bluuebunny/crossref_metadata_2025 huggingface dataset:
Simulation of magnetic holes formation in the magnetosheath
Authors: Ahmadi Narges , Germaschewski Kai , Raeder Joachim
Published: December 2017

Magnetic holes have been frequently observed in the Earth's magnetosheath and are believed to be the consequence of the nonlinear evolution of the mirror instability. Mirror mode perturbations mainly form as magnetic holes in regions where the plasma is marginally mirror stable with respect to the linear instability criterion. We present an expanding box particle-in-cell simulation to mimic the changing conditions in the magnetosheath as the plasma is convected through it that produces mirror mode magnetic holes. We show that in the initial nonlinear evolution, where the plasma conditions are mirror unstable, the magnetic peaks are dominant, while later, as the plasma relaxes toward marginal stability, the fluctuations evolve into deep magnetic holes. While the averaged plasma parameters in the simulation remain close to the mirror instability threshold, the local plasma in the magnetic holes is highly unstable to mirror instability and locally mirror stable in the magnetic peaks.
Multi-state effective Hamiltonian and size-consistency corrections in stochastic configuration interactions
Authors: Ten-no Seiichiro L.
Published: December 2017

Model space quantum Monte Carlo (MSQMC) is an extension of full configuration interaction QMC that allows us to calculate quasi-degenerate and excited electronic states by sampling the effective Hamiltonian in the model space. We introduce a novel algorithm based on the state-selective partitioning for the effective Hamiltonian using left eigenvectors to calculate several electronic states simultaneously at much less computational cost than the original MSQMC with the energy-dependent partitioning. The sampling of walkers in MSQMC is analyzed in the single reference limit using a stochastic algorithm for higher-order perturbation energies by the analogy of the deterministic case utilizing a full configuration interaction program. We further develop size-consistency corrections of the initiator adaptation (i-MSQMC) in three different ways, i.e., the coupled electron pair approximation, a posteriori, and second-order perturbative corrections. It is clearly demonstrated that most of the initiator error is originating from the deficiency of proper scaling of correlation energy due to its truncated CI nature of the initiator approximation and that the greater part of the error can be recovered by the size-consistency corrections developed in this work.
ReS2-based interlayer tunnel field effect transistor
Authors: Mohammed Omar B. , Movva Hema C. P. , Prasad Nitin , Valsaraj Amithraj , Kang Sangwoo , Corbet Chris M. , Taniguchi Takashi , Watanabe Kenji , Register Leonard F. , Tutuc Emanuel , Banerjee Sanjay K.
Published: December 2017

In this study, we report the fabrication and characterization of a vertical resonant interlayer tunneling field-effect transistor created using exfoliated, few-layer rhenium disulfide (ReS2) flakes as the electrodes and hexagonal boron nitride as the tunnel barrier. Due to the Γ-point conduction band minimum, the ReS2 based system offers the possibility of resonant interlayer tunneling and associated low-voltage negative differential resistance (NDR) without rotational alignment of the electrode crystal orientations. Substantial NDR is observed, which appears consistent with in-plane crystal momentum conserving tunneling, although considerably broadened by scattering consistent within low mobility ReS2 flakes.
Accurate and balanced anisotropic Gaussian type orbital basis sets for atoms in strong magnetic fields
Authors: Zhu Wuming , Trickey S. B.
Published: December 2017

In high magnetic field calculations, anisotropic Gaussian type orbital (AGTO) basis functions are capable of reconciling the competing demands of the spherically symmetric Coulombic interaction and cylindrical magnetic (B field) confinement. However, the best available a priori procedure for composing highly accurate AGTO sets for atoms in a strong B field [W. Zhu et al., Phys. Rev. A 90, 022504 (2014)] yields very large basis sets. Their size is problematical for use in any calculation with unfavorable computational cost scaling. Here we provide an alternative constructive procedure. It is based upon analysis of the underlying physics of atoms in B fields that allow identification of several principles for the construction of AGTO basis sets. Aided by numerical optimization and parameter fitting, followed by fine tuning of fitting parameters, we devise formulae for generating accurate AGTO basis sets in an arbitrary B field. For the hydrogen iso-electronic sequence, a set depends on B field strength, nuclear charge, and orbital quantum numbers. For multi-electron systems, the basis set formulae also include adjustment to account for orbital occupations. Tests of the new basis sets for atoms H through C (1 ≤ Z ≤ 6) and ions Li+, Be+, and B+, in a wide B field range (0 ≤ B ≤ 2000 a.u.), show an accuracy better than a few μhartree for single-electron systems and a few hundredths to a few mHs for multi-electron atoms. The relative errors are similar for different atoms and ions in a large B field range, from a few to a couple of tens of millionths, thereby confirming rather uniform accuracy across the nuclear charge Z and B field strength values. Residual basis set errors are two to three orders of magnitude smaller than the electronic correlation energies in multi-electron atoms, a signal of the usefulness of the new AGTO basis sets in correlated wavefunction or density functional calculations for atomic and molecular systems in an external strong B field.
Trapping of sub-relativistic particles in laser driven accelerators
Authors: Hanuka Adi , Schächter Levi
Published: December 2017

