site use appeared unrelated to habitat distributions at both landscape and local scales. Results suggest prioritizing sites for conservation that are located in areas with high wetland coverage.

Regional factors rather than forest type drive the community structure of soil living oribatid mites (Acari, Oribatida).

PubMed

Erdmann, Georgia; Scheu, Stefan; Maraun, Mark

2012-06-01

Most European forests are managed by humans. However, the manner and intensity of management vary. While the effect of forest management on above-ground communities has been investigated in detail, effects on the below-ground fauna remain poorly understood. Oribatid mites are abundant microarthropods in forest soil and important decomposers in terrestrial ecosystems. Here, we investigated the effect of four forest types (i.e., managed coniferous forests; 30 and 70 years old managed beech forests; natural beech forests) on the density, diversity and community structure of oribatid mites (Acari). The study was replicated at three regions in Germany: the Swabian Alb, the Hainich and the Schorfheide. To relate changes in oribatid mite community structure to environmental factors, litter mass, pH, C and N content of litter, fine roots and C content of soil were measured. Density of oribatid mites was highest in the coniferous forests and decreased in the order 30 years old, 70 years old, and natural beech forests. Mass of the litter layer and density of oribatid mites were strongly correlated indicating that the litter layer is an important factor regulating oribatid mite densities. Diversity of oribatid mites was little affected by forest type indicating that they harbor similar numbers of niches. Species composition differed between the forest types, suggesting different types of niches. The community structure of oribatid mites differed more strongly between the three regions than between the forest types indicating that regional factors are more important than effects associated with forest type.

Relationship between mRNA secondary structure and sequence variability in Chloroplast genes: possible life history implications.

PubMed

Krishnan, Neeraja M; Seligmann, Hervé; Rao, Basuthkar J

2008-01-28

Synonymous sites are freer to vary because of redundancy in genetic code. Messenger RNA secondary structure restricts this freedom, as revealed by previous findings in mitochondrial genes that mutations at third codon position nucleotides in helices are more selected against than those in loops. This motivated us to explore the constraints imposed by mRNA secondary structure on evolutionary variability at all codon positions in general, in chloroplast systems. We found that the evolutionary variability and intrinsic secondary structure stability of these sequences share an inverse relationship. Simulations of most likely single nucleotide evolution in Psilotum nudum and Nephroselmis olivacea mRNAs, indicate that helix-forming propensities of mutated mRNAs are greater than those of the natural mRNAs for short sequences and vice-versa for long sequences. Moreover, helix-forming propensity estimated by the percentage of total mRNA in helices increases gradually with mRNA length, saturating beyond 1000 nucleotides. Protection levels of functionally important sites vary across plants and proteins: r-strategists minimize mutation costs in large genes; K-strategists do the opposite. Mrna length presumably predisposes shorter mRNAs to evolve under different constraints than longer mRNAs. The positive correlation between secondary structure protection and functional importance of sites suggests that some sites might be conserved due to packing-protection constraints at the nucleic acid level in addition to protein level constraints. Consequently, nucleic acid secondary structure a priori biases mutations. The converse (exposure of conserved sites) apparently occurs in a smaller number of cases, indicating a different evolutionary adaptive strategy in these plants. The differences between the protection levels of functionally important sites for r- and K-strategists reflect their respective molecular adaptive strategies. These converge with increasing domestication levels of K-strategists, perhaps because domestication increases reproductive output.

Biochemical and structural characterisation of the second oxidative crosslinking step during the biosynthesis of the glycopeptide antibiotic A47934.

PubMed

Ulrich, Veronika; Brieke, Clara; Cryle, Max J

2016-01-01

The chemical complexity and biological activity of the glycopeptide antibiotics (GPAs) stems from their unique crosslinked structure, which is generated by the actions of cytochrome P450 (Oxy) enzymes that affect the crosslinking of aromatic side chains of amino acid residues contained within the GPA heptapeptide precursor. Given the crucial role peptide cyclisation plays in GPA activity, the characterisation of this process is of great importance in understanding the biosynthesis of these important antibiotics. Here, we report the cyclisation activity and crystal structure of StaF, the D- O -E ring forming Oxy enzyme from A47934 biosynthesis. Our results show that the specificity of StaF is reduced when compared to Oxy enzymes catalysing C- O -D ring formation and that this activity relies on interactions with the non-ribosomal peptide synthetase via the X-domain. Despite the interaction of StaF with the A47934 X-domain being weaker than for the preceding Oxy enzyme StaH, StaF retains higher levels of in vitro activity: we postulate that this is due to the ability of the StaF/X-domain complex to allow substrate reorganisation after initial complex formation has occurred. These results highlight the importance of testing different peptide/protein carrier constructs for in vitro GPA cyclisation assays and show that different Oxy homologues can display significantly different catalytic propensities despite their overall similarities.

Expression and mutagenesis of the sea anemone toxin Av2 reveals key amino acid residues important for activity on voltage-gated sodium channels.

PubMed

Moran, Yehu; Cohen, Lior; Kahn, Roy; Karbat, Izhar; Gordon, Dalia; Gurevitz, Michael

2006-07-25

Type I sea anemone toxins are highly potent modulators of voltage-gated Na-channels (Na(v)s) and compete with the structurally dissimilar scorpion alpha-toxins on binding to receptor site-3. Although these features provide two structurally different probes for studying receptor site-3 and channel fast inactivation, the bioactive surface of sea anemone toxins has not been fully resolved. We established an efficient expression system for Av2 (known as ATX II), a highly insecticidal sea anemone toxin from Anemonia viridis (previously named A. sulcata), and mutagenized it throughout. Each toxin mutant was analyzed in toxicity and binding assays as well as by circular dichroism spectroscopy to discern the effects derived from structural perturbation from those related to bioactivity. Six residues were found to constitute the anti-insect bioactive surface of Av2 (Val-2, Leu-5, Asn-16, Leu-18, and Ile-41). Further analysis of nine Av2 mutants on the human heart channel Na(v)1.5 expressed in Xenopus oocytes indicated that the bioactive surfaces toward insects and mammals practically coincide but differ from the bioactive surface of a structurally similar sea anemone toxin, Anthopleurin B, from Anthopleura xanthogrammica. Hence, our results not only demonstrate clear differences in the bioactive surfaces of Av2 and scorpion alpha-toxins but also indicate that despite the general conservation in structure and importance of the Arg-14 loop and its flanking residues Gly-10 and Gly-20 for function, the surface of interaction between different sea anemone toxins and Na(v)s varies.

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

How Life History Can Sway the Fixation Probability of Mutants

PubMed Central

Li, Xiang-Yi; Kurokawa, Shun; Giaimo, Stefano; Traulsen, Arne

2016-01-01

In this work, we study the effects of demographic structure on evolutionary dynamics when selection acts on reproduction, survival, or both. In contrast to the previously discovered pattern that the fixation probability of a neutral mutant decreases while the population becomes younger, we show that a mutant with a constant selective advantage may have a maximum or a minimum of the fixation probability in populations with an intermediate fraction of young individuals. This highlights the importance of life history and demographic structure in studying evolutionary dynamics. We also illustrate the fundamental differences between selection on reproduction and selection on survival when age structure is present. In addition, we evaluate the relative importance of size and structure of the population in determining the fixation probability of the mutant. Our work lays the foundation for also studying density- and frequency-dependent effects in populations when demographic structures cannot be neglected. PMID:27129737

The Importance of Using Games in EFL Classrooms

ERIC Educational Resources Information Center

Gozcu, Emine; Caganaga, Cagda Kivanc

2016-01-01

This paper aims to find out how games are important and effective when used in EFL classrooms. Two different kinds of qualitative research methods: semi-structured interviews and observation were conducted in this study. Multi-method triangulation is used throughout the study. The data was carried out through audio-recorded interview and…

Food choice questionnaire revisited in four countries. Does it still measure the same?

PubMed

Januszewska, Renata; Pieniak, Zuzanna; Verbeke, Wim

2011-08-01

This study focuses on the implementation of the food choice questionnaire (FCQ) across four countries. The first objective is to examine the degree to which the factor structure of the FCQ is invariant across different populations. The second objective is to analyse the motives for food choice in different countries. The cross-sectional sample of 1420 consumers consisted of Belgians (N=458), Hungarians (N=401), Romanians (N=229) and Filipinos (N=332). Data analyses included estimation of five multi-group confirmatory factor analysis models; calculation of mean importance ratings for each food choice factor across countries; ANOVA and Tukey post hoc tests; and a rank order test of most to least important factors within each country. The results confirm that the factorial structure of the FCQ is invariant with respect to factor configuration, factor loadings and item intercept. Sensory appeal is the most important factor among all European consumers, while health, convenience and price were all among the five most important factors shaping food choice in Belgium, Hungary and Romania. For Filipinos, the most important were health, price and mood. Sensory appeal ranked on the fourth place. Copyright © 2011 Elsevier Ltd. All rights reserved.

The Cryoelectron Microscopy Structure of the Type 1 Chaperone-Usher Pilus Rod.

PubMed

Hospenthal, Manuela K; Zyla, Dawid; Costa, Tiago R D; Redzej, Adam; Giese, Christoph; Lillington, James; Glockshuber, Rudi; Waksman, Gabriel

2017-12-05

Adhesive chaperone-usher pili are long, supramolecular protein fibers displayed on the surface of many bacterial pathogens. The type 1 and P pili of uropathogenic Escherichia coli (UPEC) play important roles during urinary tract colonization, mediating attachment to the bladder and kidney, respectively. The biomechanical properties of the helical pilus rods allow them to reversibly uncoil in response to flow-induced forces, allowing UPEC to retain a foothold in the unique and hostile environment of the urinary tract. Here we provide the 4.2-Å resolution cryo-EM structure of the type 1 pilus rod, which together with the previous P pilus rod structure rationalizes the remarkable "spring-like" properties of chaperone-usher pili. The cryo-EM structure of the type 1 pilus rod differs in its helical parameters from the structure determined previously by a hybrid approach. We provide evidence that these structural differences originate from different quaternary structures of pili assembled in vivo and in vitro. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Structural analysis of the human fibroblast growth factor receptor 4 kinase.

PubMed

Lesca, E; Lammens, A; Huber, R; Augustin, M

2014-11-11

The family of fibroblast growth factor receptors (FGFRs) plays an important and well-characterized role in a variety of pathological disorders. FGFR4 is involved in myogenesis and muscle regeneration. Mutations affecting the kinase domain of FGFR4 may cause cancer, for example, breast cancer or rhabdomyosarcoma. Whereas FGFR1-FGFR3 have been structurally characterized, the structure of the FGFR4 kinase domain has not yet been reported. In this study, we present four structures of the kinase domain of FGFR4, in its apo-form and in complex with different types of small-molecule inhibitors. The two apo-FGFR4 kinase domain structures show an activation segment similar in conformation to an autoinhibitory segment observed in the hepatocyte growth factor receptor kinase but different from the known structures of other FGFR kinases. The structures of FGFR4 in complex with the type I inhibitor Dovitinib and the type II inhibitor Ponatinib reveal the molecular interactions with different types of kinase inhibitors and may assist in the design and development of FGFR4 inhibitors. Copyright © 2014 Elsevier Ltd. All rights reserved.

The role of the micro-pattern and nano-topography of hydroxyapatite bioceramics on stimulating osteogenic differentiation of mesenchymal stem cells.

PubMed

Zhao, Cancan; Wang, Xiaoya; Gao, Long; Jing, Linguo; Zhou, Quan; Chang, Jiang

2018-06-01

The micro/nano hybrid structure is considered to be a biomaterial characteristic to stimulate osteogenesis by mimicking the three-dimensional structure of the bone matrix. However, the mechanism of the hybrid structure induced osteogenic differentiation of stem cells is still unknown. For elucidating the mechanisms, one of the challenge is to directly fabricate micro/nano hybrid structure on bioceramics because of its brittleness. In this study, hydroxyapatite (HA) bioceramics with the micro/nano hybrid structure were firstly fabricated via a hydrothermal treatment and template method, and the effect of the different surface structures on the expression of integrins, BMP2 signaling pathways and cell-cell communication was investigated. Interestingly, the results suggested that the osteogenic differentiation induced by micro/nano structures was modulated first through activating integrins and then further activating BMP2 signaling pathway and cell-cell communication, while activated BMP2 could in turn activate integrins and Cx43-related cell-cell communication. Furthermore, differences in activation of integrins, BMP2 signaling pathway, and gap junction-mediated cell-cell communication were observed, in which nanorod and micropattern structures activated different integrin subunits, BMP downstream receptors and Cx43. This finding may explain the synergistic effect of the micro/nano hybrid structure on the activation of osteogenic differentiation of BMSCs. Based on our study, we concluded that the different activation mechanisms of micro- and nano-structures led to the synergistic stimulatory effect on integrin activation and osteogenesis, in which not only the direct contact of cells on micro/nano structure played an important role, but also other surface characteristics such as protein adsorption might contribute to the bioactive effect. The micro/nano hybrid structure has been found to have synergistic bioactivity on osteogenesis. However, it is still a challenge to fabricate the hybrid structure directly on the bioceramics, and the role of micro- and nano-structure, in particular the mechanism of the micro/nano-hybrid structure induced stem cell differentiation is still unknown. In this study, we firstly fabricated hydroxyapatite bioceramics with the micro/nano hybrid structure, and then investigated the effect of different surface structure on expression of integrins, BMP2 signaling pathways and cell-cell communication. Interestingly, we found that the osteogenic differentiation induced by structure was modulated first through activating integrins and then further activating BMP2 signaling pathway and cell-cell communication, and activated BMP2 could in turn activate some integrin subunits and Cx43-related cell-cell communication. Furthermore, differences in activation of integrins, BMP2 signaling pathway, and gap junction-mediated cell-cell communication were observed, in which nanorod and micropattern structures activated different integrin subunits, BMP downstream receptors and Cx43. This finding may explain the synergistic effect of the micro/nano hybrid structure on the activation of osteogenic differentiation of BMSCs. Based on our study, we concluded that the different activation mechanisms of micro- and nano-structures led to the synergistic stimulatory effect on integrin activation and osteogenesis, in which not only the direct contact of cells on micro/nano structure played an important role, but also other surface characteristics such as protein adsorption might contribute to the bioactive effect. Copyright © 2018 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

A fine structure genetic analysis evaluating ecoregional adaptability of a Bos taurus breed (Hereford)

USDA-ARS?s Scientific Manuscript database

Ecoregional differences contribute to genetic environmental interactions and impact animal performance. These differences may become more important under climate change scenarios. Utilizing genetic diversity within a species to address such problems has not been fully explored. In this study Herefor...

Environmental and spatial drivers of taxonomic, functional, and phylogenetic characteristics of bat communities in human-modified landscapes.

PubMed

Cisneros, Laura M; Fagan, Matthew E; Willig, Michael R

2016-01-01

Assembly of species into communities following human disturbance (e.g., deforestation, fragmentation) may be governed by spatial (e.g., dispersal) or environmental (e.g., niche partitioning) mechanisms. Variation partitioning has been used to broadly disentangle spatial and environmental mechanisms, and approaches utilizing functional and phylogenetic characteristics of communities have been implemented to determine the relative importance of particular environmental (or niche-based) mechanisms. Nonetheless, few studies have integrated these quantitative approaches to comprehensively assess the relative importance of particular structuring processes. We employed a novel variation partitioning approach to evaluate the relative importance of particular spatial and environmental drivers of taxonomic, functional, and phylogenetic aspects of bat communities in a human-modified landscape in Costa Rica. Specifically, we estimated the amount of variation in species composition (taxonomic structure) and in two aspects of functional and phylogenetic structure (i.e., composition and dispersion) along a forest loss and fragmentation gradient that are uniquely explained by landscape characteristics (i.e., environment) or space to assess the importance of competing mechanisms. The unique effects of space on taxonomic, functional and phylogenetic structure were consistently small. In contrast, landscape characteristics (i.e., environment) played an appreciable role in structuring bat communities. Spatially-structured landscape characteristics explained 84% of the variation in functional or phylogenetic dispersion, and the unique effects of landscape characteristics significantly explained 14% of the variation in species composition. Furthermore, variation in bat community structure was primarily due to differences in dispersion of species within functional or phylogenetic space along the gradient, rather than due to differences in functional or phylogenetic composition. Variation among bat communities was related to environmental mechanisms, especially niche-based (i.e., environmental) processes, rather than spatial mechanisms. High variation in functional or phylogenetic dispersion, as opposed to functional or phylogenetic composition, suggests that loss or gain of niche space is driving the progressive loss or gain of species with particular traits from communities along the human-modified gradient. Thus, environmental characteristics associated with landscape structure influence functional or phylogenetic aspects of bat communities by effectively altering the ways in which species partition niche space.

Environmental and spatial drivers of taxonomic, functional, and phylogenetic characteristics of bat communities in human-modified landscapes

PubMed Central

Fagan, Matthew E.; Willig, Michael R.

2016-01-01

Background Assembly of species into communities following human disturbance (e.g., deforestation, fragmentation) may be governed by spatial (e.g., dispersal) or environmental (e.g., niche partitioning) mechanisms. Variation partitioning has been used to broadly disentangle spatial and environmental mechanisms, and approaches utilizing functional and phylogenetic characteristics of communities have been implemented to determine the relative importance of particular environmental (or niche-based) mechanisms. Nonetheless, few studies have integrated these quantitative approaches to comprehensively assess the relative importance of particular structuring processes. Methods We employed a novel variation partitioning approach to evaluate the relative importance of particular spatial and environmental drivers of taxonomic, functional, and phylogenetic aspects of bat communities in a human-modified landscape in Costa Rica. Specifically, we estimated the amount of variation in species composition (taxonomic structure) and in two aspects of functional and phylogenetic structure (i.e., composition and dispersion) along a forest loss and fragmentation gradient that are uniquely explained by landscape characteristics (i.e., environment) or space to assess the importance of competing mechanisms. Results The unique effects of space on taxonomic, functional and phylogenetic structure were consistently small. In contrast, landscape characteristics (i.e., environment) played an appreciable role in structuring bat communities. Spatially-structured landscape characteristics explained 84% of the variation in functional or phylogenetic dispersion, and the unique effects of landscape characteristics significantly explained 14% of the variation in species composition. Furthermore, variation in bat community structure was primarily due to differences in dispersion of species within functional or phylogenetic space along the gradient, rather than due to differences in functional or phylogenetic composition. Discussion Variation among bat communities was related to environmental mechanisms, especially niche-based (i.e., environmental) processes, rather than spatial mechanisms. High variation in functional or phylogenetic dispersion, as opposed to functional or phylogenetic composition, suggests that loss or gain of niche space is driving the progressive loss or gain of species with particular traits from communities along the human-modified gradient. Thus, environmental characteristics associated with landscape structure influence functional or phylogenetic aspects of bat communities by effectively altering the ways in which species partition niche space. PMID:27761338

Analyzing the nursing organizational structure and process from a scheduling perspective.

PubMed

Maenhout, Broos; Vanhoucke, Mario

2013-09-01

The efficient and effective management of nursing personnel is of critical importance in a hospital's environment comprising approximately 25 % of the hospital's operational costs. The nurse organizational structure and the organizational processes highly affect the nurses' working conditions and the provided quality of care. In this paper, we investigate the impact of different nurse organization structures and different organizational processes for a real-life situation in a Belgian university hospital. In order to make accurate nurse staffing decisions, the employed solution methodology incorporates shift scheduling characteristics in order to overcome the deficiencies of the many phase-specific methodologies that are proposed in the academic literature.

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

PubMed Central

Estabrook, Ryne

2015-01-01

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

Quantitative Analysis of Defects in Silicon. [to predict energy conversion efficiency of silicon samples for solar cells

NASA Technical Reports Server (NTRS)

Natesh, R.; Smith, J. M.; Qidwai, H. A.; Bruce, T.

1979-01-01

The evaluation and prediction of the conversion efficiency for a variety of silicon samples with differences in structural defects, such as grain boundaries, twin boundaries, precipitate particles, dislocations, etc. are discussed. Quantitative characterization of these structural defects, which were revealed by etching the surface of silicon samples, is performed by using an image analyzer. Due to different crystal growth and fabrication techniques the various types of silicon contain a variety of trace impurity elements and structural defects. The two most important criteria in evaluating the various silicon types for solar cell applications are cost and conversion efficiency.

Definitive Mineralogical Analysis of Martian Rocks and Soil Using the CheMin XRD/XRF Instrument and the USDC Sampler

NASA Technical Reports Server (NTRS)

Blake, D. F.; Sarrazin, P.; Chipera, S. J.; Bish, D. L.; Vaniman, D. T.; Bar-Cohen, Y.; Sherrit, S.; Collins, S.; Boyer, B.; Bryson, C.

2003-01-01

The search for evidence of extant or extinct life on Mars will initially be a search for evidence of present or past conditions supportive of life (e.g., evidence of water), not for life itself. Definitive evidence of past or present water activity lies in the discovery of: * Hydrated minerals: The "rock type" hosting the hydrated minerals could be igneous, metamorphic, or sedimentary, with only a minor hydrated mineral phase. Therefore, the identification of minor phases is important. * Clastic sediments: Clastic sediments are commonly identified by the fact that they contain minerals of disparate origin that could only have come together as a mechanical mixture. Therefore, the identification of all minerals present in a mixture to ascertain mineralogical source regions is important. * Hydrothermal precipitates and chemical sediments: Some chemical precipitates are uniquely identified only by their structure. For example, Opal A, Opal CT, tridymite, crystobalite, high and low Quartz all have the same composition (SiO2) but different crystal structures indicative of different environments - from hydrothermal hydrothermal formation to low temperature precipitation. Other silica types such as stishovite can provide evidence of shock metamorphism. Therefore, identification of crystal structures and structural polymorphs is important. The elucidation of the nature of the Mars soil will require the identification of mineral components that can unravel its history and the history of the Mars atmosphere.

Improving cancer care in Europe: Which institutional health structures might be beneficial and why? 1. European Roundtable Meeting (ERTM), 16th May 2014, Berlin, Germany.

PubMed

Ortmann, Olaf; Helbig, U; Torode, J

2016-01-01

Bringing the knowledge and expertise of different European countries and the European Commission together for an analysis of the different factors being beneficent or rather opposing for high quality in cancer care. A specific focus is set on the structures and views in European nations on implementation processes. Due to the variation of National Cancer Control Plans (NCCPs) the preferences for implementation strategies differ. For quality achievement the involvement of the different stakeholders is beneficial. Common sense was the importance of NCCPs. However, it was consensus between participants that a bottom-up approach that considers the needs of different professional groups involved in cancer care and also the views of patients is of critical importance for successful implementation. Functioning cancer registries and evidence-based guidelines with standard of care are fundamental for quality measurement. There is consensus between participants of the meeting that NCCPs are essential for improvement of cancer care. However, national preferences and the views of patients and caregivers have to be included to guarantee successful implementation.

Implication of the cause of differences in 3D structures of proteins with high sequence identity based on analyses of amino acid sequences and 3D structures.

PubMed

Matsuoka, Masanari; Sugita, Masatake; Kikuchi, Takeshi

2014-09-18

Proteins that share a high sequence homology while exhibiting drastically different 3D structures are investigated in this study. Recently, artificial proteins related to the sequences of the GA and IgG binding GB domains of human serum albumin have been designed. These artificial proteins, referred to as GA and GB, share 98% amino acid sequence identity but exhibit different 3D structures, namely, a 3α bundle versus a 4β + α structure. Discriminating between their 3D structures based on their amino acid sequences is a very difficult problem. In the present work, in addition to using bioinformatics techniques, an analysis based on inter-residue average distance statistics is used to address this problem. It was hard to distinguish which structure a given sequence would take only with the results of ordinary analyses like BLAST and conservation analyses. However, in addition to these analyses, with the analysis based on the inter-residue average distance statistics and our sequence tendency analysis, we could infer which part would play an important role in its structural formation. The results suggest possible determinants of the different 3D structures for sequences with high sequence identity. The possibility of discriminating between the 3D structures based on the given sequences is also discussed.

Combinatorics and synchronization in natural semiotics

NASA Astrophysics Data System (ADS)

Orsucci, Franco; Giuliani, Alessandro; Webber, Charles; Zbilut, Joseph; Fonagy, Peter; Mazza, Marianna

2006-03-01

In this study the derivation of an objective metrics to appreciate the degree of structuring of written and spoken texts is presented. The proposed metrics is based on the scoring of recurrences inside a text by means of the application of recurrence quantification analysis (RQA), a nonlinear technique widely used in other fields of sciences. The adopted approach allowed us to create a ranking of different poems strictly related to their prosodic structure and, more importantly, the possibility to recognize the same structure across different languages, to define a level of structuring typical of spoken texts and identifying the progressive synchronization of a dyadic relation between two speakers in terms of relative complexity of their speeches. These results suggest the possibility of introducing objective measurement methods into humanities studies.

Chemical control of orbital polarization in artificially structured transition-metal oxides: La2NiXO6 (X=B,Al,Ga,In) from first principles

NASA Astrophysics Data System (ADS)

Han, M. J.; Marianetti, C. A.; Millis, A. J.

2010-10-01

The application of modern layer-by-layer growth techniques to transition-metal oxide materials raises the possibility of creating new classes of materials with rationally designed correlated electron properties. An important step toward this goal is the demonstration that electronic structure can be controlled by atomic composition. In compounds with partially occupied transition-metal d shells, one important aspect of the electronic structure is the relative occupancy of different d orbitals. Previous work has established that strain and quantum confinement can be used to influence orbital occupancy. In this paper we demonstrate a different modality for orbital control in transition-metal oxide heterostructures, using density-functional band calculations supplemented by a tight-binding analysis to show that the choice of nontransition-metal counterion X in transition-metal oxide heterostructures composed of alternating LaNiO3 and LaXO3 units strongly affects orbital occupancy, changing the magnitude and in some cases the sign of the orbital polarization.

Chalcones: structural requirements for antioxidant, estrogenic and antiproliferative activities.

PubMed

Calliste, C A; Le Bail, J C; Trouillas, P; Pouget, C; Habrioux, G; Chulia, A J; Duroux, J L

2001-01-01

Flavonoids are largely studied for their biological properties and particularly for their scavenging and antioxidant activities. In the present study, we first evaluated the antioxidant and the estrogenic actions of chalcones, then we tested their effects on MCF-7 cell proliferation. Chalcones are unique in the flavonoids family in lacking a heterocyclic C ring. We tested substituted chalcones with different numbers and different positions of the hydroxy groups: 2'-hydroxychalcone, 4'-hydroxychalcone, 4-hydroxychalcone, 2',4-dihydroxychalcone, isoliquiritigenin, 2',4'-dihydroxychalcone, phloretin and naringenin chalcone. For the antioxidant tests we established the importance of the alpha-beta double bond and the 6'-hydroxy group. The establishment of the structure-activity relationship for the estrogenic properties showed a correlation between the antioxidant and the estrogenic properties. The importance of conformation and hydroxy group positions observed for chalcones, having antioxidant and estrogenic properties, was also observed on MCF-7 cell growth with the same structure-activity relationship. The role of electron and hydrogen transfer in the correlation between these three biological activities was discussed.

Co-acclimation of bacterial communities under stresses of hydrocarbons with different structures

PubMed Central

Wang, Hui; Wang, Bin; Dong, Wenwen; Hu, Xiaoke

2016-01-01

Crude oil is a complex mixture of hydrocarbons with different structures; its components vary in bioavailability and toxicity. It is important to understand how bacterial communities response to different hydrocarbons and their co-acclimation in the process of degradation. In this study, microcosms with the addition of structurally different hydrocarbons were setup to investigate the successions of bacterial communities and the interactions between different bacterial taxa. Hydrocarbons were effectively degraded in all microcosms after 40 days. High-throughput sequencing offered a great quantity of data for analyzing successions of bacterial communities. The results indicated that the bacterial communities responded dramatically different to various hydrocarbons. KEGG database and PICRUSt were applied to predict functions of individual bacterial taxa and networks were constructed to analyze co-acclimations between functional bacterial groups. Almost all functional genes catalyzing degradation of different hydrocarbons were predicted in bacterial communities. Most of bacterial taxa were believed to conduct biodegradation processes via interactions with each other. This study addressed a few investigated area of bacterial community responses to structurally different organic pollutants and their co-acclimation and interactions in the process of biodegradation. The study could provide useful information to guide the bioremediation of crude oil pollution. PMID:27698451

Efficacy of very fast simulated annealing global optimization method for interpretation of self-potential anomaly by different forward formulation over 2D inclined sheet type structure

NASA Astrophysics Data System (ADS)

Biswas, A.; Sharma, S. P.

2012-12-01

Self-Potential anomaly is an important geophysical technique that measures the electrical potential due natural source of current in the Earth's subsurface. An inclined sheet type model is a very familiar structure associated with mineralization, fault plane, groundwater flow and many other geological features which exhibits self potential anomaly. A number of linearized and global inversion approaches have been developed for the interpretation of SP anomaly over different structures for various purposes. Mathematical expression to compute the forward response over a two-dimensional dipping sheet type structures can be described in three different ways using five variables in each case. Complexities in the inversion using three different forward approaches are different. Interpretation of self-potential anomaly using very fast simulated annealing global optimization has been developed in the present study which yielded a new insight about the uncertainty and equivalence in model parameters. Interpretation of the measured data yields the location of the causative body, depth to the top, extension, dip and quality of the causative body. In the present study, a comparative performance of three different forward approaches in the interpretation of self-potential anomaly is performed to assess the efficacy of the each approach in resolving the possible ambiguity. Even though each forward formulation yields the same forward response but optimization of different sets of variable using different forward problems poses different kinds of ambiguity in the interpretation. Performance of the three approaches in optimization has been compared and it is observed that out of three methods, one approach is best and suitable for this kind of study. Our VFSA approach has been tested on synthetic, noisy and field data for three different methods to show the efficacy and suitability of the best method. It is important to use the forward problem in the optimization that yields the best result without any ambiguity and smaller uncertainty. Keywords: SP anomaly, inclined sheet, 2D structure, forward problems, VFSA Optimization,

Structure and Typical Profiles of Elementary Teacher Students' View of Mathematics

ERIC Educational Resources Information Center

Hannula, Markku S.; Kaasila, Raimo; Laine, Anu; Pehkonen, Erkki

2005-01-01

The elementary school teachers' view of mathematics is important because it will influence the way they will teach mathematics. Based on a survey study in three Finnish universities we explored the structure of student teachers view of mathematics and also the different belief profiles that they had. The core of student teachers' view consisted of…

Pyramidal Cells in Prefrontal Cortex of Primates: Marked Differences in Neuronal Structure Among Species

PubMed Central

Elston, Guy N.; Benavides-Piccione, Ruth; Elston, Alejandra; Manger, Paul R.; DeFelipe, Javier

2010-01-01

The most ubiquitous neuron in the cerebral cortex, the pyramidal cell, is characterized by markedly different dendritic structure among different cortical areas. The complex pyramidal cell phenotype in granular prefrontal cortex (gPFC) of higher primates endows specific biophysical properties and patterns of connectivity, which differ from those in other cortical regions. However, within the gPFC, data have been sampled from only a select few cortical areas. The gPFC of species such as human and macaque monkey includes more than 10 cortical areas. It remains unknown as to what degree pyramidal cell structure may vary among these cortical areas. Here we undertook a survey of pyramidal cells in the dorsolateral, medial, and orbital gPFC of cercopithecid primates. We found marked heterogeneity in pyramidal cell structure within and between these regions. Moreover, trends for gradients in neuronal complexity varied among species. As the structure of neurons determines their computational abilities, memory storage capacity and connectivity, we propose that these specializations in the pyramidal cell phenotype are an important determinant of species-specific executive cortical functions in primates. PMID:21347276

Different effects of the TAR structure on HIV-1 and HIV-2 genomic RNA translation

PubMed Central

Soto-Rifo, Ricardo; Limousin, Taran; Rubilar, Paulina S.; Ricci, Emiliano P.; Décimo, Didier; Moncorgé, Olivier; Trabaud, Mary-Anne; André, Patrice; Cimarelli, Andrea; Ohlmann, Théophile

2012-01-01

The 5′-untranslated region (5′-UTR) of the genomic RNA of human immunodeficiency viruses type-1 (HIV-1) and type-2 (HIV-2) is composed of highly structured RNA motifs essential for viral replication that are expected to interfere with Gag and Gag-Pol translation. Here, we have analyzed and compared the properties by which the viral 5′-UTR drives translation from the genomic RNA of both human immunodeficiency viruses. Our results showed that translation from the HIV-2 gRNA was very poor compared to that of HIV-1. This was rather due to the intrinsic structural motifs in their respective 5′-UTR without involvement of any viral protein. Further investigation pointed to a different role of TAR RNA, which was much inhibitory for HIV-2 translation. Altogether, these data highlight important structural and functional differences between these two human pathogens. PMID:22121214

Annealing effects on the structural and magnetic properties of off-stoichiometric Fe-Mn-Ga ferromagnetic shape memory alloys

DOE PAGES

Chen, Yan; Bei, Hongbin; Dela Cruz, Clarina R; ...

2016-05-07

Annealing plays an important role in modifying structures and properties of ferromagnetic shape memory alloys (FSMAs). The annealing effect on the structures and magnetic properties of off-stoichiometric Fe 45Mn 26Ga 29 FSMA has been investigated at different elevated temperatures. Rietveld refinements of neutron diffraction patterns display that the formation of the γ phase in Fe 45Mn 26Ga 29 annealed at 1073 K increases the martensitic transformation temperature and reduces the thermal hysteresis in comparison to the homogenized sample. The phase segregation of a Fe-rich cubic phase and a Ga-rich cubic phase occurs at the annealing temperature of 773 K. Themore » atomic occupancies of the alloys are determined thanks to the neutron's capability of differentiating transition metals. The annealing effects at different temperatures introduce a different magnetic characteristic that is associated with distinctive structural changes in the crystal.« less

Collagens--structure, function, and biosynthesis.

PubMed

Gelse, K; Pöschl, E; Aigner, T

2003-11-28

The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different collagen types identified so far. Collagens are centrally involved in the formation of fibrillar and microfibrillar networks of the extracellular matrix, basement membranes as well as other structures of the extracellular matrix. This review focuses on the distribution and function of various collagen types in different tissues. It introduces their basic structural subunits and points out major steps in the biosynthesis and supramolecular processing of fibrillar collagens as prototypical members of this protein family. A final outlook indicates the importance of different collagen types not only for the understanding of collagen-related diseases, but also as a basis for the therapeutical use of members of this protein family discussed in other chapters of this issue.

Momentum-based morphometric analysis with application to Parkinson's disease

NASA Astrophysics Data System (ADS)

Chen, Jingyun; Khan, Ali R.; McKeown, Martin J.; Beg, Mirza F.

2011-03-01

We apply the initial momentum shape representation of diffeomorphic metric mapping from a template region of interest (ROI) to a given ROI as a morphometic marker in Parkinson's disease. We used a three-step segmentation-registrationmomentum process to derive feature vectors from ROIs in a group of 42 subjects consisting of 19 Parkinson's Disease (PD) subjects and 23 normal control (NC) subjects. Significant group differences between PD and NC subjects were detected in four basal ganglia structures including the caudate, putamen, thalamus and globus pallidus. The magnitude of regionally significant between-group differences detected ranged between 34-75%. Visualization of the different structural deformation pattern between-groups revealed that some parts of basal ganglia structure actually hypertrophy, presumably as a compensatory response to more widespread atrophy. Our results of both hypertrophy and atrophy in the same structures further demonstrate the importance of morphological measures as opposed to overall volume in the assessment of neurodegenerative disease.

Structure of New Zealand sweetpotato starch.

PubMed

Zhu, Fan; Xie, Qian

2018-05-15

New Zealand sweetpotatoes (kumara) (Ipomoea batatas) represent unique genetic resources for sweetpotato diversity, though they are much under-studied. In this study, 7 New Zealand sweetpotato varieties with commercial significance were collected for the characterization of the molecular and granular structure of the starches. In particular, the internal molecular structure of the amylopectins was detailed by chromatographic and enzymatic techniques. Maize and potato starches with normal amylose contents, which are among the most important commercial starch sources, were employed for comparison. The results revealed a degree of diversity in amylose composition, unit and internal chain composition, granule size distribution, and degree of crystallinity among the 7 sweetpotato starches. All the sweetpotato starches showed C A -type polymorph. The sweetpotato amylopectins have intermediate amounts of both short and long internal unit chains among amylopectins of different botanical sources. The differences in the structure of sweetpotato starches suggest differences in physicochemical properties. Copyright © 2018 Elsevier Ltd. All rights reserved.

An environmental decision framework applied to marine engine control technologies.

PubMed

Corbett, James J; Chapman, David

2006-06-01

This paper develops a decision framework for considering emission control technologies on marine engines, informed by standard decision theory, with an open structure that may be adapted by operators with specific vessel and technology attributes different from those provided here. Attributes relate objectives important to choosing control technologies with specific alternatives that may meet several of the objectives differently. The transparent framework enables multiple stakeholders to understand how different subjective judgments and varying attribute properties may result in different technology choices. Standard scoring techniques ensure that attributes are not biased by subjective scoring and that weights are the primary quantitative input where subjective preferences are exercised. An expected value decision structure is adopted that considers probabilities (likelihood) that a given alternative can meet its claims; alternative decision criteria are discussed. Capital and annual costs are combined using a net present value approach. An iterative approach is advocated that allows for screening and disqualifying alternatives that do not meet minimum conditions for acceptance, such as engine warranty or U.S. Coast Guard requirements. This decision framework assists vessel operators in considering explicitly important attributes and in representing choices clearly to other stakeholders concerned about reducing air pollution from vessels. This general decision structure may also be applied similarly to other environmental controls in marine applications.

Interaction between birds and macrofauna within food webs of six intertidal habitats of the Wadden Sea.

PubMed

Horn, Sabine; de la Vega, Camille; Asmus, Ragnhild; Schwemmer, Philipp; Enners, Leonie; Garthe, Stefan; Binder, Kirsten; Asmus, Harald

2017-01-01

The determination of food web structures using Ecological Network Analysis (ENA) is a helpful tool to get insight into complex ecosystem processes. The intertidal area of the Wadden Sea is structured into diverse habitat types which differ in their ecological functioning. In the present study, six different intertidal habitats (i.e. cockle field, razor clam field, mud flat, mussel bank, sand flat and seagrass meadow) were analyzed using ENA to determine similarities and characteristic differences in the food web structure of the systems. All six systems were well balanced between their degree of organization and their robustness. However, they differed in their detailed features. The cockle field and the mussel bank exhibited a strong dependency on external imports. The razor clam field appeared to be a rather small system with low energy transfer. In the mud flat microphytobenthos was used as a main food source and the system appeared to be sensitive to perturbations. Bird predation was the most pronounced in the sand flat and the seagrass meadow and led to an increase in energy transfer and parallel trophic cycles in these habitats. Habitat diversity appears to be an important trait for the Wadden Sea as each subsystem seems to have a specific role in the overall functioning of the entire ecosystem.

Interaction between birds and macrofauna within food webs of six intertidal habitats of the Wadden Sea

PubMed Central

Horn, Sabine; de la Vega, Camille; Asmus, Ragnhild; Schwemmer, Philipp; Enners, Leonie; Garthe, Stefan; Binder, Kirsten; Asmus, Harald

2017-01-01

The determination of food web structures using Ecological Network Analysis (ENA) is a helpful tool to get insight into complex ecosystem processes. The intertidal area of the Wadden Sea is structured into diverse habitat types which differ in their ecological functioning. In the present study, six different intertidal habitats (i.e. cockle field, razor clam field, mud flat, mussel bank, sand flat and seagrass meadow) were analyzed using ENA to determine similarities and characteristic differences in the food web structure of the systems. All six systems were well balanced between their degree of organization and their robustness. However, they differed in their detailed features. The cockle field and the mussel bank exhibited a strong dependency on external imports. The razor clam field appeared to be a rather small system with low energy transfer. In the mud flat microphytobenthos was used as a main food source and the system appeared to be sensitive to perturbations. Bird predation was the most pronounced in the sand flat and the seagrass meadow and led to an increase in energy transfer and parallel trophic cycles in these habitats. Habitat diversity appears to be an important trait for the Wadden Sea as each subsystem seems to have a specific role in the overall functioning of the entire ecosystem. PMID:28489869

Individual differences in brain structure and resting brain function underlie cognitive styles: evidence from the Embedded Figures Test.

PubMed

Hao, Xin; Wang, Kangcheng; Li, Wenfu; Yang, Wenjing; Wei, Dongtao; Qiu, Jiang; Zhang, Qinglin

2013-01-01

Cognitive styles can be characterized as individual differences in the way people perceive, think, solve problems, learn, and relate to others. Field dependence/independence (FDI) is an important and widely studied dimension of cognitive styles. Although functional imaging studies have investigated the brain activation of FDI cognitive styles, the combined structural and functional correlates with individual differences in a large sample have never been investigated. In the present study, we investigated the neural correlates of individual differences in FDI cognitive styles by analyzing the correlations between Embedded Figures Test (EFT) score and structural neuroimaging data [regional gray matter volume (rGMV) was assessed using voxel-based morphometry (VBM)]/functional neuroimaging data [resting-brain functions were measured by amplitude of low-frequency fluctuation (ALFF)] throughout the whole brain. Results showed that the increased rGMV in the left inferior parietal lobule (IPL) was associated with the EFT score, which might be the structural basis of effective local processing. Additionally, a significant positive correlation between ALFF and EFT score was found in the fronto-parietal network, including the left inferior parietal lobule (IPL) and the medial prefrontal cortex (mPFC). We speculated that the left IPL might be associated with superior feature identification, and mPFC might be related to cognitive inhibition of global processing bias. These results suggested that the underlying neuroanatomical and functional bases were linked to the individual differences in FDI cognitive styles and emphasized the important contribution of superior local processing ability and cognitive inhibition to field-independent style.

Individual Differences in Brain Structure and Resting Brain Function Underlie Cognitive Styles: Evidence from the Embedded Figures Test

PubMed Central

Hao, Xin; Wang, Kangcheng; Li, Wenfu; Yang, Wenjing; Wei, Dongtao; Qiu, Jiang; Zhang, Qinglin

2013-01-01

Cognitive styles can be characterized as individual differences in the way people perceive, think, solve problems, learn, and relate to others. Field dependence/independence (FDI) is an important and widely studied dimension of cognitive styles. Although functional imaging studies have investigated the brain activation of FDI cognitive styles, the combined structural and functional correlates with individual differences in a large sample have never been investigated. In the present study, we investigated the neural correlates of individual differences in FDI cognitive styles by analyzing the correlations between Embedded Figures Test (EFT) score and structural neuroimaging data [regional gray matter volume (rGMV) was assessed using voxel-based morphometry (VBM)] / functional neuroimaging data [resting-brain functions were measured by amplitude of low-frequency fluctuation (ALFF)] throughout the whole brain. Results showed that the increased rGMV in the left inferior parietal lobule (IPL) was associated with the EFT score, which might be the structural basis of effective local processing. Additionally, a significant positive correlation between ALFF and EFT score was found in the fronto-parietal network, including the left inferior parietal lobule (IPL) and the medial prefrontal cortex (mPFC). We speculated that the left IPL might be associated with superior feature identification, and mPFC might be related to cognitive inhibition of global processing bias. These results suggested that the underlying neuroanatomical and functional bases were linked to the individual differences in FDI cognitive styles and emphasized the important contribution of superior local processing ability and cognitive inhibition to field-independent style. PMID:24348991

Ensemble-based evaluation for protein structure models.

