bluuebunny/crossref_metadata_2025 huggingface dataset:
Femtosecond time-resolved electronic relaxation dynamics in tetrathiafulvalene
Authors: Staedter D. , Thiré N. , Polizzi L. , Mairesse Y. , Mayer P. , Blanchet V.
Published: May 2015

In the present paper, the ultrafast electronic relaxation of tetrathiafulvalene (TTF) initiated around 4 eV is studied by femtosecond time-resolved velocity-map imaging. The goal is to investigate the broad double structure observed in the absorption spectrum at this energy. By monitoring the transients of the parent cation and its fragments and by varying the pump and the probe wavelengths, two internal conversions and intramolecular vibrational relaxation are detected both on the order of a few hundred of femtoseconds. Photoelectron images permit the assignment of a dark electronic state involved in the relaxation. In addition, the formation of the dimer of TTF has been observed.
de Finetti reductions for correlations
Authors: Arnon-Friedman Rotem , Renner Renato
Published: May 2015

When analysing quantum information processing protocols, one has to deal with large entangled systems, each consisting of many subsystems. To make this analysis feasible, it is often necessary to identify some additional structures. de Finetti theorems provide such a structure for the case where certain symmetries hold. More precisely, they relate states that are invariant under permutations of subsystems to states in which the subsystems are independent of each other. This relation plays an important role in various areas, e.g., in quantum cryptography or state tomography, where permutation invariant systems are ubiquitous. The known de Finetti theorems usually refer to the internal quantum state of a system and depend on its dimension. Here, we prove a different de Finetti theorem where systems are modelled in terms of their statistics under measurements. This is necessary for a large class of applications widely considered today, such as device independent protocols, where the underlying systems and the dimensions are unknown and the entire analysis is based on the observed correlations.
Coagulation kinetics beyond mean field theory using an optimised Poisson representation
Authors: Burnett James , Ford Ian J.
Published: May 2015

Binary particle coagulation can be modelled as the repeated random process of the combination of two particles to form a third. The kinetics may be represented by population rate equations based on a mean field assumption, according to which the rate of aggregation is taken to be proportional to the product of the mean populations of the two participants, but this can be a poor approximation when the mean populations are small. However, using the Poisson representation, it is possible to derive a set of rate equations that go beyond mean field theory, describing pseudo-populations that are continuous, noisy, and complex, but where averaging over the noise and initial conditions gives the mean of the physical population. Such an approach is explored for the simple case of a size-independent rate of coagulation between particles. Analytical results are compared with numerical computations and with results derived by other means. In the numerical work, we encounter instabilities that can be eliminated using a suitable “gauge” transformation of the problem [P. D. Drummond, Eur. Phys. J. B 38, 617 (2004)] which we show to be equivalent to the application of the Cameron-Martin-Girsanov formula describing a shift in a probability measure. The cost of such a procedure is to introduce additional statistical noise into the numerical results, but we identify an optimised gauge transformation where this difficulty is minimal for the main properties of interest. For more complicated systems, such an approach is likely to be computationally cheaper than Monte Carlo simulation.
A systematic comparison of different approaches of density functional theory for the study of electrical double layers
Authors: Yang Guomin , Liu Longcheng
Published: May 2015

Based on the best available knowledge of density functional theory (DFT), the reference-fluid perturbation method is here extended to yield different approaches that well account for the cross correlations between the Columbic interaction and the hard-sphere exclusion in an inhomogeneous ionic hard-sphere fluid. In order to quantitatively evaluate the advantage and disadvantage of different approaches in describing the interfacial properties of electrical double layers, this study makes a systematic comparison against Monte Carlo simulations over a wide range of conditions. The results suggest that the accuracy of the DFT approaches is well correlated to a coupling parameter that describes the coupling strength of electrical double layers by accounting for the steric effect and that can be used to classify the systems into two regimes. In the weak-coupling regime, the approaches based on the bulk-fluid perturbation method are shown to be more accurate than the counterparts based on the reference-fluid perturbation method, whereas they exhibit the opposite behavior in the strong-coupling regime. More importantly, the analysis indicates that, with a suitable choice of the reference fluid, the weighted correlation approximation (WCA) to DFT gives the best account of the coupling effect of the electrostatic-excluded volume correlations. As a result, a piecewise WCA approach can be developed that is robust enough to describe the structural and thermodynamic properties of electrical double layers over both weak- and strong-coupling regimes.
A novel method for determining sky view factor for isotropic diffuse radiations for a collector in obstacles-free or urban sites
Authors: Rehman Naveed ur , Siddiqui Mubashir Ali
Published: May 2015

