bluuebunny/crossref_metadata_2025 huggingface dataset:
Magnetoresistance in graphene-based ferromagnetic/ferromagnetic barrier/superconductor junction
Authors: Hajati Y. , Zargar Shoushtari M. , Rashedi G.
Published: June 2012

We study the magnetoresistance (MR) and spin transport in a graphene-based ferromagnetic/ferromagnetic barrier/s-wave superconductor (FFBS) junction for two regimes including retro-Andreev reflection (AR) (EF = 100Δ0) and retroreflection crossing over to specular Andreev reflection (EF = Δ0). We observed that the variation of exchange energy in the ferromagnetic region h1 has a stronger effect on the amplitude of the MR oscillations rather than length, exchange energy, and effective gate potential in the FB region in both regimes. In the EF = 100Δ0 regime, the higher values of exchange energy h1 approach EF, which decrease the amplitude of the MR oscillations with respect to FB length. By increasing the exchange energy up to h1 > EF, a phase shift occurs for the peaks of the MR curves and the amplitude of the MR oscillations reaches its maximum value at the exchange energy hc = 2EF + U0. Furthermore, in the EF = Δ0 regime, at the exchange energy h1 = eV, the amplitude of the MR oscillations approaches its maximum value. At this value of energy of carriers eV + h1 − EF (Dirac point), the sign of the energy will be reversed and a transition from the retroreflection to the specular Andreev reflection occurs. Thus, in this regime (EF = Δ0), by observing the maximum of the MR at specified values of eV and h1, we can measure the Fermi energy of the graphene. While in the EF = 100Δ0 regime, the MR versus bias energy can be tuned from the positive to negative values by varying h1, but in the EF = Δ0 regime, the MR shows only the positive values. In addition, we have investigated the spin conductance in both regimes.
A parameter-free, solid-angle based, nearest-neighbor algorithm
Authors: van Meel Jacobus A. , Filion Laura , Valeriani Chantal , Frenkel Daan
Published: June 2012

We propose a parameter-free algorithm for the identification of nearest neighbors. The algorithm is very easy to use and has a number of advantages over existing algorithms to identify nearest-neighbors. This solid-angle based nearest-neighbor algorithm (SANN) attributes to each possible neighbor a solid angle and determines the cutoff radius by the requirement that the sum of the solid angles is 4π. The algorithm can be used to analyze 3D images, both from experiments as well as theory, and as the algorithm has a low computational cost, it can also be used “on the fly” in simulations. In this paper, we describe the SANN algorithm, discuss its properties, and compare it to both a fixed-distance cutoff algorithm and to a Voronoi construction by analyzing its behavior in bulk phases of systems of carbon atoms, Lennard-Jones particles and hard spheres as well as in Lennard-Jones systems with liquid-crystal and liquid-vapor interfaces.
Conversion of basal plane dislocations to threading edge dislocations in 4H-SiC epilayers by high temperature annealing
Authors: Zhang Xuan , Tsuchida Hidekazu
Published: June 2012

Conversion of basal plane dislocations (BPDs) to threading edge dislocations (TEDs) is found in 4H-SiC epilayers after being annealed simply at high temperatures. Grazing incidence reflection synchrotron x-ray topography for the dislocations in the epilayers before and after annealing confirmed that some of the BPDs in the epilayers had converted to TEDs from the epilayer surface by the annealing. Observations on the dislocation behavior during annealing are explained in detail, and the mechanism of BPD conversion is discussed. It is argued that the conversion proceeds through the cross slip of constricted BPD segments towards the surface on the prismatic plane driven by the image force as well as TED glide driven by the line tension. Certain kinetic processes during annealing may facilitate the formation of constriction.
Balanced detection for interferometry with a noisy source
Authors: Robinson E. C. , Trägårdh J. , Lindsay I. D. , Gersen H.
Published: June 2012

Optical properties of nanostructures depend on size, shape, material, and local environment. These characteristics can be probed interferometrically, given a broadband source. However, broadband supercontinuum sources are intrinsically noisy, limiting the measurement sensitivity. In this article we describe the application of an auto-balancing technique to reduce the noise in a broadband supercontinuum source, thus increasing the signal to noise ratio. We show a noise reduction of 41 dB allowing optical powers as small as 0.01 pW to be interferometrically detected with a 5 ms integration time.
On a Bargmann transform and coherent states for the n-sphere
Authors: Díaz-Ortiz Erik I. , Villegas-Blas Carlos
Published: June 2012

We introduce a Bargmann transform for the Hilbert space L2(Sn), n ⩾ 2, and study semiclassical properties of the associated coherent states defined on the n-sphere Sn. In particular, we prove an Egorov-type theorem for the Berezin symbol related to a pseudo-differential operator on L2(Sn).
Size-extensive vibrational self-consistent field methods with anharmonic geometry corrections
Authors: Hermes Matthew R. , Keçeli Murat , Hirata So
Published: June 2012

