bluuebunny/crossref_metadata_2025 huggingface dataset:
Oriented nanometric aggregates of partially inverted zinc ferrite: One-step processing and tunable high-frequency magnetic properties
Authors: Sai Ranajit , Endo Yasushi , Shimada Yutaka , Yamaguchi Masahiro , Shivashankar S. A.
Published: April 2015

In this work, it is demonstrated that the in situ growth of oriented nanometric aggregates of partially inverted zinc ferrite can potentially pave a way to alter and tune magnetocrystalline anisotropy that, in turn, dictates ferromagnetic resonance frequency (fFMR) by inducing strain due to aggregation. Furthermore, the influence of interparticle interaction on magnetic properties of the aggregates is investigated. Mono-dispersed zinc ferrite nanoparticles (<5 nm) with various degrees of aggregation were prepared through decomposition of metal-organic compounds of zinc (II) and iron (III) in an alcoholic solution under controlled microwave irradiation, below 200 °C. The nanocrystallites were found to possess high degree of inversion (>0.5). With increasing order of aggregation in the samples, saturation magnetization (at 5 K) is found to decrease from 38 emu/g to 24 emu/g, while coercivity is found to increase gradually by up to 100% (525 Oe to 1040 Oe). Anisotropy-mediated shift of fFMR has also been measured and discussed. In essence, the result exhibits an easy way to control the magnetic characteristics of nanocrystalline zinc ferrite, boosted with significant degree of inversion, at GHz frequencies.
How electronic dynamics with Pauli exclusion produces Fermi-Dirac statistics
Authors: Nguyen Triet S. , Nanguneri Ravindra , Parkhill John
Published: April 2015

It is important that any dynamics method approaches the correct population distribution at long times. In this paper, we derive a one-body reduced density matrix dynamics for electrons in energetic contact with a bath. We obtain a remarkable equation of motion which shows that in order to reach equilibrium properly, rates of electron transitions depend on the density matrix. Even though the bath drives the electrons towards a Boltzmann distribution, hole blocking factors in our equation of motion cause the electronic populations to relax to a Fermi-Dirac distribution. These factors are an old concept, but we show how they can be derived with a combination of time-dependent perturbation theory and the extended normal ordering of Mukherjee and Kutzelnigg for a general electronic state. The resulting non-equilibrium kinetic equations generalize the usual Redfield theory to many-electron systems, while ensuring that the orbital occupations remain between zero and one. In numerical applications of our equations, we show that relaxation rates of molecules are not constant because of the blocking effect. Other applications to model atomic chains are also presented which highlight the importance of treating both dephasing and relaxation. Finally, we show how the bath localizes the electron density matrix.
Fourier-transform spectroscopy and potential construction of the (2)1Π state in KCs
Authors: Birzniece I. , Nikolayeva O. , Tamanis M. , Ferber R.
Published: April 2015

The paper presents an empirical pointwise potential energy curve (PEC) of the (2)1Π state of the KCs molecule constructed by applying the Inverted Perturbation Approach routine. The experimental term values in the energy range E(v′, J′) ∈ [15 407; 16 579] cm−1 involved in the fit were based on Fourier-Transform spectroscopy data obtained with 0.01 cm−1 accuracy from the laser-induced (2)1Π → X1Σ+ fluorescence spectra. Buffer gas Ar was used to facilitate the appearance of rotation relaxation lines in the spectra, thus enlarging the (2)1Π data set and allowing determination of the Λ-splitting constants. The data set included vibrational v′ ∈ [0, 28] and rotational J′ ∈ [7, 274] quantum numbers covering about 67% of the potential well. The present PEC reproduces the overall set of data included in the fit with a standard deviation of 0.5 cm−1. The obtained value of the Λ-doubling constant q = + 1.8 × 10−6 cm−1 for J′ > 50 and v′ ∈ [0, 6] is in an excellent agreement with q = + 1.84 × 10−6 cm−1 reported in Kim, Lee, and Stolyarov [J. Mol. Spectrosc. 256, 57-67 (2009)].
The energetic of (CH2F2)2 investigated by TDL IR spectroscopy and DFT computations: From collision induced relaxation of ro-vibrational transitions to non-covalent interactions
Authors: Tasinato Nicola , Turchetto Arianna , Stoppa Paolo , Charmet Andrea Pietropolli , Giorgianni Santi
Published: April 2015

Difluoromethane (CH2F2) is an atmospheric pollutant presenting strong absorptions within the 8–12 μm atmospheric window, hence it can contribute to global warming. Its dimer, (CH2F2)2, is bound through weak hydrogen bonds (wHBs). Theoretically, wHBs are of paramount importance in biological systems, though their modeling at density functional theory (DFT) level requires dispersion correlations to be accounted for. In this work, the binding energy (3.1 ± 0.5 kcal mol−1) of (CH2F2)2 is experimentally derived from the foreign broadening coefficients of the monomer compound, collisionally perturbed by a range of damping gases. Measurements are carried out on CH2F2 ro-vibrational transitions by means of tunable diode laser spectroscopy. Six stationary points on the potential energy surface (PES) of the dimer are investigated at DFT level by using some of the last generation density functionals (DFs). The Minnesota M06 suite of functionals as well as range separated DFs and DFs augmented by the non-local (NL) van der Waals (vdW) dispersion corrections are considered. DFT results are compared to reference values at the estimated complete basis set (CBS) limit of CCSD(T) theory (coupled cluster with singles and doubles augmented by a perturbational estimate of connected triples) and to the experimental binding energy. The M06-2X, M06-HF, VV10, BLYP-NL, and B3LYP-NL DFs reproduce CCSD(T)/CBS binding energies with a mean absolute deviation <0.4 kcal mol−1 and about the same deviation from the experimental value. The present results are of twofold relevance: (i) they show that binding energy of homodimers can be conveniently obtained from the monomer’s foreign broadening coefficients and that the correct simulation of hydrogen bonds involved in (CH2F2)2 needs non-covalent interactions to be included into DFT; (ii) O2- and N2-pressure broadening parameters represent fundamental data for exploiting the efficacy of remote sensing measurements employed to retrieve temperature and concentration profiles of our atmosphere.
Super-Joule heating in graphene and silver nanowire network
Authors: Maize Kerry , Das Suprem R. , Sadeque Sajia , Mohammed Amr M. S. , Shakouri Ali , Janes David B. , Alam Muhammad A.
Published: April 2015

