bluuebunny/crossref_metadata_2025 huggingface dataset:
Eucken correction in high-temperature gases with electronic excitation
Authors: Istomin V. A. , Kustova E. V. , Mekhonoshina M. A.
Published: May 2014

In the present paper, thermal conductivity coefficient of high-temperature molecular and atomic gases with excited electronic states is studied using both the kinetic theory algorithm developed by authors earlier and the well known simple expression for the thermal conductivity coefficient proposed by Eucken and generalized by Hirschfelder. The influence of large collision diameters of excited states on the thermal conductivity is discussed. The limit of validity of the Eucken correction is evaluated on the basis of the kinetic theory calculations; an improved model suitable for air species under high-temperature conditions is proposed.
Measurement of modal birefringence in optical waveguides based on the Mach-Zehnder interferometer
Authors: Zhong Ze Bing , Fu Zhi Cheng , Shi Jian Dong , Tan Qi Long , Huang Wo Bin , Huang Xu Guang
Published: May 2014

A method for measuring the birefringence in planar waveguide circuits is theoretically proposed and validated. The method is based on the Mach-Zehnder interference and by measuring the spectral shift due to orthogonal polarization states. The birefringence of a silica waveguide is measured to be 2.33 × 10−4 at nearby 1550 nm. In addition, the birefringence variations with the wavelength and its dependence on the external stress are investigated with the proposed method experimentally. The results in measuring birefringence demonstrate a high accuracy with the order of 10−5, a wide dynamic range from 10−5 to 10−3, and a characteristic of multi-wavelength evaluation.
Stochastic quasi-steady state approximations for asymptotic solutions of the chemical master equation
Authors: Alarcón Tomás
Published: May 2014

In this paper, we propose two methods to carry out the quasi-steady state approximation in stochastic models of enzyme catalytic regulation, based on WKB asymptotics of the chemical master equation or of the corresponding partial differential equation for the generating function. The first of the methods we propose involves the development of multiscale generalisation of a WKB approximation of the solution of the master equation, where the separation of time scales is made explicit which allows us to apply the quasi-steady state approximation in a straightforward manner. To the lowest order, the multi-scale WKB method provides a quasi-steady state, Gaussian approximation of the probability distribution. The second method is based on the Hamilton-Jacobi representation of the stochastic process where, as predicted by large deviation theory, the solution of the partial differential equation for the corresponding characteristic function is given in terms of an effective action functional. The optimal transition paths between two states are then given by those paths that maximise the effective action. Such paths are the solutions of the Hamilton equations for the Hamiltonian associated to the effective action functional. The quasi-steady state approximation is applied to the Hamilton equations thus providing an approximation to the optimal transition paths and the transition time between two states. Using this approximation we predict that, unlike the mean-field quasi-steady approximation result, the rate of enzyme catalysis depends explicitly on the initial number of enzyme molecules. The accuracy and validity of our approximated results as well as that of our predictions regarding the behaviour of the stochastic enzyme catalytic models are verified by direct simulation of the stochastic model using Gillespie stochastic simulation algorithm.
Multifractal subgrid-scale modeling within a variational multiscale method for large-eddy simulation of passive-scalar mixing in turbulent flow at low and high Schmidt numbers
Authors: Rasthofer U. , Burton G. C. , Wall W. A. , Gravemeier V.
Published: May 2014

Multifractal subgrid-scale modeling embedded into a variational multiscale method is proposed for large-eddy simulation of passive-scalar mixing in turbulent incompressible flow. In this subgrid-scale modeling approach, subgrid-scale velocity and scalar field are directly approximated by a multifractal reconstruction process replicating the actual physics of turbulent flows. Problems from low to high Schmidt numbers (i.e., Sc ≈ 1 to Sc ≫ 1) are considered in this work. Starting from preceding work, in this study, multifractal subgrid-scale modeling is further detailed by refining the approximation process within the scalar field. Thereby, appropriate multifractal subgrid-scale modeling for passive-scalar mixing is derived in comprehensive form for the entire range of Schmidt numbers. The near-wall behavior of the multifractal subgrid-scale modeling approach is investigated for wall-bounded turbulent flows with passive-scalar mixing. The method is validated for passive-scalar mixing in turbulent channel flow for a broad range of Schmidt numbers in between 1 and 1000. Excellent performance is stated for all Schmidt numbers, in particular when comparing the results obtained with the proposed method to results provided by other methods widely used in the literature. An analysis of the subgrid-scale scalar-variance transfer highlights the influence of the multifractal subgrid-scale modeling within the variational multiscale method. The near-wall behavior of the proposed method is investigated via the transfer coefficient, for which results consistent with the theoretical correlation are obtained.
Integrable and superintegrable Hamiltonian systems with four dimensional real Lie algebras as symmetry of the systems
Authors: Abedi-Fardad J. , Rezaei-Aghdam A. , Haghighatdoost Gh.
Published: May 2014

We construct integrable and superintegrable Hamiltonian systems using the realizations of four dimensional real Lie algebras as a symmetry of the system with the phase space $\mathbb {R}^{4}$R4 and $\mathbb {R}^{6}$R6. Furthermore, we construct some integrable and superintegrable Hamiltonian systems for which the symmetry Lie group is also the phase space of the system.
Phenomenological modelling of first order phase transitions in magnetic systems
Authors: Melikhov Yevgen , Hadimani R. L. , Raghunathan Arun
Published: May 2014

