bluuebunny/crossref_metadata_2025 huggingface dataset:
Theoretical spectroscopic characterization at low temperatures of methyl hydroperoxide and three S-analogs
Authors: Dalbouha S. , Senent M. L. , Komiha N.
Published: February 2015

The low temperature spectra of the detectable species methyl hydroperoxide (CH3OOH) and three sulfur analogs, the two isomers of methanesulfenic acid (CH3SOH and CH3OSH) and the methyl hydrogen disulfide (CH3SSH), are predicted from highly correlated ab initio methods (CCSD(T) and CCSD(T)-F12). Rotational parameters, anharmonic frequencies, torsional energy barriers, torsional energy levels, and their splittings are provided. Our computed parameters should help for the characterization and the identification of these organic compounds in laboratory and in the interstellar medium.
Sanov and central limit theorems for output statistics of quantum Markov chains
Authors: van Horssen Merlijn , Guţă Mădălin
Published: February 2015

In this paper, we consider the statistics of repeated measurements on the output of a quantum Markov chain. We establish a large deviations result analogous to Sanov’s theorem for the multi-site empirical measure associated to finite sequences of consecutive outcomes of a classical stochastic process. Our result relies on the construction of an extended quantum transition operator (which keeps track of previous outcomes) in terms of which we compute moment generating functions, and whose spectral radius is related to the large deviations rate function. As a corollary to this, we obtain a central limit theorem for the empirical measure. Such higher level statistics may be used to uncover critical behaviour such as dynamical phase transitions, which are not captured by lower level statistics such as the sample mean. As a step in this direction, we give an example of a finite system whose level-1 (empirical mean) rate function is independent of a model parameter while the level-2 (empirical measure) rate is not.
Asymptotics for Toeplitz determinants: Perturbation of symbols with a gap
Authors: Charlier Christophe , Claeys Tom
Published: February 2015

We study the determinants of Toeplitz matrices as the size of the matrices tends to infinity, in the particular case where the symbol has two jump discontinuities and tends to zero on an arc of the unit circle at a sufficiently fast rate. We generalize an asymptotic expansion by Widom [Indiana Univ. Math. J. 21, 277–283 (1971)], which was known for symbols supported on an arc. We highlight applications of our results in the circular unitary ensemble and in the study of Fredholm determinants associated to the sine kernel.
Parameter-induced stochastic resonance based on spectral entropy and its application to weak signal detection
Authors: Zhang Jinjing , Zhang Tao
Published: February 2015

The parameter-induced stochastic resonance based on spectral entropy (PSRSE) method is introduced for the detection of a very weak signal in the presence of strong noise. The effect of stochastic resonance on the detection is optimized using parameters obtained in spectral entropy analysis. Upon processing employing the PSRSE method, the amplitude of the weak signal is enhanced and the noise power is reduced, so that the frequency of the signal can be estimated with greater precision through spectral analysis. While the improvement in the signal-to-noise ratio is similar to that obtained using the Duffing oscillator algorithm, the computational cost reduces from O(N2) to O(N). The PSRSE approach is applied to the frequency measurement of a weak signal made by a vortex flow meter. The results are compared with those obtained applying the Duffing oscillator algorithm.
An early warning indicator for atmospheric blocking events using transfer operators
Authors: Tantet Alexis , van der Burgt Fiona R. , Dijkstra Henk A.
Published: February 2015

The existence of persistent midlatitude atmospheric flow regimes with time-scales larger than 5–10 days and indications of preferred transitions between them motivates to develop early warning indicators for such regime transitions. In this paper, we use a hemispheric barotropic model together with estimates of transfer operators on a reduced phase space to develop an early warning indicator of the zonal to blocked flow transition in this model. It is shown that the spectrum of the transfer operators can be used to study the slow dynamics of the flow as well as the non-Markovian character of the reduction. The slowest motions are thereby found to have time scales of three to six weeks and to be associated with meta-stable regimes (and their transitions) which can be detected as almost-invariant sets of the transfer operator. From the energy budget of the model, we are able to explain the meta-stability of the regimes and the existence of preferred transition paths. Even though the model is highly simplified, the skill of the early warning indicator is promising, suggesting that the transfer operator approach can be used in parallel to an operational deterministic model for stochastic prediction or to assess forecast uncertainty.
Reduced thermal conductivity by nanoscale intergrowths in perovskite like layered structure La2Ti2O7
Authors: Khaliq Jibran , Li Chunchun , Chen Kan , Shi Baogui , Ye Haitao , Grande Antonio M. , Yan Haixue , Reece Michael J.
Published: February 2015

The effect of substitution and oxidation-reduction on the thermal conductivity of perovskite-like layered structure (PLS) ceramics was investigated in relation to mass contrast and non-stoichiometry. Sr (acceptor) was substituted on the A site, while Ta (donor) was substituted on the B site of La2Ti2O7. Substitution in PLS materials creates atomic scale disorders to accommodate the non-stoichiometry. High resolution transmission electron microscopy and X ray diffraction revealed that acceptor substitution in La2Ti2O7 produced nanoscale intergrowths of n = 5 layered phase, while donor substitution produced nanoscale intergrowths of n = 3 layered phase. As a result of these nanoscale intergrowths, the thermal conductivity value reduced by as much as ∼20%. Pure La2Ti2O7 has a thermal conductivity value of ∼1.3 W/m K which dropped to a value of ∼1.12 W/m K for Sr doped La2Ti2O7 and ∼0.93 W/m K for Ta doped La2Ti2O7 at 573 K.
Unusually high critical current of clean P-doped BaFe2As2 single crystalline thin film
Authors: Kurth F. , Tarantini C. , Grinenko V. , Hänisch J. , Jaroszynski J. , Reich E. , Mori Y. , Sakagami A. , Kawaguchi T. , Engelmann J. , Schultz L. , Holzapfel B. , Ikuta H. , Hühne R. , Iida K.
Published: February 2015