A novel method for computing sky view factor for isotropic diffuse radiations on tilted collectors located in obstacle free and urban sites has been introduced in this paper. The proposed method involves disintegrating the hemispherical sky vault around collector into small portions (sky elements). Collector is a flat receiving surface, positioned at a particular tilt angle and facing a specific azimuthal orientation. The three-dimensional celestial vault is transformed into a two-dimensional plane. This plane is converted into a computer graphic raster image for computing. Each pixel of raster image represents a sky element. Color (gray shade) of every pixel describes specific weight which depends upon sky element's solid angle and incidence angle with respect to collector. Sky view factor is evaluated by taking ratio of the sum of color codes of all the pixels for tilted collector to that of horizontal collector. Sky view factors at different tilt angles for obstacle free sites are evaluated and results are found in good agreement with Liu Jordan method. To evaluate sky view factor for urban sites having obstacles (e.g., buildings, trees, etc.) that may cause sky blocking, the obstacles are taken into account by projecting them onto the celestial vault. Their projections are transformed onto a two dimensional plane and then onto the raster image. For enhancing the applicability of the proposed method, so as to analyze sites with complex sky blocking obstacles, the approach is developed such that it can be computer programmed easily. Small portions of sky can be located and analyzed in a program using a specially developed coordinate system recognized by various programing languages. The program results in grey scaled raster images presenting radiances received by the collector, coming from different portions of the sky. Comparison of sky view factors obtained from the proposed method with existing methods published in literature is also presented. Results show that the proposed methodology is in good agreement with Liu Jordan method and provides more logical results as compared to results published in literature for urban sites with obstacles. The deviations between results are quantified and discussed.
Interaction between random heterogeneously charged surfaces in an electrolyte solution
Authors: Bakhshandeh Amin , dos Santos Alexandre P. , Diehl Alexandre , Levin Yan
Published: May 2015

We study, using Monte Carlo simulations, the interaction between infinite heterogeneously charged surfaces inside an electrolyte solution. The surfaces are overall neutral with quenched charged domains. An average over the quenched disorder is performed to obtain the net force. We find that the interaction between the surfaces is repulsive at short distances and is attractive for larger separations.
Surface plasmon resonance induced Er3+ photoluminescence enhancement in tellurite glass
Authors: Fares Hssen , Elhouichet Habib , Gelloz Bernard , Férid Mokhtar
Published: May 2015

The melt quenching method is used to prepare tellurite glasses co-activated with erbium ions and silver nanoparticles (Ag NPs). The glass samples are characterized by x-ray diffraction, UV-vis-NIR absorption, transmission electron microscopy (TEM) imaging, and photoluminescence spectroscopy. The XRD pattern shows no sharp peak indicating an amorphous nature of the glasses. The presence of Ag NPs is confirmed from TEM micrograph. The absorption spectra reveal not only the peaks due to Er3+ ions, but also the surface plasmon resonance band of silver NPs in the 510–535 nm range. The J-O model has been applied to the room temperature absorption intensities of Er3+ (4f11) transitions to establish the so-called J-O intensity parameters: Ω2, Ω4, and Ω6. The intensity parameters are used to determine the radiative decay rates (emission probabilities of transitions) and branching ratios of the Er3+ transitions from the excited state J manifolds to the lower-lying J' manifolds. Intensified of 1.53 μm band is obtained for the sample containing 0.5 mol. % of AgNO3 (Ag0.5 glass) using for excitation a laser operating at 980 nm. The simultaneous influence of the Ag NPs → Er3+ energy transfer and the contribution of the intensified local field effect due to the silver NPs give origin to the enhancement of both the Photoluminescence (PL) intensity and the PL lifetime relative to the 4I13/2 → 4I15/2 transition, whereas the quenching is ascribed to the energy transfer from Er3+ ions to silver NPs. Based on the analysis of the temperature dependence of the PL intensity and decay time, we identified a weak back transfer process from Er to the glass host that makes the quenching of the PL intensity weak. Large magnitudes of calculated emission cross-section (σe), effective bandwidth (Δλeff), and bandwidth quality factor (FWHM × σe) relatives to 4I13/2 → 4I15/2 transition in Er doped Ag0.5 glass have been shown. They indicate that this glass sample has good prospect as a gain medium applied for 1.53 μm band broad and high-gain erbium-doped fiber amplifiers.
Interfacial and bulk polaron masses in Zn1−xMgxO/ZnO heterostructures examined by terahertz time-domain cyclotron spectroscopy
Authors: Lloyd-Hughes J. , Failla M. , Ye J. , Jones S. P. P. , Teo K. L. , Jagadish C.
Published: May 2015

The cyclotron resonance of polarons in Zn1−xMgxO/ZnO heterostructures (with 0.15<x<0.22) was studied by terahertz time-domain spectroscopy. Low-temperature magnetoconductivity spectra of the 2D electron gas at the Zn1−xMgxO/ZnO interface determined the polaron density, mass, and scattering rate. The cyclotron mass of 2D polarons was found to increase significantly with magnetic field B from 0.24 me at B = 2 T to 0.37 me at B = 7.5 T. A nonlinear cyclotron frequency with B was also observed for 3D polarons in ZnO. The findings are discussed in the context of polaron mass renormalization driven by the electron-LO-phonon and electron-acoustic phonon interactions.
Note: An analyzer for field detection of H2S by using cavity ring-down at 1.57 μm
Authors: Siciliani de Cumis M. , Viciani S. , Galli I. , Mazzotti D. , Sorci F. , Severi M. , D’Amato F.
Published: May 2015

A prototype analyzer for the detection of hydrogen sulfide (H2S), based on cavity ring-down spectroscopy, is described. The device exploits, whenever possible, optical fibers, in order to simplify the alignment and to improve the stability. A trade-off between low detection level and simplicity has been pursued. The experimental results obtained during tests on different kinds of H2S samples are shown.
Synchrotron-based analysis of chromium distributions in multicrystalline silicon for solar cells
Authors: Jensen Mallory Ann , Hofstetter Jasmin , Morishige Ashley E. , Coletti Gianluca , Lai Barry , Fenning David P. , Buonassisi Tonio
Published: May 2015

