bluuebunny/crossref_metadata_2025 huggingface dataset:
Communication: Towards first principles theory of relaxation in supercooled liquids formulated in terms of cooperative motion
Authors: Freed Karl F.
Published: October 2014

A general theory of the long time, low temperature dynamics of glass-forming fluids remains elusive despite the almost 20 years since the famous pronouncement by the Nobel Laureate P. W. Anderson, “The deepest and most interesting unsolved problem in solid state theory is probably the theory of the nature of glass and the glass transition” [Science 267, 1615 (1995)]. While recent work indicates that Adam-Gibbs theory (AGT) provides a framework for computing the structural relaxation time of supercooled fluids and for analyzing the properties of the cooperatively rearranging dynamical strings observed in low temperature molecular dynamics simulations, the heuristic nature of AGT has impeded general acceptance due to the lack of a first principles derivation [G. Adam and J. H. Gibbs, J. Chem. Phys. 43, 139 (1965)]. This deficiency is rectified here by a statistical mechanical derivation of AGT that uses transition state theory and the assumption that the transition state is composed of elementary excitations of a string-like form. The strings are assumed to form in equilibrium with the mobile particles in the fluid. Hence, transition state theory requires the strings to be in mutual equilibrium and thus to have the size distribution of a self-assembling system, in accord with the simulations and analyses of Douglas and co-workers. The average relaxation rate is computed as a grand canonical ensemble average over all string sizes, and use of the previously determined relation between configurational entropy and the average cluster size in several model equilibrium self-associating systems produces the AGT expression in a manner enabling further extensions and more fundamental tests of the assumptions.
Regrowth-free single-mode quantum cascade lasers with power consumption below 1 W
Authors: Briggs Ryan M. , Frez Clifford , Borgentun Carl E. , Forouhar Siamak
Published: October 2014

We report on single-mode distributed-feedback quantum cascade lasers emitting at 4.8 μm with continuous-wave threshold power consumption as low as 0.76 W at 20 °C and 0.98 W at 50 °C. Following growth of the laser active region and semiconductor cladding layers by a single molecular beam epitaxy process, devices with 4-μm-wide ridges and vertical sidewall gratings were fabricated using plasma etching and standard dielectric and metal deposition processes. In terms of mode stability, output power, and efficiency, we show that lasers with 1-mm cavity length and high-reflectivity back-facet coatings can match the performance of buried heterostructure devices, but with the advantage of requiring only a single epitaxial growth step.
Localized surface plasmon resonance enhanced ultraviolet emission and F-P lasing from single ZnO microflower
Authors: Lin Yi , Li Jitao , Xu Chunxiang , Fan Xuemei , Wang Baoping
Published: October 2014

In this work, monodispersed ZnO microflowers are fabricated by a vapor phase transport method, and Au nanoparticles (NPs) are directly decorated on the surface of the ZnO microflowers. The micro-photoluminescence of a single ZnO microflower demonstrates that the near band-edge emission is tremendously enhanced while the defect-related emission is completely suppressed after Au decoration. The average enhancement factor reaches up to 65 fold. The enhancement mechanism is assumed to be the electron transfer from excited Au NPs to the ZnO microflower induced by the localized surface plasmon resonance based on the time-resolved photoluminescence. The enhanced F-P lasing from a single ZnO sample is further realized.
Fano-induced solar absorption enhancement in thin organic photovoltaic cells
Authors: Le Khai Q. , Alù Andrea
Published: October 2014

We explore the enhancement mechanisms associated with combined Fano resonances in metasurfaces, demonstrating enhanced absorption efficiency of thin-film organic solar cells over a moderately broad bandwidth of operation. An integrated AM1.5G (air mass 1.5 global solar energy) absorption enhancement of up to 44.6% is obtained, corresponding to an increase in solar absorption at normal incidence from 48% to 69.4%. Fano resonances are induced in arrays of four asymmetric-arranged nanodisks (nanopillars) with small inter-disk gaps, incorporated into an organic thin-film. They are shown to play a dominant role in light-trapping enhancement, mediated by combined localized surface plasmon resonances.
Dynamic behavior of microscale particles controlled by standing bulk acoustic waves
Authors: Greenhall J. , Guevara Vasquez F. , Raeymaekers B.
Published: October 2014

We analyze the dynamic behavior of a spherical microparticle submerged in a fluid medium, driven to the node of a standing bulk acoustic wave created by two opposing transducers. We derive the dynamics of the fluid-particle system taking into account the acoustic radiation force and the time-dependent and time-independent drag force acting on the particle. Using this dynamic model, we characterize the transient and steady-state behavior of the fluid-particle system as a function of the particle and fluid properties and the transducer operating parameters. The results show that the settling time and percent overshoot of the particle trajectory are dependent on the ratio of the acoustic radiation force and time-independent damping force. In addition, we show that the particle oscillates around the node of the standing wave with an amplitude that depends on the ratio of the time-dependent drag forces and the particle inertia.
Turn on of new electronic paths in Fe-SiO2 granular thin film
Authors: Boff M. A. S. , Hinrichs R. , Canto B. , Mesquita F. , Baptista D. L. , Fraga G. L. F. , Pereira L. G.
Published: October 2014