We investigate the longitudinal and transverse dynamics of sub-relativistic electrons during the trapping process, as facilitated by an adiabatically tapered dielectric structure. The characteristics of the trapped electrons are studied for different initial conditions and structure's parameters. A set of optimal parameters that exemplify our approach are presented. Specifically, we determine the condition where the transverse emittance is preserved during the trapping process.
The importance of nuclear quantum effects in spectral line broadening of optical spectra and electrostatic properties in aromatic chromophores
Authors: Law Y. K. , Hassanali A. A.
Published: December 2017

In this work, we examine the importance of nuclear quantum effects on capturing the line broadening and vibronic structure of optical spectra. We determine the absorption spectra of three aromatic molecules indole, pyridine, and benzene using time dependent density functional theory with several molecular dynamics sampling protocols: force-field based empirical potentials, ab initio simulations, and finally path-integrals for the inclusion of nuclear quantum effects. We show that the absorption spectrum for all these chromophores are similarly broadened in the presence of nuclear quantum effects regardless of the presence of hydrogen bond donor or acceptor groups. We also show that simulations incorporating nuclear quantum effects are able to reproduce the heterogeneous broadening of the absorption spectra even with empirical force fields. The spectral broadening associated with nuclear quantum effects can be accounted for by the broadened distribution of chromophore size as revealed by a particle in the box model. We also highlight the role that nuclear quantum effects have on the underlying electronic structure of aromatic molecules as probed by various electrostatic properties.
Observing non-equilibrium state of transport through graphene channel at the nano-second time-scale
Authors: Mishra Abhishek , Meersha Adil , Raghavan Srinivasan , Shrivastava Mayank
Published: December 2017

Electrical performance of a graphene FET is drastically affected by electron-phonon inelastic scattering. At high electric fields, the out-of-equilibrium population of optical phonons equilibrates by emitting acoustic phonons, which dissipate the energy to heat sinks. The equilibration time of the process is governed by thermal diffusion time, which is few nano-seconds for a typical graphene FET. The nano-second time-scale of the process keeps it elusive to conventional steady-state or DC measurement systems. Here, we employ a time-domain reflectometry-based technique to electrically probe the device for few nano-seconds and investigate the non-equilibrium state. For the first time, the transient nature of electrical transport through graphene FET is revealed. A maximum change of 35% in current and 50% in contact resistance is recorded over a time span of 8 ns, while operating graphene FET at a current density of 1 mA/μm. The study highlights the role of intrinsic heating (scattering) in deciding metal-graphene contact resistance and transport through the graphene channel.
On spintronics-based nano-scale power electronics
Authors: Mayergoyz I. D. , Tyagi S.
Published: December 2017

It is suggested to explore achievements in spintronics for future design of nanoscale power converters. In contrast with traditional semiconductor switch-mode power converters, spintronics based power conversion may be achieved without repetitive (high-frequency) switching.
Temperature-dependent vibrational spectra and structure of liquid water from classical and quantum simulations with the MB-pol potential energy function
Authors: Reddy Sandeep K. , Moberg Daniel R. , Straight Shelby C. , Paesani Francesco
Published: December 2017

The structure of liquid water as a function of temperature is investigated through the modeling of infrared and Raman spectra along with structural order parameters calculated from classical and quantum molecular dynamics simulations with the MB-pol many-body potential energy function. The magnitude of nuclear quantum effects is also monitored by comparing the vibrational spectra obtained from classical and centroid molecular dynamics, both in intensities and peak positions. The observed changes in spectral activities are shown to reflect changes in the underlying structure of the hydrogen-bond network and are found to be particularly sensitive to many-body effects in the representation of the electrostatic interactions. Overall, good agreement is found with the experimental spectra, which provides further evidence for the accuracy of MB-pol in predicting the properties of water.
The temperature dependence of magnetic anisotropy of Nd-Fe-B thin films
Authors: Sato Takuya , Hashimoto Ryuji , Tanaka Yoshitomo , Suzuki Kenichi , Enokido Yasushi , Choi Kyung-Ku , Suzuki Takao
Published: December 2017

The magnetic properties of Nd-Fe-B thin films with the three different compositions (#1: Nd12.6Fe81.5B5.9, #2: Nd14.6Fe78.1B7.4 and #3: Nd22.6Fe66.2B11.2) are discussed. With increasing Nd content, the c-axis orientation along the film normal is enhanced. It is found that sample #2 possesses the saturation magnetization Ms very close to that for Nd2Fe14B over a temperature range from 100 to about 300K. The magnetic anisotropy constant Ku2 for sample #2 is the highest among those samples, but smaller by about 20%, as compared to that for Nd2Fe14B. It is of interest to note that the temperature TR at which Ku1 changes its sign is lower by about 30K as compared to that previously reported for Nd2Fe14B. The reason for this discrepancy is not clear, but could be due to the presence of the minority phases of Nd-rich compounds and also a possible contribution of the magneto-elastic effect to the net magnetic anisotropy.
Development of device for quantifying magnetic nanoparticle tracers accumulating in sentinel lymph nodes
Authors: Kuwahata Akihiro , Kaneko Miki , Chikaki Shinichi , Kusakabe Moriaki , Sekino Masaki
Published: December 2017

