bluuebunny/crossref_metadata_2025 huggingface dataset:
High-resolution and high-sensitivity phase-contrast imaging by focused hard x-ray ptychography with a spatial filter
Authors: Takahashi Yukio , Suzuki Akihiro , Furutaku Shin , Yamauchi Kazuto , Kohmura Yoshiki , Ishikawa Tetsuya
Published: March 2013

We demonstrate high-resolution and high-sensitivity x-ray phase-contrast imaging of a weakly scattering extended object by scanning coherent diffractive imaging, i.e., ptychography, using a focused x-ray beam with a spatial filter. We develop the x-ray illumination optics installed with the spatial filter to collect coherent diffraction patterns with a high signal-to-noise ratio. We quantitatively visualize the object with a slight phase shift (∼λ/320) at spatial resolution better than 17 nm in a field of view larger than ∼2×2μm2. The present coherent method has a marked potential for high-resolution and wide-field-of-view observation of weakly scattering objects such as biological soft tissues.
Formation process of perovskite-type hydride LiNiH3: In situ synchrotron radiation X-ray diffraction study
Authors: Sato Ryutaro , Saitoh Hiroyuki , Endo Naruki , Takagi Shigeyuki , Matsuo Motoaki , Aoki Katsutoshi , Orimo Shin-ichi
Published: March 2013

The formation process of perovskite-type hydride LiNiH3 was investigated using in situ synchrotron X-ray diffraction measurements. A mixture of LiH and Ni was hydrogenated at 873 K and 3 GPa, and the structural changes associated with hydrogenation were observed. Time-resolved diffraction profiles showed a three-step reaction: hydrogenation of Ni to NiHx, formation of LiyNi1–yH solid solution, and conversion to perovskite-type hydride LiNiH3. The solid solution, which has never been reported, plays the role of the precursor in the perovskite formation and its presence is apparently critical for synthesizing perovskite-type hydrides.
Terahertz emission and detection both based on high-Tc superconductors: Towards an integrated receiver
Authors: An D. Y. , Yuan J. , Kinev N. , Li M. Y. , Huang Y. , Ji M. , Zhang H. , Sun Z. L. , Kang L. , Jin B. B. , Chen J. , Li J. , Gross B. , Ishii A. , Hirata K. , Hatano T. , Koshelets V. P. , Koelle D. , Kleiner R. , Wang H. B. , Xu W. W. , Wu P. H.
Published: March 2013

We have combined a stand-alone Bi2Sr2CaCu2O8 intrinsic Josephson junction stack, emitting terahertz radiation, with a YBa2Cu3O7 grain boundary Josephson junction acting as detector. The detector is mounted on a lens, positioned 1.2 cm away from the emitter on a similar lens. With the emitter radiating at 0.5 THz, we observed up to 7 Shapiro steps on the current-voltage characteristic of the detector. The ac current induced in this junction was 0.9 mA, and the dissipated power was 1.8 μW. The setup, although far from being optimized, may be considered as a first step towards an integrated high-Tc receiver.
Predominant growth of non-polar a-plane (Al,Ga)N on patterned c-plane sapphire by hydride vapor phase epitaxy
Authors: Mogilatenko A. , Hagedorn S. , Richter E. , Zeimer U. , Goran D. , Weyers M. , Tränkle G.
Published: March 2013

We report for the first time on predominant growth of non-polar a-plane (Al,Ga)N layers on patterned c-plane AlN/sapphire templates with ridges oriented along the [11¯00]Al2O3 direction. The layers were grown by hydride vapor phase epitaxy. During the first stages of the growth (Al,Ga)N nucleates simultaneously on top of the ridges, inside the trenches and on the trench sidewalls. As a result, two different (Al,Ga)N orientations are formed with respect to the horizontal growth front: c-plane (Al,Ga)N on the c-plane ridges as well as inside the trenches and a-plane (Al,Ga)N on the trench sidewalls. The growth rate of a-plane (Al,Ga)N exceeds that of c-plane regions, which leads to the complete overgrowth of c-plane (Al,Ga)N by the a-plane oriented material.
Improved Ohmic contacts to plasma etched n-Al0.5Ga0.5N by annealing under nitrogen ambient before metal deposition
Authors: Zhang Wei , Zhang Jianbao , Wu Zhihao , Chen Shengchang , Li Yang , Tian Yu , Dai Jiangnan , Chen Changqing , Fang Yanyan
Published: March 2013

The contact characteristics of Ti/Al and Ti/Al/Ni/Au contacts to as-grown, plasma etched and plasma etched + annealed in N2 n-Al0.5Ga0.5N epilayers were compared. After a rapid thermal annealing, both Ti/Al and Ti/Al/Ni/Au contacts to as-grown and plasma etched + annealed in N2 n-Al0.5Ga0.5N became truly Ohmic, whereas the contacts to plasma etched samples still remained rectifying. Surface atomic concentration analysis indicates the N vacancies resulting from plasma treatment act more as deep-level states rather than shallow donors. However, these deep-level states could be effectively removed by annealing the plasma etched n-Al0.5Ga0.5N under N2 ambient, and as a result, the Fermi level was elevated toward conduction band edge, facilitating the formation of Ohmic contacts.
Effect of Mn substitution on the magnetic and magneto-transport properties of Fe3−xMnxSi (0 ≤ x ≤ 1.25) alloys
Authors: Pal Lakhan , Suresh K. G. , Nigam A. K.
Published: March 2013

