bluuebunny/crossref_metadata_2025 huggingface dataset:
Localized surface plasmon resonance anisotropy in template aligned silver nanoparticles: A case of biaxial metal optics
Authors: Ranjan Mukesh , Bhatnagar Mukul , Mukherjee Subroto
Published: March 2015

Generalized ellipsometry is used to extract the dielectric functions of self-aligned silver nanoparticles on silicon ripple patterns which account for the anisotropic Localized Surface Plasmon Resonance shown by such nanostructures. The biaxial nature of dielectric functions shows its presence through the modified in-plane plasmonic behaviour as compared to the case of random nanoparticles. The nature of in-plane optical coupling and out of plane metallic behavior is further investigated by tuning the interparticle gap along the ripple direction and also varying the ripple periodicity. Thus, we propose that generalized ellipsometry may be used as an effective process monitoring technique to develop anisotropic plasmonic substrates with potential applications in photovoltaic systems as a plasmonic back reflector.
Influence of electrically induced refraction and absorption on the measurement of spin current by pockels effect in GaAs
Authors: Liu Houquan , She Weilong
Published: March 2015

The pockels effect could be utilized to measure spin current in semiconductors for linear electro-optic coefficient can be induced by spin current. When dc electric field is applied, the carriers will shift in k space, which could lead to the change of refraction and absorption coefficients. In this paper, we investigate the influence of the induced change of the refraction and absorption coefficients on the measurement of spin current by pockels effect in GaAs.
Donor-doping and reduced leakage current in Nb-doped Na0.5Bi0.5TiO3
Authors: Li Ming , Li Linhao , Zang Jiadong , Sinclair Derek C.
Published: March 2015

Low levels of so-called “donor-doping” in titanate-based perovskite oxides such as La for Ba, Sr, and Nb for Ti in (Ba, Sr)TiO3 can significantly reduce the resistivity of these typical (d0) dielectric materials and expand application areas to positive temperature coefficient resistors, thermoelectrics, conductive wafers as thin film substrates, and solid oxide fuel cell anode materials. Here, we show low levels of Nb-doping (≤1 at. %) on the Ti-site in the well-known lead-free piezoelectric perovskite oxide Na0.5Bi0.5TiO3 (NBT) produces completely different behaviours whereby much higher resistivity is obtained, therefore indicating a different donor-doping (substitution) mechanism. There is a switch in conduction mechanism from oxygen-ions in undoped NBT with an activation energy (Ea) of <0.9 eV to electronic (band gap) conduction in 0.5–1 at. % Nb-doped NBT with Ea ∼ 1.5–1.8 eV. This demonstrates the necessity of further systematic doping studies to elucidate the defect chemistry of NBT which is clearly different to that of (Ba,Sr)TiO3. This defect chemistry needs to be understood if NBT-based materials are going to be manufactured on a large scale for commercial applications. This study also illustrates different donor-doping mechanisms to exist within the family of d0 titanate-based perovskites.
Magnetocaloric properties, exchange bias, and critical behavior of Ge substituted Ni50Mn36Sn14 Heusler alloys
Authors: Raji G. R. , Uthaman Bhagya , Thomas Senoy , Suresh K. G. , Raama Varma Manoj
Published: March 2015

The effect of Ge substitution on the magnetic, magnetocaloric, and exchange bias properties of Heusler alloy system Ni50Mn36Sn14-xGex (x = 1, 2) has been investigated. With the increase of Ge content, the cell volume decreases due to the smaller Ge radius and the martensitic transition temperature increases, while the Curie temperature of the austenite phase shows a small decrease. Metamagnetic behavior is observed in the low temperature magnetization isotherms for x = 1, whereas it is less pronounced in x = 2. The maximum magnetic entropy changes associated with the martensitic transition are 7.8 J/kg K and 2.3 J/kg K for x = 1 and 2, respectively, for a field change of 5 T. Relative cooling power is found to be more in the vicinity of the Curie temperature of the austenite phase, compared to that at the martensitic transition temperature in both x = 1 and 2. At low temperatures, both the samples exhibit exchange bias effect, with x = 2 showing higher value of exchange bias field. This is ascribed to the coexistence of ferromagnetic and antiferromagnetic interactions in these alloys. Further, the critical behavior of the austenite phase of both the alloys is studied and the values of the critical exponents are found to be different from the mean field values, which is attributed to the magnetic inhomogeneity originated due to Ge substitution.
Electromechanical magnetization switching
Authors: Chudnovsky Eugene M. , Jaafar Reem
Published: March 2015

We show that the magnetization of a torsional oscillator that, in addition to the magnetic moment also possesses an electrical polarization, can be switched by the electric field that ignites mechanical oscillations at the frequency comparable to the frequency of the ferromagnetic resonance. The 180° switching arises from the spin-rotation coupling and is not prohibited by the different symmetry of the magnetic moment and the electric field as in the case of a stationary magnet. Analytical equations describing the system have been derived and investigated numerically. Phase diagrams showing the range of parameters required for the switching have been obtained.
Superconductivity of magnetic Sm-substituted LaCo2B2
Authors: Wang Y. , Ren W. J. , Duan T. F. , Li D. , Li J. , Zhang Z. D.
Published: March 2015

