bluuebunny/crossref_metadata_2025 huggingface dataset:
Colour and texture feature‐based image retrieval by using Hadamard matrix in discrete wavelet transform
Authors: Farsi Hassan , Mohamadzadeh Sajad
Published: June 2013

Image retrieval is one of the most applicable image processing techniques, which has been used extensively. Feature extraction is one of the most important procedures used for interpretation and indexing images in content‐based image retrieval systems. Effective storage, indexing and managing a large number of image collections is a critical challenge in computer systems. There are many proposed methods to overcome these problems. However, the rate of accurate image retrieval and speed of retrieval is still an interesting field of research. In this study, the authors propose a new method based on combination of Hadamard matrix and discrete wavelet transform (HDWT) in hue‐min‐max‐difference colour space. An average normalised rank and combination of precision and recall are considered as metrics to evaluate and compare the proposed method against different methods. The obtained results show that the use of HDWT provides better performance in comparison with Haar discrete wavelet transform, colour layout descriptor, dominant colour descriptor and scalable colour descriptor, Padua point and histogram intersection.
Using macroscopic information in image segmentation
Authors: Khan Asmar Azar , Xydeas Costas , Ahmed Hassan
Published: June 2013

Post‐processing ‘macroscopically’ output‐segmented images obtained from conventional image segmentation (IS) techniques, leads into the concept of micro–macro IS (MMIS). MMIS pays extra attention to information extracted from relatively large image regions and as a result, overall system segmentation performance improves both subjectively and objectively. The proposed post‐processing scheme is generic, in the sense that can be used together with any other existing segmentation approach. Thus given an input‐segmented image, MMIS has the ability to automatically select an appropriate number of regions and classes in a way that helps object‐oriented visual information to become more apparent in the final segmented output image. Computer simulation results clearly indicate that significant IS performance benefits can be obtained by augmenting conventional IS schemes within an MMIS framework, with or without input images being corrupted by additive Gaussian noise
Two anisotropic fourth‐order partial differential equations for image inpainting
Authors: Li Peng , Li Shuai‐Jie , Yao Zheng‐An , Zhang Zu‐Jin
Published: June 2013

In this study, the authors propose two fourth‐order partial differential equations (PDEs) to inpaint the image. By analysing those anisotropic fourth‐order PDEs and comparing their diffusion images, the authors confirm they are forward diffusion or backward diffusion. A numerical algorithm is presented using a finite‐difference method and analyse the stability of discretisation. Finally, they show various experimental results and conclude that the proposed new models are better than the second‐order and third‐order PDEs, especially for weakening the blocky effects.
Generalised parallel‐coupled line and interdigital filters with unusually broad upper stop bandwidth:synthesis and design in homogeneous media
Authors: Fathelbab Wael M.
Published: June 2013

The synthesis and design of generalised parallel‐coupled line and interdigital filters suitable for realisation in a homogeneous media are proposed in this study. The filters comprise novel coupled line sections whose synthesis is discussed in detail leading to the derivation of formulae to evaluate their modal‐impedances. It will be shown that the proposed filters comprise asymmetrically coupled stepped‐impedance resonators and are capable of realising broad upper stopbands. Filter examples are synthesised and subsequently realised in suspended‐substrate stripline technology were simulated utilising High Frequency System Simulator (HFSS) show close correspondence to theoretical predictions.
Multiphysics design and experimental verification of a quad‐band dichroic mirror for deep space ground stations
Authors: Pasian Marco , Formaggi Marco , Bozzi Maurizio , Carli Fabio , Perregrini Luca , Philippou Glafkos , Dauron Guillaume
Published: June 2013

This study presents the multi‐disciplinary approach used to study a quad‐band dichroic mirror to be installed in the European Space Agency deep space antennas. Traditional electromagnetic (EM) analyses based on a uniform plane wave incidence were augmented by advanced numerical techniques to investigate the impact of the dichroic mirror on the overall antenna performance. In addition, along with the EM design, a parallel study considering mechanical, thermal and power‐handling aspects allowed their impact on the EM behaviour of the dichroic mirror to be evaluated. This comprehensive study permitted an optimum design to be achieved for the dichroic mirror, which accounts for the actual operational conditions of the mirror itself when installed in the antenna. The device was manufactured and measured, verifying also the mechanical and thermal theoretical predictions, obtaining an excellent agreement between simulations and experimental results.
Unidirectional wideband circularly polarised aperture antennas backed with artificial magnetic conductor reflectors
Authors: Agarwal Kush , Nasimuddin  , Alphones Arokiaswami
Published: June 2013