Microstructurally clean, isovalently P-doped BaFe2As2 (Ba-122) single crystalline thin films have been prepared on MgO (001) substrates by molecular beam epitaxy. These films show a superconducting transition temperature (Tc) of over 30 K although P content is around 0.22, which is lower than the optimal one for single crystals (i.e., 0.33). The enhanced Tc at this doping level is attributed to the in-plane tensile strain. The strained film shows high transport self-field critical current densities (Jc) of over 6 MA/cm2 at 4.2 K, which are among the highest for Fe based superconductors (FeSCs). In-field Jc exceeds 0.1 MA/cm2 at μ0H=35 T for H‖ab and μ0H=18 T for H‖c at 4.2 K, respectively, in spite of moderate upper critical fields compared to other FeSCs with similar Tc. Structural investigations reveal no defects or misoriented grains pointing to strong pinning centers. We relate this unexpected high Jc to a strong enhancement of the vortex core energy at optimal Tc, driven by in-plane strain and doping. These unusually high Jc make P-doped Ba-122 very favorable for high-field magnet applications.
Simulation studies on architecture dependence of unentangled polymer melts
Authors: Xu Xiaolei , Chen Jizhong , An Lijia
Published: February 2015

The dependences of the properties of linear, ring, star, and H-shaped polymer melts on architecture are investigated by nonequilibrium molecular dynamics simulations. We find that zero-shear viscosities η0 for various architectures follow a universal relation, η0=Cη〈Rg02〉, where Cη is a constant and 〈Rg02〉 the equilibrium mean-square radius of gyration, in the unentangled regime. This law is also found valid for asymmetrical polymers but invalid for polymers with a hard core, such as stars with many arms and short arm lengths. In the unentangled regime, from the point of view of polymer size, the relaxation times show weak dependences on architecture, but the architecture dependence of the diffusion coefficient is still apparent. Then, we examine unentangled melts of various architectures having the same size over a wide range of shear rates covering linear and nonlinear viscoelastic regimes and find that the rheological quantities, namely, viscosity, first and second normal stress differences, are independent of architecture. In contrast, the polymer deformation shows an apparent dependence on architecture in the nonlinear regime. These findings shall shed significant light on the nature of rheological behaviors of unentangled melts.
Spatially separated charge densities of electrons and holes in organic-inorganic halide perovskites
Authors: Li Dan , Liang Chunjun , Zhang Huimin , Zhang Chunxiu , You Fangtian , He Zhiqun
Published: February 2015

Solution-processable methylammonium lead trihalide perovskites exhibit remarkable high-absorption and low-loss properties for solar energy conversion. Calculation from density functional theory indicates the presence of non-equivalent halogen atoms in the unit cell because of the specific orientation of the organic cation. Considering the 〈100〉 orientation as an example, I1, one of the halogen atoms, differs from the other iodine atoms (I2 and I3) in terms of its interaction with the organic cation. The valance-band-maximum (VBM) and conduction-band-minimum (CBM) states are derived mainly from 5p orbital of I1 atom and 6p orbital of Pb atom, respectively. The spatially separated charge densities of the electrons and holes justify the low recombination rate of the pure iodide perovskite. Chlorine substitution further strengthens the unique position of the I1 atom, leading to more localized charge density around the I1 atom and less charge density around the other atoms at the VBM state. The less overlap of charge densities between the VBM and CBM states explains the relatively lower carrier recombination rate of the iodine-chlorine mixed perovskite. Chlorine substitution significantly reduces the effective mass at a direction perpendicular to the Pb-Cl bond and organic axis, enhancing the carrier transport property of the mixed perovskite in this direction.
Sub-tesla-field magnetization of vibrated magnetic nanoreagents for screening tumor markers
Authors: Chieh Jen-Jie , Huang Kai-Wen , Shi Jin-Cheng
Published: February 2015

Magnetic nanoreagents (MNRs), consisting of liquid solutions and magnetic nanoparticles (MNPs) coated with bioprobes, have been widely used in biomedical disciplines. For in vitro tests of serum biomarkers, numerous MNR-based magnetic immunoassay methods or schemes have been developed; however, their applications are limited. In this study, a vibrating sample magnetometer (VSM) was used for screening tumor biomarkers based on the same MNRs as those used in other immunoassay methods. The examination mechanism is that examined tumor biomarkers are typically conjugated to the bioprobes coated on MNPs to form magnetic clusters. Consequently, the sub-Tesla-field magnetization (Msub-T) of MNRs, including magnetic clusters, exceeds that of MNRs containing only separate MNPs. For human serum samples, proteins other than the targeted biomarkers induce the formation of magnetic clusters with increased Msub-T because of weak nonspecific binding. In this study, this interference problem was suppressed by the vibration condition in the VSM and analysis. Based on a referenced Msub-T,0 value defined by the average Msub-T value of a normal person's serum samples, including general proteins and few tumor biomarkers, the difference ΔMsub-T between the measured Msub-T and the reference Msub-T,0 determined the expression of only target tumor biomarkers in the tested serum samples. By using common MNRs with an alpha-fetoprotein-antibody coating, this study demonstrated that a current VSM can perform clinical screening of hepatocellular carcinoma.
Effect of substitutional defects on Kambersky damping in L1 magnetic materials
Authors: Qu T. , Victora R. H.
Published: February 2015