First order phase transitions may occur in several magnetic systems, with two structural phases having different magnetic properties each and a structural transition between them. Here, a novel physics based phenomenological model of such systems is proposed, in which magnetization is represented by the volumetric amounts of ferromagnetism (described by extended Jiles-Atherton theory) and paramagnetism (described by the Curie-Weiss law) in respective phases. An identification procedure to extract material parameters from experimental data is proposed. The proposed phenomenological approach was successfully applied to magnetocaloric Gd5(SixGe1−x)4 system and also has the potential to describe the behavior of Griffiths phase magnetic systems.
Regulation of electron temperature gradient turbulence by zonal flows driven by trapped electron modes
Authors: Asahi Y. , Ishizawa A. , Watanabe T.-H. , Tsutsui H. , Tsuji-Iio S.
Published: May 2014

Turbulent transport caused by electron temperature gradient (ETG) modes was investigated by means of gyrokinetic simulations. It was found that the ETG turbulence can be regulated by meso-scale zonal flows driven by trapped electron modes (TEMs), which are excited with much smaller growth rates than those of ETG modes. The zonal flows of which radial wavelengths are in between the ion and the electron banana widths are not shielded by trapped ions nor electrons, and hence they are effectively driven by the TEMs. It was also shown that an E × B shearing rate of the TEM-driven zonal flows is larger than or comparable to the growth rates of long-wavelength ETG modes and TEMs, which make a main contribution to the turbulent transport before excitation of the zonal flows.
Role of multilayer-like interference effects on the transient optical response of Si3N4 films pumped with free-electron laser pulses
Authors: Casolari F. , Bencivenga F. , Capotondi F. , Giangrisostomi E. , Manfredda M. , Mincigrucci R. , Pedersoli E. , Principi E. , Masciovecchio C. , Kiskinova M.
Published: May 2014

X-ray/optical cross-correlation methods are attracting increasing interest for exploring transient states of matter using ultrashort free-electron laser (FEL) pulses. Our paper shows that in such studies the difference in the penetration depth of the FEL-pump and the infrared (IR) probe pulses become important, in particular, when exploring the changes in the optical properties of solid targets. We discuss the role of interference effects, using a phenomenological model with excited and unperturbed slabs. The reliability of this model was experimentally verified by measuring the transient optical response of free-standing and silicon (Si) supported silicon nitride (Si3N4) films, simultaneously in reflection and transmission, using s- and p-polarized IR light. The changes in the Si3N4 optical refractive index, induced by the FEL pulses, have fully been described in the frame of the proposed model. The experimental results confirm that the differences, observed in the FEL-induced transient reflectance and transmittance of the Si3N4 targets with different thicknesses, arise from multilayer-like interferometric phenomena.
Determination of the spontaneous polarization of wurtzite (Mg,Zn)O
Authors: Stölzel Marko , Müller Alexander , Benndorf Gabriele , Lorenz Michael , Patzig Christian , Höche Thomas , Grundmann Marius
Published: May 2014

We report on the experimental determination of the spontaneous polarization of wurtzite-(Mg,Zn)O by examination of the recombination dynamics of polar ZnO/(Mg,Zn)O quantum wells (QWs). The thickness-dependent decay time of the unscreened single-exciton states inside the QWs was modeled by a self-consistent solution of Schrödinger- and Poisson-equation to deduce the total polarization across the QW for different Mg-contents inside the barriers. By the separation of the piezoelectric components of the polarization, a linear increase in spontaneous polarization with increasing Mg-content x of P/x = (0.151 ± 0.015) C/m2 was determined for Mgx Zn1−x O.
Significant enhancement in thermoelectric properties of polycrystalline Pr-doped SrTiO3−δ ceramics originating from nonuniform distribution of Pr dopants
Authors: Dehkordi Arash Mehdizadeh , Bhattacharya Sriparna , He Jian , Alshareef Husam N. , Tritt Terry M.
Published: May 2014

Recently, we have reported a significant enhancement (>70% at 500 °C) in the thermoelectric power factor (PF) of bulk polycrystalline Pr-doped SrTiO3 ceramics employing a novel synthesis strategy which led to the highest ever reported values of PF among doped polycrystalline SrTiO3. It was found that the formation of Pr-rich grain boundary regions gives rise to an enhancement in carrier mobility. In this Letter, we investigate the electronic and thermal transport in Sr1−xPrxTiO3 ceramics in order to determine the optimum doping concentration and to evaluate the overall thermoelectric performance. Simultaneous enhancement in the thermoelectric power factor and reduction in thermal conductivity in these samples resulted in more than 30% improvement in the dimensionless thermoelectric figure of merit (ZT) for the whole temperature range over all previously reported maximum values. Maximum ZT value of 0.35 was obtained at 500 °C.
Hybrid model of atmospheric pressure Ar/O2/TiCl4 radio-frequency capacitive discharge for TiO2 deposition
Authors: Leblanc A. , Ding Ke , Lieberman M. A. , Wang De Xin , Zhang Jing , Jun Shi Jian
Published: May 2014