PubMed

Jamroz, Michal; Kolinski, Andrzej; Kihara, Daisuke

2016-06-15

Comparing protein tertiary structures is a fundamental procedure in structural biology and protein bioinformatics. Structure comparison is important particularly for evaluating computational protein structure models. Most of the model structure evaluation methods perform rigid body superimposition of a structure model to its crystal structure and measure the difference of the corresponding residue or atom positions between them. However, these methods neglect intrinsic flexibility of proteins by treating the native structure as a rigid molecule. Because different parts of proteins have different levels of flexibility, for example, exposed loop regions are usually more flexible than the core region of a protein structure, disagreement of a model to the native needs to be evaluated differently depending on the flexibility of residues in a protein. We propose a score named FlexScore for comparing protein structures that consider flexibility of each residue in the native state of proteins. Flexibility information may be extracted from experiments such as NMR or molecular dynamics simulation. FlexScore considers an ensemble of conformations of a protein described as a multivariate Gaussian distribution of atomic displacements and compares a query computational model with the ensemble. We compare FlexScore with other commonly used structure similarity scores over various examples. FlexScore agrees with experts' intuitive assessment of computational models and provides information of practical usefulness of models. https://bitbucket.org/mjamroz/flexscore dkihara@purdue.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Ensemble-based evaluation for protein structure models

PubMed Central

Jamroz, Michal; Kolinski, Andrzej; Kihara, Daisuke

2016-01-01

Motivation: Comparing protein tertiary structures is a fundamental procedure in structural biology and protein bioinformatics. Structure comparison is important particularly for evaluating computational protein structure models. Most of the model structure evaluation methods perform rigid body superimposition of a structure model to its crystal structure and measure the difference of the corresponding residue or atom positions between them. However, these methods neglect intrinsic flexibility of proteins by treating the native structure as a rigid molecule. Because different parts of proteins have different levels of flexibility, for example, exposed loop regions are usually more flexible than the core region of a protein structure, disagreement of a model to the native needs to be evaluated differently depending on the flexibility of residues in a protein. Results: We propose a score named FlexScore for comparing protein structures that consider flexibility of each residue in the native state of proteins. Flexibility information may be extracted from experiments such as NMR or molecular dynamics simulation. FlexScore considers an ensemble of conformations of a protein described as a multivariate Gaussian distribution of atomic displacements and compares a query computational model with the ensemble. We compare FlexScore with other commonly used structure similarity scores over various examples. FlexScore agrees with experts’ intuitive assessment of computational models and provides information of practical usefulness of models. Availability and implementation: https://bitbucket.org/mjamroz/flexscore Contact: dkihara@purdue.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27307633

Placement of molecules in (not out of) the cell

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

Dauter, Zbigniew, E-mail: dauter@anl.gov

2013-01-01

The importance of presenting macromolecular structures in unified, standard ways is discussed. To uniquely describe a crystal structure, it is sufficient to specify the crystal unit cell and symmetry, and describe the unique structural motif which is repeated by the space-group symmetry throughout the whole crystal. It is somewhat arbitrary how such a unique motif can be defined and positioned with respect to the unit-cell origin. As a result of such freedom, some isomorphous structures are presented in the Protein Data Bank in different locations and appear as if they have different atomic coordinates, despite being completely equivalent structurally. Thismore » may easily confuse those users of the PDB who are less familiar with crystallographic symmetry transformations. It would therefore be beneficial for the community of PDB users to introduce standard rules for locating crystal structures of macromolecules in the unit cells of various space groups.« less

Emollient product design: objective measurements of formulation structure, texture and performance, and subjective assessments of user acceptability.

PubMed

Antonijević, M D; Owusu-Ware, S; Sanchon-Lopez, B

2018-06-01

The choice of prescribed emollients is usually based on cost and patient preference. Differences in formulations can affect user acceptability. To compare the physical performance, user acceptability and various product design features of two emollient gels that are prescribed in the UK and alleged to be therapeutically interchangeable because their formulations are described as having the same contents of oily ingredients. We found that here are in fact significant measurable differences between the structure and performance of the two formulations, which materially affect their user acceptability. These differences are attributed to the use of different types of gelling agents and other ingredients of differing grades/quality and concentrations, and probably due to the formulations being made by different manufacturing processes. We also identified other product design features that are important to user appeal, including the type of container in which the formulations are presented, the type of dispensing devices provided, and the nature and form of the supplied user instructions. Patients and prescribers should be aware that there can be important differences in performance and user appeal between emollients, even between products that, superficially, may appear to be very similar. These important performance aspects should be characterized for new emollient introductions to encourage better informed product selection. © 2018 The Authors. Clinical and Experimental Dermatology published by John Wiley & Sons Ltd on behalf of British Association of Dermatologists, North American Clinical Dermatologic Society and St Johns Dermatological Society.

Function in the Human Connectome: Task-fMRI and Individual Differences in Behavior

PubMed Central

Barch, Deanna M.; Burgess, Gregory C.; Harms, Michael P.; Petersen, Steven E.; Schlaggar, Bradley L.; Corbetta, Maurizio; Glasser, Matthew F.; Curtiss, Sandra; Dixit, Sachin; Feldt, Cindy; Nolan, Dan; Bryant, Edward; Hartley, Tucker; Footer, Owen; Bjork, James M.; Poldrack, Russ; Smith, Steve; Johansen-Berg, Heidi; Snyder, Abraham Z.; Van Essen, David C.

2014-01-01

The primary goal of the Human Connectome Project (HCP) is to delineate the typical patterns of structural and functional connectivity in the healthy adult human brain. However, we know that there are important individual differences in such patterns of connectivity, with evidence that this variability is associated with alterations in important cognitive and behavioral variables that affect real world function. The HCP data will be a critical stepping-off point for future studies that will examine how variation in human structural and functional connectivity play a role in adult and pediatric neurological and psychiatric disorders that account for a huge amount of public health resources. Thus, the HCP is collecting behavioral measures of a range of motor, sensory, cognitive and emotional processes that will delineate a core set of functions relevant to understanding the relationship between brain connectivity and human behavior. In addition, the HCP is using task-fMRI (tfMRI) to help delineate the relationships between individual differences in the neurobiological substrates of mental processing and both functional and structural connectivity, as well as to help characterize and validate the connectivity analyses to be conducted on the structural and functional connectivity data. This paper describes the logic and rationale behind the development of the behavioral, individual difference, and tfMRI batteries and provides preliminary data on the patterns of activation associated with each of the fMRI tasks, at both a group and individual level. PMID:23684877

Network analysis of returns and volume trading in stock markets: The Euro Stoxx case

NASA Astrophysics Data System (ADS)

Brida, Juan Gabriel; Matesanz, David; Seijas, Maria Nela

2016-02-01

This study applies network analysis to analyze the structure of the Euro Stoxx market during the long period from 2002 up to 2014. The paper generalizes previous research on stock market networks by including asset returns and volume trading as the main variables to study the financial market. A multidimensional generalization of the minimal spanning tree (MST) concept is introduced, by adding the role of trading volume to the traditional approach which only includes price returns. Additionally, we use symbolization methods to the raw data to study the behavior of the market structure in different, normal and critical, situations. The hierarchical organization of the network is derived, and the MST for different sub-periods of 2002-2014 is created to illustrate how the structure of the market evolves over time. From the structural topologies of these trees, different clusters of companies are identified and analyzed according to their geographical and economic links. Two important results are achieved. Firstly, as other studies have highlighted, at the time of the financial crisis after 2008 the network becomes a more centralized one. Secondly and most important, during our second period of analysis, 2008-2014, we observe that hierarchy becomes more country-specific where different sub-clusters of stocks belonging to France, Germany, Spain or Italy are found apart from their business sector group. This result may suggest that during this period of time financial investors seem to be worried most about country specific economic circumstances.

Self-Regulation across Different Contexts: Findings in Young Albanian Children

ERIC Educational Resources Information Center

von Suchodoletz, Antje; Uka, Fitim; Larsen, Ross A. A. A.

2015-01-01

Research Findings: The importance of self-regulation for children's successful academic performance has led to greatly increased interest in this topic in recent years. However, less is known about the interrelations among self-regulatory processes across different contexts. The present study investigated the structure of self-regulation in young…

Optimal Design for Two-Level Random Assignment and Regression Discontinuity Studies

ERIC Educational Resources Information Center

Rhoads, Christopher H.; Dye, Charles

2016-01-01

An important concern when planning research studies is to obtain maximum precision of an estimate of a treatment effect given a budget constraint. When research designs have a "multilevel" or "hierarchical" structure changes in sample size at different levels of the design will impact precision differently. Furthermore, there…

Pragmatics Fragmented: The Factor Structure of the Dutch Children's Communication Checklist (CCC)

ERIC Educational Resources Information Center

Geurts, Hilde M.; Hartman, Catharina; Verte, Sylvie; Oosterlaan, Jaap; Roeyers, Herbert; Sergeant, Joseph A.

2009-01-01

Background: A number of disorders are associated with pragmatic difficulties. Instruments that can make subdivisions within the larger construct of pragmatics could be important tools for disentangling profiles of pragmatic difficulty in different disorders. The deficits underlying the observed pragmatic difficulties may be different for different…

District nurses' prescribing practice and its link to structural conditions.

PubMed

Blanck, Susanne; Engström, Maria

2015-10-01

To describe district nurses' (DNs') prescribing practice and examine associations between DNs' self-reported prescribing frequency, opinions about prescribing, and structural conditions/empowerment. A cross-sectional and correlational design was employed. Data were collected during 2012 using questionnaires and a prescribing register. A random sample of 150 DNs from 32 primary care centers in Sweden was invited. DNs' ability to prescribe is used to a relatively small extent and access to "opportunities" and "informal power" seems to be the most important structural empowerment conditions for increased prescribing frequency and positive opinions about prescribing. The results support Kanter's theory of structural empowerment. This article regarding restricted prescribing shows how important structural conditions/empowerment is to DNs' prescribing and employers have to enhance nurses' access to especially the structures "opportunities" and "informal power" to increase nurse prescribing. More targeted support and training are needed in different prescribing areas to make use of DNs' prescription qualification to a greater extent. ©2015 American Association of Nurse Practitioners.

Key vortical structure causing laminar-turbulent transition in a boundary layer disturbed by a short-duration jet

NASA Astrophysics Data System (ADS)

Yoshikawa, Joe; Nishio, Yu; Izawa, Seiichiro; Fukunishi, Yu

2018-01-01

Numerical simulations are carried out to discover the flow structure that plays an important role in the laminar-turbulent transition process of a boundary layer on a flat plate. The boundary layer is destabilized by ejecting a short-duration jet from a hole in the surface. When the jet velocity is set to 20% of the uniform-flow velocity, a laminar-turbulent transition takes place, whereas in the 18% case, the disturbances created by the jet decay downstream. It is found that in both cases, hairpin vortices are generated; however, these first-generation hairpins do not directly cause the transition. Only in the 20% case does a new hairpin vortex of a different shape with wider distance between the legs appear. The new hairpin grows with time and evokes the generation of vortical structures one after another around it, turning the flow turbulent. It is found that the difference between the two cases is whether or not one of the first-generation hairpin vortices gets connected with the nearby longitudinal vortices. Only when the connection is successful is the new hairpin vortex with wider distance between the legs created. For each of several cases tested with changing jet-ejecting conditions, no difference is found in the importance of the role of the hairpin structure. Therefore, we conclude that the hairpin vortex with widespread legs is a key structure in the transition to turbulence.

Aging Differences in Ethnic Skin

PubMed Central

Buainain De Castro Maymone, Mayra; Kundu, Roopal V.

2016-01-01

Aging is an inevitable and complex process that can be described clinically as features of wrinkles, sunspots, uneven skin color, and sagging skin. These cutaneous effects are influenced by both intrinsic and extrinsic factors and often are varied based on ethnic origin given underlying structural and functional differences. The authors sought to provide updated information on facets of aging and how it relates to ethnic variation given innate differences in skin structure and function. Publications describing structural and functional principles of ethnic and aging skin were primarily found through a PubMed literature search and supplemented with a review of textbook chapters. The most common signs of skin aging despite skin type are dark spots, loss of elasticity, loss of volume, and rhytides. Skin of color has many characteristics that make its aging process unique. Those of Asian, Hispanic, and African American descent have distinct facial structures. Differences in the concentration of epidermal melanin makes darkly pigmented persons more vulnerable to dyspigmentation, while a thicker and more compact dermis makes facial lines less noticeable. Ethnic skin comprises a large portion of the world population. Therefore, it is important to understand the unique structural and functional differences among ethnicities to adequately treat the signs of aging. PMID:26962390

A US Army Reserve (USAR) Noncommissioned Officer (NCO) Tacit Knowledge Inventory: Flexible Structure for Squad-Level Leader Self-Development

DTIC Science & Technology

2008-06-01

biases about people or racism 6 Very Important THEN you will quickly learn to change your mind or hide your true feelings AND you will 5 Moderately...Very Important race, religion, gender or culture AND you want to build an effective team THEN you Moderately Important must educate yourself AND your...Soldiers on 4 Important cultural, racial, religious, or gender -related differences in the Soldiers which may impact Moderately Unimportant how

Machine Learning and Network Analysis of Molecular Dynamics Trajectories Reveal Two Chains of Red/Ox-specific Residue Interactions in Human Protein Disulfide Isomerase.

PubMed

Karamzadeh, Razieh; Karimi-Jafari, Mohammad Hossein; Sharifi-Zarchi, Ali; Chitsaz, Hamidreza; Salekdeh, Ghasem Hosseini; Moosavi-Movahedi, Ali Akbar

2017-06-16

The human protein disulfide isomerase (hPDI), is an essential four-domain multifunctional enzyme. As a result of disulfide shuffling in its terminal domains, hPDI exists in two oxidation states with different conformational preferences which are important for substrate binding and functional activities. Here, we address the redox-dependent conformational dynamics of hPDI through molecular dynamics (MD) simulations. Collective domain motions are identified by the principal component analysis of MD trajectories and redox-dependent opening-closing structure variations are highlighted on projected free energy landscapes. Then, important structural features that exhibit considerable differences in dynamics of redox states are extracted by statistical machine learning methods. Mapping the structural variations to time series of residue interaction networks also provides a holistic representation of the dynamical redox differences. With emphasizing on persistent long-lasting interactions, an approach is proposed that compiled these time series networks to a single dynamic residue interaction network (DRIN). Differential comparison of DRIN in oxidized and reduced states reveals chains of residue interactions that represent potential allosteric paths between catalytic and ligand binding sites of hPDI.

Different Scalable Implementations of Collision and Streaming for Optimal Computational Performance of Lattice Boltzmann Simulations

NASA Astrophysics Data System (ADS)

Geneva, Nicholas; Wang, Lian-Ping

2015-11-01

In the past 25 years, the mesoscopic lattice Boltzmann method (LBM) has become an increasingly popular approach to simulate incompressible flows including turbulent flows. While LBM solves more solution variables compared to the conventional CFD approach based on the macroscopic Navier-Stokes equation, it also offers opportunities for more efficient parallelization. In this talk we will describe several different algorithms that have been developed over the past 10 plus years, which can be used to represent the two core steps of LBM, collision and streaming, more effectively than standard approaches. The application of these algorithms spans LBM simulations ranging from basic channel to particle laden flows. We will cover the essential detail on the implementation of each algorithm for simple 2D flows, to the challenges one faces when using a given algorithm for more complex simulations. The key is to explore the best use of data structure and cache memory. Two basic data structures will be discussed and the importance of effective data storage to maximize a CPU's cache will be addressed. The performance of a 3D turbulent channel flow simulation using these different algorithms and data structures will be compared along with important hardware related issues.

Household Location and Schools in Metropolitan Areas with Heterogeneous Suburbs; Tiebout, Alonso, and Government Policy. NBER Working Paper No. 15915

ERIC Educational Resources Information Center

Hanushek, Eric A.; Yilmaz, Kuzey

2010-01-01

An important element in considering school finance policies is that households are not passive but instead respond to policies. Household behavior is especially important in considering how households affect the spatial structure of metropolitan areas where different jurisdictions incorporate bundles of advantages and disadvantages. This paper…

The elusive structural role of ubiquitinated histones.

PubMed

Moore, Susan C; Jason, Laure; Ausió, Juan

2002-01-01

It is increasingly apparent that histone posttranslational modifications are important in chromatin structure and dynamics. However, histone ubiquitination has received little attention. Histones H1, H3, H2A, and H2B can be ubiquitinated in vivo, but the most prevalent are uH2A and uH2B. The size of this modification suggests some sort of structural impact. Physiological observations suggest that ubiquitinated histones may have multiple functions and structural effects. Ubiquitinated histones have been correlated with transcriptionally active DNA, implying that it may prevent chromatin folding or help maintain an open conformation. Also, in some organisms during spermiogenesis, a process involving extensive chromatin remodeling, uH2A levels increase just prior to histone replacement by protamines. Determination of chromatin's structural changes resulting from histone ubiquitination is therefore important. Recent work using reconstituted nucleosomes and chromatin fibers containing uH2A indicate that in the absence of linker histones, ubiquitination has little structural impact. DNase I digests and analytical ultracentrifugation of reconstituted ubiquitinated nucleosomes show no structural differences. Solubility assays using reconstituted chromatin fibers in the presence of divalent ions demonstrate that uH2A fibers are slightly more prone to aggregation than controls, and analytical ultracentrifugation results with different MgCl2 and NaCl concentrations determined that chromatin folding is not affected by this modification. Additional work to assess possible synergistic affects with histone acetylation also precludes any structural implications. Protamine displacement experiments concluded that the presence of uH2A does not significantly affect the ability of the protamines to displace histones. In addition, uH2A does not interfere with histone H1 binding to the nucleosome. While work with uH2B remains insufficient to come to any definitive conclusions about its structural impact, current work with uH-2A indicates that, contrary to predictions, this histone modification does not affect either nucleosome or chromatin structure. Consequently, the search for a structural role for ubiquitinated histones continues and their effect on and importance in chromatin dynamics remains elusive.

Tree community variation in a tropical continental island according to slope aspect and human interference.

PubMed

Gonçalves, Nathan B; Nettesheim, Felipe C; Conde, Marilena M S

2018-01-01

Associating description of unrecorded tropical tree community structure to sampling approaches that can help determine mechanisms behind floristic variation is important to further the comprehension of how plant species coexist at tropical forests. Thus, this study had the goals of (i) evaluating tree community structure on the continental island of Marambaia (23°4'37.09"S; 43°59'2.15"W) and (ii) testing the prediction that there are local scale changes in a tropical tree community structure between slopes facing different geographic orientation and with distinct human interference history. We established 60 (0.6 ha) sampling units in three different slope sites with distinct predominant geographic orientation and human interference. We sampled all woody trees with diameter at breast height (dbh) ≥ 5 cm. We found a total of 1.170 individuals representing 220 species, 120 genera and 50 families. The overall tree community structure and structural descriptors (abundance of individuals, basal area, species richness and diversity) varied extensively between the sites. The evidence presented here supports that local scale topography variations and human interference history can be important factors contributing to the known floristic heterogeneity of the Atlantic Rainforest. Future work on the study area should focus on disentangling effects from distinct causal factors over tree community variation and species occurrence.

Sensitivity and Limitations of Structures from X-ray and Neutron-Based Diffraction Analyses of Transition Metal Oxide Lithium-Battery Electrodes

DOE PAGES

Liu, Hao; Liu, Haodong; Lapidus, Saul H.; ...

2017-06-21

Lithium transition metal oxides are an important class of electrode materials for lithium-ion batteries. Binary or ternary (transition) metal doping brings about new opportunities to improve the electrode’s performance and often leads to more complex stoichiometries and atomic structures than the archetypal LiCoO 2. Rietveld structural analyses of X-ray and neutron diffraction data is a widely-used approach for structural characterization of crystalline materials. But, different structural models and refinement approaches can lead to differing results, and some parameters can be difficult to quantify due to the inherent limitations of the data. Here, through the example of LiNi 0.8Co 0.15Al 0.05Omore » 2 (NCA), we demonstrated the sensitivity of various structural parameters in Rietveld structural analysis to different refinement approaches and structural models, and proposed an approach to reduce refinement uncertainties due to the inexact X-ray scattering factors of the constituent atoms within the lattice. Furthermore, this refinement approach was implemented for electrochemically-cycled NCA samples and yielded accurate structural parameters using only X-ray diffraction data. The present work provides the best practices for performing structural refinement of lithium transition metal oxides.« less

Sensitivity and Limitations of Structures from X-ray and Neutron-Based Diffraction Analyses of Transition Metal Oxide Lithium-Battery Electrodes

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

Liu, Hao; Liu, Haodong; Lapidus, Saul H.

Lithium transition metal oxides are an important class of electrode materials for lithium-ion batteries. Binary or ternary (transition) metal doping brings about new opportunities to improve the electrode’s performance and often leads to more complex stoichiometries and atomic structures than the archetypal LiCoO 2. Rietveld structural analyses of X-ray and neutron diffraction data is a widely-used approach for structural characterization of crystalline materials. But, different structural models and refinement approaches can lead to differing results, and some parameters can be difficult to quantify due to the inherent limitations of the data. Here, through the example of LiNi 0.8Co 0.15Al 0.05Omore » 2 (NCA), we demonstrated the sensitivity of various structural parameters in Rietveld structural analysis to different refinement approaches and structural models, and proposed an approach to reduce refinement uncertainties due to the inexact X-ray scattering factors of the constituent atoms within the lattice. Furthermore, this refinement approach was implemented for electrochemically-cycled NCA samples and yielded accurate structural parameters using only X-ray diffraction data. The present work provides the best practices for performing structural refinement of lithium transition metal oxides.« less

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

PubMed

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

2014-10-01

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

Structural Integrity of Proteins under Applied Bias during Solid-State Nanopore Translocation

NASA Astrophysics Data System (ADS)

Hasan, Mohammad R.; Khanzada, Raja Raheel; Mahmood, Mohammed A. I.; Ashfaq, Adnan; Iqbal, Samir M.

2015-03-01

The translocation behavior of proteins through solid-state nanopores can be used as a new way to detect and identify proteins. The ionic current through a nanopore that flows under applied bias gets perturbed when a biomolecule traverses the Nanopore. It is important for a protein detection scheme to know of any changes in the three-dimensional structure of the molecule during the process. Here we report the data on structural integrity of protein during translocation through nanopore under different applied biases. Nanoscale Molecular Dynamic was used to establish a framework to study the changes in protein structures as these travelled across the nanopore. The analysis revealed the contributions of structural changes of protein to its ionic current signature. As a model, thrombin protein crystalline structure was imported and positioned inside a 6 nm diameter pore in a 6 nm thick silicon nitride membrane. The protein was solvated in 1 M KCl at 295 K and the system was equilibrated for 20 ns to attain its minimum energy state. The simulation was performed at different electric fields from 0 to 1 kCal/(mol.Å.e). RMSD, radial distribution function, movement of the center of mass and velocity of the protein were calculated. The results showed linear increments in the velocity and perturbations in ionic current profile with increasing electric potential. Support Acknowledged from NSF through ECCS-1201878.

Structural studies of Pseudomonas and Chromobacterium ω-aminotransferases provide insights into their differing substrate specificity

PubMed Central

Sayer, Christopher; Isupov, Michail N.; Westlake, Aaron; Littlechild, Jennifer A.

2013-01-01

The crystal structures and inhibitor complexes of two industrially important ω-aminotransferase enzymes from Pseudomonas aeruginosa and Chromobacterium violaceum have been determined in order to understand the differences in their substrate specificity. The two enzymes share 30% sequence identity and use the same amino acceptor, pyruvate; however, the Pseudomonas enzyme shows activity towards the amino donor β-alanine, whilst the Chromobacterium enzyme does not. Both enzymes show activity towards S-α-methylbenzylamine (MBA), with the Chromobacterium enzyme having a broader substrate range. The crystal structure of the P. aeruginosa enzyme has been solved in the holo form and with the inhibitor gabaculine bound. The C. violaceum enzyme has been solved in the apo and holo forms and with gabaculine bound. The structures of the holo forms of both enzymes are quite similar. There is little conformational difference observed between the inhibitor complex and the holoenzyme for the P. aeruginosa aminotransferase. In comparison, the crystal structure of the C. violaceum gabaculine complex shows significant structural rearrangements from the structures of both the apo and holo forms of the enzyme. It appears that the different rigidity of the protein scaffold contributes to the substrate specificity observed for the two ω-­aminotransferases. PMID:23519665

Leaving Group Ability Observably Affects Transition State Structure in a Single Enzyme Active Site.

PubMed

Roston, Daniel; Demapan, Darren; Cui, Qiang

2016-06-15

A reaction's transition state (TS) structure plays a critical role in determining reactivity and has important implications for the design of catalysts, drugs, and other applications. Here, we explore TS structure in the enzyme alkaline phosphatase using hybrid Quantum Mechanics/Molecular Mechanics simulations. We find that minor perturbations to the substrate have major effects on TS structure and the way the enzyme stabilizes the TS. Substrates with good leaving groups (LGs) have little cleavage of the phosphorus-LG bond at the TS, while substrates with poor LGs have substantial cleavage of that bond. The results predict nonlinear free energy relationships for a single rate-determining step, and substantial differences in kinetic isotope effects for different substrates; both trends were observed in previous experimental studies, although the original interpretations differed from the present model. Moreover, due to different degrees of phosphorus-LG bond cleavage at the TS for different substrates, the LG is stabilized by different interactions at the TS: while a poor LG is directly stabilized by an active site zinc ion, a good LG is mainly stabilized by active site water molecules. Our results demonstrate the considerable plasticity of TS structure and stabilization in enzymes. Furthermore, perturbations to reactivity that probe TS structure experimentally (i.e., substituent effects) may substantially perturb the TS they aim to probe, and thus classical experimental approaches such as free energy relations should be interpreted with care.

Structural comparison of nickel electrodes and precursor phases

NASA Technical Reports Server (NTRS)

Cornilsen, Bahne C.; Shan, Xiaoyin; Loyselle, Patricia

1989-01-01

Researchers summarize previous Raman spectroscopic results and discuss important structural differences in the various phases of active mass and active mass precursors. Raman spectra provide unique signatures for these phases, and allow one to distinguish each phase, even when the compound is amorphous to x rays (i.e., does not scatter x rays because of a lack of order and/or small particle size). The structural changes incurred during formation, charge and discharge, cobalt addition, and aging are discussed. The oxidation states and dopant contents are explained in terms of the nonstoichiometric structures.

Virtual screening of compound libraries.

PubMed

Cerqueira, Nuno M F S A; Sousa, Sérgio F; Fernandes, Pedro A; Ramos, Maria João

2009-01-01

During the last decade, Virtual Screening (VS) has definitively established itself as an important part of the drug discovery and development process. VS involves the selection of likely drug candidates from large libraries of chemical structures by using computational methodologies, but the generic definition of VS encompasses many different methodologies. This chapter provides an introduction to the field by reviewing a variety of important aspects, including the different types of virtual screening methods, and the several steps required for a successful virtual screening campaign within a state-of-the-art approach, from target selection to postfilter application. This analysis is further complemented with a small collection important VS success stories.

Hydration in drug design. 3. Conserved water molecules at the ligand-binding sites of homologous proteins

NASA Astrophysics Data System (ADS)

Poornima, C. S.; Dean, P. M.

1995-12-01

Water molecules are known to play an important rôle in mediating protein-ligand interactions. If water molecules are conserved at the ligand-binding sites of homologous proteins, such a finding may suggest the structural importance of water molecules in ligand binding. Structurally conserved water molecules change the conventional definition of `binding sites' by changing the shape and complementarity of these sites. Such conserved water molecules can be important for site-directed ligand/drug design. Therefore, five different sets of homologous protein/protein-ligand complexes have been examined to identify the conserved water molecules at the ligand-binding sites. Our analysis reveals that there are as many as 16 conserved water molecules at the FAD binding site of glutathione reductase between the crystal structures obtained from human and E. coli. In the remaining four sets of high-resolution crystal structures, 2-4 water molecules have been found to be conserved at the ligand-binding sites. The majority of these conserved water molecules are either bound in deep grooves at the protein-ligand interface or completely buried in cavities between the protein and the ligand. All these water molecules, conserved between the protein/protein-ligand complexes from different species, have identical or similar apolar and polar interactions in a given set. The site residues interacting with the conserved water molecules at the ligand-binding sites have been found to be highly conserved among proteins from different species; they are more conserved compared to the other site residues interacting with the ligand. These water molecules, in general, make multiple polar contacts with protein-site residues.

Structural color mechanism in the Papilio blumei butterfly.

PubMed

Lo, Mei-Ling; Lee, Cheng-Chung

2014-02-01

The structural color found in biological systems has complicated nanostructure. It is very important to determine its color mechanism. In this study, the 2D photonic crystal structures of the Papilio blumei butterfly were constructed, and the corresponding reflectance spectra were simulated by the finite-difference time-domain method. The structural color of the butterfly depends on the incident angle of light, film thickness, film material (film refractive index), and the size of the air hole (effective refractive index). Analysis of simulations can help us understand the hue, brightness, and saturation of structural color on the butterfly wing. As a result, the analysis can help us fabricate expected structural color.

Shape-related characteristics of age-related differences in subcortical structures.

PubMed

Madan, Christopher R

2018-01-11

With an increasing aging population, it is important to understand biological markers of aging. Subcortical volume is known to differ with age; additionally considering shape-related characteristics may provide a better index of age-related differences. Fractal dimensionality is more sensitive to age-related differences, but is borne out of mathematical principles, rather than neurobiological relevance. We considered four distinct measures of shape and how they relate to aging and fractal dimensionality: surface-to-volume ratio, sphericity, long-axis curvature, and surface texture. Structural MRIs from a combined sample of over 600 healthy adults were used to measure age-related differences in the structure of the thalamus, putamen, caudate, and hippocampus. For each, volume and fractal dimensionality were calculated, as well as four distinct shape measures. These measures were examined for their utility in explaining age-related variability in brain structure. The four shape measures were able to account for 80%-90% of the variance in fractal dimensionality. Of the distinct shape measures, surface-to-volume ratio was the most sensitive biomarker. Though volume is often used to characterize inter-individual differences in subcortical structures, our results demonstrate that additional measures can be useful complements. Our results indicate that shape characteristics are useful biological markers of aging.

Importance of inoculum properties on the structure and growth of bacterial communities during Recolonisation of humus soil with different pH.

PubMed

Pettersson, Marie; Bååth, Erland

2013-08-01

The relationship between community structure and growth and pH tolerance of a soil bacterial community was studied after liming in a reciprocal inoculum study. An unlimed (UL) humus soil with a pH of 4.0 was fumigated with chloroform for 4 h, after which < 1 % of the initial bacterial activity remained. Half of the fumigated soil was experimentally limed (EL) to a pH of 7.6. Both the UL and the EL soil were then reciprocally inoculated with UL soil or field limed (FL) soil with a pH of 6.2. The FL soil was from a 15-year-old experiment. The structural changes were measured on both bacteria in soil and on bacteria able to grow on agar plates using phospholipids fatty acid (PLFA) and denaturing gradient gel electrophoresis (DGGE) analysis. The developing community pH tolerance and bacterial growth were also monitored over time using thymidine incorporation. The inoculum source had a significant impact on both growth and pH tolerance of the bacterial community in the EL soil. These differences between the EL soil inoculated with UL soil and FL soil were correlated to structural changes, as evidenced by both PLFA and DGGE analyses on the soil. Similar correlations were seen to the fraction of the community growing on agar plates. There were, however, no differences between the soil bacterial communities in the unlimed soils with different inocula. This study showed the connection between the development of function (growth), community properties (pH tolerance) and the structure of the bacterial community. It also highlighted the importance of both the initial properties of the community and the selection pressure after environmental changes in shaping the resulting microbial community.

Impact of Protein-Metal Ion Interactions on the Crystallization of Silk Fibroin Protein

NASA Astrophysics Data System (ADS)

Hu, Xiao; Lu, Qiang; Kaplan, David; Cebe, Peggy

2009-03-01

Proteins can easily form bonds with a variety of metal ions, which provides many unique biological functions for the protein structures, and therefore controls the overall structural transformation of proteins. We use advanced thermal analysis methods such as temperature modulated differential scanning calorimetry and quasi-isothermal TMDSC, combined with Fourier transform infrared spectroscopy, and scanning electron microscopy, to investigate the protein-metallic ion interactions in Bombyx mori silk fibroin proteins. Silk samples were mixed with different metal ions (Ca^2+, K^+, Ma^2+, Na^+, Cu^2+, Mn^2+) with different mass ratios, and compared with the physical conditions in the silkworm gland. Results show that all metallic ions can directly affect the crystallization behavior and glass transition of silk fibroin. However, different ions tend to have different structural impact, including their role as plasticizer or anti-plasticizer. Detailed studies reveal important information allowing us better to understand the natural silk spinning and crystallization process.

Non-anticoagulant effects of low molecular weight heparins in inflammatory disorders: A review.

PubMed

Yan, Yishu; Ji, Yang; Su, Nan; Mei, Xiang; Wang, Yi; Du, Shanshan; Zhu, Wenming; Zhang, Chong; Lu, Yuan; Xing, Xin-Hui

2017-03-15

Low molecular weight heparins (LMWHs) are produced by chemical or enzymatic depolymerization of unfractionated heparin (UFH). Besides their well-known anticoagulant effects, LMWHs have also been reported to exhibit numerous anti-inflammatory properties. Previous studies have, however, shown that different production processes result in unique structural characteristics of LMWHs. The structural variations may help explain the different therapeutic spectrums in disease treatment for non-anticoagulant effects. In the present review, we summarize major advances in understanding and exploiting the anti-inflammatory disorder activities of LMWHs, based on mechanistic studies, preclinical experiments and clinical trials. We highlight differences in these activities of commercially available LMWHs produced using different manufacturing processes. We stress the importance of structure-activity relationship (SAR) studies on the non-anticoagulant effects of LMWHs and discuss strategies for exploring new clinical indications. Copyright © 2016 Elsevier Ltd. All rights reserved.

Towards predictive molecular dynamics simulations of DNA: electrostatics and solution/crystal environments

NASA Astrophysics Data System (ADS)

Babin, Volodymr; Baucom, Jason; Darden, Thomas; Sagui, Celeste

2006-03-01

We have investigated to what extend molecular dynamics (MD) simulatons can reproduce DNA sequence-specific features, given different electrostatic descriptions and different cell environments. For this purpose, we have carried out multiple unrestrained MD simulations of the duplex d(CCAACGTTGG)2. With respect to the electrostatic descriptions, two different force fields were studied: a traditional description based on atomic point charges and a polarizable force field. With respect to the cell environment, the difference between crystal and solution environments is emphasized, as well as the structural importance of divalent ions. By imposing the correct experimental unit cell environment, an initial configuration with two ideal B-DNA duplexes in the unit cell is shown to converge to the crystallographic structure. To the best of our knowledge, this provides the first example of a multiple nanosecond MD trajectory that shows and ideal structure converging to an experimental one, with a significant decay of the RMSD.

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.

Residual Stress Measurement and Calibration for A7N01 Aluminum Alloy Welded Joints by Using Longitudinal Critically Refracted ( LCR) Wave Transmission Method

NASA Astrophysics Data System (ADS)

Zhu, Qimeng; Chen, Jia; Gou, Guoqing; Chen, Hui; Li, Peng; Gao, W.

2016-10-01

Residual stress measurement and control are highly important for the safety of structures of high-speed trains, which is critical for the structure design. The longitudinal critically refracted wave technology is the most widely used method in measuring residual stress with ultrasonic method, but its accuracy is strongly related to the test parameters, namely the flight time at the free-stress condition ( t 0), stress coefficient ( K), and initial stress (σ0) of the measured materials. The difference of microstructure in the weld zone, heat affected zone, and base metal (BM) results in the divergence of experimental parameters. However, the majority of researchers use the BM parameters to determine the residual stress in other zones and ignore the initial stress (σ0) in calibration samples. Therefore, the measured residual stress in different zones is often high in errors and may result in the miscalculation of the safe design of important structures. A serious problem in the ultrasonic estimation of residual stresses requires separation between the microstructure and the acoustoelastic effects. In this paper, the effects of initial stress and microstructure on stress coefficient K and flight time t 0 at free-stress conditions have been studied. The residual stress with or without different corrections was investigated. The results indicated that the residual stresses obtained with correction are more accurate for structure design.

The effects of thinning intensity on snag and cavity tree abundance in an Appalachian hardwood stand

Treesearch

Aaron T. Graves; Mary Ann Fajvan; Gary W. Miller

2000-01-01

Traditional silvicultural practices focus on manipulating forest vegetation structure for commodity production. Structural features important to wildlife, such as snags, trees with decay, and cavity trees are also affected by forest management, but these effects are often not quantified. This study measured the effects of different thinning intensities (45, 60, and 75...

Comprehensive comparative analysis and identification of RNA-binding protein domains: multi-class classification and feature selection.

PubMed

Jahandideh, Samad; Srinivasasainagendra, Vinodh; Zhi, Degui

2012-11-07

RNA-protein interaction plays an important role in various cellular processes, such as protein synthesis, gene regulation, post-transcriptional gene regulation, alternative splicing, and infections by RNA viruses. In this study, using Gene Ontology Annotated (GOA) and Structural Classification of Proteins (SCOP) databases an automatic procedure was designed to capture structurally solved RNA-binding protein domains in different subclasses. Subsequently, we applied tuned multi-class SVM (TMCSVM), Random Forest (RF), and multi-class ℓ1/ℓq-regularized logistic regression (MCRLR) for analysis and classifying RNA-binding protein domains based on a comprehensive set of sequence and structural features. In this study, we compared prediction accuracy of three different state-of-the-art predictor methods. From our results, TMCSVM outperforms the other methods and suggests the potential of TMCSVM as a useful tool for facilitating the multi-class prediction of RNA-binding protein domains. On the other hand, MCRLR by elucidating importance of features for their contribution in predictive accuracy of RNA-binding protein domains subclasses, helps us to provide some biological insights into the roles of sequences and structures in protein-RNA interactions.

Vegetation structure of plantain-based agrosystems determines numerical dominance in community of ground-dwelling ants

PubMed Central

Dassou, Anicet Gbéblonoudo; Tixier, Philippe; Dépigny, Sylvain

2017-01-01

In tropics, ants can represent an important part of animal biomass and are known to be involved in ecosystem services, such as pest regulation. Understanding the mechanisms underlying the structuring of local ant communities is therefore important in agroecology. In the humid tropics of Africa, plantains are cropped in association with many other annual and perennial crops. Such agrosystems differ greatly in vegetation diversity and structure and are well-suited for studying how habitat-related factors affect the ant community. We analysed abundance data for the six numerically dominant ant taxa in 500 subplots located in 20 diversified, plantain-based fields. We found that the density of crops with foliage at intermediate and high canopy strata determined the numerical dominance of species. We found no relationship between the numerical dominance of each ant taxon with the crop diversity. Our results indicate that the manipulation of the densities of crops with leaves in the intermediate and high strata may help maintain the coexistence of ant species by providing different habitat patches. Further research in such agrosystems should be performed to assess if the effect of vegetation structure on ant abundance could result in efficient pest regulation. PMID:29152414

Interfacial Shear Strength of Multilayer Graphene Oxide Films.

PubMed

Daly, Matthew; Cao, Changhong; Sun, Hao; Sun, Yu; Filleter, Tobin; Singh, Chandra Veer

2016-02-23

Graphene oxide (GO) is considered as one of the most promising layered materials with tunable physical properties and applicability in many important engineering applications. In this work, the interfacial behavior of multilayer GO films was directly investigated via GO-to-GO friction force microscopy, and the interfacial shear strength (ISS) was measured to be 5.3 ± 3.2 MPa. Based on high resolution atomic force microscopy images and the available chemical data, targeted molecular dynamics simulations were performed to evaluate the influence of functional structure, topological defects, and interlayer registry on the shear response of the GO films. Theoretical values for shear strength ranging from 17 to 132 MPa were predicted for the different structures studied, providing upper bounds for the ISS. Computational results also revealed the atomic origins of the stochastic nature of friction measurements. Specifically, the wide scatter in experimental measurements was attributed to variations in functional structure and topological defects within the sliding volume. The findings of this study provide important insight for understanding the significant differences in strength between monolayer and bulk graphene oxide materials and can be useful for engineering topological structures with tunable mechanical properties.

Vegetation structure of plantain-based agrosystems determines numerical dominance in community of ground-dwelling ants.

PubMed

Dassou, Anicet Gbéblonoudo; Tixier, Philippe; Dépigny, Sylvain; Carval, Dominique

2017-01-01

In tropics, ants can represent an important part of animal biomass and are known to be involved in ecosystem services, such as pest regulation. Understanding the mechanisms underlying the structuring of local ant communities is therefore important in agroecology. In the humid tropics of Africa, plantains are cropped in association with many other annual and perennial crops. Such agrosystems differ greatly in vegetation diversity and structure and are well-suited for studying how habitat-related factors affect the ant community. We analysed abundance data for the six numerically dominant ant taxa in 500 subplots located in 20 diversified, plantain-based fields. We found that the density of crops with foliage at intermediate and high canopy strata determined the numerical dominance of species. We found no relationship between the numerical dominance of each ant taxon with the crop diversity. Our results indicate that the manipulation of the densities of crops with leaves in the intermediate and high strata may help maintain the coexistence of ant species by providing different habitat patches. Further research in such agrosystems should be performed to assess if the effect of vegetation structure on ant abundance could result in efficient pest regulation.

Role of ice structuring proteins on freezing-thawing cycles of pasta sauces.

PubMed

Calderara, Marianna; Deorsola, Fabio A; Bensaid, Samir; Fino, Debora; Russo, Nunzio; Geobaldo, Francesco

2016-12-01

The freezing of the food is one of the most important technological developments for the storage of food in terms of quality and safety. The aim of this work was to study the role of an ice structuring protein (ISP) on freezing-thawing cycles of different solutions and commercial Italian pasta sauces. Ice structuring proteins were related to the modification of the structure of ice. The results showed that the freezing time of an aqueous solution containing the protein was reduced to about 20% with respect to a pure water solution. The same effect was demonstrated in sugar-containing solutions and in lipid-containing sauces. The study proved a specific role of ISP during thawing, inducing a time decrease similar to that of freezing and even more important in the case of tomato-based sauces. This work demonstrated the role of ISP in the freezing-thawing process, showing a significant reduction of processing in the freezing and thawing phase by adding the protein to pure water and different sugar-, salt- and lipid-containing solutions and commercial sauces, with considerable benefits for the food industry in terms of costs and food quality.

A pilot cluster randomized controlled trial of structured goal-setting following stroke.

PubMed

Taylor, William J; Brown, Melanie; William, Levack; McPherson, Kathryn M; Reed, Kirk; Dean, Sarah G; Weatherall, Mark

2012-04-01

To determine the feasibility, the cluster design effect and the variance and minimal clinical importance difference in the primary outcome in a pilot study of a structured approach to goal-setting. A cluster randomized controlled trial. Inpatient rehabilitation facilities. People who were admitted to inpatient rehabilitation following stroke who had sufficient cognition to engage in structured goal-setting and complete the primary outcome measure. Structured goal elicitation using the Canadian Occupational Performance Measure. Quality of life at 12 weeks using the Schedule for Individualised Quality of Life (SEIQOL-DW), Functional Independence Measure, Short Form 36 and Patient Perception of Rehabilitation (measuring satisfaction with rehabilitation). Assessors were blinded to the intervention. Four rehabilitation services and 41 patients were randomized. We found high values of the intraclass correlation for the outcome measures (ranging from 0.03 to 0.40) and high variance of the SEIQOL-DW (SD 19.6) in relation to the minimally importance difference of 2.1, leading to impractically large sample size requirements for a cluster randomized design. A cluster randomized design is not a practical means of avoiding contamination effects in studies of inpatient rehabilitation goal-setting. Other techniques for coping with contamination effects are necessary.

Chimaeric sounds reveal dichotomies in auditory perception

PubMed Central

Smith, Zachary M.; Delgutte, Bertrand; Oxenham, Andrew J.

2008-01-01

By Fourier's theorem1, signals can be decomposed into a sum of sinusoids of different frequencies. This is especially relevant for hearing, because the inner ear performs a form of mechanical Fourier transform by mapping frequencies along the length of the cochlear partition. An alternative signal decomposition, originated by Hilbert2, is to factor a signal into the product of a slowly varying envelope and a rapidly varying fine time structure. Neurons in the auditory brainstem3–6 sensitive to these features have been found in mammalian physiological studies. To investigate the relative perceptual importance of envelope and fine structure, we synthesized stimuli that we call ‘auditory chimaeras’, which have the envelope of one sound and the fine structure of another. Here we show that the envelope is most important for speech reception, and the fine structure is most important for pitch perception and sound localization. When the two features are in conflict, the sound of speech is heard at a location determined by the fine structure, but the words are identified according to the envelope. This finding reveals a possible acoustic basis for the hypothesized ‘what’ and ‘where’ pathways in the auditory cortex7–10. PMID:11882898

[Development of intelligence in old age].

PubMed

Rott, C

1990-01-01

This article attempts to find the structure of a selected spectrum of intelligence. A combination of longitudinal and cross-sectional methods is applied. Two dimensions were found, which can be named as "crystallized" and "fluid" abilities (in the sense of Horn & Cattell). Whereas, the crystallized abilities do not show any systematic variation from age 61 to 83, fluid abilities decline with age. Schaie's three-component-model is not able to describe differences and variations of crystallized intelligence. Within fluid intelligence, age changes are more important than cohort differences. There are hints that structural changes take place.

Polymer separations by liquid interaction chromatography: principles - prospects - limitations.

PubMed

Radke, Wolfgang

2014-03-28

Most heterogeneities of polymers with respect to different structural features cannot be resolved by only size exclusion chromatography (SEC), the most frequently applied mode of polymer chromatography. Instead, methods of interaction chromatography became increasingly important. However, despite the increasing applications the principles and potential of polymer interaction chromatography are still often unknown to a large number of polymer scientists. The present review will explain the principles of the different modes of polymer chromatography. Based on selected examples it will be shown which separation techniques can be successfully applied for separations with respect to the different structural features of polymers. Copyright © 2013 Elsevier B.V. All rights reserved.

Brain structural connectivity and context-dependent extinction memory.