Effect of partial Mn substitution for Fe in Fe3Si on the structural, magnetic, transport, and magnetotransport properties has been studied. Mn substitution is found to induce a re-entrant antiferromagnetic phase at low temperatures. The increase in the antiferromagnetic exchange causes a gradual decrease in the Curie temperature and the saturation magnetization. Temperature dependence of the electrical resistivity data shows that the high temperature resistivity is dominated by electron-phonon scattering, while below the re-entry temperature (TR), electron-magnon scattering is dominant. These results are in agreement with the reported spin polarization studies and indicate that the reentrant behavior is detrimental to half metallicity. Application of a field causes negative magnetoresistance (MR) above TR. However, at 5 K, the magnetoresistance is found to be positive, with the magnitude increasing with x. For x > 0.8, field induced irreversibility has been found in MR vs. field isotherms at 5 K, which indicates that the re-entrant phase has competing magnetic interactions. Canted magnetic structure known to exist in this system is assumed to be responsible for this anomalous behaviour.
Simulation and modeling of the electronic structure of GaAs damage clusters
Authors: Moussa Jonathan E. , Foiles Stephen M. , Schultz Peter A.
Published: March 2013

In an effort to build a stronger microscopic foundation for radiation damage models in gallium arsenide (GaAs), the electronic properties of radiation-induced damage clusters are studied with atomistic simulations. Molecular dynamics simulations are used to access the time and length scales required for direct simulation of a collision cascade, and density functional theory simulations are used to calculate the electronic properties of isolated damaged clusters that are extracted from these cascades. To study the physical properties of clusters, we analyze the statistics of a randomly generated ensemble of damage clusters because no single cluster adequately represents this class of defects. The electronic properties of damage clusters are accurately described by a classical model of the electrical charging of a semiconducting sphere embedded in a uniform dielectric. The effective band gap of the cluster depends on the degree of internal structural damage, and the gap closes to form a metal in the high-damage limit. We estimate the Fermi level of this metallic state, which corresponds to high-energy amorphous GaAs, to be 0.46±0.07 eV above the valence band edge of crystalline GaAs.
Experimental investigation of the ribbon-array ablation process
Authors: Li Zhenghong , Xu Rongkun , Chu Yanyun , Yang Jianlun , Xu Zeping , Ding Ning , Ye Fan , Chen Faxin , Xue Feibiao , Ning Jiamin , Qin Yi , Meng Shijian , Hu Qingyuan , Si Fenni , Feng Jinghua , Zhang Faqiang , Chen Jinchuan , Li Linbo , Chen Dingyang , Zhou Xiuwen
Published: March 2013

Ablation processes of ribbon-array loads, as well as wire-array loads for comparison, were investigated on Qiangguang-1 accelerator. The ultraviolet framing images indicate that the ribbon-array loads have stable passages of currents, which produce axially uniform ablated plasma. The end-on x-ray framing camera observed the azimuthally modulated distribution of the early ablated ribbon-array plasma and the shrink process of the x-ray radiation region. Magnetic probes measured the total and precursor currents of ribbon-array and wire-array loads, and there exists no evident difference between the precursor currents of the two types of loads. The proportion of the precursor current to the total current is 15% to 20%, and the start time of the precursor current is about 25 ns later than that of the total current. The melting time of the load material is about 16 ns, when the inward drift velocity of the ablated plasma is taken to be 1.5 × 107 cm/s.
Sublattice magnetizations of ultrathin alloy [Co1−cGdc]n nanojunctions between Co leads using the combined effective field theory and mean field theory methods
Authors: Abou Ghantous M. , Khater A. , Ashokan V. , Ghader D.
Published: March 2013

The cobalt and gadolinium sublattice magnetizations of ultrathin cobalt-gadolinium alloy nanojunctions [Co1−cGdc]n between Co leads are investigated using the effective field theory (EFT) and mean field theory (MFT) methods. The n hcp atomic layers at homogeneous concentrations c are considered to model structurally the alloy nanojunction. In particular, the Ising EFT serves to determine the appropriate exchange constants for Co and Gd, characterized by their fundamental spins, by calculating their single-site spin correlations, magnetizations, and Curie temperatures, in good agreement with experimental data in the ordered phase. The EFT results seed the MFT calculations for the nanojunction from the interface inwards. The combined EFT and MFT analysis yields the sublattice magnetizations for the Co and Gd sites, and compensation effects, on the individual layers of the nanojunctions, as a function of concentration, temperature, and nanojunction thickness. We observe that these magnetic variables are different for the first few layers near the nanojunction interfaces but tend to limiting solutions in the core layers. The exchange constants and sublattice magnetizations calculated by this combined approach and referenced to the fundamental Co and Gd spins, are necessary elements for the self-consistent analysis of the spin dynamics of the system and the quantum transport of lead magnons across the nanojunctions.
Time resolved gain and excess noise properties of InGaAs/InAlAs avalanche photodiodes with cascaded discrete gain layer multiplication regions
Authors: Williams George M. , Ramirez David A. , Hayat Majeed M. , Huntington Andrew S.
Published: March 2013

