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

Orientation dependence of microfracture behavior in a dual-phase high-strength low-alloy steel

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

Suh, D.; Lee, S.; Kim, N.J.

1997-02-01

In selecting the processing conditions and evaluating the reliability of structural materials, microscopic observations and identification of the fracture mechanisms in local cracking behavior are required. An important instance in the failure of the local brittle zone (LBZ) in the welding zone. The LBZ, which is very brittle, is the coarse-grained heat-affected zone near the fusion line, a zone known to be critical to the fracture toughness of welded parts. Thus, maintaining stable fracture resistance by predicting the microfracture behavior is important when using high-strength low-alloy (HSLA) steels in offshore structural steel welds. Depending on the thermal cycles involved duringmore » welding, the ferrite/martensite structure can have various morphologies of martensite particles, for example, fibrous and blocky martensite. In summary, in situ SEM fracture tests reveal that in the L-oriented IQ DCB specimen, a microcrack tends to propagate relatively uniformly throughout the ferrite and well-distributed fine fibrous martensite, yielding good elongation with high strength level. Also, the IQ structure in the T orientation shows similar microfracture behavior. On the other hand, in the SQ structure, where blocky-type martensite is mixed with ferrite, strain is localized into shear bands mostly in the ferrite region, and a local microcrack propagates along the strain-localized band formed in the ferrite, resulting in the SQ structure in the T orientation, where the ferrite-martensite bands are parallel to the notch direction, the martensite cannot act as an efficient barrier to microcrack advance, and thus the tensile ductility is decreased.« less

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

Kamiya, Shoji; Sato, Hisashi; Nishida, Masahiro

Reliability of electronic devices has been an issue of serious importance. One of the potential factors to spoil the reliability is possible local drops of strength on the interface of multilayered structure. A new technique for the evaluation of local interface adhesion energy was applied to the interface between Cu and cap layer in a Cu damascene interconnect structure, in order to elucidate variation in adhesion strength as a function of measurement location.

ProBiS-database: precalculated binding site similarities and local pairwise alignments of PDB structures.

PubMed

Konc, Janez; Cesnik, Tomo; Konc, Joanna Trykowska; Penca, Matej; Janežič, Dušanka

2012-02-27

ProBiS-Database is a searchable repository of precalculated local structural alignments in proteins detected by the ProBiS algorithm in the Protein Data Bank. Identification of functionally important binding regions of the protein is facilitated by structural similarity scores mapped to the query protein structure. PDB structures that have been aligned with a query protein may be rapidly retrieved from the ProBiS-Database, which is thus able to generate hypotheses concerning the roles of uncharacterized proteins. Presented with uncharacterized protein structure, ProBiS-Database can discern relationships between such a query protein and other better known proteins in the PDB. Fast access and a user-friendly graphical interface promote easy exploration of this database of over 420 million local structural alignments. The ProBiS-Database is updated weekly and is freely available online at http://probis.cmm.ki.si/database.

Locating Structural Centers: A Density-Based Clustering Method for Community Detection

PubMed Central

Liu, Gongshen; Li, Jianhua; Nees, Jan P.

2017-01-01

Uncovering underlying community structures in complex networks has received considerable attention because of its importance in understanding structural attributes and group characteristics of networks. The algorithmic identification of such structures is a significant challenge. Local expanding methods have proven to be efficient and effective in community detection, but most methods are sensitive to initial seeds and built-in parameters. In this paper, we present a local expansion method by density-based clustering, which aims to uncover the intrinsic network communities by locating the structural centers of communities based on a proposed structural centrality. The structural centrality takes into account local density of nodes and relative distance between nodes. The proposed algorithm expands a community from the structural center to the border with a single local search procedure. The local expanding procedure follows a heuristic strategy as allowing it to find complete community structures. Moreover, it can identify different node roles (cores and outliers) in communities by defining a border region. The experiments involve both on real-world and artificial networks, and give a comparison view to evaluate the proposed method. The result of these experiments shows that the proposed method performs more efficiently with a comparative clustering performance than current state of the art methods. PMID:28046030

Inference for local autocorrelations in locally stationary models.

PubMed

Zhao, Zhibiao

2015-04-01

For non-stationary processes, the time-varying correlation structure provides useful insights into the underlying model dynamics. We study estimation and inferences for local autocorrelation process in locally stationary time series. Our constructed simultaneous confidence band can be used to address important hypothesis testing problems, such as whether the local autocorrelation process is indeed time-varying and whether the local autocorrelation is zero. In particular, our result provides an important generalization of the R function acf() to locally stationary Gaussian processes. Simulation studies and two empirical applications are developed. For the global temperature series, we find that the local autocorrelations are time-varying and have a "V" shape during 1910-1960. For the S&P 500 index, we conclude that the returns satisfy the efficient-market hypothesis whereas the magnitudes of returns show significant local autocorrelations.

Data analysis and detection methods for on-line health monitoring of bridge structures

DOT National Transportation Integrated Search

2002-06-01

Developing an efficient structural health monitoring (SHM) technique is important for reducing potential hazards posed : to the public by damaged civil structures. The ultimate goal of applying SHM is to real-time detect, localize, and quantify : the...

Mixture models for protein structure ensembles.

PubMed

Hirsch, Michael; Habeck, Michael

2008-10-01

Protein structure ensembles provide important insight into the dynamics and function of a protein and contain information that is not captured with a single static structure. However, it is not clear a priori to what extent the variability within an ensemble is caused by internal structural changes. Additional variability results from overall translations and rotations of the molecule. And most experimental data do not provide information to relate the structures to a common reference frame. To report meaningful values of intrinsic dynamics, structural precision, conformational entropy, etc., it is therefore important to disentangle local from global conformational heterogeneity. We consider the task of disentangling local from global heterogeneity as an inference problem. We use probabilistic methods to infer from the protein ensemble missing information on reference frames and stable conformational sub-states. To this end, we model a protein ensemble as a mixture of Gaussian probability distributions of either entire conformations or structural segments. We learn these models from a protein ensemble using the expectation-maximization algorithm. Our first model can be used to find multiple conformers in a structure ensemble. The second model partitions the protein chain into locally stable structural segments or core elements and less structured regions typically found in loops. Both models are simple to implement and contain only a single free parameter: the number of conformers or structural segments. Our models can be used to analyse experimental ensembles, molecular dynamics trajectories and conformational change in proteins. The Python source code for protein ensemble analysis is available from the authors upon request.

The influence of the local structure on proton transport in a solid oxide proton conductor La 0.8 Ba 1.2 GaO 3.9

DOE PAGES

Cheng, Yongqiang; Balachandran, Janakiraman; Bi, Zhonghe; ...

2017-07-18

The local structure around the mobile ions influences their dynamics. The knowledge about the relationship between these properties is of fundamental importance and may lead the way for development of improved solid state ionic conductors. Here, we use inelastic neutron scattering and ab initio modeling to study a representative proton conductor, La 0.8Ba 1.2GaO 3.9, where different local structures are possible for the same stoichiometry. The intrinsic correlations between the local bonding environment and the dynamical behavior of protons are presented. In particular, we identify how the local Ba/La concentration affects the proton vibrational frequencies, hydrogen bond strength, O–H rotationsmore » and in turn long-range proton mobility. Furthermore, possible mechanism for proton transport, through the inter-tetrahedral bond switching, O–H rotations and tetrahedral reorientation is anticipated.« less

Bringing together local culture and rural development: findings from Ireland, Pennsylvania and Alaska

Treesearch

M.A. Brennan; Courtney G. Flint; A.E. Luloff

2009-01-01

The developmental trajectories of communities are routinely explained by reference to economic history, human capital deficits, or the structure of local labour markets. The role of local culture in understanding community development or in interpreting empirical research has received less attention. We believe culture plays an important independent role in shaping...

Discriminative structural approaches for enzyme active-site prediction.

PubMed

Kato, Tsuyoshi; Nagano, Nozomi

2011-02-15

Predicting enzyme active-sites in proteins is an important issue not only for protein sciences but also for a variety of practical applications such as drug design. Because enzyme reaction mechanisms are based on the local structures of enzyme active-sites, various template-based methods that compare local structures in proteins have been developed to date. In comparing such local sites, a simple measurement, RMSD, has been used so far. This paper introduces new machine learning algorithms that refine the similarity/deviation for comparison of local structures. The similarity/deviation is applied to two types of applications, single template analysis and multiple template analysis. In the single template analysis, a single template is used as a query to search proteins for active sites, whereas a protein structure is examined as a query to discover the possible active-sites using a set of templates in the multiple template analysis. This paper experimentally illustrates that the machine learning algorithms effectively improve the similarity/deviation measurements for both the analyses.

Time-dependent local and average structural evolution of δ-phase 239Pu-Ga alloys

DOE PAGES

Smith, Alice I.; Page, Katharine L.; Siewenie, Joan E.; ...

2016-08-05

Here, plutonium metal is a very unusual element, exhibiting six allotropes at ambient pressure, between room temperature and its melting point, a complicated phase diagram, and a complex electronic structure. Many phases of plutonium metal are unstable with changes in temperature, pressure, chemical additions, or time. This strongly affects structure and properties, and becomes of high importance, particularly when considering effects on structural integrity over long periods of time [1]. This paper presents a time-dependent neutron total scattering study of the local and average structure of naturally aging δ-phase 239Pu-Ga alloys, together with preliminary results on neutron tomography characterization.

Performance Analysis of Local Ensemble Kalman Filter

NASA Astrophysics Data System (ADS)

Tong, Xin T.

2018-03-01

Ensemble Kalman filter (EnKF) is an important data assimilation method for high-dimensional geophysical systems. Efficient implementation of EnKF in practice often involves the localization technique, which updates each component using only information within a local radius. This paper rigorously analyzes the local EnKF (LEnKF) for linear systems and shows that the filter error can be dominated by the ensemble covariance, as long as (1) the sample size exceeds the logarithmic of state dimension and a constant that depends only on the local radius; (2) the forecast covariance matrix admits a stable localized structure. In particular, this indicates that with small system and observation noises, the filter error will be accurate in long time even if the initialization is not. The analysis also reveals an intrinsic inconsistency caused by the localization technique, and a stable localized structure is necessary to control this inconsistency. While this structure is usually taken for granted for the operation of LEnKF, it can also be rigorously proved for linear systems with sparse local observations and weak local interactions. These theoretical results are also validated by numerical implementation of LEnKF on a simple stochastic turbulence in two dynamical regimes.

Online social activity reflects economic status

NASA Astrophysics Data System (ADS)

Liu, Jin-Hu; Wang, Jun; Shao, Junming; Zhou, Tao

2016-09-01

To characterize economic development and diagnose the economic health condition, several popular indices such as gross domestic product (GDP), industrial structure and income growth are widely applied. However, computing these indices based on traditional economic census is usually costly and resources consuming, and more importantly, following a long time delay. In this paper, we analyzed nearly 200 million users' activities for four consecutive years in the largest social network (Sina Microblog) in China, aiming at exploring latent relationships between the online social activities and local economic status. Results indicate that online social activity has a strong correlation with local economic development and industrial structure, and more interestingly, allows revealing the macro-economic structure instantaneously with nearly no cost. Beyond, this work also provides a new venue to identify risky signal in local economic structure.

The Structure of Policy Networks for Injury and Violence Prevention in 15 US Cities

PubMed Central

Jonson-Reid, Melissa; Carothers, Bobbi J.; Fowler, Patrick

2017-01-01

Objectives: Changes in policy can reduce violence and injury; however, little is known about how partnerships among organizations influence policy development, adoption, and implementation. To understand partnerships among organizations working on injury and violence prevention (IVP) policy, we examined IVP policy networks in 15 large US cities. Methods: In summer 2014, we recruited 15 local health departments (LHDs) to participate in the study. They identified an average of 28.9 local partners (SD = 10.2) working on IVP policy. In late 2014, we sent survey questionnaires to 434 organizations, including the 15 LHDs and their local partners, about their partnerships and the importance of each organization to local IVP policy efforts; 319 participated. We used network methods to examine the composition and structure of the policy networks. Results: Each IVP policy network included the LHD and an average of 21.3 (SD = 6.9) local partners. On average, nonprofit organizations constituted 50.7% of networks, followed by government agencies (26.3%), schools and universities (11.8%), coalitions (11.2%), voluntary organizations (9.6%), hospitals (8.5%), foundations (2.2%), and for-profit organizations (0.7%). Government agencies were perceived as important by the highest proportion of partners. Perceived importance was significantly associated with forming partnerships in most networks; odds ratios ranged from 1.07 (95% CI, 1.02-1.13) to 2.35 (95% CI, 1.68-3.28). Organization type was significantly associated with partnership formation in most networks after controlling for an organization’s importance to the network. Conclusions: Several strategies could strengthen local IVP policy networks, including (1) developing connections with partners from sectors that are not well integrated into the networks and (2) encouraging indirect or less formal connections with important but missing partners and partner types. PMID:28426291

The Structure of Policy Networks for Injury and Violence Prevention in 15 US Cities.

PubMed

Harris, Jenine K; Jonson-Reid, Melissa; Carothers, Bobbi J; Fowler, Patrick

Changes in policy can reduce violence and injury; however, little is known about how partnerships among organizations influence policy development, adoption, and implementation. To understand partnerships among organizations working on injury and violence prevention (IVP) policy, we examined IVP policy networks in 15 large US cities. In summer 2014, we recruited 15 local health departments (LHDs) to participate in the study. They identified an average of 28.9 local partners (SD = 10.2) working on IVP policy. In late 2014, we sent survey questionnaires to 434 organizations, including the 15 LHDs and their local partners, about their partnerships and the importance of each organization to local IVP policy efforts; 319 participated. We used network methods to examine the composition and structure of the policy networks. Each IVP policy network included the LHD and an average of 21.3 (SD = 6.9) local partners. On average, nonprofit organizations constituted 50.7% of networks, followed by government agencies (26.3%), schools and universities (11.8%), coalitions (11.2%), voluntary organizations (9.6%), hospitals (8.5%), foundations (2.2%), and for-profit organizations (0.7%). Government agencies were perceived as important by the highest proportion of partners. Perceived importance was significantly associated with forming partnerships in most networks; odds ratios ranged from 1.07 (95% CI, 1.02-1.13) to 2.35 (95% CI, 1.68-3.28). Organization type was significantly associated with partnership formation in most networks after controlling for an organization's importance to the network. Several strategies could strengthen local IVP policy networks, including (1) developing connections with partners from sectors that are not well integrated into the networks and (2) encouraging indirect or less formal connections with important but missing partners and partner types.

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.

Bacterial translation elongation factor EF-Tu interacts and colocalizes with actin-like MreB protein.

PubMed

Defeu Soufo, Hervé Joël; Reimold, Christian; Linne, Uwe; Knust, Tobias; Gescher, Johannes; Graumann, Peter L

2010-02-16

We show that translation initiation factor EF-Tu plays a second important role in cell shape maintenance in the bacterium Bacillus subtilis. EF-Tu localizes in a helical pattern underneath the cell membrane and colocalizes with MreB, an actin-like cytoskeletal element setting up rod cell shape. The localization of MreB and of EF-Tu is interdependent, but in contrast to the dynamic MreB filaments, EF-Tu structures are more static and may serve as tracks for MreB filaments. In agreement with this idea, EF-Tu and MreB interact in vivo and in vitro. Lowering of the EF-Tu levels had a minor effect on translation but a strong effect on cell shape and on the localization of MreB, and blocking of the function of EF-Tu in translation did not interfere with the localization of MreB, showing that, directly or indirectly, EF-Tu affects the cytoskeletal MreB structure and thus serves two important functions in a bacterium.

Probing the structural and dynamical properties of liquid water with models including non-local electron correlation

NASA Astrophysics Data System (ADS)

Del Ben, Mauro; Hutter, Jürg; VandeVondele, Joost

2015-08-01

Water is a ubiquitous liquid that displays a wide range of anomalous properties and has a delicate structure that challenges experiment and simulation alike. The various intermolecular interactions that play an important role, such as repulsion, polarization, hydrogen bonding, and van der Waals interactions, are often difficult to reproduce faithfully in atomistic models. Here, electronic structure theories including all these interactions at equal footing, which requires the inclusion of non-local electron correlation, are used to describe structure and dynamics of bulk liquid water. Isobaric-isothermal (NpT) ensemble simulations based on the Random Phase Approximation (RPA) yield excellent density (0.994 g/ml) and fair radial distribution functions, while various other density functional approximations produce scattered results (0.8-1.2 g/ml). Molecular dynamics simulation in the microcanonical (NVE) ensemble based on Møller-Plesset perturbation theory (MP2) yields dynamical properties in the condensed phase, namely, the infrared spectrum and diffusion constant. At the MP2 and RPA levels of theory, ice is correctly predicted to float on water, resolving one of the anomalies as resulting from a delicate balance between van der Waals and hydrogen bonding interactions. For several properties, obtaining quantitative agreement with experiment requires correction for nuclear quantum effects (NQEs), highlighting their importance, for structure, dynamics, and electronic properties. A computed NQE shift of 0.6 eV for the band gap and absorption spectrum illustrates the latter. Giving access to both structure and dynamics of condensed phase systems, non-local electron correlation will increasingly be used to study systems where weak interactions are of paramount importance.

Predicting residue-wise contact orders in proteins by support vector regression.

PubMed

Song, Jiangning; Burrage, Kevin

2006-10-03

The residue-wise contact order (RWCO) describes the sequence separations between the residues of interest and its contacting residues in a protein sequence. It is a new kind of one-dimensional protein structure that represents the extent of long-range contacts and is considered as a generalization of contact order. Together with secondary structure, accessible surface area, the B factor, and contact number, RWCO provides comprehensive and indispensable important information to reconstructing the protein three-dimensional structure from a set of one-dimensional structural properties. Accurately predicting RWCO values could have many important applications in protein three-dimensional structure prediction and protein folding rate prediction, and give deep insights into protein sequence-structure relationships. We developed a novel approach to predict residue-wise contact order values in proteins based on support vector regression (SVR), starting from primary amino acid sequences. We explored seven different sequence encoding schemes to examine their effects on the prediction performance, including local sequence in the form of PSI-BLAST profiles, local sequence plus amino acid composition, local sequence plus molecular weight, local sequence plus secondary structure predicted by PSIPRED, local sequence plus molecular weight and amino acid composition, local sequence plus molecular weight and predicted secondary structure, and local sequence plus molecular weight, amino acid composition and predicted secondary structure. When using local sequences with multiple sequence alignments in the form of PSI-BLAST profiles, we could predict the RWCO distribution with a Pearson correlation coefficient (CC) between the predicted and observed RWCO values of 0.55, and root mean square error (RMSE) of 0.82, based on a well-defined dataset with 680 protein sequences. Moreover, by incorporating global features such as molecular weight and amino acid composition we could further improve the prediction performance with the CC to 0.57 and an RMSE of 0.79. In addition, combining the predicted secondary structure by PSIPRED was found to significantly improve the prediction performance and could yield the best prediction accuracy with a CC of 0.60 and RMSE of 0.78, which provided at least comparable performance compared with the other existing methods. The SVR method shows a prediction performance competitive with or at least comparable to the previously developed linear regression-based methods for predicting RWCO values. In contrast to support vector classification (SVC), SVR is very good at estimating the raw value profiles of the samples. The successful application of the SVR approach in this study reinforces the fact that support vector regression is a powerful tool in extracting the protein sequence-structure relationship and in estimating the protein structural profiles from amino acid sequences.

PBxplore: a tool to analyze local protein structure and deformability with Protein Blocks

PubMed Central

Craveur, Pierrick; Joseph, Agnel Praveen; Jallu, Vincent

2017-01-01

This paper describes the development and application of a suite of tools, called PBxplore, to analyze the dynamics and deformability of protein structures using Protein Blocks (PBs). Proteins are highly dynamic macromolecules, and a classical way to analyze their inherent flexibility is to perform molecular dynamics simulations. The advantage of using small structural prototypes such as PBs is to give a good approximation of the local structure of the protein backbone. More importantly, by reducing the conformational complexity of protein structures, PBs allow analysis of local protein deformability which cannot be done with other methods and had been used efficiently in different applications. PBxplore is able to process large amounts of data such as those produced by molecular dynamics simulations. It produces frequencies, entropy and information logo outputs as text and graphics. PBxplore is available at https://github.com/pierrepo/PBxplore and is released under the open-source MIT license. PMID:29177113

Recognition of Local DNA Structures by p53 Protein

PubMed Central

Brázda, Václav; Coufal, Jan

2017-01-01

p53 plays critical roles in regulating cell cycle, apoptosis, senescence and metabolism and is commonly mutated in human cancer. These roles are achieved by interaction with other proteins, but particularly by interaction with DNA. As a transcription factor, p53 is well known to bind consensus target sequences in linear B-DNA. Recent findings indicate that p53 binds with higher affinity to target sequences that form cruciform DNA structure. Moreover, p53 binds very tightly to non-B DNA structures and local DNA structures are increasingly recognized to influence the activity of wild-type and mutant p53. Apart from cruciform structures, p53 binds to quadruplex DNA, triplex DNA, DNA loops, bulged DNA and hemicatenane DNA. In this review, we describe local DNA structures and summarize information about interactions of p53 with these structural DNA motifs. These recent data provide important insights into the complexity of the p53 pathway and the functional consequences of wild-type and mutant p53 activation in normal and tumor cells. PMID:28208646

HARMONY: a server for the assessment of protein structures

PubMed Central

Pugalenthi, G.; Shameer, K.; Srinivasan, N.; Sowdhamini, R.

2006-01-01

Protein structure validation is an important step in computational modeling and structure determination. Stereochemical assessment of protein structures examine internal parameters such as bond lengths and Ramachandran (φ,ψ) angles. Gross structure prediction methods such as inverse folding procedure and structure determination especially at low resolution can sometimes give rise to models that are incorrect due to assignment of misfolds or mistracing of electron density maps. Such errors are not reflected as strain in internal parameters. HARMONY is a procedure that examines the compatibility between the sequence and the structure of a protein by assigning scores to individual residues and their amino acid exchange patterns after considering their local environments. Local environments are described by the backbone conformation, solvent accessibility and hydrogen bonding patterns. We are now providing HARMONY through a web server such that users can submit their protein structure files and, if required, the alignment of homologous sequences. Scores are mapped on the structure for subsequent examination that is useful to also recognize regions of possible local errors in protein structures. HARMONY server is located at PMID:16844999

Schoolyard Microclimate

ERIC Educational Resources Information Center

Fontaine, Joseph J.; Stier, Samuel C.; Maggio, Melissa L.; Decker, Karie L.

2007-01-01

Students can gain an appreciation for the structure and function of local environments by studying the potential impacts of small changes in local microclimate on plant distribution. The concept of microclimate is easy for students to comprehend, simple to measure, exists in all schoolyards, and has important and tangible ecological implications.…

Decentralized control experiments on NASA's flexible grid

NASA Technical Reports Server (NTRS)

Ozguner, U.; Yurkowich, S.; Martin, J., III; Al-Abbass, F.

1986-01-01

Methods arising from the area of decentralized control are emerging for analysis and control synthesis for large flexible structures. In this paper the control strategy involves a decentralized model reference adaptive approach using a variable structure control. Local models are formulated based on desired damping and response time in a model-following scheme for various modal configurations. Variable structure controllers are then designed employing co-located angular rate and position feedback. In this scheme local control forces the system to move on a local sliding mode in some local error space. An important feature of this approach is that the local subsystem is made insensitive to dynamical interactions with other subsystems once the sliding surface is reached. Experiments based on the above have been performed for NASA's flexible grid experimental apparatus. The grid is designed to admit appreciable low-frequency structural dynamics, and allows for implementation of distributed computing components, inertial sensors, and actuation devices. A finite-element analysis of the grid provides the model for control system design and simulation; results of several simulations are reported on here, and a discussion of application experiments on the apparatus is presented.

The role of dispersal mode and habitat specialization for metacommunity structure of shallow beach invertebrates.

PubMed

Rodil, Iván F; Lucena-Moya, Paloma; Jokinen, Henri; Ollus, Victoria; Wennhage, Håkan; Villnäs, Anna; Norkko, Alf

2017-01-01

Metacommunity ecology recognizes the interplay between local and regional patterns in contributing to spatial variation in community structure. In aquatic systems, the relative importance of such patterns depends mainly on the potential connectivity of the specific system. Thus, connectivity is expected to increase in relation to the degree of water movement, and to depend on the specific traits of the study organism. We examined the role of environmental and spatial factors in structuring benthic communities from a highly connected shallow beach network using a metacommunity approach. Both factors contributed to a varying degree to the structure of the local communities suggesting that environmental filters and dispersal-related mechanisms played key roles in determining abundance patterns. We categorized benthic taxa according to their dispersal mode (passive vs. active) and habitat specialization (generalist vs. specialist) to understand the relative importance of environment and dispersal related processes for shallow beach metacommunities. Passive dispersers were predicted by a combination of environmental and spatial factors, whereas active dispersers were not spatially structured and responded only to local environmental factors. Generalists were predicted primarily by spatial factors, while specialists were only predicted by local environmental factors. The results suggest that the role of the spatial component in metacommunity organization is greater in open coastal waters, such as shallow beaches, compared to less-connected environmentally controlled aquatic systems. Our results also reveal a strong environmental role in structuring the benthic metacommunity of shallow beaches. Specifically, we highlight the sensitivity of shallow beach macrofauna to environmental factors related to eutrophication proxies.

The role of dispersal mode and habitat specialization for metacommunity structure of shallow beach invertebrates

PubMed Central

Lucena-Moya, Paloma; Jokinen, Henri; Ollus, Victoria; Wennhage, Håkan; Villnäs, Anna; Norkko, Alf

2017-01-01

Metacommunity ecology recognizes the interplay between local and regional patterns in contributing to spatial variation in community structure. In aquatic systems, the relative importance of such patterns depends mainly on the potential connectivity of the specific system. Thus, connectivity is expected to increase in relation to the degree of water movement, and to depend on the specific traits of the study organism. We examined the role of environmental and spatial factors in structuring benthic communities from a highly connected shallow beach network using a metacommunity approach. Both factors contributed to a varying degree to the structure of the local communities suggesting that environmental filters and dispersal-related mechanisms played key roles in determining abundance patterns. We categorized benthic taxa according to their dispersal mode (passive vs. active) and habitat specialization (generalist vs. specialist) to understand the relative importance of environment and dispersal related processes for shallow beach metacommunities. Passive dispersers were predicted by a combination of environmental and spatial factors, whereas active dispersers were not spatially structured and responded only to local environmental factors. Generalists were predicted primarily by spatial factors, while specialists were only predicted by local environmental factors. The results suggest that the role of the spatial component in metacommunity organization is greater in open coastal waters, such as shallow beaches, compared to less-connected environmentally controlled aquatic systems. Our results also reveal a strong environmental role in structuring the benthic metacommunity of shallow beaches. Specifically, we highlight the sensitivity of shallow beach macrofauna to environmental factors related to eutrophication proxies. PMID:28196112

Introducing Fe 2+ into Nickel-Iron Layered Double Hydroxide: Local Structure Modulated Water Oxidation Activity

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

Cai, Zhao; Zhou, Daojin; Wang, Maoyu

Exploring materials with regulated local structures and understanding how the atomic motifs govern the reactivity and durability of catalysts are a critical challenge for designing advanced catalysts. Here we report the tuning of the local atomic structure of nickel–iron layered double hydroxides (NiFe–LDHs) by partially substituting Ni 2+ with Fe 2+ to introduce Fe–O–Fe moieties. These Fe 2+–containing NiFe–LDHs exhibit enhanced oxygen evolution reaction (OER) activity with an ultralow overpotential of 195 mV at the current density of 10 mA/cm 2, which is among the best OER catalytic performance reported to date. In–situ X–ray absorption, Raman, and electrochemical analysis jointlymore » reveal that the Fe–O–Fe motifs could stabilize high–valent metal sites at low overpotentials, thereby enhancing the OER activity. Lastly, these results reveal the importance of tuning the local atomic structure for designing high efficiency electrocatalysts.« less

Introducing Fe2+ into Nickel-Iron Layered Double Hydroxide: Local Structure Modulated Water Oxidation Activity.

PubMed

Cai, Zhao; Zhou, Daojin; Wang, Maoyu; Bak, Seongmin; Wu, Yueshen; Wu, Zishan; Tian, Yang; Xiong, Xuya; Li, Yaping; Liu, Wen; Siahrostami, Samira; Kuang, Yun; Yang, Xiao-Qing; Duan, Haohong; Feng, Zhenxing; Wang, Hailiang; Sun, Xiaoming

2018-06-11

Exploring materials with regulated local structures and understanding how the atomic motifs govern the reactivity and durability of catalysts are a critical challenge for designing advanced catalysts. Here we report the tuning of the local atomic structure of nickel-iron layered double hydroxides (NiFe-LDHs) by partially substituting Ni2+ with Fe2+ to introduce Fe-O-Fe moieties. These Fe2+-containing NiFe-LDHs exhibit enhanced oxygen evolution reaction (OER) activity with an ultralow overpotential of 195 mV at the current density of 10 mA/cm2, which is among the best OER catalytic performance reported to date. In-situ X-ray absorption, Raman, and electrochemical analysis jointly reveal that the Fe-O-Fe motifs could stabilize high-valent metal sites at low overpotentials, thereby enhancing the OER activity. These results reveal the importance of tuning the local atomic structure for designing high efficiency electrocatalysts. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Introducing Fe 2+ into Nickel-Iron Layered Double Hydroxide: Local Structure Modulated Water Oxidation Activity

DOE PAGES

Cai, Zhao; Zhou, Daojin; Wang, Maoyu; ...

2018-06-11

Exploring materials with regulated local structures and understanding how the atomic motifs govern the reactivity and durability of catalysts are a critical challenge for designing advanced catalysts. Here we report the tuning of the local atomic structure of nickel–iron layered double hydroxides (NiFe–LDHs) by partially substituting Ni 2+ with Fe 2+ to introduce Fe–O–Fe moieties. These Fe 2+–containing NiFe–LDHs exhibit enhanced oxygen evolution reaction (OER) activity with an ultralow overpotential of 195 mV at the current density of 10 mA/cm 2, which is among the best OER catalytic performance reported to date. In–situ X–ray absorption, Raman, and electrochemical analysis jointlymore » reveal that the Fe–O–Fe motifs could stabilize high–valent metal sites at low overpotentials, thereby enhancing the OER activity. Lastly, these results reveal the importance of tuning the local atomic structure for designing high efficiency electrocatalysts.« less

Intracellular Localization and Trafficking of Serine Proteinase AhSub and Cysteine Proteinase AhCP of Acanthamoeba healyi

PubMed Central

Moon, E.-K.; Lee, S.-T.; Chung, D.-I.; Kong, H.-H.

2006-01-01

Proteinases have been proposed to play important roles in pathogenesis and various biologic actions in Acanthamoeba. Although genetic characteristics of several proteases of Acanthamoeba have been reported, the intracellular localization and trafficking of these enzymes has yet to be studied. In the present study, we analyzed the intracellular localization and trafficking of two proteinases, AhSub and AhCP, of Acanthamoeba healyi by transient transfection. Full-length AhSub-enhanced green fluorescent protein (EGFP) fusion protein was found in intracellular vesicle-like structures of transfected amoebae. Time-lapse photographs confirmed the secretion of the fluorescent material of the vesicle toward the extracellular space. The mutated AhSub, of which the pre or prepro region was deleted, was found to localize diffusely throughout the cytoplasm of the amoeba rather than concentrated in the secretory vesicle. Transfection of the construct containing the pre region only showed the same localization and trafficking of the full-length AhSub. A cysteine proteinase AhCP-EGFP fusion protein showed similar localization in the vesicle-like structure in the amoeba. However, using Lyso Tracker analysis, these vesicular structures of AhCP were confirmed to be lysosomes rather than secretory vesicles. The AhCP construct with a deletion of the prepro region showed a dispersed distribution of fluorescence in the cytoplasm of the cells. These results indicated that AhSub and AhCP would play different roles in Acanthameoba biology and that the pre region of AhSub and pro region of AhCP are important for proper intracellular localization and trafficking of each proteinase. PMID:16400174

Influence of local demography on asymptotic and transient dynamics of a yellow-bellied marmot metapopulation.

PubMed

Ozgul, Arpat; Oli, Madan K; Armitage, Kenneth B; Blumstein, Daniel T; Van Vuren, Dirk H

2009-04-01

Despite recent advances in biodemography and metapopulation ecology, we still have limited understanding of how local demographic parameters influence short- and long-term metapopulation dynamics. We used long-term data from 17 local populations, along with the recently developed methods of matrix metapopulation modeling and transient sensitivity analysis, to investigate the influence of local demography on long-term (asymptotic) versus short-term (transient) dynamics of a yellow-bellied marmot metapopulation in Colorado. Both long- and short-term dynamics depended primarily on a few colony sites and were highly sensitive to changes in demography at these sites, particularly in survival of reproductive adult females. Interestingly, the relative importance of sites differed between long- and short-term dynamics; the spatial structure and local population sizes, while insignificant for asymptotic dynamics, were influential on transient dynamics. However, considering the spatial structure was uninformative about the relative influence of local demography on metapopulation dynamics. The vital rates that were the most influential on local dynamics were also the most influential on both long- and short-term metapopulation dynamics. Our results show that an explicit consideration of local demography is essential for a complete understanding of the dynamics and persistence of spatially structured populations.

Lack of congruence in species diversity indices and community structures of planktonic groups based on local environmental factors.

PubMed

Doi, Hideyuki; Chang, Kwang-Hyeon; Nishibe, Yuichiro; Imai, Hiroyuki; Nakano, Shin-ichi

2013-01-01

The importance of analyzing the determinants of biodiversity and community composition by using multiple trophic levels is well recognized; however, relevant data are lacking. In the present study, we investigated variations in species diversity indices and community structures of the plankton taxonomic groups-zooplankton, rotifers, ciliates, and phytoplankton-under a range of local environmental factors in pond ecosystems. For each planktonic group, we estimated the species diversity index by using linear models and analyzed the community structure by using canonical correspondence analysis. We showed that the species diversity indices and community structures varied among the planktonic groups and according to local environmental factors. The observed lack of congruence among the planktonic groups may have been caused by niche competition between groups with similar trophic guilds or by weak trophic interactions. Our findings highlight the difficulty of predicting total biodiversity within a system, based upon a single taxonomic group. Thus, to conserve the biodiversity of an ecosystem, it is crucial to consider variations in species diversity indices and community structures of different taxonomic groups, under a range of local conditions.

Multiple-wavelength neutron holography with pulsed neutrons

PubMed Central

Hayashi, Kouichi; Ohoyama, Kenji; Happo, Naohisa; Matsushita, Tomohiro; Hosokawa, Shinya; Harada, Masahide; Inamura, Yasuhiro; Nitani, Hiroaki; Shishido, Toetsu; Yubuta, Kunio

2017-01-01

Local structures around impurities in solids provide important information for understanding the mechanisms of material functions, because most of them are controlled by dopants. For this purpose, the x-ray absorption fine structure method, which provides radial distribution functions around specific elements, is most widely used. However, a similar method using neutron techniques has not yet been developed. If one can establish a method of local structural analysis with neutrons, then a new frontier of materials science can be explored owing to the specific nature of neutron scattering—that is, its high sensitivity to light elements and magnetic moments. Multiple-wavelength neutron holography using the time-of-flight technique with pulsed neutrons has great potential to realize this. We demonstrated multiple-wavelength neutron holography using a Eu-doped CaF2 single crystal and obtained a clear three-dimensional atomic image around trivalent Eu substituted for divalent Ca, revealing an interesting feature of the local structure that allows it to maintain charge neutrality. The new holography technique is expected to provide new information on local structures using the neutron technique. PMID:28835917

Multiple-wavelength neutron holography with pulsed neutrons.

PubMed

Hayashi, Kouichi; Ohoyama, Kenji; Happo, Naohisa; Matsushita, Tomohiro; Hosokawa, Shinya; Harada, Masahide; Inamura, Yasuhiro; Nitani, Hiroaki; Shishido, Toetsu; Yubuta, Kunio

2017-08-01

Local structures around impurities in solids provide important information for understanding the mechanisms of material functions, because most of them are controlled by dopants. For this purpose, the x-ray absorption fine structure method, which provides radial distribution functions around specific elements, is most widely used. However, a similar method using neutron techniques has not yet been developed. If one can establish a method of local structural analysis with neutrons, then a new frontier of materials science can be explored owing to the specific nature of neutron scattering-that is, its high sensitivity to light elements and magnetic moments. Multiple-wavelength neutron holography using the time-of-flight technique with pulsed neutrons has great potential to realize this. We demonstrated multiple-wavelength neutron holography using a Eu-doped CaF 2 single crystal and obtained a clear three-dimensional atomic image around trivalent Eu substituted for divalent Ca, revealing an interesting feature of the local structure that allows it to maintain charge neutrality. The new holography technique is expected to provide new information on local structures using the neutron technique.

Molecular Epidemiology of P. vivax in Iran: High Diversity and Complex Sub-Structure Using Neutral Markers, but No Evidence of Y976F Mutation at pvmdr1.

PubMed

Hamedi, Yaghoob; Sharifi-Sarasiabi, Khojasteh; Dehghan, Farzaneh; Safari, Reza; To, Sheren; Handayuni, Irene; Trimarsanto, Hidayat; Price, Ric N; Auburn, Sarah

2016-01-01

Malaria remains endemic at low levels in the south-eastern provinces of Iran bordering Afghanistan and Pakistan, with the majority of cases attributable to P. vivax. The national guidelines recommend chloroquine (CQ) as blood-stage treatment for uncomplicated P. vivax, but the large influx of imported cases enhances the risk of introducing CQ resistance (CQR). The genetic diversity at pvmdr1, a putative modulator of CQR, and across nine putatively neutral short tandem repeat (STR) markers were assessed in P. vivax clinical isolates collected between April 2007 and January 2013 in Hormozgan Province, south-eastern Iran. One hundred blood samples were collected from patients with microscopy-confirmed P. vivax enrolled at one of five district clinics. In total 73 (73%) were autochthonous cases, 23 (23%) imported cases from Afghanistan or Pakistan, and 4 (4%) with unknown origin. 97% (97/100) isolates carried the F1076L mutation, but none carried the Y976F mutation. STR genotyping was successful in 71 (71%) isolates, including 57(57%) autochthonous and 11 (11%) imported cases. Analysis of population structure revealed 2 major sub-populations, K1 and K2, with further sub-structure within K2. The K1 sub-population had markedly lower diversity than K2 (HE = 0.06 vs HE = 0.82) suggesting that the sub-populations were sustained by distinct reservoirs with differing transmission dynamics, possibly reflecting local versus imported/introduced populations. No notable separation was observed between the local and imported cases although the sample size was limited. The contrasting low versus high diversity in the two sub-populations (K1 and K2) infers that a combination of local transmission and cross-border malaria from higher transmission regions shape the genetic make-up of the P. vivax population in south-eastern Iran. There was no molecular evidence of CQR amongst the local or imported cases, but ongoing clinical surveillance is warranted.

Structural model to evaluate the effect of participation and satisfaction on ecotourism sustainability

NASA Astrophysics Data System (ADS)

Kencana, Eka N.; Manutami, T.

2017-10-01

This paper is directed to study the effect of local community participation and visitors’ satisfaction on ecotourism sustainability at Badung regency of Bali province, Indonesia. Two important aspects regarding ecotourism sustainability had been studied, i.e. (a) economic benefits for local people and (b) tourists’ satisfaction. Applying variance-based structural equation modeling, data were collected in July 2015 from local community leaders of Kiadan Village at Badung regency and tourists whom visited this village, were analysed. Four latent variables, namely (a) community participation, (b) economic benefits, (c) tourists’ satisfaction, and (d) ecotourism sustainability, were used to build structural model. The results showed sustainability of Kiadan’s ecotourism was significantly affected by local community participation and visitors’ satisfaction although community participation’s effect slightly greater than tourists’ satisfaction with path values for participation and satisfaction as much as 0.651 and 0.627, respectively.

Local and global structural drivers for the photoactivation of the orange carotenoid protein

DOE PAGES

Gupta, Sayan; Guttman, Miklos; Leverenz, Ryan L.; ...

2015-09-18

Here, photoprotective mechanisms are of fundamental importance for the survival of photosynthetic organisms. In cyanobacteria, the orange carotenoid protein (OCP), when activated by intense blue light, binds to the light-harvesting antenna and triggers the dissipation of excess captured light energy. Using a combination of small angle X-ray scattering (SAXS), X-ray hydroxyl radical footprinting, circular dichroism, and H/D exchange mass spectrometry, we identified both the local and global structural changes in the OCP upon photoactivation. SAXS and H/D exchange data showed that global tertiary structural changes, including complete domain dissociation, occur upon photoactivation, but with alteration of secondary structure confined tomore » only the N terminus of the OCP. Microsecond radiolytic labeling identified rearrangement of the H-bonding network associated with conserved residues and structural water molecules. Collectively, these data provide experimental evidence for an ensemble of local and global structural changes, upon activation of the OCP, that are essential for photoprotection.« less

Local and global structural drivers for the photoactivation of the orange carotenoid protein

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

Gupta, Sayan; Guttman, Miklos; Leverenz, Ryan L.

Here, photoprotective mechanisms are of fundamental importance for the survival of photosynthetic organisms. In cyanobacteria, the orange carotenoid protein (OCP), when activated by intense blue light, binds to the light-harvesting antenna and triggers the dissipation of excess captured light energy. Using a combination of small angle X-ray scattering (SAXS), X-ray hydroxyl radical footprinting, circular dichroism, and H/D exchange mass spectrometry, we identified both the local and global structural changes in the OCP upon photoactivation. SAXS and H/D exchange data showed that global tertiary structural changes, including complete domain dissociation, occur upon photoactivation, but with alteration of secondary structure confined tomore » only the N terminus of the OCP. Microsecond radiolytic labeling identified rearrangement of the H-bonding network associated with conserved residues and structural water molecules. Collectively, these data provide experimental evidence for an ensemble of local and global structural changes, upon activation of the OCP, that are essential for photoprotection.« less

Evaluating different methods used in ethnobotanical and ecological studies to record plant biodiversity

PubMed Central

2014-01-01

Background This study compares the efficiency of identifying the plants in an area of semi-arid Northeast Brazil by methods that a) access the local knowledge used in ethnobotanical studies using semi-structured interviews conducted within the entire community, an inventory interview conducted with two participants using the previously collected vegetation inventory, and a participatory workshop presenting exsiccates and photographs to 32 people and b) inventory the vegetation (phytosociology) in locations with different histories of disturbance using rectangular plots and quadrant points. Methods The proportion of species identified using each method was then compared with Cochran’s Q test. We calculated the use value (UV) of each species using semi-structured interviews; this quantitative index was correlated against values of the vegetation’s structural importance obtained from the sample plot method and point-centered quarter method applied in two areas with different historical usage. The analysis sought to correlate the relative importance of plants to the local community (use value - UV) with the ecological importance of the plants in the vegetation structure (importance value - IV; relative density - RD) by using different sampling methods to analyze the two areas. Results With regard to the methods used for accessing the local knowledge, a difference was observed among the ethnobotanical methods of surveying species (Q = 13.37, df = 2, p = 0.0013): 44 species were identified in the inventory interview, 38 in the participatory workshop and 33 in the semi-structured interviews with the community. There was either no correlation between the UV, relative density (RD) and importance value (IV) of some species, or this correlation was negative. Conclusion It was concluded that the inventory interview was the most efficient method for recording species and their uses, as it allowed more plants to be identified in their original environment. To optimize researchers’ time in future studies, the use of the point-centered quarter method rather than the sample plot method is recommended. PMID:24916833

Determinants of community structure of zooplankton in heavily polluted river ecosystems

NASA Astrophysics Data System (ADS)

Xiong, Wei; Li, Jie; Chen, Yiyong; Shan, Baoqing; Wang, Weimin; Zhan, Aibin

2016-02-01

River ecosystems are among the most affected habitats globally by human activities, such as the release of chemical pollutants. However, it remains largely unknown how and to what extent many communities such as zooplankton are affected by these environmental stressors in river ecosystems. Here, we aim to determine major factors responsible for shaping community structure of zooplankton in heavily polluted river ecosystems. Specially, we use rotifers in the Haihe River Basin (HRB) in North China as a case study to test the hypothesis that species sorting (i.e. species are “filtered” by environmental factors and occur at environmental suitable sites) plays a key role in determining community structure at the basin level. Based on an analysis of 94 sites across the plain region of HRB, we found evidence that both local and regional factors could affect rotifer community structure. Interestingly, further analyses indicated that local factors played a more important role in determining community structure. Thus, our results support the species sorting hypothesis in highly polluted rivers, suggesting that local environmental constraints, such as environmental pollution caused by human activities, can be stronger than dispersal limitation caused by regional factors to shape local community structure of zooplankton at the basin level.

Localization of ultra-low frequency waves in multi-ion plasmas of the planetary magnetosphere

DOE PAGES

Kim, Eun -Hwa; Johnson, Jay R.; Lee, Dong -Hun

2015-01-01

By adopting a 2D time-dependent wave code, we investigate how mode-converted waves at the Ion-Ion Hybrid (IIH) resonance and compressional waves propagate in 2D density structures with a wide range of field-aligned wavenumbers to background magnetic fields. The simulation results show that the mode-converted waves have continuous bands across the field line consistent with previous numerical studies. These waves also have harmonic structures in frequency domain and are localized in the field-aligned heavy ion density well. Lastly, our results thus emphasize the importance of a field-aligned heavy ion density structure for ultra-low frequency wave propagation, and suggest that IIH wavesmore » can be localized in different locations along the field line.« less

The Sensitivity of Large-Eddy Simulation to Local and Nonlocal Drag Coefficients at the Lower Boundary

NASA Technical Reports Server (NTRS)

Schowalter, D. G.; DeCroix, D. S.; Lin, Y. L.; Arya, S. P.; Kaplan, M. L.

1996-01-01

It was found that the homogeneity of the surface drag coefficient plays an important role in the large scale structure of turbulence in large-eddy simulation of the convective atmospheric boundary layer. Particularly when a ground surface temperature was specified, large horizontal anisotropies occurred when the drag coefficient depended upon local velocities and heat fluxes. This was due to the formation of streamwise roll structures in the boundary layer. In reality, these structures have been found to form when shear is approximately balanced by buoyancy. The present cases, however, were highly convective. The formation was caused by particularly low values of the drag coefficient at the entrance to thermal plume structures.

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.

Development of pair distribution function analysis

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

Vondreele, R.; Billinge, S.; Kwei, G.

1996-09-01

This is the final report of a 3-year LDRD project at LANL. It has become more and more evident that structural coherence in the CuO{sub 2} planes of high-{Tc} superconducting materials over some intermediate length scale (nm range) is important to superconductivity. In recent years, the pair distribution function (PDF) analysis of powder diffraction data has been developed for extracting structural information on these length scales. This project sought to expand and develop this technique, use it to analyze neutron powder diffraction data, and apply it to problems. In particular, interest is in the area of high-{Tc} superconductors, although wemore » planned to extend the study to the closely related perovskite ferroelectric materials andother materials where the local structure affects the properties where detailed knowledge of the local and intermediate range structure is important. In addition, we planned to carry out single crystal experiments to look for diffuse scattering. This information augments the information from the PDF.« less

Cytoplasmic and nuclear localizations are important for the hypersensitive response conferred by maize autoactive Rp1-D21 protein

USDA-ARS?s Scientific Manuscript database

Disease resistance (R-) genes have been isolated from many plant species. Most encode nucleotide binding leucine-rich-repeat (NLR) proteins that trigger a rapid localized programmed cell death termed the hypersensitive response (HR) upon pathogen recognition. Despite their structural similarities, d...

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.

Local atomic and electronic structures in ferromagnetic topological insulator Cr-doped (BixSb1-x) 2Te3 studied by XAFS and ab initio calculations

NASA Astrophysics Data System (ADS)

Liu, Zhen; Wei, Xinyuan; Wang, Jiajia; Pan, Hong; Ji, Fuhao; Ye, Mao; Yang, Zhongqin; Qiao, Shan

2015-09-01

The local atomic and electronic structures around the dopants in Cr-doped (BixSb1 -x )2Te3 are studied by x-ray absorption fine structure (XAFS) measurements and first-principles calculations. Both Cr and Bi are confirmed substituting Sb sites (CrSb and BiSb). The six nearest Te atoms around Cr move towards Cr and shorten the Cr-Te bond lengths to 2.76 Å and 2.77 Å for x =0.1 and x =0.2 , respectively. Importantly, we reveal the hybridization between the Sb/Te p states and Cr d states by the presence of a pre-edge peak at Cr K -absorption edge, which is also supported by our ab initio calculations. These findings provide important clues to understand the mechanism of ferromagnetic order in this system with quantum anomalous Hall effect.

Structural Evolution of Supercritical CO2 across the Frenkel Line.

PubMed

Bolmatov, Dima; Zav'yalov, D; Gao, M; Zhernenkov, Mikhail

2014-08-21

Here, we study structural properties of the supercritical carbon dioxide and discover the existence of persistent medium-range order correlations, which make supercritical carbon dioxide nonuniform and heterogeneous on an intermediate length scale. We report on the CO2 heterogeneity shell structure where, in the first shell, both carbon and oxygen atoms experience gas-like-type interactions with short-range order correlations while within the second shell, oxygen atoms essentially exhibit a liquid-like type of interactions due to localization of transverse-like phonon packets. Importantly, we highlight a catalytic role of atoms inside of the nearest-neighbor heterogeneity shell in providing a mechanism for diffusion and proving the existence of an additional thermodynamic boundary in the supercritical carbon dioxide on an intermediate length scale. Finally, we discuss important implications for answering the intriguing question whether Venus may have had CO2 oceans and urge for an experimental detection of this persistent local-order heterogeneity.

The relative importance of regional, local, and evolutionary factors structuring cryptobenthic coral-reef assemblages

NASA Astrophysics Data System (ADS)

Ahmadia, Gabby N.; Tornabene, Luke; Smith, David J.; Pezold, Frank L.

2018-03-01

Factors shaping coral-reef fish species assemblages can operate over a wide range of spatial scales (local versus regional) and across both proximate and evolutionary time. Niche theory and neutral theory provide frameworks for testing assumptions and generating insights about the importance of local versus regional processes. Niche theory postulates that species assemblages are an outcome of evolutionary processes at regional scales followed by local-scale interactions, whereas neutral theory presumes that species assemblages are formed by largely random processes drawing from regional species pools. Indo-Pacific cryptobenthic coral-reef fishes are highly evolved, ecologically diverse, temporally responsive, and situated on a natural longitudinal diversity gradient, making them an ideal group for testing predictions from niche and neutral theories and effects of regional and local processes on species assemblages. Using a combination of ecological metrics (fish density, diversity, assemblage composition) and evolutionary analyses (testing for phylogenetic niche conservatism), we demonstrate that the structure of cryptobenthic fish assemblages can be explained by a mixture of regional factors, such as the size of regional species pools and broad-scale barriers to gene flow/drivers of speciation, coupled with local-scale factors, such as the relative abundance of specific microhabitat types. Furthermore, species of cryptobenthic fishes have distinct microhabitat associations that drive significant differences in assemblage community structure between microhabitat types, and these distinct microhabitat associations are phylogenetically conserved over evolutionary timescales. The implied differential fitness of cryptobenthic fishes across varied microhabitats and the conserved nature of their ecology are consistent with predictions from niche theory. Neutral theory predictions may still hold true for early life-history stages, where stochastic factors may be more important in explaining recruitment. Overall, through integration of ecological and evolutionary techniques, and using multiple spatial scales, our study offers a unique perspective on factors determining coral-reef fish assemblages.

The determinants of bond angle variability in protein/peptide backbones: A comprehensive statistical/quantum mechanics analysis.

PubMed

Improta, Roberto; Vitagliano, Luigi; Esposito, Luciana

2015-11-01

The elucidation of the mutual influence between peptide bond geometry and local conformation has important implications for protein structure refinement, validation, and prediction. To gain insights into the structural determinants and the energetic contributions associated with protein/peptide backbone plasticity, we here report an extensive analysis of the variability of the peptide bond angles by combining statistical analyses of protein structures and quantum mechanics calculations on small model peptide systems. Our analyses demonstrate that all the backbone bond angles strongly depend on the peptide conformation and unveil the existence of regular trends as function of ψ and/or φ. The excellent agreement of the quantum mechanics calculations with the statistical surveys of protein structures validates the computational scheme here employed and demonstrates that the valence geometry of protein/peptide backbone is primarily dictated by local interactions. Notably, for the first time we show that the position of the H(α) hydrogen atom, which is an important parameter in NMR structural studies, is also dependent on the local conformation. Most of the trends observed may be satisfactorily explained by invoking steric repulsive interactions; in some specific cases the valence bond variability is also influenced by hydrogen-bond like interactions. Moreover, we can provide a reliable estimate of the energies involved in the interplay between geometry and conformations. © 2015 Wiley Periodicals, Inc.

Distributed digital signal processors for multi-body flexible structures

NASA Technical Reports Server (NTRS)

Lee, Gordon K. F.

1992-01-01

Multi-body flexible structures, such as those currently under investigation in spacecraft design, are large scale (high-order) dimensional systems. Controlling and filtering such structures is a computationally complex problem. This is particularly important when many sensors and actuators are located along the structure and need to be processed in real time. This report summarizes research activity focused on solving the signal processing (that is, information processing) issues of multi-body structures. A distributed architecture is developed in which single loop processors are employed for local filtering and control. By implementing such a philosophy with an embedded controller configuration, a supervising controller may be used to process global data and make global decisions as the local devices are processing local information. A hardware testbed, a position controller system for a servo motor, is employed to illustrate the capabilities of the embedded controller structure. Several filtering and control structures which can be modeled as rational functions can be implemented on the system developed in this research effort. Thus the results of the study provide a support tool for many Control/Structure Interaction (CSI) NASA testbeds such as the Evolutionary model and the nine-bay truss structure.

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

Cheng, Yongqiang; Balachandran, Janakiraman; Bi, Zhonghe

The local structure around the mobile ions influences their dynamics. The knowledge about the relationship between these properties is of fundamental importance and may lead the way for development of improved solid state ionic conductors. Here, we use inelastic neutron scattering and ab initio modeling to study a representative proton conductor, La 0.8Ba 1.2GaO 3.9, where different local structures are possible for the same stoichiometry. The intrinsic correlations between the local bonding environment and the dynamical behavior of protons are presented. In particular, we identify how the local Ba/La concentration affects the proton vibrational frequencies, hydrogen bond strength, O–H rotationsmore » and in turn long-range proton mobility. Furthermore, possible mechanism for proton transport, through the inter-tetrahedral bond switching, O–H rotations and tetrahedral reorientation is anticipated.« less

Large-scale distribution patterns of mangrove nematodes: A global meta-analysis.

PubMed

Brustolin, Marco C; Nagelkerken, Ivan; Fonseca, Gustavo

2018-05-01

Mangroves harbor diverse invertebrate communities, suggesting that macroecological distribution patterns of habitat-forming foundation species drive the associated faunal distribution. Whether these are driven by mangrove biogeography is still ambiguous. For small-bodied taxa, local factors and landscape metrics might be as important as macroecology. We performed a meta-analysis to address the following questions: (1) can richness of mangrove trees explain macroecological patterns of nematode richness? and (2) do local landscape attributes have equal or higher importance than biogeography in structuring nematode richness? Mangrove areas of Caribbean-Southwest Atlantic, Western Indian, Central Indo-Pacific, and Southwest Pacific biogeographic regions. We used random-effects meta-analyses based on natural logarithm of the response ratio (lnRR) to assess the importance of macroecology (i.e., biogeographic regions, latitude, longitude), local factors (i.e., aboveground mangrove biomass and tree richness), and landscape metrics (forest area and shape) in structuring nematode richness from 34 mangroves sites around the world. Latitude, mangrove forest area, and forest shape index explained 19% of the heterogeneity across studies. Richness was higher at low latitudes, closer to the equator. At local scales, richness increased slightly with landscape complexity and decreased with forest shape index. Our results contrast with biogeographic diversity patterns of mangrove-associated taxa. Global-scale nematode diversity may have evolved independently of mangrove tree richness, and diversity of small-bodied metazoans is probably more closely driven by latitude and associated climates, rather than local, landscape, or global biogeographic patterns.

Entanglement classes of symmetric Werner states

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

Lyons, David W.; Walck, Scott N.

2011-10-15

The symmetric Werner states for n qubits, important in the study of quantum nonlocality and useful for applications in quantum information, have a surprisingly simple and elegant structure in terms of tensor products of Pauli matrices. Further, each of these states forms a unique local unitary equivalence class, that is, no two of these states are interconvertible by local unitary operations.

The Structure of Legal Education and the Legal Profession, Multidisciplinary Practice, Competition, and Globalization.

ERIC Educational Resources Information Center

Daly, Mary C.

2002-01-01

Discusses challenges facing the legal profession: the increasing importance of a law school's identity as national, regional, or local to graduates' career trajectories; disjunction between the legal academy and the profession; the threat to local and regional law schools' economic viability from online education; and emergence of new types of…

Structural basis for the regulation of nuclear import of Epstein-Barr virus nuclear antigen 1 (EBNA1) by phosphorylation of the nuclear localization signal

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

Nakada, Ryohei; Hirano, Hidemi; Structural Biology Research Center, Graduate School of Science, Nagoya University

Epstein-Barr virus (EBV) nuclear antigen 1 (EBNA1) is expressed in every EBV-positive tumor and is essential for the maintenance, replication, and transcription of the EBV genome in the nucleus of host cells. EBNA1 is a serine phosphoprotein, and it has been shown that phosphorylation of S385 in the nuclear localization signal (NLS) of EBNA1 increases the binding affinity to the nuclear import adaptor importin-α1 as well as importin-α5, and stimulates nuclear import of EBNA1. To gain insights into how phosphorylation of the EBNA1 NLS regulates nuclear import, we have determined the crystal structures of two peptide complexes of importin-α1: onemore » with S385-phosphorylated EBNA1 NLS peptide, determined at 2.0 Å resolution, and one with non-phosphorylated EBNA1 NLS peptide, determined at 2.2 Å resolution. The structures show that EBNA1 NLS binds to the major and minor NLS-binding sites of importin-α1, and indicate that the binding affinity of the EBNA1 NLS to the minor NLS-binding site could be enhanced by phosphorylation of S385 through electrostatic interaction between the phosphate group of phospho-S385 and K392 of importin-α1 (corresponding to R395 of importin-α5) on armadillo repeat 8. - Highlights: • Nuclear import of EBNA1 can be regulated by phosphorylation of NLS. • Crystal structures of importin-α1 bound to the NLS peptides of EBNA1 are solved. • Structures provide insights into how phosphorylation can regulate nuclear import.« less

Local self-uniformity in photonic networks.

PubMed

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

2017-02-17

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

Local self-uniformity in photonic networks

NASA Astrophysics Data System (ADS)

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

2017-02-01

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

EXAFS spectrum peculiarities of Y 1- xYb xNi 2B 2C

NASA Astrophysics Data System (ADS)

Cortes, R.; Fomicheva, L. N.; Menushenkov, A. P.; Meyer-Klaucke, W.; Konarev, P. V.; Tsvyashchenko, A. V.

2001-09-01

The results on the temperature dependent EXAFS studies of the local structure peculiarities of Y 1- xYb xNi 2B 2C series synthesized at a high pressure of 8 GPa are presented. The interrelation between the local structure of Y 1- xYb xNi 2B 2C and its superconducting and magnetic properties was observed supporting the model where the contributions from all type of the nearest atoms to the electron-phonon coupling are important and cannot be neglected.

Maize diversity associated with social origin and environmental variation in Southern Mexico.

PubMed

Orozco-Ramírez, Q; Ross-Ibarra, J; Santacruz-Varela, A; Brush, S

2016-05-01

While prevailing theories of crop evolution suggest that crop diversity and cultural diversity should be linked, empirical evidence for such a link remains inconclusive. In particular, few studies have investigated such patterns on a local scale. Here, we address this issue by examining the determinants of maize diversity in a local region of high cultural and biological richness in Southern Mexico. We collected maize samples from villages at low and middle elevations in two adjacent municipalities of differing ethnicity: Mixtec or Chatino. Although morphological traits show few patterns of population structure, we see clear genetic differentiation among villages, with municipality explaining a larger proportion of the differentiation than altitude. Consistent with an important role of social origin in patterning seed exchange, metapopulation model-based estimates of differentiation match the genetic data within village and ethnically distinct municipalities, but underestimate differentiation when all four villages are taken together. Our research provides insights about the importance of social origin in structuring maize diversity at the local scale.

Maize diversity associated with social origin and environmental variation in Southern Mexico

PubMed Central

Orozco-Ramírez, Q; Ross-Ibarra, J; Santacruz-Varela, A; Brush, S

2016-01-01

While prevailing theories of crop evolution suggest that crop diversity and cultural diversity should be linked, empirical evidence for such a link remains inconclusive. In particular, few studies have investigated such patterns on a local scale. Here, we address this issue by examining the determinants of maize diversity in a local region of high cultural and biological richness in Southern Mexico. We collected maize samples from villages at low and middle elevations in two adjacent municipalities of differing ethnicity: Mixtec or Chatino. Although morphological traits show few patterns of population structure, we see clear genetic differentiation among villages, with municipality explaining a larger proportion of the differentiation than altitude. Consistent with an important role of social origin in patterning seed exchange, metapopulation model-based estimates of differentiation match the genetic data within village and ethnically distinct municipalities, but underestimate differentiation when all four villages are taken together. Our research provides insights about the importance of social origin in structuring maize diversity at the local scale. PMID:26905463

Binocular stereo matching method based on structure tensor

NASA Astrophysics Data System (ADS)

Song, Xiaowei; Yang, Manyi; Fan, Yubo; Yang, Lei

2016-10-01

In a binocular visual system, to recover the three-dimensional information of the object, the most important step is to acquire matching points. Structure tensor is the vector representation of each point in its local neighborhood. Therefore, structure tensor performs well in region detection of local structure, and it is very suitable for detecting specific graphics such as pedestrians, cars and road signs in the image. In this paper, the structure tensor is combined with the luminance information to form the extended structure tensor. The directional derivatives of luminance in x and y directions are calculated, so that the local structure of the image is more prominent. Meanwhile, the Euclidean distance between the eigenvectors of key points is used as the similarity determination metric of key points in the two images. By matching, the coordinates of the matching points in the detected target are precisely acquired. In this paper, experiments were performed on the captured left and right images. After the binocular calibration, image matching was done to acquire the matching points, and then the target depth was calculated according to these matching points. By comparison, it is proved that the structure tensor can accurately acquire the matching points in binocular stereo matching.

Water: a responsive small molecule.

PubMed

Shultz, Mary Jane; Vu, Tuan Hoang; Meyer, Bryce; Bisson, Patrick

2012-01-17

Unique among small molecules, water forms a nearly tetrahedral yet flexible hydrogen-bond network. In addition to its flexibility, this network is dynamic: bonds are formed or broken on a picosecond time scale. These unique features make probing the local structure of water challenging. Despite the challenges, there is intense interest in developing a picture of the local water structure due to water's fundamental importance in many fields of chemistry. Understanding changes in the local network structure of water near solutes likely holds the key to unlock problems from analyzing parameters that determine the three dimensional structure of proteins to modeling the fate of volatile materials released into the atmosphere. Pictures of the local structure of water are heavily influenced by what is known about the structure of ice. In hexagonal I(h) ice, the most stable form of solid water under ordinary conditions, water has an equal number of donor and acceptor bonds; a kind of symmetry. This symmetric tetrahedral coordination is only approximately preserved in the liquid. The most obvious manifestation of this altered tetrahedral bonding is the greater density in the liquid compared with the solid. Formation of an interface or addition of solutes further modifies the local bonding in water. Because the O-H stretching frequency is sensitive to the environment, vibrational spectroscopy provides an excellent probe for the hydrogen-bond structure in water. In this Account, we examine both local interactions between water and small solutes and longer range interactions at the aqueous surface. Locally, the results suggest that water is not a symmetric donor or acceptor, but rather has a propensity to act as an acceptor. In interactions with hydrocarbons, action is centered at the water oxygen. For soluble inorganic salts, interaction is greater with the cation than the anion. The vibrational spectrum of the surface of salt solutions is altered compared with that of neat water. Studies of local salt-water interactions suggest that the picture of the local water structure and the ion distribution at the surface deduced from the surface vibrational spectrum should encompass both ions of the salt.

Computer simulations of local anesthetic mechanisms: Quantum chemical investigation of procaine

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

Smith, Jeremy C; Bondar, A.N.; Suhai, Sandor

2007-02-01

A description at the atomic level of detail of the interaction between local anesthetics, lipid membranes and membrane proteins, is essential for understanding the mechanism of local anesthesia. The importance of performing computer simulations to decipher the mechanism of local anesthesia is discussed here in the context of the current status of understanding of the local anesthetics action. As a first step towards accurate simulations of the interaction between local anesthetics, proteins, lipid and water molecules, here we use quantum mechanical methods to assess the charge distribution and structural properties of procaine in the presence and in the absence ofmore » water molecules. The calculations indicate that, in the absence of hydrogen-bonding water molecules, protonated procaine strongly prefers a compact structure enabled by intramolecular hydrogen bonding. In the presence of water molecules the torsional energy pro?le of procaine is modified, and hydrogen bonding to water molecules is favored relative to intra-molecular hydrogen bonding.« less

Regional-scale drivers of marine nematode distribution in Southern Ocean continental shelf sediments

NASA Astrophysics Data System (ADS)

Hauquier, Freija; Verleyen, Elie; Tytgat, Bjorn; Vanreusel, Ann

2018-07-01

Many marine meiofauna taxa seem to possess cosmopolitan species distributions, despite their endobenthic lifestyle and restricted long-distance dispersal capacities. In light of this paradox we used a metacommunity framework to study spatial turnover in free-living nematode distribution and assess the importance of local environmental conditions in explaining differences between communities in surface and subsurface sediments of the Southern Ocean continental shelf. We analysed nematode community structure in two sediment layers (0-3 cm and 3-5 cm) of locations maximum 2400 km apart. We first focused on a subset of locations to evaluate whether the genus level is sufficiently taxonomically fine-grained to study large-scale patterns in nematode community structure. We subsequently used redundancy and variation partitioning analyses to quantify the unique and combined effects of local environmental conditions and spatial descriptors on genus-level community composition. Macroecological patterns in community structure were highly congruent at the genus and species level. Nematode community composition was highly divergent between both depth strata, likely as a result of local abiotic conditions. Variation in community structure between the different regions largely stemmed from turnover (i.e. genus/species replacement) rather than nestedness (i.e. genus/species loss). The level of turnover among communities increased with geographic distance and was more pronounced in subsurface layers compared to surface sediments. Variation partitioning analysis revealed that both environmental and spatial predictors significantly explained variation in community structure. Moreover, the shared fraction of both sets of variables was high, which suggested a substantial amount of spatially structured environmental variation. Additionally, the effect of space independent of environment was much higher than the effect of environment independent of space, which shows the importance of including spatial descriptors in meiofauna and nematode community ecology. Large-scale assessment of free-living nematode diversity and abundance in the Southern Ocean shelf zone revealed strong horizontal and vertical spatial structuring in response to local environmental conditions, in combination with (most likely) dispersal limitation.

Active learning for semi-supervised clustering based on locally linear propagation reconstruction.

PubMed

Chang, Chin-Chun; Lin, Po-Yi

2015-03-01

The success of semi-supervised clustering relies on the effectiveness of side information. To get effective side information, a new active learner learning pairwise constraints known as must-link and cannot-link constraints is proposed in this paper. Three novel techniques are developed for learning effective pairwise constraints. The first technique is used to identify samples less important to cluster structures. This technique makes use of a kernel version of locally linear embedding for manifold learning. Samples neither important to locally linear propagation reconstructions of other samples nor on flat patches in the learned manifold are regarded as unimportant samples. The second is a novel criterion for query selection. This criterion considers not only the importance of a sample to expanding the space coverage of the learned samples but also the expected number of queries needed to learn the sample. To facilitate semi-supervised clustering, the third technique yields inferred must-links for passing information about flat patches in the learned manifold to semi-supervised clustering algorithms. Experimental results have shown that the learned pairwise constraints can capture the underlying cluster structures and proven the feasibility of the proposed approach. Copyright © 2014 Elsevier Ltd. All rights reserved.

Spatiotemporal dynamics of Puumala hantavirus associated with its rodent host, Myodes glareolus

PubMed Central

Weber de Melo, Vanessa; Sheikh Ali, Hanan; Freise, Jona; Kühnert, Denise; Essbauer, Sandra; Mertens, Marc; Wanka, Konrad M; Drewes, Stephan; Ulrich, Rainer G; Heckel, Gerald

2015-01-01

Many viruses significantly impact human and animal health. Understanding the population dynamics of these viruses and their hosts can provide important insights for epidemiology and virus evolution. Puumala virus (PUUV) is a European hantavirus that may cause regional outbreaks of hemorrhagic fever with renal syndrome in humans. Here, we analyzed the spatiotemporal dynamics of PUUV circulating in local populations of its rodent reservoir host, the bank vole (Myodes glareolus) during eight years. Phylogenetic and population genetic analyses of all three genome segments of PUUV showed strong geographical structuring at a very local scale. There was a high temporal turnover of virus strains in the local bank vole populations, but several virus strains persisted through multiple years. Phylodynamic analyses showed no significant changes in the local effective population sizes of PUUV, although vole numbers and virus prevalence fluctuated widely. Microsatellite data demonstrated also a temporally persisting subdivision between local vole populations, but these groups did not correspond to the subdivision in the virus strains. We conclude that restricted transmission between vole populations and genetic drift play important roles in shaping the genetic structure and temporal dynamics of PUUV in its natural host which has several implications for zoonotic risks of the human population. PMID:26136821

Connectivity and genetic structure of the queen conch on the Mesoamerican Reef

NASA Astrophysics Data System (ADS)

Machkour-M'Rabet, Salima; Cruz-Medina, Jorge; García-De León, Francisco J.; De Jesús-Navarrete, Alberto; Hénaut, Yann

2017-06-01

The queen conch ( Strombus gigas) is a commercially important marine invertebrate that is widely distributed throughout the western Atlantic, from Bermuda to Brazil. Intense exploitation has resulted in a decrease in population numbers of this species, which is listed as protected from commercial exploitation under IUCN and CITES. Previous studies on population genetics have demonstrated contrasting results in terms of the population structure of S. gigas. This research analyzed the genetic connectivity of the queen conch over a wide area of the Mesoamerican Reef System to determine whether S. gigas presents one panmictic population or a more complex structure. Furthermore, we evaluated the risk of local extinction by establishing the genetic diversity of the studied populations. High resolution was obtained for the five ISSR markers used for a total of 190 individuals, from seven localities along the Mesoamerican Reef. Our results reject the panmictic structure hypothesis for the queen conch in the study area and demonstrate genetic patchiness, indicating general homogeneity among localities that present an isolation-by-distance pattern. However, some genetic temporal variation was confirmed for the Cozumel locality. Furthermore, our results reveal self-recruitment for the Alacranes Reef aggregation and suggest sufficient connectivity with localities on the Caribbean coast to maintain high genetic diversity. With regard to genetic diversity, the results demonstrate that the queen conch is not genetically threatened in the study area. This is probably due to high annual recruitment within Caribbean queen conch aggregations, and suggests that S. gigas is a highly resilient organism. We advocate that the appropriate management of S. gigas (fishing quota and/or closed season) must be followed to attain a rapid recovery of queen conch populations. This study represents a fundamental step in the understanding of the dynamic population structure of S. gigas in the Mesoamerican Reef and is an important contribution toward improving the future management of this commercially protected species.