PubMed

Hermann, Andrea; Stark, Rudolf; Blecker, Carlo R; Milad, Mohammed R; Merz, Christian J

2017-08-01

Extinction of conditioned fear represents an important mechanism in the treatment of anxiety disorders. Return of fear after successful extinction or exposure therapy in patients with anxiety disorders might be linked to poor temporal or contextual generalization of extinction due to individual differences in brain structural connectivity. The goal of this magnetic resonance imaging study was therefore to investigate the association of context-dependent extinction recall with brain structural connectivity. Diffusion-tensor imaging was used to determine the fractional anisotropy as a measure of white matter structural integrity of fiber tracts connecting central brain regions of the fear and extinction circuit (uncinate fasciculus, cingulum). Forty-five healthy men participated in a two-day fear conditioning experiment with fear acquisition in context A and extinction learning in context B on the first day. Extinction recall in the extinction context as well as renewal in the acquisition context and a novel context C took place one day later. Renewal of conditioned fear (skin conductance responses) in the acquisition context was associated with higher structural integrity of the hippocampal part of the cingulum. Enhanced structural integrity of the cingulum might be related to stronger hippocampal modulation of the dorsal anterior cingulate cortex, a region important for modulating conditioned fear output by excitatory projections to the amygdala. This finding underpins the crucial role of individual differences in the structural integrity of relevant fiber tracts for context-dependent extinction recall and return of fear after exposure therapy in anxiety disorders. © 2017 Wiley Periodicals, Inc.

Structure of the protein core of translation initiation factor 2 in apo, GTP-bound and GDP-bound forms

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

Simonetti, Angelita; Marzi, Stefano; Fabbretti, Attilio

2013-06-01

The crystal structures of the eubacterial translation initiation factor 2 in apo form and with bound GDP and GTP reveal conformational changes upon nucleotide binding and hydrolysis, notably of the catalytically important histidine in the switch II region. Translation initiation factor 2 (IF2) is involved in the early steps of bacterial protein synthesis. It promotes the stabilization of the initiator tRNA on the 30S initiation complex (IC) and triggers GTP hydrolysis upon ribosomal subunit joining. While the structure of an archaeal homologue (a/eIF5B) is known, there are significant sequence and functional differences in eubacterial IF2, while the trimeric eukaryotic IF2more » is completely unrelated. Here, the crystal structure of the apo IF2 protein core from Thermus thermophilus has been determined by MAD phasing and the structures of GTP and GDP complexes were also obtained. The IF2–GTP complex was trapped by soaking with GTP in the cryoprotectant. The structures revealed conformational changes of the protein upon nucleotide binding, in particular in the P-loop region, which extend to the functionally relevant switch II region. The latter carries a catalytically important and conserved histidine residue which is observed in different conformations in the GTP and GDP complexes. Overall, this work provides the first crystal structure of a eubacterial IF2 and suggests that activation of GTP hydrolysis may occur by a conformational repositioning of the histidine residue.« less

Protein intrinsic disorder in plants.

PubMed

Pazos, Florencio; Pietrosemoli, Natalia; García-Martín, Juan A; Solano, Roberto

2013-09-12

To some extent contradicting the classical paradigm of the relationship between protein 3D structure and function, now it is clear that large portions of the proteomes, especially in higher organisms, lack a fixed structure and still perform very important functions. Proteins completely or partially unstructured in their native (functional) form are involved in key cellular processes underlain by complex networks of protein interactions. The intrinsic conformational flexibility of these disordered proteins allows them to bind multiple partners in transient interactions of high specificity and low affinity. In concordance, in plants this type of proteins has been found in processes requiring these complex and versatile interaction networks. These include transcription factor networks, where disordered proteins act as integrators of different signals or link different transcription factor subnetworks due to their ability to interact (in many cases simultaneously) with different partners. Similarly, they also serve as signal integrators in signaling cascades, such as those related to response to external stimuli. Disordered proteins have also been found in plants in many stress-response processes, acting as protein chaperones or protecting other cellular components and structures. In plants, it is especially important to have complex and versatile networks able to quickly and efficiently respond to changing environmental conditions since these organisms cannot escape and have no other choice than adapting to them. Consequently, protein disorder can play an especially important role in plants, providing them with a fast mechanism to obtain complex, interconnected and versatile molecular networks.

Protein intrinsic disorder in plants

PubMed Central

Pazos, Florencio; Pietrosemoli, Natalia; García-Martín, Juan A.; Solano, Roberto

2013-01-01

To some extent contradicting the classical paradigm of the relationship between protein 3D structure and function, now it is clear that large portions of the proteomes, especially in higher organisms, lack a fixed structure and still perform very important functions. Proteins completely or partially unstructured in their native (functional) form are involved in key cellular processes underlain by complex networks of protein interactions. The intrinsic conformational flexibility of these disordered proteins allows them to bind multiple partners in transient interactions of high specificity and low affinity. In concordance, in plants this type of proteins has been found in processes requiring these complex and versatile interaction networks. These include transcription factor networks, where disordered proteins act as integrators of different signals or link different transcription factor subnetworks due to their ability to interact (in many cases simultaneously) with different partners. Similarly, they also serve as signal integrators in signaling cascades, such as those related to response to external stimuli. Disordered proteins have also been found in plants in many stress-response processes, acting as protein chaperones or protecting other cellular components and structures. In plants, it is especially important to have complex and versatile networks able to quickly and efficiently respond to changing environmental conditions since these organisms cannot escape and have no other choice than adapting to them. Consequently, protein disorder can play an especially important role in plants, providing them with a fast mechanism to obtain complex, interconnected and versatile molecular networks. PMID:24062761

Bird-habitat relationships in interior Columbia Basin shrubsteppe

USGS Publications Warehouse

Earnst, S.L.; Holmes, A.L.

2012-01-01

Vegetation structure is considered an important habitat feature structuring avian communities. In the sagebrush biome, both remotely-sensed and field-acquired measures of big sagebrush (Artemisia tridentata) cover have proven valuable in understanding avian abundance. Differences in structure between the exotic annual cheatgrass (Bromus tectorum) and native bunchgrasses are also expected to be important. We used avian abundance data from 318 point count stations, coupled with field vegetation measurements and a detailed vegetation map, to model abundance for four shrub- and four grassland-associated avian species in southeastern Washington shrubsteppe. Specifically, we ask whether species distinguish between bunchgrass and cheatgrass, and whether mapped, categorical cover types adequately explain species' abundance or whether fine-grained, field-measured differences in vegetation cover are also important. Results indicate that mapped cover types alone can be useful for predicting patterns of distribution and abundance within the sagebrush biome for several avian species (five of eight studied here). However, field-measured sagebrush cover was a strong positive predictor for Sage Sparrow (Amphispiza belli), the only sagebrush obligate in this study, and a strong negative predictor for two grassland associates, Horned Lark (Eremophila alpestris) and Grasshopper Sparrow (Ammodramus savannarum). Likewise, shrub associates did not differ in abundance in sagebrush with a cheatgrass vs. bunchgrass understory, but grassland associates were more common in either bunchgrass (Horned Lark and Grasshopper Sparrow) or cheatgrass grasslands (Long-billed Curlew, Numenius americanus), or tended to use sagebrush-cheatgrass less than sagebrush-bunchgrass (Horned Lark, Grasshopper Sparrow, and Savannah Sparrow, Passerculus sandwichensis).

MOTHER-CHILD AND FATHER-CHILD PLAY INTERACTION: THE IMPORTANCE OF PARENTAL PLAYFULNESS AS A MODERATOR OF THE LINKS BETWEEN PARENTAL BEHAVIOR AND CHILD NEGATIVITY.

PubMed

Menashe-Grinberg, Atara; Atzaba-Poria, Naama

2017-11-01

Based on the premise that father-child play is an important context for children's development and that fathers "specialize" in play, similarities and differences in the role of playfulness in the father-child and mother-child relationship were examined. Participants in this study included 111 families (children's age: 1-3 years). Father-child and mother-child play interactions were videotaped and coded for parental playfulness, sensitivity, structuring, and nonintrusiveness as well as child negativity. Results indicated that mothers and fathers did not differ in playfulness and that mothers and fathers who were higher in playfulness had children with lower levels of negativity. However, playfulness differently moderated the links between parents' and children's behaviors for mothers and fathers. A double-risk pattern was found for mothers, such that the links between child negativity and maternal sensitivity, structuring, and nonintrusiveness were significant only for the subgroup of mothers with low levels of playfulness. When mothers had high levels of playfulness, these effects were negligible. For fathers, a double-buffer pattern was revealed, indicating that the links between child negativity and paternal sensitivity and structuring were significant only for fathers with high levels of playfulness. When fathers had low levels of playfulness, these effects were negligible. These findings demonstrate the important role that parental playfulness has on parent-child interaction as well as the need to examine moderation patterns separately for fathers and mothers. © 2017 Michigan Association for Infant Mental Health.

Electromagnetic resonance in the asymmetric terahertz metamaterials with triangle microstructure

NASA Astrophysics Data System (ADS)

Xing, Yuanyuan; Zhang, Xiaoyu; Zhang, Qiang; Gu, Yanping; Qian, Yunan; Lin, Xingyue; Tang, Yunhai; Cheng, Xinli; Qin, Changfa; Shen, Jiaoyan; Zang, Taocheng; Ma, Chunlan

2018-05-01

We investigate terahertz transmission properties and electromagnetic resonance modes in the asymmetric triangle structures with the change of asymmetric distance and the direction of electric field. When the THz electric field is perpendicular to the split gap of triangle, the electric field can better excite the THz absorption in the triangle structures. Importantly, electromagnetically induced transparency (EIT) characteristics are observed in the triangle structures due to the destructive interference of the different excited modes. The distributions of electric field and surface current density simulated by finite difference time domain indicate that the bright mode is excited by the side of triangle structures and dark mode is excited by the gap-side of triangle. The present study is helpful to understand the electromagnetic resonance in the asymmetric triangular metamaterials.

Expression of Glycosaminoglycan Epitopes During Zebrafish Skeletogenesis

PubMed Central

Hayes, Anthony J; Mitchell, Ruth E; Bashford, Andrew; Reynolds, Scott; Caterson, Bruce; Hammond, Chrissy L

2013-01-01

Background: The zebrafish is an important developmental model. Surprisingly, there are few studies that describe the glycosaminoglycan composition of its extracellular matrix during skeletogenesis. Glycosaminoglycans on proteoglycans contribute to the material properties of musculo skeletal connective tissues, and are important in regulating signalling events during morphogenesis. Sulfation motifs within the chain structure of glycosaminoglycans on cell-associated and extracellular matrix proteoglycans allow them to bind and regulate the sequestration/presentation of bioactive signalling molecules important in musculo-skeletal development. Results: We describe the spatio-temporal expression of different glycosaminoglycan moieties during zebrafish skeletogenesis with antibodies recognising (1) native sulfation motifs within chondroitin and keratan sulfate chains, and (2) enzyme-generated neoepitope sequences within the chain structure of chondroitin sulfate (i.e., 0-, 4-, and 6-sulfated isoforms) and heparan sulfate glycosaminoglycans. We show that all the glycosaminoglycan moieties investigated are expressed within the developing skeletal tissues of larval zebrafish. However, subtle changes in their patterns of spatio-temporal expression over the period examined suggest that their expression is tightly and dynamically controlled during development. Conclusions: The subtle differences observed in the domains of expression between different glycosaminoglycan moieties suggest differences in their functional roles during establishment of the primitive analogues of the skeleton. Developmental Dynamics 242:778–789, 2013. © 2013 Wiley Periodicals, Inc. Key Findings The developing zebrafish skeleton expresses many different glycosaminoglycan modifications. Multiple different glycosaminoglycan epitopes are dynamically expressed in the craniofacial skeleton. Expression of chondroitin sulfate moieties are dynamically expressed in the vertebral column and precede mineralisation. PMID:23576310

Brain structural covariance network centrality in maltreated youth with PTSD and in maltreated youth resilient to PTSD.

PubMed

Sun, Delin; Haswell, Courtney C; Morey, Rajendra A; De Bellis, Michael D

2018-04-10

Child maltreatment is a major cause of pediatric posttraumatic stress disorder (PTSD). Previous studies have not investigated potential differences in network architecture in maltreated youth with PTSD and those resilient to PTSD. High-resolution magnetic resonance imaging brain scans at 3 T were completed in maltreated youth with PTSD (n = 31), without PTSD (n = 32), and nonmaltreated controls (n = 57). Structural covariance network architecture was derived from between-subject intraregional correlations in measures of cortical thickness in 148 cortical regions (nodes). Interregional positive partial correlations controlling for demographic variables were assessed, and those correlations that exceeded specified thresholds constituted connections in cortical brain networks. Four measures of network centrality characterized topology, and the importance of cortical regions (nodes) within the network architecture were calculated for each group. Permutation testing and principle component analysis method were employed to calculate between-group differences. Principle component analysis is a methodological improvement to methods used in previous brain structural covariance network studies. Differences in centrality were observed between groups. Larger centrality was found in maltreated youth with PTSD in the right posterior cingulate cortex; smaller centrality was detected in the right inferior frontal cortex compared to youth resilient to PTSD and controls, demonstrating network characteristics unique to pediatric maltreatment-related PTSD. Larger centrality was detected in right frontal pole in maltreated youth resilient to PTSD compared to youth with PTSD and controls, demonstrating structural covariance network differences in youth resilience to PTSD following maltreatment. Smaller centrality was found in the left posterior cingulate cortex and in the right inferior frontal cortex in maltreated youth compared to controls, demonstrating attributes of structural covariance network topology that is unique to experiencing maltreatment. This work is the first to identify cortical thickness-based structural covariance network differences between maltreated youth with and without PTSD. We demonstrated network differences in both networks unique to maltreated youth with PTSD and those resilient to PTSD. The networks identified are important for the successful attainment of age-appropriate social cognition, attention, emotional processing, and inhibitory control. Our findings in maltreated youth with PTSD versus those without PTSD suggest vulnerability mechanisms for developing PTSD.

The Cognitive Neuroscience of Human Memory Since H.M

PubMed Central

Squire, Larry R.; Wixted, John T.

2011-01-01

Work with patient H.M., beginning in the 1950s, established key principles about the organization of memory that inspired decades of experimental work. Since H.M., the study of human memory and its disorders has continued to yield new insights and to improve understanding of the structure and organization of memory. Here we review this work with emphasis on the neuroanatomy of medial temporal lobe and diencephalic structures important for memory, multiple memory systems, visual perception, immediate memory, memory consolidation, the locus of long-term memory storage, the concepts of recollection and familiarity, and the question of how different medial temporal lobe structures may contribute differently to memory functions. PMID:21456960

Neural-network-enhanced evolutionary algorithm applied to supported metal nanoparticles

NASA Astrophysics Data System (ADS)

Kolsbjerg, E. L.; Peterson, A. A.; Hammer, B.

2018-05-01

We show that approximate structural relaxation with a neural network enables orders of magnitude faster global optimization with an evolutionary algorithm in a density functional theory framework. The increased speed facilitates reliable identification of global minimum energy structures, as exemplified by our finding of a hollow Pt13 nanoparticle on an MgO support. We highlight the importance of knowing the correct structure when studying the catalytic reactivity of the different particle shapes. The computational speedup further enables screening of hundreds of different pathways in the search for optimum kinetic transitions between low-energy conformers and hence pushes the limits of the insight into thermal ensembles that can be obtained from theory.

Postglacial dispersal patterns and mitochondrial genetic structure of the Pyrenean desman (Galemys pyrenaicus) in the northwestern region of the Iberian Peninsula.

PubMed

Querejeta, Marina; Fernández-González, Angel; Romero, Rafael; Castresana, Jose

2017-06-01

The genetic structure of small semiaquatic animals may be influenced by dispersal across both rivers and land. The relative importance of these two modes of dispersal may vary across different species and with ecological conditions and evolutionary periods. The Pyrenean desman ( Galemys pyrenaicus ) is an endemic mammal of the Iberian Peninsula with a strong phylogeographic structure and semiaquatic habits, thus making it an ideal model to study the effects of river and overland dispersal on its genetic structure. Thanks to different types of noninvasive samples, we obtained an extensive sampling of the Pyrenean desman from the northwestern region of the Iberian Peninsula and sequenced two mitochondrial DNA fragments. We then analyzed, using an isolation-by-distance approach, the correlation between phylogenetic distances and geographical distances measured along both river networks and land to infer the relative importance of river and overland dispersal. We found that the correlations in the whole area and in a large basin were consistent with an effect of overland dispersal, which may be due to the postglacial colonization of new territories using terrestrial corridors and, possibly, a more extensive fluvial network that may have been present during the Holocene. However, in a small basin, likely to be less influenced by the impact of ancient postglacial dispersal, the correlations suggested significant overall effects of both overland and river dispersal, as expected for a semiaquatic mammal. Therefore, different scales and geographical regions reflect different aspects of the evolutionary history and ecology of this semiaquatic species using this isolation-by-distance method. The results we obtained may have crucial implications for the conservation of the Pyrenean desman because they reinforce the importance of interbasin dispersal for this species in the studied area and the need to protect the whole riverine ecosystem, including rivers, upland streams and terrestrial corridors between basins.

PRISM-EM: template interface-based modelling of multi-protein complexes guided by cryo-electron microscopy density maps.

PubMed

Kuzu, Guray; Keskin, Ozlem; Nussinov, Ruth; Gursoy, Attila

2016-10-01

The structures of protein assemblies are important for elucidating cellular processes at the molecular level. Three-dimensional electron microscopy (3DEM) is a powerful method to identify the structures of assemblies, especially those that are challenging to study by crystallography. Here, a new approach, PRISM-EM, is reported to computationally generate plausible structural models using a procedure that combines crystallographic structures and density maps obtained from 3DEM. The predictions are validated against seven available structurally different crystallographic complexes. The models display mean deviations in the backbone of <5 Å. PRISM-EM was further tested on different benchmark sets; the accuracy was evaluated with respect to the structure of the complex, and the correlation with EM density maps and interface predictions were evaluated and compared with those obtained using other methods. PRISM-EM was then used to predict the structure of the ternary complex of the HIV-1 envelope glycoprotein trimer, the ligand CD4 and the neutralizing protein m36.

Importance of intrinsic properties of dense caseinate dispersions for structure formation.

PubMed

Manski, Julita M; van Riemsdijk, Lieke E; van der Goot, Atze J; Boom, Remko M

2007-11-01

Rheological measurements of dense calcium caseinate and sodium caseinate dispersions (> or =15%) provided insight into the factors determining shear-induced structure formation in caseinates. Calcium caseinate at a sufficiently high concentration (30%) was shown to form highly anisotropic structures during shearing and concurrent enzymatic cross-linking. In contrast, sodium caseinate formed isotropic structures using similar processing conditions. The main difference between the two types of caseinates is the counterion present, and as a consequence, the size of structural elements and their interactions. The rheological behavior of calcium caseinate and sodium caseinate reflected these differences, yielding non-monotonic and shear thinning flow behavior for calcium caseinate whereas sodium caseinate behaved only slightly shear thinning. It appears that the intrinsic properties of the dense caseinate dispersions, which are reflected in their rheological behavior, affect the structure formation that was found after applying shear. Therefore, rheological measurements are useful to obtain an indication of the structure formation potential of caseinate dispersions.

Mesoscopic modeling of structural and thermodynamic properties of fluids confined by rough surfaces.

PubMed

Terrón-Mejía, Ketzasmin A; López-Rendón, Roberto; Gama Goicochea, Armando

2015-10-21

The interfacial and structural properties of fluids confined by surfaces of different geometries are studied at the mesoscopic scale using dissipative particle dynamics simulations in the grand canonical ensemble. The structure of the surfaces is modeled by a simple function, which allows us to simulate readily different types of surfaces through the choice of three parameters only. The fluids we have modeled are confined either by two smooth surfaces or by symmetrically and asymmetrically structured walls. We calculate structural and thermodynamic properties such as the density, temperature and pressure profiles, as well as the interfacial tension profiles for each case and find that a structural order-disorder phase transition occurs as the degree of surface roughness increases. However, the magnitude of the interfacial tension is insensitive to the structuring of the surfaces and depends solely on the magnitude of the solid-fluid interaction. These results are important for modern nanotechnology applications, such as in the enhanced recovery of oil, and in the design of porous materials with specifically tailored properties.

Coordination of physiological and structural traits in Amazon forest trees

NASA Astrophysics Data System (ADS)

Patiño, S.; Fyllas, N. M.; Baker, T. R.; Paiva, R.; Quesada, C. A.; Santos, A. J. B.; Schwarz, M.; Ter Steege, H.; Phillips, O. L.; Lloyd, J.

2011-05-01

Many plant traits covary in a non-random manner reflecting interdependencies associated with "ecological strategy" dimensions. To understand how plants modulate their structural investments to best maintain and utilise their physiological capabilities, data on leaf and leaflet size and the ratio of leaf area to sapwood area (ΦLS) obtained for 1040 tree species located in 53 tropical forest plots across the Amazon Basin were incorporated into an analysis utilising existing data on species maximum height (Hmax), seed size, leaf mass per unit area (MA), foliar nutrients and δ13C and branch xylem density (ρx). Utilising a common principal components approach allowing eigenvalues to vary between two soil fertility dependent species groups, five genetically controlled trait dimensions were identified. The first involves primarily cations, foliar carbon and MA and is associated with differences in foliar construction costs. The second relates to the classic "leaf economic spectrum", but with increased individual leaf areas and a higher ΦLS newly identified components. The third relates primarily to increasing Hmax and hence variations in light acquisition strategy involving greater MA, reductions in ΦLS and less negative δ13C. Although these first three dimensions were more important for species from high fertility sites the final two dimensions were more important for low fertility species and were associated with variations linked to reproductive and shade tolerance strategies. Environmental conditions also influenced structural traits with ρx decreasing with increased soil fertility and decreasing with increased temperatures. This soil fertility response appears to be synchronised with increases in foliar nutrient concentrations and reductions in foliar [C]. Leaf and leaflet area and ΦLS were less responsive to the environment than ρx. Thus although genetically determined foliar traits such as those associated with leaf construction costs coordinate independently of structural characteristics, others tend to covary with leaf size, ΦLS, S tolerance strategies. Several traits such as MA and [C] are important components of more than one dimension with their ambiguous nature reflecting different underlying causes of variation. Environmental effects on structural and physiological characteristics are also coordinated but in a different way to the gamut of linkages associated with genotypic differences.

Nonmetro Poverty: Assessing the Effect of the 1990s.

ERIC Educational Resources Information Center

Jolliffe, Dean

2003-01-01

During the 1990s, the poverty rate in nonmetropolitan areas declined to a record low of 13.4 percent. Drawing on census data, aspects of nonmetro poverty during the 1990s are outlined, including effects of urbanization, regional differences, racial and ethnic differences, importance of family structure, needs for assistance and human services,…

Causal Models of Role Stressor Antecedents and Consequences: The Importance of Occupational Differences.

ERIC Educational Resources Information Center

Bacharach, Samuel; Bamberger, Peter

1992-01-01

Survey data from 215 nurses (10 male) and 430 civil engineers (10 female) supported the plausibility of occupation-specific models (positing direct paths between role stressors, antecedents, and consequences) compared to generic models. A weakness of generic models is the tendency to ignore differences in occupational structure and culture. (SK)

Extended Family Ties among Mexicans, Puerto Ricans, and Whites: Superintegration or Disintegration?

ERIC Educational Resources Information Center

Sarkisian, Natalia; Gerena, Mariana; Gerstel, Naomi

2006-01-01

Addressing recent theoretical debates, this study examined the differences in extended family integration among Mexicans, Puerto Ricans, and Whites, as well as the importance of culture and structure in explaining these differences. Our findings showed Whites and Latinos/as have distinctive patterns of extended family integration: Mexicans and…

Role of different salt marsh plants on metal retention in an urban estuary (Lima estuary, NW Portugal)

NASA Astrophysics Data System (ADS)

Almeida, C. M. R.; Mucha, Ana P.; Teresa Vasconcelos, M.

2011-01-01

The aim of the present work was to understand the role different salt marsh plants on metal distribution and retention in the Lima River estuary (NW Portugal), which to our knowledge have not been ascertained in this area yet. The knowledge of these differences is an important requirement for the development of appropriate management strategies, and is poorly described for Eurosiberian estuaries, like the one selected. In addition it is important to understand the difference among introduced and native salt marsh plants. In this work, metal levels (Cd, Cr, Cu, Fe, Mn, Ni, Pb and Zn) were surveyed (by atomic absorption spectrometry) in sediments from sites vegetated with Juncus maritimus, Spartina patens, Phragmites australis and Triglochin striata (rhizo-sediments), in non-vegetated sediments and in the different tissues of the plants (roots, rhizomes and aerial shoots). In general, rhizo-sediments had higher metal concentrations than non-vegetated sediments, a feature that seems common to sediments colonized by salt marsh plants of different estuarine areas. All plants concentrated metals, at least Cd, Cu and Zn (and Pb for T. striata) in their belowground structures ([ M] belowground tissues/[ M] non-vegetated sediment > 1). However, when considered per unit of salt marsh area, the different selected plants played a different role on sediment metal distribution and retention. Triglochin striata retained a significant metal burden in it belowground structures (root plus rhizomes) acting like a possible phyto-stabilizer, whereas P. australis had an higher metal burden in aboveground tissues acting as a possible phyto-extractor. As for J. maritimus and S. patens, metal burden distribution between above and belowground structures depended on the metal, with J. maritimus retaining, for instance, much more Cd and Cu in the aboveground than in the belowground structures. Therefore, the presence of invasive and exotic plants in some areas of the salt marsh may considerably affect metal distribution and retention in the estuarine region.

Relationships between structural complexity, coral traits, and reef fish assemblages

NASA Astrophysics Data System (ADS)

Darling, Emily S.; Graham, Nicholas A. J.; Januchowski-Hartley, Fraser A.; Nash, Kirsty L.; Pratchett, Morgan S.; Wilson, Shaun K.

2017-06-01

With the ongoing loss of coral cover and the associated flattening of reef architecture, understanding the links between coral habitat and reef fishes is of critical importance. Here, we investigate whether considering coral traits and functional diversity provides new insights into the relationship between structural complexity and reef fish communities, and whether coral traits and community composition can predict structural complexity. Across 157 sites in Seychelles, Maldives, the Chagos Archipelago, and Australia's Great Barrier Reef, we find that structural complexity and reef zone are the strongest and most consistent predictors of reef fish abundance, biomass, species richness, and trophic structure. However, coral traits, diversity, and life histories provided additional predictive power for models of reef fish assemblages, and were key drivers of structural complexity. Our findings highlight that reef complexity relies on living corals—with different traits and life histories—continuing to build carbonate skeletons, and that these nuanced relationships between coral assemblages and habitat complexity can affect the structure of reef fish assemblages. Seascape-level estimates of structural complexity are rapid and cost effective with important implications for the structure and function of fish assemblages, and should be incorporated into monitoring programs.

The importance of humin in soil characterisation: A study on Amazonian soils using different fluorescence techniques.

PubMed

Tadini, Amanda Maria; Nicolodelli, Gustavo; Mounier, Stephane; Montes, Célia Regina; Milori, Débora Marcondes Bastos Pereira

2015-12-15

Soil organic matter (SOM) is a complex mixture of molecules with different physicochemical properties, with humic substances (HS) being the main component as it represents around 20-50% of SOM structure. Soil of the Amazon region is considered one of the larger carbon pools of the world; thus, studies of the humic fractions are important for understanding the dynamics of organic matter (OM) in these soils. The aim of this study was to use laser-induced fluorescence spectroscopy (LIFS) and a combination of excitation-emission matrix (EEM) fluorescence with Parallel Factor Analysis (CP/PARAFAC) to assess the characteristics of humin (HU) extracted from Amazonian soils. The results obtained using LIFS showed that there was an increasing gradient of humification degree with depth, the deeper horizon presenting a higher amount of aromatic groups in the structure of HU. From the EEM, the contribution of two fluorophores with similar behaviour in the structures of HU and whole soil was assessed. Additionally, the results showed that the HU fraction might represent a larger fraction of SOM than previously thought: about 80-93% of some Amazon soils. Therefore, HU is an important humic fraction, thus indicating its role in environmental analysis, mainly in soil analysis. Copyright © 2015 Elsevier B.V. All rights reserved.

Influence of habitat heterogeneity on the community structure of deep-sea harpacticoid communities from a canyon and an escarpment site on the continental rise off California

NASA Astrophysics Data System (ADS)

Thistle, David; Sedlacek, Linda; Carman, Kevin R.; Barry, James P.

2017-05-01

The sediment-covered deep-sea floor was initially thought to be environmentally homogeneous. Recent work has shown otherwise, and deep-sea ecologists have been searching for ecologically important environmental heterogeneities on different spatial and temporal scales, with particular interest in canyons. Here we report results for harpacticoid copepods from a site at 3262 m depth in the axis of Monterey Canyon and one on an escarpment 46 km away at 3090 m depth. Multivariate community analyses revealed significant differences between sites in community structure. Absolute abundance, the ratio of subadult copepodites to adults, species density, the proportion of the harpacticoid individuals that emerged, and the proportion that lived in tubes were significantly lower at the canyon site than at the escarpment site. The proportion of the harpacticoid individuals that belonged to the surface-dweller life-style group was significantly higher than at the escarpment site. These marked differences imply that ecologically important environmental heterogeneities exist. We speculate that differences between the sites in food conditions and sediment grain-size distributions are among them.

The structural damages of lens crystallins induced by peroxynitrite and methylglyoxal, two causative players in diabetic complications and preventive role of lens antioxidant components.

PubMed

Moghadam, Sogand Sasan; Oryan, Ahmad; Kurganov, Boris I; Tamaddon, Ali-Mohammad; Alavianehr, Mohammad Mehdi; Moosavi-Movahedi, Ali Akbar; Yousefi, Reza

2017-10-01

Peroxynitrite (PON) and methylglyoxal (MGO), two diabetes-associated compounds, are believed to be important causative players in development of diabetic cataracts. In the current study, different spectroscopic methods, gel electrophoresis, lens culture and microscopic assessments were applied to examine the impact of individual, subsequent or simultaneous modification of lens crystallins with MGO and PON on their structure, oligomerization and aggregation. The protein modifications were confirmed with detection of the significantly increased quantity of carbonyl groups and decreased levels of sulfhydryl, tyrosine and tryptophan. Also, lens proteins modification with these chemical agents was accompanied with important structural alteration, oligomerization, disulfide/chromophore mediated protein crosslinking and important proteolytic instability. All these structural damages were more pronounced when the lens proteins were modified in the presence of both mentioned chemical agents, either in sequential or simultaneous manner. Ascorbic acid and glutathione, as the main components of lens antioxidant defense mechanism, were also capable to markedly prevent the damaging effects of PON and MGO on lens crystallins, as indicated by gel electrophoresis. The results of this study may highlight the importance of lens antioxidant defense system in protection of crystallins against the structural insults induced by PON and MGO during chronic hyperglycemia in the diabetic patients. Copyright © 2017 Elsevier B.V. All rights reserved.

Insights into Structural and Mechanistic Features of Viral IRES Elements

PubMed Central

Martinez-Salas, Encarnacion; Francisco-Velilla, Rosario; Fernandez-Chamorro, Javier; Embarek, Azman M.

2018-01-01

Internal ribosome entry site (IRES) elements are cis-acting RNA regions that promote internal initiation of protein synthesis using cap-independent mechanisms. However, distinct types of IRES elements present in the genome of various RNA viruses perform the same function despite lacking conservation of sequence and secondary RNA structure. Likewise, IRES elements differ in host factor requirement to recruit the ribosomal subunits. In spite of this diversity, evolutionarily conserved motifs in each family of RNA viruses preserve sequences impacting on RNA structure and RNA–protein interactions important for IRES activity. Indeed, IRES elements adopting remarkable different structural organizations contain RNA structural motifs that play an essential role in recruiting ribosomes, initiation factors and/or RNA-binding proteins using different mechanisms. Therefore, given that a universal IRES motif remains elusive, it is critical to understand how diverse structural motifs deliver functions relevant for IRES activity. This will be useful for understanding the molecular mechanisms beyond cap-independent translation, as well as the evolutionary history of these regulatory elements. Moreover, it could improve the accuracy to predict IRES-like motifs hidden in genome sequences. This review summarizes recent advances on the diversity and biological relevance of RNA structural motifs for viral IRES elements. PMID:29354113

Effects of hydrophobic and dipole-dipole interactions on the conformational transitions of a model polypeptide

NASA Astrophysics Data System (ADS)

Mu, Yan; Gao, Yi Qin

2007-09-01

We studied the effects of hydrophobicity and dipole-dipole interactions between the nearest-neighbor amide planes on the secondary structures of a model polypeptide by calculating the free energy differences between different peptide structures. The free energy calculations were performed with low computational costs using the accelerated Monte Carlo simulation (umbrella sampling) method, with a bias-potential method used earlier in our accelerated molecular dynamics simulations. It was found that the hydrophobic interaction enhances the stability of α helices at both low and high temperatures but stabilizes β structures only at high temperatures at which α helices are not stable. The nearest-neighbor dipole-dipole interaction stabilizes β structures under all conditions, especially in the low temperature region where α helices are the stable structures. Our results indicate clearly that the dipole-dipole interaction between the nearest neighboring amide planes plays an important role in determining the peptide structures. Current research provides a more unified and quantitative picture for understanding the effects of different forms of interactions on polypeptide structures. In addition, the present model can be extended to describe DNA/RNA, polymer, copolymer, and other chain systems.

The H0 function, a new index for detecting structural/topological complexity information in undirected graphs

NASA Astrophysics Data System (ADS)

Buscema, Massimo; Asadi-Zeydabadi, Masoud; Lodwick, Weldon; Breda, Marco

2016-04-01

Significant applications such as the analysis of Alzheimer's disease differentiated from dementia, or in data mining of social media, or in extracting information of drug cartel structural composition, are often modeled as graphs. The structural or topological complexity or lack of it in a graph is quite often useful in understanding and more importantly, resolving the problem. We are proposing a new index we call the H0function to measure the structural/topological complexity of a graph. To do this, we introduce the concept of graph pruning and its associated algorithm that is used in the development of our measure. We illustrate the behavior of our measure, the H0 function, through different examples found in the appendix. These examples indicate that the H0 function contains information that is useful and important characteristics of a graph. Here, we restrict ourselves to undirected.

Langley's CSI evolutionary model: Phase 2

NASA Technical Reports Server (NTRS)

Horta, Lucas G.; Reaves, Mercedes C.; Elliott, Kenny B.; Belvin, W. Keith; Teter, John E.

1995-01-01

Phase 2 testbed is part of a sequence of laboratory models, developed at NASA Langley Research Center, to enhance our understanding on how to model, control, and design structures for space applications. A key problem with structures that must perform in space is the appearance of unwanted vibrations during operations. Instruments, design independently by different scientists, must share the same vehicle causing them to interact with each other. Once in space, these problems are difficult to correct and therefore, prediction via analysis design, and experiments is very important. Phase 2 laboratory model and its predecessors are designed to fill a gap between theory and practice and to aid in understanding important aspects in modeling, sensor and actuator technology, ground testing techniques, and control design issues. This document provides detailed information on the truss structure and its main components, control computer architecture, and structural models generated along with corresponding experimental results.

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.

Peptide-Lipid Interactions: Experiments and Applications

PubMed Central

Galdiero, Stefania; Falanga, Annarita; Cantisani, Marco; Vitiello, Mariateresa; Morelli, Giancarlo; Galdiero, Massimiliano

2013-01-01

The interactions between peptides and lipids are of fundamental importance in the functioning of numerous membrane-mediated cellular processes including antimicrobial peptide action, hormone-receptor interactions, drug bioavailability across the blood-brain barrier and viral fusion processes. Moreover, a major goal of modern biotechnology is obtaining new potent pharmaceutical agents whose biological action is dependent on the binding of peptides to lipid-bilayers. Several issues need to be addressed such as secondary structure, orientation, oligomerization and localization inside the membrane. At the same time, the structural effects which the peptides cause on the lipid bilayer are important for the interactions and need to be elucidated. The structural characterization of membrane active peptides in membranes is a harsh experimental challenge. It is in fact accepted that no single experimental technique can give a complete structural picture of the interaction, but rather a combination of different techniques is necessary. PMID:24036440

Modal loss mechanism of micro-structured VCSELs studied using full vector FDTD method.

PubMed

Jo, Du-Ho; Vu, Ngoc Hai; Kim, Jin-Tae; Hwang, In-Kag

2011-09-12

Modal properties of vertical cavity surface-emitting lasers (VCSELs) with holey structures are studied using a finite difference time domain (FDTD) method. We investigate loss behavior with respect to the variation of structural parameters, and explain the loss mechanism of VCSELs. We also propose an effective method to estimate the modal loss based on mode profiles obtained using FDTD simulation. Our results could provide an important guideline for optimization of the microstructures of high-power single-mode VCSELs.

Surface and electronic structure of Bi-Ca-Sr-Cu-O superconductors studied by LEED, UPS and XPS

NASA Astrophysics Data System (ADS)

Shen, Z.-X.; Lindberg, P. A. P.; Wells, B. O.; Lindau, I.; Spicer, W. E.; Mitzi, D. B.; Eom, C. B.; Kapitulnik, A.; Geballe, T. H.; Soukiassian, P.

1989-02-01

Single crystal and polycrystalline samples of Bi2CaSr2Cu2O8 have been studied by various surface sensitive techniques, including low energy electron diffraction (LEED), ultraviolet photoemission spectroscopy (UPS) and x-ray photoemission spectroscopy (XPS). The surface structure of the single crystals was characterized by LEED to be consistent with that of the bulk structure. Our data suggest that Bi2CaSr2Cu2O8 single crystals are very stable in the ultrahigh vacuu. No change of XPS spectra with temperature was observed. We have also studied the electronic structure of Bi2Sr2CuO6, which has a lower superconducting transition temperature Tc. Comparing the electronic structure of the two Bi-Ca-Sr-Cu-O superconductors, an important difference in the density of states near EF was observed which seems to be related to the difference in Tc.

Probabilistic-Based Modeling and Simulation Assessment

DTIC Science & Technology

2010-06-01

developed to determine the relative importance of structural components of the vehicle under differnet crash and blast scenarios. With the integration of...the vehicle under different crash and blast scenarios. With the integration of the high fidelity neck and head model, a methodology to calculate the...parameter variability, correlation, and multiple (often competing) failure metrics. Important scenarios include vehicular collisions, blast /fragment

Comparison of topological clustering within protein networks using edge metrics that evaluate full sequence, full structure, and active site microenvironment similarity.

PubMed

Leuthaeuser, Janelle B; Knutson, Stacy T; Kumar, Kiran; Babbitt, Patricia C; Fetrow, Jacquelyn S

2015-09-01

The development of accurate protein function annotation methods has emerged as a major unsolved biological problem. Protein similarity networks, one approach to function annotation via annotation transfer, group proteins into similarity-based clusters. An underlying assumption is that the edge metric used to identify such clusters correlates with functional information. In this contribution, this assumption is evaluated by observing topologies in similarity networks using three different edge metrics: sequence (BLAST), structure (TM-Align), and active site similarity (active site profiling, implemented in DASP). Network topologies for four well-studied protein superfamilies (enolase, peroxiredoxin (Prx), glutathione transferase (GST), and crotonase) were compared with curated functional hierarchies and structure. As expected, network topology differs, depending on edge metric; comparison of topologies provides valuable information on structure/function relationships. Subnetworks based on active site similarity correlate with known functional hierarchies at a single edge threshold more often than sequence- or structure-based networks. Sequence- and structure-based networks are useful for identifying sequence and domain similarities and differences; therefore, it is important to consider the clustering goal before deciding appropriate edge metric. Further, conserved active site residues identified in enolase and GST active site subnetworks correspond with published functionally important residues. Extension of this analysis yields predictions of functionally determinant residues for GST subgroups. These results support the hypothesis that active site similarity-based networks reveal clusters that share functional details and lay the foundation for capturing functionally relevant hierarchies using an approach that is both automatable and can deliver greater precision in function annotation than current similarity-based methods. © 2015 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

Molecular Docking, Molecular Dynamics, and Structure-Activity Relationship Explorations of 14-Oxygenated N-Methylmorphinan-6-ones as Potent μ-Opioid Receptor Agonists.

PubMed

Noha, Stefan M; Schmidhammer, Helmut; Spetea, Mariana

2017-06-21

Among opioids, morphinans are of major importance as the most effective analgesic drugs acting primarily via μ-opioid receptor (μ-OR) activation. Our long-standing efforts in the field of opioid analgesics from the class of morphinans led to N-methylmorphinan-6-ones differently substituted at positions 5 and 14 as μ-OR agonists inducing potent analgesia and fewer undesirable effects. Herein we present the first thorough molecular modeling study and structure-activity relationship (SAR) explorations aided by docking and molecular dynamics (MD) simulations of 14-oxygenated N-methylmorphinan-6-ones to gain insights into their mode of binding to the μ-OR and interaction mechanisms. The structure of activated μ-OR provides an essential model for how ligand/μ-OR binding is encoded within small chemical differences in otherwise structurally similar morphinans. We reveal important molecular interactions that these μ-agonists share and distinguish them. The molecular docking outcomes indicate the crucial role of the relative orientation of the ligand in the μ-OR binding site, influencing the propensity of critical non-covalent interactions that are required to facilitate ligand/μ-OR interactions and receptor activation. The MD simulations point out minor differences in the tendency to form hydrogen bonds by the 4,5α-epoxy group, along with the tendency to affect the 3-7 lock switch. The emerged SARs reveal the subtle interplay between the substituents at positions 5 and 14 in the morphinan scaffold by enabling the identification of key structural elements that determine the distinct pharmacological profiles. This study provides a significant structural basis for understanding ligand binding and μ-OR activation by the 14-oxygenated N-methylmorphinan-6-ones, which should be useful for guiding drug design.

Comparison of topological clustering within protein networks using edge metrics that evaluate full sequence, full structure, and active site microenvironment similarity

PubMed Central

Leuthaeuser, Janelle B; Knutson, Stacy T; Kumar, Kiran; Babbitt, Patricia C; Fetrow, Jacquelyn S

2015-01-01

The development of accurate protein function annotation methods has emerged as a major unsolved biological problem. Protein similarity networks, one approach to function annotation via annotation transfer, group proteins into similarity-based clusters. An underlying assumption is that the edge metric used to identify such clusters correlates with functional information. In this contribution, this assumption is evaluated by observing topologies in similarity networks using three different edge metrics: sequence (BLAST), structure (TM-Align), and active site similarity (active site profiling, implemented in DASP). Network topologies for four well-studied protein superfamilies (enolase, peroxiredoxin (Prx), glutathione transferase (GST), and crotonase) were compared with curated functional hierarchies and structure. As expected, network topology differs, depending on edge metric; comparison of topologies provides valuable information on structure/function relationships. Subnetworks based on active site similarity correlate with known functional hierarchies at a single edge threshold more often than sequence- or structure-based networks. Sequence- and structure-based networks are useful for identifying sequence and domain similarities and differences; therefore, it is important to consider the clustering goal before deciding appropriate edge metric. Further, conserved active site residues identified in enolase and GST active site subnetworks correspond with published functionally important residues. Extension of this analysis yields predictions of functionally determinant residues for GST subgroups. These results support the hypothesis that active site similarity-based networks reveal clusters that share functional details and lay the foundation for capturing functionally relevant hierarchies using an approach that is both automatable and can deliver greater precision in function annotation than current similarity-based methods. PMID:26073648

Reflection and transmission for layered composite materials

NASA Technical Reports Server (NTRS)

Graglia, Roberto D.; Uslenghi, Piergiorgio L. E.

1991-01-01

A layered planar structure consisting of different bianisotropic materials separated by jump-immittance sheets is considered. Reflection and transmission coefficients are determined via a chain-matrix algorithm. Applications are important for radomes and radar-absorbing materials.

Study on CO2 gasification reactivity and physical characteristics of biomass, petroleum coke and coal chars.

PubMed

Huo, Wei; Zhou, Zhijie; Chen, Xueli; Dai, Zhenghua; Yu, Guangsuo

2014-05-01

Gasification reactivities of six different carbonaceous material chars with CO2 were determined by a Thermogravimetric Analyzer (TGA). Gasification reactivities of biomass chars are higher than those of coke and coal chars. In addition, physical structures and chemical components of these chars were systematically tested. It is found that the crystalline structure is an important factor to evaluate gasification reactivities of different chars and the crystalline structures of biomass chars are less order than those of coke and coal chars. Moreover, initial gasification rates of these chars were measured at high temperatures and with relatively large particle sizes. The method of calculating the effectiveness factor η was used to quantify the effect of pore diffusion on gasification. The results show that differences in pore diffusion effects among gasification with various chars are prominent and can be attributed to different intrinsic gasification reactivities and physical characteristics of different chars. Copyright © 2014 Elsevier Ltd. All rights reserved.