In this work, superconductivity with a maximum superconducting transition onset temperature TC of 3.6 K is reported in La1-xSmxCo2B2 in the concentration range 0.12 ≤ x ≤ 0.20. Substitution of magnetic Sm ions with 4f electrons for La is beneficial for superconductivity in the system. The low upper critical field of La0.8Sm0.2Co2B2 suggests that the dominant magnetic-field suppressing superconducting mechanism is the orbit pair-breaking effect. A special specific-heat anomaly is observed around TC.
The effect of varying Co layer thickness on the time-temperature characteristics of Co/Sb semimetal embedded magnetic nanoparticles
Authors: Madden M. R. , Alshammary T. , Grove B. , Phillips J. , Reaz K. , Hensley S. , Kenning G. G.
Published: March 2015

We report the effect of varying cobalt thickness on the temperature-dependent time decay of the electrical resistance of Co/Sb multilayer samples. We find that for a given temperature, a five fold change in the Co thickness produces a 100 fold change in the characteristic decay time of the resistance. We find that the characteristic decay time, as a function of temperature, follows an Arrhenius law. During deposition, the Co evolves single domain magnetic nanoparticles, on the Sb, in either a Volmer-Weber or Stranski-Krastanov growth mode. This metastable state is then encased in 2.5 nm of Sb producing an embedded nanoparticle system. Scanning tunneling microscopy measurements taken before sample aging (annealing at a given temperature for enough time to complete the resistance decay) and after aging show that these nanoparticles undergo morphological transformations during aging. These transformations lead to well defined time dependent decays in both the magnetization and the electrical resistance, making this material an excellent candidate for an electronic time-temperature sensor.
Reflection and transmission of light waves from the air-magnetoplasma interface: Spatial and angular Imbert-Fedorov shifts
Authors: Borhanian Jafar
Published: March 2015

We have investigated the reflection and transmission of an electromagnetic wave from the air-magnetoplasma interface. The reflection and transmission coefficients are obtained for an arbitrary polarized incident wave. The spatial and angular Imbert-Fedorov (IF) shifts are discussed. The numerical results are presented to study the dependence of the reflection and transmission coefficients and IF shifts on relevant parameters of the system. The plasma and wave parameters can be used to control the reflection coefficients and IF shifts.
Flux-driven simulations of turbulence collapse
Authors: Park G. Y. , Kim S. S. , Jhang Hogun , Diamond P. H. , Rhee T. , Xu X. Q.
Published: March 2015

Using three-dimensional nonlinear simulations of tokamak turbulence, we show that an edge transport barrier (ETB) forms naturally once input power exceeds a threshold value. Profiles, turbulence-driven flows, and neoclassical coefficients are evolved self-consistently. A slow power ramp-up simulation shows that ETB transition is triggered by the turbulence-driven flows via an intermediate phase which involves coherent oscillation of turbulence intensity and E×B flow shear. A novel observation of the evolution is that the turbulence collapses and the ETB transition begins when RT > 1 at t = tR (RT: normalized Reynolds power), while the conventional transition criterion (ωE×B>γlin where ωE×B denotes mean flow shear) is satisfied only after t = tC ( >tR), when the mean flow shear grows due to positive feedback.
Production of negative hydrogen ions on metal grids
Authors: Oohara W. , Maetani Y. , Takeda Takashi , Takeda Toshiaki , Yokoyama H. , Kawata K.
Published: March 2015

Negative hydrogen ions are produced on a nickel grid with positive-ion irradiation. In order to investigate the production mechanism, a copper grid without the chemisorption of hydrogen atoms and positive helium ions without negative ionization are used for comparison. Positive hydrogen ions reflected on the metal surface obtain two electrons from the surface and become negatively ionized. It is found that the production yield of negative ions by desorption ionization of chemisorbed hydrogen atoms seems to be small, and the production is a minor mechanism.
Anisotropic behavior of exchange bias effect in tensile-deformed Pt3Fe single crystal
Authors: Kobayashi Satoru , Morita Ryo
Published: March 2015

Plastic strain in Pt3Fe causes changes in the atomic arrangement around the {111} glide plane and induces ferromagnetism even at room temperature. We have performed detailed magnetization measurements on a Pt3Fe single crystal with plastic strains of 11.6% under magnetic fields in various directions with respect to the [100] strain axis in order to elucidate the reversal mechanism of induced ferromagnetic domains. We observed that by decreasing the angle between the magnetization direction and strain axis, hysteresis loops are strongly sheared, which is associated with a large increase in coercivity. We also observed that an exchange bias effect appears for all field orientations, but the exchange field maximizes for an intermediate field direction. On the other hand, both phenomena are insensitive to magnetic fields perpendicular to the [100] strain axis. These observations were explained by a single-domain model with uniaxial anisotropy along the [100] strain axis.
Spin wave eigenmodes in single and coupled sub-150 nm rectangular permalloy dots
Authors: Carlotti G. , Tacchi S. , Gubbiotti G. , Madami M. , Dey H. , Csaba G. , Porod W.
Published: March 2015

We present the results of a Brillouin light scattering investigation of thermally excited spin wave eigenmodes in square arrays of either isolated rectangular dots of permalloy or twins of dipolarly coupled elements, placed side-by-side or head-to-tail. The nanodots, fabricated by e-beam lithography and lift-off, are 20 nm thick and have the major size D in the range between 90 nm and 150 nm. The experimental spectra show the presence of two main peaks, corresponding to modes localized either at the edges or in the center of the dots. Their frequency dependence on the dot size and on the interaction with adjacent elements has been measured and successfully interpreted on the basis of dynamical micromagnetic simulations. The latter enabled us also to describe the spatial profile of the eigenmodes, putting in evidence the effects induced by the dipolar interaction between coupled dots. In particular, in twinned dots the demagnetizing field is appreciably modified in proximity of the “internal edges” if compared to the “external” ones, leading to a splitting of the edge mode. These results can be relevant for the exploitation of sub-150 nm magnetic dots in new applications, such as magnonic metamaterials, bit-patterned storage media, and nano-magnetic logic devices.
Short-lived species detection of nitrous acid by external-cavity quantum cascade laser based quartz-enhanced photoacoustic absorption spectroscopy
Authors: Yi Hongming , Maamary Rabih , Gao Xiaoming , Sigrist Markus W. , Fertein Eric , Chen Weidong
Published: March 2015