A hybrid global-analytical model of an atmospheric pressure radio-frequency driven capacitive discharge is applied to determine the plasma conditions for TiO2 film deposition. The feed gas is mainly argon with a small fraction of O2 and a smaller fraction of TiCl4. Variations of the discharge parameters and species densities with O2 concentration, discharge power, and flow rate are determined. A simplified chemistry model is developed and compared with the simulation results, showing good agreement. For a base case with Ar/O2/TiCl4 flow rates of 203/30/0.17 sccm, the results indicate that a minimum O2 fraction of 7.3 × 10−4 is required for pure (un-chlorinated) TiO2 film deposition that the active precursor species is TiO2Cl3, with subsequent abstraction of Cl atoms by dissociative electron attachment and that the deposition rates are around 1 nm/s.
An original method to evaluate the transport parameters and reconstruct the electric field in solid-state photodetectors
Authors: Santi A. , Zanichelli M. , Piacentini G. , Pavesi M. , Cola A. , Farella I.
Published: May 2014

A method for reconstructing the spatial profile of the electric field along the thickness of a generic bulk solid-state photodetector is proposed. Furthermore, the mobility and lifetime of both electrons and holes can be evaluated contextually. The method is based on a procedure of minimization built up from current transient profiles induced by laser pulses in a planar detector at different applied voltages. The procedure was tested in CdTe planar detectors for X- and Gamma rays. The devices were measured in a single-carrier transport configuration by impinging laser light on the sample cathode. This method could be suitable for many other devices provided that they are made of materials with sufficiently high resistivity, i.e., with a sufficiently low density of intrinsic carriers.
Temperature and field dependent effective hole mobility and impact ionization at extremely high fields in amorphous selenium
Authors: Kabir M. Z. , Hijazi Nour
Published: May 2014

An analytical model for the electric field and temperature dependent effective drift mobility of holes in amorphous selenium (a-Se) has been developed by considering density of states distribution near the valence band, field enhancement release rate from the shallow traps, and carrier heating. The models for the field-dependent microscopic mobility and momentum relaxation mean free path considering carrier heating are also proposed. The models are fitted with the published experimental results on effective hole mobility and impact ionization with wide variations of applied electric fields and temperatures. The fittings of the model with the published experimental data on the effective hole mobility reveal that, while the effective hole drift mobility increases with increasing temperature and field, the microscopic mobility and momentum relaxation mean free path in a-Se decreases with increasing electric field. A better fitting considering thermally activated tunneling for the field-enhancement release rate indicates that the shallow hole traps in a-Se are neutral defects.
Structural investigation on GexSb10Se90−x glasses using x-ray photoelectron spectra
Authors: Wei Wen-Hou , Xiang Shen , Xu Si-Wei , Fang Liang , Wang Rong-Ping
Published: May 2014

The structure of GexSb10Se90−x glasses (x = 7.5, 10, 15, 20, 25, 27.5, 30, and 32.5 at. %) has been investigated by x-ray photoelectron spectroscopy (XPS). Different structural units have been extracted and characterized by decomposing XPS core level spectra, the evolution of the relative concentration of each structural unit indicates that, the relative contributions of Se-trimers and Se-Se-Ge(Sb) structure decrease with increasing Ge content until they become zero at chemically stoichiometric glasses of Ge25Sb10Se65, and then the homopolar bonds like Ge-Ge and Sb-Sb begin to appear in the spectra. Increase of homopolar bonds will extend band-tails into the gap and narrow the optical band gap. Thus, the glass with a stoichiometric composition generally has fewer defective bonds and larger optical bandgap.
Superconducting cascade electron refrigerator
Authors: Camarasa-Gómez M. , Di Marco A. , Hekking F. W. J. , Winkelmann C. B. , Courtois H. , Giazotto F.
Published: May 2014

The design and operation of an electronic cooler based on a combination of superconducting tunnel junctions is described. The cascade extraction of hot-quasiparticles, which stems from the energy gaps of two different superconductors, allows for a normal metal to be cooled down to about 100 mK starting from a bath temperature of 0.5 K. We discuss the practical implementation, potential performance, and limitations of such a device.
When smaller is better: leaf hydraulic conductance and drought vulnerability correlate to leaf size and venation density across four Coffea arabica genotypes
Authors: Nardini Andrea , Õunapuu-Pikas Eele , Savi Tadeja
Published: May 2014

Leaf hydraulic conductance (Kleaf) and drought vulnerability in terms of leaf water potential inducing 50% loss of Kleaf (P50), were assessed in four genotypes of Coffea arabica L. We tested three hypotheses: (1) leaf P50 is lower in small leaves with higher vein densities; (2) lower P50 translates into lower Kleaf, limiting gas exchange rates and higher leaf mass per unit area (LMA); (3) P50 values are coordinated with symplastic drought tolerance. We found partial support for Hypotheses 1 and 3, but not for Hypothesis 2. Significant correlations existed among leaf size, vein network and drought resistance. Smaller leaves displayed higher major vein density, higher Kleaf and more negative P50. Kleaf was correlated with leaf gas exchange rates. A negative relationship was observed between Kleaf and LMA, whereas P50 was found to be positively correlated with LMA. Across coffee genotypes, reduced leaf surface area and increased vein density shifts P50 towards more negative values while not translating into higher LMA or lower Kleaf. Breeding crop varieties for both increased safety of the leaf hydraulic system towards drought-induced dysfunction and high gas exchange rates per unit of leaf area is probably a feasible target for future adaptation of crops to climate change scenarios.
Experimental confirmation of the MWIR and LWIR grey body assumption for vegetation fire flame emissivity
Authors: Johnston J. M. , Wooster M. J. , Lynham T. J.
Published: May 2014