Kambersky damping, representing the loss of magnetic energy from the electrons to the lattice through the spin orbit interaction, is calculated for L10 FePt, FePd, CoPt, and CoPd alloys versus chemical degree of order. When more substitutional defects exist in the alloys, damping is predicted to increase due to the increase of the spin-flip channels allowed by the broken symmetry. It is demonstrated that this corresponds to an enhanced density of states (DOS) at the Fermi level, owing to the rounding of the DOS with loss of long-range order. Both the damping and the DOS of the Co-based alloy are found to be less affected by the disorder. Pd-based alloys are predicted to have lower damping than Pt-based alloys, making them more suitable for high density spintronic applications.
Indium clustering in a-plane InGaN quantum wells as evidenced by atom probe tomography
Authors: Tang Fengzai , Zhu Tongtong , Oehler Fabrice , Fu Wai Yuen , Griffiths James T. , Massabuau Fabien C.-P. , Kappers Menno J. , Martin Tomas L. , Bagot Paul A. J. , Moody Michael P. , Oliver Rachel A.
Published: February 2015

Atom probe tomography (APT) has been used to characterize the distribution of In atoms within non-polar a-plane InGaN quantum wells (QWs) grown on a GaN pseudo-substrate produced using epitaxial lateral overgrowth. Application of the focused ion beam microscope enabled APT needles to be prepared from the low defect density regions of the grown sample. A complementary analysis was also undertaken on QWs having comparable In contents grown on polar c-plane sample pseudo-substrates. Both frequency distribution and modified nearest neighbor analyses indicate a statistically non-randomized In distribution in the a-plane QWs, but a random distribution in the c-plane QWs. This work not only provides insights into the structure of non-polar a-plane QWs but also shows that APT is capable of detecting as-grown nanoscale clustering in InGaN and thus validates the reliability of earlier APT analyses of the In distribution in c-plane InGaN QWs which show no such clustering.
Strain and lattice orientation distribution in SiN/Ge complementary metal–oxide–semiconductor compatible light emitting microstructures by quick x-ray nano-diffraction microscopy
Authors: Chahine G. A. , Zoellner M. H. , Richard M.-I. , Guha S. , Reich C. , Zaumseil P. , Capellini G. , Schroeder T. , Schülli T. U.
Published: February 2015

This paper presents a study of the spatial distribution of strain and lattice orientation in CMOS-fabricated strained Ge microstripes using high resolution x-ray micro-diffraction. The recently developed model-free characterization tool, based on a quick scanning x-ray diffraction microscopy technique can image strain down to levels of 10−5 (Δa/a) with a spatial resolution of ∼0.5 μm. Strain and lattice tilt are extracted using the strain and orientation calculation software package X-SOCS. The obtained results are compared with the biaxial strain distribution obtained by lattice parameter-sensitive μ-Raman and μ-photoluminescence measurements. The experimental data are interpreted with the help of finite element modeling of the strain relaxation dynamics in the investigated structures.
Outstanding field emission properties of wet-processed titanium dioxide coated carbon nanotube based field emission devices
Authors: Xu Jinzhuo , Xu Peng , Ou-Yang Wei , Chen Xiaohong , Guo Pingsheng , Li Jun , Piao Xianqing , Wang Miao , Sun Zhuo
Published: February 2015

Field emission devices using a wet-processed composite cathode of carbon nanotube films coated with titanium dioxide exhibit outstanding field emission characteristics, including ultralow turn on field of 0.383 V μm−1 and threshold field of 0.657 V μm−1 corresponding with a very high field enhancement factor of 20 000, exceptional current stability, and excellent emission uniformity. The improved field emission properties are attributed to the enhanced edge effect simultaneously with the reduced screening effect, and the lowered work function of the composite cathode. In addition, the highly stable electron emission is found due to the presence of titanium dioxide nanoparticles on the carbon nanotubes, which prohibits the cathode from the influence of ions and free radical created in the emission process as well as residual oxygen gas in the device. The high-performance solution-processed composite cathode demonstrates great potential application in vacuum electronic devices.
Piezoelectric ZnO-nanorod-structured pressure sensors using GaN-based field-effect-transistor
Authors: Lee Ching-Ting , Chiu Ying-Shuo
Published: February 2015

To utilize the piezoelectric property of ZnO nanorods, the ZnO nanorod array was grown on the AlGaN/GaN field-effect-transistor as the pressure sensors. The drain-source current of the ZnO nanorod-structured-AlGaN/GaN FET pressure sensors can be effectively modulated by the induced gate voltage caused from the piezoelectric phenomenon of ZnO nanorods under different pressures. The pressure sensors revealed the linearly response current under the pressure from 19.6 mN/mm2 to 490 mN/mm2. The ratio of the response current achieved 2.67% under the pressure of 490 mN/mm2. The induced piezoelectric potential under different pressure was also calculated and obtained in this work.
Evolution of the ferromagnetic resonance spectrum of a hexagonal antidot lattice with film thickness: Experiment and numerical simulations
Authors: Vovk A. , Golub V. , Salyuk O. , Krivoruchko V. N. , Marchenko A. I.
Published: February 2015

