bluuebunny/crossref_metadata_2025 huggingface dataset:
Observation of spectral composition and polarization of sub-terahertz emission from dense plasma during relativistic electron beam–plasma interaction
Authors: Arzhannikov A. V. , Burdakov A. V. , Burmasov V. S. , Gavrilenko D. E. , Ivanov I. A. , Kasatov A. A. , Kuznetsov S. A. , Mekler K. I. , Polosatkin S. V. , Postupaev V. V. , Rovenskikh A. F. , Sinitsky S. L. , Sklyarov V. F. , Vyacheslavov L. N.
Published: August 2014

The paper presents results of measurements of sub-terahertz electromagnetic emission from magnetized plasma during injection of a powerful relativistic electron beam of microsecond duration in plasma with the density of 3 × 1014 cm−3. It was found that the spectrum of the radiation concentrated in three distinct regions with high level of spectral power density. The first region is located near f1 = 100 GHz; the second one is in the vicinity of 190 GHz, and the third region is in the frequency interval f3 = 280–340 GHz. Polarization vectors of the emission in the first and third regions (f1 and f3) are directed mainly perpendicular to the magnetic field in the plasma. At the same time, the polarization of the radiation in the vicinity of f2 = 190 GHz is parallel to the magnetic field. The most likely mechanism of electromagnetic wave generation in the frequency regions f1 and f2 is the linear conversion of the plasma oscillations into the electromagnetic waves on strong gradients of the plasma density. The third region is situated in the vicinity of second harmonic of electron plasma frequency, and we explain this emission by the coalescence of the upper-hybrid oscillations at high level turbulence in plasma.
Communication: Using multiple tethers to stabilize proteins on surfaces
Authors: Loong Brandon K. , Knotts Thomas A.
Published: August 2014

Protein surface interactions are important in many applications in biotechnology including protein arrays, but these technologies have not lived up to their transformative potential because it is difficult to attach proteins to surfaces in a manner that preserves function and theoretical understanding of the relevant phenomena remains limited. Here is reported the effect of using multiple tethers to attach a protein (lysozyme) to a surface and the effects on the structure and stability of the molecule. The simulations show how using two tethers can drastically change the folding mechanism such that a protein that is initially unstable and inactive when attached using a single tether can become more stable and functional when two tethers are used. The results offer hope that the rational design of protein arrays is possible.
Design and realization of one-dimensional double hetero-structure photonic crystals for infrared-radar stealth-compatible materials applications
Authors: Wang Zhixun , Cheng Yongzhi , Nie Yan , Wang Xian , Gong Rongzhou
Published: August 2014

In this paper, a new type one-dimensional (1D) double hetero-structure composite photonic crystal (CPC) for infrared-radar stealth-compatible materials applications was proposed and studied numerically and experimentally. First, based on transfer matrix method of thin-film optical theory, the propagation characteristics of the proposed structure comprising a stack of different alternating micrometer-thick layers of germanium and zinc sulfide were investigated numerically. Calculation results exhibit that this 1D single hetero-structure PC could achieve a flat high reflectivity gradually with increasing the number of the alternating media layers in a single broadband range. Then, based on principles of distributed Bragg reflector micro-cavity, a 1D double hetero-structure CPC comprising four PCs with thickness of 0.797 μm, 0.592 μm, 1.480 μm, and 2.114 μm, respectively, was proposed. Calculation results exhibit that this CPC could achieve a high reflectance of greater than 0.99 in the wavelength ranges of 3–5 μm and 8–14 μm and agreed well with experiment. Further experiments exhibit that the infrared emissivity of the proposed CPC is as low as 0.073 and 0.042 in the wavelength ranges of 3–5 μm and 8–12 μm, respectively. In addition, the proposed CPC can be used to construct infrared-radar stealth-compatible materials due to its high transmittance in radar wave band.
Heterojunction of single-walled capped carbon nanotube and zinc phthalocyanine with high energy conversion efficiency
Authors: Ono Shota , Kuwahara Riichi , Ohno Kaoru
Published: August 2014

We propose a heterojunction of capped carbon nanotube (CNT) and zinc phthalocyanine as a solar cell. The charge separation mechanism at the interface is investigated using the density functional theory, through an analysis of the spatial profile of the Kohn-Sham wave functions. Estimated energy conversion efficiency of the capped CNT-based solar cells is quite larger than that of C60-based ones, offering an essential idea to overcome the difficulty to increase the efficiency.
The luminescence of BaF2 nanoparticles upon high-energy excitation
Authors: Vistovskyy V. V. , Zhyshkovych A. V. , Halyatkin O. O. , Mitina N. E. , Zaichenko A. S. , Rodnyi P. A. , Vasil'ev A. N. , Gektin A. V. , Voloshinovskii A. S.
Published: August 2014

The dependence of X-ray excited luminescence intensity on BaF2 nanoparticle size was studied. A sharp decrease of self-trapped exciton luminescence intensity was observed when the nanoparticle size is less than 80 nm. The main mechanism of the luminescence quenching is caused by the escape of electrons from the nanoparticles. Escape of electrons from nanoparticles is confirmed by the considerable increase of luminescence intensity of the polystyrene scintillator with embedded BaF2 nanoparticles comparing with pure polystyrene scintillator.
Computational synthesis of single-layer GaN on refractory materials
Authors: Singh Arunima K. , Hennig Richard G.
Published: August 2014