The reflection coefficient phase is studied for four different artificial magnetic conductors (AMCs) having canonical frequency selective surface (FSS)‐type two‐dimensional periodic structures to be used as back reflectors for an aperture antenna. The bidirectional circularly polarised (CP) radiation of the octagonal‐shaped aperture (OSA) antenna is made unidirectional using these AMC surfaces as ground planes. The antenna height measured from the upper surface of AMC reflector to the OSA radiator is chosen to be small to realise low‐profile antenna: 0.0825λo at the lowest analysis frequency of 4.5 GHz. Different antenna parameters like voltage standing wave ratio (VSWR) of 2, 3‐dB axial ratio (AR) bandwidth, gain, and front‐to‐back ratio are studied and compared for these four AMCs and the conventionally used perfect electric conductor (PEC) ground plane as back reflectors. Four different aperture shapes with fixed aperture perimeter are designed to integrate with the square‐loop AMC as back reflector to realise a low‐profile unidirectional wideband CP aperture antenna. Hexagonal‐shaped aperture antenna over the square‐loop AMC shows the largest measured 3‐dB AR bandwidth of 23.33% (5.65–7.05 GHz), VSWR of 2 bandwidth of 36.67% (5.16–7.36 GHz), and the gain of around 7 dBic over the band for overall antenna volume of 0.72λo × 0.60λo × 0.19λo at 6.0 GHz.
Vibrationally induced charge transfer in a bimolecular model complex in vacuo
Authors: Knurr Benjamin J. , McCoy Anne B. , Weber J. Mathias
Published: June 2013

We report vibrationally induced charge transfer from nitromethane anion to methyliodide in a molecular complex. Excitation of a CH stretching vibrational transition in either of the molecular constituents results in dissociative electron transfer to the CH3I molecule, resulting in I− product anions. Solvation of the pre-reactive complex with more than two Ar atoms leads to complete quenching of the reaction and can be used to estimate the barrier for this reaction. We discuss the results in the framework of electronic structure calculations and compare the intra-complex electron transfer with vibrationally mediated electron emission in bare nitromethane anion.
Classical limits of quantum mechanics on a non-commutative configuration space
Authors: Benatti Fabio , Gouba Laure
Published: June 2013

We consider a model of non-commutative quantum mechanics given by two harmonic oscillators over a non-commutative two dimensional configuration space. We study possible ways of removing the non-commutativity based on the classical limit context known as anti-Wick quantization. We show that removal of non-commutativity from the configuration space and from the canonical operators is not commuting operation.
Solvent effect on electronic absorption, fluorescence, and phosphorescence of acetone in water: Revisited by quantum mechanics/molecular mechanics (QM/MM) simulations
Authors: Ma Haibo , Ma Yingjin
Published: June 2013

The accurate simulation of fluorescence and phosphorescence spectra in solution remains a huge challenge due to the difficulty of simulating excited state dynamics in condensed phase. In this work we revisit the solvent effect on the electronic absorption, fluorescence, and phosphorescence of acetone by virtue of quantum mechanics/molecular mechanics (QM/MM) equilibrium state dynamics simulations for both the ground state (S0) and the lowest excited singlet (S1) and triplet (T1) states of aqueous acetone, which use periodic boundary conditions and hundreds of explicit solvent molecules and are free of empirical electrostatic fittings for excited states. Our calculated solvent effects on acetone's n → π* (S0 → S1) absorption (0.25–0.31 eV) and n ← π* (S1 → S0) emission (0.03–0.04 eV) as well as the Stokes shift (0.22–0.27 eV) are in good accordance with the experimental results (0.19 to 0.31, −0.02 to 0.05, and 0.14 to 0.33 eV, respectively). We also predict small water effects (−0.05 to 0.03 eV) for S1 → T1 and T1 → S0 phosphorescence emissions of acetone, which have no experimental data to date. For the recent dispute about the magnitude of the solvent effect for acetone's S1 → S0 fluorescence, we confirm that such effect is very small, agreeing well with the experimental determinations and most recent theoretical calculations. The large solvent effect for electronic absorption and small or negligible one for fluorescence and phosphorescence are shown to be related with much reduced dipole moments of acetone and accordingly much less hydrogen bonds for aqueous acetone in the electronic excited states S1 and T1 comparing to the ground state S0. We also disclose that solvent polarization effects are relatively small for all the electronic transitions of aqueous acetone involved in this work through the investigation of the QM region size effect on QM/MM results.
Three-dimensional confinement of vapor in nanostructures for sub-Doppler optical resolution
Authors: Ballin Philippe , Moufarej Elias , Maurin Isabelle , Laliotis Athanasios , Bloch Daniel
Published: June 2013

We confine a Cs thermal vapor in the interstitial regions of a glass opal. We perform linear reflection spectroscopy on a cell whose window is covered with a thin film (10 or 20 layers) of ∼1000 nm (or 400 nm) diameter glass spheres and observe sub-Doppler structures in the optical spectrum for a large range of oblique incidences. This original feature associated with the inner (3-dimensional) confinement of the vapor in the interstitial regions of the opal evokes a Dicke narrowing. We finally consider possible micron-size references for optical frequency clocks based on weak, hard to saturate, molecular lines.
Nanosecond-scale timing jitter for single photon detection in transition edge sensors
Authors: Lamas-Linares Antia , Calkins Brice , Tomlin Nathan A. , Gerrits Thomas , Lita Adriana E. , Beyer Jörn , Mirin Richard P. , Woo Nam Sae
Published: June 2013