The temperature and emissivity of forest fire flames play a key role in understanding fire behaviour, modelling fire spread and calculating fire parameters by means of active fire thermal remote sensing. Essential to many of these is the often-made assumption that vegetation fire flames behave as grey bodies in the infrared (IR). Although the emissivity of flames and its relationship to flame depth has been measured experimentally using thermal imagers working in the long-wave IR (LWIR, 8–12µm), no published study has yet demonstrated relationships in the important mid-wave IR (MWIR, 3–5µm) spectral region, nor conclusively demonstrated that assumptions about grey body behaviour across these two important IR atmospheric windows fit well with reality. Our study explores these issues using measurements of boreal forest fuels burned with flame depths ranging from 0.2 to 4.2 m. Observations of two stable black body sources made through the differing flame depths were used to explore flame spectral emissivities and their relationship to flame depth. We found essentially the same relationship between flame emissivity and flame depth for both spectral regions, (extinction coefficient K=0.7 m–1), confirming that the grey body assumption for forest fire flames in the MWIR and LWIR atmospheric windows appears valid for the fire conditions encountered here.
First light of the Gemini Planet Imager
Authors: Macintosh Bruce , Graham James R. , Ingraham Patrick , Konopacky Quinn , Marois Christian , Perrin Marshall , Poyneer Lisa , Bauman Brian , Barman Travis , Burrows Adam S. , Cardwell Andrew , Chilcote Jeffrey , De Rosa Robert J. , Dillon Daren , Doyon Rene , Dunn Jennifer , Erikson Darren , Fitzgerald Michael P. , Gavel Donald , Goodsell Stephen , Hartung Markus , Hibon Pascale , Kalas Paul , Larkin James , Maire Jerome , Marchis Franck , Marley Mark S. , McBride James , Millar-Blanchaer Max , Morzinski Katie , Norton Andrew , Oppenheimer B. R. , Palmer David , Patience Jennifer , Pueyo Laurent , Rantakyro Fredrik , Sadakuni Naru , Saddlemyer Leslie , Savransky Dmitry , Serio Andrew , Soummer Remi , Sivaramakrishnan Anand , Song Inseok , Thomas Sandrine , Wallace J. Kent , Wiktorowicz Sloane , Wolff Schuyler
Published: May 2014

Significance

Direct detection—spatially resolving the light of a planet from the light of its parent star—is an important technique for characterizing exoplanets. It allows observations of giant exoplanets in locations like those in our solar system, inaccessible by other methods. The Gemini Planet Imager (GPI) is a new instrument for the Gemini South telescope. Designed and optimized only for high-contrast imaging, it incorporates advanced adaptive optics, diffraction control, a near-infrared spectrograph, and an imaging polarimeter. During first-light scientific observations in November 2013, GPI achieved contrast performance that is an order of magnitude better than conventional adaptive optics imagers.
Priming by the variability of visual information
Authors: Michael Elizabeth , de Gardelle Vincent , Summerfield Christopher
Published: May 2014

Significance

Sensory systems in the mammalian brain adapt to the context provided by the local environment. The high-level statistics of visual information, such as the central tendency (mean) or heterogeneity (variance) of features or objects, provide important contextual cues for perception. Here, we show that participants categorize a “target” array faster when it occurs in the context of a preceding “prime” array with similar levels feature variance, even when prime and target features are drawn from different categories. This finding suggests that humans rapidly extract and adapt to the variance of visual information. Adaptation to variance may facilitate gain control in heterogeneous or cluttered environments, and contribute to ecologically important behaviors, such as detection in camouflage.
Indirect detection of dark matter with γ rays
Authors: Funk Stefan
Published: May 2014

The details of what constitutes the majority of the mass that makes up dark matter in the Universe remains one of the prime puzzles of cosmology and particle physics today—80 y after the first observational indications. Today, it is widely accepted that dark matter exists and that it is very likely composed of elementary particles, which are weakly interacting and massive [weakly interacting massive particles (WIMPs)]. As important as dark matter is in our understanding of cosmology, the detection of these particles has thus far been elusive. Their primary properties such as mass and interaction cross sections are still unknown. Indirect detection searches for the products of WIMP annihilation or decay. This is generally done through observations of γ-ray photons or cosmic rays. Instruments such as the Fermi large-area telescope, high-energy stereoscopic system, major atmospheric gamma-ray imaging Cherenkov, and very energetic radiation imaging telescope array, combined with the future Cherenkov telescope array, will provide important complementarity to other search techniques. Given the expected sensitivities of all search techniques, we are at a stage where the WIMP scenario is facing stringent tests, and it can be expected that WIMPs will be either be detected or the scenario will be so severely constrained that it will have to be rethought. In this sense, we are on the threshold of discovery. In this article, I will give a general overview of the current status and future expectations for indirect searches of dark matter (WIMP) particles.
Energy efficiency and allometry of movement of swimming and flying animals
Authors: Bale Rahul , Hao Max , Bhalla Amneet Pal Singh , Patankar Neelesh A.
Published: May 2014