The electrical properties of Fe-SiO2 have been studied in the low-field regime (eΔV ≪ kBT), varying the injected current and the bias potential. Superparamagnetism and a resistance drop of 4400 Ω (for a voltage variation of 15 V) were observed at room temperature. This resistance drop increased at lower temperatures. The electrical properties were described with the “Mott variable range hopping” model explaining the behavior of the electrical resistance and the electronic localization length as due to the activation of new electronic paths between more distant grains. This non-ohmic resistance at room temperature can be important for properties dependent of electrical current (magnetoresistance, Hall effect, and magnetoimpedance).
Reversible modulated mid-infrared absorption of Ag/TiO2 by photoinduced interfacial charge transfer
Authors: Xu S. C. , Li L. , Pan S. S. , Luo Y. Y. , Zhang Y. X. , Li G. H.
Published: October 2014

An enhanced mid-infrared absorption in Ag nanoparticles-decorated TiO2 microflowers was reported. It was found that the mid-infrared absorption of the Ag/TiO2 complex depends strongly on the content and size of Ag nanoparticles, the higher the Ag nanoparticles content, the stronger the infrared absorption. The average reflectivity in the entire mid-infrared region of the microflowers drops from 57.6% to 10.5% after Ag nanoparticles decoration. Reversible modulated mid-infrared absorption properties were found in the Ag/TiO2 complexes upon alternative illumination of visible and UV light due to the photoinduced interfacial electron transfer between TiO2 semiconductor and Ag nanoparticles.
Virtually pure near-infrared electroluminescence from exciplexes at polyfluorene/hexaazatrinaphthylene interfaces
Authors: Tregnago G. , Fléchon C. , Choudhary S. , Gozalvez C. , Mateo-Alonso A. , Cacialli F.
Published: October 2014

Electronic processes at the heterojunction between chemically different organic semiconductors are of special significance for devices such as light-emitting diodes (LEDs) and photovoltaic diodes. Here, we report the formation of an exciplex state at the heterojunction of an electron-transporting material, a functionalized hexaazatrinaphthylene, and a hole-transporting material, poly(9,9-dioctylfluorene-alt-N-(4-butylphenyl)diphenylamine) (TFB). The energetics of the exciplex state leads to a spectral shift of ∼1 eV between the exciton and the exciplex peak energies (at 2.58 eV and 1.58 eV, respectively). LEDs incorporating such bulk heterojunctions display complete quenching of the exciton luminescence, and a nearly pure near-infrared electroluminescence arising from the exciplex (at ∼1.52 eV) with >98% of the emission at wavelengths above 700 nm at any operational voltage.
The effects of surface bond relaxation on electronic structure of Sb2Te3 nano-films by first-principles calculation
Authors: Li C. , Zhao Y. F. , Fu C. X. , Chi B. Q. , Gong Y. Y. , Sun C. Q.
Published: October 2014

The effects of vertical compressive stress on Sb2Te3 nano-films have been investigated by the first principles calculation, including stability, electronic structure, crystal structure, and bond order. It is found that the band gap of nano-film is sensitive to the stress in Sb2Te3 nano-film and the critical thickness increases under compressive stress. The band gap and band order of Sb2Te3 film has been affected collectively by the surface and internal crystal structures, the contraction ratio between surface bond length of nano-film and the corresponding bond length of bulk decides the band order of Sb2Te3 film.
Exploration of stable compounds, crystal structures, and superconductivity in the Be-H system
Authors: Yu Shuyin , Zeng Qingfeng , Oganov Artem R. , Hu Chaohao , Frapper Gilles , Zhang Litong
Published: October 2014

Using first-principles variable-composition evolutionary methodology, we explored the high-pressure structures of beryllium hydrides between 0 and 400 GPa. We found that BeH2 remains the only stable compound in this pressure range. The pressure-induced transformations are predicted as Ibam→P3̄m1→R3̄m→Cmcm→P4/nmm, which occur at 24, 139, 204 and 349 GPa, respectively. P3̄m1 and R3̄m structures are layered polytypes based on close packings of H atoms with Be atoms filling all octahedral voids in alternating layers. Cmcm and P4/nmm contain two-dimensional triangular networks with each layer forming a kinked slab in the ab-plane. P3̄m1 and R3̄m are semiconductors while Cmcm and P4/nmm are metallic. We have explored superconductivity of both metal phases, and found large electron-phonon coupling parameters of λ = 0.63 for Cmcm with a Tc of 32.1-44.1 K at 250 GPa and λ = 0.65 for P4/nmm with a Tc of 46.1-62.4 K at 400 GPa. The dependence of Tc on pressure indicates that Tc initially increases to a maximum of 45.1 K for Cmcm at 275 GPa and 97.0 K for P4/nmm at 365 GPa, and then decreases with increasing pressure for both phases.
Determination of constitutive parameters of homogeneous metamaterial slabs by a novel calibration-independent method
Authors: Hasar U. C. , Buldu G. , Bute M. , Barroso J. J. , Karacali T. , Ertugrul M.
Published: October 2014