Chromium (Cr) can degrade silicon wafer-based solar cell efficiencies at concentrations as low as 1010 cm−3. In this contribution, we employ synchrotron-based X-ray fluorescence microscopy to study chromium distributions in multicrystalline silicon in as-grown material and after phosphorous diffusion. We complement quantified precipitate size and spatial distribution with interstitial Cr concentration and minority carrier lifetime measurements to provide insight into chromium gettering kinetics and offer suggestions for minimizing the device impacts of chromium. We observe that Cr-rich precipitates in as-grown material are generally smaller than iron-rich precipitates and that Cri point defects account for only one-half of the total Cr in the as-grown material. This observation is consistent with previous hypotheses that Cr transport and CrSi2 growth are more strongly diffusion-limited during ingot cooling. We apply two phosphorous diffusion gettering profiles that both increase minority carrier lifetime by two orders of magnitude and reduce [Cri] by three orders of magnitude to ≈1010 cm−3. Some Cr-rich precipitates persist after both processes, and locally high [Cri] after the high-temperature process indicates that further optimization of the chromium gettering profile is possible.
Coalescence of GaAs on (001) Si nano-trenches based on three-stage epitaxial lateral overgrowth
Authors: He Yunrui , Wang Jun , Hu Haiyang , Wang Qi , Huang Yongqing , Ren Xiaomin
Published: May 2015

The coalescence of selective area grown GaAs regions has been performed on patterned 1.8 μm GaAs buffer layer on Si via metal-organic chemical vapor deposition. We propose a promising method of three-stage epitaxial lateral overgrowth (ELO) to achieve uniform coalescence and flat surface. Rough surface caused by the coalescence of different growth fronts is smoothened by this method. Low root-mean-square surface roughness of 6.29 nm has been obtained on a 410-nm-thick coalesced ELO GaAs layer. Cross-sectional transmission electron microscope study shows that the coalescence of different growth fronts will induce some new dislocations. However, the coalescence-induced dislocations tend to mutually annihilate and only a small part of them reach the GaAs surface. High optical quality of the ELO GaAs layer has been confirmed by low temperature (77 K) photoluminescence measurements. This research promises a very large scale integration platform for the monolithic integration of GaAs-based device on Si.
Estimating the CCSD basis-set limit energy from small basis sets: basis-set extrapolations vs additivity schemes
Authors: Spackman Peter R. , Karton Amir
Published: May 2015

Coupled cluster calculations with all single and double excitations (CCSD) converge exceedingly slowly with the size of the one-particle basis set. We assess the performance of a number of approaches for obtaining CCSD correlation energies close to the complete basis-set limit in conjunction with relatively small DZ and TZ basis sets. These include global and system-dependent extrapolations based on the A + B/Lα two-point extrapolation formula, and the well-known additivity approach that uses an MP2-based basis-set-correction term. We show that the basis set convergence rate can change dramatically between different systems(e.g.it is slower for molecules with polar bonds and/or second-row elements). The system-dependent basis-set extrapolation scheme, in which unique basis-set extrapolation exponents for each system are obtained from lower-cost MP2 calculations, significantly accelerates the basis-set convergence relative to the global extrapolations. Nevertheless, we find that the simple MP2-based basis-set additivity scheme outperforms the extrapolation approaches. For example, the following root-mean-squared deviations are obtained for the 140 basis-set limit CCSD atomization energies in the W4-11 database: 9.1 (global extrapolation), 3.7 (system-dependent extrapolation), and 2.4 (additivity scheme) kJ mol–1. The CCSD energy in these approximations is obtained from basis sets of up to TZ quality and the latter two approaches require additional MP2 calculations with basis sets of up to QZ quality. We also assess the performance of the basis-set extrapolations and additivity schemes for a set of 20 basis-set limit CCSD atomization energies of larger molecules including amino acids, DNA/RNA bases, aromatic compounds, and platonic hydrocarbon cages. We obtain the following RMSDs for the above methods: 10.2 (global extrapolation), 5.7 (system-dependent extrapolation), and 2.9 (additivity scheme) kJ mol–1.
Conservation genetics and geographic patterns of genetic variation of the vulnerable officinal herb Fritillaria walujewii (Liliaceae)
Authors: Su Zhihao , Pan Borong , Sanderson Stewart C. , Shi Xiaojun , Jiang Xiaolong
Published: May 2015

The Chinese herb Fritillaria walujewii Regel is an important officinal species that is vulnerable because of over-harvesting. Here, we examined the geographic pattern of genetic variation across the species entire range, to study its evolution process and give implication needed for the conservation. Nine haplotypes were detected on the basis of three chloroplast spacers. The most common haplotype was central in the haplotype network and was distributed widely from the Yili Valley to the eastern Tianshan Mountains. Genetic variation primarily occurred among populations and SAMOVA groups and the analysis of genetic structure showed a significant correlation between genetic and geographical distance. The fragmented distribution of F. walujewii in deep valleys may cause gene-flow barriers among distant populations and, along with genetic drift, has caused high genetic structure in the species. We identified Xinyuan County as the centre of diversification of F. walujewii, and speculated that populations in the eastern Tianshan Mountains were colonised from the Yili Valley. In relation to conservation management, we identified Xinyuan and Zhaosu County as having a high degree of genetic diversity and these should be the areas of the greatest focus for conservation.
Change in chirality of semiconducting single-walled carbon nanotubes can overcome anionic surfactant stabilisation: a systematic study of aggregation kinetics
Authors: Khan Iftheker A. , Flora Joseph R. V. , Afrooz A. R. M. Nabiul , Aich Nirupam , Schierz P. Ariette , Ferguson P. Lee , Sabo-Attwood Tara , Saleh Navid B.
Published: May 2015