Transistors, sensors, and transparent conductors based on randomly assembled nanowire networks rely on multi-component percolation for unique and distinctive applications in flexible electronics, biochemical sensing, and solar cells. While conduction models for 1-D and 1-D/2-D networks have been developed, typically assuming linear electronic transport and self-heating, the model has not been validated by direct high-resolution characterization of coupled electronic pathways and thermal response. In this letter, we show the occurrence of nonlinear “super-Joule” self-heating at the transport bottlenecks in networks of silver nanowires and silver nanowire/single layer graphene hybrid using high resolution thermoreflectance (TR) imaging. TR images at the microscopic self-heating hotspots within nanowire network and nanowire/graphene hybrid network devices with submicron spatial resolution are used to infer electrical current pathways. The results encourage a fundamental reevaluation of transport models for network-based percolating conductors.
Analysis of negative capacitance and self-heating in organic semiconductor devices
Authors: Knapp Evelyne , Ruhstaller Beat
Published: April 2015

In admittance spectroscopy of organic semiconductor devices, negative capacitance values arise at low frequency and high voltages. This study aims at explaining the influence of self-heating on the frequency-dependent capacitance and demonstrates its impact on steady-state and dynamic experiments. Therefore, a one dimensional numerical drift-diffusion model extended by the heat equation is presented. We calculate the admittance with two approaches: a Fourier method that is applied to time domain data and a numerically efficient sinusoidal steady state analysis (S3A), which is based on the linearization of the equations around the operating point. The simulation results coincide well with the experimental findings from reference [H. Okumoto and T. Tsutsui, Appl. Phys. Express 7, 061601 (2014)] where the negative capacitance effect of an organic device becomes weaker with better cooling of the structure. Linking the frequency- and time-domain with the Fourier approach supports an effortless interpretation of the negative capacitance. Namely, we find that negative capacitance originates from self-heating induced current enhancement.
Entropy-scaling laws for diffusion coefficients in liquid metals under high pressures
Authors: Cao Qi-Long , Shao Ju-Xiang , Wang Pan-Pan , Wang Fan-Hou
Published: April 2015

Molecular dynamic simulations on the liquid copper and tungsten are used to investigate the empirical entropy-scaling laws D*=A exp(BSex), proposed independently by Rosenfeld and Dzugutov for diffusion coefficient, under high pressure conditions. We show that the scaling laws hold rather well for them under high pressure conditions. Furthermore, both the original diffusion coefficients and the reduced diffusion coefficients exhibit an Arrhenius relationship DM=DM0 exp(−EM/KBT), (M=un,R,D) and the activation energy EM increases with increasing pressure, the diffusion pre-exponential factors (DR0 and DD0) are nearly independent of the pressure and element. The pair correlation entropy, S2, depends linearly on the reciprocal temperature S2=−ES/T, and the activation energy, ES, increases with increasing pressure. In particular, the ratios of the activation energies (Eun, ER, and ED) obtained from diffusion coefficients to the activation energy, ES, obtained from the entropy keep constants in the whole pressure range. Therefore, the entropy-scaling laws for the diffusion coefficients and the Arrhenius law are linked via the temperature dependence of entropy.
Spin orbit torque based electronic neuron
Authors: Sengupta Abhronil , Choday Sri Harsha , Kim Yusung , Roy Kaushik
Published: April 2015

A device based on current-induced spin-orbit torque (SOT) that functions as an electronic neuron is proposed in this work. The SOT device implements an artificial neuron's thresholding (transfer) function. In the first step of a two-step switching scheme, a charge current places the magnetization of a nano-magnet along the hard-axis, i.e., an unstable point for the magnet. In the second step, the SOT device (neuron) receives a current (from the synapses) which moves the magnetization from the unstable point to one of the two stable states. The polarity of the synaptic current encodes the excitatory and inhibitory nature of the neuron input and determines the final orientation of the magnetization. A resistive crossbar array, functioning as synapses, generates a bipolar current that is a weighted sum of the inputs. The simulation of a two layer feed-forward artificial neural network based on the SOT electronic neuron shows that it consumes ∼3× lower power than a 45 nm digital CMOS implementation, while reaching ∼80% accuracy in the classification of 100 images of handwritten digits from the MNIST dataset.
Electric-field-induced angular dependence of magnetic anisotropy in a FeCo/Pb(Mg1/3Nb2/3)O3-PbTiO3 heterostructure
Authors: Yang Chengcheng , Wang Fenglong , Dong Chunhui , Sui Wenbo , Jiang Changjun , Xue Desheng
Published: April 2015