Significance

Is a whale or a tuna more efficient? The answer depends on the definition of efficiency. If one uses cost of transport, defined as the energy required to move unit distance, then the tuna wins. If energy of transporting unit mass over unit distance is used then the whale wins. We address this ambiguity by rationally deriving a new efficiency measure called the energy-consumption coefficient (CE), which is a nondimensional measure of fuel consumption.CEis a fundamental metric to quantify efficiency of self-propelled bodies analogous to the drag coefficient (Cd) to quantify aerodynamic shapes of vehicles. The analysis also leads to allometric scalings of frequency and velocity of swimming and flying organisms over more than 20 orders of magnitude of mass.
Room temperature hyperpolarization of nuclear spins in bulk
Authors: Tateishi Kenichiro , Negoro Makoto , Nishida Shinsuke , Kagawa Akinori , Morita Yasushi , Kitagawa Masahiro
Published: May 2014

Significance

Nuclear spins are only slightly aligned even in the strong magnetic fields of superconducting magnets because the magnetic energy of nuclear spin is much smaller than thermal energy. This is the major reason for the low sensitivity of NMR spectroscopy. Using electron spins in thermal equilibrium, which have 660 times higher magnetic energy, the sensitivity can be enhanced by at most this factor through a method called dynamic nuclear polarization. Utilizing photo-excited nonthermalized electrons instead, we demonstrate an enhancement factor of 250,000 at room temperature, which can be applied to a wide range of fields including NMR, MRI, and physics.
Rapid short-term cooling following the Chicxulub impact at the Cretaceous–Paleogene boundary
Authors: Vellekoop Johan , Sluijs Appy , Smit Jan , Schouten Stefan , Weijers Johan W. H. , Sinninghe Damsté Jaap S. , Brinkhuis Henk
Published: May 2014

Significance

Here, for the first time (to our knowledge), we are able to demonstrate unambiguously that the impact at the Cretaceous–Paleogene boundary (K–Pg, ∼66 Mya) was followed by a so-called “impact winter.” This impact winter was the result of the injection of large amounts of dust and aerosols into the stratosphere and significantly reduced incoming solar radiation for decades. Therefore, this phase will have been a key contributory element in the extinctions of many biological clades, including the dinosaurs. The K–Pg boundary impact presents a unique event in Earth history because it caused global change at an unparalleled rate. This detailed portrayal of the environmental consequences of the K–Pg impact and aftermath aids in our understanding of truly rapid climate change.
Speciation of a group I intron into a lariat capping ribozyme
Authors: Meyer Mélanie , Nielsen Henrik , Oliéric Vincent , Roblin Pierre , Johansen Steinar D. , Westhof Eric , Masquida Benoît
Published: May 2014

Significance

We report the crystal structures of precleavage and postcleavage forms of the lariat-capping (LC) ribozyme. The structures show how domains from an ancestral group I ribozyme have evolved due to loss of selection pressure for self-splicing. Instead, a branching activity has been selected, resulting in capping the downstream mRNA by a 3-nt lariat stabilized by the ribozyme core. The LC ribozyme constitutes an original ribozyme family with an unexpected 3D structure that departs significantly from that of group I introns. The structures also elucidate the regulatory domain’s role in transmitting a signal for cleavage to the ribozyme. The characterization of this natural evolutionary RNA speciation event is, to our knowledge, the first described at such an intricate level.
Outer-membrane lipoprotein LpoB spans the periplasm to stimulate the peptidoglycan synthase PBP1B
Authors: Egan Alexander J. F. , Jean Nicolas L. , Koumoutsi Alexandra , Bougault Catherine M. , Biboy Jacob , Sassine Jad , Solovyova Alexandra S. , Breukink Eefjan , Typas Athanasios , Vollmer Waldemar , Simorre Jean-Pierre
Published: May 2014

Significance

Bacteria surround their cytoplasmic membrane with an essential heteropolymer, the peptidoglycan (PG) sacculus, to maintain osmotic stability and cell shape. Cells enlarge their sacculus by using cytoplasmic membrane-anchored PG synthases, which are guided by cytoskeletal elements. Gram-negative bacteria have a thin, mainly single-layered sacculus, connected to the outer membrane. Outer-membrane–anchored lipoproteins were recently found to be essential for PG growth. Here, we present the structure of the outer membrane protein LpoB of
Escherichia coli
, which is required for the function of the major PG synthase PBP1B. LpoB has a long, flexible N-terminal stretch enabling it to span the periplasm and reach its docking site in PBP1B, the noncatalytic UvrB domain 2 homolog domain, to stimulate PG growth.
Structural and functional brain rewiring clarifies preserved interhemispheric transfer in humans born without the corpus callosum
Authors: Tovar-Moll Fernanda , Monteiro Myriam , Andrade Juliana , Bramati Ivanei E. , Vianna-Barbosa Rodrigo , Marins Theo , Rodrigues Erika , Dantas Natalia , Behrens Timothy E. J. , de Oliveira-Souza Ricardo , Moll Jorge , Lent Roberto
Published: May 2014