Environmental context
Chirally enriched semiconducting single-walled carbon nanotubes (SWNTs) are some of the most utilised nanomaterials. Although chirality of SWNTs is known to influence their electronic properties and interfacial interaction, the interplay between chirality and surfactant structure in SWNT stability is not well understood. This study investigates these interactions, providing data to better assess the environmental fate of SWNTs.

Abstract
Single-walled carbon nanotubes’ (SWNT) effectiveness in applications is enhanced by debundling or stabilisation. Anionic surfactants are known to effectively stabilise SWNTs. However, the role of specific chirality on surfactant-stabilised SWNT aggregation has not been studied to date. The aggregation behaviour of chirally enriched (6,5) and (7,6) semiconducting SWNTs, functionalised with three anionic surfactants – sodium dodecyl sulfate, sodium dodecyl benzene sulfonate and sodium deoxycholate – was evaluated with time-resolved dynamic light scattering. A wide range of mono- (NaCl) and divalent (CaCl2) electrolytes as well as a 2.5mg total organic carbon (TOC) L–1 Suwannee River humic acid were used as background chemistry. Overall, sodium dodecyl benzene sulfonate showed the most effectiveness in stabilising SWNTs, followed by sodium deoxycholate and sodium dodecyl sulfate. However, the larger diameter (7,6) chirality tubes (compared to (6,5) diameter), compromised the surfactant stability due to enhanced van der Waals interaction. The presence of divalent electrolytes overshadowed the chirality effects and resulted in similar aggregation behaviour for both the SWNT samples. Molecular modelling results elucidated key differences in surfactant conformation on SWNT surfaces and identified interaction energy changes between the two chiralities to delineate aggregation mechanisms. The stability of SWNTs increased in the presence of Suwannee River humic acid under 10mM monovalent and mixed-electrolyte conditions. The results suggest that change in chirality can overcome surfactant stabilisation of semiconducting SWNTs. SWNT stability can also be strongly influenced by the anionic surfactant structure.
Genomic expression profiles in cumulus cells derived from germinal vesicle and MII mouse oocytes
Authors: Shao Li , Chian Ri-Cheng , Xu Yixin , Yan Zhengjie , Zhang Yihui , Gao Chao , Gao Li , Liu Jiayin , Cui Yugui
Published: May 2015

Cumulus cells (CCs) are distinct from other granulosa cells and the mutual communication between CCs and oocytes is essential for the establishment of oocyte competence. In the present study we assessed genomic expression profiles in mouse CCs before and after oocyte maturation in vitro. Microarray analysis revealed significant changes in gene expression in CCs between the germinal vesicle (GV) and metaphase II (MII) stages, with 2615 upregulated and 2808 downregulated genes. Genes related to epidermal growth factor, extracellular matrix (Ptgs2, Ereg, Tnfaip6 and Efemp1), mitochondrial metabolism (Fdx1 and Aifm2), gap junctions and the cell cycle (Gja1, Gja4, Ccnd2, Ccna2 and Ccnb2) were highlighted as being differentially expressed between the two development stages. Real-time polymerase chain reaction confirmed the validity and reproducibility of the results for the selected differentially expressed genes. Similar expression patterns were identified by western blot analysis for some functional proteins, including EFEMP1, FDX1, GJA1 and CCND2, followed by immunofluorescence localisation. These genes may be potential biomarkers for oocyte developmental competence following fertilisation and will be investigated further in future studies.
Understanding the quality of data: a concept map for ‘the thinking behind the doing’ in scientific practice
Authors: Roberts Ros , Johnson Philip
Published: May 2015

Recent school science curriculum developments in many countries emphasise that scientists derive evidence for their claims through different approaches; that such practices are bound up with disciplinary knowledge; and that the quality of data should be appreciated. This position paper presents an understanding of the validity of data as a set of conceptual relationships, illustrating the application of the network of ideas and their inter‐relationships necessary for the ‘thinking behind the doing’ with examples from practice. We explore ways in which this understanding of data is inherently related to underpinning disciplinary ideas. We suggest how the recognition of a conceptual basis for understanding the quality of data represents an ontological shift with respect to widespread characterisations of scientific practices which addresses some long‐standing issues in science education research, policy, curricula and practice.
The breadth and mnemonic consequences of the youth bias
Authors: Koppel Jonathan , Berntsen Dorthe
Published: May 2015