To understand the distribution of the in-plane magnetic anisotropy under a dc electric field, FeCo films deposited onto Pb(Mg1/3Nb2/3)O3-PbTiO3 (011)-orientated substrates by RF-magnetron sputtering were investigated. Vibrating sample magnetometer was performed and the occurrence of switching was demonstrated of the magnetization easy axis in FeCo films upon applying solely a dc electric field. A theoretical calculation was performed to provide a simplified account of the magnetoelastic contribution to the magnetic anisotropy. Quantification of the angular distribution of the magnetic anisotropy field under various electric fields was obtained, which can contribute to realizing low-loss electric-field-turning devices.
Co thickness dependence of structural and magnetic properties in spin quantum cross devices utilizing stray magnetic fields
Authors: Kaiju H. , Kasa H. , Komine T. , Mori S. , Misawa T. , Abe T. , Nishii J.
Published: April 2015

We investigate the Co thickness dependence of the structural and magnetic properties of Co thin-film electrodes sandwiched between borate glasses in spin quantum cross (SQC) devices that utilize stray magnetic fields. We also calculate the Co thickness dependence of the stray field between the two edges of Co thin-film electrodes in SQC devices using micromagnetic simulation. The surface roughness of Co thin films with a thickness of less than 20 nm on borate glasses is shown to be as small as 0.18 nm, at the same scanning scale as the Co film thickness, and the squareness of the hysteresis loop is shown to be as large as 0.96–1.0. As a result of the establishment of polishing techniques for Co thin-film electrodes sandwiched between borate glasses, we successfully demonstrate the formation of smooth Co edges and the generation of stray magnetic fields from Co edges. Theoretical calculation reveals that a strong stray field beyond 6 kOe is generated when the Co thickness is greater than 10 nm at a junction gap distance of 5 nm. From these experimental and calculation results, it can be concluded that SQC devices with a Co thickness of 10–20 nm can be expected to function as spin-filter devices.
New expression for collisionless magnetic reconnection rate
Authors: Klimas Alex
Published: April 2015

For 2D, symmetric, anti-parallel, collisionless magnetic reconnection, new expressions for the reconnection rate in the electron diffusion region are introduced. It is shown that these expressions can be derived in just a few simple steps from a physically intuitive starting point; the derivations are given in their entirety, and the validity of each step is confirmed. The predictions of these expressions are compared to the results of several long-duration, open-boundary particle-in-cell reconnection simulations to demonstrate excellent agreement.
Effect of aligned ferromagnetic particles on strain sensitivity of multi-walled carbon nanotube/polydimethylsiloxane sensors
Authors: Jang S. H. , Yin H. M.
Published: April 2015

A strain sensor using chain-structured ferromagnetic particles (FPs) in a multi-walled carbon nanotube (MWCNT)/polydimethylsiloxane (PDMS) nanocomposite was fabricated under a magnetic field and its strain sensitivity was evaluated at different material proportions. When the proportion of MWCNTs that are well dispersed in PDMS is higher than the percolation threshold, the strain sensitivity reduces with the increase of MWCNTs, in general; whereas a higher volume fraction of FPs produces a higher strain sensitivity when the chain-structure of FPs sustains. The mechanisms causing this interesting phenomenon have been demonstrated through the microstructural evolution and micromechanics-based modeling. These findings indicate that an optimal design of the volume fraction of FPs and MWCNTs exists to achieve the best strain sensitivity of this type of sensors. It is demonstrated that the nanocomposites containing 20 vol. % of nickel particles and 0.35 wt. % MWCNTs exhibit a high strain sensitivity of ∼80.
Note: Optical and electronic design of an amplitude-modulated continuous-wave laser scanner for high-accuracy distance measurement
Authors: Jang Junhwan , Hwang Sungui , Park Kyihwan
Published: April 2015

To utilize a time-of-flight-based laser scanner as a distance measurement sensor, the measurable distance and accuracy are the most important performance parameters to consider. For these purposes, the optical system and electronic signal processing of the laser scanner should be optimally designed in order to reduce a distance error caused by the optical crosstalk and wide dynamic range input. Optical system design for removing optical crosstalk problem is proposed in this work. Intensity control is also considered to solve the problem of a phase-shift variation in the signal processing circuit caused by object reflectivity. The experimental results for optical system and signal processing design are performed using 3D measurements.
Turbulent bands in plane-Poiseuille flow at moderate Reynolds numbers
Authors: Xiong Xiangming , Tao Jianjun , Chen Shiyi , Brandt Luca
Published: April 2015

In this letter, we show via numerical simulations that the typical flow structures appearing in transitional channel flows at moderate Reynolds numbers are not spots but isolated turbulent bands, which have much longer lifetimes than the spots. Localized perturbations can evolve into isolated turbulent bands by continuously growing obliquely when the Reynolds number is larger than 660. However, interactions with other bands and local perturbations cause band breaking and decay. The competition between the band extension and breaking does not lead to a sustained turbulence until Re becomes larger than about 1000. Above this critical value, the bands split, providing an effective mechanism for turbulence spreading.
Commentary: The Hash House Harriers and the winding path to materials discovery
Authors: Canfield Paul C.
Published: April 2015