Significance

Individuals subjected to surgical transection of the corpus callosum (“split-brains”) fail to transfer information between the cerebral hemispheres, a condition known as “disconnection syndrome.” On the other hand, subjects born without the callosum (callosal dysgenesis, CD) typically show preserved interhemispheric communication. To clarify this paradox, which has defied neuroscientists for decades, we investigated CD subjects using functional and structural neuroimaging and neuropsychological tests. Results demonstrated the existence of anomalous interhemispheric tracts that cross through the midbrain and ventral forebrain, linking the parietal cortices bilaterally. These findings provide an explanation for the preserved cross-transfer of tactile information between hemispheres in CD. We suggest that this condition is associated with extensive brain rewiring, generating a new circuitry that provides functional compensatory interhemispheric integration.
Highly efficient integration and expression of
piggyBac
-derived cassettes in the honeybee (
Apis mellifera
)
Authors: Schulte Christina , Theilenberg Eva , Müller-Borg Marion , Gempe Tanja , Beye Martin
Published: May 2014

Significance

We report the first to our knowledge genetically engineered honeybees, which are important pollinators and interesting biological models for the study of social and complex behaviors as well as caste and sexual development. This genetic manipulation tool will enable systematic studies of biological processes in an organism building complex societies. We demonstrate highly efficient integration and expression of
piggyBac
-derived cassettes in the honeybee that make this system applicable to colony-based screening approaches and useful for an average beekeeping facility. This cassette was stably and efficiently transmitted and expressed in progeny by two different promoters, offering the prospect for activation or inhibition of gene functions under conditions of stage- and tissue-specific promoters.
A C⋅As lyase for degradation of environmental organoarsenical herbicides and animal husbandry growth promoters
Authors: Yoshinaga Masafumi , Rosen Barry P.
Published: May 2014

Significance

Organoarsenicals are used as herbicides, pesticides, antimicrobial growth promoters, and chemical warfare agents. Environmental organoarsenicals are microbially degraded, but the molecular mechanisms of breakdown are unknown. We previously identified a two-step pathway of degradation involving sequential reduction and C⋅As bond cleavage. Here we report cloning of the gene and characterization of the gene product for a C⋅As lyase, ArsI, a member of the family of type I extradiol dioxygenases. ArsI is the only enzyme shown to be involved in degradation of the reduced forms of the herbicide monosodium methylarsonic acid and the antimicrobial growth promoter roxarsone. As
arsI
genes are widely distributed in bacteria, ArsI-catalyzed organoarsenic degradation is proposed to have an impact on the arsenic biogeocycle.
Cryo-EM near-atomic structure of a dsRNA fungal virus shows ancient structural motifs preserved in the dsRNA viral lineage
Authors: Luque Daniel , Gómez-Blanco Josué , Garriga Damiá , Brilot Axel F. , González José M. , Havens Wendy M. , Carrascosa José L. , Trus Benes L. , Verdaguer Nuria , Ghabrial Said A. , Castón José R.
Published: May 2014

Significance

Viruses that are seemingly unrelated in genomic studies, and which infect hosts in different domains of life, show similarities in virion structure that indicate deep evolutionary relationships. We report the cryo-EM structure, at near-atomic resolution, of the fungal dsRNA
Penicillium chrysogenum
virus. Its capsid protein is a duplication of a single primordial α-helical domain. This domain has a fold that is conserved among dsRNA viruses; it has increased its complexity through an early gene duplication event, followed by insertion of distinct segments in preferential “hotspots.” We show evidence that this preserved hallmark indicates an ancestral fold, and we suggest a relationship among current viral lineages.
The conserved AAA-ATPase Msp1 confers organelle specificity to tail-anchored proteins
Authors: Okreglak Voytek , Walter Peter
Published: May 2014

Significance

Membrane protein targeting to the endoplasmic reticulum, peroxisomes, and mitochondria requires specialized machinery to ensure the appropriate localization of proteins, which is important for defining organelle identity. Additional specificity is provided by sensing and degrading proteins that are mistargeted to an inappropriate compartment. One class of membrane proteins, which contain a hydrophobic segment at their extreme C terminus (called tail-anchored proteins), are prone to be mistargeted; however, how cells cope with this burden is unknown. In this work, we identify a conserved ATPase of the outer mitochondrial membrane, Msp1, which we propose functions as an extraction engine to remove and initiate degradation of an inappropriately targeted tail-anchored protein. In this way, Msp1 serves to enhance the fidelity of protein localization.
Temporal patterns of gene expression in developing maize endosperm identified through transcriptome sequencing
Authors: Li Guosheng , Wang Dongfang , Yang Ruolin , Logan Kyle , Chen Hao , Zhang Shanshan , Skaggs Megan I. , Lloyd Alan , Burnett William J. , Laurie John D. , Hunter Brenda G. , Dannenhoffer Joanne M. , Larkins Brian A. , Drews Gary N. , Wang Xiangfeng , Yadegari Ramin
Published: May 2014

Significance

In flowering plants, double fertilization gives rise to an embryo and the endosperm, an absorptive storage structure that supports embryogenesis and seedling germination. In cereal grains, endosperm comprises a large proportion of the mature seed, contains large amounts of carbohydrates and proteins, and is an important source of food, feed, and industrial raw materials. This study provides a comprehensive profile of the genes expressed in the early developing endosperm in maize. We also show how a series of temporal programs of gene expression correlate with progressive functional and cellular specializations.
Redemption of autoantibodies on anergic B cells by variable-region glycosylation and mutation away from self-reactivity
Authors: Sabouri Zahra , Schofield Peter , Horikawa Keisuke , Spierings Emily , Kipling David , Randall Katrina L. , Langley David , Roome Brendan , Vazquez-Lombardi Rodrigo , Rouet Romain , Hermes Jana , Chan Tyani D. , Brink Robert , Dunn-Walters Deborah K. , Christ Daniel , Goodnow Christopher C.
Published: May 2014