To predict pulse detection performance when implemented in high speed photoreceivers, temporally resolved measurements of a 10-stage InAlAs/InGaAs single carrier multiplication (SCM) avalanche photodiode (APD)'s avalanche response to short multi-photon laser pulses were explained using instantaneous (time resolved) pulse height statistics of the device's impulse response. Numeric models of the junction carrier populations as a function of the time following injection of a primary photo-electron were used to create the probability density functions (pdfs) of the instances of the avalanche buildup process. The numeric pdfs were used to generate low frequency gain and excess noise models, which were in good agreement with analytic models of multiple discrete low-gain-stage APDs and with measured excess noise data. The numeric models were then used to generate the instantaneous and cumulative instantaneous low order statistics of the instances of the impulse response. It is shown that during the early times of the impulse response, the SCM APDs have lower excess noise than the pseudo-DC measurements and the common APD models used to describe them. The methods of determining the time resolved low order statistics of APDs are described and the importance of using time-resolved models of APD gain and noise is discussed.
Model for the J-V characteristics of degraded polymer solar cells
Authors: Kumar Pankaj , Gaur Ankita
Published: March 2013

An equivalent circuit model was developed for polymer solar cells (PSCs), which explains correctly their behavior under different test conditions. We examine here the validity of that model for degraded PSCs. For that purpose, investigations were carried out on solar cells based on the interpenetrating bulk heterojunctions of poly(3-hehylthiophene) and phenyl[6,6] C61 butyric acid methyl ester. Current density-voltage (J-V) characteristics were measured in dark and under illumination at different time intervals. The characteristics of fresh solar cells are explained well by the developed model, with exponential dependence of photocurrent on applied voltage. However, the degraded characteristics showed space charge limited conduction and the characteristics could be explained well by the same model but with different voltage dependence of photocurrent.
High-quality formation of multiply stacked SiGe-on-insulator structures by temperature-modulated successive rapid-melting-growth
Authors: Tojo Yuki , Matsumura Ryo , Yokoyama Hiroyuki , Kurosawa Masashi , Toko Kaoru , Sadoh Taizoh , Miyao Masanobu
Published: March 2013

Laterally and vertically modulated SiGe-on-insulator (SGOI) structures are essential to integrate functional device-arrays with various energy-band-gaps and/or lattice-constants. We develop the temperature-modulated successive rapid-melting-growth (RMG) method, where Si-concentration dependent RMG processing is combined with non-destructive crystallinity-analysis. First, SGOI is formed by segregation-controlled RMG of SiGe by using Si-substrate as crystalline-seed. Polarized-Raman-scattering measurements non-destructively reveal the lateral-epitaxial-growth of SGOI with graded SiGe-concentration profiles. Second, Ge-on-insulator (GOI) is stacked on SGOI by using SGOI as crystalline-seed, where RMG temperature is selected between the melting-points of Ge and underlying SGOI. This achieves defect-free, multiply-stacked GOI on graded-SGOI structure, which demonstrates 3-dimensionally modulated SiGe-concentration profiles on Si-platform.
Fully balanced heat interferometer
Authors: Martínez-Pérez M. J. , Giazotto F.
Published: March 2013

A tunable and balanced heat interferometer is proposed and analyzed. The device consists of two superconductors linked together to form a double-loop interrupted by three parallel-coupled Josephson junctions. Both superconductors are held at different temperatures, allowing the heat currents flowing through the structure to interfere. We demonstrate that thermal transport is coherently modulated through the application of a magnetic flux. Furthermore, such modulation can be tailored at will or even suppressed through the application of an extra control flux. Such a device allows for a versatile operation appearing as an attractive key to the onset of low-temperature coherent caloritronic circuits.
Terahertz-field-driven sub-picosecond optical switching enabled by large third-order optical nonlinearity in a one-dimensional Mott insulator
Authors: Yada Hiroyuki , Miyamoto Tatsuya , Okamoto Hiroshi
Published: March 2013

Sub-picosecond modulation of the optical reflectivity (R) using terahertz electric-field (ETHz) pulses was achieved in a typical one-dimensional Mott insulator, the bromine-bridged nickel compound, [Ni(chxn)2Br]Br2 (chxn: cyclohexanediamine). The reflectivity change (ΔR/R) at around the Mott-gap transition peak (∼1.3 eV) was ∼1% for ETHz ∼45 kV/cm, and proportional to the square of ETHz. The relaxation time of ΔR/R was under 0.1 ps, enabling optical switching with a high repetition rate in the near-infrared region. The electric-field and probe-energy dependences of ΔR/R demonstrate that the modulation is due to large third-order optical nonlinearity of one-dimensional Mott insulators.
Direct imaging of radiative decay of surface plasmon polaritons in nanohole arrays by cross-polarization microscopy
Authors: Cao Z. L. , Ong H. C.
Published: March 2013

We employ angle- and polarization-resolved optical microscope to image the radiative decay patterns of surface plasmon polaritons (SPPs) in Au nanohole array. By controlling the incident angle, we excite desired SPP mode and image its radiative decay under cross-polarization configuration. The experimental results are supported by temporal coupled mode theory and confirmed by finite-difference time-domain simulations and analytical calculations. Our approach is effective in studying the decay process of any particular SPP mode in periodic structures and thus is useful in understanding SPP mediated Raman scattering and fluorescence.
Rapid formation of Cu/Cu3Sn/Cu joints using ultrasonic bonding process at ambient temperature
Authors: Li Mingyu , Li Zhuolin , Xiao Yong , Wang Chunqing
Published: March 2013

Wafer bonding using Sn interlayer and silicon bond components with Ti/Ni/Cu metallization was achieved by ultrasonic bonding at ambient temperature for 4 s under 0.6 MPa. High-melting-point joint which fully consisted of Cu3Sn intermetallic compounds was formed with a high shear strength of 65.8 MPa and a low electrical resistivity of 67.3 μΩ · cm. Experimental results showed that ultrasonic vibration induced steep temperature rise at rubbing interface, melting solid solder, and sequent ultrasonic effects at the liquid Sn/solid Cu interface dominated the mechanism and kinetics of rapid formation of Cu3Sn joint.
Transient thermoreflectance from graphene composites with matrix of indium and copper
Authors: Zheng H. , Jagannadham K.
Published: March 2013