The synthesis of single-layer materials relies on suitable substrates. In this paper, we identify suitable substrates for the stabilization and growth of single-layer GaN and characterize the effect of the substrate on the electronic structure of single-layer GaN. We identify two classes of epitaxial substrates, refractory metal diborides and transition-metal dichalcogenides. We find that the refractory diborides provide epitaxial stabilization for the growth and functionalization of single layer GaN. We show that chemical interactions of single layer GaN with the diboride substrates result in n-type doping of the single-layer GaN. Transition-metal dichalcogenides, on the other hand, although epitaxially matched, cannot provide sufficient thermodynamic stabilization for the growth of single layer GaN. Nonetheless, energy band alignments of GaN/metal chalcogenides show that they make good candidates for heterostructures.
Doubling the electrocaloric cooling of poled ferroelectric materials by bipolar cycling
Authors: Basso Vittorio , Gerard Jean-François , Pruvost Sébastien
Published: August 2014

We have investigated the entropy change in the ferroelectric phase of poly(vinylidene fluoride-trifluoroethylene) 70/30 films by direct heat flux calorimetry using Peltier cell heat flux sensors. We find that by applying a negative electric field to a positively poled state, the entropy can be further increased without any significantly change of the remanent polarization or the domain structure. By cycling between positive and negative values of the electric field, the electrocaloric effect (ECE) can be then improved by a factor of 2. As an example, we measured, around the positive remanence Pr = 60 × 10−3 C m−2, a fully reversible entropy change |Δs| = 1 J kg−1K−1 for a field change from 40 × 106 to −40 × 106 V m−1 and a maximum of |Δs| = 3.2 J kg−1K−1 for an asymmetric field change from 200 × 106 to −40 × 106 V m−1. This effect can be exploited to significantly increase the range of operating temperature for ECE materials below their Curie temperature.
Deep-ultraviolet light emission properties of nonpolar M-plane AlGaN quantum wells
Authors: Banal Ryan G. , Taniyasu Yoshitaka , Yamamoto Hideki
Published: August 2014

Deep-ultraviolet (deep-UV) light emissions from nonpolar (10-10) M-plane AlxGa1−xN/AlyGa1−yN multiple quantum wells (MQWs) were studied by photoluminescence spectroscopy. The nonpolar M-plane AlGaN MQWs showed shorter emission wavelength than the polar (0001) C-plane ones, mainly because of the absence of the quantum-confined Stark effect. The deep-UV light emissions from the M-plane AlGaN MQWs showed stronger polarization with electric field E parallel to the c-axis (E||c) than the C-plane ones. The different polarization properties between the M- and C-plane AlGaN MQWs can be explained in terms of in-plane lattice strain and anisotropy of the effective hole mass.
Low dielectric loss and weak frequency dependence of dielectric permittivity of the CeO2/polystyrene nanocomposite films
Authors: Zhang Liang , Chen Shuo , Yuan Shuai , Wang Dongrui , Hu Peng-Hao , Dang Zhi-Min
Published: August 2014

Nanocomposite films with cerium oxide (CeO2) nanoparticles as functional fillers and polystyrene (PS) as polymer matrix were prepared using solution casting method. Physical properties including both weak frequency dependence of dielectric permittivity and low dielectric loss were experimentally discovered in the CeO2/PS nanocomposite films. To improve the dielectric properties of films further, the surface of CeO2 nanoparticles was treated by H2O2 to increase the homogeneity of the nanocomposite film, which was confirmed by scanning electron microscopy (SEM) results. Furthermore, it was found that both the filler size and the filler volume fraction played a role on the dielectric properties of the nanocomposite films.
Excess-hole induced high temperature polarized state and its correlation with the multiferroicity in single crystalline DyMnO3
Authors: Zou Tao , Dun Zhiling , Cao Huibo , Zhu Mengze , Coulter Daniel , Zhou Haidong , Ke Xianglin
Published: August 2014

Controlling the ferroelectricity and magnetism in multiferroic materials has been an important research topic. We report the formation of a highly polarized state in multiferroic DyMnO3 single crystals which develops well above the magnetic transition temperatures, and we attribute it to the thermally stimulated depolarization current effect of excess holes forming Mn4+ ions in the system. We also show that this high temperature polarized state intimately correlates with the lower temperature ferroelectric state that is induced by the incommensurate spiral magnetic order of Mn spins. This study demonstrates an efficient approach to tune the multiferroicity in the manganite system.
Origin of electrons emitted into vacuum from InGaN light emitting diodes
Authors: Iveland Justin , Piccardo Marco , Martinelli Lucio , Peretti Jacques , Choi Joo Won , Young Nathan , Nakamura Shuji , Speck James S. , Weisbuch Claude
Published: August 2014