Experimental and theoretical studies of the evolution of the ferromagnetic resonance spectrum with film thickness for hexagonal lattice of antidots have been reported. We found three different quasi-uniform modes in the resonance spectrum. Calculations of the local dynamic susceptibility tensor show that these modes are related to the resonances from quasiuniformly magnetized regions of the hexagonal antidot array unit cell. The increase of the film thickness results in the broadening of the resonance lines as well as the appearance of additional resonance lines. Good qualitative correlation of the theory and experiment was obtained. Additional relaxation mechanisms due to magnetic inhomogeneities are also discussed.
Symmetry-dependent interfacial reconstruction to compensate polar discontinuity at perovskite oxide interfaces (LaAlO3/SrTiO3 and LaAlO3/CaTiO3)
Authors: Lee Joohwi , Choi Jong Kwon , Moon Seon Young , Park Jaehong , Kim Jin-Sang , Hwang Cheol Seong , Baek Seung-Hyub , Choi Jung-Hae , Chang Hye Jung
Published: February 2015

We report the crystal symmetry-dependency of the interfacial reconstruction to relieve the polar discontinuity at the complex oxide heterointerfaces. We chose LaAlO3/SrTiO3 and LaAlO3/CaTiO3 interfaces as model systems, where the neutral TiO2 and the positive LaO+ layers form the polar discontinuity at the interface with TiO2-terminated (001) cubic SrTiO3 and orthorhombic CaTiO3. Using scanning transmission electron microscopy, we observed that the interlayer distance abnormally increased at the interface. We performed the first-principles calculations to understand the detailed atomic displacement at the interfaces having no oxygen vacancy and intermixing. Our results show that cations were reconstructed in different ways depending on the crystal symmetry through the octahedral tilts and atomic displacements to compensate the polar discontinuity at the interfaces. Our results imply that the interfacial reconstructions have to be considered along with the ionic compensation (intermixing) and electronic compensation (two dimensional electron gas) to fully understand the interfacial phenomena.
Magnetic versus nonmagnetic ion substitution effects in gapless semiconductor PbPdO2
Authors: Lee Kyujoon , Choo Seong-Min , Jung Myung-Hwa
Published: February 2015

PbPdO2 is a gapless semiconductor, of which the physical properties are easily tuned by external parameters such as temperature, magnetic field, and chemical doping. We have studied the physical properties tuned by magnetic and nonmagnetic ion substitutions. When Pd in PbPdO2 is substituted by Zn, that is, divalent and nonmagnetic with 3d10 (S = 0), the electrical resistivity decreases and the magnetic properties are not changed to remain diamagnetic. However, by substituting Cu2+ (3d9) with S = 1/2, the electrical resistivity increases and the magnetization shows paramagnetic behavior. Another noticeable feature in the magnetic versus nonmagnetic ion substitution is found in the magneto-transport data. The magnetoresistance for PbPd0.9Cu0.1O2 is positive, compared with the negative behavior for PbPd0.9Zn0.1O2. These results propose that chemical dopants play an important role in optimizing the tunability of the physical properties of gapless semiconductors.
Nanoscale thermal conductivity spectroscopy by using gold nano-islands heat absorbers
Authors: Oyake Takafumi , Sakata Masanori , Shiomi Junichiro
Published: February 2015

A measurement technique of quasi-ballistic thermal transport in tens of nanometers has been developed by using time-domain thermoreflectance of gold nano-islands. The suppressed apparent thermal conductivity of transparent substrates (fused quartz, crystal quartz, and sapphire) due to quasi-ballistic thermal transport is obtained through the transient temperature change of the gold nano-islands formed on the substrate surface, and the size effect of thermal conductivity in the range of tens of nanometers is quantified by varying the gold nano-island sizes. Furthermore, characteristic phonon mean free paths of the substrates were obtained by fitting the measured size effect with a solution of a Boltzmann transport equation. The results identify that the size-effect of amorphous fused quartz at room temperature becomes significant when the size is reduced below 60 nm.
Direct minority carrier transport characterization of InAs/InAsSb superlattice nBn photodetectors
Authors: Zuo Daniel , Liu Runyu , Wasserman Daniel , Mabon James , He Zhao-Yu , Liu Shi , Zhang Yong-Hang , Kadlec Emil A. , Olson Benjamin V. , Shaner Eric A.
Published: February 2015

We present an extensive characterization of the minority carrier transport properties in an nBn mid-wave infrared detector incorporating a Ga-free InAs/InAsSb type-II superlattice as the absorbing region. Using a modified electron beam induced current technique in conjunction with time-resolved photoluminescence, we were able to determine several important transport parameters of the absorber region in the device, which uses a barrier layer to reduce dark current. For a device at liquid He temperatures, we report a minority carrier diffusion length of 750 nm and a minority carrier lifetime of 200 ns, with a vertical diffusivity of 3 × 10−2 cm2/s. We also report on the device's optical response characteristics at 78 K.
Distinctive translational and self-rotational motion of lymphoma cells in an optically induced non-rotational alternating current electric field
Authors: Liang Wenfeng , Zhang Ke , Yang Xieliu , Liu Lianqing , Yu Haibo , Zhang Weijing
Published: February 2015

