bluuebunny/crossref_metadata_2025 huggingface dataset:
Finite domain simulations with adaptive boundaries: Accurate potentials and nonequilibrium movesets
Authors: Wagoner Jason A. , Pande Vijay S.
Published: December 2013

We extend the theory of hybrid explicit/implicit solvent models to include an explicit domain that grows and shrinks in response to a solute's evolving configuration. The goal of this model is to provide an appropriate but not excessive amount of solvent detail, and the inclusion of an adjustable boundary provides a significant computational advantage for solutes that explore a range of configurations. In addition to the theoretical development, a successful implementation of this method requires (1) an efficient moveset that propagates the boundary as a new coordinate of the system, and (2) an accurate continuum solvent model with parameters that are transferable to an explicit domain of any size. We address these challenges and develop boundary updates using Monte Carlo moves biased by nonequilibrium paths. We obtain the desired level of accuracy using a “decoupling interface” that we have previously shown to remove boundary artifacts common to hybrid solvent models. Using an uncharged, coarse-grained solvent model, we then study the efficiency of nonequilibrium paths that a simulation takes by quantifying the dissipation. In the spirit of optimization, we study this quantity over a range of simulation parameters.
A transferable coarse-grained model for diphenylalanine: How to represent an environment driven conformational transition
Authors: Dalgicdir Cahit , Sensoy Ozge , Peter Christine , Sayar Mehmet
Published: December 2013

One of the major challenges in the development of coarse grained (CG) simulation models that aim at biomolecular structure formation processes is the correct representation of an environment-driven conformational change, for example, a folding/unfolding event upon interaction with an interface or upon aggregation. In the present study, we investigate this transferability challenge for a CG model using the example of diphenylalanine. This dipeptide displays a transition from a trans-like to a cis-like conformation upon aggregation as well as upon transfer from bulk water to the cyclohexane/water interface. Here, we show that one can construct a single CG model that can reproduce both the bulk and interface conformational behavior and the segregation between hydrophobic/hydrophilic medium. While the general strategy to obtain nonbonded interactions in the present CG model is to reproduce solvation free energies of small molecules representing the CG beads in the respective solvents, the success of the model strongly depends on nontrivial decisions one has to make to capture the delicate balance between the bonded and nonbonded interactions. In particular, we found that the peptide's conformational behavior is qualitatively affected by the cyclohexane/water interaction potential, an interaction that does not directly involve the peptide at all but merely influences the properties of the hydrophobic/hydrophilic interface. Furthermore, we show that a small modification to improve the structural/conformational properties of the CG model could dramatically alter the thermodynamic properties.
Probing the photoluminescence properties of gold nanoclusters by fluorescence lifetime correlation spectroscopy
Authors: Yuan C. T. , Lin C. A. , Lin T. N. , Chang W. H. , Shen J. L. , Cheng H. W. , Tang J.
Published: December 2013

Gold nanoclusters (Au NCs) have attracted much attention for promising applications in biological imaging owing to their tiny sizes and biocompatibility. So far, most efforts have been focused on the strategies for fabricating high-quality Au NCs and then characterized by conventional ensemble measurement. Here, a fusion single-molecule technique combining fluorescence correlation spectroscopy and time-correlated single-photon counting can be successfully applied to probe the photoluminescence (PL) properties for sparse Au NCs. In this case, the triplet-state dynamics and diffusion process can be observed simultaneously and the relevant time constants can be derived. This work provides a complementary insight into the PL mechanism at the molecular levels for Au NCs in solution.
Mixed-field orientation of molecules without rotational symmetry
Authors: Hansen Jonas L. , Omiste Juan J. , Nielsen Jens H. , Pentlehner Dominik , Küpper Jochen , González-Férez Rosario , Stapelfeldt Henrik
Published: December 2013

The mixed-field orientation of an asymmetric-rotor molecule with its permanent dipole moment nonparallel to the principal axes of polarizability is investigated experimentally and theoretically. We find that for the typical case of a strong, nonresonant laser field and a weak static electric field complete 3D orientation is induced if the laser field is elliptically polarized and if its major and minor polarization axes are not parallel to the static field. For a linearly polarized laser field solely the dipole moment component along the most polarizable axis of the molecule is relevant resulting in 1D orientation even when the laser polarization and the static field are nonparallel. Simulations show that the dipole moment component perpendicular to the most-polarizable axis becomes relevant in a strong dc electric field combined with the laser field. This offers an alternative approach to 3D orientation by combining a linearly polarized laser field and a strong dc electric field arranged at an angle equal to the angle between the most polarizable axis of the molecule and its permanent dipole moment.
Trace gas analysis from glazes by means of a compact photothermal deflection spectroscopy apparatus
Authors: Leahu G. , Voti R. Li , Paoloni S. , Sibilia C. , Bertolotti M.
Published: December 2013

A portable photothermal deflection spectroscopy apparatus for accurate analysis of gas mixtures containing volatile organic substances is presented. The main technical aspects of the photothermal deflection cell, and of the gas sampling equipment are discussed in details. Finally, we present a straightforward industrial application of the apparatus concerning the qualitative and quantitative analysis of the gas emissions from thermal treatment of ceramic glazes.
Incorporation kinetics in mixed anion compound semiconductor alloys
Authors: Millunchick Joanna M. , Anderson Evan M. , Pearson Chris , Sarney Wendy L. , Svensson Stefan P.
Published: December 2013