Significance

Antibodies are selected to bind microbial but not self-antigens, because binding to self would compete with binding microbes, shorten antibody half-life, and cause autoimmunity. Self-tolerance is actively acquired in part by discarding self-binding antibodies before the body is exposed to a microbe or vaccine. The experiments here provide evidence of an opposite mechanism, allowing antibodies that initially bind both foreign and self-antigens to acquire self/non-self discrimination during the course of an immune response through somatic hypermutation away from self-reactivity. In addition to selection for lower-affinity binding to self, antibody variants were selected with fewer binding sites available to bind self-antigen because most were occupied by N-linked carbohydrate, possibly explaining the frequent occurrence of N-linked glycosylation of antibody variable domains.
Atg16L1 T300A variant decreases selective autophagy resulting in altered cytokine signaling and decreased antibacterial defense
Authors: Lassen Kara G. , Kuballa Petric , Conway Kara L. , Patel Khushbu K. , Becker Christine E. , Peloquin Joanna M. , Villablanca Eduardo J. , Norman Jason M. , Liu Ta-Chiang , Heath Robert J. , Becker Morgan L. , Fagbami Lola , Horn Heiko , Mercer Johnathan , Yilmaz Omer H. , Jaffe Jacob D. , Shamji Alykhan F. , Bhan Atul K. , Carr Steven A. , Daly Mark J. , Virgin Herbert W. , Schreiber Stuart L. , Stappenbeck Thaddeus S. , Xavier Ramnik J.
Published: May 2014

Significance

Although advances in human genetics have shaped our understanding of many complex diseases, little is known about the mechanism of action of alleles that influence disease. By using mice expressing a Crohn disease (CD)-associated risk polymorphism (Atg16L1 T300A), we show that Atg16L1 T300A-expressing mice demonstrate abnormalities in Paneth cells (similar to patients with the risk polymorphism) and goblet cells. We show that Atg16L1 T300A protein is more susceptible to caspase-mediated cleavage than WT autophagy related 16-like 1 (Atg16L1), resulting in decreased protein stability and effects on antibacterial autophagy and inflammatory cytokine production. We also identify interacting proteins that contribute to autophagy-dependent immune responses. Understanding how ATG16L1 T300A modulates autophagy-dependent immune responses sheds light on the mechanisms that underlie initiation and progression of CD.
Survey of Intersex Largemouth Bass from Impoundments in Georgia USA
Authors: Kellock Kristen A. , Trushel Brittany E. , Ely Patrick C. , Jennings Cecil A. , Bringolf Robert B.
Published: May 2014

Intersex fish are increasingly being reported worldwide, primarily in rivers that receive treated wastewater, but few studies have investigated intersex in waters that do not receive wastewater. In a recent reconnaissance survey of intersex fish in North America, a high rate of intersex was reported for Largemouth Bass Micropterus salmoides in some southeastern U.S. rivers; however, the occurrence of intersex in impoundments has not been well described, especially on a statewide scale. Therefore, our objective for this project was to survey the occurrence of intersex Largemouth Bass in a variety of impoundment habitats across Georgia. Largemouth Bass were collected from 11 impoundments without direct municipal or agricultural wastewater inputs. Gonads from all male Largemouth Bass were evaluated for the incidence and severity of the intersex condition based on presence and arrangement of testicular oocytes. Overall 48% of male Largemouth Bass collected from impoundments were intersex, which was found in 9 of the 11 impoundments. Among impoundments, incidence of intersex ranged from 0 to 82% of the males sampled and surface area of the impoundment was a significant predictor of intersex incidence. Intersex fish were smaller than normal males, but population‐level effects of intersex and causative factors of endocrine disruption in the impoundments remain unknown. The high incidence of intersex males in small impoundments demonstrates that the condition is not confined to rivers and suggests that factors other than those previously associated with intersex (i.e., municipal wastewater) may be involved.
Determinate Versus Indeterminate Fecundity in American Shad, an Anadromous Clupeid
Authors: Hyle A. Reid , McBride Richard S. , Olney John E.
Published: May 2014

Historical fecundity estimates of American Shad Alosa sapidissima used a determinate method that estimated annual fecundity as the standing stock of oocytes at a single point of time prior to spawning. Such fecundity estimates have been (1) reported for populations from the Canadian Maritimes to Florida, (2) applied to hypothesis tests of life history evolution, and (3) used in demographic models to advise management policy. However, American Shad have asynchronous development of yolked oocyte clutches, which suggests that new oocytes could arise after spawning commences, biasing the results of a determinate fecundity method downward. If so, annual fecundity should be a product of batch size and the number of batches—an indeterminate fecundity method. We investigated oocyte recruitment, atresia, and spawning intervals using gonad histology of females from the Mattaponi River, Virginia. Batch size (i.e., the number of hydrated oocytes prior to a spawning event) was estimated using a gravimetric method. Spawning duration was obtained from an independent acoustic tagging study. A size hiatus between primary and secondary oocytes was only evident in some individuals during spawning, so we conclude that an indeterminate fecundity method is necessary for this population of American Shad. Atresia was evident during spawning but was low at the end of the 2002 spawning season. Females spawned every 2.2–2.9 d, releasing 11–17 batches per season. Batch fecundity (range: 12,700–81,400) was 23% higher for repeat versus virgin spawners. A bootstrapped estimate of potential annual fecundity for a virgin female—as calculated with an indeterminate fecundity method—was 478,000–544,000 eggs (95% confidence interval), about double the previous (determinate) estimates from this river system (260,000 and 288,000). Until more comparisons are done with other populations, we urge caution in using the many published determinate fecundity estimates of American Shad and other Alosa species.
Abundance, Distribution, and Diet of a Small‐Bodied Ecotype of Windowpane
Authors: Hanson John Mark , Wilson Tamara
Published: May 2014