We have recently demonstrated the existence of the youth bias, referring to a tendency to favour adolescence and early adulthood over other lifetime periods when making inferences about the timing of important public events across the lifespan of a typical individual within one's culture. The youth bias integrates two discrete lines of research, that is, the literature on the privileged status of adolescence and early adulthood in human memory and cognition, and the literature on cognitive biases. Here we first examined whether the youth bias holds for specific categories of public events (i.e., deaths of public figures, United States presidential elections, and sporting events). We then investigated the possible role of the youth bias in structuring recall for public events, by probing, within subjects, for the relation between: (1) these expectations of the timing, in a typical person's life, of the most important exemplar from each public event category, and (2) the age at which the cited event occurred on a recall question asking participants to cite the most important exemplar, in their own lifetime, from each category. We found a youth bias for each category. Additionally, responses to the youth bias question were correlated with the age at which the recalled event occurred, but only where particularly salient historical events did not play a central role in driving recall (i.e., for sporting events). We conclude that the youth bias holds across different types of public events and provides a default structure for organizing recall of public events.
‘Dying of the Fifth Act’: Corneille's (Un)Natural Deaths
Authors: Harris Joseph
Published: May 2015

Generally speaking, deaths in tragedy involve murder or suicide. This article brings together a handful of disparate cases, from within Corneille's dramatic work, of deaths that do not fit into this typical tragic schema. Such deaths held something of a fascination for Corneille throughout his career: between his comedy
L'Illusion comique
(1635) and his swansong tragedy
Suréna
(1674), four of his female characters die of a broken heart, and one man is struck down by a lethal haemorrhage. Although these ‘(un)natural deaths’ clearly compromise
vraisemblance
, the very backbone of seventeenth-century dramaturgy, Corneille is also keen to harness their potential benefits as a source of dramatic, ethical, or emotional effect. This article traces the various techniques that Corneille adopts in order to integrate such causally problematic deaths into his plays. As I argue, although Corneille never settles for a single strategy (sometimes refusing to re-use even techniques he deems successful), he increasingly tends to draw on his rhetorical skills to ‘prepare’ these potentially awkward deaths on a thematic or poetic level. This becomes most poignantly clear at the end of his final tragedy
Suréna
, which reworks elements of his earlier ‘(un)natural deaths’ to unexpectedly elegiac effect.
Descemet Stripping Automated Endothelial Keratoplasty for Endothelial Dysfunction in Xeroderma Pigmentosum: A Clinicopathological Correlation and Review of Literature
Authors: Vira Divya , Fernandes Merle , Mittal Ruchi
Published: May 2015

Xeroderma pigmentosum (XP) mainly affects the ocular surface; however, endothelial damage may also occur. We would like to report changes in the endothelial–Descemet layer and review the literature on similar findings in patients with XP, including the role of Descemet stripping automated endothelial keratoplasty (DSAEK) in the management of a 21-year-old man who presented with nonresolving corneal edema in the right eye after excision biopsy for conjunctival intraepithelial neoplasia. His best-corrected visual acuity (BCVA) was 20/200 in the right eye and 20/20 in the left eye. On general examination, there was patchy hyperpigmentation of the exposed areas of skin suggestive of XP. On examination of the right eye, there was stromal edema involving the exposed half of cornea. The left eye appeared normal. Pachymetry readings were 860 and 600 μm in the right and left eye, respectively. Descemet stripping automated endothelial keratoplasty was performed for endothelial dysfunction and the stripped endothelium, and Descemet membrane (DM) was sent for histopathologic evaluation. Postoperatively, the donor lenticule was well apposed and the overlying stromal edema resolved. The patient achieved a BCVA of 20/30 in the right eye without progression of corneal scarring at 1-year follow-up. In the meanwhile, however, the left eye developed corneal edema. Histopathology revealed gross attenuation of endothelial cells with uniform thickness of the DM. Corneal endothelial dysfunction in XP is amenable to treatment with DSAEK.
Not so colourful after all: eggshell pigments constrain avian eggshell colour space
Authors: Hanley Daniel , Grim Tomáš , Cassey Phillip , Hauber Mark E.
Published: May 2015

Birds' eggshells are renowned for their striking colours and varied patterns. Although often considered exceptionally diverse, we report that avian eggshell coloration, sampled here across the full phylogenetic diversity of birds, occupies only 0.08–0.10% of the avian perceivable colour space. The concentrations of the two known tetrapyrrole eggshell pigments (protoporphyrin and biliverdin) are generally poor predictors of colour, both intra- and interspecifically. Here, we show that the constrained diversity of eggshell coloration can be accurately predicted by colour mixing models based on the relative contribution of both pigments and we demonstrate that the models' predictions can be improved by accounting for the reflectance of the eggshell's calcium carbonate matrix. The establishment of these proximate links between pigmentation and colour will enable future tests of hypotheses on the functions of perceived avian eggshell colours that depend on eggshell chemistry. More generally, colour mixing models are not limited to avian eggshell colours but apply to any natural colour. Our approach illustrates how modelling can aid the understanding of constraints on phenotypic diversity.
Punctuated equilibrium in the large-scale evolution of programming languages
Authors: Valverde Sergi , Solé Ricard V.
Published: May 2015

The analogies and differences between biological and cultural evolution have been explored by evolutionary biologists, historians, engineers and linguists alike. Two well-known domains of cultural change are language and technology. Both share some traits relating the evolution of species, but technological change is very difficult to study. A major challenge in our way towards a scientific theory of technological evolution is how to properly define evolutionary trees or clades and how to weight the role played by horizontal transfer of information. Here, we study the large-scale historical development of programming languages, which have deeply marked social and technological advances in the last half century. We analyse their historical connections using network theory and reconstructed phylogenetic networks. Using both data analysis and network modelling, it is shown that their evolution is highly uneven, marked by innovation events where new languages are created out of improved combinations of different structural components belonging to previous languages. These radiation events occur in a bursty pattern and are tied to novel technological and social niches. The method can be extrapolated to other systems and consistently captures the major classes of languages and the widespread horizontal design exchanges, revealing a punctuated evolutionary path.
A comprehensive analysis of the growth rate of stress corrosion cracks
Authors: Lee D. , Huang Y. , Achenbach J. D.
Published: May 2015