We present a kinetic model predicting anion incorporation in InAsSb. Included are the effects of As desorption, Sb segregation, and Sb displacement by As, any of which may be limited by the In flux if it is comparatively larger. The model captures experimental data over a range of growth conditions for the InAsSb system using activation energies for desorption and Sb segregation found in literature. The activation energy for Sb displacement found in this work is 1.3 eV. This model is general and should be valid for other mixed anion systems, or, appropriately modified, mixed cation systems and mixed anion/cation systems such as AlInAsSb.
Local network structure of a-SiC:H and its correlation with dielectric function
Authors: Kageyama Shota , Matsuki Nobuyuki , Fujiwara Hiroyuki
Published: December 2013

The microscopic disordered structures of hydrogenated amorphous silicon carbide (a-Si1−xCx:H) layers with different carbon contents have been determined based on the correlations between the dielectric function in the ultraviolet/visible region and the local bonding states studied by high-sensitivity infrared attenuated total reflection spectroscopy. We find that the microscopic structure of the a-Si1−xCx:H layers fabricated by plasma-enhanced chemical vapor deposition shows a sharp structural transition at a boundary of x = 6.3 at. %. In the regime of x ≤ 6.3 at. %, (i) the amplitude of the a-SiC:H dielectric function reduces and (ii) the SiH2 content increases drastically with x, even though most of the C atoms are introduced into the tetrahedral sites without bonding with H. In the regime of x > 6.3 at. %, on the other hand, (i) the amplitude of the dielectric function reduces further and (ii) the concentration of the sp3 CHn (n = 2,3) groups increases. Moreover, we obtained the direct evidence that the sp2 C bonding state in the a-SiC matrix exists in the configuration of C = CH2 and the generation of the graphite-like C = CH2 unit suppresses the band gap widening significantly. At high C contents of x > 6.3 at. %, the a-SiC:H layers show quite porous structures due to the formation of microvoids terminated with the SiH2/CHn groups. By taking the SiH2/CHn microvoid generation in the network and the high-energy shift of the dielectric function by the local bonding states into account, the a-SiC:H dielectric function model has been established. From the analysis using this model, we have confirmed that the a-SiC:H optical properties in the ultraviolet/visible region are determined almost completely by the local network structures.
Global solar irradiation prediction using a multi-gene genetic programming approach
Authors: Pan Indranil , Pandey Daya Shankar , Das Saptarshi
Published: December 2013

In this paper, a nonlinear symbolic regression technique using an evolutionary algorithm known as multi-gene genetic programming (MGGP) is applied for a data-driven modelling between the dependent and the independent variables. The technique is applied for modelling the measured global solar irradiation and validated through numerical simulations. The proposed modelling technique shows improved results over the fuzzy logic and artificial neural network (ANN) based approaches as attempted by contemporary researchers. The method proposed here results in nonlinear analytical expressions, unlike those with neural networks which is essentially a black box modelling approach. This additional flexibility is an advantage from the modelling perspective and helps to discern the important variables which affect the prediction. Due to the evolutionary nature of the algorithm, it is able to get out of local minima and converge to a global optimum unlike the back-propagation (BP) algorithm used for training neural networks. This results in a better percentage fit than the ones obtained using neural networks by contemporary researchers. Also a hold-out cross validation is done on the obtained genetic programming (GP) results which show that the results generalize well to new data and do not over-fit the training samples. The multi-gene GP results are compared with those obtained using its single-gene version and also the same with four classical regression models in order to show the effectiveness of the adopted approach.
Complex dynamics of a nonlinear voter model with contrarian agents
Authors: Tanabe Shoma , Masuda Naoki
Published: December 2013

We investigate mean-field dynamics of a nonlinear opinion formation model with congregator and contrarian agents. Each agent assumes one of the two possible states. Congregators imitate the state of other agents with a rate that increases with the number of other agents in the opposite state, as in the linear voter model and nonlinear majority voting models. Contrarians flip the state with a rate that increases with the number of other agents in the same state. The nonlinearity controls the strength of the majority voting and is used as a main bifurcation parameter. We show that the model undergoes a rich bifurcation scenario comprising the egalitarian equilibrium, two symmetric lopsided equilibria, limit cycle, and coexistence of different types of stable equilibria with intertwining attractive basins.
Selective charge doping of chemical vapor deposition-grown graphene by interface modification
Authors: Wang Shengnan , Suzuki Satoru , Furukawa Kazuaki , Orofeo Carlo M. , Takamura Makoto , Hibino Hiroki
Published: December 2013

The doping and scattering effect of substrate on the electronic properties of chemical vapor deposition (CVD)-grown graphene are revealed. Wet etching the underlying SiO2 of graphene and depositing self-assembled monolayers (SAMs) of organosilane between graphene and SiO2 are used to modify various substrates for CVD graphene transistors. Comparing with the bare SiO2 substrate, the carrier mobility of CVD graphene on modified substrate is enhanced by almost 5-fold; consistently the residual carrier concentration is reduced down to 1011 cm−2. Moreover, scalable and reliable p- and n-type graphene and graphene p-n junction are achieved on various silane SAMs with different functional groups.
Resonant carrier-phonon scattering in graphene under Landau quantization
Authors: Wendler Florian , Knorr Andreas , Malic Ermin
Published: December 2013