Analysis of Aerodynamic Load of LSU-03 (LAPAN Surveillance UAV-03) Propeller

NASA Astrophysics Data System (ADS)

Rahmadi Nuranto, Awang; Jamaludin Fitroh, Ahmad; Syamsudin, Hendri

2018-04-01

The existing propeller of the LSU-03 aircraft is made of wood. To improve structural strength and obtain better mechanical properties, the propeller will be redesigned usingcomposite materials. It is necessary to simulate and analyze the design load. This research paper explainsthe simulation and analysis of aerodynamic load prior to structural design phase of composite propeller. Aerodynamic load calculations are performed using both the Blade Element Theory(BET) and the Computational Fluid Dynamic (CFD)simulation. The result of both methods show a close agreement, the different thrust forces is only 1.2 and 4.1% for two type mesh. Thus the distribution of aerodynamic loads along the surface of the propeller blades of the 3-D CFD simulation results are considered valid and ready to design the composite structure. TheCFD results is directly imported to the structure model using the Direct Import CFD / One-Way Fluid Structure Interaction (FSI) method. Design load of propeller is chosen at the flight condition at speed of 20 km/h at 7000 rpm.

Structure of FGFR3 transmembrane domain dimer: implications for signaling and human pathologies.

PubMed

Bocharov, Eduard V; Lesovoy, Dmitry M; Goncharuk, Sergey A; Goncharuk, Marina V; Hristova, Kalina; Arseniev, Alexander S

2013-11-05

Fibroblast growth factor receptor 3 (FGFR3) transduces biochemical signals via lateral dimerization in the plasma membrane, and plays an important role in human development and disease. Eight different pathogenic mutations, implicated in cancers and growth disorders, have been identified in the FGFR3 transmembrane segment. Here, we describe the dimerization of the FGFR3 transmembrane domain in membrane-mimicking DPC/SDS (9/1) micelles. In the solved NMR structure, the two transmembrane helices pack into a symmetric left-handed dimer, with intermolecular stacking interactions occurring in the dimer central region. Some pathogenic mutations fall within the helix-helix interface, whereas others are located within a putative alternative interface. This implies that although the observed dimer structure is important for FGFR3 signaling, the mechanism of FGFR3-mediated transduction across the membrane is complex. We propose an FGFR3 signaling mechanism that is based on the solved structure, available structures of isolated soluble FGFR domains, and published biochemical and biophysical data. Copyright © 2013 Elsevier Ltd. All rights reserved.

Sex-based differences in brain alterations across chronic pain conditions

PubMed Central

Gupta, Arpana; Mayer, Emeran A; Fling, Connor; Labus, Jennifer S; Naliboff, Bruce D; Hong, Jui-Yang; Kilpatrick, Lisa A

2016-01-01

Common brain mechanisms are thought to play a significant role across a multitude of chronic pain syndromes. In addition, there is strong evidence for the existence of sex differences in the prevalence of chronic pain and in the neurobiology of pain. Thus, it is important to consider sex when developing general principals of pain neurobiology. The goal of the current review is to evaluate what is known about sex-specific brain alterations across multiple chronic pain populations. A total of 15 sex difference and 143 single-sex manuscripts were identified out of 412 chronic pain neuroimaging manuscripts. Results from sex difference studies indicate more prominent primary sensorimotor structural and functional alterations in female chronic pain patients compared to male chronic pain patients; differences in the nature and degree of insula alterations, with greater insula reactivity in male patients; differences in the degree of anterior cingulate structural alterations; and differences in emotional-arousal reactivity. Qualitative comparisons of male-specific and female-specific studies appear to be consistent with the results from sex difference studies. Given these differences, mixed-sex studies of chronic pain risk creating biased data or missing important information and single-sex studies have limited generalizability. The advent of large scale neuroimaging databases will likely aid in building a more comprehensive understanding of sex differences and commonalities in brain mechanisms underlying chronic pain. PMID:27870423

Sex-based differences in brain alterations across chronic pain conditions.

PubMed

Gupta, Arpana; Mayer, Emeran A; Fling, Connor; Labus, Jennifer S; Naliboff, Bruce D; Hong, Jui-Yang; Kilpatrick, Lisa A

2017-01-02

Common brain mechanisms are thought to play a significant role across a multitude of chronic pain syndromes. In addition, there is strong evidence for the existence of sex differences in the prevalence of chronic pain and in the neurobiology of pain. Thus, it is important to consider sex when developing general principals of pain neurobiology. The goal of the current Mini-Review is to evaluate what is known about sex-specific brain alterations across multiple chronic pain populations. A total of 15 sex difference and 143 single-sex articles were identified from among 412 chronic pain neuroimaging articles. Results from sex difference studies indicate more prominent primary sensorimotor structural and functional alterations in female chronic pain patients compared with male chronic pain patients: differences in the nature and degree of insula alterations, with greater insula reactivity in male patients; differences in the degree of anterior cingulate structural alterations; and differences in emotional-arousal reactivity. Qualitative comparisons of male-specific and female-specific studies appear to be consistent with the results from sex difference studies. Given these differences, mixed-sex studies of chronic pain risk creating biased data or missing important information and single-sex studies have limited generalizability. The advent of large-scale neuroimaging databases will likely aid in building a more comprehensive understanding of sex differences and commonalities in brain mechanisms underlying chronic pain. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Variation of M···H-C Interactions in Square-Planar Complexes of Nickel(II), Palladium(II), and Platinum(II) Probed by Luminescence Spectroscopy and X-ray Diffraction at Variable Pressure.

PubMed

Poirier, Stéphanie; Lynn, Hudson; Reber, Christian; Tailleur, Elodie; Marchivie, Mathieu; Guionneau, Philippe; Probert, Michael R

2018-06-12

Luminescence spectra of isoelectronic square-planar d 8 complexes with 3d, 4d, and 5d metal centers show d-d luminescence with an energetic order different from that of the spectrochemical series, indicating that additional structural effects, such as different ligand-metal-ligand angles, are important factors. Variable-pressure luminescence spectra of square-planar nickel(II), palladium(II), and platinum(II) complexes with dimethyldithiocarbamate ({CH 3 } 2 DTC) ligands and their deuterated analogues show unexpected variations of the shifts of their maxima. High-resolution crystal structures and crystal structures at variable pressure for [Pt{(CH 3 ) 2 DTC} 2 ] indicate that intermolecular M···H-C interactions are at the origin of these different shifts.

Ion Spectral Structures Observed by the Van Allen Probes and Cluster

NASA Astrophysics Data System (ADS)

Ferradas, C.; Zhang, J.; Luo, H.; Kistler, L. M.; Spence, H. E.; Larsen, B.; Skoug, R. M.; Funsten, H. O.; Reeves, G. D.

2014-12-01

During the last decades several missions have recorded the presence of dynamic spectral features of energetic ions in the inner magnetosphere. Previous studies have revealed single "nose-like" structures occurring alone and simultaneous nose-like structures (up to three). In this study we also include signatures of new types of ion structure, namely "trunk-like" and "tusk-like" structures. All the ion structures are named after the characteristic shapes of energy bands or gaps in the energy-time spectrograms of in situ measured ion fluxes. They constitute the observational signatures of ion acceleration, transport, and loss in the global magnetosphere. Multi-spacecraft analysis of these structures is important to understand their spatial distribution and temporal evolution. Mass spectrometers onboard Cluster (in a polar orbit) and the Van Allen Probes (in an equatorial orbit) measure energetic hydrogen, helium, and oxygen ions near the inner edge of the plasma sheet, where these ion structures are observed. We present a statistical study of the ion structures, using >1-year measurements from the two missions during the Van Allen Probes era. The results provide important details about the spatial distribution (dependence on geocentric distance and magnetic local time), spectral features of the structures (e.g., characteristic energy and differences among species), and geomagnetic and solar wind conditions under which these structures occur.

[Rapid ecological assessment of tropical fish communities in a gold mine area of Costa Rica].

PubMed

Espinoza Mendiola, Mario

2008-12-01

Gold mining impacts have generated a great concern regarding aquatic systems and habitat fragmentation. Anthropogenic disturbances on the structure and heterogeneity of a system can have an important effect on aquatic community stability. Ecological rapid assessments (1996, 2002, and 2007) were employed to determine the structure, composition and distribution of tropical fish communities in several rivers and smaller creeks from a gold mining area in Cerro Crucitas, Costa Rica. In addition, species composition and relative abundance were related with habitat structure. A total of 35 species were registered, among which sardine Astyanax aeneus (Characidae) and livebearer Alfaro cultratus (Poeciliidae) were the most abundant fish (71%). The highest species richness was observed in Caño Crucitas (s=19) and Minas Creek (s=18). Significant differences in fish communities structure and composition from Infiernillo river and Minas creek were observed (lamda = 0.0, F(132, 66) = 2.24, p < 0.001). Presence and/or absence of certain species such as Dormitor gobiomorus, Rhamdia nicaraguensis, Parachromis loiseillei and Atractosteus tropicus explained most of the spatial variation among sites. Habitat structure also contributed to explain differences among sites (lamda = 0.004, F(60.183) = 5.52, p < 0.001). Substratum (soft and hard bottom types) and habitat attributes (elevation, width and depth) explained most of the variability observed in Infiernillo River, Caño Crucitas and Tamagá Creek. In addition, a significant association between fish species and habitat structure was observed. This study reveals a high complexity in tropical fish communities that inhabit a gold mine area. Furthermore, it highlights the importance of habitat heterogeneity in fish community dynamics. The loss and degradation of aquatic systems in Cerro Crucitas can have a strong negative effect on fish community structure and composition of local species. A better understanding of the use of specific habitats that serve as essential fish habitats can improve tropical fish conservation and management strategies, thus increasing local diversity, and thereby, the biological importance of the area.

The shear response of copper bicrystals with Σ11 symmetric and asymmetric tilt grain boundaries by molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Zhang, Liang; Lu, Cheng; Tieu, Kiet; Zhao, Xing; Pei, Linqing

2015-04-01

Grain boundaries (GBs) are important microstructure features and can significantly affect the properties of nanocrystalline materials. Molecular dynamics simulation was carried out in this study to investigate the shear response and deformation mechanisms of symmetric and asymmetric Σ11<1 1 0> tilt GBs in copper bicrystals. Different deformation mechanisms were reported, depending on GB inclination angles and equilibrium GB structures, including GB migration coupled to shear deformation, GB sliding caused by local atomic shuffling, and dislocation nucleation from GB. The simulation showed that migrating Σ11(1 1 3) GB under shear can be regarded as sliding of GB dislocations and their combination along the boundary plane. A non-planar structure with dissociated intrinsic stacking faults was prevalent in Σ11 asymmetric GBs of Cu. This type of structure can significantly increase the ductility of bicrystal models under shear deformation. A grain boundary can be a source of dislocation and migrate itself at different stress levels. The intrinsic free volume involved in the grain boundary area was correlated with dislocation nucleation and GB sliding, while the dislocation nucleation mechanism can be different for a grain boundary due to its different equilibrium structures.Grain boundaries (GBs) are important microstructure features and can significantly affect the properties of nanocrystalline materials. Molecular dynamics simulation was carried out in this study to investigate the shear response and deformation mechanisms of symmetric and asymmetric Σ11<1 1 0> tilt GBs in copper bicrystals. Different deformation mechanisms were reported, depending on GB inclination angles and equilibrium GB structures, including GB migration coupled to shear deformation, GB sliding caused by local atomic shuffling, and dislocation nucleation from GB. The simulation showed that migrating Σ11(1 1 3) GB under shear can be regarded as sliding of GB dislocations and their combination along the boundary plane. A non-planar structure with dissociated intrinsic stacking faults was prevalent in Σ11 asymmetric GBs of Cu. This type of structure can significantly increase the ductility of bicrystal models under shear deformation. A grain boundary can be a source of dislocation and migrate itself at different stress levels. The intrinsic free volume involved in the grain boundary area was correlated with dislocation nucleation and GB sliding, while the dislocation nucleation mechanism can be different for a grain boundary due to its different equilibrium structures. Electronic supplementary information (ESI) available: Movies show the evolution of different grain boundaries under shear deformation: S-0, S-54.74, S-70.53-A, S-70.53-B, S-90. See DOI: 10.1039/c4nr07496c

Changes in Soil Fungal Community Structure with Increasing Disturbance Frequency.

PubMed

Cho, Hyunjun; Kim, Mincheol; Tripathi, Binu; Adams, Jonathan

2017-07-01

Although disturbance is thought to be important in many ecological processes, responses of fungal communities to soil disturbance have been little studied experimentally. We subjected a soil microcosm to physical disturbance, at a range of frequencies designed to simulate ecological disturbance events. We analyzed the fungal community structure using Illumina HiSeq sequencing of the ITS1 region. Fungal diversity was found to decline with the increasing disturbance frequencies, with no sign of the "humpback" pattern found in many studies of larger sedentary organisms. There is thus no evidence of an effect of release from competition resulting from moderate disturbance-which suggests that competition and niche overlap may not be important in limiting soil fungal diversity. Changing disturbance frequency also led to consistent differences in community composition. There were clear differences in OTU-level composition, with different disturbance treatments each having distinct fungal communities. The functional profile of fungal groups (guilds) was changed by the level of disturbance frequency. These predictable differences in community composition suggest that soil fungi can possess different niches in relation to disturbance frequency, or time since last disturbance. Fungi appear to be most abundant relative to bacteria at intermediate disturbance frequencies, on the time scale we studied here.

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

The effectiveness of a structured education pulmonary rehabilitation programme for improving the health status of people with moderate and severe chronic obstructive pulmonary disease in primary care: the PRINCE cluster randomised trial.

PubMed

Casey, Dympna; Murphy, Kathy; Devane, Declan; Cooney, Adeline; McCarthy, Bernard; Mee, Lorraine; Newell, John; O'Shea, Eamon; Scarrott, Carl; Gillespie, Paddy; Kirwan, Collette; Murphy, Andrew W

2013-10-01

To evaluate the effectiveness of a structured education pulmonary rehabilitation programme on the health status of people with chronic obstructive pulmonary disease (COPD). Two-arm, cluster randomised controlled trial. 32 general practices in the Republic of Ireland. 350 participants with a diagnosis of moderate or severe COPD. Experimental group received a structured education pulmonary rehabilitation programme, delivered by the practice nurse and physiotherapist. Control group received usual care. Health status as measured by the Chronic Respiratory Questionnaire (CRQ) at baseline and at 12-14 weeks postcompletion of the programme. Participants allocated to the intervention group had statistically significant higher mean change total CRQ scores (adjusted mean difference (MD) 1.11, 95% CI 0.35 to 1.87). However, the CI does not exclude a smaller difference than the one that was prespecified as clinically important. Participants allocated to the intervention group also had statistically significant higher mean CRQ Dyspnoea scores after intervention (adjusted MD 0.49, 95% CI 0.20 to 0.78) and CRQ Physical scores (adjusted MD 0.37, 95% CI 0.14 to 0.60). However, CIs for both the CRQ Dyspnoea and CRQ Physical subscales do not exclude smaller differences as prespecified as clinically important. No other statistically significant differences between groups were seen. A primary care based structured education pulmonary rehabilitation programme is feasible and may increase local accessibility to people with moderate and severe COPD. ISRCTN52403063.

Structural flexibility and protein adaptation to temperature: Molecular dynamics analysis of malate dehydrogenases of marine molluscs.

PubMed

Dong, Yun-Wei; Liao, Ming-Ling; Meng, Xian-Liang; Somero, George N

2018-02-06

Orthologous proteins of species adapted to different temperatures exhibit differences in stability and function that are interpreted to reflect adaptive variation in structural "flexibility." However, quantifying flexibility and comparing flexibility across proteins has remained a challenge. To address this issue, we examined temperature effects on cytosolic malate dehydrogenase (cMDH) orthologs from differently thermally adapted congeners of five genera of marine molluscs whose field body temperatures span a range of ∼60 °C. We describe consistent patterns of convergent evolution in adaptation of function [temperature effects on K M of cofactor (NADH)] and structural stability (rate of heat denaturation of activity). To determine how these differences depend on flexibilities of overall structure and of regions known to be important in binding and catalysis, we performed molecular dynamics simulation (MDS) analyses. MDS analyses revealed a significant negative correlation between adaptation temperature and heat-induced increase of backbone atom movements [root mean square deviation (rmsd) of main-chain atoms]. Root mean square fluctuations (RMSFs) of movement by individual amino acid residues varied across the sequence in a qualitatively similar pattern among orthologs. Regions of sequence involved in ligand binding and catalysis-termed mobile regions 1 and 2 (MR1 and MR2), respectively-showed the largest values for RMSF. Heat-induced changes in RMSF values across the sequence and, importantly, in MR1 and MR2 were greatest in cold-adapted species. MDS methods are shown to provide powerful tools for examining adaptation of enzymes by providing a quantitative index of protein flexibility and identifying sequence regions where adaptive change in flexibility occurs.

Trends in Asset Structure between Not-for-Profit and Investor Owned Hospitals

PubMed Central

Song, Paula H.; Reiter, Kristin L.

2010-01-01

The delivery of health care is a capital intensive industry and thus hospital investment strategy continues to be an important area of interest for both health policy and research. Much attention has been given to hospitals’ capital investment policies with relatively little attention to investments in financial assets, which serve an important role in NFP hospitals. This study describes and analyzes trends in aggregate asset structure between NFP and IO hospitals during the post-capital based PPS implementation period, providing the first documentation of long-term trends in hospital investment. We find hospitals’ aggregate asset structure differs significantly based on ownership, size, and profitability. For both NFP and IO hospitals, financial securities have remained consistent over time, while fixed asset representation has declined in IO hospitals. PMID:20519429

Impact of Sampling Schemes on Demographic Inference: An Empirical Study in Two Species with Different Mating Systems and Demographic Histories

PubMed Central

St. Onge, K. R.; Palmé, A. E.; Wright, S. I.; Lascoux, M.

2012-01-01

Most species have at least some level of genetic structure. Recent simulation studies have shown that it is important to consider population structure when sampling individuals to infer past population history. The relevance of the results of these computer simulations for empirical studies, however, remains unclear. In the present study, we use DNA sequence datasets collected from two closely related species with very different histories, the selfing species Capsella rubella and its outcrossing relative C. grandiflora, to assess the impact of different sampling strategies on summary statistics and the inference of historical demography. Sampling strategy did not strongly influence the mean values of Tajima’s D in either species, but it had some impact on the variance. The general conclusions about demographic history were comparable across sampling schemes even when resampled data were analyzed with approximate Bayesian computation (ABC). We used simulations to explore the effects of sampling scheme under different demographic models. We conclude that when sequences from modest numbers of loci (<60) are analyzed, the sampling strategy is generally of limited importance. The same is true under intermediate or high levels of gene flow (4Nm > 2–10) in models in which global expansion is combined with either local expansion or hierarchical population structure. Although we observe a less severe effect of sampling than predicted under some earlier simulation models, our results should not be seen as an encouragement to neglect this issue. In general, a good coverage of the natural range, both within and between populations, will be needed to obtain a reliable reconstruction of a species’s demographic history, and in fact, the effect of sampling scheme on polymorphism patterns may itself provide important information about demographic history. PMID:22870403

Different secondary structure elements as scaffolds for protein folding transition states of two homologous four-helix bundles.

PubMed

Teilum, Kaare; Thormann, Thorsten; Caterer, Nigel R; Poulsen, Heidi I; Jensen, Peter H; Knudsen, Jens; Kragelund, Birthe B; Poulsen, Flemming M

2005-04-01

Comparison of the folding processes for homologue proteins can provide valuable information about details in the interactions leading to the formation of the folding transition state. Here the folding kinetics of 18 variants of yACBP and 3 variants of bACBP have been studied by Phi-value analysis. In combination with Phi-values from previous work, detailed insight into the transition states for folding of both yACBP and bACBP has been obtained. Of the 16 sequence positions that have been studied in both yACBP and bACBP, 5 (V12, I/L27, Y73, V77, and L80) have high Phi-values and appear to be important for the transition state formation in both homologues. Y31, A34, and A69 have high Phi-values only in yACBP, while F5, A9, and I74 have high Phi-values only in bACBP. Thus, additional interactions between helices A2 and A4 appear to be important for the transition state of yACBP, whereas additional interactions between helices A1 and A4 appear to be important for the transition state of bACBP. To examine whether these differences could be assigned to different packing of the residues in the native state, a solution structure of yACBP was determined by NMR. Small changes in the packing of the hydrophobic side-chains, which strengthen the interactions between helices A2 and A4, are observed in yACBP relative to bACBP. It is suggested that different structure elements serve as scaffolds for the folding of the 2 ACBP homologues. (c) 2005 Wiley-Liss, Inc.

Comparison of the structures of three circoviruses: chicken anemia virus, porcine circovirus type 2, and beak and feather disease virus.

PubMed

Crowther, R A; Berriman, J A; Curran, W L; Allan, G M; Todd, D

2003-12-01

Circoviruses are small, nonenveloped icosahedral animal viruses characterized by circular single-stranded DNA genomes. Their genomes are the smallest possessed by animal viruses. Infections with circoviruses, which can lead to economically important diseases, frequently result in virus-induced damage to lymphoid tissue and immunosuppression. Within the family Circoviridae, different genera are distinguished by differences in genomic organization. Thus, Chicken anemia virus is in the genus Gyrovirus, while porcine circoviruses and Beak and feather disease virus belong to the genus CIRCOVIRUS: Little is known about the structures of circoviruses. Accordingly, we investigated the structures of these three viruses with a view to determining whether they are related. Three-dimensional maps computed from electron micrographs showed that all three viruses have a T=1 organization with capsids formed from 60 subunits. Porcine circovirus type 2 and beak and feather disease virus show similar capsid structures with flat pentameric morphological units, whereas chicken anemia virus has stikingly different protruding pentagonal trumpet-shaped units. It thus appears that the structures of viruses in the same genus are related but that those of viruses in different genera are unrelated.

Photosynthetic light capture and processing from cell to canopy

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

Stenberg, P.; DeLucia, E.H.; Schoettle, A.W.

1995-07-01

We have addressed the unique structural features of conifers, as they relate to photosynthetic production, at different levels of organization (from needle to canopy). Many concepts and measures must be defined for conifers so that they are consistent with the structural properties of needles and shoots. Consistency is needed in comparing the photosynthetic performance of conifers and broad leaves, wherein it is important to distinguish the effect of structural factors on light capture from differences in the photosynthetic response at a fixed interception. Needles differ from broad leaves both with respect to inner structure and external shape, which includes amore » continuum from nearly flat to cylindrical. For nonflat three-dimensional objects such as for conifer needles, total surface area is the natural measure. The meaning of the one-sided area of needles is not clear, but consistency requires that it be defined as half the total needle surface area, as concluded. Characteristic structural factors of conifers that affect their ability to harvest light are a deep canopy combined with a small needle size, which create an important penumbra effect, and the clustering of needles on shoots, which creates a discontinuous distribution of needle area. These factors imply that, at a fixed leaf area index, the intercepted PAR would be smaller in coniferous than in broad-leafed canopies, but the vertical gradient of light in conifers is less steep and light reaching the lower canopy is all penumbral (diffuse). Conifers can maintain a higher leaf area index, and this may be accomplished by a more even distribution of light between shoots at different locations in the canopy and also because shade shoots have a structure that effectively intercepts light. Broad leaves in general have higher maximum photosynthetic rates than do needles, and yet conifers are at least equally productive on a stand basis. Possible reasons are discussed.« less

X-ray and Neutron Scattering Study of the Formation of Core–Shell-Type Polyoxometalates

DOE PAGES

Yin, Panchao; Wu, Bin; Mamontov, Eugene; ...

2016-02-05

A typical type of core-shell polyoxometalates can be obtained through the Keggin-type polyoxometalate-templated growth of a layer of spherical shell structure of {Mo 72Fe 30}. Small angle X-ray scattering is used to study the structural features and stability of the core-shell structures in aqueous solutions. Time-resolved small angle X-ray scattering is applied to monitor the synthetic reactions and a three-stage formation mechanism is proposed to describe the synthesis of the core-shell polyoxometalates based on the monitoring results. Quasi-elastic and inelastic neutron scattering are used to probe the dynamics of water molecules in the core-shell structures and two different types ofmore » water molecules, the confined and structured water, are observed. These water molecules play an important role in bridging core and shell structures and stabilizing the cluster structures. A typical type of core shell polyoxometalates can be obtained through the Keggin-type polyoxometalate-templated growth of a layer of spherical shell structure of {Mo 72Fe 30}. Small-angle X-ray scattering is used to study the structural features and stability of the core shell structures in aqueous solutions. Time-resolved small-angle X-ray scattering is applied to monitor the synthetic reactions, and a three-stage formation mechanism is proposed to describe the synthesis of the core shell polyoxometalates based on the monitoring results. New protocols have been developed by fitting the X-ray data with custom physical models, which provide more convincing, objective, and completed data interpretation. Quasi-elastic and inelastic neutron scattering are used to probe the dynamics of water molecules in the core shell structures, and two different types of water molecules, the confined and structured water, are observed. These water molecules play an important role in bridging core and shell structures and stabilizing the cluster structures.« less

The BepiColombo Spacecraft: The Mercury Transfer Module Structure Qualification Test Campaign Description

NASA Astrophysics Data System (ADS)

Martin Zurdo, M. J.

2012-07-01

The BepiColombo is a space mission to Mercury (ESA in cooperation with Japan Aerospace Exploration Agency). The spacecraft consist of three different structures: two orbiters responsible for the scientific mission (MPO and MMO) and one service module, Mercury Transfer Module (MTM), which provides propulsion and services during the journey to Mercury. Taking into account only the MTM structure, the companies involved are ASTRIUM GERMANY acting as the prime contractor and ASTRIUM UK acting as the co- prime contractor company. EADS CASA Espacio (ECE) in Spain is the company responsible for the final design, manufacturing and qualification of the MTM structure. The test campaign specimen is the MTM core structure, which corresponds to the central cone with the structure floors, shear panels and tank support structure. This test campaign qualifies the primary load path and its primary interfaces; the rest of the MTM structure is qualified by system level vibration test. In order to qualify the MTM structure, three different kinds of qualification tests have been performed: stiffness test, global strength test and local tests in different specific areas. The most relevant test during the campaign is the global strength test case, in which several external loads are introduced (different interfaces) simulating the load introduction for a selected critical flight case. There are two important items in the qualification test campaign: 1. The instrumentation of the structure, with two main functions: to control the specimen under test loads, and to demonstrate the qualification of the structure. 2. The set-up structure, designed by ECE to allow the correct load introduction on each testing case during the whole test campaign. This paper describes the MTM structure test campaign from the definition of the loads applied in each test to the qualification of the complete structure.

Progress on Discrete Fracture Network models with implications on the predictions of permeability and flow channeling structure

NASA Astrophysics Data System (ADS)

Darcel, C.; Davy, P.; Le Goc, R.; Maillot, J.; Selroos, J. O.

2017-12-01

We present progress on Discrete Fracture Network (DFN) flow modeling, including realistic advanced DFN spatial structures and local fracture transmissivity properties, through an application to the Forsmark site in Sweden. DFN models are a framework to combine fracture datasets from different sources and scales and to interpolate them in combining statistical distributions and stereological relations. The resulting DFN upscaling function - size density distribution - is a model component key to extrapolating fracture size densities between data gaps, from borehole core up to site scale. Another important feature of DFN models lays in the spatial correlations between fractures, with still unevaluated consequences on flow predictions. Indeed, although common Poisson (i.e. spatially random) models are widely used, they do not reflect these geological evidences for more complex structures. To model them, we define a DFN growth process from kinematic rules for nucleation, growth and stopping conditions. It mimics in a simplified way the geological fracturing processes and produces DFN characteristics -both upscaling function and spatial correlations- fully consistent with field observations. DFN structures are first compared for constant transmissivities. Flow simulations for the kinematic and equivalent Poisson DFN models show striking differences: with the kinematic DFN, connectivity and permeability are significantly smaller, down to a difference of one order of magnitude, and flow is much more channelized. Further flow analyses are performed with more realistic transmissivity distribution conditions (sealed parts, relations to fracture sizes, orientations and in-situ stress field). The relative importance of the overall DFN structure in the final flow predictions is discussed.

Soil and plant factors driving the community of soil-borne microorganisms across chronosequences of secondary succession of chalk grasslands with a neutral pH.

PubMed

Kuramae, Eiko; Gamper, Hannes; van Veen, Johannes; Kowalchuk, George

2011-08-01

Although soil pH has been shown to be an important factor driving microbial communities, relatively little is known about the other potentially important factors that shape soil-borne microbial community structure. This study examined plant and microbial communities across a series of neutral pH fields (pH=7.0-7.5) representing a chronosequence of secondary succession after former arable fields were taken out of production. These fields ranged from 17 to >66 years since the time of abandonment, and an adjacent arable field was included as a reference. Hierarchical clustering analysis, nonmetric multidimensional scaling and analysis of similarity of 52 different plant species showed that the plant community composition was significantly different in the different chronosequences, and that plant species richness and diversity increased with time since abandonment. The microbial community structure, as analyzed by phylogenetic microarrays (PhyloChips), was significantly different in arable field and the early succession stage, but no distinct microbial communities were observed for the intermediate and the late succession stages. The most determinant factors in shaping the soil-borne microbial communities were phosphorous and NH(4)(+). Plant community composition and diversity did not have a significant effect on the belowground microbial community structure or diversity. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Foam injection molding of thermoplastic elastomers: Blowing agents, foaming process and characterization of structural foams

NASA Astrophysics Data System (ADS)

Ries, S.; Spoerrer, A.; Altstaedt, V.

2014-05-01

Polymer foams play an important role caused by the steadily increasing demand to light weight design. In case of soft polymers, like thermoplastic elastomers (TPE), the haptic feeling of the surface is affected by the inner foam structure. Foam injection molding of TPEs leads to so called structural foam, consisting of two compact skin layers and a cellular core. The properties of soft structural foams like soft-touch, elastic and plastic behavior are affected by the resulting foam structure, e.g. thickness of the compact skins and the foam core or density. This inner structure can considerably be influenced by different processing parameters and the chosen blowing agent. This paper is focused on the selection and characterization of suitable blowing agents for foam injection molding of a TPE-blend. The aim was a high density reduction and a decent inner structure. Therefore DSC and TGA measurements were performed on different blowing agents to find out which one is appropriate for the used TPE. Moreover a new analyzing method for the description of processing characteristics by temperature dependent expansion measurements was developed. After choosing suitable blowing agents structural foams were molded with different types of blowing agents and combinations and with the breathing mold technology in order to get lower densities. The foam structure was analyzed to show the influence of the different blowing agents and combinations. Finally compression tests were performed to estimate the influence of the used blowing agent and the density reduction on the compression modulus.

Multi-object segmentation framework using deformable models for medical imaging analysis.

PubMed

Namías, Rafael; D'Amato, Juan Pablo; Del Fresno, Mariana; Vénere, Marcelo; Pirró, Nicola; Bellemare, Marc-Emmanuel

2016-08-01

Segmenting structures of interest in medical images is an important step in different tasks such as visualization, quantitative analysis, simulation, and image-guided surgery, among several other clinical applications. Numerous segmentation methods have been developed in the past three decades for extraction of anatomical or functional structures on medical imaging. Deformable models, which include the active contour models or snakes, are among the most popular methods for image segmentation combining several desirable features such as inherent connectivity and smoothness. Even though different approaches have been proposed and significant work has been dedicated to the improvement of such algorithms, there are still challenging research directions as the simultaneous extraction of multiple objects and the integration of individual techniques. This paper presents a novel open-source framework called deformable model array (DMA) for the segmentation of multiple and complex structures of interest in different imaging modalities. While most active contour algorithms can extract one region at a time, DMA allows integrating several deformable models to deal with multiple segmentation scenarios. Moreover, it is possible to consider any existing explicit deformable model formulation and even to incorporate new active contour methods, allowing to select a suitable combination in different conditions. The framework also introduces a control module that coordinates the cooperative evolution of the snakes and is able to solve interaction issues toward the segmentation goal. Thus, DMA can implement complex object and multi-object segmentations in both 2D and 3D using the contextual information derived from the model interaction. These are important features for several medical image analysis tasks in which different but related objects need to be simultaneously extracted. Experimental results on both computed tomography and magnetic resonance imaging show that the proposed framework has a wide range of applications especially in the presence of adjacent structures of interest or under intra-structure inhomogeneities giving excellent quantitative results.

Aryl- and alkyl-phosphorus-containing flame retardants induced mitochondrial impairment and cell death in Chinese hamster ovary (CHO-k1) cells.

PubMed

Huang, Chao; Li, Na; Yuan, Shengwu; Ji, Xiaoya; Ma, Mei; Rao, Kaifeng; Wang, Zijian

2017-11-01

Phosphorus-containing flame retardants (PFRs) are increasingly in demand worldwide as replacements for brominated flame retardants (BFRs), but insufficient available toxicological information on PFRs makes assessing their health risks challenging. Mitochondria are important targets of various environmental pollutants, and mitochondrial dysfunction may lead to many common diseases. In the present study, mitochondria impairment-related endpoints were measured by a high content screening (HCS) assay for 11 selected non-halogen PFRs in Chinese hamster ovary (CHO-k1) cells. A cluster analysis was used to categorize these PFRs into three groups according to their structural characteristics and results from the HCS assay. Two groups, containing long-chain alkyl-PFRs and all aryl-PFRs, were found to cause mitochondrial impairment but showed different mechanisms of toxicity. Due to the high correlation between cell death and mitochondrial impairment, two PFRs with different structures, trihexyl phosphate (THP) and cresyl diphenyl phosphate (CDP), were selected and compared with chlorpyrifos (CPF) to elucidate their mechanism of inducing cell death. THP (an alkyl-PFR) was found to utilize a similar pathway as CPF to induce apoptosis. However, cell death induced by CDP (an aryl-PFR) was different from classical necrosis based on experiments to discriminate among the different modes of cell death. These results confirm that mitochondria might be important targets for some PFRs and that differently structured PFRs could function via distinct mechanisms of toxicity. Copyright © 2017 Elsevier Ltd. All rights reserved.

Regional mechanics determine collagen fiber structure in healing myocardial infarcts.

PubMed

Fomovsky, Gregory M; Rouillard, Andrew D; Holmes, Jeffrey W

2012-05-01

Following myocardial infarction, the mechanical properties of the healing infarct are an important determinant of heart function and the risk of progression to heart failure. In particular, mechanical anisotropy (having different mechanical properties in different directions) in the healing infarct can preserve pump function of the heart. Based on reports of different collagen structures and mechanical properties in various animal models, we hypothesized that differences in infarct size, shape, and/or location produce different patterns of mechanical stretch that guide evolving collagen fiber structure. We tested the effects of infarct shape and location using a combined experimental and computational approach. We studied mechanics and collagen fiber structure in cryoinfarcts in 53 Sprague-Dawley rats and found that regardless of shape or orientation, cryoinfarcts near the equator of the left ventricle stretched primarily in the circumferential direction and developed circumferentially aligned collagen, while infarcts at the apex stretched similarly in the circumferential and longitudinal directions and developed randomly oriented collagen. In a computational model of infarct healing, an effect of mechanical stretch on fibroblast and collagen alignment was required to reproduce the experimental results. We conclude that mechanical environment determines collagen fiber structure in healing myocardial infarcts. Our results suggest that emerging post-infarction therapies that alter regional mechanics will also alter infarct collagen structure, offering both potential risks and novel therapeutic opportunities. Copyright © 2012 Elsevier Ltd. All rights reserved.

Regional Mechanics Determine Collagen Fiber Structure in Healing Myocardial Infarcts

PubMed Central

Fomovsky, Gregory M.; Rouillard, Andrew D.; Holmes, Jeffrey W.

2012-01-01

Following myocardial infarction, the mechanical properties of the healing infarct are an important determinant of heart function and the risk of progression to heart failure. In particular, mechanical anisotropy (having different mechanical properties in different directions) in the healing infarct can preserve pump function of the heart. Based on reports of different collagen structures and mechanical properties in various animal models, we hypothesized that differences in infarct size, shape, and/or location produce different patterns of mechanical stretch that guide evolving collagen fiber structure. We tested the effects of infarct shape and location using a combined experimental and computational approach. We studied mechanics and collagen fiber structure in cryoinfarcts in 53 Sprague-Dawley rats and found that regardless of shape or orientation, cryoinfarcts near the equator of the left ventricle stretched primarily in the circumferential direction and developed circumferentially aligned collagen, while infarcts at the apex stretched similarly in the circumferential and longitudinal direction and developed randomly oriented collagen. In a computational model of infarct healing, an effect of mechanical stretch on fibroblast and collagen alignment was required to reproduce the experimental results. We conclude that mechanical environment determines collagen fiber structure in healing myocardial infarcts. Our results suggest that emerging post-infarction therapies that alter regional mechanics will also alter infarct collagen structure, offering both potential risks and novel therapeutic opportunities. PMID:22418281

Effects of species' similarity and dominance on the functional and phylogenetic structure of a plant meta-community.

PubMed

Chalmandrier, L; Münkemüller, T; Lavergne, S; Thuiller, W

2015-01-01

Different assembly processes drive the spatial structure of meta-communities (beta-diversity). Recently, functional and phylogenetic diversities have been suggested as indicators of these assembly processes. Assuming that diversity is a good proxy for niche overlap, high beta-diversity along environmental gradients should be the result of environmental filtering while low beta-diversity should stem from competitive interactions. So far, studies trying to disentangle the relative importance of these assembly processes have provided mixed results. One reason for this may be that these studies often rely on a single measure of diversity and thus implicitly make a choice on how they account for species relative abundances and how species similarities are captured by functional traits or phylogeny. Here, we tested the effect of gradually scaling the importance of dominance (the weight given to dominant vs. rare species) and species similarity (the weight given to small vs. large similarities) on resulting beta-diversity patterns of an alpine plant meta-community. To this end, we combined recent extensions of the Hill numbers framework with Pagel's phylogenetic tree transformation approach. We included functional (based on the leaf-height-seed spectrum) and phylogenetic facets of beta-diversity in our analysis and explicitly accounted for effects of environmental and spatial covariates. We found that functional beta-diversity, was high when the same weight was given to dominant vs. rare species and to large vs. small species' similarities. In contrast, phylogenetic beta-diversity was low when greater weight was given to dominant species and small species' similarities. Those results suggested that different environments along the gradients filtered different species according to their functional traits, while, the same competitive lineages dominated communities across the gradients. Our results highlight that functional vs. phylogenetic facets, presence-absence vs. abundance structure and different weights of species' dissimilarity provide complementary and important information on the drivers of meta-community structure. By utilizing the full extent of information provided by the flexible frameworks of Hill numbers and Pagel's tree transformation, we propose a new approach to disentangle the patterns resulting from different assembly processes.

EEG Characteristic Extraction Method of Listening Music and Objective Estimation Method Based on Latency Structure Model in Individual Characteristics

NASA Astrophysics Data System (ADS)

Ito, Shin-Ichi; Mitsukura, Yasue; Nakamura Miyamura, Hiroko; Saito, Takafumi; Fukumi, Minoru

EEG is characterized by the unique and individual characteristics. Little research has been done to take into account the individual characteristics when analyzing EEG signals. Often the EEG has frequency components which can describe most of the significant characteristics. Then there is the difference of importance between the analyzed frequency components of the EEG. We think that the importance difference shows the individual characteristics. In this paper, we propose a new EEG extraction method of characteristic vector by a latency structure model in individual characteristics (LSMIC). The LSMIC is the latency structure model, which has personal error as the individual characteristics, based on normal distribution. The real-coded genetic algorithms (RGA) are used for specifying the personal error that is unknown parameter. Moreover we propose an objective estimation method that plots the EEG characteristic vector on a visualization space. Finally, the performance of the proposed method is evaluated using a realistic simulation and applied to a real EEG data. The result of our experiment shows the effectiveness of the proposed method.

Spectrally tuned structural and pigmentary coloration of birdwing butterfly wing scales.

PubMed

Wilts, Bodo D; Matsushita, Atsuko; Arikawa, Kentaro; Stavenga, Doekele G

2015-10-06

The colourful wing patterns of butterflies play an important role for enhancing fitness; for instance, by providing camouflage, for interspecific mate recognition, or for aposematic display. Closely related butterfly species can have dramatically different wing patterns. The phenomenon is assumed to be caused by ecological processes with changing conditions, e.g. in the environment, and also by sexual selection. Here, we investigate the birdwing butterflies, Ornithoptera, the largest butterflies of the world, together forming a small genus in the butterfly family Papilionidae. The wings of these butterflies are marked by strongly coloured patches. The colours are caused by specially structured wing scales, which act as a chirped multilayer reflector, but the scales also contain papiliochrome pigments, which act as a spectral filter. The combined structural and pigmentary effects tune the coloration of the wing scales. The tuned colours are presumably important for mate recognition and signalling. By applying electron microscopy, (micro-)spectrophotometry and scatterometry we found that the various mechanisms of scale coloration of the different birdwing species strongly correlate with the taxonomical distribution of Ornithoptera species. © 2015 The Author(s).

Spectrally tuned structural and pigmentary coloration of birdwing butterfly wing scales

PubMed Central

Wilts, Bodo D.; Matsushita, Atsuko; Arikawa, Kentaro; Stavenga, Doekele G.

2015-01-01

The colourful wing patterns of butterflies play an important role for enhancing fitness; for instance, by providing camouflage, for interspecific mate recognition, or for aposematic display. Closely related butterfly species can have dramatically different wing patterns. The phenomenon is assumed to be caused by ecological processes with changing conditions, e.g. in the environment, and also by sexual selection. Here, we investigate the birdwing butterflies, Ornithoptera, the largest butterflies of the world, together forming a small genus in the butterfly family Papilionidae. The wings of these butterflies are marked by strongly coloured patches. The colours are caused by specially structured wing scales, which act as a chirped multilayer reflector, but the scales also contain papiliochrome pigments, which act as a spectral filter. The combined structural and pigmentary effects tune the coloration of the wing scales. The tuned colours are presumably important for mate recognition and signalling. By applying electron microscopy, (micro-)spectrophotometry and scatterometry we found that the various mechanisms of scale coloration of the different birdwing species strongly correlate with the taxonomical distribution of Ornithoptera species. PMID:26446560

Aging and social networks in Spain: the importance of pubs and churches.

PubMed

Buz, José; Sanchez, Marta; Levenson, Michael R; Aldwin, Carolyn M

2014-01-01

We examined whether the social convoy model and socioemotional selectivity theory apply in collectivistic cultures by examining the contextual factors which are hypothesized to mediate age-related differences in social support in a collectivist European country. Five hundred Spanish community-dwelling older adults (Mean age = 74.78, SD = 7.76, range = 60-93) were interviewed to examine structural aspects of their social networks. We found that age showed highly complex relationships with network size and frequency of interaction, depending on the network circle and the mediation of cultural factors. Family structure was important for social relations in the inner circle, while pubs and churches were important for peripheral relations. Surprisingly, pub attendance was the most important variable for maintenance of social support of peripheral network members. In general, the results support the applicability of the social convoy and socioemotional selectivity constructs to social support among Spanish older adults.

Vertical structure use by the Stout Iguana (Cyclura pinguis) on Guana Island, BVI

USGS Publications Warehouse

Cheek, Christopher A.; Hlavaty, Shay; Perkins, Rebecca N.; Peyton, Mark A.; Ryan, Caitlin N.; Zavaleta, Jennifer C.; Boal, Clint W.; Perry, Gad

2013-01-01

The Stout Iguana (Cyclura pinguis) is a critically endangered species endemic to the Puerto Rico Bank and currently restricted to the British Virgin Islands (BVI). Our study on Guana Island, BVI, focused on vertical structure use. Based on previous incidental observations, we hypothesized that Stout Iguanas use vertical structures and that adults and juveniles use such structures differently. In October 2011, we documented movement and vertical structure use by adult (n = 4) and juvenile (n = 11) iguanas with tracking bobbins. We recorded structure types used, heights attained on structures, distances between structures, and structure sizes. We found that Stout Iguanas used vertical structure more than previously documented. Trees comprised a significantly greater (P < 0.001) proportion of structures used by juveniles than by adults, whereas rocks comprised the greatest proportion of structures used by adults. In addition to differential structure use, juveniles climbed significantly higher (2.4 vs. 0.9 m on average; P < 0.001) than adults. We found no difference in the diameter or distance between structures used by adults and juveniles. Our results suggest that vertical structure use may be an important habitat element for free-ranging juvenile Stout Iguanas. Habitat management that provides vertical structure may be advantageous for the conservation of this species.

Evaluation of multiple-scale 3D characterization for coal physical structure with DCM method and synchrotron X-ray CT.

PubMed

Wang, Haipeng; Yang, Yushuang; Yang, Jianli; Nie, Yihang; Jia, Jing; Wang, Yudan

2015-01-01

Multiscale nondestructive characterization of coal microscopic physical structure can provide important information for coal conversion and coal-bed methane extraction. In this study, the physical structure of a coal sample was investigated by synchrotron-based multiple-energy X-ray CT at three beam energies and two different spatial resolutions. A data-constrained modeling (DCM) approach was used to quantitatively characterize the multiscale compositional distributions at the two resolutions. The volume fractions of each voxel for four different composition groups were obtained at the two resolutions. Between the two resolutions, the difference for DCM computed volume fractions of coal matrix and pores is less than 0.3%, and the difference for mineral composition groups is less than 0.17%. This demonstrates that the DCM approach can account for compositions beyond the X-ray CT imaging resolution with adequate accuracy. By using DCM, it is possible to characterize a relatively large coal sample at a relatively low spatial resolution with minimal loss of the effect due to subpixel fine length scale structures.