The developed device with electromagnetic coils and small permanent magnets quantifies the iron contents of superparamagnetic iron oxide nanoparticles for sentinel lymph node (SLN) biopsy. To remove diamagnetic and paramagnetic components and detect only superparamagnetic components, a 2nd harmonics signal is detected by a gradiometer under a moderate AC magnetic field (1–2 mT) with the fundamental frequency (2.944 kHz) of the coils and DC magnetic field (1–2 mT) of the magnets. The detection limit with a signal-to-noise ratio of 5 is approximately 0.28 μg of iron, and the device has a wide dynamic range of 104, 0.28 μg–2.8 mg. Additional coils and permanent magnets play an important role producing the optimum distribution of AC/DC magnetic fields for an iron distribution-independent and SLN size-independent quantification. We demonstrated the quantification of the iron in phantoms, which have a size of 3–20 mm with varied iron distributions and contain magnetic nanoparticles numerically. These results indicate that the developed device is useful for quantifying the magnetic nanoparticles accumulating in SLNs.
S2p core level spectroscopy of short chain oligothiophenes
Authors: Baseggio O. , Toffoli D. , Stener M. , Fronzoni G. , de Simone M. , Grazioli C. , Coreno M. , Guarnaccio A. , Santagata A. , D’Auria M.
Published: December 2017

The Near-Edge X-ray-Absorption Fine-Structure (NEXAFS) and X-ray Photoemission Spectroscopy (XPS) of short-chain oligothiophenes (thiophene, 2,2′-bithiophene, and 2,2′:5′,2″-terthiophene) in the gas phase have been measured in the sulfur L2,3-edge region. The assignment of the spectral features is based on the relativistic two-component zeroth-order regular approximation time dependent density functional theory approach. The calculations allow us to estimate both the contribution of the spin-orbit splitting and of the molecular-field splitting to the sulfur binding energies and give results in good agreement with the experimental measurements. The deconvolution of the calculated S2p NEXAFS spectra into the two manifolds of excited states converging to the LIII and LII edges facilitates the attribution of the spectral structures. The main S2p NEXAFS features are preserved along the series both as concerns the energy positions and the nature of the transitions. This behaviour suggests that the electronic and geometrical environment of the sulfur atom in the three oligomers is relatively unaffected by the increasing chain length. This trend is also observed in the XPS spectra. The relatively simple structure of S2p NEXAFS spectra along the series reflects the localized nature of the virtual states involved in the core excitation process.
Effects of the magnetic field variation on the spin wave interference in a magnetic cross junction
Authors: Balynskiy M. , Chiang H. , Kozhevnikov A. , Dudko G. , Filimonov Y. , Balandin A. A. , Khitun A.
Published: December 2017

This article reports results of the investigation of the effect of the external magnetic field variation on the spin wave interference in a magnetic cross junction. The experiments were performed using a micrometer scale Y3Fe5O12 cross structure with a set of micro-antennas fabricated on the edges of the cross arms. Two of the antennas were used for the spin wave excitation while a third antenna was used for detecting the inductive voltage produced by the interfering spin waves. It was found that a small variation of the bias magnetic field may result in a significant change of the output inductive voltage. The effect is most prominent under the destructive interference condition. The maximum response exceeds 30 dB per 0.1 Oe at room temperature. It takes a relatively small bias magnetic field variation of about 1 Oe to drive the system from the destructive to the constructive interference conditions. The switching is accompanied by a significant, up to 50 dB, change in the output voltage. The obtained results demonstrate a feasibility of the efficient spin wave interference control by an external magnetic field, which may be utilized for engineering novel type of magnetometers and magnonic logic devices.
Room-temperature magnetoelectric effect in a chiral smectic liquid crystal
Authors: Ueda H. , Akita T. , Uchida Y. , Kimura T.
Published: December 2017

A direct magnetoelectric effect, an induction of electric polarization by a magnetic field, was observed at room temperature in a chiral smectic liquid crystal without magnetic metals or radicals. Our detailed measurements of the magnetoelectric effect and the magnetodielectric effect suggest a unique origin of the magnetoelectric coupling in the liquid crystal, that is, a magnetic-field manipulation of the molecular orientation state, which is closely coupled with a local electric dipole moment due to the chirality-induced symmetry breaking. This unconventional strategy based on the softness of liquid crystals provides one of the promising directions towards the achievement of room-temperature metal-free magnetoelectrics.
Burying non-radiative defects in InGaN underlayer to increase InGaN/GaN quantum well efficiency
Authors: Haller C. , Carlin J.-F. , Jacopin G. , Martin D. , Butté R. , Grandjean N.
Published: December 2017

The insertion of an InGaN underlayer (UL) is known to strongly improve the performance of InGaN/GaN quantum well (QW) based blue light emitting diodes (LEDs). However, the actual physical mechanism responsible for it is still unclear. We thus conduct a systematic study and investigate different hypotheses. To this aim, InGaN/GaN single (S) QWs are grown on sapphire and GaN free-standing substrates with or without InGaN UL. This allows us to conclude that (i) improvement of LED performance is due to a higher internal quantum efficiency of the InGaN/GaN SQW and (ii) reduction of structural defects is not at play. Furthermore, we show that neither the surface morphology nor the strain of the top GaN layer before the growth of the QW is affected by the InGaN UL. Finally, we find that the beneficial effect of the InGaN UL is still present after 100 nm of GaN. This result combined with band structure modelling rules out the hypothesis of higher QW oscillator strength induced by a reduction of the internal electric field due to band bending. In conclusion, we demonstrate that the increase in InGaN/GaN QW efficiency is the consequence of a reduction of non-radiative recombination centers in the QW itself, independent of the dislocation density.
Spectroscopic study of native defects in the semiconductor to metal phase transition in V2O5 nanostructure
Authors: Basu Raktima , Dhara Sandip
Published: December 2017