In the size-extensive vibrational self-consistent field (XVSCF) method introduced earlier [M. Keçeli and S. Hirata, J. Chem. Phys. 135, 134108 (2011)]10.1063/1.3644895, only a small subset of even-order force constants that can form connected diagrams were used to compute extensive total energies and intensive transition frequencies. The mean-field potentials of XVSCF formed with these force constants have been shown to be effectively harmonic, making basis functions, quadrature, or matrix diagonalization in the conventional VSCF method unnecessary. We introduce two size-consistent VSCF methods, XVSCF(n) and XVSCF[n], for vibrationally averaged geometries in addition to energies and frequencies including anharmonic effects caused by up to the nth-order force constants. The methods are based on our observations that a small number of odd-order force constants of certain types can form open, connected diagrams isomorphic to the diagram of the mean-field potential gradients and that these nonzero gradients shift the potential minima by intensive amounts, which are interpreted as anharmonic geometry corrections. XVSCF(n) evaluates these mean-field gradients and force constants at the equilibrium geometry and estimates this shift accurately, but approximately, neglecting the coupling between these two quantities. XVSCF[n] solves the coupled equations for geometry corrections and frequencies with an iterative algorithm, giving results that should be identical to those of VSCF when applied to an infinite system. We present the diagrammatic and algebraic definitions, algorithms, and initial implementations as well as numerical results of these two methods. The results show that XVSCF(n) and XVSCF[n] reproduce the vibrationally averaged geometries of VSCF for naphthalene and anthracene in their ground and excited vibrational states accurately at fractions of the computational cost.
Pulse fluence dependent nanograting inscription on the surface of fused silica
Authors: Liang Feng , Vallée Réal , Leang Chin See
Published: June 2012

Pulse fluence dependent nanograting inscription on the surface of fused silica is investigated. The nanograting period is found to decrease with the increase of the incident pulse fluence. Local intensity distribution and incubation effect are responsible for the change of the nanograting period.
First results from the J-TEXT high-resolution three-wave polarimeter-interferometer
Authors: Chen J. , Zhuang G. , Wang Z. J. , Gao L. , Li Q. , Chen W. , Brower D. L. , Ding W. X.
Published: June 2012

A laser-based far-infrared polarimeter-interferometer system utilizing the three-wave technique has been implemented on the J-TEXT tokamak. The polarimeter determines the Faraday effect by measuring the phase difference between two collinear, counter-rotating, circularly polarized laser beams. The first results of the polarimeter-interferometer designed for J-TEXT have been obtained in the most recent J-TEXT experimental campaign. Simultaneous polarimetric and interferometric measurement is achieved, with phase resolution up to 0.1°, at bandwidth of 50 kHz. The temporal resolution, which is dependent on the laser's frequency offset, is ∼1 μs. Continual spatial measurement covering 45 cm (80% of the plasma cross-section) is realized by utilizing 1D parabolic beam expansion optics. Three initial test chords are installed and future plans call for expansion up to 30 chords with 1.5 cm chord spacing, providing high spatial resolution for measurement of electron density and current density profiles. Reliability of both polarimetric and interferometric measurement is confirmed by comparison with computation and data from a hydrocyanic acid (HCN) interferometer. With the high temporal and phase resolution, perturbations associated with the sawtooth cycle and MHD activity have been observed.
Self-consistent numerical dispersion relation of the ablative Rayleigh-Taylor instability of double ablation fronts in inertial confinement fusion
Authors: Yañez C. , Sanz J. , Olazabal-Loumé M.
Published: June 2012

The linear stability analysis of accelerated double ablation fronts is carried out numerically with a self-consistent approach. Accurate hydrodynamic profiles are taken into account in the theoretical model by means of a fitting parameters method using 1D simulation results. Numerical dispersion relation is compared to an analytical sharp boundary model [Yañez et al., Phys. Plasmas 18, 052701 (2011)] showing an excellent agreement for the radiation dominated regime of very steep ablation fronts, and the stabilization due to smooth profiles. 2D simulations are presented to validate the numerical self-consistent theory.
Simulating the magnetized liner inertial fusion plasma confinement with smaller-scale experiments
Authors: Ryutov D. D. , Cuneo M. E. , Herrmann M. C. , Sinars D. B. , Slutz S. A.
Published: June 2012

The recently proposed magnetized liner inertial fusion approach to a Z-pinch driven fusion [Slutz et al., Phys. Plasmas 17, 056303 (2010)] is based on the use of an axial magnetic field to provide plasma thermal insulation from the walls of the imploding liner. The characteristic plasma transport regimes in the proposed approach cover parameter domains that have not been studied yet in either magnetic confinement or inertial confinement experiments. In this article, an analysis is presented of the scalability of the key physical processes that determine the plasma confinement. The dimensionless scaling parameters are identified and conclusion is drawn that the plasma behavior in scaled-down experiments can correctly represent the full-scale plasma, provided these parameters are approximately the same in two systems. This observation is important in that smaller-scale experiments typically have better diagnostic access and more experiments per year are possible.
Electromagnetic modeling of edge coupled quantum well infrared photodetectors
Authors: Choi K. K.
Published: June 2012