Interspecific analysis of covariance structure in the masticatory apparatus of galagos.

PubMed

Vinyard, Christopher J

2007-01-01

The primate masticatory apparatus (MA) is a functionally integrated set of features, each of which performs important functions in biting, ingestive, and chewing behaviors. A comparison of morphological covariance structure among species for these MA features will help us to further understand the evolutionary history of this region. In this exploratory analysis, the covariance structure of the MA is compared across seven galago species to investigate 1) whether there are differences in covariance structure in this region, and 2) if so, how has this covariation changed with respect to size, MA form, diet, and/or phylogeny? Ten measurements of the MA functionally related to bite force production and load resistance were obtained from 218 adults of seven galago species. Correlation matrices were generated for these 10 dimensions and compared among species via matrix correlations and Mantel tests. Subsequently, pairwise covariance disparity in the MA was estimated as a measure of difference in covariance structure between species. Covariance disparity estimates were correlated with pairwise distances related to differences in body size, MA size and shape, genetic distance (based on cytochrome-b sequences) and percentage of dietary foods to determine whether one or more of these factors is linked to differences in covariance structure. Galagos differ in MA covariance structure. Body size appears to be a major factor correlated with differences in covariance structure among galagos. The largest galago species, Otolemur crassicaudatus, exhibits large differences in body mass and covariance structure relative to other galagos, and thus plays a primary role in creating this association. MA size and shape do not correlate with covariance structure when body mass is held constant. Diet also shows no association. Genetic distance is significantly negatively correlated with covariance disparity when body mass is held constant, but this correlation appears to be a function of the small body size and large genetic distance for Galagoides demidoff. These exploratory results indicate that changing body size may have been a key factor in the evolution of the galago MA.

Development and modeling of self-deployable structures

NASA Astrophysics Data System (ADS)

Neogi, Depankar

Deployable space structures are prefabricated structures which can be transformed from a closed, compact configuration to a predetermined expanded form in which they are stable and can bear loads. The present research effort investigates a new family of deployable structures, called the Self-Deployable Structures (SDS). Unlike other deployable structures, which have rigid members, the SDS members are flexible while the connecting joints are rigid. The joints store the predefined geometry of the deployed structure in the collapsed state. The SDS is stress-free in both deployed and collapsed configurations and results in a self-standing structure which acquires its structural properties after a chemical reaction. Reliability of deployment is one of the most important features of the SDS, since it does not rely on mechanisms that can lock during deployment. The unit building block of these structures is the self-deployable structural element (SDSE). Several SDSE members can be linked to generate a complex building block such as a triangular or a tetrahedral structure. Different SDSE and SDS concepts are investigated in the research work, and the performance of SDS's are experimentally and theoretically explored. Triangular and tetrahedral prototype SDS have been developed and presented. Theoretical efforts include modeling the behavior of 2-dimensional SDSs. Using this design tool, engineers can study the effects of different packing configurations and deployment sequence; and perform optimization on the collapsed state of a structure with different external constraints. The model also predicts if any lockup or entanglement occurs during deployment.

Application of high explosion cratering data to planetary problems

NASA Technical Reports Server (NTRS)

Oberbeck, V. R.

1977-01-01

The present paper deals with the conditions of explosion or nuclear cratering required to simulate impact crater formation. Some planetary problems associated with three different aspects of crater formation are discussed, and solutions based on high-explosion data are proposed. Structures of impact craters and some selected explosion craters formed in layered media are examined and are related to the structure of lunar basins. The mode of ejection of material from impact craters is identified using explosion analogs. The ejection mode is shown to have important implications for the origin of material in crater and basin deposits. Equally important are the populations of secondary craters on lunar and planetary surfaces.

Expression of interest: transcriptomics and the designation of conservation units.

PubMed

Hansen, Michael M

2010-05-01

An important task within conservation genetics consists in defining intraspecific conservation units. Most conceptual frameworks involve two steps: (i) identifying demographically independent units, and (ii) evaluating their degree of adaptive divergence. Whereas a plethora of methods are available for delineating genetic population structure, assessment of functional genetic divergence remains a challenge. In this issue, Tymchuk et al. (2010) study Atlantic salmon (Salmo salar) populations using both microsatellite markers and analysis of global gene expression. They show that important gene expression differences exist that can be interpreted in the context of different ecological conditions experienced by the populations, along with the populations' histories. This demonstrates an important potential role of transcriptomics for designating conservation units.

Effects of functional groups and ionization on the structure of alkanethiol coated gold nanoparticles

NASA Astrophysics Data System (ADS)

Bolintineanu, Dan S.; Lane, J. Matthew D.; Grest, Gary S.

2013-03-01

We report fully atomistic molecular dynamics simulations of alkanethiol coated gold nanoparticles solvated in water and decane. The structure of the coatings is analyzed as a function of various functional end groups, including amine and carboxyl groups in different neutralization states. We study the effects of charge in the end groups for two different chain lengths (10 and 18 carbons) and different counterions (mono- and divalent). For the longer alkanes we find significant local phase segregation of chains on the nanoparticle surface, which results in highly asymmetric coating structures. In general, the charged end groups attenuate this effect by enhancing the water solubility of the nanoparticles. Based on the coating structures and density profiles, we can qualitatively infer the overall solubility of the nanoparticles. The asymmetry in the alkanethiol coatings is also likely to have a significant effect on aggregation behavior. More importantly, our simulations suggest the ability to modulate end group charge states (e.g. by changing the pH of the solution) in order to control coating structure, and therefore control solubility and aggregation behavior.

Does Compound I Vary Significantly between Isoforms of Cytochrome P450?

PubMed Central

2011-01-01

The cytochrome P450 (CYP) enzymes are important in many areas, including pharmaceutical development. Subtle changes in the electronic structure of the active species, Compound I, have been postulated previously to account partly for the experimentally observed differences in reactivity between isoforms. Current predictive models of CYP metabolism typically assume an identical Compound I in all isoforms. Here we present a method to calculate the electronic structure and to estimate the Fe–O bond enthalpy of Compound I, and apply it to several human and bacterial CYP isoforms. Conformational flexibility is accounted for by sampling large numbers of structures from molecular dynamics simulations, which are subsequently optimized with density functional theory (B3LYP) based quantum mechanics/molecular mechanics. The observed differences in Compound I between human isoforms are small: They are generally smaller than the spread of values obtained for the same isoform starting from different initial structures. Hence, it is unlikely that the variation in activity between human isoforms is due to differences in the electronic structure of Compound I. A larger difference in electronic structure is observed between the human isoforms and P450cam and may be explained by the slightly different hydrogen-bonding environment surrounding the cysteinyl sulfur. The presence of substrate in the active site of all isoforms studied appears to cause a slight decrease in the Fe–O bond enthalpy, apparently due to displacement of water out of the active site, suggesting that Compound I is less stable in the presence of substrate. PMID:21863858

Compartments in a marine food web associated with phylogeny, body mass, and habitat structure.

PubMed

Rezende, Enrico L; Albert, Eva M; Fortuna, Miguel A; Bascompte, Jordi

2009-08-01

A long-standing question in community ecology is whether food webs are organized in compartments, where species within the same compartment interact frequently among themselves, but show fewer interactions with species from other compartments. Finding evidence for this community organization is important since compartmentalization may strongly affect food web robustness to perturbation. However, few studies have found unequivocal evidence of compartments, and none has quantified the suite of mechanisms generating such a structure. Here, we combine computational tools from the physics of complex networks with phylogenetic statistical methods to show that a large marine food web is organized in compartments, and that body size, phylogeny, and spatial structure are jointly associated with such a compartmentalized structure. Sharks account for the majority of predatory interactions within their compartments. Phylogenetically closely related shark species tend to occupy different compartments and have divergent trophic levels, suggesting that competition may play an important role structuring some of these compartments. Current overfishing of sharks has the potential to change the structural properties, which might eventually affect the stability of the food web.

Visualization and manipulating the image of a formal data structure (FDS)-based database

NASA Astrophysics Data System (ADS)

Verdiesen, Franc; de Hoop, Sylvia; Molenaar, Martien

1994-08-01

A vector map is a terrain representation with a vector-structured geometry. Molenaar formulated an object-oriented formal data structure for 3D single valued vector maps. This FDS is implemented in a database (Oracle). In this study we describe a methodology for visualizing a FDS-based database and manipulating the image. A data set retrieved by querying the database is converted into an import file for a drawing application. An objective of this study is that an end-user can alter and add terrain objects in the image. The drawing application creates an export file, that is compared with the import file. Differences between these files result in updating the database which involves checks on consistency. In this study Autocad is used for visualizing and manipulating the image of the data set. A computer program has been written for the data exchange and conversion between Oracle and Autocad. The data structure of the FDS is compared to the data structure of Autocad and the data of the FDS is converted into the structure of Autocad equal to the FDS.

Unique structural modulation of a non-native substrate by cochaperone DnaJ.

PubMed

Tiwari, Satyam; Kumar, Vignesh; Jayaraj, Gopal Gunanathan; Maiti, Souvik; Mapa, Koyeli

2013-02-12

The role of bacterial DnaJ protein as a cochaperone of DnaK is strongly appreciated. Although DnaJ unaccompanied by DnaK can bind unfolded as well as native substrate proteins, its role as an individual chaperone remains elusive. In this study, we demonstrate that DnaJ binds a model non-native substrate with a low nanomolar dissociation constant and, more importantly, modulates the structure of its non-native state. The structural modulation achieved by DnaJ is different compared to that achieved by the DnaK-DnaJ complex. The nature of structural modulation exerted by DnaJ is suggestive of a unique unfolding activity on the non-native substrate by the chaperone. Furthermore, we demonstrate that the zinc binding motif along with the C-terminal substrate binding domain of DnaJ is necessary and sufficient for binding and the subsequent binding-induced structural alterations of the non-native substrate. We hypothesize that this hitherto unknown structural alteration of non-native states by DnaJ might be important for its chaperoning activity by removing kinetic traps of the folding intermediates.

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

Insights into Photosystem II from Isomorphous Difference Fourier Maps of Femtosecond X-ray Diffraction Data and Quantum Mechanics/Molecular Mechanics Structural Models.

PubMed

Wang, Jimin; Askerka, Mikhail; Brudvig, Gary W; Batista, Victor S

2017-02-10

Understanding structure-function relations in photosystem II (PSII) is important for the development of biomimetic photocatalytic systems. X-ray crystallography, computational modeling, and spectroscopy have played central roles in elucidating the structure and function of PSII. Recent breakthroughs in femtosecond X-ray crystallography offer the possibility of collecting diffraction data from the X-ray free electron laser (XFEL) before radiation damage of the sample, thereby overcoming the main challenge of conventional X-ray diffraction methods. However, the interpretation of XFEL data from PSII intermediates is challenging because of the issues regarding data-processing, uncertainty on the precise positions of light oxygen atoms next to heavy metal centers, and different kinetics of the S-state transition in microcrystals compared to solution. Here, we summarize recent advances and outstanding challenges in PSII structure-function determination with emphasis on the implementation of quantum mechanics/molecular mechanics techniques combined with isomorphous difference Fourier maps, direct methods, and high-resolution spectroscopy.

Assessment of Protein Side-Chain Conformation Prediction Methods in Different Residue Environments

PubMed Central

Peterson, Lenna X.; Kang, Xuejiao; Kihara, Daisuke

2016-01-01

Computational prediction of side-chain conformation is an important component of protein structure prediction. Accurate side-chain prediction is crucial for practical applications of protein structure models that need atomic detailed resolution such as protein and ligand design. We evaluated the accuracy of eight side-chain prediction methods in reproducing the side-chain conformations of experimentally solved structures deposited to the Protein Data Bank. Prediction accuracy was evaluated for a total of four different structural environments (buried, surface, interface, and membrane-spanning) in three different protein types (monomeric, multimeric, and membrane). Overall, the highest accuracy was observed for buried residues in monomeric and multimeric proteins. Notably, side-chains at protein interfaces and membrane-spanning regions were better predicted than surface residues even though the methods did not all use multimeric and membrane proteins for training. Thus, we conclude that the current methods are as practically useful for modeling protein docking interfaces and membrane-spanning regions as for modeling monomers. PMID:24619909

The Structure Lacuna

PubMed Central

Boeyens, Jan C.A.; Levendis, Demetrius C.

2012-01-01

Molecular symmetry is intimately connected with the classical concept of three-dimensional molecular structure. In a non-classical theory of wave-like interaction in four-dimensional space-time, both of these concepts and traditional quantum mechanics lose their operational meaning, unless suitably modified. A required reformulation should emphasize the importance of four-dimensional effects like spin and the symmetry effects of space-time curvature that could lead to a fundamentally different understanding of molecular symmetry and structure in terms of elementary number theory. Isolated single molecules have no characteristic shape and macro-biomolecules only develop robust three-dimensional structure in hydrophobic response to aqueous cellular media. PMID:22942753

Parametric computational study of sheaths in multicomponent Ar/O2 plasma

NASA Astrophysics Data System (ADS)

Hromadka, J.; Ibehej, T.; Hrach, R.

2018-02-01

Our study is devoted to sheath structures emerging in Ar/O2 plasma. By means of two dimensional PIC/MCC computer model two configurations were investigated - sheath structure in the vicinity of a cylindrical Langmuir probe for two different biases and changes of the sheath structure when a cylindrical probe passes into a semi-planar probe. It was shown that O+ ions play important role in shielding out negative bias of a solid immersed in Ar/O2 plasma and edge effects of a semi-planar probe on its sheath structure were evaluated.

Composite Fuselage Technology

NASA Technical Reports Server (NTRS)

Lagace, Paul A.

1999-01-01

Work was conducted over a ten-year period to address the central issue of damage in primary load-bearing aircraft composite structure, specifically fuselage structure. This included the three facets of damage resistance, damage tolerance, and damage arrest. Experimental, analytical, and numerical work was conducted in order to identify and better understand the mechanisms that control the structural behavior of fuselage structures in their response to the three aspects of damage. Furthermore, work was done to develop straightforward design methodologies that can be employed by structural designers in preliminary design stages to make intelligent choices concerning the material, layup, and structural configurations so that a more efficient structure with structural integrity can be designed and built. Considerable progress was made towards achieving these goals via this work. In regard to damage tolerance considerations, the following were identified as important effects: composite layup and associated orthotropy/structural anisotropy, specifics of initial local damage mechanisms, role of longitudinal versus hoop stress, and large deformation and associated geometric nonlinearity. Means were established to account for effects of radius and for the nonlinear response. In particular, nondimensional parameters were identified to characterize the importance of nonlinearity in the response of pressurized cylinders. This led to the establishment of a iso-nonlinear-error plot for reference in structural design. Finally, in the case of damage tolerance, the general approach of the original methodology to predict the failure pressure involving extending basic plate failure data by accounting for the local stress intensification was accomplished for the general case by accounting for the mechanisms noted by utilizing the capability of the STAGS finite element code and numerically calculating the local stress intensification for the particular configuration to be considered. For the issue of damage arrest, placement of and configuration of stiffeners (including stiffener curvature), and magnitude and orientation of principal strains due to local bending were found to be key considerations. Means were established to account for stiffener effectiveness quantitatively based on radius, slit size, stiffener curvature' and relative bending stifffiesses involved. Geometric nonlinearity was also found to play an - 24 - important role here. Furthermore, it was determined that damage propagation is controlled by different mechanisms (hoop stress versus flapping stress and the associated factors involved in each) depending upon the direction of damage propagation. This latter item results in an inability to scale these phenomena in one test due to the different factors involved. Finally, the importance of shell curvature and associated instability in response to transverse loading including impact were found to be important considerations in damage resistance. A technique, involving asymmetric meshing of a finite element mesh, was developed to predict this behavior and showed excellent correlation with experimental results. Further details of these ten years of work are presented herein with references made to the fourteen documents produced during this work where full details can be found. Implications of this work are discussed and recommendations made. Although it is clear that there is more work to be done to fully understand composite fuselage technology and specifically the overall issue of damage in primary load-bearing composite structures, important understanding and capability has been extended via this work.

Formation of propagation invariant laser beams with anamorphic optical systems

NASA Astrophysics Data System (ADS)

Soskind, Y. G.

2015-03-01

Propagation invariant structured laser beams play an important role in several photonics applications. A majority of propagation invariant beams are usually produced in the form of laser modes emanating from stable laser cavities. This work shows that anamorphic optical systems can be effectively employed to transform input propagation invariant laser beams and produce a variety of alternative propagation invariant structured laser beam distributions with different shapes and phase structures. This work also presents several types of anamorphic lens systems suitable for transforming the input laser modes into a variety of structured propagation invariant beams. The transformations are applied to different laser mode types, including Hermite-Gaussian, Laguerre-Gaussian, and Ince-Gaussian field distributions. The influence of the relative azimuthal orientation between the input laser modes and the anamorphic optical systems on the resulting transformed propagation invariant beams is presented as well.

Structure and physical properties of silkworm cocoons

PubMed Central

Chen, Fujia; Porter, David; Vollrath, Fritz

2012-01-01

Silkworm cocoons have evolved a wide range of different structures and combinations of physical and chemical properties in order to cope with different threats and environmental conditions. We present our observations and measurements on 25 diverse types of cocoons in a first attempt to correlate physical properties with the structure and morphology of the cocoons. These two architectural parameters appear to be far more important than the material properties of the silk fibres themselves. We consider tensile and compressive mechanical properties and gas permeation of the cocoon walls, and in each case identify mechanisms or models that relate these properties to cocoon structure, usually based upon non-woven fibre composites. These properties are of relevance also for synthetic non-woven composite materials and our studies will help formulate bio-inspired design principles for new materials. PMID:22552916

Fluid transport and coherent structures of translating and flapping wings.

PubMed

Eldredge, Jeff D; Chong, Kwitae

2010-03-01

The Lagrangian coherent structures (LCSs) of simple wing cross sections in various low Reynolds number motions are extracted from high-fidelity numerical simulation data and examined in detail. The entrainment process in the wake of a translating ellipse is revealed by studying the relationship between attracting structures in the wake and upstream repelling structures, with the help of blocks of tracer particles. It is shown that a series of slender lobes in the repelling LCS project upstream from the front of the ellipse and "pull" fluid into the wake. Each lobe is paired with a corresponding wake vortex, into which the constituent fluid particles are folded. Flexible and rigid foils in flapping motion are studied, and the resulting differences in coherent structures are used to elucidate their differences in force generation. The clarity with which these flow structures are revealed, compared to the vorticity or velocity fields, provides new insight into the vortex shedding mechanisms that play an important role in unsteady aerodynamics.

Stochastic Time Models of Syllable Structure

PubMed Central

Shaw, Jason A.; Gafos, Adamantios I.

2015-01-01

Drawing on phonology research within the generative linguistics tradition, stochastic methods, and notions from complex systems, we develop a modelling paradigm linking phonological structure, expressed in terms of syllables, to speech movement data acquired with 3D electromagnetic articulography and X-ray microbeam methods. The essential variable in the models is syllable structure. When mapped to discrete coordination topologies, syllabic organization imposes systematic patterns of variability on the temporal dynamics of speech articulation. We simulated these dynamics under different syllabic parses and evaluated simulations against experimental data from Arabic and English, two languages claimed to parse similar strings of segments into different syllabic structures. Model simulations replicated several key experimental results, including the fallibility of past phonetic heuristics for syllable structure, and exposed the range of conditions under which such heuristics remain valid. More importantly, the modelling approach consistently diagnosed syllable structure proving resilient to multiple sources of variability in experimental data including measurement variability, speaker variability, and contextual variability. Prospects for extensions of our modelling paradigm to acoustic data are also discussed. PMID:25996153

Which similarity measure is better for analyzing protein structures in a molecular dynamics trajectory?

PubMed

Cossio, Pilar; Laio, Alessandro; Pietrucci, Fabio

2011-06-14

An important step in the computer simulation of the dynamics of biomolecules is the comparison of structures in a trajectory by exploiting a measure of distance. This allows distinguishing structures which are geometrically similar from those which are different. By analyzing microseconds-long all-atom molecular dynamics simulations of a polypeptide, we find that a distance based on backbone dihedral angles performs very well in distinguishing structures that are kinetically correlated from those that are not, while the widely used C(α) root mean square distance performs more poorly. The root mean square difference between contact matrices turns out instead to be the metric providing the highest clustering coefficient, namely, according to this similarity measure, the neighbors of a structure are also, on average, neighbors among themselves. We also propose a combined distance measure which, for the system considered here, performs well both for distinguishing structures which are distant in time and for giving a consistent cluster analysis. This journal is © the Owner Societies 2011

CHIRAL CHLORDANE SIGNATURES IN USGS NATIONAL WATER-QUALITY ASSESSMENT PROGRAM SEDIMENT SAMPLES

EPA Science Inventory

More than 260 important environmental contaminants are chiral (having structures that are nonsuperimposible mirror images). Although enantiomer pairs have identical physical-chemical properties, their toxicity, biodegradation, and environmental fate often are different. Cyclodex...

Differences between Mobile Learning Environmental Preferences of High School Teachers and Students in Taiwan: A Structural Equation Model Analysis

ERIC Educational Resources Information Center

Lai, Chiu-Lin; Hwang, Gwo-Jen; Liang, Jyh-Chong; Tsai, Chin-Chung

2016-01-01

Mobile technology has been increasingly applied to educational settings in the past decade. Although researchers have attempted to investigate both students' and teachers' preferences regarding mobile learning, few studies have investigated the differences between the two, an understanding of which is important for developing effective mobile…

Coping with an Insecure Employment Environment: The Differing Roles of Protean and Boundaryless Career Orientations

ERIC Educational Resources Information Center

Briscoe, Jon P.; Henagan, Stephanie C.; Burton, James P.; Murphy, Wendy M.

2012-01-01

In this paper, we utilize a sample of working adults (N = 362) in the context of the recent economic recession to explore the coping mechanisms associated with different career attitudes and their subsequent impact on important individual work outcomes. Results of structural equation modeling (SEM) demonstrated that boundaryless mindset and…

Adolescents' Commitment to Developing Talent: The Role of Peers in Continuing Motivation for Sports and the Arts.

ERIC Educational Resources Information Center

Patrick, Helen; Ryan, Allison M.; Alfeld-Liro, Corinne; Fredericks, Jennifer A.; Hruda, Ludmila Z.; Eccles, Jacquelynne S.

1999-01-01

Conducted semi-structured in-depth interviews with 41 adolescents talented in sports or the arts to study the importance of peer relationships in their continued involvement in their talent activities, sex differences in attitudes, and possible differences by activity domain. Peers generally played a supportive role, although females were more…

Frog tongue surface microstructures: functional and evolutionary patterns

PubMed Central

Gorb, Stanislav N

2016-01-01

Summary Frogs (Lissamphibia: Anura) use adhesive tongues to capture fast moving, elusive prey. For this, the tongues are moved quickly and adhere instantaneously to various prey surfaces. Recently, the functional morphology of frog tongues was discussed in context of their adhesive performance. It was suggested that the interaction between the tongue surface and the mucus coating is important for generating strong pull-off forces. However, despite the general notions about its importance for a successful contact with the prey, little is known about the surface structure of frog tongues. Previous studies focused almost exclusively on species within the Ranidae and Bufonidae, neglecting the wide diversity of frogs. Here we examined the tongue surface in nine different frog species, comprising eight different taxa, i.e., the Alytidae, Bombinatoridae, Megophryidae, Hylidae, Ceratophryidae, Ranidae, Bufonidae, and Dendrobatidae. In all species examined herein, we found fungiform and filiform papillae on the tongue surface. Further, we observed a high degree of variation among tongues in different frogs. These differences can be seen in the size and shape of the papillae, in the fine-structures on the papillae, as well as in the three-dimensional organization of subsurface tissues. Notably, the fine-structures on the filiform papillae in frogs comprise hair-like protrusions (Megophryidae and Ranidae), microridges (Bufonidae and Dendrobatidae), or can be irregularly shaped or absent as observed in the remaining taxa examined herein. Some of this variation might be related to different degrees of adhesive performance and may point to differences in the spectra of prey items between frog taxa. PMID:27547606

Centrality measures in temporal networks with time series analysis

NASA Astrophysics Data System (ADS)

Huang, Qiangjuan; Zhao, Chengli; Zhang, Xue; Wang, Xiaojie; Yi, Dongyun

2017-05-01

The study of identifying important nodes in networks has a wide application in different fields. However, the current researches are mostly based on static or aggregated networks. Recently, the increasing attention to networks with time-varying structure promotes the study of node centrality in temporal networks. In this paper, we define a supra-evolution matrix to depict the temporal network structure. With using of the time series analysis, the relationships between different time layers can be learned automatically. Based on the special form of the supra-evolution matrix, the eigenvector centrality calculating problem is turned into the calculation of eigenvectors of several low-dimensional matrices through iteration, which effectively reduces the computational complexity. Experiments are carried out on two real-world temporal networks, Enron email communication network and DBLP co-authorship network, the results of which show that our method is more efficient at discovering the important nodes than the common aggregating method.

Interplay between abiotic factors and species assemblages mediated by the ecosystem engineer Sabellaria alveolata (Annelida: Polychaeta)

NASA Astrophysics Data System (ADS)

Jones, Auriane G.; Dubois, Stanislas F.; Desroy, Nicolas; Fournier, Jérôme

2018-01-01

Sabellaria alveolata is a gregarious polychaete that uses sand particles to build three-dimensional structures known as reefs, fixed atop rocks or built on soft sediments. These structures are known to modify the local grain-size distribution and to host a highly diversified macrofauna, altered when the reef undergoes disturbances. The goal of this study was to investigate the different sedimentary and biological changes associated with the presence of a S. alveolata reef over two contrasting seasons (late winter and late summer), and how these changes were linked. Three different sediments were considered: the engineered sediment (the actual reef), the associated sediment (the soft sediment surrounding the reef structures) and a control soft sediment (i.e. no reef structures in close proximity). Univariate and multivariate comparisons of grain-size distribution, soft sediment characteristics (organic matter content, chlorophyll a, pheopigments and carbohydrate concentrations) and macrofauna were conducted between the different sediment types at both seasons and between the two seasons for each sediment type. A distance-based redundancy analyses (dbRDA) was used to investigate the link between the different environmental parameters and the macrofauna assemblages. Finally, we focused on a disturbance continuum of the engineered sediments proxied by an increase in the mud present in these sediments. The effects of a continuous and increasing disturbance on the associated fauna were investigated using pairwise beta diversity indices (Sørensen and Bray-Curtis dissimilarities and their decomposition into turnover and nestedness). Results showed a significant effect of the reef on the local sediment distribution (coarser sediments compared to the control) and on the benthic primary production (higher in the associated sediments). At both seasons, S. alveolata biomass and sediment principal mode were the environmental parameters which best differentiated the engineered, associated and control sediment assemblages. These two parameters are under the ecosystem engineer's influence stressing its importance in structuring benthic macrofauna. Furthermore, in late summer but not in late winter, presence/absence and abundance-based beta diversity were positively correlated to our disturbance proxy (mud content) a tendency driven by a species replacement and a rise in the associated fauna density. Our first set of results highlight the importance of S. alveolata reefs as benthic primary production enhancers via their physical structure and their biological activity. The results obtained using beta diversity indices emphasize the importance of recruitment in structuring the reef's macrofauna and - paradoxically - the ecological value of S. alveolata degraded forms as biodiversity and recruitment promoters.

A Novel Cofactor-binding Mode in Bacterial IMP Dehydrogenases Explains Inhibitor Selectivity*

PubMed Central

Makowska-Grzyska, Magdalena; Kim, Youngchang; Maltseva, Natalia; Osipiuk, Jerzy; Gu, Minyi; Zhang, Minjia; Mandapati, Kavitha; Gollapalli, Deviprasad R.; Gorla, Suresh Kumar; Hedstrom, Lizbeth; Joachimiak, Andrzej

2015-01-01

The steadily rising frequency of emerging diseases and antibiotic resistance creates an urgent need for new drugs and targets. Inosine 5′-monophosphate dehydrogenase (IMP dehydrogenase or IMPDH) is a promising target for the development of new antimicrobial agents. IMPDH catalyzes the oxidation of IMP to XMP with the concomitant reduction of NAD+, which is the pivotal step in the biosynthesis of guanine nucleotides. Potent inhibitors of bacterial IMPDHs have been identified that bind in a structurally distinct pocket that is absent in eukaryotic IMPDHs. The physiological role of this pocket was not understood. Here, we report the structures of complexes with different classes of inhibitors of Bacillus anthracis, Campylobacter jejuni, and Clostridium perfringens IMPDHs. These structures in combination with inhibition studies provide important insights into the interactions that modulate selectivity and potency. We also present two structures of the Vibrio cholerae IMPDH in complex with IMP/NAD+ and XMP/NAD+. In both structures, the cofactor assumes a dramatically different conformation than reported previously for eukaryotic IMPDHs and other dehydrogenases, with the major change observed for the position of the NAD+ adenosine moiety. More importantly, this new NAD+-binding site involves the same pocket that is utilized by the inhibitors. Thus, the bacterial IMPDH-specific NAD+-binding mode helps to rationalize the conformation adopted by several classes of prokaryotic IMPDH inhibitors. These findings offer a potential strategy for further ligand optimization. PMID:25572472

Bipolar disorder type I and II show distinct relationships between cortical thickness and executive function.

PubMed

Abé, C; Rolstad, S; Petrovic, P; Ekman, C-J; Sparding, T; Ingvar, M; Landén, M

2018-06-15

Frontal cortical abnormalities and executive function impairment co-occur in bipolar disorder. Recent studies have shown that bipolar subtypes differ in the degree of structural and functional impairments. The relationships between cognitive performance and cortical integrity have not been clarified and might differ across patients with bipolar disorder type I, II, and healthy subjects. Using a vertex-wise whole-brain analysis, we investigated how cortical integrity, as measured by cortical thickness, correlates with executive performance in patients with bipolar disorder type I, II, and controls (N = 160). We found focal associations between executive function and cortical thickness in the medial prefrontal cortex in bipolar II patients and controls, but not in bipolar I disorder. In bipolar II patients, we observed additional correlations in lateral prefrontal and occipital regions. Our findings suggest that bipolar disorder patients show altered structure-function relationships, and importantly that those relationships may differ between bipolar subtypes. The findings are line with studies suggesting subtype-specific neurobiological and cognitive profiles. This study contributes to a better understanding of brain structure-function relationships in bipolar disorder and gives important insights into the neuropathophysiology of diagnostic subtypes. © 2018 The Authors Acta Psychiatrica Scandinavica Published by John Wiley & Sons Ltd.

What Drives National Differences in Intensive Grandparental Childcare in Europe?

PubMed Central

Glaser, Karen; Price, Debora; Ribe, Eloi; Tinker, Anthea

2016-01-01

Objectives. Grandparents play an important role in looking after grandchildren, although intensive grandparental childcare varies considerably across Europe. Few studies have explicitly investigated the extent to which such cross-national variations are associated with national level differences in individual demographic and socio-economic distributions along with contextual-structural and cultural factors (e.g., variations in female labor force participation, childcare provision, and cultural attitudes). Methods. We used multilevel models to examine associations between intensive grandparental childcare and contextual-structural and cultural factors, after controlling for grandparent, parent, and child characteristics using nationally representative data from the Survey of Health, Ageing and Retirement in Europe. Results. Even controlling for cross-national differences in demographic and socio-economic distributions, contextual-structural factors play an important role in explaining grandparental childcare variations in Europe. In particular, higher levels of intensive grandparental childcare are found in countries with low labor force participation among younger and older women, and low formal childcare provision, where mothers in paid work largely rely on grandparental support on an almost daily basis. Discussion. Encouraging older women to remain in paid work is likely to have an impact on grandchild care which in turn may affect mothers’ employment, particularly in Southern European countries where there is little formal childcare. PMID:25783973

Effect of aggregate structure on VOC gas adsorption onto volcanic ash soil.

PubMed

Hamamoto, Shoichiro; Seki, Katsutoshi; Miyazaki, Tsuyoshi

2009-07-15

The understanding of the gaseous adsorption process and the parameters of volatile organic compounds such as organic solvents or fuels onto soils is very important in the analysis of the transport or fate of these chemicals in soils. Batch adsorption experiments with six different treatments were conducted to determine the adsorption of isohexane, a gaseous aliphatic, onto volcanic ash soil (Tachikawa loam). The measured gas adsorption coefficient for samples of Tachikawa loam used in the first three treatments, Control, AD (aggregate destroyed), and AD-OMR (aggregate destroyed and organic matter removed), implied that the aggregate structure of volcanic ash soil as well as organic matter strongly enhanced gas adsorption under the dry condition, whereas under the wet condition, the aggregate structure played an important role in gas adsorption regardless of the insolubility of isohexane. In the gas adsorption experiments for the last three treatments, soils were sieved in different sizes of mesh and were separated into three different aggregate or particle size fractions (2.0-1.0mm, 1.0-0.5mm, and less than 0.5mm). Tachikawa loam with a larger size fraction showed higher gas adsorption coefficient, suggesting the higher contributions of macroaggregates to isohexane gas adsorption under dry and wet conditions.

Fine-tuning the extent and dynamics of binding cleft opening as a potential general regulatory mechanism in parvulin-type peptidyl prolyl isomerases

NASA Astrophysics Data System (ADS)

Czajlik, András; Kovács, Bertalan; Permi, Perttu; Gáspári, Zoltán

2017-03-01

Parvulins or rotamases form a distinct group within peptidyl prolyl cis-trans isomerases. Their exact mode of action as well as the role of conserved residues in the family are still not unambiguously resolved. Using backbone S2 order parameters and NOEs as restraints, we have generated dynamic structural ensembles of three distinct parvulins, SaPrsA, TbPin1 and CsPinA. The resulting ensembles are in good agreement with the experimental data but reveal important differences between the three enzymes. The largest difference can be attributed to the extent of the opening of the substrate binding cleft, along which motional mode the three molecules occupy distinct regions. Comparison with a wide range of other available parvulin structures highlights structural divergence along the bottom of the binding cleft acting as a hinge during the opening-closing motion. In the prototype WW-domain containing parvulin, Pin1, this region is also important in forming contacts with the WW domain known to modulate enzymatic activity of the catalytic domain. We hypothesize that modulation of the extent and dynamics of the identified ‘breathing motion’ might be one of the factors responsible for functional differences in the distinct parvulin subfamilies.

Creative females have larger white matter structures: Evidence from a large sample study.

PubMed

Takeuchi, Hikaru; Taki, Yasuyuki; Nouchi, Rui; Yokoyama, Ryoichi; Kotozaki, Yuka; Nakagawa, Seishu; Sekiguchi, Atsushi; Iizuka, Kunio; Yamamoto, Yuki; Hanawa, Sugiko; Araki, Tsuyoshi; Makoto Miyauchi, Carlos; Shinada, Takamitsu; Sakaki, Kohei; Sassa, Yuko; Nozawa, Takayuki; Ikeda, Shigeyuki; Yokota, Susumu; Daniele, Magistro; Kawashima, Ryuta

2017-01-01

The importance of brain connectivity for creativity has been theoretically suggested and empirically demonstrated. Studies have shown sex differences in creativity measured by divergent thinking (CMDT) as well as sex differences in the structural correlates of CMDT. However, the relationships between regional white matter volume (rWMV) and CMDT and associated sex differences have never been directly investigated. In addition, structural studies have shown poor replicability and inaccuracy of multiple comparisons over the whole brain. To address these issues, we used the data from a large sample of healthy young adults (776 males and 560 females; mean age: 20.8 years, SD = 0.8). We investigated the relationship between CMDT and WMV using the newest version of voxel-based morphometry (VBM). We corrected for multiple comparisons over whole brain using the permutation-based method, which is known to be quite accurate and robust. Significant positive correlations between rWMV and CMDT scores were observed in widespread areas below the neocortex specifically in females. These associations with CMDT were not observed in analyses of fractional anisotropy using diffusion tensor imaging. Using rigorous methods, our findings further supported the importance of brain connectivity for creativity as well as its female-specific association. Hum Brain Mapp 38:414-430, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Ultrasound elastography to determine the layered mechanical properties of articular cartilage and the importance of such structural characteristics under load.

PubMed

McCredie, Alexandra J; Stride, Eleanor; Saffari, Nader

2009-01-01

Articular cartilage is an important load bearing surface in joints. Prone to damage and with limited self-repair ability, it is of interest to tissue engineers. Tissue implant design requires full mechanical characterisation of healthy native tissue. A layered organisation of reinforcing collagen fibrils exists in healthy articular cartilage and is believed to be important for correct tissue function. However, the effect of this on the local depth-dependent elasticity is poorly characterised. In this study, quasi-static ultrasound elastography is used both to compare the depth-dependent elastic properties of cartilage structures with two different fibril arrangements and to monitor changes in the elastic properties of engineered samples during development. Results show global and local elastic properties of the native tissues and highlight the differences caused by fibril architecture. At increasing culture periods, results from the engineered tissue demonstrate an increase in elastic stiffness and the time taken to reach equilibrium under a quasi-static displacement. The study suggests suitability of ultrasound elastography for design and monitoring engineered articular cartilage.

Examining drivers of the emissions embodied in trade

PubMed Central

Wu, Leying; Wang, Zheng

2017-01-01

Emissions embodied in provincial trade (EEPT) have important effects on provinces’ responsibilities for carbon emission reductions. Based on a multi-regional input-output model, we calculated EEPT for China’s 30 provinces in 2002, 2007 and 2010, and we attempted to determine the drivers of EEPT. The results showed that, during this period, the ratio of EEPT to production-based emissions increased over time, reaching 40.24% in 2010. In consideration of its important role in carbon emissions, we analyzed the factors attributable to EEPT through structure decomposition analysis. The decomposition results showed that final demand and carbon emission intensity were two major factors in EEPT, while the final demand in other provinces and the carbon emission intensity in the local province were major factors for Emissions embodied in provincial exports and the final demand in the local province and the carbon emission intensity in other provinces were major factors for Emissions embodied in provincial imports. Regarding the differences among the EEPT of different provinces, changes in the structure of trade were the primary reason. PMID:28426769

Origin, evolution and function of the hemipteran perimicrovillar membrane with emphasis on Reduviidae that transmit Chagas disease.

PubMed

Gutiérrez-Cabrera, A E; Córdoba-Aguilar, A; Zenteno, E; Lowenberger, C; Espinoza, B

2016-06-01

The peritrophic matrix is a chitin-protein structure that envelops the food bolus in the midgut of the majority of insects, but is absent in some groups which have, instead, an unusual extra-cellular lipoprotein membrane named the perimicrovillar membrane. The presence of the perimicrovillar membrane (PMM) allows these insects to exploit restricted ecological niches during all life stages. It is found only in some members of the superorder Paraneoptera and many of these species are of medical and economic importance. In this review we present an overview of the midgut and the digestive system of insects with an emphasis on the order Paraneoptera and differences found across phylogenetic groups. We discuss the importance of the PMM in Hemiptera and the apparent conservation of this structure among hemipteran groups, suggesting that the basic mechanism of PMM production is the same for different hemipteran species. We propose that the PMM is intimately involved in the interaction with parasites and as such should be a target for biological and chemical control of hemipteran insects of economic and medical importance.

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.

Frequency-tunable circular polarization beam splitter using a graphene-dielectric sub-wavelength film.

PubMed

Chen, Tuo; He, Sailing

2014-08-11

Manipulating the circular polarization of light is of great importance in chemistry and biology, as chiral molecules exhibit different physiological properties when exposed to different circularly polarized waves. Here we suggest a graphene/dielectric-stacked structure, which has both the properties of an epsilon-near-zero material and the high Hall conductivity of graphene. The proposed sub-wavelength structure demonstrates efficient manipulation of circular polarization properties of light. In a quite broad frequency range and at a large oblique incidence angle, the present magnetically active structure is transparent for one circularly polarized wave, and opaque for another. Such an effect can be further tuned by changing the magnitude of the applied magnetic field and chemical potential of graphene.

Vortex Structure Effects on Impingement, Effusion, and Cross Flow Cooling of a Double Wall Configuration

NASA Astrophysics Data System (ADS)

Ligrani, P. M.

2018-03-01

A variety of different types of vortices and vortex structures have important influences on thermal protection, heat transfer augmentation, and cooling performance of impingement cooling, effusion cooling, and cross flow cooling. Of particular interest are horseshoe vortices, which form around the upstream portions of effusion coolant concentrations just after they exit individual holes, hairpin vortices, which develop nearby and adjacent to effusion coolant trajectories, and Kelvin-Helmholtz vortices which form within the shear layers that form around each impingement cooling jet. The influences of these different vortex structures are described as they affect and alter the thermal performance of effusion cooling, impingement cooling, and cross flow cooling, as applied to a double wall configuration.

Origami structures for tunable thermal expansion

NASA Astrophysics Data System (ADS)

Boatti, Elisa; Bertoldi, Katia

Materials with engineered thermal expansion, capable of achieving targeted and extreme area/volume changes in response to variations in temperature, are important for a number of aerospace, optical, energy, and microelectronic applications. While most of the proposed structures with tunable coefficient of thermal expansion consist of bi-material 2D or 3D lattices, here we propose a periodic metastructure based on a bilayer Miura-Ori origami fold. We combine experiments and simulations to demonstrate that by tuning the geometrical and mechanical parameters an extremely broad range of thermal expansion coefficients can be obtained, spanning both negative and positive values. Additionally, the thermal properties along different directions can be adjusted independently. Differently from all previously reported systems, the proposed structure is non-porous.

Tuning the effective parameters in (Ta/Cu/[Ni/Co]x/Ta) multilayers with perpendicular magnetic anisotropy

NASA Astrophysics Data System (ADS)

Ayareh, Zohreh; Moradi, Mehrdad; Mahmoodi, Saman

2018-06-01

In this paper, we report perpendicular magnetic anisotropy (PMA) in a (Ta/Cu/[Ni/Co]x/Ta) multilayers structure. These typical structures usually include a multilayer of ferromagnetic and transition metal thin films. Usually, magnetic anisotropy is characterized by magnetization loops determined by magnetometer or magneto-optical Kerr effect (MOKE). The interface between ferromagnetic and metallic layers plays an important role in magnetic anisotropy evolution from out-of-plane to in-plane in (Ta/Cu/[Ni/Co]/Ta) structure. Obtained results from MOKE and magnetometry of these samples show that they have different easy axes due to change in thickness of Cu as spacer layer and difference in number of repetition of [Ni/Co] stacks.

The importance of dunes on a variety of planetary surfaces

USGS Publications Warehouse

Titus, Timothy N.; Zimbelman, James R.; Radebaugh, Jani

2015-01-01

Scientists observe aeolian bed forms, or dune-like structures, throughout the solar system in a range of locations, from bodies with only transient atmospheres, such as comets, to places with thick atmospheres, such as Venus and the Earth’s ocean floor. Determining the source of sand and the different dune formations that result are thus important to understanding solar system and planetary evolution.

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

Ordered patterns and structures via interfacial self-assembly: superlattices, honeycomb structures and coffee rings.

PubMed

Ma, Hongmin; Hao, Jingcheng

2011-11-01

Self-assembly is now being intensively studied in chemistry, physics, biology, and materials engineering and has become an important "bottom-up" approach to create intriguing structures for different applications. Self-assembly is not only a practical approach for creating a variety of nanostructures, but also shows great superiority in building hierarchical structures with orders on different length scales. The early work in self-assembly focused on molecular self-assembly in bulk solution, including the resultant dye aggregates, liposomes, vesicles, liquid crystals, gels and so on. Interfacial self-assembly has been a great concern over the last two decades, largely because of the unique and ingenious roles of this method for constructing materials at interfaces, such as self-assembled monolayers, Langmuir-Blodgett films, and capsules. Nanocrystal superlattices, honeycomb films and coffee rings are intriguing structural materials with more complex features and can be prepared by interfacial self-assembly on different length scales. In this critical review, we outline the recent development in the preparation and application of colloidal nanocrystal superlattices, honeycomb-patterned macroporous structures by the breath figure method, and coffee-ring-like patterns (247 references). This journal is © The Royal Society of Chemistry 2011

Force field dependent solution properties of glycine oligomers

PubMed Central

Drake, Justin A.

2015-01-01

Molecular simulations can be used to study disordered polypeptide systems and to generate hypotheses on the underlying structural and thermodynamic mechanisms that govern their function. As the number of disordered protein systems investigated with simulations increase, it is important to understand how particular force fields affect the structural properties of disordered polypeptides in solution. To this end, we performed a comparative structural analysis of Gly3 and Gly10 in aqueous solution from all-atom, microsecond MD simulations using the CHARMM 27 (C27), CHARMM 36 (C36), and Amber ff12SB force fields. For each force field, Gly3 and Gly10 were simulated for at least 300 ns and 1 μs, respectively. Simulating oligoglycines of two different lengths allows us to evaluate how force field effects depend on polypeptide length. Using a variety of structural metrics (e.g. end-to-end distance, radius of gyration, dihedral angle distributions), we characterize the distribution of oligoglycine conformers for each force field and show that each sample conformation space differently, yielding considerably different structural tendencies of the same oligoglycine model in solution. Notably, we find that C36 samples more extended oligoglycine structures than both C27 and ff12SB. PMID:25952623

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.