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.

Potential of tourism and recreational postindustrial city (Radzionków GIS-based case study)

NASA Astrophysics Data System (ADS)

Ślesak, Barbara; Absalon, Damian; Pytel, Sławomir

2014-10-01

The paper presents an analysis of the land structure use in the town Radzionków. The study area, despite of the industrial past, distinguished by a large proportion of green areas: parks, forests, agricultural lands, recreational areas. The study shows how important is the role of shaping the image of the municipality as an interesting tourist, plays right policy and how important local municipal authorities may support use of local tourism resources through appropriate and targeted use of space (Municipal Development Plan).

Critical Velocity for Shear Localization in A Mature Mylonitic Rock Analogue

NASA Astrophysics Data System (ADS)

Takahashi, M.; van den Ende, M.; Niemeijer, A. R.; Spiers, C. J.

2016-12-01

Highly localized slip zones, seen within ductile shear zones developed in nature, such as pseudotachylite bands occurring within mylonites, are widely recognized as evidence for earthquake nucleation and/or propagation within and overprinting the ductile regime. To understand brittle/frictional localization processes in ductile shear zones and to connect these to earthquake nucleation and propagation processes, we performed large velocity step-change tests on a brine-saturated, 80:20 (wt. %) halite and muscovite gouge mixture, after forming a mature mylonitic structure through pressure solution creep at low-velocity. The sharp increase in sliding strength that occurs in response to an instantaneous upward velocity-step (direct effect) is an important parameter in determining the potential for and nature of seismic rupture nucleation. We obtained reproducible results regarding low velocity mechanical behavior compared with previous work of Niemeijer and Spiers, [2006], but also obtained new insights into the effects of sudden increases in slip velocity on localization and strength evolution, at velocities above a specific critical velocity Vc ( 20 μm/sec). We found that once a ductile, mylonitic structure has developed in a shear zone, subsequent cataclastic deformation at high velocity (> Vc) is consistently localized in a narrow zone characterized by fine grains of halite aligned in arrays between foliated muscovite Due to this intense localization, structures presumably developed under low velocity conditions were still preserved in large parts of the gouge body. This switch to localized deformation is controlled by the imposed velocity, and becomes most apparent at velocities over Vc. In addition, the direct effect a decreases rapidly when the velocity exceeds Vc. This implies that slip can localize and accelerate towards seismic velocities more or less instantly once Vc is exceeded. Obtaining a measure for Vc in natural faults is therefore of key importance for understanding earthquake nucleation and propagation.

The structure of MgO-SiO2 glasses at elevated pressure.

PubMed

Wilding, Martin; Guthrie, Malcolm; Kohara, Shinji; Bull, Craig L; Akola, Jaakko; Tucker, Matt G

2012-06-06

The magnesium silicate system is an important geophysical analogue and neutron diffraction data from glasses formed in this system may also provide an initial framework for understanding the structure-dependent properties of related liquids that are important during planetary formation. Neutron diffraction data collected in situ for a single composition (38 mol% SiO(2)) magnesium silicate glass sample shows local changes in structure as pressure is increased from ambient conditions to 8.6 GPa at ambient temperature. A method for obtaining the fully corrected, total structure factor, S(Q), has been developed that allows accurate structural characterization as this weakly scattering glass sample is compressed. The measured S(Q) data indicate changes in chemical ordering with pressure and the real-space transforms show an increase in Mg-O coordination number and a distortion of the local environment around magnesium ions. We have used reverse Monte Carlo methods to compare the high pressure and ambient pressure structures and also compare the high pressure form with a more silica-poor glass (Mg(2)SiO(4)) that represents the approach to a more dense, void-free and topologically ordered structure. The Mg-O coordination number increases with pressure and we also find that the degree of continuous connectivity of Si-O bonds increases via a collapse of interstices.

Remote sensing of vegetation 3-D structure for biodiversity and habitat: Review and implications for lidar and radar spaceborne missions

Treesearch

K.M. Bergen; S.J. Goetz; R.O. Dubayah; G.M. Henebry; C.T. Hunsaker; M.L. Imhoff; R.F. Nelson; G.G. Parker; V.C. Radeloff

2009-01-01

Biodiversity and habitat face increasing pressures due to human and natural influences that alter vegetation structure. Because of the inherent difficulty of measuring forested vegetation three-dimensional (3-D) structure on the ground, this important component of biodiversity and habitat has been, until recently, largely restricted to local measurements, or at larger...

On decoupling of volatility smile and term structure in inverse option pricing

NASA Astrophysics Data System (ADS)

Egger, Herbert; Hein, Torsten; Hofmann, Bernd

2006-08-01

Correct pricing of options and other financial derivatives is of great importance to financial markets and one of the key subjects of mathematical finance. Usually, parameters specifying the underlying stochastic model are not directly observable, but have to be determined indirectly from observable quantities. The identification of local volatility surfaces from market data of European vanilla options is one very important example of this type. As with many other parameter identification problems, the reconstruction of local volatility surfaces is ill-posed, and reasonable results can only be achieved via regularization methods. Moreover, due to the sparsity of data, the local volatility is not uniquely determined, but depends strongly on the kind of regularization norm used and a good a priori guess for the parameter. By assuming a multiplicative structure for the local volatility, which is motivated by the specific data situation, the inverse problem can be decomposed into two separate sub-problems. This removes part of the non-uniqueness and allows us to establish convergence and convergence rates under weak assumptions. Additionally, a numerical solution of the two sub-problems is much cheaper than that of the overall identification problem. The theoretical results are illustrated by numerical tests.

The Lamb wave bandgap variation of a locally resonant phononic crystal subjected to thermal deformation

NASA Astrophysics Data System (ADS)

Zhu, Yun; Li, Zhen; Li, Yue-ming

2018-05-01

A study on dynamical characteristics of a ternary locally resonant phononic crystal (PC) plate (i.e., hard scatterer with soft coating periodically disperse in stiff host matrix) is carried out in this paper. The effect of thermal deformation on the structure stiffness, which plays an important role in the PC's dynamical characteristics, is considered. Results show that both the start and the stop frequency of bandgap shift to higher range with the thermal deformation. In particular, the characteristics of band structure change suddenly at critical buckling temperature. The effect of thermal deformation could be utilized for tuning of phononic band structures, which can promote their design and further applications.

Imaging of matrix-disorder in normal and pathological human dermis using nonlinear optical microscopy

NASA Astrophysics Data System (ADS)

Zhuo, Shuangmu; Chen, Jianxin; Xie, Shusen; Zheng, Liqin; Jiang, Xingshan

2009-11-01

In dermis, collagen and elastin are important structural proteins of extracellular maxtrix. The matrix-disorder is associated with various physiologic processes, such as localized scleroderma, anetoderma, photoaging. In this work, we demonstrate the capability of nonlinear optical microscopy in imaging structural proteins in normal and pathological human dermis.

Downscaling Indicators of Forest Habitat Structure from National Assessments

Treesearch

Kurt H. Riitters

2005-01-01

Downscaling is an important problem because consistent large-area assessments of forest habitat structure, while feasible, are only feasible when using relatively coarse data and indicators. Techniques are needed to enable more detailed and local interpretations of the national statistics. Using the results of national assessments from land-cover maps, this paper...

Bayesian comparison of protein structures using partial Procrustes distance.

PubMed

Ejlali, Nasim; Faghihi, Mohammad Reza; Sadeghi, Mehdi

2017-09-26

An important topic in bioinformatics is the protein structure alignment. Some statistical methods have been proposed for this problem, but most of them align two protein structures based on the global geometric information without considering the effect of neighbourhood in the structures. In this paper, we provide a Bayesian model to align protein structures, by considering the effect of both local and global geometric information of protein structures. Local geometric information is incorporated to the model through the partial Procrustes distance of small substructures. These substructures are composed of β-carbon atoms from the side chains. Parameters are estimated using a Markov chain Monte Carlo (MCMC) approach. We evaluate the performance of our model through some simulation studies. Furthermore, we apply our model to a real dataset and assess the accuracy and convergence rate. Results show that our model is much more efficient than previous approaches.

Distributed rewiring model for complex networking: The effect of local rewiring rules on final structural properties.

PubMed

López Chavira, Magali Alexander; Marcelín-Jiménez, Ricardo

2017-01-01

The study of complex networks has become an important subject over the last decades. It has been shown that these structures have special features, such as their diameter, or their average path length, which in turn are the explanation of some functional properties in a system such as its fault tolerance, its fragility before attacks, or the ability to support routing procedures. In the present work, we study some of the forces that help a network to evolve to the point where structural properties are settled. Although our work is mainly focused on the possibility of applying our ideas to Information and Communication Technologies systems, we consider that our results may contribute to understanding different scenarios where complex networks have become an important modeling tool. Using a discrete event simulator, we get each node to discover the shortcuts that may connect it with regions away from its local environment. Based on this partial knowledge, each node can rewire some of its links, which allows modifying the topology of the entire underlying graph to achieve new structural properties. We proposed a distributed rewiring model that creates networks with features similar to those found in complex networks. Although each node acts in a distributed way and seeking to reduce only the trajectories of its packets, we observed a decrease of diameter and an increase in clustering coefficient in the global structure compared to the initial graph. Furthermore, we can find different final structures depending on slight changes in the local rewiring rules.

Emergence of scale-free close-knit friendship structure in online social networks.

PubMed

Cui, Ai-Xiang; Zhang, Zi-Ke; Tang, Ming; Hui, Pak Ming; Fu, Yan

2012-01-01

Although the structural properties of online social networks have attracted much attention, the properties of the close-knit friendship structures remain an important question. Here, we mainly focus on how these mesoscale structures are affected by the local and global structural properties. Analyzing the data of four large-scale online social networks reveals several common structural properties. It is found that not only the local structures given by the indegree, outdegree, and reciprocal degree distributions follow a similar scaling behavior, the mesoscale structures represented by the distributions of close-knit friendship structures also exhibit a similar scaling law. The degree correlation is very weak over a wide range of the degrees. We propose a simple directed network model that captures the observed properties. The model incorporates two mechanisms: reciprocation and preferential attachment. Through rate equation analysis of our model, the local-scale and mesoscale structural properties are derived. In the local-scale, the same scaling behavior of indegree and outdegree distributions stems from indegree and outdegree of nodes both growing as the same function of the introduction time, and the reciprocal degree distribution also shows the same power-law due to the linear relationship between the reciprocal degree and in/outdegree of nodes. In the mesoscale, the distributions of four closed triples representing close-knit friendship structures are found to exhibit identical power-laws, a behavior attributed to the negligible degree correlations. Intriguingly, all the power-law exponents of the distributions in the local-scale and mesoscale depend only on one global parameter, the mean in/outdegree, while both the mean in/outdegree and the reciprocity together determine the ratio of the reciprocal degree of a node to its in/outdegree. Structural properties of numerical simulated networks are analyzed and compared with each of the four real networks. This work helps understand the interplay between structures on different scales in online social networks.

Emergence of Scale-Free Close-Knit Friendship Structure in Online Social Networks

PubMed Central

Cui, Ai-Xiang; Zhang, Zi-Ke; Tang, Ming; Hui, Pak Ming; Fu, Yan

2012-01-01

Although the structural properties of online social networks have attracted much attention, the properties of the close-knit friendship structures remain an important question. Here, we mainly focus on how these mesoscale structures are affected by the local and global structural properties. Analyzing the data of four large-scale online social networks reveals several common structural properties. It is found that not only the local structures given by the indegree, outdegree, and reciprocal degree distributions follow a similar scaling behavior, the mesoscale structures represented by the distributions of close-knit friendship structures also exhibit a similar scaling law. The degree correlation is very weak over a wide range of the degrees. We propose a simple directed network model that captures the observed properties. The model incorporates two mechanisms: reciprocation and preferential attachment. Through rate equation analysis of our model, the local-scale and mesoscale structural properties are derived. In the local-scale, the same scaling behavior of indegree and outdegree distributions stems from indegree and outdegree of nodes both growing as the same function of the introduction time, and the reciprocal degree distribution also shows the same power-law due to the linear relationship between the reciprocal degree and in/outdegree of nodes. In the mesoscale, the distributions of four closed triples representing close-knit friendship structures are found to exhibit identical power-laws, a behavior attributed to the negligible degree correlations. Intriguingly, all the power-law exponents of the distributions in the local-scale and mesoscale depend only on one global parameter, the mean in/outdegree, while both the mean in/outdegree and the reciprocity together determine the ratio of the reciprocal degree of a node to its in/outdegree. Structural properties of numerical simulated networks are analyzed and compared with each of the four real networks. This work helps understand the interplay between structures on different scales in online social networks. PMID:23272067

Local structure distortion induced by Ti dopants boosting the pseudocapacitance of RuO2-based supercapacitors

NASA Astrophysics Data System (ADS)

Chen, I.-Li; Wei, Yu-Chen; Lu, Kueih-Tzu; Chen, Tsan-Yao; Hu, Chi-Chang; Chen, Jin-Ming

2015-09-01

Binary oxides with atomic ratios of Ru/Ti = 90/10, 70/30, and 50/50 were fabricated using H2O2-oxidative precipitation with the assistance of a cetyltrimethylammonium bromide (CTAB) template, followed by a thermal treatment at 200 °C. The characteristics of electron structure and local structure extracted from X-ray absorption spectroscopy (XAS) and transmission electron microscopy (TEM) analyses indicate that incorporation of Ti into the RuO2 lattice produces not only the local structural distortion of the RuO6 octahedra in (Ru-Ti)O2 with an increase in the central Ru-Ru distance but also a local crystallization of RuO2. Among the three binary oxides studied, (Ru70-Ti30)O2 exhibits a capacitance improvement of about 1.4-fold relative to the CTAB-modified RuO2, mainly due to the enhanced crystallinity of the distorted RuO6 structure rather than the surface area effect. Upon increasing the extent of Ti doping, the deteriorated supercapacitive performance of (Ru50-Ti50)O2 results from the formation of localized nano-clusters of TiO2 crystallites. These results provide insight into the important role of Ti doping in RuO2 that boosts the pseudocapacitive performance for RuO2-based supercapacitors. The present result is crucial for the design of new binary oxides for supercapacitor applications with extraordinary performance.Binary oxides with atomic ratios of Ru/Ti = 90/10, 70/30, and 50/50 were fabricated using H2O2-oxidative precipitation with the assistance of a cetyltrimethylammonium bromide (CTAB) template, followed by a thermal treatment at 200 °C. The characteristics of electron structure and local structure extracted from X-ray absorption spectroscopy (XAS) and transmission electron microscopy (TEM) analyses indicate that incorporation of Ti into the RuO2 lattice produces not only the local structural distortion of the RuO6 octahedra in (Ru-Ti)O2 with an increase in the central Ru-Ru distance but also a local crystallization of RuO2. Among the three binary oxides studied, (Ru70-Ti30)O2 exhibits a capacitance improvement of about 1.4-fold relative to the CTAB-modified RuO2, mainly due to the enhanced crystallinity of the distorted RuO6 structure rather than the surface area effect. Upon increasing the extent of Ti doping, the deteriorated supercapacitive performance of (Ru50-Ti50)O2 results from the formation of localized nano-clusters of TiO2 crystallites. These results provide insight into the important role of Ti doping in RuO2 that boosts the pseudocapacitive performance for RuO2-based supercapacitors. The present result is crucial for the design of new binary oxides for supercapacitor applications with extraordinary performance. Electronic supplementary information (ESI) available: A series of Ru K-edge EXAFS spectra fitting results for RuO2 together with oxides with different Ru-Ti atomic ratios treated at 200 °C. See DOI: 10.1039/c5nr03660g

Modeling non-locality of plasmonic excitations with a fictitious film

NASA Astrophysics Data System (ADS)

Kong, Jiantao; Shvonski, Alexander; Kempa, Krzysztof

Non-local effects, requiring a wavevector (q) dependent dielectric response are becoming increasingly important in studies of plasmonic and metamaterial structures. The phenomenological hydrodynamic approximation (HDA) is the simplest, and most often used model, but it often fails. We show that the d-function formalism, exact to first order in q, is a powerful and simple-to-use alternative. Recently, we developed a mapping of the d-function formalism into a purely local fictitious film. This geometric mapping allows for non-local extensions of any local calculation scheme, including FDTD. We demonstrate here, that such mapped FDTD simulation of metallic nanoclusters agrees very well with various experiments.

Electron band structure of the high pressure cubic phase of AlH3

NASA Astrophysics Data System (ADS)

Shi, Hongliang; Zarifi, Niliffar; Yim, Wai-Leung; Tse, J. S.

2012-07-01

The electronic band structure of the cubic Pm3n phase of AlH3 stable above 100 GPa is examined with semi-local, Tran-Blaha modified Becke-Johnson local density approximation (TB-mBJLDA), screened hybrid density functionals and GW methods. The shift of the conduction band to higher energy with increasing pressure is predicted by all methods. However, there are significant differences in detail band structure. In the pressure range from 90 to160 GPa, semi-local, hybrid functional and TB-mBJLDA calculations predicted that AlH3 is a poor metal. In comparison, GW calculations show a gap opening at 160 GPa and AlH3 becomes a small gap semi-conductor. From the trends of the calculated band shifts, it can be concluded that the favourable conditions leading to the nesting of Fermi surfaces predicted by semi-local calculation have disappeared if the exchange term is included. The results highlight the importance of the correction to the exchange energy on the band structure of hydrogen dominant dense metal hydrides at high pressure hydrides and may help to rationalize the absence of superconductivity in AlH3 from experimental measurements.

Local food in Iceland: identifying behavioral barriers to increased production and consumption

NASA Astrophysics Data System (ADS)

Ósk Halldórsdóttir, Þórhildur; Nicholas, Kimberly A.

2016-11-01

Increased production and consumption of local food may reduce the negative environmental, social, and economic impacts of industrialized and globalized food production. Here we examined potential barriers to increasing production and consumption of food produced in Iceland. First, we developed a new framework to address the behaviors of production and consumption simultaneously, to comprehensively analyze their potential barriers. We examined structural barriers by estimating the food production capacity of Iceland, and cultural and personal barriers through survey data on cultural norms and purchasing behavior from Matís, a research and development company. We found no structural barriers preventing Iceland from increasing production of local cereals, which would compliment current local production of meat and dairy and reduce reliance on imports, currently at 50% of the daily caloric intake. However, if food production became entirely local without changing the current mix of crops grown, there would be a 50% reduction in diversity (from 50 to 25 items in eight out of ten food categories). We did not identify any cultural barriers, as survey results demonstrated that consumers hold generally positive worldviews towards local food, with 88% satisfied with local food they had purchased. More than two-thirds of consumers regarded supporting the local farmer and considerations such as environmentally friendly production, fewer food miles, lower carbon footprint as important. However, they rated the local food they have access to as lower in meeting sustainability criteria, showing that they make justifications for not choosing local food in practice. This is a personal barrier to increased consumption of local food, and implies that marketing strategies and general knowledge connected to local food in Iceland might be improved. Although the results apply to the case of Iceland, the method of identifying behavioral barriers to change is applicable to other countries, regions, or foodsheds interested in assessing their food security through an analysis of local food.

GOSSIP: a method for fast and accurate global alignment of protein structures.

PubMed

Kifer, I; Nussinov, R; Wolfson, H J

2011-04-01

The database of known protein structures (PDB) is increasing rapidly. This results in a growing need for methods that can cope with the vast amount of structural data. To analyze the accumulating data, it is important to have a fast tool for identifying similar structures and clustering them by structural resemblance. Several excellent tools have been developed for the comparison of protein structures. These usually address the task of local structure alignment, an important yet computationally intensive problem due to its complexity. It is difficult to use such tools for comparing a large number of structures to each other at a reasonable time. Here we present GOSSIP, a novel method for a global all-against-all alignment of any set of protein structures. The method detects similarities between structures down to a certain cutoff (a parameter of the program), hence allowing it to detect similar structures at a much higher speed than local structure alignment methods. GOSSIP compares many structures in times which are several orders of magnitude faster than well-known available structure alignment servers, and it is also faster than a database scanning method. We evaluate GOSSIP both on a dataset of short structural fragments and on two large sequence-diverse structural benchmarks. Our conclusions are that for a threshold of 0.6 and above, the speed of GOSSIP is obtained with no compromise of the accuracy of the alignments or of the number of detected global similarities. A server, as well as an executable for download, are available at http://bioinfo3d.cs.tau.ac.il/gossip/.

Investigating homology between proteins using energetic profiles.

PubMed

Wrabl, James O; Hilser, Vincent J

2010-03-26

Accumulated experimental observations demonstrate that protein stability is often preserved upon conservative point mutation. In contrast, less is known about the effects of large sequence or structure changes on the stability of a particular fold. Almost completely unknown is the degree to which stability of different regions of a protein is generally preserved throughout evolution. In this work, these questions are addressed through thermodynamic analysis of a large representative sample of protein fold space based on remote, yet accepted, homology. More than 3,000 proteins were computationally analyzed using the structural-thermodynamic algorithm COREX/BEST. Estimated position-specific stability (i.e., local Gibbs free energy of folding) and its component enthalpy and entropy were quantitatively compared between all proteins in the sample according to all-vs.-all pairwise structural alignment. It was discovered that the local stabilities of homologous pairs were significantly more correlated than those of non-homologous pairs, indicating that local stability was indeed generally conserved throughout evolution. However, the position-specific enthalpy and entropy underlying stability were less correlated, suggesting that the overall regional stability of a protein was more important than the thermodynamic mechanism utilized to achieve that stability. Finally, two different types of statistically exceptional evolutionary structure-thermodynamic relationships were noted. First, many homologous proteins contained regions of similar thermodynamics despite localized structure change, suggesting a thermodynamic mechanism enabling evolutionary fold change. Second, some homologous proteins with extremely similar structures nonetheless exhibited different local stabilities, a phenomenon previously observed experimentally in this laboratory. These two observations, in conjunction with the principal conclusion that homologous proteins generally conserved local stability, may provide guidance for a future thermodynamically informed classification of protein homology.

Local structural order and relaxation effects in metal-chalcogenide glasses

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

Saleh, Z.M.

1990-01-01

Nuclear quadrupole resonance (NQR) and nuclear magnetic resonance (NMR) have been employed to study the local structural order and the relaxation mechanisms in metal-arsenic-chalcogenide glasses for metal concentrations within the glass forming region. The glass forming region in the Cu-As-S and Cu-As-se glassy systems extends approximately to 6 and 25 at. % copper, respectively. In the composition Cu[sub x](As[sub 2/5]Ch[sub 3/5])[sub 1[minus]x], where Ch = S or Se, there is evidence of dramatic changes in the local structure as copper is added to the system. One important change is the formation of As-As bonds which are absent in As[sub 2]Ch[submore » 3]. The [sup 75]As NQR measurements indicate that the density of these bonds increases with copper concentration x. These results are consistent with the predictions of a model proposed recently to explain the local structural order in glassy metal chalcogenides. While NQR data show that arsenic atoms are threefold coordinated, EXAFs measurements have shown that copper is fourfold coordinated within the glass forming ranges in both systems. The NMR measurements confirm this result and quantitatively determine the local environment around the copper nuclei. For the naturally occurring mineral luzonite (Cu[sub 3]AsS[sub 4]) copper is fourfold coordinated. The known structure of this mineral has been used as a guide to understanding the local structure in the glasses. Copper and arsenic nuclear relaxation measurements were used to study the dynamics of these systems. The temperature and frequency dependence of the spin-lattice and spin-spin relaxation times have been carefully measured to determine the relaxation mechanisms.« less

Local topography shapes fine-scale spatial genetic structure in the Arkansas Valley evening primrose, Oenothera harringtonii (Onagraceae).

PubMed

Rhodes, Matthew K; Fant, Jeremie B; Skogen, Krissa A

2014-01-01

Identifying factors that shape the spatial distribution of genetic variation is crucial to understanding many population- and landscape-level processes. In this study, we explore fine-scale spatial genetic structure in Oenothera harringtonii (Onagraceae), an insect-pollinated, gravity-dispersed herb endemic to the grasslands of south-central and southeastern Colorado, USA. We genotyped 315 individuals with 11 microsatellite markers and utilized a combination of spatial autocorrelation analyses and landscape genetic models to relate life history traits and landscape features to dispersal processes. Spatial genetic structure was consistent with theoretical expectations of isolation by distance, but this pattern was weak (Sp = 0.00374). Anisotropic analyses indicated that spatial genetic structure was markedly directional, in this case consistent with increased dispersal along prominent slopes. Landscape genetic models subsequently confirmed that spatial genetic variation was significantly influenced by local topographic heterogeneity, specifically that geographic distance, elevation and aspect were important predictors of spatial genetic structure. Among these variables, geographic distance was ~68% more important than elevation in describing spatial genetic variation, and elevation was ~42% more important than aspect after removing the effect of geographic distance. From these results, we infer a mechanism of hydrochorous seed dispersal along major drainages aided by seasonal monsoon rains. Our findings suggest that landscape features may shape microevolutionary processes at much finer spatial scales than typically considered, and stress the importance of considering how particular dispersal vectors are influenced by their environmental context. © The American Genetic Association 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

The domain organization of the bacterial intermediate filament-like protein crescentin is important for assembly and function

PubMed Central

Cabeen, Matthew T; Herrmann, Harald; Jacobs-Wagner, Christine

2011-01-01

Crescentin is a bacterial filament-forming protein that exhibits domain organization features found in metazoan intermediate filament (IF) proteins. Structure-function studies of eukaryotic IFs have been hindered by a lack of simple genetic systems and easily quantifiable phenotypes. Here we exploit the characteristic localization of the crescentin structure along the inner curvature of Caulobacter crescentus cells and the loss of cell curvature associated with impaired crescentin function to analyze the importance of the domain organization of crescentin. By combining biochemistry and ultrastructural analysis in vitro with cellular localization and functional studies, we show that crescentin requires its distinctive domain organization, and furthermore that different structural elements have distinct structural and functional contributions. The head domain can be functionally subdivided into two subdomains; the first (amino-terminal) is required for function but not assembly, while the second is necessary for structure assembly. The rod domain is similarly required for structure assembly, and the linker L1 appears important to prevent runaway assembly into nonfunctional aggregates. The data also suggest that the stutter and the tail domain have critical functional roles in stabilizing crescentin structures against disassembly by monovalent cations in the cytoplasm. This study suggests that the IF-like behavior of crescentin is a consequence of its domain organization, implying that the IF protein layout is an adaptable cytoskeletal motif, much like the actin and tubulin folds, that is broadly exploited for various functions throughout life from bacteria to humans. © 2011 Wiley-Liss, Inc. PMID:21360832

Domino structures evolution in strike-slip shear zones; the importance of the cataclastic flow

NASA Astrophysics Data System (ADS)

Moreira, N.; Dias, R.

2018-05-01

The Porto-Tomar-Ferreira do Alentejo dextral Shear Zone is one of the most important structures of the Iberian Variscides. In its vicinity, close to Abrantes (Central Portugal), a localized heterogeneous strain pattern developed in a decimetric metamorphic siliceous multilayer. This complex pattern was induced by the D2 dextral shearing of the early S0//S1 foliation in brittle-ductile conditions, giving rise to three main shear zone families. One of these families, with antithetic kinematics, delimits blocks with rigid clockwise rotation surrounded by coeval cataclasites, generating a local domino structure. The proposed geometrical and kinematic analysis, coupled with statistical studies, highlights the relation between subsidiary shear zones and the main shear zone. Despite the heterogeneous strain pattern, a quantitative approach of finite strain was applied based on the restoration of the initial fracture pattern. This approach shows the importance of the cataclastic flow coupled with the translational displacement of the domino domain in solving space problems related to the rigid block rotation. Such processes are key in allowing the rigid block rotation inside shear zones whenever the simple shear component is a fundamental mechanism.

Soil resources and topography shape local tree community structure in tropical forests

PubMed Central

Baldeck, Claire A.; Harms, Kyle E.; Yavitt, Joseph B.; John, Robert; Turner, Benjamin L.; Valencia, Renato; Navarrete, Hugo; Davies, Stuart J.; Chuyong, George B.; Kenfack, David; Thomas, Duncan W.; Madawala, Sumedha; Gunatilleke, Nimal; Gunatilleke, Savitri; Bunyavejchewin, Sarayudh; Kiratiprayoon, Somboon; Yaacob, Adzmi; Supardi, Mohd N. Nur; Dalling, James W.

2013-01-01

Both habitat filtering and dispersal limitation influence the compositional structure of forest communities, but previous studies examining the relative contributions of these processes with variation partitioning have primarily used topography to represent the influence of the environment. Here, we bring together data on both topography and soil resource variation within eight large (24–50 ha) tropical forest plots, and use variation partitioning to decompose community compositional variation into fractions explained by spatial, soil resource and topographic variables. Both soil resources and topography account for significant and approximately equal variation in tree community composition (9–34% and 5–29%, respectively), and all environmental variables together explain 13–39% of compositional variation within a plot. A large fraction of variation (19–37%) was spatially structured, yet unexplained by the environment, suggesting an important role for dispersal processes and unmeasured environmental variables. For the majority of sites, adding soil resource variables to topography nearly doubled the inferred role of habitat filtering, accounting for variation in compositional structure that would previously have been attributable to dispersal. Our results, illustrated using a new graphical depiction of community structure within these plots, demonstrate the importance of small-scale environmental variation in shaping local community structure in diverse tropical forests around the globe. PMID:23256196

MR Anatomy of Deep Brain Nuclei with Special Reference to Specific Diseases and Deep Brain Stimulation Localization

PubMed Central

Telford, Ryan; Vattoth, Surjith

2014-01-01

Summary Diseases affecting the basal ganglia and deep brain structures vary widely in etiology and include metabolic, infectious, ischemic, and neurodegenerative conditions. Some neurologic diseases, such as Wernicke encephalopathy or pseudohypoparathyroidism, require specific treatments, which if unrecognized could lead to further complications. Other pathologies, such as hypertrophic olivary degeneration, if not properly diagnosed may be mistaken for a primary medullary neoplasm and create unnecessary concern. The deep brain structures are complex and can be difficult to distinguish on routine imaging. It is imperative that radiologists first understand the intrinsic anatomic relationships between the different basal ganglia nuclei and deep brain structures with magnetic resonance (MR) imaging. It is important to understand the "normal" MR signal characteristics, locations, and appearances of these structures. This is essential to recognizing diseases affecting the basal ganglia and deep brain structures, especially since most of these diseases result in symmetrical, and therefore less noticeable, abnormalities. It is also crucial that neurosurgeons correctly identify the deep brain nuclei presurgically for positioning deep brain stimulator leads, the most important being the subthalamic nucleus for Parkinson syndromes and the thalamic ventral intermediate nucleus for essential tremor. Radiologists will be able to better assist clinicians in diagnosis and treatment once they are able to accurately localize specific deep brain structures. PMID:24571832

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.

Binding ligand prediction for proteins using partial matching of local surface patches.

PubMed

Sael, Lee; Kihara, Daisuke

2010-01-01

Functional elucidation of uncharacterized protein structures is an important task in bioinformatics. We report our new approach for structure-based function prediction which captures local surface features of ligand binding pockets. Function of proteins, specifically, binding ligands of proteins, can be predicted by finding similar local surface regions of known proteins. To enable partial comparison of binding sites in proteins, a weighted bipartite matching algorithm is used to match pairs of surface patches. The surface patches are encoded with the 3D Zernike descriptors. Unlike the existing methods which compare global characteristics of the protein fold or the global pocket shape, the local surface patch method can find functional similarity between non-homologous proteins and binding pockets for flexible ligand molecules. The proposed method improves prediction results over global pocket shape-based method which was previously developed by our group.

Binding Ligand Prediction for Proteins Using Partial Matching of Local Surface Patches

PubMed Central

Sael, Lee; Kihara, Daisuke

2010-01-01

Functional elucidation of uncharacterized protein structures is an important task in bioinformatics. We report our new approach for structure-based function prediction which captures local surface features of ligand binding pockets. Function of proteins, specifically, binding ligands of proteins, can be predicted by finding similar local surface regions of known proteins. To enable partial comparison of binding sites in proteins, a weighted bipartite matching algorithm is used to match pairs of surface patches. The surface patches are encoded with the 3D Zernike descriptors. Unlike the existing methods which compare global characteristics of the protein fold or the global pocket shape, the local surface patch method can find functional similarity between non-homologous proteins and binding pockets for flexible ligand molecules. The proposed method improves prediction results over global pocket shape-based method which was previously developed by our group. PMID:21614188

Credit networks and systemic risk of Chinese local financing platforms: Too central or too big to fail?. -based on different credit correlations using hierarchical methods

NASA Astrophysics Data System (ADS)

He, Fang; Chen, Xi

2016-11-01

The accelerating accumulation and risk concentration of Chinese local financing platforms debts have attracted wide attention throughout the world. Due to the network of financial exposures among institutions, the failure of several platforms or regions of systemic importance will probably trigger systemic risk and destabilize the financial system. However, the complex network of credit relationships in Chinese local financing platforms at the state level remains unknown. To fill this gap, we presented the first complex networks and hierarchical cluster analysis of the credit market of Chinese local financing platforms using the ;bottom up; method from firm-level data. Based on balance-sheet channel, we analyzed the topology and taxonomy by applying the analysis paradigm of subdominant ultra-metric space to an empirical data in 2013. It is remarked that we chose to extract the network of co-financed financing platforms in order to evaluate the effect of risk contagion from platforms to bank system. We used the new credit similarity measure by combining the factor of connectivity and size, to extract minimal spanning trees (MSTs) and hierarchical trees (HTs). We found that: (1) the degree distributions of credit correlation backbone structure of Chinese local financing platforms are fat tailed, and the structure is unstable with respect to targeted failures; (2) the backbone is highly hierarchical, and largely explained by the geographic region; (3) the credit correlation backbone structure based on connectivity and size is significantly heterogeneous; (4) key platforms and regions of systemic importance, and contagion path of systemic risk are obtained, which are contributed to preventing systemic risk and regional risk of Chinese local financing platforms and preserving financial stability under the framework of macro prudential supervision. Our approach of credit similarity measure provides a means of recognizing ;systemically important; institutions and regions for a targeted policy with risk minimization which gives a flexible and comprehensive consideration to both aspects of ;too big to fail; and ;too central to fail;.

Humanitarian engineering placements in our own communities

NASA Astrophysics Data System (ADS)

VanderSteen, J. D. J.; Hall, K. R.; Baillie, C. A.

2010-05-01

There is an increasing interest in the humanitarian engineering curriculum, and a service-learning placement could be an important component of such a curriculum. International placements offer some important pedagogical advantages, but also have some practical and ethical limitations. Local community-based placements have the potential to be transformative for both the student and the community, although this potential is not always seen. In order to investigate the role of local placements, qualitative research interviews were conducted. Thirty-two semi-structured research interviews were conducted and analysed, resulting in a distinct outcome space. It is concluded that local humanitarian engineering placements greatly complement international placements and are strongly recommended if international placements are conducted. More importantly it is seen that we are better suited to address the marginalised in our own community, although it is often easier to see the needs of an outside populace.

The demographic consequences of growing older and bigger in oyster populations.

PubMed

Moore, Jacob L; Lipcius, Romuald N; Puckett, Brandon; Schreiber, Sebastian J

2016-10-01

Structured population models, particularly size- or age-structured, have a long history of informing conservation and natural resource management. While size is often easier to measure than age and is the focus of many management strategies, age-structure can have important effects on population dynamics that are not captured in size-only models. However, relatively few studies have included the simultaneous effects of both age- and size-structure. To better understand how population structure, particularly that of age and size, impacts restoration and management decisions, we developed and compared a size-structured integral projection model (IPM) and an age- and size-structured IPM, using a population of Crassostrea gigas oysters in the northeastern Pacific Ocean. We analyzed sensitivity of model results across values of local retention that give populations decreasing in size to populations increasing in size. We found that age- and size-structured models yielded the best fit to the demographic data and provided more reliable results about long-term demography. Elasticity analysis showed that population growth rate was most sensitive to changes in the survival of both large (>175 mm shell length) and small (<75 mm shell length) oysters, indicating that a maximum size limit, in addition to a minimum size limit, could be an effective strategy for maintaining a sustainable population. In contrast, the purely size-structured model did not detect the importance of large individuals. Finally, patterns in stable age and stable size distributions differed between populations decreasing in size due to limited local retention and populations increasing in size due to high local retention. These patterns can be used to determine population status and restoration success. The methodology described here provides general insight into the necessity of including both age- and size-structure into modeling frameworks when using population models to inform restoration and management decisions. © 2016 by the Ecological Society of America.

The Best Possible Intentions Testing Prophylactic Approaches on Humans in Developing Countries

PubMed Central

2013-01-01

Debates on human experiments in developing countries focus on ethical principles such as informed consent, accountability, involvement of the concerned communities, and the improvement of local health services. Public health specialists who conducted human experiments in Rio de Janeiro (1902–1905) and in Guatemala (1947–1948) believed, however, that they were acting in the best interests of local populations, were aware of the importance of informed consent, were closely collaborating with local health professionals, and were contributing to the development of local health structures. Nevertheless, their investigations went dramatically wrong. An initial desire to conduct ethically and scientifically sound studies was undermined by pressure to obtain results and to save the researchers’ initial investment, the possibility of freely using hospitalized patients as experimental participants, uncritical help from local professional elites, and structural pitfalls of experimenting with severely deprived people. These elements can still be found in trials of preventive methods in the Global South. PMID:23237168

Are Low-Income Canadians Financially Literate? Placing Financial Literacy in the Context of Personal and Structural Constraints

ERIC Educational Resources Information Center

Buckland, Jerry

2010-01-01

This article argues that financial literacy varies across socioeconomic groups and their neighborhoods, in part because of the adult learning that occurs within a local context. The study begins by explaining that financial literacy needs vary across socioeconomic groups and that there are important structural factors affecting the financial…

Habitat, topographical, and geographical components structuring shrubsteppe bird communities

USGS Publications Warehouse

Knick, S.T.; Rotenberry, J.T.; Leu, M.

2008-01-01

Landscapes available to birds to select for breeding locations are arrayed along multiple dimensions. Identifying the primary gradients structuring shrubsteppe bird communities in the western United States is important because widespread habitat loss and alteration are shifting the environmental template on which these birds depend. We integrated field habitat surveys, GIS coverages, and bird counts from 61 Breeding Bird Survey routes located in shrubsteppe habitats across a >800 000 km2 region to determine the gradients of habitat, topography, and geography underlying bird communities. A small set of habitat features dominated the primary environmental gradients in a canonical ordination; the 13 species in the shrubsteppe bird community were closely packed along the first two axes. Using hierarchical variance partitioning, we identified habitat as the most important pure (31% explained variation) or shared component. Topography (9%) and geography (4%) were minor components but each shared a larger contribution with habitat (habitat-topography 21%; habitat-geography 22%) in explaining the organization of the bird community. In a second tier partition of habitat structure, pure composition (% land cover) was more important (45%) than configuration (patch size and edge) (7%); the two components shared 27% of the explained variation in the bird community axes. Local (9%), community (14%), and landscape (10%) levels contributed equally. Adjacent organizational levels had a larger shared contribution (local-community 26%; community-landscape 27%) than more separated local-landscape levels (21%). Extensive conversion of shrubsteppe habitats to agriculture, exotic annual grasslands, or pinyon (Pinus spp.)-juniper (Juniperus spp.) woodlands is occurring along the primary axes of habitat structure. Because the shrubsteppe bird community was organized along short gradients dominated by habitat features, relatively small shifts in their available environment will exert a strong influence on these bird populations in the absence of buffering by alternative gradients. ?? 2008 The Authors.

Fusion of multichannel local and global structural cues for photo aesthetics evaluation.

PubMed

Luming Zhang; Yue Gao; Zimmermann, Roger; Qi Tian; Xuelong Li

2014-03-01

Photo aesthetic quality evaluation is a fundamental yet under addressed task in computer vision and image processing fields. Conventional approaches are frustrated by the following two drawbacks. First, both the local and global spatial arrangements of image regions play an important role in photo aesthetics. However, existing rules, e.g., visual balance, heuristically define which spatial distribution among the salient regions of a photo is aesthetically pleasing. Second, it is difficult to adjust visual cues from multiple channels automatically in photo aesthetics assessment. To solve these problems, we propose a new photo aesthetics evaluation framework, focusing on learning the image descriptors that characterize local and global structural aesthetics from multiple visual channels. In particular, to describe the spatial structure of the image local regions, we construct graphlets small-sized connected graphs by connecting spatially adjacent atomic regions. Since spatially adjacent graphlets distribute closely in their feature space, we project them onto a manifold and subsequently propose an embedding algorithm. The embedding algorithm encodes the photo global spatial layout into graphlets. Simultaneously, the importance of graphlets from multiple visual channels are dynamically adjusted. Finally, these post-embedding graphlets are integrated for photo aesthetics evaluation using a probabilistic model. Experimental results show that: 1) the visualized graphlets explicitly capture the aesthetically arranged atomic regions; 2) the proposed approach generalizes and improves four prominent aesthetic rules; and 3) our approach significantly outperforms state-of-the-art algorithms in photo aesthetics prediction.

Ferroelectric Domain Structure and Local Piezoelectric Properties of Lead-Free (Ka0.5Na0.5)NbO3 and BiFeO3-Based Piezoelectric Ceramics

PubMed Central

Alikin, Denis; Turygin, Anton; Kholkin, Andrei; Shur, Vladimir

2017-01-01

Recent advances in the development of novel methods for the local characterization of ferroelectric domains open up new opportunities not only to image, but also to control and to create desired domain configurations (domain engineering). The morphotropic and polymorphic phase boundaries that are frequently used to increase the electromechanical and dielectric performance of ferroelectric ceramics have a tremendous effect on the domain structure, which can serve as a signature of complex polarization states and link local and macroscopic piezoelectric and dielectric responses. This is especially important for the study of lead-free ferroelectric ceramics, which is currently replacing traditional lead-containing materials, and great efforts are devoted to increasing their performance to match that of lead zirconate titanate (PZT). In this work, we provide a short overview of the recent progress in the imaging of domain structure in two major families of ceramic lead-free systems based on BiFeO3 (BFO) and (Ka0.5Na0.5)NbO3 (KNN). This can be used as a guideline for the understanding of domain processes in lead-free piezoelectric ceramics and provide further insight into the mechanisms of structure–property relationship in these technologically important material families. PMID:28772408

Local structure distortion induced by Ti dopants boosting the pseudocapacitance of RuO2-based supercapacitors.

PubMed

Chen, I-Li; Wei, Yu-Chen; Lu, Kueih-Tzu; Chen, Tsan-Yao; Hu, Chi-Chang; Chen, Jin-Ming

2015-10-07

Binary oxides with atomic ratios of Ru/Ti = 90/10, 70/30, and 50/50 were fabricated using H2O2-oxidative precipitation with the assistance of a cetyltrimethylammonium bromide (CTAB) template, followed by a thermal treatment at 200 °C. The characteristics of electron structure and local structure extracted from X-ray absorption spectroscopy (XAS) and transmission electron microscopy (TEM) analyses indicate that incorporation of Ti into the RuO2 lattice produces not only the local structural distortion of the RuO6 octahedra in (Ru-Ti)O2 with an increase in the central Ru-Ru distance but also a local crystallization of RuO2. Among the three binary oxides studied, (Ru70-Ti30)O2 exhibits a capacitance improvement of about 1.4-fold relative to the CTAB-modified RuO2, mainly due to the enhanced crystallinity of the distorted RuO6 structure rather than the surface area effect. Upon increasing the extent of Ti doping, the deteriorated supercapacitive performance of (Ru50-Ti50)O2 results from the formation of localized nano-clusters of TiO2 crystallites. These results provide insight into the important role of Ti doping in RuO2 that boosts the pseudocapacitive performance for RuO2-based supercapacitors. The present result is crucial for the design of new binary oxides for supercapacitor applications with extraordinary performance.

Localization of mRNA in vertebrate axonal compartments by in situ hybridization.

PubMed

Sotelo-Silveira, José Roberto; Calliari, Aldo; Kun, Alejandra; Elizondo, Victoria; Canclini, Lucía; Sotelo, José Roberto

2011-01-01

The conclusive demonstration of RNA in vertebrate axons by in situ hybridization (ISH) has been elusive. We review the most important reasons for difficulties, including low concentration of axonal RNAs, localization in specific cortical domains, and the need to isolate axons. We demonstrate the importance of axon micro-dissection to obtain a whole mount perspective of mRNA distribution in the axonal territory. We describe a protocol to perform fluorescent ISH in isolated axons and guidelines for the preservation of structural and molecular integrity of cortical RNA-containing domains (e.g., Periaxoplasmic Ribosomal Plaques, or PARPs) in isolated axoplasm.

Ab-initio atomic level stress and role of d-orbitals in CuZr, CuZn and CuY

NASA Astrophysics Data System (ADS)

Ojha, Madhusudan; Nicholson, Don M.; Egami, Takeshi

2015-03-01

Atomic level stress offers a new tool to characterize materials within the local approximation to density functional theory (DFT). Ab-initio atomic level stresses in B2 structures of CuZr, CuZn and CuY are calculated and results are explained on the basis of d-orbital contributions to Density of States (DOS). The overlap of d-orbital DOS plays an important role in the relative magnitude of atomic level stresses in these structures. The trends in atomic level stresses that we observed in these simple B2 structures are also seen in complex structures such as liquids, glasses and solid solutions. The stresses are however modified by the different coordination and relaxed separation distances in these complex structures. We used the Locally Self-Consistent Multiple Scattering (LSMS) code and Vienna Ab-initio Simulation Package (VASP) for ab-initio calculations.

Situation analysis of procurement and production of multiple micronutrient supplements in 12 lower and upper middle-income countries.

PubMed

Monterrosa, Eva C; Beesabathuni, Kalpana; van Zutphen, Kesso G; Steiger, Georg; Kupka, Roland; Fleet, Alison; Kraemer, Klaus

2017-12-26

Globally, there are few vitamin and mineral ingredient manufacturers. To support local, in-country or regional procurement and production of multiple micronutrient supplements (MMS), the following production scenarios are possible: (a) straight ingredients of vitamins and minerals forms imported or locally produced that are mixed, tableted, or encapsulated and packaged by a local manufacturer; (b) import or local production of a vitamin and minerals premix that is tableted or encapsulated and packaged locally; (c) import of a bulk, finished product (tablets or capsules) that is packaged and branded; and (d) or import of a branded packaged product. This paper is a situation analysis of the market, manufacturing, and policy factors that are driving the production of MMS in 12 lower and upper middle-income countries. Key informants completed a self-administered structured questionnaire, which examined the local context of products available in the market and their cost, regulations and policies, in Brazil, Colombia, Guatemala, Mexico, Peru, Bangladesh, India, Vietnam, Ghana, Kenya, Nigeria, and South Africa. Our study found that although most countries have the capacity to produce locally MMS, the major barriers observed for sustainable and affordable production include (a) poor technical capacity and policies for ensuring quality along the value chain and (b) lack of policy coherence to incentivize local production and lower the manufacture and retail price of MMS. Also, better guidelines and government oversight will be required because not one country had an MMS formulation that matched the globally recommended formulation of the United Nations Multiple Micronutrient Preparation (UNIMMAP). © 2018 John Wiley & Sons Ltd.

Activation of preexisting transverse structures in an evolving magmatic rift in East Africa

NASA Astrophysics Data System (ADS)

Muirhead, J. D.; Kattenhorn, S. A.

2018-01-01

Inherited crustal weaknesses have long been recognized as important factors in strain localization and basin development in the East African Rift System (EARS). However, the timing and kinematics (e.g., sense of slip) of transverse (rift-oblique) faults that exploit these weaknesses are debated, and thus the roles of inherited weaknesses at different stages of rift basin evolution are often overlooked. The mechanics of transverse faulting were addressed through an analysis of the Kordjya fault of the Magadi basin (Kenya Rift). Fault kinematics were investigated from field and remote-sensing data collected on fault and joint systems. Our analysis indicates that the Kordjya fault consists of a complex system of predominantly NNE-striking, rift-parallel fault segments that collectively form a NNW-trending array of en echelon faults. The transverse Kordjya fault therefore reactivated existing rift-parallel faults in ∼1 Ma lavas as oblique-normal faults with a component of sinistral shear. In all, these fault motions accommodate dip-slip on an underlying transverse structure that exploits the Aswa basement shear zone. This study shows that transverse faults may be activated through a complex interplay among magma-assisted strain localization, preexisting structures, and local stress rotations. Rather than forming during rift initiation, transverse structures can develop after the establishment of pervasive rift-parallel fault systems, and may exhibit dip-slip kinematics when activated from local stress rotations. The Kordjya fault is shown here to form a kinematic linkage that transfers strain to a newly developing center of concentrated magmatism and normal faulting. It is concluded that recently activated transverse faults not only reveal the effects of inherited basement weaknesses on fault development, but also provide important clues regarding developing magmatic and tectonic systems as young continental rift basins evolve.

Manipulation of local optical properties and structures in molybdenum-disulfide monolayers using electric field-assisted near-field techniques.

PubMed

Nozaki, Junji; Fukumura, Musashi; Aoki, Takaaki; Maniwa, Yutaka; Yomogida, Yohei; Yanagi, Kazuhiro

2017-04-05

Remarkable optical properties, such as quantum light emission and large optical nonlinearity, have been observed in peculiar local sites of transition metal dichalcogenide monolayers, and the ability to tune such properties is of great importance for their optoelectronic applications. For that purpose, it is crucial to elucidate and tune their local optical properties simultaneously. Here, we develop an electric field-assisted near-field technique. Using this technique we can clarify and tune the local optical properties simultaneously with a spatial resolution of approximately 100 nm due to the electric field from the cantilever. The photoluminescence at local sites in molybdenum-disulfide (MoS 2 ) monolayers is reversibly modulated, and the inhomogeneity of the charge neutral points and quantum yields is suggested. We successfully etch MoS 2 crystals and fabricate nanoribbons using near-field techniques in combination with an electric field. This study creates a way to tune the local optical properties and to freely design the structural shapes of atomic monolayers using near-field optics.

Robust Measurement via A Fused Latent and Graphical Item Response Theory Model.

PubMed

Chen, Yunxiao; Li, Xiaoou; Liu, Jingchen; Ying, Zhiliang

2018-03-12

Item response theory (IRT) plays an important role in psychological and educational measurement. Unlike the classical testing theory, IRT models aggregate the item level information, yielding more accurate measurements. Most IRT models assume local independence, an assumption not likely to be satisfied in practice, especially when the number of items is large. Results in the literature and simulation studies in this paper reveal that misspecifying the local independence assumption may result in inaccurate measurements and differential item functioning. To provide more robust measurements, we propose an integrated approach by adding a graphical component to a multidimensional IRT model that can offset the effect of unknown local dependence. The new model contains a confirmatory latent variable component, which measures the targeted latent traits, and a graphical component, which captures the local dependence. An efficient proximal algorithm is proposed for the parameter estimation and structure learning of the local dependence. This approach can substantially improve the measurement, given no prior information on the local dependence structure. The model can be applied to measure both a unidimensional latent trait and multidimensional latent traits.

Geographical ecology of the palms (Arecaceae): determinants of diversity and distributions across spatial scales

PubMed Central

Eiserhardt, Wolf L.; Svenning, Jens-Christian; Kissling, W. Daniel; Balslev, Henrik

2011-01-01

Background The palm family occurs in all tropical and sub-tropical regions of the world. Palms are of high ecological and economical importance, and display complex spatial patterns of species distributions and diversity. Scope This review summarizes empirical evidence for factors that determine palm species distributions, community composition and species richness such as the abiotic environment (climate, soil chemistry, hydrology and topography), the biotic environment (vegetation structure and species interactions) and dispersal. The importance of contemporary vs. historical impacts of these factors and the scale at which they function is discussed. Finally a hierarchical scale framework is developed to guide predictor selection for future studies. Conclusions Determinants of palm distributions, composition and richness vary with spatial scale. For species distributions, climate appears to be important at landscape and broader scales, soil, topography and vegetation at landscape and local scales, hydrology at local scales, and dispersal at all scales. For community composition, soil appears important at regional and finer scales, hydrology, topography and vegetation at landscape and local scales, and dispersal again at all scales. For species richness, climate and dispersal appear to be important at continental to global scales, soil at landscape and broader scales, and topography at landscape and finer scales. Some scale–predictor combinations have not been studied or deserve further attention, e.g. climate on regional to finer scales, and hydrology and topography on landscape and broader scales. The importance of biotic interactions – apart from general vegetation structure effects – for the geographic ecology of palms is generally underexplored. Future studies should target scale–predictor combinations and geographic domains not studied yet. To avoid biased inference, one should ideally include at least all predictors previously found important at the spatial scale of investigation. PMID:21712297

Intracellular Localization and Cellular Factors Interaction of HTLV-1 and HTLV-2 Tax Proteins: Similarities and Functional Differences

PubMed Central

Bertazzoni, Umberto; Turci, Marco; Avesani, Francesca; Di Gennaro, Gianfranco; Bidoia, Carlo; Romanelli, Maria Grazia

2011-01-01

Human T-lymphotropic viruses type 1 (HTLV-1) and type 2 (HTLV-2) present very similar genomic structures but HTLV-1 is more pathogenic than HTLV-2. Is this difference due to their transactivating Tax proteins, Tax-1 and Tax-2, which are responsible for viral and cellular gene activation? Do Tax-1 and Tax-2 differ in their cellular localization and in their interaction pattern with cellular factors? In this review, we summarize Tax-1 and Tax-2 structural and phenotypic properties, their interaction with factors involved in signal transduction and their localization-related behavior within the cell. Special attention will be given to the distinctions between Tax-1 and Tax-2 that likely play an important role in their transactivation activity. PMID:21994745

Characterization of the Bm61 of the Bombyx mori nucleopolyhedrovirus.

PubMed

Shen, Hongxing; Chen, Keping; Yao, Qin; Zhou, Yang

2009-07-01

orf61 (bm61) of Bombyx mori Nucleopolyhedrovirus (BmNPV) is a highly conserved baculovirus gene, suggesting that it performs an important role in the virus life cycle whose function is unknown. In this study, we describe the characterization of bm61. Quantitative polymerase chain reaction (qPCR) and western blot analysis demonstrated that bm61 was expressed as a late gene. Immunofluorescence analysis by confocal microscopy showed that BM61 protein was localized on nuclear membrane and in intranuclear ring zone of infected cells. Structure localization of the BM61 in BV and ODV by western analysis demonstrated that BM61 was the protein of both BV and ODV. In addition, our data indicated that BM61 was a late structure protein localized in nucleus.

Local Descriptors of Dynamic and Nondynamic Correlation.

PubMed

Ramos-Cordoba, Eloy; Matito, Eduard

2017-06-13

Quantitatively accurate electronic structure calculations rely on the proper description of electron correlation. A judicious choice of the approximate quantum chemistry method depends upon the importance of dynamic and nondynamic correlation, which is usually assesed by scalar measures. Existing measures of electron correlation do not consider separately the regions of the Cartesian space where dynamic or nondynamic correlation are most important. We introduce real-space descriptors of dynamic and nondynamic electron correlation that admit orbital decomposition. Integration of the local descriptors yields global numbers that can be used to quantify dynamic and nondynamic correlation. Illustrative examples over different chemical systems with varying electron correlation regimes are used to demonstrate the capabilities of the local descriptors. Since the expressions only require orbitals and occupation numbers, they can be readily applied in the context of local correlation methods, hybrid methods, density matrix functional theory, and fractional-occupancy density functional theory.

Sound localization in the alligator.

PubMed

Bierman, Hilary S; Carr, Catherine E

2015-11-01

In early tetrapods, it is assumed that the tympana were acoustically coupled through the pharynx and therefore inherently directional, acting as pressure difference receivers. The later closure of the middle ear cavity in turtles, archosaurs, and mammals is a derived condition, and would have changed the ear by decoupling the tympana. Isolation of the middle ears would then have led to selection for structural and neural strategies to compute sound source localization in both archosaurs and mammalian ancestors. In the archosaurs (birds and crocodilians) the presence of air spaces in the skull provided connections between the ears that have been exploited to improve directional hearing, while neural circuits mediating sound localization are well developed. In this review, we will focus primarily on directional hearing in crocodilians, where vocalization and sound localization are thought to be ecologically important, and indicate important issues still awaiting resolution. Copyright © 2015 Elsevier B.V. All rights reserved.

How Connecticut health directors deal with public health budget cuts at the local level.

PubMed

Prust, Margaret L; Clark, Kathleen; Davis, Brigette; Pallas, Sarah W; Kertanis, Jennifer; O'Keefe, Elaine; Araas, Michael; Iyer, Neel S; Dandorf, Stewart; Platis, Stephanie; Humphries, Debbie

2015-04-01

We investigated the perspectives of local health jurisdiction (LHJ) directors on coping mechanisms used to respond to budget reductions and constraints on their decision-making. We conducted in-depth interviews with 17 LHJ directors. Interviews were audio recorded, transcribed, and analyzed using the constant comparative method. LHJ directors use a range of coping mechanisms, including identifying alternative revenue sources, adjusting services, amending staffing arrangements, appealing to local political leaders, and forming strategic partnerships. LHJs also face constraints on their decision-making because of state and local statutory requirements, political priorities, pressures from other LHJs, and LHJ structure. LHJs respond creatively to budget cuts to maintain important public health services. Some LHJ adjustments to administrative resources may obscure the long-term costs of public health budget cuts in such areas as staff morale and turnover. Not all coping strategies are available to each LHJ because of the contextual constraints of its locality, pointing to important policy questions on identifying optimum jurisdiction size and improving efficiency.

Energy Based Topology Optimization of Morphing Wings a Multidisciplinary Global/Local Design Approach

DTIC Science & Technology

2006-12-01

subsystem that drives the active materials to achieve the desired shape changes. As opposed to fixed wing structures in which the aerodynamic and...structures and aerodynamics occur in conjunction with the active material and electronic subsystem interactions that involve transfer of energy from a source...which the aerodynamic and structure integration for the entire wing is the most important interaction mechanism, in the case of a morphing wing

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

Mixed severity fire effects within the Rim fire: Relative importance of local climate, fire weather, topography, and forest structure

Treesearch

Van R. Kane; C. Alina Cansler; Nicholas A. Povak; Jonathan T. Kane; Robert J. McGaughey; James A. Lutz; Derek J. Churchill; Malcolm P. North

2015-01-01

Recent and projected increases in the frequency and severity of large wildfires in the western U.S. makes understanding the factors that strongly affect landscape fire patterns a management priority for optimizing treatment location. We compared the influence of variations in the local environment on burn severity patterns on the large 2013 Rim fire that burned under...

Discontinuities, cross-scale patterns, and the organizationof ecosystems

EPA Science Inventory

Ecological structures and processes occur at specific spatiotemporal scales, and interactions that occur across multiple scales mediate scale-specific (e.g., individual,community, local, or regional) responses to disturbance. Despite the importance of scale,explicitly incorporat...

Understanding and quantifying urban forest structure, functions, and value

Treesearch

David J. Nowak; Daniel E. Crane; Jeffrey T. Walton; Daniel B. Twardus; John F. Dwyer

2002-01-01

Trees in urban areas can have a significant impact on human health and the environment. Unfortunately, there is relatively little data about the structure, health, functions, and long-term changes in this important resource. In the United States, a number of efforts are underway to assess urban forest attributes at the local to national scales. In addition, tools are...

Analyzing canopy structure in Pacific Northwest old-growth forests with a stand-scale crown model

Treesearch

Robert Van Pelt; Malcolm P. North

1996-01-01

I n forests, the canopy is the locale of critical ecosystem processes such as photosynthesis and evapotranspiration. and it provides essential habitat for a highly diverse array of animals, plants, and other organisms. Despite its importance, the structure of the canopy as a whole has had little quantitative study because limited access makes quantification difficult...

Structural Connectivity Networks of Transgender People

PubMed Central

Hahn, Andreas; Kranz, Georg S.; Küblböck, Martin; Kaufmann, Ulrike; Ganger, Sebastian; Hummer, Allan; Seiger, Rene; Spies, Marie; Winkler, Dietmar; Kasper, Siegfried; Windischberger, Christian; Swaab, Dick F.; Lanzenberger, Rupert

2015-01-01

Although previous investigations of transsexual people have focused on regional brain alterations, evaluations on a network level, especially those structural in nature, are largely missing. Therefore, we investigated the structural connectome of 23 female-to-male (FtM) and 21 male-to-female (MtF) transgender patients before hormone therapy as compared with 25 female and 25 male healthy controls. Graph theoretical analysis of whole-brain probabilistic tractography networks (adjusted for differences in intracranial volume) showed decreased hemispheric connectivity ratios of subcortical/limbic areas for both transgender groups. Subsequent analysis revealed that this finding was driven by increased interhemispheric lobar connectivity weights (LCWs) in MtF transsexuals and decreased intrahemispheric LCWs in FtM patients. This was further reflected on a regional level, where the MtF group showed mostly increased local efficiencies and FtM patients decreased values. Importantly, these parameters separated each patient group from the remaining subjects for the majority of significant findings. This work complements previously established regional alterations with important findings of structural connectivity. Specifically, our data suggest that network parameters may reflect unique characteristics of transgender patients, whereas local physiological aspects have been shown to represent the transition from the biological sex to the actual gender identity. PMID:25217469

Local Chemical Ordering and Negative Thermal Expansion in PtNi Alloy Nanoparticles.

PubMed

Li, Qiang; Zhu, He; Zheng, Lirong; Fan, Longlong; Wang, Na; Rong, Yangchun; Ren, Yang; Chen, Jun; Deng, Jinxia; Xing, Xianran

2017-12-13

An atomic insight into the local chemical ordering and lattice strain is particular interesting to recent emerging bimetallic nanocatalysts such as PtNi alloys. Here, we reported the atomic distribution, chemical environment, and lattice thermal evolution in full-scale structural description of PtNi alloy nanoparticles (NPs). The different segregation of elements in the well-faceted PtNi nanoparticles is convinced by extended X-ray absorption fine structure (EXAFS). Atomic pair distribution function (PDF) study evidences the coexistence of the face-centered cubic and tetragonal ordering parts in the local environment of PtNi nanoparticles. Further reverse Monte Carlo (RMC) simulation with PDF data obviously exposed the segregation as Ni and Pt in the centers of {111} and {001} facets, respectively. Layer-by-layer statistical analysis up to 6 nm for the local atomic pairs revealed the distribution of local tetragonal ordering on the surface. This local coordination environment facilitates the distribution of heteroatomic Pt-Ni pairs, which plays an important role in the negative thermal expansion of Pt 41 Ni 59 NPs. The present study on PtNi alloy NPs from local short-range coordination to long-range average lattice provides a new perspective on tailoring physical properties in nanomaterials.

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

Paterson, Carolyn P.; Ayalew, Lisanework E.; Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK S7N 5E3 S7N 5B4 Canada

The L1 region of bovine adenovirus (BAdV)-3 encodes a non-structural protein designated 52K. Anti-52K serum detected a protein of 40 kDa, which localized to the nucleus but not to the nucleolus in BAdV-3-infected or transfected cells. Analysis of mutant 52K proteins suggested that three basic residues ({sup 105}RKR{sup 107}) of the identified domain (amino acids {sup 102}GMPRKRVLT{sup 110}) are essential for nuclear localization of 52K. The nuclear import of a GST-52K fusion protein utilizes the classical importin {alpha}/{beta}-dependent nuclear transport pathway. The 52K protein is preferentially bound to the cellular nuclear import receptor importin {alpha}3. Although deletion of amino acidmore » 102-110 is sufficient to abrogate the nuclear localization of 52K, amino acid 90-133 are required for interaction with importin-{alpha}3 and localizing a cytoplasmic protein to the nucleus. These results suggest that 52K contains a bipartite NLS, which preferentially utilize an importin {alpha}3 nuclear import receptor-mediated pathway to transport 52K to the nucleus.« less

CNNH_PSS: protein 8-class secondary structure prediction by convolutional neural network with highway.

PubMed

Zhou, Jiyun; Wang, Hongpeng; Zhao, Zhishan; Xu, Ruifeng; Lu, Qin

2018-05-08

Protein secondary structure is the three dimensional form of local segments of proteins and its prediction is an important problem in protein tertiary structure prediction. Developing computational approaches for protein secondary structure prediction is becoming increasingly urgent. We present a novel deep learning based model, referred to as CNNH_PSS, by using multi-scale CNN with highway. In CNNH_PSS, any two neighbor convolutional layers have a highway to deliver information from current layer to the output of the next one to keep local contexts. As lower layers extract local context while higher layers extract long-range interdependencies, the highways between neighbor layers allow CNNH_PSS to have ability to extract both local contexts and long-range interdependencies. We evaluate CNNH_PSS on two commonly used datasets: CB6133 and CB513. CNNH_PSS outperforms the multi-scale CNN without highway by at least 0.010 Q8 accuracy and also performs better than CNF, DeepCNF and SSpro8, which cannot extract long-range interdependencies, by at least 0.020 Q8 accuracy, demonstrating that both local contexts and long-range interdependencies are indeed useful for prediction. Furthermore, CNNH_PSS also performs better than GSM and DCRNN which need extra complex model to extract long-range interdependencies. It demonstrates that CNNH_PSS not only cost less computer resource, but also achieves better predicting performance. CNNH_PSS have ability to extracts both local contexts and long-range interdependencies by combing multi-scale CNN and highway network. The evaluations on common datasets and comparisons with state-of-the-art methods indicate that CNNH_PSS is an useful and efficient tool for protein secondary structure prediction.

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

PubMed

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

2016-01-01

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

Si-centered capped trigonal prism ordering in liquid Pd 82Si 18 alloy study by first-principles calculations

DOE PAGES

Dong, F.; Yue, G. Q.; Ames Lab. and Iowa State Univ., Ames, IA; ...

2017-03-24

First-principles molecular dynamic (MD) simulation and X-ray diffraction were employed to study the local structures of Pd–Si liquid at the eutectic composition (Pd 82Si 18). Here, a strong repulsion is found between Si atoms, and Si atoms prefer to be evenly distributed in the liquid. The dominate local structures around Si atoms are found to be with of a trigonal prism capped by three half-octahedra and an archimedean anti-prism. The populations of these clusters increase significantly upon cooling, and may play an important role in the formation of Pd 82Si 18 alloy glass.

Si-centered capped trigonal prism ordering in liquid Pd 82Si 18 alloy study by first-principles calculations

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

Dong, F.; Yue, G. Q.; Ames Lab. and Iowa State Univ., Ames, IA

First-principles molecular dynamic (MD) simulation and X-ray diffraction were employed to study the local structures of Pd–Si liquid at the eutectic composition (Pd 82Si 18). Here, a strong repulsion is found between Si atoms, and Si atoms prefer to be evenly distributed in the liquid. The dominate local structures around Si atoms are found to be with of a trigonal prism capped by three half-octahedra and an archimedean anti-prism. The populations of these clusters increase significantly upon cooling, and may play an important role in the formation of Pd 82Si 18 alloy glass.

Participation of Xenopus Elr-type Proteins in Vegetal mRNA Localization during Oogenesis*

PubMed Central

Arthur, Patrick K.; Claussen, Maike; Koch, Susanne; Tarbashevich, Katsiaryna; Jahn, Olaf; Pieler, Tomas

2009-01-01

Directional transport of specific mRNAs is of primary biological relevance. In Xenopus oocytes, mRNA localization to the vegetal pole is important for germ layer formation and germ cell development. Using a biochemical approach, we identified Xenopus Elr-type proteins, homologs of the Hu/ELAV proteins, as novel components of the vegetal mRNA localization machinery. They bind specifically to the localization elements of several different vegetally localizing Xenopus mRNAs, and they are part of one RNP together with other localization proteins, such as Vg1RBP and XStaufen 1. Blocking Elr-type protein binding by either localization element mutagenesis or antisense morpholino oligonucleotide-mediated masking of their target RNA structures, as well as overexpression of wild type and mutant ElrB proteins, interferes with vegetal localization in Xenopus oocytes. PMID:19458392

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.

Local Structure Evolution and Modes of Charge Storage in Secondary Li–FeS 2 Cells

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

Butala, Megan M.; Mayo, Martin; Doan-Nguyen, Vicky V. T.