In this paper, the translational motion and self-rotational behaviors of the Raji cells, a type of B-cell lymphoma cell, in an optically induced, non-rotational, electric field have been characterized by utilizing a digitally programmable and optically activated microfluidics chip with the assistance of an externally applied AC bias potential. The crossover frequency spectrum of the Raji cells was studied by observing the different linear translation responses of these cells to the positive and negative optically induced dielectrophoresis force generated by a projected light pattern. This digitally projected spot served as the virtual electrode to generate an axisymmetric and non-uniform electric field. Then, the membrane capacitance of the Raji cells could be directly measured. Furthermore, Raji cells under this condition also exhibited a self-rotation behavior. The repeatable and controlled self-rotation speeds of the Raji cells to the externally applied frequency and voltage were systematically investigated and characterized via computer-vision algorithms. The self-rotational speed of the Raji cells reached a maximum value at 60 kHz and demonstrated a quadratic relationship with respect to the applied voltage. Furthermore, optically projected patterns of four orthogonal electrodes were also employed as the virtual electrodes to manipulate the Raji cells. These results demonstrated that Raji cells located at the center of the four electrode pattern could not be self-rotated. Instead any Raji cells that deviated from this center area would also self-rotate. Most importantly, the Raji cells did not exhibit the self-rotational behavior after translating and rotating with respect to the center of any two adjacent electrodes. The spatial distributions of the electric field generated by the optically projected spot and the pattern of four electrodes were also modeled using a finite element numerical simulation. These simulations validated that the electric field distributions were non-uniform and non-rotational. Hence, the non-uniform electric field must play a key role in the self-rotation of the Raji cells. As a whole, this study elucidates an optoelectric-coupled microfluidics-based mechanism for cellular translation and self-rotation that can be used to extract the dielectric properties of the cells without using conventional metal-based microelectrodes. This technique may provide a simpler method for label-free identification of cancerous cells with many associated clinical applications.
Supplementation for beef cattle on Marandu grass pastures with different herbage allowances
Authors: De Oliveira A. P. , Casagrande D. R. , Bertipaglia L. M. A. , Barbero R. P. , Berchielli T. T. , Ruggieri A. C. , Reis R. A.
Published: February 2015

The objective of this study was to evaluate the performance of beef heifers on Stapf. cv. Marandu grass pastures that were managed at three herbage allowances under continuous grazing with a variable stocking rate and were provided with mineral mix supplement or supplements with energy and protein. Seventy-two test heifers and 48 put-and-take heifers were used in a randomised design in a 3 × 2 factorial arrangement [three herbage allowances (1.5, 2.0, and 2.5 kg of green dry matter/kg of bodyweight, and two supplementation levels (mineral mix or 0.3% bodyweight of a mineral–protein–energy supplement)], with two replicates per treatment (paddocks), to maintain the pre-established forage allowance. No significant difference was observed in the gain per hectare as a function of the herbage allowance, but 2.5 kg green dry matter/kg bodyweight provided the greatest average daily gain of bodyweight (0.605 kg/animal/day). The energy/protein supplementation provided the greatest average daily gain compared with animals fed only the mineral mix. The supplements in the diet of beef heifers fed at 0.3% of bodyweight increased bodyweight gains without compromising the gain per hectare at different herbage allowances.
An integrated approach to bovine oocyte quality: from phenotype to genes
Authors: Angulo Leslie , Guyader-Joly Catherine , Auclair Sylvain , Hennequet-Antier Christelle , Papillier Pascal , Boussaha Mekki , Fritz Sébastien , Hugot Karine , Moreews François , Ponsart Claire , Humblot Patrice , Dalbies-Tran Rozenn
Published: February 2015

In cattle, early embryonic failure plays a major role in the limitation of reproductive performance and is influenced by genetic effects. Suboptimal oocyte quality, including an inadequate store of maternal factors, is suspected to contribute to this phenomenon. In the present study, 13 Montbeliarde cows were phenotyped on oocyte quality, based on their ability to produce viable embryos after in vitro maturation, fertilisation and culture for 7 days. This discriminated two groups of animals, exhibiting developmental rates below 18.8% or above 40.9% (relative to cleaved embryos). Using microarrays, transcriptomic profiles were compared between oocytes collected in vivo from these two groups of animals. The difference in oocyte development potential was associated with changes in transcripts from 60 genes in immature oocytes and 135 genes in mature oocytes (following Bonferroni 5% correction). Of these, 16 and 32 genes were located in previously identified fertility quantitative trait loci. A subset of differential genes was investigated on distinct samples by reverse transcription–quantitative polymerase chain reaction. For SLC25A16, PPP1R14C, ROBO1, AMDHD1 and MEAF6 transcripts, differential expression was confirmed between high and low oocyte potential animals. Further sequencing and searches for polymorphisms will pave the way for implementing their use in genomic selection.
Use of an organotypic mammalian in vitro follicle growth assay to facilitate female reproductive toxicity screening
Authors: Xu Yuanming , Duncan Francesca E. , Xu Min , Woodruff Teresa K.
Published: February 2015