The mechanism responsible for efficiency droop in InGaN light-emitting diodes (LEDs) has long been elusive due to indirect measurement techniques used for its identification. Auger recombination is unique among proposed efficiency droop mechanisms, in that it is the only mechanism capable of generating hot carriers. In a previous study [J. Iveland et al., Phys. Rev. Lett. 110, 177406 (2013)], we performed electron energy analysis of electrons emitted into vacuum from a forward biased InGaN LED that had been brought into negative electron affinity by cesiation. Three peaks were observed in the energy spectrum of vacuum emitted electrons. In this Letter, we unambiguously identify the origin of the peaks. The two higher energy peaks correspond to accumulation of electrons transported to the surface in the bulk Γ and side L conduction band valleys. The L-valley peak is a direct signature of a hot Auger electron population. The lower energy peak results from surface photoemission induced by the internal LED light emitted from the InGaN quantum wells. Two control experiments were performed. In the first, a simple GaN pn junction generated only a single Γ peak in electroemission. In the second, selective detection of the photoemission from an LED under modulated light excitation and DC electrical injection confirms that only the low energy peak is photogenerated and that LED light is incapable of generating Γ or L-valley peaks, the latter only occurring due to the Auger effect in the LED active region.
Current-voltage characteristic and sheet resistances after annealing of femtosecond laser processed sulfur emitters for silicon solar cells
Authors: Gimpel Thomas , Guenther Kay-Michael , Kontermann Stefan , Schade Wolfgang
Published: August 2014

The characteristics of laser doped sulfur emitters are strongly dependent on annealing processes. We show how annealing increases the efficiency of silicon solar cells with such an emitter. Sheet resistance analysis reveals that up to an annealing temperature of 400 °C the emitter sheet resistivity increases. A lower sulfur donor concentration is concluded, which likely occurs by means of sulfur diffusion and capturing of sulfur donors at intrinsic silicon defects. Above that temperature, the emitter sheet resistance decreases, which we find to originate from healing of laser induced structural defects involving traps within the depletion zone of the silicon pn-junction.
On the nature of a supposed water model
Authors: Heckmann Lotta , Drossel Barbara
Published: August 2014

A cell model that has been proposed by Stanley and Franzese in 2002 for modeling water is based on Potts variables that represent the possible orientations of bonds between water molecules. We show that in the liquid phase, where all cells are occupied by a molecule, the Hamiltonian of the cell model can be rewritten as a Hamiltonian of a conventional Potts model, albeit with two types of coupling constants. We argue that such a model, while having a first-order phase transition, cannot display the critical end point that is postulated for the phase transition between a high- and low-density liquid. A closer look at the mean-field calculations that claim to find such an end point in the cell model reveals that the mean-field theory is constructed such that the symmetry constraints on the order parameter are violated. This is equivalent to introducing an external field. The introduction of such a field can be given a physical justification due to the fact that water does not have the type of long-range order occurring in the Potts model.
Carbon nanotube based flexible counter electrode for quasi-solid state dye sensitized solar cells
Authors: Zhang Jing , Feng Jiangwei , Hong Yang , Hu Zhelu , Xia Kai , Wang Peiqing , Zhu Yuejin
Published: August 2014

Low temperature fabrication of carbon nanotube based conductive composite polymer (CNT-CCP) film on conductive flexible substrate indium tin oxide coated polyethylene terephthalate film (ITO-PET) is developed as a low cost alternative to the Pt counter electrode especially for flexible quasi-solid state dye sensitized solar cells (DSSCs). The formation of three-dimensional carbon nanotube network provides the conductivity pathway which is improved with the carbon nanotube content and the film thickness increase. More importantly, the conductivity of CNT-CCP films greatly influences the performance of DSSCs. With high conductivity, good catalytic activity and especially the good consistence of the CNT-CCP with the polymer electrolyte, flexible CNT-CCP/ITO-PET counter electrode for the DSSC with the quasi-solid state composite polymer electrolyte exhibits performance of 4.24% (0.95Sun, AM1.5), which is 87% of the quasi-solid state DSSC with Pt counter electrode (4.87%). It indicates the CNT-CCP type counter electrode is promising for the flexible DSSCs.
Who are the sexual partners of transgender individuals? Differences in demographic characteristics and risk behaviours of San Francisco HIV testing clients with transgender sexual partners compared with overall testers
Authors: Wilson Erin C. , Chen Yea-Hung , Raad Nayla , Raymond H. Fisher , Dowling Teri , McFarland Willi
Published: August 2014

Background
Research to examine the sexual networks of transgender people may be the key to understanding why transwomen are at high risk of contracting HIV. Methods: Bivariate and multivariate analysis of San Francisco HIV county counselling and testing data from 2010 was conducted to compare demographic factors and risk behaviours of the partners of transgender people (PTG) to HIV testing clients overall. Results: Of the 13 754 clients overall, 477 reported having sex with a transgender person in the past 12 months. PTG were significantly more likely to be transgender, Latino, multiracial or ‘other’, and identify as bisexual. In multivariate analyses, PTG were significantly more likely to have used and injected drugs in the past 12 months; in bivariate analysis, PTG had a significantly higher likelihood of having unprotected vaginal or anal sex. PTG who had engaged in vaginal or anal sex in the past 12 months had an HIV positivity of 0.6% compared with 1.1% for non-PTG. Conclusions: People who report having transgender sexual partners engage in higher-risk behaviours than other HIV testers yet had a lower HIV positivity. Potential explanations for the discrepancy between higher-risk behaviours and lower HIV positivity for PTG may be engagement in HIV-protective behaviours like regular HIV testing and lower risk seropositioning being the insertive sexual partner. Future studies on the sexual networks of transgender people, and sexual and risk behaviours of PTG may elucidate the HIV risk for both PTG and their transgender partners.
Prevalence, correlates and attitudes towards sexting among young people in Melbourne, Australia
Authors: Yeung Timothy H. , Horyniak Danielle R. , Vella Alyce M. , Hellard Margaret E. , Lim Megan S. C.
Published: August 2014