2017-03-27

In the pursuit of high-capacity electrochemical energy storage, a promising domain of research involves conversion reaction schemes, wherein electrode materials are fully transformed during charge and discharge. There are, however, numerous difficulties in realizing theoretical capacity and high rate capability in many conversion schemes. Here we employ operando studies to understand the conversion material FeS2, focusing on the local structure evolution of this relatively reversible material. X-ray absorption spectroscopy, pair distribution function analysis, and first-principles calculations of intermediate structures shed light on the mechanism of charge storage in the Li-FeS2 system, with some general principles emerging for charge storage inmore » chalcogenide materials. Focusing on second and later charge/discharge cycles, we find small, disordered domains that locally resemble Fe and Li2S at the end of the first discharge. Upon charge, this is converted to a Li-Fe-S composition whose local structure reveals tetrahedrally coordinated Fe. With continued charge, this ternary composition displays insertion extraction behavior at higher potentials and lower Li content. The finding of hybrid modes of charge storage, rather than simple conversion, points to the important role of intermediates that appear to store charge by mechanisms that more closely resemble intercalation.« less

Imaging chromatin nanostructure with binding-activated localization microscopy based on DNA structure fluctuations

PubMed Central

Szczurek, Aleksander; Klewes, Ludger; Xing, Jun; Gourram, Amine; Birk, Udo; Knecht, Hans; Dobrucki, Jurek W.; Mai, Sabine

2017-01-01

Abstract Advanced light microscopy is an important tool for nanostructure analysis of chromatin. In this report we present a general concept for Single Molecule localization Microscopy (SMLM) super-resolved imaging of DNA-binding dyes based on modifying the properties of DNA and the dye. By careful adjustment of the chemical environment leading to local, reversible DNA melting and hybridization control over the fluorescence signal of the DNA-binding dye molecules can be introduced. We postulate a transient binding as the basis for our variation of binding-activated localization microscopy (BALM). We demonstrate that several intercalating and minor-groove binding DNA dyes can be used to register (optically isolate) only a few DNA-binding dye signals at a time. To highlight this DNA structure fluctuation-assisted BALM (fBALM), we applied it to measure, for the first time, nanoscale differences in nuclear architecture in model ischemia with an anticipated structural resolution of approximately 50 nm. Our data suggest that this approach may open an avenue for the enhanced microscopic analysis of chromatin nano-architecture and hence the microscopic analysis of nuclear structure aberrations occurring in various pathological conditions. It may also become possible to analyse nuclear nanostructure differences in different cell types, stages of development or environmental stress conditions. PMID:28082388

Diffuse Scattering from Lead-Containing Ferroelectric Perovskite Oxides

DOE PAGES

Goossens, D. J.

2013-01-01

Ferroelectric materials rely on some type of non-centrosymmetric displacement correlations to give rise to a macroscopic polarisation. These displacements can show short-range order (SRO) that is reflective of the local chemistry, and so studying it reveals important information about how the structure gives rise to the technologically useful properties. A key means of exploring this SRO is diffuse scattering. Conventional structural studies use Bragg peak intensitiesto determine the average structure. In a single crystal diffuse scattering (SCDS) experiment, the coherent scattered intensity is measured at non-integer Miller indices, and can be used to examine the population of local configurations. Thismore » is because the diffuse scattering is sensitive to two-body averages, whereas the Bragg intensity gives single-body averages. This review outlines key results of SCDS studies on several materials and explores the similarities and differences in their diffuse scattering. Random strains are considered, as are models based on a phonon-like picture or a more local-chemistry oriented picture. Limitations of the technique are discussed.« less

Voices of the poor from the margins of Bengal: structural inequities and health.

PubMed

Dutta, Mohan J; Dutta, Uttaran

2013-01-01

In opposition to the traditional approaches to health communication that treat the subaltern sectors as passive recipients of messages of enlightenment configured in top-down interventions, the culture-centered approach foregrounds the importance of listening to subaltern communities at the margins through dialogue. We build on earlier culture-centered projects in rural communities of West Bengal, India, to develop participatory research strategies for understanding the local processes through which the structural marginalization of the poor plays out in rural Bengal. Study results point toward the marginalization of the poor both communicatively and economically, attending to the ways in which communicative marginalization lies at the heart of economic oppressions. Through locally articulated concepts of "health as shortage" and "communication as shortage," community members put forth alternative rationalities of health that highlight structural resources at the heart of health. These local articulations of shortage offer an alternative rationality for organizing health promotion efforts in the rural margins of Bengal through the foregrounding of discourses of shortage.

Localized electronic structures of graphene oxide studied using scanning tunneling microscopy and spectroscopy.

PubMed

Katano, Satoshi; Wei, Tao; Sasajima, Takumi; Kasama, Ryuhei; Uehara, Yoichi

2018-06-21

We have used scanning tunneling microscopy (STM) to elucidate the nanoscale electronic structures of graphene oxide (GO). The unreduced GO layer was imaged using STM without reduction processes when deposited on a Au(111) surface covered with an octanethiolate self-assembled monolayer (C8S-SAM). The STM image of the GO sheet exhibits a grainy structure having a thickness of about 1 nm, which is in good agreement with the previous results obtained using atomic force microscopy (AFM). We found that the C8S-SAM suppresses the adsorption of water remaining on the substrate, which would be important to accomplish the nanoscale imaging of the unreduced GO by STM. Furthermore, we successfully detected the π and π* states localized in the GO sheet using scanning tunneling spectroscopy (STS). The π-π* gap energy and the gap center are not uniform within the GO sheet, indicating the existence of various sizes of the sp2 domain and evidence for the local electronic doping by the substituents.

The CLAIR model: Extension of Brodmann areas based on brain oscillations and connectivity.

PubMed

Başar, Erol; Düzgün, Aysel

2016-05-01

Since the beginning of the last century, the localization of brain function has been represented by Brodmann areas, maps of the anatomic organization of the brain. They are used to broadly represent cortical structures with their given sensory-cognitive functions. In recent decades, the analysis of brain oscillations has become important in the correlation of brain functions. Moreover, spectral connectivity can provide further information on the dynamic connectivity between various structures. In addition, brain responses are dynamic in nature and structural localization is almost impossible, according to Luria (1966). Therefore, brain functions are very difficult to localize; hence, a combined analysis of oscillation and event-related coherences is required. In this study, a model termed as "CLAIR" is described to enrich and possibly replace the concept of the Brodmann areas. A CLAIR model with optimum function may take several years to develop, but this study sets out to lay its foundation. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

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.

Aspirin locally disrupts the liquid-ordered phase

NASA Astrophysics Data System (ADS)

Alsop, Richard J.; Himbert, Sebastian; Dhaliwal, Alexander; Schmalzl, Karin; Rheinstädter, Maikel C.

2018-02-01

Local structure and dynamics of lipid membranes play an important role in membrane function. The diffusion of small molecules, the curvature of lipids around a protein and the existence of cholesterol-rich lipid domains (rafts) are examples for the membrane to serve as a functional interface. The collective fluctuations of lipid tails, in particular, are relevant for diffusion of membrane constituents and small molecules in and across membranes, and for structure and formation of membrane domains. We studied the effect of aspirin (acetylsalicylic acid, ASA) on local structure and dynamics of membranes composed of dimyristoylphosphocholine (DMPC) and cholesterol. Aspirin is a common analgesic, but is also used in the treatment of cholesterol. Using coherent inelastic neutron scattering experiments and molecular dynamics (MD) simulations, we present evidence that ASA binds to liquid-ordered, raft-like domains and disturbs domain organization and dampens collective fluctuations. By hydrogen-bonding to lipid molecules, ASA forms `superfluid' complexes with lipid molecules that can organize laterally in superlattices and suppress cholesterol's ordering effect.

A smart composite patch for the repair of aircraft structures

NASA Astrophysics Data System (ADS)

Wakha, Kelah; Samuel, Paul; Pines, Darryll J.

2005-05-01

Recent interest in bonded composite patch repair technology for aerospace systems is because this method can be carried out at a reduced cost and time and can easily be applied to complex geometric structures. This paper details the development of a dual stiffness/energy sensor for monitoring the integrity of a composite patch used to repair an aluminum structural component. The smart sensor has the ability to predict the elastic field of a given host structure based on the strain state of two sub-sensors integrated into the structure. The present study shows the possibility of using the sensor to deduce the local instantaneous host stiffness. Damaged structures are characterized by a reduction in their elastic stiffness that evolve from microstructural defects. A local smart sensor can be developed to sense the local average properties on a host. In this paper, sensors are attached to a structure and a modified Eshelby's equivalent inclusion method is used to derive the elastic properties of the host. An analytical derivation and a sensitivity analysis for the quasistatic application is given in a papers by Majed, Dasgupta, Kelah and Pines. A summary of the derivation of the dynamic Eshelby tensor is presented. This is of importance because damage detection in structures undergoing vibratory and other motions present a greater challenge than those in quasistatic motion. An in-situ health monitoring active sensor system for a real structure (an aluminum plate with an attached repair patch) under close-to real lifecycle loading conditions is developed. The detection of the onset of any damage to the structure as well as the repair patch and the subsequent monitoring of the growth of this damage constitute important goals of the system. Both experimental and finite element methods were applied. Experimental results are presented for tests of the aluminum plate with the repair patch under monotonic quasi-static and dynamic loading vibratory conditions. In summary, the study shows that smart bonded composite repair patches are very effective in the repair of thin aluminum structures since they are able to determine the integrity of the repair structure as well as the repair patch.

Post-fire tree establishment patterns at the alpine treeline ecotone: Mount Rainier National Park, Washington, USA

Treesearch

Kirk M. Stueve; Dawna L. Cerney; Regina M. Rochefort; Laurie L. Kurth

2009-01-01

Questions: Does tree establishment: (1) occur at a treeline depressed by fire, (2) cause the forest line to ascend upslope, and/or (3) alter landscape heterogeneity? (4) What abiotic and biotic local site conditions are most important in structuring establishment patterns? (5) Does the abiotic setting become more important with increasing upslope distance from the...

The role of local interaction mechanics in fiber optic smart structures

NASA Astrophysics Data System (ADS)

Sirkis, J. S.; Dasgupta, A.

1993-04-01

The concept of using 'smart' composite materials/structures with built-in self-diagnostic capabilities for health monitoring involves embedding discrete and/or distributed sensory networks in the host composite material, along with a central and/or distributed artificial intelligence capability for signal processing, data collection, interpretation and diagnostic evaluations. This article concentrates on the sensory functions in 'smart' structure applications and concentrates in particular on optical fiber sensors. Specifically, we present an overview of recent research dealing with the basic mechanics of local interactions between the embedded optical fiber sensors and the surrounding host composite. The term 'local' is defined by length scales on the order of several optical fiber diameters. We examine some generic issues, such as the 'calibration' and 'obtrusivity' of the sensor, and the inherent damage caused by the sensor inclusions to the surrounding host and vice-versa under internal and/or external applied loads. Analytical, numerical and experimental results are presented regarding the influence of local strain concentrations caused by the sensory inclusions on sensor and host performance. The important issues examined are the local mechanistic effects of optical fiber coatings on the behavior of the sensor and the host, and mechanical survivability of optical fibers experiencing quasi-static and time-varying thermomechanical loading.

Raman Microscopy: A Noninvasive Method to Visualize the Localizations of Biomolecules in the Cornea.

PubMed

Kaji, Yuichi; Akiyama, Toshihiro; Segawa, Hiroki; Oshika, Tetsuro; Kano, Hideaki

2017-11-01

In vivo and in situ visualization of biomolecules without pretreatment will be important for diagnosis and treatment of ocular disorders in the future. Recently, multiphoton microscopy, based on the nonlinear interactions between molecules and photons, has been applied to reveal the localizations of various molecules in tissues. We aimed to use multimodal multiphoton microscopy to visualize the localizations of specific biomolecules in rat corneas. Multiphoton images of the corneas were obtained from nonlinear signals of coherent anti-Stokes Raman scattering, third-order sum frequency generation, and second-harmonic generation. The localizations of the adhesion complex-containing basement membrane and Bowman layer were clearly visible in the third-order sum frequency generation images. The fine structure of type I collagen was observed in the corneal stroma in the second-harmonic generation images. The localizations of lipids, proteins, and nucleic acids (DNA/RNA) was obtained in the coherent anti-Stokes Raman scattering images. Imaging technologies have progressed significantly and been applied in medical fields. Optical coherence tomography and confocal microscopy are widely used but do not provide information on the molecular structure of the cornea. By contrast, multiphoton microscopy provides information on the molecular structure of living tissues. Using this technique, we successfully visualized the localizations of various biomolecules including lipids, proteins, and nucleic acids in the cornea. We speculate that multiphoton microscopy will provide essential information on the physiological and pathological conditions of the cornea, as well as molecular localizations in tissues without pretreatment.

Machine learning to design integral membrane channelrhodopsins for efficient eukaryotic expression and plasma membrane localization.

PubMed

Bedbrook, Claire N; Yang, Kevin K; Rice, Austin J; Gradinaru, Viviana; Arnold, Frances H

2017-10-01

There is growing interest in studying and engineering integral membrane proteins (MPs) that play key roles in sensing and regulating cellular response to diverse external signals. A MP must be expressed, correctly inserted and folded in a lipid bilayer, and trafficked to the proper cellular location in order to function. The sequence and structural determinants of these processes are complex and highly constrained. Here we describe a predictive, machine-learning approach that captures this complexity to facilitate successful MP engineering and design. Machine learning on carefully-chosen training sequences made by structure-guided SCHEMA recombination has enabled us to accurately predict the rare sequences in a diverse library of channelrhodopsins (ChRs) that express and localize to the plasma membrane of mammalian cells. These light-gated channel proteins of microbial origin are of interest for neuroscience applications, where expression and localization to the plasma membrane is a prerequisite for function. We trained Gaussian process (GP) classification and regression models with expression and localization data from 218 ChR chimeras chosen from a 118,098-variant library designed by SCHEMA recombination of three parent ChRs. We use these GP models to identify ChRs that express and localize well and show that our models can elucidate sequence and structure elements important for these processes. We also used the predictive models to convert a naturally occurring ChR incapable of mammalian localization into one that localizes well.

Machine learning to design integral membrane channelrhodopsins for efficient eukaryotic expression and plasma membrane localization

PubMed Central

Rice, Austin J.; Gradinaru, Viviana; Arnold, Frances H.

2017-01-01

There is growing interest in studying and engineering integral membrane proteins (MPs) that play key roles in sensing and regulating cellular response to diverse external signals. A MP must be expressed, correctly inserted and folded in a lipid bilayer, and trafficked to the proper cellular location in order to function. The sequence and structural determinants of these processes are complex and highly constrained. Here we describe a predictive, machine-learning approach that captures this complexity to facilitate successful MP engineering and design. Machine learning on carefully-chosen training sequences made by structure-guided SCHEMA recombination has enabled us to accurately predict the rare sequences in a diverse library of channelrhodopsins (ChRs) that express and localize to the plasma membrane of mammalian cells. These light-gated channel proteins of microbial origin are of interest for neuroscience applications, where expression and localization to the plasma membrane is a prerequisite for function. We trained Gaussian process (GP) classification and regression models with expression and localization data from 218 ChR chimeras chosen from a 118,098-variant library designed by SCHEMA recombination of three parent ChRs. We use these GP models to identify ChRs that express and localize well and show that our models can elucidate sequence and structure elements important for these processes. We also used the predictive models to convert a naturally occurring ChR incapable of mammalian localization into one that localizes well. PMID:29059183

The Energy Landscape Analysis of Cancer Mutations in Protein Kinases

PubMed Central

Dixit, Anshuman; Verkhivker, Gennady M.

2011-01-01

The growing interest in quantifying the molecular basis of protein kinase activation and allosteric regulation by cancer mutations has fueled computational studies of allosteric signaling in protein kinases. In the present study, we combined computer simulations and the energy landscape analysis of protein kinases to characterize the interplay between oncogenic mutations and locally frustrated sites as important catalysts of allostetric kinase activation. While structurally rigid kinase core constitutes a minimally frustrated hub of the catalytic domain, locally frustrated residue clusters, whose interaction networks are not energetically optimized, are prone to dynamic modulation and could enable allosteric conformational transitions. The results of this study have shown that the energy landscape effect of oncogenic mutations may be allosteric eliciting global changes in the spatial distribution of highly frustrated residues. We have found that mutation-induced allosteric signaling may involve a dynamic coupling between structurally rigid (minimally frustrated) and plastic (locally frustrated) clusters of residues. The presented study has demonstrated that activation cancer mutations may affect the thermodynamic equilibrium between kinase states by allosterically altering the distribution of locally frustrated sites and increasing the local frustration in the inactive form, while eliminating locally frustrated sites and restoring structural rigidity of the active form. The energy landsape analysis of protein kinases and the proposed role of locally frustrated sites in activation mechanisms may have useful implications for bioinformatics-based screening and detection of functional sites critical for allosteric regulation in complex biomolecular systems. PMID:21998754

Rapid recovery of genetic diversity of dogwhelk (Nucella lapillus L.) populations after local extinction and recolonization contradicts predictions from life-history characteristics.

PubMed

Colson, I; Hughes, R N

2004-08-01

The dogwhelk Nucella lapillus is a predatory marine gastropod populating North Atlantic rocky shores. As with many other gastropod species, N. lapillus was affected by tributyltin (TBT) pollution during the 1970s and 1980s, when local populations became extinct. After a partial ban on TBT in the United Kingdom in 1987, vacant sites have been recolonized. N. lapillus lacks a planktonic larval stage and is therefore expected to have limited dispersal ability. Relatively fast recolonization of some sites, however, contradicts this assumption. We compared levels of genetic diversity and genetic structuring between recolonized sites and sites that showed continuous population at three localities across the British Isles. No significant genetic effects of extinction/recolonization events were observed in SW Scotland and NE England. In SW England we observed a decrease in genetic diversity and an increase in genetic structure in recolonized populations. This last result could be an artefact, however, due to the superposition of other local factors influencing the genetic structuring of dogwhelk populations. We conclude that recolonization of vacant sites was accomplished by a relatively high number of individuals originating from several source populations (the 'migrant-pool' model of recolonization), implying that movements are more widespread than expected on the basis of development mode alone. Comparison with published data on genetic structure of marine organisms with contrasted larval dispersal supports this hypothesis. Our results also stress the importance of local factors (geographical or ecological) in determining genetic structure of dogwhelk populations. Copyright 2004 Blackwell Publishing Ltd

Shear localization in a mature mylonitic rock analog during fast slip

NASA Astrophysics Data System (ADS)

Takahashi, M.; van den Ende, M. P. A.; Niemeijer, A. R.; Spiers, C. J.

2017-02-01

Highly localized slip zones developed within ductile shear zones, such as pseudotachylyte bands occurring within mylonitic fabric rocks, are frequently interpreted as evidence for earthquake nucleation and/or propagation within the ductile regime. To understand brittle/frictional shear localization processes in ductile shear zones and to relate these to earthquake nucleation and propagation, we performed tests with large changes in velocity on a brine-saturated, 80:20 (wt %) mixture of halite and muscovite gouge after forming a mature mylonitic structure through frictional-viscous flow. The direct effect a on shear strength that occurs in response to an instantaneous upward velocity-step is an important parameter in determining the nature of seismic rupture nucleation and propagation. We obtained reproducible results regarding low-velocity mechanical behavior compared with previous work, but also obtained new insights into effects of sudden increases in slip velocity on localization and strength evolution, at velocities above a critical velocity Vc (˜20 μm/s). We found that once a ductile, mylonitic structure has developed in a shear zone, subsequent cataclastic deformation is consistently localized in a narrow zone. This switch to localized deformation is controlled by the imposed velocity and becomes most apparent at velocities above Vc. In addition, the direct effect drops rapidly when the velocity exceeds Vc. This implies that slip can accelerate toward seismic velocities almost instantly and without much loss of fracture energy, once Vc is exceeded. Obtaining a measure for Vc in natural faults is therefore of key importance for understanding earthquake nucleation and propagation in the brittle-ductile transitional regime.

When small changes matter: the role of cross-scale interactions between habitat and ecological connectivity in recovery.

PubMed

Thrush, Simon F; Hewitt, Judi E; Lohrer, Andrew M; Chiaroni, Luca D

2013-01-01

Interaction between the diversity of local communities and the degree of connectivity between them has the potential to influence local recovery rates and thus profoundly affect community dynamics in the face of the cumulative impacts that occur across regions. Although such complex interactions have been modeled, field experiments in natural ecosystems to investigate the importance of interactions between local and regional processes are rare, especially so in coastal marine seafloor habitats subjected to many types of disturbance. We conducted a defaunation experiment at eight subtidal sites, incorporating manipulation of habitat structure, to test the relative importance of local habitat features and colonist supply in influencing macrobenthic community recovery rate. Our sites varied in community composition, habitat characteristics, and hydrodynamic conditions, and we conducted the experiment in two phases, exposing defaunated plots to colonists during periods of either high or low larval colonist supply. In both phases of the experiment, five months after disturbance, we were able to develop models that explained a large proportion of variation in community recovery rate between sites. Our results emphasize that the connectivity to the regional species pool influences recovery rate, and although local habitat effects were important, the strength of these effects was affected by broader-scale site characteristics and connectivity. Empirical evidence that cross-scale interactions are important in disturbance-recovery dynamics emphasizes the complex dynamics underlying seafloor community responses to cumulative disturbance.

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.

Structural simplicity as a restraint on the structure of amorphous silicon

NASA Astrophysics Data System (ADS)

Cliffe, Matthew J.; Bartók, Albert P.; Kerber, Rachel N.; Grey, Clare P.; Csányi, Gábor; Goodwin, Andrew L.

2017-06-01

Understanding the structural origins of the properties of amorphous materials remains one of the most important challenges in structural science. In this study, we demonstrate that local "structural simplicity", embodied by the degree to which atomic environments within a material are similar to each other, is a powerful concept for rationalizing the structure of amorphous silicon (a -Si) a canonical amorphous material. We show, by restraining a reverse Monte Carlo refinement against pair distribution function (PDF) data to be simpler, that the simplest model consistent with the PDF is a continuous random network (CRN). A further effect of producing a simple model of a -Si is the generation of a (pseudo)gap in the electronic density of states, suggesting that structural homogeneity drives electronic homogeneity. That this method produces models of a -Si that approach the state-of-the-art without the need for chemically specific restraints (beyond the assumption of homogeneity) suggests that simplicity-based refinement approaches may allow experiment-driven structural modeling techniques to be developed for the wide variety of amorphous semiconductors with strong local order.

A general strategy to solve the phase problem in RNA crystallography

PubMed Central

Keel, Amanda Y.; Rambo, Robert P.; Batey, Robert T.; Kieft, Jeffrey S.

2007-01-01

SUMMARY X-ray crystallography of biologically important RNA molecules has been hampered by technical challenges, including finding a heavy-atom derivative to obtain high-quality experimental phase information. Existing techniques have drawbacks, severely limiting the rate at which important new structures are solved. To address this need, we have developed a reliable means to localize heavy atoms specifically to virtually any RNA. By solving the crystal structures of thirteen variants of the G·U wobble pair cation binding motif we have identified an optimal version that when inserted into an RNA helix introduces a high-occupancy cation binding site suitable for phasing. This “directed soaking” strategy can be integrated fully into existing RNA and crystallography methods, potentially increasing the rate at which important structures are solved and facilitating routine solving of structures using Cu-Kα radiation. The success of this method has been proven in that it has already been used to solve several novel crystal structures. PMID:17637337

Probing the band structure and local electronic properties of low-dimensional semiconductor structures

NASA Astrophysics Data System (ADS)

Walrath, Jenna Cherie

Low-dimensional semiconductor structures are important for a wide variety of applications, and recent advances in nanoscale fabrication are paving the way for increasingly precise nano-engineering of a wide range of materials. It is therefore essential that the physics of materials at the nanoscale are thoroughly understood to unleash the full potential of nanotechnology, requiring the development of increasingly sophisticated instrumentation and modeling. Of particular interest is the relationship between the local density of states (LDOS) of low-dimensional structures and the band structure and local electronic properties. This dissertation presents the investigation of the band structure, LDOS, and local electronic properties of nanostructures ranging from zero-dimensional (0D) quantum dots (QDs) to two-dimensional (2D) thin films, synthesizing computational and experimental approaches including Poisson-Schrodinger band structure calculations, scanning tunneling microscopy (STM), scanning tunneling spectroscopy (STS), and scanning thermoelectric microscopy (SThEM). A method is presented for quantifying the local Seebeck coefficient (S) with SThEM, using a quasi-3D conversion matrix approach to directly convert temperature gradient-induced voltages S. For a GaAs p-n junction, the resulting S-profile is consistent with that computed using the free carrier concentration profile. This combined computational-experimental approach is expected to enable nanoscale measurements of S across a wide variety of heterostructure interfaces. The local carrier concentration, n, is profiled across epitaxial InAs/GaAs QDs, where SThEM is used to profile the temperature gradient-induced voltage, which is converted to a profile of the local S and finally to an n profile. The S profile is converted to a conduction band-edge profile and compared with Poisson-Schrodinger band-edge simulations. The combined computational-experimental approach suggests a reduced n in the QD center in comparison to that of the 2D alloy layer. The surface composition and band structure of ordered horizontal Sb2Te3 nanowires induced by femtosecond laser irradiation of a thin film are investigated, revealing a band gap modulation between buried Sb2Te3 nanowires and the surrounding insulating material. Finally, STM and STS are used to investigate the band structure of BiSbTe alloys at room temperature, revealing both the Fermi level and Dirac point located inside the bulk bandgap, indicating bulk-like insulating behavior with accessible surface states.

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

Structural determination of importin alpha in complex with beak and feather disease virus capsid nuclear localization signal

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

Patterson, Edward I.; EH Graham Centre for Agricultural Innovation; Dombrovski, Andrew K.

2013-09-06

Highlights: •Circovirus capsid proteins contain large nuclear localization signals (NLS). •A method of nuclear import has not been elucidated. •Beak and feather disease virus (BFDV) capsid NLS was crystallized with importin α. •The structure showed BFDV NLS binding to the major site of importin α. •Result shows implications for mechanism of nuclear transport for all circoviruses. -- Abstract: Circoviruses represent a rapidly increasing genus of viruses that infect a variety of vertebrates. Replication requires shuttling viral molecules into the host cell nucleus, a process facilitated by capsid-associated protein (Cap). Whilst a nuclear localization signal (NLS) has been shown to mediatemore » nuclear translocation, the mode of nuclear transport remains to be elucidated. To better understand this process, beak and feather disease virus (BFDV) Cap NLS was crystallized with nuclear import receptor importin-α (Impα). Diffraction yielded structural data to 2.9 Å resolution, and the binding site on both Impα and BFDV Cap NLS were well resolved. The binding mechanism for the major site is likely conserved across circoviruses as supported by the similarity of NLSs in circovirus Caps. This finding illuminates a crucial step for infection of host cells by this viral family, and provides a platform for rational drug design against the binding interface.« less

Local adaptation in Trinidadian guppies alters stream ecosystem structure at landscape scales despite high environmental variability

USGS Publications Warehouse

Simon, Troy N.; Bassar, Ronald D.; Binderup, Andrew J.; Flecker, Alex S.; Freeman, Mary C.; Gilliam, James F.; Marshall, Michael C.; Thomas, Steve A.; Travis, Joseph; Reznick, David N.; Pringle, Catherine M.

2017-01-01

While previous studies have shown that evolutionary divergence alters ecological processes in small-scale experiments, a major challenge is to assess whether such evolutionary effects are important in natural ecosystems at larger spatial scales. At the landscape scale, across eight streams in the Caroni drainage, we found that the presence of locally adapted populations of guppies (Poecilia reticulata) is associated with reduced algal biomass and increased invertebrate biomass, while the opposite trends were true in streams with experimentally introduced populations of non-locally adapted guppies. Exclusion experiments conducted in two separate reaches of a single stream showed that guppies with locally adapted phenotypes significantly reduced algae with no effect on invertebrates, while non-adapted guppies had no effect on algae but significantly reduced invertebrates. These divergent effects of phenotype on stream ecosystems are comparable in strength to the effects of abiotic factors (e.g., light) known to be important drivers of ecosystem condition. They also corroborate the results of previous experiments conducted in artificial streams. Our results demonstrate that local adaptation can produce phenotypes with significantly different effects in natural ecosystems at a landscape scale, within a tropical watershed, despite high variability in abiotic factors: five of the seven physical and chemical parameters measured across the eight study streams varied by more than one order of magnitude. Our findings suggest that ecosystem structure is, in part, an evolutionary product and not simply an ecological pattern.

Altered structural development and accelerated succession from intermediate-scale wind disturbance in Quercus stands on the Cumberland Plateau, USA

Treesearch

Stephen D White; Justin L. Hart; Callie J. Schweitzer; Daniel C. Dey

2015-01-01

Natural disturbances play important roles in shaping the structure and composition of all forest ecosystems and can be used to inform silvicultural practices. Canopy disturbances are often classified along a gradient ranging from highly localized, gap-scale events to stand-replacing events. Wind storms such as downbursts, derechos, and low intensity tornadoes typically...

Relative importance of local- and large-scale drivers of alpine soil microarthropod communities.

PubMed

Mitchell, Ruth J; Urpeth, Hannah M; Britton, Andrea J; Black, Helaina; Taylor, Astrid R

2016-11-01

Nitrogen (N) deposition and climate are acknowledged drivers of change in biodiversity and ecosystem function at large scales. However, at a local scale, their impact on functions and community structure of organisms is filtered by drivers like habitat quality and food quality/availability. This study assesses the relative impact of large-scale factors, N deposition and climate (rainfall and temperature), versus local-scale factors of habitat quality and food quality/availability on soil fauna communities at 15 alpine moss-sedge heaths along an N deposition gradient in the UK. Habitat quality and food quality/availability were the primary drivers of microarthropod communities. No direct impacts of N deposition on the microarthropod community were observed, but induced changes in habitat quality (decline in moss cover and depth) and food quality (decreased vegetation C:N) associated with increased N deposition strongly suggest an indirect impact of N. Habitat quality and climate explained variation in the composition of the Oribatida, Mesostigmata, and Collembola communities, while only habitat quality significantly impacted the Prostigmata. Food quality and prey availability were important in explaining the composition of the oribatid and mesostigmatid mite communities, respectively. This study shows that, in alpine habitats, soil microarthropod community structure responds most strongly to local-scale variation in habitat quality and food availability rather than large-scale variation in climate and pollution. However, given the strong links between N deposition and the key habitat quality parameters, we conclude that N deposition indirectly drives changes in the soil microarthropod community, suggesting a mechanism by which large-scale drivers indirectly impacts these functionally important groups.

Environmental species sorting dominates forest-bird community assembly across scales.

PubMed

Özkan, Korhan; Svenning, Jens-Christian; Jeppesen, Erik

2013-01-01

Environmental species sorting and dispersal are seen as key factors in community assembly, but their relative importance and scale dependence remain uncertain, as the extent to which communities are consistently assembled throughout their biomes. To address these issues, we analysed bird metacommunity structure in a 1200-km(2) forested landscape (Istranca Forests) in Turkish Thrace at the margin of the Western Palaearctic (WP) temperate-forest biome. First, we used spatial regressions and Mantel tests to assess the relative importance of environmental and spatial factors as drivers of local species richness and composition within the metacommunity. Second, we analysed species' abundance-occupancy relationship across the metacommunity and used null models to assess whether occupancy is determined by species' environmental niches. Third, we used generalized linear models to test for links between species' metacommunity-wide occupancy and their broader WP regional populations and assessed whether these links are consistent with environmental species sorting. There was strong environmental control on local species richness and composition patterns within the metacommunity, but non-environmental spatial factors had also an important joint role. Null model analyses on randomized communities showed that species' occupancy across the metacommunity was strongly determined by species' environmental niches, with occupancy being related to niche position marginality. Species' metacommunity-wide occupancy correlated with their local abundance as well as with their range size and total abundance for the whole WP, suggesting that the same assembly mechanisms act consistently across local to regional scales. A species specialization index that was estimated by bird species' habitat use across France, incorporating both niche position and breadth, was significantly related to species' occupancy and abundance at both metacommunity and WP regional scales. Hence, the same niche-related assembly mechanisms appear to act consistently across the WP region. Overall, our results suggest that the structure of the Istranca Forest' bird metacommunity was predominantly controlled by environmental species sorting in a manner consistent with the broader WP region. However, variability in local community structure was also linked to purely spatial factors, albeit more weakly. © 2012 The Authors. Journal of Animal Ecology © 2012 British Ecological Society.

The problem and promise of scale dependency in community phylogenetics.

PubMed

Swenson, Nathan G; Enquist, Brian J; Pither, Jason; Thompson, Jill; Zimmerman, Jess K

2006-10-01

The problem of scale dependency is widespread in investigations of ecological communities. Null model investigations of community assembly exemplify the challenges involved because they typically include subjectively defined "regional species pools." The burgeoning field of community phylogenetics appears poised to face similar challenges. Our objective is to quantify the scope of the problem of scale dependency by comparing the phylogenetic structure of assemblages across contrasting geographic and taxonomic scales. We conduct phylogenetic analyses on communities within three tropical forests, and perform a sensitivity analysis with respect to two scaleable inputs: taxonomy and species pool size. We show that (1) estimates of phylogenetic overdispersion within local assemblages depend strongly on the taxonomic makeup of the local assemblage and (2) comparing the phylogenetic structure of a local assemblage to a species pool drawn from increasingly larger geographic scales results in an increased signal of phylogenetic clustering. We argue that, rather than posing a problem, "scale sensitivities" are likely to reveal general patterns of diversity that could help identify critical scales at which local or regional influences gain primacy for the structuring of communities. In this way, community phylogenetics promises to fill an important gap in community ecology and biogeography research.

Research on local resonance and Bragg scattering coexistence in phononic crystal

NASA Astrophysics Data System (ADS)

Dong, Yake; Yao, Hong; Du, Jun; Zhao, Jingbo; Jiang, Jiulong

2017-04-01

Based on the finite element method (FEM), characteristics of the local resonance band gap and the Bragg scattering band gap of two periodically-distributed vibrator structures are studied. Conditions of original anti-resonance generation are theoretically derived. The original anti-resonance effect leads to localization of vibration. Factors which influence original anti-resonance band gap are analyzed. The band gap width and the mass ratio between two vibrators are closely correlated to each other. Results show that the original anti-resonance band gap has few influencing factors. In the locally resonant structure, the Bragg scattering band gap is found. The mass density of the elastic medium and the elasticity modulus have an important impact on the Bragg band gap. The coexistence of the two mechanisms makes the band gap larger. The band gap covered 90% of the low frequencies below 2000 Hz. All in all, the research could provide references for studying the low-frequency and broad band gap of phononic crystal.

A comparative study of theoretical graph models for characterizing structural networks of human brain.

PubMed

Li, Xiaojin; Hu, Xintao; Jin, Changfeng; Han, Junwei; Liu, Tianming; Guo, Lei; Hao, Wei; Li, Lingjiang

2013-01-01

Previous studies have investigated both structural and functional brain networks via graph-theoretical methods. However, there is an important issue that has not been adequately discussed before: what is the optimal theoretical graph model for describing the structural networks of human brain? In this paper, we perform a comparative study to address this problem. Firstly, large-scale cortical regions of interest (ROIs) are localized by recently developed and validated brain reference system named Dense Individualized Common Connectivity-based Cortical Landmarks (DICCCOL) to address the limitations in the identification of the brain network ROIs in previous studies. Then, we construct structural brain networks based on diffusion tensor imaging (DTI) data. Afterwards, the global and local graph properties of the constructed structural brain networks are measured using the state-of-the-art graph analysis algorithms and tools and are further compared with seven popular theoretical graph models. In addition, we compare the topological properties between two graph models, namely, stickiness-index-based model (STICKY) and scale-free gene duplication model (SF-GD), that have higher similarity with the real structural brain networks in terms of global and local graph properties. Our experimental results suggest that among the seven theoretical graph models compared in this study, STICKY and SF-GD models have better performances in characterizing the structural human brain network.

Analysis of the HIV-2 protease's adaptation to various ligands: characterization of backbone asymmetry using a structural alphabet.

PubMed

Triki, Dhoha; Cano Contreras, Mario Enrique; Flatters, Delphine; Visseaux, Benoit; Descamps, Diane; Camproux, Anne-Claude; Regad, Leslie

2018-01-15

The HIV-2 protease (PR2) is a homodimer of 99 residues with asymmetric assembly and binding various ligands. We propose an exhaustive study of the local structural asymmetry between the two monomers of all available PR2 structures complexed with various inhibitors using a structural alphabet approach. On average, PR2 exhibits asymmetry in 31% of its positions-i.e., exhibiting different backbone local conformations in the two monomers. This asymmetry was observed all along its structure, particularly in the elbow and flap regions. We first differentiated structural asymmetry conserved in most PR2 structures from the one specific to some PR2. Then, we explored the origin of the detected asymmetry in PR2. We localized asymmetry that could be induced by PR2's flexibility, allowing transition from the semi-open to closed conformations and the asymmetry potentially induced by ligand binding. This latter could be important for the PR2's adaptation to diverse ligands. Our results highlighted some differences between asymmetry of PR2 bound to darunavir and amprenavir that could explain their differences of affinity. This knowledge is critical for a better description of PR2's recognition and adaptation to various ligands and for a better understanding of the resistance of PR2 to most PR2 inhibitors, a major antiretroviral class.

Local structure of dilute aqueous DMSO solutions, as seen from molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Idrissi, Abdenacer; Marekha, Bogdan A.; Barj, Mohammed; Miannay, François Alexandre; Takamuku, Toshiyuki; Raptis, Vasilios; Samios, Jannis; Jedlovszky, Pál

2017-06-01

The information about the structure of dimethyl sulfoxide (DMSO)-water mixtures at relatively low DMSO mole fractions is an important step in order to understand their cryoprotective properties as well as the solvation process of proteins and amino acids. Classical MD simulations, using the potential model combination that best reproduces the free energy of mixing of these compounds, are used to analyze the local structure of DMSO-water mixtures at DMSO mole fractions below 0.2. Significant changes in the local structure of DMSO are observed around the DMSO mole fraction of 0.1. The array of evidence, based on the cluster and the metric and topological parameters of the Voronoi polyhedra distributions, indicates that these changes are associated with the simultaneous increase of the number of DMSO-water and decrease of water-water hydrogen bonds with increasing DMSO concentration. The inversion between the dominance of these two types of H-bonds occurs around XDMSO = 0.1, above which the DMSO-DMSO interactions also start playing an important role. In other words, below the DMSO mole fraction of 0.1, DMSO molecules are mainly solvated by water molecules, while above it, their solvation shell consists of a mixture of water and DMSO. The trigonal, tetrahedral, and trigonal bipyramidal distributions of water shift to lower corresponding order parameter values indicating the loosening of these orientations. Adding DMSO does not affect the hydrogen bonding between a reference water molecule and its first neighbor hydrogen bonded water molecules, while it increases the bent hydrogen bond geometry involving the second ones. The close-packed local structure of the third, fourth, and fifth water neighbors also is reinforced. In accordance with previous theoretical and experimental data, the hydrogen bonding between water and the first, the second, and the third DMSO neighbors is stronger than that with its corresponding water neighbors. At a given DMSO mole fraction, the behavior of the intensity of the high orientational order parameter values indicates that water molecules are more ordered in the vicinity of the hydrophilic group while their structure is close-packed near the hydrophobic group of DMSO.

DOS cones along atomic chains

NASA Astrophysics Data System (ADS)

Kwapiński, Tomasz

2017-03-01

The electron transport properties of a linear atomic chain are studied theoretically within the tight-binding Hamiltonian and the Green’s function method. Variations of the local density of states (DOS) along the chain are investigated. They are crucial in scanning tunnelling experiments and give important insight into the electron transport mechanism and charge distribution inside chains. It is found that depending on the chain parity the local DOS at the Fermi level can form cone-like structures (DOS cones) along the chain. The general condition for the local DOS oscillations is obtained and the linear behaviour of the local density function is confirmed analytically. DOS cones are characterized by a linear decay towards the chain which is in contrast to the propagation properties of charge density waves, end states and Friedel oscillations in one-dimensional systems. We find that DOS cones can appear due to non-resonant electron transport, the spin-orbit scattering or for chains fabricated on a substrate with localized electrons. It is also shown that for imperfect chains (e.g. with a reduced coupling strength between two neighboring sites) a diamond-like structure of the local DOS along the chain appears.

[Assessment tools in early detection of osteoporosis in dentistry].

PubMed

Knezović Zlatarić, Dubravka; Pandurić, Josip; Korsić, Mirko; Dodig, Damir

2007-03-01

Osteoporosis, one of the major skeletal diseases in older age, is characterised by low bone mass and microarchitectural deterioration with a resulting increase in bone fragility and hence susceptibility to fracture. In this review we analyse the systemic and local factors associated with oral bone mass loss. Systemic factors most often correlated with the oral bone mass loss include osteoporosis, renal diseases, hormonal disorders, diet and the impact of different drugs on the bony structure. Chronic periodontal disease, early loss of teeth or the effect of inadequate prosthodontic appliance on the residual ridge are the local factors associated with mandibular bone loss. Different assessment tools for the assessment of mandibular oral bone loss have been proposed, such as DXA absorptiometry, quantitative computed tomography, intraoral microdensitometry, SCORE index and the assessment of the thickness and quality of the mandibular inferior cortical border. Qualitative and quantitative assessment of the mandibular bony structure is of great importance in all fields of dentistry - from periodontology to endodontics and prosthodontics, especially in dental implantology. It is important to make the correct indication prior to dental implant therapy, and taking into account the systemic and local factors mentioned above, assess both the actual quality and quantity of the mandible.

Truss systems and shape optimization

NASA Astrophysics Data System (ADS)

Pricop, Mihai Victor; Bunea, Marian; Nedelcu, Roxana

2017-07-01

Structure optimization is an important topic because of its benefits and wide applicability range, from civil engineering to aerospace and automotive industries, contributing to a more green industry and life. Truss finite elements are still in use in many research/industrial codesfor their simple stiffness matrixand are naturally matching the requirements for cellular materials especially considering various 3D printing technologies. Optimality Criteria combined with Solid Isotropic Material with Penalization is the optimization method of choice, particularized for truss systems. Global locked structures areobtainedusinglocally locked lattice local organization, corresponding to structured or unstructured meshes. Post processing is important for downstream application of the method, to make a faster link to the CAD systems. To export the optimal structure in CATIA, a CATScript file is automatically generated. Results, findings and conclusions are given for two and three-dimensional cases.

Estimating 3D positions and velocities of projectiles from monocular views.

PubMed

Ribnick, Evan; Atev, Stefan; Papanikolopoulos, Nikolaos P

2009-05-01

In this paper, we consider the problem of localizing a projectile in 3D based on its apparent motion in a stationary monocular view. A thorough theoretical analysis is developed, from which we establish the minimum conditions for the existence of a unique solution. The theoretical results obtained have important implications for applications involving projectile motion. A robust, nonlinear optimization-based formulation is proposed, and the use of a local optimization method is justified by detailed examination of the local convexity structure of the cost function. The potential of this approach is validated by experimental results.

Combining density functional theory (DFT) and pair distribution function (PDF) analysis to solve the structure of metastable materials: the case of metakaolin.

PubMed

White, Claire E; Provis, John L; Proffen, Thomas; Riley, Daniel P; van Deventer, Jannie S J

2010-04-07

Understanding the atomic structure of complex metastable (including glassy) materials is of great importance in research and industry, however, such materials resist solution by most standard techniques. Here, a novel technique combining thermodynamics and local structure is presented to solve the structure of the metastable aluminosilicate material metakaolin (calcined kaolinite) without the use of chemical constraints. The structure is elucidated by iterating between least-squares real-space refinement using neutron pair distribution function data, and geometry optimisation using density functional modelling. The resulting structural representation is both energetically feasible and in excellent agreement with experimental data. This accurate structural representation of metakaolin provides new insight into the local environment of the aluminium atoms, with evidence of the existence of tri-coordinated aluminium. By the availability of this detailed chemically feasible atomic description, without the need to artificially impose constraints during the refinement process, there exists the opportunity to tailor chemical and mechanical processes involving metakaolin and other complex metastable materials at the atomic level to obtain optimal performance at the macro-scale.

Skeletal adaptation to external loads optimizes mechanical properties: fact or fiction

NASA Technical Reports Server (NTRS)

Turner, R. T.

2001-01-01

The skeleton adapts to a changing mechanical environment but the widely held concept that bone cells are programmed to respond to local mechanical loads to produce an optimal mechanical structure is not consistent with the high frequency of bone fractures. Instead, the author suggests that other important functions of bone compete with mechanical adaptation to determine structure. As a consequence of competing demands, bone architecture never achieves an optimal mechanical structure. c2001 Lippincott Williams & Wilkins, Inc.

Failure mechanisms in energy-absorbing composite structures

NASA Astrophysics Data System (ADS)

Johnson, Alastair F.; David, Matthew

2010-11-01

Quasi-static tests are described for determination of the energy-absorption properties of composite crash energy-absorbing segment elements under axial loads. Detailed computer tomography scans of failed specimens were used to identify local compression crush failure mechanisms at the crush front. These mechanisms are important for selecting composite materials for energy-absorbing structures, such as helicopter and aircraft sub-floors. Finite element models of the failure processes are described that could be the basis for materials selection and future design procedures for crashworthy structures.

Topology-guided deformable registration with local importance preservation for biomedical images

NASA Astrophysics Data System (ADS)

Zheng, Chaojie; Wang, Xiuying; Zeng, Shan; Zhou, Jianlong; Yin, Yong; Feng, Dagan; Fulham, Michael

2018-01-01

The demons registration (DR) model is well recognized for its deformation capability. However, it might lead to misregistration due to erroneous diffusion direction when there are no overlaps between corresponding regions. We propose a novel registration energy function, introducing topology energy, and incorporating a local energy function into the DR in a progressive registration scheme, to address these shortcomings. The topology energy that is derived from the topological information of the images serves as a direction inference to guide diffusion transformation to retain the merits of DR. The local energy constrains the deformation disparity of neighbouring pixels to maintain important local texture and density features. The energy function is minimized in a progressive scheme steered by a topology tree graph and we refer to it as topology-guided deformable registration (TDR). We validated our TDR on 20 pairs of synthetic images with Gaussian noise, 20 phantom PET images with artificial deformations and 12 pairs of clinical PET-CT studies. We compared it to three methods: (1) free-form deformation registration method, (2) energy-based DR and (3) multi-resolution DR. The experimental results show that our TDR outperformed the other three methods in regard to structural correspondence and preservation of the local important information including texture and density, while retaining global correspondence.

Species mobility and landscape context determine the importance of local and landscape-level attributes.

PubMed

Fuentes-Montemayor, Elisa; Watts, Kevin; Macgregor, Nicholas A; Lopez-Gallego, Zeltia; J Park, Kirsty

2017-07-01

Conservation strategies to tackle habitat loss and fragmentation require actions at the local (e.g., improving/expanding existing habitat patches) and landscape level (e.g., creating new habitat in the matrix). However, the relative importance of these actions for biodiversity is still poorly understood, leading to debate on how to prioritize conservation activities. Here, we assess the relative importance of local vs. landscape-level attributes in determining the use of woodlands by bats in fragmented landscapes; we also compare the role of habitat amount in the surrounding landscape per se vs. a combination of both habitat amount and configuration and explore whether the relative importance of these attributes varies with species mobility and landscape context. We conducted acoustic surveys in 102 woodland patches in the UK that form part of the WrEN project (www.wren-project.com), a large-scale natural experiment designed to study the effects of 160 yr of woodland creation on biodiversity and inform landscape-scale conservation. We used multivariate analysis and a model-selection approach to assess the relative importance of local (e.g., vegetation structure) and landscape-level (e.g., amount/configuration of surrounding land types) attributes on bat occurrence and activity levels. Species mobility was an important trait determining the relative importance of local vs. landscape-level attributes for different bat species. Lower mobility species were most strongly influenced by local habitat quality; the landscape became increasingly important for higher mobility species. At the landscape-scale, a combination of habitat amount and configuration appeared more important than habitat amount alone for lower mobility species, while the opposite was observed for higher mobility species. Regardless of species mobility, landscape-level attributes appeared more important for bats in a more homogeneous and intensively farmed landscape. Conservation strategies involving habitat creation and restoration should take into account the mobility of target species and prioritize landscape-level actions in more homogeneous and intensively farmed landscapes where habitat loss and fragmentation have been more severe. © 2017 by the Ecological Society of America.

Thermostability of In Vitro Evolved Bacillus subtilis Lipase A: A Network and Dynamics Perspective

PubMed Central

Srivastava, Ashutosh; Sinha, Somdatta

2014-01-01

Proteins in thermophilic organisms remain stable and function optimally at high temperatures. Owing to their important applicability in many industrial processes, such thermostable proteins have been studied extensively, and several structural factors attributed to their enhanced stability. How these factors render the emergent property of thermostability to proteins, even in situations where no significant changes occur in their three-dimensional structures in comparison to their mesophilic counter-parts, has remained an intriguing question. In this study we treat Lipase A from Bacillus subtilis and its six thermostable mutants in a unified manner and address the problem with a combined complex network-based analysis and molecular dynamic studies to find commonality in their properties. The Protein Contact Networks (PCN) of the wild-type and six mutant Lipase A structures developed at a mesoscopic scale were analyzed at global network and local node (residue) level using network parameters and community structure analysis. The comparative PCN analysis of all proteins pointed towards important role of specific residues in the enhanced thermostability. Network analysis results were corroborated with finer-scale molecular dynamics simulations at both room and high temperatures. Our results show that this combined approach at two scales can uncover small but important changes in the local conformations that add up to stabilize the protein structure in thermostable mutants, even when overall conformation differences among them are negligible. Our analysis not only supports the experimentally determined stabilizing factors, but also unveils the important role of contacts, distributed throughout the protein, that lead to thermostability. We propose that this combined mesoscopic-network and fine-grained molecular dynamics approach is a convenient and useful scheme not only to study allosteric changes leading to protein stability in the face of negligible over-all conformational changes due to mutations, but also in other molecular networks where change in function does not accompany significant change in the network structure. PMID:25122499

Gauge Field Localization on Deformed Branes

NASA Astrophysics Data System (ADS)

Tofighi, A.; Moazzen, M.; Farokhtabar, A.

2016-02-01

In this paper, we utilise the Chumbes-Holf da Silva-Hott (CHH) mechanism to investigate the issue of gauge field localization on a deformed brane constructed with one scalar field, which can be coupled to gravity minimally or non-minimally. The study of deformed defects is important because they contain internal structures which may have implications in braneworld models. With the CHH mechanism, we find that the massless zero mode of gauge field, in the case of minimal or non-minimal coupling is localized on the brane. Moreover, in the case of non-minimal coupling, it is shown that, when the non-minimal coupling constant is larger than its critical value, then the zero mode is localized on each sub brane.

How Connecticut Health Directors Deal With Public Health Budget Cuts at the Local Level

PubMed Central

Prust, Margaret L.; Clark, Kathleen; Davis, Brigette; Pallas, Sarah W.; Kertanis, Jennifer; O’Keefe, Elaine; Araas, Michael; Iyer, Neel S.; Dandorf, Stewart; Platis, Stephanie

2015-01-01

Objectives. We investigated the perspectives of local health jurisdiction (LHJ) directors on coping mechanisms used to respond to budget reductions and constraints on their decision-making. Methods. We conducted in-depth interviews with 17 LHJ directors. Interviews were audio recorded, transcribed, and analyzed using the constant comparative method. Results. LHJ directors use a range of coping mechanisms, including identifying alternative revenue sources, adjusting services, amending staffing arrangements, appealing to local political leaders, and forming strategic partnerships. LHJs also face constraints on their decision-making because of state and local statutory requirements, political priorities, pressures from other LHJs, and LHJ structure. Conclusions. LHJs respond creatively to budget cuts to maintain important public health services. Some LHJ adjustments to administrative resources may obscure the long-term costs of public health budget cuts in such areas as staff morale and turnover. Not all coping strategies are available to each LHJ because of the contextual constraints of its locality, pointing to important policy questions on identifying optimum jurisdiction size and improving efficiency. PMID:25689206

Local magnetic moments in iron and nickel at ambient and Earth's core conditions.

PubMed

Hausoel, A; Karolak, M; Şaşιoğlu, E; Lichtenstein, A; Held, K; Katanin, A; Toschi, A; Sangiovanni, G

2017-07-12

Some Bravais lattices have a particular geometry that can slow down the motion of Bloch electrons by pre-localization due to the band-structure properties. Another known source of electronic localization in solids is the Coulomb repulsion in partially filled d or f orbitals, which leads to the formation of local magnetic moments. The combination of these two effects is usually considered of little relevance to strongly correlated materials. Here we show that it represents, instead, the underlying physical mechanism in two of the most important ferromagnets: nickel and iron. In nickel, the van Hove singularity has an unexpected impact on the magnetism. As a result, the electron-electron scattering rate is linear in temperature, in violation of the conventional Landau theory of metals. This is true even at Earth's core pressures, at which iron is instead a good Fermi liquid. The importance of nickel in models of geomagnetism may have therefore to be reconsidered.

Local magnetic moments in iron and nickel at ambient and Earth’s core conditions

PubMed Central

Hausoel, A.; Karolak, M.; Şaşιoğlu, E.; Lichtenstein, A.; Held, K.; Katanin, A.; Toschi, A.; Sangiovanni, G.

2017-01-01

Some Bravais lattices have a particular geometry that can slow down the motion of Bloch electrons by pre-localization due to the band-structure properties. Another known source of electronic localization in solids is the Coulomb repulsion in partially filled d or f orbitals, which leads to the formation of local magnetic moments. The combination of these two effects is usually considered of little relevance to strongly correlated materials. Here we show that it represents, instead, the underlying physical mechanism in two of the most important ferromagnets: nickel and iron. In nickel, the van Hove singularity has an unexpected impact on the magnetism. As a result, the electron–electron scattering rate is linear in temperature, in violation of the conventional Landau theory of metals. This is true even at Earth’s core pressures, at which iron is instead a good Fermi liquid. The importance of nickel in models of geomagnetism may have therefore to be reconsidered. PMID:28799538

Does stability in local community composition depend on temporal variation in rates of dispersal and connectivity?

NASA Astrophysics Data System (ADS)

Valanko, Sebastian; Norkko, Joanna; Norkko, Alf

2015-04-01

In ecology understanding variation in connectivity is central for how biodiversity is maintained. Field studies on dispersal and temporal dynamics in community regulating processes are, however, rare. We test the short-term temporal stability in community composition in a soft-sediment benthic community by determining among-sampling interval similarity in community composition. We relate stability to in situ measures of connectivity (wind, wave, current energy) and rates of dispersal (quantified in different trap types). Waves were an important predictor of when local community taxa are most likely to disperse in different trap-types, suggesting that wave energy is important for connectivity in a region. Community composition at the site was variable and changed stochastically over time. We found changes in community composition (occurrence, abundance, dominance) to be greater at times when connectivity and rates of dispersal were low. In response to periods of lower connectedness dominant taxa in the local community only exhibited change in their relative abundance. In contrast, locally less abundant taxa varied in both their presence, as well as in relative abundance. Constancy in connectivity and rates of dispersal promotes community stability and persistence, suggesting that local community composition will be impacted by changes in the spatial extent over which immigration and emigration operates in the region. Few empirical studies have actually measured dispersal directly in a multi-species context to demonstrate the role it plays in maintaining local community structure. Even though our study does not evaluate coexistence over demographic time scales, it importantly demonstrates that dispersal is not only important in initial recruitment or following a disturbance, but also key in maintaining local community composition.

Extended electron energy loss fine structure simulation of the local boron environment in sodium aluminoborosilicate glasses containing gadolinium

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

Qian, Morris; Li, Hong; Li, Liyu

Gadolinium can be dissolved in sodium-alumino-borosilicate glasses up to 47 wt% in a baseline borosilicate glass (mol%) 20 B2O3, 5 Al2O3, 60 SiO2,and 20 Na2O. Understanding of Gd dissolution in borosilicate melts is important in glass formulation optimization. Electron energy loss fine structure (ELFS) spectroscopy is chosen, which provides well resolved local atomic structure information for both amorphous and crystalline materials with high sensitivity to low Z elements such as Al, B, Na, O, and Si where the x-ray absorption fine structure (XAFS) technique faces experimental difficulty. In this study, we report our results of boron K-edge ELFS study. Twomore » borosilicate glass samples with 30 and 47 mass% Gd2O3, B20Gd30 and B20Gd47were chosen for B K-edge ELFS study. EEL spectra were acquired on a Philips 430 TEM equipped with Gatan PEELS system 666 and EL/P 2.1 software with Custom function AcqLong. The ELFS data analysis was performed using UWELFS, UWXAFS and FEFF software. From our Gd solubility study, the local structure of Gd in the borate environment possibly resembles double chain structure found in crystalline Gd(BO2)3 as proposed by Chakraborty et al. The B/Gd ratio's in both glasses are smaller then 3, which means the excess Gd atoms in the Si-sites would be 17 and 60 mol% of the total Gd atoms, respectively according to the model, yet the local environment of borate sites saturated with Gd should be remained. To verity above hypothesis, the double chain structure model was applied to fit boron K-edge. The model was shown to well fit experimental boron K-edge EELS spectra for both glasses with some degree of distance distortion which is understandable in amorphous structure. Therefore, it is very likely that Gd stabilized in borate sites has a local structure resembling the double chain Gd(BO2)3 structure as proposed by our solubility study and literature.« less

A multi-scaled approach to evaluating the fish assemblage structure within southern Appalachian streams USA.

USGS Publications Warehouse

Kirsch, Joseph; Peterson, James T.

2014-01-01

There is considerable uncertainty about the relative roles of stream habitat and landscape characteristics in structuring stream-fish assemblages. We evaluated the relative importance of environmental characteristics on fish occupancy at the local and landscape scales within the upper Little Tennessee River basin of Georgia and North Carolina. Fishes were sampled using a quadrat sample design at 525 channel units within 48 study reaches during two consecutive years. We evaluated species–habitat relationships (local and landscape factors) by developing hierarchical, multispecies occupancy models. Modeling results suggested that fish occupancy within the Little Tennessee River basin was primarily influenced by stream topology and topography, urban land coverage, and channel unit types. Landscape scale factors (e.g., urban land coverage and elevation) largely controlled the fish assemblage structure at a stream-reach level, and local-scale factors (i.e., channel unit types) influenced fish distribution within stream reaches. Our study demonstrates the utility of a multi-scaled approach and the need to account for hierarchy and the interscale interactions of factors influencing assemblage structure prior to monitoring fish assemblages, developing biological management plans, or allocating management resources throughout a stream system.

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

PubMed Central

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

2016-01-01

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

Failure analysis of thick composite cylinders under external pressure

NASA Technical Reports Server (NTRS)

Caiazzo, A.; Rosen, B. W.

1992-01-01

Failure of thick section composites due to local compression strength and overall structural instability is treated. Effects of material nonlinearity, imperfect fiber architecture, and structural imperfections upon anticipated failure stresses are determined. Comparisons with experimental data for a series of test cylinders are described. Predicting the failure strength of composite structures requires consideration of stability and material strength modes of failure using linear and nonlinear analysis techniques. Material strength prediction requires the accurate definition of the local multiaxial stress state in the material. An elasticity solution for the linear static analysis of thick anisotropic cylinders and rings is used herein to predict the axisymmetric stress state in the cylinders. Asymmetric nonlinear behavior due to initial cylinder out of roundness and the effects of end closure structure are treated using finite element methods. It is assumed that local fiber or ply waviness is an important factor in the initiation of material failure. An analytical model for the prediction of compression failure of fiber composites, which includes the effects of fiber misalignments, matrix inelasticity, and multiaxial applied stresses is used for material strength calculations. Analytical results are compared to experimental data for a series of glass and carbon fiber reinforced epoxy cylinders subjected to external pressure. Recommendations for pretest characterization and other experimental issues are presented. Implications for material and structural design are discussed.

A new wave front shape-based approach for acoustic source localization in an anisotropic plate without knowing its material properties.

PubMed

Sen, Novonil; Kundu, Tribikram

2018-07-01

Estimating the location of an acoustic source in a structure is an important step towards passive structural health monitoring. Techniques for localizing an acoustic source in isotropic structures are well developed in the literature. Development of similar techniques for anisotropic structures, however, has gained attention only in the recent years and has a scope of further improvement. Most of the existing techniques for anisotropic structures either assume a straight line wave propagation path between the source and an ultrasonic sensor or require the material properties to be known. This study considers different shapes of the wave front generated during an acoustic event and develops a methodology to localize the acoustic source in an anisotropic plate from those wave front shapes. An elliptical wave front shape-based technique was developed first, followed by the development of a parametric curve-based technique for non-elliptical wave front shapes. The source coordinates are obtained by minimizing an objective function. The proposed methodology does not assume a straight line wave propagation path and can predict the source location without any knowledge of the elastic properties of the material. A numerical study presented here illustrates how the proposed methodology can accurately estimate the source coordinates. Copyright © 2018 Elsevier B.V. All rights reserved.

The return of the city-state: urban governance and the New York City H1N1 pandemic.

PubMed

Hoffman, Lily M

2013-02-01

This article examines New York City's response to the 2009 H1N1 pandemic in the context of the post-9/11 US security regime. While the federal level 'all-hazards' approach made for greater depth of support, it also generated unrealistic assumptions at odds with an effective local response. The combination of structurally induced opportunity and actor specific strengths (size, expertise) made for effective local governance by the New York City Department of Health and Mental Hygiene. By underlining the importance of locality as a first line of defence and linking defence function to policy initiative in regard to health governance, this study illustrates the continuing relevance of Weber's insight into the institutional structure of the city. © 2012 The Author. Sociology of Health & Illness © 2012 Foundation for the Sociology of Health & Illness/Blackwell Publishing Ltd.

Using local chromatin structure to improve CRISPR/Cas9 efficiency in zebrafish.

PubMed

Chen, Yunru; Zeng, Shiyang; Hu, Ruikun; Wang, Xiangxiu; Huang, Weilai; Liu, Jiangfang; Wang, Luying; Liu, Guifen; Cao, Ying; Zhang, Yong

2017-01-01

Although the CRISPR/Cas9 has been successfully applied in zebrafish, considerable variations in efficiency have been observed for different gRNAs. The workload and cost of zebrafish mutant screening is largely dependent on the mutation rate of injected embryos; therefore, selecting more effective gRNAs is especially important for zebrafish mutant construction. Besides the sequence features, local chromatin structures may have effects on CRISPR/Cas9 efficiency, which remain largely unexplored. In the only related study in zebrafish, nucleosome organization was not found to have an effect on CRISPR/Cas9 efficiency, which is inconsistent with recent studies in vitro and in mammalian cell lines. To understand the effects of local chromatin structure on CRISPR/Cas9 efficiency in zebrafish, we first determined that CRISPR/Cas9 introduced genome editing mainly before the dome stage. Based on this observation, we reanalyzed our published nucleosome organization profiles and generated chromatin accessibility profiles in the 256-cell and dome stages using ATAC-seq technology. Our study demonstrated that chromatin accessibility showed positive correlation with CRISPR/Cas9 efficiency, but we did not observe a clear correlation between nucleosome organization and CRISPR/Cas9 efficiency. We constructed an online database for zebrafish gRNA selection based on local chromatin structure features that could prove beneficial to zebrafish homozygous mutant construction via CRISPR/Cas9.

Subcellular localization of calcium and Ca-ATPase activity during nuclear maturation in Bufo arenarum oocytes.

PubMed

Ramos, Inés; Cisint, Susana B; Crespo, Claudia A; Medina, Marcela F; Fernández, Silvia N

2009-08-01

The localization of calcium and Ca-ATPase activity in Bufo arenarum oocytes was investigated by ultracytochemical techniques during progesterone-induced nuclear maturation, under in vitro conditions. No Ca2+ deposits were detected in either control oocytes or progesterone-treated ones for 1-2 h. At the time when nuclear migration started, electron dense deposits of Ca2+ were visible in vesicles, endoplasmic reticulum cisternae and in the space between the annulate lamellae membranes. Furthermore, Ca-ATPase activity was also detected in these membrane structures. As maturation progressed, the cation deposits were observed in the cytomembrane structures, which underwent an important reorganization and redistribution. Thus, they moved from the subcortex and became located predominantly in the oocyte cortex area when nuclear maturation ended. Ca2+ stores were observed in vesicles surrounding or between the cortical granules, which are aligned close to the plasma membrane. The positive Ca-ATPase reaction in these membrane structures could indicate that the calcium deposit is an ATP-dependent process. Our results suggest that during oocyte maturation calcium would be stored in membrane structures where it remains available for release at the time of fertilization. Data obtained under our experimental conditions indicate that calcium from the extracellular medium would be important for the oocyte maturation process.

Bird diversity along a gradient of fragmented habitats of the Cerrado.

PubMed

Jesus, Shayana DE; Pedro, Wagner A; Bispo, Arthur A

2018-01-01

Understanding the factors that affect biodiversity is of central interest to ecology, and essential to species conservation and ecosystems management. We sampled bird communities in 17 forest fragments in the Cerrado biome, the Central-West region of Brazil. We aimed to know the communities structure pattern and the influence of geographical distance and environmental variables on them, along a gradient of fragmented habitats at both local and landscape scales. Eight structural variables of the fragments served as an environmental distance measurement at the local scale while five metrics served as an environmental distance measurement at the landscape scale. Species presence-absence data were used to calculate the dissimilarity index. Beta diversity was calculated using three indices (βsim, βnes and βsor), representing the spatial species turnover, nestedness and total beta diversity, respectively. Spatial species turnover was the predominant pattern in the structure of the communities. Variations in beta diversity were explained only by the environmental variables of the landscape with spatial configuration being more important than the composition. This fact indicates that, in Cerrado of Goiás avian communities structure, deterministic ecological processes associated to differences in species responses to landscape fragmentation are more important than stochastic processes driven by species dispersal.

Community Detection in Complex Networks via Clique Conductance.

PubMed

Lu, Zhenqi; Wahlström, Johan; Nehorai, Arye

2018-04-13

Network science plays a central role in understanding and modeling complex systems in many areas including physics, sociology, biology, computer science, economics, politics, and neuroscience. One of the most important features of networks is community structure, i.e., clustering of nodes that are locally densely interconnected. Communities reveal the hierarchical organization of nodes, and detecting communities is of great importance in the study of complex systems. Most existing community-detection methods consider low-order connection patterns at the level of individual links. But high-order connection patterns, at the level of small subnetworks, are generally not considered. In this paper, we develop a novel community-detection method based on cliques, i.e., local complete subnetworks. The proposed method overcomes the deficiencies of previous similar community-detection methods by considering the mathematical properties of cliques. We apply the proposed method to computer-generated graphs and real-world network datasets. When applied to networks with known community structure, the proposed method detects the structure with high fidelity and sensitivity. When applied to networks with no a priori information regarding community structure, the proposed method yields insightful results revealing the organization of these complex networks. We also show that the proposed method is guaranteed to detect near-optimal clusters in the bipartition case.

Deformation-induced spatiotemporal fluctuation, evolution and localization of strain fields in a bulk metallic glass

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

Wu, Yuan; Bei, Hongbin; Wang, Yanli

Deformation behavior and local strain evolutions upon loading and unloading of a bulk metallic glass (BMG) were systematically investigated by in situ digital image correlation (DIC). Distinct fluctuations and irreversible local strains were observed before the onset of macroscopic yielding. Statistical analysis shows that these fluctuations might be related to intrinsic structural heterogeneities, and that the evolution history and characteristics of local strain fields play an important role in the subsequent initiation of shear bands. Effects of sample size, pre-strain, and loading conditions were systematically analyzed in terms of the probability distributions of the resulting local strain fields. It ismore » found that a higher degree of local shear strain heterogeneity corresponds to a more ductile stressestrain curve. Implications of these findings are discussed for the design of new materials.« less

Deformation-induced spatiotemporal fluctuation, evolution and localization of strain fields in a bulk metallic glass

DOE PAGES

Wu, Yuan; Bei, Hongbin; Wang, Yanli; ...

2015-05-16

Deformation behavior and local strain evolutions upon loading and unloading of a bulk metallic glass (BMG) were systematically investigated by in situ digital image correlation (DIC). Distinct fluctuations and irreversible local strains were observed before the onset of macroscopic yielding. Statistical analysis shows that these fluctuations might be related to intrinsic structural heterogeneities, and that the evolution history and characteristics of local strain fields play an important role in the subsequent initiation of shear bands. Effects of sample size, pre-strain, and loading conditions were systematically analyzed in terms of the probability distributions of the resulting local strain fields. It ismore » found that a higher degree of local shear strain heterogeneity corresponds to a more ductile stressestrain curve. Implications of these findings are discussed for the design of new materials.« less

Metacommunity theory as a multispecies, multiscale framework for studying the influence of river network structure on riverine communities and ecosystems

USGS Publications Warehouse

Brown, B.L.; Swan, C.M.; Auerbach, D.A.; Campbell, Grant E.H.; Hitt, N.P.; Maloney, K.O.; Patrick, C.

2011-01-01

Explaining the mechanisms underlying patterns of species diversity and composition in riverine networks is challenging. Historically, community ecologists have conceived of communities as largely isolated entities and have focused on local environmental factors and interspecific interactions as the major forces determining species composition. However, stream ecologists have long embraced a multiscale approach to studying riverine ecosystems and have studied both local factors and larger-scale regional factors, such as dispersal and disturbance. River networks exhibit a dendritic spatial structure that can constrain aquatic organisms when their dispersal is influenced by or confined to the river network. We contend that the principles of metacommunity theory would help stream ecologists to understand how the complex spatial structure of river networks mediates the relative influences of local and regional control on species composition. From a basic ecological perspective, the concept is attractive because new evidence suggests that the importance of regional processes (dispersal) depends on spatial structure of habitat and on connection to the regional species pool. The role of local factors relative to regional factors will vary with spatial position in a river network. From an applied perspective, the long-standing view in ecology that local community composition is an indicator of habitat quality may not be uniformly applicable across a river network, but the strength of such bioassessment approaches probably will depend on spatial position in the network. The principles of metacommunity theory are broadly applicable across taxa and systems but seem of particular consequence to stream ecology given the unique spatial structure of riverine systems. By explicitly embracing processes at multiple spatial scales, metacommunity theory provides a foundation on which to build a richer understanding of stream communities.

S-wave attenuation of the shallow sediments in the North China basin based on borehole seismograms of local earthquakes

NASA Astrophysics Data System (ADS)

Wang, Sheng; Li, Zhiwei

2018-06-01

S-wave velocity and attenuation structures of shallow sediments play important roles in accurate prediction of strong ground motion. However, it is more difficult to investigate the attenuation than velocity structures. In this study, we developed a new approach for estimating frequency-dependent S-wave attenuation (Q_S^{ - 1}) structures of shallow sediments based on multiple time window analysis of borehole seismograms from local earthquakes. Multiple time windows for separating direct and surface-reflected S-waves in local earthquake waveforms at borehole stations are selected with a global optimization scheme. With respect to different time windows, the transfer functions between direct and surface-reflected S-waves are achieved with a weighted averaging scheme, based on which frequency dependent Q_S^{ - 1} values are obtained. Synthetic tests suggest that the proposed method can restore robust and reliableQ_S^{ - 1} values, especially when the dataset of local earthquakes is not abundant. We utilize this method for local earthquake waveforms at 14 borehole seismic stations in the North China basin, and obtain Q_S^{ - 1} values in 2 ˜ 10 Hz frequency band, as well as average {V_P}, {V_S} and {V_P}/{{}}{V_S} ratio for shallow sediments deep to a few hundred meters. Results suggest that Q_S^{ - 1} values are to 0.01˜0.06, and generally decrease with frequency. The average attenuation structure of shallow sediments within the depth of a few hundred meters beneath 14 borehole stations in the North China basin can be modeled as Q_S^{ - 1} = 0.056{f^{ - 0.61}}. It is generally consistent with the attenuation structure of sedimentary basins in other areas, such as Mississippi Embayment sediments in the United States and Sendai basin in Japan.