Vanadium is a transition metal with multiple oxidation states and V2O5 is the most stable form among them. Besides catalysis, chemical sensing, and photo-chromatic applications, V2O5 is also reported to exhibit a semiconductor to metal transition (SMT) at a temperature range of 530–560 K. Even though there are debates in using the term “SMT” for V2O5, the metallic behavior above the transition temperature and its origin are of great interest in the scientific community. In this study, V2O5 nanostructures were deposited on a SiO2/Si substrate by the vapour transport method using Au as a catalyst. Temperature dependent electrical measurement confirms the SMT in V2O5 without any structural change. Temperature dependent photoluminescence analysis proves the appearance of oxygen vacancy related peaks due to reduction of V2O5 above the transition temperature, as also inferred from temperature dependent Raman spectroscopic studies. The newly evolved defect levels in the V2O5 electronic structure with increasing temperature are also understood from the downward shift of the bottom most split-off conduction bands due to breakdown of pdπ bonds leading to metallic behavior in V2O5 above the transition temperature.
Probing resonant energy transfer in collisions of ammonia with Rydberg helium atoms by microwave spectroscopy
Authors: Zhelyazkova V. , Hogan S. D.
Published: December 2017

We present the results of experiments demonstrating the spectroscopic detection of Förster resonance energy transfer from NH3 in the X1A1 ground electronic state to helium atoms in 1sns 3S1 Rydberg levels, where n = 37 and n = 40. For these values of n, the 1sns 3S1 → 1snp 3PJ transitions in helium lie close to resonance with the ground-state inversion transitions in NH3 and can be tuned through resonance using electric fields of less than 10 V/cm. In the experiments, energy transfer was detected by direct state-selective electric field ionization of the 3S1 and 3PJ Rydberg levels and by monitoring the population of the 3DJ levels following pulsed microwave transfer from the 3PJ levels. Detection by microwave spectroscopic methods represents a highly state selective, low-background approach to probing the collisional energy transfer process and the environment in which the atom-molecule interactions occur. The experimentally observed electric-field dependence of the resonant energy transfer process, probed both by direct electric field ionization and by microwave transfer, agrees well with the results of calculations performed using a simple theoretical model of the energy transfer process. For measurements performed in zero electric field with atoms prepared in the 1s40s 3S1 level, the transition from a regime in which a single energy transfer channel can be isolated for detection to one in which multiple collision channels begin to play a role has been identified as the NH3 density was increased.
Interface roughening in irradiated oxide dispersion strengthened steels
Authors: Ribis J. , Leprêtre F.
Published: December 2017

Oxide Dispersion Strengthened steels are considered as promising candidates for nuclear applications as cladding tubes for GEN IV reactors. These materials are reinforced by a fine dispersion of nano-oxides whose semi-coherent flat interfaces constitute trapping sites for radiation-induced point defects. However, the sink strength of such interfaces may change under irradiation since the interfaces become damaged themselves. Therefore, the behavior of semi-coherent flat interfaces under irradiation is under concern. After ion irradiation up to 150 dPa at 500 °C, High Resolution Transmission Electron Microscopy images show that interfaces are no longer sharp but present an irregular mound morphology owing to the destabilization by the nuclear cascade collisions of incoming ions. Further, the kinetic roughening of the interfaces appears to increase with the irradiation dose. However, the low magnitude of the roughness suggests that the interfaces are remarkably stable under irradiation.
Influence of substrate on structural, morphological and optical properties of TiO2 thin films deposited by reaction magnetron sputtering
Authors: Zhu Xinghua , Gu Peng , Wu Haihua , Yang Dingyu , Sun Hui , Wangyang Peihua , Li Jitao , Tian Haibo
Published: December 2017

Titanium dioxide (TiO2) films have been prepared by DC reaction magnetron sputtering technique on different substrates (glass, SiO2, platinum electrode-Pt, Silicon-Si). X-ray diffraction (XRD) patterns showed that all TiO2 films were grown along the preferred orientation of (110) plane. Samples on Si and Pt substrates are almost monophasic rutile, however, samples on glass and SiO2 substrates accompanied by a weak anatase structure. Atomic force microscopy (AFM) images revealed uniform grain distribution except for films on Pt substrates. Photoluminescence (PL) spectra showed obvious intrinsic emission band, but films on glass was accompanied by a distinct defect luminescence region. Raman spectroscopy suggested that all samples moved to high wavenumbers and films on glass moved obviously.
New Products
Authors: Mandelis Andreas
Published: December 2017

In order to supplement manufacturers’ information, this Department will welcome the submission by our readers of brief communications reporting measurements on the physical properties of materials which supersede earlier data or suggest new research applications.
Economic networks: Heterogeneity-induced vulnerability and loss of synchronization
Authors: Colon Célian , Ghil Michael
Published: December 2017

Interconnected systems are prone to propagation of disturbances, which can undermine their resilience to external perturbations. Propagation dynamics can clearly be affected by potential time delays in the underlying processes. We investigate how such delays influence the resilience of production networks facing disruption of supply. Interdependencies between economic agents are modeled using systems of Boolean delay equations (BDEs); doing so allows us to introduce heterogeneity in production delays and in inventories. Complex network topologies are considered that reproduce realistic economic features, including a network of networks. Perturbations that would otherwise vanish can, because of delay heterogeneity, amplify and lead to permanent disruptions. This phenomenon is enabled by the interactions between short cyclic structures. Difference in delays between two interacting, and otherwise resilient, structures can in turn lead to loss of synchronization in damage propagation and thus prevent recovery. Finally, this study also shows that BDEs on complex networks can lead to metastable relaxation oscillations, which are damped out in one part of a network while moving on to another part.
Bosonic quadratic Hamiltonians
Authors: Dereziński Jan
Published: December 2017