Screening of pharmaceutical, chemical and environmental compounds for their effects on reproductive health relies on in vivo studies. More robust and efficient methods to assess these effects are needed. Herein we adapted and validated an organotypic in vitro follicle growth (IVFG) assay to determine the impact of compounds on markers of ovarian function. We isolated mammalian follicles and cultured them in the presence of compounds with: (1) known fertotoxicity (i.e. toxicity to the reproductive system; cyclophosphamide and cisplatin); (2) no known fertotoxicity (nalbuphine); and (3) unknown fertotoxicity (Corexit EC 9500 A; CE, Nalco, Chicago, IL, USA). For each compound, we assayed follicle growth, hormone production and the ability of follicle-enclosed oocytes to resume meiosis and produce a mature egg. Cyclophosphamide and cisplatin caused dose-dependent disruption of follicle dynamics, whereas nalbuphine did not. The reproductive toxicity of CE, an oil dispersant used heavily during the 2010 Deepwater Horizon oil spill, has never been examined in a mammalian system. In the present study, CE compromised follicle morphology and functional parameters. Our findings demonstrate that this IVFG assay system can be used to distinguish fertotoxic from non-toxic compounds, providing an in vitro tool to assess the effects of chemical compounds on reproductive function and health.
Expression and immunolocalisation of follicle-stimulating hormone receptors in gonads of newborn and adult female horses
Authors: Scarlet Dragos , Walter Ingrid , Hlavaty Juraj , Aurich Christine
Published: February 2015

In mares, FSH and its receptor (FSHR) are essential for ovarian function. The objective of the present study was to analyse FSHR gene expression at the mRNA and protein levels in ovarian tissue from newborn and adult horses. Expression of mRNA was analysed by reverse transcription polymerase chain reaction, whereas FSHR protein was visualised by immunohistochemistry (IHC), immunofluorescence labelling (IF) and western blot. FSHR mRNA was detected in ovarian follicles and luteal tissue from adult mares, as well as in the ovaries of neonates. Follicular growth up to 4 mm in diameter was already present in neonates. Using IHC and IF, FSHR protein was detected in granulosa cells, cumulus cells and inconsistently in oocytes, independent of the animal’s age or the stage of folliculogenesis. A lower FSHR expression was observed in theca cells in comparison to granulosa cells. FSHR was abundant in the ovarian stroma cells of neonates but not of adults. Luteal cells stained positive for FSHR independent of the stage of corpus luteum development. The presence of FSHR protein in various cell populations of the ovary was confirmed by western blot. In conclusion, FSHR is present in horse ovaries consistently from birth onwards and expression remains constant during the oestrous cycle.
New approaches to cataloguing and understanding evolutionary diversity: a perspective from Australian herpetology
Authors: Oliver Paul , Keogh J. Scott , Moritz Craig
Published: February 2015

Species are a fundamental unit for all fields of biology but conceptual and practical limitations have hampered the process of identifying and describing species in many organismal groups. One outcome of these challenges is the accumulation of genetically divergent lineages and morphologically distinctive populations that are ‘known’, but remain of uncertain taxonomic status and evolutionary significance. These lineages are also currently not effectively incorporated into evolutionary studies or conservation planning and management. Here we suggest three ways to address this issue. First, there is a need to develop improved frameworks to systematically capture taxonomically unrecognised lineage diversity. Second, increased utilisation of metadata frameworks will allow better recording and dissemination of biodiversity information. Finally, emerging genomic and analytical techniques will provide powerful new tools to improve our identification and understanding of evolutionary lineages.
Coding principles of the canonical cortical microcircuit in the avian brain
Authors: Calabrese Ana , Woolley Sarah M. N.
Published: February 2015

Significance

A six-layered neocortex is a hallmark feature of the mammalian brain. Connections among layers and progressive changes in the neural coding properties of each layer define a microcircuit thought to perform the computations underlying complex behavior. Birds lack a six-layered cortex. Yet, they demonstrate complex cognition and behavior. Recent anatomical studies propose that adjacent regions of the avian pallium are homologs of neocortical layers. Here, we show that the avian auditory pallium exhibits the same information-processing principles that define the mammalian neocortical microcircuit. Results suggest that the cortical microcircuit evolved in a common ancestor of mammals and birds and provide a physiological explanation for neural processes that give rise to complex behavior in the absence of cortical lamination.
Hybrid origins and the earliest stages of diploidization in the highly successful recent polyploid
Capsella bursa-pastoris
Authors: Douglas Gavin M. , Gos Gesseca , Steige Kim A. , Salcedo Adriana , Holm Karl , Josephs Emily B. , Arunkumar Ramesh , Ågren J. Arvid , Hazzouri Khaled M. , Wang Wei , Platts Adrian E. , Williamson Robert J. , Neuffer Barbara , Lascoux Martin , Slotte Tanja , Wright Stephen I.
Published: February 2015

Significance

Plants have undergone repeated rounds of whole-genome duplication, followed by gene degeneration and loss. Using whole-genome resequencing, we examined the origins of the recent tetraploid
Capsella bursa-pastoris
and the earliest stages of genome evolution after polyploidization. We conclude the species had a hybrid origin from two distinct
Capsella
lineages within the past 100,000–300,000 y. Our analyses suggest the absence of rapid gene loss but provide evidence that the species has large numbers of inactivating mutations, many of which were inherited from the parental species. Our results suggest that genome evolution following polyploidy is determined not only by genome redundancy but also by demography, the mating system, and the evolutionary history of the parental species.
RING finger protein 121 facilitates the degradation and membrane localization of voltage-gated sodium channels
Authors: Ogino Kazutoyo , Low Sean E. , Yamada Kenta , Saint-Amant Louis , Zhou Weibin , Muto Akira , Asakawa Kazuhide , Nakai Junichi , Kawakami Koichi , Kuwada John Y. , Hirata Hiromi
Published: February 2015