Transient thermoreflectance was measured from In and In-graphene composite films pressed on to different substrates that include Si, GaAs, Cu and Cu-graphene composite. Measurements were also made from Al film deposited on substrates of Cu and Cu-graphene composite. The experimental results were modeled using solution to the thermal diffusion equation to determine the thermal conductivity of the phases and thermal conductance of the interface. The In-graphene and Cu-graphene composites are found to spread the heat more rapidly than In and Cu, respectively. The interface thermal conductance of In or In-graphene film pressed on to Cu was found to be smaller than the observed values for metal-metal contacts reported in the literature although higher than the value observed for the interface between Pb-Sn eutectic solder alloy bonded to Cu. The interface thermal conductance between Al film deposited on mechanically polished Cu or Cu-graphene composite is also found to be much lower than the value observed previously. The smaller value of interface thermal conductance of either In or In-gr or Al film on different substrates is explained by absence of atomic level bonding, presence of rough surfaces with incomplete contact and oxygen or water vapor at the interface.
Titanium catalyzed silicon nanowires and nanoplatelets
Authors: Usman Mohammad A. U. , Smith Brady J. , Jackson Justin B. , De Long Matthew C. , Miller Mark S.
Published: March 2013

Silicon nanowires, nanoplatelets, and other morphologies resulted from silicon growth catalyzed by thin titanium layers. The nanowires have diameters down to 5 nm and lengths to tens of micrometers. The two-dimensional platelets, in some instances with filigreed, snow flake-like shapes, had thicknesses down to the 10 nm scale and spans to several micrometers. These platelets grew in a narrow temperature range around 900 celsius, apparently representing a new silicon crystallite morphology at this length scale. We surmise that the platelets grow with a faceted dendritic mechanism known for larger crystals nucleated by titanium silicide catalyst islands.
Characterisation and optimisation of PECVD SiNx as an antireflection coating and passivation layer for silicon solar cells
Authors: Wan Yimao , McIntosh Keith R. , Thomson Andrew F.
Published: March 2013

In this work, we investigate how the film properties of silicon nitride (SiNx) depend on its deposition conditions when formed by plasma enhanced chemical vapour deposition (PECVD). The examination is conducted with a Roth & Rau AK400 PECVD reactor, where the varied parameters are deposition temperature, pressure, gas flow ratio, total gas flow, microwave plasma power and radio-frequency bias voltage. The films are evaluated by Fourier transform infrared spectroscopy to determine structural properties, by spectrophotometry to determine optical properties, and by capacitance–voltage and photoconductance measurements to determine electronic properties. After reporting on the dependence of SiNx properties on deposition parameters, we determine the optimized deposition conditions that attain low absorption and low recombination. On the basis of SiNx growth models proposed in the literature and of our experimental results, we discuss how each process parameter affects the deposition rate and chemical bond density. We then focus on the effective surface recombination velocity Seff, which is of primary importance to solar cells. We find that for the SiNx prepared in this work, 1) Seff does not correlate universally with the bulk structural and optical properties such as chemical bond densities and refractive index, and 2) Seff depends primarily on the defect density at the SiNx-Si interface rather than the insulator charge. Finally, employing the optimized deposition condition, we achieve a relatively constant and low Seff,UL on low-resistivity (≤1.1 Ωcm) p- and n-type c-Si substrates over a broad range of n = 1.85–4.07. The results of this study demonstrate that the trade-off between optical transmission and surface passivation can be circumvented. Although we focus on photovoltaic applications, this study may be useful for any device for which it is desirable to maximize light transmission and surface passivation.
Seminal characteristics, sperm fatty acids, and blood biochemical attributes in breeder roosters orally administered with sage (Salvia officinalis) extract
Authors: Ommati M. M. , Zamiri M. J. , Akhlaghi A. , Atashi H. , Jafarzadeh M. R. , Rezvani M. R. , Saemi F.
Published: March 2013

Seminal characteristics and blood biochemical attributes were studied in breeder roosters orally administered with sage extract (SG), an herbal extract well known to have potent antioxidant activities. Sixty roosters (34 weeks old) were randomly allotted to five treatment groups to receive no SG, or orally administered with 110, 210, 320, or 420 mg SG/kg liveweight for 8 weeks. Semen samples were evaluated weekly. Blood samples were taken fortnightly and a total of 21 biochemical indices were measured to unmask the effects of SG (especially the adverse ones) on the clinical profile. Excluding the sperm concentration and seminal content of thiobarbituric acid reactive substances (sperm membrane lipid peroxidation index), other seminal traits exhibited one of the linear, quadratic, or cubic responses to the various levels of SG. The most improvements in total live sperm number and sperm membrane integrity (as determined by the hypoosmotic swelling test) were observed in birds receiving 210 and 320 mg SG/kg liveweight, respectively. Serum testosterone level was generally higher (cubically, P = 0.015), but serum copper was lower (linearly, P = 0.014) in SG-administered birds. Birds receiving 320 and 420 mg SG showed a decreased content of C18 : 2(n-6) in sperm plasma membrane. Other biochemical attributes or sperm fatty acids were not affected. It seems that most improvement in the seminal characteristics could be achieved 5–6 weeks following the administration of 210 and 320 mg SG/kg liveweight without any apparent adverse effect on the blood biochemical indices. The improvements, however, could not be attributed to the antioxidative effect of SG. Although it is hypothesised that an increased serum testosterone might have been involved, the underlying mechanism(s) remain(s) to be clarified.
Identification of QTLs involved in pod-shatter resistance in Brassica napus L.
Authors: Wen Y. C. , Zhang S. F. , Yi B. , Wen J. , Wang J. P. , Zhu J. C. , He J. P. , Cao J. H.
Published: March 2013