This paper is a synthesis of earlier results supplemented by new results to define a comprehensive analysis of the growth rate of stress corrosion cracking (SCC). Two mechanisms, anodic dissolution (AD) and hydrogen embrittlement (HE), have been considered to calculate the SCC growth rate of AA 7050-T6 for a surface-breaking crack with blunt tip in an aqueous environment. The relative contributions of each mechanism and their mutual interactions have been quantitatively assessed. Results show that AD provides critical conditions for HE, which explains in part a stepwise propagation of the crack. Finally, the total crack growth rate due to the combined effects of AD and HE has been determined, and numerical results have been compared with experimental data, and a calculation of the crack growth rate for a practical configuration has been presented.
Organic fields sustain weed metacommunity dynamics in farmland landscapes
Authors: Henckel Laura , Börger Luca , Meiss Helmut , Gaba Sabrina , Bretagnolle Vincent
Published: May 2015

Agro-ecosystems constitute essential habitat for many organisms. Agricultural intensification, however, has caused a strong decline of farmland biodiversity. Organic farming (OF) is often presented as a more biodiversity-friendly practice, but the generality of the beneficial effects of OF is debated as the effects appear often species- and context-dependent, and current research has highlighted the need to quantify the relative effects of local- and landscape-scale management on farmland biodiversity. Yet very few studies have investigated the landscape-level effects of OF; that is to say, how the biodiversity of a field is affected by the presence or density of organically farmed fields in the surrounding landscape. We addressed this issue using the metacommunity framework, with weed species richness in winter wheat within an intensively farmed landscape in France as model system. Controlling for the effects of local and landscape structure, we showed that OF leads to higher local weed diversity and that the presence of OF in the landscape is associated with higher local weed biodiversity also for conventionally farmed fields, and may reach a similar biodiversity level to organic fields in field margins. Based on these results, we derive indications for improving the sustainable management of farming systems.
Sensory-based niche partitioning in a multiple predator–multiple prey community
Authors: Falk Jay J. , ter Hofstede Hannah M. , Jones Patricia L. , Dixon Marjorie M. , Faure Paul A. , Kalko Elisabeth K. V. , Page Rachel A.
Published: May 2015

Many predators and parasites eavesdrop on the communication signals of their prey. Eavesdropping is typically studied as dyadic predator–prey species interactions; yet in nature, most predators target multiple prey species and most prey must evade multiple predator species. The impact of predator communities on prey signal evolution is not well understood. Predators could converge in their preferences for conspicuous signal properties, generating competition among predators and natural selection on particular prey signal features. Alternatively, predator species could vary in their preferences for prey signal properties, resulting in sensory-based niche partitioning of prey resources. In the Neotropics, many substrate-gleaning bats use the mate-attraction songs of male katydids to locate them as prey. We studied mechanisms of niche partitioning in four substrate-gleaning bat species and found they are similar in morphology, echolocation signal design and prey-handling ability, but each species preferred different acoustic features of male song in 12 sympatric katydid species. This divergence in predator preference probably contributes to the coexistence of many substrate-gleaning bat species in the Neotropics, and the substantial diversity in the mate-attraction signals of katydids. Our results provide insight into how multiple eavesdropping predator species might influence prey signal evolution through sensory-based niche partitioning.
Oceanisphaera psychrotolerans sp. nov., isolated from coastal sediment samples
Authors: Zhou Shan , Wang Huimin , Wang Yanwei , Ma Kedong , He Mingxiong , Chen Xiaorong , Kong Delong , Guo Xiang , Ruan Zhiyong , Zhao Bin
Published: May 2015

A novel aerobic, Gram-staining-negative bacterium, designated strain LAM-WHM-ZCT, was isolated from coastal sediment samples from the Bohai Sea, near Yantai, China. Cells of LAM-WHM-ZCT were non-motile, short-rod- or coccoid-shaped. The temperature and pH ranges for growth were 4–40  °C (optimum: 20–33  °C) and pH 5–9 (optimum: pH 7.5). The strain did not require NaCl for growth but tolerated up to 10 % NaCl (w/v). The major fatty acids of strain LAM-WHM-ZCT were summed feature 3, C12 : 0, C16 : 0, summed feature 2 and summed feature 8. The predominant respiratory quinone was ubiquinone Q-8. The main polar lipids were diphosphatidyglycerol, phosphatigylethanolamine, phosphatidyglycerol, one phospholipid and four unidentified glycolipids. The DNA G+C content was 59.3 mol% as determined by the melting temperature (T
m) method. Analysis of the 16S rRNA gene sequence indicated that the isolate represented a member of the genus Oceanisphaera and was closely related to Oceanisphaera arctica KCTC 23013T, Oceanisphaera litoralis DSM 15406T, Oceanisphaera sediminis KACC 15117T and Oceanisphaera donghaensis KCTC 12522T with 97.7 %, 97.1 %, 96.6 % and 96.6 % sequence similarity, respectively. The DNA–DNA hybridization values between strain LAM-WHM-ZCT and the four reference strains were 47.4 ± 2.8 %, 33.5 ± 2.2 %, 28.4 ± 1.8 % and 13.7 ± 0.8 %, respectively. Based on its phenotypic and genotypic properties, strain LAM-WHM-ZCT is suggested to represent a novel species of the genus Oceanisphaera, for which the name Oceanisphaera psychrotolerans sp. nov. is proposed. The type strain is LAM-WHM-ZCT ( = ACCC 06516T = JCM 30466T).
Thermoactinomyces guangxiensis sp. nov., a thermophilic actinomycete isolated from mushroom compost
Authors: Wu Hao , Liu Bin , Pan Shangli
Published: May 2015