We present a microscopic study on the phonon-induced inter-Landau level carrier relaxation in graphene. Our approach is based on the density matrix formalism giving access to time-resolved relaxation dynamics in graphene under Landau quantization. We find a drastically enhanced scattering via optical phonons at specific magnetic fields predicting clear still unobserved signatures in experimental differential transmission spectra.
Detailed balance limit of power conversion efficiency for organic photovoltaics
Authors: Seki Kazuhiko , Furube Akihiro , Yoshida Yuji
Published: December 2013

A fundamental difference between inorganic photovoltaic (IPV) and organic photovoltaic (OPV) cells is that charges are generated at the interface in OPV cells, while free charges can be generated in the bulk in IPV cells. In OPV cells, charge generation involves intrinsic energy losses to dissociate excitons at the interface between the donor and acceptor. By taking into account the energy losses, we show the theoretical limits of the power conversion efficiency set by radiative recombination of the carriers on the basis of the detailed balance relation between radiation from the cell and black-body radiation.
Analysis of carrier behavior in C60/P(VDF-TrFE) double-layer capacitor by using electric-field-induced optical second-harmonic generation measurement
Authors: Cui Xiaojin , Taguchi Dai , Manaka Takaaki , Iwamoto Mitsumasa
Published: December 2013

By using displacement current measurement (DCM) and electric-field-induced optical second-harmonic generation (EFISHG) measurement, we studied the carrier behavior in the indium-tin oxide (ITO)/Poly(vinylidene fluoride-trifluoroethylene) (P(VDF-TrFE))/C60/Au(or Al) capacitors. Two DCM peaks appeared asymmetrically at around −35.5 V and +30.0 V in the dark. Correspondingly, the EFISHG response from the C60 layer was observed, but the peak positions were different with respect to DCM ones. The results show that the spontaneous polarization of the ferroelectric P(VDF-TrFE) polymeric layer directly affects the electric field in the C60 layer, and thus governs the carrier motion in this layer. As a result, the C60 layer serves like an insulator in the dark, while electrons and holes are captured and released at the interface in response to the turn-over of spontaneous polarization of ferroelectric layer. On the other hand, under white light illumination, C60 layer serves like a conductor due to the increase of photogenerated mobile carriers, and these carriers dominate the carrier motions therein. Our findings here will be helpful for analyzing carrier behaviors in organic electronic devices using ferroelectric polymers.
Giant zero field cooled spontaneous exchange bias effect in phase separated La1.5Sr0.5CoMnO6
Authors: Krishna Murthy J. , Venimadhav A.
Published: December 2013

We report a giant zero field cooled exchange bias (ZEB) effect (∼0.65 T) in La1.5Sr0.5CoMnO6 sample. Magnetic study has revealed a reentrant spin glass ∼90 K, phase separation to spin glass and ferromagnetic phases below 50 K and canted antiferromagnetic transition ∼10 K. A small conventional exchange bias (CEB) is established with the advent of spontaneous phase separation down to 10 K. Giant ZEB and enhanced CEB effects are found only below 10 K and are attributed to the large unidirectional anisotropy at the interface of isothermally field induced ferromagnetic phase and canted antiferromagnetic background.
Computational and experimental characterization of high-brightness beams for femtosecond electron imaging and spectroscopy
Authors: Portman J. , Zhang H. , Tao Z. , Makino K. , Berz M. , Duxbury P. M. , Ruan C.-Y.
Published: December 2013

Using a multilevel fast multipole method, coupled with the shadow imaging of femtosecond photoelectron pulses for validation, we quantitatively elucidate the photocathode, space charge, and virtual cathode physics, which fundamentally limit the spatiotemporal and spectroscopic resolution and throughput of ultrafast electron microscope (UEM) systems. We present a simple microscopic description to capture the nonlinear beam dynamics based on a two-fluid picture and elucidate an unexpected dominant role of image potential pinning in accelerating the emittance growth process. These calculations set theoretical limits on the performance of UEM systems and provide useful guides for photocathode design for high-brightness electron beam systems.
Characterization of SiGe/Si multi-quantum wells for infrared sensing
Authors: Moeen M. , Salemi A. , Kolahdouz M. , Östling M. , Radamson H. H.
Published: December 2013

SiGe epitaxial layers are integrated as an active part in thermal detectors. To improve their performance, deeper understanding of design parameters, such as thickness, well periodicity, quality, and strain amount, of the layers/interfaces is required. Oxygen (2–2500 × 10−9 Torr) was exposed prior or during epitaxy of SiGe/Si multilayers. In this range, samples with 10 nTorr oxygen were processed to investigate layer quality and noise measurements. Temperature coefficient of resistance was also measured to evaluate the thermal response. These results demonstrate sensitivity of SiGe-based devices to size and location of defects in the structure.
Intersublevel dephasing in InAs/GaAs quantum dots below the Reststrahlen band
Authors: Teich M. , Stephan D. R. , Winnerl S. , Schneider H. , Wilson L. R. , Helm M.
Published: December 2013