Fine-Scale Analysis Reveals Cryptic Landscape Genetic Structure in Desert Tortoises

PubMed Central

Latch, Emily K.; Boarman, William I.; Walde, Andrew; Fleischer, Robert C.

2011-01-01

Characterizing the effects of landscape features on genetic variation is essential for understanding how landscapes shape patterns of gene flow and spatial genetic structure of populations. Most landscape genetics studies have focused on patterns of gene flow at a regional scale. However, the genetic structure of populations at a local scale may be influenced by a unique suite of landscape variables that have little bearing on connectivity patterns observed at broader spatial scales. We investigated fine-scale spatial patterns of genetic variation and gene flow in relation to features of the landscape in desert tortoise (Gopherus agassizii), using 859 tortoises genotyped at 16 microsatellite loci with associated data on geographic location, sex, elevation, slope, and soil type, and spatial relationship to putative barriers (power lines, roads). We used spatially explicit and non-explicit Bayesian clustering algorithms to partition the sample into discrete clusters, and characterize the relationships between genetic distance and ecological variables to identify factors with the greatest influence on gene flow at a local scale. Desert tortoises exhibit weak genetic structure at a local scale, and we identified two subpopulations across the study area. Although genetic differentiation between the subpopulations was low, our landscape genetic analysis identified both natural (slope) and anthropogenic (roads) landscape variables that have significantly influenced gene flow within this local population. We show that desert tortoise movements at a local scale are influenced by features of the landscape, and that these features are different than those that influence gene flow at larger scales. Our findings are important for desert tortoise conservation and management, particularly in light of recent translocation efforts in the region. More generally, our results indicate that recent landscape changes can affect gene flow at a local scale and that their effects can be detected almost immediately. PMID:22132143

Fine-scale analysis reveals cryptic landscape genetic structure in desert tortoises.

PubMed

Latch, Emily K; Boarman, William I; Walde, Andrew; Fleischer, Robert C

2011-01-01

Characterizing the effects of landscape features on genetic variation is essential for understanding how landscapes shape patterns of gene flow and spatial genetic structure of populations. Most landscape genetics studies have focused on patterns of gene flow at a regional scale. However, the genetic structure of populations at a local scale may be influenced by a unique suite of landscape variables that have little bearing on connectivity patterns observed at broader spatial scales. We investigated fine-scale spatial patterns of genetic variation and gene flow in relation to features of the landscape in desert tortoise (Gopherus agassizii), using 859 tortoises genotyped at 16 microsatellite loci with associated data on geographic location, sex, elevation, slope, and soil type, and spatial relationship to putative barriers (power lines, roads). We used spatially explicit and non-explicit Bayesian clustering algorithms to partition the sample into discrete clusters, and characterize the relationships between genetic distance and ecological variables to identify factors with the greatest influence on gene flow at a local scale. Desert tortoises exhibit weak genetic structure at a local scale, and we identified two subpopulations across the study area. Although genetic differentiation between the subpopulations was low, our landscape genetic analysis identified both natural (slope) and anthropogenic (roads) landscape variables that have significantly influenced gene flow within this local population. We show that desert tortoise movements at a local scale are influenced by features of the landscape, and that these features are different than those that influence gene flow at larger scales. Our findings are important for desert tortoise conservation and management, particularly in light of recent translocation efforts in the region. More generally, our results indicate that recent landscape changes can affect gene flow at a local scale and that their effects can be detected almost immediately.

Collaboration of general practitioners and exercise providers in promotion of physical activity a written survey among general practitioners.

PubMed

Leemrijse, C J; de Bakker, D H; Ooms, L; Veenhof, C

2015-08-06

General practitioners have an ideal position to motivate inactive patients to increase their physical activity. Most patients are able to exercise in regular local facilities outside the health care setting. The purpose of this study was to get insight into general practitioners perceptions and current practices regarding referral of patients to local exercise facilities. Furthermore, collaboration with exercise providers in the community was investigated, and motivators and barriers for referral. A written questionnaire sent to a representative random sample of 800 Dutch general practitioners. Descriptive statistics and Chi(2) tests were used. All responding general practitioners (340) recommend their patients to take more exercise when necessary and 87 % say to refer patients sometimes. Limited motivation of the patient (44 %) and reduced health status (34 %) are the most mentioned barriers for advising patients to increase physical activity. When referred, most patients are send to a physical therapist (69 %) but also local exercise facilities were mentioned (54 %). The most important barrier for referring patients to local exercise activities are patients limited financial possibilities (46 %). Restricted knowledge of local exercise- or sport facilities was an additional barrier (19 %). There is little structural collaboration between general practitioners and exercise providers, but when collaboration exists general practitioners refer more often. Positive experiences of patients (67 %), affordable offers (59 %) and information of local exercise facilities (46 %) are seen as important promoting factors for referral. Although 32 % of the general practitioners think that good collaboration would be stimulating, regular meetings with sports and exercise providers were considered the least important for increasing referral (3 %). Dutch physicians have a positive attitude towards stimulating physical activity but referral to local exercise facilities is low. Referral is partly hindered by restricted knowledge of local exercise facilities. Although general practitioners think that collaboration is important for physical activity promotion, it should not cost them much extra time. A coordinator with knowledge of the local situation can facilitate contacts between GP practices and sports providers.

Hierarchical drivers of reef-fish metacommunity structure.

PubMed

MacNeil, M Aaron; Graham, Nicholas A J; Polunin, Nicholas V C; Kulbicki, Michel; Galzin, René; Harmelin-Vivien, Mireille; Rushton, Steven P

2009-01-01

Coral reefs are highly complex ecological systems, where multiple processes interact across scales in space and time to create assemblages of exceptionally high biodiversity. Despite the increasing frequency of hierarchically structured sampling programs used in coral-reef science, little progress has been made in quantifying the relative importance of processes operating across multiple scales. The vast majority of reef studies are conducted, or at least analyzed, at a single spatial scale, ignoring the implicitly hierarchical structure of the overall system in favor of small-scale experiments or large-scale observations. Here we demonstrate how alpha (mean local number of species), beta diversity (degree of species dissimilarity among local sites), and gamma diversity (overall species richness) vary with spatial scale, and using a hierarchical, information-theoretic approach, we evaluate the relative importance of site-, reef-, and atoll-level processes driving the fish metacommunity structure among 10 atolls in French Polynesia. Process-based models, representing well-established hypotheses about drivers of reef-fish community structure, were assembled into a candidate set of 12 hierarchical linear models. Variation in fish abundance, biomass, and species richness were unevenly distributed among transect, reef, and atoll levels, establishing the relative contribution of variation at these spatial scales to the structure of the metacommunity. Reef-fish biomass, species richness, and the abundance of most functional-groups corresponded primarily with transect-level habitat diversity and atoll-lagoon size, whereas detritivore and grazer abundances were largely correlated with potential covariates of larval dispersal. Our findings show that (1) within-transect and among-atoll factors primarily drive the relationship between alpha and gamma diversity in this reef-fish metacommunity; (2) habitat is the primary correlate with reef-fish metacommunity structure at multiple spatial scales; and (3) inter-atoll connectedness was poorly correlated with the nonrandom clustering of reef-fish species. These results demonstrate the importance of modeling hierarchical data and processes in understanding reef-fish metacommunity structure.

Submarine groundwater discharge as an important nutrient source influencing nutrient structure in coastal water of Daya Bay, China

NASA Astrophysics Data System (ADS)

Wang, Xuejing; Li, Hailong; Zheng, Chunmiao; Yang, Jinzhong; Zhang, Yan; Zhang, Meng; Qi, Zhanhui; Xiao, Kai; Zhang, Xiaolang

2018-03-01

As an important nutrient source for coastal waters, submarine groundwater discharge (SGD) has long been largely ignored in Daya Bay, China. In this study, we estimate the fluxes of SGD and associated nutrients into this region using a 224Ra mass balance model and assess the contribution/importance of nutrients by SGD, benthic sediments, local rivers, and atmospheric deposition. The results of 224Ra mass balance show that the estimated SGD ranges from (2.76 ± 1.43) × 106 m3/d to (1.03 ± 0.53) × 107 m3/d with an average of (6.32 ± 2.42) × 106 m3/d, about 16 times the total discharge rate of local rivers. The nutrient loading from SGD is estimated to be (1.05-1.99) × 105 mol/d for NO3-N, (4.04-12.16) × 103 mol/d for DIP, and (3.54-11.35) × 105 mol/d for Si. Among these considered nutrient sources, we find that SGD is the primary source for Si and NO3-N, contributing 68% and 42% of all considered sources, respectively. The atmospheric NO3-N flux is comparable to that from SGD. The local rivers are the most important source for DIP, contributing 75% of all considered sources. SGD with high N:P ratio (NO3-N/DIP) of 37.0 delivers not only a large quantity of nutrients, but also changes nutrient structure in coastal water. Based on a DIP budget, primary productivity is evaluated to be 54-73 mg C/m2 d, in which SGD accounts for approximately 30% of total production. This study indicates that SGD is a key source of nutrients to coastal waters and may cause an obvious change of primary production and nutrient structure in Daya Bay.

Investigations of the local environment and macroscopic alignment behavior of novel polymerizeable lyotropic liquid crystals using nuclear magnetic resonance

NASA Astrophysics Data System (ADS)

Juang, Elizabeth

In this dissertation, a variety of NMR techniques were used to explore the local environment of novel polymerizeable lyotropic liquid crystals (LLC). The LLC monomers examined in this study self-assemble in the presence of a small amount of water to form uniform, nanometer-scale tubes with aqueous interiors. The phase architecture is retained upon photopolymerization to yield the resulting nanoporous material. By dissolving reactive precursors into the aqueous phase, well- structured nancomposite materials have also been formed. Proposed uses for these novel polymerizeable LLCs are as porous water filtration membranes, as heterogeneous organic catalysts, and as nanocomposite materials for load bearing and optical applications. In order to better exploit these polymerizeable LLCs for materials development, the local environment must be examined. In addition, the macroscopic orientation of these materials remains an important step in their advancement. Various NMR studies were conducted on these novel LLCs. NMR T1 relaxation measurements were conducted to elucidate the local environment and dynamics of the 23Na counterions located inside the aqueous channels. 2H NMR line shape analyses were used to characterize the local structure and dynamics near the hydrophilic headgroup. 29 Si NMR studies were performed on silica nanocomposites formed with these LLC structures. Finally, the macroscopic alignment behavior of these novel LLCs using shear and magnetic fields was examined.

Genetic population structure in an equatorial sparrow: roles for culture and geography.

PubMed

Danner, J E; Fleischer, R C; Danner, R M; Moore, I T

2017-06-01

Female preference for local cultural traits has been proposed as a barrier to breeding among animal populations. As such, several studies have found correlations between male bird song dialects and population genetics over relatively large distances. To investigate whether female choice for local dialects could act as a barrier to breeding between nearby and contiguous populations, we tested whether variation in male song dialects explains genetic structure among eight populations of rufous-collared sparrows (Zonotrichia capensis) in Ecuador. Our study sites lay along a transect, and adjacent study sites were separated by approximately 25 km, an order of magnitude less than previously examined for this and most other species. This transect crossed an Andean ridge and through the Quijos River Valley, both of which may be barriers to gene flow. Using a variance partitioning approach, we show that song dialect is important in explaining population genetics, independent of the geographic variables: distance, the river valley and the Andean Ridge. This result is consistent with the hypothesis that song acts as a barrier to breeding among populations in close proximity. In addition, songs of contiguous populations differed by the same degree or more than between two populations previously shown to exhibit female preference for local dialect, suggesting that birds from these populations would also breed preferentially with locals. As expected, all geographic variables (distance, the river valley and the Andean Ridge) also predicted population genetic structure. Our results have important implications for the understanding whether, and at what spatial scale, culture can affect population divergence. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Tidal Channel Diatom Assemblages Reflect within Wetland Environmental Conditions and Land Use at Multiple Scales

EPA Science Inventory

We characterized regional patterns of the tidal channel benthic diatom community and examined the relative importance of local wetland and surrounding landscape level factors measured at multiple scales in structuring this assemblage. Surrounding land cover was characterized at ...

Precambrian Basement Structure Map of the Continental United States - An Interpretation of Geologic and Aeromagnetic Data

USGS Publications Warehouse

Sims, Paul K.; Saltus, Richard W.; Anderson, Eric D.

2008-01-01

The Precambrian basement rocks of the continental United States are largely covered by younger sedimentary and volcanic rocks, and the availability of updated aeromagnetic data (NAMAG, 2002) provides a means to infer major regional basement structures and tie together the scattered, but locally abundant, geologic information. Precambrian basement structures in the continental United States have strongly influenced later Proterozoic and Phanerozoic tectonism within the continent, and there is a growing awareness of the utility of these structures in deciphering major younger tectonic and related episodes. Interest in the role of basement structures in the evolution of continents has been recently stimulated, particularly by publications of the Geological Society of London (Holdsworth and others, 1998; Holdsworth and others, 2001). These publications, as well as others, stress the importance of reactivation of basement structures in guiding the subsequent evolution of continents. Knowledge of basement structures is an important key to understanding the geology of continental interiors.

Two-dimensional joint inversion of Magnetotelluric and local earthquake data: Discussion on the contribution to the solution of deep subsurface structures

NASA Astrophysics Data System (ADS)

Demirci, İsmail; Dikmen, Ünal; Candansayar, M. Emin

2018-02-01

Joint inversion of data sets collected by using several geophysical exploration methods has gained importance and associated algorithms have been developed. To explore the deep subsurface structures, Magnetotelluric and local earthquake tomography algorithms are generally used individually. Due to the usage of natural resources in both methods, it is not possible to increase data quality and resolution of model parameters. For this reason, the solution of the deep structures with the individual usage of the methods cannot be fully attained. In this paper, we firstly focused on the effects of both Magnetotelluric and local earthquake data sets on the solution of deep structures and discussed the results on the basis of the resolving power of the methods. The presence of deep-focus seismic sources increase the resolution of deep structures. Moreover, conductivity distribution of relatively shallow structures can be solved with high resolution by using MT algorithm. Therefore, we developed a new joint inversion algorithm based on the cross gradient function in order to jointly invert Magnetotelluric and local earthquake data sets. In the study, we added a new regularization parameter into the second term of the parameter correction vector of Gallardo and Meju (2003). The new regularization parameter is enhancing the stability of the algorithm and controls the contribution of the cross gradient term in the solution. The results show that even in cases where resistivity and velocity boundaries are different, both methods influence each other positively. In addition, the region of common structural boundaries of the models are clearly mapped compared with original models. Furthermore, deep structures are identified satisfactorily even with using the minimum number of seismic sources. In this paper, in order to understand the future studies, we discussed joint inversion of Magnetotelluric and local earthquake data sets only in two-dimensional space. In the light of these results and by means of the acceleration on the three-dimensional modelling and inversion algorithms, it is thought that it may be easier to identify underground structures with high resolution.

A Landscape Approach to Invasive Species Management.

PubMed

Lurgi, Miguel; Wells, Konstans; Kennedy, Malcolm; Campbell, Susan; Fordham, Damien A

2016-01-01

Biological invasions are not only a major threat to biodiversity, they also have major impacts on local economies and agricultural production systems. Once established, the connection of local populations into metapopulation networks facilitates dispersal at landscape scales, generating spatial dynamics that can impact the outcome of pest-management actions. Much planning goes into landscape-scale invasive species management. However, effective management requires knowledge on the interplay between metapopulation network topology and management actions. We address this knowledge gap using simulation models to explore the effectiveness of two common management strategies, applied across different extents and according to different rules for selecting target localities in metapopulations with different network topologies. These management actions are: (i) general population reduction, and (ii) reduction of an obligate resource. The reduction of an obligate resource was generally more efficient than population reduction for depleting populations at landscape scales. However, the way in which local populations are selected for management is important when the topology of the metapopulation is heterogeneous in terms of the distribution of connections among local populations. We tested these broad findings using real-world scenarios of European rabbits (Oryctolagus cuniculus) infesting agricultural landscapes in Western Australia. Although management strategies targeting central populations were more effective in simulated heterogeneous metapopulation structures, no difference was observed in real-world metapopulation structures that are highly homogeneous. In large metapopulations with high proximity and connectivity of neighbouring populations, different spatial management strategies yield similar outcomes. Directly considering spatial attributes in pest-management actions will be most important for metapopulation networks with heterogeneously distributed links. Our modelling framework provides a simple approach for identifying the best possible management strategy for invasive species based on metapopulation structure and control capacity. This information can be used by managers trying to devise efficient landscape-oriented management strategies for invasive species and can also generate insights for conservation purposes.

Detection of Escaping Lyman Continuum Radiation in Two Local Starbursts Using FUSE

NASA Astrophysics Data System (ADS)

Leitet, E.; Bergvall, N.; Andersson, B.-G.; Zackrisson, E.

2007-05-01

Dwarf galaxies may play a significant role in the reionization history of the universe, and as such also for the history of structure formation. These galaxies are however too faint to be observed at high redshifts, and it is therefore important to establish the amount of Lyman continuum (LyC) radiation that escape local starbursting dwarf galaxies. The amount of leakage is important to know also in order to improve models of star formation and spectral evolution of galaxies, which if neglected, might lead to false conclusions about the properties of the galaxies themself. Previous attempts to directly observe the leakage of hydrogen-ionizing radiation from local galaxies has before this resulted only in one successful case. In Bergvall et al. (2006 A&A 448, 513) an escape fraction of 4-10 % for the blue compact galaxy Haro 11, was found. In this work the detection and quantification of the LyC escape fractions for two additional local starburst galaxies using the Far Ultraviolet Spectroscopic Explorer, FUSE, is presented. The detections were made using FUSE archival data reduced with the latest, and much improved, pipeline. The LyC continuum can be seen as a faint structure between the Lyman limit of the target galaxies and the Milky Way. From line profile fitting it was found that both galaxies have high column densities of neutral gas, indicating that the LyC radiation is escaping through holes in the ISM. The escape fractions are calculated using spectral evolutionary models, based on the f(900Å), f(960Å) and f(Ha) fluxes. The fact that LyC leakage now is detected in three local starbursting dwarf galaxies is going to have a deep impact on future research on structure formation and galaxy evolution. The next challenge would be to statistically determine the escape fraction in extended surveys of starbursting dwarf galaxies.

The spatial structure of chronic morbidity: evidence from UK census returns.

PubMed

Dutey-Magni, Peter F; Moon, Graham

2016-08-24

Disease prevalence models have been widely used to estimate health, lifestyle and disability characteristics for small geographical units when other data are not available. Yet, knowledge is often lacking about how to make informed decisions around the specification of such models, especially regarding spatial assumptions placed on their covariance structure. This paper is concerned with understanding processes of spatial dependency in unexplained variation in chronic morbidity. 2011 UK census data on limiting long-term illness (LLTI) is used to look at the spatial structure in chronic morbidity across England and Wales. The variance and spatial clustering of the odds of LLTI across local authority districts (LADs) and middle layer super output areas are measured across 40 demographic cross-classifications. A series of adjacency matrices based on distance, contiguity and migration flows are tested to examine the spatial structure in LLTI. Odds are then modelled using a logistic mixed model to examine the association with district-level covariates and their predictive power. The odds of chronic illness are more dispersed than local age characteristics, mortality, hospitalisation rates and chance alone would suggest. Of all adjacency matrices, the three-nearest neighbour method is identified as the best fitting. Migration flows can also be used to construct spatial weights matrices which uncover non-negligible autocorrelation. Once the most important characteristics observable at the LAD-level are taken into account, substantial spatial autocorrelation remains which can be modelled explicitly to improve disease prevalence predictions. Systematic investigation of spatial structures and dependency is important to develop model-based estimation tools in chronic disease mapping. Spatial structures reflecting migration interactions are easy to develop and capture autocorrelation in LLTI. Patterns of spatial dependency in the geographical distribution of LLTI are not comparable across ethnic groups. Ethnic stratification of local health information is needed and there is potential to further address complexity in prevalence models by improving access to disaggregated data.

Climate effects and feedback structure determining weed population dynamics in a long-term experiment.

PubMed

Lima, Mauricio; Navarrete, Luis; González-Andujar, José Luis

2012-01-01

Pest control is one of the areas in which population dynamic theory has been successfully applied to solve practical problems. However, the links between population dynamic theory and model construction have been less emphasized in the management and control of weed populations. Most management models of weed population dynamics have emphasized the role of the endogenous process, but the role of exogenous variables such as climate have been ignored in the study of weed populations and their management. Here, we use long-term data (22 years) on two annual weed species from a locality in Central Spain to determine the importance of endogenous and exogenous processes (local and large-scale climate factors). Our modeling study determined two different feedback structures and climate effects in the two weed species analyzed. While Descurainia sophia exhibited a second-order feedback and low climate influence, Veronica hederifolia was characterized by a first-order feedback structure and important effects from temperature and rainfall. Our results strongly suggest the importance of theoretical population dynamics in understanding plant population systems. Moreover, the use of this approach, discerning between the effect of exogenous and endogenous factors, can be fundamental to applying weed management practices in agricultural systems and to controlling invasive weedy species. This is a radical change from most approaches currently used to guide weed and invasive weedy species managements.

Climate Effects and Feedback Structure Determining Weed Population Dynamics in a Long-Term Experiment

PubMed Central

Lima, Mauricio; Navarrete, Luis; González-Andujar, José Luis

2012-01-01

Pest control is one of the areas in which population dynamic theory has been successfully applied to solve practical problems. However, the links between population dynamic theory and model construction have been less emphasized in the management and control of weed populations. Most management models of weed population dynamics have emphasized the role of the endogenous process, but the role of exogenous variables such as climate have been ignored in the study of weed populations and their management. Here, we use long-term data (22 years) on two annual weed species from a locality in Central Spain to determine the importance of endogenous and exogenous processes (local and large-scale climate factors). Our modeling study determined two different feedback structures and climate effects in the two weed species analyzed. While Descurainia sophia exhibited a second-order feedback and low climate influence, Veronica hederifolia was characterized by a first-order feedback structure and important effects from temperature and rainfall. Our results strongly suggest the importance of theoretical population dynamics in understanding plant population systems. Moreover, the use of this approach, discerning between the effect of exogenous and endogenous factors, can be fundamental to applying weed management practices in agricultural systems and to controlling invasive weedy species. This is a radical change from most approaches currently used to guide weed and invasive weedy species managements. PMID:22272362

Structure of Benthic Communities along the Taiwan Latitudinal Gradient

PubMed Central

De Palmas, Stéphane; Kuo, Chao-Yang; Hsieh, Hernyi Justin; Chen, Chaolun Allen

2016-01-01

The distribution and the structure of benthic assemblages vary with latitude. However, few studies have described benthic communities along large latitudinal gradients, and patterns of variation are not fully understood. Taiwan, lying between 21.90°N and 25.30°N, is located at the center of the Philippine-Japan arc and lies at the northern margin of coral reef development. A wide range of habitats is distributed along this latitudinal gradient, from extensive fringing coral reefs at the southern coast to non-reefal communities at the north. In this study, we examined the structure of benthic communities around Taiwan, by comparing its assemblages in four regions, analyzing the effects of the latitudinal gradient, and highlighting regional characteristics. A total of 25 sites, 125 transects, and 2,625 photographs were used to analyze the benthic communities. Scleractinian corals present an obvious gradient of increasing diversity from north to south, whereas macro-algae diversity is higher on the north-eastern coast. At the country scale, Taiwanese coral communities were dominated by turf algae (49%). At the regional scale, we observed an important heterogeneity that may be caused by local disturbances and habitat degradation that smooths out regional differences. In this context, our observations highlight the importance of managing local stressors responsible for reef degradation. Overall, this study provides an important baseline upon which future changes in benthic assemblages around Taiwan can be assessed. PMID:27513665

Local changes in neocortical circuit dynamics coincide with the spread of seizures to thalamus in a model of epilepsy.

PubMed

Neubauer, Florian B; Sederberg, Audrey; MacLean, Jason N

2014-01-01

During the generalization of epileptic seizures, pathological activity in one brain area recruits distant brain structures into joint synchronous discharges. However, it remains unknown whether specific changes in local circuit activity are related to the aberrant recruitment of anatomically distant structures into epileptiform discharges. Further, it is not known whether aberrant areas recruit or entrain healthy ones into pathological activity. Here we study the dynamics of local circuit activity during the spread of epileptiform discharges in the zero-magnesium in vitro model of epilepsy. We employ high-speed multi-photon imaging in combination with dual whole-cell recordings in acute thalamocortical (TC) slices of the juvenile mouse to characterize the generalization of epileptic activity between neocortex and thalamus. We find that, although both structures are exposed to zero-magnesium, the initial onset of focal epileptiform discharge occurs in cortex. This suggests that local recurrent connectivity that is particularly prevalent in cortex is important for the initiation of seizure activity. Subsequent recruitment of thalamus into joint, generalized discharges is coincident with an increase in the coherence of local cortical circuit activity that itself does not depend on thalamus. Finally, the intensity of population discharges is positively correlated between both brain areas. This suggests that during and after seizure generalization not only the timing but also the amplitude of epileptiform discharges in thalamus is entrained by cortex. Together these results suggest a central role of neocortical activity for the onset and the structure of pathological recruitment of thalamus into joint synchronous epileptiform discharges.

Local changes in neocortical circuit dynamics coincide with the spread of seizures to thalamus in a model of epilepsy

PubMed Central

Neubauer, Florian B.; Sederberg, Audrey; MacLean, Jason N.

2014-01-01

During the generalization of epileptic seizures, pathological activity in one brain area recruits distant brain structures into joint synchronous discharges. However, it remains unknown whether specific changes in local circuit activity are related to the aberrant recruitment of anatomically distant structures into epileptiform discharges. Further, it is not known whether aberrant areas recruit or entrain healthy ones into pathological activity. Here we study the dynamics of local circuit activity during the spread of epileptiform discharges in the zero-magnesium in vitro model of epilepsy. We employ high-speed multi-photon imaging in combination with dual whole-cell recordings in acute thalamocortical (TC) slices of the juvenile mouse to characterize the generalization of epileptic activity between neocortex and thalamus. We find that, although both structures are exposed to zero-magnesium, the initial onset of focal epileptiform discharge occurs in cortex. This suggests that local recurrent connectivity that is particularly prevalent in cortex is important for the initiation of seizure activity. Subsequent recruitment of thalamus into joint, generalized discharges is coincident with an increase in the coherence of local cortical circuit activity that itself does not depend on thalamus. Finally, the intensity of population discharges is positively correlated between both brain areas. This suggests that during and after seizure generalization not only the timing but also the amplitude of epileptiform discharges in thalamus is entrained by cortex. Together these results suggest a central role of neocortical activity for the onset and the structure of pathological recruitment of thalamus into joint synchronous epileptiform discharges. PMID:25232306

Habitat structure mediates biodiversity effects on ecosystem properties

PubMed Central

Godbold, J. A.; Bulling, M. T.; Solan, M.

2011-01-01

Much of what we know about the role of biodiversity in mediating ecosystem processes and function stems from manipulative experiments, which have largely been performed in isolated, homogeneous environments that do not incorporate habitat structure or allow natural community dynamics to develop. Here, we use a range of habitat configurations in a model marine benthic system to investigate the effects of species composition, resource heterogeneity and patch connectivity on ecosystem properties at both the patch (bioturbation intensity) and multi-patch (nutrient concentration) scale. We show that allowing fauna to move and preferentially select patches alters local species composition and density distributions, which has negative effects on ecosystem processes (bioturbation intensity) at the patch scale, but overall positive effects on ecosystem functioning (nutrient concentration) at the multi-patch scale. Our findings provide important evidence that community dynamics alter in response to localized resource heterogeneity and that these small-scale variations in habitat structure influence species contributions to ecosystem properties at larger scales. We conclude that habitat complexity forms an important buffer against disturbance and that contemporary estimates of the level of biodiversity required for maintaining future multi-functional systems may need to be revised. PMID:21227969

Importance of conduction electron correlation in a Kondo lattice, Ce₂CoSi₃.

PubMed

Patil, Swapnil; Pandey, Sudhir K; Medicherla, V R R; Singh, R S; Bindu, R; Sampathkumaran, E V; Maiti, Kalobaran

2010-06-30

Kondo systems are usually described by the interaction of the correlation induced local moments with the highly itinerant conduction electrons. Here, we study the role of electron correlations among conduction electrons in the electronic structure of a Kondo lattice compound, Ce₂CoSi₃, using high resolution photoemission spectroscopy and ab initio band structure calculations, where Co 3d electrons contribute in the conduction band. High energy resolution employed in the measurements helped to reveal the signatures of Ce 4f states derived Kondo resonance features at the Fermi level and the dominance of Co 3d contributions at higher binding energies in the conduction band. The lineshape of the experimental Co 3d band is found to be significantly different from that obtained from the band structure calculations within the local density approximations, LDA. Consideration of electron-electron Coulomb repulsion, U, among Co 3d electrons within the LDA + U method leads to a better representation of experimental results. The signature of an electron correlation induced satellite feature is also observed in the Co 2p core level spectrum. These results clearly demonstrate the importance of the electron correlation among conduction electrons in deriving the microscopic description of such Kondo systems.

Habitat structure mediates biodiversity effects on ecosystem properties.

PubMed

Godbold, J A; Bulling, M T; Solan, M

2011-08-22

Much of what we know about the role of biodiversity in mediating ecosystem processes and function stems from manipulative experiments, which have largely been performed in isolated, homogeneous environments that do not incorporate habitat structure or allow natural community dynamics to develop. Here, we use a range of habitat configurations in a model marine benthic system to investigate the effects of species composition, resource heterogeneity and patch connectivity on ecosystem properties at both the patch (bioturbation intensity) and multi-patch (nutrient concentration) scale. We show that allowing fauna to move and preferentially select patches alters local species composition and density distributions, which has negative effects on ecosystem processes (bioturbation intensity) at the patch scale, but overall positive effects on ecosystem functioning (nutrient concentration) at the multi-patch scale. Our findings provide important evidence that community dynamics alter in response to localized resource heterogeneity and that these small-scale variations in habitat structure influence species contributions to ecosystem properties at larger scales. We conclude that habitat complexity forms an important buffer against disturbance and that contemporary estimates of the level of biodiversity required for maintaining future multi-functional systems may need to be revised.

Energy level alignment at molecule-metal interfaces from an optimally tuned range-separated hybrid functional

DOE PAGES

Liu, Zhen-Fei; Egger, David A.; Refaely-Abramson, Sivan; ...

2017-02-21

The alignment of the frontier orbital energies of an adsorbed molecule with the substrate Fermi level at metal-organic interfaces is a fundamental observable of significant practical importance in nanoscience and beyond. Typical density functional theory calculations, especially those using local and semi-local functionals, often underestimate level alignment leading to inaccurate electronic structure and charge transport properties. Here, we develop a new fully self-consistent predictive scheme to accurately compute level alignment at certain classes of complex heterogeneous molecule-metal interfaces based on optimally tuned range-separated hybrid functionals. Starting from a highly accurate description of the gas-phase electronic structure, our method by constructionmore » captures important nonlocal surface polarization effects via tuning of the long-range screened exchange in a range-separated hybrid in a non-empirical and system-specific manner. We implement this functional in a plane-wave code and apply it to several physisorbed and chemisorbed molecule-metal interface systems. Our results are in quantitative agreement with experiments, the both the level alignment and work function changes. This approach constitutes a new practical scheme for accurate and efficient calculations of the electronic structure of molecule-metal interfaces.« less

Local structure of scalar flux in turbulent passive scalar mixing

NASA Astrophysics Data System (ADS)

Konduri, Aditya; Donzis, Diego

2012-11-01

Understanding the properties of scalar flux is important in the study of turbulent mixing. Classical theories suggest that it mainly depends on the large scale structures in the flow. Recent studies suggest that the mean scalar flux reaches an asymptotic value at high Peclet numbers, independent of molecular transport properties of the fluid. A large DNS database of isotropic turbulence with passive scalars forced with a mean scalar gradient with resolution up to 40963, is used to explore the structure of scalar flux based on the local topology of the flow. It is found that regions of small velocity gradients, where dissipation and enstrophy are small, constitute the main contribution to scalar flux. On the other hand, regions of very small scalar gradient (and scalar dissipation) become less important to the scalar flux at high Reynolds numbers. The scaling of the scalar flux spectra is also investigated. The k - 7 / 3 scaling proposed by Lumley (1964) is observed at high Reynolds numbers, but collapse is not complete. A spectral bump similar to that in the velocity spectrum is observed close to dissipative scales. A number of features, including the height of the bump, appear to reach an asymptotic value at high Schmidt number.

Energy level alignment at molecule-metal interfaces from an optimally tuned range-separated hybrid functional

NASA Astrophysics Data System (ADS)

Liu, Zhen-Fei; Egger, David A.; Refaely-Abramson, Sivan; Kronik, Leeor; Neaton, Jeffrey B.

2017-03-01

The alignment of the frontier orbital energies of an adsorbed molecule with the substrate Fermi level at metal-organic interfaces is a fundamental observable of significant practical importance in nanoscience and beyond. Typical density functional theory calculations, especially those using local and semi-local functionals, often underestimate level alignment leading to inaccurate electronic structure and charge transport properties. In this work, we develop a new fully self-consistent predictive scheme to accurately compute level alignment at certain classes of complex heterogeneous molecule-metal interfaces based on optimally tuned range-separated hybrid functionals. Starting from a highly accurate description of the gas-phase electronic structure, our method by construction captures important nonlocal surface polarization effects via tuning of the long-range screened exchange in a range-separated hybrid in a non-empirical and system-specific manner. We implement this functional in a plane-wave code and apply it to several physisorbed and chemisorbed molecule-metal interface systems. Our results are in quantitative agreement with experiments, the both the level alignment and work function changes. Our approach constitutes a new practical scheme for accurate and efficient calculations of the electronic structure of molecule-metal interfaces.

Ethnobotany, traditional knowledge and socioeconomic importance of native drink among the Oraon tribe of Malda district in India

PubMed Central

Saha, Manas Ranjan; Rai, Ritu; Kar, Pallab; Sen, Arnab; Sarker, Dilip De

2015-01-01

Aim: Preparation of daily traditional drink by the indigenous tribes is a common phenomenon in India. Oraon tribes in Malda district of West Bengal, India are very much practiced in making of their own native brew, known as Chullu. Therefore, the aim of this study was to explore the whole Chullu procedure technology of the region and its socioeconomic effect on Oraon. Ethnomedicinal investigation of local plants involved in Chullu preparation was another aspect of this study. Materials and Methods: The present study was conducted from April 2012 to June 2013. Consecutive field surveys were performed to collect information from Chullu producers to focus the procedure technology of local brew by means of semi-structured individual interviews, informal interviews and group discussion. A semi-structured questionnaire process was also performed to obtain the information regarding the ethnic use of plant species involved in Chullu preparation. Results: The present study revealed that four medicinal plant species along with rice having strong local ethnomedicinal value were used to prepare this indigenous drink. Oraon prepare the brew using their unique home-made distillation process. Commercialization of this local brew represents an alternative income to develop their economic condition, especially for poor households. The index of importance value was considered to evaluate the importance, usage, and knowledge of the five studied species. Conclusion: It could be concluded that practices of Chullu preparation represent a bonding between ethnic knowledge and Oraon people of the province. Commercialization of Chullu may be considered as a source of alternative way of income for poor households in the region. PMID:26401382

Methodology of determining soil structure in important groundwater areas: case studies in Kauvonkangas, Finnish Lapland

NASA Astrophysics Data System (ADS)

Kupila, Juho

2016-04-01

Finland is fully self-sufficient in clean groundwater and even has a capacity of exportation. There are approx. 6000 groundwater areas with a total yield of 5.4 million m3/day. Currently only 10% of this groundwater resource is in use. For the efficient and safe exploitation of these areas in the future, detailed modeling of soil structure is an important method in groundwater surveys. 3D -models improve the general knowledge of linkage between land use planning and groundwater protection. Results can be used as a base information in water supply service development and when performing the measures needed in case of environmental accidents. Also, when creating the groundwater flow models the collected information is utilized and is usually the main data source. Geological Survey of Finland has carried out soil structure studies in co-operation with authorities, municipalities and the local water suppliers. The main objectives of these projects are to determine the geological structure of groundwater area for estimating the validity of the present exclusion area, the quantity of ground water volume and recharge capability and possible risks to the groundwater. Research areas are usually under an active water supply service. Kauvonkangas groundwater area is located in the municipality of Tervola, in Southern part of Finnish Lapland. Extent of the area is 7.9 km2 and it is an important water source for the local and nearby population centers. There are two active water supply companies in the area. Field studies in the project will include general geological and hydrological mapping, soil drilling with observation pipe installation, test pumping and water sampling. Geophysical measures will play a key-role, including ground penetrating radar (GPR) and gravimetric measurements. Studies will be carried out in spring and summer 2016. The main results will be the models of the bedrock and groundwater level and main characteristics of the soil layers in the area. Results will also include the main flow directions of the groundwater. Structure models will be done with Groundhog -software. Kauvonkangas -project is funded by local water supply companies Meri-Lapin Vesi and Tervolan Vesi, Ministry of Agriculture and Forestry, and Geological Survey of Finland.

Electron microscopy study of gold nanoparticles deposited on transition metal oxides.

PubMed

Akita, Tomoki; Kohyama, Masanori; Haruta, Masatake

2013-08-20

Many researchers have investigated the catalytic performance of gold nanoparticles (GNPs) supported on metal oxides for various catalytic reactions of industrial importance. These studies have consistently shown that the catalytic activity and selectivity depend on the size of GNPs, the kind of metal oxide supports, and the gold/metal oxide interface structure. Although researchers have proposed several structural models for the catalytically active sites and have identified the specific electronic structures of GNPs induced by the quantum effect, recent experimental and theoretical studies indicate that the perimeter around GNPs in contact with the metal oxide supports acts as an active site in many reactions. Thus, it is of immense importance to investigate the detailed structures of the perimeters and the contact interfaces of gold/metal oxide systems by using electron microscopy at an atomic scale. This Account describes our investigation, at the atomic scale using electron microscopy, of GNPs deposited on metal oxides. In particular, high-resolution transmission electron microscopy (HRTEM) and high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM) are valuable tools to observe local atomic structures, as has been successfully demonstrated for various nanoparticles, surfaces, and material interfaces. TEM can be applied to real powder catalysts as received without making special specimens, in contrast to what is typically necessary to observe bulk materials. For precise structure analyses at an atomic scale, model catalysts prepared by using well-defined single-crystalline substrates are also adopted for TEM observations. Moreover, aberration-corrected TEM, which has high spatial resolution under 0.1 nm, is a promising tool to observe the interface structure between GNPs and metal oxide supports including oxygen atoms at the interfaces. The oxygen atoms in particular play an important role in the behavior of gold/metal oxide interfaces, because they may participate in catalytic reaction steps. Detailed information about the interfacial structures between GNPs and metal oxides provides valuable structure models for theoretical calculations which can elucidate the local electronic structure effective for activating a reactant molecule. Based on our observations with HRTEM and HAADF-STEM, we report the detailed structure of gold/metal oxide interfaces.

The emergence of place-based conservation [Chapter 1

Treesearch

Daniel R. Williams; William P. Stewart; Linda E. Kruger

2013-01-01

Place has emerged as a significant topic within conservation research and practice. The transformative changes connected to contemporary conservation are related to recognition of multi-scaled, social-ecological dynamics; emergent, multiscaled governance structures; and rising importance of place-specific meanings and local knowledge. These transformative changes are...

Chimera regimes in a ring of oscillators with local nonlinear interaction

NASA Astrophysics Data System (ADS)

Shepelev, Igor A.; Zakharova, Anna; Vadivasova, Tatiana E.

2017-03-01

One of important problems concerning chimera states is the conditions of their existence and stability. Until now, it was assumed that chimeras could arise only in ensembles with nonlocal character of interactions. However, this assumption is not exactly right. In some special cases chimeras can be realized for local type of coupling [1-3]. We propose a simple model of ensemble with local coupling when chimeras are realized. This model is a ring of linear oscillators with the local nonlinear unidirectional interaction. Chimera structures in the ring are found using computer simulations for wide area of values of parameters. Diagram of the regimes on plane of control parameters is plotted and scenario of chimera destruction are studied when the parameters are changed.

The use of SWOT analysis to explore and prioritize conservation and development strategies for local cattle breeds.

PubMed

Martín-Collado, D; Díaz, C; Mäki-Tanila, A; Colinet, F; Duclos, D; Hiemstra, S J; Gandini, G

2013-06-01

SWOT (Strengths, Weaknesses, Opportunities and Threats) analysis is a tool widely used to help in decision making in complex systems. It suits to exploring the issues and measures related to the conservation and development of local breeds, as it allows the integration of many driving factors influencing breed dynamics. We developed a quantified SWOT method as a decision-making tool for identification and ranking of conservation and development strategies of local breeds, and applied it to a set of 13 cattle breeds of six European countries. The method has four steps: definition of the system, identification and grouping of the driving factors, quantification of the importance of driving factors and identification and prioritization of the strategies. The factors were determined following a multi-stakeholder approach and grouped with a three-level structure. Animal genetic resources expert groups ranked the factors, and a quantification process was implemented to identify and prioritize strategies. The proposed SWOT methodology allows analyzing the dynamics of local cattle breeds in a structured and systematic way. It is a flexible tool developed to assist different stakeholders in defining the strategies and actions. The quantification process allows the comparison of the driving factors and the prioritization of the strategies for the conservation and development of local cattle breeds. We identified 99 factors across the breeds. Although the situation is very heterogeneous, the future of these breeds may be promising. The most important strengths and weaknesses were related to production systems and farmers. The most important opportunities were found in marketing new products, whereas the most relevant threats were found in selling the current products. The across-breed strategies utility decreased as they gained specificity. Therefore, the strategies at European level should focus on general aspects and be flexible enough to be adapted to the country and breed specificities.

Lateral extrusion of a thermally weakened pluton overburden (Campiglia Marittima, Tuscany)

NASA Astrophysics Data System (ADS)

Vezzoni, Simone; Rocchi, Sergio; Dini, Andrea

2017-10-01

The ascent and emplacement of magmas in the upper crust modify the local pre-existing thermal and rheological settings. Such changes have important effects in producing anomalous structures, mass extrusion, rock fracturing, and in some conditions, hydrothermal mineralizations. In the Campiglia Marittima area, detailed field mapping led to the reconstruction of a local deformation history that overlaps, chronologically and spatially, with regional extension. This local deformation was triggered at the Miocene-Pliocene boundary by the intrusion of a monzogranitic pluton beneath a carbonate sedimentary sequence. The emplacement of the pluton produced a perturbation in the rheological behaviour of the carbonate host rocks, producing transient ductile conditions in the very shallow crust. The carbonate rocks were thermally weakened and flowed laterally, accumulating downslope of the pluton roof, mainly toward the east. As the thermal anomaly was decaying, the brittle-ductile boundary moved progressively back towards the pluton, and large tension gash-shaped volumes of fractured marble were generated. These fractured volumes were exploited by rising hydrothermal fluids generating sigmoidal skarn bodies and ore shoots. This work presents the Campiglia Marittima case study as a prime example of structural interference between regional extensional structures and local, lateral mass extrusion in a transient ductile rheological regime triggered by pluton emplacement.

The structure of the Myo4p globular tail and its function in ASH1 mRNA localization.

PubMed

Heuck, Alexander; Fetka, Ingrid; Brewer, Daniel N; Hüls, Daniela; Munson, Mary; Jansen, Ralf-Peter; Niessing, Dierk

2010-05-03

Type V myosin (MyoV)-dependent transport of cargo is an essential process in eukaryotes. Studies on yeast and vertebrate MyoV showed that their globular tails mediate binding to the cargo complexes. In Saccharomyces cerevisiae, the MyoV motor Myo4p interacts with She3p to localize asymmetric synthesis of HO 1 (ASH1) mRNA into the bud of dividing cells. A recent study showed that localization of GFP-MS2-tethered ASH1 particles does not require the Myo4p globular tail, challenging the supposed role of this domain. We assessed ASH1 mRNA and Myo4p distribution more directly and found that their localization is impaired in cells expressing globular tail-lacking Myo4p. In vitro studies further show that the globular tail together with a more N-terminal linker region is required for efficient She3p binding. We also determined the x-ray structure of the Myo4p globular tail and identify a conserved surface patch important for She3p binding. The structure shows pronounced similarities to membrane-tethering complexes and indicates that Myo4p may not undergo auto-inhibition of its motor domain.

Landscape matrix mediates occupancy dynamics of Neotropical avian insectivores

USGS Publications Warehouse

Kennedy, Christina M.; Campbell Grant, Evan H.; Neel, Maile C.; Fagan, William F.; Marpa, Peter P.

2011-01-01

In addition to patch-level attributes (i.e., area and isolation), the nature of land cover between habitat patches (the matrix) may drive colonization and extinction dynamics in fragmented landscapes. Despite a long-standing recognition of matrix effects in fragmented systems, an understanding of the relative impacts of different types of land cover on patterns and dynamics of species occurrence remains limited. We employed multi-season occupancy models to determine the relative influence of patch area, patch isolation, within-patch vegetation structure, and landscape matrix on occupancy dynamics of nine Neotropical nsectivorous birds in 99 forest patches embedded in four matrix types (agriculture, suburban evelopment, bauxite mining, and forest) in central Jamaica. We found that within-patch vegetation structure and the matrix type between patches were more important than patch area and patch isolation in determining local colonization and local extinction probabilities, and that the effects of patch area, isolation, and vegetation structure on occupancy dynamics tended to be matrix and species dependent. Across the avian community, the landscape matrix influenced local extinction more than local colonization, indicating that extinction processes, rather than movement, likely drive interspecific differences in occupancy dynamics. These findings lend crucial empirical support to the hypothesis that species occupancy dynamics in fragmented systems may depend greatly upon the landscape context.

Lateral extrusion of a thermally weakened pluton overburden (Campiglia Marittima, Tuscany)

NASA Astrophysics Data System (ADS)

Vezzoni, Simone; Rocchi, Sergio; Dini, Andrea

2018-06-01

The ascent and emplacement of magmas in the upper crust modify the local pre-existing thermal and rheological settings. Such changes have important effects in producing anomalous structures, mass extrusion, rock fracturing, and in some conditions, hydrothermal mineralizations. In the Campiglia Marittima area, detailed field mapping led to the reconstruction of a local deformation history that overlaps, chronologically and spatially, with regional extension. This local deformation was triggered at the Miocene-Pliocene boundary by the intrusion of a monzogranitic pluton beneath a carbonate sedimentary sequence. The emplacement of the pluton produced a perturbation in the rheological behaviour of the carbonate host rocks, producing transient ductile conditions in the very shallow crust. The carbonate rocks were thermally weakened and flowed laterally, accumulating downslope of the pluton roof, mainly toward the east. As the thermal anomaly was decaying, the brittle-ductile boundary moved progressively back towards the pluton, and large tension gash-shaped volumes of fractured marble were generated. These fractured volumes were exploited by rising hydrothermal fluids generating sigmoidal skarn bodies and ore shoots. This work presents the Campiglia Marittima case study as a prime example of structural interference between regional extensional structures and local, lateral mass extrusion in a transient ductile rheological regime triggered by pluton emplacement.

Atom-scale depth localization of biologically important chemical elements in molecular layers.

PubMed

Schneck, Emanuel; Scoppola, Ernesto; Drnec, Jakub; Mocuta, Cristian; Felici, Roberto; Novikov, Dmitri; Fragneto, Giovanna; Daillant, Jean

2016-08-23

In nature, biomolecules are often organized as functional thin layers in interfacial architectures, the most prominent examples being biological membranes. Biomolecular layers play also important roles in context with biotechnological surfaces, for instance, when they are the result of adsorption processes. For the understanding of many biological or biotechnologically relevant phenomena, detailed structural insight into the involved biomolecular layers is required. Here, we use standing-wave X-ray fluorescence (SWXF) to localize chemical elements in solid-supported lipid and protein layers with near-Ångstrom precision. The technique complements traditional specular reflectometry experiments that merely yield the layers' global density profiles. While earlier work mostly focused on relatively heavy elements, typically metal ions, we show that it is also possible to determine the position of the comparatively light elements S and P, which are found in the most abundant classes of biomolecules and are therefore particularly important. With that, we overcome the need of artificial heavy atom labels, the main obstacle to a broader application of high-resolution SWXF in the fields of biology and soft matter. This work may thus constitute the basis for the label-free, element-specific structural investigation of complex biomolecular layers and biological surfaces.

Solitary plasma rings and magnetic field generation involving gravity and differential rotation

NASA Astrophysics Data System (ADS)

Coppi, B.

2012-12-01

A new theoretical framework for describing how magnetic fields are generated and amplified is provided by finding magneto-gravitational modes that involve gravity, density gradients, and differential rotation in an essential way. Other factors, such as the presence of a high temperature particle population or of a temperature gradient, can contribute to their excitation. These modes identified by a linearized analysis are shown to be important for the evolution of plasma disks surrounding black holes toward different configurations. Since the nonlinear development of these modes can lead to radially localized regions with a relatively small differential rotation, new stationary structures have been identified, in the (fully) nonlinear limit, which are localized radially over regions with negligible gradients of the rotation frequency. These structures, characterized by solitary plasma rings, do not involve a pre-existing "seed" magnetic field, unlike other configurations found previously. The relevant magnetic energy density is comparable to the gravitationally confined plasma pressure. The "source" of these configurations is the combination of the gravitational force and of the plasma density gradient orthogonal to it that is an important factor in the theory of magneto-gravitational modes, another important factor being an anisotropy of the plasma pressure.

Atom-scale depth localization of biologically important chemical elements in molecular layers

PubMed Central

Schneck, Emanuel; Scoppola, Ernesto; Drnec, Jakub; Mocuta, Cristian; Felici, Roberto; Novikov, Dmitri; Fragneto, Giovanna; Daillant, Jean

2016-01-01

In nature, biomolecules are often organized as functional thin layers in interfacial architectures, the most prominent examples being biological membranes. Biomolecular layers play also important roles in context with biotechnological surfaces, for instance, when they are the result of adsorption processes. For the understanding of many biological or biotechnologically relevant phenomena, detailed structural insight into the involved biomolecular layers is required. Here, we use standing-wave X-ray fluorescence (SWXF) to localize chemical elements in solid-supported lipid and protein layers with near-Ångstrom precision. The technique complements traditional specular reflectometry experiments that merely yield the layers’ global density profiles. While earlier work mostly focused on relatively heavy elements, typically metal ions, we show that it is also possible to determine the position of the comparatively light elements S and P, which are found in the most abundant classes of biomolecules and are therefore particularly important. With that, we overcome the need of artificial heavy atom labels, the main obstacle to a broader application of high-resolution SWXF in the fields of biology and soft matter. This work may thus constitute the basis for the label-free, element-specific structural investigation of complex biomolecular layers and biological surfaces. PMID:27503887

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

Kitiashvili, I. N.; Mansour, N. N.; Wray, A. A.

Magnetic fields are usually observed in the quiet Sun as small-scale elements that cover the entire solar surface (the “salt-and-pepper” patterns in line-of-sight magnetograms). By using 3D radiative MHD numerical simulations, we find that these fields result from a local dynamo action in the top layers of the convection zone, where extremely weak “seed” magnetic fields (e.g., from a 10{sup −6} G) can locally grow above the mean equipartition field to a stronger than 2000 G field localized in magnetic structures. Our results reveal that the magnetic flux is predominantly generated in regions of small-scale helical downflows. We find thatmore » the local dynamo action takes place mostly in a shallow, about 500 km deep, subsurface layer, from which the generated field is transported into the deeper layers by convective downdrafts. We demonstrate that the observed dominance of vertical magnetic fields at the photosphere and horizontal fields above the photosphere can be explained by small-scale magnetic loops produced by the dynamo. Such small-scale loops play an important role in the structure and dynamics of the solar atmosphere and their detection in observations is critical for understanding the local dynamo action on the Sun.« less

Kinetic Model of Electric Potentials in Localized Collisionless Plasma Structures under Steady Quasi-gyrotropic Conditions

NASA Technical Reports Server (NTRS)

Schindler, K.; Birn, J.; Hesse, M.

2012-01-01

Localized plasma structures, such as thin current sheets, generally are associated with localized magnetic and electric fields. In space plasmas localized electric fields not only play an important role for particle dynamics and acceleration but may also have significant consequences on larger scales, e.g., through magnetic reconnection. Also, it has been suggested that localized electric fields generated in the magnetosphere are directly connected with quasi-steady auroral arcs. In this context, we present a two-dimensional model based on Vlasov theory that provides the electric potential for a large class of given magnetic field profiles. The model uses an expansion for small deviation from gyrotropy and besides quasineutrality it assumes that electrons and ions have the same number of particles with their generalized gyrocenter on any given magnetic field line. Specializing to one dimension, a detailed discussion concentrates on the electric potential shapes (such as "U" or "S" shapes) associated with magnetic dips, bumps, and steps. Then, it is investigated how the model responds to quasi-steady evolution of the plasma. Finally, the model proves useful in the interpretation of the electric potentials taken from two existing particle simulations.

Efficient O(N) integration for all-electron electronic structure calculation using numeric basis functions

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

Havu, V.; Fritz Haber Institute of the Max Planck Society, Berlin; Blum, V.

2009-12-01

We consider the problem of developing O(N) scaling grid-based operations needed in many central operations when performing electronic structure calculations with numeric atom-centered orbitals as basis functions. We outline the overall formulation of localized algorithms, and specifically the creation of localized grid batches. The choice of the grid partitioning scheme plays an important role in the performance and memory consumption of the grid-based operations. Three different top-down partitioning methods are investigated, and compared with formally more rigorous yet much more expensive bottom-up algorithms. We show that a conceptually simple top-down grid partitioning scheme achieves essentially the same efficiency as themore » more rigorous bottom-up approaches.« less

'Long-Cell Action' Corrosion: A Basic Mechanism Hidden Behind Components Degradation Issues in Nuclear Power Plants

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

Genn Saji

2006-07-01

In spite of industries' effort over the last 40 years, corrosion-related issues continue to be one of the largest unresolved problems for nuclear power plants worldwide. There are several types of strange corrosion phenomena from the point of view of our current understanding of corrosion science established in other fields. Some of these are IGSCC, PWSCC, AOA, and FAC (Erosion-Corrosion). Through studying and coping with diverse corrosion phenomena, the author believes that they share a common basis with respect to the assumed corrosion mechanism (e.g., 'local cell action' hypothesis). In general, local cell action is rarely severe since it producesmore » a fairly uniform corrosion. The 'long cell action' that transports electrons through structures far beyond the region of local cell corrosion activities has been identified as a basic mechanism in soil corrosion. If this mechanism is assumed in nuclear power plants, the structure becomes anodic in the area where the potential is less positive and cathodic where this potential is more positive. Metallic ions generated at anodic corrosion sites are transported to remote cathodic sites through the circulation of water and deposits as corrosion products. The SCC, FAC (E-C) and PWSCC occur in the anodic sites as the structure itself acts as a short-circuiting conductor between the two sites, the action is similar to a galvanic cell but in a very large scale. This situation is the same as a battery that has been short-circuited at the terminals. No apparent external potential difference exists between the two electrodes, but an electrochemical reaction is still taking place inside the battery cell with a large internal short current. In this example what is important is the potential difference between the local coolant and the surface of the structural material. Long cell action corrosion is likely enhancing the local cell action's anodic corrosion activities, such as SCC, FAC/E-C, and PWSCC. It tends to be more hazardous because of its localized nature compared with the local cell action corrosion. There exist various mechanisms (electrochemical cell configurations) that induce such potential differences, including: ionic concentration, aeration, temperature, flow velocity, radiation and corrosion potentials. In this paper, the author will discuss these potential differences and their relevance to the un-resolved corrosion issues in nuclear power plants. Due to the importance of this potential mechanism the author is calling for further verification experiments as a joint international project. (author)« less

Modelling the structure of Zr-rich Pb(Zr1-xTix)O3, x = 0.4 by a multiphase approach.

PubMed

Bogdanov, Alexander; Mysovsky, Andrey; Pickard, Chris J; Kimmel, Anna V

2016-10-12

Solid solution perovskite Pb(Zr 1-x Ti x )O 3 (PZT) is an industrially important material. Despite the long history of experimental and theoretical studies, the structure of this material is still under intensive discussion. In this work, we have applied structure searching coupled with density functional theory methods to provide a multiphase description of this material at x = 0.4. We demonstrate that the permutational freedom of B-site cations leads to the stabilisation of a variety of local phases reflecting a relatively flat energy landscape of PZT. Using a set of predicted local phases we reproduce the experimental pair distribution function (PDF) profile with high accuracy. We introduce a complex multiphase picture of the structure of PZT and show that additional monoclinic and rhombohedral phases account for a better description of the experimental PDF profile. We propose that such a multiphase picture reflects the entropy reached in the sample during the preparation process.

[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.

Sustainability of Metal Structures via Spray-Clad Remanufacturing

NASA Astrophysics Data System (ADS)

Smith, Gregory M.; Sampath, Sanjay

2018-04-01

Structural reclamation and remanufacturing is an important future design consideration to allow sustainable recovery of degraded structural metals. Heavy machinery and infrastructure components subjected to extended use and/or environment induced degradation require costly and time-consuming replacement. If these parts can be remanufactured to original tolerances, and returned to service with "as good or better" performance, significant reductions in materials, cost, and environmental impact can be achieved. Localized additive restoration via thermal or cold spray methods is a promising approach in recovering and restoring original design strength of degraded metals. The advent of high velocity spray deposition technologies has allowed deposition of near full density materials. In this review, the fundamental scientific and technological elements of such local additive restoration is contemplated including materials, processes, and methodologies to assess the capabilities of such remanufactured systems. This points to sustainable material reclamation, as well as a route toward resource and process sustainability.

Structural damage to periodontal tissues at varying rate of anesthetic injection.

PubMed

Sarapultseva, Maria; Sarapultsev, Alexey; Medvedeva, Svetlana; Danilova, Irina

2018-04-01

Incorrect administration of an anesthetic during local anesthesia is one of the most important causes of pain symptoms in patients scheduled for dental procedures. The current study assessed the severity of damage to periodontal tissue following different rates of anesthetic administration. The research was conducted on 50 outbred male rats with a body mass of 180-240 g. The anesthetic used was 1% articaine. The results showed that administration of the anesthetic at a rapid pace caused structural damage to the periodontal tissue. Further, signs of impaired microcirculation were noted at all rates of administration. Biochemical studies demonstrated changes in the level of glucose and enzymes with the rapid introduction of the anesthetic, indicating severe systemic stress response of the body. Injection of local anesthetic at any rate of introduction induces vascular congestion in the microcirculatory bloodstream and exudative reactions. Rapid introduction of an anesthetic causes progression of structural changes in the gingival tissue.

Local spin-density-wave order inside vortex cores in multiband superconductors

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

Mishra, Vivek; Koshelev, Alexei E.

Coexistence of antiferromagnetic order with superconductivity in many families of newly discovered iron-based superconductors has renewed interest to this old problem. Due to competition between the two types of order, one can expect appearance of the antiferromagnetism inside the cores of the vortices generated by the external magnetic field. The structure of a vortex in type II superconductors holds significant importance from the theoretical and the application points of view. In this paper, we consider the internal vortex structure in a two-band s± superconductor near a spin-density-wave instability. We treat the problem in a completely self-consistent manner within the quasiclassicalmore » Eilenberger formalism. We study the structure of the s± superconducting order and magnetic field-induced spin-density-wave order near an isolated vortex. Finally, we examine the effect of this spin-density-wave state inside the vortex cores on the local density of states.« less

Local spin-density-wave order inside vortex cores in multiband superconductors

DOE PAGES

Mishra, Vivek; Koshelev, Alexei E.

2015-08-13

Coexistence of antiferromagnetic order with superconductivity in many families of newly discovered iron-based superconductors has renewed interest to this old problem. Due to competition between the two types of order, one can expect appearance of the antiferromagnetism inside the cores of the vortices generated by the external magnetic field. The structure of a vortex in type II superconductors holds significant importance from the theoretical and the application points of view. In this paper, we consider the internal vortex structure in a two-band s± superconductor near a spin-density-wave instability. We treat the problem in a completely self-consistent manner within the quasiclassicalmore » Eilenberger formalism. We study the structure of the s± superconducting order and magnetic field-induced spin-density-wave order near an isolated vortex. Finally, we examine the effect of this spin-density-wave state inside the vortex cores on the local density of states.« less

Texture feature extraction based on a uniformity estimation method for local brightness and structure in chest CT images.

PubMed

Peng, Shao-Hu; Kim, Deok-Hwan; Lee, Seok-Lyong; Lim, Myung-Kwan

2010-01-01

Texture feature is one of most important feature analysis methods in the computer-aided diagnosis (CAD) systems for disease diagnosis. In this paper, we propose a Uniformity Estimation Method (UEM) for local brightness and structure to detect the pathological change in the chest CT images. Based on the characteristics of the chest CT images, we extract texture features by proposing an extension of rotation invariant LBP (ELBP(riu4)) and the gradient orientation difference so as to represent a uniform pattern of the brightness and structure in the image. The utilization of the ELBP(riu4) and the gradient orientation difference allows us to extract rotation invariant texture features in multiple directions. Beyond this, we propose to employ the integral image technique to speed up the texture feature computation of the spatial gray level dependent method (SGLDM). Copyright © 2010 Elsevier Ltd. All rights reserved.

The role of syntax in complex networks: Local and global importance of verbs in a syntactic dependency network

NASA Astrophysics Data System (ADS)

Čech, Radek; Mačutek, Ján; Žabokrtský, Zdeněk

2011-10-01

Syntax of natural language has been the focus of linguistics for decades. The complex network theory, being one of new research tools, opens new perspectives on syntax properties of the language. Despite numerous partial achievements, some fundamental problems remain unsolved. Specifically, although statistical properties typical for complex networks can be observed in all syntactic networks, the impact of syntax itself on these properties is still unclear. The aim of the present study is to shed more light on the role of syntax in the syntactic network structure. In particular, we concentrate on the impact of the syntactic function of a verb in the sentence on the complex network structure. Verbs play the decisive role in the sentence structure (“local” importance). From this fact we hypothesize the importance of verbs in the complex network (“global” importance). The importance of verb in the complex network is assessed by the number of links which are directed from the node representing verb to other nodes in the network. Six languages (Catalan, Czech, Dutch, Hungarian, Italian, Portuguese) were used for testing the hypothesis.

Limited Pollen Dispersal Contributes to Population Genetic Structure but Not Local Adaptation in Quercus oleoides Forests of Costa Rica.

PubMed

Deacon, Nicholas John; Cavender-Bares, Jeannine

2015-01-01

Quercus oleoides Cham. and Schlect., tropical live oak, is a species of conservation importance in its southern range limit of northwestern Costa Rica. It occurs in high-density stands across a fragmented landscape spanning a contrasting elevation and precipitation gradient. We examined genetic diversity and spatial genetic structure in this geographically isolated and genetically distinct population. We characterized population genetic diversity at 11 nuclear microsatellite loci in 260 individuals from 13 sites. We monitored flowering time at 10 sites, and characterized the local environment in order to compare observed spatial genetic structure to hypotheses of isolation-by-distance and isolation-by-environment. Finally, we quantified pollen dispersal distances and tested for local adaptation through a reciprocal transplant experiment in order to experimentally address these hypotheses. High genetic diversity is maintained in the population and the genetic variation is significantly structured among sampled sites. We identified 5 distinct genetic clusters and average pollen dispersal predominately occurred over short distances. Differences among sites in flowering phenology and environmental factors, however, were not strictly associated with genetic differentiation. Growth and survival of upland and lowland progeny in their native and foreign environments was expected to exhibit evidence of local adaptation due to the more extreme dry season in the lowlands. Seedlings planted in the lowland garden experienced much higher mortality than seedlings in the upland garden, but we did not identify evidence for local adaptation. Overall, this study indicates that the Costa Rican Q. oleoides population has a rich population genetic history. Despite environmental heterogeneity and habitat fragmentation, isolation-by-distance and isolation-by-environment alone do not explain spatial genetic structure. These results add to studies of genetic structure by examining a common, tropical tree over multiple habitats and provide information for managers of a successional forest in a protected area.

Damage detection of rotating wind turbine blades using local flexibility method and long-gauge fiber Bragg grating sensors

NASA Astrophysics Data System (ADS)

Hsu, Ting-Yu; Shiao, Shen-Yuan; Liao, Wen-I.

2018-01-01

Wind turbines are a cost-effective alternative energy source; however, their blades are susceptible to damage. Therefore, damage detection of wind turbine blades is of great importance for condition monitoring of wind turbines. Many vibration-based structural damage detection techniques have been proposed in the last two decades. The local flexibility method, which can determine local stiffness variations of beam-like structures by using measured modal parameters, is one of the most promising vibration-based approaches. The local flexibility method does not require a finite element model of the structure. A few structural modal parameters identified from the ambient vibration signals both before and after damage are required for this method. In this study, we propose a damage detection approach for rotating wind turbine blades using the local flexibility method based on the dynamic macro-strain signals measured by long-gauge fiber Bragg grating (FBG)-based sensors. A small wind turbine structure was constructed and excited using a shaking table to generate vibration signals. The structure was designed to have natural frequencies as close as possible to those of a typical 1.5 MW wind turbine in real scale. The optical fiber signal of the rotating blades was transmitted to the data acquisition system through a rotary joint fixed inside the hollow shaft of the wind turbine. Reversible damage was simulated by aluminum plates attached to some sections of the wind turbine blades. The damaged locations of the rotating blades were successfully detected using the proposed approach, with the extent of damage somewhat over-estimated. Nevertheless, although the specimen of wind turbine blades cannot represent a real one, the results still manifest that FBG-based macro-strain measurement has potential to be employed to obtain the modal parameters of the rotating wind turbines and then locations of wind turbine segments with a change of rigidity can be estimated effectively by utilizing these identified parameters.

Efficient organ localization using multi-label convolutional neural networks in thorax-abdomen CT scans

NASA Astrophysics Data System (ADS)

Efrain Humpire-Mamani, Gabriel; Arindra Adiyoso Setio, Arnaud; van Ginneken, Bram; Jacobs, Colin

2018-04-01

Automatic localization of organs and other structures in medical images is an important preprocessing step that can improve and speed up other algorithms such as organ segmentation, lesion detection, and registration. This work presents an efficient method for simultaneous localization of multiple structures in 3D thorax-abdomen CT scans. Our approach predicts the location of multiple structures using a single multi-label convolutional neural network for each orthogonal view. Each network takes extra slices around the current slice as input to provide extra context. A sigmoid layer is used to perform multi-label classification. The output of the three networks is subsequently combined to compute a 3D bounding box for each structure. We used our approach to locate 11 structures of interest. The neural network was trained and evaluated on a large set of 1884 thorax-abdomen CT scans from patients undergoing oncological workup. Reference bounding boxes were annotated by human observers. The performance of our method was evaluated by computing the wall distance to the reference bounding boxes. The bounding boxes annotated by the first human observer were used as the reference standard for the test set. Using the best configuration, we obtained an average wall distance of 3.20~+/-~7.33 mm in the test set. The second human observer achieved 1.23~+/-~3.39 mm. For all structures, the results were better than those reported in previously published studies. In conclusion, we proposed an efficient method for the accurate localization of multiple organs. Our method uses multiple slices as input to provide more context around the slice under analysis, and we have shown that this improves performance. This method can easily be adapted to handle more organs.

Designing and evaluating the MULTICOM protein local and global model quality prediction methods in the CASP10 experiment

PubMed Central

2014-01-01

Background Protein model quality assessment is an essential component of generating and using protein structural models. During the Tenth Critical Assessment of Techniques for Protein Structure Prediction (CASP10), we developed and tested four automated methods (MULTICOM-REFINE, MULTICOM-CLUSTER, MULTICOM-NOVEL, and MULTICOM-CONSTRUCT) that predicted both local and global quality of protein structural models. Results MULTICOM-REFINE was a clustering approach that used the average pairwise structural similarity between models to measure the global quality and the average Euclidean distance between a model and several top ranked models to measure the local quality. MULTICOM-CLUSTER and MULTICOM-NOVEL were two new support vector machine-based methods of predicting both the local and global quality of a single protein model. MULTICOM-CONSTRUCT was a new weighted pairwise model comparison (clustering) method that used the weighted average similarity between models in a pool to measure the global model quality. Our experiments showed that the pairwise model assessment methods worked better when a large portion of models in the pool were of good quality, whereas single-model quality assessment methods performed better on some hard targets when only a small portion of models in the pool were of reasonable quality. Conclusions Since digging out a few good models from a large pool of low-quality models is a major challenge in protein structure prediction, single model quality assessment methods appear to be poised to make important contributions to protein structure modeling. The other interesting finding was that single-model quality assessment scores could be used to weight the models by the consensus pairwise model comparison method to improve its accuracy. PMID:24731387

Designing and evaluating the MULTICOM protein local and global model quality prediction methods in the CASP10 experiment.

PubMed

Cao, Renzhi; Wang, Zheng; Cheng, Jianlin

2014-04-15

Protein model quality assessment is an essential component of generating and using protein structural models. During the Tenth Critical Assessment of Techniques for Protein Structure Prediction (CASP10), we developed and tested four automated methods (MULTICOM-REFINE, MULTICOM-CLUSTER, MULTICOM-NOVEL, and MULTICOM-CONSTRUCT) that predicted both local and global quality of protein structural models. MULTICOM-REFINE was a clustering approach that used the average pairwise structural similarity between models to measure the global quality and the average Euclidean distance between a model and several top ranked models to measure the local quality. MULTICOM-CLUSTER and MULTICOM-NOVEL were two new support vector machine-based methods of predicting both the local and global quality of a single protein model. MULTICOM-CONSTRUCT was a new weighted pairwise model comparison (clustering) method that used the weighted average similarity between models in a pool to measure the global model quality. Our experiments showed that the pairwise model assessment methods worked better when a large portion of models in the pool were of good quality, whereas single-model quality assessment methods performed better on some hard targets when only a small portion of models in the pool were of reasonable quality. Since digging out a few good models from a large pool of low-quality models is a major challenge in protein structure prediction, single model quality assessment methods appear to be poised to make important contributions to protein structure modeling. The other interesting finding was that single-model quality assessment scores could be used to weight the models by the consensus pairwise model comparison method to improve its accuracy.