Action of plant proteinase inhibitors on enzymes of physiopathological importance.

PubMed

Oliva, Maria Luiza V; Sampaio, Misako U

2009-09-01

Obtained from leguminous seeds, various plant proteins inhibit animal proteinases, including human, and can be considered for the development of compounds with biological activity. Inhibitors from the Bowman-Birk and plant Kunitz-type family have been characterized by proteinase specificity, primary structure and reactive site. Our group mostly studies the genus Bauhinia, mainly the species bauhinioides, rufa, ungulata and variegata. In some species, more than one inhibitor was characterized, exhibiting different properties. Although proteins from this group share high structural similarity, they present differences in proteinase inhibition, explored in studies using diverse biological models.

Sex Differences in Gray Matter Volume of the Right Anterior Hippocampus Explain Sex Differences in Three-Dimensional Mental Rotation

PubMed Central

Wei, Wei; Chen, Chuansheng; Dong, Qi; Zhou, Xinlin

2016-01-01

Behavioral studies have reported that males perform better than females in 3-dimensional (3D) mental rotation. Given the important role of the hippocampus in spatial processing, the present study investigated whether structural differences in the hippocampus could explain the sex difference in 3D mental rotation. Results showed that after controlling for brain size, males had a larger anterior hippocampus, whereas females had a larger posterior hippocampus. Gray matter volume (GMV) of the right anterior hippocampus was significantly correlated with 3D mental rotation score. After controlling GMV of the right anterior hippocampus, sex difference in 3D mental rotation was no longer significant. These results suggest that the structural difference between males’ and females’ right anterior hippocampus was a neurobiological substrate for the sex difference in 3D mental rotation. PMID:27895570

Structure and Kinetic Stability of the p63 Tetramerization Domain

PubMed Central

Natan, Eviatar; Joerger, Andreas C.

2012-01-01

The p53 family of transcription factors—comprising p53, p63 and p73—plays an important role in tumor prevention and development. Essential to their function is the formation of tetramers, allowing cooperative binding to their DNA response elements. We solved crystal structures of the human p63 tetramerization domain, showing that p63 forms a dimer of dimers with D2 symmetry composed of highly intertwined monomers. The primary dimers are formed via an intramolecular β-sheet and hydrophobic helix packing (H1), a hallmark of all p53 family members. Like p73, but unlike p53, p63 requires a second helix (H2) to stabilize the architecture of the tetramer. In order to investigate the impact of structural differences on tetramer stability, we measured the subunit exchange reaction of p53 family homotetramers by nanoflow electrospray mass spectrometry. There were differences in both the kinetics and the pattern of the exchange reaction, with the p53 and p63 tetramers exhibiting much faster exchange kinetics than p73. The structural similarity between p63 and p73 rationalizes previous observations that p63 and p73 form mixed tetramers, and the kinetic data reveal the dissociation of the p73 homotetramers as the rate-limiting step for heterotetramer formation. Differential stability of the tetramers may play an important role in the cross talk between different isoforms and regulation of p53, p63 and p73 function in the cell cycle. PMID:22100306

Geomorphology Drives Amphibian Beta Diversity in Atlantic Forest Lowlands of Southeastern Brazil

PubMed Central

Luiz, Amom Mendes; Leão-Pires, Thiago Augusto; Sawaya, Ricardo J.

2016-01-01

Beta diversity patterns are the outcome of multiple processes operating at different scales. Amphibian assemblages seem to be affected by contemporary climate and dispersal-based processes. However, historical processes involved in present patterns of beta diversity remain poorly understood. We assess and disentangle geomorphological, climatic and spatial drivers of amphibian beta diversity in coastal lowlands of the Atlantic Forest, southeastern Brazil. We tested the hypothesis that geomorphological factors are more important in structuring anuran beta diversity than climatic and spatial factors. We obtained species composition via field survey (N = 766 individuals), museum specimens (N = 9,730) and literature records (N = 4,763). Sampling area was divided in four spatially explicit geomorphological units, representing historical predictors. Climatic descriptors were represented by the first two axis of a Principal Component Analysis. Spatial predictors in different spatial scales were described by Moran Eigenvector Maps. Redundancy Analysis was implemented to partition the explained variation of species composition by geomorphological, climatic and spatial predictors. Moreover, spatial autocorrelation analyses were used to test neutral theory predictions. Beta diversity was spatially structured in broader scales. Shared fraction between climatic and geomorphological variables was an important predictor of species composition (13%), as well as broad scale spatial predictors (13%). However, geomorphological variables alone were the most important predictor of beta diversity (42%). Historical factors related to geomorphology must have played a crucial role in structuring amphibian beta diversity. The complex relationships between geomorphological history and climatic gradients generated by the Serra do Mar Precambrian basements were also important. We highlight the importance of combining spatially explicit historical and contemporary predictors for understanding and disentangling major drivers of beta diversity patterns. PMID:27171522

Geomorphology Drives Amphibian Beta Diversity in Atlantic Forest Lowlands of Southeastern Brazil.

PubMed

Luiz, Amom Mendes; Leão-Pires, Thiago Augusto; Sawaya, Ricardo J

2016-01-01

Beta diversity patterns are the outcome of multiple processes operating at different scales. Amphibian assemblages seem to be affected by contemporary climate and dispersal-based processes. However, historical processes involved in present patterns of beta diversity remain poorly understood. We assess and disentangle geomorphological, climatic and spatial drivers of amphibian beta diversity in coastal lowlands of the Atlantic Forest, southeastern Brazil. We tested the hypothesis that geomorphological factors are more important in structuring anuran beta diversity than climatic and spatial factors. We obtained species composition via field survey (N = 766 individuals), museum specimens (N = 9,730) and literature records (N = 4,763). Sampling area was divided in four spatially explicit geomorphological units, representing historical predictors. Climatic descriptors were represented by the first two axis of a Principal Component Analysis. Spatial predictors in different spatial scales were described by Moran Eigenvector Maps. Redundancy Analysis was implemented to partition the explained variation of species composition by geomorphological, climatic and spatial predictors. Moreover, spatial autocorrelation analyses were used to test neutral theory predictions. Beta diversity was spatially structured in broader scales. Shared fraction between climatic and geomorphological variables was an important predictor of species composition (13%), as well as broad scale spatial predictors (13%). However, geomorphological variables alone were the most important predictor of beta diversity (42%). Historical factors related to geomorphology must have played a crucial role in structuring amphibian beta diversity. The complex relationships between geomorphological history and climatic gradients generated by the Serra do Mar Precambrian basements were also important. We highlight the importance of combining spatially explicit historical and contemporary predictors for understanding and disentangling major drivers of beta diversity patterns.

Population structure of Aphis spiraecola (Hemiptera: Aphididae) on pear trees in China identified using microsatellites.

PubMed

Cao, Jinjun; Li, Jie; Niu, Jianqun; Liu, Xiaoxia; Zhang, Qingwen

2012-04-01

The spiraea aphid (Aphis spiraecola Patch) is a primary pest of fruit trees, particularly pear trees in China. Despite the economic importance of this pest, little is known about its genetic structure or its patterns of dispersal at local and regional scales; however, knowledge of these characteristics is important for establishing effective control strategies for this pest. The genetic variability of 431 individuals from 21 populations on pear trees in China was investigated using eight polymorphic microsatellite loci. The high polymorphism of these markers was evident from the expected heterozygosity value (He = 0.824) and the Polymorphism Information Content (PIC = 0.805), indicating that the spiraea aphid maintains a high level of genetic diversity. The analysis of molecular variance revealed a middle level of population differentiation (F(ST) = 0.1478) among A. spiraecola populations. This result is consistent with the results of the STRUCTURE analysis (K = 3), the unweighted pair-group method with arithmetic average tree and the Mantel test (r = 0.6392; P < 0.05). Our results indicate high levels of genetic exchange in the spiraea aphid, possibly facilitated by geography and climate. Our findings emphasize the importance of considering regional differences in studies of population structure, even when strong isolation-by-distance influences the genetic population structure of species.

Inter-annual differences of ichthyofauna structure of the Guadiana estuary and adjacent coastal area (SE Portugal/SW Spain): Before and after Alqueva dam construction

NASA Astrophysics Data System (ADS)

Chícharo, M. Alexandra; Chícharo, Luis; Morais, Pedro

2006-10-01

The objective of this study was to evaluate how inter-annual changes in the volume of freshwater input and water parameters (salinity, temperature, major dissolved nutrients, seston and chlorophyll a) affect fish assemblages in the Guadiana estuary (South Portugal). During the sampling period (two distinct hydrological years), 56 fish species were identified. Anchovies ( Engraulis encrasicolus) and barbells ( Barbus species) dominated the abundances in the high inflow year (2001), but Pomatoschistus species were the most important taxa in the low inflow year (2002). Barbells and Portuguese toadfish ( Halobatrachus didactylus) dominated the biomass in both years under different inflow conditions, but a reduction in barbells' biomass occurred during the low inflow year. Multivariate analysis indicated a persistent spatial structuring of the estuarine community for both years and in different seasonal periods. Changes in salinity and seston, which were mainly due to changes in freshwater input, had an important influence on the structure of the fish assemblages. In 2002, the increased salinity in the upper estuary allowed colonization by marine species of an area that usually contains freshwater, decreasing even more the habitat for indigenous freshwater species in the downstream area of the Guadiana River. There was also a decrease in the abundances of planktivorous and omnivorous fishes and an increase in carnivorous fishes during the low inflow year. As fishes in these systems are important regulators of processes in the trophic web, changes in the dominant feeding groups can have consequences on water quality, particularly in relation to the occurrence of plankton blooms.

Contrasting Patterns in Solitary and Eusocial Bees While Responding to Landscape Features in the Brazilian Cerrado: a Multiscaled Perspective.

PubMed

Silva, D P; Nogueira, D S; De Marco, P

2017-06-01

Landscape structure is an important determinant of biological fluxes and species composition, but species do not respond equally to landscape features or spatial extents. Evaluating "multi-scale" responses of species to landscape structure is an important framework to be considered, allowing insights about habitat requirements for different groups. We evaluated the response of Brazilian Cerrado's bees (eusocial vs. solitary ones) to both the amount and isolation of remnant vegetation in eight nested multiple-local scales. Response variables included abundance, observed, and estimated species richness, and beta diversity (split into nestedness and turnover resultant dissimilarities). Eusocial species' abundance responded to landscape structure at narrow scales of fragment isolation (250 m of radius from sampling sites), while solitary species' abundance responded to broader scales to fragment area (2000 m). Eusocial species nestedness also responded to landscape features in broader scales (1500 m), especially to increasing fragment isolation. However, all the remaining response variables did not respond to any other landscape variables in any spatial scale considered. Such contrasting responses of the abundances of eusocial vs. solitary species are related to the inherent life-history traits of each group. Important attributes in this context are different requirements on food resources, population features, and flight abilities. Species-specific dispersal abilities may be the main determinants of the nested patterns found for eusocial species at 1500 m. Considering these results, we suggest that different bee groups are considered separately in further landscape analyses, especially in other Brazilian biomes, for a better understanding of landscape effects on these organisms.

Differential investment in visual and olfactory brain areas reflects behavioural choices in hawk moths

PubMed Central

Stöckl, Anna; Heinze, Stanley; Charalabidis, Alice; el Jundi, Basil; Warrant, Eric; Kelber, Almut

2016-01-01

Nervous tissue is one of the most metabolically expensive animal tissues, thus evolutionary investments that result in enlarged brain regions should also result in improved behavioural performance. Indeed, large-scale comparative studies in vertebrates and invertebrates have successfully linked differences in brain anatomy to differences in ecology and behaviour, but their precision can be limited by the detail of the anatomical measurements, or by only measuring behaviour indirectly. Therefore, detailed case studies are valuable complements to these investigations, and have provided important evidence linking brain structure to function in a range of higher-order behavioural traits, such as foraging experience or aggressive behaviour. Here, we show that differences in the size of both lower and higher-order sensory brain areas reflect differences in the relative importance of these senses in the foraging choices of hawk moths, as suggested by previous anatomical work in Lepidopterans. To this end we combined anatomical and behavioural quantifications of the relative importance of vision and olfaction in two closely related hawk moth species. We conclude that differences in sensory brain volume in these hawk moths can indeed be interpreted as differences in the importance of these senses for the animal’s behaviour. PMID:27185464

Examining predator–prey body size, trophic level and body mass across marine and terrestrial mammals

PubMed Central

Tucker, Marlee A.; Rogers, Tracey L.

2014-01-01

Predator–prey relationships and trophic levels are indicators of community structure, and are important for monitoring ecosystem changes. Mammals colonized the marine environment on seven separate occasions, which resulted in differences in species' physiology, morphology and behaviour. It is likely that these changes have had a major effect upon predator–prey relationships and trophic position; however, the effect of environment is yet to be clarified. We compiled a dataset, based on the literature, to explore the relationship between body mass, trophic level and predator–prey ratio across terrestrial (n = 51) and marine (n = 56) mammals. We did not find the expected positive relationship between trophic level and body mass, but we did find that marine carnivores sit 1.3 trophic levels higher than terrestrial carnivores. Also, marine mammals are largely carnivorous and have significantly larger predator–prey ratios compared with their terrestrial counterparts. We propose that primary productivity, and its availability, is important for mammalian trophic structure and body size. Also, energy flow and community structure in the marine environment are influenced by differences in energy efficiency and increased food web stability. Enhancing our knowledge of feeding ecology in mammals has the potential to provide insights into the structure and functioning of marine and terrestrial communities. PMID:25377460

Capillary electrophoretic study of dibasic acids of different structures: Relation to separation of oxidative intermediates in remediation

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

Yu, Z.; Cocke, D.L.

Dicarboxylic acids are important in environmental chemistry because they are intermediates in oxidative processes involved in natural remediation and waste management processes such as oxidative detoxification and advanced oxidation. Capillary electrophoresis (CE), a promising technique for separating and analyzing these intermediates, has been used to examine a series of dibasic acids of different structures and conformations. This series includes malonic acid, succinic acid, glutaric acid, adipic acid, pimelic acid, maleic acid, fumaric acid, phthalic acid, and trans, trans-muconic acid. The CE parameters as well as structural variations (molecular structure and molecular isomers, buffer composition, pH, applied voltage, injection mode, current,more » temperature, and detection wavelength) that affect the separations and analytical results have been examined in this study. Those factors that affect the separation have been delineated. Among these parameters, the pH has been found to be the most important, which affects the double-layer of the capillary wall, the electro-osmotic flow and analyte mobility. The optimum pH for separating these dibasic acids, as well as the other parameters are discussed in detail and related to the development of methods for analyzing oxidation intermediates in oxidative waste management procedures.« less

Biomimetic photonic materials with tunable structural colors.

PubMed

Xu, Jun; Guo, Zhiguang

2013-09-15

Nature is a huge gallery of art involving nearly perfect structures and forms over the millions of years developing. Inspiration from natural structures exhibiting structural colors is first discussed. We give some examples of natural one-, two-, and three-dimensional photonic structures. This review article presents a brief summary of recent progress on bio-inspired photonic materials with variable structural colors, including the different facile and efficient routes to construct the nano-architectures, and the development of the artificial variable structural color photonic materials. Besides the superior optical properties, the excellent functions such as robust mechanical strength, good wettability are also mentioned, as well as the technical importance in various applications. This review will provide significant insight into the fabrication, design and application of the structural color materials. Copyright © 2013 Elsevier Inc. All rights reserved.

Photonic band structures solved by a plane-wave-based transfer-matrix method.

PubMed

Li, Zhi-Yuan; Lin, Lan-Lan

2003-04-01

Transfer-matrix methods adopting a plane-wave basis have been routinely used to calculate the scattering of electromagnetic waves by general multilayer gratings and photonic crystal slabs. In this paper we show that this technique, when combined with Bloch's theorem, can be extended to solve the photonic band structure for 2D and 3D photonic crystal structures. Three different eigensolution schemes to solve the traditional band diagrams along high-symmetry lines in the first Brillouin zone of the crystal are discussed. Optimal rules for the Fourier expansion over the dielectric function and electromagnetic fields with discontinuities occurring at the boundary of different material domains have been employed to accelerate the convergence of numerical computation. Application of this method to an important class of 3D layer-by-layer photonic crystals reveals the superior convergency of this different approach over the conventional plane-wave expansion method.

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.

Risk Behavior and Perception Among Youths Residing in Urban Public Housing Developments

PubMed Central

Li, Xiaoming; Stanton, Bonita; Black, Maureen M.; Romer, Daniel; Ricardo, Izabel; Kaljee, Linda

1994-01-01

The scientific literature and popular media suggest that variations in housing structure and neighborhood influence risk behaviors among youths living in low-income urban communities. To explore the importance of these factors on early sexual intercourse, substance use, drug trafficking, and school truancy, data from a community-based survey, conducted in six public housing developments in a major eastern metropolis, were analyzed. The survey group consisted of 300 youths aged 9 through 15 years. There were minimal differences in three potential mediators of risk behaviors (e.g., perceived social support, parenting style, and perceived risk exposure) and in self-reported adolescent risk behaviors among youths residing in different housing developments and between youths residing in high-rise and in low-rise structures. These findings do not support the hypothesis that within a risk-dense low-income environment, variations in building structure or in neighborhood are associated with differences in adolescent risk behaviors. PMID:19313105

Rigidity and pH dependent Morphology of Beta-Lactoglobulin Spherulites

NASA Astrophysics Data System (ADS)

Gayetsky, Lisa; Armstead, Douglas

2008-03-01

Beta-Lactoglobulin is a milk protein that will denature in acidic solution (less than 2.0 pH) and if heated for extended periods (greater than 18 hours) it will form radial structures called Spherulites. Spherulites, along with the amyloid fibrils that compose them, are of practical importance because they form in the human body and cause the amyloidosis diseases. Different amyloidosis are caused by different types of denatured proteins occurring in different parts of the body. Since it is believed that Spherulite formation is a generic protein characteristic, Beta-Lactoglobulin is a legitimate and easy to use protein to study these structures. In this study we are quantifying the shape of Beta-Lactoglobulin Spherulites to determine if the pH of the protein solution has an impact on the morphology due to side chain interactions or other causes. We are also testing the rigidity of these structures to determine the relevance of small shape changes.

Aging and the segmentation of narrative film.

PubMed

Kurby, Christopher A; Asiala, Lillian K E; Mills, Steven R

2014-01-01

The perception of event structure in continuous activity is important for everyday comprehension. Although the segmentation of experience into events is a normal concomitant of perceptual processing, previous research has shown age differences in the ability to perceive structure in naturalistic activity, such as a movie of someone washing a car. However, past research has also shown that older adults have a preserved ability to comprehend events in narrative text, which suggests that narrative may improve the event processing of older adults. This study tested whether there are age differences in event segmentation at the intersection of continuous activity and narrative: narrative film. Younger and older adults watched and segmented a narrative film, The Red Balloon, into coarse and fine events. Changes in situational features, such as changes in characters, goals, and objects predicted segmentation. Analyses revealed little age-difference in segmentation behavior. This suggests the possibility that narrative structure supports event understanding for older adults.

Development of the Noise-Resistant and Sound Focusing Accessory of Ultrasonic Leak Detector for Spacecraft on Orbit

NASA Astrophysics Data System (ADS)

Sun, W.; Yan, R. X.; Sun, L. C.; Shao, R. P.

2017-12-01

Ultrasonic signal produced by the gas leak is so week that it is difficult to detect, and easily interfered. So developing the noise-resistant and sound focusing accessory for the ultrasonic leak detector is very important for improving ultrasonic leak detector sensitivity and noise-resistant capability. Based on the theory analysis of the leak ultrasonic signal reverberation and anacampsis, the 5A06 aluminium alloy and nylon were selected as the material of noise-resistant and sound focusing accessory by calculation and compare. Then the circular cone trumpet structure was design as the accessory main structure, and the nylon expansion port, nylon shrinking port and aluminium alloy expansion port structures were manufactured. The different structure characters were shown by the contrasting experiment. The results indicate that the nylon expansion circular cone trumpet structure has better sound focusing performance and it can improve the testing sound pressure amplitude 10 bigger than the detector without the accessory. And the aluminium alloy expansion circular cone trumpet structure has better noise-resistant ability than others. These conclusions are very important for the spacecraft leak detection and it can provide some references for the design of the noise-resistant and sound focusing structure.

Connecting Structure-Property and Structure-Function Relationships across the Disciplines of Chemistry and Biology: Exploring Student Perceptions.

PubMed

Kohn, Kathryn P; Underwood, Sonia M; Cooper, Melanie M

2018-06-01

While many university students take science courses in multiple disciplines, little is known about how they perceive common concepts from different disciplinary perspectives. Structure-property and structure-function relationships have long been considered important explanatory concepts in the disciplines of chemistry and biology, respectively. Fourteen university students concurrently enrolled in introductory chemistry and biology courses were interviewed to explore their perceptions regarding 1) the meaning of structure, properties, and function; 2) the presentation of these concepts in their courses; and 3) how these concepts might be related. Findings suggest that the concepts of structure and properties were interpreted similarly between chemistry and biology, but students more closely associated the discussion of structure-property relationships with their chemistry courses and structure-function with biology. Despite receiving little in the way of instructional support, nine students proposed a coherent conceptual relationship, indicating that structure determines properties, which determine function. Furthermore, students described ways in which they connected and benefited from their understanding. Though many students are prepared to make these connections, we would encourage instructors to engage in cross-disciplinary conversations to understand the shared goals and disciplinary distinctions regarding these important concepts in an effort to better support students unable to construct these connections for themselves.

Student perception and conceptual development as represented by student mental models of atomic structure

NASA Astrophysics Data System (ADS)

Park, Eun Jung

The nature of matter based upon atomic theory is a principal concept in science; hence, how to teach and how to learn about atoms is an important subject for science education. To this end, this study explored student perceptions of atomic structure and how students learn about this concept by analyzing student mental models of atomic structure. Changes in student mental models serve as a valuable resource for comprehending student conceptual development. Data was collected from students who were taking the introductory chemistry course. Responses to course examinations, pre- and post-questionnaires, and pre- and post-interviews were used to analyze student mental models of atomic structure. First, this study reveals that conceptual development can be achieved, either by elevating mental models toward higher levels of understanding or by developing a single mental model. This study reinforces the importance of higher-order thinking skills to enable students to relate concepts in order to construct a target model of atomic structure. Second, Bohr's orbital structure seems to have had a strong influence on student perceptions of atomic structure. With regard to this finding, this study suggests that it is instructionally important to teach the concept of "orbitals" related to "quantum theory." Third, there were relatively few students who had developed understanding at the level of the target model, which required student understanding of the basic ideas of quantum theory. This study suggests that the understanding of atomic structure based on the idea of quantum theory is both important and difficult. Fourth, this study included different student assessments comprised of course examinations, questionnaires, and interviews. Each assessment can be used to gather information to map out student mental models. Fifth, in the comparison of the pre- and post-interview responses, this study showed that high achieving students moved toward more improved models or to advanced levels of understanding. The analysis of mental models in this study has provided information describing student understanding of the nature and structure of an atom. In addition to an assessment of student cognition, information produced from this study can serve as an important resource for curriculum development, teacher education, and instruction.

Cannibals in space: the coevolution of cannibalism and dispersal in spatially structured populations.

PubMed

Rudolf, Volker H W; Kamo, Masashi; Boots, Mike

2010-05-01

The propensity for cannibalism varies considerably both within and between species. Currently we have little understanding of both the causes of this variation and its evolutionary consequences for other life-history traits. We examine how different levels of spatial structure affect the evolution of cannibalism and how cannibalism in turn drives the evolution of dispersal. Using pair approximations and simulations, we show that cannibalism can easily evolve in spatially structured populations as long as some dispersal exists. Furthermore, for a wide range of intermediate levels of spatial structure, we find the possibility of evolutionary branching leading to polymorphism in cannibalism. We also show that cannibalism itself can have important evolutionary consequences and select for increased dispersal rates, thus helping to determine the spatial structure of populations. The coevolution of cannibalism and dispersal results in the evolution of various alternative life-history strategies with different dispersal and cannibalism regimes. Which strategy evolves depends on the environmental conditions that determine initial cannibalism rates. Our results therefore suggest that differences in spatial structure could explain variation in the propensity for cannibalism and cannibalistic polyphenism. Furthermore, results emphasize that cannibalism can drive the evolution of other life-history traits and determine the spatial structure of natural populations.

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.

Trends in asset structure between not-for-profit and investor-owned hospitals.

PubMed

Song, Paula H; Reiter, Kristin L

2010-12-01

The delivery of health care is a capital-intensive industry, and thus, hospital investment strategy continues to be an important area of interest for both health policy and research. Much attention has been given to hospitals' capital investment policies with relatively little attention to investments in financial assets, which serve an important role in not-for-profit (NFP) hospitals. This study describes and analyzes trends in aggregate asset structure between NFP and investor-owned (IO) hospitals during the post-capital-based prospective payment system implementation period, providing the first documentation of long-term trends in hospital investment. The authors find hospitals' aggregate asset structure differs significantly based on ownership, size, and profitability. For both NFP and IO hospitals, financial securities have remained consistent over time, while fixed asset representation has declined in IO hospitals.

Organization structure as a moderator of the relationship between procedural justice, interactional justice, perceived organizational support, and supervisory trust.

PubMed

Ambrose, Maureen L; Schminke, Marshall

2003-04-01

Organizational justice researchers recognize the important role organization context plays in justice perceptions, yet few studies systematically examine contextual variables. This article examines how 1 aspect of context--organizational structure--affects the relationship between justice perceptions and 2 types of social exchange relationships, organizational and supervisory. The authors suggest that under different structural conditions, procedural and interactional justice will play differentially important roles in determining the quality of organizational social exchange (as evidenced by perceived organizational support [POS]) and supervisory social exchange (as evidenced by supervisory trust). In particular, the authors hypothesized that the relationship between procedural justice and POS would be stronger in mechanistic organizations and that the relationship between interactional justice and supervisory trust would be stronger in organic organizations. The authors' results support these hypotheses.

Deletion of a gene cluster encoding pectin degrading enzymes in Caldicellulosiruptor bescii reveals an important role for pectin in plant biomass recalcitrance

DOE PAGES

Chung, Daehwan; Pattathil, Sivakumar; Biswal, Ajaya K.; ...

2014-10-10

A major obstacle, and perhaps the most important economic barrier to the effective use of plant biomass for the production of fuels, chemicals, and bioproducts, is our current lack of knowledge of how to efficiently and effectively deconstruct wall polymers for their subsequent use as feedstocks. Plants represent the most desired source of renewable energy and hydrocarbons because they fix CO 2, making their use carbon neutral. Their biomass structure, however, is a barrier to deconstruction, and this is often referred to as recalcitrance. Members of the bacterial genus Caldicellulosiruptor have the ability to grow on unpretreated plant biomass andmore » thus provide an assay for plant deconstruction and biomass recalcitrance. Using recently developed genetic tools for manipulation of these bacteria, a deletion of a gene cluster encoding enzymes for pectin degradation was constructed, and the resulting mutant was reduced in its ability to grow on both dicot and grass biomass, but not on soluble sugars. The plant biomass from three phylogenetically diverse plants, Arabidopsis (a herbaceous dicot), switchgrass (a monocot grass), and poplar (a woody dicot), was used in these analyses. These biomass types have cell walls that are significantly different from each other in both structure and composition. While pectin is a relatively minor component of the grass and woody dicot substrates, the reduced growth of the mutant on all three biomass types provides direct evidence that pectin plays an important role in biomass recalcitrance. Glycome profiling of the plant material remaining after growth of the mutant on Arabidopsis biomass compared to the wild-type revealed differences in the rhamnogalacturonan I, homogalacturonan, arabinogalactan, and xylan profiles. In contrast, only minor differences were observed in the glycome profiles of the switchgrass and poplar biomass. In conclusion, the combination of microbial digestion and plant biomass analysis provides a new and important platform to identify plant wall structures whose presence reduces the ability of microbes to deconstruct plant walls and to identify enzymes that specifically deconstruct those structures.« less

A family of zeolites with controlled pore size prepared using a top-down method

NASA Astrophysics Data System (ADS)

Roth, Wieslaw J.; Nachtigall, Petr; Morris, Russell E.; Wheatley, Paul S.; Seymour, Valerie R.; Ashbrook, Sharon E.; Chlubná, Pavla; Grajciar, Lukáš; Položij, Miroslav; Zukal, Arnošt; Shvets, Oleksiy; Čejka, Jiří

2013-07-01

The properties of zeolites, and thus their suitability for different applications, are intimately connected with their structures. Synthesizing specific architectures is therefore important, but has remained challenging. Here we report a top-down strategy that involves the disassembly of a parent zeolite, UTL, and its reassembly into two zeolites with targeted topologies, IPC-2 and IPC-4. The three zeolites are closely related as they adopt the same layered structure, and they differ only in how the layers are connected. Choosing different linkers gives rise to different pore sizes, enabling the synthesis of materials with predetermined pore architectures. The structures of the resulting zeolites were characterized by interpreting the X-ray powder-diffraction patterns through models using computational methods; IPC-2 exhibits orthogonal 12- and ten-ring channels, and IPC-4 is a more complex zeolite that comprises orthogonal ten- and eight-ring channels. We describe how this method enables the preparation of functional materials and discuss its potential for targeting other new zeolites.

Observation of creep behavior of cellulose electro-active paper (EAPap) actuator

NASA Astrophysics Data System (ADS)

Kim, Joo-Hyung; Lee, Sang-Woo; Yun, Gyu-Young; Yang, Chulho; Kim, Heung Soo; Kim, Jaehwan

2009-03-01

Understanding of creep effects on actuating mechanisms is important to precisely figure out the behavior of material. Creep behaviors of cellulose based Electro-Active Paper (EAPap) were studied under different constant loading conditions. We found the structural modification of microfibrils in EAPap after creep test. Structural differences of as-prepared and after creep tested samples were compared by SEM measurements. From the measured creep behaviors by different loading conditions, two different regions of induced strain and current were clearly observed as the measurement time increased. It is consider that local defects may occur and becomes micro-dimple or micro-crack formations in lower load cases as localized deformation proceeds, while the shrinkage of diameter of elongated fibers was observed only at the high level of loading. Therefore, cellulose nanofibers may play a role to be against the creep load and prevent the localized structural deformations. The results provide useful creep behavior and mechanism to understand the mechanical behavior of thin visco-elastic EAPap actuator.

Exploring ischemia-induced vascular lesions and potential pharmacological intervention strategies.

PubMed

Aliev, G; Obrenovich, M E; Seyidova, D; de la Torre, J C

2005-01-01

Structural changes in vessels under the influence of ischemia play an important role in the pathogenesis of many diseases, most important of which are stroke and myocardial infarction or myocardial insult. Over the years, information has been gathered, which implicate a role for ischemic vascular changes in the pathogenesis of crush-syndrome, atherosclerosis and other vascular diseases. When blood vessels are damaged they become unresponsive to a stimulus, which normally elicits vasodilatation and can lead to intraluminal thrombosis and ischemic events. The aim of this review is to explore the structural changes seen in vessels affected by ischemia reperfusion injury. With ischemia, the development of observable changes to vascular structure is multifactorial. One key factor is reperfusion ischemic injury. Moreover, the duration of the ischemic event is an important factor when determining both the prognosis and the type of morphological change that is observable in affected vessel walls. In this regard, the deleterious progression of blood flow impairment and its severity depends on the specific organ involved and the type of tissue affected. Further, there are regional differences within affected tissues and the degree of microvascular injury is well correlated with differences in the nature and severity of the ischemic event. Any method aimed at preventing and treating ischemic reperfusion injuries in vessels, based on these investigations, should likewise be able to decrease the early signs of brain, cerebrovascular and heart injury and preserve normal cellular architecture.

Asymmetric interactions in the adenosine-binding pockets of the MS2 coat protein dimer

PubMed Central

Powell, Amy J; Peabody, David S

2001-01-01

Background The X-ray structure of the MS2 coat protein-operator RNA complex reveals the existence of quasi-synmetric interactions of adenosines -4 and -10 in pockets formed on different subunits of the coat protein dimer. Both pockets utilize the same five amino acid residues, namely Val29, Thr45, Ser47, Thr59, and Lys61. We call these sites the adenosine-binding pockets. Results We present here a heterodimer complementation analysis of the contributions of individual A-pocket amino acids to the binding of A-4 and A-10 in different halves of the dimer. Various substitutions of A-pocket residues were introduced into one half of single-chain coat protein heterodimers where they were tested for their abilities to complement Y85H or T91I substitutions (defects in the A-4 and A-10 half-sites, respectively) present in the other dimer half. Conclusions These experiments provide functional tests of interactions predicted from structural analyses, demonstrating the importance of certain amino acid-nucleotide contacts observed in the crystal structure, and showing that others make little or no contribution to the stability of the complex. In summary, Val29 and Lys61 form important stabilizing interactions with both A-4 and A-10. Meanwhile, Ser47 and Thr59 interact primarily with A-10. The important interactions with Thr45 are restricted to A-4. PMID:11504563

Structural comparison of chromosomal and exogenous dihydrofolate reductase from Staphylococcus aureus in complex with the potent inhibitor trimethoprim

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

Heaslet, Holly; Harris, Melissa; Fahnoe, Kelly

2010-09-02

Dihydrofolate reductase (DHFR) is the enzyme responsible for the NADPH-dependent reduction of 5,6-dihydrofolate to 5,6,7,8-tetrahydrofolate, an essential cofactor in the synthesis of purines, thymidylate, methionine, and other key metabolites. Because of its importance in multiple cellular functions, DHFR has been the subject of much research targeting the enzyme with anticancer, antibacterial, and antimicrobial agents. Clinically used compounds targeting DHFR include methotrexate for the treatment of cancer and diaminopyrimidines (DAPs) such as trimethoprim (TMP) for the treatment of bacterial infections. DAP inhibitors of DHFR have been used clinically for >30 years and resistance to these agents has become widespread. Methicillin-resistant Staphylococcusmore » aureus (MRSA), the causative agent of many serious nosocomial and community acquired infections, and other gram-positive organisms can show resistance to DAPs through mutation of the chromosomal gene or acquisition of an alternative DHFR termed 'S1 DHFR.' To develop new therapies for health threats such as MRSA, it is important to understand the molecular basis of DAP resistance. Here, we report the crystal structure of the wild-type chromosomal DHFR from S. aureus in complex with NADPH and TMP. We have also solved the structure of the exogenous, TMP resistant S1 DHFR, apo and in complex with TMP. The structural and thermodynamic data point to important molecular differences between the two enzymes that lead to dramatically reduced affinity of DAPs to S1 DHFR. These differences in enzyme binding affinity translate into reduced antibacterial activity against strains of S. aureus that express S1 DHFR.« less

Nonhydrostatic simulation of hyperpycnal river plumes on sloping continental shelves: Flow structures and nonhydrostatic effect

NASA Astrophysics Data System (ADS)

Tseng, Chien-Yung; Chou, Yi-Ju

2018-04-01

A three-dimensional nonhydrostatic coastal model SUNTANS is used to study hyperpycnal plumes on sloping continental shelves with idealized domain setup. The study aims to examine the nonhydrostatic effect of the plunging hyperpycnal plume and the associated flow structures on different shelf slopes. The unstructured triangular grid in SUNTANS allows for local refinement of the grid size for regions in which the flow varies abruptly, while retaining low-cost computation using the coarse grid resolution for regions in which the flow is more uniform. These nonhydrostatic simulations reveal detailed three-dimensional flow structures in both transient and steady states. Via comparison with the hydrostatic simulation, we show that the nonhydrostatic effect is particularly important before plunging, when the plume is subject to significant changes in both the along-shore and vertical directions. After plunging, where the plume becomes an undercurrent that is more spatially uniform, little difference is found between the hydrostatic and nonhydrostatic simulations in the present gentle- and mild-slope cases. A grid-dependence study shows that the nonhydrostatic effect can be seen only when the grid resolution is sufficiently fine that the calculation is not overly diffusive. A depth-integrated momentum budget analysis is then conducted to show that the flow convergence due to plunging is an important factor in the three-dimensional flow structures. Moreover, it shows that the nonhydrostatic effect becomes more important as the slope increases, and in the steep-slope case, neglect of transport of the vertical momentum during plunging in the hydrostatic case further leads to an erroneous prediction for the undercurrent.

Folding a Protein with Equal Probability of Being Helix or Hairpin

PubMed Central

Lin, Chun-Yu; Chen, Nan-Yow; Mou, Chung Yu

2012-01-01

We explore the possibility for the native structure of a protein being inherently multiconformational in an ab initio coarse-grained model. Based on the Wang-Landau algorithm, the complete free energy landscape for the designed sequence 2DX4: INYWLAHAKAGYIVHWTA is constructed. It is shown that 2DX4 possesses two nearly degenerate native structures: one is a helix structure with the other a hairpinlike structure, and their free energy difference is <2% of that of local minima. Two degenerate native structures are stabilized by an energy barrier of ∼10 kcal/mol. Furthermore, the hydrogen-bond and dipole-dipole interactions are found to be two major competing interactions in transforming one conformation into the other. Our results indicate that two degenerate native structures are stabilized by subtle balance between different interactions in proteins. In particular, for small proteins, balance between the hydrogen-bond and dipole-dipole interactions happens for proteins of sizes being ∼18 amino acids and is shown to the main driving mechanism for the occurrence of degeneracy. These results provide important clues to the study of native structures of proteins. PMID:22828336

Crystal structure of a putative exo-β-1,3-galactanase from Bifidobacterium bifidum S17

PubMed Central

Godoy, Andre S.; de Lima, Mariana Z. T.; Camilo, Cesar M.; Polikarpov, Igor

2016-01-01

Given the current interest in second-generation biofuels, carbohydrate-active enzymes have become the most important tool to overcome the structural recalcitrance of the plant cell wall. While some glycoside hydrolase families have been exhaustively described, others remain poorly characterized, especially with regard to structural information. The family 43 glycoside hydrolases are a diverse group of inverting enzymes; the available structure information on these enzymes is mainly from xylosidases and arabinofuranosidase. Currently, only one structure of an exo-β-1,3-galactanase is available. Here, the production, crystallization and structure determination of a putative exo-β-1,3-galactanase from Bifidobacterium bifidum S17 (BbGal43A) are described. BbGal43A was successfully produced and showed activity towards synthetic galactosides. BbGal43A was subsequently crystallized and data were collected to 1.4 Å resolution. The structure shows a single-domain molecule, differing from known homologues, and crystal contact analysis predicts the formation of a dimer in solution. Further biochemical studies are necessary to elucidate the differences between BbGal43A and its characterized homologues. PMID:27050262

Parallel aeroelastic computations for wing and wing-body configurations

NASA Technical Reports Server (NTRS)

Byun, Chansup

1994-01-01

The objective of this research is to develop computationally efficient methods for solving fluid-structural interaction problems by directly coupling finite difference Euler/Navier-Stokes equations for fluids and finite element dynamics equations for structures on parallel computers. This capability will significantly impact many aerospace projects of national importance such as Advanced Subsonic Civil Transport (ASCT), where the structural stability margin becomes very critical at the transonic region. This research effort will have direct impact on the High Performance Computing and Communication (HPCC) Program of NASA in the area of parallel computing.

Developing Regionalized Models of Lithospheric Thickness and Velocity Structure Across Eurasia and the Middle East from Jointly Inverting P-Wave and S-Wave Receiver Functions with Rayleigh Wave Group and Phase Velocities

DTIC Science & Technology

2010-09-01

lithospheric velocity structure for a wide variety of tectonic regions throughout Eurasia and the Middle East. We expect the regionalized models will improve...constructed by combining the 1D joint inversion models within each tectonic region and validated through regional waveform modeling. The velocity models thus...important differences in lithospheric structure between the cratonic regions of Eastern Europe and the tectonic regions of Western Europe and the

Microscopic structural descriptor of liquid water

NASA Astrophysics Data System (ADS)

Shi, Rui; Tanaka, Hajime

2018-03-01

The microscopic structure of liquid water has been believed to be the key to the understanding of the unique properties of this extremely important substance. Many structural descriptors have been developed for revealing local structural order in water, but their properties are still not well understood. The essential difficulty comes from structural fluctuations due to thermal noise, which are intrinsic to the liquid state. The most popular and widely used descriptors are the local structure index (LSI) and d5. Recently, Russo and Tanaka [Nat. Commun. 3, 3556 (2014)] introduced a new descriptor ζ which measures the translational order between the first and second shells considering hydrogen bonding (H-bonding) in the first shell. In this work, we compare the performance of these three structural descriptors for a popular water model known as TIP5P water. We show that local structural ordering can be properly captured only by the structural descriptor ζ, but not by the other two descriptors particularly at a high temperature, where thermal noise effects are severe. The key difference of ζ from LSI and d5 is that only ζ considers H-bonding which is crucial to detect high translational and tetrahedral order of not only oxygen but also hydrogen atoms. The importance of H-bonding is very natural, considering the fact that the locally favored structures are stabilized by energy gain due to the formation of four hydrogen bonds between the central water molecule and its neighboring ones in the first shell. Our analysis of the water structure by using ζ strongly supports the two-state model of water: water is a dynamic mixture of locally favored (ordered) and normal-liquid (disordered) structures. This work demonstrates the importance of H-bonding in the characterization of water's structures and provides a useful structural descriptor for water-type tetrahedral liquids to study their structure and dynamics.

Effects of hedgerows on bats and bush crickets at different spatial scales

NASA Astrophysics Data System (ADS)

Lacoeuilhe, Aurélie; Machon, Nathalie; Julien, Jean-François; Kerbiriou, Christian

2016-02-01

Biodiversity is threatened by the loss and fragmentation of habitats. The role of hedgerows in maintaining biodiversity is well established, but few studies have addressed the importance for biodiversity of the intrinsic characteristics of hedgerows and the quality of hedgerow networks along a spatial scale. We examined three quality indices providing information at different territorial levels: density in the landscape, structural diversity and wood production. We performed an acoustic survey in a grassland to estimate the species abundance and community composition of bats (9 taxa) and bush crickets (11 species). Using an approach based on species and traits, we assessed how hedgerow quality influenced the activity of these taxa at different spatial scales (from 50 to 1000 m) and focused on three types of traits: bush cricket mobility ability, bat foraging strategy and habitat specialization. In general, our results showed the importance of hedgerow quality for bats and bush crickets, but the strength of the association between taxa and hedgerows varied substantially among the species and the spatial scales. Although it depends on the taxa, the production, density and structural diversity of hedgerows each had an overall positive effect. Our results suggested that these effects were generally more important at large scales. The scale effect of the production index is the best predictor of activity for bat and bush cricket taxa and traits. Our results showed the importance of hedgerow quality for the ecology of bat and bush cricket communities and could be used to improve conservation management.

Exploring new topography-based subgrid spatial structures for improving land surface modeling

DOE PAGES

Tesfa, Teklu K.; Leung, Lai-Yung Ruby

2017-02-22

Topography plays an important role in land surface processes through its influence on atmospheric forcing, soil and vegetation properties, and river network topology and drainage area. Land surface models with a spatial structure that captures spatial heterogeneity, which is directly affected by topography, may improve the representation of land surface processes. Previous studies found that land surface modeling, using subbasins instead of structured grids as computational units, improves the scalability of simulated runoff and streamflow processes. In this study, new land surface spatial structures are explored by further dividing subbasins into subgrid structures based on topographic properties, including surface elevation,more » slope and aspect. Two methods (local and global) of watershed discretization are applied to derive two types of subgrid structures (geo-located and non-geo-located) over the topographically diverse Columbia River basin in the northwestern United States. In the global method, a fixed elevation classification scheme is used to discretize subbasins. The local method utilizes concepts of hypsometric analysis to discretize each subbasin, using different elevation ranges that also naturally account for slope variations. The relative merits of the two methods and subgrid structures are investigated for their ability to capture topographic heterogeneity and the implications of this on representations of atmospheric forcing and land cover spatial patterns. Results showed that the local method reduces the standard deviation (SD) of subgrid surface elevation in the study domain by 17 to 19 % compared to the global method, highlighting the relative advantages of the local method for capturing subgrid topographic variations. The comparison between the two types of subgrid structures showed that the non-geo-located subgrid structures are more consistent across different area threshold values than the geo-located subgrid structures. Altogether the local method and non-geo-located subgrid structures effectively and robustly capture topographic, climatic and vegetation variability, which is important for land surface modeling.« less

Exploring new topography-based subgrid spatial structures for improving land surface modeling

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

Tesfa, Teklu K.; Leung, Lai-Yung Ruby

Topography plays an important role in land surface processes through its influence on atmospheric forcing, soil and vegetation properties, and river network topology and drainage area. Land surface models with a spatial structure that captures spatial heterogeneity, which is directly affected by topography, may improve the representation of land surface processes. Previous studies found that land surface modeling, using subbasins instead of structured grids as computational units, improves the scalability of simulated runoff and streamflow processes. In this study, new land surface spatial structures are explored by further dividing subbasins into subgrid structures based on topographic properties, including surface elevation,more » slope and aspect. Two methods (local and global) of watershed discretization are applied to derive two types of subgrid structures (geo-located and non-geo-located) over the topographically diverse Columbia River basin in the northwestern United States. In the global method, a fixed elevation classification scheme is used to discretize subbasins. The local method utilizes concepts of hypsometric analysis to discretize each subbasin, using different elevation ranges that also naturally account for slope variations. The relative merits of the two methods and subgrid structures are investigated for their ability to capture topographic heterogeneity and the implications of this on representations of atmospheric forcing and land cover spatial patterns. Results showed that the local method reduces the standard deviation (SD) of subgrid surface elevation in the study domain by 17 to 19 % compared to the global method, highlighting the relative advantages of the local method for capturing subgrid topographic variations. The comparison between the two types of subgrid structures showed that the non-geo-located subgrid structures are more consistent across different area threshold values than the geo-located subgrid structures. Altogether the local method and non-geo-located subgrid structures effectively and robustly capture topographic, climatic and vegetation variability, which is important for land surface modeling.« less

The effect of structurally related impurities on crystallinity reduction of sulfamethazine by grinding.