Edge coupling through a 45° facet is the standard approach in characterizing quantum well infrared photodetector materials. From the spectral responsivity, the material absorption coefficient can be deduced from a classical model. However, this classical model has not been closely examined by a rigorous theory. In this work, we apply finite element electromagnetic modeling to obtain the detector quantum efficiency under this geometry and compare the result with the classical prediction. Remarkably, we find that both models give the same result at this particular angle while they differ significantly at other angles.
An energy-tunable positronium beam produced using the photodetachment of the positronium negative ion
Authors: Michishio K. , Tachibana T. , Suzuki R. H. , Wada K. , Yagishita A. , Hyodo T. , Nagashima Y.
Published: June 2012

We report here the production of an energy-tunable monoenergetic positronium beam using photodetachment of the positronium negative ion, a bound state of one positron and two electrons. The ions were produced efficiently by bombarding a Na-coated tungsten surface with a pulsed slow positron beam and accelerated using a static electric field. On irradiating the ions with a high intensity pulsed laser light, a positronium beam with a hitherto unrealized energy range of up to 1.9 keV has been produced in an ultra high vacuum environment.
A broadband vibrational energy harvester
Authors: Van Blarigan Louis , Danzl Per , Moehlis Jeff
Published: June 2012

We propose a design for an energy harvester which has the potential to harvest vibrational energy over a broad range of ambient frequencies. The device uses two flexible ceramic piezoelectric elements arranged in a buckled configuration in the absence of vibrations. Experimental data show that this design allows enhanced harvesting of energy relative to a comparable cantilever design, both for periodic and stochastic vibrations. Moreover, the data suggest that this harvester has its peak energy generation when it responds with chaotic vibrations.
Free radicals induced in aqueous solution by non-contact atmospheric-pressure cold plasma
Authors: Tani Atsushi , Ono Yusuke , Fukui Satoshi , Ikawa Satoshi , Kitano Katsuhisa
Published: June 2012

To understand plasma-induced chemical processing in liquids, we investigated the formation of free radicals in aqueous solution exposed to different types of non-contact atmospheric-pressure helium plasma using the spin-trapping technique. Both hydroxyl radical (OH·) and superoxide anion radical (O2−·) adducts were observed when neutral oxygen gas was additionally supplied to the plasma. In particular, O2−· can be dominantly induced in the solution via oxygen flow into the afterglow gas of helium plasma. This type of plasma treatment can potentially be used in medical applications to control infectious diseases, because the O2−· is crucial for sterilization of liquids via atmospheric-pressure plasma.
Visible light emission and energy transfer processes in Sm-doped nitride films
Authors: Zanatta A. R.
Published: June 2012

Even though the great interest in studying the near-infrared light emission due to Er3+ ions for telecommunication purposes, efficient visible radiation can be achieved from many different rare-earth (RE) ions. In fact, visible and/or near-infrared light emission takes place in RE-doped wide bandgap semiconductors following either photon or electron excitation, suggesting their technological potential in devices such as light-emitting diodes (LED's) and flat-panel displays, for example. Taking into consideration these aspects, the present contribution reports on the investigation of AlN, BeN, GeN, and SiN thin films doped with samarium. The samples were prepared by sputtering and as a result of the deposition method and conditions they present an amorphous structure and Sm concentrations in the low 0.5 at. %. After deposition, the samples were submitted to thermal annealing treatments and investigated by different spectroscopic techniques. A detailed examination of the experimental data allowed to identify optical transitions due to Sm3+ and Sm2+ ions as well as differences in their mechanisms of photon excitation and recombination. Moreover, it is shown that the Sm-related spectral features and emission intensity are susceptible, respectively, to the atomic environment the Sm3+/Sm2+ ions experience and to the presence of non-radiative recombination centers.
Laser-assisted sol-gel growth and characteristics of ZnO thin films
Authors: Su Kim Min , Kim Soaram , Leem Jae-Young
Published: June 2012

ZnO thin films were grown on Si(100) substrates by a sol-gel method assisted by laser beam irradiation with a 325 nm He-Cd laser. In contrast to conventional sol-gel ZnO thin films, the surface morphology of the laser-assisted sol-gel thin films was much smoother, and the residual stress in the films was relaxed by laser irradiation. The luminescent properties of the films were also enhanced by laser irradiation, especially, by irradiation during the deposition and post-heat treatment stages. The incident laser beam is thought to play several roles, such as annihilating defects by accelerating crystallization during heat treatment, enhancing the surface migration of atoms and molecules, and relaxing the ZnO matrix structure during crystallization.
Introduction to Focus Issue: Statistical mechanics and billiard-type dynamical systems
Authors: Leonel Edson D. , Beims Marcus W. , Bunimovich Leonid A.
Published: June 2012

Dynamical systems of the billiard type are of fundamental importance for the description of numerous phenomena observed in many different fields of research, including statistical mechanics, Hamiltonian dynamics, nonlinear physics, and many others. This Focus Issue presents the recent progress in this area with contributions from the mathematical as well as physical stand point.
Structure and electrical properties of 〈001〉 textured (Ba0.85Ca0.15)(Ti0.9Zr0.1)O3 lead-free piezoelectric ceramics
Authors: Ye S. K. , Fuh J. Y. H. , Lu L.
Published: June 2012

