bluuebunny/crossref_metadata_2025 huggingface dataset:
A coarse-grained model with implicit salt for RNAs: Predicting 3D structure, stability and salt effect
Authors: Shi Ya-Zhou , Wang Feng-Hua , Wu Yuan-Yan , Tan Zhi-Jie
Published: September 2014

To bridge the gap between the sequences and 3-dimensional (3D) structures of RNAs, some computational models have been proposed for predicting RNA 3D structures. However, the existed models seldom consider the conditions departing from the room/body temperature and high salt (1M NaCl), and thus generally hardly predict the thermodynamics and salt effect. In this study, we propose a coarse-grained model with implicit salt for RNAs to predict 3D structures, stability, and salt effect. Combined with Monte Carlo simulated annealing algorithm and a coarse-grained force field, the model folds 46 tested RNAs (≤45 nt) including pseudoknots into their native-like structures from their sequences, with an overall mean RMSD of 3.5 Å and an overall minimum RMSD of 1.9 Å from the experimental structures. For 30 RNA hairpins, the present model also gives the reliable predictions for the stability and salt effect with the mean deviation ∼ 1.0 °C of melting temperatures, as compared with the extensive experimental data. In addition, the model could provide the ensemble of possible 3D structures for a short RNA at a given temperature/salt condition.
Frequency-dependent failure mechanisms of nanocrystalline gold interconnect lines under general alternating current
Authors: Luo X. M. , Zhang B. , Zhang G. P.
Published: September 2014

Thermal fatigue failure of metallization interconnect lines subjected to alternating currents (AC) is becoming a severe threat to the long-term reliability of micro/nanodevices with increasing electrical current density/power. Here, thermal fatigue failure behaviors and damage mechanisms of nanocrystalline Au interconnect lines on the silicon glass substrate have been investigated by applying general alternating currents (the pure alternating current coupled with a direct current (DC) component) with different frequencies ranging from 0.05 Hz to 5 kHz. We observed both thermal fatigue damages caused by Joule heating-induced cyclic strain/stress and electromigration (EM) damages caused by the DC component. Besides, the damage formation showed a strong electrically-thermally-mechanically coupled effect and frequency dependence. At lower frequencies, thermal fatigue damages were dominant and the main damage forms were grain coarsening with grain boundary (GB) cracking/voiding and grain thinning. At higher frequencies, EM damages took over and the main damage forms were GB cracking/voiding of smaller grains and hillocks. Furthermore, the healing effect of the reversing current was considered to elucidate damage mechanisms of the nanocrystalline Au lines generated by the general AC. Lastly, a modified model was proposed to predict the lifetime of the nanocrystalline metal interconnect lines, i.e., that was a competing drift velocity-based approach based on the threshold time required for reverse diffusion/healing to occur.
Characterization and versatile applications of low hydrogen content SiOCN grown by plasma-enhanced chemical vapor deposition
Authors: Hamm Steven C. , Waidmann Jacob , Mathai Joseph C. , Gangopadhyay Keshab , Currano Luke , Gangopadhyay Shubhra
Published: September 2014

Low hydrogen content silicon oxycarbonitride (SiOCN) thin films were grown by plasma-enhanced chemical vapor deposition exploiting hydrogen dilution with silane/methane/nitrous oxide or tetramethylsilane/nitrous oxide precursors. The effects of deposition temperature were compared by investigating the compositional, optical, mechanical, and electrical properties of films grown at 100 °C, 250 °C, and 400 °C at thicknesses ranging from 50 nm to 10 μm. The dielectric constant and high breakdown strength of the films remain relatively constant at between 4–5 and 6.8 ± 0.2 MV cm−1 to 9.1 ± 0.3 MV cm−1, respectively, despite the differences in deposition temperature. Other properties of the films include excellent transparency in the visible regime, high nanoindentation hardness (4 to 12 GPa), and relatively low measured stress on Si (−20 to −300 MPa). Overall, the results of this work show that these SiOCN films can be used in a wide variety of applications, including as a dielectric within high voltage capacitors, transparent abrasion-resistant coatings for plastic windows, coatings on flexible substrates, a metal diffusion barrier for low-k dielectrics and polymer films, or within various microelectronic fabrication steps or systems.
Communication: Coupled-cluster interpretation of the photoelectron spectrum of ${\rm Au}_{3}^{-}$ Au 3−
Authors: Bauman Nicholas P. , Hansen Jared A. , Ehara Masahiro , Piecuch Piotr
Published: September 2014