Materials science research can be both very demanding and extremely rewarding. In this Commentary, in my own research of new electronic and magnetic materials, I give numerous exemplars of the path followed to materials discovery. I also highlight the parallels between my research experiences with the pastime of running. I hope that my thoughts will help guide junior researchers along the often tortuous and exciting path to new materials and that I can teach them to be open minded and persistent about following new lines of discovery. “No-pain, no-gain” applies to many things in life, running and scientific research being just two examples, but I hope in the case of scientific research that I can convince you the gain normally outweighs the pain.
Strain-compensated (Ga,In)N/(Al,Ga)N/GaN multiple quantum wells for improved yellow/amber light emission
Authors: Lekhal K. , Damilano B. , Ngo H. T. , Rosales D. , De Mierry P. , Hussain S. , Vennéguès P. , Gil B.
Published: April 2015

Yellow/amber (570–600 nm) emitting InxGa1−xN/AlyGa1−yN/GaN multiple quantum wells (QWs) have been grown by metal organic chemical vapor deposition on GaN-on- sapphire templates. When the (Al,Ga)N thickness of the barrier increases, the room temperature photoluminescence is red-shifted while its yield increases. This is attributed to an increase of the QW internal electric field and an improvement of the material quality due to the compensation of the compressive strain of the InxGa1−xN QWs by the AlyGa1−yN layers, respectively.
Nonlinear optical absorption tuning in Bi3.15Nd0.85Ti3O12 ferroelectric thin films by thickness
Authors: Li S. , Zhong X. L. , Cheng G. H. , Liu X. , Zhang Y. , Wang J. B. , Song H. J. , Tan C. B. , Li B.
Published: April 2015

The tunability of nonlinear optical (NLO) absorption in Bi3.15Nd0.85Ti3O12 (BNT) ferroelectric thin films was investigated through the open aperture Z-scan method with femtosecond laser pulses at the wavelength of 800 nm. NLO absorption responses of the BNT films were observed to be highly sensitive to the film thickness. As the film thickness increases from 106.8 to 139.7 nm, the NLO absorption changes from saturable absorption (SA) to reverse saturable absorption (RSA). When the film thickness further increases to 312.9 nm, the RSA effect is enhanced. A band-gap-related competition between the ground-state excitation and the two-photon absorption is responsible for the absorption switching behavior. Such a tunable NLO absorption can widen the photonic application of the BNT thin films.
Electronic band structure of compressively strained Ge1−xSnx with x < 0.11 studied by contactless electroreflectance
Authors: Zelazna K. , Polak M. P. , Scharoch P. , Serafinczuk J. , Gladysiewicz M. , Misiewicz J. , Dekoster J. , Kudrawiec R.
Published: April 2015

Contactless electroreflectance is applied to study direct optical transitions from the heavy hole, light hole, and spin-orbit split-off band to the conduction band in compressively strained Ge1−xSnx layers of various Sn concentrations at room temperature. It is shown that the energies of these transitions are in very good agreement with theoretical predictions, which take into account non-linear variation of bandgap and spin-orbit splitting plus the strain-related shifts obtained from the Bir-Pikus theory. The bowing parameter for the direct bandgap has been determined to be 1.8 ± 0.2 eV and agree with this one obtained within ab initio calculations, which is 1.97 eV (for indirect bandgap the bowing parameter is 0.26 eV).
Magnetothermopower, magnetic entropy change, and magnetoresistance in ferromagnetic cobaltites: R0.7Sr0.3CoO3 (R = La and Gd)
Authors: Kumar Pawan , Mahendiran R.
Published: April 2015

We compare the impact effect of external magnetic fields on the magnetic entropy (Sm), electrical resistivity, and thermopower in two metallic oxides R0.7Sr0.3CoO3 that become ferromagnetic below TC = 240 K and 117 K for R = La3+(4f0) and Gd3+(4f7), respectively. While Gd0.7Sr0.3CoO3 shows unusually high values of negative magnetothermopower (≈−35.5%), magnetic entropy change (ΔSm ≈ −12 J/kg K), and negative magnetoresistance (≈−3.7%) at 10 K for a field change of 5 T, these effects are absent in the La sample at 10 K. We suggest that the large ΔSm arises from the field-induced suppression of spin fluctuations associated with localized 4f7 moments of Gd3+ ions, but magnetic interaction among Co ions dictates magnetoresistance and magnetothermopower. Magnetization data indicate that while Co3+ ions adopt intermediate spin state (S = 1) in the La compound, major fraction of them transforms into low spin state (S = 0) in the Gd sample. Hence, the Gd sample is microscopically heterogeneous with a mixture of ferromagnetic metallic and paramagnetic metallic clusters. Spin dependent scattering at the surface of ferromagnetic clusters may be the cause for the coexistence of magnetothermopower and magnetoresistance in this compound. A close correlation between the magnetoresistance and the magnetothermopower is reported.
Vegetation dynamics and mesophication in response to conifer encroachment within an ultramafic system
Authors: Burgess J. , Szlavecz K. , Rajakaruna N. , Lev S. , Swan C.
Published: April 2015