Simulation of light in-coupling through an aperture probe to investigate light propagation in a thin layer for opto-electronic application

NASA Astrophysics Data System (ADS)

Ermes, Markus; Lehnen, Stephan; Cao, Zhao; Bittkau, Karsten; Carius, Reinhard

2015-06-01

In thin optoelectronic devices, like organic light emitting diodes (OLED) or thin-film solar cells (TFSC), light propagation, which is initiated by a local point source, is of particular importance. In OLEDs, light is generated in the layer by the luminescence of single molecules, whereas in TFSCs, light is coupled into the devices by scattering at small surface features. In both applications, light propagation within the active layers has a significant impact on the optical device performance. Scanning near-field optical microscopy (SNOM) using aperture probes is a powerful tool to investigate this propagation with a high spatial resolution. Dual-probe SNOM allows simulating the local light generation by an illumination probe as well as the detection of the light propagated through the layer. In our work, we focus on the light propagation in thin silicon films as used in thin-film silicon solar cells. We investigate the light-in-coupling from an illuminating probe via rigorous solution of Maxwell's equations using a Finite-Difference Time-Domain approach, especially to gain insight into the light distribution inside a thin layer, which is not accessible in the experiment. The structures investigated include at and structured surfaces with varying illumination positions and wavelengths. From the performed simulations, we define a "spatial sensitivity" which is characteristic for the local structure and illumination position. This quantity can help to identify structures which are beneficial as well as detrimental to absorption inside the investigated layer. We find a strong dependence of the spatial sensitivity on the surface structure as well as both the absorption coefficient and the probe position. Furthermore, we investigate inhomogeneity in local light propagation resulting from different surface structures and illumination positions.

Antarctic glossopterid diversity on a local scale: the presence of multiple megasporophyll genera, Upper Permian, Mt. Achernar, Transantarctic Mountains, Antarctica.

PubMed

Ryberg, Patricia E; Taylor, Edith L; Taylor, Thomas N

2012-09-01

The glossopterids are a group of plants that thrived during a time of global warming similar to what is happening on the Earth today as well as the transition from archaic plant groups to the ancestors of modern groups. The diversity of the glossopterid clade is based on the megasporangiate structures assigned to the group, because the vegetative and pollen-bearing structures vary little. The presence of numerous reproductive genera from a single Upper Permian locality in the central Transantarctic Mountains provides important data on local glossopterid diversity in Antarctica. Impression/compression fossils were imaged with a Leica 5000C digital camera on a dissecting microscope or a Fujifilm FinePix S1pro digital camera. Two megasporangiate taxa are described: Scutum leiophyllum, which represents the first confirmed record of the genus in Antarctica, and Lidgettoniopsis ramulus, a new morphology consisting of a pinnate structure with oppositely attached megasporophylls. Plumsteadia ovata specimens indicate that this genus can be larger than previously recorded and illustrate the vegetative surface with a distinct midrib. The presence of a laminar, multiovulate structure and a pinnate structure at the same site indicates that local-level glossopterid diversity in Antarctica is greater than previously hypothesized. The discovery of a new megasporophyll morphology in Antarctica (confirming the presence of three distinctive morphologies on the continent) shows that Antarctic glossopterid heterogeneity is on a par with other Gondwanan continents. The diversity of the Antarctic landscape reveals that high polar latitudes can sustain a diverse ecosystem during times of global warming.

Microsatellite variation in Donax trunculus from the Iberian Peninsula, with particular attention to Galician estuaries (NW Spain)

NASA Astrophysics Data System (ADS)

Nantón, A.; Arias-Pérez, A.; Freire, R.; Fernández-Pérez, J.; Nóvoa, S.; Méndez, J.

2017-10-01

Genetic variation and population structure information is essential for conservation and stock management policies. The wedge clam Donax trunculus is an important fishing resource in the Iberian Peninsula and in some areas, such as the northwestern Spain, wild stocks have decreased greatly. Despite this, information is mainly from the southwestern Atlantic to the northwestern Mediterranean of the Iberian Peninsula. In this study, fifteen microsatellite loci were examined at 17 localities along the Iberian Peninsula to characterize its genetic diversity and population structure. Particular attention was paid to the northwestern Atlantic area, and to test if the pattern previously described for this species is confirmed when localities distributed across the Atlantic coast are included and different microsatellite markers are used. All localities displayed similar allelic richness values and heterozygosity levels but when genetic diversity levels were compared among groups of localities, tests were significant and samples from the northwestern area (Galicia) showed the lowest values. The analysis of population structure indicated that localities from the Atlantic coast are genetically homogeneous although some samples showed significant pairwise Fst values. These values were low and Bayesian analysis of genetic differentiation did not show a consistent structure along the Atlantic coast of the Iberian Peninsula. However, Atlantic samples were genetically different from those located in Mediterranean coast, which may be explained by the existence of the Almeria-Oran front. Moreover, Fuengirola, locality situated in the Alboran Sea between the Strait of Gibraltar and Mediterranean Sea, showed significant differences from all remaining localities included in the study. Overall, the data showed the existence of genetic homogeneity along the Atlantic coast of the Iberian Peninsula and support the three management units (Atlantic Ocean, the Alboran Sea and the northwestern Mediterranean) previously described in this species. Reduced diversity in the northwestern Spain samples could be related to the exploitation of this resource.

Identification of Germ Plasm-Associated Transcripts by Microarray Analysis of Xenopus Vegetal Cortex RNA

PubMed Central

Cuykendall, Tawny N.; Houston, Douglas W.

2011-01-01

RNA localization is a common mechanism for regulating cell structure and function. Localized RNAs in Xenopus oocytes are critical for early development, including germline specification by the germ plasm. Despite the importance of these localized RNAs, only approximately 25 have been identified and fewer are functionally characterized. Using microarrays, we identified a large set of localized RNAs from the vegetal cortex. Overall, our results indicate a minimum of 275 localized RNAs in oocytes, or 2–3% of maternal transcripts, which are in general agreement with previous findings. We further validated vegetal localization for 24 candidates and further characterized three genes expressed in the germ plasm. We identified novel germ plasm expression for reticulon 3.1, exd2 (a novel exonuclease-domain encoding gene), and a putative noncoding RNA. Further analysis of these and other localized RNAs will likely identify new functions of germ plasm and facilitate the identification of cis-acting RNA localization elements. PMID:20503379

Collective Cellular Decision-Making Gives Developmental Plasticity: A Model of Signaling in Branching Roots

NASA Astrophysics Data System (ADS)

McCleery, W. Tyler; Mohd-Radzman, Nadiatul A.; Grieneisen, Veronica A.

Cells within tissues can be regarded as autonomous entities that respond to their local environment and signaling from neighbors. Cell coordination is particularly important in plants, where root architecture must strategically invest resources for growth to optimize nutrient acquisition. Thus, root cells are constantly adapting to environmental cues and neighbor communication in a non-linear manner. To explain such plasticity, we view the root as a swarm of coupled multi-cellular structures, ''metamers'', rather than as a continuum of identical cells. These metamers are individually programmed to achieve a local objective - developing a lateral root primordia, which aids in local foraging of nutrients. Collectively, such individual attempts may be halted, structuring root architecture as an emergent behavior. Each metamer's decision to branch is coordinated locally and globally through hormone signaling, including processes of controlled diffusion, active polar transport, and dynamic feedback. We present a physical model of the signaling mechanism that coordinates branching decisions in response to the environment. This work was funded by the European Commission 7th Framework Program, Project No. 601062, SWARM-ORGAN.

Free energy landscape of a minimalist salt bridge model.

PubMed

Li, Xubin; Lv, Chao; Corbett, Karen M; Zheng, Lianqing; Wu, Dongsheng; Yang, Wei

2016-01-01

Salt bridges are essential to protein stability and dynamics. Despite the importance, there has been scarce of detailed discussion on how salt bridge partners interact with each other in distinct solvent exposed environments. In this study, employing a recent generalized orthogonal space tempering (gOST) method, we enabled efficient molecular dynamics simulation of repetitive breaking and reforming of salt bridge structures within a minimalist salt-bridge model, the Asp-Arg dipeptide and thereby were able to map its detailed free energy landscape in aqueous solution. Free energy surface analysis shows that although individually-solvated states are more favorable, salt-bridge states still occupy a noticeable portion of the overall population. Notably, the competing forces, e.g. intercharge attractions that drive the formation of salt bridges and solvation forces that pull the charged groups away from each other, are energetically comparable. As the result, the salt bridge stability is highly tunable by local environments; for instance when local water molecules are perturbed to interact more strongly with each other, the population of the salt-bridge states is likely to increase. Our results reveal the critical role of local solvent structures in modulating salt-bridge partner interactions and imply the importance of water fluctuations on conformational dynamics that involves solvent accessible salt bridge formations. © 2015 The Protein Society.

Relative importance of local habitat complexity and regional factors for assemblages of oribatid mites (Acari: Oribatida) in Sphagnum peat bogs.

PubMed

Minor, M A; Ermilov, S G; Philippov, D A; Prokin, A A

2016-11-01

We investigated communities of oribatid mites in five peat bogs in the north-west of the East European plain. We aimed to determine the extent to which geographic factors (latitude, separation distance), local environment (Sphagnum moss species, ground water level, biogeochemistry) and local habitat complexity (diversity of vascular plants and bryophytes in the surrounding plant community) influence diversity and community composition of Oribatida. There was a significant north-to-south increase in Oribatida abundance. In the variance partitioning, spatial factors explained 33.1 % of variability in abundance across samples; none of the environmental factors were significant. Across all bogs, Oribatida species richness and community composition were similar in Sphagnum rubellum and Sphagnum magellanicum, but significantly different and less diverse in Sphagnum cuspidatum. Sphagnum microhabitat explained 52.2 % of variability in Oribatida species richness, whereas spatial variables explained only 8.7 %. There was no distance decay in community similarity between bogs with increased geographical distance. The environmental variables explained 34.9 % of the variance in community structure, with vascular plants diversity, bryophytes diversity, and ground water level all contributing significantly; spatial variables explained 15.1 % of the total variance. Overall, only 50 % of the Oribatida community variance was explained by the spatial structure and environmental variables. We discuss relative importance of spatial and local environmental factors, and make general inferences about the formation of fauna in Sphagnum bogs.

Applications of X Radiography to Examination of Nuclear Graphite; APPLICATIONS DE LA RADIOGRAPHIE X A L'EXAMEN DU GRAPHITE NUCLEAIRE

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

Magnier, P.

1960-06-01

A technique which determines some important elements in the structure of graphite, osme dislocation lines, the presence of some dense impurities, and the local decreases in density, which develop in the course of oxidation, is described. (P.C.H.)

Import of a major mitochondrial enzyme depends on synergy between two distinct helices of its presequence

USDA-ARS?s Scientific Manuscript database

The human mitochondrial glutamate dehydrogenase isozymes (hGDH1 and 2) are abundant matrix-localized proteins encoded by nuclear genes. The proteins are synthesized in the cytoplasm, with an atypically long N-terminal mitochondrial targeting sequence (MTS). The results of secondary structure predi...

StralSV: assessment of sequence variability within similar 3D structures and application to polio RNA-dependent RNA polymerase.

PubMed

Zemla, Adam T; Lang, Dorothy M; Kostova, Tanya; Andino, Raul; Ecale Zhou, Carol L

2011-06-02

Most of the currently used methods for protein function prediction rely on sequence-based comparisons between a query protein and those for which a functional annotation is provided. A serious limitation of sequence similarity-based approaches for identifying residue conservation among proteins is the low confidence in assigning residue-residue correspondences among proteins when the level of sequence identity between the compared proteins is poor. Multiple sequence alignment methods are more satisfactory--still, they cannot provide reliable results at low levels of sequence identity. Our goal in the current work was to develop an algorithm that could help overcome these difficulties by facilitating the identification of structurally (and possibly functionally) relevant residue-residue correspondences between compared protein structures. Here we present StralSV (structure-alignment sequence variability), a new algorithm for detecting closely related structure fragments and quantifying residue frequency from tight local structure alignments. We apply StralSV in a study of the RNA-dependent RNA polymerase of poliovirus, and we demonstrate that the algorithm can be used to determine regions of the protein that are relatively unique, or that share structural similarity with proteins that would be considered distantly related. By quantifying residue frequencies among many residue-residue pairs extracted from local structural alignments, one can infer potential structural or functional importance of specific residues that are determined to be highly conserved or that deviate from a consensus. We further demonstrate that considerable detailed structural and phylogenetic information can be derived from StralSV analyses. StralSV is a new structure-based algorithm for identifying and aligning structure fragments that have similarity to a reference protein. StralSV analysis can be used to quantify residue-residue correspondences and identify residues that may be of particular structural or functional importance, as well as unusual or unexpected residues at a given sequence position. StralSV is provided as a web service at http://proteinmodel.org/AS2TS/STRALSV/.

Computational measurement of joint space width and structural parameters in normal hips.

PubMed

Nishii, Takashi; Shiomi, Toshiyuki; Sakai, Takashi; Takao, Masaki; Yoshikawa, Hideki; Sugano, Nobuhiko

2012-05-01

Joint space width (JSW) of hip joints on radiographs in normal population may vary by related factors, but previous investigations were insufficient due to limitations of sources of radiographs, inclusion of subjects with osteoarthritis, and manual measurement techniques. We investigated influential factors on JSW using semiautomatic computational software on pelvic radiographs in asymptomatic subjects without radiological osteoarthritic findings. Global and local JSW at the medial, middle, and lateral compartments, and the hip structural parameters were measured in asymptomatic, normal 150 cases (300 hips), using a customized computational software. Reliability of measurement in global and local JSWs was high with intraobserver reproducibility (intraclass correlation coefficient) ranging from 0.957 to 0.993 and interobserver reproducibility ranging from 0.925 to 0.985. There were significant differences among three local JSWs, with the largest JSW at the lateral compartment. Global and medial local JSWs were significantly larger in the right hip, and global, medial and middle local JSWs were significantly smaller in women. Global and local JSWs were inversely correlated with CE angle and positively correlated with horizontal distance of the head center, but not correlated with body mass index in men and women. They were positively correlated with age and inversely correlated with vertical distance of the head center only in men. There were interindividual variations of JSW in normal population, depending on sites of the weight-bearing area, side, gender, age, and hip structural parameters. For accurate diagnosis and assessment of hip osteoarthritis, consideration of those influential factors other than degenerative change is important.

The devil is in the detail: brain dynamics in preparation for a global-local task.

PubMed

Leaver, Echo E; Low, Kathy A; DiVacri, Assunta; Merla, Arcangelo; Fabiani, Monica; Gratton, Gabriele

2015-08-01

When analyzing visual scenes, it is sometimes important to determine the relevant "grain" size. Attention control mechanisms may help direct our processing to the intended grain size. Here we used the event-related optical signal, a method possessing high temporal and spatial resolution, to examine the involvement of brain structures within the dorsal attention network (DAN) and the visual processing network (VPN) in preparation for the appropriate level of analysis. Behavioral data indicate that the small features of a hierarchical stimulus (local condition) are more difficult to process than the large features (global condition). Consistent with this finding, cues predicting a local trial were associated with greater DAN activation. This activity was bilateral but more pronounced in the left hemisphere, where it showed a frontal-to-parietal progression over time. Furthermore, the amount of DAN activation, especially in the left hemisphere and in parietal regions, was predictive of subsequent performance. Although local cues elicited left-lateralized DAN activity, no preponderantly right activity was observed for global cues; however, the data indicated an interaction between level of analysis (local vs. global) and hemisphere in VPN. They further showed that local processing involves structures in the ventral VPN, whereas global processing involves structures in the dorsal VPN. These results indicate that in our study preparation for analyzing different size features is an asymmetric process, in which greater preparation is required to focus on small rather than large features, perhaps because of their lesser salience. This preparation involves the same DAN used for other attention control operations.

Prolonged exposure to particulate chromate inhibits RAD51 nuclear import mediator proteins.

PubMed

Browning, Cynthia L; Wise, John Pierce

2017-09-15

Particulate hexavalent chromium (Cr(VI)) is a human lung carcinogen and a human health concern. The induction of structural chromosome instability is considered to be a driving mechanism of Cr(VI)-induced carcinogenesis. Homologous recombination repair protects against Cr(VI)-induced chromosome damage, due to its highly accurate repair of Cr(VI)-induced DNA double strand breaks. However, recent studies demonstrate Cr(VI) inhibits homologous recombination repair through the misregulation of RAD51. RAD51 is an essential protein in HR repair that facilitates the search for a homologous sequence. Recent studies show prolonged Cr(VI) exposure prevents proper RAD51 subcellular localization, causing it to accumulate in the cytoplasm. Since nuclear import of RAD51 is crucial to its function, this study investigated the effect of Cr(VI) on the RAD51 nuclear import mediators, RAD51C and BRCA2. We show acute (24h) Cr(VI) exposure induces the proper localization of RAD51C and BRCA2. In contrast, prolonged (120h) exposure increased the cytoplasmic localization of both proteins, although RAD51C localization was more severely impaired. These results correlate temporally with the previously reported Cr(VI)-induced RAD51 cytoplasmic accumulation. In addition, we found Cr(VI) does not inhibit interaction between RAD51 and its nuclear import mediators. Altogether, our results suggest prolonged Cr(VI) exposure inhibits the nuclear import of RAD51C, and to a lesser extent, BRCA2, which results in the cytoplasmic accumulation of RAD51. Cr(VI)-induced inhibition of nuclear import may play a key role in its carcinogenic mechanism since the nuclear import of many tumor suppressor proteins and DNA repair proteins is crucial to their function. Copyright © 2017 Elsevier Inc. All rights reserved.

Complex structures of different CaFe2As2 samples

PubMed Central

Saparov, Bayrammurad; Cantoni, Claudia; Pan, Minghu; Hogan, Thomas C.; II, William Ratcliff; Wilson, Stephen D.; Fritsch, Katharina; Gaulin, Bruce D.; Sefat, Athena S.

2014-01-01

The interplay between magnetism and crystal structures in three CaFe2As2 samples is studied. For the nonmagnetic quenched crystals, different crystalline domains with varying lattice parameters are found, and three phases (orthorhombic, tetragonal, and collapsed tetragonal) coexist between TS = 95 K and 45 K. Annealing of the quenched crystals at 350°C leads to a strain relief through a large (~1.3%) expansion of the c-parameter and a small (~0.2%) contraction of the a-parameter, and to local ~0.2 Å displacements at the atomic-level. This annealing procedure results in the most homogeneous crystals for which the antiferromagnetic and orthorhombic phase transitions occur at TN/TS = 168(1) K. In the 700°C-annealed crystal, an intermediate strain regime takes place, with tetragonal and orthorhombic structural phases coexisting between 80 to 120 K. The origin of such strong shifts in the transition temperatures are tied to structural parameters. Importantly, with annealing, an increase in the Fe-As length leads to more localized Fe electrons and higher local magnetic moments on Fe ions. Synergistic contribution of other structural parameters, including a decrease in the Fe-Fe distance, and a dramatic increase of the c-parameter, which enhances the Fermi surface nesting in CaFe2As2, are also discussed. PMID:24844399

Investigation of the Effect of the Tortuous Pore Structure on Water Diffusion through a Polymer Film Using Lattice Boltzmann Simulations.

PubMed

Gebäck, Tobias; Marucci, Mariagrazia; Boissier, Catherine; Arnehed, Johan; Heintz, Alexei

2015-04-23

Understanding how the pore structure influences the mass transport through a porous material is important in several applications, not the least in the design of polymer film coatings intended to control drug release. In this study, a polymer film made of ethyl cellulose and hydroxypropyl cellulose was investigated. The 3D structure of the films was first experimentally characterized using confocal laser scanning microscopy data and then mathematically reconstructed for the whole film thickness. Lattice Boltzmann simulations were performed to compute the effective diffusion coefficient of water in the film and the results were compared to experimental data. The local porosities and pore sizes were also analyzed to determine how the properties of the internal film structure affect the water effective diffusion coefficient. The results show that the top part of the film has lower porosity, lower pore size, and lower connectivity, which results in a much lower effective diffusion coefficient in this part, largely determining the diffusion rate through the entire film. Furthermore, the local effective diffusion coefficients were not proportional to the local film porosity, indicating that the results cannot be explained by a single tortuosity factor. In summary, the proposed methodology of combining microscopy data, mass transport simulations, and pore space analysis can give valuable insights on how the film structure affects the mass transport through the film.

Adapt-Mix: learning local genetic correlation structure improves summary statistics-based analyses

PubMed Central

Park, Danny S.; Brown, Brielin; Eng, Celeste; Huntsman, Scott; Hu, Donglei; Torgerson, Dara G.; Burchard, Esteban G.; Zaitlen, Noah

2015-01-01

Motivation: Approaches to identifying new risk loci, training risk prediction models, imputing untyped variants and fine-mapping causal variants from summary statistics of genome-wide association studies are playing an increasingly important role in the human genetics community. Current summary statistics-based methods rely on global ‘best guess’ reference panels to model the genetic correlation structure of the dataset being studied. This approach, especially in admixed populations, has the potential to produce misleading results, ignores variation in local structure and is not feasible when appropriate reference panels are missing or small. Here, we develop a method, Adapt-Mix, that combines information across all available reference panels to produce estimates of local genetic correlation structure for summary statistics-based methods in arbitrary populations. Results: We applied Adapt-Mix to estimate the genetic correlation structure of both admixed and non-admixed individuals using simulated and real data. We evaluated our method by measuring the performance of two summary statistics-based methods: imputation and joint-testing. When using our method as opposed to the current standard of ‘best guess’ reference panels, we observed a 28% decrease in mean-squared error for imputation and a 73.7% decrease in mean-squared error for joint-testing. Availability and implementation: Our method is publicly available in a software package called ADAPT-Mix available at https://github.com/dpark27/adapt_mix. Contact: noah.zaitlen@ucsf.edu PMID:26072481

iSS-PseDNC: identifying splicing sites using pseudo dinucleotide composition.

PubMed

Chen, Wei; Feng, Peng-Mian; Lin, Hao; Chou, Kuo-Chen

2014-01-01

In eukaryotic genes, exons are generally interrupted by introns. Accurately removing introns and joining exons together are essential processes in eukaryotic gene expression. With the avalanche of genome sequences generated in the postgenomic age, it is highly desired to develop automated methods for rapid and effective detection of splice sites that play important roles in gene structure annotation and even in RNA splicing. Although a series of computational methods were proposed for splice site identification, most of them neglected the intrinsic local structural properties. In the present study, a predictor called "iSS-PseDNC" was developed for identifying splice sites. In the new predictor, the sequences were formulated by a novel feature-vector called "pseudo dinucleotide composition" (PseDNC) into which six DNA local structural properties were incorporated. It was observed by the rigorous cross-validation tests on two benchmark datasets that the overall success rates achieved by iSS-PseDNC in identifying splice donor site and splice acceptor site were 85.45% and 87.73%, respectively. It is anticipated that iSS-PseDNC may become a useful tool for identifying splice sites and that the six DNA local structural properties described in this paper may provide novel insights for in-depth investigations into the mechanism of RNA splicing.

Helminth parasite communities of allopatric populations of the frog Leptodactylus podicipinus from Pantanal, Brazil.

PubMed

Campião, K M; da Silva, R J; Ferreira, V L

2014-03-01

Several factors may influence the structure of parasite communities in amphibian hosts. In this study, we describe the helminth parasites of three allopatric populations of the frog Leptodactylus podicipinus and test whether host size and sex were determinants of the structure and composition of the helminth communities. One hundred and twenty-three anurans were collected from three different study sites within the Pantanal wetlands and surveyed for helminth parasites. We found 14 helminth taxa: 7 species of nematodes, 4 species of trematodes, 1 species of cestodes, 1 species of acanthocephalan and one unidentified cyst. Host sex and size did not cause significant differences in helminth abundance or richness. The structure of helminth communities from the three study sites varied in terms of species composition, abundance and diversity. Six out of 14 helminth taxa were found in the three localities. Among those, the nematodes Cosmocerca podicipinus and Rhabdias sp., the trematode Catadiscus propinquus and the helminth cyst showed significant differences in mean abundances. We suggest that such differences found among the three component communities are driven by biotic and abiotic factors operating locally. Moreover, these differences stress the importance of local conditions, such as hydrologic characteristics and landscape composition, on helminth community structure.

Surface layer protein characterization by small angle x-ray scattering and a fractal mean force concept: from protein structure to nanodisk assemblies.

PubMed

Horejs, Christine; Pum, Dietmar; Sleytr, Uwe B; Peterlik, Herwig; Jungbauer, Alois; Tscheliessnig, Rupert

2010-11-07

Surface layers (S-layers) are the most commonly observed cell surface structure of prokaryotic organisms. They are made up of proteins that spontaneously self-assemble into functional crystalline lattices in solution, on various solid surfaces, and interfaces. While classical experimental techniques failed to recover a complete structural model of an unmodified S-layer protein, small angle x-ray scattering (SAXS) provides an opportunity to study the structure of S-layer monomers in solution and of self-assembled two-dimensional sheets. For the protein under investigation we recently suggested an atomistic structural model by the use of molecular dynamics simulations. This structural model is now refined on the basis of SAXS data together with a fractal assembly approach. Here we show that a nondiluted critical system of proteins, which crystallize into monomolecular structures, might be analyzed by SAXS if protein-protein interactions are taken into account by relating a fractal local density distribution to a fractal local mean potential, which has to fulfill the Poisson equation. The present work demonstrates an important step into the elucidation of the structure of S-layers and offers a tool to analyze the structure of self-assembling systems in solution by means of SAXS and computer simulations.

Surface layer protein characterization by small angle x-ray scattering and a fractal mean force concept: From protein structure to nanodisk assemblies

NASA Astrophysics Data System (ADS)

Horejs, Christine; Pum, Dietmar; Sleytr, Uwe B.; Peterlik, Herwig; Jungbauer, Alois; Tscheliessnig, Rupert

2010-11-01

Surface layers (S-layers) are the most commonly observed cell surface structure of prokaryotic organisms. They are made up of proteins that spontaneously self-assemble into functional crystalline lattices in solution, on various solid surfaces, and interfaces. While classical experimental techniques failed to recover a complete structural model of an unmodified S-layer protein, small angle x-ray scattering (SAXS) provides an opportunity to study the structure of S-layer monomers in solution and of self-assembled two-dimensional sheets. For the protein under investigation we recently suggested an atomistic structural model by the use of molecular dynamics simulations. This structural model is now refined on the basis of SAXS data together with a fractal assembly approach. Here we show that a nondiluted critical system of proteins, which crystallize into monomolecular structures, might be analyzed by SAXS if protein-protein interactions are taken into account by relating a fractal local density distribution to a fractal local mean potential, which has to fulfill the Poisson equation. The present work demonstrates an important step into the elucidation of the structure of S-layers and offers a tool to analyze the structure of self-assembling systems in solution by means of SAXS and computer simulations.

Surface layer protein characterization by small angle x-ray scattering and a fractal mean force concept: From protein structure to nanodisk assemblies

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

Horejs, Christine; Pum, Dietmar; Sleytr, Uwe B.

2010-11-07

Surface layers (S-layers) are the most commonly observed cell surface structure of prokaryotic organisms. They are made up of proteins that spontaneously self-assemble into functional crystalline lattices in solution, on various solid surfaces, and interfaces. While classical experimental techniques failed to recover a complete structural model of an unmodified S-layer protein, small angle x-ray scattering (SAXS) provides an opportunity to study the structure of S-layer monomers in solution and of self-assembled two-dimensional sheets. For the protein under investigation we recently suggested an atomistic structural model by the use of molecular dynamics simulations. This structural model is now refined on themore » basis of SAXS data together with a fractal assembly approach. Here we show that a nondiluted critical system of proteins, which crystallize into monomolecular structures, might be analyzed by SAXS if protein-protein interactions are taken into account by relating a fractal local density distribution to a fractal local mean potential, which has to fulfill the Poisson equation. The present work demonstrates an important step into the elucidation of the structure of S-layers and offers a tool to analyze the structure of self-assembling systems in solution by means of SAXS and computer simulations.« less

Parameterized centrality metric for network analysis

NASA Astrophysics Data System (ADS)

Ghosh, Rumi; Lerman, Kristina

2011-06-01

A variety of metrics have been proposed to measure the relative importance of nodes in a network. One of these, alpha-centrality [P. Bonacich, Am. J. Sociol.0002-960210.1086/228631 92, 1170 (1987)], measures the number of attenuated paths that exist between nodes. We introduce a normalized version of this metric and use it to study network structure, for example, to rank nodes and find community structure of the network. Specifically, we extend the modularity-maximization method for community detection to use this metric as the measure of node connectivity. Normalized alpha-centrality is a powerful tool for network analysis, since it contains a tunable parameter that sets the length scale of interactions. Studying how rankings and discovered communities change when this parameter is varied allows us to identify locally and globally important nodes and structures. We apply the proposed metric to several benchmark networks and show that it leads to better insights into network structure than alternative metrics.

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

The local implementation of a chronic disease management model for childhood overweight and obesity.

PubMed

Brink-Melis, Willy J; Derksen, Elze R E; Westerman, Marjan J; Renders, Carry M; Seidell, Jacob C; Visscher, Tommy L S

2012-01-01

The aim of this study is to determine opportunities and barriers regarding the management of overweight and obese children in daily practice, and to show the value of using focus groups when developing an action plan for childhood overweight management in a local context. Seven focus groups and four semi-structured interviews were conducted with 29 professionals from nine different care disciplines and 7 parents of overweight and obese children aged 4-19 years. After thorough analysis of the focus groups, issues concerning finding the most appropriate care and realising a long-term weight management in daily practice have become clear. Some examples of these issues are: lack of awareness, reluctance to discuss and refer, mutual cooperation, contradictory advice and expectations of treatment and lack of effective support strategies. Focus groups deliver important information on local issues that are important for the development and implementation of a childhood overweight management action plan. And, besides delivering necessary information, focus groups lead to an increased awareness and willingness to improve childhood overweight management in a local context. Copyright © 2012 S. Karger GmbH, Freiburg.

Importance of nuclear localization for the apoptosis-induced activity of a fungal galectin AAL (Agrocybe aegerita lectin)

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

Liang, Yi; Feng, Lei; Tong, Xin

2009-08-28

Agrocybe aegerita lectin (AAL) was identified previously in our group as a novel galectin from medicinal fungi Agrocybe aegerita, and has been shown to effectively induce cancer cell cycle arrest and apoptosis in vitro and tumor regression in vivo. Here, AAL was observed to translocate into the HeLa cell nucleus and induce cell apoptosis when it was predominantly in the nucleus. The N-terminus and C-terminus of AAL were required for nuclear localization. Site mutated proteins were generated based on AAL structure. Dimer interface mutant I25G, carbohydrate recognition domain (CRD) mutant R63H, and loop region mutant L33A could not enter themore » nucleus and lost the ability to induce apoptosis. CRD mutant H59Q and loop region mutant I144G maintained nuclear localization activity, and H59Q retained residual bioability but I144G had no activity, indicating that nuclear localization is important but not sufficient for AAL to become apoptotically active. Our findings provide a novel antitumor mechanism of fungal galectin.« less

Efficient iris recognition by characterizing key local variations.

PubMed

Ma, Li; Tan, Tieniu; Wang, Yunhong; Zhang, Dexin

2004-06-01

Unlike other biometrics such as fingerprints and face, the distinct aspect of iris comes from randomly distributed features. This leads to its high reliability for personal identification, and at the same time, the difficulty in effectively representing such details in an image. This paper describes an efficient algorithm for iris recognition by characterizing key local variations. The basic idea is that local sharp variation points, denoting the appearing or vanishing of an important image structure, are utilized to represent the characteristics of the iris. The whole procedure of feature extraction includes two steps: 1) a set of one-dimensional intensity signals is constructed to effectively characterize the most important information of the original two-dimensional image; 2) using a particular class of wavelets, a position sequence of local sharp variation points in such signals is recorded as features. We also present a fast matching scheme based on exclusive OR operation to compute the similarity between a pair of position sequences. Experimental results on 2255 iris images show that the performance of the proposed method is encouraging and comparable to the best iris recognition algorithm found in the current literature.

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.

Altered Brain Network Segregation in Fragile X Syndrome Revealed by Structural Connectomics.

PubMed

Bruno, Jennifer Lynn; Hosseini, S M Hadi; Saggar, Manish; Quintin, Eve-Marie; Raman, Mira Michelle; Reiss, Allan L

2017-03-01

Fragile X syndrome (FXS), the most common inherited cause of intellectual disability and autism spectrum disorder, is associated with significant behavioral, social, and neurocognitive deficits. Understanding structural brain network topology in FXS provides an important link between neurobiological and behavioral/cognitive symptoms of this disorder. We investigated the connectome via whole-brain structural networks created from group-level morphological correlations. Participants included 100 individuals: 50 with FXS and 50 with typical development, age 11-23 years. Results indicated alterations in topological properties of structural brain networks in individuals with FXS. Significantly reduced small-world index indicates a shift in the balance between network segregation and integration and significantly reduced clustering coefficient suggests that reduced local segregation shifted this balance. Caudate and amygdala were less interactive in the FXS network further highlighting the importance of subcortical region alterations in the neurobiological signature of FXS. Modularity analysis indicates that FXS and typically developing groups' networks decompose into different sets of interconnected sub networks, potentially indicative of aberrant local interconnectivity in individuals with FXS. These findings advance our understanding of the effects of fragile X mental retardation protein on large-scale brain networks and could be used to develop a connectome-level biological signature for FXS. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Advanced prior modeling for 3D bright field electron tomography

NASA Astrophysics Data System (ADS)

Sreehari, Suhas; Venkatakrishnan, S. V.; Drummy, Lawrence F.; Simmons, Jeffrey P.; Bouman, Charles A.

2015-03-01

Many important imaging problems in material science involve reconstruction of images containing repetitive non-local structures. Model-based iterative reconstruction (MBIR) could in principle exploit such redundancies through the selection of a log prior probability term. However, in practice, determining such a log prior term that accounts for the similarity between distant structures in the image is quite challenging. Much progress has been made in the development of denoising algorithms like non-local means and BM3D, and these are known to successfully capture non-local redundancies in images. But the fact that these denoising operations are not explicitly formulated as cost functions makes it unclear as to how to incorporate them in the MBIR framework. In this paper, we formulate a solution to bright field electron tomography by augmenting the existing bright field MBIR method to incorporate any non-local denoising operator as a prior model. We accomplish this using a framework we call plug-and-play priors that decouples the log likelihood and the log prior probability terms in the MBIR cost function. We specifically use 3D non-local means (NLM) as the prior model in the plug-and-play framework, and showcase high quality tomographic reconstructions of a simulated aluminum spheres dataset, and two real datasets of aluminum spheres and ferritin structures. We observe that streak and smear artifacts are visibly suppressed, and that edges are preserved. Also, we report lower RMSE values compared to the conventional MBIR reconstruction using qGGMRF as the prior model.

StralSV: assessment of sequence variability within similar 3D structures and application to polio RNA-dependent RNA polymerase

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

Zemla, A; Lang, D; Kostova, T

2010-11-29

Most of the currently used methods for protein function prediction rely on sequence-based comparisons between a query protein and those for which a functional annotation is provided. A serious limitation of sequence similarity-based approaches for identifying residue conservation among proteins is the low confidence in assigning residue-residue correspondences among proteins when the level of sequence identity between the compared proteins is poor. Multiple sequence alignment methods are more satisfactory - still, they cannot provide reliable results at low levels of sequence identity. Our goal in the current work was to develop an algorithm that could overcome these difficulties and facilitatemore » the identification of structurally (and possibly functionally) relevant residue-residue correspondences between compared protein structures. Here we present StralSV, a new algorithm for detecting closely related structure fragments and quantifying residue frequency from tight local structure alignments. We apply StralSV in a study of the RNA-dependent RNA polymerase of poliovirus and demonstrate that the algorithm can be used to determine regions of the protein that are relatively unique or that shared structural similarity with structures that are distantly related. By quantifying residue frequencies among many residue-residue pairs extracted from local alignments, one can infer potential structural or functional importance of specific residues that are determined to be highly conserved or that deviate from a consensus. We further demonstrate that considerable detailed structural and phylogenetic information can be derived from StralSV analyses. StralSV is a new structure-based algorithm for identifying and aligning structure fragments that have similarity to a reference protein. StralSV analysis can be used to quantify residue-residue correspondences and identify residues that may be of particular structural or functional importance, as well as unusual or unexpected residues at a given sequence position.« less

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.

Potential energy surface fitting by a statistically localized, permutationally invariant, local interpolating moving least squares method for the many-body potential: Method and application to N{sub 4}

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

Bender, Jason D.; Doraiswamy, Sriram; Candler, Graham V., E-mail: truhlar@umn.edu, E-mail: candler@aem.umn.edu

2014-02-07

Fitting potential energy surfaces to analytic forms is an important first step for efficient molecular dynamics simulations. Here, we present an improved version of the local interpolating moving least squares method (L-IMLS) for such fitting. Our method has three key improvements. First, pairwise interactions are modeled separately from many-body interactions. Second, permutational invariance is incorporated in the basis functions, using permutationally invariant polynomials in Morse variables, and in the weight functions. Third, computational cost is reduced by statistical localization, in which we statistically correlate the cutoff radius with data point density. We motivate our discussion in this paper with amore » review of global and local least-squares-based fitting methods in one dimension. Then, we develop our method in six dimensions, and we note that it allows the analytic evaluation of gradients, a feature that is important for molecular dynamics. The approach, which we call statistically localized, permutationally invariant, local interpolating moving least squares fitting of the many-body potential (SL-PI-L-IMLS-MP, or, more simply, L-IMLS-G2), is used to fit a potential energy surface to an electronic structure dataset for N{sub 4}. We discuss its performance on the dataset and give directions for further research, including applications to trajectory calculations.« less

Influence of local meshing size on stress intensity factor of orthopedic lag screw

NASA Astrophysics Data System (ADS)

Husain, M. N.; Daud, R.; Basaruddin, K. S.; Mat, F.; Bajuri, M. Y.; Arifin, A. K.

2017-09-01

Linear elastic fracture mechanics (LEFM) concept is generally used to study the influence of crack on the performance of structures. In order to study the LEFM concept on damaged structure, the usage of finite element analysis software is implemented to do the simulation of the structure. Mesh generation is one of the most crucial procedures in finite element method. For the structure that crack or damaged, it is very important to determine the accurate local meshing size at the crack tip of the crack itself in order to get the accurate value of stress intensity factor, KI. Pre crack will be introduced to the lag screw based on the von mises' stress result that had been performed in previous research. This paper shows the influence of local mesh arrangement on numerical value of the stress intensity factor, KI obtained by the displacement method. This study aims to simulate the effect of local meshing which is the singularity region on stress intensity factor, KI to the critical point of failure in screw. Five different set of wedges meshing size are introduced during the simulation of finite element analysis. The number of wedges used to simulate this research is 8, 10, 14, 16 and 20. There are three set of numerical equations used to validate the results which are brown and srawley, gross and brown and Tada equation. The result obtained from the finite element software (ANSYS APDL) has a positive agreement with the numerical analysis which is Brown and Srawley compared to other numerical formula. Radius of first row size of 0.014 and singularity element with 14 numbers of wedges is proved to be the best local meshing for this study.

A multistate dynamic site occupancy model for spatially aggregated sessile communities

USGS Publications Warehouse

Fukaya, Keiichi; Royle, J. Andrew; Okuda, Takehiro; Nakaoka, Masahiro; Noda, Takashi

2017-01-01

Estimation of transition probabilities of sessile communities seems easy in principle but may still be difficult in practice because resampling error (i.e. a failure to resample exactly the same location at fixed points) may cause significant estimation bias. Previous studies have developed novel analytical methods to correct for this estimation bias. However, they did not consider the local structure of community composition induced by the aggregated distribution of organisms that is typically observed in sessile assemblages and is very likely to affect observations.We developed a multistate dynamic site occupancy model to estimate transition probabilities that accounts for resampling errors associated with local community structure. The model applies a nonparametric multivariate kernel smoothing methodology to the latent occupancy component to estimate the local state composition near each observation point, which is assumed to determine the probability distribution of data conditional on the occurrence of resampling error.By using computer simulations, we confirmed that an observation process that depends on local community structure may bias inferences about transition probabilities. By applying the proposed model to a real data set of intertidal sessile communities, we also showed that estimates of transition probabilities and of the properties of community dynamics may differ considerably when spatial dependence is taken into account.Results suggest the importance of accounting for resampling error and local community structure for developing management plans that are based on Markovian models. Our approach provides a solution to this problem that is applicable to broad sessile communities. It can even accommodate an anisotropic spatial correlation of species composition, and may also serve as a basis for inferring complex nonlinear ecological dynamics.

Overlapping communities from dense disjoint and high total degree clusters

NASA Astrophysics Data System (ADS)

Zhang, Hongli; Gao, Yang; Zhang, Yue

2018-04-01

Community plays an important role in the field of sociology, biology and especially in domains of computer science, where systems are often represented as networks. And community detection is of great importance in the domains. A community is a dense subgraph of the whole graph with more links between its members than between its members to the outside nodes, and nodes in the same community probably share common properties or play similar roles in the graph. Communities overlap when nodes in a graph belong to multiple communities. A vast variety of overlapping community detection methods have been proposed in the literature, and the local expansion method is one of the most successful techniques dealing with large networks. The paper presents a density-based seeding method, in which dense disjoint local clusters are searched and selected as seeds. The proposed method selects a seed by the total degree and density of local clusters utilizing merely local structures of the network. Furthermore, this paper proposes a novel community refining phase via minimizing the conductance of each community, through which the quality of identified communities is largely improved in linear time. Experimental results in synthetic networks show that the proposed seeding method outperforms other seeding methods in the state of the art and the proposed refining method largely enhances the quality of the identified communities. Experimental results in real graphs with ground-truth communities show that the proposed approach outperforms other state of the art overlapping community detection algorithms, in particular, it is more than two orders of magnitude faster than the existing global algorithms with higher quality, and it obtains much more accurate community structure than the current local algorithms without any priori information.

Assessment of existing local houses condition as analysis tools for shore housing improvement program in Weriagar district, Bintuni Bay

NASA Astrophysics Data System (ADS)

Firmansyah, F.; Fernando, A.; Allo, I. P. R.

2018-01-01

The housing assessment is a part of the pre-feasibility study inThe Shore Housing Improvement Program in Weriagar District, West Papua. The housing assessment was conducted to identify the physical condition of existing houses. The parameters of assessment formulated from local references, practices and also national building regulation that covers each building system components, such as building structure/frame, building floor, building cover, and building roof. This study aims to explains lessons from local practices and references, used as the formula to generate assessment parameter, elaborate with Indonesia building regulation. The result of housing assessment were used as a basis to develop the house improvement strategy, the design alternative for housing improvement and further planning recommendations. The local knowledges involved in housing improvement program expected that the local-based approach could respect to the local build culture, respect the local environment, and the most important can offer best suitable solutions for functional utility and livability.

Dental Public Health In Action: Putting Oral Health on the Local Public Health Agenda.

PubMed

Walker, I F; Eapen-Simon, S; Gibson, S

2018-04-18

Oral health is a key public health issue across England. In Wakefield in the north of England, local data suggested the oral health of local children was significantly worse than the national average. This paper describes the work undertaken by Wakefield Council to strategically address this issue. A structured process was adopted. Key lessons include; having senior ownership from the Director of Public Health, partnership working across all key stakeholders, utilising dental public health expertise from Public Health England and the use of extensive engagement with stakeholders. Through this work, oral health is now identified with greater importance in Wakefield as a public health issue. Actions are now strategically co-ordinated across stakeholders to improve oral health in local children. Copyright© 2018 Dennis Barber Ltd.

Structural short-range order of the β-Ti phase in bulk Ti-Fe-(Sn) nanoeutectic composites

NASA Astrophysics Data System (ADS)

Das, J.; Eckert, J.; Theissmann, R.

2006-12-01

The authors report lattice distortion and "ω-like" structural short-range order (SRO) of the β-Ti phase in a Ti-Fe-(Sn) bulk nanoeutectic composite prepared by slow cooling from the melt. The nanoeuetctic phases are chemically homogeneous, but the addition of Sn releases the local lattice strain, modifies the structural SRO, and prevents the formation of stacking faults in the body centered cubic (bcc) β-Ti phase resulting in improved plastic deformability. The elastic properties and the structural SRO of the β-Ti phase are proposed to be important parameters for developing advanced high strength, ductile Ti-base nanocomposite alloys.

Demographics and Case Studies of Galactic Outflows in the Local Universe

NASA Astrophysics Data System (ADS)

Rupke, David

2017-07-01

Galactic outflows driven by both star formation and active black holes are an important driver of galaxy evolution. The local universe is a sensitive laboratory for understanding the scaling relations that characterize these winds and the physics that govern them. I will review what we know from statistical studies about the prevalance and properties of nearby galactic winds and how these properties depend on those of the host galaxy or power source. I will also highlight detailed case studies of key objects that illustrate the multiphase structure of these winds.

The f ( R ) halo mass function in the cosmic web

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

Braun-Bates, F. von; Winther, H.A.; Alonso, D.

An important indicator of modified gravity is the effect of the local environment on halo properties. This paper examines the influence of the local tidal structure on the halo mass function, the halo orientation, spin and the concentration-mass relation. We use the excursion set formalism to produce a halo mass function conditional on large-scale structure. Our simple model agrees well with simulations on large scales at which the density field is linear or weakly non-linear. Beyond this, our principal result is that f ( R ) does affect halo abundances, the halo spin parameter and the concentration-mass relationship in anmore » environment-independent way, whereas we find no appreciable deviation from \\text(ΛCDM) for the mass function with fixed environment density, nor the alignment of the orientation and spin vectors of the halo to the eigenvectors of the local cosmic web. There is a general trend for greater deviation from \\text(ΛCDM) in underdense environments and for high-mass haloes, as expected from chameleon screening.« less

Nucleophosmin integrates within the nucleolus via multi-modal interactions with proteins displaying R-rich linear motifs and rRNA.

PubMed

Mitrea, Diana M; Cika, Jaclyn A; Guy, Clifford S; Ban, David; Banerjee, Priya R; Stanley, Christopher B; Nourse, Amanda; Deniz, Ashok A; Kriwacki, Richard W

2016-02-02

The nucleolus is a membrane-less organelle formed through liquid-liquid phase separation of its components from the surrounding nucleoplasm. Here, we show that nucleophosmin (NPM1) integrates within the nucleolus via a multi-modal mechanism involving multivalent interactions with proteins containing arginine-rich linear motifs (R-motifs) and ribosomal RNA (rRNA). Importantly, these R-motifs are found in canonical nucleolar localization signals. Based on a novel combination of biophysical approaches, we propose a model for the molecular organization within liquid-like droplets formed by the N-terminal domain of NPM1 and R-motif peptides, thus providing insights into the structural organization of the nucleolus. We identify multivalency of acidic tracts and folded nucleic acid binding domains, mediated by N-terminal domain oligomerization, as structural features required for phase separation of NPM1 with other nucleolar components in vitro and for localization within mammalian nucleoli. We propose that one mechanism of nucleolar localization involves phase separation of proteins within the nucleolus.

Ripple-modulated electronic structure of a 3D topological insulator.

PubMed

Okada, Yoshinori; Zhou, Wenwen; Walkup, D; Dhital, Chetan; Wilson, Stephen D; Madhavan, V

2012-01-01

Three-dimensional topological insulators host linearly dispersing states with unique properties and a strong potential for applications. An important ingredient in realizing some of the more exotic states in topological insulators is the ability to manipulate local electronic properties. Direct analogy to the Dirac material graphene suggests that a possible avenue for controlling local properties is via a controlled structural deformation such as the formation of ripples. However, the influence of such ripples on topological insulators is yet to be explored. Here we use scanning tunnelling microscopy to determine the effects of one-dimensional buckling on the electronic properties of Bi(2)Te(3.) By tracking spatial variations of the interference patterns generated by the Dirac electrons we show that buckling imposes a periodic potential, which locally modulates the surface-state dispersion. This suggests that forming one- and two-dimensional ripples is a viable method for creating nanoscale potential landscapes that can be used to control the properties of Dirac electrons in topological insulators.

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

Datta, Kaustuv; Neder, Reinhard B.; Chen, Jun

Revelation of unequivocal structural information at the atomic level for complex systems is uniquely important for deeper and generic understanding of the structure property connections and a key challenge in materials science. Here in this paper we report an experimental study of the local structure by applying total elastic scattering and Raman scattering analyses to an important non-relaxor ferroelectric solid solution exhibiting the so-called composition-induced morphotropic phase boundary (MPB), where concomitant enhancement of physical properties have been detected. The powerful combination of static and dynamic structural probes enabled us to derive direct correspondence between the atomic-level structural correlations and reportedmore » properties. The atomic pair distribution functions obtained from the neutron total scattering experiments were analysed through big-box atom-modelling implementing reverse Monte Carlo method, from which distributions of magnitudes and directions of off-centred cationic displacements were extracted. We found that an enhanced randomness of the displacement-directions for all ferroelectrically active cations combined with a strong dynamical coupling between the A- and B-site cations of the perovskite structure, can explain the abrupt amplification of piezoelectric response of the system near MPB. Finally, altogether this provides a more fundamental basis in inferring structure-property connections in similar systems including important implications in designing novel and bespoke materials.« less

Atomic scale chemical tomography of human bone

NASA Astrophysics Data System (ADS)

Langelier, Brian; Wang, Xiaoyue; Grandfield, Kathryn

2017-01-01

Human bone is a complex hierarchical material. Understanding bone structure and its corresponding composition at the nanometer scale is critical for elucidating mechanisms of biomineralization under healthy and pathological states. However, the three-dimensional structure and chemical nature of bone remains largely unexplored at the nanometer scale due to the challenges associated with characterizing both the structural and chemical integrity of bone simultaneously. Here, we use correlative transmission electron microscopy and atom probe tomography for the first time, to our knowledge, to reveal structures in human bone at the atomic level. This approach provides an overlaying chemical map of the organic and inorganic constituents of bone on its structure. This first use of atom probe tomography on human bone reveals local gradients, trace element detection of Mg, and the co-localization of Na with the inorganic-organic interface of bone mineral and collagen fibrils, suggesting the important role of Na-rich organics in the structural connection between mineral and collagen. Our findings provide the first insights into the hierarchical organization and chemical heterogeneity in human bone in three-dimensions at its smallest length scale - the atomic level. We demonstrate that atom probe tomography shows potential for new insights in biomineralization research on bone.

Non-contact local temperature measurement inside an object using an infrared point detector

NASA Astrophysics Data System (ADS)

Hisaka, Masaki

2017-04-01

Local temperature measurement in deep areas of objects is an important technique in biomedical measurement. We have investigated a non-contact method for measuring temperature inside an object using a point detector for infrared (IR) light. An IR point detector with a pinhole was constructed and the radiant IR light emitted from the local interior of the object is photodetected only at the position of pinhole located in imaging relation. We measured the thermal structure of the filament inside the miniature bulb using the IR point detector, and investigated the temperature dependence at approximately human body temperature using a glass plate positioned in front of the heat source.

New Insight into the Local Structure of Hydrous Ferric Arsenate Using Full-Potential Multiple Scattering Analysis, Density Functional Theory Calculations, and Vibrational Spectroscopy.

PubMed

Wang, Shaofeng; Ma, Xu; Zhang, Guoqing; Jia, Yongfeng; Hatada, Keisuke

2016-11-15

Hydrous ferric arsenate (HFA) is an important arsenic-bearing precipitate in the mining-impacted environment and hydrometallurgical tailings. However, there is no agreement on its local atomic structure. The local structure of HFA was reprobed by employing a full-potential multiple scattering (FPMS) analysis, density functional theory (DFT) calculations, and vibrational spectroscopy. The FPMS simulations indicated that the coordination number of the As-Fe, Fe-As, or both in HFA was approximately two. The DFT calculations constructed a structure of HFA with the formula of Fe(HAsO 4 ) x (H 2 AsO 4 ) 1-x (OH) y ·zH 2 O. The presence of protonated arsenate in HFA was also evidenced by vibrational spectroscopy. The As and Fe K-edge X-ray absorption near-edge structure spectra of HFA were accurately reproduced by FPMS simulations using the chain structure, which was also a reasonable model for extended X-Ray absorption fine structure fitting. The FPMS refinements indicated that the interatomic Fe-Fe distance was approximately 5.2 Å, consistent with that obtained by Mikutta et al. (Environ. Sci. Technol. 2013, 47 (7), 3122-3131) using wavelet analysis. All of the results suggested that HFA was more likely to occur as a chain with AsO 4 tetrahedra and FeO 6 octahedra connecting alternately in an isolated bidentate-type fashion. This finding is of significance for understanding the fate of arsenic and the formation of ferric arsenate minerals in an acidic environment.

Changes in local surface structure and Sr depletion in Fe-implanted SrTiO3 (001)

NASA Astrophysics Data System (ADS)

Lobacheva, O.; Yiu, Y. M.; Chen, N.; Sham, T. K.; Goncharova, L. V.

2017-01-01

Local surface structure of single crystal strontium titanate SrTiO3 (001) samples implanted with Fe in the range of concentrations between 2 × 1014 to 2 × 1016 Fe/cm2 at 30 keV has been investigated. In order to facilitate Fe substitution (doping), implanted samples were annealed in oxygen at 350 °C. Sr depletion was observed from the near-surface layers impacted by the ion-implantation process, as revealed by Rutherford Backscattering Spectrometry (RBS), X-ray photoelectron spectroscopy (XPS), X-ray Absorption Near Edge Spectroscopy (XANES), and Atomic Force Microscopy (AFM). Hydrocarbon contaminations on the surface may contribute to the mechanisms of Sr depletion, which have important implications for Sr(Ti1-xFex)O3-δ materials in gas sensing applications.

A New Approach of evaluating the damage in simply-supported reinforced concrete beam by Local mean decomposition (LMD)

NASA Astrophysics Data System (ADS)

Zhang, Xuebing; Liu, Ning; Xi, Jiaxin; Zhang, Yunqi; Zhang, Wenchun; Yang, Peipei

2017-08-01

How to analyze the nonstationary response signals and obtain vibration characters is extremely important in the vibration-based structural diagnosis methods. In this work, we introduce a more reasonable time-frequency decomposition method termed local mean decomposition (LMD) to instead the widely-used empirical mode decomposition (EMD). By employing the LMD method, one can derive a group of component signals, each of which is more stationary, and then analyze the vibration state and make the assessment of structural damage of a construction or building. We illustrated the effectiveness of LMD by a synthetic data and an experimental data recorded in a simply-supported reinforced concrete beam. Then based on the decomposition results, an elementary method of damage diagnosis was proposed.

Computational methods and traveling wave solutions for the fourth-order nonlinear Ablowitz-Kaup-Newell-Segur water wave dynamical equation via two methods and its applications

NASA Astrophysics Data System (ADS)

Ali, Asghar; Seadawy, Aly R.; Lu, Dianchen

2018-05-01

The aim of this article is to construct some new traveling wave solutions and investigate localized structures for fourth-order nonlinear Ablowitz-Kaup-Newell-Segur (AKNS) water wave dynamical equation. The simple equation method (SEM) and the modified simple equation method (MSEM) are applied in this paper to construct the analytical traveling wave solutions of AKNS equation. The different waves solutions are derived by assigning special values to the parameters. The obtained results have their importance in the field of physics and other areas of applied sciences. All the solutions are also graphically represented. The constructed results are often helpful for studying several new localized structures and the waves interaction in the high-dimensional models.

Ground Layer Plant Species Turnover and Beta Diversity in Southern-European Old-Growth Forests

PubMed Central

Sabatini, Francesco Maria; Burrascano, Sabina; Tuomisto, Hanna; Blasi, Carlo

2014-01-01

Different assembly processes may simultaneously affect local-scale variation of species composition in temperate old-growth forests. Ground layer species diversity reflects chance colonization and persistence of low-dispersal species, as well as fine-scale environmental heterogeneity. The latter depends on both purely abiotic factors, such as soil properties and topography, and factors primarily determined by overstorey structure, such as light availability. Understanding the degree to which plant diversity in old-growth forests is associated with structural heterogeneity and/or to dispersal limitation will help assessing the effectiveness of silvicultural practices that recreate old-growth patterns and structures for the conservation or restoration of plant diversity. We used a nested sampling design to assess fine-scale species turnover, i.e. the proportion of species composition that changes among sampling units, across 11 beech-dominated old-growth forests in Southern Europe. For each stand, we also measured a wide range of environmental and structural variables that might explain ground layer species turnover. Our aim was to quantify the relative importance of dispersal limitation in comparison to that of stand structural heterogeneity while controlling for other sources of environmental heterogeneity. For this purpose, we used multiple regression on distance matrices at the within-stand extent, and mixed effect models at the extent of the whole dataset. Species turnover was best predicted by structural and environmental heterogeneity, especially by differences in light availability and in topsoil nutrient concentration and texture. Spatial distances were significant only in four out of eleven stands with a relatively low explanatory power. This suggests that structural heterogeneity is a more important driver of local-scale ground layer species turnover than dispersal limitation in southern European old-growth beech forests. PMID:24748155

In vivo subcellular localization of Mal de Rio Cuarto virus (MRCV) non-structural proteins in insect cells reveals their putative functions

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

Maroniche, Guillermo A.; Mongelli, Vanesa C.; Llauger, Gabriela

2012-09-01

The in vivo subcellular localization of Mal de Rio Cuarto virus (MRCV, Fijivirus, Reoviridae) non-structural proteins fused to GFP was analyzed by confocal microscopy. P5-1 showed a cytoplasmic vesicular-like distribution that was lost upon deleting its PDZ binding TKF motif, suggesting that P5-1 interacts with cellular PDZ proteins. P5-2 located at the nucleus and its nuclear import was affected by the deletion of its basic C-termini. P7-1 and P7-2 also entered the nucleus and therefore, along with P5-2, could function as regulators of host gene expression. P6 located in the cytoplasm and in perinuclear cloud-like inclusions, was driven to P9-1more » viroplasm-like structures and co-localized with P7-2, P10 and {alpha}-tubulin, suggesting its involvement in viroplasm formation and viral intracellular movement. Finally, P9-2 was N-glycosylated and located at the plasma membrane in association with filopodia-like protrusions containing actin, suggesting a possible role in virus cell-to-cell movement and spread.« less

Mapping in vitro local material properties of intact and disrupted virions at high resolution using multi-harmonic atomic force microscopy.

PubMed

Cartagena, Alexander; Hernando-Pérez, Mercedes; Carrascosa, José L; de Pablo, Pedro J; Raman, Arvind

2013-06-07

Understanding the relationships between viral material properties (stiffness, strength, charge density, adhesion, hydration, viscosity, etc.), structure (protein sub-units, genome, surface receptors, appendages), and functions (self-assembly, stability, disassembly, infection) is of significant importance in physical virology and nanomedicine. Conventional Atomic Force Microscopy (AFM) methods have measured a single physical property such as the stiffness of the entire virus from nano-indentation at a few points which severely limits the study of structure-property-function relationships. We present an in vitro dynamic AFM technique operating in the intermittent contact regime which synthesizes anharmonic Lorentz-force excited AFM cantilevers to map quantitatively at nanometer resolution the local electro-mechanical force gradient, adhesion, and hydration layer viscosity within individual φ29 virions. Furthermore, the changes in material properties over the entire φ29 virion provoked by the local disruption of its shell are studied, providing evidence of bacteriophage depressurization. The technique significantly generalizes recent multi-harmonic theory (A. Raman, et al., Nat. Nanotechnol., 2011, 6, 809-814) and enables high-resolution in vitro quantitative mapping of multiple material properties within weakly bonded viruses and nanoparticles with complex structure that otherwise cannot be observed using standard AFM techniques.

A local immunization strategy for networks with overlapping community structure

NASA Astrophysics Data System (ADS)

Taghavian, Fatemeh; Salehi, Mostafa; Teimouri, Mehdi

2017-02-01

Since full coverage treatment is not feasible due to limited resources, we need to utilize an immunization strategy to effectively distribute the available vaccines. On the other hand, the structure of contact network among people has a significant impact on epidemics of infectious diseases (such as SARS and influenza) in a population. Therefore, network-based immunization strategies aim to reduce the spreading rate by removing the vaccinated nodes from contact network. Such strategies try to identify more important nodes in epidemics spreading over a network. In this paper, we address the effect of overlapping nodes among communities on epidemics spreading. The proposed strategy is an optimized random-walk based selection of these nodes. The whole process is local, i.e. it requires contact network information in the level of nodes. Thus, it is applicable to large-scale and unknown networks in which the global methods usually are unrealizable. Our simulation results on different synthetic and real networks show that the proposed method outperforms the existing local methods in most cases. In particular, for networks with strong community structures, high overlapping membership of nodes or small size communities, the proposed method shows better performance.

A Study into the Impact of Physical Structures on the Runway Velocity Field at the Atlantic City International Airport

NASA Astrophysics Data System (ADS)

King, David, Jr.; Manson, Russell; Trout, Joseph; Decicco, Nicholas; Rios, Manny

2015-04-01

Wake vortices are generated by airplanes in flight. These vortices decay slowly and may persist for several minutes after their creation. These vortices and associated smaller scale turbulent structures present a hazard to incoming flights. It is for this reason that incoming flights are timed to arrive after these vortices have dissipated. Local weather conditions, mainly prevailing winds, can affect the transport and evolution of these vortices; therefore, there is a need to fully understand localized wind patterns at the airport-sized mircoscale. Here we have undertaken a computational investigation into the impacts of localized wind flows and physical structures on the velocity field at Atlantic City International Airport. The simulations are undertaken in OpenFOAM, an open source computational fluid dynamics software package, using an optimized geometric mesh of the airport. Initial conditions for the simulations are based on historical data with the option to run simulations based on projected weather conditions imported from the Weather Research & Forcasting (WRF) Model. Sub-grid scale turbulence is modeled using a Large Eddy Simulation (LES) approach. The initial results gathered from the WRF Model simulations and historical weather data analysis are presented elsewhere.

Aurora Kinase B, a novel regulator of TERF1 binding and telomeric integrity

PubMed Central

Chan, Foong Lyn; Vinod, Benjamin; Novy, Karel; Schittenhelm, Ralf B.; Huang, Cheng; Udugama, Maheshi; Nunez-Iglesias, Juan; Lin, Jane I.; Hii, Linda; Chan, Julie; Pickett, Hilda A.; Daly, Roger J.

2017-01-01

Abstract AURKB (Aurora Kinase B) is a serine/threonine kinase better known for its role at the mitotic kinetochore during chromosome segregation. Here, we demonstrate that AURKB localizes to the telomeres in mouse embryonic stem cells, where it interacts with the essential telomere protein TERF1. Loss of AURKB function affects TERF1 telomere binding and results in aberrant telomere structure. In vitro kinase experiments successfully identified Serine 404 on TERF1 as a putative AURKB target site. Importantly, in vivo overexpression of S404-TERF1 mutants results in fragile telomere formation. These findings demonstrate that AURKB is an important regulator of telomere structural integrity. PMID:29040668

Coastal evolution and littoral cells distribution in Northern Tuscany (Italy)

NASA Astrophysics Data System (ADS)

Anfuso, Giorgio; Pranzini, Enzo; Vitale, Giovanni

2010-05-01

This paper deals with a 64-km-long coastal physiographic unit located in the northern littoral of Tuscany (Italy). The investigated area recorded important erosion problems in last century due to the reduction in sediment input from rivers and to the feeding effect of ports and shore protection structures. Vertical aerial photographs and direct field surveys (with RTK-GPS and total station) were used for the reconstruction of coastline changes at medium-long temporal scales. The littoral is a microtidal environment and most frequent and severe storms approach from the 245° direction, with maximum one year recurrence Hs values between 3.5 and 4.0 m, less frequent and severe storms approach from the 180° and 200° directions. Concerning coastal evolution for the 1938-2005 period, important accretion was recorded updrift of two harbours (300 at Viareggio and 100 m at Carrara port in a convergence area (100 m at Marina di Pietrasanta), whereas severe erosion occurred downcoast of Carrara harbour (-130 m at Marina dei Ronchi) and at the northern (unprotected) side of the Arno River mouth (with maximum values of 400 m). Locally breakwaters and groins were implemented to solve erosion problems but the structures only - and not always - solved problems at local scale shifting erosion downdrift. Coastal compartmentalisation controlled the longshore distribution of erosion/accretion patterns and it was strongly forced by natural and human structures and coastal orientation in relation to wave approaching fronts. Three main littoral cells were formed by four natural limits: i) Punta Bianca Promontory, which works as a fixed absolute limit; ii) Marina di Pietrasanta, a convergent, free limit; iii) the Arno River Mouth, a divergent limit; and, iv) Livorno harbour, which works as an absolute fixed southern limit. In it is important to highlight that human structures interfere with natural sediment transport within major cells creating small sub-cells. This way, the general natural trend determined by coastal compartmentalisation is only slightly affected by human structures which give rise to erosion/accretion areas within most important cells. In detail, the most important structures are Carrara and Viareggio ports which constitute artificial, fixed limits which allow little transport in a given direction, depending on their protrusion and wave characteristics. They allow periodic, almost unidirectional, transport that, according to field observations, takes place along narrow zones parallel to the shoreline, extending to a variable depth (6-10 m), depending on wave conditions and bottom morphology. Furthermore, bypassing of limits takes place locally as a consequence of bed load sand transport onto longshore bars and only fine sediments bypass the structures. In detail, Carrara port only permits transport in one predominant direction (southward) and Viareggio port probably records a bi-directional transport, even if prevails the northward directed one. Last, obtained results are useful to improve the understanding of coastal processes to manage littoral sediment transport in a sustainable manner and to minimise needs for structural interventions. For this is sufficient to identify independent cells and partially dependent sub-cells for shoreline management units, if not adverse impacts will be inevitability transmitted to the downdrift unit.

Local diurnal wind-driven variabiity and upwelling in a small coastal embayment

NASA Astrophysics Data System (ADS)

Walter, R. K.; Reid, E. C.; Davis, K. A.; Armenta, K. J.; Merhoff, K.; Nidzieko, N.

2017-12-01

The oceanic response to high-frequency local diurnal wind forcing is examined in a small coastal embayment located along an understudied stretch of the central California coast. We show that local diurnal wind forcing is the dominant control on nearshore temperature variability and circulation patterns. A complex empirical orthogonal function (CEOF) analysis of velocities in San Luis Obispo Bay reveals that the first-mode CEOF amplitude time series, which accounts for 47.9% of the variance, is significantly coherent with the local wind signal at the diurnal frequency and aligns with periods of weak and strong wind forcing. The diurnal evolution of the hydrographic structure and circulation in the bay is examined using both individual events and composite-day averages. During the late afternoon, the local wind strengthens and results in a sheared flow with near-surface warm waters directed out of the bay and a compensating flow of colder waters into the bay over the bottom portion of the water column. This cold water intrusion into the bay causes isotherms to shoal toward the surface and delivers subthermocline waters to shallow reaches of the bay, representing a mechanism for small-scale upwelling. When the local winds relax, the warm water mass advects back into the bay in the form of a buoyant plume front. Local diurnal winds are expected to play an important role in nearshore dynamics and local upwelling in other small coastal embayments with important implications for various biological and ecological processes.

Local diurnal wind-driven variability and upwelling in a small coastal embayment

NASA Astrophysics Data System (ADS)

Walter, Ryan K.; Reid, Emma C.; Davis, Kristen A.; Armenta, Kevin J.; Merhoff, Kevin; Nidzieko, Nicholas J.

2017-02-01

The oceanic response to high-frequency local diurnal wind forcing is examined in a small coastal embayment located along an understudied stretch of the central California coast. We show that local diurnal wind forcing is the dominant control on nearshore temperature variability and circulation patterns. A complex empirical orthogonal function (CEOF) analysis of velocities in San Luis Obispo Bay reveals that the first-mode CEOF amplitude time series, which accounts for 47.9% of the variance, is significantly coherent with the local wind signal at the diurnal frequency and aligns with periods of weak and strong wind forcing. The diurnal evolution of the hydrographic structure and circulation in the bay is examined using both individual events and composite-day averages. During the late afternoon, the local wind strengthens and results in a sheared flow with near-surface warm waters directed out of the bay and a compensating flow of colder waters into the bay over the bottom portion of the water column. This cold water intrusion into the bay causes isotherms to shoal toward the surface and delivers subthermocline waters to shallow reaches of the bay, representing a mechanism for small-scale upwelling. When the local winds relax, the warm water mass advects back into the bay in the form of a buoyant plume front. Local diurnal winds are expected to play an important role in nearshore dynamics and local upwelling in other small coastal embayments with important implications for various biological and ecological processes.

A qualitative evaluation of a Local Professional Network programme "Baby Teeth DO Matter".

PubMed

Brocklehurst, P; Bridgman, C; Davies, G

2013-12-01

The objective of this study was to use a qualitative approach to examine the perceptions of dentists who led a health promotion programme entitled "Baby Teeth DO Matter". Semi-structured interviews were undertaken with a variety of participants in a health promotional programme facilitated by a shadow Local Professional Network. These were then recorded and transcribed verbatim. The transcripts were line numbered and subjected to thematic analysis to develop a coding frame. Overarching themes were developed from the coded transcripts by organising them into clusters based on the similarity of their meaning and checked against the coded extracts and the raw data. General Dental Practice. General Dental Practitioners. A Greater Manchester-wide prevention programme entitled "Baby teeth DO Matter". To determine the perceptions of involved clinicians and whether "clinically owned and clinically led" services add value. Eight codes were generated: "Success of the project", "Down-stream to up-stream", "Importance of clinically led and clinically owned", "Keeping the approach simple", "Importance of networking", "Importance of Dental Public Health", "Importance of task and finish" and "Threats to the future of the Local Professional Network". These were organised into three over-arching themes. "Clinically Led and Clinically Owned" projects appear to empower local practitioners and add value. They encourage community-facing practitioners, build capacity and develop personal skills;--all in accordance with the fundamental principles of the Ottawa Charter. Distributed leadership was seen to be effective and Dental Public Health input, "Task and Finishing", resources and clarity of communication were all considered to be of critical importance.