Spectroscopic detection of short-lived gaseous nitrous acid (HONO) at 1254.85 cm−1 was realized by off-beam coupled quartz-enhanced photoacoustic spectroscopy (QEPAS) in conjunction with an external cavity quantum cascade lasers (EC-QCL). High sensitivity monitoring of HONO was performed within a very small gas-sample volume (of ∼40 mm3) allowing a significant reduction (of about 4 orders of magnitude) of air sampling residence time which is highly desired for accurate quantification of chemically reactive short-lived species. Calibration of the developed QEPAS-based HONO sensor was carried out by means of lab-generated HONO samples whose concentrations were determined by direct absorption spectroscopy involving a ∼109.5 m multipass cell and a distributed feedback QCL. A minimum detection limit (MDL) of 66 ppbv (1 σ) HONO was achieved at 70 mbar using a laser output power of 50 mW and 1 s integration time, which corresponded to a normalized noise equivalent absorption coefficient of 3.6 × 10−8 cm−1 W/Hz1/2. This MDL was down to 7 ppbv at the optimal integration time of 150 s. The corresponding 1σ minimum detected absorption coefficient is ∼1.1 × 10−7 cm−1 (MDL ∼ 3 ppbv) in 1 s and ∼1.1 × 10−8 cm−1 (MDL ∼ 330 pptv) in 150 s, respectively, with 1 W laser power.
Bottom-gate coplanar graphene transistors with enhanced graphene adhesion on atomic layer deposition Al2O3
Authors: Park Dong-Wook , Mikael Solomon , Chang Tzu-Hsuan , Gong Shaoqin , Ma Zhenqiang
Published: March 2015

A graphene transistor with a bottom-gate coplanar structure and an atomic layer deposition (ALD) aluminum oxide (Al2O3) gate dielectric is demonstrated. Wetting properties of ALD Al2O3 under different deposition conditions are investigated by measuring the surface contact angle. It is observed that the relatively hydrophobic surface is suitable for adhesion between graphene and ALD Al2O3. To achieve hydrophobic surface of ALD Al2O3, a methyl group (CH3)-terminated deposition method has been developed and compared with a hydroxyl group (OH)-terminated deposition. Based on this approach, bottom-gate coplanar graphene field-effect transistors are fabricated and characterized. A post-thermal annealing process improves the performance of the transistors by enhancing the contacts between the source/drain metal and graphene. The fabricated transistor shows an Ion/Ioff ratio, maximum transconductance, and field-effect mobility of 4.04, 20.1 μS at VD = 0.1 V, and 249.5 cm2/V·s, respectively.
Ptychographic x-ray imaging of surfaces on crystal truncation rod
Authors: Zhu Chenhui , Harder Ross , Diaz Ana , Komanicky Vladimir , Barbour Andi , Xu Ruqing , Huang Xiaojing , Liu Yaohua , Pierce Michael S. , Menzel Andreas , You Hoydoo
Published: March 2015

Ptychography is a high-resolution imaging technique, which does not require lenses for image magnification and which provides phase contrast with high sensitivity. Here, we propose to use x-ray ptychography for the imaging of surface structure in crystalline samples. We show that ptychography can be used to image atomic step structures using coherent diffraction patterns recorded along the crystal truncation rod of a crystal surface. In a proof-of-concept experiment on a Pt (111) sample, we present ptychographic reconstructions showing features consistent with surface steps. Due to the penetration power of x-rays, this method could find interesting applications for the study of surface structures under buried interfaces or in harsh environments.
Exact solutions of the incompressible dissipative Hall magnetohydrodynamics
Authors: Xia Zhenwei , Yang Weihong
Published: March 2015

By using analytical method, the exact solutions of the incompressible dissipative Hall magnetohydrodynamics (MHD) equations are derived. It is found that a phase difference may occur between the velocity and magnetic field fluctuations when the kinetic and magnetic Reynolds numbers are both very large. Since velocity and magnetic field fluctuations are both circular polarized, the phase difference makes them no longer parallel or anti-parallel like that in the incompressible ideal Hall MHD.
A vibration energy harvester using five-phase laminate composite transducer based on nanocrystalline soft magnetic alloy
Authors: Qiu Jing , Wen Yumei , Li Ping , Chen Hengjia , Yang Jin
Published: March 2015

In this research, a vibration energy harvester employing the FeCuNbSiB/Terfenol-D/PZT/Terfenol-D/FeCuNbSiB five-phase laminate composite transducer to convert mechanical vibration energy into electrical energy was presented. The electric output performance of the proposed vibration energy harvester has been investigated. It was found that appropriate FeCuNbSiB layer thickness was propitious to the electric output characteristics. Compared to traditional vibration energy harvester using Terfenol-D/PZT/Terfenol-D (MPM) transducer, the experimental results show that the proposed vibration energy harvester provides a remarkably enhanced output power performance. When the thickness of FeCuNbSiB layer was 30 μm, the optimum output power of vibration energy harvester achieved 4.00 mW/g for an acceleration of 0.8 g at frequency of 34.5 Hz, which was 1.29 times as great as that of traditional MPM transducer. Remarkably, this power is a very encouraging power figure and the proposed vibration energy harvester has great potential as far as its application in wireless sensor network.
Determination of the Schottky barrier height of ferromagnetic contacts to few-layer phosphorene
Authors: Anugrah Yoska , Robbins Matthew C. , Crowell Paul A. , Koester Steven J.
Published: March 2015