Seed loss caused by pod-shatter during harvesting is one of the main problems in rapeseed production worldwide. Quantitative trait loci (QTLs) for pod-shatter based on genetic mapping would help breeders develop cultivars resistant to pod-shatter. In this study, we constructed a genetic map of Brassica napus containing 107 simple sequence repeat (SSR) markers and 68 sequence-related amplified polymorphism (SRAP) markers using a doubled-haploid (DH) population of 276 lines derived from the cross H155 × Qva. This map covered 1382.8 cM with an average marker interval of 7.9 cM. In total, 13 QTLs for pod-shatter resistance were identified in this DH population at two experimental sites (in Wuhan and Zhengzhou); three of the QTLs were present at both locations. At Zhengzhou, nine QTLs, identified in linkage groups A1, A7, A8, C5, and C8, together explained 49.0% of the phenotypic variation. At Wuhan, four QTLs were mapped on the A1, A4, A7, and C8 linkage groups. These QTLs explained 38.6% of the phenotypic variation. These results may serve as a valuable basis for further molecular dissection of pod-shatter resistance in B. napus, and for development of the markers related to QTLs that may be useful for marker-assisted selection of pod-shatter resistant cultivars.
Improved stomatal regulation and ion partitioning boosts salt tolerance in grafted melon
Authors: Orsini Francesco , Sanoubar Rabab , Oztekin Golgen Bahar , Kappel Noemi , Tepecik Mahmut , Quacquarelli Cristina , Tuzel Yuksel , Bona Stefano , Gianquinto Giorgio
Published: March 2013

Grafted plants are often more tolerant to salinity than nongrafted controls. In order to distinguish differential response components in grafted melon (Cucumis melo L.), salt stress was imposed on several rootstock–scion combinations in four experiments. The rootstock used was an interspecific squash (Cucurbita maxima Duch. × Cucurbita moschate Duch.), RS841, combined with two cantaloupe (C. melo var. cantalupensis) cultivars, namely London and Brennus, against both self-grafted and nongrafted controls. Physiological, morphological and biochemical adaptations to 0, 40 and 80 mM NaCl were monitored. Upon salinity, plant biomass and leaf area were improved by grafting per se, since self-grafted plants performed similarly to the heterografted ones. However, improvements in the exclusion of Na+ and the uptake of K+ were due only to the rootstock genotype, since ionic composition was similar in self-grafted and nongrafted plants. These results indicate that the favourable effects of grafting on plant growth cannot be ascribed to a more efficient exclusion of Na+ or enhanced nutrient uptake. On the other hand, growth improvements in both self- and heterografted plants were associated with a more efficient control of stomatal functions (changes in stomatal index and water relations), which may indicate that the grafting incision may alter hormonal signalling between roots and shoots.
Effect of hCG administration during corpus luteum establishment on subsequent corpus luteum development and circulating progesterone concentrations in beef heifers
Authors: Maillo V. , Duffy P. , O'Hara L. , de Frutos C. , Kelly A. K. , Lonergan P. , Rizos D.
Published: March 2013

This study examined the effect of a single administration of human chorionic gonadotrophin (hCG) on Day 1 to 4 after oestrus on corpus luteum (CL) development and circulating progesterone (P4). Oestrus-synchronized heifers (n = 43) were administered a single intramuscular injection of saline on Day 1 (control) or 3000 IU hCG on Day 1, 2, 3 or 4 after oestrus. Administration of hCG on Day 1 had no effect on CL area, on Day 2 increased CL area from Day 6 to 12 (P < 0.05), on Day 3 increased CL area from Day 9 to 11, while on Day 4 increased CL size on Days 9 and 10 (P < 0.05). Administration of hCG on Day 4 induced the formation of an accessory CL in 89% of heifers, resulting in a significant increase in total luteal tissue area on the ovaries compared with all other groups. Consistent with the effects on the CL, hCG on Day 1 did not affect P4 concentrations, on Day 2 significantly increased P4 compared with the control from Day 6 to 11 (P < 0.05), on Day 3 resulted in a non-significant increase in P4 while hCG on Day 4 increased P4 from Day 8 to 13 compared with the control (P < 0.05). In conclusion, administration of hCG as early as Day 2 after oestrus results in increased P4 in circulation from Day 6, which should have beneficial downstream effects in terms of uterine receptivity and conceptus elongation.
Role for compartmentalization in nephron progenitor differentiation
Authors: Brown Aaron C. , Muthukrishnan Sree Deepthi , Guay Justin A. , Adams Derek C. , Schafer Dillon A. , Fetting Jennifer L. , Oxburgh Leif
Published: March 2013