Transition edge sensors (TES) have the highest reported efficiencies (>98%) for single photon detection in the visible and near infrared. Experiments in quantum information and foundations of physics that rely on this efficiency have started incorporating these detectors. However, their range of applicability has been hindered by slow operation both in recovery time and timing jitter. We show how a conventional tungsten-TES can be operated with jitter times of ≈4 ns, providing a practical simplification for experiments that rely on simultaneous high efficiency and low timing uncertainty, such as loophole free Bell inequalities and device independent quantum cryptography.
Optical frequency comb with an absolute linewidth of 0.6 Hz–1.2 Hz over an octave spectrum
Authors: Fang Su , Chen Haiqin , Wang Tianyin , Jiang Yanyi , Bi Zhiyi , Ma Longsheng
Published: June 2013

We demonstrate a narrow-linewidth optical frequency comb based on a femtosecond Ti:sapphire laser by precisely phase-locking it to a subhertz-linewidth Nd:YAG laser at 1064 nm. Each comb tooth inherits the phase coherence and frequency stability of the subhertz-linewidth laser. By comparing against other independent narrow-linewidth lasers, we measured the absolute linewidth of the comb teeth to be 0.6 Hz–1.2 Hz over an octave spectrum.
Time dependence of magnetization reversal when beginning with pre-existing nucleation sites
Authors: Windsor Y. W. , Gerber A. , Korenblit I. Ya. , Karpovski M.
Published: June 2013

We use measurements of time and field dependent magnetization reversal in Co/Pd multilayers with perpendicular anisotropy to detect the presence of dilute enclaves of opposite magnetization within a magnetized ferromagnet. Such enclaves are stable due to dipolar fields generated by the surrounding material, and their presence at the onset of reversal can speed the process by orders of magnitude. The field required to suppress these nuclei and reach true magnetic saturation is found to be an order of magnitude higher than the observable macroscopic saturation field. Fatuzzo–Labrune model is extended to describe magnetization reversal starting with ready nucleation domains.
Phenotypic deconstruction of gene circuitry
Authors: Lomnitz Jason G. , Savageau Michael A.
Published: June 2013

It remains a challenge to obtain a global perspective on the behavioral repertoire of complex nonlinear gene circuits. In this paper, we describe a method for deconstructing complex systems into nonlinear sub-systems, based on mathematically defined phenotypes, which are then represented within a system design space that allows the repertoire of qualitatively distinct phenotypes of the complex system to be identified, enumerated, and analyzed. This method efficiently characterizes large regions of system design space and quickly generates alternative hypotheses for experimental testing. We describe the motivation and strategy in general terms, illustrate its use with a detailed example involving a two-gene circuit with a rich repertoire of dynamic behavior, and discuss experimental means of navigating the system design space.
On electric conduction of amorphous silicon carbonitride derived from a polymeric precursor
Authors: Chen Yaohan , Yang Fuqian , An Linan
Published: June 2013

A long-existing problem that the conductivity of amorphous silicon carbonitrides derived from polymeric precursor increases significantly with pyrolysis temperature is investigated. We show that the conductivity exhibited an Arrhenius dependence on pyrolysis temperature, with the activation energy of ∼3.41 eV. Structural analysis using Raman spectroscopy reveals that the free carbon within the material undergoes a sp3-to-sp2 transition as pyrolysis temperature increases, with the activation energy of ∼3.6 eV. We conclude that the pyrolysis-temperature induced increase in the conductivity is mainly due to the increase in the conductivity of the free carbon. A simple model is proposed to correlate the two.
Fabrication and tuning of plasmonic optical nanoantennas around droplet epitaxy quantum dots by cathodoluminescence
Authors: Nogues Gilles , Merotto Quentin , Bachelier Guillaume , Hye Lee Eun , Dong Song Jin
Published: June 2013

We use cathodoluminescence to locate droplet epitaxy quantum dots with a precision ≲50 nm before fabricating nanoantennas in their vicinity by electron-beam lithography. Cathodoluminescence is further used to evidence the effect of the antennas as a function of their length on the light emitted by the dot. Experimental results are in good agreement with numerical simulations of the structures.
Crystal structure and properties of CdxZn1−xO alloys across the full composition range
Authors: Detert D. M. , Lim S. H. M. , Tom K. , Luce A. V. , Anders A. , Dubon O. D. , Yu K. M. , Walukiewicz W.
Published: June 2013

We have synthesized CdxZn1−xO alloys across the full composition range. The structural mismatch of the two endpoint compounds splits the alloy into two regions of distinct optical and electrical behavior. The wurtzite phase alloys at compositions 0 < x < 0.69 exhibit a decrease in the absorption edge across the visible range and an increase in the conductivity with increasing Cd content. A phase transition to the rocksalt structure is observed above x = 0.69 along with a step increase in the electron mobility and the absorption edge. The intrinsic bandgap of these alloys was determined taking into account the carrier filling and renormalization effects.
Experimental demonstration of one-way slow wave in waveguide involving gyromagnetic photonic crystals
Authors: Yang Yan , Poo Yin , Wu Rui-xin , Gu Yan , Chen Ping
Published: June 2013