〈001〉 textured (Ba0.85Ca0.15)(Ti0.9Zr0.1)O3 (BCTZ) lead-free piezoelectric ceramics were prepared by templated-grain growth method using BaTiO3 as template. The degree of orientation and the microstructure of the ceramics with different amount of template were investigated. The electrical properties of the textured-ceramics in the optimized condition were dramatically enhanced compared with randomly-oriented BCTZ ceramics. The textured BCTZ ceramics showed high piezoelectric constants d33 = 470 pC/N and d31 = −170 pC/N, and high electromechanical coupling factors kp = 44% and k31 = 22%. In addition, the Curie point of the textured ceramics revealed an increase with the template content.
Energy consumption, industrial structure, and economic growth patterns in China: A study based on provincial data
Authors: Yu Lihong , He Yuan
Published: June 2012

There are two important paths to transform the economic growth pattern in China: upgrading industrial structure and adjusting energy structure. However, industrial structure depends on the stage of economic development; energy structure depends on resource endowments. Thus, the start times and development paths of China’s economic growth differ from region to region. The changes and differences in industrial structure, energy structure, and the corresponding energy (coal) intensity in one decade are analyzed based on provincial cross-sectional data in 2009 and 2000. It is found that Chinese provinces have different growth patterns due to the difference of resource endowment, industrial structure, and the internal industrial transfer. Moreover, the potential paths of economic growth pattern transformation in provinces in China are analyzed. It should be a common direction to make the industrial structure light and energy structure low-carbon, but the road maps of regional transformation vary significantly.
Correlation between threshold voltage and channel dopant concentration in negative-type metal-oxide-semiconductor field-effect transistors studied by atom probe tomography
Authors: Takamizawa H. , Shimizu Y. , Inoue K. , Toyama T. , Yano F. , Nishida A. , Mogami T. , Okada N. , Kato M. , Uchida H. , Kitamoto K. , Miyagi T. , Kato J. , Nagai Y.
Published: June 2012

The correlation between threshold voltage (VT) and channel boron concentration in silicon-based 65 nm node negative-type metal-oxide-semiconductor field-effect transistors was studied by atom probe tomography (APT). VT values were determined for one million transistors in a single chip, and transistors having a ±4σ deviation from the median VT were analyzed using APT. VT and the channel boron concentration were positively correlated. This is consistent with the relationship between the average boron concentration of wafers implanted with different channel doses and the median VT of the million transistors. APT is suitable for the study of dopant-distribution-based device failure mechanisms.
Achievements and Opportunities in Initiating Governance for Urban Sustainability
Authors: Smith Riley , Wiek Arnim
Published: June 2012

The concept of urban sustainability governance has developed as an institutional guiding concept to holistically address the vitality of cities under a long-term perspective and is based on the collaborative efforts of government, administration, business, science, and the civil society. Yet, the initiation and implementation of this guiding concept faces a variety of barriers, including deficient conceptualization, unfamiliarity, detrimental organizational structures, and inertia. We examine the initiation of urban sustainability governance in the City of Richmond, British Columbia, Canada. On the basis of the reviews of administrative documents and interviews with staff across various administrative levels and units, we reflect on achievements and shortcomings against guidelines of urban sustainability governance spelled out in the literature. Our study indicates accomplishments in the conceptualization of a vision and overall framework to operate from, but also a number of deficits in specifying sustainability targets, applying governance principles, and evaluating impacts. Additionally, we discuss how administrative structures influence how urban sustainability governance is being implemented. We draw conclusions regarding general factors for succeeding in the initiation and implementation of urban sustainability governance.
Who Benefits and Who Loses from Flood Risk Reduction?
Authors: Penning-Rowsell Edmund C , Pardoe Joanna
Published: June 2012

The distributional effects of investment for the reduction of flood risk are explored, with the UK as an example. Using three case studies, we initially investigate the ‘gainers’ and the ‘losers’ from three contrasting engineering-oriented flood alleviation and land drainage schemes, the results of which appear to show that property owners at risk of flooding were the gainers and the general flood-free taxpayer was the loser. An analysis of flood damages, however, shows that those losing work from repairing or replacing flood damaged goods are a primary loser group as risk is reduced. Investigating insurance cover for flooding (near-universal in the UK) also shows that the principal real gainers appear to be insurance companies and their shareholders, since premiums generally do not appear to fall as risk is reduced. The implication of these novel results are evaluated both for the UK and, briefly, for elsewhere in the world.
(Un)Sustainable Territories: Causes of the Speculative Bubble in Spain (1996–2010) and its Territorial, Environmental, and Sociopolitical Consequences
Authors: Romero Juan , Jimenez Fernando , Villoria Manuel
Published: June 2012

In this paper we analyse the causes of the Spanish property model and its territorial, social, and political consequences. Particular attention is paid to sociopolitical contexts. These consequences include excessive dependence on economic activity and employment in the housing construction sector, the irreversible disappearance of landmarks in the country's collective history and culture, and examples of ‘policy capture’, especially at local and regional levels. This lengthy process has led to corruption in town planning and an increase in poor policy decisions, greatly harming Spain's reputation.
Engineering Enzymes for Energy Production
Authors: Ollis David L. , Liu Jian-Wei , Stevenson Bradley J.
Published: June 2012