A calibration-independent line-line method for broadband and simultaneous constitutive parameters determination of homogeneous metamaterial (MM) slabs is proposed. It is shown that the sufficient condition for parameters retrieval by the proposed method is to measure uncalibrated (raw) complex scattering parameters of measurement cells (different air regions in free-space) which are completely and partially loaded by the two identical metamaterial slabs. The stability of derived equations for different measurement uncertainty cases is analyzed. We have validated the proposed method by using simulated scattering parameters of a MM slab with split-ring-resonators and then by comparing the extracted electromagnetic parameters with those of a general method used in the literature in the cases with and without a small offset in reference-plane positions (as well as other measurement errors). From this comparison, we note that while the general method does not eliminate those errors, the proposed method not only does not introduce the non-physical anti-resonance behavior but also removes the measurement errors arising from different mechanisms such as inaccurate reference-plane positions and mismatched connections.
Solution for acoustic field of thermo-acoustic emission from arbitrary source
Authors: Hu Hanping , Wang Dongdong , Wang Zedong
Published: October 2014

In this work, an expression for acoustic field of thermo-acoustic (TA) emission from arbitrary source is presented by deriving the solutions of TA emission from spherical surface and point source in gas and then taking advantage of the point sources superposition and the surface heat distribution factor. Accordingly, the computational analysis of acoustic pressure field of TA emission is extended to three-dimensional cases. The theory developed in this work is in good agreement with the experimental results and applicable for solving many complex and important TA emission problems including nanothermophones and phased array and impulse-driven TA emissions.
Ferroelectric gate tunnel field-effect transistors with low-power steep turn-on
Authors: Lee M. H. , Wei Y.-T. , Lin J.-C. , Chen C.-W. , Tu W.-H. , Tang M.
Published: October 2014

Using a ferroelectric PbZrTiO3 gate stack, the range of the steep subthreshold swing in tunnel field-effect transistors was extended by 3.5 orders of magnitude demonstrating an improvement in the swing (by approximately double the slope). The drain conductance (gd) shows only 16% enhancement with large V DS (∼−1.5V) indicates internal voltage amplification with ferroelectric negative capacitance effect beneficial to small lateral drain-source bias voltages (−0.1 V). The concept of coupling the ferroelectric polarization is proposed. The power consumption is also discussed in low-power applications of steep subthreshold slope devices.
Separating astrophysical sources from indirect dark matter signals
Authors: Siegal-Gaskins Jennifer M.
Published: October 2014

Indirect searches for products of dark matter annihilation and decay face the challenge of identifying an uncertain and subdominant signal in the presence of uncertain backgrounds. Two valuable approaches to this problem are (
i
) using analysis methods which take advantage of different features in the energy spectrum and angular distribution of the signal and backgrounds and (
ii
) more accurately characterizing backgrounds, which allows for more robust identification of possible signals. These two approaches are complementary and can be significantly strengthened when used together. I review the status of indirect searches with gamma rays using two promising targets, the Inner Galaxy and the isotropic gamma-ray background. For both targets, uncertainties in the properties of backgrounds are a major limitation to the sensitivity of indirect searches. I then highlight approaches which can enhance the sensitivity of indirect searches using these targets.
Functional specialization of stomatal bHLHs through modification of DNA-binding and phosphoregulation potential
Authors: Davies Kelli A. , Bergmann Dominique C.
Published: October 2014

Significance

Developmental complexity often parallels expansion of transcription factor families, and highly similar proteins can play related but distinct roles in the development of cell lineages and cell types. Comparative sequence analyses can point to regions of proteins that may be involved in specialization, but complementary functional approaches are required to confirm these roles. Using the “natural laboratory” of stomatal development in which closely related basic helix–loop–helix (bHLH) transcription factors regulate distinct sequential processes, we assign functions to unique domains and identify functional divergences hidden within regions of sequence identity.
PhosphoPICK: modelling cellular context to map kinase-substrate phosphorylation events
Authors: Patrick Ralph , Lê Cao Kim-Anh , Kobe Bostjan , Bodén Mikael
Published: October 2014

Motivation: The determinants of kinase-substrate phosphorylation can be found both in the substrate sequence and the surrounding cellular context. Cell cycle progression, interactions with mediating proteins and even prior phosphorylation events are necessary for kinases to maintain substrate specificity. While much work has focussed on the use of sequence-based methods to predict phosphorylation sites, there has been very little work invested into the application of systems biology to understand phosphorylation. Lack of specificity in many kinase substrate binding motifs means that sequence methods for predicting kinase binding sites are susceptible to high false-positive rates.

Results: We present here a model that takes into account protein–protein interaction information, and protein abundance data across the cell cycle to predict kinase substrates for 59 human kinases that are representative of important biological pathways. The model shows high accuracy for substrate prediction (with an average AUC of 0.86) across the 59 kinases tested. When using the model to complement sequence-based kinase-specific phosphorylation site prediction, we found that the additional information increased prediction performance for most comparisons made, particularly on kinases from the CMGC family. We then used our model to identify functional overlaps between predicted CDK2 substrates and targets from the E2F family of transcription factors. Our results demonstrate that a model harnessing context data can account for the short-falls in sequence information and provide a robust description of the cellular events that regulate protein phosphorylation.

Availability and implementation: The method is freely available online as a web server at the website http://bioinf.scmb.uq.edu.au/phosphopick .