We discuss self-adjoint operators given formally by expressions quadratic in bosonic creation and annihilation operators. We give conditions when they can be defined as self-adjoint operators, possibly after an infinite renormalization. We also discuss explicit formulas for their infimum. Our main motivation comes from local quantum field theory, which furnishes interesting examples of bosonic quadratic Hamiltonians that require an infinite renormalization.
Causes and consequences of decreasing atmospheric organic aerosol in the United States
Authors: Ridley D. A. , Heald C. L. , Ridley K. J. , Kroll J. H.
Published: December 2017

Significance

Ambient particulate matter (PM) was responsible for four million premature deaths globally in 2012. The deleterious health impacts of PM motivated the US Environmental Protection Agency (EPA) to curtail emission of PM and precursor gases. The 2011 EPA report to Congress on the efficacy of the Clean Air Act estimated a dramatic reduction in human mortality resulting from these emissions controls. Surface measurements from 1990 to 2012 indicate a significant US-wide decline in the organic portion of the PM, not accounted for in the EPA report. We show that the decline in organic aerosol is mediated primarily through changes in vehicle and residential fuel-burning emissions, indicating that the Clean Air Act is even more beneficial to US air quality than currently appreciated.
Evaluating the contribution of rare variants to type 2 diabetes and related traits using pedigrees
Authors: Jun Goo , Manning Alisa , Almeida Marcio , Zawistowski Matthew , Wood Andrew R. , Teslovich Tanya M. , Fuchsberger Christian , Feng Shuang , Cingolani Pablo , Gaulton Kyle J. , Dyer Thomas , Blackwell Thomas W. , Chen Han , Chines Peter S. , Choi Sungkyoung , Churchhouse Claire , Fontanillas Pierre , King Ryan , Lee SungYoung , Lincoln Stephen E. , Trubetskoy Vasily , DePristo Mark , Fingerlin Tasha , Grossman Robert , Grundstad Jason , Heath Alison , Kim Jayoun , Kim Young Jin , Laramie Jason , Lee Jaehoon , Li Heng , Liu Xuanyao , Livne Oren , Locke Adam E. , Maller Julian , Mazur Alexander , Morris Andrew P. , Pollin Toni I. , Ragona Derek , Reich David , Rivas Manuel A. , Scott Laura J. , Sim Xueling , Tearle Rick G. , Teo Yik Ying , Williams Amy L. , Zöllner Sebastian , Curran Joanne E. , Peralta Juan , Akolkar Beena , Bell Graeme I. , Burtt Noël P. , Cox Nancy J. , Florez Jose C. , Hanis Craig L. , McKeon Catherine , Mohlke Karen L. , Seielstad Mark , Wilson James G. , Atzmon Gil , Below Jennifer E. , Dupuis Josée , Nicolae Dan L. , Lehman Donna , Park Taesung , Won Sungho , Sladek Robert , Altshuler David , McCarthy Mark I. , Duggirala Ravindranath , Boehnke Michael , Frayling Timothy M. , Abecasis Gonçalo R. , Blangero John
Published: December 2017

Significance

Contributions of rare variants to common and complex traits such as type 2 diabetes (T2D) are difficult to measure. This paper describes our results from deep whole-genome analysis of large Mexican-American pedigrees to understand the role of rare-sequence variations in T2D and related traits through enriched allele counts in pedigrees. Our study design was well-powered to detect association of rare variants if rare variants with large effects collectively accounted for large portions of risk variability, but our results did not identify such variants in this sample. We further quantified the contributions of common and rare variants in gene expression profiles and concluded that rare expression quantitative trait loci explain a substantive, but minor, portion of expression heritability.
High-resolution structure of podovirus tail adaptor suggests repositioning of an octad motif that mediates the sequential tail assembly
Authors: Liang Lingfei , Zhao Haiyan , An Bowen , Tang Liang
Published: December 2017

Significance

Many dsDNA bacteriophages possess a tail that encodes functions essential for viral life cycles. Assembly of such a molecular machine has been shown to occur in a sequential manner. Here, we report the high-resolution crystal structure of the tail adaptor protein gp7 from
Shigella
phage Sf6. Comparative structural studies reveal that the N-terminal portion undergoes structural rearrangement by repositioning two consecutive repeats of a conserved octad sequence motif, turning the molecule from the preassembly state to the postassembly state, which creates the binding site for the next tail component to attach to. These results provide a structural basis for a mechanism of repositioning of sequence motifs by which the adaptor protein mediates the sequential assembly of the phage tail.
Low-lying excited states in crystalline perylene
Authors: Rangel Tonatiuh , Rinn Andre , Sharifzadeh Sahar , da Jornada Felipe H. , Pick André , Louie Steven G. , Witte Gregor , Kronik Leeor , Neaton Jeffrey B. , Chatterjee Sangam
Published: December 2017