The biological, ecological, and evolutionary significance of serpentine habitats has long been recognised. We used an integrated physiochemical dataset combining plot spatial data with temporal data from tree cores to evaluate changes in soils and vegetation. Data suggest that this unique habitat is undergoing a transition, endangering local biodiversity and endemic plant species. The objective of this work was to analyse the vegetation dynamics of a xeric serpentine savanna located in the Mid-Atlantic, USA. We employed vegetation surveys of 32 10 × 15 m quadrats to obtain woody species composition, density, basal area, and developed a spatial physiochemical dataset of substrate geochemistry to independently summarise the data using regression and ordination techniques. This information was interpreted alongside historical, dendrochronologic and soil stable carbon isotopic data to evaluate successional dynamics. Comparisons among geologic, pedologic and vegetation environmental drivers indicated broad correlations across an environmental gradient, corresponding to a grassland to forest transition. The woodland communities appear to be part of a complex soil moisture and chemistry gradient that affects the extent, density, basal area and species composition of these communities. Over the gradient, there is an increase in α diversity, a decrease in the density of xeric and invasive species, and an increase in stem density of more mesic species. Dendrochronology suggests poor recruitment of xeric species and concomitant increase in more mesic species. The data indicated that former C4-dominated grasslands were initially invaded by conifers and are now experiencing mesophication, with growing dominance by Acer, Nyssa and more mesic Quercus and Fagus species.
US protected lands mismatch biodiversity priorities
Authors: Jenkins Clinton N. , Van Houtan Kyle S. , Pimm Stuart L. , Sexton Joseph O.
Published: April 2015

Significance

The United States has one of the oldest and most sophisticated systems of protected areas in the world. Given the large amount of information on the country’s biodiversity, and the potential resources available, one might expect it to do well in protecting biodiversity. We find that it does not. The United States protected areas do not adequately cover the country’s unique species. To improve the coverage, we map priorities for multiple taxa and recommend specific areas for immediate conservation attention. These areas contain a mix of public and private land, meaning that major progress in conservation will require actions in both the public and private sectors, and will succeed only if done in the correct areas.
Productive mRNA stem loop-mediated transcriptional slippage: Crucial features in common with intrinsic terminators
Authors: Penno Christophe , Sharma Virag , Coakley Arthur , O’Connell Motherway Mary , van Sinderen Douwe , Lubkowska Lucyna , Kireeva Maria L. , Kashlev Mikhail , Baranov Pavel V. , Atkins John F.
Published: April 2015

Significance

Perturbation of transcription register by RNA polymerase, transcription slippage, is used to yield additional protein products. Known functionally important cases involve a small number of short sequences without secondary structure. The discovery reported here of the dependence of a newly identified motif on nascent RNA forming a stem loop structure within the RNA exit channel of the polymerase greatly extends the potential for a broad variety of putative slippage sequences, especially as the phenomenon has been observed with both bacterial and eukaryotic RNA polymerases. Characterization of the mechanism involved shows similarities with, and differences from, intrinsic transcription termination, which also depends on formation of RNA stem loop structures. Our findings reveal novel insights to RNA polymerase versatility and functioning.
Cadherin-related family member 3, a childhood asthma susceptibility gene product, mediates rhinovirus C binding and replication
Authors: Bochkov Yury A. , Watters Kelly , Ashraf Shamaila , Griggs Theodor F. , Devries Mark K. , Jackson Daniel J. , Palmenberg Ann C. , Gern James E.
Published: April 2015

Significance

The rhinovirus C (RV-C) species was first identified in 2006 and is a major cause of acute respiratory illnesses in children and hospitalizations for exacerbations of asthma. In this study, we discovered that expression of human cadherin-related family member 3 (CDHR3), a transmembrane protein with yet unknown biological function, enables RV-C binding and replication in normally unsusceptible host cells. Intriguingly, we found that a coding SNP (rs6967330, C
529
Y) in CDHR3, previously linked to wheezing illnesses and hospitalizations for childhood asthma by genetic analysis, also mediates enhanced RV-C binding and increased progeny yields in vitro. Finally, using structural modeling, we identified potential binding sites in CDHR3 domains 1 and 2 interacting with viral capsid surface regions that are highly conserved among RV-C types.
Sterile inflammation in the spleen during atherosclerosis provides oxidation-specific epitopes that induce a protective B-cell response
Authors: Grasset Emilie K. , Duhlin Amanda , Agardh Hanna E. , Ovchinnikova Olga , Hägglöf Thomas , Forsell Mattias N. , Paulsson-Berne Gabrielle , Hansson Göran K. , Ketelhuth Daniel F. J. , Karlsson Mikael C. I.
Published: April 2015

Significance

In this study we investigate the origin of the protective B-cell response in the spleen in atherosclerosis. We find an ongoing B-cell activation with production of antibodies against oxidation-specific epitopes. In addition, this response can be accelerated using apoptotic cells alone that reduce lesion development and serum cholesterol in a B-cell–dependent manner. This study pinpoints the spleen as an important organ for atherosclerosis-associated immunity and provides novel pathways to use for treatment.
Mosaic nature of the mitochondrial proteome: Implications for the origin and evolution of mitochondria
Authors: Gray Michael W.
Published: April 2015

Comparative studies of the mitochondrial proteome have identified a conserved core of proteins descended from the α-proteobacterial endosymbiont that gave rise to the mitochondrion and was the source of the mitochondrial genome in contemporary eukaryotes. A surprising result of phylogenetic analyses is the relatively small proportion (10–20%) of the mitochondrial proteome displaying a clear α-proteobacterial ancestry. A large fraction of mitochondrial proteins typically has detectable homologs only in other eukaryotes and is presumed to represent proteins that emerged specifically within eukaryotes. A further significant fraction of the mitochondrial proteome consists of proteins with homologs in prokaryotes, but without a robust phylogenetic signal affiliating them with specific prokaryotic lineages. The presumptive evolutionary source of these proteins is quite different in contending models of mitochondrial origin.
Pain-enhancing mechanism through interaction between TRPV1 and anoctamin 1 in sensory neurons
Authors: Takayama Yasunori , Uta Daisuke , Furue Hidemasa , Tominaga Makoto
Published: April 2015