Contact:  m.boden@uq.edu.au

Supplementary information:  Supplementary data are available at Bioinformatics online.
A stochastic automaton model for simulating kinesin processivity
Authors: Khataee Hamidreza , Liew Alan Wee-Chung
Published: October 2014

Motivation: Cellular interactions of kinesin-1, an adenosine triphosphate (ATP)-driven motor protein capable of undergoing multiple steps on a microtubule (MT), affect its mechanical processivity, the number of steps taken per encounter with MT. Even though the processivity of kinesin has been widely studied, a detailed study of the factors that affect the stepping of the motor along MT is still lacking.

Results: We model the cellular interactions of kinesin as a probabilistic timed automaton and use the model to simulate the mechanical processivity of the motor. Theoretical analysis suggests: (i) backward stepping tends to be powered by ATP hydrolysis, rather than ATP synthesis, (ii) backward stepping powered by ATP synthesis is more likely to happen with limiting ATP concentration ([ATP]) at high loads and (iii) with increasing load the frequency of backward stepping powered by ATP hydrolysis at high [ATP] is greater than that powered by ATP synthesis at limiting [ATP]. Together, the higher frequency of backward stepping powered by ATP hydrolysis than by ATP synthesis is found to be a reason for the more dramatic falling of kinesin processivity with rising load at high [ATP] compared with that at low [ATP]. Simulation results further show that the processivity of kinesin can be determined by the number of ATP hydrolysis and synthesis kinetic cycles taken by the motor before becoming inactive. It is also found that the duration of a backward stepping cycle at high loads is more likely to be less than that of a forward stepping cycle.

Contact:  h.r.khataee@griffithuni.edu.au or a.liew@griffith.edu.au .
Integrative data analysis indicates an intrinsic disordered domain character of Argonaute-binding motifs
Authors: Zielezinski Andrzej , Karlowski Wojciech M.
Published: October 2014

Motivation: Argonaute-interacting WG/GW proteins are characterized by the presence of repeated sequence motifs containing glycine (G) and tryptophan (W). The motifs seem to be remarkably adaptive to amino acid substitutions and their sequences show non-contiguity. Our previous approach to the detection of GW domains, based on scoring their gross amino acid composition, allowed annotation of several novel proteins involved in gene silencing. The accumulation of new experimental data and more advanced applications revealed some deficiency of the algorithm in prediction selectivity. Additionally, W-motifs, though critical in gene regulation, have not yet been annotated in any available online resources.

Results: We present an improved set of computational tools allowing efficient management and annotation of W-based motifs involved in gene silencing. The new prediction algorithms provide novel functionalities by annotation of the W-containing domains at the local sequence motif level rather than by overall compositional properties. This approach represents a significant improvement over the previous method in terms of prediction sensitivity and selectivity. Application of the algorithm allowed annotation of a comprehensive list of putative Argonaute-interacting proteins across eukaryotes. An in-depth characterization of the domains’ properties indicates its intrinsic disordered character. In addition, we created a knowledge-based portal (whub) that provides access to tools and information on RNAi-related tryptophan-containing motifs.

Availability and implementation: The web portal and tools are freely available at http://www.comgen.pl/whub .

Contact:  wmk@amu.edu.pl

Supplementary information:  Supplementary data are available at Bioinformatics online.
Tabhu: tools for antibody humanization
Authors: Olimpieri Pier Paolo , Marcatili Paolo , Tramontano Anna
Published: October 2014

Summary: Antibodies are rapidly becoming essential tools in the clinical practice, given their ability to recognize their cognate antigens with high specificity and affinity, and a high yield at reasonable costs in model animals. Unfortunately, when administered to human patients, xenogeneic antibodies can elicit unwanted and dangerous immunogenic responses. Antibody humanization methods are designed to produce molecules with a better safety profile still maintaining their ability to bind the antigen. This can be accomplished by grafting the non-human regions determining the antigen specificity into a suitable human template. Unfortunately, this procedure may results in a partial or complete loss of affinity of the grafted molecule that can be restored by back-mutating some of the residues of human origin to the corresponding murine ones. This trial-and-error procedure is hard and involves expensive and time-consuming experiments. Here we present tools for antibody humanization (Tabhu) a web server for antibody humanization. Tabhu includes tools for human template selection, grafting, back-mutation evaluation, antibody modelling and structural analysis, helping the user in all the critical steps of the humanization experiment protocol.

Availability:  http://www.biocomputing.it/tabhu

Contact:  anna.tramontano@uniroma1.it , pierpaolo.olimpieri@uniroma1.it

Supplementary information : Supplementary data are available at Bioinformatics online.
Deciphering the origin of flowering plants
Authors: Wang By Ling
Published: October 2014

Colorful flowers decorate our planet with their appealing forms, yet their enigmatic evolutionary origin and rapid early diversification have been regarded as the ‘Goldbach conjecture’ of paleobotany. Else Marie Friis is a prominent professor who in 1981 was the first to identify the small angiosperm flowers that changed our perception of ancestral flowers and opened up a new direction in the study of angiosperm evolution. As a foreign member of Chinese Academy of Sciences (CAS), Professor Friis helps strengthen the scholarly communication and cooperation between China and Europe, especially in paleobotany. NSR got the chance to talk to Professor Friis about her research and developments in this field during her last visit to China. Professor Zhonghe Zhou, a paleontologist at the Institute of Vertebrate Paleontology and Paleoanthropology, CAS, joined the interview.
Incumbency Effects in a Comparative Perspective: Evidence from Brazilian Mayoral Elections
Authors: De Magalhaes Leandro
Published: October 2014