Phosphorene, the 2D analogue of black phosphorus, is a promising material for studying spin transport due to its low spin-orbit coupling and its ½ nuclear spin, which could allow the study of hyperfine effects. In this work, the properties of permalloy (Py) and cobalt (Co) contacts to few-layer phosphorene are presented. The Schottky barrier height was extracted and determined as a function of gate bias. Flat-band barrier heights, relative to the valence band edge, of 110 meV and 200 meV were determined for Py and Co, respectively. These results are important for future studies of spin transport in phosphorene.
Bending stiffness and interlayer shear modulus of few-layer graphene
Authors: Chen Xiaoming , Yi Chenglin , Ke Changhong
Published: March 2015

Interlayer shear deformation occurs in the bending of multilayer graphene with unconstrained ends, thus influencing its bending rigidity. Here, we investigate the bending stiffness and interlayer shear modulus of few-layer graphene through examining its self-folding conformation on a flat substrate using atomic force microscopy in conjunction with nonlinear mechanics modeling. The results reveal that the bending stiffness of 2–6 layers graphene follows a square-power relationship with its thickness. The interlayer shear modulus is found to be in the range of 0.36–0.49 GPa. The research findings show that the weak interlayer shear interaction has a substantial stiffening effect for multilayer graphene.
Application of UV photoluminescence imaging spectroscopy for stacking faults identification on thick, lightly n-type doped, 4°-off 4H-SiC epilayers
Authors: Thierry-Jebali N. , Kawahara C. , Miyazawa T. , Tsuchida H. , Kimoto T.
Published: March 2015

This paper deals with the description and the application of an original photoluminescence (PL) imaging technique on thick, lighly n-type doped 4H-SiC epilayers for in-grown stacking fault (SF) identification. This technique, call “photoluminescence imaging spectroscopy” (PLIS), compares different PL imaging pictures in order to create a new picture which displays the location and an approximation of the maximum photoemission wavelength of SFs at room temperature. Five types of SF have been detected and identified by PLIS on two different wafers. The origin of SF type modification during the growth is also discussed in this work.
Real-time maximum a-posteriori image reconstruction for fluorescence microscopy
Authors: Jabbar Anwar A. , Dilipkumar Shilpa , C K Rasmi , Rajan K. , Mondal Partha P.
Published: March 2015

Rapid reconstruction of multidimensional image is crucial for enabling real-time 3D fluorescence imaging. This becomes a key factor for imaging rapidly occurring events in the cellular environment. To facilitate real-time imaging, we have developed a graphics processing unit (GPU) based real-time maximum a-posteriori (MAP) image reconstruction system. The parallel processing capability of GPU device that consists of a large number of tiny processing cores and the adaptability of image reconstruction algorithm to parallel processing (that employ multiple independent computing modules called threads) results in high temporal resolution. Moreover, the proposed quadratic potential based MAP algorithm effectively deconvolves the images as well as suppresses the noise. The multi-node multi-threaded GPU and the Compute Unified Device Architecture (CUDA) efficiently execute the iterative image reconstruction algorithm that is ≈200-fold faster (for large dataset) when compared to existing CPU based systems.
Three-dimensional super-resolution imaging for fluorescence emission difference microscopy
Authors: You Shangting , Kuang Cuifang , Li Shuai , Liu Xu , Ding Zhihua
Published: March 2015

We propose a method theoretically to break the diffraction limit and to improve the resolution in all three dimensions for fluorescence emission difference microscopy. We produce two kinds of hollow focal spot by phase modulation. By incoherent superposition, these two kinds of focal spot yield a 3D hollow focal spot. The optimal proportion of these two kinds of spot is given in the paper. By employing 3D hollow focal spot, super-resolution image can be yielded by means of fluorescence emission difference microscopy, with resolution enhanced both laterally and axially. According to computation result, size of point spread function of three-dimensional super-resolution imaging is reduced by about 40% in all three spatial directions with respect to confocal imaging.
Identification and characteristics of ZnO/MgO core-shell nanowires
Authors: Yang S. , Wang L. , Wang Y. , Li L. , Wang T. , Jiang Z.
Published: March 2015

In this paper, ZnO/MgO core-shell nanowires are synthesized based on a one-step chemical vapor deposition (CVD) method. The scanning electron microscopy (SEM) images of core-shell nanowires indicate that Mg addition has little influence on the morphology of the synthesizing products. High crystalline quality ZnO/MgO core-shell nanowires instead of ZnMgO ternary compounds are identified by X-ray diffraction (XRD) patterns, transmission electron microscopy (TEM) images, selected area electron diffraction (SAED) pattern and photoluminescence (PL) spectra. The experimental results show that the ultraviolet (UV) emission of these samples with MgO shell is 12 times higher than that of the corresponding bare ZnO nanowires, and the suppression of the green emission is only 1/45 of the bare ZnO nanowires. It is also found that PL properties are proportional to Mg ratio. The UV emission enhancement and green emission suppression are due to the passivation of surface defects and the improvement of ZnO crystalline quality. The results are very useful for the development of optical devices based on nanowires.
Ambient ionisation mass spectrometry for lipid profiling and structural analysis of mammalian oocytes, preimplantation embryos and stem cells
Authors: Ferreira Christina R. , Jarmusch Alan K. , Pirro Valentina , Alfaro Clint M. , González-Serrano Andres F. , Niemann Heiner , Wheeler Matthew B. , Rabel Rathnaweera A. C. , Hallett Judy E. , Houser Rebecca , Kaufman Annemarie , Cooks R. Graham
Published: March 2015