Background
‘Sexting’ is the exchange of sexually explicit material via communication technologies. Despite significant media attention, there has been little examination of sexting in the Australian setting. This study aimed to provide insight into sexting behaviours and attitudes among young Australians. Methods: A cross-sectional survey was conducted with a convenience sample of people aged 16–29 years attending a music festival (n = 1372). Correlates of lifetime sexting were determined using multivariate logistic regression. Attitudes towards and perceived consequences of sexting were explored in focus group discussions (FGDs) with 39 young people. Results: Forty percent of survey participants reported that they had ever sent or received a sext (48% of males, 36% of females), most commonly with a regular partner. Lower levels of education, greater recreational spending, greater number of sexual partners, inconsistent condom use with a regular partner, identifying as being nonheterosexual and risky alcohol consumption were all independent correlates of sexting. FGD participants made a clear distinction between consensual creating, sending and possessing of sexts, and nonconsensual sharing of sexts. Positive outcomes of consensual sexting included flirting and sexual experimentation, with sexting perceived as a normalised aspect of sexual interaction. Conclusions: Sexting is a common and normalised practice among young Australians. Our findings highlight the distinction in young people’s minds between consensual sexting and the nonconsensual sharing or circulation of sexts, which is not currently well recognised in sexuality education, the media or the law.
Time trends in adolescent sexual behaviour in Italy
Authors: Marino Claudia , Vieno Alessio , Lenzi Michela , Santinello Massimo
Published: August 2014

Background
There has been little research investigating sexual health in Italy. The aim of the present study was to present time trends over 8 years in sexual behaviour among adolescents. Methods: This study is part of the Health Behaviour in School-aged Children study (sample: 3983 adolescents aged 15 years; 51.9% girls). Measures included sexual initiation, condom use and age of first sexual intercourse. Results: No variation was observed in the prevalence of sexual initiation and in condom use. The mean age of first sexual intercourse decreased among surveyed adolescents. Conclusions: Considering the tendency of Italian adolescents to begin having intercourse at an earlier age, increased knowledge on sexual behaviours is needed to improve sexual health.
Spliceostatin hemiketal biosynthesis in
Burkholderia
spp. is catalyzed by an iron/α-ketoglutarate–dependent dioxygenase
Authors: Eustáquio Alessandra S. , Janso Jeffrey E. , Ratnayake Anokha S. , O’Donnell Christopher J. , Koehn Frank E.
Published: August 2014

Significance

Spliceostatins are bacterial natural products that show promising anticancer activity. Understanding how the bacterium makes spliceostatins will aid efforts toward a sustainable route for their production. Moreover, altering the chemical structure of a natural product is usually necessary to improve its pharmaceutical properties. For example, the parent spliceostatin molecule contains an unstable hemiketal chemical group. Contrary to previous hypotheses, we report on the identification of a dioxygenase enzyme responsible for hemiketal biosynthesis. Deletion of the corresponding dioxygenase gene led to a strain that produces exclusively spliceostatin congeners that are more stable than, and as active as, the parent compound, when derivatized to increase cell permeability. The strain generated in this study will be the basis for future development.
Dynamic regulation of human endogenous retroviruses mediates factor-induced reprogramming and differentiation potential
Authors: Ohnuki Mari , Tanabe Koji , Sutou Kenta , Teramoto Ito , Sawamura Yuka , Narita Megumi , Nakamura Michiko , Tokunaga Yumie , Nakamura Masahiro , Watanabe Akira , Yamanaka Shinya , Takahashi Kazutoshi
Published: August 2014

Significance

In this study, we found that human endogenous retoriviruses type-H (HERV-Hs) are transiently hyperactivated during reprogramming toward induced pluripotent stem cells (iPSCs) and play important roles in this process. However, when reprogramming is complete and cells acquire full pluripotency, HERV-H activity should decrease to levels comparable with those in embryonic stem cells because failure to resilence this activity leads to the differentiation-defective phenotype in neural lineage. We also found that during reprogramming, reprogramming factors, including POU class 5 homeobox 1 (OCT3/4), sex determining region Y-box 2 (SOX2), and Krüppel-like factor 4 (KLF4) (OSK) bind to and activate long-terminal repeats of HERV-Hs. KLF4 possibly precludes Tripartite motif containing 28 and recruits not only OCT3/4 and SOX2, but also E1A binding protein p300 (p300) histone acethyltransferase on HERV-H loci. Therefore, OKSM-induced HERV-H activation constitutes an unanticipated and critical mechanism for iPSC formation.
Tracking global changes induced in the CD4 T-cell receptor repertoire by immunization with a complex antigen using short stretches of CDR3 protein sequence
Authors: Thomas Niclas , Best Katharine , Cinelli Mattia , Reich-Zeliger Shlomit , Gal Hilah , Shifrut Eric , Madi Asaf , Friedman Nir , Shawe-Taylor John , Chain Benny
Published: August 2014

Motivation: The clonal theory of adaptive immunity proposes that immunological responses are encoded by increases in the frequency of lymphocytes carrying antigen-specific receptors. In this study, we measure the frequency of different T-cell receptors (TcR) in CD4 + T cell populations of mice immunized with a complex antigen, killed Mycobacterium tuberculosis , using high throughput parallel sequencing of the TcR β chain. Our initial hypothesis that immunization would induce repertoire convergence proved to be incorrect, and therefore an alternative approach was developed that allows accurate stratification of TcR repertoires and provides novel insights into the nature of CD4 + T-cell receptor recognition.