High rerunning rates among incumbents and among the two major parties allow studies of U.S. incumbency advantage to bypass the selection problem of who chooses to rerun. In countries where rerunning is not widespread among individuals or parties, estimation using methods developed for the United States may result in a sample selection bias. In countries with party switching, there may be a disconnect between party and individual estimates. This article proposes a definition of incumbency advantage that is valid for countries that present any of these characteristics and that is valid for cross-country comparison: the effect of incumbency for anindividualpolitician on theunconditionalprobability of winning. I illustrate the issues raised in this article with evidence from Brazilian mayoral elections.
Factors Associated with Improved Survival after Resection of Pancreatic Adenocarcinoma
Authors: Call Tyler R. , Pace Nathan L. , Thorup Datus B. , Maxfield Derric , Chortkoff Ben , Christensen Joslin , Mulvihill Sean J.
Published: October 2014

AbstractAbstract

A model based on retrospective analysis of the records of 144 patients who underwent resection of pancreatic adenocarcinoma between 2001 and 2011 predicted median survival of patients to whom dexamethasone is administered and who have epidural analgesia would be increased from 370 days to 651 days compared to similar patients receiving neither dexamethasone nor epidural analgesia.

Background:

Several retrospective studies suggest that perioperative care and anesthetic management for cancer resection may influence cancer recurrence or patient survival. Various intraoperative techniques such as paravertebral blocks, decreased opioid use, immunomodulation, and perioperative antiinflammatory administration, have previously been assessed for improved patient survival. The aim of this study was to assess associations between perioperative management and survival in patients undergoing resection of pancreatic adenocarcinoma.

Methods:

Survival data and anesthetic records for 144 patients who had surgical resection of pancreatic adenocarcinoma from 2001 to 2012 were obtained and associations were sought between survival and 19 predefined variables. The authors performed a propensity weighted multivariable statistical analysis using Cox proportional hazards.

Results:

Median length of survival was 562 days with 95% confidence interval (471, 680). In a multivariable Cox proportional hazard model of survival, the authors found increased survival in patients who received perioperative epidural analgesia and/or intraoperative dexamethasone. There was a 44% hazard ratio reduction, hazard ratio = 0.56, 95% confidence interval (0.38, 0.87), with dexamethasone. Adjuvant postoperative chemotherapy was associated with longer survival. A decrease in survival was noted in patients who received intraoperative blood transfusions, had poorer histologic grade, and advanced tumor stage.

Conclusions:

The authors report an association between perioperative dexamethasone administration and improved survival in human pancreatic adenocarcinoma patients. An association between use of epidural anesthesia during primary pancreatic cancer surgery and prolonged survival was also observed. Previously identified associations between perioperative blood transfusions and poor tumor histologic grade and decreased survival were confirmed. Further investigations regarding the use of perioperative dexamethasone and neuraxial anesthesia in this patient population are warranted.
Association Mapping across Numerous Traits Reveals Patterns of Functional Variation in Maize
Authors: Wallace Jason G , Bradbury Peter , Zhang Nengyi , Gibon Yves , Stitt Mark , Buckler Edward
Published: October 2014

Phenotypic variation in natural populations results from a combination of genetic effects, environmental effects, and gene-by-environment interactions. Despite the vast amount of genomic data becoming available, many pressing questions remain about the nature of genetic mutations that underlie functional variation. We present the results of combining genome-wide association analysis of 41 different phenotypes in ~5,000 inbred maize lines to analyze patterns of high-resolution genetic association among of 28.9 million single-nucleotide polymorphisms (SNPs) and ~800,000 copy-number variants (CNVs). We show that genic and intergenic regions have opposite patterns of enrichment, minor allele frequencies, and effect sizes, implying tradeoffs among the probability that a given polymorphism will have an effect, the detectable size of that effect, and its frequency in the population. We also find that genes tagged by GWAS are enriched for regulatory functions and are ~50% more likely to have a paralog than expected by chance, indicating that gene regulation and neofunctionalization are strong drivers of phenotypic variation. These results will likely apply to many other organisms, especially ones with large and complex genomes like maize.
Massive bursts of transposable element activity in Drosophila
Authors: Kofler Robert , Nolte Viola , Schlötterer Christian
Published: October 2014

The evolutionary dynamics of transposable element (TE) insertions have been of continued interest since TE activity has important implications for genome evolution and adaptation. Here, we infer the transposition dynamics of TEs by comparing their abundance in naturalD. melanogasterandD. simulanspopulations. Sequencing pools of more than 550 South African flies to at least 320-fold coverage, we determined the genome wide TE insertion frequencies in both species. We show that 46 (49%) TE families inD. melanogasterand 44 (47%) inD. simulansexperienced a recent burst of activity. The bursts of activity affected different TE families in the two species. While inD. melanogasterretrotransposons predominated, DNA transposons showed higher activity levels inD. simulans. We propose that the observed TE dynamics are the outcome of the demographic history of the two species, with habitat expansion triggering a period of rapid evolution.
A simple method for constructing magneticEscherichia coli
Authors: Sun Mengyi , Lu Yong-jun
Published: October 2014