Using transient four-wave mixing in the terahertz range, we have measured the s-p inter-sublevel dephasing time in self-assembled InAs/GaAs quantum dots for transition energies below the Reststrahlen band. Dephasing times of up to 600 ps at a photon energy of 18 meV have been determined. By comparing pump-probe and four-wave mixing measurements, we show that there is no significant influence of any pure dephasing process at low temperature. The linear temperature dependence is consistent with acoustic phonon scattering.
Reversing Property Rights: Practice‐Based Approaches for Controlling Agricultural Nonpoint‐source Water Pollution When Emissions Aggregate Nonlinearly
Authors: Rabotyagov Sergey S. , Valcu Adriana M. , Kling Catherine L.
Published: December 2013

Nonpoint‐source water pollution remains a major issue despite decades of research and sizable conservation programs. We suggest that by taking advantage of contemporary modeling and optimization approaches, good approximations to physical relationships can be constructed so that even in the presence of unobservable field emissions and nonlinear fate and transport relationships, standard economic tools of command‐and‐control requirements, performance standards, and trading can be implemented. The Boone River Watershed in the U.S. state of Iowa is used for empirical demonstration. Although the approach can be used to construct voluntary conservation policies, the described policies involve imposing requirements on agricultural polluters rather than relying on voluntary actions alone.
JEPETTO: a Cytoscape plugin for gene set enrichment and topological analysis based on interaction networks
Authors: Winterhalter Charles , Widera Paweł , Krasnogor Natalio
Published: December 2013

Summary: JEPETTO (Java Enrichment of Pathways Extended To TOpology) is a Cytoscape 3.x plugin performing integrative human gene set analysis. It identifies functional associations between genes and known cellular pathways, and processes using protein interaction networks and topological analysis. The plugin integrates information from three separate web servers we published previously, specializing in enrichment analysis, pathways expansion and topological matching. This integration substantially simplifies the analysis of user gene sets and the interpretation of the results. We demonstrate the utility of the JEPETTO plugin on a set of misregulated genes associated with Alzheimer’s disease.

Availability: Source code and binaries are freely available for download at http://apps.cytoscape.org/apps/jepetto, implemented in Java and multi-platform. Installable directly via Cytoscape plugin manager. Released under the GNU General Public Licence.

Contact:  jepetto.plugin@gmail.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
WiggleTools: parallel processing of large collections of genome-wide datasets for visualization and statistical analysis
Authors: Zerbino Daniel R. , Johnson Nathan , Juettemann Thomas , Wilder Steven P. , Flicek Paul
Published: December 2013

Motivation: Using high-throughput sequencing, researchers are now generating hundreds of whole-genome assays to measure various features such as transcription factor binding, histone marks, DNA methylation or RNA transcription. Displaying so much data generally leads to a confusing accumulation of plots. We describe here a multithreaded library that computes statistics on large numbers of datasets (Wiggle, BigWig, Bed, BigBed and BAM), generating statistical summaries within minutes with limited memory requirements, whether on the whole genome or on selected regions.

Availability and Implementation: The code is freely available under Apache 2.0 license at www.github.com/Ensembl/Wiggletools

Contact:  zerbino@ebi.ac.uk or flicek@ebi.ac.uk
SurpriseMe: an integrated tool for network community structure characterization using Surprise maximization
Authors: Aldecoa Rodrigo , Marín Ignacio
Published: December 2013

Summary: Detecting communities and densely connected groups may contribute to unravel the underlying relationships among the units present in diverse biological networks (e.g. interactomes, coexpression networks, ecological networks). We recently showed that communities can be precisely characterized by maximizing Surprise, a global network parameter. Here, we present SurpriseMe, a tool that integrates the outputs of seven of the best algorithms available to estimate the maximum Surprise value. SurpriseMe also generates distance matrices that allow visualizing the relationships among the solutions generated by the algorithms. We show that the communities present in small- and medium-sized networks, with up to 10 000 nodes, can be easily characterized: on standard PC computers, these analyses take less than an hour. Also, four of the algorithms may rapidly analyze networks with up to 100 000 nodes, given enough memory resources. Because of its performance and simplicity, SurpriseMe is a reference tool for community structure characterization.

Availability and implementation: SurpriseMe is implemented in Perl and C/C++. It compiles and runs on any UNIX-based operating system, including Linux and Mac OS/X, using standard libraries. The source code is freely and publicly available under the GPL 3.0 license at http://github.com/raldecoa/SurpriseMe/releases.