Significance

The capsaicin receptor transient receptor potential cation channel vanilloid 1 (TRPV1) and anoctamin 1 (ANO1) work as receptors activated by noxious stimuli in sensory nerve endings. It is believed that activation of the two channels causes cation influx and anion efflux, respectively, both of which lead to depolarization. We show that ANO1 is activated by calcium ions entering neurons through TRPV1 activation based on their physical binding on the cell membrane. Indeed, both capsaicin-activated inward currents in sensory neurons and capsaicin-induced pain-related behaviors in mice were inhibited significantly by ANO1 blockade. To our knowledge, this is the first evidence for a mechanism by which interaction between TRPV1 and ANO1 functions as a pain-enhancing mechanism.
Fishing amplifies forage fish population collapses
Authors: Essington Timothy E. , Moriarty Pamela E. , Froehlich Halley E. , Hodgson Emma E. , Koehn Laura E. , Oken Kiva L. , Siple Margaret C. , Stawitz Christine C.
Published: April 2015

Significance

Forage fish provide substantial benefits to both humans and ocean food webs, but these benefits may be in conflict unless there are effective policies governing human activities, such as fishing. Collapses of forage fish induce widespread ecological effects on dependent predators, but attributing collapses to fishing has been difficult because of natural fluctuations of these stocks. We implicate fishing in forage fish stock collapses by showing that high fishing rates are maintained when stock productivity is in rapid decline. As a consequence, the magnitude and frequency but not duration of stock collapses are far greater than expected from natural fluctuations. Risk-based management policies would provide substantial ecological benefits with little effect on fishery catches.
A modular toolkit to inhibit proline-rich motif–mediated protein–protein interactions
Authors: Opitz Robert , Müller Matthias , Reuter Cédric , Barone Matthias , Soicke Arne , Roske Yvette , Piotukh Kirill , Huy Peter , Beerbaum Monika , Wiesner Burkhard , Beyermann Michael , Schmieder Peter , Freund Christian , Volkmer Rudolf , Oschkinat Hartmut , Schmalz Hans-Günther , Kühne Ronald
Published: April 2015

Significance

Protein–protein interactions mediated by proline-rich motifs are involved in regulation of many important signaling cascades. Protein domains specialized in recognition of these motifs expose a flat and relatively rigid binding site that preferentially interacts with sequences adopting a left-handed polyproline helix II. Here, we present a toolkit of new chemical entities that enables rational construction of selective small-molecule inhibitors for these protein domains. As proof of principle, we developed a selective, cell-permeable inhibitor of
Drosophila
enabled (Ena)/vasodilator-stimulated phosphoprotein (VASP) homology 1 (EVH1) domains of the Ena/VASP protein family. Invasive breast-cancer cells treated with our EVH1 inhibitor showed strongly reduced cell invasion.
RETRACTED: Stochastic induction of persister cells by HipA through (p)ppGpp-mediated activation of mRNA endonucleases
Authors: Germain Elsa , Roghanian Mohammad , Gerdes Kenn , Maisonneuve Etienne
Published: April 2015

The model organism
Escherichia coli
codes for at least 11 type II toxin–antitoxin (TA) modules, all implicated in bacterial persistence (multidrug tolerance). Ten of these encode messenger RNA endonucleases (mRNases) inhibiting translation by catalytic degradation of mRNA, and the 11th module,
hipBA
, encodes HipA (high persister protein A) kinase, which inhibits glutamyl tRNA synthetase (GltX). In turn, inhibition of GltX inhibits translation and induces the stringent response and persistence. Previously, we presented strong support for a model proposing (p)ppGpp (guanosine tetra and penta-phosphate) as the master regulator of persistence. Stochastic variation of [(p)ppGpp] in single cells induced TA-encoded mRNases via a pathway involving polyphosphate and Lon protease. Polyphosphate activated Lon to degrade all known type II antitoxins of
E. coli
. In turn, the activated mRNases induced persistence and multidrug tolerance. However, even though it was known that activation of HipA stimulated (p)ppGpp synthesis, our model did not explain how
hipBA
induced persistence. Here we show that, in support of and consistent with our initial model, HipA-induced persistence depends not only on (p)ppGpp but also on the 10 mRNase-encoding TA modules, Lon protease, and polyphosphate. Importantly, observations with single cells convincingly show that the high level of (p)ppGpp caused by activation of HipA does not induce persistence in the absence of TA-encoded mRNases. Thus, slow growth per se does not induce persistence in the absence of TA-encoded toxins, placing these genes as central effectors of bacterial persistence.
Potential role for snoRNAs in PKR activation during metabolic stress
Authors: Youssef Osama A. , Safran Sarah A. , Nakamura Takahisa , Nix David A. , Hotamisligil Gökhan S. , Bass Brenda L.
Published: April 2015