Magnetic force can serve as an ideal way to control the spatial behavior of microorganisms, because of its flexibility and penetrability. By incubation with the biocompatible compound, ammonium ferric citrate, as an iron source, we magnetizedEscherichia coli, the most programmable chassis in synthetic biology. To enhance the magnetization efficiency, the ferritin protein, FtnA, fromE. coliwas cloned and overexpressed in strain BL21(DE3). The magnetization effect was observed within 30 min after harvest of bacteria, and the concentration of ammonium ferric acid used could be as low as 0.5 mM. Using different shapes of magnetic fields, different patterns could be generated easily. Our method may set up the foundation for a rational design of spatial structure of cell communities, which is important for their actual application.
Estimating genotype error rates from high-coverage next-generation sequence data
Authors: Wall Jeffrey D. , Tang Ling Fung , Zerbe Brandon , Kvale Mark N. , Kwok Pui-Yan , Schaefer Catherine , Risch Neil
Published: October 2014

Exome and whole-genome sequencing studies are becoming increasingly common, but little is known about the accuracy of the genotype calls made by the commonly used platforms. Here we use replicate high-coverage sequencing of blood and saliva DNA samples from four European-American individuals to estimate lower bounds on the error rates of Complete Genomics and Illumina HiSeq whole-genome and whole-exome sequencing. Error rates for nonreference genotype calls range from 0.1% to 0.6%, depending on the platform and the depth of coverage. Additionally, we found (1) no difference in the error profiles or rates between blood and saliva samples; (2) Complete Genomics sequences had substantially higher error rates than Illumina sequences had; (3) error rates were higher (up to 6%) for rare or unique variants; (4) error rates generally declined with genotype quality (GQ) score, but in a nonlinear fashion for the Illumina data, likely due to loss of specificity of GQ scores greater than 60; and (5) error rates increased with increasing depth of coverage for the Illumina data. These findings, especially (3)–(5), suggest that caution should be taken in interpreting the results of next-generation sequencing-based association studies, and even more so in clinical application of this technology in the absence of validation by other more robust sequencing or genotyping methods.
ArabidopsisTTG2 RegulatesTRYExpression through Enhancement of Activator Complex-Triggered Activation
Authors: Pesch Martina , Dartan Burcu , Birkenbihl Rainer , Somssich Imre E. , Hülskamp Martin
Published: October 2014

Trichome patterning in Arabidopsis thaliana is regulated by a regulatory feedback loop of the trichome promoting factors TRANSPARENT TESTA GLABRA1 (TTG1), GLABRA3 (GL3)/ENHANCER OF GL3 (EGL3), and GL1 and a group of homologous R3MYB proteins that act as their inhibitors. Together, they regulate the temporal and spatial expression of GL2 and TTG2, which are considered to control trichome cell differentiation. In this work, we show that TTG2 is a specific activator of TRY (but not CPC or GL2). The WRKY protein TTG2 binds to W-boxes in a minimal promoter fragment of TRY, and these W-boxes are essential for rescue of the try mutant phenotype. We further show that TTG2 alone is not able to activate TRY expression, but rather drastically enhances the activation by TTG1 and GL3. As TTG2 physically interacts with TTG1 and because TTG2 can associate with GL3 through its interaction with TTG1, we propose that TTG2 enhances the activity of TTG1 and GL3 by forming a protein complex.
Myrosin Idioblast Cell Fate and Development Are Regulated by theArabidopsisTranscription Factor FAMA, the Auxin Pathway, and Vesicular Trafficking
Authors: Li Meng , Sack Fred D.
Published: October 2014

Crucifer shoots harbor a glucosinolate-myrosinase system that defends against insect predation. Arabidopsis thaliana myrosinase (thioglucoside glucohydrolase [TGG]) accumulates in stomata and in myrosin idioblasts (MIs). This work reports that the basic helix-loop-helix transcription factor FAMA that is key to stomatal development is also expressed in MIs. The loss of FAMA function abolishes MI fate as well as the expression of the myrosinase genes TGG1 and TGG2. MI cells have previously been reported to be located in the phloem. Instead, we found that MIs arise from the ground meristem rather than provascular tissues and thus are not homologous with phloem. Moreover, MI patterning and morphogenesis are abnormal when the function of the ARF-GEF gene GNOM is lost as well as when auxin efflux and vesicular trafficking are chemically disrupted. Stomata and MI cells constitute part of a wider system that reduces plant predation, the so-called “mustard oil bomb,” in which vacuole breakage in cells harboring myrosinase and glucosinolate yields a brew toxic to many animals, especially insects. This identification of the gene that confers the fate of MIs, as well as stomata, might facilitate the development of strategies for engineering crops to mitigate predation.
Habitat evaluation for outbreak of Yangtze voles (Microtus fortis) and management implications
Authors: XU Zhenggang , ZHAO Yunlin , LI Bo , ZHANG Meiwen , SHEN Guo , WANG Yong
Published: October 2014