Results: To track the changes induced by immunization within this heterogeneous repertoire, the sequence data were classified by counting the frequency of different clusters of short (3 or 4) continuous stretches of amino acids within the antigen binding complementarity determining region 3 (CDR3) repertoire of different mice. Both unsupervised (hierarchical clustering) and supervised (support vector machine) analyses of these different distributions of sequence clusters differentiated between immunized and unimmunized mice with 100% efficiency. The CD4 + TcR repertoires of mice 5 and 14 days postimmunization were clearly different from that of unimmunized mice but were not distinguishable from each other. However, the repertoires of mice 60 days postimmunization were distinct both from naive mice and the day 5/14 animals. Our results reinforce the remarkable diversity of the TcR repertoire, resulting in many diverse private TcRs contributing to the T-cell response even in genetically identical mice responding to the same antigen. However, specific motifs defined by short stretches of amino acids within the CDR3 region may determine TcR specificity and define a new approach to TcR sequence classification.

Availability and implementation: The analysis was implemented in R and Python, and source code can be found in Supplementary Data .

Contact:  b.chain@ucl.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
DNAApp: a mobile application for sequencing data analysis
Authors: Nguyen Phi-Vu , Verma Chandra Shekhar , Gan Samuel Ken-En
Published: August 2014

Summary: There have been numerous applications developed for decoding and visualization of ab1 DNA sequencing files for Windows and MAC platforms, yet none exists for the increasingly popular smartphone operating systems. The ability to decode sequencing files cannot easily be carried out using browser accessed Web tools. To overcome this hurdle, we have developed a new native app called DNAApp that can decode and display ab1 sequencing file on Android and iOS. In addition to in-built analysis tools such as reverse complementation, protein translation and searching for specific sequences, we have incorporated convenient functions that would facilitate the harnessing of online Web tools for a full range of analysis. Given the high usage of Android/iOS tablets and smartphones, such bioinformatics apps would raise productivity and facilitate the high demand for analyzing sequencing data in biomedical research.

Availability and implementation: The Android version of DNAApp is available in Google Play Store as ‘DNAApp’, and the iOS version is available in the App Store. More details on the app can be found at www.facebook.com/APDLab ; www.bii.a-star.edu.sg/research/trd/apd.php

The DNAApp user guide is available at http://tinyurl.com/DNAAppuser , and a video tutorial is available on Google Play Store and App Store, as well as on the Facebook page.

Contact:  samuelg@bii.a-star.edu.sg
Thresher: an improved algorithm for peak height thresholding of microbial community profiles
Authors: Starke Verena , Steele Andrew
Published: August 2014

Motivation: This article presents Thresher, an improved technique for finding peak height thresholds for automated rRNA intergenic spacer analysis (ARISA) profiles. We argue that thresholds must be sample dependent, taking community richness into account. In most previous fragment analyses, a common threshold is applied to all samples simultaneously, ignoring richness variations among samples and thereby compromising cross-sample comparison. Our technique solves this problem, and at the same time provides a robust method for outlier rejection, selecting for removal any replicate pairs that are not valid replicates.

Results : Thresholds are calculated individually for each replicate in a pair, and separately for each sample. The thresholds are selected to be the ones that minimize the dissimilarity between the replicates after thresholding. If a choice of threshold results in the two replicates in a pair failing a quantitative test of similarity, either that threshold or that sample must be rejected. We compare thresholded ARISA results with sequencing results, and demonstrate that the Thresher algorithm outperforms conventional thresholding techniques.

Availability and Implementation : The software is implemented in R, and the code is available at http://verenastarke.wordpress.com or by contacting the author.

Contact : vstarke@ciw.edu or http://verenastarke.wordpress.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
A method for calculating a meta-analytical prior for the natural mortality rate using multiple life history correlates
Authors: Hamel Owen S.
Published: August 2014