Windowpanes Scophthalmus aquosus were collected during demersal trawl surveys in Northumberland Strait in the southern Gulf of St. Lawrence, Canada, during July and August 2001–2012. Abundance indices showed relatively little variation between years. Windowpanes were widely distributed in the strait, with 95% of the population occurring in water <23m deep and with a temperature of >9.5°C. The Windowpanes collected were small, all <30cm total length. Fish of all sizes fed mainly on sevenspine bay shrimp Crangon septemspinosa, followed by mysids and (for fish >20cm) sand lances Ammodytes spp. and juvenile Atlantic Herring Harengus harengus. Small (<10‐cm) individuals also ate crab megalops larvae. The mysids consumed on sandy–gravel substrates were Mysis spp.; those consumed on mud bottom were mainly Neomysis americana. Cannibalism was low, consisting of two individuals <1.6cm.
Passive Acoustic Monitoring to Detect Spawning in Large‐Bodied Catostomids
Authors: Straight Carrie A. , Freeman Byron J. , Freeman Mary C.
Published: May 2014

Documenting timing, locations, and intensity of spawning can provide valuable information for conservation and management of imperiled fishes. However, deep, turbid or turbulent water, or occurrence of spawning at night, can severely limit direct observations. We have developed and tested the use of passive acoustics to detect distinctive acoustic signatures associated with spawning events of two large‐bodied catostomid species (River RedhorseMoxostoma carinatumand Robust RedhorseMoxostoma robustum) in river systems in north Georgia. We deployed a hydrophone with a recording unit at four different locations on four different dates when we could both record and observe spawning activity. Recordings captured 494 spawning events that we acoustically characterized using dominant frequency, 95% frequency, relative power, and duration. We similarly characterized 46 randomly selected ambient river noises. Dominant frequency did not differ between redhorse species and ranged from 172.3 to 14,987.1Hz. Duration of spawning events ranged from 0.65 to 11.07s, River Redhorse having longer durations than Robust Redhorse. Observed spawning events had significantly higher dominant and 95% frequencies than ambient river noises. We additionally tested software designed to automate acoustic detection. The automated detection configurations correctly identified 80–82% of known spawning events, and falsely indentified spawns 6–7% of the time when none occurred. These rates were combined over all recordings; rates were more variable among individual recordings. Longer spawning events were more likely to be detected. Combined with sufficient visual observations to ascertain species identities and to estimate detection error rates, passive acoustic recording provides a useful tool to study spawning frequency of large‐bodied fishes that displace gravel during egg deposition, including several species of imperiled catostomids.
Relationships among Walleye Population Characteristics and Genetic Diversity in Northern Wisconsin Lakes
Authors: Waterhouse Matthew D. , Sloss Brian L. , Isermann Daniel A.
Published: May 2014

The maintenance of genetic integrity is an important goal of fisheries management, yet little is known regarding the effects of management actions (e.g., stocking, harvest regulations) on the genetic diversity of many important fish species. Furthermore, relationships between population characteristics and genetic diversity remain poorly understood. We examined relationships among population demographics (abundance, recruitment, sex ratio, and mean age of the breeding population), stocking intensity, and genetic characteristics (heterozygosity, effective number of alleles, allelic richness, Wright's inbreeding coefficient, effective population size [Ne], mean d2 [a measure of inbreeding], mean relatedness, and pairwise population ΦST estimates) for 15 populations of Walleye Sander vitreus in northern Wisconsin. We also tested for potential demographic and genetic influences on Walleye body condition and early growth. Combinations of demographic variables explained 47.1–79.8% of the variation in genetic diversity. Skewed sex ratios contributed to a reduction in Ne and subsequent increases in genetic drift and relatedness among individuals within populations; these factors were correlated to reductions in allelic richness and early growth rate. Levels of inbreeding were negatively related to both age‐0 abundance and mean age, suggesting Ne was influenced by recruitment and generational overlap. A negative relationship between the effective number of alleles and body condition suggests stocking affected underlying genetic diversity of recipient populations and the overall productivity of the population. These relationships may result from poor performance of stocked fish, outbreeding depression, or density‐dependent factors. An isolation‐by‐distance pattern of genetic diversity was apparent in nonstocked populations, but was disrupted in stocked populations, suggesting that stocking affected genetic structure. Overall, demographic factors were related to genetic diversity and stocking appeared to alter allelic frequencies and the genetic structure of Walleye populations in Wisconsin, possibly resulting in disruption of local adaptation.