Harvesting the energy of sunlight can be achieved with a variety of processes and as one becomes obsolete, others will need to be developed to replace it. The direct conversion of sunlight into electrical energy could be used to provide power. Energy could also be obtained by combusting hydrogen produced by splitting of water with sunlight. None of these direct approaches will entirely satisfy the entire energy needs of a modern economy and the conversion of biological materials into liquid fuels for transport and other applications may prove to be important for tomorrow’s energy needs. In fact, biofuels such as bioethanol and biodiesel are already used in many countries. However, the long-term viability of these fuels depends on the efficiency of the processes used to produce them. We outline here a method by which ethanol can be produced using enzymes that can be optimized for this purpose.
An Institutional Approach to Solar Fuels Research
Authors: Messinger Johannes
Published: June 2012

This account gives a brief overview of various directions in current solar fuels research. On that basis, the necessity for an interdisciplinary approach is argued, and an institutional way for promoting this development is presented using the example of the Chemistry Biology Centre (KBC) at Umeå University in Sweden.
Perspectives for Photobiology in Molecular Solar Fuels
Authors: Hingorani Kastoori , Hillier Warwick
Published: June 2012

This paper presents an overview of the prospects for bio-solar energy conversion. The Global Artificial Photosynthesis meeting at Lord Howe Island (14–18 August 2011) underscored the dependence that the world has placed on non-renewable energy supplies, particularly for transport fuels, and highlighted the potential of solar energy. Biology has used solar energy for free energy gain to drive chemical reactions for billions of years. The principal conduits for energy conversion on earth are photosynthetic reaction centres – but can they be harnessed, copied and emulated? In this communication, we initially discuss algal-based biofuels before investigating bio-inspired solar energy conversion in artificial and engineered systems. We show that the basic design and engineering principles for assembling photocatalytic proteins can be used to assemble nanocatalysts for solar fuel production.
Identifying resistance genes to Leptosphaeria maculans in Australian Brassica napus cultivars based on reactions to isolates with known avirulence genotypes
Authors: Marcroft Steve J. , Elliott Vicki L. , Cozijnsen Anton J. , Salisbury Phillip A. , Howlett Barbara J. , Van de Wouw Angela P.
Published: June 2012

Blackleg disease, caused by the fungus Leptosphaeria maculans, is the major disease of canola (Brassica napus) worldwide. A set of 12 Australian L. maculans isolates was developed and used to characterise seedling resistance in 127 Australian cultivars and advanced breeding lines. Plant mortality data used to assess the effectiveness of seedling resistance in canola growing regions of Australia showed that Rlm3 and Rlm4 resistance genes were less effective than other seedling resistance genes. This finding was consistent with regional surveys of the pathogen, which showed the frequency of Rlm4-attacking isolates was >70% in fungal populations over a 10-year period. Differences in adult plant resistance were identified in a subset of Australian cultivars, indicating that some adult gene resistance is isolate-specific.
Surface roughness directed self-assembly of patchy particles into colloidal micelles
Authors: Kraft Daniela J. , Ni Ran , Smallenburg Frank , Hermes Michiel , Yoon Kisun , Weitz David A. , van Blaaderen Alfons , Groenewold Jan , Dijkstra Marjolein , Kegel Willem K.
Published: June 2012

Colloidal particles with site-specific directional interactions, so called “patchy particles”, are promising candidates for bottom-up assembly routes towards complex structures with rationally designed properties. Here we present an experimental realization of patchy colloidal particles based on material independent depletion interaction and surface roughness. Curved, smooth patches on rough colloids are shown to be exclusively attractive due to their different overlap volumes. We discuss in detail the case of colloids with one patch that serves as a model for molecular surfactants both with respect to their geometry and their interactions. These one-patch particles assemble into clusters that resemble surfactant micelles with the smooth and attractive sides of the colloids located at the interior. We term these clusters “colloidal micelles”. Direct Monte Carlo simulations starting from a homogeneous state give rise to cluster size distributions that are in good agreement with those found in experiments. Important differences with surfactant micelles originate from the colloidal character of our model system and are investigated by simulations and addressed theoretically. Our new “patchy” model system opens up the possibility for self-assembly studies into finite-sized superstructures as well as crystals with as of yet inaccessible structures.
Origin and evolution of carnivorism in the Ascomycota (fungi)
Authors: Yang Ence , Xu Lingling , Yang Ying , Zhang Xinyu , Xiang Meichun , Wang Chengshu , An Zhiqiang , Liu Xingzhong
Published: June 2012