PubMed

Hamada, Yoshito; Ono, Makoto; Ohara, Motomu; Yonemochi, Etsuo

2016-12-30

In this study, the effect of structurally related impurities on crystallinity reduction of sulfamethazine by grinding was evaluated. The crystallinity of sulfamethazine was not decreased when it was ground alone. However, when structurally related impurities with sulfonamide derivatives were blended, the crystallinity of sulfamethazine was decreased by grinding. Other materials without a sulfonamide moiety showed no such effect. The Raman spectra of sulfamethazine demonstrated that there was a difference between its crystalline and amorphous states within its sulfonamide structure. It was suggested that the sulfonamide structure of the impurities was important in causing the inhibition of recrystallization of sulfamethazine during grinding. Copyright © 2016 Elsevier B.V. All rights reserved.

Right- and left-handed three-helix proteins. I. Experimental and simulation analysis of differences in folding and structure.

PubMed

Glyakina, Anna V; Pereyaslavets, Leonid B; Galzitskaya, Oxana V

2013-09-01

Despite the large number of publications on three-helix protein folding, there is no study devoted to the influence of handedness on the rate of three-helix protein folding. From the experimental studies, we make a conclusion that the left-handed three-helix proteins fold faster than the right-handed ones. What may explain this difference? An important question arising in this paper is whether the modeling of protein folding can catch the difference between the protein folding rates of proteins with similar structures but with different folding mechanisms. To answer this question, the folding of eight three-helix proteins (four right-handed and four left-handed), which are similar in size, was modeled using the Monte Carlo and dynamic programming methods. The studies allowed us to determine the orders of folding of the secondary-structure elements in these domains and amino acid residues which are important for the folding. The obtained data are in good correlation with each other and with the experimental data. Structural analysis of these proteins demonstrated that the left-handed domains have a lesser number of contacts per residue and a smaller radius of cross section than the right-handed domains. This may be one of the explanations of the observed fact. The same tendency is observed for the large dataset consisting of 332 three-helix proteins (238 right- and 94 left-handed). From our analysis, we found that the left-handed three-helix proteins have some less-dense packing that should result in faster folding for some proteins as compared to the case of right-handed proteins. Copyright © 2013 Wiley Periodicals, Inc.

Relationships between adaptive and neutral genetic diversity and ecological structure and functioning: a meta-analysis

PubMed Central

Whitlock, Raj

2014-01-01

Understanding the effects of intraspecific genetic diversity on the structure and functioning of ecological communities is a fundamentally important part of evolutionary ecology and may also have conservation relevance in identifying the situations in which genetic diversity coincides with species-level diversity.Early studies within this field documented positive relationships between genetic diversity and ecological structure, but recent studies have challenged these findings. Conceptual synthesis has been hampered because studies have used different measures of intraspecific variation (phenotypically adaptive vs. neutral) and have considered different measures of ecological structure in different ecological and spatial contexts. The aim of this study is to strengthen conceptual understanding by providing an empirical synthesis quantifying the relationship between genetic diversity and ecological structure.Here, I present a meta-analysis of the relationship between genetic diversity within plant populations and the structure and functioning of associated ecological communities (including 423 effect sizes from 70 studies). I used Bayesian meta-analyses to examine (i) the strength and direction of this relationship, (ii) the extent to which phenotypically adaptive and neutral (molecular) measures of diversity differ in their association with ecological structure and (iii) variation in outcomes among different measures of ecological structure and in different ecological contexts.Effect sizes measuring the relationship between adaptive diversity (genotypic richness) and both community- and ecosystem-level ecological responses were small, but significantly positive. These associations were supported by genetic effects on species richness and productivity, respectively.There was no overall association between neutral genetic diversity and measures of ecological structure, but a positive correlation was observed under a limited set of demographic conditions. These results suggest that adaptive and neutral genetic diversity should not be treated as ecologically equivalent measures of intraspecific variation.Synthesis. This study advances the debate over whether relationships between genetic diversity and ecological structure are either simply positive or negative, by showing how the strength and direction of these relationships changes with different measures of diversity and in different ecological contexts. The results provide a solid foundation for assessing when and where an expanded synthesis between ecology and genetics will be most fruitful. PMID:25210204

Detection of core-periphery structure in networks based on 3-tuple motifs

NASA Astrophysics Data System (ADS)

Ma, Chuang; Xiang, Bing-Bing; Chen, Han-Shuang; Small, Michael; Zhang, Hai-Feng

2018-05-01

Detecting mesoscale structure, such as community structure, is of vital importance for analyzing complex networks. Recently, a new mesoscale structure, core-periphery (CP) structure, has been identified in many real-world systems. In this paper, we propose an effective algorithm for detecting CP structure based on a 3-tuple motif. In this algorithm, we first define a 3-tuple motif in terms of the patterns of edges as well as the property of nodes, and then a motif adjacency matrix is constructed based on the 3-tuple motif. Finally, the problem is converted to find a cluster that minimizes the smallest motif conductance. Our algorithm works well in different CP structures: including single or multiple CP structure, and local or global CP structures. Results on the synthetic and the empirical networks validate the high performance of our method.

Off-axis volcano-tectonic activity during continental rifting: Insights from the transversal Goba-Bonga lineament, Main Ethiopian Rift (East Africa)

NASA Astrophysics Data System (ADS)

Corti, Giacomo; Sani, Federico; Agostini, Samuele; Philippon, Melody; Sokoutis, Dimitrios; Willingshofer, Ernst

2018-03-01

The Main Ethiopian Rift, East Africa, is characterized by the presence of major, enigmatic structures which strike approximately orthogonal to the trend of the rift valley. These structures are marked by important deformation and magmatic activity in an off-axis position in the plateaus surrounding the rift. In this study, we present new structural data based on a remote and field analysis, complemented with analogue modelling experiments, and new geochemical analysis of volcanic rocks sampled in different portions of one of these transversal structures: the Goba-Bonga volcano-tectonic lineament (GBVL). This integrated analysis shows that the GBVL is associated with roughly E-W-trending prominent volcano-tectonic activity affecting the western plateau. Within the rift floor, the approximately E-W alignment of Awasa and Corbetti calderas likely represent expressions of the GBVL. Conversely, no tectonic or volcanic features of similar (E-W) orientation have been recognized on the eastern plateau. Analogue modelling suggests that the volcano-tectonic features of the GBVL have probably been controlled by the presence of a roughly E-W striking pre-existing discontinuity beneath the western plateau, which did not extend beneath the eastern plateau. Geochemical analysis supports this interpretation and indicates that, although magmas have the same sub-lithospheric mantle source, limited differences in magma evolution displayed by products found along the GBVL may be ascribed to the different tectonic framework to the west, to the east, and in the axial zone of the rift. These results support the importance of the heterogeneous nature of the lithosphere and the spatial variations of its structure in controlling the architecture of continental rifts and the distribution of the related volcano-tectonic activity.

Characterization of the allosteric binding pocket of human liver fructose-1,6-bisphosphatase by protein crystallography and inhibitor activity studies.

PubMed

Iversen, L F; Brzozowski, M; Hastrup, S; Hubbard, R; Kastrup, J S; Larsen, I K; Naerum, L; Nørskov-Lauridsen, L; Rasmussen, P B; Thim, L; Wiberg, F C; Lundgren, K

1997-05-01

The structures of three complexes of human fructose-1,6-bisphosphatase (FB) with the allosteric inhibitor AMP and two AMP analogues have been determined and all fully refined. The data used for structure determination were collected at cryogenic temperature (110 K), and with the use of synchrotron radiation. The structures reveal a common mode of binding for AMP and formycine monophosphate (FMP). 5-Amino-4-carboxamido-1 beta-D-5-phosphate-ribofuranosyl-1H-imidazole (AICAR-P) shows an unexpected mode of binding to FB, different from that of the other two ligands. The imidazole ring of AICAR-P is rotated 180 degrees compared to the AMP and FMP bases. This rotation results in a slightly different hydrogen bonding pattern and minor changes in the water structure in the binding pocket. Common features of binding are seen for the ribose and phosphate moieties of all three compounds. Although binding in a different mode, AICAR-P is still capable of making all the important interactions with the residues building the allosteric binding pocket. The IC50 values of AMP, FMP, and AICAR-P were determined to be 1.7, 1.4, and 20.9 microM, respectively. Thus, the approximately 10 times lower potency of AICAR-P is difficult to explain solely from the variations observed in the binding pocket. Only one water molecule in the allosteric binding pocket was found to be conserved in all four subunits in all three structures. This water molecule coordinates to a phosphate oxygen atom and the N7 atom of the AMP molecule, and to similarly situated atoms in the FMP and AICAR-P complexes. This implies an important role of the conserved water molecule in binding of the ligand.

Characterization of the allosteric binding pocket of human liver fructose-1,6-bisphosphatase by protein crystallography and inhibitor activity studies.

PubMed Central

Iversen, L. F.; Brzozowski, M.; Hastrup, S.; Hubbard, R.; Kastrup, J. S.; Larsen, I. K.; Naerum, L.; Nørskov-Lauridsen, L.; Rasmussen, P. B.; Thim, L.; Wiberg, F. C.; Lundgren, K.

1997-01-01

The structures of three complexes of human fructose-1,6-bisphosphatase (FB) with the allosteric inhibitor AMP and two AMP analogues have been determined and all fully refined. The data used for structure determination were collected at cryogenic temperature (110 K), and with the use of synchrotron radiation. The structures reveal a common mode of binding for AMP and formycine monophosphate (FMP). 5-Amino-4-carboxamido-1 beta-D-5-phosphate-ribofuranosyl-1H-imidazole (AICAR-P) shows an unexpected mode of binding to FB, different from that of the other two ligands. The imidazole ring of AICAR-P is rotated 180 degrees compared to the AMP and FMP bases. This rotation results in a slightly different hydrogen bonding pattern and minor changes in the water structure in the binding pocket. Common features of binding are seen for the ribose and phosphate moieties of all three compounds. Although binding in a different mode, AICAR-P is still capable of making all the important interactions with the residues building the allosteric binding pocket. The IC50 values of AMP, FMP, and AICAR-P were determined to be 1.7, 1.4, and 20.9 microM, respectively. Thus, the approximately 10 times lower potency of AICAR-P is difficult to explain solely from the variations observed in the binding pocket. Only one water molecule in the allosteric binding pocket was found to be conserved in all four subunits in all three structures. This water molecule coordinates to a phosphate oxygen atom and the N7 atom of the AMP molecule, and to similarly situated atoms in the FMP and AICAR-P complexes. This implies an important role of the conserved water molecule in binding of the ligand. PMID:9144768

Effects of atmospheric relative humidity on Stratum Corneum structure at the molecular level: ex vivo Raman spectroscopy analysis.

PubMed

Vyumvuhore, Raoul; Tfayli, Ali; Duplan, Hélène; Delalleau, Alexandre; Manfait, Michel; Baillet-Guffroy, Arlette

2013-07-21

Skin hydration plays an important role in the optimal physical properties and physiological functions of the skin. Despite the advancements in the last decade, dry skin remains the most common characteristic of human skin disorders. Thus, it is important to understand the effect of hydration on Stratum Corneum (SC) components. In this respect, our interest consists in correlating the variations of unbound and bound water content in the SC with structural and organizational changes in lipids and proteins using a non-invasive technique: Raman spectroscopy. Raman spectra were acquired on human SC at different relative humidity (RH) levels (4-75%). The content of different types of water, bound and free, was measured using the second derivative and curve fitting of the Raman bands in the range of 3100-3700 cm(-1). Changes in lipidic order were evaluated using νC-C and νC-H. To analyze the effect of RH on the protein structure, we examined in the Amide I region, the Fermi doublet of tyrosine, and the νasymCH3 vibration. The contributions of totally bound water were found not to vary with humidity, while partially bound water varied with three different rates. Unbound water increased greatly when all sites for bound water were saturated. Lipid organization as well as protein deployment was found to be optimal at intermediate RH values (around 60%), which correspond to the maximum of SC water binding capacity. This analysis highlights the relationship between bound water, the SC barrier state and the protein structure and elucidates the optimal conditions. Moreover, our results showed that increased content of unbound water in the SC induces disorder in the structures of lipids and proteins.

Ole e 13 is the unique food allergen in olive: Structure-functional, substrates docking, and molecular allergenicity comparative analysis.

PubMed

Jimenez-Lopez, J C; Robles-Bolivar, P; Lopez-Valverde, F J; Lima-Cabello, E; Kotchoni, S O; Alché, J D

2016-05-01

Thaumatin-like proteins (TLPs) are enzymes with important functions in pathogens defense and in the response to biotic and abiotic stresses. Last identified olive allergen (Ole e 13) is a TLP, which may also importantly contribute to food allergy and cross-allergenicity to pollen allergen proteins. The goals of this study are the characterization of the structural-functionality of Ole e 13 with a focus in its catalytic mechanism, and its molecular allergenicity by extensive analysis using different molecular computer-aided approaches covering a) functional-regulatory motifs, b) comparative study of linear sequence, 2-D and 3D structural homology modeling, c) molecular docking with two different β-D-glucans, d) conservational and evolutionary analysis, e) catalytic mechanism modeling, and f) IgE-binding, B- and T-cell epitopes identification and comparison to other allergenic TLPs. Sequence comparison, structure-based features, and phylogenetic analysis identified Ole e 13 as a thaumatin-like protein. 3D structural characterization revealed a conserved overall folding among plants TLPs, with mayor differences in the acidic (catalytic) cleft. Molecular docking analysis using two β-(1,3)-glucans allowed to identify fundamental residues involved in the endo-1,3-β-glucanase activity, and defining E84 as one of the conserved residues of the TLPs responsible of the nucleophilic attack to initiate the enzymatic reaction and D107 as proton donor, thus proposing a catalytic mechanism for Ole e 13. Identification of IgE-binding, B- and T-cell epitopes may help designing strategies to improve diagnosis and immunotherapy to food allergy and cross-allergenic pollen TLPs. Copyright © 2016 Elsevier Inc. All rights reserved.

Perception of patterns of musical beat distribution in phonological developmental dyslexia: significant longitudinal relations with word reading and reading comprehension.

PubMed

Goswami, Usha; Huss, Martina; Mead, Natasha; Fosker, Tim; Verney, John P

2013-05-01

In a recent study, we reported that the accurate perception of beat structure in music ('perception of musical meter') accounted for over 40% of the variance in single word reading in children with and without dyslexia (Huss et al., 2011). Performance in the musical task was most strongly associated with the auditory processing of rise time, even though beat structure was varied by manipulating the duration of the musical notes. Here we administered the same musical task a year later to 88 children with and without dyslexia, and used new auditory processing measures to provide a more comprehensive picture of the auditory correlates of the beat structure task. We also measured reading comprehension and nonword reading in addition to single word reading. One year later, the children with dyslexia performed more poorly in the musical task than younger children reading at the same level, indicating a severe perceptual deficit for musical beat patterns. They now also had significantly poorer perception of sound rise time than younger children. Longitudinal analyses showed that the musical beat structure task was a significant longitudinal predictor of development in reading, accounting for over half of the variance in reading comprehension along with a linguistic measure of phonological awareness. The non-linguistic musical beat structure task is an important independent longitudinal and concurrent predictor of variance in reading attainment by children. The different longitudinal versus concurrent associations between musical beat perception and auditory processing suggest that individual differences in the perception of rhythmic timing are an important shared neural basis for individual differences in children in linguistic and musical processing. Copyright © 2012 Elsevier Ltd. All rights reserved.

Validity of the growth model of the 'computerized visual perception assessment tool for Chinese characters structures'.

PubMed

Wu, Huey-Min; Li, Cheng-Hsaun; Kuo, Bor-Chen; Yang, Yu-Mao; Lin, Chin-Kai; Wan, Wei-Hsiang

2017-08-01

Morphological awareness is the foundation for the important developmental skills involved with vocabulary, as well as understanding the meaning of words, orthographic knowledge, reading, and writing. Visual perception of space and radicals in two-dimensional positions of Chinese characters' morphology is very important in identifying Chinese characters. The important predictive variables of special and visual perception in Chinese characters identification were investigated in the growth model in this research. The assessment tool is the "Computerized Visual Perception Assessment Tool for Chinese Characters Structures" developed by this study. There are two constructs, basic stroke and character structure. In the basic stroke, there are three subtests of one, two, and more than three strokes. In the character structure, there are three subtests of single-component character, horizontal-compound character, and vertical-compound character. This study used purposive sampling. In the first year, 551 children 4-6 years old participated in the study and were monitored for one year. In the second year, 388 children remained in the study and the successful follow-up rate was 70.4%. This study used a two-wave cross-lagged panel design to validate the growth model of the basic stroke and the character structure. There was significant correlation of the basic stroke and the character structure at different time points. The abilities in the basic stroke and in the character structure steadily developed over time for preschool children. Children's knowledge of the basic stroke effectively predicted their knowledge of the basic stroke and the character structure. Copyright © 2017 Elsevier Ltd. All rights reserved.

Protein structure similarity from Principle Component Correlation analysis.

PubMed

Zhou, Xiaobo; Chou, James; Wong, Stephen T C

2006-01-25

Owing to rapid expansion of protein structure databases in recent years, methods of structure comparison are becoming increasingly effective and important in revealing novel information on functional properties of proteins and their roles in the grand scheme of evolutionary biology. Currently, the structural similarity between two proteins is measured by the root-mean-square-deviation (RMSD) in their best-superimposed atomic coordinates. RMSD is the golden rule of measuring structural similarity when the structures are nearly identical; it, however, fails to detect the higher order topological similarities in proteins evolved into different shapes. We propose new algorithms for extracting geometrical invariants of proteins that can be effectively used to identify homologous protein structures or topologies in order to quantify both close and remote structural similarities. We measure structural similarity between proteins by correlating the principle components of their secondary structure interaction matrix. In our approach, the Principle Component Correlation (PCC) analysis, a symmetric interaction matrix for a protein structure is constructed with relationship parameters between secondary elements that can take the form of distance, orientation, or other relevant structural invariants. When using a distance-based construction in the presence or absence of encoded N to C terminal sense, there are strong correlations between the principle components of interaction matrices of structurally or topologically similar proteins. The PCC method is extensively tested for protein structures that belong to the same topological class but are significantly different by RMSD measure. The PCC analysis can also differentiate proteins having similar shapes but different topological arrangements. Additionally, we demonstrate that when using two independently defined interaction matrices, comparison of their maximum eigenvalues can be highly effective in clustering structurally or topologically similar proteins. We believe that the PCC analysis of interaction matrix is highly flexible in adopting various structural parameters for protein structure comparison.

Electronic structure and mechanical properties of osmium borides, carbides and nitrides from first principles

NASA Astrophysics Data System (ADS)

Liang, Yongcheng; Zhao, Jianzhi; Zhang, Bin

2008-06-01

The stabilities, mechanical properties and electronic structures of osmium boride (OsB), carbide (OsC) and nitride (OsN), in the tungsten carbide (WC), rocksalt (NaCl), cesium chloride (CsCl) and zinc blende (ZnS) structures respectively, are systematically predicted by calculations from first-principles. Only four phases, namely, OsB(WC), OsB(CsCl), OsC(WC), and OsC(ZnS), are mechanically stable, and none is a superhard compound, contrary to previous speculation. Most importantly, we find that the changing trends of bulk modulus and shear modulus are completely different for OsB, OsC and OsN in same hexagonal WC structure, which indicates that the underlying sources of hardness and incompressibility are fundamentally different: the former is determined by bonding nature while the latter is closely associated with valence electron density.

Thermoelectric microdevice fabricated by a MEMS-like electrochemical process

NASA Technical Reports Server (NTRS)

Snyder, G. Jeffrey; Lim, James R.; Huang, Chen-Kuo; Fleurial, Jean-Pierre

2003-01-01

Microelectromechanical systems (MEMS) are the basis of many rapidly growing technologies, because they combine miniature sensors and actuators with communications and electronics at low cost. Commercial MEMS fabrication processes are limited to silicon-based materials or two-dimensional structures. Here we show an inexpensive, electrochemical technique to build MEMS-like structures that contain several different metals and semiconductors with three-dimensional bridging structures. We demonstrate this technique by building a working microthermoelectric device. Using repeated exposure and development of multiple photoresist layers, several different metals and thermoelectric materials are fabricated in a three-dimensional structure. A device containing 126 n-type and p-type (Bi, Sb)2Te3 thermoelectric elements, 20 microm tall and 60 microm in diameter with bridging metal interconnects, was fabricated and cooling demonstrated. Such a device should be of technological importance for precise thermal control when operating as a cooler, and for portable power when operating as a micro power generator.

MEAs and 3D nanoelectrodes: electrodeposition as tool for a precisely controlled nanofabrication.

PubMed

Weidlich, Sabrina; Krause, Kay J; Schnitker, Jan; Wolfrum, Bernhard; Offenhäusser, Andreas

2017-01-31

Microelectrode arrays (MEAs) are gaining increasing importance for the investigation of signaling processes between electrogenic cells. However, efficient cell-chip coupling for robust and long-term electrophysiological recording and stimulation still remains a challenge. A possible approach for the improvement of the cell-electrode contact is the utilization of three-dimensional structures. In recent years, various 3D electrode geometries have been developed, but we are still lacking a fabrication approach that enables the formation of different 3D structures on a single chip in a controlled manner. This, however, is needed to enable a direct and reliable comparison of the recording capabilities of the different structures. Here, we present a method for a precisely controlled deposition of nanoelectrodes, enabling the fabrication of multiple, well-defined types of structures on our 64 electrode MEAs towards a rapid-prototyping approach to 3D electrodes.

Role of thermal history in atomic dynamics of chalcogenide glass: A case study on Ge{sub 20}Te{sub 80} glass

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

Sharma, Yashika; Kalra, Geetanjali; Murugavel, Sevi, E-mail: murug@physics.du.ac.in

The non-existence of thermodynamic equilibrium in glasses, their thermal history plays a very crucial role in explaining the relaxation behavior in various time scales and its configurational states. More importantly, the associated relaxation behavior is related mainly to the structural phenomenon of the glasses. Here, we report the dependence of quenching rate on the variation of structural units. The local structures of these glasses are monitored by recording the Raman spectroscopy and related to the different configurational states. The observed variations in structural differences are reflected in the measured density of the corresponding glasses. The quenching rate dependent of themore » relative fractions of edge-shared and corner-shared GeTe{sub 4} tetrahedral units are shown to be consistent with the corresponding variations in the measured density values.« less

THz wavefront manipulation based on metal waveguides

NASA Astrophysics Data System (ADS)

Wu, Mengru; Lang, Tingting; Shen, Changyu; Shi, Guohua; Han, Zhanghua

2018-07-01

In this paper, two waveguiding structures for arbitrary wavefront manipulation in the terahertz spectral region were proposed, designed and characterized. The first structure consists of parallel stack copper plates forming an array of parallel-plate waveguides (PPWGs). The second structure is three-dimensional metal rectangular waveguides array. The phase delay of the input wave after passing through the waveguide array is mainly determined by the effective index of the waveguides. Therefore, the waveguide array can be engineered using different core width distribution to generate any desired light beam. Examples, working at the frequency of 0.3 THz show that good focusing phenomenon with different focus lengths and spot sizes were observed, as well as arbitrarily tilted propagation of incident plane waves. The structure introduces a new method to perform wavefront manipulation, and can be utilized in many important applications in terahertz imaging and communication systems.

Diagnostics and structure

NASA Technical Reports Server (NTRS)

Vial, J. C.

1986-01-01

The structure of prominences and the diagnostic techniques used to evaluate their physical parameters are discussed. These include electron temperature, various densities (n sub p, n sub e, n sub l), ionization degree, velocities, and magnetic field vector. UV and radio measurements have already evidenced the existence of different temperature regions, corresponding to different geometrical locations, e.g., the so called Prominence-Corona (P-C) interface. Velocity measurements are important for considering formation and mass balance of prominences but there are conflicting velocity measurements which have led to the basic question: what structure is actually observed at a given wavelength; what averaging is performed within the projected slit area during the exposure time? In optically thick lines, the question of the formation region of the radiation along the line of sight is also not a trivial one. The same is true for low resolution measurements of the magnetic field. Coupling diagnostics with structure is now a general preoccupation.

Dynamic multifactor clustering of financial networks

NASA Astrophysics Data System (ADS)

Ross, Gordon J.

2014-02-01

We investigate the tendency for financial instruments to form clusters when there are multiple factors influencing the correlation structure. Specifically, we consider a stock portfolio which contains companies from different industrial sectors, located in several different countries. Both sector membership and geography combine to create a complex clustering structure where companies seem to first be divided based on sector, with geographical subclusters emerging within each industrial sector. We argue that standard techniques for detecting overlapping clusters and communities are not able to capture this type of structure and show how robust regression techniques can instead be used to remove the influence of both sector and geography from the correlation matrix separately. Our analysis reveals that prior to the 2008 financial crisis, companies did not tend to form clusters based on geography. This changed immediately following the crisis, with geography becoming a more important determinant of clustering structure.

Mobile genes in the human microbiome are structured from global to individual scales

PubMed Central

Brito, IL; Jupiter, SD; Jenkins, AP; Naisilisili, W; Tamminen, M; Smillie, CS; Wortman, JR; Birren, BW; Xavier, RJ; Blainey, PC; Singh, AK; Gevers, D; Alm, EJ

2016-01-01

Recent work has underscored the importance of the microbiome in human health, largely attributing differences in phenotype to differences in the species present across individuals1,2,3,4,5. But mobile genes can confer profoundly different phenotypes on different strains of the same species. Little is known about the function and distribution of mobile genes in the human microbiome, and in particular whether the gene pool is globally homogenous or constrained by human population structure. Here, we investigate this question by comparing the mobile genes found in the microbiomes of 81 metropolitan North Americans with that of 172 agrarian Fiji islanders using a combination of single-cell genomics and metagenomics. We find large differences in mobile gene content between the Fijian and North American microbiomes, with functional variation that mirrors known dietary differences such as the excess of plant-based starch degradation genes. Remarkably, differences are also observed between the mobile gene pools of proximal Fijian villages, even though microbiome composition across villages is similar. Finally, we observe high rates of recombination leading to individual-specific mobile elements, suggesting that the abundance of some genes may reflect environmental selection rather than dispersal limitation. Together, these data support the hypothesis that human activities and behaviors provide selective pressures that shape mobile gene pools, and that acquisition of mobile genes is important to colonizing specific human populations. PMID:27409808

The Halophile protein database.

PubMed

Sharma, Naveen; Farooqi, Mohammad Samir; Chaturvedi, Krishna Kumar; Lal, Shashi Bhushan; Grover, Monendra; Rai, Anil; Pandey, Pankaj

2014-01-01

Halophilic archaea/bacteria adapt to different salt concentration, namely extreme, moderate and low. These type of adaptations may occur as a result of modification of protein structure and other changes in different cell organelles. Thus proteins may play an important role in the adaptation of halophilic archaea/bacteria to saline conditions. The Halophile protein database (HProtDB) is a systematic attempt to document the biochemical and biophysical properties of proteins from halophilic archaea/bacteria which may be involved in adaptation of these organisms to saline conditions. In this database, various physicochemical properties such as molecular weight, theoretical pI, amino acid composition, atomic composition, estimated half-life, instability index, aliphatic index and grand average of hydropathicity (Gravy) have been listed. These physicochemical properties play an important role in identifying the protein structure, bonding pattern and function of the specific proteins. This database is comprehensive, manually curated, non-redundant catalogue of proteins. The database currently contains 59 897 proteins properties extracted from 21 different strains of halophilic archaea/bacteria. The database can be accessed through link. Database URL: http://webapp.cabgrid.res.in/protein/ © The Author(s) 2014. Published by Oxford University Press.

Forging the ring: from fungal septins' divergent roles in morphology, septation and virulence to factors contributing to their assembly into higher order structures.

PubMed

Vargas-Muñiz, Jose M; Juvvadi, Praveen R; Steinbach, William J

2016-09-01

Septins are a conserved family of GTP-binding proteins that are distributed across different lineages of the eukaryotes, with the exception of plants. Septins perform a myriad of functions in fungal cells, ranging from controlling morphogenetic events to contributing to host tissue invasion and virulence. One key attribute of the septins is their ability to assemble into heterooligomeric complexes that organizse into higher order structures. In addition to the established role of septins in the model budding yeast, Saccharomyces cerevisiae, their importance in other fungi recently emerges. While newer roles for septins are being uncovered in these fungi, the mechanism of how septins assemble into a complex and their regulation is only beginning to be comprehended. In this review, we summarize recent findings on the role of septins in different fungi and focus on how the septin complexes of different fungi are organized in vitro and in vivo. Furthermore, we discuss on how phosphorylation/dephosphorylation can serve as an important mechanism of septin complex assembly and regulation.

Probing the Complexities of Structural Changes in Layered Oxide Cathode Materials for Li-Ion Batteries during Fast Charge-Discharge Cycling and Heating.

PubMed

Hu, Enyuan; Wang, Xuelong; Yu, Xiqian; Yang, Xiao-Qing

2018-02-20

The rechargeable lithium-ion battery (LIB) is the most promising energy storage system to power electric vehicles with high energy density and long cycling life. However, in order to meet customers' demands for fast charging, the power performances of current LIBs need to be improved. From the cathode aspect, layer-structured cathode materials are widely used in today's market and will continue to play important roles in the near future. The high rate capability of layered cathode materials during charging and discharging is critical to the power performance of the whole cell and the thermal stability is closely related to the safety issues. Therefore, the in-depth understanding of structural changes of layered cathode materials during high rate charging/discharging and the thermal stability during heating are essential in developing new materials and improving current materials. Since structural changes take place from the atomic level to the whole electrode level, combination of characterization techniques covering multilength scales is quite important. In many cases, this means using comprehensive tools involving diffraction, spectroscopy, and imaging to differentiate the surface from the bulk and to obtain structural/chemical information with different levels of spatial resolution. For example, hard X-ray spectroscopy can yield the bulk information and soft X-ray spectroscopy can give the surface information; X-ray based imaging techniques can obtain spatial resolution of tens of nanometers, and electron-based microcopy can go to angstroms. In addition to challenges associated with different spatial resolution, the dynamic nature of structural changes during high rate cycling and heating requires characterization tools to have the capability of collecting high quality data in a time-resolved fashion. Thanks to the advancement in synchrotron based techniques and high-resolution electron microscopy, high temporal and spatial resolutions can now be achieved. In this Account, we focus on the recent works studying kinetic and thermal properties of layer-structured cathode materials, especially the structural changes during high rate cycling and the thermal stability during heating. Advanced characterization techniques relating to the rate capability and thermal stability will be introduced. The different structure evolution behavior of cathode materials cycled at high rate will be compared with that cycled at low rate. Different response of individual transition metals and the inhomogeneity in chemical distribution will be discussed. For the thermal stability, the relationship between structural changes and oxygen release will be emphatically pointed out. In all these studies being reviewed, advanced characterization techniques are critically applied to reveal complexities at multiscale in layer-structured cathode materials.

Street tree structural differences and associated stormwater benefits in metropolitan Cincinnati, Ohio, USA

EPA Science Inventory

Green infrastructure approaches leverage vegetation and soil to improve environmental quality. Municipal street trees are crucial components of urban green infrastructure because they provide stormwater interception benefits and other ecosystem services. Thus, it is important to ...

Millimeter Wave Atmospheric Radiometry Observations.

DTIC Science & Technology

1981-03-27

structure of the atmosphere would be very important. Rufton [20] combined thermal sensor technology for microthermal measurements with radiosonde...fromT2 h n relationships with CT(h) at least for optical effects. Bufton obtained the mean-square temperature difference between two microthermal probes

Comparing large-scale computational approaches to epidemic modeling: agent-based versus structured metapopulation models.

PubMed

Ajelli, Marco; Gonçalves, Bruno; Balcan, Duygu; Colizza, Vittoria; Hu, Hao; Ramasco, José J; Merler, Stefano; Vespignani, Alessandro

2010-06-29

In recent years large-scale computational models for the realistic simulation of epidemic outbreaks have been used with increased frequency. Methodologies adapt to the scale of interest and range from very detailed agent-based models to spatially-structured metapopulation models. One major issue thus concerns to what extent the geotemporal spreading pattern found by different modeling approaches may differ and depend on the different approximations and assumptions used. We provide for the first time a side-by-side comparison of the results obtained with a stochastic agent-based model and a structured metapopulation stochastic model for the progression of a baseline pandemic event in Italy, a large and geographically heterogeneous European country. The agent-based model is based on the explicit representation of the Italian population through highly detailed data on the socio-demographic structure. The metapopulation simulations use the GLobal Epidemic and Mobility (GLEaM) model, based on high-resolution census data worldwide, and integrating airline travel flow data with short-range human mobility patterns at the global scale. The model also considers age structure data for Italy. GLEaM and the agent-based models are synchronized in their initial conditions by using the same disease parameterization, and by defining the same importation of infected cases from international travels. The results obtained show that both models provide epidemic patterns that are in very good agreement at the granularity levels accessible by both approaches, with differences in peak timing on the order of a few days. The relative difference of the epidemic size depends on the basic reproductive ratio, R0, and on the fact that the metapopulation model consistently yields a larger incidence than the agent-based model, as expected due to the differences in the structure in the intra-population contact pattern of the approaches. The age breakdown analysis shows that similar attack rates are obtained for the younger age classes. The good agreement between the two modeling approaches is very important for defining the tradeoff between data availability and the information provided by the models. The results we present define the possibility of hybrid models combining the agent-based and the metapopulation approaches according to the available data and computational resources.

Bayesian shrinkage approach for a joint model of longitudinal and survival outcomes assuming different association structures.

PubMed

Andrinopoulou, Eleni-Rosalina; Rizopoulos, Dimitris

2016-11-20

The joint modeling of longitudinal and survival data has recently received much attention. Several extensions of the standard joint model that consists of one longitudinal and one survival outcome have been proposed including the use of different association structures between the longitudinal and the survival outcomes. However, in general, relatively little attention has been given to the selection of the most appropriate functional form to link the two outcomes. In common practice, it is assumed that the underlying value of the longitudinal outcome is associated with the survival outcome. However, it could be that different characteristics of the patients' longitudinal profiles influence the hazard. For example, not only the current value but also the slope or the area under the curve of the longitudinal outcome. The choice of which functional form to use is an important decision that needs to be investigated because it could influence the results. In this paper, we use a Bayesian shrinkage approach in order to determine the most appropriate functional forms. We propose a joint model that includes different association structures of different biomarkers and assume informative priors for the regression coefficients that correspond to the terms of the longitudinal process. Specifically, we assume Bayesian lasso, Bayesian ridge, Bayesian elastic net, and horseshoe. These methods are applied to a dataset consisting of patients with a chronic liver disease, where it is important to investigate which characteristics of the biomarkers have an influence on survival. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 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.

Separate effects of sex hormones and sex chromosomes on brain structure and function revealed by high-resolution magnetic resonance imaging and spatial navigation assessment of the Four Core Genotype mouse model.

PubMed

Corre, Christina; Friedel, Miriam; Vousden, Dulcie A; Metcalf, Ariane; Spring, Shoshana; Qiu, Lily R; Lerch, Jason P; Palmert, Mark R

2016-03-01

Males and females exhibit several differences in brain structure and function. To examine the basis for these sex differences, we investigated the influences of sex hormones and sex chromosomes on brain structure and function in mice. We used the Four Core Genotype (4CG) mice, which can generate both male and female mice with XX or XY sex chromosome complement, allowing the decoupling of sex chromosomes from hormonal milieu. To examine whole brain structure, high-resolution ex vivo MRI was performed, and to assess differences in cognitive function, mice were trained on a radial arm maze. Voxel-wise and volumetric analyses of MRI data uncovered a striking independence of hormonal versus chromosomal influences in 30 sexually dimorphic brain regions. For example, the bed nucleus of the stria terminalis and the parieto-temporal lobe of the cerebral cortex displayed steroid-dependence while the cerebellar cortex, corpus callosum, and olfactory bulbs were influenced by sex chromosomes. Spatial learning and memory demonstrated strict hormone-dependency with no apparent influence of sex chromosomes. Understanding the influences of chromosomes and hormones on brain structure and function is important for understanding sex differences in brain structure and function, an endeavor that has eventual implications for understanding sex biases observed in the prevalence of psychiatric disorders.

Auditory psychophysics and perception.

PubMed

Hirsh, I J; Watson, C S

1996-01-01

In this review of auditory psychophysics and perception, we cite some important books, research monographs, and research summaries from the past decade. Within auditory psychophysics, we have singled out some topics of current importance: Cross-Spectral Processing, Timbre and Pitch, and Methodological Developments. Complex sounds and complex listening tasks have been the subject of new studies in auditory perception. We review especially work that concerns auditory pattern perception, with emphasis on temporal aspects of the patterns and on patterns that do not depend on the cognitive structures often involved in the perception of speech and music. Finally, we comment on some aspects of individual difference that are sufficiently important to question the goal of characterizing auditory properties of the typical, average, adult listener. Among the important factors that give rise to these individual differences are those involved in selective processing and attention.

An optimal transportation approach for nuclear structure-based pathology.

PubMed

Wang, Wei; Ozolek, John A; Slepčev, Dejan; Lee, Ann B; Chen, Cheng; Rohde, Gustavo K

2011-03-01

Nuclear morphology and structure as visualized from histopathology microscopy images can yield important diagnostic clues in some benign and malignant tissue lesions. Precise quantitative information about nuclear structure and morphology, however, is currently not available for many diagnostic challenges. This is due, in part, to the lack of methods to quantify these differences from image data. We describe a method to characterize and contrast the distribution of nuclear structure in different tissue classes (normal, benign, cancer, etc.). The approach is based on quantifying chromatin morphology in different groups of cells using the optimal transportation (Kantorovich-Wasserstein) metric in combination with the Fisher discriminant analysis and multidimensional scaling techniques. We show that the optimal transportation metric is able to measure relevant biological information as it enables automatic determination of the class (e.g., normal versus cancer) of a set of nuclei. We show that the classification accuracies obtained using this metric are, on average, as good or better than those obtained utilizing a set of previously described numerical features. We apply our methods to two diagnostic challenges for surgical pathology: one in the liver and one in the thyroid. Results automatically computed using this technique show potentially biologically relevant differences in nuclear structure in liver and thyroid cancers.

An optimal transportation approach for nuclear structure-based pathology

PubMed Central

Wang, Wei; Ozolek, John A.; Slepčev, Dejan; Lee, Ann B.; Chen, Cheng; Rohde, Gustavo K.

2012-01-01

Nuclear morphology and structure as visualized from histopathology microscopy images can yield important diagnostic clues in some benign and malignant tissue lesions. Precise quantitative information about nuclear structure and morphology, however, is currently not available for many diagnostic challenges. This is due, in part, to the lack of methods to quantify these differences from image data. We describe a method to characterize and contrast the distribution of nuclear structure in different tissue classes (normal, benign, cancer, etc.). The approach is based on quantifying chromatin morphology in different groups of cells using the optimal transportation (Kantorovich-Wasserstein) metric in combination with the Fisher discriminant analysis and multidimensional scaling techniques. We show that the optimal transportation metric is able to measure relevant biological information as it enables automatic determination of the class (e.g. normal vs. cancer) of a set of nuclei. We show that the classification accuracies obtained using this metric are, on average, as good or better than those obtained utilizing a set of previously described numerical features. We apply our methods to two diagnostic challenges for surgical pathology: one in the liver and one in the thyroid. Results automatically computed using this technique show potentially biologically relevant differences in nuclear structure in liver and thyroid cancers. PMID:20977984

Quasi-static elastography comparison of hyaline cartilage structures

NASA Astrophysics Data System (ADS)

McCredie, A. J.; Stride, E.; Saffari, N.

2009-11-01

Joint cartilage, a load bearing structure in mammals, has only limited ability for regeneration after damage. For tissue engineers to design functional constructs, better understanding of the properties of healthy tissue is required. Joint cartilage is a specialised structure of hyaline cartilage; a poroviscoelastic solid containing fibril matrix reinforcements. Healthy joint cartilage is layered, which is thought to be important for correct tissue function. However, the behaviour of each layer during loading is poorly understood. Ultrasound elastography provides access to depth-dependent information in real-time for a sample during loading. A 15 MHz focussed transducer provided details from scatterers within a small fixed region in each sample. Quasi-static loading was applied to cartilage samples while ultrasonic signals before and during compressions were recorded. Ultrasonic signals were processed to provide time-shift profiles using a sum-squared difference method and cross-correlation. Two structures of hyaline cartilage have been tested ultrasonically and mechanically to determine method suitability for monitoring internal deformation differences under load and the effect of the layers on the global mechanical material behaviour. Results show differences in both the global mechanical properties and the ultrasonically tested strain distributions between the two structures tested. It was concluded that these differences are caused primarily by the fibril orientations.

Crystal structure of the Leishmania major peroxidase–cytochrome c complex

PubMed Central

Jasion, Victoria S.; Doukov, Tzanko; Pineda, Stephanie H.; Li, Huiying; Poulos, Thomas L.

2012-01-01

The causative agent of leishmaniasis is the protozoan parasite Leishmania major. Part of the host protective mechanism is the production of reactive oxygen species including hydrogen peroxide. In response, L. major produces a peroxidase, L. major peroxidase (LmP), that helps to protect the parasite from oxidative stress. LmP is a heme peroxidase that catalyzes the peroxidation of mitochondrial cytochrome c. We have determined the crystal structure of LmP in a complex with its substrate, L. major cytochrome c (LmCytc) to 1.84 Å, and compared the structure to its close homolog, the yeast cytochrome c peroxidase–cytochrome c complex. The binding interface between LmP and LmCytc has one strong and one weak ionic interaction that the yeast system lacks. The differences between the steady-state kinetics correlate well with the Lm redox pair being more dependent on ionic interactions, whereas the yeast redox pair depends more on nonpolar interactions. Mutagenesis studies confirm that the ion pairs at the intermolecular interface are important to both kcat and KM. Despite these differences, the electron transfer path, with respect to the distance between hemes, along the polypeptide chain is exactly the same in both redox systems. A potentially important difference, however, is the side chains involved. LmP has more polar groups (Asp and His) along the pathway compared with the nonpolar groups (Leu and Ala) in the yeast system, and as a result, the electrostatic environment along the presumed electron transfer path is substantially different. PMID:23100535

Structure and reactivity of oxalate surface complexes on lepidocrocite derived from infrared spectroscopy, DFT-calculations, adsorption, dissolution and photochemical experiments

NASA Astrophysics Data System (ADS)

Borowski, Susan C.; Biswakarma, Jagannath; Kang, Kyounglim; Schenkeveld, Walter D. C.; Hering, Janet G.; Kubicki, James D.; Kraemer, Stephan M.; Hug, Stephan J.

2018-04-01

Oxalate, together with other ligands, plays an important role in the dissolution of iron(hdyr)oxides and the bio-availability of iron. The formation and properties of oxalate surface complexes on lepidocrocite were studied with a combination of infrared spectroscopy (IR), density functional theory (DFT) calculations, dissolution, and photochemical experiments. IR spectra measured as a function of time, concentration, and pH (50-200 μM oxalate, pH 3-7) showed that several surface complexes are formed at different rates and in different proportions. Measured spectra could be separated into three contributions described by Gaussian line shapes, with frequencies that agreed well with the theoretical frequencies of three different surface complexes: an outer-sphere complex (OS), an inner-sphere monodentate mononuclear complex (MM), and a bidentate mononuclear complex (BM) involving one O atom from each carboxylate group. At pH 6, OS was formed at the highest rate. The contribution of BM increased with decreasing pH. In dissolution experiments, lepidocrocite was dissolved at rates proportional to the surface concentration of BM, rather than to the total adsorbed concentration. Under UV-light (365 nm), BM was photolyzed at a higher rate than MM and OS. Although the comparison of measured spectra with calculated frequencies cannot exclude additional possible structures, the combined results allowed the assignment of three main structures with different reactivities consistent with experiments. The results illustrate the importance of the surface speciation of adsorbed ligands in dissolution and photochemical reactions.