Rodent pests severely damage agricultural crops. Outbreak risk models of rodent pests often do not include sufficient information regarding geographic variation. Habitat plays an important role in rodent–pest outbreak risk, and more information about the relationship between habitat and crop protection is urgently needed. The goal of the present study was to provide an outbreak risk map for the Dongting Lake region and to understand the relationship between rodent–pest outbreak variation and habitat distribution. The main rodent pests in the Dongting Lake region are Yangtze voles (Microtus fortis). These pests cause massive damage in outbreak years, most notably in 2007. Habitat evaluation and ecological details were obtained by analyzing the correlation between habitat suitability and outbreak risk, as indicated by population density and historical events. For the source‐sink population, 96.18% of Yangtze vole disaster regions were covered by a 10‐km buffer zone of suitable habitat in 2007. Historical outbreak frequency and peak population density were significantly correlated with the proportion of land covered by suitable habitat (r = 0.68, P = 0.04 and r = 0.76, P = 0.03, respectively). The Yangtze vole population tends to migrate approximately 10 km in outbreak years. Here, we propose a practical method for habitat evaluation that can be used to create integrated pest management plans for rodent pests when combined with basic information on the biology, ecology and behavior of the target species.
Screening of Tea Extract and Theaflavins for Inhibitory Effects on the Biological Activity and Production of Staphylococcal Enterotoxin A
Authors: Shimamura Yuko , Aoki Natsumi , Sugiyama Yuka , Nakayama Tsutomu , Masuda Shuichi
Published: October 2014

This study aimed to develop a novel method with tea extracts and its components, to reduce the risk of foodborne illnesses caused by the bacterial toxin staphylococcal enterotoxin A (SEA). The potential effect of tea extracts, theaflavins, and epitheaflagallin on staphylococcal growth was studied. A broth microdilution method was used to determine the minimum inhibitory concentration of these samples against an SEA‐producing strain, Staphylococcus aureus C‐29. The following assays were performed to evaluate various effects on concentrations of no effect on staphylococcal growth. The interactions of theaflavin‐rich green tea extracts (TGE), theaflavins, and epitheaflagallin to cultured S. aureus C‐29 were determined using Western blot analysis. As a result, all samples suppressed the binding affinity of the anti‐SEA antibody to SEA. Since these samples could react directly with SEA, we examined whether they could bind to SEA. Our results demonstrated that binding of the anti‐SEA antibody to 4 theaflavins‐treated SEA was inhibited in a dose‐dependent manner. On the other hand, the production of SEA was significantly decreased by treatment with TGE and epitheaflagallin. Based on the finding that TGE and epitheaflagallin inhibit the production of SEA, we further examined the relative expression levels of sea toxin‐encoding genes after treatment with TGE and epitheaflagallin with real‐time RT‐PCR. TGE and epitheaflagallin significantly supressed the gene transcription of SEA in S. aureus C‐29. We then tested whether the samples block the biological activity of SEA in murine spleen cells. TGE, theaflavins, and epitheaflagallin became inactivated the biological activity of SEA. These results suggest that edible and safe compounds in tea can be used to inactivate both pathogens and toxins.
Phenolic Profile and Antioxidant Activity of Extracts Prepared from Fermented Heat‐Stabilized Defatted Rice Bran
Authors: Webber Daniel M. , Hettiarachchy Navam S. , Li Ruiqi , Horax Ronny , Theivendran Sivarooban
Published: October 2014

Heat‐stabilized, defatted rice bran (HDRB) serves as a potential source of phenolic compounds which have numerous purported health benefits. An estimated 70% of phenolics present in rice bran are esterified to the arabinoxylan residues of the cell walls. Release of such compounds could provide a value‐added application for HDRB. The objective of this study was to extract and quantify phenolics from HDRB using fermentation technology. Out of 8 organisms selected for rice bran fermentation, Bacillus subtilis subspecies subtilis had the maximum phenolic release of 26.8 mg ferulic acid equivalents (FAE) per gram HDRB. Response surface methodology was used to further optimize the release of rice bran phenolics. An optimum of 28.6 mg FAE/g rice bran was predicted at 168 h, 0.01% inoculation level, and 100 mg HDRB/mL. Fermentation of HDRB for 96 h with B. subtilis subspecies subtilis resulted in a significant increase in phenolic yield, phenolic concentration, and radical scavenging capacity. Fermented rice bran had 4.86 mg gentistic acid, 1.38 mg caffeic acid, 6.03 mg syringic acid, 19.02 mg (‐)‐epicatechin, 4.08 mg p‐courmaric acid, 4.64 mg ferulic acid, 10.04 mg sinapic acid, and 17.59 mg benzoic acid per 100 g fermented extract compared to 0.65 mg p‐courmaric acid and 0.36 mg ferulic acid per 100 g nonfermented extract. The high phenolic content and antioxidant activity of fermented HDRB extract indicates that rice bran fermentation under optimized condition is a potential means of meeting the demand for an effective and affordable antioxidant.
Characterization of Physicochemical Properties and IgE‐Binding of Soybean Proteins Derived from the HHP‐Treated Seeds
Authors: Yang Hui , Yang Anshu , Gao Jinyan , Chen Hongbing
Published: October 2014