Lipids play fundamental roles in mammalian embryo preimplantation development and cell fate. Triacylglycerol accumulates in oocytes and blastomeres as lipid droplets, phospholipids influence membrane functional properties, and essential fatty acid metabolism is important for maintaining the stemness of cells cultured in vitro. The growing impact that lipids have in the field of developmental biology makes analytical approaches to analyse structural information of great interest. This paper describes the concept and presents the results of lipid profiling by mass spectrometry (MS) of oocytes and preimplantation embryos, with special focus on ambient ionisation. Based on our previous experience with oocytes and embryos, we aim to convey that ambient MS is also valuable for stem cell differentiation analysis. Ambient ionisation MS allows the detection of a wide range of lipid classes (e.g. free fatty acids, cholesterol esters, phospholipids) in single oocytes, embryos and cell pellets, which are informative of in vitro culture impact, developmental and differentiation stages. Background on MS principles, the importance of underused MS scan modes for structural analysis of lipids, and statistical approaches used for data analysis are covered. We envisage that MS alone or in combination with other techniques will have a profound impact on the understanding of lipid metabolism, particularly in early embryo development and cell differentiation research.
Applying metabolomic analyses to the practice of embryology: physiology, development and assisted reproductive technology
Authors: Krisher Rebecca L. , Heuberger Adam L. , Paczkowski Melissa , Stevens John , Pospisil Courtney , Prather Randall S. , Sturmey Roger G. , Herrick Jason R. , Schoolcraft William B.
Published: March 2015

The advent of metabolomics technology and its application to small samples has allowed us to non-invasively monitor the metabolic activity of embryos in a complex culture environment. The aim of this study was to apply metabolomics technology to the analysis of individual embryos from several species during in vitro development to gain an insight into the metabolomics pathways used by embryos and their relationship with embryo quality. Alanine is produced by both in vivo- and in vitro-derived human, murine, bovine and porcine embryos. Glutamine is also produced by the embryos of these four species, but only those produced in vitro. Across species, blastocysts significantly consumed amino acids from the culture medium, whereas glucose was not significantly taken up. There are significant differences in the metabolic profile of in vivo- compared with in vitro-produced embryos at the blastocyst stage. For example, in vitro-produced murine embryos consume arginine, asparagine, glutamate and proline, whereas in vivo-produced embryos do not. Human embryos produce more alanine, glutamate and glutamine, and consume less pyruvate, at the blastocyst compared with cleavage stages. Glucose was consumed by human blastocysts, but not at a high enough level to reach significance. Consumption of tyrosine by cleavage stage human embryos is indicative of blastocyst development, although tyrosine consumption is not predictive of blastocyst quality. Similarly, although in vivo-produced murine blastocysts consumed less aspartate, lactate, taurine and tyrosine than those produced in vitro, consumption of these four amino acids by in vitro-derived embryos with high octamer-binding transcription factor 4 (Oct4) expression, indicative of high quality, did not differ from those with low Oct4 expression. Further application of metabolomic technologies to studies of the consumption and/or production of metabolites from individual embryos in a complete culture medium could transform our understanding of embryo physiology and improve our ability to produce developmentally competent embryos in vitro.
Salinity-induced differences in soil microbial communities around the hypersaline Lake Urmia
Authors: Barin Mohsen , Aliasgharzad Nasser , Olsson Pål Axel , Rasouli-Sadaghiani MirHassan
Published: March 2015

Lake Urmia in north-western Iran is one of the largest hypersaline lakes in the world, and agricultural production in the surrounding area is limited by soil salinity. We investigated the effects of salinity on belowground microbial communities in soils collected from fields of cultivated onions (Allium cepa L.) and lucerne (Medicago sativa L.), and sites with the native halophyte samphire (Salicornia europaea L.). We tested the hypotheses that salinity reduces microbial biomass and changes the structure of the microbial community. The physical and chemical properties of soil samples were analysed, and phospholipid fatty acids were identified as signatures for various microbial groups. We found that the organic carbon (OC) content was the dominant determinant of microbial biomass. We also found linear relationships between OC and the biomass of various groups of organisms across the wide salinity gradient studied. Salinity, on the other hand, caused changes in the microbial fatty acid composition that indicated adaptation to stress and favoured saprotrophic fungi over bacteria, and Gram-negative bacteria over Gram-positive. Principal component analysis showed that salinity variables and microbial stress indices formed one group, and OC and microbial biomass another. The importance of OC for high microbial biomass in severely stressed soils indicates that OC amendment may be used to mitigate salt stress and as a method of managing saline soils.
Stable solar-driven oxidation of water by semiconducting photoanodes protected by transparent catalytic nickel oxide films
Authors: Sun Ke , Saadi Fadl H. , Lichterman Michael F. , Hale William G. , Wang Hsin-Ping , Zhou Xinghao , Plymale Noah T. , Omelchenko Stefan T. , He Jr-Hau , Papadantonakis Kimberly M. , Brunschwig Bruce S. , Lewis Nathan S.
Published: March 2015