Carnivorism is one of the basic life strategies of fungi. Carnivorous fungi possess the ability to trap and digest their preys by sophisticated trapping devices. However, the origin and development of fungal carnivorism remains a gap in evolution biology. In this study, five protein-encoding genes were used to construct the phylogeny of the carnivorous fungi in the phylum Ascomycota; these fungi prey on nematodes by means of specialized trapping structures such as constricting rings and adhesive traps. Our analysis revealed a definitive pattern of evolutionary development for these trapping structures. Molecular clock calibration based on two fossil records revealed that fungal carnivorism diverged from saprophytism about 419 Mya, which was after the origin of nematodes about 550–600 Mya. Active carnivorism (fungi with constricting rings) and passive carnivorism (fungi with adhesive traps) diverged from each other around 246 Mya, shortly after the occurrence of the Permian–Triassic extinction event about 251.4 Mya. The major adhesive traps evolved around 198–208 Mya, which was within the time frame of the Triassic–Jurassic extinction event about 201.4 Mya. However, no major carnivorous ascomycetes divergence was correlated to the Cretaceous–Tertiary extinction event, which occurred more recently (about 65.5 Mya). Therefore, a causal relationship between mass extinction events and fungal carnivorism evolution is not validated in this study. More evidence including additional fossil records is needed to establish if fungal carnivorism evolution was a response to mass extinction events.
Isotype modulates epitope specificity, affinity, and antiviral activities of anti–HIV-1 human broadly neutralizing 2F5 antibody
Authors: Tudor Daniela , Yu Huifeng , Maupetit Julien , Drillet Anne-Sophie , Bouceba Tahar , Schwartz-Cornil Isabelle , Lopalco Lucia , Tuffery Pierre , Bomsel Morgane
Published: June 2012

The constant heavy chain (CH1) domain affects antibody affinity and fine specificity, challenging the paradigm that only variable regions contribute to antigen binding. To investigate the role of the CH1 domain, we constructed IgA2 from the broadly neutralizing anti–HIV-1 2F5 IgG1, and compared 2F5 IgA2 and IgG binding affinity and functional activities. We found that 2F5 IgA2 bound to the gp41 membrane proximal external region with higher affinity than IgG1. Functionally, compared with IgG1, 2F5 IgA2 more efficiently blocked HIV-1 transcytosis across epithelial cells and CD4
+
cell infection by R5 HIV-1. The 2F5 IgG1 and IgA2 acted synergistically to fully block HIV-1 transfer from Langerhans to autologous CD4
+
T cells and to inhibit CD4
+
T-cell infection. Epitope mapping performed by screening a random peptide library and
in silico
docking modeling suggested that along with the 2F5 IgG canonical ELDKWA epitope on gp41, the IgG1 recognized an additional 3D-conformational epitope on the gp41 C-helix. In contrast, the IgA2 epitope included a unique conformational motif on the gp41
N
-helix. Overall, the CH1 region of 2F5 contributes to shape its epitope specificity, antibody affinity, and functional activities. In the context of sexually transmitted infections such as HIV-1/AIDS, raising a mucosal IgA-based vaccine response should complement an IgG-based vaccine response in blocking HIV-1 transmission.
Homology and homoplasy of swimming behaviors and neural circuits in the Nudipleura (Mollusca, Gastropoda, Opisthobranchia)
Authors: Newcomb James M. , Sakurai Akira , Lillvis Joshua L. , Gunaratne Charuni A. , Katz Paul S.
Published: June 2012

How neural circuit evolution relates to behavioral evolution is not well understood. Here the relationship between neural circuits and behavior is explored with respect to the swimming behaviors of the Nudipleura (Mollusca, Gastropoda, Opithobranchia). Nudipleura is a diverse monophyletic clade of sea slugs among which only a small percentage of species can swim. Swimming falls into a limited number of categories, the most prevalent of which are rhythmic left–right body flexions (LR) and rhythmic dorsal–ventral body flexions (DV). The phylogenetic distribution of these behaviors suggests a high degree of homoplasy. The central pattern generator (CPG) underlying DV swimming has been well characterized in
Tritonia diomedea
and in
Pleurobranchaea californica
. The CPG for LR swimming has been elucidated in
Melibe leonina
and
Dendronotus iris
, which are more closely related. The CPGs for the categorically distinct DV and LR swimming behaviors consist of nonoverlapping sets of homologous identified neurons, whereas the categorically similar behaviors share some homologous identified neurons, although the exact composition of neurons and synapses in the neural circuits differ. The roles played by homologous identified neurons in categorically distinct behaviors differ. However, homologous identified neurons also play different roles even in the swim CPGs of the two LR swimming species. Individual neurons can be multifunctional within a species. Some of those functions are shared across species, whereas others are not. The pattern of use and reuse of homologous neurons in various forms of swimming and other behaviors further demonstrates that the composition of neural circuits influences the evolution of behaviors.
From chemotaxis to the cognitive map: The function of olfaction
Authors: Jacobs Lucia F.
Published: June 2012

A paradox of vertebrate brain evolution is the unexplained variability in the size of the olfactory bulb (OB), in contrast to other brain regions, which scale predictably with brain size. Such variability appears to be the result of selection for olfactory function, yet there is no obvious concordance that would predict the causal relationship between OB size and behavior. This discordance may derive from assuming the primary function of olfaction is odorant discrimination and acuity. If instead the primary function of olfaction is navigation, i.e., predicting odorant distributions in time and space, variability in absolute OB size could be ascribed and explained by variability in navigational demand. This olfactory spatial hypothesis offers a single functional explanation to account for patterns of olfactory system scaling in vertebrates, the primacy of olfaction in spatial navigation, even in visual specialists, and proposes an evolutionary scenario to account for the convergence in olfactory structure and function across protostomes and deuterostomes. In addition, the unique percepts of olfaction may organize odorant information in a parallel map structure. This could have served as a scaffold for the evolution of the parallel map structure of the mammalian hippocampus, and possibly the arthropod mushroom body, and offers an explanation for similar flexible spatial navigation strategies in arthropods and vertebrates.
Adaptive evolution of voltage-gated sodium channels: The first 800 million years
Authors: Zakon Harold H.
Published: June 2012