Contact:  imarin@ibv.csic.es
Observing the quantum anomalous Hall effect
Authors: Wang Ling
Published: December 2013

Soon after the article ‘Experimental Observation of the Quantum Anomalous Hall Effect (QAHE) in a Magnetic Topological Insulator’ was published online in Science, Qikun Xue, the team leader of this fabulous work from Tsinghua University, was flooded with requests for interviews. This is not so surprising. Physicists have been waiting for the observation of the QAHE for over 20 years, and, until 2013, there had been few groundbreaking experimental results. ‘The honor absolutely belongs to the entire group, especially our budding scientists’, Xue declared, Xucun Ma and Ke He, two scientists of Institute of Physics, CAS, are certainly among them. In 2009, Ma and He commenced their journey to find a unique material that could demonstrate the QAHE under the leadership of Xue.
Topological insulating phase in commonly used semiconductors
Authors: Chang Kai
Published: December 2013

Interface polarization between commonly used semiconductors provides a possible method to drive commonly used semiconductors into their topological insulating phase.
Causal Inference in Conjoint Analysis: Understanding Multidimensional Choices via Stated Preference Experiments
Authors: Hainmueller Jens , Hopkins Daniel J. , Yamamoto Teppei
Published: December 2013

Survey experiments are a core tool for causal inference. Yet, the design of classical survey experiments prevents them from identifying which components of a multidimensional treatment are influential. Here, we show howconjoint analysis, an experimental design yet to be widely applied in political science, enables researchers to estimate the causal effects of multiple treatment components and assess several causal hypotheses simultaneously. In conjoint analysis, respondents score a set of alternatives, where each has randomly varied attributes. Here, we undertake a formal identification analysis to integrate conjoint analysis with the potential outcomes framework for causal inference. We propose a new causal estimand and show that it can be nonparametrically identified and easily estimated from conjoint data using a fully randomized design. The analysis enables us to propose diagnostic checks for the identification assumptions. We then demonstrate the value of these techniques through empirical applications to voter decision making and attitudes toward immigrants.
Roseomonas soli sp. nov., isolated from an agricultural soil cultivated with Chinese cabbage (Brassica campestris)
Authors: Kim Dong-Uk , Ka Jong-Ok
Published: December 2013

A bacterial strain, designated 5N26T, was isolated from an agricultural soil cultivated with Chinese cabbage (Brassica campestris). Cells of this strain were Gram-reaction-negative, strictly aerobic, motile, non-spore-forming rods, and catalase- and urease-negative. The major fatty acids of strain 5N26Twere C16 : 0(7.5 %), C18 : 12-OH (13.4 %) and summed feature 8 (C18 : 1ω6cand/or C18 : 1ω7c; 63.2 %). The polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylmonomethylethanolamine and one unidentified aminolipid. The G+C content of the genomic DNA of strain 5N26Twas 68.3 mol%. 16S rRNA gene sequence analysis showed that strain 5N26Twas phylogenetically related toRoseomonas lacusTH-G33TandRoseomonas terraeDS-48T(97.0 % and 96.6 % sequence similarity, respectively). The results of genotypic and phenotypic data showed that strain 5N26Tcould be distinguished from phylogenetically related species, and that this strain represented a novel species within the genusRoseomonas, for which the nameRoseomonas solisp. nov. (type strain 5N26T = KACC 16376T = NBRC 109097T) is proposed.
Sphaerisporangium rufum sp. nov., an endophytic actinomycete from roots of Oryza sativa L
Authors: Mingma Ratchanee , Duangmal Kannika , Trakulnaleamsai Savitr , Thamchaipenet Arinthip , Matsumoto Atsuko , Takahashi Yoko
Published: December 2013

An endophytic actinomycete, strain R10-82T, isolated from surface-sterilized roots of rice (Oryza sativa L.) was studied using a polyphasic approach. Strain R10-82T produced branching substrate mycelia and developed spherical spore vesicles on aerial hyphae containing non-motile spores. The major cellular fatty acids were iso-C16 : 0, iso-C14 : 0 and 10-methyl C17 : 0. The predominant menaquinones were MK-9, MK-9(H2), MK-9(H4) and MK-9(H6). Rhamnose, ribose, madurose, mannose and glucose were detected in whole-cell hydrolysates. The diagnostic phospholipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol mannosides, hydroxylphosphatidylethanolamine and ninhydrin-positive phosphoglycolipids. These morphological and chemotaxonomic data were similar to those of the genus

Sphaerisporangium

. Analysis of the 16S rRNA gene sequence revealed that strain R10-82T was related most closely to

Sphaerisporangium cinnabarinum

JCM 3291T (98.3 % similarity). The DNA G+C content of strain R10-82T was 74 mol%. DNA–DNA relatedness data in combination with differences in the biochemical and physiological properties suggested that strain R10-82T should be classified as representing a novel species of the genus

Sphaerisporangium

, for which the name Sphaerisporangium rufum is proposed. The type strain is R10-82T ( = BCC 51287T = NBRC 109079T). An emended description of the genus

Sphaerisporangium

is also provided.
Discovery of urchin-associated densoviruses (family Parvoviridae) in coastal waters of the Big Island, Hawaii
Authors: Gudenkauf Brent M. , Eaglesham James B. , Aragundi William M. , Hewson Ian
Published: December 2013

Echinoderms are important constituents of marine ecosystems, where they may influence the recruitment success of benthic flora and fauna, and are important consumers of detritus and plant materials. There are currently no described viruses of echinoderms. We used a viral metagenomic approach to examine viral consortia within three urchins –Colobocentrotus atratus,Tripneustes gratillaandEchinometra mathaei– which are common constituents of reef communities in the Hawaiian archipelago. Metagenomic libraries revealed the presence of bacteriophages and densoviruses (familyParvoviridae) in tissues of all three urchins. Densoviruses are known typically to infect terrestrial and aquatic arthropods. Urchin-associated densoviruses were detected by quantitative PCR in all tissues tested, and were also detected in filtered suspended matter (>0.2 µm) from plankton and in sediments at several locations near to where the urchins were collected for metagenomic analysis. To the best of our knowledge, this is the first report of echinoderm-associated viruses, which extends the known host range of parvoviruses.
Estimation of the in vivo recombination rate for a plant RNA virus
Authors: Tromas Nicolas , Zwart Mark P. , Poulain Maïté , Elena Santiago F.
Published: December 2013