Embryonic nephron progenitor cells are segregated in molecularly distinct compartments of unknown function. Our study reveals an integral role for bone morphogenetic protein-SMAD in promoting transition of progenitors from the primitive Cbp/p300-interacting transactivator 1 expressing (CITED1+) compartment to the uniquely sine oculis-related homeobox 2 expressing (SIX2-only) compartment where they become inducible by wingless-type mouse mammary tumor virus integration site family member (WNT)/β-catenin signaling. Significantly, CITED1
+
cells are refractory to WNT/β-catenin induction. We propose a model in which the primitive CITED1
+
compartment is refractory to induction by WNT9b/β-catenin, ensuring maintenance of undifferentiated progenitor cells for future nephrogenesis. Bone morphogenetic protein 7-SMAD is then required for transition to a distinct compartment in which cells become inducible by WNT9b/β-catenin, allowing them to progress toward epithelialization.
From mechanical folding trajectories to intrinsic energy landscapes of biopolymers
Authors: Hinczewski Michael , Gebhardt J. Christof M. , Rief Matthias , Thirumalai D.
Published: March 2013

In single-molecule laser optical tweezer (LOT) pulling experiments, a protein or RNA is juxtaposed between DNA handles that are attached to beads in optical traps. The LOT generates folding trajectories under force in terms of time-dependent changes in the distance between the beads. How to construct the full intrinsic folding landscape (without the handles and beads) from the measured time series is a major unsolved problem. By using rigorous theoretical methods—which account for fluctuations of the DNA handles, rotation of the optical beads, variations in applied tension due to finite trap stiffness, as well as environmental noise and limited bandwidth of the apparatus—we provide a tractable method to derive intrinsic free-energy profiles. We validate the method by showing that the exactly calculable intrinsic free-energy profile for a generalized Rouse model, which mimics the two-state behavior in nucleic acid hairpins, can be accurately extracted from simulated time series in a LOT setup regardless of the stiffness of the handles. We next apply the approach to trajectories from coarse-grained LOT molecular simulations of a coiled-coil protein based on the GCN4 leucine zipper and obtain a free-energy landscape that is in quantitative agreement with simulations performed without the beads and handles. Finally, we extract the intrinsic free-energy landscape from experimental LOT measurements for the leucine zipper.
New Trans-Arctic shipping routes navigable by midcentury
Authors: Smith Laurence C. , Stephenson Scott R.
Published: March 2013

Recent historic observed lows in Arctic sea ice extent, together with climate model projections of additional ice reductions in the future, have fueled speculations of potential new trans-Arctic shipping routes linking the Atlantic and Pacific Oceans. However, numerical studies of how projected geophysical changes in sea ice will realistically impact ship navigation are lacking. To address this deficiency, we analyze seven climate model projections of sea ice properties, assuming two different climate change scenarios [representative concentration pathways (RCPs) 4.5 and 8.5] and two vessel classes, to assess future changes in peak season (September) Arctic shipping potential. By midcentury, changing sea ice conditions enable expanded September navigability for common open-water ships crossing the Arctic along the Northern Sea Route over the Russian Federation, robust new routes for moderately ice-strengthened (Polar Class 6) ships over the North Pole, and new routes through the Northwest Passage for both vessel classes. Although numerous other nonclimatic factors also limit Arctic shipping potential, these findings have important economic, strategic, environmental, and governance implications for the region.
Mouse alarm pheromone shares structural similarity with predator scents
Authors: Brechbühl Julien , Moine Fabian , Klaey Magali , Nenniger-Tosato Monique , Hurni Nicolas , Sporkert Frank , Giroud Christian , Broillet Marie-Christine
Published: March 2013

Sensing the chemical warnings present in the environment is essential for species survival. In mammals, this form of danger communication occurs via the release of natural predator scents that can involuntarily warn the prey or by the production of alarm pheromones by the stressed prey alerting its conspecifics. Although we previously identified the olfactory Grueneberg ganglion as the sensory organ through which mammalian alarm pheromones signal a threatening situation, the chemical nature of these cues remains elusive. We here identify, through chemical analysis in combination with a series of physiological and behavioral tests, the chemical structure of a mouse alarm pheromone. To successfully recognize the volatile cues that signal danger, we based our selection on their activation of the mouse olfactory Grueneberg ganglion and the concomitant display of innate fear reactions. Interestingly, we found that the chemical structure of the identified mouse alarm pheromone has similar features as the sulfur-containing volatiles that are released by predating carnivores. Our findings thus not only reveal a chemical Leitmotiv that underlies signaling of fear, but also point to a double role for the olfactory Grueneberg ganglion in intraspecies as well as interspecies communication of danger.
Quantification of excess risk for diabetes for those born in times of hunger, in an entire population of a nation, across a century
Authors: Thurner Stefan , Klimek Peter , Szell Michael , Duftschmid Georg , Endel Gottfried , Kautzky-Willer Alexandra , Kasper David C.
Published: March 2013

Based on a unique dataset comprising all 325,000 Austrian patients that were under pharmaceutical treatment for diabetes during 2006 and 2007, we measured the excess risk of developing diabetes triggered by undernourishment in early life. We studied the percentage of all diabetes patients in the total population specifically for each year of birth, from 1917 to 2007. We found a massive excess risk of diabetes in people born during the times of the three major famines and immediately after, which occurred in Austria in the 20th century: 1918–1919, 1938, and 1946–1947. Depending on the region, there was an up to 40% higher chance of having diabetes when born in 1919–1921, compared with 1918 or 1922, where age-specific typical diabetes ratios are observed. The excess risk for diabetes was practically absent in those provinces of Austria that were less affected by the famines. We show that diabetes rates exhibit nontrivial, age-specific sex differences, and correlate with the economic wealth of the region. Our results might be of relevance for establishing higher awareness in the health system for those born in high-risk years, and underline the importance of ensuring sufficient nutrition in prenatal and early stages of life.
Identification of genetic variants influencing the human plasma proteome
Authors: Johansson Åsa , Enroth Stefan , Palmblad Magnus , Deelder André M. , Bergquist Jonas , Gyllensten Ulf
Published: March 2013