Significance

Voltage-gated sodium channels (NaV) are known to form clusters at the membranes of excitable cells; however, what governs their transport is largely unknown. We found that the endoplasmic reticulum (ER) andcis-Golgi associated ubiquitin ligase really interesting new gene (RING) finger protein 121 (RNF121) mediates the degradation and membrane localization of NaV. This apparent quality control of NaVensures the transport of properly folded channels to the membranes of excitable cells. To our knowledge, this is the first pathologically relevant identification of a voltage-gated ion channel as a substrate for ER-associated protein degradation, whose degradation is governed by an ER- and Golgi-associated E3-ubiquitin ligase.
EF-hand protein Ca
2+
buffers regulate Ca
2+
influx and exocytosis in sensory hair cells
Authors: Pangršič Tina , Gabrielaitis Mantas , Michanski Susann , Schwaller Beat , Wolf Fred , Strenzke Nicola , Moser Tobias
Published: February 2015

Significance

Ca
2+
ions serve as a key cellular signal and are tightly controlled. One mechanism to limit free Ca
2+
ions is buffering by Ca
2+
-binding proteins, which are strongly expressed in sensory hair cells of the ear. Here we studied how genetic disruption of the Ca
2+
-binding proteins parvalbumin-α, calbindin-D28k, and calretinin affects exocytosis and sound encoding at the synapses of mouse inner hair cells (IHCs) and spiral ganglion neurons (SGNs). Mutant IHCs showed increased exocytosis, but the sound-evoked spiking activity in SGNs was unaltered. Together with mathematical modeling, this finding indicates that a large fraction of exocytosis in mutant IHCs occurred outside synapses. We conclude that Ca
2+
-binding proteins shape presynaptic Ca
2+
signals to restrict exocytosis to active zones, thus enabling metabolically efficient sound encoding.
Evidence and implications of higher-order scaling in the environmental variation of animal population growth
Authors: Ferguson Jake M. , Ponciano José M.
Published: February 2015

Significance

We show that the variation of plant and animal populations through time can provide basic insights into how populations interact with their environment, even when environmental covariates are unobserved. We contrasted the effects of two types of temporal variation on population dynamics showing that fluctuations in the strength of competition among individuals can change a well-known scaling relation between the population variance and population abundances. The scaling of the population variance is explored using a large database of time series, as well as two well-studied ungulate populations. Our results suggest that higher-order variance scaling may be present in many animal populations, both reducing the long-run population variance relative to the standard model and providing important information on how populations are regulated by their environment.
Parameter-free methods distinguish Wnt pathway models and guide design of experiments
Authors: MacLean Adam L. , Rosen Zvi , Byrne Helen M. , Harrington Heather A.
Published: February 2015

Significance

The canonical Wnt/β-catenin signaling pathway is important for essential cellular functions and is implicated in many diseases. We introduce a new mathematical model that focuses on β-catenin degradation and protein shuttling between cellular compartments. We compare our model to others and show that all fit to time-dependent experimental data. To evade this parameter problem, we use algebraic methods and characterize model features that are independent of the choice of parameter values. We find that multiple responses to Wnt are feasible under certain conditions for the new model, but not for the others; moreover, we provide dependencies between species (variables) that inform future experiments and model discrimination. We also highlight the wide applicability of these tools across problems in systems biology.
Focus on the success of others leads to selfish behavior
Authors: van den Berg Pieter , Molleman Lucas , Weissing Franz J.
Published: February 2015

Significance

We report on a two-step decision-making experiment. The first part shows that humans differ consistently in the way they learn from others. Some individuals are success-based learners, who try to identify successful peers and mimic their behavior. Others are frequency-based learners, who tend to adopt the most frequent behavior in their group. The second part reveals that these differences in social learning have important consequences for the outcome of social interactions. In situations where participants had to choose between a selfish option and an option benefitting their group, groups of frequency-based learners achieved considerably higher levels of cooperation than groups of success-based learners. This is the first clear experimental evidence that learning strategies are an important determinant of social behavior.
Hunger promotes acquisition of nonfood objects
Authors: Xu Alison Jing , Schwarz Norbert , Wyer Robert S.
Published: February 2015

Significance

Hunger is assumed to motivate eating, which satisfies the caloric needs underlying the motivation. However, hunger’s influence extends beyond food consumption to the acquisition of nonfood items that cannot satisfy the underlying need (e.g., binder clips), suggesting that domain-specific motives can influence behavior in unrelated domains that are irrelevant to the motive. This is likely to occur when the domain-specific response includes concepts and behaviors that can also guide decisions in other domains.
Discovery of multiple hidden allosteric sites by combining Markov state models and experiments
Authors: Bowman Gregory R. , Bolin Eric R. , Hart Kathryn M. , Maguire Brendan C. , Marqusee Susan
Published: February 2015