Differential receptive field organizations give rise to nearly identical neural correlations across three parallel sensory maps in weakly electric fish

PubMed Central

2017-01-01

Understanding how neural populations encode sensory information thereby leading to perception and behavior (i.e., the neural code) remains an important problem in neuroscience. When investigating the neural code, one must take into account the fact that neural activities are not independent but are actually correlated with one another. Such correlations are seen ubiquitously and have a strong impact on neural coding. Here we investigated how differences in the antagonistic center-surround receptive field (RF) organization across three parallel sensory maps influence correlations between the activities of electrosensory pyramidal neurons. Using a model based on known anatomical differences in receptive field center size and overlap, we initially predicted large differences in correlated activity across the maps. However, in vivo electrophysiological recordings showed that, contrary to modeling predictions, electrosensory pyramidal neurons across all three segments displayed nearly identical correlations. To explain this surprising result, we incorporated the effects of RF surround in our model. By systematically varying both the RF surround gain and size relative to that of the RF center, we found that multiple RF structures gave rise to similar levels of correlation. In particular, incorporating known physiological differences in RF structure between the three maps in our model gave rise to similar levels of correlation. Our results show that RF center overlap alone does not determine correlations which has important implications for understanding how RF structure influences correlated neural activity. PMID:28863136

Changes in diversity, abundance, and structure of soil bacterial communities in Brazilian Savanna under different land use systems.

PubMed

Rampelotto, Pabulo Henrique; de Siqueira Ferreira, Adão; Barboza, Anthony Diego Muller; Roesch, Luiz Fernando Wurdig

2013-10-01

The Brazilian Savanna, also known as "Cerrado", is the richest and most diverse savanna in the world and has been ranked as one of the main hotspots of biodiversity. The Cerrado is a representative biome in Central Brazil and the second largest biome in species diversity of South America. Nevertheless, large areas of native vegetation have been converted to agricultural land including grain production, livestock, and forestry. In this view, understanding how land use affects microbial communities is fundamental for the sustainable management of agricultural ecosystems. The aim of this work was to analyze and compare the soil bacterial communities from the Brazilian Cerrado associated with different land use systems using high throughput pyrosequencing of 16S rRNA genes. Relevant differences were observed in the abundance and structure of bacterial communities in soils under different land use systems. On the other hand, the diversity of bacterial communities was not relevantly changed among the sites studied. Land use systems had also an important impact on specific bacterial groups in soil, which might change the soil function and the ecological processes. Acidobacteria, Proteobacteria, and Actinobacteria were the most abundant groups in the Brazilian Cerrado. These findings suggest that more important than analyzing the general diversity is to analyze the composition of the communities. Since soil type was the same among the sites, we might assume that land use was the main factor defining the abundance and structure of bacterial communities.

Conformation switching of AIM2 PYD domain revealed by NMR relaxation and MD simulation.

PubMed

Wang, Haobo; Yang, Lijiang; Niu, Xiaogang

2016-04-29

Protein absent in melanoma 2 (AIM2) is a double-strand DNA (ds DNA) sensor mainly located in cytoplasm of cell. It includes one N terminal PYD domain and one C terminal HIN domain. When the ds DNA such as DNA viruses and bacteria entered cytoplasm, the HIN domain of AIM2 will recognize and bind to DNA, and the PYD domain will bind to ASC protein which will result in the formation of AIM2 inflammasome. Three AIM2 PYD domain structures have been solved, but every structure yields a unique conformation around the α3 helix region. To understand why different AIM2 PYD structures show different conformations in this region, we use NMR relaxation techniques to study the backbone dynamics of mouse AIM2 PYD domain and perform molecular dynamics (MD) simulations on both mouse and human AIM2 PYD structures. Our results indicate that this region is highly flexible in both mouse and human AIM2 PYD domains, and the PYD domain may exist as a conformation ensemble in solution. Different environment makes the population vary among pre-existing conformational substrates of the ensemble, which may be the reason why different AIM2 PYD structures were observed under different conditions. Further docking analysis reveals that the conformation switching may be important for the autoinhibition of the AIM2 protein. Copyright © 2016 Elsevier Inc. All rights reserved.

Asparagine-linked oligosaccharides on lutropin, follitropin, and thyrotropin: distributions of sulfated and sialylated oligosaccharides on bovine, ovine, and human pituitary glycoprotein hormones

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

Green, E.D.; Baenziger, J.U.

1988-01-05

The asparagine-linked oligosaccharides on the pituitary glycoprotein hormones lutropin (LH), follitropin (FSH), and thyrotropin (TSH) consist of a heterogeneous array of neutral, sulfated, sialylated, and sulfated/sialylated structures. In this study, the authors determined the relative quantities of the various asparagine-linked oligosaccharides on LH, FSH, and TSH from these three animal species. The proportions of sulfated versus sialylated oligosaccharides varied markedly among the different hormones. Both hormone- and animal species-specific differences in the types and distributions of sulfated, sialylated, and sulfated/sialylated structures were evident. In particular, LH and FSH, which are synthesized in the same pituitary cell and bear ..cap alpha..-subunitsmore » with the identical amino acid sequence, contained significantly different distributions of sulfated and sialylated oligosaccharides. For all three animal species, the ratio of sialylated to sulfated oligosaccharides differed by >10-fold for LH and FSH, with sulfated structures dominating on LH and sialylated structures on FSH. Sialylated oligosaccharides were also heterogeneous with respect to sialic acid linkage (..cap alpha..2,3 versus ..cap alpha..2,6). The differences in oligosaccharide structures among the various pituitary glycoprotein hormones as well as among the various glycosylation sites within a single hormone support the hypothesis that glycosylation may serve important functional roles in the expression and/or regulation of hormone bioactivity.« less

Round window chamber and fustis: endoscopic anatomy and surgical implications.

PubMed

Marchioni, Daniele; Soloperto, Davide; Colleselli, Elena; Tatti, Maria Fatima; Patel, Nirmal; Jufas, Nicholas

2016-11-01

The round window region is of critical importance in the anatomy of the middle ear. The aim of this paper is to describe its anatomy from an endoscopic point of view, emphasizing structures that have important surgical implications, in particular the fustis and the subcochlear canaliculus. The fustis, a smooth bony structure that forms the floor of the round window region, is a constant and important structure. It seems to indicate the round window membrane and the correct position of scala tympani. A structure connecting the round window region to the petrous apex, named the subcochlear canaliculus, is also described. A retrospective review of video recordings of endoscopic dissection and surgical procedures, carried out between June 2014 and February 2015, was conducted across two Tertiary university referral centers. A total of 42 dissections were analyzed in the study. We observed the fustis in all the cases and we identify two different anatomical conformations. The subcochlear canaliculus was found in 81.0 %, with a pneumatization direct to the petrous apex in 47.7 %. Conformation and limits of the round window niche may influence the surgical view of the round window membrane. Endoscopic approaches allow a very detailed view, which enables a comprehensive exploration of the round window region. Accurate knowledge of the anatomical relationships of this region has important advantages during middle ear surgery.

Computer-aided drug design for AMP-activated protein kinase activators.

PubMed

Wang, Zhanli; Huo, Jianxin; Sun, Lidan; Wang, Yongfu; Jin, Hongwei; Yu, Hui; Zhang, Liangren; Zhou, Lishe

2011-09-01

AMP-activated protein kinase (AMPK) is an important therapeutic target for the potential treatment of metabolic disorders, cardiovascular disease and cancer. Recently, various classes of compounds that activate AMPK by direct or indirect interactions have been reported. The importance of computer-aided drug design approaches in the search for potent activators of AMPK is now established, including structure-based design, ligand-based design, fragment-based design, as well as structural analysis. This review article highlights the computer-aided drug design approaches utilized to discover of activators targeting AMPK. The principles, advantages or limitation of the different methods are also being discussed together with examples of applications taken from the literatures.

Metal Transport across Biomembranes: Emerging Models for a Distinct Chemistry*

PubMed Central

Argüello, José M.; Raimunda, Daniel; González-Guerrero, Manuel

2012-01-01

Transition metals are essential components of important biomolecules, and their homeostasis is central to many life processes. Transmembrane transporters are key elements controlling the distribution of metals in various compartments. However, due to their chemical properties, transition elements require transporters with different structural-functional characteristics from those of alkali and alkali earth ions. Emerging structural information and functional studies have revealed distinctive features of metal transport. Among these are the relevance of multifaceted events involving metal transfer among participating proteins, the importance of coordination geometry at transmembrane transport sites, and the presence of the largely irreversible steps associated with vectorial transport. Here, we discuss how these characteristics shape novel transition metal ion transport models. PMID:22389499

Metal transport across biomembranes: emerging models for a distinct chemistry.

PubMed

Argüello, José M; Raimunda, Daniel; González-Guerrero, Manuel

2012-04-20

Transition metals are essential components of important biomolecules, and their homeostasis is central to many life processes. Transmembrane transporters are key elements controlling the distribution of metals in various compartments. However, due to their chemical properties, transition elements require transporters with different structural-functional characteristics from those of alkali and alkali earth ions. Emerging structural information and functional studies have revealed distinctive features of metal transport. Among these are the relevance of multifaceted events involving metal transfer among participating proteins, the importance of coordination geometry at transmembrane transport sites, and the presence of the largely irreversible steps associated with vectorial transport. Here, we discuss how these characteristics shape novel transition metal ion transport models.

High Energy Density in Azobenzene-based Materials for Photo-Thermal Batteries via Controlled Polymer Architecture and Polymer-Solvent Interactions.

PubMed

Jeong, Seung Pyo; Renna, Lawrence A; Boyle, Connor J; Kwak, Hyunwook S; Harder, Edward; Damm, Wolfgang; Venkataraman, Dhandapani

2017-12-19

Energy densities of ~510 J/g (max: 698 J/g) have been achieved in azobenzene-based syndiotactic-rich poly(methacrylate) polymers. The processing solvent and polymer-solvent interactions are important to achieve morphologically optimal structures for high-energy density materials. This work shows that morphological changes of solid-state syndiotactic polymers, driven by different solvent processings play an important role in controlling the activation energy of Z-E isomerization as well as the shape of the DSC exotherm. Thus, this study shows the crucial role of processing solvents and thin film structure in achieving higher energy densities.

Study of Barley Grain Molecular Structure for Ruminants Using DRIFT, FTIR-ATR and Synchrotron Radiation Infrared Microspectroscopy (SR-IMS): A Review

NASA Astrophysics Data System (ADS)

Yu, Peiqiang

2012-05-01

Barley inherent structures are highly associated with nutrient utilization and availability in both humans and animals. Barley has different degradation kinetics compared with other cereal grains. It has a relatively higher degradation rate and extent, which often cause digestive disorder in the rumen. Therefore understanding barley inherent structure at cellular and molecular levels and processing-induced structure changes is important, because we can manipulate barley inherent structures and digestive behaviors. Several molecular spectroscopy techniques can be used to detect barley inherent structures at cellular and molecular levels. This article reviews several applications of the IR molecular spectral bioanalytical techniques - DRIFT, FT/IR-ATR and SR-IMS for barley chemistry, molecular structure and molecular nutrition research

The first mammalian aldehyde oxidase crystal structure: insights into substrate specificity.

PubMed

Coelho, Catarina; Mahro, Martin; Trincão, José; Carvalho, Alexandra T P; Ramos, Maria João; Terao, Mineko; Garattini, Enrico; Leimkühler, Silke; Romão, Maria João

2012-11-23

Aldehyde oxidases have pharmacological relevance, and AOX3 is the major drug-metabolizing enzyme in rodents. The crystal structure of mouse AOX3 with kinetics and molecular docking studies provides insights into its enzymatic characteristics. Differences in substrate and inhibitor specificities can be rationalized by comparing the AOX3 and xanthine oxidase structures. The first aldehyde oxidase structure represents a major advance for drug design and mechanistic studies. Aldehyde oxidases (AOXs) are homodimeric proteins belonging to the xanthine oxidase family of molybdenum-containing enzymes. Each 150-kDa monomer contains a FAD redox cofactor, two spectroscopically distinct [2Fe-2S] clusters, and a molybdenum cofactor located within the protein active site. AOXs are characterized by broad range substrate specificity, oxidizing different aldehydes and aromatic N-heterocycles. Despite increasing recognition of its role in the metabolism of drugs and xenobiotics, the physiological function of the protein is still largely unknown. We have crystallized and solved the crystal structure of mouse liver aldehyde oxidase 3 to 2.9 Å. This is the first mammalian AOX whose structure has been solved. The structure provides important insights into the protein active center and further evidence on the catalytic differences characterizing AOX and xanthine oxidoreductase. The mouse liver aldehyde oxidase 3 three-dimensional structure combined with kinetic, mutagenesis data, molecular docking, and molecular dynamics studies make a decisive contribution to understand the molecular basis of its rather broad substrate specificity.

Investigation of structure in the modular light pipe component for LED automotive lamp

NASA Astrophysics Data System (ADS)

Chen, Hsi-Chao; Zhou, Yang; Huang, Chien-Sheng; Jhong, Wan-Ling; Cheng, Bo-Wei; Jhang, Jhe-Ming

2014-09-01

Light-Emitting Diodes (LEDs) have the advantages of small length, long lifetime, fast response time (μs), low voltage, good mechanical properties and environmental protection. Furthermore, LEDs could replace the halogen lamps to avoid the mercury pollution and economize the use of energy. Therefore, the LEDs could instead of the traditional lamp in the future and became an important light source. The proposal of this study was to investigate the effects of the structure and length of the reflector component for a LED automotive lamp. The novel LED automotive lamp was assembled by several different modularization columnar. The optimized design of the different structure and the length to the reflector was simulated by software TracePro. The design result must met the vehicle regulation of United Nations Economic Commission for Europe (UNECE) such as ECE-R19 etc. The structure of the light pipe could be designed by two steps structure. Then constitute the proper structure and choose different power LED to meet the luminous intensity of the vehicle regulation. The simulation result shows the proper structure and length has the best total luminous flux and a high luminous efficiency for the system. Also, the stray light could meet the vehicle regulation of ECE R19. Finally, the experimental result of the selected structure and length of the light pipe could match the simulation result above 80%.

Atomic force microscopy study of the structure function relationships of the biofilm-forming bacterium Streptococcus mutans

NASA Astrophysics Data System (ADS)

Cross, Sarah E.; Kreth, Jens; Zhu, Lin; Qi, Fengxia; Pelling, Andrew E.; Shi, Wenyuan; Gimzewski, James K.

2006-02-01

Atomic force microscopy (AFM) has garnered much interest in recent years for its ability to probe the structure, function and cellular nanomechanics inherent to specific biological cells. In particular, we have used AFM to probe the important structure-function relationships of the bacterium Streptococcus mutans. S. mutans is the primary aetiological agent in human dental caries (tooth decay), and is of medical importance due to the virulence properties of these cells in biofilm initiation and formation, leading to increased tolerance to antibiotics. We have used AFM to characterize the unique surface structures of distinct mutants of S. mutans. These mutations are located in specific genes that encode surface proteins, thus using AFM we have resolved characteristic surface features for mutant strains compared to the wild type. Ultimately, our characterization of surface morphology has shown distinct differences in the local properties displayed by various S. mutans strains on the nanoscale, which is imperative for understanding the collective properties of these cells in biofilm formation.

Identity related to living situation in six individuals with congenital quadriplegia.

PubMed

Robey, Kenneth L

2008-01-01

This study was a preliminary examination of structural aspects of identity, particularly identity associated with living situation, in individuals who have quadriplegia due to cerebral palsy. A hierarchical classes algorithm (HICLAS) was used to construct idiographic 'identity structure' models for three individuals who are living in an inpatient hospital setting and for three individuals living in community-based group residences. Indices derived from the models indicate that the identity 'myself as one who has a disability' was structurally superordinate (i.e., resided at a high hierarchical level) for all six participants, suggesting a high level of importance of this identity in participants' sense of self. The models also indicate that while identity associated with one's particular living situation was superordinate for persons living in the hospital, it was not for persons living in community residences. While conclusions based on this small sample are necessarily limited, the data suggest that identity associated with living situation might differ in structural centrality, and presumably subjective importance, for persons living in inpatient versus community-based settings.

Crystal Structure of PKG I:cGMP Complex Reveals a cGMP-Mediated Dimeric Interface that Facilitates cGMP-Induced Activation

DOE PAGES

Kim, Jeong Joo; Lorenz, Robin; Arold, Stefan T.; ...

2016-04-07

Cyclic guanosine monophosphate (cGMP)-dependent protein kinase (PKG) is a key regulator of smooth muscle and vascular tone and represents an important drug target for treating hypertensive diseases and erectile dysfunction. Despite its importance, its activation mechanism is not fully understood. To understand the activation mechanism, we determined a 2.5 Å crystal structure of the PKG I regulatory (R) domain bound with cGMP, which represents the activated state. Here, although we used a monomeric domain for crystallization, the structure reveals that two R domains form a symmetric dimer where the cGMP bound at high-affinity pockets provide critical dimeric contacts. Small-angle X-raymore » scattering and mutagenesis support this dimer model, suggesting that the dimer interface modulates kinase activation. Finally, structural comparison with the homologous cyclic AMP-dependent protein kinase reveals that PKG is drastically different from protein kinase A in its active conformation, suggesting a novel activation mechanism for PKG.« less

Architecture and data processing alternatives for the TSE computer. Volume 3: Execution of a parallel counting algorithm using array logic (Tse) devices

NASA Technical Reports Server (NTRS)

Metcalfe, A. G.; Bodenheimer, R. E.

1976-01-01

A parallel algorithm for counting the number of logic-l elements in a binary array or image developed during preliminary investigation of the Tse concept is described. The counting algorithm is implemented using a basic combinational structure. Modifications which improve the efficiency of the basic structure are also presented. A programmable Tse computer structure is proposed, along with a hardware control unit, Tse instruction set, and software program for execution of the counting algorithm. Finally, a comparison is made between the different structures in terms of their more important characteristics.

Structural insights into the inactivation of CRISPR-Cas systems by diverse anti-CRISPR proteins.

PubMed

Zhu, Yuwei; Zhang, Fan; Huang, Zhiwei

2018-03-19

A molecular arms race is progressively being unveiled between prokaryotes and viruses. Prokaryotes utilize CRISPR-mediated adaptive immune systems to kill the invading phages and mobile genetic elements, and in turn, the viruses evolve diverse anti-CRISPR proteins to fight back. The structures of several anti-CRISPR proteins have now been reported, and here we discuss their structural features, with a particular emphasis on topology, to discover their similarities and differences. We summarize the CRISPR-Cas inhibition mechanisms of these anti-CRISPR proteins in their structural context. Considering anti-CRISPRs in this way will provide important clues for studying their origin and evolution.

A structural diagnostics diagram for metallofullerenes encapsulating metal carbides and nitrides.

PubMed

Maki, Sachiko; Nishibori, Eiji; Terauchi, Ikuya; Ishihara, Masayuki; Aoyagi, Shinobu; Sakata, Makoto; Takata, Masaki; Umemoto, Hisashi; Inoue, Takashi; Shinohara, Hisanori

2013-01-16

Systematic structural studies of 24 different kinds of endohedral metallofullerenes, M(x)C(2n) (M = La, Y, Sc, Lu, Ti, Eu, Er, Hf, Sc(3)N; 34 ≤ n ≤ 43), as 1:1 cocrystals with solvent toluene molecules have been carried out using synchrotron radiation powder diffraction. Thirteen of the 24 molecular structures, including five metal carbides, one metal nitride endohedral fullerene, and one hollow fullerene, have been determined by a combination of the maximum entropy method and Rietveld refinement of the X-ray diffraction data obtained. We have found that the volume for one fullerene and one toluene molecule depends linearly on the number of carbon atoms in the fullerene cage. Fifteen different kinds of metal carbide endohedral fullerenes have been identified, which can be structurally characterized from the obtained lattice constants using only this linear dependence. The linear dependence found in the present study provides a metallofullerene diagnostics diagram that may have universal importance for structural characterization of the so-called cluster endohedral fullerenes.

Numerical simulation of colloidal self-assembly of super-hydrophobic arachnid cerotegument structures.

PubMed

Filippov, Alexander É; Wolff, Jonas O; Seiter, Michael; Gorb, Stanislav N

2017-10-07

Certain arachnids exhibit complex coatings of their exoskeleton, consisting of globular structures with complex surface features. This, so-called, cerotegument is formed by a multi-component colloidal secretion that self-assembles and cures on the body surface, and leads to high water repellency. Previous ultrastructural studies revealed the involvement of different glandular cells that contribute different components to the secretion mixture, but the overall process of self-assembly into the complex regular structures observed remained highly unclear. Here we study this process from a theoretical point of view, starting from the so-called Tammes-problem. We show that slight changes of simple parameters lead to a variety of morphologies that are highly similar to the ones observed in the species specific cerotegument structures of whip-spiders. These results are not only important for our understanding of the formation of globular hierarchical structures in nature, but also for the fabrication of novel surface coatings by colloidal lithography. Copyright © 2017 Elsevier Ltd. All rights reserved.

The First Mammalian Aldehyde Oxidase Crystal Structure

PubMed Central

Coelho, Catarina; Mahro, Martin; Trincão, José; Carvalho, Alexandra T. P.; Ramos, Maria João; Terao, Mineko; Garattini, Enrico; Leimkühler, Silke; Romão, Maria João

2012-01-01

Aldehyde oxidases (AOXs) are homodimeric proteins belonging to the xanthine oxidase family of molybdenum-containing enzymes. Each 150-kDa monomer contains a FAD redox cofactor, two spectroscopically distinct [2Fe-2S] clusters, and a molybdenum cofactor located within the protein active site. AOXs are characterized by broad range substrate specificity, oxidizing different aldehydes and aromatic N-heterocycles. Despite increasing recognition of its role in the metabolism of drugs and xenobiotics, the physiological function of the protein is still largely unknown. We have crystallized and solved the crystal structure of mouse liver aldehyde oxidase 3 to 2.9 Å. This is the first mammalian AOX whose structure has been solved. The structure provides important insights into the protein active center and further evidence on the catalytic differences characterizing AOX and xanthine oxidoreductase. The mouse liver aldehyde oxidase 3 three-dimensional structure combined with kinetic, mutagenesis data, molecular docking, and molecular dynamics studies make a decisive contribution to understand the molecular basis of its rather broad substrate specificity. PMID:23019336

Sequence, Structural Analysis and Metrics to Define the Unique Dynamic Features of the Flap Regions Among Aspartic Proteases.

PubMed

McGillewie, Lara; Ramesh, Muthusamy; Soliman, Mahmoud E

2017-10-01

Aspartic proteases are a class of hydrolytic enzymes that have been implicated in a number of diseases such as HIV, malaria, cancer and Alzheimer's. The flap region of aspartic proteases is a characteristic unique structural feature of these enzymes; and found to have a profound impact on protein overall structure, function and dynamics. Flap dynamics also plays a crucial role in drug binding and drug resistance. Therefore, understanding the structure and dynamic behavior of this flap regions is crucial in the design of potent and selective inhibitors against aspartic proteases. Defining metrics that can describe the flap motion/dynamics has been a challenging topic in literature. This review is the first attempt to compile comprehensive information on sequence, structure, motion and metrics used to assess the dynamics of the flap region of different aspartic proteases in "one pot". We believe that this review would be of critical importance to the researchers from different scientific domains.

Substrate temperature effect on the structural anisotropy in amorphous Tb-Fe films

NASA Astrophysics Data System (ADS)

Harris, V. G.; Hellman, F.; Elam, W. T.; Koon, N. C.

1993-05-01

Using extended x-ray absorption fine structures (EXAFS) measurements we have investigated the atomic environment around the Fe atom in a series of amorphous Tb0.26Fe0.74 films having different magnetic anisotropy energies owing to different deposition temperatures. The polarization properties of synchrotron radiation allowed the separate study of structure parallel and perpendicular to the sample plane. An anisotropy between these two structures was observed. Modeling results indicate this anisotropy is due to anisotropic pair correlations where the Fe-Fe pairs are statistically preferred in-plane and the Fe-Tb pairs out-of-plane. The amplitude of this anisotropy scales with both the substrate temperature and the magnetic anisotropy energy. A ≊1% in-plane compression of the Fe-Fe distance was measured between the in-plane and out-of-plane structure of the sample grown at 77 K. This sample had no detectable local chemical anisotropy suggesting that intrinsic stress plays an important role in determining its magnetic anisotropy.

Recent advances in biomimetic sensing technologies.

PubMed

Johnson, E A C; Bonser, R H C; Jeronimidis, G

2009-04-28

The importance of biological materials has long been recognized from the molecular level to higher levels of organization. Whereas, in traditional engineering, hardness and stiffness are considered desirable properties in a material, biology makes considerable and advantageous use of softer, more pliable resources. The development, structure and mechanics of these materials are well documented and will not be covered here. The purpose of this paper is, however, to demonstrate the importance of such materials and, in particular, the functional structures they form. Using only a few simple building blocks, nature is able to develop a plethora of diverse materials, each with a very different set of mechanical properties and from which a seemingly impossibly large number of assorted structures are formed. There is little doubt that this is made possible by the fact that the majority of biological 'materials' or 'structures' are based on fibres and that these fibres provide opportunities for functional hierarchies. We show how these structures have inspired a new generation of innovative technologies in the science and engineering community. Particular attention is given to the use of insects as models for biomimetically inspired innovations.

Benthic community structure, diversity, and productivity in the shallow Barents Sea bank (Svalbard Bank).

PubMed

Kędra, Monika; Renaud, Paul E; Andrade, Hector; Goszczko, Ilona; Ambrose, William G

2013-01-01

The Barents Sea is among the most productive areas in the world oceans, and its shallow banks exhibit particularly high rates of primary productivity reaching over 300 g C m -2 year -1 . Our study focused on the Svalbard Bank, an important feeding area for fishes and whales. In order to investigate how benthic community structure and benthic secondary production vary across environmental gradients and through time, we sampled across the bank and compared results with a similar study conducted 85 years ago. Considerable variability in community structure and function across bank corresponded with differences in the physical structure of the habitat, including currents, sedimentation regimes and sediment type, and overlying water masses. Despite an intensive scallop fishery and climatic shifts that have taken place since the last survey in the 1920s, benthic community structure was very similar to that from the previous survey, suggesting strong system resilience. Primary and secondary production over shallow banks plays a large role in the Barents Sea and may act as a carbon subsidy to surrounding fish populations, of which many are of commercial importance.

Statistical inference of protein structural alignments using information and compression.

PubMed

Collier, James H; Allison, Lloyd; Lesk, Arthur M; Stuckey, Peter J; Garcia de la Banda, Maria; Konagurthu, Arun S

2017-04-01

Structural molecular biology depends crucially on computational techniques that compare protein three-dimensional structures and generate structural alignments (the assignment of one-to-one correspondences between subsets of amino acids based on atomic coordinates). Despite its importance, the structural alignment problem has not been formulated, much less solved, in a consistent and reliable way. To overcome these difficulties, we present here a statistical framework for the precise inference of structural alignments, built on the Bayesian and information-theoretic principle of Minimum Message Length (MML). The quality of any alignment is measured by its explanatory power-the amount of lossless compression achieved to explain the protein coordinates using that alignment. We have implemented this approach in MMLigner , the first program able to infer statistically significant structural alignments. We also demonstrate the reliability of MMLigner 's alignment results when compared with the state of the art. Importantly, MMLigner can also discover different structural alignments of comparable quality, a challenging problem for oligomers and protein complexes. Source code, binaries and an interactive web version are available at http://lcb.infotech.monash.edu.au/mmligner . arun.konagurthu@monash.edu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

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

Onoufriou, T.; Simpson, R.J.; Protopapas, M.

This paper presents the development and application of reliability based inspection planning techniques for floaters. Based on previous experience from jacket structure applications optimized inspection planning (OIP) techniques for floaters are developed. The differences between floaters and jacket structures in relation to fatigue damage, redundancy levels and inspection practice are examined and reflected in the proposed methodology. The application and benefits of these techniques is demonstrated through representative analyses and important trends are highlighted through the results of a parametric sensitivity study.

Bodily Integrity and Male Circumcision: An Islamic Perspective

PubMed Central

Alahmad, Ghiath; Dekkers, Wim

2012-01-01

The notion of bodily integrity forms an important part of the value-structure of many religions and cultures. In this paper, we explore the notion of bodily integrity in Islam using male circumcision as the focus of the discussion. Our aim is to contribute to a better understanding of the Muslim perspective and of the differences and similarities between Western and Islamic ethical structures, in particular, regarding the concept of bodily integrity. PMID:23610746

Robot arm system for automatic satellite capture and berthing

NASA Technical Reports Server (NTRS)

Nishida, Shinichiro; Toriu, Hidetoshi; Hayashi, Masato; Kubo, Tomoaki; Miyata, Makoto

1994-01-01

Load control is one of the most important technologies for capturing and berthing free flying satellites by a space robot arm because free flying satellites have different motion rates. The performance of active compliance control techniques depend on the location of the force sensor and the arm's structural compliance. A compliance control technique for the robot arm's structural elasticity and a consideration for an end-effector appropriate for it are presented in this paper.

Modelling and Holographic Visualization of Space Radiation-Induced DNA Damage

NASA Technical Reports Server (NTRS)

Plante, Ianik

2017-01-01

Space radiation is composed by a mixture of ions of different energies. Among these, heavy inos are of particular importance because their health effects are poorly understood. In. the recent years, a software named RITRACKS (Relativistic Ion Tracks) was developed to simulate the detailed radiation track structure, several DNA models and DNA damage. As the DNA structure is complex due to packing, it is difficult to the damage using a regular computer screen.

How to benchmark methods for structure-based virtual screening of large compound libraries.

PubMed

Christofferson, Andrew J; Huang, Niu

2012-01-01

Structure-based virtual screening is a useful computational technique for ligand discovery. To systematically evaluate different docking approaches, it is important to have a consistent benchmarking protocol that is both relevant and unbiased. Here, we describe the designing of a benchmarking data set for docking screen assessment, a standard docking screening process, and the analysis and presentation of the enrichment of annotated ligands among a background decoy database.

In Situ Monitoring of Ni-based Catalysts during the Synthesis of Propylene Carbonate

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

Ramin, Michael; Reimann, Sven; Grunwaldt, Jan-Dierk

2007-02-02

Three different nickel complexes were catalytically tested in the synthesis of propylene carbonate by carbon dioxide insertion. XAS measurements of the as prepared catalysts confirmed the differences in the structure which led to the varying catalytic activity. The structure of one of the active nickel-based catalysts was followed in situ by X-ray absorption spectroscopy using a specially designed batch reactor cell. The novel batch reactor allows in situ studies in dense carbon dioxide at elevated temperature and high pressure (up to 200 bar) even at the low energy of the nickel K-edge. Hence, important information on the fate of themore » ligands and structural changes under reaction conditions could be gained providing new insight into the reaction mechanism.« less

Learning processes in the professional development of mental health counselors: knowledge restructuring and illness script formation.

PubMed

Strasser, Josef; Gruber, Hans

2015-05-01

An important part of learning processes in the professional development of counselors is the integration of declarative knowledge and professional experience. It was investigated in-how-far mental health counselors at different levels of expertise (experts, intermediates, novices) differ in their availability of experience-based knowledge structures. Participants were prompted with 20 client problems. They had to explain those problems, the explanations were analyzed using think-aloud protocols. The results show that experts' knowledge is organized in script-like structures that integrate declarative knowledge and professional experience and help experts in accessing relevant information about cases. Novices revealed less integrated knowledge structures. It is concluded that knowledge restructuring and illness script formation are crucial parts of the professional learning of counselors.

Effect of the structure and mechanical properties of the near-surface layer of lithium niobate single crystals on the manufacture of integrated optic circuits

NASA Astrophysics Data System (ADS)

Sosunov, A. V.; Ponomarev, R. S.; Yur'ev, V. A.; Volyntsev, A. B.

2017-01-01

This paper shows that the near-surface layer of a lithium niobate single layer 15 μm in depth is essentially different from the rest of the volume of the material from the standpoint of composition, structure, and mechanical properties. The pointed out differences are due to the effect of cutting, polishing, and smoothing of the lithium niobate plates, which increase the density of point defects and dislocations. The increasing density of the structural defects leads to uncontrollable changes in the conditions of the formations of waveguides and the drifting of characteristics of integrated optical circuits. The results obtained are very important for the manufacture of lithium niobate based integrated optical circuits.

Temporal structure of neuronal population oscillations with empirical model decomposition

NASA Astrophysics Data System (ADS)

Li, Xiaoli

2006-08-01

Frequency analysis of neuronal oscillation is very important for understanding the neural information processing and mechanism of disorder in the brain. This Letter addresses a new method to analyze the neuronal population oscillations with empirical mode decomposition (EMD). Following EMD of neuronal oscillation, a series of intrinsic mode functions (IMFs) are obtained, then Hilbert transform of IMFs can be used to extract the instantaneous time frequency structure of neuronal oscillation. The method is applied to analyze the neuronal oscillation in the hippocampus of epileptic rats in vivo, the results show the neuronal oscillations have different descriptions during the pre-ictal, seizure onset and ictal periods of the epileptic EEG at the different frequency band. This new method is very helpful to provide a view for the temporal structure of neural oscillation.

Hooked on α-d-galactosidases: from biomedicine to enzymatic synthesis.

PubMed

Bakunina, Irina Yu; Balabanova, Larissa A; Pennacchio, Angela; Trincone, Antonio

2016-01-01

α-d-Galactosidases (EC 3.2.1.22) are enzymes employed in a number of useful bio-based applications. We have depicted a comprehensive general survey of α-d-galactosidases from different origin with special emphasis on marine example(s). The structures of natural α-galactosyl containing compounds are described. In addition to 3D structures and mechanisms of action of α-d-galactosidases, different sources, natural function and genetic regulation are also covered. Finally, hydrolytic and synthetic exploitations as free or immobilized biocatalysts are reviewed. Interest in the synthetic aspects during the next years is anticipated for access to important small molecules by green technology with an emphasis on alternative selectivity of this class of enzymes from different sources.

Impact of Early and Late Visual Deprivation on the Structure of the Corpus Callosum: A Study Combining Thickness Profile with Surface Tensor-Based Morphometry.

PubMed

Shi, Jie; Collignon, Olivier; Xu, Liang; Wang, Gang; Kang, Yue; Leporé, Franco; Lao, Yi; Joshi, Anand A; Leporé, Natasha; Wang, Yalin

2015-07-01

Blindness represents a unique model to study how visual experience may shape the development of brain organization. Exploring how the structure of the corpus callosum (CC) reorganizes ensuing visual deprivation is of particular interest due to its important functional implication in vision (e.g., via the splenium of the CC). Moreover, comparing early versus late visually deprived individuals has the potential to unravel the existence of a sensitive period for reshaping the CC structure. Here, we develop a novel framework to capture a complete set of shape differences in the CC between congenitally blind (CB), late blind (LB) and sighted control (SC) groups. The CCs were manually segmented from T1-weighted brain MRI and modeled by 3D tetrahedral meshes. We statistically compared the combination of local area and thickness at each point between subject groups. Differences in area are found using surface tensor-based morphometry; thickness is estimated by tracing the streamlines in the volumetric harmonic field. Group differences were assessed on this combined measure using Hotelling's T(2) test. Interestingly, we observed that the total callosal volume did not differ between the groups. However, our fine-grained analysis reveals significant differences mostly localized around the splenium areas between both blind groups and the sighted group (general effects of blindness) and, importantly, specific dissimilarities between the LB and CB groups, illustrating the existence of a sensitive period for reorganization. The new multivariate statistics also gave better effect sizes for detecting morphometric differences, relative to other statistics. They may boost statistical power for CC morphometric analyses.

IMPACT OF EARLY AND LATE VISUAL DEPRIVATION ON THE STRUCTURE OF THE CORPUS CALLOSUM: A STUDY COMBINING THICKNESS PROFILE WITH SURFACE TENSOR-BASED MORPHOMETRY

PubMed Central

Shi, Jie; Collignon, Olivier; Xu, Liang; Wang, Gang; Kang, Yue; Leporé, Franco; Lao, Yi; Joshi, Anand A.

2015-01-01

Blindness represents a unique model to study how visual experience may shape the development of brain organization. Exploring how the structure of the corpus callosum (CC) reorganizes ensuing visual deprivation is of particular interest due to its important functional implication in vision (e.g. via the splenium of the CC). Moreover, comparing early versus late visually deprived individuals has the potential to unravel the existence of a sensitive period for reshaping the CC structure. Here, we develop a novel framework to capture a complete set of shape differences in the CC between congenitally blind (CB), late blind (LB) and sighted control (SC) groups. The CCs were manually segmented from T1-weighted brain MRI and modeled by 3D tetrahedral meshes. We statistically compared the combination of local area and thickness at each point between subject groups. Differences in area are found using surface tensor-based morphometry; thickness is estimated by tracing the streamlines in the volumetric harmonic field. Group differences were assessed on this combined measure using Hotelling’s T2 test. Interestingly, we observed that the total callosal volume did not differ between the groups. However, our fine-grained analysis reveals significant differences mostly localized around the splenium areas between both blind groups and the sighted group (general effects of blindness) and, importantly, specific dissimilarities between the LB and CB groups, illustrating the existence of a sensitive period for reorganization. The new multivariate statistics also gave better effect sizes for detecting morphometric differences, relative to other statistics. They may boost statistical power for CC morphometric analyses. PMID:25649876

Estimating the Effect of Health Insurance on Personal Prescription Drug Importation

PubMed Central

Zullo, Andrew R.; Howe, Chanelle J.; Galárraga, Omar

2016-01-01

Personal prescription drug importation occurs in the United States because of the high cost of U.S. medicines and lower cost of foreign equivalents. Importation carries a risk of exposure to counterfeit (i.e., falsified, fraudulent), adulterated, and substandard drugs. Inadequate health insurance may increase the risk of importation. We use inverse probability weighted marginal structural models and data on 87,494 individuals from the 2011-2013 National Health Interview Survey to estimate the marginal association between no health insurance and importation within U.S. subpopulations. The marginal prevalence difference [95% confidence limits] for those without (prevalence = 0.031) versus those with health insurance was 0.016 [0.011, 0.021]. The prevalence difference was higher among persons who were Hispanic, born in Latin America, Russia, or Europe, traveled to developing countries, and did not use the Internet to fill prescriptions or to find health information. Health insurance coverage may effectively reduce importation, especially among particular subpopulations. PMID:26837427

Water-mediated contacts in the trp-repressor operator complex recognition process.

PubMed

Wibowo, Fajar R; Rauch, Christine; Trieb, Michael; Wellenzohn, Bernd; Liedl, Klaus R

2004-04-15

Water-mediated contacts are known as an important recognition tool in trp-repressor operator systems. One of these contacts involves two conserved base pairs (G(6).C(-6) and A(5). T(-5)) and three amino acids (Lys 72, Ile 79, and Ala 80). To investigate the nature of these contacts, we analyzed the X-ray structure (PDB code: 1TRO) of the trp-repressor operator complex by means of molecular dynamics simulations. This X-ray structure contains two dimers that exhibit structural differences. From these two different starting structures, two 10 ns molecular dynamics simulations have been performed. Both of our simulations show an increase of water molecules in the major groove at one side of the dimer, while the other side remains unchanged compared to the X-ray structure. Though the maximum residence time of the concerned water molecules decreases with an increase of solvent at the interface, these water molecules continue to play an important role in mediating DNA-protein contacts. This is shown by new stable amino acids-DNA distances and a long water residence time compared to free DNA simulation. To maintain stability of the new contacts, the preferential water binding site on O6(G6) is extended. This extension agrees with mutation experiment data on A5 and G6, which shows different relative affinity due to mutation on these bases [A. Joachimiak, T. E. Haran, P. B. Sigler, EMBO Journal 1994, Vol. 13, No. (2) pp. 367-372]. Due to the rearrangements in the system, the phosphate of the base G6 is able to interconvert to the B(II) substate, which is not observed on the other half side of the complex. The decrease of the number of hydrogen bonds between protein and DNA backbone could be the initial step of the dissociation process of the complex, or in other words an intermediate complex conformation of the association process. Thus, we surmise that these features show the importance of water-mediated contacts in the trp-repressor operator recognition process. Copyright 2004 Wiley Periodicals, Inc.

Variations in the structural and functional diversity of zooplankton over vertical and horizontal environmental gradients en route to the Arctic Ocean through the Fram Strait.

PubMed

Gluchowska, Marta; Trudnowska, Emilia; Goszczko, Ilona; Kubiszyn, Anna Maria; Blachowiak-Samolyk, Katarzyna; Walczowski, Waldemar; Kwasniewski, Slawomir

2017-01-01

A multi-scale approach was used to evaluate which spatial gradient of environmental variability is the most important in structuring zooplankton diversity in the West Spitsbergen Current (WSC). The WSC is the main conveyor of warm and biologically rich Atlantic water to the Arctic Ocean through the Fram Strait. The data set included 85 stratified vertical zooplankton samples (obtained from depths up to 1000 metres) covering two latitudinal sections (76°30'N and 79°N) located across the multi-path WSC system. The results indicate that the most important environmental variables shaping the zooplankton structural and functional diversity and standing stock variability are those associated with depth, whereas variables acting in the horizontal dimension are of lesser importance. Multivariate analysis of the zooplankton assemblages, together with different univariate descriptors of zooplankton diversity, clearly illustrated the segregation of zooplankton taxa in the vertical plane. The epipelagic zone (upper 200 m) hosted plentiful, Oithona similis-dominated assemblages with a high proportion of filter-feeding zooplankton. Although total zooplankton abundance declined in the mesopelagic zone (200-1000 m), zooplankton assemblages in that zone were more diverse and more evenly distributed, with high contributions from both herbivorous and carnivorous taxa. The vertical distribution of integrated biomass (mg DW m-2) indicated that the total zooplankton biomass in the epipelagic and mesopelagic zones was comparable. Environmental gradients acting in the horizontal plane, such as the ones associated with different ice cover and timing of the spring bloom, were reflected in the latitudinal variability in protist community structure and probably caused differences in succession in the zooplankton community. High abundances of Calanus finmarchicus in the WSC core branch suggest the existence of mechanisms advantageous for higher productivity or/and responsible for physical concentration of zooplankton. Our results indicate that regional hydrography plays a primary role in shaping zooplankton variability in the WSC on the way to the Arctic Ocean, with additional effects caused by biological factors related to seasonality in pelagic ecosystem development, resulting in regional differences in food availability or biological production between the continental slope and the deep ocean regions.

Landscape structure affects specialists but not generalists in naturally fragmented grasslands

USGS Publications Warehouse

Miller, Jesse E.D.; Damschen, Ellen Ingman; Harrison, Susan P.; Grace, James B.

2015-01-01

Understanding how biotic communities respond to landscape spatial structure is critically important for conservation management as natural landscapes become increasingly fragmented. However, empirical studies of the effects of spatial structure on plant species richness have found inconsistent results, suggesting that more comprehensive approaches are needed. In this study, we asked how landscape structure affects total plant species richness and the richness of a guild of specialized plants in a multivariate context. We sampled herbaceous plant communities at 56 dolomite glades (insular, fire-adapted grasslands) across the Missouri Ozarks, and used structural equation modeling (SEM) to analyze the relative importance of landscape structure, soil resource availability, and fire history for plant communities. We found that landscape spatial structure-defined as the area-weighted proximity of glade habitat surrounding study sites (proximity index)-had a significant effect on total plant species richness, but only after we controlled for environmental covariates. Richness of specialist species, but not generalists, was positively related to landscape spatial structure. Our results highlight that local environmental filters must be considered to understand the influence of landscape structure on communities, and that unique species guilds may respond differently to landscape structure than the community as a whole. These findings suggest that both local environment and landscape context should be considered when developing management strategies for species of conservation concern in fragmented habitats.

Multi-attribute integrated measurement of node importance in complex networks.

PubMed

Wang, Shibo; Zhao, Jinlou

2015-11-01

The measure of node importance in complex networks is very important to the research of networks stability and robustness; it also can ensure the security of the whole network. Most researchers have used a single indicator to measure the networks node importance, so that the obtained measurement results only reflect certain aspects of the networks with a loss of information. Meanwhile, because of the difference of networks topology, the nodes' importance should be described by combining the character of the networks topology. Most of the existing evaluation algorithms cannot completely reflect the circumstances of complex networks, so this paper takes into account the degree of centrality, the relative closeness centrality, clustering coefficient, and topology potential and raises an integrated measuring method to measure the nodes' importance. This method can reflect nodes' internal and outside attributes and eliminate the influence of network structure on the node importance. The experiments of karate network and dolphin network show that networks topology structure integrated measure has smaller range of metrical result than a single indicator and more universal. Experiments show that attacking the North American power grid and the Internet network with the method has a faster convergence speed than other methods.