Genetic variants influencing the transcriptome have been extensively studied. However, the impact of the genetic factors on the human proteome is largely unexplored, mainly due to lack of suitable high-throughput methods. Here we present unique and comprehensive identification of genetic variants affecting the human plasma protein profile by combining high-throughput and high-resolution mass spectrometry (MS) with genome-wide SNP data. We identified and quantified the abundance of 1,056 tryptic-digested peptides, representing 163 proteins in the plasma of 1,060 individuals from two population-based cohorts. The abundance level of almost one-fifth (19%) of the peptides was found to be heritable, with heritability ranging from 0.08 to 0.43. The levels of 60 peptides from 25 proteins, 15% of the proteins studied, were influenced by
cis
-acting SNPs. We identified and replicated individual
cis
-acting SNPs (combined
P
value ranging from 3.1 × 10
−52
to 2.9 × 10
−12
) influencing 11 peptides from 5 individual proteins. These SNPs represent both regulatory SNPs and nonsynonymous changes defining well-studied disease alleles such as the ɛ4 allele of apolipoprotein E (APOE), which has been shown to increase risk of Alzheimer's disease. Our results show that high-throughput mass spectrometry represents a promising method for large-scale characterization of the human proteome, allowing for both quantification and sequencing of individual proteins. Abundance and peptide composition of a protein plays an important role in the etiology, diagnosis, and treatment of a number of diseases. A better understanding of the genetic impact on the plasma proteome is therefore important for evaluating potential biomarkers and therapeutic agents for common diseases.
Structure of the trypanosome cyanide-insensitive alternative oxidase
Authors: Shiba Tomoo , Kido Yasutoshi , Sakamoto Kimitoshi , Inaoka Daniel Ken , Tsuge Chiaki , Tatsumi Ryoko , Takahashi Gen , Balogun Emmanuel Oluwadare , Nara Takeshi , Aoki Takashi , Honma Teruki , Tanaka Akiko , Inoue Masayuki , Matsuoka Shigeru , Saimoto Hiroyuki , Moore Anthony L. , Harada Shigeharu , Kita Kiyoshi
Published: March 2013

In addition to haem copper oxidases, all higher plants, some algae, yeasts, molds, metazoans, and pathogenic microorganisms such as
Trypanosoma brucei
contain an additional terminal oxidase, the cyanide-insensitive alternative oxidase (AOX). AOX is a diiron carboxylate protein that catalyzes the four-electron reduction of dioxygen to water by ubiquinol. In
T. brucei,
a parasite that causes human African sleeping sickness, AOX plays a critical role in the survival of the parasite in its bloodstream form. Because AOX is absent from mammals, this protein represents a unique and promising therapeutic target. Despite its bioenergetic and medical importance, however, structural features of any AOX are yet to be elucidated. Here we report crystal structures of the trypanosomal alternative oxidase in the absence and presence of ascofuranone derivatives. All structures reveal that the oxidase is a homodimer with the nonhaem diiron carboxylate active site buried within a four-helix bundle. Unusually, the active site is ligated solely by four glutamate residues in its oxidized inhibitor-free state; however, inhibitor binding induces the ligation of a histidine residue. A highly conserved Tyr220 is within 4 Å of the active site and is critical for catalytic activity. All structures also reveal that there are two hydrophobic cavities per monomer. Both inhibitors bind to one cavity within 4 Å and 5 Å of the active site and Tyr220, respectively. A second cavity interacts with the inhibitor-binding cavity at the diiron center. We suggest that both cavities bind ubiquinol and along with Tyr220 are required for the catalytic cycle for O
2
reduction.
Groups of piecewise projective homeomorphisms
Authors: Monod Nicolas
Published: March 2013

The group of piecewise projective homeomorphisms of the line provides straightforward torsion-free counterexamples to the so-called von Neumann conjecture. The examples are so simple that many additional properties can be established.
Activation of the sympathetic nervous system mediates hypophagic and anxiety-like effects of CB
1
receptor blockade
Authors: Bellocchio Luigi , Soria-Gómez Edgar , Quarta Carmelo , Metna-Laurent Mathilde , Cardinal Pierre , Binder Elke , Cannich Astrid , Delamarre Anna , Häring Martin , Martín-Fontecha Mar , Vega David , Leste-Lasserre Thierry , Bartsch Dusan , Monory Krisztina , Lutz Beat , Chaouloff Francis , Pagotto Uberto , Guzman Manuel , Cota Daniela , Marsicano Giovanni
Published: March 2013

Complex interactions between periphery and the brain regulate food intake in mammals. Cannabinoid type-1 (CB
1
) receptor antagonists are potent hypophagic agents, but the sites where this acute action is exerted and the underlying mechanisms are not fully elucidated. To dissect the mechanisms underlying the hypophagic effect of CB
1
receptor blockade, we combined the acute injection of the CB
1
receptor antagonist rimonabant with the use of conditional
CB