Invasive plant erodes local song diversity in a migratory passerine

Treesearch

Yvette K. Ortega; Aubree Benson; Erick Greene

2014-01-01

Exotic plant invasions threaten ecosystems globally, but we still know little about the specific consequences for animals. Invasive plants can alter the quality of breeding habitat for songbirds, thereby impacting important demographic traits such as dispersal, philopatry, and age structure. These demographic effects may in turn alter song-learning conditions to affect...

Source-sink dynamics sustain central stonerollers (Campostoma anomalum) in a heavily urbanized catchment

Treesearch

Eric R. Waits; Mark J. Bagley; Michael J. Blum; Frank H. McCormick; James M. Lazorchak

2008-01-01

Relating local demographic processes to spatial structure (e.g. habitat heterogeneity) is essential for understanding population and species persistence (Hanski & Gilpin, 1997; Fagan, 2002). Yet few studies have tested general hypotheses about the importance of spatial patterns in determining population dynamics within river­stream networks (Lowe, Likens &...

The Case against Public Sector Unions

ERIC Educational Resources Information Center

McGinnis, John O.; Schanzenbach, Max

2010-01-01

State and local governments today are, with few exceptions, in deep financial distress. While some governors can offer the recession, the housing crisis, or the loss of an important industry as an excuse for poor finances, many states are simply structurally insolvent. In this article, the authors discuss the primary cause of the states' long-term…

The Roots of Urban Discontent: Public Policy, Municipal Institutions, and the Ghetto.

ERIC Educational Resources Information Center

Rossi, Peter H.; And Others

The central concern of this volume is to examine the interrelationships between three levels of urban social structure: (1) local public policy-makers, comprised of elected public officials, the heads of major municipal departments, and "civic notables," or persons who play important roles in urban civic life; (2) "institutional agents," or…

Nanomotor dynamics in a chemically oscillating medium

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

Robertson, Bryan, E-mail: bryan.robertson@mail.utoronto.ca; Kapral, Raymond, E-mail: rkapral@chem.utoronto.ca

2015-04-21

Synthetic nanomotors powered by chemical reactions have potential uses as cargo transport vehicles in both in vivo and in vitro applications. In many situations, motors will have to operate in out-of-equilibrium complex chemically reacting media, which supply fuel to the motors and remove the products they produce. Using molecular simulation and mean-field theory, this paper describes some of the new features that arise when a chemically powered nanomotor, operating through a diffusiophoretic mechanism, moves in an environment that supports an oscillatory chemical reaction network. It is shown how oscillations in the concentrations in chemical species in the environment give risemore » to oscillatory motor dynamics. More importantly, since the catalytic reactions on the motor that are responsible for its propulsion couple to the bulk phase reaction network, the motor can change its local environment. This process can give rise to distinctive spatiotemporal structures in reaction-diffusion media that occur as a result of active motor motion. Such locally induced nonequilibrium structure will play an important role in applications that involve motor dynamics in complex chemical media.« less

Changes in Brain Structural Networks and Cognitive Functions in Testicular Cancer Patients Receiving Cisplatin-Based Chemotherapy.

PubMed

Amidi, Ali; Hosseini, S M Hadi; Leemans, Alexander; Kesler, Shelli R; Agerbæk, Mads; Wu, Lisa M; Zachariae, Robert

2017-12-01

Cisplatin-based chemotherapy may have neurotoxic effects within the central nervous system. The aims of this study were 1) to longitudinally investigate the impact of cisplatin-based chemotherapy on whole-brain networks in testicular cancer patients undergoing treatment and 2) to explore whether possible changes are related to decline in cognitive functioning. Sixty-four newly orchiectomized TC patients underwent structural magnetic resonance imaging (T1-weighted and diffusion-weighted imaging) and cognitive testing at baseline prior to further treatment and again at a six-month follow-up. At follow-up, 22 participants had received cisplatin-based chemotherapy (CT) while 42 were in active surveillance (S). Brain structural networks were constructed for each participant, and network properties were investigated using graph theory and longitudinally compared across groups. Cognitive functioning was evaluated using standardized neuropsychological tests. All statistical tests were two-sided. Compared with the S group, the CT group demonstrated altered global and local brain network properties from baseline to follow-up as evidenced by decreases in important brain network properties such as small-worldness (P = .04), network clustering (P = .04), and local efficiency (P = .02). In the CT group, poorer overall cognitive performance was associated with decreased small-worldness (r = -0.46, P = .04) and local efficiency (r = -0.51, P = .02), and verbal fluency was associated with decreased local efficiency (r = -0.55, P = .008). Brain structural networks may be disrupted following treatment with cisplatin-based chemotherapy. Impaired brain networks may underlie poorer performance over time on both specific and nonspecific cognitive functions in patients undergoing chemotherapy. To the best of our knowledge, this is the first study to longitudinally investigate changes in structural brain networks in a cancer population, providing novel insights regarding the neurobiological mechanisms of cancer-related cognitive impairment.

Very high resolution Earth Observation features for testing the direct and indirect effects of landscape structure on local habitat quality

NASA Astrophysics Data System (ADS)

Mairota, Paola; Cafarelli, Barbara; Labadessa, Rocco; Lovergine, Francesco P.; Tarantino, Cristina; Nagendra, Harini; Didham, Raphael K.

2015-02-01

Modelling the empirical relationships between habitat quality and species distribution patterns is the first step to understanding human impacts on biodiversity. It is important to build on this understanding to develop a broader conceptual appreciation of the influence of surrounding landscape structure on local habitat quality, across multiple spatial scales. Traditional models which report that 'habitat amount' in the landscape is sufficient to explain patterns of biodiversity, irrespective of habitat configuration or spatial variation in habitat quality at edges, implicitly treat each unit of habitat as interchangeable and ignore the high degree of interdependence between spatial components of land-use change. Here, we test the contrasting hypothesis, that local habitat units are not interchangeable in their habitat attributes, but are instead dependent on variation in surrounding habitat structure at both patch- and landscape levels. As the statistical approaches needed to implement such hierarchical causal models are observation-intensive, we utilise very high resolution (VHR) Earth Observation (EO) images to rapidly generate fine-grained measures of habitat patch internal heterogeneities over large spatial extents. We use linear mixed-effects models to test whether these remotely-sensed proxies for habitat quality were influenced by surrounding patch or landscape structure. The results demonstrate the significant influence of surrounding patch and landscape context on local habitat quality. They further indicate that such an influence can be direct, when a landscape variable alone influences the habitat structure variable, and/or indirect when the landscape and patch attributes have a conjoined effect on the response variable. We conclude that a substantial degree of interaction among spatial configuration effects is likely to be the norm in determining the ecological consequences of habitat fragmentation, thus corroborating the notion of the spatial context dependence of habitat quality.

Magnetorotational instability: nonmodal growth and the relationship of global modes to the shearing box

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

Squire, J.; Bhattacharjee, A.

2014-12-10

We study magnetorotational instability (MRI) using nonmodal stability techniques. Despite the spectral instability of many forms of MRI, this proves to be a natural method of analysis that is well-suited to deal with the non-self-adjoint nature of the linear MRI equations. We find that the fastest growing linear MRI structures on both local and global domains can look very different from the eigenmodes, invariably resembling waves shearing with the background flow (shear waves). In addition, such structures can grow many times faster than the least stable eigenmode over long time periods, and be localized in a completely different region ofmore » space. These ideas lead—for both axisymmetric and non-axisymmetric modes—to a natural connection between the global MRI and the local shearing box approximation. By illustrating that the fastest growing global structure is well described by the ordinary differential equations (ODEs) governing a single shear wave, we find that the shearing box is a very sensible approximation for the linear MRI, contrary to many previous claims. Since the shear wave ODEs are most naturally understood using nonmodal analysis techniques, we conclude by analyzing local MRI growth over finite timescales using these methods. The strong growth over a wide range of wave-numbers suggests that nonmodal linear physics could be of fundamental importance in MRI turbulence.« less

Protein functional features are reflected in the patterns of mRNA translation speed.

PubMed

López, Daniel; Pazos, Florencio

2015-07-09

The degeneracy of the genetic code makes it possible for the same amino acid string to be coded by different messenger RNA (mRNA) sequences. These "synonymous mRNAs" may differ largely in a number of aspects related to their overall translational efficiency, such as secondary structure content and availability of the encoded transfer RNAs (tRNAs). Consequently, they may render different yields of the translated polypeptides. These mRNA features related to translation efficiency are also playing a role locally, resulting in a non-uniform translation speed along the mRNA, which has been previously related to some protein structural features and also used to explain some dramatic effects of "silent" single-nucleotide-polymorphisms (SNPs). In this work we perform the first large scale analysis of the relationship between three experimental proxies of mRNA local translation efficiency and the local features of the corresponding encoded proteins. We found that a number of protein functional and structural features are reflected in the patterns of ribosome occupancy, secondary structure and tRNA availability along the mRNA. One or more of these proxies of translation speed have distinctive patterns around the mRNA regions coding for certain protein local features. In some cases the three patterns follow a similar trend. We also show specific examples where these patterns of translation speed point to the protein's important structural and functional features. This support the idea that the genome not only codes the protein functional features as sequences of amino acids, but also as subtle patterns of mRNA properties which, probably through local effects on the translation speed, have some consequence on the final polypeptide. These results open the possibility of predicting a protein's functional regions based on a single genomic sequence, and have implications for heterologous protein expression and fine-tuning protein function.

Fatigue Technology Assessment and Strategies for Fatigue Avoidance in Marine Structures

DTIC Science & Technology

1992-06-01

time history. xii MODELING ERROR (Xme) : Typically defined as the ratio of actual behavior of the structure to the one predicted by the model. It is...and temperature changes may be important to fatigue in a local component, these loadings are not a major concern in the global behavior of typical...Reference 3.1) to assess fracture behavior in a low toughness HAZ indicated that a small low- toughness area in the HAZ can be masked by the higher

Plasma jets in the near-Earth's magnetotail (Julius Bartels Medal Lecture)

NASA Astrophysics Data System (ADS)

Nakamura, Rumi

2014-05-01

The Earth's magnetosphere is formed as a consequence of the interaction between the magnetized solar wind and the terrestrial magnetic field. While the large-scale and average (>hours) properties of the Earth's magnetotail current sheet can be well described by overall solar wind-magnetosphere interaction, the most dramatic energy conversion process takes place in an explosive manner involving transient (up to several minutes) and localized (up to a few RE) phenomena in the plasma sheet/current sheet regions. One of the most clear observables of such processes are the localized and transient plasma jets called Bursty bulk flows (BBF), embedding velocity peaks of 1-min duration, which are called flow bursts. This talk is a review of the current understanding of these plasma jets by highlighting the results from multi-spacecraft observations by the Cluster and THEMIS spacecraft. The first four-spacecraft mission Cluster crossed the near-Earth plasma sheet with inter-spacecraft distance of about 250 km to 10000 km, ideal for studying local structures of the flow bursts. The five-spacecraft THEMIS mission , separated by larger distances , succeeded to monitor the large-scale evolution of the fast flows from the mid-tail to the inner magnetosphere. Multi-point observations of BBFS have established the importance of measuring local gradients of the fields and the plasma to understand the BBF structures such as the spatial scales and 3D structure of localized Earthward convecting flux tubes. Among others the magnetic field disturbance forming at the front of BBF, called dipolarization front (DF), has been intensively studied. From the propagation properties of DF relative to the flows and by comparing with ionospheric data, the evolution of the fast flows in terms of magnetosphere-ionospheric coupling through field-aligned currents are established. An important aspect of BBF is the interaction of the Earthward plasma jets and the Earth's dipole field. Multi-point observations combined with ground-based observations enabled to resolve how the BBFs are braked , diverted, or bounced back at the high-pressure gradient region. The multi-point capabilities in space enabled to study the BBF structure as well as large-scale evolution of BBFs. These processes are also universal processes in space plasmas and are, for example, associated with the reconnection process during the solar flares or leading to auroral phenomena at different planets.

Patch size and landscape effects on density and nesting success of grassland birds

USGS Publications Warehouse

Winter, Maiken; Johnson, Douglas H.; Shaffer, Jill A.; Donovan, Therese M.; Svedarsky, W. Daniel

2006-01-01

Current management recommendations for grassland birds in North America emphasize providing large patches of grassland habitat within landscapes that have few forest or shrubland areas. These Bird Conservation Areas are being proposed under the assumption that large patches of habitat in treeless landscapes will maintain viable populations of grassland birds. This assumption requires that patch size and landscape features affect density and nesting success of grassland birds, and that these effects are consistent among years and regions and across focal species. However, these assumptions have not yet been validated for grassland birds, and the relative importance of local vegetation structure, patch size, and landscape composition on grassland bird populations is not well known. In addition, factors influencing grassland bird nesting success have been investigated mostly in small-scale and short-duration studies. To develop management guidelines for grassland birds, we tested the spatial and temporal repeatability of the influence of patch size and landscape composition on density and nesting success of 3 grassland passerines, after controlling for local-scale vegetation structure, climate, and—when analyzing nest success—bird density. We conducted our study during 4 years (1998–2001) in 44 study plots that were set up in 3 regions of the northern tallgrass prairie in Minnesota and North Dakota, USA. In these study plots we measured density and nesting success of clay-colored sparrows (Spizella pallida), Savannah sparrows (Passerculus sandwichensis), and bobolinks (Dolichonyx oryzivorus). Statistical models indicated that density was influenced by patch size, landscape, region, and local vegetation structure more so than by local vegetation structure alone. Both magnitude and direction of the response of density to patch size varied among regions, years, and species. In contrast, the direction of landscape effects was consistent among regions, years, and between Savannah sparrows and bobolinks. In each species, this landscape effect was independent of patch size. Nesting success was not clearly influenced by patch size or landscape composition, and none of the factors that influenced avian density also influenced nesting success in any of the 3 species. General statements on “optimal habitat” for grassland birds should therefore be viewed cautiously. Instead, long-term studies in different regions as well as a deeper understanding of the local system are needed to determine which factors are most important for grassland birds in a particular area.

Karyopherin α 3 and karyopherin α 4 proteins mediate the nuclear import of methyl-CpG binding protein 2.

PubMed

Baker, Steven Andrew; Lombardi, Laura Marie; Zoghbi, Huda Yahya

2015-09-11

Methyl-CpG binding protein 2 (MeCP2) is a nuclear protein with important roles in regulating chromatin structure and gene expression, and mutations in MECP2 cause Rett syndrome (RTT). Within the MeCP2 protein sequence, the nuclear localization signal (NLS) is reported to reside between amino acids 255-271, and certain RTT-causing mutations overlap with the MeCP2 NLS, suggesting that they may alter nuclear localization. One such mutation, R270X, is predicted to interfere with the localization of MeCP2, but recent in vivo studies have demonstrated that this mutant remains entirely nuclear. To clarify the mechanism of MeCP2 nuclear import, we isolated proteins that interact with the NLS and identified karyopherin α 3 (KPNA3 or Kap-α3) and karyopherin α 4 (KPNA4 or Kap-α4) as key binding partners of MeCP2. MeCP2-R270X did not interact with KPNA4, consistent with a requirement for an intact NLS in this interaction. However, this mutant retains binding to KPNA3, accounting for the normal localization of MeCP2-R270X to the nucleus. These data provide a mechanism for MeCP2 nuclear import and have implications for the design of therapeutics aimed at modulating the function of MeCP2 in RTT patients. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

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

Anomalous van der Waals-Casimir interactions on graphene: A concerted effect of temperature, retardation, and non-locality

NASA Astrophysics Data System (ADS)

Ambrosetti, Alberto; Silvestrelli, Pier Luigi

2018-04-01

Dispersion forces play a major role in graphene, largely influencing adhesion of adsorbate moieties and stabilization of functional multilayered structures. However, the reliable prediction of dispersion interactions on graphene up to the relevant ˜10 nm scale is an extremely challenging task: in fact, electromagnetic retardation effects and the highly non-local character of π electrons can imply sizeable qualitative variations of the interaction with respect to known pairwise approaches. Here we address both issues, determining the finite-temperature van der Waals (vdW)-Casimir interaction for point-like and extended adsorbates on graphene, explicitly accounting for the non-local dielectric permittivity. We find that temperature, retardation, and non-locality play a crucial role in determining the actual vdW scaling laws and the stability of both atomic and larger molecular adsorbates. Our results highlight the importance of these effects for a proper description of systems of current high interest, such as graphene interacting with biomolecules, and self-assembly of complex nanoscale structures. Due to the generality of our approach and the observed non-locality of other 2D materials, our results suggest non-trivial vdW interactions from hexagonal mono-layered materials from group 14 of the periodic table, to transition metal dichalcogenides.

Anomalous van der Waals-Casimir interactions on graphene: A concerted effect of temperature, retardation, and non-locality.

PubMed

Ambrosetti, Alberto; Silvestrelli, Pier Luigi

2018-04-07

Dispersion forces play a major role in graphene, largely influencing adhesion of adsorbate moieties and stabilization of functional multilayered structures. However, the reliable prediction of dispersion interactions on graphene up to the relevant ∼10 nm scale is an extremely challenging task: in fact, electromagnetic retardation effects and the highly non-local character of π electrons can imply sizeable qualitative variations of the interaction with respect to known pairwise approaches. Here we address both issues, determining the finite-temperature van der Waals (vdW)-Casimir interaction for point-like and extended adsorbates on graphene, explicitly accounting for the non-local dielectric permittivity. We find that temperature, retardation, and non-locality play a crucial role in determining the actual vdW scaling laws and the stability of both atomic and larger molecular adsorbates. Our results highlight the importance of these effects for a proper description of systems of current high interest, such as graphene interacting with biomolecules, and self-assembly of complex nanoscale structures. Due to the generality of our approach and the observed non-locality of other 2D materials, our results suggest non-trivial vdW interactions from hexagonal mono-layered materials from group 14 of the periodic table, to transition metal dichalcogenides.

Remote sensing image segmentation using local sparse structure constrained latent low rank representation

NASA Astrophysics Data System (ADS)

Tian, Shu; Zhang, Ye; Yan, Yimin; Su, Nan; Zhang, Junping

2016-09-01

Latent low-rank representation (LatLRR) has been attached considerable attention in the field of remote sensing image segmentation, due to its effectiveness in exploring the multiple subspace structures of data. However, the increasingly heterogeneous texture information in the high spatial resolution remote sensing images, leads to more severe interference of pixels in local neighborhood, and the LatLRR fails to capture the local complex structure information. Therefore, we present a local sparse structure constrainted latent low-rank representation (LSSLatLRR) segmentation method, which explicitly imposes the local sparse structure constraint on LatLRR to capture the intrinsic local structure in manifold structure feature subspaces. The whole segmentation framework can be viewed as two stages in cascade. In the first stage, we use the local histogram transform to extract the texture local histogram features (LHOG) at each pixel, which can efficiently capture the complex and micro-texture pattern. In the second stage, a local sparse structure (LSS) formulation is established on LHOG, which aims to preserve the local intrinsic structure and enhance the relationship between pixels having similar local characteristics. Meanwhile, by integrating the LSS and the LatLRR, we can efficiently capture the local sparse and low-rank structure in the mixture of feature subspace, and we adopt the subspace segmentation method to improve the segmentation accuracy. Experimental results on the remote sensing images with different spatial resolution show that, compared with three state-of-the-art image segmentation methods, the proposed method achieves more accurate segmentation results.

Molecular-Scale Features that Govern the Effects of O-Glycosylation on a Carbohydrate-Binding Module

DOE PAGES

Guan, Xiaoyang; Chaffey, Patrick K.; Zeng, Chen; ...

2015-09-21

The protein glycosylation is a ubiquitous post-translational modification in all kingdoms of life. Despite its importance in molecular and cellular biology, the molecular-level ramifications of O-glycosylation on biomolecular structure and function remain elusive. Here, we took a small model glycoprotein and changed the glycan structure and size, amino acid residues near the glycosylation site, and glycosidic linkage while monitoring any corresponding changes to physical stability and cellulose binding affinity. The results of this study reveal the collective importance of all the studied features in controlling the most pronounced effects of O-glycosylation in this system. This study suggests the possibility ofmore » designing proteins with multiple improved properties by simultaneously varying the structures of O-glycans and amino acids local to the glycosylation site.« less

Hydrodynamic patterns favouring sea urchin recruitment in coastal areas: A Mediterranean study case.

PubMed

Farina, S; Quattrocchi, G; Guala, I; Cucco, A

2018-05-11

In invertebrate fisheries, sea urchin harvesting continues to grow with dramatic consequences for benthic ecosystems. The identification of areas with a marked natural recruitment and the mechanisms regulating it is crucial for the conservation of benthic communities and for planning the sustainable harvesting. This study evaluates the spatial distribution and density of recruits of the edible sea urchin Paracentrotus lividus along the Sinis + Peninsula (Sardinia) and explores its significant relationships with the local oceanographic features. Our results reveal that recruitment is favoured in areas with slow currents and high levels of confinement and trapping of the water masses. Analysis of the residual circulation indicates that the presence of local standing circulation structures promotes the sea urchin recruitment process. Our findings emphasize the importance of managing local sea urchin harvesting as a system of populations with their demographic influence mainly dependent on the most important ecological driver that is the recruitment. Copyright © 2018 Elsevier Ltd. All rights reserved.

Mapping the nuclear localization signal in the matrix protein of potato yellow dwarf virus.

PubMed

Anderson, Gavin; Jang, Chanyong; Wang, Renyuan; Goodin, Michael

2018-05-01

The ability of the matrix (M) protein of potato yellow dwarf virus (PYDV) to remodel nuclear membranes is controlled by a di-leucine motif located at residues 223 and 224 of its primary structure. This function can be uncoupled from that of its nuclear localization signal (NLS), which is controlled primarily by lysine and arginine residues immediately downstream of the LL motif. In planta localization of green fluorescent protein fusions, bimolecular fluorescence complementation assays with nuclear import receptor importin-α1 and yeast-based nuclear import assays provided three independent experimental approaches to validate the authenticity of the M-NLS. The carboxy terminus of M is predicted to contain a nuclear export signal, which is belived to be functional, given the ability of M to bind the Arabidopsis nuclear export receptor 1 (XPO1). The nuclear shuttle activity of M has implications for the cell-to-cell movement of PYDV nucleocapsids, based upon its interaction with the N and Y proteins.

Partial dispensability of Djp1's J domain in peroxisomal protein import in Saccharomyces cerevisiae results from genetic redundancy with another class II J protein, Caj1.

PubMed

Dobriyal, Neha; Tripathi, Prerna; Sarkar, Susrita; Tak, Yogesh; Verma, Amit K; Sahi, Chandan

2017-05-01

J proteins are obligate co-chaperones of Hsp70s. Via their signature J domain, all J proteins interact with their partner Hsp70s and stimulate their weak ATPase activity, which is vital for Hsp70 functions. The dependency of J proteins on their J domain is such that mutations in critical amino acids in the J domain often results into a null phenotype for a particular J protein. Here, we show that the J domain of Djp1, a cytosolic J protein important for peroxisomal protein import in Saccharomyces cerevisiae, is partially dispensable. A complete deletion of Djp1 J domain resulted into only partial loss in peroxisomal protein import function. Instead, the C-terminal domain of Djp1 was found to be essential for proper localization of the peroxisomal targeted GFP-PTS1. Furthermore, we show that Caj1, another cytosolic J protein, also has some role in peroxisomal protein import. Caj1 was found to be partially redundant with Djp1 as cells lacking both Djp1 and Caj1 resulted into a much more severe defect in GFP-PTS1 localization. Based on these results, we propose that dispensability of J domains could be attributed to genetic redundancy between different J proteins sharing common structural topology and cellular localization.

[Innovation in pharmaceutical and health biotechnology industries: challenges for a virtuous agenda].

PubMed

Vargas, Marco; Gadelha, Carlos Augusto Grabois; Costa, Laís Silveira; Maldonado, José

2012-12-01

Pharmaceutical and biotechnology industries comprise a major production subsystem of the health industrial complex in Brazil. It stands out for both its economic importance and its prominent role in developing new technologies in strategic areas. Strengthening the local production of generic drugs in the last decade has significantly increased the number of Brazilian companies in the local pharmaceutical market and has been an important turning point for this industry's growth. However, there remain major structural bottlenecks both in terms of production and continuous innovation. These bottlenecks reveal the high vulnerability of the Brazilian National Health System and point to the need of public policies that promote strengthening the production base and innovation in the pharmaceutical industry and that at the same time meet health-related social demands in health in Brazil.

Computing the Partition Function for Kinetically Trapped RNA Secondary Structures

PubMed Central

Lorenz, William A.; Clote, Peter

2011-01-01

An RNA secondary structure is locally optimal if there is no lower energy structure that can be obtained by the addition or removal of a single base pair, where energy is defined according to the widely accepted Turner nearest neighbor model. Locally optimal structures form kinetic traps, since any evolution away from a locally optimal structure must involve energetically unfavorable folding steps. Here, we present a novel, efficient algorithm to compute the partition function over all locally optimal secondary structures of a given RNA sequence. Our software, RNAlocopt runs in time and space. Additionally, RNAlocopt samples a user-specified number of structures from the Boltzmann subensemble of all locally optimal structures. We apply RNAlocopt to show that (1) the number of locally optimal structures is far fewer than the total number of structures – indeed, the number of locally optimal structures approximately equal to the square root of the number of all structures, (2) the structural diversity of this subensemble may be either similar to or quite different from the structural diversity of the entire Boltzmann ensemble, a situation that depends on the type of input RNA, (3) the (modified) maximum expected accuracy structure, computed by taking into account base pairing frequencies of locally optimal structures, is a more accurate prediction of the native structure than other current thermodynamics-based methods. The software RNAlocopt constitutes a technical breakthrough in our study of the folding landscape for RNA secondary structures. For the first time, locally optimal structures (kinetic traps in the Turner energy model) can be rapidly generated for long RNA sequences, previously impossible with methods that involved exhaustive enumeration. Use of locally optimal structure leads to state-of-the-art secondary structure prediction, as benchmarked against methods involving the computation of minimum free energy and of maximum expected accuracy. Web server and source code available at http://bioinformatics.bc.edu/clotelab/RNAlocopt/. PMID:21297972

Robust hashing with local models for approximate similarity search.

PubMed

Song, Jingkuan; Yang, Yi; Li, Xuelong; Huang, Zi; Yang, Yang

2014-07-01

Similarity search plays an important role in many applications involving high-dimensional data. Due to the known dimensionality curse, the performance of most existing indexing structures degrades quickly as the feature dimensionality increases. Hashing methods, such as locality sensitive hashing (LSH) and its variants, have been widely used to achieve fast approximate similarity search by trading search quality for efficiency. However, most existing hashing methods make use of randomized algorithms to generate hash codes without considering the specific structural information in the data. In this paper, we propose a novel hashing method, namely, robust hashing with local models (RHLM), which learns a set of robust hash functions to map the high-dimensional data points into binary hash codes by effectively utilizing local structural information. In RHLM, for each individual data point in the training dataset, a local hashing model is learned and used to predict the hash codes of its neighboring data points. The local models from all the data points are globally aligned so that an optimal hash code can be assigned to each data point. After obtaining the hash codes of all the training data points, we design a robust method by employing l2,1 -norm minimization on the loss function to learn effective hash functions, which are then used to map each database point into its hash code. Given a query data point, the search process first maps it into the query hash code by the hash functions and then explores the buckets, which have similar hash codes to the query hash code. Extensive experimental results conducted on real-life datasets show that the proposed RHLM outperforms the state-of-the-art methods in terms of search quality and efficiency.

Serotype-specific differences in dengue virus non-structural protein 5 nuclear localization.

PubMed

Hannemann, Holger; Sung, Po-Yu; Chiu, Han-Chen; Yousuf, Amjad; Bird, Jim; Lim, Siew Pheng; Davidson, Andrew D

2013-08-02

The four serotypes of dengue virus (DENV-1 to -4) cause the most important arthropod-borne viral disease of humans. DENV non-structural protein 5 (NS5) contains enzymatic activities required for capping and replication of the viral RNA genome that occurs in the host cytoplasm. However, previous studies have shown that DENV-2 NS5 accumulates in the nucleus during infection. In this study, we examined the nuclear localization of NS5 for all four DENV serotypes. We demonstrate for the first time that there are serotypic differences in NS5 nuclear localization. Whereas the DENV-2 and -3 proteins accumulate in the nucleus, DENV-1 and -4 NS5 are predominantly if not exclusively localized to the cytoplasm. Comparative studies on the DENV-2 and -4 NS5 proteins revealed that the difference in DENV-4 NS5 nuclear localization was not due to rapid nuclear export but rather the lack of a functional nuclear localization sequence. Interaction studies using DENV-2 and -4 NS5 and human importin-α isoforms failed to identify an interaction that supported the differential nuclear localization of NS5. siRNA knockdown of the human importin-α isoform KPNA2, corresponding to the murine importin-α isoform previously shown to bind to DENV-2 NS5, did not substantially affect DENV-2 NS5 nuclear localization, whereas knockdown of importin-β did. The serotypic differences in NS5 nuclear localization did not correlate with differences in IL-8 gene expression. The results show that NS5 nuclear localization is not strictly required for virus replication but is more likely to have an auxiliary function in the life cycle of specific DENV serotypes.

Serotype-specific Differences in Dengue Virus Non-structural Protein 5 Nuclear Localization*

PubMed Central

Hannemann, Holger; Sung, Po-Yu; Chiu, Han-Chen; Yousuf, Amjad; Bird, Jim; Lim, Siew Pheng; Davidson, Andrew D.

2013-01-01

The four serotypes of dengue virus (DENV-1 to -4) cause the most important arthropod-borne viral disease of humans. DENV non-structural protein 5 (NS5) contains enzymatic activities required for capping and replication of the viral RNA genome that occurs in the host cytoplasm. However, previous studies have shown that DENV-2 NS5 accumulates in the nucleus during infection. In this study, we examined the nuclear localization of NS5 for all four DENV serotypes. We demonstrate for the first time that there are serotypic differences in NS5 nuclear localization. Whereas the DENV-2 and -3 proteins accumulate in the nucleus, DENV-1 and -4 NS5 are predominantly if not exclusively localized to the cytoplasm. Comparative studies on the DENV-2 and -4 NS5 proteins revealed that the difference in DENV-4 NS5 nuclear localization was not due to rapid nuclear export but rather the lack of a functional nuclear localization sequence. Interaction studies using DENV-2 and -4 NS5 and human importin-α isoforms failed to identify an interaction that supported the differential nuclear localization of NS5. siRNA knockdown of the human importin-α isoform KPNA2, corresponding to the murine importin-α isoform previously shown to bind to DENV-2 NS5, did not substantially affect DENV-2 NS5 nuclear localization, whereas knockdown of importin-β did. The serotypic differences in NS5 nuclear localization did not correlate with differences in IL-8 gene expression. The results show that NS5 nuclear localization is not strictly required for virus replication but is more likely to have an auxiliary function in the life cycle of specific DENV serotypes. PMID:23770669

A new method to detect transitory signatures and local time/space variability structures in the climate system: the scale-dependent correlation analysis

NASA Astrophysics Data System (ADS)

Rodó, Xavier; Rodríguez-Arias, Miquel-Àngel

2006-10-01

The study of transitory signals and local variability structures in both/either time and space and their role as sources of climatic memory, is an important but often neglected topic in climate research despite its obvious importance and extensive coverage in the literature. Transitory signals arise either from non-linearities, in the climate system, transitory atmosphere-ocean couplings, and other processes in the climate system evolving after a critical threshold is crossed. These temporary interactions that, though intense, may not last long, can be responsible for a large amount of unexplained variability but are normally considered of limited relevance and often, discarded. With most of the current techniques at hand these typology of signatures are difficult to isolate because the low signal-to-noise ratio in midlatitudes, the limited recurrence of the transitory signals during a customary interval of data considered. Also, there is often a serious problem arising from the smoothing of local or transitory processes if statistical techniques are applied, that consider all the length of data available, rather than taking into account the size of the specific variability structure under investigation. Scale-dependent correlation (SDC) analysis is a new statistical method capable of highlighting the presence of transitory processes, these former being understood as temporary significant lag-dependent autocovariance in a single series, or covariance structures between two series. This approach, therefore, complements other approaches such as those resulting from the families of wavelet analysis, singular-spectrum analysis and recurrence plots. A main feature of SDC is its high-performance for short time series, its ability to characterize phase-relationships and thresholds in the bivariate domain. Ultimately, SDC helps tracking short-lagged relationships among processes that locally or temporarily couple and uncouple. The use of SDC is illustrated in the present paper by means of some synthetic time-series examples of increasing complexity, and it is compared with wavelet analysis in order to provide a well-known reference of its capabilities. A comparison between SDC and companion techniques is also addressed and results are exemplified for the specific case of some relevant El Niño-Southern Oscillation teleconnections.

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.

Phylogenetic turnover along local environmental gradients in tropical forest communities.

PubMed

Baldeck, C A; Kembel, S W; Harms, K E; Yavitt, J B; John, R; Turner, B L; Madawala, S; Gunatilleke, N; Gunatilleke, S; Bunyavejchewin, S; Kiratiprayoon, S; Yaacob, A; Supardi, M N N; Valencia, R; Navarrete, H; Davies, S J; Chuyong, G B; Kenfack, D; Thomas, D W; Dalling, J W

2016-10-01

While the importance of local-scale habitat niches in shaping tree species turnover along environmental gradients in tropical forests is well appreciated, relatively little is known about the influence of phylogenetic signal in species' habitat niches in shaping local community structure. We used detailed maps of the soil resource and topographic variation within eight 24-50 ha tropical forest plots combined with species phylogenies created from the APG III phylogeny to examine how phylogenetic beta diversity (indicating the degree of phylogenetic similarity of two communities) was related to environmental gradients within tropical tree communities. Using distance-based redundancy analysis we found that phylogenetic beta diversity, expressed as either nearest neighbor distance or mean pairwise distance, was significantly related to both soil and topographic variation in all study sites. In general, more phylogenetic beta diversity within a forest plot was explained by environmental variables this was expressed as nearest neighbor distance versus mean pairwise distance (3.0-10.3 % and 0.4-8.8 % of variation explained among plots, respectively), and more variation was explained by soil resource variables than topographic variables using either phylogenetic beta diversity metric. We also found that patterns of phylogenetic beta diversity expressed as nearest neighbor distance were consistent with previously observed patterns of niche similarity among congeneric species pairs in these plots. These results indicate the importance of phylogenetic signal in local habitat niches in shaping the phylogenetic structure of tropical tree communities, especially at the level of close phylogenetic neighbors, where similarity in habitat niches is most strongly preserved.

Tissue heterogeneity in structure and conductivity contribute to cell survival during irreversible electroporation ablation by “electric field sinks”

PubMed Central

Golberg, Alexander; Bruinsma, Bote G.; Uygun, Basak E.; Yarmush, Martin L.

2015-01-01

Irreversible electroporation (IRE) is an emerging, minimally invasive technique for solid tumors ablation, under clinical investigation for cancer therapy. IRE affects only the cell membrane, killing cells while preserving the extracellular matrix structure. Current reports indicate tumors recurrence rate after IRE averaging 31% of the cases, of which 10% are local recurrences. The mechanisms for these recurrences are not known and new explanations for incomplete cell death are needed. Using finite elements method for electric field distribution, we show that presence of vascular structures with blood leads to the redistribution of electric fields leading to the areas with more than 60% reduced electric field strength in proximity to large blood vessels and clustered vessel structures. In an in vivo rat model of liver IRE ablation, we show that cells located in the proximity of larger vessel structures and in proximity of clustered vessel structures appear less affected by IRE ablation than cells in the tissue parenchyma or in the proximity of small, more isolated vessels. These findings suggest a role for “electric field sinks” in local tumors recurrences after IRE and emphasize the importance of the precise mapping of the targeted organ structure and conductivity for planning of electroporation procedures. PMID:25684630

Tissue heterogeneity in structure and conductivity contribute to cell survival during irreversible electroporation ablation by "electric field sinks".

PubMed

Golberg, Alexander; Bruinsma, Bote G; Uygun, Basak E; Yarmush, Martin L

2015-02-16

Irreversible electroporation (IRE) is an emerging, minimally invasive technique for solid tumors ablation, under clinical investigation for cancer therapy. IRE affects only the cell membrane, killing cells while preserving the extracellular matrix structure. Current reports indicate tumors recurrence rate after IRE averaging 31% of the cases, of which 10% are local recurrences. The mechanisms for these recurrences are not known and new explanations for incomplete cell death are needed. Using finite elements method for electric field distribution, we show that presence of vascular structures with blood leads to the redistribution of electric fields leading to the areas with more than 60% reduced electric field strength in proximity to large blood vessels and clustered vessel structures. In an in vivo rat model of liver IRE ablation, we show that cells located in the proximity of larger vessel structures and in proximity of clustered vessel structures appear less affected by IRE ablation than cells in the tissue parenchyma or in the proximity of small, more isolated vessels. These findings suggest a role for "electric field sinks" in local tumors recurrences after IRE and emphasize the importance of the precise mapping of the targeted organ structure and conductivity for planning of electroporation procedures.

Flow directionality, mountain barriers and functional traits determine diatom metacommunity structuring of high mountain streams.

PubMed

Dong, Xiaoyu; Li, Bin; He, Fengzhi; Gu, Yuan; Sun, Meiqin; Zhang, Haomiao; Tan, Lu; Xiao, Wen; Liu, Shuoran; Cai, Qinghua

2016-04-19

Stream metacommunities are structured by a combination of local (environmental filtering) and regional (dispersal) processes. The unique characters of high mountain streams could potentially determine metacommunity structuring, which is currently poorly understood. Aiming at understanding how these characters influenced metacommunity structuring, we explored the relative importance of local environmental conditions and various dispersal processes, including through geographical (overland), topographical (across mountain barriers) and network (along flow direction) pathways in shaping benthic diatom communities. From a trait perspective, diatoms were categorized into high-profile, low-profile and motile guild to examine the roles of functional traits. Our results indicated that both environmental filtering and dispersal processes influenced metacommunity structuring, with dispersal contributing more than environmental processes. Among the three pathways, stream corridors were primary pathway. Deconstructive analysis suggested different responses to environmental and spatial factors for each of three ecological guilds. However, regardless of traits, dispersal among streams was limited by mountain barriers, while dispersal along stream was promoted by rushing flow in high mountain stream. Our results highlighted that directional processes had prevailing effects on metacommunity structuring in high mountain streams. Flow directionality, mountain barriers and ecological guilds contributed to a better understanding of the roles that mountains played in structuring metacommunity.

Conformations of the HIV-1 protease: A crystal structure data set analysis.

PubMed

Palese, Luigi Leonardo

2017-11-01

The HIV protease is an important drug target for HIV/AIDS therapy, and its structure and function have been extensively investigated. This enzyme performs an essential role in viral maturation by processing specific cleavage sites in the Gag and Gag-Pol precursor polyproteins so as to release their mature forms. This 99 amino acid aspartic protease works as a homodimer, with the active site localized in a central cavity capped by two flexible flap regions. The dimer presents closed or open conformations, which are involved in the substrate binding and release. Here the results of the analysis of a HIV-1 protease data set containing 552 dimer structures are reported. Different dimensionality reduction methods have been used in order to get information from this multidimensional database. Most of the structures in the data set belong to two conformational clusters. An interesting observation that comes from the analysis of these data is that some protease sequences are localized preferentially in specific areas of the conformational landscape of this protein. Copyright © 2017 Elsevier B.V. All rights reserved.

Three-dimensional mapping of microcircuit correlation structure

PubMed Central

Cotton, R. James; Froudarakis, Emmanouil; Storer, Patrick; Saggau, Peter; Tolias, Andreas S.

2013-01-01

Great progress has been made toward understanding the properties of single neurons, yet the principles underlying interactions between neurons remain poorly understood. Given that connectivity in the neocortex is locally dense through both horizontal and vertical connections, it is of particular importance to characterize the activity structure of local populations of neurons arranged in three dimensions. However, techniques for simultaneously measuring microcircuit activity are lacking. We developed an in vivo 3D high-speed, random-access two-photon microscope that is capable of simultaneous 3D motion tracking. This allows imaging from hundreds of neurons at several hundred Hz, while monitoring tissue movement. Given that motion will induce common artifacts across the population, accurate motion tracking is absolutely necessary for studying population activity with random-access based imaging methods. We demonstrate the potential of this imaging technique by measuring the correlation structure of large populations of nearby neurons in the mouse visual cortex, and find that the microcircuit correlation structure is stimulus-dependent. Three-dimensional random access multiphoton imaging with concurrent motion tracking provides a novel, powerful method to characterize the microcircuit activity in vivo. PMID:24133414

Understanding cage effects in imidazolium ionic liquids by 129Xe NMR: MD simulations and relativistic DFT calculations.

PubMed

Saielli, Giacomo; Bagno, Alessandro; Castiglione, Franca; Simonutti, Roberto; Mauri, Michele; Mele, Andrea

2014-12-04

(129)Xe NMR has been recently employed to probe the local structure of ionic liquids (ILs). However, no theoretical investigation has been yet reported addressing the problem of the dependence of the chemical shift of xenon on the cage structure of the IL. Therefore, we present here a study of the chemical shift of (129)Xe in two ionic liquids, [bmim][Cl] and [bmim][PF6], by a combination of classical MD simulations and relativistic DFT calculations of the xenon shielding constant. The bulk structure of the two ILs is investigated by means of the radial distribution functions, paying special attention to the local structure, volume, and charge distribution of the cage surrounding the xenon atom. Relativistic DFT calculations, based on the ZORA formalism, on clusters extracted from the trajectory files of the two systems, yield an average relative chemical shift in good agreement with the experimental data. Our results demonstrate the importance of the cage volume and the average charge surrounding the xenon nucleus in the IL cage as the factors determining the effective shielding.

Thalamic reticular nucleus induces fast and local modulation of arousal state

PubMed Central

Lewis, Laura D; Voigts, Jakob; Flores, Francisco J; Schmitt, L Ian; Wilson, Matthew A

2015-01-01

During low arousal states such as drowsiness and sleep, cortical neurons exhibit rhythmic slow wave activity associated with periods of neuronal silence. Slow waves are locally regulated, and local slow wave dynamics are important for memory, cognition, and behaviour. While several brainstem structures for controlling global sleep states have now been well characterized, a mechanism underlying fast and local modulation of cortical slow waves has not been identified. Here, using optogenetics and whole cortex electrophysiology, we show that local tonic activation of thalamic reticular nucleus (TRN) rapidly induces slow wave activity in a spatially restricted region of cortex. These slow waves resemble those seen in sleep, as cortical units undergo periods of silence phase-locked to the slow wave. Furthermore, animals exhibit behavioural changes consistent with a decrease in arousal state during TRN stimulation. We conclude that TRN can induce rapid modulation of local cortical state. DOI: http://dx.doi.org/10.7554/eLife.08760.001 PMID:26460547

Universality Classes of Interaction Structures for NK Fitness Landscapes

NASA Astrophysics Data System (ADS)

Hwang, Sungmin; Schmiegelt, Benjamin; Ferretti, Luca; Krug, Joachim

2018-07-01

Kauffman's NK-model is a paradigmatic example of a class of stochastic models of genotypic fitness landscapes that aim to capture generic features of epistatic interactions in multilocus systems. Genotypes are represented as sequences of L binary loci. The fitness assigned to a genotype is a sum of contributions, each of which is a random function defined on a subset of k ≤ L loci. These subsets or neighborhoods determine the genetic interactions of the model. Whereas earlier work on the NK model suggested that most of its properties are robust with regard to the choice of neighborhoods, recent work has revealed an important and sometimes counter-intuitive influence of the interaction structure on the properties of NK fitness landscapes. Here we review these developments and present new results concerning the number of local fitness maxima and the statistics of selectively accessible (that is, fitness-monotonic) mutational pathways. In particular, we develop a unified framework for computing the exponential growth rate of the expected number of local fitness maxima as a function of L, and identify two different universality classes of interaction structures that display different asymptotics of this quantity for large k. Moreover, we show that the probability that the fitness landscape can be traversed along an accessible path decreases exponentially in L for a large class of interaction structures that we characterize as locally bounded. Finally, we discuss the impact of the NK interaction structures on the dynamics of evolution using adaptive walk models.

Universality Classes of Interaction Structures for NK Fitness Landscapes

NASA Astrophysics Data System (ADS)

Hwang, Sungmin; Schmiegelt, Benjamin; Ferretti, Luca; Krug, Joachim

2018-02-01

Kauffman's NK-model is a paradigmatic example of a class of stochastic models of genotypic fitness landscapes that aim to capture generic features of epistatic interactions in multilocus systems. Genotypes are represented as sequences of L binary loci. The fitness assigned to a genotype is a sum of contributions, each of which is a random function defined on a subset of k ≤ L loci. These subsets or neighborhoods determine the genetic interactions of the model. Whereas earlier work on the NK model suggested that most of its properties are robust with regard to the choice of neighborhoods, recent work has revealed an important and sometimes counter-intuitive influence of the interaction structure on the properties of NK fitness landscapes. Here we review these developments and present new results concerning the number of local fitness maxima and the statistics of selectively accessible (that is, fitness-monotonic) mutational pathways. In particular, we develop a unified framework for computing the exponential growth rate of the expected number of local fitness maxima as a function of L, and identify two different universality classes of interaction structures that display different asymptotics of this quantity for large k. Moreover, we show that the probability that the fitness landscape can be traversed along an accessible path decreases exponentially in L for a large class of interaction structures that we characterize as locally bounded. Finally, we discuss the impact of the NK interaction structures on the dynamics of evolution using adaptive walk models.

Advanced fitness landscape analysis and the performance of memetic algorithms.

PubMed

Merz, Peter

2004-01-01

Memetic algorithms (MAs) have demonstrated very effective in combinatorial optimization. This paper offers explanations as to why this is so by investigating the performance of MAs in terms of efficiency and effectiveness. A special class of MAs is used to discuss efficiency and effectiveness for local search and evolutionary meta-search. It is shown that the efficiency of MAs can be increased drastically with the use of domain knowledge. However, effectiveness highly depends on the structure of the problem. As is well-known, identifying this structure is made easier with the notion of fitness landscapes: the local properties of the fitness landscape strongly influence the effectiveness of the local search while the global properties strongly influence the effectiveness of the evolutionary meta-search. This paper also introduces new techniques for analyzing the fitness landscapes of combinatorial problems; these techniques focus on the investigation of random walks in the fitness landscape starting at locally optimal solutions as well as on the escape from the basins of attractions of current local optima. It is shown for NK-landscapes and landscapes of the unconstrained binary quadratic programming problem (BQP) that a random walk to another local optimum can be used to explain the efficiency of recombination in comparison to mutation. Moreover, the paper shows that other aspects like the size of the basins of attractions of local optima are important for the efficiency of MAs and a local search escape analysis is proposed. These simple analysis techniques have several advantages over previously proposed statistical measures and provide valuable insight into the behaviour of MAs on different kinds of landscapes.

Structural Basis for Activation of Fatty Acid-binding Protein 4

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

Gillilan,R.; Ayers, S.; Noy, N.

2007-01-01

Fatty acid-binding protein 4 (FABP4) delivers ligands from the cytosol to the nuclear receptor PPAR{gamma} in the nucleus, thereby enhancing the transcriptional activity of the receptor. Notably, FABP4 binds multiple ligands with a similar affinity but its nuclear translocation is activated only by specific compounds. To gain insight into the structural features that underlie the ligand-specificity in activation of the nuclear import of FABP4, we solved the crystal structures of the protein complexed with two compounds that induce its nuclear translocation, and compared these to the apo-protein and to FABP4 structures bound to non-activating ligands. Examination of these structures indicatesmore » that activation coincides with closure of a portal loop phenylalanine side-chain, contraction of the binding pocket, a subtle shift in a helical domain containing the nuclear localization signal of the protein, and a resultant change in oligomeric state that exposes the nuclear localization signal to the solution. Comparisons of backbone displacements induced by activating ligands with a measure of mobility derived from translation, libration, screw (TLS) refinement, and with a composite of slowest normal modes of the apo state suggest that the helical motion associated with the activation of the protein is part of the repertoire of the equilibrium motions of the apo-protein, i.e. that ligand binding does not induce the activated configuration but serves to stabilize it. Nuclear import of FABP4 can thus be understood in terms of the pre-existing equilibrium hypothesis of ligand binding.« less

Soil geohazard mapping for improved asset management of UK local roads

NASA Astrophysics Data System (ADS)

Pritchard, O. G.; Hallett, S. H.; Farewell, T. S.

2015-09-01

Unclassified roads comprise 60 % of the road network in the United Kingdom (UK). The resilience of this locally important network is declining. It is considered by the Institution of Civil Engineers to be "at risk" and is ranked 26th in the world. Many factors contribute to the degradation and ultimate failure of particular road sections. However, several UK local authorities have identified that in drought conditions, road sections founded upon shrink-swell susceptible clay soils undergo significant deterioration compared with sections on non-susceptible soils. This arises from the local road network having little, if any, structural foundations. Consequently, droughts in East Anglia have resulted in millions of pounds of damage, leading authorities to seek emergency governmental funding. This paper assesses the use of soil-related geohazard assessments in providing soil-informed maintenance strategies for the asset management of the locally important road network of the UK. A case study draws upon the UK administrative county of Lincolnshire, where road assessment data have been analysed against mapped clay-subsidence risk. This reveals a statistically significant relationship between road condition and susceptible clay soils. Furthermore, incorporation of UKCP09 future climate projections within the geohazard models has highlighted roads likely to be at future risk of clay-related subsidence.

Soil geohazard mapping for improved asset management of UK local roads

NASA Astrophysics Data System (ADS)

Pritchard, O. G.; Hallett, S. H.; Farewell, T. S.

2015-05-01

Unclassified roads comprise 60% of the road network in the United Kingdom (UK). The resilience of this locally important network is declining. It is considered by the Institution of Civil Engineers to be "at risk" and is ranked 26th in the world. Many factors contribute to the degradation and ultimate failure of particular road sections. However, several UK local authorities have identified that in drought conditions, road sections founded upon shrink/swell susceptible clay soils undergo significant deterioration compared with sections on non-susceptible soils. This arises from the local road network having little, if any structural foundations. Consequently, droughts in East Anglia have resulted in millions of pounds of damage, leading authorities to seek emergency governmental funding. This paper assesses the use of soil-related geohazard assessments in providing soil-informed maintenance strategies for the asset management of the locally important road network of the UK. A case study draws upon the UK administrative county of Lincolnshire, where road assessment data have been analysed against mapped clay-subsidence risk. This reveals a statistically significant relationship between road condition and susceptible clay soils. Furthermore, incorporation of UKCP09 future climate projections within the geohazard models has highlighted roads likely to be at future risk of clay-related subsidence.

Intracellular Localization, Interactions and Functions of Capsicum Chlorosis Virus Proteins

PubMed Central

Widana Gamage, Shirani M. K.; Dietzgen, Ralf G.

2017-01-01

Tospoviruses are among the most devastating viruses of horticultural and field crops. Capsicum chlorosis virus (CaCV) has emerged as an important pathogen of capsicum and tomato in Australia and South-east Asia. Present knowledge about CaCV protein functions in host cells is lacking. We determined intracellular localization and interactions of CaCV proteins by live plant cell imaging to gain insight into the associations of viral proteins during infection. Proteins were transiently expressed as fusions to autofluorescent proteins in leaf epidermal cells of Nicotiana benthamiana and capsicum. All viral proteins localized at least partially in the cell periphery suggestive of cytoplasmic replication and assembly of CaCV. Nucleocapsid (N) and non-structural movement (NSm) proteins localized exclusively in the cell periphery, while non-structural suppressor of silencing (NSs) protein and Gc and Gn glycoproteins accumulated in both the cell periphery and the nucleus. Nuclear localization of CaCV Gn and NSs is unique among tospoviruses. We validated nuclear localization of NSs by immunofluorescence in protoplasts. Bimolecular fluorescence complementation showed self-interactions of CaCV N, NSs and NSm, and heterotypic interactions of N with NSs and Gn. All interactions occurred in the cytoplasm, except NSs self-interaction was exclusively nuclear. Interactions of a tospoviral NSs protein with itself and with N had not been reported previously. Functionally, CaCV NSs showed strong local and systemic RNA silencing suppressor activity and appears to delay short-distance spread of silencing signal. Cell-to-cell movement activity of NSm was demonstrated by trans-complementation of a movement-defective tobamovirus replicon. CaCV NSm localized at plasmodesmata and its transient expression led to the formation of tubular structures that protruded from protoplasts. The D155 residue in the 30K-like movement protein-specific LxD/N50-70G motif of NSm was critical for plasmodesmata localization and movement activity. Compared to other tospoviruses, CaCV proteins have both conserved and unique properties in terms of in planta localization, interactions and protein functions which will effect viral multiplication and movement in host plants. PMID:28443083

Intracellular Localization, Interactions and Functions of Capsicum Chlorosis Virus Proteins.

PubMed

Widana Gamage, Shirani M K; Dietzgen, Ralf G

2017-01-01

Tospoviruses are among the most devastating viruses of horticultural and field crops. Capsicum chlorosis virus (CaCV) has emerged as an important pathogen of capsicum and tomato in Australia and South-east Asia. Present knowledge about CaCV protein functions in host cells is lacking. We determined intracellular localization and interactions of CaCV proteins by live plant cell imaging to gain insight into the associations of viral proteins during infection. Proteins were transiently expressed as fusions to autofluorescent proteins in leaf epidermal cells of Nicotiana benthamiana and capsicum. All viral proteins localized at least partially in the cell periphery suggestive of cytoplasmic replication and assembly of CaCV. Nucleocapsid (N) and non-structural movement (NSm) proteins localized exclusively in the cell periphery, while non-structural suppressor of silencing (NSs) protein and Gc and Gn glycoproteins accumulated in both the cell periphery and the nucleus. Nuclear localization of CaCV Gn and NSs is unique among tospoviruses. We validated nuclear localization of NSs by immunofluorescence in protoplasts. Bimolecular fluorescence complementation showed self-interactions of CaCV N, NSs and NSm, and heterotypic interactions of N with NSs and Gn. All interactions occurred in the cytoplasm, except NSs self-interaction was exclusively nuclear. Interactions of a tospoviral NSs protein with itself and with N had not been reported previously. Functionally, CaCV NSs showed strong local and systemic RNA silencing suppressor activity and appears to delay short-distance spread of silencing signal. Cell-to-cell movement activity of NSm was demonstrated by trans -complementation of a movement-defective tobamovirus replicon. CaCV NSm localized at plasmodesmata and its transient expression led to the formation of tubular structures that protruded from protoplasts. The D 155 residue in the 30K-like movement protein-specific LxD/N 50-70 G motif of NSm was critical for plasmodesmata localization and movement activity. Compared to other tospoviruses, CaCV proteins have both conserved and unique properties in terms of in planta localization, interactions and protein functions which will effect viral multiplication and movement in host plants.

Structural polymorphism at LCR and its role in beta-globin gene regulation.

PubMed

Kukreti, Shrikant; Kaur, Harpreet; Kaushik, Mahima; Bansal, Aparna; Saxena, Sarika; Kaushik, Shikha; Kukreti, Ritushree

2010-09-01

Information on the secondary structures and conformational manifestations of eukaryotic DNA and their biological significance with reference to gene regulation and expression is limited. The human beta-globin gene Locus Control Region (LCR), a dominant regulator of globin gene expression, is a contiguous piece of DNA with five tissue-specific DNase I-hypersensitive sites (HSs). Since these HSs have a high density of transcription factor binding sites, structural interdependencies between HSs and different promoters may directly or indirectly regulate LCR functions. Mutations and SNPs may stabilize or destabilize the local secondary structures, affecting the gene expression by changes in the protein-DNA recognition patterns. Various palindromic or quasi-palindromic segments within LCR, could cause structural polymorphism and geometrical switching of DNA. This emphasizes the importance of understanding of the sequence-dependent variations of the DNA structure. Such structural motifs might act as regulatory elements. The local conformational variability of a DNA segment or action of a DNA specific protein is key to create and maintain active chromatin domains and affect transcription of various tissue specific beta-globin genes. We, summarize here the current status of beta-globin LCR structure and function. Further structural studies at molecular level and functional genomics might solve the regulatory puzzles that control the beta-globin gene locus. Copyright (c) 2010 Elsevier Masson SAS. All rights reserved.

Global and local disturbances interact to modify seagrass palatability.

PubMed

Jiménez-Ramos, Rocío; Egea, Luis G; Ortega, María J; Hernández, Ignacio; Vergara, Juan J; Brun, Fernando G

2017-01-01

Global change, such as warming and ocean acidification, and local anthropogenic disturbances, such as eutrophication, can have profound impacts on marine organisms. However, we are far from being able to predict the outcome of multiple interacting disturbances on seagrass communities. Herbivores are key in determining plant community structure and the transfer of energy up the food web. Global and local disturbances may alter the ecological role of herbivory by modifying leaf palatability (i.e. leaf traits) and consequently, the feeding patterns of herbivores. This study evaluates the main and interactive effects of factors related to global change (i.e. elevated temperature, lower pH levels and associated ocean acidification) and local disturbance (i.e. eutrophication through ammonium enrichment) on a broad spectrum of leaf traits using the temperate seagrass Cymodocea nodosa, including structural, nutritional, biomechanical and chemical traits. The effect of these traits on the consumption rates of the generalist herbivore Paracentrotus lividus (purple sea urchin) is evaluated. The three disturbances of warming, low pH level and eutrophication, alone and in combination, increased the consumption rate of seagrass by modifying all leaf traits. Leaf nutritional quality, measured as nitrogen content, was positively correlated to consumption rate. In contrast, a negative correlation was found between feeding decisions by sea urchins and structural, biomechanical and chemical leaf traits. In addition, a notable accomplishment of this work is the identification of phenolic compounds not previously reported for C. nodosa. Our results suggest that global and local disturbances may trigger a major shift in the herbivory of seagrass communities, with important implications for the resilience of seagrass ecosystems.

Think locally, act locally: detection of small, medium-sized, and large communities in large networks.

PubMed

Jeub, Lucas G S; Balachandran, Prakash; Porter, Mason A; Mucha, Peter J; Mahoney, Michael W

2015-01-01

It is common in the study of networks to investigate intermediate-sized (or "meso-scale") features to try to gain an understanding of network structure and function. For example, numerous algorithms have been developed to try to identify "communities," which are typically construed as sets of nodes with denser connections internally than with the remainder of a network. In this paper, we adopt a complementary perspective that communities are associated with bottlenecks of locally biased dynamical processes that begin at seed sets of nodes, and we employ several different community-identification procedures (using diffusion-based and geodesic-based dynamics) to investigate community quality as a function of community size. Using several empirical and synthetic networks, we identify several distinct scenarios for "size-resolved community structure" that can arise in real (and realistic) networks: (1) the best small groups of nodes can be better than the best large groups (for a given formulation of the idea of a good community); (2) the best small groups can have a quality that is comparable to the best medium-sized and large groups; and (3) the best small groups of nodes can be worse than the best large groups. As we discuss in detail, which of these three cases holds for a given network can make an enormous difference when investigating and making claims about network community structure, and it is important to take this into account to obtain reliable downstream conclusions. Depending on which scenario holds, one may or may not be able to successfully identify "good" communities in a given network (and good communities might not even exist for a given community quality measure), the manner in which different small communities fit together to form meso-scale network structures can be very different, and processes such as viral propagation and information diffusion can exhibit very different dynamics. In addition, our results suggest that, for many large realistic networks, the output of locally biased methods that focus on communities that are centered around a given seed node (or set of seed nodes) might have better conceptual grounding and greater practical utility than the output of global community-detection methods. They also illustrate structural properties that are important to consider in the development of better benchmark networks to test methods for community detection.

Think locally, act locally: Detection of small, medium-sized, and large communities in large networks

NASA Astrophysics Data System (ADS)

Jeub, Lucas G. S.; Balachandran, Prakash; Porter, Mason A.; Mucha, Peter J.; Mahoney, Michael W.

2015-01-01

It is common in the study of networks to investigate intermediate-sized (or "meso-scale") features to try to gain an understanding of network structure and function. For example, numerous algorithms have been developed to try to identify "communities," which are typically construed as sets of nodes with denser connections internally than with the remainder of a network. In this paper, we adopt a complementary perspective that communities are associated with bottlenecks of locally biased dynamical processes that begin at seed sets of nodes, and we employ several different community-identification procedures (using diffusion-based and geodesic-based dynamics) to investigate community quality as a function of community size. Using several empirical and synthetic networks, we identify several distinct scenarios for "size-resolved community structure" that can arise in real (and realistic) networks: (1) the best small groups of nodes can be better than the best large groups (for a given formulation of the idea of a good community); (2) the best small groups can have a quality that is comparable to the best medium-sized and large groups; and (3) the best small groups of nodes can be worse than the best large groups. As we discuss in detail, which of these three cases holds for a given network can make an enormous difference when investigating and making claims about network community structure, and it is important to take this into account to obtain reliable downstream conclusions. Depending on which scenario holds, one may or may not be able to successfully identify "good" communities in a given network (and good communities might not even exist for a given community quality measure), the manner in which different small communities fit together to form meso-scale network structures can be very different, and processes such as viral propagation and information diffusion can exhibit very different dynamics. In addition, our results suggest that, for many large realistic networks, the output of locally biased methods that focus on communities that are centered around a given seed node (or set of seed nodes) might have better conceptual grounding and greater practical utility than the output of global community-detection methods. They also illustrate structural properties that are important to consider in the development of better benchmark networks to test methods for community detection.

Atomic resolution holography.

PubMed

Hayashi, Kouichi

2014-11-01

Atomic resolution holography, such as X-ray fluorescence holography (XFH)[1] and photoelectron holography (PH), has the attention of researcher as an informative local structure analysis, because it provides three dimensional atomic images around specific elements within a range of a few nanometers. It can determine atomic arrangements around a specific element without any prior knowledge of structures. It is considered that the atomic resolution holographic is a third method of structural analysis at the atomic level after X-ray diffraction (XRD) and X-ray absorption fine structure (XAFS). As known by many researchers, XRD and XAFS are established methods that are widespread use in various fields. XRD and XAFS provide information on long-range translational periodicities and very local environments, respectively, whereas the atomic resolution holography gives 3D information on the local order and can visualize surrounding atoms with a large range of coordination shells. We call this feature "3D medium-range local structure observation".In addition to this feature, the atomic resolution holography is very sensitive to the displacement of atoms from their ideal positions, and one can obtain quantitative information about local lattice distortions by analyzing reconstructed atomic images[2] When dopants with different atomic radii from the matrix elements are present, the lattices around the dopants are distorted. However, using the conventional methods of structural analysis, one cannot determine the extent to which the local lattice distortions are preserved from the dopants. XFH is a good tool for solving this problem.Figure 1 shows a recent achievement on a relaxor ferroelectric of Pb(Mg1/3Nb2/3)O3 (PMN) using XFH. The structural studies of relaxor ferroelectrics have been carried out by X-ray or neutron diffractions, which suggested rhombohedral distortions of their lattices. However, their true pictures have not been obtained, yet. The Nb Kα holograms showed four separate Pb images, as shown in Fig.1. Using these images, we could obtain acute and obtuse rhombohedral structures of the crystal unit cells. Moreover, the Pb-Pb correlated images reconstructed from Pb Lα holograms showed a local structure of body center-like 2a0 ×2a0 × 2a0 superlattice, proving a rigid 3D network structural model combining the two kinds of rhombohedrons. This superstructure are believed to play an important role in the relaxor behaviour of PMN at atomic level[3].jmicro;63/suppl_1/i13/DFU047F1F1DFU047F1Fig. 1.3D images of the nearest Pb and O atoms around Nb in Pb(Mg1/3Nb2/3)O3. The cube represents 1/8 of the unit cell. © The Author 2014. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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

PubMed

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

2016-12-01

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

Electronic structures of GeSi nanoislands grown on pit-patterned Si(001) substrate

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

Ye, Han, E-mail: Dabombyh@aliyun.com; Yu, Zhongyuan

2014-11-15

Patterning pit on Si(001) substrate prior to Ge deposition is an important approach to achieve GeSi nanoislands with high ordering and size uniformity. In present work, the electronic structures of realistic uncapped pyramid, dome, barn and cupola nanoislands grown in (105) pits are systematically investigated by solving Schrödinger equation for heavy-hole, which resorts to inhomogeneous strain distribution and nonlinear composition-dependent band parameters. Uniform, partitioned and equilibrium composition profile (CP) in nanoisland and inverted pyramid structure are simulated separately. We demonstrate the huge impact of composition profile on localization of heavy-hole: wave function of ground state is confined near pit facetsmore » for uniform CP, at bottom of nanoisland for partitioned CP and at top of nanoisland for equilibrium CP. Moreover, such localization is gradually compromised by the size effect as pit filling ratio or pit size decreases. The results pave the fundamental guideline of designing nanoislands on pit-patterned substrates for desired applications.« less

The Multiple-Minima Problem in Protein Folding

NASA Astrophysics Data System (ADS)

Scheraga, Harold A.

1991-10-01

The conformational energy surface of a polypeptide or protein has many local minima, and conventional energy minimization procedures reach only a local minimum (near the starting point of the optimization algorithm) instead of the global minimum (the multiple-minima problem). Several procedures have been developed to surmount this problem, the most promising of which are: (a) build up procedure, (b) optimization of electrostatics, (c) Monte Carlo-plus-energy minimization, (d) electrostatically-driven Monte Carlo, (e) inclusion of distance restraints, (f) adaptive importance-sampling Monte Carlo, (g) relaxation of dimensionality, (h) pattern-recognition, and (i) diffusion equation method. These procedures have been applied to a variety of polypeptide structural problems, and the results of such computations are presented. These include the computation of the structures of open-chain and cyclic peptides, fibrous proteins and globular proteins. Present efforts are being devoted to scaling up these procedures from small polypeptides to proteins, to try to compute the three-dimensional structure of a protein from its amino sequence.

Principle and Reconstruction Algorithm for Atomic-Resolution Holography

NASA Astrophysics Data System (ADS)

Matsushita, Tomohiro; Muro, Takayuki; Matsui, Fumihiko; Happo, Naohisa; Hosokawa, Shinya; Ohoyama, Kenji; Sato-Tomita, Ayana; Sasaki, Yuji C.; Hayashi, Kouichi

2018-06-01

Atomic-resolution holography makes it possible to obtain the three-dimensional (3D) structure around a target atomic site. Translational symmetry of the atomic arrangement of the sample is not necessary, and the 3D atomic image can be measured when the local structure of the target atomic site is oriented. Therefore, 3D local atomic structures such as dopants and adsorbates are observable. Here, the atomic-resolution holography comprising photoelectron holography, X-ray fluorescence holography, neutron holography, and their inverse modes are treated. Although the measurement methods are different, they can be handled with a unified theory. The algorithm for reconstructing 3D atomic images from holograms plays an important role. Although Fourier transform-based methods have been proposed, they require the multiple-energy holograms. In addition, they cannot be directly applied to photoelectron holography because of the phase shift problem. We have developed methods based on the fitting method for reconstructing from single-energy and photoelectron holograms. The developed methods are applicable to all types of atomic-resolution holography.

Synthesis, crystal structure analysis, molecular docking studies and density functional theory predictions of the local reactive properties and degradation properties of a novel halochalcone

NASA Astrophysics Data System (ADS)

Arshad, Suhana; Pillai, Renjith Raveendran; Zainuri, Dian Alwani; Khalib, Nuridayanti Che; Razak, Ibrahim Abdul; Armaković, Stevan; Armaković, Sanja J.

2017-09-01

In the present study, single crystals of E)-3-(3,5-dichlorophenyl)-1-(4-fluorophenyl)prop-2-en-1-one, were prepared and structurally characterized by single crystal X-ray diffraction analysis. The molecular structure crystallized in monoclinic crystal system with P21/c space group. Sensitivity of the title molecule towards electrophilic attacks has been examined by calculations of average localized ionization energies (ALIE) and their mapping to electron density surface. Further determination of atoms that could be important reactive centres has been performed by calculations of Fukui functions. Sensitivity of title molecule towards autoxidation and hydrolysis mechanisms has been assessed by calculations of bond dissociation energies and radial distribution functions (RDF), respectively. Also, in order to explore possible binding mode of the title compound towards Dihydrofolate reductase enzyme, we have utilized in silico molecular docking to explore possible binding modes of the title compound with the DHFR enzyme.

Automatic abdominal lymph node detection method based on local intensity structure analysis from 3D x-ray CT images

NASA Astrophysics Data System (ADS)

Nakamura, Yoshihiko; Nimura, Yukitaka; Kitasaka, Takayuki; Mizuno, Shinji; Furukawa, Kazuhiro; Goto, Hidemi; Fujiwara, Michitaka; Misawa, Kazunari; Ito, Masaaki; Nawano, Shigeru; Mori, Kensaku

2013-03-01

This paper presents an automated method of abdominal lymph node detection to aid the preoperative diagnosis of abdominal cancer surgery. In abdominal cancer surgery, surgeons must resect not only tumors and metastases but also lymph nodes that might have a metastasis. This procedure is called lymphadenectomy or lymph node dissection. Insufficient lymphadenectomy carries a high risk for relapse. However, excessive resection decreases a patient's quality of life. Therefore, it is important to identify the location and the structure of lymph nodes to make a suitable surgical plan. The proposed method consists of candidate lymph node detection and false positive reduction. Candidate lymph nodes are detected using a multi-scale blob-like enhancement filter based on local intensity structure analysis. To reduce false positives, the proposed method uses a classifier based on support vector machine with the texture and shape information. The experimental results reveal that it detects 70.5% of the lymph nodes with 13.0 false positives per case.