Significance

Molecular solids are an important class of highly tunable, chemically diverse, cheap-to-process materials with promise for next-generation organic optoelectronics. Bound largely by noncovalent interactions, these materials harbor unique charge carrier generation and transport phenomena distinct from conventional semiconductors, an understanding of which requires a detailed description of the excited-state properties of molecular solids. Recent advances in synthetic techniques, ab initio theory, and spectroscopic measurements have enabled such a description, and here we perform quantitative theoretical calculations and high-resolution measurements on a high-quality single-crystal thin film of perylene, an exemplar molecular solid. We obtain excellent agreement between theory and experiment, and a clear picture of the low-lying excitations in perylene responsible for its distinctive optical properties.
Multiple origins of interdependent endosymbiotic complexes in a genus of cicadas
Authors: Łukasik Piotr , Nazario Katherine , Van Leuven James T. , Campbell Matthew A. , Meyer Mariah , Michalik Anna , Pessacq Pablo , Simon Chris , Veloso Claudio , McCutcheon John P.
Published: December 2017

Significance

Highly reduced genomes from bacteria that are long-term beneficial endosymbionts of insects often show remarkable structural stability. Endosymbionts in insects diverged by tens or hundreds of millions of years often have genomes almost completely conserved in gene order and content. Here, we show that an endosymbiont in some cicadas has repeatedly and independently fractured into complexes of distinct genomic and cellular lineages present in the same host. Individual endosymbiont lineages, having lost many of the essential ancestral genes, rely on each other for basic function and together seem to provide the same nutritional benefits as the ancestral single symbiont. These cicada endosymbionts show genomic parallels to mitochondria and provide another example of how normally stable genomes can lose structural stability.
Single-molecule FRET studies on the cotranscriptional folding of a thiamine pyrophosphate riboswitch
Authors: Uhm Heesoo , Kang Wooyoung , Ha Kook Sun , Kang Changwon , Hohng Sungchul
Published: December 2017

Significance

RNA molecules fold into functional structures as they are being synthesized by transcription. Here, we developed a single-molecule fluorescence resonance energy transfer (FRET) assay that permits real-time monitoring of the cotranscriptional folding of RNA molecules. This single-molecule FRET assay makes it possible to carry out controlled studies of the two main physical mechanisms that regulate cotranscriptional RNA folding: transcriptional pausing and transcriptional speed.
Two types of aggression in human evolution
Authors: Wrangham Richard W.
Published: December 2017

Two major types of aggression, proactive and reactive, are associated with contrasting expression, eliciting factors, neural pathways, development, and function. The distinction is useful for understanding the nature and evolution of human aggression. Compared with many primates, humans have a high propensity for proactive aggression, a trait shared with chimpanzees but not bonobos. By contrast, humans have a low propensity for reactive aggression compared with chimpanzees, and in this respect humans are more bonobo-like. The bimodal classification of human aggression helps solve two important puzzles. First, a long-standing debate about the significance of aggression in human nature is misconceived, because both positions are partly correct. The Hobbes–Huxley position rightly recognizes the high potential for proactive violence, while the Rousseau–Kropotkin position correctly notes the low frequency of reactive aggression. Second, the occurrence of two major types of human aggression solves the execution paradox, concerned with the hypothesized effects of capital punishment on self-domestication in the Pleistocene. The puzzle is that the propensity for aggressive behavior was supposedly reduced as a result of being selected against by capital punishment, but capital punishment is itself an aggressive behavior. Since the aggression used by executioners is proactive, the execution paradox is solved to the extent that the aggressive behavior of which victims were accused was frequently reactive, as has been reported. Both types of killing are important in humans, although proactive killing appears to be typically more frequent in war. The biology of proactive aggression is less well known and merits increased attention.
Locus coeruleus input to hippocampal CA3 drives single-trial learning of a novel context
Authors: Wagatsuma Akiko , Okuyama Teruhiro , Sun Chen , Smith Lillian M. , Abe Kuniya , Tonegawa Susumu
Published: December 2017

Significance

The ability to remember a new place is crucial for survival. The locus coeruleus (LC) in the brain stem is known to respond to novel sensory stimuli and can facilitate hippocampus-dependent memory, although the circuit and the role that LC plays in novelty-associated memory is unknown. We performed circuit-specific optogenetic inhibition and found that the hippocampal CA3 subregion is the crucial target of LC projections during the encoding of a novel context. Furthermore, we show with activity-dependent labeling and in vivo calcium imaging that LC inputs are necessary to provide stable neuronal representations of the context. This study provides evidence that LC neuromodulation, especially to the CA3 subregion, plays a crucial role in memory formation of a new context.
Colorectal cancer specific conditions promote
Streptococcus gallolyticus
gut colonization
Authors: Aymeric Laetitia , Donnadieu Françoise , Mulet Céline , du Merle Laurence , Nigro Giulia , Saffarian Azadeh , Bérard Marion , Poyart Claire , Robine Sylvie , Regnault Béatrice , Trieu-Cuot Patrick , Sansonetti Philippe J. , Dramsi Shaynoor
Published: December 2017

Significance

Growing evidence indicates a correlation between colorectal cancer and intestinal dysbiosis or colonization by single bacterial species such as
Streptococcus gallolyticus
subsp.
gallolyticus
(SGG), yet a causality link remains to be established. To address this point experimentally, we colonized
Apc

+/
−

Notch-inducible mice with SGG.
Apc

+/
−

is a pioneer somatic mutation driving the occurrence of polyps. We did not observe significant changes in the occurrence or development of polyps in this model. However, we observed a strong SGG colonization in
Apc