A novel thermophilic actinomycete, designated strain CD-1T, was isolated from mushroom compost in Nanning, Guangxi province, China. The strain grew at 37–55 °C (optimum 45–50 °C), pH 6.0–11.0 (optimum pH 7.0–9.0) and with 0–2.0  % NaCl (optimum 0–1.0  %), formed well-developed white aerial mycelium and pale-yellow vegetative mycelium, and single endospores (0.8–1.0 μm diameter) were borne on long sporophores (2–3 μm length). The endospores were spherical-polyhedron in shape with smooth surface. Based on its phenotypic and phylogenetic characteristics, strain CD-1T is affiliated to the genus Thermoactinomyces. It contained meso-diaminopimelic acid as the diagnostic diamino acid; the whole-cell sugars were ribose and glucose. Major fatty acids were iso-C15  :  0, C16  :  0, anteiso-C15  :  0 and iso-C17  :  0. MK-7 was the predominant menaquinone. The polar phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylethanolamine containing hydroxylated fatty acids, ninhydrin-positive glycophospholipid, an unknown phospholipid and glycolipids. The G+C content of the genomic DNA was 48.8  %. 16S rRNA gene sequence analysis showed that the organism was closely related to Lihuaxuella thermophila YIM 77831T (95.69  % sequence similarity), Thermoactinomyces daqus H-18T (95.49  %), Laceyella putida KCTC 3666T (95.05  %), Thermoactinomyces vulgaris KCTC 9076T (95.01  %) and Thermoactinomyces intermedius JCM 3312T (94.55  %). Levels of DNA–DNA relatedness between strain CD-1T and Lihuaxuella thermophila JCM 18059T, Thermoactinomyces daqus DSM 45914T, Laceyella putida JCM 8091T, Thermoactinomyces vulgaris JCM 3162T and Thermoactinomyces intermedius JCM 3312T were low (22.8, 33.3, 24.7, 29.4 and 30.0  %, respectively). A battery of phenotypic, genotypic and DNA–DNA relatedness data indicated that strain CD-1T represented a novel species of the genus Thermoactinomyces, for which the name Thermoactinomyces guangxiensis sp. nov. is proposed. The type strain is CD-1T ( = ATCC BAA-2630T = CGMCC 4.7156T).
The Cf-4 receptor-like protein associates with the BAK1 receptor-like kinase to initiate receptor endocytosis and plant immunity
Authors: Postma Jelle , Liebrand Thomas W. H. , Bi Guozhi , Evrard Alexandre , Bye Ruby R. , Mbengue Malick , Joosten Matthieu H. A. J. , Robatzek Silke
Published: May 2015

The first layer of plant immunity is activated by cell surface receptor-like kinases (RLKs) and proteins (RLPs) that detect infectious pathogens. Constitutive interaction with the RLK SUPPRESSOR OF BIR1 (SOBIR1) contributes to RLP stability and kinase activity. As RLK activation requires transphosphorylation with a second associated RLK, it remains elusive how RLPs initiate downstream signaling. To address this, we investigated functioning of Cf RLPs that mediate immunity of tomato againstCladosporium fulvum.

We employed live-cell imaging and co-immunoprecipitation in tomato andNicotiana benthamianato investigate the requirement of associated kinases for Cf activity and ligand-induced subcellular trafficking of Cf-4.

Upon elicitation with the matching effector ligands Avr4 and Avr9, BRI1-ASSOCIATED KINASE 1 (BAK1) associates with Cf-4 and Cf-9. Furthermore, Cf-4 that interacts with SOBIR1 at the plasma membrane, is recruited to late endosomes after elicitation. Significantly, BAK1 is required for Avr4-triggered endocytosis, effector-triggered defenses in Cf-4 plants and resistance of tomato againstC. fulvum.