1

-knockout mice, as well as with pharmacological modulation of different central and peripheral circuits. Fasting/refeeding experiments revealed that CB
1
receptor signaling in many specific brain neurons is dispensable for the acute hypophagic effects of rimonabant. CB
1
receptor antagonist-induced hypophagia was fully abolished by peripheral blockade of β-adrenergic transmission, suggesting that this effect is mediated by increased activity of the sympathetic nervous system. Consistently, we found that rimonabant increases gastrointestinal metabolism via increased peripheral β-adrenergic receptor signaling in peripheral organs, including the gastrointestinal tract. Blockade of both visceral afferents and glutamatergic transmission in the nucleus tractus solitarii abolished rimonabant-induced hypophagia. Importantly, these mechanisms were specifically triggered by lipid-deprivation, revealing a nutrient-specific component acutely regulated by CB
1
receptor blockade. Finally, peripheral blockade of sympathetic neurotransmission also blunted central effects of CB
1
receptor blockade, such as fear responses and anxiety-like behaviors. These data demonstrate that, independently of their site of origin, important effects of CB
1
receptor blockade are expressed via activation of peripheral sympathetic activity. Thus, CB
1
receptors modulate bidirectional circuits between the periphery and the brain to regulate feeding and other behaviors.
Host-compound foraging by intestinal microbiota revealed by single-cell stable isotope probing
Authors: Berry David , Stecher Bärbel , Schintlmeister Arno , Reichert Jochen , Brugiroux Sandrine , Wild Birgit , Wanek Wolfgang , Richter Andreas , Rauch Isabella , Decker Thomas , Loy Alexander , Wagner Michael
Published: March 2013

The animal and human intestinal mucosa secretes an assortment of compounds to establish a physical barrier between the host tissue and intestinal contents, a separation that is vital for health. Some pathogenic microorganisms as well as members of the commensal intestinal microbiota have been shown to be able to break down these secreted compounds. Our understanding of host-compound degradation by the commensal microbiota has been limited to knowledge about simplified model systems because of the difficulty in studying the complex intestinal ecosystem in vivo. In this study, we introduce an approach that overcomes previous technical limitations and allows us to observe which microbial cells in the intestine use host-derived compounds. We added stable isotope-labeled threonine i.v. to mice and combined fluorescence in situ hybridization with high-resolution secondary ion mass spectrometry imaging to characterize utilization of host proteins by individual bacterial cells. We show that two bacterial species,
Bacteroides acidifaciens
and
Akkermansia muciniphila
, are important host-protein foragers in vivo. Using gnotobiotic mice we show that microbiota composition determines the magnitude and pattern of foraging by these organisms, demonstrating that a complex microbiota is necessary in order for this niche to be fully exploited. These results underscore the importance of in vivo studies of intestinal microbiota, and the approach presented in this study will be a powerful tool to address many other key questions in animal and human microbiome research.
Omega-3 fatty acids lower blood pressure by directly activating large-conductance Ca
2+
-dependent K
+
channels
Authors: Hoshi Toshinori , Wissuwa Bianka , Tian Yutao , Tajima Nobuyoshi , Xu Rong , Bauer Michael , Heinemann Stefan H. , Hou Shangwei
Published: March 2013

Long-chain polyunsaturated omega-3 fatty acids such as docosahexaenoic acid (DHA), found abundantly in oily fish, may have diverse health-promoting effects, potentially protecting the immune, nervous, and cardiovascular systems. However, the mechanisms underlying the purported health-promoting effects of DHA remain largely unclear, in part because molecular signaling pathways and effectors of DHA are only beginning to be revealed. In vascular smooth muscle cells, large-conductance Ca
2+
- and voltage-activated K
+
(BK) channels provide a critical vasodilatory influence. We report here that DHA with an EC
50
of ∼500 nM rapidly and reversibly activates BK channels composed of the pore-forming Slo1 subunit and the auxiliary subunit β1, increasing currents by up to ∼20-fold. The DHA action is observed in cell-free patches and does not require voltage-sensor activation or Ca
2+
binding but involves destabilization of the closed conformation of the ion conduction gate. DHA lowers blood pressure in anesthetized wild-type but not in Slo1 knockout mice. DHA ethyl ester, contained in dietary supplements, fails to activate BK channels and antagonizes the stimulatory effect of DHA. Slo1 BK channels are thus receptors for long-chain omega-3 fatty acids, and these fatty acids—unlike their ethyl ester derivatives—activate the channels and lower blood pressure. This finding has practical implications for the use of omega-3 fatty acids as nutraceuticals for the general public and also for the critically ill receiving omega-3–enriched formulas.
O-GlcNAc transferase (OGT) as a placental biomarker of maternal stress and reprogramming of CNS gene transcription in development
Authors: Howerton Christopher L. , Morgan Christopher P. , Fischer David B. , Bale Tracy L.
Published: March 2013

Maternal stress is a key risk factor for neurodevelopmental disorders, including schizophrenia and autism, which often exhibit a sex bias in rates of presentation, age of onset, and symptom severity. The placenta is an endocrine tissue that functions as an important mediator in responding to perturbations in the intrauterine environment and is accessible for diagnostic purposes, potentially providing biomarkers predictive of disease. Therefore, we have used a genome-wide array approach to screen placental expression across pregnancy for gene candidates that are sex-biased and stress-responsive in mice and translate to human tissue. We identifed O-linked-N-acetylglucosamine (O-GlcNAc) transferase (OGT), an X-linked gene important in regulating proteins involved in chromatin remodeling, as fitting these criteria. Levels of both OGT and its biochemical mark, O-GlcNAcylation, were significantly lower in males and further reduced by prenatal stress. Examination of human placental tissue found similar patterns related to X chromosome dosage. As a demonstration of the importance of placental OGT in neurodevelopment, we found that hypothalamic gene expression and the broad epigenetic microRNA environment in the neonatal brain of placental-specific hemizygous OGT mice was substantially altered. These studies identified OGT as a promising placental biomarker of maternal stress exposure that may relate to sex-biased outcomes in neurodevelopment.