Imaging and reconstruction of cell cortex structures near the cell surface

NASA Astrophysics Data System (ADS)

Jin, Luhong; Zhou, Xiaoxu; Xiu, Peng; Luo, Wei; Huang, Yujia; Yu, Feng; Kuang, Cuifang; Sun, Yonghong; Liu, Xu; Xu, Yingke

2017-11-01

Total internal reflection fluorescence microscopy (TIRFM) provides high optical sectioning capability and superb signal-to-noise ratio for imaging of cell cortex structures. The development of multi-angle (MA)-TIRFM permits high axial resolution imaging and reconstruction of cellular structures near the cell surface. Cytoskeleton is composed of a network of filaments, which are important for maintenance of cell function. The high-resolution imaging and quantitative analysis of filament organization would contribute to our understanding of cytoskeleton regulation in cell. Here, we used a custom-developed MA-TIRFM setup, together with stochastic photobleaching and single molecule localization method, to enhance the lateral resolution of TIRFM imaging to about 100 nm. In addition, we proposed novel methods to perform filament segmentation and 3D reconstruction from MA-TIRFM images. Furthermore, we applied these methods to study the 3D localization of cortical actin and microtubule structures in U373 cancer cells. Our results showed that cortical actins localize ∼ 27 nm closer to the plasma membrane when compared with microtubules. We found that treatment of cells with chemotherapy drugs nocodazole and cytochalasin B disassembles cytoskeletal network and induces the reorganization of filaments towards the cell periphery. In summary, this study provides feasible approaches for 3D imaging and analyzing cell surface distribution of cytoskeletal network. Our established microscopy platform and image analysis toolkits would facilitate the study of cytoskeletal network in cells.

New Technique for Speciation of Uranium in Sediments Following Acetate-Stimulated Bioremediation

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

Not Available

2011-06-22

Acetate-stimulated bioremediation is a promising new technique for sequestering toxic uranium contamination from groundwater. The speciation of uranium in sediments after such bioremediation attempts remains unknown as a result of low uranium concentration, and is important to analyzing the stability of sequestered uranium. A new technique was developed for investigating the oxidation state and local molecular structure of uranium from field site sediments using X-Ray Absorption Spectroscopy (XAS), and was implemented at the site of a former uranium mill in Rifle, CO. Glass columns filled with bioactive Rifle sediments were deployed in wells in the contaminated Rifle aquifer and amendedmore » with a hexavalent uranium (U(VI)) stock solution to increase uranium concentration while maintaining field conditions. This sediment was harvested and XAS was utilized to analyze the oxidation state and local molecular structure of the uranium in sediment samples. Extended X-Ray Absorption Fine Structure (EXAFS) data was collected and compared to known uranium spectra to determine the local molecular structure of the uranium in the sediment. Fitting was used to determine that the field site sediments did not contain uraninite (UO{sub 2}), indicating that models based on bioreduction using pure bacterial cultures are not accurate for bioremediation in the field. Stability tests on the monomeric tetravalent uranium (U(IV)) produced by bioremediation are needed in order to assess the efficacy of acetate-stimulation bioremediation.« less

The structure of internal stresses in the uncompacted ice cover

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

Sukhorukov, K.K.

1995-12-31

Interactions between engineering structures and sea ice cover are associated with an inhomogeneous space/time field of internal stresses. Field measurements (e.g., Coon, 1989; Tucker, 1992) have revealed considerable local stresses depending on the regional stress field and ice structure. These stresses appear in different time and space scales and depend on rheologic properties of the ice. To estimate properly the stressed state a knowledge of a connection between internal stress components in various regions of the ice cover is necessary. To develop reliable algorithms for estimates of ice action on engineering structures new experimental data are required to take intomore » account both microscale (comparable with local ice inhomogeneities) and small-scale (kilometers) inhomogeneities of the ice cover. Studies of compacted ice (concentration N is nearly 1) are mostly important. This paper deals with the small-scale spatial distribution of internal stresses in the interaction zone between the ice covers of various concentrations and icebergs. The experimental conditions model a situation of the interaction between a wide structure and the ice cover. Field data on a drifting ice were collected during the Russian-US experiment in Antarctica WEDDELL-I in 1992.« less

Sleep loss and structural plasticity.

PubMed

Areal, Cassandra C; Warby, Simon C; Mongrain, Valérie

2017-06-01

Wakefulness and sleep are dynamic states during which brain functioning is modified and shaped. Sleep loss is detrimental to many brain functions and results in structural changes localized at synapses in the nervous system. In this review, we present and discuss some of the latest observations of structural changes following sleep loss in some vertebrates and insects. We also emphasize that these changes are region-specific and cell type-specific and that, most importantly, these structural modifications have functional roles in sleep regulation and brain functions. Selected mechanisms driving structural modifications occurring with sleep loss are also discussed. Overall, recent research highlights that extending wakefulness impacts synapse number and shape, which in turn regulate sleep need and sleep-dependent learning/memory. Copyright © 2017 Elsevier Ltd. All rights reserved.

Dyeing regions of oxidative hair dyes in human hair investigated by nanoscale secondary ion mass spectrometry.

PubMed

Kojima, Toru; Yamada, Hiromi; Yamamoto, Toshihiko; Matsushita, Yasuyuki; Fukushima, Kazuhiko

2013-06-01

To develop more effective oxidative hair coloring products, it is important to understand the localization of colored chromophores, which are formed from oxidative dyes, in the fine structure of hair. However, the dyeing regions of oxidative hair dyes in the fine structure of hair have not been extensively examined. In this study, we investigated the distribution and localization of colored chromophores formed by an oxidative hair coloring product in the fine structure of human hair by using a stable isotope-labeled oxidative dye with nanoscale secondary ion mass spectrometry (NanoSIMS). First, formation of the colored chromophore from a deuterium-labeled oxidative dye was examined by visible spectra similarly to a study of its formation using nonlabeled oxidative dye. Furthermore, the formation of binuclear indo dye containing deuterium in its chemical structure was confirmed using time-of-flight secondary ion mass spectrometry (TOF-SIMS) analysis. As a result of the NanoSIMS image on a cross-sectional dyed hair, although deuterium ions were detected in whole hair cross-section, quite a few of them were detected at particulate regions. These particulate regions of the dyed black hair in which deuterium ions were intensely detected were identified as melanin granules, by comparing the dyeing behaviors of black and white hair. NanoSIMS analysis revealed that melanin granules of black human hair are important dyeing regions in oxidative hair coloring. Copyright © 2013 Elsevier B.V. All rights reserved.

Making Federalism Work in Italy. OECD Economics Department Working Papers No. 590

ERIC Educational Resources Information Center

Bibbee, Alexandra

2007-01-01

Fiscal federalism can be an important complement to structural reforms and budget consolidation. Empowering sub national governments, while at the same time making them accountable to local citizens in the uses of tax money, could improve the allocation of public resources and promote catch up of the lagging regions. Italy has launched itself in…

Mapping of Functional Domains of the Lipid Kinase Phosphatidylinositol 4-Kinase Type III Alpha Involved in Enzymatic Activity and Hepatitis C Virus Replication

PubMed Central

Harak, Christian; Radujkovic, Danijela; Taveneau, Cyntia; Reiss, Simon; Klein, Rahel; Bressanelli, Stéphane

2014-01-01

ABSTRACT The lipid kinase phosphatidylinositol 4-kinase III alpha (PI4KIIIα) is an endoplasmic reticulum (ER)-resident enzyme that synthesizes phosphatidylinositol 4-phosphate (PI4P). PI4KIIIα is an essential host factor for hepatitis C virus (HCV) replication. Interaction with HCV nonstructural protein 5A (NS5A) leads to kinase activation and accumulation of PI4P at intracellular membranes. In this study, we investigated the structural requirements of PI4KIIIα in HCV replication and enzymatic activity. Therefore, we analyzed PI4KIIIα mutants for subcellular localization, reconstitution of HCV replication in PI4KIIIα knockdown cell lines, PI4P induction in HCV-positive cells, and lipid kinase activity in vitro. All mutants still interacted with NS5A and localized in a manner similar to that of the full-length enzyme, suggesting multiple regions of PI4KIIIα are involved in NS5A interaction and subcellular localization. Interestingly, the N-terminal 1,152 amino acids were dispensable for HCV replication, PI4P induction, and enzymatic function, whereas further N-terminal or C-terminal deletions were deleterious, thereby defining the minimal PI4KIIIα core enzyme at a size of ca. 108 kDa. Additional deletion of predicted functional motifs within the C-terminal half of PI4KIIIα also were detrimental for enzymatic activity and for the ability of PI4KIIIα to rescue HCV replication, with the exception of a proposed nuclear localization signal, suggesting that the entire C-terminal half of PI4KIIIα is involved in the formation of a minimal enzymatic core. This view was supported by structural modeling of the PI4KIIIα C terminus, suggesting a catalytic center formed by an N- and C-terminal lobe and an armadillo-fold motif, which is preceded by three distinct alpha-helical domains probably involved in regulation of enzymatic activity. IMPORTANCE The lipid kinase PI4KIIIα is of central importance for cellular phosphatidylinositol metabolism and is a key host cell factor of hepatitis C virus replication. However, little is known so far about the structure of this 240-kDa protein and the functional importance of specific subdomains regarding lipid kinase activity and viral replication. This work focuses on the phenotypic analysis of distinct PI4KIIIα mutants in different biochemical and cell-based assays and develops a structural model of the C-terminal enzymatic core. The results shed light on the structural and functional requirements of enzymatic activity and the determinants required for HCV replication. PMID:24920820

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

NASA Astrophysics Data System (ADS)

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

2018-05-01

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

Local structural and chemical ordering of nanosized Pt3±δCo probed by multiple-scattering x-ray absorption spectroscopy

NASA Astrophysics Data System (ADS)

Greco, Giorgia; Witkowska, Agnieszka; Principi, Emiliano; Minicucci, Marco; di Cicco, Andrea

2011-04-01

This work reports a detailed investigation of the local structure and chemical disorder of a Pt3±δCo thin film and Pt3±δCo nanoparticles. We have used a combination of techniques including x-ray absorption spectroscopy (XAS), x-ray diffraction (XRD), and high-resolution transmission electron microscopy (TEM). High-quality XAS spectra at the Co K edge and Pt L3 edge have been analyzed using double-edge multiple-scattering data analysis. Structural extended x-ray absorption fine structure (EXAFS) refinements have been performed accounting for the reduction of the coordination numbers and degeneracy of three-atom configurations, resulting from the measured size distribution and stoichiometry. The important effect of chemical ordering on pair and three-atom configurations has been studied using computer simulations based on a simple model accounting for substitutional disorder, defined by an order parameter s. It has been found that individual EXAFS signals related to the minority species (Co) are extremely sensitive to substitutional disorder so their intensities, especially those of the collinear three-atom configurations, can be used as a measure of the ordering level. The thin film has been found to be chemically disordered (s⩽0.4), in agreement with previous estimates. The Pt3±δCo nanoalloy has been found to be partially ordered (s=0.6±0.1) while the local structure around Co atoms is characterized by a higher level of structural disorder as compared to the bulk-like thin film. The robust approach for nanomaterial characterization used in this work combining different techniques can, in principle, be applied for structural refinements of any binary nanocrystalline functional system.

Protein structure prediction with local adjust tabu search algorithm

PubMed Central

2014-01-01

Background Protein folding structure prediction is one of the most challenging problems in the bioinformatics domain. Because of the complexity of the realistic protein structure, the simplified structure model and the computational method should be adopted in the research. The AB off-lattice model is one of the simplification models, which only considers two classes of amino acids, hydrophobic (A) residues and hydrophilic (B) residues. Results The main work of this paper is to discuss how to optimize the lowest energy configurations in 2D off-lattice model and 3D off-lattice model by using Fibonacci sequences and real protein sequences. In order to avoid falling into local minimum and faster convergence to the global minimum, we introduce a novel method (SATS) to the protein structure problem, which combines simulated annealing algorithm and tabu search algorithm. Various strategies, such as the new encoding strategy, the adaptive neighborhood generation strategy and the local adjustment strategy, are adopted successfully for high-speed searching the optimal conformation corresponds to the lowest energy of the protein sequences. Experimental results show that some of the results obtained by the improved SATS are better than those reported in previous literatures, and we can sure that the lowest energy folding state for short Fibonacci sequences have been found. Conclusions Although the off-lattice models is not very realistic, they can reflect some important characteristics of the realistic protein. It can be found that 3D off-lattice model is more like native folding structure of the realistic protein than 2D off-lattice model. In addition, compared with some previous researches, the proposed hybrid algorithm can more effectively and more quickly search the spatial folding structure of a protein chain. PMID:25474708

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.

Local health practices and the knowledge of medicinal plants in a Brazilian semi-arid region: environmental benefits to human health.

PubMed

Zank, Sofia; Peroni, Nivaldo; de Araújo, Elcida Lima; Hanazaki, Natalia

2015-02-23

The concept of eco-cultural health considers the dynamic interaction between humans and ecosystems, emphasizing the implications of the health of the ecosystem for the health and well-being of human populations. Ethnobotanical studies focusing on folk medicine and medicinal plants can contribute to the field of eco-cultural health if they incorporate the perspective and local knowledge of communities. We investigated the local health practices in three rural communities living within the vicinity of a protected area of sustainable use in a semi-arid region of Brazil. We analyzed the opinions of local health experts on the elements that influence human health and on how the environment contributes to this influence. We also analyzed and compared the local knowledge of medicinal plants, as knowledge of this type is an important factor when considering the interaction between environmental and human health. We performed structured interviews and free-listings with 66 local health experts. We used content analysis to systematize the elements of the influences on human health. We compared the richness of the plants cited among communities and analyzed the differences among the three communities regarding the ways in which the plants were obtained and the environments in which plants were collected. The local experts identified several influences of the environment on human health. These influences can be associated with ecosystem services, such as climatic conditions, water and air quality, recreation and medicinal and food resources. We identified 192 medicinal plant species, most of which were gathered from wild ecosystems. The most important environments for the three communities were the plateau mountain and backyards. The informants had a broad and integrated view of health, perceiving the importance of conserving the environment within the National Forest of Araripe for the health and well-being of the local populations.

Adaptive livelihood strategies for coping with water scarcity in the drylands of central Tanzania

NASA Astrophysics Data System (ADS)

Liwenga, Emma T.

In this paper, it is argued that local knowledge for adapting to water scarcity is important for integrated resource management by taking into consideration both the natural and social constraints in a particular setting based on accumulated experience. The paper examines the relevance of local knowledge in sustaining agricultural production in the semiarid areas of central Tanzania. The paper specifically focuses on how water scarcity, as the major limiting factor, is addressed in the study area using local knowledge to sustain livelihoods of its people. The study was conducted in four villages; Mzula, Ilolo, Chanhumba and Ngahelezi, situation in Mvumi Division in Dodoma Region. The study mainly employed qualitative data collection techniques. Participatory methods provided a means of exploring perceptions and gaining deeper insights regarding natural resource utilization in terms of problems and opportunities. The main data sources drawn upon in this study were documentation, group interviews and field observations. Group interviews involved discussions with a group of 6-12 people selected on the basis of gender, age and socio-economic groups. Data analysis entailed structural and content analysis within the adaptive livelihood framework in relation to management of water scarcity using local knowledge. The findings confirm that rainfall is the main limiting factor for agricultural activities in the drylands of Central Tanzania. As such, local communities have developed, through time, indigenous knowledge to cope with such environments utilizing seasonality and diversity of landscapes. Use of this local knowledge is therefore effective in managing water scarcity by ensuring a continuous production of crops throughout the year. This practice implies increased food availability and accessibility through sales of such agricultural products. Local innovations for water management, such as cultivation in sandy rivers, appear to be very important means of accessing water in these dryland areas. It can therefore be concluded that utilization of local knowledge has wide impact on integrated water resource management. These implications are important considerations for development of adaptive water system innovations at community level.

Tendency to occupy a statistically dominant spatial state of the flow as a driving force for turbulent transition.

PubMed

Chekmarev, Sergei F

2013-03-01

The transition from laminar to turbulent fluid motion occurring at large Reynolds numbers is generally associated with the instability of the laminar flow. On the other hand, since the turbulent flow characteristically appears in the form of spatially localized structures (e.g., eddies) filling the flow field, a tendency to occupy such a structured state of the flow cannot be ruled out as a driving force for turbulent transition. To examine this possibility, we propose a simple analytical model that treats the flow as a collection of localized spatial structures, each of which consists of elementary cells in which the behavior of the particles (atoms or molecules) is uncorrelated. This allows us to introduce the Reynolds number, associating it with the ratio between the total phase volume for the system and that for the elementary cell. Using the principle of maximum entropy to calculate the most probable size distribution of the localized structures, we show that as the Reynolds number increases, the elementary cells group into the localized structures, which successfully explains turbulent transition and some other general properties of turbulent flows. An important feature of the present model is that a bridge between the spatial-statistical description of the flow and hydrodynamic equations is established. We show that the basic assumptions underlying the model, i.e., that the particles are indistinguishable and elementary volumes of phase space exist in which the state of the particles is uncertain, are involved in the derivation of the Navier-Stokes equation. Taking into account that the model captures essential features of turbulent flows, this suggests that the driving force for the turbulent transition is basically the same as in the present model, i.e., the tendency of the system to occupy a statistically dominant state plays a key role. The instability of the flow at high Reynolds numbers can then be a mechanism to initiate structural rearrangement of the flow to find this state.

IUE study of the very local interstellar medium. [Copernicus spacecraft

NASA Technical Reports Server (NTRS)

Henry, R. C.; Murthy, J.; Moos, H. W.; Landsman, W. B.; Linsky, J. L.; Vidal-Madjar, A.; Gry, C.

1986-01-01

The IUE and Copernicus results for the very local interstellar medium are compared. Despite its lower resolution, IUE produces results of comparable quality, giving important confirmation of Copernicus results on the density, temperature, turbulence, and deuterium-to-hydrogen ratio in the region within 10 pc of the Sun. The stars observed are in a very low-density quarter of the galaxy: multicomponent structure seen in other directions may not be present in the direction of most of the observed stars. The exceedingly low densities observed in certain directions encourages the idea that EUV studies of certain normal stars may be possible.

Prices and availability of locally produced and imported medicines in Ethiopia and Tanzania.

PubMed

Ewen, M; Kaplan, W; Gedif, T; Justin-Temu, M; Vialle-Valentin, C; Mirza, Z; Regeer, B; Zweekhorst, M; Laing, R

2017-01-01

To assess the effect of policies supporting local medicine production to improve access to medicines. We adapted the WHO/HAI instruments measuring medicines availability and prices to differentiate local from imported products, then pilot tested in Ethiopia and Tanzania. In each outlet, prices were recorded for all products in stock for medicines on a country-specific list. Government procurement prices were also collected. Prices were compared to an international reference and expressed as median price ratios (MPR). The Ethiopian government paid more for local products (median MPR = 1.20) than for imports (median MPR = 0.84). Eight of nine medicines procured as both local and imported products were cheaper when imported. Availability was better for local products compared to imports, in the public (48% vs. 19%, respectively) and private (54% vs. 35%, respectively) sectors. Patient prices were lower for imports in the public sector (median MPR = 1.18[imported] vs. 1.44[local]) and higher in the private sector (median MPR = 5.42[imported] vs. 1.85[local]). In the public sector, patients paid 17% and 53% more than the government procurement price for local and imported products, respectively. The Tanzanian government paid less for local products (median MPR = 0.69) than imports (median MPR = 1.34). In the public sector, availability of local and imported products was 21% and 32% respectively, with patients paying slightly more for local products (median MPR = 1.35[imported] vs. 1.44[local]). In the private sector, local products were less available (21%) than imports (70%) but prices were similar (median MPR = 2.29[imported] vs. 2.27[local]). In the public sector, patients paid 135% and 65% more than the government procurement price for local and imported products, respectively. Our results show how local production can affect availability and prices, and how it can be influenced by preferential purchasing and mark-ups in the public sector. Governments need to evaluate the impact of local production policies, and adjust policies to protect patients from paying more for local products.

Expression, subcellular localization, and cis-regulatory structure of duplicated phytoene synthase genes in melon (Cucumis melo L.).

PubMed

Qin, Xiaoqiong; Coku, Ardian; Inoue, Kentaro; Tian, Li

2011-10-01

Carotenoids perform many critical functions in plants, animals, and humans. It is therefore important to understand carotenoid biosynthesis and its regulation in plants. Phytoene synthase (PSY) catalyzes the first committed and rate-limiting step in carotenoid biosynthesis. While PSY is present as a single copy gene in Arabidopsis, duplicated PSY genes have been identified in many economically important monocot and dicot crops. CmPSY1 was previously identified from melon (Cucumis melo L.), but was not functionally characterized. We isolated a second PSY gene, CmPSY2, from melon in this work. CmPSY2 possesses a unique intron/exon structure that has not been observed in other plant PSYs. Both CmPSY1 and CmPSY2 are functional in vitro, but exhibit distinct expression patterns in different melon tissues and during fruit development, suggesting differential regulation of the duplicated melon PSY genes. In vitro chloroplast import assays verified the plastidic localization of CmPSY1 and CmPSY2 despite the lack of an obvious plastid target peptide in CmPSY2. Promoter motif analysis of the duplicated melon and tomato PSY genes and the Arabidopsis PSY revealed distinctive cis-regulatory structures of melon PSYs and identified gibberellin-responsive motifs in all PSYs except for SlPSY1, which has not been reported previously. Overall, these data provide new insights into the evolutionary history of plant PSY genes and the regulation of PSY expression by developmental and environmental signals that may involve different regulatory networks.

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.

Parametric imaging of collagen structural changes in human osteoarthritic cartilage using optical polarization tractography

NASA Astrophysics Data System (ADS)

Ravanfar, Mohammadreza; Pfeiffer, Ferris M.; Bozynski, Chantelle C.; Wang, Yuanbo; Yao, Gang

2017-12-01

Collagen degeneration is an important pathological feature of osteoarthritis. The purpose of this study is to investigate whether the polarization-sensitive optical coherence tomography (PSOCT)-based optical polarization tractography (OPT) can be useful in imaging collagen structural changes in human osteoarthritic cartilage samples. OPT eliminated the banding artifacts in conventional PSOCT by calculating the depth-resolved local birefringence and fiber orientation. A close comparison between OPT and PSOCT showed that OPT provided improved visualization and characterization of the zonal structure in human cartilage. Experimental results obtained in this study also underlined the importance of knowing the collagen fiber orientation in conventional polarized light microscopy assessment. In addition, parametric OPT imaging was achieved by quantifying the surface roughness, birefringence, and fiber dispersion in the superficial zone of the cartilage. These quantitative parametric images provided complementary information on the structural changes in cartilage, which can be useful for a comprehensive evaluation of collagen damage in osteoarthritic cartilage.

Evidence For Rapid Spatiotemporal Changes in Genetic Structure of an Alien Whitefly During Initial Invasion

PubMed Central

Chu, Dong; Guo, Dong; Tao, Yunli; Jiang, Defeng; Li, Jie; Zhang, Youjun

2014-01-01

The sweetpotato whitefly Bemisia tabaci Q species is a recent invader and important pest of agricultural crops in China. This research tested the hypothesis that the Q populations that establish in agricultural fields in northern China each year are derived from multiple secondary introductions and/or local populations that overwinter in greenhouses (the pest cannot survive winters in the field in northern China). Here, we report the evidence that the Q populations in agricultural fields mainly derive from multiple secondary introductions. In addition, the common use of greenhouses during the winter in certain locations in northern China helps increase the genetic diversity and the genetic structure of the pest. The genetic structure information generated from this long-term and large-scale field analysis increases our understanding of B. tabaci Q as an invasive pest and has important implications for B. tabaci Q management. PMID:24637851

Population genetic structure of codling moth (Lepidoptera: Tortricidae) from apple orchards in central Chile.

PubMed

Fuentes-Contreras, Eduardo; Espinoza, Juan L; Lavandero, Blas; Ramírez, Claudio C

2008-02-01

Codling moth, Cydia pomonella (L.) (Lepidoptera: Tortricidae), is the main pest of pome fruits worldwide. Despite its economic importance, little is known about the genetic structure and patterns of dispersal at the local and regional scale, which are important aspects for establishing a control strategy for this pest. An analysis of genetic variability using microsatellites was performed for 11 codling moth populations in the two major apple (Malus domestica Borkh) cropping regions in central Chile. Despite the geographical distances between some populations (approximately 185 km), there was low genetic differentiation among populations (F(ST) = 0.002176), with only slight isolation by distance. Only approximately 0.2% of the genetic variability was found among the populations. Geographically structured genetic variation was independent of apple orchard management (production or abandoned). These results suggest a high genetic exchange of codling moth between orchards, possibly mediated by human activities related to fruit production.

Characterization of Microgravity Effects on Bone Structure and Strength Using Fractal Analysis

NASA Technical Reports Server (NTRS)

Acharya, Raj S.; Shackelford, Linda

1996-01-01

Protecting humans against extreme environmental conditions requires a thorough understanding of the pathophysiological changes resulting from the exposure to those extreme conditions. Knowledge of the degree of medical risk associated with the exposure is of paramount importance in the design of effective prophylactic and therapeutic measures for space exploration. Major health hazards due o musculoskeletal systems include the signs and symptoms of hypercalciuria, lengthy recovery of lost bone tissue after flight, the possibility of irreversible trabecular bone loss, the possible effect of calcification in the soft tissues, and the possible increase in fracture potential. In this research, we characterize the trabecular structure with the aid of fractal analysis. Our research to relate local trabecular structural information to microgravity conditions is an important initial step in understanding the effect of microgravity and countermeasures on bone condition and strength. The proposed research is also closely linked with Osteoporosis and will benefit the general population.

Quantifying randomness in real networks

NASA Astrophysics Data System (ADS)

Orsini, Chiara; Dankulov, Marija M.; Colomer-de-Simón, Pol; Jamakovic, Almerima; Mahadevan, Priya; Vahdat, Amin; Bassler, Kevin E.; Toroczkai, Zoltán; Boguñá, Marián; Caldarelli, Guido; Fortunato, Santo; Krioukov, Dmitri

2015-10-01

Represented as graphs, real networks are intricate combinations of order and disorder. Fixing some of the structural properties of network models to their values observed in real networks, many other properties appear as statistical consequences of these fixed observables, plus randomness in other respects. Here we employ the dk-series, a complete set of basic characteristics of the network structure, to study the statistical dependencies between different network properties. We consider six real networks--the Internet, US airport network, human protein interactions, technosocial web of trust, English word network, and an fMRI map of the human brain--and find that many important local and global structural properties of these networks are closely reproduced by dk-random graphs whose degree distributions, degree correlations and clustering are as in the corresponding real network. We discuss important conceptual, methodological, and practical implications of this evaluation of network randomness, and release software to generate dk-random graphs.

Morphometric attributes to understand palaeogeomorphological controls on mass-transport deposits offshore Brazil

NASA Astrophysics Data System (ADS)

Piedade, Aldina; Alves, Tiago; Luís Zêzere, José

2017-04-01

Mass-transport deposits form a significant part of the stratigraphic record of ancient and modern deep-water basins worldwide. Three-dimensional (3D) seismic data is used to analyse two different types of buried mass-transport deposits offshore Espírito Santo Basin (SE Brazil. Both types are developed within Early Miocene to Holocene stratigraphic units composed of sandstones, calcarenites, turbidite sands and marls. The high resolution images provided by the interpreted 3D seismic data allowed a detailed analysis of the seismic stratigraphy and internal structure of mass-transport deposits. In addition, improvements in visualisation techniques were used to compute simple morphometric attributes of buried mass-transport deposits in continental slopes. This study classifies the interpreted mass-transport deposits in two different types according to the relationship between the morphology of mass-transport deposits and the surrounding topography. Locally confined mass-transport deposits are laterally constrained by non-deformed strata that surrounds the mass-transport deposit and by the local topography of the depositional surface. Their dimensions are relatively small (area of 5.251 km2). Unconfined mass-transport deposits show a much larger volume compared to the previously type ( 87.180 km2), and local topography does not have control on their geometry. The analysis proves that local topography and geometry of the depositional surface are key controlling factors on the spatial distribution and dimensions of the two types of mass-transport deposits. However, the two types differ in size, geomorphological expression, local structural controls and run-out distance. This work importance is relate variations in the character of the depositional surface with the morphology mass-transport deposits and run-out distance. As a result of the methodology used, two different styles of mass-transport run-out are identified and local factors controlling their morphology are addressed, such as roughness and local morphology of the depositional surface. Separating these two styles, or types, of mass-transport deposits it is of critical importance to understand their mechanisms of gliding, downslope spreading and emplacement.

Predicting local adaptation in fragmented plant populations: implications for restoration genetics

PubMed Central

Pickup, Melinda; Field, David L; Rowell, David M; Young, Andrew G

2012-01-01

Understanding patterns and correlates of local adaptation in heterogeneous landscapes can provide important information in the selection of appropriate seed sources for restoration. We assessed the extent of local adaptation of fitness components in 12 population pairs of the perennial herb Rutidosis leptorrhynchoides (Asteraceae) and examined whether spatial scale (0.7–600 km), environmental distance, quantitative (QST) and neutral (FST) genetic differentiation, and size of the local and foreign populations could predict patterns of adaptive differentiation. Local adaptation varied among populations and fitness components. Including all population pairs, local adaptation was observed for seedling survival, but not for biomass, while foreign genotype advantage was observed for reproduction (number of inflorescences). Among population pairs, local adaptation increased with QST and local population size for biomass. QST was associated with environmental distance, suggesting ecological selection for phenotypic divergence. However, low FST and variation in population structure in small populations demonstrates the interaction of gene flow and drift in constraining local adaptation in R. leptorrhynchoides. Our study indicates that for species in heterogeneous landscapes, collecting seed from large populations from similar environments to candidate sites is likely to provide the most appropriate seed sources for restoration. PMID:23346235

Using a NIATx based local learning collaborative for performance improvement

PubMed Central

Roosa, Mathew; Scripa, Joseph S.; Zastowny, Thomas R.; Ford, James H.

2012-01-01

Local governments play an important role in improving substance abuse and mental health services. The structure of the local learning collaborative requires careful attention to old relationships and challenges local governmental leaders to help move participants from a competitive to collaborative environment. This study describes one county’s experience applying the NIATx process improvement model via a local learning collaborative. Local substance abuse and mental health agencies participated in two local learning collaboratives designed to improve client retention in substance abuse treatment and client access to mental health services. Results of changes implemented at the provider level on access and retention are outlined. The process of implementing evidence-based practices by using the Plan-Do-Study-Act rapid-cycle change is a powerful combination for change at the local level. Key lessons include: creating a clear plan and shared vision, recognizing that one size does not fit all, using data can help fuel participant engagement, a long collaborative may benefit from breaking it into smaller segments, and paying providers to offset costs of participation enhances their engagement. The experience gained in Onondaga County, New York, offers insights that serve as a foundation for using the local learning collaborative in other community-based organizations. PMID:21371751

Development of structural correlations and synchronization from adaptive rewiring in networks of Kuramoto oscillators

NASA Astrophysics Data System (ADS)

Papadopoulos, Lia; Kim, Jason Z.; Kurths, Jürgen; Bassett, Danielle S.

2017-07-01

Synchronization of non-identical oscillators coupled through complex networks is an important example of collective behavior, and it is interesting to ask how the structural organization of network interactions influences this process. Several studies have explored and uncovered optimal topologies for synchronization by making purposeful alterations to a network. On the other hand, the connectivity patterns of many natural systems are often not static, but are rather modulated over time according to their dynamics. However, this co-evolution and the extent to which the dynamics of the individual units can shape the organization of the network itself are less well understood. Here, we study initially randomly connected but locally adaptive networks of Kuramoto oscillators. In particular, the system employs a co-evolutionary rewiring strategy that depends only on the instantaneous, pairwise phase differences of neighboring oscillators, and that conserves the total number of edges, allowing the effects of local reorganization to be isolated. We find that a simple rule—which preserves connections between more out-of-phase oscillators while rewiring connections between more in-phase oscillators—can cause initially disordered networks to organize into more structured topologies that support enhanced synchronization dynamics. We examine how this process unfolds over time, finding a dependence on the intrinsic frequencies of the oscillators, the global coupling, and the network density, in terms of how the adaptive mechanism reorganizes the network and influences the dynamics. Importantly, for large enough coupling and after sufficient adaptation, the resulting networks exhibit interesting characteristics, including degree-frequency and frequency-neighbor frequency correlations. These properties have previously been associated with optimal synchronization or explosive transitions in which the networks were constructed using global information. On the contrary, by considering a time-dependent interplay between structure and dynamics, this work offers a mechanism through which emergent phenomena and organization can arise in complex systems utilizing local rules.

Geometry motivated alternative view on local protein backbone structures.

PubMed

Zacharias, Jan; Knapp, Ernst Walter

2013-11-01

We present an alternative to the classical Ramachandran plot (R-plot) to display local protein backbone structure. Instead of the (φ, ψ)-backbone angles relating to the chemical architecture of polypeptides generic helical parameters are used. These are the rotation or twist angle ϑ and the helical rise parameter d. Plots with these parameters provide a different view on the nature of local protein backbone structures. It allows to display the local structures in polar (d, ϑ)-coordinates, which is not possible for an R-plot, where structural regimes connected by periodicity appear disconnected. But there are other advantages, like a clear discrimination of the handedness of a local structure, a larger spread of the different local structure domains--the latter can yield a better separation of different local secondary structure motives--and many more. Compared to the R-plot we are not aware of any major disadvantage to classify local polypeptide structures with the (d, ϑ)-plot, except that it requires some elementary computations. To facilitate usage of the new (d, ϑ)-plot for protein structures we provide a web application (http://agknapp.chemie.fu-berlin.de/secsass), which shows the (d, ϑ)-plot side-by-side with the R-plot. © 2013 The Protein Society.

A predictive structural model for bulk metallic glasses

PubMed Central

Laws, K. J.; Miracle, D. B.; Ferry, M.

2015-01-01

Great progress has been made in understanding the atomic structure of metallic glasses, but there is still no clear connection between atomic structure and glass-forming ability. Here we give new insights into perhaps the most important question in the field of amorphous metals: how can glass-forming ability be predicted from atomic structure? We give a new approach to modelling metallic glass atomic structures by solving three long-standing problems: we discover a new family of structural defects that discourage glass formation; we impose efficient local packing around all atoms simultaneously; and we enforce structural self-consistency. Fewer than a dozen binary structures satisfy these constraints, but extra degrees of freedom in structures with three or more different atom sizes significantly expand the number of relatively stable, ‘bulk' metallic glasses. The present work gives a new approach towards achieving the long-sought goal of a predictive capability for bulk metallic glasses. PMID:26370667

MicroRNAfold: pre-microRNA secondary structure prediction based on modified NCM model with thermodynamics-based scoring strategy.

PubMed

Han, Dianwei; Zhang, Jun; Tang, Guiliang

2012-01-01

An accurate prediction of the pre-microRNA secondary structure is important in miRNA informatics. Based on a recently proposed model, nucleotide cyclic motifs (NCM), to predict RNA secondary structure, we propose and implement a Modified NCM (MNCM) model with a physics-based scoring strategy to tackle the problem of pre-microRNA folding. Our microRNAfold is implemented using a global optimal algorithm based on the bottom-up local optimal solutions. Our experimental results show that microRNAfold outperforms the current leading prediction tools in terms of True Negative rate, False Negative rate, Specificity, and Matthews coefficient ratio.

The complex roles of space and environment in structuring functional, taxonomic and phylogenetic beta diversity of frogs in the Atlantic Forest

PubMed Central

Luiz, Amom Mendes; Sawaya, Ricardo J.

2018-01-01

Ecological communities are complex entities that can be maintained and structured by niche-based processes such as environmental conditions, and spatial processes such as dispersal. Thus, diversity patterns may be shaped simultaneously at different spatial scales by very distinct processes. Herein we assess whether and how functional, taxonomic, and phylogenetic beta diversities of frog tadpoles are explained by environmental and/or spatial predictors. We implemented a distance–based redundancy analysis to explore variation in components of beta diversity explained by pure environmental and pure spatial predictors, as well as their interactions, at both fine and broad spatial scales. Our results indicated important but complex roles of spatial and environmental predictors in structuring phylogenetic, taxonomic and functional beta diversities. The pure fine-scales spatial fraction was more important in structuring all beta diversity components, especially to functional and taxonomical spatial turnover. Environmental variables such as canopy cover and vegetation structure were important predictors of all components, but especially to functional and taxonomic beta diversity. We emphasize that distinct factors related to environment and space are affecting distinct components of beta diversity in different ways. Although weaker, phylogenetic beta diversity, which is structured more on biogeographical scales, and thus can be represented by spatially structured processes, was more related to broad spatial processes than other components. However, selected fine-scale spatial predictors denoted negative autocorrelation, which may be revealing the existence of differences in unmeasured habitat variables among samples. Although overall important, local environmental-based processes explained better functional and taxonomic beta diversity, as these diversity components carry an important ecological value. We highlight the importance of assessing different components of diversity patterns at different scales by spatially explicit models in order to improve our understanding of community structure and help to unravel the complex nature of biodiversity. PMID:29672575

Local Crystal Structure of Antiferroelectric Bi2Mn4/3Ni2/3O6 in Commensurate and Incommensurate Phases Described by Pair Distribution Function (PDF) and Reverse Monte Carlo (RMC) Modeling.

PubMed

Szczecinski, Robert J; Chong, Samantha Y; Chater, Philip A; Hughes, Helen; Tucker, Matthew G; Claridge, John B; Rosseinsky, Matthew J

2014-04-08

The functional properties of materials can arise from local structural features that are not well determined or described by crystallographic methods based on long-range average structural models. The room temperature (RT) structure of the Bi perovskite Bi 2 Mn 4/3 Ni 2/3 O 6 has previously been modeled as a locally polar structure where polarization is suppressed by a long-range incommensurate antiferroelectric modulation. In this study we investigate the short-range local structure of Bi 2 Mn 4/3 Ni 2/3 O 6 , determined through reverse Monte Carlo (RMC) modeling of neutron total scattering data, and compare the results with the long-range incommensurate structure description. While the incommensurate structure has equivalent B site environments for Mn and Ni, the local structure displays a significantly Jahn-Teller distorted environment for Mn 3+ . The local structure displays the rock-salt-type Mn/Ni ordering of the related Bi 2 MnNiO 6 high pressure phase, as opposed to Mn/Ni clustering observed in the long-range average incommensurate model. RMC modeling reveals short-range ferroelectric correlations between Bi 3+ cations, giving rise to polar regions that are quantified for the first time as existing within a distance of approximately 12 Å. These local correlations persist in the commensurate high temperature (HT) phase, where the long-range average structure is nonpolar. The local structure thus provides information about cation ordering and B site structural flexibility that may stabilize Bi 3+ on the A site of the perovskite structure and reveals the extent of the local polar regions created by this cation.

Eco-evolutionary spatial dynamics in the Glanville fritillary butterfly.

PubMed

Hanski, Ilkka A

2011-08-30

Demographic population dynamics, gene flow, and local adaptation may influence each other and lead to coupling of ecological and evolutionary dynamics, especially in species inhabiting fragmented heterogeneous environments. Here, I review long-term research on eco-evolutionary spatial dynamics in the Glanville fritillary butterfly inhabiting a large network of approximately 4,000 meadows in Finland. The metapopulation persists in a balance between frequent local extinctions and recolonizations. The genetic spatial structure as defined by neutral markers is much more coarse-grained than the demographic spatial structure determined by the fragmented habitat, yet small-scale spatial structure has important consequences for the dynamics. I discuss three examples of eco-evolutionary spatial dynamics. (i) Extinction-colonization metapopulation dynamics influence allele frequency changes in the phosphoglucose isomerase (Pgi) gene, which leads to strong associations between genetic variation in Pgi and dispersal, recolonization, and local population dynamics. (ii) Inbreeding in local populations increases their risk for extinction, whereas reciprocal effects between inbreeding, population size, and emigration represent likely eco-evolutionary feedbacks. (iii) Genetically determined female oviposition preference for two host plant species exhibits a cline paralleling a gradient in host plant relative abundances, and host plant preference of dispersing females in relation to the host plant composition of habitat patches influences immigration (gene flow) and recolonization (founder events). Eco-evolutionary spatial dynamics in heterogeneous environments may not lead to directional evolutionary changes unless the environment itself changes, but eco-evolutionary dynamics may contribute to the maintenance of genetic variation attributable to fluctuating selection in space and time.

Localization microscopy of DNA in situ using Vybrant(®) DyeCycle™ Violet fluorescent probe: A new approach to study nuclear nanostructure at single molecule resolution.

PubMed

Żurek-Biesiada, Dominika; Szczurek, Aleksander T; Prakash, Kirti; Mohana, Giriram K; Lee, Hyun-Keun; Roignant, Jean-Yves; Birk, Udo J; Dobrucki, Jurek W; Cremer, Christoph

2016-05-01

Higher order chromatin structure is not only required to compact and spatially arrange long chromatids within a nucleus, but have also important functional roles, including control of gene expression and DNA processing. However, studies of chromatin nanostructures cannot be performed using conventional widefield and confocal microscopy because of the limited optical resolution. Various methods of superresolution microscopy have been described to overcome this difficulty, like structured illumination and single molecule localization microscopy. We report here that the standard DNA dye Vybrant(®) DyeCycle™ Violet can be used to provide single molecule localization microscopy (SMLM) images of DNA in nuclei of fixed mammalian cells. This SMLM method enabled optical isolation and localization of large numbers of DNA-bound molecules, usually in excess of 10(6) signals in one cell nucleus. The technique yielded high-quality images of nuclear DNA density, revealing subdiffraction chromatin structures of the size in the order of 100nm; the interchromatin compartment was visualized at unprecedented optical resolution. The approach offers several advantages over previously described high resolution DNA imaging methods, including high specificity, an ability to record images using a single wavelength excitation, and a higher density of single molecule signals than reported in previous SMLM studies. The method is compatible with DNA/multicolor SMLM imaging which employs simple staining methods suited also for conventional optical microscopy. Copyright © 2016. Published by Elsevier Inc.

Community involvement in constructing village health buildings in Uganda and Sierra Leone.

PubMed

Mitchell, M

1995-11-01

Three public health projects in Uganda and Sierra Leone are used to illustrate a new approach to construction of health buildings in villages. Emphasis is placed on community involvement. The health projects were comprehensive and relied on health education, employment of local village health workers, and establishment of village health committees. The objective of community involvement was described as encouragement of people to change their own diets and living conditions. This approach to primary health care is considered to be a strong basis for sustainable social development. Each of the three communities initiated the building projects slightly differently. There was a range of structures: traditional meeting halls, simple rooms with imported materials and a pit latrine, new buildings combining local and imported materials and labor, new nontraditional buildings, rehabilitated existing nontraditional buildings with imported labor and materials, and temporary mobile clinics. Community involvement was at different levels. All three projects were the result of a combined effort of national governments or mission hospitals, nongovernmental organizations, and the host community. The following should be considered before beginning construction: a suitable site, appropriate staff accommodation, the likely motivation of the host community, seasonality, local materials available, availability of skilled labor, and design. A plan of work during construction should include a building design, site supervision, transportation of local and non-local materials, unskilled labor, and skilled labor. Village health committees with or without government help would be responsible for maintenance of buildings after construction. A key feature of this approach is the assessment of the community's ability and capacity to contribute.

Oceanographic Currents and Local Ecological Knowledge Indicate, and Genetics Does Not Refute, a Contemporary Pattern of Larval Dispersal for The Ornate Spiny Lobster, Panulirus ornatus in the South-East Asian Archipelago

PubMed Central

Dao, Hoc Tan; Smith-Keune, Carolyn; Wolanski, Eric; Jones, Clive M.; Jerry, Dean R.

2015-01-01

Here we utilize a combination of genetic data, oceanographic data, and local ecological knowledge to assess connectivity patterns of the ornate spiny lobster Panulirus ornatus (Fabricius, 1798) in the South-East Asian archipelago from Vietnam to Australia. Partial mitochondrial DNA control region and 10 polymorphic microsatellites did not detect genetic structure of 216 wild P. ornatus samples from Australia, Indonesia and Vietnam. Analyses show no evidence for genetic differentiation among populations (mtDNA control region sequences ΦST = -0.008; microsatellite loci FST = 0.003). A lack of evidence for regional or localized mtDNA haplotype clusters, or geographic clusters of microsatellite genotypes, reveals a pattern of high gene flow in P. ornatus throughout the South-East Asian Archipelago. This lack of genetic structure may be due to the oceanography-driven connectivity of the pelagic lobster larvae between spawning grounds in Papua New Guinea, the Philippines and, possibly, Indonesia. The connectivity cycle necessitates three generations. The lack of genetic structure of P. ornatus population in the South-East Asian archipelago has important implications for the sustainable management of this lobster in that the species within the region needs to be managed as one genetic stock. PMID:25951344

Vortex Interactions from a Finite Span Cylinder with a Laminar Boundary Layer for Varied Parameters

NASA Astrophysics Data System (ADS)

Gildersleeve, Samantha; Amitay, Michael

2017-11-01

Flow structures around a stationary, wall-mounted, finite-span cylindrical pin were investigated experimentally over a flat plate to explore the effects of varied aspect ratio and pin mean height with respect to the local boundary layer. Nine static pin configurations were tested where the pin's mean height to the local boundary layer thickness were 0.5, 1, and 1.5 for a range of aspect ratios between 0.125 and 1.125. The freestream velocity was fixed at 11 m/s, corresponding to ReD 2800, 5600, and 8400, respectively. Three-dimensional flowfields were reconstructed and analyzed from SPIV measurements where data were collected along cross-stream planes in the wake of the pin. This study focuses on three dominant vortical patterns associated with a finite span cylinder: the arch-type vortex horseshoe vortex, and the tip vortices Results indicate that both the aspect ratio and mean height play an important role in the behavior and interactions of these vortex structures which alter the wake characteristics significantly. Understanding the mechanisms by which the vortical structures may be strengthened while reducing adverse local pressure drag are key for developing more efficient means of passive and/or active flow control through finite span cylindrical pins and will be discussed in further detail. NDSEG Fellowship for Samantha Gildersleeve.

Fatal Attraction? Intraguild Facilitation and Suppression among Predators.

PubMed

Sivy, Kelly J; Pozzanghera, Casey B; Grace, James B; Prugh, Laura R

2017-11-01

Competition and suppression are recognized as dominant forces that structure predator communities. Facilitation via carrion provisioning, however, is a ubiquitous interaction among predators that could offset the strength of suppression. Understanding the relative importance of these positive and negative interactions is necessary to anticipate community-wide responses to apex predator declines and recoveries worldwide. Using state-sponsored wolf (Canis lupus) control in Alaska as a quasi experiment, we conducted snow track surveys of apex, meso-, and small predators to test for evidence of carnivore cascades (e.g., mesopredator release). We analyzed survey data using an integrative occupancy and structural equation modeling framework to quantify the strengths of hypothesized interaction pathways, and we evaluated fine-scale spatiotemporal responses of nonapex predators to wolf activity clusters identified from radio-collar data. Contrary to the carnivore cascade hypothesis, both meso- and small predator occupancy patterns indicated guild-wide, negative responses of nonapex predators to wolf abundance variations at the landscape scale. At the local scale, however, we observed a near guild-wide, positive response of nonapex predators to localized wolf activity. Local-scale association with apex predators due to scavenging could lead to landscape patterns of mesopredator suppression, suggesting a key link between occupancy patterns and the structure of predator communities at different spatial scales.

Oceanographic Currents and Local Ecological Knowledge Indicate, and Genetics Does Not Refute, a Contemporary Pattern of Larval Dispersal for The Ornate Spiny Lobster, Panulirus ornatus in the South-East Asian Archipelago.

PubMed

Dao, Hoc Tan; Smith-Keune, Carolyn; Wolanski, Eric; Jones, Clive M; Jerry, Dean R

2015-01-01

Here we utilize a combination of genetic data, oceanographic data, and local ecological knowledge to assess connectivity patterns of the ornate spiny lobster Panulirus ornatus (Fabricius, 1798) in the South-East Asian archipelago from Vietnam to Australia. Partial mitochondrial DNA control region and 10 polymorphic microsatellites did not detect genetic structure of 216 wild P. ornatus samples from Australia, Indonesia and Vietnam. Analyses show no evidence for genetic differentiation among populations (mtDNA control region sequences ΦST = -0.008; microsatellite loci FST = 0.003). A lack of evidence for regional or localized mtDNA haplotype clusters, or geographic clusters of microsatellite genotypes, reveals a pattern of high gene flow in P. ornatus throughout the South-East Asian Archipelago. This lack of genetic structure may be due to the oceanography-driven connectivity of the pelagic lobster larvae between spawning grounds in Papua New Guinea, the Philippines and, possibly, Indonesia. The connectivity cycle necessitates three generations. The lack of genetic structure of P. ornatus population in the South-East Asian archipelago has important implications for the sustainable management of this lobster in that the species within the region needs to be managed as one genetic stock.

Evolution of spatially structured host-parasite interactions.

PubMed

Lion, S; Gandon, S

2015-01-01

Spatial structure has dramatic effects on the demography and the evolution of species. A large variety of theoretical models have attempted to understand how local dispersal may shape the coevolution of interacting species such as host-parasite interactions. The lack of a unifying framework is a serious impediment for anyone willing to understand current theory. Here, we review previous theoretical studies in the light of a single epidemiological model that allows us to explore the effects of both host and parasite migration rates on the evolution and coevolution of various life-history traits. We discuss the impact of local dispersal on parasite virulence, various host defence strategies and local adaptation. Our analysis shows that evolutionary and coevolutionary outcomes crucially depend on the details of the host-parasite life cycle and on which life-history trait is involved in the interaction. We also discuss experimental studies that support the effects of spatial structure on the evolution of host-parasite interactions. This review highlights major similarities between some theoretical results, but it also reveals an important gap between evolutionary and coevolutionary models. We discuss possible ways to bridge this gap within a more unified framework that would reconcile spatial epidemiology, evolution and coevolution. © 2014 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

Mental health network governance: comparative analysis across Canadian regions.

PubMed

Wiktorowicz, Mary E; Fleury, Marie-Josée; Adair, Carol E; Lesage, Alain; Goldner, Elliot; Peters, Suzanne

2010-10-26

Modes of governance were compared in ten local mental health networks in diverse contexts (rural/urban and regionalized/non-regionalized) to clarify the governance processes that foster inter-organizational collaboration and the conditions that support them. Case studies of ten local mental health networks were developed using qualitative methods of document review, semi-structured interviews and focus groups that incorporated provincial policy, network and organizational levels of analysis. Mental health networks adopted either a corporate structure, mutual adjustment or an alliance governance model. A corporate structure supported by regionalization offered the most direct means for local governance to attain inter-organizational collaboration. The likelihood that networks with an alliance model developed coordination processes depended on the presence of the following conditions: a moderate number of organizations, goal consensus and trust among the organizations, and network-level competencies. In the small and mid-sized urban networks where these conditions were met their alliance realized the inter-organizational collaboration sought. In the large urban and rural networks where these conditions were not met, externally brokered forms of network governance were required to support alliance based models. In metropolitan and rural networks with such shared forms of network governance as an alliance or voluntary mutual adjustment, external mediation by a regional or provincial authority was an important lever to foster inter-organizational collaboration.

Molecular cloning, structure, and chromosomal localization of the mouse LIM/homeobox gene Lhx5

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

Bertuzzi, S.; Sheng, Hui Z.; Westphal, H.

1996-09-01

Lhx5, the mouse ortholog of the Xenopus Xlim-5, is a LIM/homeobox gene expressed in the central nervous system during both embryonic development and adulthood. During development its domain of expression is mainly localized at the most anterior portion of the neural tube, and it precedes the morphological differentiation of the forebrain; for this reason we believe that Lhx5 could play an important role in forebrain patterning. Here we present the structural organization and the chromosomal localization of the Lhx5 gene. The gene is composed of five exons spanning more than 10 kb of genomic sequence. The first and second LIMmore » domains are encoded by the first and second exon, while the codons of the homeobox are split between the third and the fourth exons. The structure of Lhx5 is similar to that of other LIM/homeodomain proteins, Lxh1/lim1 and Lhx3/lim3, but differs from that of other LIM genes, such as mec3 and LMO1/Rbtn1, in which the codons for the LIM domains are interrupted by introns. We have mapped Lhx5 to the central region of mouse chromosome 5. 38 refs., 4 figs.« less

Estimation of Local Orientations in Fibrous Structures With Applications to the Purkinje System

PubMed Central

Plank, Gernot; Trayanova, Natalia A.; Vidal, René

2011-01-01

The extraction of the cardiac Purkinje system (PS) from intensity images is a critical step toward the development of realistic structural models of the heart. Such models are important for uncovering the mechanisms of cardiac disease and improving its treatment and prevention. Unfortunately, the manual extraction of the PS is a challenging and error-prone task due to the presence of image noise and numerous fiber junctions. To deal with these challenges, we propose a framework that estimates local fiber orientations with high accuracy and reconstructs the fibers via tracking. Our key contribution is the development of a descriptor for estimating the orientation distribution function (ODF), a spherical function encoding the local geometry of the fibers at a point of interest. The fiber/branch orientations are identified as the modes of the ODFs via spherical clustering and guide the extraction of the fiber centerlines. Experiments on synthetic data evaluate the sensitivity of our approach to image noise, width of the fiber, and choice of the mode detection strategy, and show its superior performance compared to those of the existing descriptors. Experiments on the free-running PS in an MR image also demonstrate the accuracy of our method in reconstructing such sparse fibrous structures. PMID:21335301

Fatal attraction? Intraguild facilitation and suppression among predators

USGS Publications Warehouse

Sivy, Kelly J.; Pozzanghera, Casey B.; Grace, James B.; Prugh, Laura R.

2017-01-01

Competition and suppression are recognized as dominant forces that structure predator communities. Facilitation via carrion provisioning, however, is a ubiquitous interaction among predators that could offset the strength of suppression. Understanding the relative importance of these positive and negative interactions is necessary to anticipate community-wide responses to apex predator declines and recoveries worldwide. Using state-sponsored wolf (Canis lupus) control in Alaska as a quasi experiment, we conducted snow track surveys of apex, meso-, and small predators to test for evidence of carnivore cascades (e.g., mesopredator release). We analyzed survey data using an integrative occupancy and structural equation modeling framework to quantify the strengths of hypothesized interaction pathways, and we evaluated fine-scale spatiotemporal responses of nonapex predators to wolf activity clusters identified from radio-collar data. Contrary to the carnivore cascade hypothesis, both meso- and small predator occupancy patterns indicated guild-wide, negative responses of nonapex predators to wolf abundance variations at the landscape scale. At the local scale, however, we observed a near guild-wide, positive response of nonapex predators to localized wolf activity. Local-scale association with apex predators due to scavenging could lead to landscape patterns of mesopredator suppression, suggesting a key link between occupancy patterns and the structure of predator communities at different spatial scales.

Tests of species-specific models reveal the importance of drought in postglacial range shifts of a Mediterranean-climate tree: insights from integrative distributional, demographic and coalescent modelling and ABC model selection.

PubMed

Bemmels, Jordan B; Title, Pascal O; Ortego, Joaquín; Knowles, L Lacey

2016-10-01

Past climate change has caused shifts in species distributions and undoubtedly impacted patterns of genetic variation, but the biological processes mediating responses to climate change, and their genetic signatures, are often poorly understood. We test six species-specific biologically informed hypotheses about such processes in canyon live oak (Quercus chrysolepis) from the California Floristic Province. These hypotheses encompass the potential roles of climatic niche, niche multidimensionality, physiological trade-offs in functional traits, and local-scale factors (microsites and local adaptation within ecoregions) in structuring genetic variation. Specifically, we use ecological niche models (ENMs) to construct temporally dynamic landscapes where the processes invoked by each hypothesis are reflected by differences in local habitat suitabilities. These landscapes are used to simulate expected patterns of genetic variation under each model and evaluate the fit of empirical data from 13 microsatellite loci genotyped in 226 individuals from across the species range. Using approximate Bayesian computation (ABC), we obtain very strong support for two statistically indistinguishable models: a trade-off model in which growth rate and drought tolerance drive habitat suitability and genetic structure, and a model based on the climatic niche estimated from a generic ENM, in which the variables found to make the most important contribution to the ENM have strong conceptual links to drought stress. The two most probable models for explaining the patterns of genetic variation thus share a common component, highlighting the potential importance of seasonal drought in driving historical range shifts in a temperate tree from a Mediterranean climate where summer drought is common. © 2016 John Wiley & Sons Ltd.

Different effects of variation in Xanthium strumarium L. (Compositae) on two insect seed predators.

PubMed

Hare, J Daniel; Futuyma, Douglas J

1978-01-01

To determine the relative importance of variation in several plant characters on susceptibility to herbivores, we examined patterns of seed predation by two monophagous insect species and patterns of variation in ten populations of the cocklebur, Xanthium strumarium. Multiple regression analysis disclosed that one seed predator was most influenced by plant chemical variation, the other was significantly influenced by both chemical and morphological variation, but variation in yet another character, general burr size, was most important in conferring resistance to both insects simultaneously. The plant populations differed most in this character. Although many of the plant characters were correlated with each other, those important in determining susceptibility to each insect species were uncorrelated and independent of those conferring resistance to both insects simultaneously.These results imply that ecological similar herbivores may be influenced by different aspects of plant variation, and that predictions of evolutionary responses of local plant populations to herbivory may require knowledge of the structure of local herbivore communities and the dynamics of their establishment.

Causal Learning with Local Computations

ERIC Educational Resources Information Center

Fernbach, Philip M.; Sloman, Steven A.

2009-01-01

The authors proposed and tested a psychological theory of causal structure learning based on local computations. Local computations simplify complex learning problems via cues available on individual trials to update a single causal structure hypothesis. Structural inferences from local computations make minimal demands on memory, require…

Electromigration and the structure of metallic nanocontacts

NASA Astrophysics Data System (ADS)

Hoffmann-Vogel, R.

2017-09-01

This article reviews efforts to structurally characterize metallic nanocontacts. While the electronic characterization of such junctions is relatively straight forward, usually it is technically challenging to study the nanocontact's structure at small length scales. However, knowing that the structure is the basis for understanding the electronic properties of the nanocontact, for example, it is necessary to explain the electronic properties by calculations based on structural models. Besides using a gate electrode, controlling the structure is an important way of understanding how the electronic transport properties can be influenced. A key to make structural information directly accessible is to choose a fabrication method that is adapted to the structural characterization method. Special emphasis is given to transmission electron microscopy fabrication and to thermally assisted electromigration methods due to their potential for obtaining information on both electrodes of the forming nanocontact. Controlled electromigration aims at studying the contact at constant temperature of the contact during electromigration compared to studies at constant temperature of the environment as done previously. We review efforts to calculate electromigration forces. We describe how hot spots are formed during electromigration. We summarize implications for the structure obtained from studies of the ballistic transport regime, tunneling, and Coulomb-blockade. We review the structure of the nanocontacts known from direct structural characterization. Single-crystalline wires allow suppressing grain boundary electromigration. In thin films, the substrate plays an important role in influencing the defect and temperature distribution. Hot-spot formation and recrystallization are observed. We add information on the local temperature and current density and on alloys important for microelectronic interconnects.

On the modal characteristics of damaging structures subjected to earthquakes

NASA Astrophysics Data System (ADS)

Carlo Ponzo, Felice; Ditommaso, Rocco; Auletta, Gianluca; Iacovino, Chiara; Mossucca, Antonello; Nigro, Antonella; Nigro, Domenico

2015-04-01

Structural Health Monitoring, especially for structures located in seismic prone areas, has assumed a meaning of great importance in last years, for the possibility to make a more objective and more rapid estimation of the damage occurred on buildings after a seismic event. In the last years many researchers are working to set-up new methodologies for Non-destructive Damage Evaluation based on the variation of the dynamic behaviour of structures under seismic loads. The NDE methods for damage detection and evaluation can be classified into four levels, according to the specific criteria provided by the Rytter. Each level of identification is correlated with specific information related to monitored structure. In fact, by increasing the level it is possible to obtain more information about the state of the health of the structures, to know if damage occurred on the structures, to quantify and localize the damage and to evaluate its impact on the monitored structure. Several authors discussed on the possibility to use the mode shape curvature to localize damage on structural elements, for example, by applying the curvature-based method to frequency response function instead of mode shape, and demonstrated the potential of this approach by considering real data. Damage detection approach based on dynamic monitoring of structural properties over time has received a considerable attention in recent scientific literature. In earthquake engineering field, the recourse to experimental research is necessary to understand the mechanical behaviour of the various structural and non-structural components. In this paper a new methodology to detect and localize a possible damage occurred on a framed structure after an earthquake is presented and discussed. The main outcomes retrieved from many numerical non linear dynamic models of reinforced concrete framed structures characterized by 3, 5 and 8 floors with different geometric configurations and designed for gravity loads only are here presented. In addition, the main results of experimental shaking table tests carried out on a steel framed model are also showed to confirm the effectiveness of the proposed procedure. Acknowledgements This study was partially funded by the Italian Civil Protection Department within the project DPC-RELUIS 2014 - RS4 ''Seismic observatory of structures and health monitoring''.

Rim Structure, Stratigraphy, and Aqueous Alteration Exposures Along Opportunity Rover's Traverse of the Noachian Endeavour Crater

NASA Technical Reports Server (NTRS)

Crumpler, L.S.; Arvidson, R. E.; Golombek, M.; Grant, J. A.; Jolliff, B. L.; Mittlefehldt, D. W.

2017-01-01

The Mars Exploration Rover Opportunity has traversed 10.2 kilometers along segments of the west rim of the 22-kilometer-diameter Noachian Endeavour impact crater as of sol 4608 (01/09/17). The stratigraphy, attitude of units, lithology, and degradation state of bedrock outcrops exposed on the crater rim have been examined in situ and placed in geologic context. Structures within the rim and differences in physical properties of the identified lithologies have played important roles in localizing outcrops bearing evidence of aqueous alteration.

Nucleophosmin integrates within the nucleolus via multi-modal interactions with proteins displaying R-rich linear motifs and rRNA

PubMed Central

Mitrea, Diana M; Cika, Jaclyn A; Guy, Clifford S; Ban, David; Banerjee, Priya R; Stanley, Christopher B; Nourse, Amanda; Deniz, Ashok A; Kriwacki, Richard W

2016-01-01

The nucleolus is a membrane-less organelle formed through liquid-liquid phase separation of its components from the surrounding nucleoplasm. Here, we show that nucleophosmin (NPM1) integrates within the nucleolus via a multi-modal mechanism involving multivalent interactions with proteins containing arginine-rich linear motifs (R-motifs) and ribosomal RNA (rRNA). Importantly, these R-motifs are found in canonical nucleolar localization signals. Based on a novel combination of biophysical approaches, we propose a model for the molecular organization within liquid-like droplets formed by the N-terminal domain of NPM1 and R-motif peptides, thus providing insights into the structural organization of the nucleolus. We identify multivalency of acidic tracts and folded nucleic acid binding domains, mediated by N-terminal domain oligomerization, as structural features required for phase separation of NPM1 with other nucleolar components in vitro and for localization within mammalian nucleoli. We propose that one mechanism of nucleolar localization involves phase separation of proteins within the nucleolus. DOI: http://dx.doi.org/10.7554/eLife.13571.001 PMID:26836305

Chromosomal localization and partial genomic structure of the human peroxisome proliferator activated receptor-gamma (hPPAR gamma) gene.

PubMed

Beamer, B A; Negri, C; Yen, C J; Gavrilova, O; Rumberger, J M; Durcan, M J; Yarnall, D P; Hawkins, A L; Griffin, C A; Burns, D K; Roth, J; Reitman, M; Shuldiner, A R

1997-04-28

We determined the chromosomal localization and partial genomic structure of the coding region of the human PPAR gamma gene (hPPAR gamma), a nuclear receptor important for adipocyte differentiation and function. Sequence analysis and long PCR of human genomic DNA with primers that span putative introns revealed that intron positions and sizes of hPPAR gamma are similar to those previously determined for the mouse PPAR gamma gene[13]. Fluorescent in situ hybridization localized hPPAR gamma to chromosome 3, band 3p25. Radiation hybrid mapping with two independent primer pairs was consistent with hPPAR gamma being within 1.5 Mb of marker D3S1263 on 3p25-p24.2. These sequences of the intron/exon junctions of the 6 coding exons shared by hPPAR gamma 1 and hPPAR gamma 2 will facilitate screening for possible mutations. Furthermore, D3S1263 is a suitable polymorphic marker for linkage analysis to evaluate PPAR gamma's potential contribution to genetic susceptibility to obesity, lipoatrophy, insulin resistance, and diabetes.

Evolution of the Orszag-Tang vortex system in a compressible medium. II - Supersonic flow

NASA Technical Reports Server (NTRS)

Picone, J. Michael; Dahlburg, Russell B.

1991-01-01

A study is presented on the effect of embedded supersonic flows and the resulting emerging shock waves on phenomena associated with MHD turbulence, including reconnection, the formation of current sheets and vortex structures, and the evolution of spatial and temporal correlations among physical variables. A two-dimensional model problem, the Orszag-Tang (1979) vortex system, is chosen, which involves decay from nonrandom initial conditions. The system is doubly periodic, and the initial conditions consist of single-mode solenoidal velocity and magnetic fields, each containing X points and O points. The initial mass density is flat, and the initial pressure fluctuations are incompressible, balancing the local forces for a magnetofluid of unit mass density. Results on the evolution of the local structure of the flow field, the global properties of the system, and spectral correlations are presented. The important dynamical properties and observational consequences of embedded supersonic regions and emerging shocks in the Orszag-Tang model of an MHD system undergoing reconnection are discussed. Conclusions are drawn regarding the effects of local supersonic regions on MHD turbulence.

Locally adaptive MR intensity models and MRF-based segmentation of multiple sclerosis lesions

NASA Astrophysics Data System (ADS)

Galimzianova, Alfiia; Lesjak, Žiga; Likar, Boštjan; Pernuš, Franjo; Špiclin, Žiga

2015-03-01

Neuroimaging biomarkers are an important paraclinical tool used to characterize a number of neurological diseases, however, their extraction requires accurate and reliable segmentation of normal and pathological brain structures. For MR images of healthy brains the intensity models of normal-appearing brain tissue (NABT) in combination with Markov random field (MRF) models are known to give reliable and smooth NABT segmentation. However, the presence of pathology, MR intensity bias and natural tissue-dependent intensity variability altogether represent difficult challenges for a reliable estimation of NABT intensity model based on MR images. In this paper, we propose a novel method for segmentation of normal and pathological structures in brain MR images of multiple sclerosis (MS) patients that is based on locally-adaptive NABT model, a robust method for the estimation of model parameters and a MRF-based segmentation framework. Experiments on multi-sequence brain MR images of 27 MS patients show that, compared to whole-brain model and compared to the widely used Expectation-Maximization Segmentation (EMS) method, the locally-adaptive NABT model increases the accuracy of MS lesion segmentation.

Nucleophosmin integrates within the nucleolus via multi-modal interactions with proteins displaying R-rich linear motifs and rRNA

DOE PAGES

Mitrea, Diana M.; Cika, Jaclyn A.; Guy, Clifford S.; ...

2016-02-02

In this study, the nucleolus is a membrane-less organelle formed through liquid-liquid phase separation of its components from the surrounding nucleoplasm. Here, we show that nucleophosmin (NPM1) integrates within the nucleolus via a multi-modal mechanism involving multivalent interactions with proteins containing arginine-rich linear motifs (R-motifs) and ribosomal RNA (rRNA). Importantly, these R-motifs are found in canonical nucleolar localization signals. Based on a novel combination of biophysical approaches, we propose a model for the molecular organization within liquid-like droplets formed by the N-terminal domain of NPM1 and R-motif peptides, thus providing insights into the structural organization of the nucleolus. We identifymore » multivalency of acidic tracts and folded nucleic acid binding domains, mediated by N-terminal domain oligomerization, as structural features required for phase separation of NPM1 with other nucleolar components in vitro and for localization within mammalian nucleoli. We propose that one mechanism of nucleolar localization involves phase separation of proteins within the nucleolus.« less

Local phase space and edge modes for diffeomorphism-invariant theories

NASA Astrophysics Data System (ADS)

Speranza, Antony J.

2018-02-01

We discuss an approach to characterizing local degrees of freedom of a subregion in diffeomorphism-invariant theories using the extended phase space of Donnelly and Freidel [36]. Such a characterization is important for defining local observables and entanglement entropy in gravitational theories. Traditional phase space constructions for subregions are not invariant with respect to diffeomorphisms that act at the boundary. The extended phase space remedies this problem by introducing edge mode fields at the boundary whose transformations under diffeomorphisms render the extended symplectic structure fully gauge invariant. In this work, we present a general construction for the edge mode symplectic structure. We show that the new fields satisfy a surface symmetry algebra generated by the Noether charges associated with the edge mode fields. For surface-preserving symmetries, the algebra is universal for all diffeomorphism-invariant theories, comprised of diffeomorphisms of the boundary, SL(2, ℝ) transformations of the normal plane, and, in some cases, normal shearing transformations. We also show that if boundary conditions are chosen such that surface translations are symmetries, the algebra acquires a central extension.

Specific Non-Local Interactions Are Not Necessary for Recovering Native Protein Dynamics

PubMed Central

Dasgupta, Bhaskar; Kasahara, Kota; Kamiya, Narutoshi; Nakamura, Haruki; Kinjo, Akira R.

2014-01-01

The elastic network model (ENM) is a widely used method to study native protein dynamics by normal mode analysis (NMA). In ENM we need information about all pairwise distances, and the distance between contacting atoms is restrained to the native value. Therefore ENM requires O(N2) information to realize its dynamics for a protein consisting of N amino acid residues. To see if (or to what extent) such a large amount of specific structural information is required to realize native protein dynamics, here we introduce a novel model based on only O(N) restraints. This model, named the ‘contact number diffusion’ model (CND), includes specific distance restraints for only local (along the amino acid sequence) atom pairs, and semi-specific non-local restraints imposed on each atom, rather than atom pairs. The semi-specific non-local restraints are defined in terms of the non-local contact numbers of atoms. The CND model exhibits the dynamic characteristics comparable to ENM and more correlated with the explicit-solvent molecular dynamics simulation than ENM. Moreover, unrealistic surface fluctuations often observed in ENM were suppressed in CND. On the other hand, in some ligand-bound structures CND showed larger fluctuations of buried protein atoms interacting with the ligand compared to ENM. In addition, fluctuations from CND and ENM show comparable correlations with the experimental B-factor. Although there are some indications of the importance of some specific non-local interactions, the semi-specific non-local interactions are mostly sufficient for reproducing the native protein dynamics. PMID:24625758

G-LoSA: An efficient computational tool for local structure-centric biological studies and drug design.