We experimentally demonstrate that electromagnetic waves in the waveguide comprising gyromagnetic photonic crystals (GMPCs) and a metal cladding are robust one-way slow waves in the frequency range of the chiral edge states of GMPC. Measured with phase shift technique in microwave regime, the group velocity of the wave could be one order of magnitude smaller than the speed of light with group index up to 15.6. The one-way wave with much slower group velocity is shown by retailoring the waveguide further. This waveguide provides a potential way to realize robust slow-light transmission lines in electromagnetic or optical systems.
Giant magnetoelectric effect in vacuum
Authors: Kirchhof Christine , Krantz Matthias , Teliban Iulian , Jahns Robert , Marauska Stephan , Wagner Bernhard , Knöchel Reinhard , Gerken Martina , Meyners Dirk , Quandt Eckhard
Published: June 2013

Magnetoelectric (ME) thin film cantilever type sensors made of AlN and FeCoSiB are operated in vacuum, reducing air damping and thus increasing the ME coefficient and improving the limit of detection (LOD) for ac-magnetic fields. Depending on the sensor geometry, the response is increased by a factor of 5 resulting in a ME coefficient of 20 kV/cmOe at 152 Hz and by a factor of 11 with 12 kV/cmOe at 4.7 kHz and an improvement in LOD by an order of magnitude. Modelling these cantilevers reveals dominant contributions of viscoelastic and molecular damping above and intrinsic damping below 10−2 mbar, respectively.
Probing electron acceleration and x-ray emission in laser-plasma accelerators
Authors: Thaury C. , Ta Phuoc K. , Corde S. , Brijesh P. , Lambert G. , Mangles S. P. D. , Bloom M. S. , Kneip S. , Malka V.
Published: June 2013

While laser-plasma accelerators have demonstrated a strong potential in the acceleration of electrons up to giga-electronvolt energies, few experimental tools for studying the acceleration physics have been developed. In this paper, we demonstrate a method for probing the acceleration process. A second laser beam, propagating perpendicular to the main beam, is focused on the gas jet few nanosecond before the main beam creates the accelerating plasma wave. This second beam is intense enough to ionize the gas and form a density depletion, which will locally inhibit the acceleration. The position of the density depletion is scanned along the interaction length to probe the electron injection and acceleration, and the betatron X-ray emission. To illustrate the potential of the method, the variation of the injection position with the plasma density is studied.
Spatiotemporal evolution of dielectric driven cogenerated dust density waves
Authors: Sarkar Sanjib , Bose M. , Mukherjee S. , Pramanik J.
Published: June 2013

An experimental observation of spatiotemporal evolution of dust density waves (DDWs) in cogenerated dusty plasma in the presence of modified field induced by glass plate is reported. Various DDWs, such as vertical, oblique, and stationary, were detected simultaneously for the first time. Evolution of spatiotemporal complexity like bifurcation in propagating wavefronts is also observed. As dust concentration reaches extremely high value, the DDW collapses. Also, the oblique and nonpropagating mode vanishes when we increase the number of glass plates, while dust particles were trapped above each glass plates showing only vertical DDWs.
The World Reference Base for Soils (WRB) and Soil Taxonomy: an appraisal of their application to the soils of the Northern Rivers of New South Wales
Authors: Morand David T.
Published: June 2013

Few soil surveys in New South Wales have utilised international soil classifications. Extensive morphological and laboratory data collected during soil surveys in the Northern Rivers region provided a strong basis for correlation with the World Reference Base for Soil Resources (WRB), Soil Taxonomy (ST), and the Australian Soil Classification (ASC). Of the 32 reference soil groups comprising the WRB, 20 were present locally; nine of the 12 ST orders were present. After re-classification of soils, correlation of the ASC with the WRB and ST was undertaken. Soils not requiring extensive laboratory analysis for classification and sharing similar central concepts were the more straightforward to correlate. Several ASC orders have unique central concepts and were therefore difficult to correlate with any one WRB reference soil group or ST order/suborder. Other soils were difficult to correlate due to differences in definitions of similar diagnostic criteria. This is most applicable to soils with strong texture-contrast and those with natric conditions. Such soils are not adequately differentiated to suit the Northern Rivers conditions. Of the two international schemes, the WRB was easier to apply locally due to the relative simplicity of the scheme. Considering certain aspects of Australian soils would improve the applicability of the WRB as a truly international framework for soil classification and correlation. Amendments to both the ASC and WRB are suggested.
Acidity fractions in acid sulfate soils and sediments: contributions of schwertmannite and jarosite
Authors: Vithana Chamindra L. , Sullivan Leigh A. , Bush Richard T. , Burton Edward D.
Published: June 2013