Voltage-gated Na
+
-permeable (Nav) channels form the basis for electrical excitability in animals. Nav channels evolved from Ca
2+
channels and were present in the common ancestor of choanoflagellates and animals, although this channel was likely permeable to both Na
+
and Ca
2+
. Thus, like many other neuronal channels and receptors, Nav channels predated neurons. Invertebrates possess two Nav channels (Nav1 and Nav2), whereas vertebrate Nav channels are of the Nav1 family. Approximately 500 Mya in early chordates Nav channels evolved a motif that allowed them to cluster at axon initial segments, 50 million years later with the evolution of myelin, Nav channels “capitalized” on this property and clustered at nodes of Ranvier. The enhancement of conduction velocity along with the evolution of jaws likely made early gnathostomes fierce predators and the dominant vertebrates in the ocean. Later in vertebrate evolution, the Nav channel gene family expanded in parallel in tetrapods and teleosts (∼9 to 10 genes in amniotes, 8 in teleosts). This expansion occurred during or after the late Devonian extinction, when teleosts and tetrapods each diversified in their respective habitats, and coincided with an increase in the number of telencephalic nuclei in both groups. The expansion of Nav channels may have allowed for more sophisticated neural computation and tailoring of Nav channel kinetics with potassium channel kinetics to enhance energy savings. Nav channels show adaptive sequence evolution for increasing diversity in communication signals (electric fish), in protection against lethal Nav channel toxins (snakes, newts, pufferfish, insects), and in specialized habitats (naked mole rats).
Shared developmental and evolutionary origins for neural basis of vocal–acoustic and pectoral–gestural signaling
Authors: Bass Andrew H. , Chagnaud Boris P.
Published: June 2012

Acoustic signaling behaviors are widespread among bony vertebrates, which include the majority of living fishes and tetrapods. Developmental studies in sound-producing fishes and tetrapods indicate that central pattern generating networks dedicated to vocalization originate from the same caudal hindbrain rhombomere (rh) 8-spinal compartment. Together, the evidence suggests that vocalization and its morphophysiological basis, including mechanisms of vocal–respiratory coupling that are widespread among tetrapods, are ancestral characters for bony vertebrates. Premotor-motor circuitry for pectoral appendages that function in locomotion and acoustic signaling develops in the same rh8-spinal compartment. Hence, vocal and pectoral phenotypes in fishes share both developmental origins and roles in acoustic communication. These findings lead to the proposal that the coupling of more highly derived vocal and pectoral mechanisms among tetrapods, including those adapted for nonvocal acoustic and gestural signaling, originated in fishes. Comparative studies further show that rh8 premotor populations have distinct neurophysiological properties coding for equally distinct behavioral attributes such as call duration. We conclude that neural network innovations in the spatiotemporal patterning of vocal and pectoral mechanisms of social communication, including forelimb gestural signaling, have their evolutionary origins in the caudal hindbrain of fishes.
Functionalization of a protosynaptic gene expression network
Authors: Conaco Cecilia , Bassett Danielle S. , Zhou Hongjun , Arcila Mary Luz , Degnan Sandie M. , Degnan Bernard M. , Kosik Kenneth S.
Published: June 2012

Assembly of a functioning neuronal synapse requires the precisely coordinated synthesis of many proteins. To understand the evolution of this complex cellular machine, we tracked the developmental expression patterns of a core set of conserved synaptic genes across a representative sampling of the animal kingdom. Coregulation, as measured by correlation of gene expression over development, showed a marked increase as functional nervous systems emerged. In the earliest branching animal phyla (Porifera), in which a nearly complete set of synaptic genes exists in the absence of morphological synapses, these “protosynaptic” genes displayed a lack of global coregulation although small modules of coexpressed genes are readily detectable by using network analysis techniques. These findings suggest that functional synapses evolved by exapting preexisting cellular machines, likely through some modification of regulatory circuitry. Evolutionarily ancient modules continue to operate seamlessly within the synapses of modern animals. This work shows that the application of network techniques to emerging genomic and expression data can provide insights into the evolution of complex cellular machines such as the synapse.
Cortical evolution in mammals: The bane and beauty of phenotypic variability
Authors: Krubitzer Leah A. , Seelke Adele M. H.
Published: June 2012

Evolution by natural selection, the unifying theory of all biological sciences, provides a basis for understanding how phenotypic variability is generated at all levels of organization from genes to behavior. However, it is important to distinguish what is the target of selection vs. what is transmitted across generations. Physical traits, behaviors, and the extended phenotype are all selected features of an individual, but genes that covary with different aspects of the targets of selection are inherited. Here we review the variability in cortical organization, morphology, and behavior that have been observed across species and describe similar types of variability within species. We examine sources of variability and the constraints that limit the types of changes that evolution has and can produce. Finally, we underscore the importance of how genes and genetic regulatory networks are deployed and interact within an individual, and their relationship to external, physical forces within the environment that shape the ultimate phenotype.
The remarkable, yet not extraordinary, human brain as a scaled-up primate brain and its associated cost
Authors: Herculano-Houzel Suzana
Published: June 2012