Significance

The development of efficient artificial photosynthetic systems, designed to store solar energy in chemical bonds, requires the pairing of stable light-absorbing electrodes for both the oxidative and reductive half-reactions. The development of such systems has been hindered in part by the lack of semiconducting photoanodes that are stable under the conditions required for the production of O
2
(g) from water. We demonstrate herein that a reactively sputtered NiO
x
layer provides a transparent, antireflective, conductive, chemically stable, inherently catalytic coating that stabilizes many efficient and technologically important semiconducting photoanodes under viable system operating conditions, thereby allowing the use of these materials in an integrated system for the sustainable, direct production of fuels from sunlight.
The Fe-S cluster-containing NEET proteins mitoNEET and NAF-1 as chemotherapeutic targets in breast cancer
Authors: Bai Fang , Morcos Faruck , Sohn Yang-Sung , Darash-Yahana Merav , Rezende Celso O. , Lipper Colin H. , Paddock Mark L. , Song Luhua , Luo Yuting , Holt Sarah H. , Tamir Sagi , Theodorakis Emmanuel A. , Jennings Patricia A. , Onuchic José N. , Mittler Ron , Nechushtai Rachel
Published: March 2015

Significance

Cancer is a leading cause of mortality worldwide, with the identification of novel drug targets and chemotherapeutic agents being a high priority in the fight against it. The NEET proteins mitoNEET (mNT) and nutrient-deprivation autophagy factor-1 (NAF-1) were recently shown to be required for cancer cell proliferation. Utilizing a combination of experimental and computational techniques, we identified a derivative of the mitocan cluvenone that binds to NEET proteins at the vicinity of their 2Fe-2S clusters and facilitates their destabilization. The new drug displays a high specificity in the selective killing of human epithelial breast cancer cells, without any apparent effects on normal breast cells. Our results identify the 2Fe-2S clusters of NEET proteins as a novel target in the chemotherapeutic treatment of breast cancer.
miR2GO: comparative functional analysis for microRNAs
Authors: Bhattacharya Anindya , Cui Yan
Published: March 2015

Summary: miR2GO is a web-based platform for comparative analyses of human miRNA functions. It includes two programs: miRmut2GO and miRpair2GO. miRmut2GO implements a knowledge-based method to assess the functional effects of genetic and somatic mutations in microRNA seed regions. The functional effects of a mutation are analysed by semantic comparison of enriched gene ontology (GO) annotations of the target gene sets for the wild-type and mutated alleles. miRpair2GO compares the functions of two different miRNAs based on the enriched functional annotations of their target gene sets.

Availability and implementation: The miR2GO web server is available at http://compbio.uthsc.edu/miR2GO.

Contact:  ycui2@uthsc.edu
Assessment of multidrug resistance, clonality and virulence in non-PCV-13 Streptococcus pneumoniae serotypes in Canada, 2011–13
Authors: Golden Alyssa R. , Adam Heather J. , Gilmour Matthew W. , Baxter Melanie R. , Martin Irene , Nichol Kimberly A. , Demczuk Walter H. B. , Hoban Daryl J. , Zhanel George G.
Published: March 2015

Objectives

Serotype replacement in Streptococcus pneumoniae following the implementation of a new vaccine has been associated with the emergence of non-vaccine serotypes as prominent causes of invasive pneumococcal disease (IPD). The aim of this study was to characterize specific non-PCV-13 serotypes 15A, 22F, 33F and 35B from IPD, isolated in Canada post-PCV-13 introduction in 2010.

Methods

Of 3802 IPD isolates collected from across Canada in 2011–13, 18.4% were found to be serotypes 15A, 22F, 33F and 35B. These 699 isolates were subjected to antimicrobial susceptibility testing, PFGE, MLST, molecular detection of pneumococcal pili and comparison with Pneumococcal Molecular Epidemiology Network (PMEN) clones.

Results

This study demonstrated clonal spread of specific STs, including MDR ST63 and its Sweden15A-25-related variants, the increasingly common ST433 and a variant of piliated, penicillin-non-susceptible ST558, related to PMEN clone Utah35B-24 (ST377). New STs of serotype 33F were identified. Several potential capsular switching events were identified within these serotypes.

Conclusions

Non-PCV-13 serotype 22F is increasing in Canada through the rapid clonal expansion of ST433. Numerous new STs associated with serotype 33F indicate the potential divergence of the serotype. Serotypes 15A and 35B in Canada are related to international clones of S. pneumoniae.
The Minimum Data Set 3.0 Cognitive Function Scale
Authors: Thomas Kali S. , Dosa David , Wysocki Andrea , Mor Vincent
Published: March 2015

Background:

The Minimum Data Set (MDS) 3.0 introduced the Brief Interview for Mental Status (BIMS), a short performance-based cognitive screener for nursing home (NH) residents. Not all residents are able to complete the BIMS and are consequently assessed by staff. We designed a Cognitive Function Scale (CFS) integrating self-report and staff-report data and present evidence of the scale’s construct validity.

Design:

A retrospective cohort study.

Subjects:

The subjects consisted of 3 cohorts: (1) long-stay NH residents (N=941,077) and (2) new admissions (N=2,066,580) during 2011–2012, and (3) residents with the older MDS 2.0 assessment in 2010 and the newer MDS 3.0 assessment (n=688,511).

Measures:

MDS 3.0 items were used to create a single, integrated 4-category hierarchical CFS that was compared with residents’ prior MDS 2.0 Cognitive Performance Scale scores and other concurrent MDS 3.0 measures of construct validity.