Our observations indicate that RLP-mediated immune signaling and endocytosis require ligand-induced recruitment of BAK1, reminiscent of BAK1 interaction and subcellular fate of the FLAGELLIN SENSING 2 RLK. This reveals that diverse classes of cell surface immune receptors share common requirements for signaling initiation and endocytosis.
Rust fungal effectors mimic host transit peptides to translocate into chloroplasts
Authors: Petre Benjamin , Lorrain Cécile , Saunders Diane G.O. , Duplessis Sébastien , Kamoun Sophien
Published: May 2015

Parasite effector proteins target various host cell compartments to alter host processes and promote infection. How effectors cross membrane-rich interfaces to reach these compartments is a major question in effector biology. Growing evidence suggests that effectors use molecular mimicry to subvert host cell machinery for protein sorting. We recently identified CTP1 (chloroplast-targetedprotein 1), a candidate effector from the poplar leaf rust fungusMelampsora larici-populinathat carries a predicted transit peptide and accumulates in chloroplasts. Here, we show that the CTP1 transit peptide is necessary and sufficient for accumulation in the stroma of chloroplasts, and is cleaved after translocation. CTP1 is part of aMelampsora-specific family of polymorphic secreted proteins whose members translocate and are processed in chloroplasts in a N-terminal signal-dependent manner. Our findings reveal that fungi have evolved effector proteins that mimic plant-specific sorting signals to traffic within plant cells.
Attention selectively gates afferent signal transmission to area V4
Authors: Grothe Iris , Rotermund David , Neitzel Simon David , Mandon Sunita , Ernst Udo Alexander , Kreiter Andreas Kurt , Pawelzik Klaus Richard
Published: May 2015

Selective attention causes visual cortical neurons to act as if only one of multiple stimuli are within their receptive fields. This suggests that attention employs a, yet unknown, neuronal gating mechanism for transmitting only the information that is relevant for the current behavioral context. We introduce an experimental paradigm to causally investigate this putative gating and the mechanism underlying selective attention by determining the signal availability of two time-varying stimuli in local field potentials of V4 neurons. We find transmission of the low frequency (<20Hz) components only from the attended visual input signal and that the higher frequencies from both stimuli are attenuated. A minimal model implementing routing by synchrony replicates the attentional gating effect and explains the spectral transfer characteristics of the signals. It supports the proposal that selective gamma-band synchrony subserves signal routing in cortex and further substantiates our experimental finding that attention selectively gates signals already at the level of afferent synaptic input.
piRNA-directed cleavage of meiotic transcripts regulates spermatogenesis
Authors: Goh Wee Siong Sho , Falciatori Ilaria , Tam Oliver H. , Burgess Ralph , Meikar Oliver , Kotaja Noora , Hammell Molly , Hannon Gregory J.
Published: May 2015

MIWI catalytic activity is required for spermatogenesis, indicating that piRNA-guided cleavage is critical for germ cell development. To identify meiotic piRNA targets, we augmented the mouse piRNA repertoire by introducing a human meiotic piRNA cluster. This triggered a spermatogenesis defect by inappropriately targeting the piRNA machinery to mouse mRNAs essential for germ cell development. Analysis of such de novo targets revealed a signature for pachytene piRNA target recognition. This enabled identification of both transposable elements and meiotically expressed protein-coding genes as targets of native piRNAs. Cleavage of genic targets began at the pachytene stage and resulted in progressive repression through meiosis, driven at least in part via the ping-pong cycle. Our data support the idea that meiotic piRNA populations must be strongly selected to enable successful spermatogenesis, both driving the response away from essential genes and directing the pathway toward mRNA targets that are regulated by small RNAs in meiotic cells.
The structure of hookworm platelet inhibitor (HPI), a CAP superfamily member fromAncylostoma caninum
Authors: Ma Dongying , Francischetti Ivo M. B. , Ribeiro Jose M. C. , Andersen John F.
Published: May 2015

Secreted protein components of hookworm species include a number of representatives of the cysteine-rich/antigen 5/pathogenesis-related 1 (CAP) protein family known asAncylostoma-secreted proteins (ASPs). Some of these have been considered as candidate antigens for the development of vaccines against hookworms. The functions of most CAP superfamily members are poorly understood, but one form, the hookworm platelet inhibitor (HPI), has been isolated as a putative antagonist of the platelet integrins αIIbβ3and α2β1. Here, the crystal structure of HPI is described and its structural features are examined in relation to its possible function. The HPI structure is similar to those of other ASPs and shows incomplete conservation of the sequence motifs CAP1 and CAP2 that are considered to be diagnostic of CAP superfamily members. The asymmetric unit of the HPI crystal contains a dimer with an extensive interaction interface, but chromatographic measurements indicate that it is primarily monomeric in solution. In the dimeric structure, the putative active-site cleft areas from both monomers are united into a single negatively charged depression. A potential Lys-Gly-Asp disintegrin-like motif was identified in the sequence of HPI, but is not positioned at the apex of a tight turn, making it unlikely that it interacts with the integrin. Recombinant HPI produced inEscherichia coliwas found not to inhibit the adhesion of human platelets to collagen or fibrinogen, despite having a native structure as shown by X-ray diffraction. This result corroborates previous analyses of recombinant HPI and suggests that it might require post-translational modification or have a different biological function.
Crystallographic study of a novel DNA-binding domain of human HLTF involved in the template-switching pathway to avoid the replication arrest caused by DNA damage
Authors: Ikegaya Yuzu , Hara Kodai , Hishiki Asami , Yokoyama Hideshi , Hashimoto Hiroshi
Published: May 2015

HLTF is a pivotal protein in the template-switching pathway that allows DNA synthesis to continue even in the presence of DNA damage by utilizing a newly synthesized undamaged strand as a template. HLTF has a novel DNA-binding domain termed HIRAN that has been recently found in various proteins, although its detailed function remains unclear. In this study, the HIRAN domain of human HLTF was successfully crystallized. The crystals belonged to space groupP41212 orP43212, with unit-cell parametersa=b= 130.0,c= 150.1 Å.