Phylogenomic evidence suggested that recombination is an important evolutionary force for potyviruses, one of the larger families of plant RNA viruses. However, mixed-genotype potyvirus infections are marked by low levels of cellular coinfection, precluding template switching and recombination events between virus genotypes during genomic RNA replication. To reconcile these conflicting observations, we evaluated thein vivorecombination rate (rg) ofTobacco etch virus(TEV; genusPotyvirus, familyPotyviridae) by coinfecting plants with pairs of genotypes marked with engineered restriction sites as neutral markers. The recombination rate was then estimated using two different approaches: (i) a classical approach that assumed recombination between marked genotypes can occur in the whole virus population, rendering an estimate ofrg = 7.762×10−8recombination events per nucleotide site per generation, and (ii) an alternative method that assumed recombination between marked genotypes can occur only in coinfected cells, rendering a much higher estimate ofrg = 3.427×10−5recombination events per nucleotide site per generation. This last estimate is similar to the TEV mutation rate, suggesting that recombination should be at least as important as point mutation in creating variability. Finally, we compared our mutation and recombination rate estimates to those reported for animal RNA viruses. Our analysis suggested that high recombination rates may be an unavoidable consequence of selection for fast replication at the cost of low fidelity.
Recovery of a chemically synthesized Japanese encephalitis virus reveals two critical adaptive mutations in NS2B and NS4A
Authors: Li Xiao-Dan , Li Xiao-Feng , Ye Han-Qing , Deng Cheng-Lin , Ye Qing , Shan Chao , Shang Bao-Di , Xu Lin-Lin , Li Shi-Hua , Cao Sheng-Bo , Yuan Zhi-Ming , Shi Pei-Yong , Qin Cheng-Feng , Zhang Bo
Published: December 2013

A full-length genome infectious clone is a powerful tool for functional assays in virology. In this study, using a chemical synthesized complete genome of Japanese encephalitis virus (JEV) strain SA14 (GenBank accession no. U14163), we constructed a full-length genomic cDNA clone of JEV. The recovered virus from the cDNA clone replicated poorly in baby hamster kidney (BHK-21) cells and in suckling mice brain. Following serial passage in BHK-21 cells, adaptive mutations within the NS2B and NS4A proteins were recovered in the passaged viruses leading to viruses with a large-plaque phenotype. Mutagenesis analysis, using a genome-length RNA and a replicon of JEV, demonstrated that the adaptive mutations restored replication to different degrees, and the restoration efficiencies were in the order: NS2B-T102M<NS4A-R79K<NS2B-T102M+NS4A-R79K. An in vivo virulence assay in mice showed that the recombinant virus containing double mutations showed similar virulence to the WT SA14 (GenBank accession no. M55506). This study reports the first chemically synthesized JEV. A reverse genetics assay demonstrated that substitutions of NS2B-T102M and NS4A-R79K altered JEV replication.
Sufficient Amounts of Functional HOP2/MND1 Complex Promote Interhomolog DNA Repair but Are Dispensable for Intersister DNA Repair during Meiosis in Arabidopsis
Authors: Uanschou Clemens , Ronceret Arnaud , Von Harder Mona , De Muyt Arnaud , Vezon Daniel , Pereira Lucie , Chelysheva Liudmila , Kobayashi Wataru , Kurumizaka Hitoshi , Schlögelhofer Peter , Grelon Mathilde
Published: December 2013

During meiosis, homologous recombination (HR) is essential to repair programmed DNA double-strand breaks (DSBs), and a dedicated protein machinery ensures that the homologous chromosome is favored over the nearby sister chromatid as a repair template. The HOMOLOGOUS-PAIRING PROTEIN2/MEIOTIC NUCLEAR DIVISION PROTEIN1 (HOP2/MND1) protein complex has been identified as a crucial factor of meiotic HR in Arabidopsis thaliana, since loss of either MND1 or HOP2 results in failure of DNA repair. We isolated two mutant alleles of HOP2 (hop2-2 and hop2-3) that retained the capacity to repair meiotic DSBs via the sister chromatid but failed to use the homologous chromosome. We show that in these alleles, the recombinases RADIATION SENSITIVE51 (RAD51) and DISRUPTED MEIOTIC cDNA1 (DMC1) are loaded, but only the intersister DNA repair pathway is activated. The hop2-2 phenotype is correlated with a decrease in HOP2/MND1 complex abundance. In hop2-3, a truncated HOP2 protein is produced that retains its ability to bind to DMC1 and DNA but forms less stable complexes with MND1 and fails to efficiently stimulate DMC1-driven D-loop formation. Genetic analyses demonstrated that in the absence of DMC1, HOP2/MND1 is dispensable for RAD51-mediated intersister DNA repair, while in the presence of DMC1, a minimal amount of functional HOP2/MND1 is essential to drive intersister DNA repair.
Exploring the consequences of reducing survey effort for detecting individual and temporal variability in survival
Authors: Lahoz‐Monfort José J. , Harris Michael P. , Morgan Byron J. T. , Freeman Stephen N. , Wanless Sarah
Published: December 2013

Long‐term monitoring programmes often involve substantial input of skilled staff time. In mark–recapture studies, considerable effort is usually devoted to both marking and recapturing/resighting individuals. Given increasing budgetary constraints, it is essential to streamline field protocols to minimize data redundancy while still achieving targets such as detecting trends or ecological effects.