The natural mortality rate M is an important parameter for understanding population dynamics, and is extraordinarily difficult to estimate for many fish species. The uncertainty associated with M translates into increased uncertainty in fishery stock assessments. Estimation of M within a stock assessment model is complicated by its confounding with other life history and fishery parameters which are also uncertain, some of which are typically estimated within the model. Ageing error and variation in growth, which may not be fully modelled, can also affect estimation of M, as can various assumptions, including the form of the stock–recruitment function (e.g. Beverton–Holt, Ricker) and the level of compensation (or steepness), which may be fixed (or limited by a prior) in the model. To avoid these difficulties, stock assessors often assume point estimates for M derived from meta-analytical relationships between M and more easily measured life history characteristics, such as growth rate or longevity. However, these relationships depend on estimates of M for a great number of species, and those estimates are also subject to errors and biases (as are, to a lesser extent, the other life history parameters). Therefore, at the very least, some measure of uncertainty in M should be calculated and used for evaluating uncertainty in stock assessments and management strategy evaluations. Given error-free data on M and the covariate(s) for a meta-analysis, prediction intervals would provide the appropriate measure of uncertainty in M. In contrast, if the relationship between the covariate(s) and M is exact and the only error is in the estimates of M used for the meta-analysis, confidence intervals would appropriate. Using multiple published meta-analyses of M’s relationship with various life history correlates, and beginning with the uncertainty interval calculations, I develop a method for creating combined priors for M for use in stock assessment.
ERAP1 functions override the intrinsic selection of specific antigens as immunodominant peptides, thereby altering the potency of antigen-specific cytolytic and effector memory T-cell responses
Authors: Rastall David P. W. , Aldhamen Yasser A. , Seregin Sergey S. , Godbehere Sarah , Amalfitano Andrea
Published: August 2014

Endoplasmic reticulum aminopeptidase 1 (ERAP1) is a critical component of the adaptive immune system that has been shown to increase or decrease the presentation of specific peptides on MHC class I molecules. Here, we have demonstrated that ERAP1 functions are not only important during the presentation of antigen-derived peptides, but these functions can also completely change which antigen-derived peptides ultimately become selected as immunodominant T-cell epitopes. Our results suggest that ERAP1 may do this by destroying epitopes that would otherwise become immunodominant in the absence of adequate ERAP1 functionality. We further establish that ERAP1-mediated influences on T-cell functions are both qualitative and quantitative, by demonstrating that loss of ERAP1 function redirects CTL killing toward a different set of antigen-derived epitopes and increases the percent of antigen-specific memory T cells elicited by antigen exposure. As a result, our studies suggest that normal ERAP1 activity can act to suppress the numbers of T effector memory cells that respond to a given antigen. This unique finding may shed light on why certain ERAP1 single nucleotide polymorphisms are associated with several autoimmune diseases, for example, by significantly altering the robustness and quality of CD8+ T-cell memory responses to antigen-derived peptides.
Responses of macrophages to the danger signals released from necrotic cells
Authors: Kimura Toshifumi , Kobayashi Shuhei , Hanihara-Tatsuzawa Fumito , Sayama Aoi , MaruYama Takashi , Muta Tatsushi
Published: August 2014

The immune system maintains homeostasis by recognizing and responding to cell death caused by various stresses. The immune response is considered to be elicited by ‘danger signals’ released from necrotic cells. However, the identity of the danger signals remains elusive. In this study, we focused on the expression of chemokines by macrophages stimulated with necrotic cells. In mouse bone-marrow-derived macrophages, the chemokine monocyte chemoattractant protein (MCP)-3 was induced at both the mRNA and protein levels in response to heat-killed murine cells. The induction of MCP-3 was also observed in MyD88-deficient macrophages, indicating that Toll-like receptors and the IL-1 receptor are not involved in this response. Consistent with this observation, the activation of NF-κB was not detected in RAW264.7 macrophages stimulated with necrotic cells. Treatments with proteinase K, DNaseI or RNaseA did not affect the ‘stimulating activity’ of necrotic cells. In contrast, treatment with apyrase, which removes phosphates from nucleoside tri- and di-phosphates, abolished the inducing activity. Purified UDP at 30 µM concentration elicited similar induction of MCP-3 in RAW264.7 macrophages. Small interfering RNA-mediated knock-down of the UDP receptor P2Y6 in RAW264.7 cells significantly reduced the induction of MCP-3 in response to necrotic cells, but not its induction by lipopolysaccharide. Furthermore, ectopic expression of the P2Y6 receptor in HEK293 cells conferred responsiveness to necrotic cells. These results suggest that UDP released by necrotic cells plays a critical role as an endogenous danger signal and that P2Y6 is required for the induction of MCP-3 in response to necrotic cells.
REVIEW: Properties of Cereal Brans: A Review
Authors: Chinma Chiemela Enyinnaya , Ramakrishnan Yogeshini , Ilowefah Muna , Hanis‐Syazwani Mat , Muhammad Kharidah
Published: August 2014

Cereal brans are functional ingredients with high nutritive value and enormous health properties. Cereal brans have not been fully utilized in food systems despite their health benefits. This review presents an overview on the physical, chemical, microbiological, functional, and sensory properties of cereal brans for possible comparisons and selection to enhance the utilization of this underutilized milling fraction.
Frequency of Verticillium Species in Commercial Spinach Fields and Transmission of V. dahliae from Spinach to Subsequent Lettuce Crops
Authors: Short D. P. G. , Gurung S. , Koike S. T. , Klosterman S. J. , Subbarao K. V.
Published: August 2014