Significance

Animals respond to stress in many ways, including initiating cell death to eliminate damaged cells. Protein kinase RNA-activated (PKR) is a protein that senses stress, and it promotes cell death by phosphorylating eIF2α to block protein synthesis in damaged cells. PKR is activated by metabolic stress, such as that associated with obesity, and this activation depends on its RNA-binding domain. Here we investigated whether endogenous RNA triggers PKR activation in response to lipid exposure. Our results indicate that a noncoding RNA, the small nucleolar RNA (snoRNA), binds PKR during cellular metabolic stress, and multiple experiments suggest snoRNAs also activate PKR during metabolic stress. snoRNAs have established roles in RNA modification, and our studies suggest they have additional roles in metabolic stress.
Insights into the origins of fish hunting in venomous cone snails from studies of
Conus tessulatus
Authors: Aman Joseph W. , Imperial Julita S. , Ueberheide Beatrix , Zhang Min-Min , Aguilar Manuel , Taylor Dylan , Watkins Maren , Yoshikami Doju , Showers-Corneli Patrice , Safavi-Hemami Helena , Biggs Jason , Teichert Russell W. , Olivera Baldomero M.
Published: April 2015

Significance

Only rarely is it possible to reconstruct molecular events that trigger the radiation of new lineages. Here we report key evidence that allows reconstruction of the transition from worm hunting to fish hunting among the species-rich family (Conidae) of marine cone snails (>700 species), which resulted in the emergence of multiple biodiverse piscivorous clades. A priori, the evolution of fish-hunting specialists would seem extremely improbable in a lineage of slowly moving snails that cannot swim, unlike their fish prey. The combination of results from molecular neuroscience, phylogenetic analysis, and chemical biology demonstrates that an ancestral cone snail venom peptide similar to δ-conotoxin TsVIA, a defensive venom component, preadapted a worm-hunting cone snail lineage, enabling the shift to a piscivorous lifestyle.
Long-acting progestin-only contraceptives impair endometrial vasculature by inhibiting uterine vascular smooth muscle cell survival
Authors: Kayisli Umit A. , Basar Murat , Guzeloglu-Kayisli Ozlem , Semerci Nihan , Atkinson Helen C. , Shapiro John , Summerfield Taryn , Huang S. Joseph , Prelle Katja , Schatz Frederick , Lockwood Charles J.
Published: April 2015

Significance

Over a million unintended pregnancies occur in the United States each year because of either discontinuation or misuse of contraceptives. The major reason for discontinuation of long-acting progestin-only contraceptives (LAPCs) is the occurrence of abnormal uterine bleeding (AUB). Uncovering the mechanisms underlying LAPC-induced AUB is essential to prevent their discontinuation. We found that LAPCs reduce proliferation of human and guinea pig endometrial vascular smooth muscle cells (VSMCs), resulting in production of thin-walled hyperdilated fragile microvessels. In cultured VSMCs, chemokine (C-C motif) ligand 2 reverses LAPC-mediated inhibition of VSMC proliferation, suggesting that LAPCs impair endometrial vascular integrity and that chemokine ligand 2 administration may prevent LAPC-induced AUB.
Rgg protein structure–function and inhibition by cyclic peptide compounds
Authors: Parashar Vijay , Aggarwal Chaitanya , Federle Michael J. , Neiditch Matthew B.
Published: April 2015

Significance

Peptide pheromones regulate developmental processes, including virulence, in Gram-positive bacteria. Immature propeptide pheromones are synthesized, secreted, and undergo proteolytic maturation to serve as intercellular signals. The regulator gene of glucosyltransferase (Rgg) transcription factors are a large family of receptors that directly bind pheromones transported to the cytosol. Here we report X-ray crystal structures of a
Streptococcus
Rgg protein alone and complexed with cyclosporin A, which is a potent inhibitor of pheromone signaling. Based on these structures and extensive genetic and biochemical studies, we mapped the pheromone-binding site, discovered mechanistic aspects of Rgg regulation, and determined how cyclosporin A and its nonimmunosuppressive analog valspodar function to inhibit pheromone-mediated receptor activation. We conclude that similar compounds targeting bacterial pheromone receptors have potential for therapeutic applications.
Ovary ecdysteroidogenic hormone requires a receptor tyrosine kinase to activate egg formation in the mosquito
Aedes aegypti
Authors: Vogel Kevin J. , Brown Mark R. , Strand Michael R.
Published: April 2015

Significance

Mosquitoes are important because several species transmit pathogens that cause major diseases of humans and other vertebrates. Mosquitoes acquire and transmit pathogens because most species must consume blood from a vertebrate host to produce eggs. Thus, a promising strategy for disease control is to interfere with mosquito reproduction. Blood feeding triggers the release of ovary ecdysteroidogenic hormone (OEH) from the mosquito brain, which is a key regulator of egg formation. To function, however, OEH must bind a receptor, which was previously unknown. Here we identify an OEH receptor and show that it is required for egg formation. Targeting OEH–receptor interactions provides opportunities for reducing mosquito reproduction and disease transmission.
Identity-specific coding of future rewards in the human orbitofrontal cortex
Authors: Howard James D. , Gottfried Jay A. , Tobler Philippe N. , Kahnt Thorsten
Published: April 2015

Significance

To make adaptive choices based on reward-predicting stimuli, organisms must take into account information about both the value and the specific identity of the reward to be obtained. Using appetizing food odors and pattern-based functional magnetic resonance imaging, we show that the human orbitofrontal cortex encodes future rewards in the form of identity-specific value codes. That is, even if valued the same, different expected rewards, such as pizza and chocolate cake, are differently encoded in this region. We further show that identity-specific and -general value coding regions are functionally linked to distinct regions, providing a novel account for the neural circuitry that underlies integration of both sensory and affective information to guide reward-related behavior.
Seizure-like activity in a juvenile Angelman syndrome mouse model is attenuated by reducing
Arc
expression
Authors: Mandel-Brehm Caleigh , Salogiannis John , Dhamne Sameer C. , Rotenberg Alexander , Greenberg Michael E.
Published: April 2015