+/
−

mice at the expense of resident enterococci. We related this ecological substitution to activation of a SGG-specific bacteriocin whose activity is induced in vivo by the detergent effect of an increased concentration of secondary bile acids in relation to oncogenic situation.
Body weight homeostat that regulates fat mass independently of leptin in rats and mice
Authors: Jansson John-Olov , Palsdottir Vilborg , Hägg Daniel A. , Schéle Erik , Dickson Suzanne L. , Anesten Fredrik , Bake Tina , Montelius Mikael , Bellman Jakob , Johansson Maria E. , Cone Roger D. , Drucker Daniel J. , Wu Jianyao , Aleksic Biljana , Törnqvist Anna E. , Sjögren Klara , Gustafsson Jan-Åke , Windahl Sara H. , Ohlsson Claes
Published: December 2017

Significance

The only known homeostatic regulator of fat mass is the leptin system. We hypothesized that there is a second homeostat regulating body weight with an impact on fat mass. In this study we have added and removed weight loads from experimental animals and measured the effects on the biological body weight. The results demonstrate that there is a body weight homeostat that regulates fat mass independently of leptin. As the body weight-reducing effect of increased loading was dependent on osteocytes, we propose that there is a sensor for body weight in the long bones of the lower extremities acting as “body scales.” This is part of a body weight homeostat, “gravitostat,” that keeps body weight and body fat mass constant.
Field- and clinically derived estimates of
Wolbachia
-mediated blocking of dengue virus transmission potential in
Aedes aegypti
mosquitoes
Authors: Carrington Lauren B. , Tran Bich Chau Nguyen , Le Nhat Thanh Hoang , Luong Tai Thi Hue , Nguyen Truong Thanh , Nguyen Phong Thanh , Nguyen Chau Van Vinh , Nguyen Huong Thi Cam , Vu Trung Tuan , Vo Long Thi , Le Dui Thi , Vu Nhu Tuyet , Nguyen Giang Thi , Luu Hung Quoc , Dang Anh Duc , Hurst Timothy P. , O’Neill Scott L. , Tran Vi Thuy , Kien Duong Thi Hue , Nguyen Nguyet Minh , Wolbers Marcel , Wills Bridget , Simmons Cameron P.
Published: December 2017

Significance

In laboratory experiments,
Wolbachia
(
w
Mel strain)-infected
Aedes aegypti
are refractory to disseminated arboviral infections. Yet previous characterizations of
w
Mel-mediated blocking have not considered several biologically and ecologically important factors likely to influence the virus–mosquito interaction. After direct feeding on 141 viremic dengue patients, we demonstrate
w
Mel lowers dengue virus (DENV) transmission potential and lengthens the extrinsic incubation period. Subsequently, using established field populations of wild-type and
w
Mel-infected
Ae. aegypti
, we compared field- versus laboratory-rearing conditions on mosquito susceptibility to disseminated DENV infection. The magnitude of
w
Mel-mediated virus blocking was even greater when mosquitoes developed under field conditions. These clinically and ecologically relevant findings support
Wolbachia
introgression into
Ae. aegypti
populations as a biocontrol method to reduce the transmission of DENV and other arboviruses.
Interfacial curvature effects on the monolayer morphology and dynamics of a clinical lung surfactant
Authors: Sachan Amit Kumar , Zasadzinski Joseph A.
Published: December 2017

Significance

Confocal microscopy provides high-resolution images of highly curved interfaces with the surprising result that the morphology of phase-separated lung surfactant monolayers changes dramatically as the interfacial curvature approaches alveolar dimensions (radius, ∼100 µm). This is due to the anisotropic bending properties of the semicrystalline liquid-condensed (LC) domains that lead to a transition between discrete, discontinuous domains on a flat interface to an interconnected meshwork on alveolar-size bubbles. This may have important implications toward understanding the dilatational properties of the monolayer-covered interfaces which can dictate lung stability during breathing.
Cell-specific and region-specific transcriptomics in the multiple sclerosis model: Focus on astrocytes
Authors: Itoh Noriko , Itoh Yuichiro , Tassoni Alessia , Ren Emily , Kaito Max , Ohno Ai , Ao Yan , Farkhondeh Vista , Johnsonbaugh Hadley , Burda Josh , Sofroniew Michael V. , Voskuhl Rhonda R.
Published: December 2017

Significance

Molecular mechanisms underlying distinct disabilities during neurological diseases may differ based on the neurological pathway involved. Multiple sclerosis (MS) is multifocal, characterized by distinct disabilities affecting walking, vision, cognition, and fatigue. Neuroprotective treatments tailored for each disability may be more effective than nonspecific treatments aiming to reduce a composite of disabilities in clinical trials. Here, we use the MS model to apply a cell-specific and region-specific gene expression approach to discover targets in distinct neuroanatomic regions. Altered cholesterol synthesis gene expression in astrocytes in spinal cord and optic nerve was identified as a potential target for walking and visual disabilities, respectively. This disability-specific discovery approach represents a strategy for finding neuroprotective treatments for multifocal neurodegenerative diseases.
Developmental origins of mosaic evolution in the avian cranium
Authors: Felice Ryan N. , Goswami Anjali
Published: December 2017