Verticillium wilt caused by V. dahliae is a devastating disease of lettuce in California (CA). The disease is currently restricted to a small geographic area in central coastal CA, even though cropping patterns in other coastal lettuce production regions in the state are similar. Infested spinach seed has been implicated in the introduction of V. dahliae into lettuce fields but direct evidence linking this inoculum to wilt epidemics in lettuce is lacking. In this study, 100 commercial spinach fields in four coastal CA counties were surveyed to evaluate the frequency of Verticillium species recovered from spinach seedlings and the area under spinach production in each county was assessed. Regardless of the county, V. isaacii was the most frequently isolated species from spinach followed by V. dahliae and, less frequently, V. klebahnii. The frequency of recovery of Verticillium species was unrelated to the occurrence of Verticillium wilt on lettuce in the four counties but was related to the area under spinach production in individual counties. The transmission of V. dahliae from infested spinach seeds to lettuce was investigated in microplots. Verticillium wilt developed on lettuce following two or three plantings of Verticillium-infested spinach, in independent experiments. The pathogen recovered from the infected lettuce from microplots was confirmed as V. dahliae by polymerase chain reaction assays. In a greenhouse study, transmission of a green fluorescence protein-tagged mutant strain of V. dahliae from spinach to lettuce roots was demonstrated, after two cycles of incorporation of infected spinach residue into the soil. This study presents conclusive evidence that V. dahliae introduced via spinach seed can cause Verticillium wilt in lettuce.
A Simulation Model for Epidemics of Stem Rust in Ryegrass Seed Crops
Authors: Pfender W. F. , Upper D.
Published: August 2014

A simulation model (STEMRUST_G, named for stem rust of grasses) was created for stem rust (caused by Puccinia graminis subsp. graminicola) in perennial ryegrass grown to maturity as a seed crop. The model has a daily time step and is driven by weather data and an initial input of disease severity from field observation. Key aspects of plant growth are modeled. Disease severity is modeled as rust population growth, where individuals are pathogen colonies (pustules) grouped in cohorts defined by date of initiation and plant part infected. Infections due to either aerial spread or within-plant contact spread are modeled. Pathogen cohorts progress through life stages that are modeled as disease cycle components (colony establishment, latent period, infectious period, and sporulation) affected by daily weather variables, plant growth, and fungicide application. Fungicide effects on disease cycle components are modeled for two commonly used active ingredients, applied preinfection or postinfection. Previously validated submodels for certain disease cycle components formed the framework for integrating additional processes, and the complete model was calibrated with field data from 10 stem rust epidemics. Discrepancies between modeled outcomes and the calibration data (log10[modeled] − log10[observed]) had a mean near zero but considerable variance, with 1 standard deviation = 0.5 log10 units (3.2-fold). It appears that a large proportion of the modeling error variance may be due to variability in field observations of disease severity. An action threshold for fungicide application was derived empirically, using a constructed weather input file favorable for disease development. The action threshold is a negative threshold, representing a level of disease (latent plus visible) below which damaging levels of disease are unable to develop before the yield-critical crop stage. The model is in the public domain and available on the Internet.
Testing the Independent Action Hypothesis of Plant Pathogen Mode of Action: A Simple and Powerful New Approach
Authors: Zwart Mark P. , Elena Santiago F.
Published: August 2014

The independent action hypothesis is a simple model of pathogen infection that can make many useful predictions on infection kinetics and, therefore, a number of different tests of independent action have been developed. However, some of these analyses are rather sophisticated, limiting their appeal to experimentalists, and it is also unclear how well the different tests perform. Here, we developed and evaluated a simple and robust new test of independent action. Our new test is based on using a constant inoculum dose of one pathogen variant, varying the dose of a second variant, and then quantifying the infection response for the first variant. We simulated infection data in which we introduced deviations from independent action, experimental variation, or both. Simulations showed that our new procedure has many advantages over the existing tests of independent action, especially if only systemic-infection data are available. We also performed experimental tests of our new procedure using two marked Tobacco etch virus (TEV) variants. We found minor deviations from the independent action model, which were not detected by previous tests using existing methods, exemplifying the utility of this approach. We discuss the implications for TEV infection kinetics and consider how to reconcile different dose-dependent effects.
Threshold Microsclerotial Inoculum for Cotton Verticillium Wilt Determined Through Wet-Sieving and Real-Time Quantitative PCR
Authors: Wei Feng , Fan Rong , Dong Haitao , Shang Wenjing , Xu Xiangming , Zhu Heqin , Yang Jiarong , Hu Xiaoping
Published: August 2014

Quantification of Verticillium dahliae microsclerotia is an important component of wilt management on a range of crops. Estimation of microsclerotia by dry or wet sieving and plating of soil samples on semiselective medium is a commonly used technique but this method is resource-intensive. We developed a new molecular quantification method based on Synergy Brands (SYBR) Green real-time quantitative polymerase chain reaction of wet-sieving samples (wet-sieving qPCR). This method can detect V. dahliae microsclerotia as low as 0.5 CFU g−1 of soil. There was a high correlation (r = 0.98) between the estimates of conventional plating analysis and the new wet-sieving qPCR method for 40 soil samples. To estimate the inoculum threshold for cotton wilt, >400 soil samples were taken from the rhizosphere of individual plants with or without visual wilt symptoms in experimental and commercial cotton fields at the boll-forming stage. Wilt inoculum was estimated using the wet-sieving qPCR method and related to wilt development. The estimated inoculum threshold varied with cultivar, ranging from 4.0 and 7.0 CFU g−1 of soil for susceptible and resistant cultivars, respectively. In addition, there was an overall relationship of wilt incidence with inoculum density across 31 commercial fields where a single composite soil sample was taken at each field, with an estimated inoculum threshold of 11 CFU g−1 of soil. These results suggest that wilt risk can be predicted from the estimated soil inoculum density using the new wet-sieving qPCR method. We recommend the use of 4.0 and 7.0 CFU g−1 as an inoculum threshold on susceptible and resistant cultivars, respectively, in practical risk prediction schemes.
Associations Between Body Mass and Revision Surgical Outcomes in Adult Scoliosis
Authors: Fu Lingjie , Chang Michael S. , Crandall Dennis G. , Revella Jan
Published: August 2014