Results:

The new CFS suggests that 28% of the long-stay cohort in 2011–2012 were cognitively intact, 22% were mildly impaired, 33% were moderately impaired, and 17% were severely impaired. For the admission cohort, the CFS noted 56% as cognitively intact, 23% as mildly impaired, 17% as moderately impaired, and 4% as severely impaired. The CFS corresponded closely with residents’ prior MDS 2.0 Cognitive Performance Scale scores and with performance of Activities of Daily Living, and nurses’ judgments of function and behavior in both the admission and long-stay cohorts.

Conclusions:

The new CFS is valuable to researchers as it provides a single, integrated measure of NH residents’ cognitive function, regardless of the mode of assessment.
Cellular responses to a prolonged delay in mitosis are determined by a DNA damage response controlled by Bcl-2 family proteins
Authors: Colin Didier J. , Hain Karolina O. , Allan Lindsey A. , Clarke Paul R.
Published: March 2015

Anti-cancer drugs that disrupt mitosis inhibit cell proliferation and induce apoptosis, although the mechanisms of these responses are poorly understood. Here, we characterize a mitotic stress response that determines cell fate in response to microtubule poisons. We show that mitotic arrest induced by these drugs produces a temporally controlled DNA damage response (DDR) characterized by the caspase-dependent formation of γH2AX foci in non-apoptotic cells. Following exit from a delayed mitosis, this initial response results in activation of DDR protein kinases, phosphorylation of the tumour suppressor p53 and a delay in subsequent cell cycle progression. We show that this response is controlled by Mcl-1, a regulator of caspase activation that becomes degraded during mitotic arrest. Chemical inhibition of Mcl-1 and the related proteins Bcl-2 and Bcl-x
L
by a BH3 mimetic enhances the mitotic DDR, promotes p53 activation and inhibits subsequent cell cycle progression. We also show that inhibitors of DDR protein kinases as well as BH3 mimetics promote apoptosis synergistically with taxol (paclitaxel) in a variety of cancer cell lines. Our work demonstrates the role of mitotic DNA damage responses in determining cell fate in response to microtubule poisons and BH3 mimetics, providing a rationale for anti-cancer combination chemotherapies.
Chryseobacterium shandongense sp. nov., isolated from soil
Authors: Yang Fan , Liu Hong-ming , Zhang Rong , Chen Ding-bin , Wang Xiang , Li Shun-peng , Hong Qing
Published: March 2015

YF-3T is a Gram-stain-negative, non-motile, non-spore-forming, yellow–orange, rod-shaped bacterium. Optimal growth conditions were at 30 °C, pH 7.0 and 1 % (w/v) NaCl. Phylogenetic analysis, on the basis of the 16S rRNA gene sequence, showed that strain YF-3T was closely related to the strains Chryseobacterium hispalense AG13T and Chryseobacterium taiwanense Soil-3-27T with 98.71 % and 96.93 % sequence similarity, respectively. Strain YF-3T contained MK-6 as the main menaquinone and had a polyamine pattern with sym-homospermidine as the major component. Its major polar lipid was phosphatidylethanolamine. The dominant fatty acids of strain YF-3T were iso-C15 : 0, iso-C17 : 0 3-OH, summed feature 9 (comprising iso-C17 : 1ω9c and/or C16 : 0 10-methyl) and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c). The DNA G+C content of strain YF-3T was 37 mol%. The DNA–DNA relatedness levels between strain YF-3T and the most closely related strains, C. hispalense AG13T and C. taiwanense Soil-3-27T, were 31.7 ± 2.1 % and 28.4 ± 5.4 %, respectively. Based on these results, a novel species named Chryseobacterium shandongense sp. nov. is proposed. The type strain is YF-3T ( = CCTCC AB 2014060T = JCM 30154T).
Measuring forces and stressesin situin living tissues
Authors:   “Forces in tissues” workshop participants
Published: March 2015

Development, homeostasis and regeneration of tissues result from the interaction of genetics and mechanics. Kinematics and rheology are two main classes of measurements respectively providing deformations and mechanical properties of a material. They are now applied to living tissues and have contributed to the better understanding of their mechanics. Due to the complexity of living tissues, however, a third class of mechanical measurements, that of in situ forces and stresses, appears to be increasingly important to elaborate realistic models of tissue mechanics. We review here several emerging techniques of this class, their fields of applications, their advantages and limitations, and their validations. We argue that they will strongly impact on our understanding of developmental biology in the near future.
The RNA helicase MOV10L1 binds piRNA precursors to initiate piRNA processing
Authors: Vourekas Anastassios , Zheng Ke , Fu Qi , Maragkakis Manolis , Alexiou Panagiotis , Ma Jing , Pillai Ramesh S. , Mourelatos Zissimos , Wang P. Jeremy
Published: March 2015

Piwi–piRNA (Piwi-interacting RNA) ribonucleoproteins (piRNPs) enforce retrotransposon silencing, a function critical for preserving the genome integrity of germ cells. The molecular functions of most of the factors that have been genetically implicated in primary piRNA biogenesis are still elusive. Here we show that MOV10L1 exhibits 5′-to-3′ directional RNA-unwinding activity in vitro and that a point mutation that abolishes this activity causes a failure in primary piRNA biogenesis in vivo. We demonstrate that MOV10L1 selectively binds piRNA precursor transcripts and is essential for the generation of intermediate piRNA processing fragments that are subsequently loaded to Piwi proteins. Multiple analyses suggest an intimate coupling of piRNA precursor processing with elements of local secondary structures such as G quadruplexes. Our results support a model in which MOV10L1 RNA helicase activity promotes unwinding and funneling of the single-stranded piRNA precursor transcripts to the endonuclease that catalyzes the first cleavage step of piRNA processing.
Origin and domestication of papaya Yh chromosome
Authors: VanBuren Robert , Zeng Fanchang , Chen Cuixia , Zhang Jisen , Wai Ching Man , Han Jennifer , Aryal Rishi , Gschwend Andrea R. , Wang Jianping , Na Jong-Kuk , Huang Lixian , Zhang Lingmao , Miao Wenjing , Gou Jiqing , Arro Jie , Guyot Romain , Moore Richard C. , Wang Ming-Li , Zee Francis , Charlesworth Deborah , Moore Paul H. , Yu Qingyi , Ming Ray
Published: March 2015