In Australia, the assessment of acidity hazard in acid sulfate soils requires the estimation of operationally defined acidity fractions such as actual acidity, potential sulfidic acidity, and retained acidity. Acid–base accounting approaches in Australia use these acidity fractions to estimate the net acidity of acid sulfate soils materials. Retained acidity is the acidity stored in the secondary Fe/Al hydroxy sulfate minerals, such as jarosite, natrojarosite, schwertmannite, and basaluminite. Retained acidity is usually measured as either net acid-soluble sulfur (SNAS) or residual acid soluble sulfur (SRAS). In the present study, contributions of schwertmannite and jarosite to the retained acidity, actual acidity, and potential sulfidic acidity fractions were systematically evaluated using SNAS and SRAS techniques. The data show that schwertmannite contributed considerably to the actual acidity fraction and that it does not contribute solely to the retained acidity fraction as has been previously conceptualised. As a consequence, SNAS values greatly underestimated the schwertmannite content. For soil samples in which jarosite is the only mineral present, a better estimate of the added jarosite content can be obtained by using a correction factor of 2 to SNAS values to account for the observed 50–60% recovery. Further work on a broader range of jarosite samples is needed to determine whether this correction factor has broad applicability. The SRAS was unable to reliably quantify either the schwertmannite or the jarosite content and, therefore, is not suitable for quantification of the retained acidity fraction. Potential sulfidic acidity in acid sulfate soils is conceptually derived from reduced inorganic sulfur minerals and has been estimated by the peroxide oxidation approach, which is used to derive the SRAS values. However, both schwertmannite and jarosite contributed to the peroxide-oxidisable sulfur fraction, implying a major potential interference by those two minerals to the determination of potential sulfidic acidity in acid sulfate soils through the peroxide oxidation approach.
Anisotropic growth shapes intestinal tissues during embryogenesis
Authors: Ben Amar Martine , Jia Fei
Published: June 2013

Embryogenesis offers a real laboratory for pattern formation, buckling, and postbuckling induced by growth of soft tissues. Each part of our body is structured in multiple adjacent layers: the skin, the brain, and the interior of organs. Each layer has a complex biological composition presenting different elasticity. Generated during fetal life, these layers will experience growth and remodeling in the early postfertilization stages. Here, we focus on a herringbone pattern occurring in fetal intestinal tissues. Common to many mammalians, this instability is a precursor of the villi, finger-like projections into the lumen. For avians (chicks’ and turkeys’ embryos), it has been shown that, a few days after fertilization, the mucosal epithelium of the duodenum is smooth, and then folds emerge, which present 2 d later a pronounced zigzag instability. Many debates and biological studies are devoted to this specific morphology, which regulates the cell renewal in the intestine. After reviewing experimental results about duodenum morphogenesis, we show that a model based on simplified hypothesis for the growth of the mesenchyme can explain buckling and postbuckling instabilities. Being completely analytical, it is based on biaxial compressive stresses due to differential growth between layers and it predicts quantitatively the morphological changes. The growth anisotropy increasing with time, the competition between folds and zigzags, is proved to occur as a secondary instability. The model is compared with available experimental data on chick’s duodenum and can be applied to other intestinal tissues, the zigzag being a common and spectacular microstructural pattern of intestine embryogenesis.
Outsourcing CO
2
within China
Authors: Feng Kuishuang , Davis Steven J. , Sun Laixiang , Li Xin , Guan Dabo , Liu Weidong , Liu Zhu , Hubacek Klaus
Published: June 2013

Recent studies have shown that the high standard of living enjoyed by people in the richest countries often comes at the expense of CO
2
emissions produced with technologies of low efficiency in less affluent, developing countries. Less apparent is that this relationship between developed and developing can exist within a single country’s borders, with rich regions consuming and exporting high-value goods and services that depend upon production of low-cost and emission-intensive goods and services from poorer regions in the same country. As the world’s largest emitter of CO
2
, China is a prominent and important example, struggling to balance rapid economic growth and environmental sustainability across provinces that are in very different stages of development. In this study, we track CO
2
emissions embodied in products traded among Chinese provinces and internationally. We find that 57% of China’s emissions are related to goods that are consumed outside of the province where they are produced. For instance, up to 80% of the emissions related to goods consumed in the highly developed coastal provinces are imported from less developed provinces in central and western China where many low–value-added but high–carbon-intensive goods are produced. Without policy attention to this sort of interprovincial carbon leakage, the less developed provinces will struggle to meet their emissions intensity targets, whereas the more developed provinces might achieve their own targets by further outsourcing. Consumption-based accounting of emissions can thus inform effective and equitable climate policy within China.
Interplay between insulin signaling, juvenile hormone, and vitellogenin regulates maternal effects on polyphenism in ants
Authors: Libbrecht Romain , Corona Miguel , Wende Franziska , Azevedo Dihego O. , Serrão Jose E. , Keller Laurent
Published: June 2013

Polyphenism is the phenomenon in which alternative phenotypes are produced by a single genotype in response to environmental cues. An extreme case is found in social insects, in which reproductive queens and sterile workers that greatly differ in morphology and behavior can arise from a single genotype. Experimental evidence for maternal effects on caste determination, the differential larval development toward the queen or worker caste, was recently documented in
Pogonomyrmex
seed harvester ants, in which only colonies with a hibernated queen produce new queens. However, the proximate mechanisms behind these intergenerational effects have remained elusive. We used a combination of artificial hibernation, hormonal treatments, gene expression analyses, hormone measurements, and vitellogenin quantification to investigate how the combined effect of environmental cues and hormonal signaling affects the process of caste determination in
Pogonomyrmex rugosus
. The results show that the interplay between insulin signaling, juvenile hormone, and vitellogenin regulates maternal effects on the production of alternative phenotypes and set vitellogenin as a likely key player in the intergenerational transmission of information. This study reveals how hibernation triggers the production of new queens in
Pogonomyrmex
ant colonies. More generally, it provides important information on maternal effects by showing how environmental cues experienced by one generation can translate into phenotypic variation in the next generation.
From perception to pleasure: Music and its neural substrates
Authors: Zatorre Robert J. , Salimpoor Valorie N.
Published: June 2013