We evaluated different levels of field effort investment in marking and resighting individuals by resampling existing mark–recapture–recovery data to construct plausible scenarios of changes in field protocols. We demonstrate the method with 26 years data from a common guillemotUria aalgemonitoring programme at a majorNorthSea colony. We also assess the impact of stopping the ringing of chicks on our ability to study population demography using integrated population models (IPM) fitted to data including information on breeding adults. Different data sets were removed artificially to explore the ability to compensate for missing data.

Current ringing effort at this colony appears adequate but resighting effort could be halved while still maintaining the capacity to monitor first‐year survival and detect the effect of hatch date on survival prospects.

TheIPMappears robust for estimating survival, productivity or abundance of the breeding population, but has limited capacity to recover year‐specific first‐year survival when chick data are omitted. If productivity were not monitored, the inclusion of chick data would be essential to estimate it, albeit imprecisely.

Synthesis and applications. Post‐study evaluation can help streamline existing long‐term environmental monitoring programmes. To our knowledge, this study is the first use of data thinning of existing mark–recapture–recovery data to identify potential field effort reductions. We also highlight how alternative monitoring scenarios can be evaluated with integrated population models when data are collected on different aspects of demography and abundance. When effort reduction is necessary, both approaches provide decision‐support tools for adjusting field protocols to collect demographic data. The framework has broad applicability to other taxa and demographic parameters, provided suitable long‐term data are available, and we discuss its use in different contexts.
An economic model of aboriginal fire‐stick farming
Authors: Wilman Elizabeth A.
Published: December 2013

Australian Aborigines faced a resource management problem, which they addressed though burning regimes, referred to as fire‐stick farming. While dynamic economic analysis is clearly applicable, to date there have been no attempts to use it to model burning regimes. This paper develops a delayed‐response optimal‐control model to describe Aboriginal fire‐stick farming. The model explains a collective welfare maximizing burning regime that successfully controlled wildfires, protected the resources essential to survival, and, incidentally, produced a biodiverse landscape and limited greenhouse gas emissions. When the parameters of the model are changed to reflect the current institutional realities of reduced access to the land, and less direct dependence on it, traditional Aboriginal burning is prevented or delayed, fuel loads build up and uncontrolled fires are more likely to occur, damaging previously protected species. If Aboriginal burning is to be used to control fires successfully in a modern resource management context, it is necessary to adjust for changes in the institutional incentive structure. Payments for carbon offsets are an example of replacing lost incentives with new ones.
Factors Related to Public Health Data Sharing between Local and State Health Departments
Authors: Vest Joshua R. , Issel L. Michele
Published: December 2013

Objective

Public health organizations increasingly face the need to be able to share data among themselves and ultimately with other providers. We examined what factors contribute to public health organizations' data exchange capabilities.

Data Sources

National Association of County and City Health Officials' 2008 National Profile of Local Health Departments survey was linked to the Association of State and Territorial Health Official's 2007 Profile of State Public Health Survey.

Study Design

We conducted a cross‐sectional analysis of organizational factors associated with gaps in data sharing between state health agencies (SHAs) and local health departments (LHDs) in the areas of childhood immunizations, vital records, and reportable conditions.

Data Collection

Based on reported information system (IS) capabilities, we created a binary variable that measured whether bidirectional data sharing was structurally possible between an LHD and its respective SHA.

Principal Findings

The proportion of LHDs experiencing a data sharing gap was 34.0 percent for immunizations, 69.8 percent for vital records, and 81.8 percent for reportable conditions. Increased SHA technological capacity and size reduced the odds of gaps.

Conclusions

Improving the IS capabilities of public health agencies may be the key to their remaining relevant in the currently evolving health care system.
White But Not Quite: Normalizing Colonial Conquests Through Spatial Mimicry
Authors: Ram Mori
Published: December 2013

The role of mimicry in the construction and deconstruction of social identities has enriched our understanding of power relations considerably. However, as a spatial practice, mimicry has received scant consideration. In what ways can space itself become an object of mimicry? What strategies and practices are involved in this process and with what political objectives? The current paper treats these questions by analyzing processes of mimetic spatial production aiming to transform the Israeli‐occupied territory of Mount Hermon into an “ordinary” western ski resort. Yet this concerted effort produces a variety of tensions and contradictions that ultimately undo the normalization of the colonial space, comprising a test case of the convoluted ways in which mimicry of space, not merely in space, generates various forms of slippage, excess and ambivalence.
Barrio Women's Invited and Invented Spaces Against Urban Elitisation in Chacao, Venezuela
Authors: Velásquez Atehortúa Juan
Published: December 2013