The aim of this work was to evaluate the characterization of physicochemical properties and IgE‐binding of soybean proteins derived from the high hydrostatic pressure (HHP) treated seeds. Soybean seeds were treated by HHP at different pressures, and changes in the physicochemical properties of soybean proteins were characterized by proteins solubility, free sulfhydryl (SH) content, surface hydrophobicity, and secondary structures. Sodium dodecyl sulphate‐polyacrylamide gel electrophoresis (SDS‐PAGE) and enzyme‐linked immunoabsorbent assay (ELISA) were used to define the proteins patterns and IgE‐binding ability. The results showed that HHP treatment in the ranges of 0 to 500 MPa led to a slight but gradual decline in free SH content. The solubility and hydrophobicity of soybean proteins increased sharply from 100 to 200 MPa, and gradually decreased upon the further increase of pressure. The α‐helix and β‐sheets contents of soybean proteins decreased, while the random coil content increased. The SDS‐PAGE showed that HHP treatment of 100 to 200 MPa could dissociate the proteins, breaking the aggregates into smaller units, while the treatment ranging from 300 to 500 MPa could induce the proteins aggregation into larger units. Moreover, the ELISA revealed that the IgE‐binding of soybean proteins after HHP treatment at 200 MPa decreased 61.7% compared to the untreated group. Our findings suggested that HHP processing could not only modify the physicochemical properties of soybean proteins, but also significantly reduce its IgE‐binding at an appropriate pressure level.
Urine albumin–creatinine ratio in women with gestational diabetes: Its link with glycaemic status
Authors: Wong Vincent W. , Chong Shanley , Jalaludin Bin , Russell Hamish , Depczynski Barbara
Published: October 2014

Background

Micro‐albuminuria has been established as a marker for micro‐vascular disease. Spot urine albumin‐to‐creatinine ratio (UACR), even in the high normal range, predicts future cardiovascular events. The value of UACR in women with gestational diabetes mellitus (GDM) during pregnancy is uncertain.

Aim

The objectives of this study were to assess the associations between UACR (performed at the time of GDM diagnosis) and various maternal parameters and to evaluate its correlation with pregnancy outcomes.

Materials and Methods

We conducted a retrospective review of women with GDM who attended antenatal clinics at a single centre between March 2010 and September 2013.

Results

Among 1015 women included in this study, high UACR levels were associated with advancing maternal age, maternal obesity, gestational hypertension, elevated glycosylated haemoglobin (HbA1c) and high fasting glucose level. After adjustments for various maternal factors, only advancing age, HbA1c and fasting glucose level were associated with UACR. In terms of pregnancy outcomes, elevated UACR was not associated with adverse events, but was a predictor for pre‐eclampsia.

Conclusions

The finding that UACR was associated with glycaemic status in women with GDM suggests early micro‐vascular disease may be present in women who had greater degree of hyperglycaemia. This raises the question of whether women with GDM and elevated UACR may be at higher risk of developing cardiovascular disease in the future. Long‐term follow‐up of this subgroup of women would be worthwhile.
Risks and benefits of hysteroscopy and endometrial sampling as a standard procedure for assessing serendipitous findings of endometrial thickening in postmenopausal women
Authors: Aston Benjamin , Weaver Edward
Published: October 2014

A retrospective study was undertaken of 35 asymptomatic postmenopausal women undergoing hysteroscopy, dilatation and curettage (H D&C) for an incidental finding of thickened endometrium to assess the rate of significant pathological findings, cost per finding and complication rate of any procedures performed. This study found one case of endometrial adenocarcinoma (1/35; 3%) at an estimated cost per significant finding of $507,116 with an estimated 11.6 complication events per finding.
Can we identify changes in fascial paravaginal supports after childbirth?
Authors: Cassadó‐Garriga Jordi , Wong Vivien , Shek Kalai , Dietz Hans Peter
Published: October 2014

Background

Defects of anterior vaginal wall fascia are generally assumed to be factors in the aetiology of cystocele. However, to date, there is very little information on diagnosis by imaging.

Aim

To document the appearance of vaginal fornices before and after childbirth using 4D ultrasound volume data sets as an aid in diagnosing paravaginal defects of the anterior vaginal wall.

Materials and Methods

This study was performed by re‐analysing data sets obtained in a previously published study involving ante‐ and postpartum pelvic floor assessment by ultrasound. Two hundred and two nulliparous women had been seen at a mean gestation of 37.2 weeks at two tertiary hospitals. One hundred and sixty‐three returned 3 months postpartum. All the participants underwent an interview and 4D translabial ultrasound at both antepartum and postpartum appointments. The integrity of vaginal fornices and levator ani was assessed by tomographic ultrasound.

Results

Vaginal fornices were assessed in both ante‐ and postnatal volumes, and loss of forniceal tenting was found in 85 patients (52%). On average, seven slices were affected (range, 1–16). On multivariate analysis, controlling for potential confounders, including partial/complete avulsion, loss of forniceal tenting remained independently associated with increased cystocele descent (P = 0.005).

Conclusions

Vaginal childbirth is associated with loss of tenting of the vaginal fornices, independent of levator trauma, and also with impaired anterior vaginal wall support. This evidence suggests the existence of paravaginal defects and may imply a role for such defects in the causation of anterior vaginal wall prolapse.