Significance

Studies reconstructing morphological evolution have long relied on simple representations of organismal form or on limited sampling of species, hindering a comprehensive understanding of the factors shaping biological diversity. Here, we combine high-resolution 3D quantification of skull shape with dense taxonomic sampling across a major vertebrate clade, birds, to demonstrate that the avian skull is formed of multiple semi-independent regions that epitomize mosaic evolution, with cranial regions and major lineages evolving with distinct rates and modes. We further show that the evolvability of different cranial regions reflects their disparate embryonic origins. Finally, we present a hypothetical reconstruction of the ancestral bird skull using this high-resolution shape data to generate a detailed estimate of extinct forms in the absence of well-preserved three-dimensional fossils.
ATM and ATR play complementary roles in the behavior of excitatory and inhibitory vesicle populations
Authors: Cheng Aifang , Zhao Teng , Tse Kai-Hei , Chow Hei-Man , Cui Yong , Jiang Liwen , Du Shengwang , Loy Michael M. T. , Herrup Karl
Published: December 2017

Significance

The symptoms of neurological diseases such as autism and schizophrenia are often attributed to a loss of excitatory/inhibitory balance of neural network function. By showing that ATR and ATM impact inhibitory and excitatory vesicle trafficking differently, our work expands the known repertoire of cytoplasmic functions for the two kinases and provides a new perspective on the origins of the symptoms of ataxia-telangiectasia (A-T) and Seckel syndrome (ATM and ATR deficiency, respectively). While these findings have their most immediate implications for the neurologic and cognitive symptoms of A-T and Seckel syndrome, they have potential relevance to a much broader range of neurologic conditions.
Identification of fusion genes and characterization of transcriptome features in T-cell acute lymphoblastic leukemia
Authors: Chen Bing , Jiang Lu , Zhong Meng-Ling , Li Jian-Feng , Li Ben-Shang , Peng Li-Jun , Dai Yu-Ting , Cui Bo-Wen , Yan Tian-Qi , Zhang Wei-Na , Weng Xiang-Qin , Xie Yin-Yin , Lu Jing , Ren Rui-Bao , Chen Su-Ning , Hu Jian-Da , Wu De-Pei , Chen Zhu , Tang Jing-Yan , Huang Jin-Yan , Mi Jian-Qing , Chen Sai-Juan
Published: December 2017

Significance

To get more insights into the disease mechanism of T-cell acute lymphoblastic leukemia (T-ALL), particularly in an adult group, we addressed the genomic landscape in 130 patients, including 61 cases of adult T-ALL. A number of new genetic aberrations were identified using integrated transcriptome and genomic analysis. Distinct T-ALL subgroups were defined according to the interplay among different genetic abnormalities and gene transcription patterns. Characterization of genomic features of T-ALL is valuable not only for a better understanding of leukemogenesis, but also for patient stratification and tailored therapy.
Heat activation is intrinsic to the pore domain of TRPV1
Authors: Zhang Feng , Jara-Oseguera Andres , Chang Tsg-Hui , Bae Chanhyung , Hanson Sonya M. , Swartz Kenton J.
Published: December 2017

Significance

The TRPV1 channel is an important detector of noxious heat, yet the location of the heat sensor and the mechanism of heat activation remain poorly understood. Here we used structure-based engineering between the heat-activated TRPV1 channel and the Shaker Kv channel to demonstrate that transplantation of the pore domain of TRPV1 into Shaker gives rise to functional channels that can be activated by a TRPV1-selective tarantula toxin and by noxious heat, demonstrating that the pore of TRPV1 contains the structural elements sufficient for activation by temperature.
Hybrid speciation leads to novel male secondary sexual ornamentation of an Amazonian bird
Authors: Barrera-Guzmán Alfredo O. , Aleixo Alexandre , Shawkey Matthew D. , Weir Jason T.
Published: December 2017

Significance

Hybridization between species can produce reproductively isolated lineages by combining parental genotypes in novel ways. Here, we used thousands of genetic markers to demonstrate that the recently rediscovered golden-crowned manakin represents an avian hybrid species from the Amazon basin. This hybrid species has a unique golden-colored crown patch used for display, which differs from the brilliant white coloration of the parental species. We used microscopy to demonstrate that, despite its unique coloration, the crown has intermediate color-producing morphological features at the nanoscale. We propose that these intermediate features disrupted the high reflectivity of the parental species, resulting in a dull hybrid population. Selection then sequestered carotenoids to the crown to compensate for its low reflectivity.
Global warming leads to more uniform spring phenology across elevations
Authors: Vitasse Yann , Signarbieux Constant , Fu Yongshuo H.
Published: December 2017

One hundred years ago, Andrew D. Hopkins estimated the progressive delay in tree leaf-out with increasing latitude, longitude, and elevation, referred to as “Hopkins’ bioclimatic law.” What if global warming is altering this well-known law? Here, based on ∼20,000 observations of the leaf-out date of four common temperate tree species located in 128 sites at various elevations in the European Alps, we found that the elevation-induced phenological shift (EPS) has significantly declined from 34 d⋅1,000 m
−1
conforming to Hopkins’ bioclimatic law in 1960, to 22 d⋅1,000 m
−1
in 2016, i.e., −35%. The stronger phenological advance at higher elevations, responsible for the reduction in EPS, is most likely to be connected to stronger warming during late spring as well as to warmer winter temperatures. Indeed, under similar spring temperatures, we found that the EPS was substantially reduced in years when the previous winter was warmer. Our results provide empirical evidence for a declining EPS over the last six decades. Future climate warming may further reduce the EPS with consequences for the structure and function of mountain forest ecosystems, in particular through changes in plant–animal interactions, but the actual impact of such ongoing change is today largely unknown.