Significance

Angelman syndrome (AS) is a human neurodevelopmental disorder caused by mutation of a specific gene,
UBE3A
. Studies of behavior in adult mouse models of AS reveal abnormalities similar to those observed in humans with AS. Because AS affects children, we hypothesized that it might be helpful to study this disorder using juvenile mice. We found that young AS mice display aberrant communication and motor behaviors and increased brain activity. Reducing the expression of the synaptic protein ARC reverses abnormal brain activity in AS mice, but has no effect on communication and motor behaviors in these mice. These findings suggest new approaches for identifying the neural circuits that are defective in AS, and for developing therapies for treating this disorder.
Stratifying tumour subtypes based on copy number alteration profiles using next-generation sequence data
Authors: Gusnanto Arief , Tcherveniakov Peter , Shuweihdi Farag , Samman Manar , Rabbitts Pamela , Wood Henry M.
Published: April 2015

Motivation: The role of personalized medicine and target treatment in the clinical management of cancer patients has become increasingly important in recent years. This has made the task of precise histological substratification of cancers crucial. Increasingly, genomic data are being seen as a valuable classifier. Specifically, copy number alteration (CNA) profiles generated by next-generation sequencing (NGS) can become a determinant for tumours subtyping. The principle purpose of this study is to devise a model with good prediction capability for the tumours histological subtypes as a function of both the patients covariates and their genome-wide CNA profiles from NGS data.

Results: We investigate a logistic regression for modelling tumour histological subtypes as a function of the patients’ covariates and their CNA profiles, in a mixed model framework. The covariates, such as age and gender, are considered as fixed predictors and the genome-wide CNA profiles are considered as random predictors. We illustrate the application of this model in lung and oral cancer datasets, and the results indicate that the tumour histological subtypes can be modelled with a good fit. Our cross-validation indicates that the logistic regression exhibits the best prediction relative to other classification methods we considered in this study. The model also exhibits the best agreement in the prediction between smooth-segmented and circular binary-segmented CNA profiles.

Availability and implementation: An R package to run a logistic regression is available in http://www1.maths.leeds.ac.uk/~arief/R/CNALR/.

Contact:  a.gusnanto@leeds.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Gene selection for the reconstruction of stem cell differentiation trees: a linear programming approach
Authors: Ghadie Mohamed A. , Japkowicz Nathalie , Perkins Theodore J.
Published: April 2015

Motivation: Stem cell differentiation is largely guided by master transcriptional regulators, but it also depends on the expression of other types of genes, such as cell cycle genes, signaling genes, metabolic genes, trafficking genes, etc. Traditional approaches to understanding gene expression patterns across multiple conditions, such as principal components analysis or K-means clustering, can group cell types based on gene expression, but they do so without knowledge of the differentiation hierarchy. Hierarchical clustering can organize cell types into a tree, but in general this tree is different from the differentiation hierarchy itself.

Methods: Given the differentiation hierarchy and gene expression data at each node, we construct a weighted Euclidean distance metric such that the minimum spanning tree with respect to that metric is precisely the given differentiation hierarchy. We provide a set of linear constraints that are provably sufficient for the desired construction and a linear programming approach to identify sparse sets of weights, effectively identifying genes that are most relevant for discriminating different parts of the tree.

Results: We apply our method to microarray gene expression data describing 38 cell types in the hematopoiesis hierarchy, constructing a weighted Euclidean metric that uses just 175 genes. However, we find that there are many alternative sets of weights that satisfy the linear constraints. Thus, in the style of random-forest training, we also construct metrics based on random subsets of the genes and compare them to the metric of 175 genes. We then report on the selected genes and their biological functions. Our approach offers a new way to identify genes that may have important roles in stem cell differentiation.

Contact:  tperkins@ohri.ca

Supplementary information:  Supplementary data are available at Bioinformatics online.
What is a Concussion?
Authors: Brody David L
Published: April 2015

A concussion is a traumatic brain injury, but not an immediately life threatening one. A traumatic brain injury occurs when a sudden force is applied to the brain from outside. But not every force causes a concussion. In fact, most do not. The scalp, skull, and dura do a pretty good job protecting our brains from most of what happens to us on a daily basis. A traumatic brain injury means that the force applied to the brain caused a disruption in the brain’s structure, an impairment of the brain’s function, or both. A CT scan or an MRI scan may be negative, but this does not mean that there has not been a concussion. Traumatic brain injury, especially concussion, is a clinical diagnosis, not based on any lab test or scan. Typically, patients with concussion have Glasgow Coma Scale between 13 and 15.
Fatigue
Authors: Brody David L
Published: April 2015

A systematic approach to fatigue: figure out how bad it is; rule out the complaint of concussion-related fatigue as an excuse to get out of school, work, or unpleasant chores at home by asking the collateral source about how fatigued the patient acts in everyday life; rule out depression; rule out a primary sleep disorder; rule out alcohol, sedating medications, and other drugs; rule out withdrawal from stimulants; rule out a systemic cause such as hypotension, hypoxemia, renal failure, liver failure, anemia, hyponatremia, hypothyroidism, vitamin D deficiency, or chronic urinary tract infection. If these are not present or fatigue persists after treatment, consider prescribing one or more of the following: a very gradually progressive exercise program, bright light treatment, complete alcohol cessation, a diet that is low in refined sugar, a stimulant, amantadine, and modafinil.