Sex in papaya is controlled by a pair of nascent sex chromosomes. Females are XX, and two slightly different Y chromosomes distinguish males (XY) and hermaphrodites (XYh). The hermaphrodite-specific region of the Yh chromosome (HSY) and its X chromosome counterpart were sequenced and analyzed previously. We now report the sequence of the entire male-specific region of the Y (MSY). We used a BAC-by-BAC approach to sequence the MSY and resequence the Y regions of 24 wild males and the Yh regions of 12 cultivated hermaphrodites. The MSY and HSY regions have highly similar gene content and structure, and only 0.4% sequence divergence. The MSY sequences from wild males include three distinct haplotypes, associated with the populations’ geographic locations, but gene flow is detected for other genomic regions. The Yh sequence is highly similar to one Y haplotype (MSY3) found only in wild dioecious populations from the north Pacific region of Costa Rica. The low MSY3-Yh divergence supports the hypothesis that hermaphrodite papaya is a product of human domestication. We estimate that Yh arose only ∼4000 yr ago, well after crop plant domestication in Mesoamerica >6200 yr ago but coinciding with the rise of the Maya civilization. The Yh chromosome has lower nucleotide diversity than the Y, or the genome regions that are not fully sex-linked, consistent with a domestication bottleneck. The identification of the ancestral MSY3 haplotype will expedite investigation of the mutation leading to the domestication of the hermaphrodite Yh chromosome. In turn, this mutation should identify the gene that was affected by the carpel-suppressing mutation that was involved in the evolution of males.
Characterization and Survival of Environmental Escherichia coli O26 Isolates in Ground Beef and Environmental Samples
Authors: Palmer Christine E. , Bratcher Christy L. , Singh Manpreet , Wang Luxin
Published: March 2015

In addition to Escherichia coli O157:H7, shiga toxin‐producing E. coli (STEC) O26 was added to the zero‐tolerance adulterant list together with other 5 non‐O157 STEC serogroups in 2012. Four farm O26 isolates were used in this study; they were obtained from a on‐farm survey study conducted in Alabama. The presence of 3 major pathogenic genes (stx1, stx2, and eaeA) was determined through multiplex polymerase chain reaction (PCR). Two major pathogenic gene profiles were observed: 3 of the farm isolates contain only the eaeA gene whereas 1 farm isolate has both the eaeA and the stx1 genes. No significant difference was seen among the 4 farm isolates in the antibiotic resistance tests. To test their survival in ground beef and environmental samples, 2 inoculums were prepared and inoculated at various concentrations into samples of ground beef, bovine feces, bedding materials, and trough water. One inoculum was made of 3 farm isolates containing only the eaeA gene and another inoculum contained the isolate with both the eaeA and stx1 genes. Inoculated beef samples were stored at 4 °C for 10 d and the inoculated environmental samples were stored at ambient temperature for 30 d. Results showed that virulence gene profiles do not have an impact on O26's ability to survive in ground beef and in environment (P > 0.05). The inoculation levels, sample types as well as the storage times are the major factors that impact O26 survival (P < 0.05).
A high‐fat plus fructose diet produces a vascular prostanoid alterations in the rat
Authors: Peredo H. A. , Lee H. , Donoso A. S. , Andrade V. , Sánchez Eluchans N. , Puyó A. M.
Published: March 2015

In the rat, a high‐fat (HF) plus fructose (F) diet produces cardiovascular and metabolic alterations that resemble human metabolic syndrome. Prostanoids (PR), cyclo‐oxygenase‐derived arachidonic acid metabolites, have vasoactive properties and mediate inflammation.

The aim of this study was to analyse the effect of a HF+F diet on blood pressure (BP), metabolic parameters and mesenteric vascular bed PR production in male Sprague–Dawley rats.

Four groups were studied over 9 weeks (n = 6 each): control (C), standard diet (SD) and tap water to drink; F+SD and 10% w/v F solution to drink; HF 50% (w/w) bovine fat added to SD and tap water; and HFF, both treatments. PR were determined by HPLC.

Blood pressure was elevated in all experimental groups. Triglyceridaemia, insulinaemia and HOMA‐IR were increased in the F and HF groups. HF+F animals showed elevated glycaemia, insulinaemia, HOMA‐IR and triglyceridaemia. F decreased the vasodilator prostanoids PGI2 and PGE2 in the mesenteric vascular bed. Body weight was not significantly altered. In HFF, production of PGE2, PGF2alpha and TXB2 was elevated.

The increased BP in HF and HFF could be partly attributed to the imbalance in vascular PR production towards vasoconstrictors. On the other hand, this dietary modification could induce inflammation, which would explain the elevation of PGE2. In the F group, hypertension could be related to decreased vasodilator PRs.

The simultaneous administration of HF and F in the rat produces deleterious effects greater than observed when treatments are applied separately.