Music has existed in human societies since prehistory, perhaps because it allows expression and regulation of emotion and evokes pleasure. In this review, we present findings from cognitive neuroscience that bear on the question of how we get from perception of sound patterns to pleasurable responses. First, we identify some of the auditory cortical circuits that are responsible for encoding and storing tonal patterns and discuss evidence that cortical loops between auditory and frontal cortices are important for maintaining musical information in working memory and for the recognition of structural regularities in musical patterns, which then lead to expectancies. Second, we review evidence concerning the mesolimbic striatal system and its involvement in reward, motivation, and pleasure in other domains. Recent data indicate that this dopaminergic system mediates pleasure associated with music; specifically, reward value for music can be coded by activity levels in the nucleus accumbens, whose functional connectivity with auditory and frontal areas increases as a function of increasing musical reward. We propose that pleasure in music arises from interactions between cortical loops that enable predictions and expectancies to emerge from sound patterns and subcortical systems responsible for reward and valuation.
Stabilization of a protein conferred by an increase in folded state entropy
Authors: Dagan Shlomi , Hagai Tzachi , Gavrilov Yulian , Kapon Ruti , Levy Yaakov , Reich Ziv
Published: June 2013

Entropic stabilization of native protein structures typically relies on strategies that serve to decrease the entropy of the unfolded state. Here we report, using a combination of experimental and computational approaches, on enhanced thermodynamic stability conferred by an increase in the configurational entropy of the folded state. The enhanced stability is observed upon modifications of a loop region in the enzyme acylphosphatase and is achieved despite significant enthalpy losses. The modifications that lead to increased stability, as well as those that result in destabilization, however, strongly compromise enzymatic activity, rationalizing the preservation of the native loop structure even though it does not provide the protein with maximal stability or kinetic foldability.
Genome of
Phaeocystis globosa
virus PgV-16T highlights the common ancestry of the largest known DNA viruses infecting eukaryotes
Authors: Santini Sebastien , Jeudy Sandra , Bartoli Julia , Poirot Olivier , Lescot Magali , Abergel Chantal , Barbe Valérie , Wommack K. Eric , Noordeloos Anna A. M. , Brussaard Corina P. D. , Claverie Jean-Michel
Published: June 2013

Large dsDNA viruses are involved in the population control of many globally distributed species of eukaryotic phytoplankton and have a prominent role in bloom termination. The genus
Phaeocystis
(
Haptophyta
,
Prymnesiophyceae
) includes several high-biomass-forming phytoplankton species, such as
Phaeocystis globosa
, the blooms of which occur mostly in the coastal zone of the North Atlantic and the North Sea. Here, we report the 459,984-bp-long genome sequence of
P. globosa
virus strain PgV-16T, encoding 434 proteins and eight tRNAs and, thus, the largest fully sequenced genome to date among viruses infecting algae. Surprisingly, PgV-16T exhibits no phylogenetic affinity with other viruses infecting microalgae (e.g., phycodnaviruses), including those infecting
Emiliania huxleyi
, another ubiquitous bloom-forming haptophyte. Rather, PgV-16T belongs to an emerging clade (the Megaviridae) clustering the viruses endowed with the largest known genomes, including Megavirus, Mimivirus (both infecting acanthamoeba), and a virus infecting the marine microflagellate grazer
Cafeteria roenbergensis
. Seventy-five percent of the best matches of PgV-16T–predicted proteins correspond to two viruses [Organic Lake phycodnavirus (OLPV)1 and OLPV2] from a hypersaline lake in Antarctica (Organic Lake), the hosts of which are unknown. As for OLPVs and other Megaviridae, the PgV-16T sequence data revealed the presence of a virophage-like genome. However, no virophage particle was detected in infected
P. globosa
cultures. The presence of many genes found only in Megaviridae in its genome and the presence of an associated virophage strongly suggest that PgV-16T shares a common ancestry with the largest known dsDNA viruses, the host range of which already encompasses the earliest diverging branches of domain Eukarya.
Solid surface tension measured by a liquid drop under a solid film
Authors: Nadermann Nichole , Hui Chung-Yuen , Jagota Anand
Published: June 2013

We show that a drop of liquid a few hundred microns in diameter placed under a solid, elastic, thin film (∼10 μm thick) causes it to bulge by tens of microns. The deformed shape is governed by equilibrium of tensions exerted by the various interfaces and the solid film, a form of Neumann’s triangle. Unlike Young’s equation, which specifies the contact angles at the junction of two fluids and a (rigid) solid, and is fundamentally underdetermined, both tensions in the solid film can be determined here if the liquid–vapor surface tension is known independently. Tensions in the solid film have a contribution from elastic stretch and a constant residual component. The residual component, extracted by extrapolation to films of vanishing thickness and supported by analysis of the elastic deformation, is interpreted as the solid–fluid surface tension, demonstrating that compliant thin-film structures can be used to measure solid surface tensions.
Genetic and archaeological perspectives on the initial modern human colonization of southern Asia
Authors: Mellars Paul , Gori Kevin C. , Carr Martin , Soares Pedro A. , Richards Martin B.
Published: June 2013