Outright victories against urban elitisation are rare in the current urban revolution. This article highlights how urban elitisation is confronted in Chacao, the most elite and urban part of Venezuela. Initially it reviews how this urban elitisation created the main economic, political and military strongholds of the opposition to the Bolivarian revolution. Then, in contesting it, the urban and Bolivarian revolutions feed each other through women's participation in invited and invented spaces of citizenship. From such spaces, Chacao women in their settler's movement organised struggles of insurgent citizenship to stop elitist urban renewal agendas and develop further forms of insurgent urbanism to conduct an urban renewal from below and establish a New Socialist Community for 600 families. They emerged as a revolutionary class to implement Bolivarian policies addressing the inefficiency and opportunism of the bureaucratic state and contesting urban elitisation with an anti‐capitalist and anti‐imperialist insurgent urbanism.
Rheumatoid arthritis and outcomes in first and subsequent births based on data from a national birth registry
Authors: Wallenius Marianne , Salvesen Kjell Å. , Daltveit Anne K. , Skomsvoll Johan F.
Published: December 2013

Objective

To examine associations between rheumatoid arthritis (RA) and pregnancy outcomes in first and subsequent births.

Design

Cohort study.

Setting

Study based on data registered in the Medical Birth Registry of Norway from the period 1 December 1998 to 31 December 2009.

Population

Singleton births in women recorded with RA (n = 1496) and reference deliveries from the general population (n = 625 642).

Methods

Outcomes of first and subsequent births were analyzed separately. First birth was defined as the first delivery of nulliparous women. Associations between RA and maternal and perinatal outcomes were assessed in logistic regression analyses and adjusted for maternal age at delivery, gestational age, smoking habits and for previous cesarean section when relevant.

Main outcome measures

Maternal and perinatal outcomes.

Results

Vaginal bleeding was observed more often among women with RA both in first pregnancy [adjusted odds ratio (aOR) 1.8, 95% CI 1.3–2.4] and in subsequent pregnancies (aOR 1.4, 95% CI 1.1–1.9). Elective cesarean section was more common among women with RA both in the first birth (aOR 2.0, 95% CI 1.4–2.8) and in subsequent births (aOR 1.5, 95% CI 1.2–2.0). Preterm delivery was more frequent among women with RA than the reference population in first pregnancy (aOR 1.5, 95% CI 1.1–2.0) and in subsequent pregnancies (aOR 1.5, 95% CI 1.1–1.9).

Conclusion

Complications and poor pregnancy outcomes were more often observed in women with RA and the greatest differences were observed in the first pregnancy.
Reliability of histological malignancy grade, ER and HER2 status on core needle biopsy vs surgical specimen in breast cancer
Authors: Munch‐Petersen Helga D. , Rasmussen Birgitte B. , Balslev Eva
Published: December 2013

Early determination of malignancy grade and biomarkers in primary breast cancer is important when planning the treatment with neoadjuvant therapy and breast‐conserving surgery. The aim of this study was to assess the reliability of malignancy grade on core needle biopsies, and to compare the concordance of ER and HER2 status on core needle biopsies vs surgical specimens. Eighty‐nine patients with invasive ductal or lobular carcinoma were included. Malignancy grade was upgraded by one degree in 23.0%. The mitotic count had most impact on the malignancy grade, and may be underestimated on core needle biopsies compared with surgical specimens. ER status was concordant in core needle biopsies and surgical specimens in 98.0%, but should be repeated when doubtfully negative. HER2 status was concordant in 84.0% prior to FISH‐HER2. Including FISH‐HER2 data, the core needle biopsies showed a final total concordance of 95.4%. In conclusion, ER and HER2 are useful markers in core needle biopsies, providing a reliable base for preoperative decisions in neoadjuvant chemotherapy, and may be omitted on surgical specimens with certain precautions and exceptions. Determination of malignancy grade should be repeated on surgical specimens, and one should be aware of underestimation on core needle biopsies.
Diversity of bla genes and low incidence of CTX‐M in plasmid‐mediated AmpC‐producing Escherichia coli clinical isolates
Authors: Galán‐Sánchez Fátima , Aznar‐Marín Pilar , Marín‐Casanova Pilar , Rodríguez‐Iglesias Manuel
Published: December 2013

The aim of this study was to characterize plasmid‐mediated AmpC (pAmpC)‐producing Escherichia coli clinical isolates. A total of 101 strains with AmpC‐susceptibility pattern were prospectively included. All isolates were tested by multiplex PCR to detect different bla genes. Phylogenetic groups were determined by a multiplex PCR assay. Antimicrobial susceptibility was tested by a microdilution commercial method. Presence of blapAmpC was detected in 79 (78.2%) of the strains; in these pAmpC‐producing isolates, blaTEM was detected in 41 (51.9%) strains, blaSHV in 5 (6.3%) strains, blaOXA in 3 (3.8%) strains, and blaCTX‐M in 3 (3.8%) strains. blaVIM and blaKPC were detected in one strain. Sixteen strains belonged to phylogroup A, 27 to B1, 20 to B2, and 16 to D. As conclusion, the majority of the strains of E. coli with AmpC‐susceptibility pattern are pAmpC positive, although the association of extended‐spectrum beta‐lactamases (ESBL) and pAmpC is unusual.