Neuroscientists have become used to a number of “facts” about the human brain: It has 100 billion neurons and 10- to 50-fold more glial cells; it is the largest-than-expected for its body among primates and mammals in general, and therefore the most cognitively able; it consumes an outstanding 20% of the total body energy budget despite representing only 2% of body mass because of an increased metabolic need of its neurons; and it is endowed with an overdeveloped cerebral cortex, the largest compared with brain size. These facts led to the widespread notion that the human brain is literally extraordinary: an outlier among mammalian brains, defying evolutionary rules that apply to other species, with a uniqueness seemingly necessary to justify the superior cognitive abilities of humans over mammals with even larger brains. These facts, with deep implications for neurophysiology and evolutionary biology, are not grounded on solid evidence or sound assumptions, however. Our recent development of a method that allows rapid and reliable quantification of the numbers of cells that compose the whole brain has provided a means to verify these facts. Here, I review this recent evidence and argue that, with 86 billion neurons and just as many nonneuronal cells, the human brain is a scaled-up primate brain in its cellular composition and metabolic cost, with a relatively enlarged cerebral cortex that does not have a relatively larger number of brain neurons yet is remarkable in its cognitive abilities and metabolism simply because of its extremely large number of neurons.
A Field‐based Bioenergetics Model for Estimating Time‐Varying Food Consumption and Growth
Authors: van Poorten Brett T. , Walters Carl J. , Taylor Nathan G.
Published: June 2012

Bioenergetics models are often used to describe the implications of changes in growth and consumption of specific wild populations, and yet most parameters are derived from a variety of laboratory studies on other populations or species, leading to questions regarding the validity of predictions. A novel bioenergetics approach was recently developed where many parameters are estimated from the population being modeled, but growth and consumption are assumed invariant over time, which would not hold true when manipulations to the system are known or suspected. In the present paper, a bioenergetics model with many key parameters estimated from field data are presented where temporal deviations in growth rates were directly estimated. A series of rainbow trout Oncorhynchus mykiss and northern pikeminnow Ptychocheilus oregonensis populations, which have undergone various population manipulations, were used to evaluate the model. Further, the model was fit to a series of rainbow trout size‐classes stocked into each of the study lakes to compare with their wild counterparts and evaluate intercohort differences in growth and consumption. We found the model with time‐varying consumption was more parsimonious compared with models where growth and consumption were assumed to be constant over time. Our field data demonstrated how the model can detect different patterns in growth and consumption across populations and species. The model detected highly variable growth and consumption in rainbow trout over time and between populations but did not seem to be particularly influenced by past population manipulations. By contrast, northern pikeminnow demonstrated differences between lakes, but showed little temporal variation in growth and consumption. Stocked rainbow trout demonstrated similar growth rates to their wild counterparts, helping to validate growth estimates. Our bioenergetics model moves beyond existing ones by allowing measurement and process errors to be explicitly represented, while also permitting growth and consumption to vary over time.
Geology as a Structuring Mechanism of Stream Fish Communities
Authors: Neff Margaret R. , Jackson Donald A.
Published: June 2012

We examined the influence of the Precambrian Shield, a broad‐scale geological feature of North America, on stream abiotic conditions and on the associated fish communities relative to an adjacent series of sites located on sedimentary geology (i.e., “off‐Shield” streams) in south‐central Ontario, Canada. Constrained and unconstrained multivariate analyses were used to quantify relationships in fish species composition, abiotic variables, and fish species’ functional traits. The results showed that for low‐order lotic systems, streams located on the Precambrian Shield had fish communities that were distinctly different from those of off‐Shield streams. Lotic fish communities on the Shield were associated with higher velocity, increased amounts of instream woody debris, higher dissolved oxygen, and shrub–marsh landscapes. In contrast, off‐Shield communities were characterized by higher conductivity, alkalinity, water temperature, and turbidity and were frequently surrounded by meadow and cultivated or pastured land. In general, off‐Shield sites were more species rich and were associated with species preferring a wide variety of habitats, whereas Shield sites were associated with a subset of the regional species pool that had more specific habitat associations. Overall, our results show that these sharp geological discontinuities result in distinct abiotic environments and fish communities between Shield and off‐Shield low‐order lotic systems within a small geographic range.
Acyclic embeddings of open Riemann surfaces into new examples of elliptic manifolds
Authors: Ritter Tyson
Published: June 2012

The geometric notion of ellipticity for complex manifolds was introduced by Gromov in his seminal 1989 paper on the Oka principle and is a sufficient condition for a manifold to be Oka. In the current paper we present contributions to three open questions involving elliptic and Oka manifolds. We show that quotients of

C

n

\mathbb {C}^n

by discrete groups of affine transformations are elliptic. Combined with an example of Margulis, this yields new examples of elliptic manifolds with free fundamental groups and vanishing higher homotopy. Finally we show that every open Riemann surface embeds acyclically into an elliptic manifold, giving a partial answer to a question of Lárusson.