It has been argued recently that the initial dispersal of anatomically modern humans from Africa to southern Asia occurred before the volcanic “supereruption” of the Mount Toba volcano (Sumatra) at ∼74,000 y before present (B.P.)—possibly as early as 120,000 y B.P. We show here that this “pre-Toba” dispersal model is in serious conflict with both the most recent genetic evidence from both Africa and Asia and the archaeological evidence from South Asian sites. We present an alternative model based on a combination of genetic analyses and recent archaeological evidence from South Asia and Africa. These data support a coastally oriented dispersal of modern humans from eastern Africa to southern Asia ∼60–50 thousand years ago (ka). This was associated with distinctively African microlithic and “backed-segment” technologies analogous to the African “Howiesons Poort” and related technologies, together with a range of distinctively “modern” cultural and symbolic features (highly shaped bone tools, personal ornaments, abstract artistic motifs, microblade technology, etc.), similar to those that accompanied the replacement of “archaic” Neanderthal by anatomically modern human populations in other regions of western Eurasia at a broadly similar date.
Bach2 maintains T cells in a naive state by suppressing effector memory-related genes
Authors: Tsukumo Shin-ichi , Unno Midori , Muto Akihiko , Takeuchi Arata , Kometani Kohei , Kurosaki Tomohiro , Igarashi Kazuhiko , Saito Takashi
Published: June 2013

The transcriptional repressor BTB and CNC homology 2 (Bach2) is thought to be mainly expressed in B cells with specific functions such as class switch recombination and somatic hypermutation, but its function in T cells is not known. We found equal
Bach2
expression in T cells and analyzed its function using Bach2-deficient (−/−) mice. Although T-cell development was normal, numbers of peripheral naive T cells were decreased, which rapidly produced Th2 cytokines after TCR stimulation. Bach2
−/−
naive T cells highly expressed genes related to effector-memory T cells such as CCR4, ST-2 and Blimp-1. Enhanced expression of these genes induced Bach2
−/−
naive T cells to migrate toward CCR4-ligand and respond to IL33. Forced expression of Bach2 restored the expression of these genes. Using Chromatin Immunoprecipitation (ChIP)-seq analysis, we identified S100 calcium binding protein a, Heme oxigenase 1, and prolyl hydroxylase 3 as Bach2 direct target genes, which are highly expressed in effector-memory T cells. These findings indicate that Bach2 suppresses effector memory-related genes to maintain the naive T-cell state and regulates generation of effector-memory T cells.
Ca
2+
/calmodulin-dependent protein kinase kinase β phosphorylation of Sirtuin 1 in endothelium is atheroprotective
Authors: Wen Liang , Chen Zhen , Zhang Fan , Cui Xiaopei , Sun Wei , Geary Greg G. , Wang Yinsheng , Johnson David A. , Zhu Yi , Chien Shu , Shyy John Y.-J.
Published: June 2013

Significance

Different flow patterns in the arterial tree determine the severity and topographic distribution of atherosclerosis. Atheroprotective flow exerts anti-inflammatory and antioxidative effects on vascular endothelial cells, and the underlying mechanism involves the flow-induced upregulation of Sirtuin (SIRT)1. This study reveals that athero-protective flow activates Ca
2+
/calmodulin-dependent protein kinase kinase (CaMKK)β, which, in turn, phosphorylates SIRT1 at Ser-27 and Ser-47 to increase the stability and activity of SIRT1. The mechanosensitive CaMKKβ-SIRT1 pathway alleviates inflammatory and redox status in the endothelium. Such a conclusion is evident from the drastically increased atherosclerosis in mice lacking CaMKKβ or endothelial SIRT1.
Yukiko Yamashita: The centrosomes get there first
Authors: Sedwick Caitlin
Published: June 2013

Yamashita studies how germline stem cells orient their asymmetric cell divisions.
Changes in RNA polymerase II progression influence somatic hypermutation of Ig-related genes by AID
Authors: Kodgire Prashant , Mukkawar Priyanka , Ratnam Sarayu , Martin Terence E. , Storb Ursula
Published: June 2013

Somatic hypermutation (SHM) of Ig genes is initiated by the activation-induced cytidine deaminase (AID), and requires target gene transcription. We previously proposed that AID may associate with the RNA polymerase II (Pol). Here, to determine aspects of the transcription process required for SHM, we knocked-in a transcription terminator into an Ig gene variable region in DT40 chicken B cell line. We found that the human β-globin terminator was an efficient inhibitor of downstream transcription in these cells. The terminator reduced mutations downstream of the poly(A) signal, suggesting that the process of transcription is essential for efficient SHM and that AID has better access to its target when Pol is in the elongating rather than terminating mode. Mutations upstream of the poly(A) site were almost doubled in the active terminator clones compared with an inactivated terminator, and this region showed more single-stranded DNA, indicating that Pol pausing assists SHM. Moreover, the nontranscribed DNA strand was the preferred SHM target upstream of the active terminator. Pol pausing during poly(A) site recognition may facilitate persistence of negative supercoils, exposing the coding single strand and possibly allowing the nascent RNA intermittent reannealing with the template strand, for prolonged access of AID.
Conformational changes in the catalytically inactive nucleotide-binding site of CFTR
Authors: Csanády László , Mihályi Csaba , Szollosi Andras , Töröcsik Beáta , Vergani Paola
Published: June 2013