Study Design:

Retrospective cohort study.

Objective:

To determine whether an association exists between high body mass index (BMI>25 kg/m2) and surgical outcomes in revision adult scoliosis patients.

Summary of Background Data:

Obesity is thought to be associated with increased surgical complications and inferior clinical outcomes in adults. There are no studies analyzing the effect of obesity on surgical outcomes in revision patients for adult scoliosis.

Methods:

Forty-five consecutive revision adult scoliosis patients (35 women and 10 men; mean age, 62.7±9.3 y) with a minimum follow-up of 2 years were included in this study. Patients were divided into 2 groups according to BMI: overweight (BMI≥25 kg/m2, n=27) and nonoverweight (<25 kg/m2, n=18). Radiographic measures, Oswestry Disability Index (ODI), Visual Analog Scale (VAS), as well as comorbidities and complications were reviewed and compared at preoperative and 2-year follow-up.

Results:

No significant differences in surgical methods, complication rates, or radiographic measures were found between the 2 groups except for the greater preoperative and final follow-up thoracic kyphosis in the overweight group (P<0.05). A higher comorbidity rate of circulatory disorders (33.3% vs. 0%, P=0.018) and diabetes (25.9% vs. 0%, P=0.053) was observed in the overweight group, as well as a higher preoperative VAS score (7.1±1.7 vs. 5.2±2.9, P=0.031). At 2-year follow-up, VAS and ODI improvements for both groups showed significant and similar improvement from preoperative (P<0.01).

Conclusions:

Overweight revision adult scoliosis patients had higher thoracic kyphosis and more significant preoperative pain compared with normal-weight individuals. Overweight patients also had significantly higher rates of medical comorbidities. However, BMI did not affect the functional outcome of surgical correction or perioperative complication rates. Overweight patients benefited from surgery just as much as nonoverweight patients at 2-year follow-up.
M-type potassium conductance controls the emergence of neural phase codes: a combined experimental and neuron modelling study
Authors: Kwag Jeehyun , Jang Hyun Jae , Kim Mincheol , Lee Sujeong
Published: August 2014

Rate and phase codes are believed to be important in neural information processing. Hippocampal place cells provide a good example where both coding schemes coexist during spatial information processing. Spike rate increases in the place field, whereas spike phase precesses relative to the ongoing theta oscillation. However, what intrinsic mechanism allows for a single neuron to generate spike output patterns that contain both neural codes is unknown. Using dynamic clamp, we simulate an
in vivo
-like subthreshold dynamics of place cells to
in vitro
CA1 pyramidal neurons to establish an
in vitro
model of spike phase precession. Using this
in vitro
model, we show that membrane potential oscillation (MPO) dynamics is important in the emergence of spike phase codes: blocking the slowly activating, non-inactivating K
+
current (
I
M
), which is known to control subthreshold MPO, disrupts MPO and abolishes spike phase precession. We verify the importance of adaptive
I
M
in the generation of phase codes using both an adaptive integrate-and-fire and a Hodgkin–Huxley (HH) neuron model. Especially, using the HH model, we further show that it is the perisomatically located
I
M
with slow activation kinetics that is crucial for the generation of phase codes. These results suggest an important functional role of
I
M
in single neuron computation, where
I
M
serves as an intrinsic mechanism allowing for dual rate and phase coding in single neurons.
The multi-layered protective cuticle of Collembola: a chemical analysis
Authors: Nickerl Julia , Tsurkan Mikhail , Hensel René , Neinhuis Christoph , Werner Carsten
Published: August 2014

Collembola, also known as springtails, are soil-dwelling arthropods that typically respire through the cuticle. To avoid suffocating in wet conditions, Collembola have evolved a complex, hierarchically nanostructured, cuticle surface that repels water with remarkable efficiency. In order to gain a more profound understanding of the cuticle characteristics, the chemical composition and architecture of the cuticle ofTetrodontophora bielanensiswas studied. A stepwise removal of the different cuticle layers enabled controlled access to each layer that could be analysed separately by chemical spectrometry methods and electron microscopy. We found a cuticle composition that consisted of three characteristic layers, namely, a chitin-rich lamellar base structure overlaid by protein-rich nanostructures, and a lipid-rich envelope. The specific functions, composition and biological characteristics of each cuticle layer are discussed with respect to adaptations of Collembola to their soil habitat. It was found that the non-wetting characteristics base on a rather typical arthropod cuticle surface chemistry which confirms the decisive role of the cuticle topography.