Significance

Rational drug design efforts typically focus on identifying inhibitors that bind to protein active sites. Pockets that are not present in crystallographic structures yet can exert allosteric (i.e., long-range) control over distant active sites present an exciting alternative. However, identifying these hidden allosteric sites is extremely challenging because one usually has to simultaneously find a small molecule that binds to and stabilizes the open conformation of the pocket. Here, we present a means of combining advances in computer modeling—using Markov state models to capture long timescale dynamics—with biophysical experiments to identify hidden allosteric sites without requiring the simultaneous discovery of drug-like compounds that bind them. Using this technology, we discover multiple hidden allosteric sites in a single protein.
Allosteric and hyperekplexic mutant phenotypes investigated on an α
1
glycine receptor transmembrane structure
Authors: Moraga-Cid Gustavo , Sauguet Ludovic , Huon Christèle , Malherbe Laurie , Girard-Blanc Christine , Petres Stéphane , Murail Samuel , Taly Antoine , Baaden Marc , Delarue Marc , Corringer Pierre-Jean
Published: February 2015

Significance

Pentameric ligand-gated ion channels (pLGICs) mediate neuronal communication in the central nervous system. Upon the neurotransmitter binding, these receptors undergo a rapid conformational change to open an integral ion channel. Mutations impairing the function of pLGICs are known to cause hyperekplexic, myasthenic, and epileptic syndromes. Here, we studied how the local perturbations caused by single mutations result in an alteration of the protein function. Using a chimeric protein assembled by the transmembrane domain of the human glycine receptors fused to the extracellular domain of the bacterial pLGIC GLIC, we performed functional experiments in parallel with X-ray crystallography. On this basis, we propose a molecular mechanism for channel opening that accounts for the phenotypes of several mutants causing hyperekplexia.
Conductance enlargement in picoscale electroburnt graphene nanojunctions
Authors: Sadeghi Hatef , Mol Jan A. , Lau Chit Siong , Briggs G. Andrew D. , Warner Jamie , Lambert Colin J.
Published: February 2015

Significance

Continuation of Moore’s law to the sub–10-nm scale requires the development of new technologies for creating electrode nanogaps, in architectures which allow a third electrostatic gate. Electroburnt graphene junctions (EGNs) have the potential to fulfill this need, provided their properties at the moment of gap formation can be understood and controlled. In contrast with mechanically controlled break junctions, whose conductance decreases monotonically as the junction approaches rupture, we show that EGNs exhibit a surprising conductance enlargement just before breaking, which signals the formation of a picoscale current path formed from a single sp
2
bond. Just as Schottky barriers are a common feature of semiconductor interfaces, conductance enlargement is a common property of EGNs and will be unavoidably encountered by all research groups working on the development of this new technology.
Interplay among nucleosomal DNA, histone tails, and corepressor CoREST underlies LSD1-mediated H3 demethylation
Authors: Pilotto Simona , Speranzini Valentina , Tortorici Marcello , Durand Dominique , Fish Alexander , Valente Sergio , Forneris Federico , Mai Antonello , Sixma Titia K. , Vachette Patrice , Mattevi Andrea
Published: February 2015

Significance

The correct and regulated readout of epigenetic marks on chromatin is essential to modulate gene expression in living cells. The regulation of chromatin accessibility is ensured by such epigenetic tags, which form a platform for the binding of specific enzymatic modules. A clear example of this mechanism is represented by the histone demethylase LSD1-CoREST, which removes methylation marks from lysine 4 of histone protein H3. We developed a crosslinking technology to capture this histone demethylase in contact with the nucleosome and used this methodology to explore the structural and biophysical properties of this complex. This is one of the very few successful attempts to visualize the molecular mechanism underlying the recognition of the nucleosomal substrate by a histone-modifying enzyme complex.
Essential functions of primate frontopolar cortex in cognition
Authors: Boschin Erica A. , Piekema Carinne , Buckley Mark J.
Published: February 2015

Significance

The frontopolar cortex (FPC) is a large region occupying the anterior portion of the brain’s frontal lobe, and has been suggested to play a role in complex, higher order behavior. However, the specific contributions of this area toward this type of behavior are still unclear. Using an animal model, we show that localized lesions to the FPC of nonhuman primates selectively impair the ability of the animal to learn rapidly about novel objects and rules, although sparing its ability to draw upon previously established knowledge about objects and rules. These findings suggest that the FPC makes a crucial contribution to the exploration and rapid acquisition of novel behavioral options, which is, in turn, an essential aspect of complex, higher order behavior.
Multimodular biosensors reveal a novel platform for activation of G proteins by growth factor receptors
Authors: Midde Krishna K. , Aznar Nicolas , Laederich Melanie B. , Ma Gary S. , Kunkel Maya T. , Newton Alexandra C. , Ghosh Pradipta
Published: February 2015

Significance

Long-held tenets in the field of signal transduction are that G proteins are activated exclusively by G protein-coupled receptors and that growth factor receptor tyrosine kinases (RTKs) do not have the wherewithal to do the same. In this work we created fluorescent biosensors derived from the multimodular signal transducer Gα-interacting vesicle-associated protein (GIV), an unusual protein that binds RTKs and activates G proteins, and used them in FRET and bimolecular fluorescent complementation assays to visualize RTK–GIV–G protein signaling complexes directly in single living cells. These studies not only provide evidence that GIV serves as a platform for transactivation of G proteins by growth factor RTKs but also illuminate the spatial and temporal dynamics of such noncanonical G protein signaling.