A central step in the gating of the cystic fibrosis transmembrane conductance regulator (CFTR) chloride channel is the association of its two cytosolic nucleotide-binding domains (NBDs) into a head-to-tail dimer, with two nucleotides bound at the interface. Channel opening and closing, respectively, are coupled to formation and disruption of this tight NBD dimer. CFTR is an asymmetric adenosine triphosphate (ATP)-binding cassette protein in which the two interfacial-binding sites (composite sites 1 and 2) are functionally different. During gating, the canonical, catalytically active nucleotide-binding site (site 2) cycles between dimerized prehydrolytic (state O1), dimerized post-hydrolytic (state O2), and dissociated (state C) forms in a preferential C→O1→O2→C sequence. In contrast, the catalytically inactive nucleotide-binding site (site 1) is believed to remain associated, ATP-bound, for several gating cycles. Here, we have examined the possibility of conformational changes in site 1 during gating, by studying gating effects of perturbations in site 1.

Previous work showed that channel closure is slowed, both under hydrolytic and nonhydrolytic conditions, by occupancy of site 1 by N6-(2-phenylethyl)-ATP (P-ATP) as well as by the site-1 mutation H1348A (NBD2 signature sequence). Here, we found that P-ATP prolongs wild-type (WT) CFTR burst durations by selectively slowing (>2×) transition O1→O2 and decreases the nonhydrolytic closing rate (transition O1→C) of CFTR mutants K1250A (∼4×) and E1371S (∼3×). Mutation H1348A also slowed (∼3×) the O1→O2 transition in the WT background and decreased the nonhydrolytic closing rate of both K1250A (∼3×) and E1371S (∼3×) background mutants. Neither P-ATP nor the H1348A mutation affected the 1:1 stoichiometry between ATP occlusion and channel burst events characteristic to WT CFTR gating in ATP. The marked effect that different structural perturbations at site 1 have on both steps O1→C and O1→O2 suggests that the overall conformational changes that CFTR undergoes upon opening and coincident with hydrolysis at the active site 2 include significant structural rearrangement at site 1.
Journal print subscription price increases no longer reflect actual costs
Authors: GANTZ Paula
Published: June 2013

Journal subscription prices and their annual increases have traditionally been reported as and based on institutional print prices. This methodology for calculating price inflation and its budgetary impact on libraries no longer reflects the actual costs to the purchasing institution. Other factors – particularly digital acquisition, bundled licensing and consortia deals, a large growth in published content and the commensurate growth in usage – have altered and significantly changed the real cost of scholarly journals. While the print‐based method of evaluating subscription price increases shows a three‐fold increase in costs from 1990 to 2010, the real effect is only 9% after taking all these factors into consideration. Librarians and publishers should work together to adopt a more reasoned and transparent approach to evaluating institutional investment in serials collections
Mechanisms Regulating Grain Contamination with Trichothecenes Translocated from the Stem Base of Wheat (Triticum aestivum) Infected withFusarium culmorum
Authors: Winter Mark , Koopmann Birger , Döll Katharina , Karlovsky Petr , Kropf Ute , Schlüter Klaus , von Tiedemann Andreas
Published: June 2013

Factors limiting trichothecene contamination of mature wheat grains after Fusarium infection are of major interest in crop production. In addition to ear infection, systemic translocation of deoxynivalenol (DON) may contribute to mycotoxin levels in grains after stem base infection with toxigenic Fusarium spp. However, the exact and potential mechanisms regulating DON translocation into wheat grains from the plant base are still unknown. We analyzed two wheat cultivars differing in susceptibility to Fusarium head blight (FHB), which were infected at the stem base with Fusarium culmorum in climate chamber experiments. Fungal DNA was found only in the infected stem base tissue, whereas DON and its derivative, DON-3-glucoside (D3G), were detected in upper plant parts. Although infected stem bases contained more than 10,000 μg kg–1dry weight (DW) of DON and mean levels of DON after translocation in the ear and husks reached 1,900 μg kg–1DW, no DON or D3G was detectable in mature grains. D3G quantification revealed that DON detoxification took mainly place in the stem basis, where ≤50% of DON was metabolized into D3G. Enhanced expression of a gene putatively encoding a uridine diphosphate-glycosyltransferase (GenBank accession number FG985273) was observed in the stem base after infection with F. culmorum. Resistance to F. culmorum stem base infection, DON glycosylation in the stem base, and mycotoxin translocation were unrelated to cultivar resistance to FHB. Histological studies demonstrated that the vascular transport of DON labeled with fluorescein as a tracer from the peduncle to the grain was interrupted by a barrier zone at the interface between grain and rachilla, formerly described as “xylem discontinuity”. This is the first study to demonstrate the effective control of influx of systemically translocated fungal mycotoxins into grains at the rachilla–seed interface by the xylem discontinuity tissue in wheat ears.