PubMed

Lee, Hui Sun; Im, Wonpil

2016-04-01

Molecular recognition by protein mostly occurs in a local region on the protein surface. Thus, an efficient computational method for accurate characterization of protein local structural conservation is necessary to better understand biology and drug design. We present a novel local structure alignment tool, G-LoSA. G-LoSA aligns protein local structures in a sequence order independent way and provides a GA-score, a chemical feature-based and size-independent structure similarity score. Our benchmark validation shows the robust performance of G-LoSA to the local structures of diverse sizes and characteristics, demonstrating its universal applicability to local structure-centric comparative biology studies. In particular, G-LoSA is highly effective in detecting conserved local regions on the entire surface of a given protein. In addition, the applications of G-LoSA to identifying template ligands and predicting ligand and protein binding sites illustrate its strong potential for computer-aided drug design. We hope that G-LoSA can be a useful computational method for exploring interesting biological problems through large-scale comparison of protein local structures and facilitating drug discovery research and development. G-LoSA is freely available to academic users at http://im.compbio.ku.edu/GLoSA/. © 2016 The Protein Society.

Size versus electronic factors in transition metal carbide and TCP phase stability

NASA Astrophysics Data System (ADS)

Pettifor, D. G.; Seiser, B.; Margine, E. R.; Kolmogorov, A. N.; Drautz, R.

2013-09-01

The contributions of atomic size and electronic factors to the structural stability of transition metal carbides and topologically close-packed (TCP) phases are investigated. The hard-sphere model that has been used by Cottrell to rationalize the occurrence of the octahedral and trigonal local coordination polyhedra within the transition metal carbides is shown to have limitations in TiC since density functional theory (DFT) predicts that the second most metastable phase closest to the B1 (NaCl) ground state takes the B? (BN) structure type with 5-atom local coordination polyhedra with very short Ti-C bond lengths. The importance of electronic factors in the TCP phases is demonstrated by DFT predictions that the A15, ? and ? phases are stabilized between groups VI and VII of the elemental transition metals, whereas the ? and Laves phases are destabilized. The origin of this difference is related to the bimodal shape parameter of the electronic density of states by using the bond-order potential expansion of the structural energy within a canonical tight-binding model. The importance of the size factor in the TCP phases is illustrated by the DFT heats of formation for the binary systems Mo-Re, Mo-Ru, Nb-Re and Nb-Ru which show that the ? and Laves phases become more and more stable compared to A15, ? and ? as the size factor increases from Mo-Re through to Nb-Ru.

SonoNet: Real-Time Detection and Localisation of Fetal Standard Scan Planes in Freehand Ultrasound.

PubMed

Baumgartner, Christian F; Kamnitsas, Konstantinos; Matthew, Jacqueline; Fletcher, Tara P; Smith, Sandra; Koch, Lisa M; Kainz, Bernhard; Rueckert, Daniel

2017-11-01

Identifying and interpreting fetal standard scan planes during 2-D ultrasound mid-pregnancy examinations are highly complex tasks, which require years of training. Apart from guiding the probe to the correct location, it can be equally difficult for a non-expert to identify relevant structures within the image. Automatic image processing can provide tools to help experienced as well as inexperienced operators with these tasks. In this paper, we propose a novel method based on convolutional neural networks, which can automatically detect 13 fetal standard views in freehand 2-D ultrasound data as well as provide a localization of the fetal structures via a bounding box. An important contribution is that the network learns to localize the target anatomy using weak supervision based on image-level labels only. The network architecture is designed to operate in real-time while providing optimal output for the localization task. We present results for real-time annotation, retrospective frame retrieval from saved videos, and localization on a very large and challenging dataset consisting of images and video recordings of full clinical anomaly screenings. We found that the proposed method achieved an average F1-score of 0.798 in a realistic classification experiment modeling real-time detection, and obtained a 90.09% accuracy for retrospective frame retrieval. Moreover, an accuracy of 77.8% was achieved on the localization task.

Understanding the challenges of service change – learning from acute pain services in the UK

PubMed Central

Powell, AE; Davies, HTO; Bannister, J; Macrae, WA

2009-01-01

Summary Objectives To explore organizational difficulties faced when implementing national policy recommendations in local contexts. Design Qualitative case study involving semi-structured interviews with health professionals and managers working in and around acute pain services. Setting Three UK acute hospital organizations. Main outcome measures Identification of the content, context and process factors impacting on the implementation of the national policy recommendations on acute pain services; insights into and deeper understanding of the generic obstacles to change facing service improvements. Results The process of implementing policy recommendations and improving services in each of the three organizations was undermined by multiple factors relating to: doubts and disagreements about the nature of the change; challenging local organizational contexts; and the beliefs, attitudes and responses of health professionals and managers. The impact of these factors was compounded by the interaction between them. Conclusions Local implementation of national policies aimed at service improvement can be undermined by multiple interacting factors. Particularly important are the pre-existing local organizational contexts and histories, and the deeply-ingrained attitudes, beliefs and assumptions of diverse staff groups. Without close attention to all of these underlying issues and how they interact in individual organizations against the background of local and national contexts, more resources or further structural change are unlikely to deliver the intended improvements in patient care. PMID:19208870

Structure Determination of Mycobacterium tuberculosis Serine Protease Hip1 (Rv2224c)

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

Naffin-Olivos, Jacqueline L.; Daab, Andrew; White, Andre

The Mycobacterium tuberculosis (Mtb) serine protease Hip1 (hydrolase important for pathogenesis; Rv2224c) promotes tuberculosis (TB) pathogenesis by impairing host immune responses through proteolysis of a protein substrate, Mtb GroEL2. The cell surface localization of Hip1 and its immunomodulatory functions make Hip1 a good drug target for new adjunctive immune therapies for TB. Here, we report the crystal structure of Hip1 to a resolution of 2.6 Å and the kinetic studies of the enzyme against model substrates and the protein GroEL2. The structure shows a two-domain protein, one of which contains the catalytic residues that are the signature of a serinemore » protease. Surprisingly, a threonine is located within the active site close enough to hydrogen bond with the catalytic residues Asp463 and His490. Mutation of this residue, Thr466, to alanine established its importance for function. Our studies provide insights into the structure of a member of a novel family of proteases. Knowledge of the Hip1 structure will aid in designing inhibitors that could block Hip1 activity« less

Structure Determination of Mycobacterium tuberculosis Serine Protease Hip1 (Rv2224c).

PubMed

Naffin-Olivos, Jacqueline L; Daab, Andrew; White, Andre; Goldfarb, Nathan E; Milne, Amy C; Liu, Dali; Baikovitz, Jacqueline; Dunn, Ben M; Rengarajan, Jyothi; Petsko, Gregory A; Ringe, Dagmar

2017-05-02

The Mycobacterium tuberculosis (Mtb) serine protease Hip1 (hydrolase important for pathogenesis; Rv2224c) promotes tuberculosis (TB) pathogenesis by impairing host immune responses through proteolysis of a protein substrate, Mtb GroEL2. The cell surface localization of Hip1 and its immunomodulatory functions make Hip1 a good drug target for new adjunctive immune therapies for TB. Here, we report the crystal structure of Hip1 to a resolution of 2.6 Å and the kinetic studies of the enzyme against model substrates and the protein GroEL2. The structure shows a two-domain protein, one of which contains the catalytic residues that are the signature of a serine protease. Surprisingly, a threonine is located within the active site close enough to hydrogen bond with the catalytic residues Asp463 and His490. Mutation of this residue, Thr466, to alanine established its importance for function. Our studies provide insights into the structure of a member of a novel family of proteases. Knowledge of the Hip1 structure will aid in designing inhibitors that could block Hip1 activity.

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.

Wait time management strategies for scheduled care: what makes them succeed?

PubMed

Pomey, Marie-Pascale; Forest, Pierre-Gerlier; Sanmartin, Claudia; De Coster, Carolyn; Drew, Madeleine

2010-02-01

To assess experts' perceptions of the contextual and local factors that promote or inhibit the implementation of waiting time management strategies (WTMS) in Canadian healthcare organizations. We conducted 16 semi-structured interviews and one focus group with individuals involved in WTMS at the federal, provincial or organizational level. The most frequently cited local factor was physicians' participation. Physicians' leadership made the greatest difference in bringing resistant physicians on board. To be effective, however, local leadership had to be supported by senior management. Alignment of financial incentives between the contextual and local levels was also frequently cited, and interviewees stressed the importance of tools used to design, monitor, evaluate and prioritize WTMS. Finding the right balance between supportive resources and tools and an effective management system is a tough challenge. But achieving this balance will help reconcile contradictions between top-down and bottom-up WTMS.

Wait Time Management Strategies for Scheduled Care: What Makes Them Succeed?

PubMed Central

Pomey, Marie-Pascale; Forest, Pierre-Gerlier; Sanmartin, Claudia; De Coster, Carolyn; Drew, Madeleine

2010-01-01

Objectives: To assess experts' perceptions of the contextual and local factors that promote or inhibit the implementation of waiting time management strategies (WTMS) in Canadian healthcare organizations. Methods: We conducted 16 semi-structured interviews and one focus group with individuals involved in WTMS at the federal, provincial or organizational level. Results: The most frequently cited local factor was physicians' participation. Physicians' leadership made the greatest difference in bringing resistant physicians on board. To be effective, however, local leadership had to be supported by senior management. Alignment of financial incentives between the contextual and local levels was also frequently cited, and interviewees stressed the importance of tools used to design, monitor, evaluate and prioritize WTMS. Conclusions: Finding the right balance between supportive resources and tools and an effective management system is a tough challenge. But achieving this balance will help reconcile contradictions between top-down and bottom-up WTMS. PMID:21286269

Global Anisotropies in TeV Cosmic Rays Related to the Sun's Local Galactic Environment from IBEX

NASA Technical Reports Server (NTRS)

Schwadron, N. A.; Adams, F. C.; Christian, E. R.; Desiati, P.; Frisch, P.; Funsten, H. O.; Jokipii, J. R.; McComas, D. J.; Moebius, E.; Zank, G. P.

2014-01-01

Observations with the Interstellar Boundary Explorer (IBEX) have shown enhanced energetic neutral atom (ENA) emission from a narrow, circular ribbon likely centered on the direction of the local interstellar medium (LISM) magnetic field. Here, we show that recent determinations of the local interstellar velocity, based on interstellar atom measurements with IBEX, are consistent with the interstellar modulation of high-energy (tera-electron volts, TeV) cosmic rays and diffusive propagation from supernova sources revealed in global anisotropy maps of ground-based high-energy cosmic-ray observatories (Milagro, Asg, and IceCube). Establishing a consistent local interstellar magnetic field direction using IBEX ENAs at hundreds to thousands of eV and galactic cosmic rays at tens of TeV has wide-ranging implications for the structure of our heliosphere and its interactions with the LISM, which is particularly important at the time when the Voyager spacecraft are leaving our heliosphere.

Global anisotropies in TeV cosmic rays related to the Sun's local galactic environment from IBEX.

PubMed

Schwadron, N A; Adams, F C; Christian, E R; Desiati, P; Frisch, P; Funsten, H O; Jokipii, J R; McComas, D J; Moebius, E; Zank, G P

2014-02-28

Observations with the Interstellar Boundary Explorer (IBEX) have shown enhanced energetic neutral atom (ENA) emission from a narrow, circular ribbon likely centered on the direction of the local interstellar medium (LISM) magnetic field. Here, we show that recent determinations of the local interstellar velocity, based on interstellar atom measurements with IBEX, are consistent with the interstellar modulation of high-energy (tera-electron volts, TeV) cosmic rays and diffusive propagation from supernova sources revealed in global anisotropy maps of ground-based high-energy cosmic-ray observatories (Milagro, Asγ, and IceCube). Establishing a consistent local interstellar magnetic field direction using IBEX ENAs at hundreds to thousands of eV and galactic cosmic rays at tens of TeV has wide-ranging implications for the structure of our heliosphere and its interactions with the LISM, which is particularly important at the time when the Voyager spacecraft are leaving our heliosphere.

Analysing taxonomic structures and local ecological processes in temperate forests in North Eastern China.

PubMed

Fan, Chunyu; Tan, Lingzhao; Zhang, Chunyu; Zhao, Xiuhai; von Gadow, Klaus

2017-10-30

One of the core issues of forest community ecology is the exploration of how ecological processes affect community structure. The relative importance of different processes is still under debate. This study addresses four questions: (1) how is the taxonomic structure of a forest community affected by spatial scale? (2) does the taxonomic structure reveal effects of local processes such as environmental filtering, dispersal limitation or interspecific competition at a local scale? (3) does the effect of local processes on the taxonomic structure vary with the spatial scale? (4) does the analysis based on taxonomic structures provide similar insights when compared with the use of phylogenetic information? Based on the data collected in two large forest observational field studies, the taxonomic structures of the plant communities were analyzed at different sampling scales using taxonomic ratios (number of genera/number of species, number of families/number of species), and the relationship between the number of higher taxa and the number of species. Two random null models were used and the "standardized effect size" (SES) of taxonomic ratios was calculated, to assess possible differences between the observed and simulated taxonomic structures, which may be caused by specific ecological processes. We further applied a phylogeny-based method to compare results with those of the taxonomic approach. As expected, the taxonomic ratios decline with increasing grain size. The quantitative relationship between genera/families and species, described by a linearized power function, showed a good fit. With the exception of the family-species relationship in the Jiaohe study area, the exponents of the genus/family-species relationships did not show any scale dependent effects. The taxonomic ratios of the observed communities had significantly lower values than those of the simulated random community under the test of two null models at almost all scales. Null Model 2 which considered the spatial dispersion of species generated a taxonomic structure which proved to be more consistent with that in the observed community. As sampling sizes increased from 20 m × 20 m to 50 m × 50 m, the magnitudes of SESs of taxonomic ratios increased. Based on the phylogenetic analysis, we found that the Jiaohe plot was phylogenetically clustered at almost all scales. We detected significant phylogenetically overdispersion at the 20 m × 20 m and 30 m × 30 m scales in the Liangshui plot. The results suggest that the effect of abiotic filtering is greater than the effects of interspecific competition in shaping the local community at almost all scales. Local processes influence the taxonomic structures, but their combined effects vary with the spatial scale. The taxonomic approach provides similar insights as the phylogenetic approach, especially when we applied a more conservative null model. Analysing taxonomic structure may be a useful tool for communities where well-resolved phylogenetic data are not available.

Soil nutrients influence spatial distributions of tropical tree species.

PubMed

John, Robert; Dalling, James W; Harms, Kyle E; Yavitt, Joseph B; Stallard, Robert F; Mirabello, Matthew; Hubbell, Stephen P; Valencia, Renato; Navarrete, Hugo; Vallejo, Martha; Foster, Robin B

2007-01-16

The importance of niche vs. neutral assembly mechanisms in structuring tropical tree communities remains an important unsettled question in community ecology [Bell G (2005) Ecology 86:1757-1770]. There is ample evidence that species distributions are determined by soils and habitat factors at landscape (<10(4) km(2)) and regional scales. At local scales (<1 km(2)), however, habitat factors and species distributions show comparable spatial aggregation, making it difficult to disentangle the importance of niche and dispersal processes. In this article, we test soil resource-based niche assembly at a local scale, using species and soil nutrient distributions obtained at high spatial resolution in three diverse neotropical forest plots in Colombia (La Planada), Ecuador (Yasuni), and Panama (Barro Colorado Island). Using spatial distribution maps of >0.5 million individual trees of 1,400 species and 10 essential plant nutrients, we used Monte Carlo simulations of species distributions to test plant-soil associations against null expectations based on dispersal assembly. We found that the spatial distributions of 36-51% of tree species at these sites show strong associations to soil nutrient distributions. Neutral dispersal assembly cannot account for these plant-soil associations or the observed niche breadths of these species. These results indicate that belowground resource availability plays an important role in the assembly of tropical tree communities at local scales and provide the basis for future investigations on the mechanisms of resource competition among tropical tree species.

Localization microscopy of DNA in situ using Vybrant{sup ®} DyeCycle™ Violet fluorescent probe: A new approach to study nuclear nanostructure at single molecule resolution

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

Żurek-Biesiada, Dominika; Szczurek, Aleksander T.; Prakash, Kirti

Higher order chromatin structure is not only required to compact and spatially arrange long chromatids within a nucleus, but have also important functional roles, including control of gene expression and DNA processing. However, studies of chromatin nanostructures cannot be performed using conventional widefield and confocal microscopy because of the limited optical resolution. Various methods of superresolution microscopy have been described to overcome this difficulty, like structured illumination and single molecule localization microscopy. We report here that the standard DNA dye Vybrant{sup ®} DyeCycle™ Violet can be used to provide single molecule localization microscopy (SMLM) images of DNA in nuclei ofmore » fixed mammalian cells. This SMLM method enabled optical isolation and localization of large numbers of DNA-bound molecules, usually in excess of 10{sup 6} signals in one cell nucleus. The technique yielded high-quality images of nuclear DNA density, revealing subdiffraction chromatin structures of the size in the order of 100 nm; the interchromatin compartment was visualized at unprecedented optical resolution. The approach offers several advantages over previously described high resolution DNA imaging methods, including high specificity, an ability to record images using a single wavelength excitation, and a higher density of single molecule signals than reported in previous SMLM studies. The method is compatible with DNA/multicolor SMLM imaging which employs simple staining methods suited also for conventional optical microscopy. - Highlights: • Super-resolution imaging of nuclear DNA with Vybrant Violet and blue excitation. • 90nm resolution images of DNA structures in optically thick eukaryotic nuclei. • Enhanced resolution confirms the existence of DNA-free regions inside the nucleus. • Optimized imaging conditions enable multicolor super-resolution imaging.« less

Atomic-level structural correlations across the morphotropic phase boundary of a ferroelectric solid solution: xBiMg 1/2Ti 1/2O 3-(1$-$x)PbTiO 3

DOE PAGES

Datta, Kaustuv; Neder, Reinhard B.; Chen, Jun; ...

2017-03-28

Revelation of unequivocal structural information at the atomic level for complex systems is uniquely important for deeper and generic understanding of the structure property connections and a key challenge in materials science. Here in this paper we report an experimental study of the local structure by applying total elastic scattering and Raman scattering analyses to an important non-relaxor ferroelectric solid solution exhibiting the so-called composition-induced morphotropic phase boundary (MPB), where concomitant enhancement of physical properties have been detected. The powerful combination of static and dynamic structural probes enabled us to derive direct correspondence between the atomic-level structural correlations and reportedmore » properties. The atomic pair distribution functions obtained from the neutron total scattering experiments were analysed through big-box atom-modelling implementing reverse Monte Carlo method, from which distributions of magnitudes and directions of off-centred cationic displacements were extracted. We found that an enhanced randomness of the displacement-directions for all ferroelectrically active cations combined with a strong dynamical coupling between the A- and B-site cations of the perovskite structure, can explain the abrupt amplification of piezoelectric response of the system near MPB. Finally, altogether this provides a more fundamental basis in inferring structure-property connections in similar systems including important implications in designing novel and bespoke materials.« less

An Assessment of the State-of-the-Art in Multidisciplinary Aeromechanical Analyses

DTIC Science & Technology

2008-01-01

monolithic formulations. In summary, for aerospace structures, partitioned formulations provide fundamental advantages over fully coupled ones, in addition...important frequencies of local analysis directly to global analysis using detailed modeling. Performed ju- diciously, based on a fundamental understanding of...in 2000 has com- prehensively described the problem, and reviewed the status of fundamental understanding, experimental data, and analytical

Positron annihilation in perovskite superconductors; Theory and experiment

NASA Astrophysics Data System (ADS)

Turchi, P. E. A.; Wachs, A. L.; Jean, Y. C.; Howell, R. H.; Wetzler, K. H.; Fluss, M. J.

1988-06-01

Positron Annihilation Spectroscopy is shown to be of potential value for probing the electronic structure and the changes accompanying the superconducting transition of the new high T c materials. The experimental results of electron-positron momentum distribution for La 2CuO 4 agree with a ligand field approach, suggesting a strong electron localization and the importance of the covalency.

Politics and Education Policy into Practice: Conversations with Former Secretaries of State

ERIC Educational Resources Information Center

Abbott, Ian

2015-01-01

Set against a period of rapid change, education has grown in political importance and policy development has moved from the local authority to central government with a key role being played by the Secretary of State. Based on a series of semi-structured interviews, with 10 politicians who have served as Secretary of State for Education, this…

Study of the effect of short ranged ordering on the magnetism in FeCr alloys

NASA Astrophysics Data System (ADS)

Jena, Ambika Prasad; Sanyal, Biplab; Mookerjee, Abhijit

2014-01-01

For the study of magnetism in systems where the local environment plays an important role, we propose a marriage between the Monte Carlo simulation and Zunger's special quasi-random structures. We apply this technique on disordered FeCr alloys and show that our estimates of the transition temperature is in good agreement with earlier experiments.

Development and mechanical properties of structural materials from lunar simulant

NASA Technical Reports Server (NTRS)

Desai, Chandra S.

1991-01-01

Development of versatile engineering materials from locally available materials in space is an important step toward establishment of outposts such as on the moon and Mars. Here development of the technologies for manufacture of structural and construction materials on the moon, utilizing local lunar soil (regolith), without the use of water, is an important element for habitats and explorations in space. It is also vital that the mechanical behavior such as strength and flexural properties, fracture toughness, ductility, and deformation characteristics are defined toward establishment of the ranges of engineering applications of the materials developed. The objectives include two areas: (1) thermal liquefaction of lunar simulant (at about 1100 C) with different additives (fibers, powders, etc.); and (2) development and use of a traxial test device in which lunar simulants are first compacted under cycles of loading, and then tested with different vacuums and initial confining or insitu stress. The second area was described in previous progress reports and publications; since the presently available device allows vacuum levels up to only 10(exp -4) torr, it is recommended that a vacuum pump that can allow higher levels of vacuum is acquired.

Immunogold scanning electron microscopy can reveal the polysaccharide architecture of xylem cell walls

PubMed Central

Sun, Yuliang; Juzenas, Kevin

2017-01-01

Abstract Immunofluorescence microscopy (IFM) and immunogold transmission electron microscopy (TEM) are the two main techniques commonly used to detect polysaccharides in plant cell walls. Both are important in localizing cell wall polysaccharides, but both have major limitations, such as low resolution in IFM and restricted sample size for immunogold TEM. In this study, we have developed a robust technique that combines immunocytochemistry with scanning electron microscopy (SEM) to study cell wall polysaccharide architecture in xylem cells at high resolution over large areas of sample. Using multiple cell wall monoclonal antibodies (mAbs), this immunogold SEM technique reliably localized groups of hemicellulosic and pectic polysaccharides in the cell walls of five different xylem structures (vessel elements, fibers, axial and ray parenchyma cells, and tyloses). This demonstrates its important advantages over the other two methods for studying cell wall polysaccharide composition and distribution in these structures. In addition, it can show the three-dimensional distribution of a polysaccharide group in the vessel lateral wall and the polysaccharide components in the cell wall of developing tyloses. This technique, therefore, should be valuable for understanding the cell wall polysaccharide composition, architecture and functions of diverse cell types. PMID:28398585

Nak regulates localization of clathrin sites in higher-order dendrites to promote local dendrite growth.

PubMed

Yang, Wei-Kang; Peng, Yu-Huei; Li, Hsun; Lin, Hsiu-Chen; Lin, Yu-Ching; Lai, Tzu-Ting; Suo, Hsien; Wang, Chien-Hsiang; Lin, Wei-Hsiang; Ou, Chan-Yen; Zhou, Xin; Pi, Haiwei; Chang, Henry C; Chien, Cheng-Ting

2011-10-20

During development, dendrites arborize in a field several hundred folds of their soma size, a process regulated by intrinsic transcription program and cell adhesion molecule (CAM)-mediated interaction. However, underlying cellular machineries that govern distal higher-order dendrite extension remain largely unknown. Here, we show that Nak, a clathrin adaptor-associated kinase, promotes higher-order dendrite growth through endocytosis. In nak mutants, both the number and length of higher-order dendrites are reduced, which are phenocopied by disruptions of clathrin-mediated endocytosis. Nak interacts genetically with components of the endocytic pathway, colocalizes with clathrin puncta, and is required for dendritic localization of clathrin puncta. More importantly, these Nak-containing clathrin structures preferentially localize to branching points and dendritic tips that are undergoing active growth. We present evidence that the Drosophila L1-CAM homolog Neuroglian is a relevant cargo of Nak-dependent internalization, suggesting that localized clathrin-mediated endocytosis of CAMs facilitates the extension of nearby higher-order dendrites. Copyright © 2011 Elsevier Inc. All rights reserved.

Study on Finite Element Model Updating in Highway Bridge Static Loading Test Using Spatially-Distributed Optical Fiber Sensors

PubMed Central

Wu, Bitao; Lu, Huaxi; Chen, Bo; Gao, Zhicheng

2017-01-01

A finite model updating method that combines dynamic-static long-gauge strain responses is proposed for highway bridge static loading tests. For this method, the objective function consisting of static long-gauge stains and the first order modal macro-strain parameter (frequency) is established, wherein the local bending stiffness, density and boundary conditions of the structures are selected as the design variables. The relationship between the macro-strain and local element stiffness was studied first. It is revealed that the macro-strain is inversely proportional to the local stiffness covered by the long-gauge strain sensor. This corresponding relation is important for the modification of the local stiffness based on the macro-strain. The local and global parameters can be simultaneously updated. Then, a series of numerical simulation and experiments were conducted to verify the effectiveness of the proposed method. The results show that the static deformation, macro-strain and macro-strain modal can be predicted well by using the proposed updating model. PMID:28753912

Study on Finite Element Model Updating in Highway Bridge Static Loading Test Using Spatially-Distributed Optical Fiber Sensors.

PubMed

Wu, Bitao; Lu, Huaxi; Chen, Bo; Gao, Zhicheng

2017-07-19

A finite model updating method that combines dynamic-static long-gauge strain responses is proposed for highway bridge static loading tests. For this method, the objective function consisting of static long-gauge stains and the first order modal macro-strain parameter (frequency) is established, wherein the local bending stiffness, density and boundary conditions of the structures are selected as the design variables. The relationship between the macro-strain and local element stiffness was studied first. It is revealed that the macro-strain is inversely proportional to the local stiffness covered by the long-gauge strain sensor. This corresponding relation is important for the modification of the local stiffness based on the macro-strain. The local and global parameters can be simultaneously updated. Then, a series of numerical simulation and experiments were conducted to verify the effectiveness of the proposed method. The results show that the static deformation, macro-strain and macro-strain modal can be predicted well by using the proposed updating model.

Mechanisms of dendritic mRNA transport and its role in synaptic tagging

PubMed Central

Doyle, Michael; Kiebler, Michael A

2011-01-01

The localization of RNAs critically contributes to many important cellular processes in an organism, such as the establishment of polarity, asymmetric division and migration during development. Moreover, in the central nervous system, the local translation of mRNAs is thought to induce plastic changes that occur at synapses triggered by learning and memory. Here, we will critically review the physiological functions of well-established dendritically localized mRNAs and their associated factors, which together form ribonucleoprotein particles (RNPs). Second, we will discuss the life of a localized transcript from transcription in the nucleus to translation at the synapse and introduce the concept of the ‘RNA signature' that is characteristic for each transcript. Finally, we present the ‘sushi belt model' of how localized RNAs within neuronal RNPs may dynamically patrol multiple synapses rather than being anchored at a single synapse. This new model integrates our current understanding of synaptic function ranging from synaptic tagging and capture to functional and structural reorganization of the synapse upon learning and memory. PMID:21878995

Characteristics of Extreme Geoelectric Fields and Their Possible Causes: Localized Peak Enhancements

NASA Astrophysics Data System (ADS)

Pulkkinen, A. A.; Ngwira, C. M.; Bernabeu, E.; Eichner, J.; Viljanen, A.; Crowley, G.

2015-12-01

One of the major challenges pertaining to extreme geomagnetic storms is to understand the basic processes associated with the development of dynamic magnetosphere-ionosphere currents, which generate large induced surface geoelectric fields. Previous studies point out the existence of localized peak geoelectric field enhancements during extreme storms. We examined induced global geoelectric fields derived from ground-based magnetometer recordings for 12 extreme geomagnetic storms between the years 1982--2005. However for the present study, an in-depth analysis was performed for two important extreme storms, October 29, 2003 and March 13, 1989. The primary purpose of this paper is to provide further evidence on the existence of localized peak geoelectric field enhancements, and to show that the structure of the geoelectric field during these localized extremes at single sites can differ greatly from globally and regionally averaged fields. Although the physical processes that govern the development of these localized extremes are still not clear, we discuss some possible causes.

A fingerprint classification algorithm based on combination of local and global information

NASA Astrophysics Data System (ADS)

Liu, Chongjin; Fu, Xiang; Bian, Junjie; Feng, Jufu

2011-12-01

Fingerprint recognition is one of the most important technologies in biometric identification and has been wildly applied in commercial and forensic areas. Fingerprint classification, as the fundamental procedure in fingerprint recognition, can sharply decrease the quantity for fingerprint matching and improve the efficiency of fingerprint recognition. Most fingerprint classification algorithms are based on the number and position of singular points. Because the singular points detecting method only considers the local information commonly, the classification algorithms are sensitive to noise. In this paper, we propose a novel fingerprint classification algorithm combining the local and global information of fingerprint. Firstly we use local information to detect singular points and measure their quality considering orientation structure and image texture in adjacent areas. Furthermore the global orientation model is adopted to measure the reliability of singular points group. Finally the local quality and global reliability is weighted to classify fingerprint. Experiments demonstrate the accuracy and effectivity of our algorithm especially for the poor quality fingerprint images.

Evaluating the quality of NMR structures by local density of protons.

PubMed

Ban, Yih-En Andrew; Rudolph, Johannes; Zhou, Pei; Edelsbrunner, Herbert

2006-03-01

Evaluating the quality of experimentally determined protein structural models is an essential step toward identifying potential errors and guiding further structural refinement. Herein, we report the use of proton local density as a sensitive measure to assess the quality of nuclear magnetic resonance (NMR) structures. Using 256 high-resolution crystal structures with protons added and optimized, we show that the local density of different proton types display distinct distributions. These distributions can be characterized by statistical moments and are used to establish local density Z-scores for evaluating both global and local packing for individual protons. Analysis of 546 crystal structures at various resolutions shows that the local density Z-scores increase as the structural resolution decreases and correlate well with the ClashScore (Word et al. J Mol Biol 1999;285(4):1711-1733) generated by all atom contact analysis. Local density Z-scores for NMR structures exhibit a significantly wider range of values than for X-ray structures and demonstrate a combination of potentially problematic inflation and compression. Water-refined NMR structures show improved packing quality. Our analysis of a high-quality structural ensemble of ubiquitin refined against order parameters shows proton density distributions that correlate nearly perfectly with our standards derived from crystal structures, further validating our approach. We present an automated analysis and visualization tool for proton packing to evaluate the quality of NMR structures. 2005 Wiley-Liss, Inc.

Non-localized trapping effects in AlGaN/GaN heterojunction field-effect transistors subjected to on-state bias stress

NASA Astrophysics Data System (ADS)

Hu, Cheng-Yu; Hashizume, Tamotsu

2012-04-01

For AlGaN/GaN heterojunction field-effect transistors, on-state-bias-stress (on-stress)-induced trapping effects were observed across the entire drain access region, not only at the gate edge. However, during the application of on-stress, the highest electric field was only localized at the drain side of the gate edge. Using the location of the highest electric field as a reference, the trapping effects at the gate edge and at the more distant access region were referred to as localized and non-localized trapping effect, respectively. Using two-dimensional-electron-gas sensing-bar (2DEG-sensing-bar) and dual-gate structures, the non-localized trapping effects were investigated and the trap density was measured to be ˜1.3 × 1012 cm-2. The effect of passivation was also discussed. It was found that both surface leakage currents and hot electrons are responsible for the non-localized trapping effects with hot electrons having the dominant effect. Since hot electrons are generated from the 2DEG channel, it is highly likely that the involved traps are mainly in the GaN buffer layer. Using monochromatic irradiation (1.24-2.81 eV), the trap levels responsible for the non-localized trapping effects were found to be located at 0.6-1.6 eV from the valence band of GaN. Both trap-assisted impact ionization and direct channel electron injection are proposed as the possible mechanisms of the hot-electron-related non-localized trapping effect. Finally, using the 2DEG-sensing-bar structure, we directly confirmed that blocking gate injected electrons is an important mechanism of Al2O3 passivation.

Subcellular Localization of Arabidopsis 3-Hydroxy-3-Methylglutaryl-Coenzyme A Reductase1

PubMed Central

Leivar, Pablo; González, Víctor M.; Castel, Susanna; Trelease, Richard N.; López-Iglesias, Carmen; Arró, Montserrat; Boronat, Albert; Campos, Narciso; Ferrer, Albert; Fernàndez-Busquets, Xavier

2005-01-01

Plants produce diverse isoprenoids, which are synthesized in plastids, mitochondria, endoplasmic reticulum (ER), and the nonorganellar cytoplasm. 3-Hydroxy-3-methylglutaryl-coenzyme A reductase (HMGR) catalyzes the synthesis of mevalonate, a rate-limiting step in the cytoplasmic pathway. Several branches of the pathway lead to the synthesis of structurally and functionally varied, yet essential, isoprenoids. Several HMGR isoforms have been identified in all plants examined. Studies based on gene expression and on fractionation of enzyme activity suggested that subcellular compartmentalization of HMGR is an important intracellular channeling mechanism for the production of the specific classes of isoprenoids. Plant HMGR has been shown previously to insert in vitro into the membrane of microsomal vesicles, but the final in vivo subcellular localization(s) remains controversial. To address the latter in Arabidopsis (Arabidopsis thaliana) cells, we conducted a multipronged microscopy and cell fractionation approach that included imaging of chimeric HMGR green fluorescent protein localizations in transiently transformed cell leaves, immunofluorescence confocal microscopy in wild-type and stably transformed seedlings, immunogold electron microscopy examinations of endogenous HMGR in seedling cotyledons, and sucrose density gradient analyses of HMGR-containing organelles. Taken together, the results reveal that endogenous Arabidopsis HMGR is localized at steady state within ER as expected, but surprisingly also predominantly within spherical, vesicular structures that range from 0.2- to 0.6-μm diameter, located in the cytoplasm and within the central vacuole in differentiated cotyledon cells. The N-terminal region, including the transmembrane domain of HMGR, was found to be necessary and sufficient for directing HMGR to ER and the spherical structures. It is believed, although not directly demonstrated, that these vesicle-like structures are derived from segments of HMGR-ER. Nevertheless, they represent a previously undescribed subcellular compartment likely capable of synthesizing mevalonate, which provides new evidence for multiorganelle compartmentalization of the isoprenoid biosynthetic pathways in plants. PMID:15618432

Studying local earthquakes in the area Baltic-Bothnia Megashear using the data of the POLENET/LAPNET temporary array

NASA Astrophysics Data System (ADS)

Usoltseva, Olga; Kozlovskaya, Elena

2016-07-01

Earthquakes in areas within continental plates are still not completely understood, and progress on understanding intraplate seismicity is slow due to a short history of instrumental seismology and sparse regional seismic networks in seismically non-active areas. However, knowledge about position and depth of seismogenic structures in such areas is necessary in order to estimate seismic hazard for such critical facilities such as nuclear power plants and nuclear waste deposits. In the present paper we address the problem of seismicity in the intraplate area of northern Fennoscandia using the information on local events recorded by the POLENET/LAPNET (Polar Earth Observing Network) temporary seismic array during the International Polar Year 2007-2009. We relocate the seismic events using the program HYPOELLIPS (a computer program for determining local earthquake hypocentral parameters) and grid search method. We use the first arrivals of P waves of local events in order to calculate a 3-D tomographic P wave velocity model of the uppermost crust (down to 20 km) for a selected region inside the study area and show that the velocity heterogeneities in the upper crust correlate well with known tectonic units. We compare the position of the velocity heterogeneities with the seismogenic structures delineated by epicentres of relocated events and demonstrate that these structures generally do not correlate with the crustal units formed as a result of crustal evolution in the Archaean and Palaeoproterozoic. On the contrary, they correlate well with the postglacial faults located in the area of the Baltic-Bothnia Megashear (BBMS). Hypocentres of local events have depths down to 30 km. We also obtain the focal mechanism of a selected event with good data quality. The focal mechanism is of oblique type with strike-slip prevailing. Our results demonstrate that the Baltic-Bothnia Megashear is an important large-scale, reactivated tectonic structure that has to be taken into account when estimating seismic hazard in northern Fennoscandia.

Ethnobotanical and economic value of Ravenala madagascariensis Sonn. in Eastern Madagascar.

PubMed

Rakotoarivelo, Nivo; Razanatsima, Aina; Rakotoarivony, Fortunat; Rasoaviety, Lucien; Ramarosandratana, Aro Vonjy; Jeannoda, Vololoniaina; Kuhlman, Alyse R; Randrianasolo, Armand; Bussmann, Rainer W

2014-07-15

Known worldwide as the "traveler's tree", the Malagasy endemic species Ravenala madagascariensis Sonn. (Strelitziaceae) is considered as an iconic symbol of Madagascar. It is a widespread species in the eastern part of the country with four different varieties which are well represented in Ambalabe community. All of them are used for different purposes and the species represents an important cultural value in the lives of the local population. However, uses of Ravenala are only generally well known by local population. Thus, in this study, we report on the different uses of Ravenala and its importance to the Ambalabe local people. Semi-structured interviews among 116 people, 59 men and 57 women with ages ranging from 17 to 84 years old, free listing and market surveys were conducted in order to collect the vernacular names, the uses of Ravenala madagascariensis and the price of plant parts sold in local market. Then, the uses were categorized according to Cámara-Leret et al. classification. Different parts of the plant are currently used by local population, which are grouped as heart, trunk, leaves, petioles and rachis. Seven categories of use were recorded, most cited include: human food, utensils and tools, and house building. The most commonly used parts are trunk, heart, leaves and petioles for which the price varies between $3-15. Uses mentioned for construction (floor, roofs and wall), human food and utensils and tools are the most frequent and salient for local population. But the use of the plant as first materials for house building is revealed to be the most important for them. Ravenala madagascariensis is very important to the Ambalabe communities because for local population, it represents the Betsimisaraka cultural and traditional use of the plant for house building. Moreover, none of its parts are discarded. The harvest and sale of R. madagascariensis for building materials can also provide an additional source of income to the family. Besides, using Ravenala in house construction reduces the use of slow growing trees and contributes to the sustainable use of natural forest resources.

Trophic cascades in rocky shore tide pools: distinguishing lethal and nonlethal effects.

PubMed

Trussell, Geoffrey C; Ewanchuk, Patrick J; Bertness, Mark D; Silliman, Brian R

2004-05-01

The effects of predators on the density of their prey can have positive indirect effects on the abundance of the prey's resource via a trophic cascade. This concept has strongly influenced contemporary views of how communities are structured. However, predators also can transmit indirect effects by inducing changes in prey traits. We show that the mere presence of predator risk cues can initiate a trophic cascade in rocky shore tide pools. In large (mean surface area =9 m2), natural tide pools, we manipulated crab density and their foraging ability to examine the relative importance of lethal (density-mediated) and non-lethal (trait-mediated) predator effects to algal community development. We found that perceived predation risk reduced snail density as much as the direct predation treatment, showing that green crab predation was not an important factor regulating local snail density. Instead, snail emigration away from resident crabs appears to be the most important factor regulating local snail density. As a result, the abundance of ephemeral green algae was similar in the predation risk and direct predation treatments, suggesting that the consumption of snails by crabs plays a minimal role in mediating the trophic cascade. Increased attention to trait-mediated effects that are transmitted by predator-induced changes in prey behavior may change our view of how predators exert their strong influence on community structure.

Element speciation during nuclear glass alteration

NASA Astrophysics Data System (ADS)

Galoisy, L.; Calas, G.; Bergeron, B.; Jollivet, P.; Pelegrin, E.

2011-12-01

Assessing the long-term behavior of nuclear glasses implies the prediction of their long-term performance. An important controlling parameter is their evolution during interaction with water under conditions simulating geological repositories. After briefly recalling the major characteristics of the local and medium-range structure of borosilicate glasses of nuclear interest, we will present some structural features of this evolution. Specific structural tools used to determine the local structure of glass surfaces include synchrotron-radiation x-ray absorption spectroscopy with total electron yield detection. The evolution of the structure of glass surface has been determined at the Zr-, Fe-, Si- and Al-K edges and U-LIII edge. During alteration in near- or under-saturated conditions, some elements such as Fe change coordination, as other elements such as Zr only suffer structural modifications in under-saturated conditions. Uranium exhibits a modification of its speciation from an hexa-coordinated U(VI) in the borosilicate glass to an uranyl group in the gel. These structural modifications may explain the chemical dependence of the initial alteration rate and the transition to the residual regime. They also illustrate the molecular-scale origin of the processes at the origin of the glass-to-gel transformation. Eventually, they explain the provisional trapping of U by the alteration gel: the uranium retention factors in the gel depend on the alteration conditions, and thus on the nature of the resulting gel and on the trapping conditions.

The dual role of fragments in fragment-assembly methods for de novo protein structure prediction

PubMed Central

Handl, Julia; Knowles, Joshua; Vernon, Robert; Baker, David; Lovell, Simon C.

2013-01-01

In fragment-assembly techniques for protein structure prediction, models of protein structure are assembled from fragments of known protein structures. This process is typically guided by a knowledge-based energy function and uses a heuristic optimization method. The fragments play two important roles in this process: they define the set of structural parameters available, and they also assume the role of the main variation operators that are used by the optimiser. Previous analysis has typically focused on the first of these roles. In particular, the relationship between local amino acid sequence and local protein structure has been studied by a range of authors. The correlation between the two has been shown to vary with the window length considered, and the results of these analyses have informed directly the choice of fragment length in state-of-the-art prediction techniques. Here, we focus on the second role of fragments and aim to determine the effect of fragment length from an optimization perspective. We use theoretical analyses to reveal how the size and structure of the search space changes as a function of insertion length. Furthermore, empirical analyses are used to explore additional ways in which the size of the fragment insertion influences the search both in a simulation model and for the fragment-assembly technique, Rosetta. PMID:22095594

A simple extension to the CMASA method for the prediction of catalytic residues in the presence of single point mutations.

PubMed

Flores, David I; Sotelo-Mundo, Rogerio R; Brizuela, Carlos A

2014-01-01

The automatic identification of catalytic residues still remains an important challenge in structural bioinformatics. Sequence-based methods are good alternatives when the query shares a high percentage of identity with a well-annotated enzyme. However, when the homology is not apparent, which occurs with many structures from the structural genome initiative, structural information should be exploited. A local structural comparison is preferred to a global structural comparison when predicting functional residues. CMASA is a recently proposed method for predicting catalytic residues based on a local structure comparison. The method achieves high accuracy and a high value for the Matthews correlation coefficient. However, point substitutions or a lack of relevant data strongly affect the performance of the method. In the present study, we propose a simple extension to the CMASA method to overcome this difficulty. Extensive computational experiments are shown as proof of concept instances, as well as for a few real cases. The results show that the extension performs well when the catalytic site contains mutated residues or when some residues are missing. The proposed modification could correctly predict the catalytic residues of a mutant thymidylate synthase, 1EVF. It also successfully predicted the catalytic residues for 3HRC despite the lack of information for a relevant side chain atom in the PDB file.

Variation in the population structure of Yukon River chum and coho salmon: Evaluating the potential impact of localized habitat degradation

USGS Publications Warehouse

Olsen, J.B.; Spearman, William J.; Sage, G.K.; Miller, S.J.; Flannery, B.G.; Wenburg, J.K.

2004-01-01

We used microsatellite and mitochondrial DNA-restriction fragment length polymorphism (mtDNA-RFLP) analyses to test the hypothesis that chum salmon Oncorhynchus keta and coho salmon O. kisutch in the Yukon River, Alaska, exhibit population structure at differing spatial scales. If the hypothesis is true, then the risk of losing genetic diversity because of habitat degradation from a gold mine near a Yukon River tributary could differ between the two species. For each species, collections were made from two tributaries in both the Innoko and Tanana rivers, which are tributaries to the lower and middle Yukon River. The results revealed a large difference in the degree and spatial distribution of population structure between the two species. For chum salmon, the microsatellite loci (F-statistic [FST] = 0.021) and mtDNA (F ST = -0.008) revealed a low degree of interpopulation genetic diversity on a relatively large geographic scale. This large-scale population structure should minimize, although not eliminate, the risk of genetic diversity loss due to localized habitat degradation. For coho salmon, the microsatellites (FST = 0.091) and mtDNA (FST = 0.586) revealed a high degree of interpopulation genetic diversity on a relatively small geographic scale. This small-scale population structure suggests that coho salmon are at a relatively high risk of losing genetic diversity due to lo-calized habitat degradation. Our study underscores the importance of a multispecies approach for evaluating the potential impact of land-use activities on the genetic diversity of Pacific salmon.

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

PubMed

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

2013-01-01

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

Local pulmonary structure classification for computer-aided nodule detection

NASA Astrophysics Data System (ADS)

Bahlmann, Claus; Li, Xianlin; Okada, Kazunori

2006-03-01

We propose a new method of classifying the local structure types, such as nodules, vessels, and junctions, in thoracic CT scans. This classification is important in the context of computer aided detection (CAD) of lung nodules. The proposed method can be used as a post-process component of any lung CAD system. In such a scenario, the classification results provide an effective means of removing false positives caused by vessels and junctions thus improving overall performance. As main advantage, the proposed solution transforms the complex problem of classifying various 3D topological structures into much simpler 2D data clustering problem, to which more generic and flexible solutions are available in literature, and which is better suited for visualization. Given a nodule candidate, first, our solution robustly fits an anisotropic Gaussian to the data. The resulting Gaussian center and spread parameters are used to affine-normalize the data domain so as to warp the fitted anisotropic ellipsoid into a fixed-size isotropic sphere. We propose an automatic method to extract a 3D spherical manifold, containing the appropriate bounding surface of the target structure. Scale selection is performed by a data driven entropy minimization approach. The manifold is analyzed for high intensity clusters, corresponding to protruding structures. Techniques involve EMclustering with automatic mode number estimation, directional statistics, and hierarchical clustering with a modified Bhattacharyya distance. The estimated number of high intensity clusters explicitly determines the type of pulmonary structures: nodule (0), attached nodule (1), vessel (2), junction (>3). We show accurate classification results for selected examples in thoracic CT scans. This local procedure is more flexible and efficient than current state of the art and will help to improve the accuracy of general lung CAD systems.

How do glycerol and dimethyl sulphoxide affect local tetrahedral structure of water around a nonpolar solute at low temperature? Importance of preferential interaction.

PubMed

Daschakraborty, Snehasis

2018-04-07

Glycerol and dimethyl sulphoxide (DMSO) have vital roles in cryoprotection of living cells, tissues, etc. The above action has been directly linked with disruption of hydrogen (H-) bond structure and dynamics of water by these cosolvents at bulk region and around various complex units, such as peptide, amino acid, protein, and lipid membrane. However, the disruption of the local structure of the water solvent around a purely hydrophobic solute is still not studied extensively. The latter is also important in the context of stabilization of protein from cold denaturation. Through all-atom molecular dynamics simulation, we have investigated the comparative effect of glycerol and DMSO on the orientational order of water around a nonpolar solute at -5 °C. A steady reduction of the tetrahedral order of water is observed at bulk (>10 Å distance from the solute) and solute interface (<5.5 Å distance from the solute) with increasing the cosolvent concentration. Contrasting roles of glycerol and DMSO have been evidenced. While DMSO affects the H-bond structure of the interfacial water more than that of the bulk water, glycerol affects the water structure almost uniformly at all regions around the solute. Furthermore, while glycerol helps to retain water molecules at the interface, DMSO significantly reduces the water content in that region. We have put forward a plausible mechanism for these contrasting roles of these cosolvents. The solute-cosolvent hydrophobic-interaction-induced orientational alignment of an interfacial cosolvent molecule determines whether the involvement of the cosolvent molecules in H-bonding with solvent water in the interface is akin to the bulk region or not.

How do glycerol and dimethyl sulphoxide affect local tetrahedral structure of water around a nonpolar solute at low temperature? Importance of preferential interaction

NASA Astrophysics Data System (ADS)

Daschakraborty, Snehasis

2018-04-01

Glycerol and dimethyl sulphoxide (DMSO) have vital roles in cryoprotection of living cells, tissues, etc. The above action has been directly linked with disruption of hydrogen (H-) bond structure and dynamics of water by these cosolvents at bulk region and around various complex units, such as peptide, amino acid, protein, and lipid membrane. However, the disruption of the local structure of the water solvent around a purely hydrophobic solute is still not studied extensively. The latter is also important in the context of stabilization of protein from cold denaturation. Through all-atom molecular dynamics simulation, we have investigated the comparative effect of glycerol and DMSO on the orientational order of water around a nonpolar solute at -5 °C. A steady reduction of the tetrahedral order of water is observed at bulk (>10 Å distance from the solute) and solute interface (<5.5 Å distance from the solute) with increasing the cosolvent concentration. Contrasting roles of glycerol and DMSO have been evidenced. While DMSO affects the H-bond structure of the interfacial water more than that of the bulk water, glycerol affects the water structure almost uniformly at all regions around the solute. Furthermore, while glycerol helps to retain water molecules at the interface, DMSO significantly reduces the water content in that region. We have put forward a plausible mechanism for these contrasting roles of these cosolvents. The solute-cosolvent hydrophobic-interaction-induced orientational alignment of an interfacial cosolvent molecule determines whether the involvement of the cosolvent molecules in H-bonding with solvent water in the interface is akin to the bulk region or not.

Explaining local-scale species distributions: relative contributions of spatial autocorrelation and landscape heterogeneity for an avian assemblage

USGS Publications Warehouse

Mattsson, Brady J.; Zipkin, Elise F.; Gardner, Beth; Blank, Peter J.; Sauer, John R.; Royle, J. Andrew

2013-01-01

Understanding interactions between mobile species distributions and landcover characteristics remains an outstanding challenge in ecology. Multiple factors could explain species distributions including endogenous evolutionary traits leading to conspecific clustering and endogenous habitat features that support life history requirements. Birds are a useful taxon for examining hypotheses about the relative importance of these factors among species in a community. We developed a hierarchical Bayes approach to model the relationships between bird species occupancy and local landcover variables accounting for spatial autocorrelation, species similarities, and partial observability. We fit alternative occupancy models to detections of 90 bird species observed during repeat visits to 316 point-counts forming a 400-m grid throughout the Patuxent Wildlife Research Refuge in Maryland, USA. Models with landcover variables performed significantly better than our autologistic and null models, supporting the hypothesis that local landcover heterogeneity is important as an exogenous driver for species distributions. Conspecific clustering alone was a comparatively poor descriptor of local community composition, but there was evidence for spatial autocorrelation in all species. Considerable uncertainty remains whether landcover combined with spatial autocorrelation is most parsimonious for describing bird species distributions at a local scale. Spatial structuring may be weaker at intermediate scales within which dispersal is less frequent, information flows are localized, and landcover types become spatially diversified and therefore exhibit little aggregation. Examining such hypotheses across species assemblages contributes to our understanding of community-level associations with conspecifics and landscape composition.

Explaining local-scale species distributions: relative contributions of spatial autocorrelation and landscape heterogeneity for an avian assemblage.

PubMed

Mattsson, Brady J; Zipkin, Elise F; Gardner, Beth; Blank, Peter J; Sauer, John R; Royle, J Andrew

2013-01-01

Understanding interactions between mobile species distributions and landcover characteristics remains an outstanding challenge in ecology. Multiple factors could explain species distributions including endogenous evolutionary traits leading to conspecific clustering and endogenous habitat features that support life history requirements. Birds are a useful taxon for examining hypotheses about the relative importance of these factors among species in a community. We developed a hierarchical Bayes approach to model the relationships between bird species occupancy and local landcover variables accounting for spatial autocorrelation, species similarities, and partial observability. We fit alternative occupancy models to detections of 90 bird species observed during repeat visits to 316 point-counts forming a 400-m grid throughout the Patuxent Wildlife Research Refuge in Maryland, USA. Models with landcover variables performed significantly better than our autologistic and null models, supporting the hypothesis that local landcover heterogeneity is important as an exogenous driver for species distributions. Conspecific clustering alone was a comparatively poor descriptor of local community composition, but there was evidence for spatial autocorrelation in all species. Considerable uncertainty remains whether landcover combined with spatial autocorrelation is most parsimonious for describing bird species distributions at a local scale. Spatial structuring may be weaker at intermediate scales within which dispersal is less frequent, information flows are localized, and landcover types become spatially diversified and therefore exhibit little aggregation. Examining such hypotheses across species assemblages contributes to our understanding of community-level associations with conspecifics and landscape composition.

Explaining Local-Scale Species Distributions: Relative Contributions of Spatial Autocorrelation and Landscape Heterogeneity for an Avian Assemblage

PubMed Central

Mattsson, Brady J.; Zipkin, Elise F.; Gardner, Beth; Blank, Peter J.; Sauer, John R.; Royle, J. Andrew

2013-01-01

Understanding interactions between mobile species distributions and landcover characteristics remains an outstanding challenge in ecology. Multiple factors could explain species distributions including endogenous evolutionary traits leading to conspecific clustering and endogenous habitat features that support life history requirements. Birds are a useful taxon for examining hypotheses about the relative importance of these factors among species in a community. We developed a hierarchical Bayes approach to model the relationships between bird species occupancy and local landcover variables accounting for spatial autocorrelation, species similarities, and partial observability. We fit alternative occupancy models to detections of 90 bird species observed during repeat visits to 316 point-counts forming a 400-m grid throughout the Patuxent Wildlife Research Refuge in Maryland, USA. Models with landcover variables performed significantly better than our autologistic and null models, supporting the hypothesis that local landcover heterogeneity is important as an exogenous driver for species distributions. Conspecific clustering alone was a comparatively poor descriptor of local community composition, but there was evidence for spatial autocorrelation in all species. Considerable uncertainty remains whether landcover combined with spatial autocorrelation is most parsimonious for describing bird species distributions at a local scale. Spatial structuring may be weaker at intermediate scales within which dispersal is less frequent, information flows are localized, and landcover types become spatially diversified and therefore exhibit little aggregation. Examining such hypotheses across species assemblages contributes to our understanding of community-level associations with conspecifics and landscape composition. PMID:23393564

Social Position Influencing the Water Perception Gap Between Local Leaders and Constituents in a Socio-Hydrological System

NASA Astrophysics Data System (ADS)

Haeffner, Melissa; Jackson-Smith, Douglas; Flint, Courtney G.

2018-02-01

How well city leaders represent their constituents and meet their needs are key concerns in transitioning to local sustainable water governance. To date, however, there is little research documenting the influence of social position between elected leaders who make policy, career staff water managers who design and operate systems and implement policies, and the members of the public whose individual water use behaviors are important drivers of water sustainability outcomes. In this study, we ask: "How does social position explain variation in water perceptions and concerns between different actors in a socio-hydrological system?" Using a mixed method approach with survey and interview data, we explore the ways that positioning within the governance system, geographic context, and citizen engagement in local government mediate perceptions of the urban water system. Regardless of local biophysical water supply conditions, residents showed most concern about future water shortages and high water costs, while their leaders were consistently most concerned about deteriorating local water infrastructure. Further, constituents who received water-related information directly from public utility mailings or served on community committees and boards had perceptions that were more aligned with leaders' concerns. The importance of social structure over natural and built environments in shaping water issue perceptions underscores the value of social analysis in socio-hydrology studies. Further, practitioners looking to increase consensus for a transition to sustainable water governance might work to develop institutional mechanisms to increase opportunities for water user involvement in local water system governance.

Second harmonic generation from small particle aggregates

NASA Astrophysics Data System (ADS)

Mochan, W. Luis; Ortiz, Guillermo P.; Mendoza, Bernardo S.; Brudny, Vera L.

2001-03-01

Novel nanofabrication techniques are capable of producing nanoparticles with controled structures which include small clusters, self-assembled particles, quantum dots, vesicles, etc. The non-linear optical scattering of these structures are important for applications, and can be used for their physical characterization. The second harmonic (SH) field radiated by a single small spherical particle has surface and bulk, dipolar and quadrupolar contributions of similar intensities and is strongly dependent of the local environment of the particle [1], in contrast to the linear case. In this work we calculate the nonlinear scattering by particle aggregates and we investigate the effects on the SH generation of the disorder induced field fluctuations and of the localization of light. We acknowledge the partial support from DGAPA-UNAM (grant IN110999), Conacyt (31120-E and 26651-E), CIP and UBACyT. [1] Vera L. Brudny, Bernardo S. Mendoza, and W. Luis Mochán, Phys. Rev. B 62, 11152 (2000).

Learning from eponyms: George F. Odland and Odland bodies

PubMed Central

Joshi, Rajiv

2014-01-01

Odland bodies (lamellar) bodies are small sub-cellular structures of size 200-300 nm that are present in the upper spinous and granular cell layers of the epidermis. These act as processing and repository areas for lipids that contribute to the epidermal permeability barrier. They also contain proteases, cathepsin D, kallikrein and other proteins including corneo-desmosins. Recent information also credits them with a role in the local innate immune response as they contain beta 2 defensins, which are anti-microbial peptides with potent activity against Gram-negative bacteria and candida. Odland bodies are important for maintaining homeostasis of the epidermis and are involved in epidermal permeability barrier function, desquamation of keratinocytes, formation of the cornified envelope and in local anti-microbial immunity. This article reviews the structure and functions of these bodies with a brief biography of George F. Odland who first described these bodies in 1960 and whose name is eponymically associated with them. PMID:25165659

Intense upconversion luminescence and effect of local environment for Tm3+/Yb3+ co-doped novel TeO2-BiCl3 glass system.

PubMed

Wang, Guonian; Dai, Shixun; Zhang, Junjie; Wen, Lei; Yang, Jianhu; Jiang, Zhonghong

2006-05-15

We present the results of a study that uses theoretical and experimental methods to investigate the characteristics of the upconversion luminescence of Tm3+/Yb3+ codoped TeO2-BiCl3 glass system as a function of the BiCl3 fraction. These glasses are potentially important in the design of upconversion fiber lasers. Effect of local environment around Tm3+ on upconversion fluorescence intensity was analyzed by theoretical calculations. The structure and spectroscopic properties were investigated in the experiments by measuring the Raman spectra, IR transmission spectra, and absorption and fluorescence intensities at room temperature. The results indicate that blue luminescence quantum efficiency increases with increasing BiCl3 content from 10 to 60 mol%, which were interpreted by the increase of asymmetry of glass structure, decrease of phonon energy and removing of OH- groups.

Effects of local structural transformation of lipid-like compounds on delivery of messenger RNA

NASA Astrophysics Data System (ADS)

Li, Bin; Luo, Xiao; Deng, Binbin; Giancola, Jolynn B.; McComb, David W.; Schmittgen, Thomas D.; Dong, Yizhou

2016-02-01

Lipid-like nanoparticles (LLNs) have shown great potential for RNA delivery. Lipid-like compounds are key components in LLNs. In this study, we investigated the effects of local structural transformation of lipid-like compounds on delivery of messenger RNA. Our results showed that position change of functional groups on lipid-like compounds can dramatically improve delivery efficiency. We then optimized formulation ratios of TNT-b10 LLNs, a lead material, increasing delivery efficiency over 2-fold. More importantly, pegylated TNT-b10 LLNs is stable for over four weeks and is over 10-fold more efficient than that of its counterpart TNT-a10 LLNs. Additionally, the optimal formulation O-TNT-b10 LLNs is capable of delivering mRNA encoding luciferase in vivo. These results provide useful insights into the design of next generation LLNs for mRNA delivery.

Crystal Structure of human Karyopherin β2 bound to the PY-NLS of Saccharomyces cerevisiae Nab2

PubMed Central

Soniat, Michael; Sampathkumar, Parthasarathy; Collett, Garen; Gizzi, Anthony S.; Banu, Radhika N.; Bhosle, Rahul C.; Chamala, Swetha; Chowdhury, Sukanya; Fiser, Andras; Glenn, Alan S.; Hammonds, James; Hillerich, Brandan; Khafizov, Kamil; Love, James D.; Matikainen, Bridget; Seidel, Ronald D.; Toro, Rafael; Kumar, P. Rajesh; Bonanno, Jeffery B.; Chook, Yuh Min; Almo, Steven C.

2013-01-01

Import-Karyopherin or Importin proteins bind nuclear localization signals (NLSs) to mediate the import of proteins into the cell nucleus. Karyopherin β2 or Kapβ2, also known as Transportin, is a member of this transporter family responsible for the import of numerous RNA binding proteins. Kapβ2 recognizes a targeting signal termed the PY-NLS that lies within its cargos to target them through the nuclear pore complex. The recognition of PY-NLS by Kapβ2 is conserved throughout eukaryotes. Kap104, the Kapβ2 homolog in Saccharomyces cerevisiae, recognizes PY-NLSs in cargos Nab2, Hrp1, and Tfg2. We have determined the crystal structure of Kapβ2 bound to the PY-NLS of the mRNA processing protein Nab2 at 3.05-Å resolution. A seven-residue segment of the PY-NLS of Nab2 is observed to bind Kapβ2 in an extended conformation and occupies the same PY-NLS binding site observed in other Kapβ2•PY-NLS structures. PMID:23535894

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

Zhu, Li; Fuhrer, Tobias; Schaefer, Bastian

Measuring similarities/dissimilarities between atomic structures is important for the exploration of potential energy landscapes. However, the cell vectors together with the coordinates of the atoms, which are generally used to describe periodic systems, are quantities not directly suitable as fingerprints to distinguish structures. Based on a characterization of the local environment of all atoms in a cell, we introduce crystal fingerprints that can be calculated easily and define configurational distances between crystalline structures that satisfy the mathematical properties of a metric. This distance between two configurations is a measure of their similarity/dissimilarity and it allows in particular to distinguish structures.more » The new method can be a useful tool within various energy landscape exploration schemes, such as minima hopping, random search, swarm intelligence algorithms, and high-throughput screenings.« less

Molecular simulation investigation of the nanorheology of an entangled polymer melt

NASA Astrophysics Data System (ADS)

Karim, Mir; Khare, Rajesh; Indei, Tsutomu; Schieber, Jay

2014-03-01

Knowledge of the ``local rheology'' is important for viscoelastic systems that contain significant structural and dynamic heterogeneities, such as cellular and extra-cellular crowded environments. For homogeneous viscoelastic media, a study of probe particle motion provides information on the microstructural evolution of the medium in response to the probe particle motion. Over the last two decades, probe particle rheology has emerged as a leading experimental technique for capturing local rheology of complex fluids. In recent work [M. Karim, S. C. Kohale, T. Indei, J. D. Schieber, and R. Khare, Phys. Rev. E86, 051501 (2012)], we showed that this approach can be used in molecular dynamics (MD) simulations to study the nanoscale viscoelastic properties of an unentangled polymer melt; an important conclusion of that work was that medium and particle inertia play a crucial role in analysis of the particle rheology simulation data. MD simulations have a natural advantage that they enable study of deformation and dynamics over a small length scale around the moving probe particle. In this work, the approach is extended to compare the motion of a nanoscale probe in melts of entangled and unentangled chains. The simulations will be used to elucidate the differences between the local responses of these media to the probe particle motion. In particular, results will be presented for the differences in the resultant velocity and stress fields as well as any possible structural asymmetry developed around the moving probe particle in the entangled and unentangled cases.

Monitoring the Damage State of Fiber Reinforced Composites Using an FBG Network for Failure Prediction.

PubMed

Kocaman, Esat Selim; Akay, Erdem; Yilmaz, Cagatay; Turkmen, Halit Suleyman; Misirlioglu, Ibrahim Burc; Suleman, Afzal; Yildiz, Mehmet

2017-01-03

A structural health monitoring (SHM) study of biaxial glass fibre-reinforced epoxy matrix composites under a constant, high strain uniaxial fatigue loading is performed using fibre Bragg grating (FBG) optical sensors embedded in composites at various locations to monitor the evolution of local strains, thereby understanding the damage mechanisms. Concurrently, the temperature changes of the samples during the fatigue test have also been monitored at the same locations. Close to fracture, significant variations in local temperatures and strains are observed, and it is shown that the variations in temperature and strain can be used to predict imminent fracture. It is noted that the latter information cannot be obtained using external strain gages, which underlines the importance of the tracking of local strains internally.

Monitoring the Damage State of Fiber Reinforced Composites Using an FBG Network for Failure Prediction

PubMed Central

Kocaman, Esat Selim; Akay, Erdem; Yilmaz, Cagatay; Turkmen, Halit Suleyman; Misirlioglu, Ibrahim Burc; Suleman, Afzal; Yildiz, Mehmet

2017-01-01

A structural health monitoring (SHM) study of biaxial glass fibre-reinforced epoxy matrix composites under a constant, high strain uniaxial fatigue loading is performed using fibre Bragg grating (FBG) optical sensors embedded in composites at various locations to monitor the evolution of local strains, thereby understanding the damage mechanisms. Concurrently, the temperature changes of the samples during the fatigue test have also been monitored at the same locations. Close to fracture, significant variations in local temperatures and strains are observed, and it is shown that the variations in temperature and strain can be used to predict imminent fracture. It is noted that the latter information cannot be obtained using external strain gages, which underlines the importance of the tracking of local strains internally. PMID:28772393

Local perceptions on factors influencing the introduction of international healthcare accreditation in Pakistan.

PubMed

Sax, Sylvia; Marx, Michael

2014-12-01

One contributor to poor health outcomes in developing countries is weak health systems; key to strengthening them are interventions to improve quality of health services. Though the value of healthcare accreditation is increasingly recognized, there are few case studies exploring its adaptation in developing countries. The aim of our study in Pakistan was to identify perceived factors influencing the adaptation of international healthcare accreditation within a developing country context. We used qualitative methods including semi-structured interviews, a structured group discussion, focus groups and non-participant observation of management meetings. Data analysis used a grounded theory approach and a conceptual framework adapted from implementation science. Using our conceptual framework categories of 'inner' and 'outer' setting, we found six perceived inner health system factors that could influence the introduction of healthcare accreditation and two 'outer' setting factors, perceived as external to the health system but able to influence its introduction. Our research identified that there is no 'one size fits all' approach to introducing healthcare accreditation as a means to improve healthcare quality. Those planning to support healthcare accreditation, such as national and provincial ministries and international development partners, need to understand how the three components of healthcare accreditation fit into the local health system and into the broader political and social environment. In our setting this included moving to supportive and transparent external evaluation mechanisms, with a first step of using locally developed and agreed standards. In addition, sustainable implementation of the three components was seen as a major challenge, especially establishment of a well-managed, transparent accreditation agency able to lead processes such as training and support for peer surveyors. Consideration of local change mechanisms and cultural practices is important in designing a local accreditation approach. The results of our study are important for health systems strengthening in Pakistan and in other developing countries. Published by Oxford University Press in association with The London School of Hygiene and Tropical Medicine © The Author 2013; all rights reserved.

Protein Sub-Nuclear Localization Based on Effective Fusion Representations and Dimension Reduction Algorithm LDA.

PubMed

Wang, Shunfang; Liu, Shuhui

2015-12-19

An effective representation of a protein sequence plays a crucial role in protein sub-nuclear localization. The existing representations, such as dipeptide composition (DipC), pseudo-amino acid composition (PseAAC) and position specific scoring matrix (PSSM), are insufficient to represent protein sequence due to their single perspectives. Thus, this paper proposes two fusion feature representations of DipPSSM and PseAAPSSM to integrate PSSM with DipC and PseAAC, respectively. When constructing each fusion representation, we introduce the balance factors to value the importance of its components. The optimal values of the balance factors are sought by genetic algorithm. Due to the high dimensionality of the proposed representations, linear discriminant analysis (LDA) is used to find its important low dimensional structure, which is essential for classification and location prediction. The numerical experiments on two public datasets with KNN classifier and cross-validation tests showed that in terms of the common indexes of sensitivity, specificity, accuracy and MCC, the proposed fusing representations outperform the traditional representations in protein sub-nuclear localization, and the representation treated by LDA outperforms the untreated one.

Protein Sub-Nuclear Localization Based on Effective Fusion Representations and Dimension Reduction Algorithm LDA

PubMed Central

Wang, Shunfang; Liu, Shuhui

2015-01-01

An effective representation of a protein sequence plays a crucial role in protein sub-nuclear localization. The existing representations, such as dipeptide composition (DipC), pseudo-amino acid composition (PseAAC) and position specific scoring matrix (PSSM), are insufficient to represent protein sequence due to their single perspectives. Thus, this paper proposes two fusion feature representations of DipPSSM and PseAAPSSM to integrate PSSM with DipC and PseAAC, respectively. When constructing each fusion representation, we introduce the balance factors to value the importance of its components. The optimal values of the balance factors are sought by genetic algorithm. Due to the high dimensionality of the proposed representations, linear discriminant analysis (LDA) is used to find its important low dimensional structure, which is essential for classification and location prediction. The numerical experiments on two public datasets with KNN classifier and cross-validation tests showed that in terms of the common indexes of sensitivity, specificity, accuracy and MCC, the proposed fusing representations outperform the traditional representations in protein sub-nuclear localization, and the representation treated by LDA outperforms the untreated one. PMID:26703574

Subcellular localization of acyl-CoA binding protein in Aspergillus oryzae is regulated by autophagy machinery.

PubMed

Kawaguchi, Kouhei; Kikuma, Takashi; Higuchi, Yujiro; Takegawa, Kaoru; Kitamoto, Katsuhiko

2016-11-04

In eukaryotic cells, acyl-CoA binding protein (ACBP) is important for cellular activities, such as in lipid metabolism. In the industrially important fungus Aspergillus oryzae, the ACBP, known as AoACBP, has been biochemically characterized, but its physiological function is not known. In the present study, although we could not find any phenotype of AoACBP disruptants in the normal growth conditions, we examined the subcellular localization of AoACBP to understand its physiological function. Using an enhanced green fluorescent protein (EGFP)-tagged AoACBP construct we showed that AoACBP localized to punctate structures in the cytoplasm, some of which moved inside the cells in a microtubule-dependent manner. Further microscopic analyses showed that AoACBP-EGFP co-localized with the autophagy marker protein AoAtg8 tagged with red fluorescent protein (mDsRed). Expression of AoACBP-EGFP in disruptants of autophagy-related genes revealed aggregation of AoACBP-EGFP fluorescence in the cytoplasm of Aoatg1, Aoatg4 and Aoatg8 disruptant cells. However, in cells harboring disruption of Aoatg15, which encodes a lipase for autophagic body, puncta of AoACBP-EGFP fluorescence accumulated in vacuoles, indicating that AoACBP is transported to vacuoles via the autophagy machinery. Collectively, these results suggest the existence of a regulatory mechanism between AoACBP localization and autophagy. Copyright © 2016 Elsevier Inc. All rights reserved.