We use the scalar relativistic ionized equation-of-motion coupled-cluster approaches, correlating valence and semi-core electrons and including up to 3-hole-2-particle terms in the ionizing operator, to investigate the photoelectron spectrum of \documentclass[12pt]{minimal}\begin{document}${\rm Au}_{3}^{-}$\end{document} Au 3−. We provide an accurate assignment of peaks and shoulders in the experimental photoelectron spectrum of \documentclass[12pt]{minimal}\begin{document}${\rm Au}_{3}^{-}$\end{document} Au 3− for the first time.
The ac-magnetic susceptibility and dielectric response of complex spin ordering processes in Mn3O4
Authors: Thota Subhash , Singh Kiran , Nayak Sanjib , Simon Ch. , Kumar Jitendra , Prellier Wilfrid
Published: September 2014

We report a meticulous study of the ac-magnetization dynamics (χac(T)), relative dielectric permittivity εr(T), and magneto-dielectric (Δεr/εr(H)) response of various complex magnetic transitions that occur below the ferrimagnetic Néel temperature TN of Mn3O4. Besides the known sequence of transitions at TN ∼ 42.75 K, T1 ∼ 39 K, and T2 ∼ 34 K, the existence of a new anomaly reported recently at 38 K (T*) has been successfully probed by χac(T) and εr(T) measurements. The effect of external dc-bias fields (HDC) and driving frequency (f) on the above mentioned transitions has been investigated in consonance with the εr(T) and Δεr/εr(T,H) results. For the first time, we observed a clear hysteresis of about 5.15 K in the zero-field εr(T) across the incommensurate-to-commensurate transition T2 ∼ 34 K, which provides evidence to the first-order nature of this transition. The Arrott plot (H/M vs. M2) criterion has been used to distinguish the nature of all the sequential transitions that take place below TN.
Angular distribution of light emission from compound-eye cornea with conformal fluorescent coating
Authors: Martín-Palma Raúl J. , Miller Amy E. , Pulsifer Drew P. , Lakhtakia Akhlesh
Published: September 2014

The complex morphology of the apposition compound eyes of insects of many species provides them a wide angular field of view. This characteristic makes these eyes attractive for bioreplication as artificial sources of light. The cornea of a blowfly eye was conformally coated with a fluorescent thin film with the aim of achieving wide field-of-view emission. On illumination by shortwave-ultraviolet light, the conformally coated eye emitted visible light whose intensity showed a weaker angular dependence than a fluorescent thin film deposited on a flat surface.
Advanced numerical technique for analysis of surface and bulk acoustic waves in resonators using periodic metal gratings
Authors: Naumenko Natalya F.
Published: September 2014

A numerical technique characterized by a unified approach for the analysis of different types of acoustic waves utilized in resonators in which a periodic metal grating is used for excitation and reflection of such waves is described. The combination of the Finite Element Method analysis of the electrode domain with the Spectral Domain Analysis (SDA) applied to the adjacent upper and lower semi-infinite regions, which may be multilayered and include air as a special case of a dielectric material, enables rigorous simulation of the admittance in resonators using surface acoustic waves, Love waves, plate modes including Lamb waves, Stonely waves, and other waves propagating along the interface between two media, and waves with transient structure between the mentioned types. The matrix formalism with improved convergence incorporated into SDA provides fast and robust simulation for multilayered structures with arbitrary thickness of each layer. The described technique is illustrated by a few examples of its application to various combinations of LiNbO3, isotropic silicon dioxide and silicon with a periodic array of Cu electrodes. The wave characteristics extracted from the admittance functions change continuously with the variation of the film and plate thicknesses over wide ranges, even when the wave nature changes. The transformation of the wave nature with the variation of the layer thicknesses is illustrated by diagrams and contour plots of the displacements calculated at resonant frequencies.
A stepped leader model for lightning including charge distribution in branched channels
Authors: Shi Wei , Li Qingmin , Zhang Li
Published: September 2014

The stepped leader process in negative cloud-to-ground lightning plays a vital role in lightning protection analysis. As lightning discharge usually presents significant branched or tortuous channels, the charge distribution along the branched channels and the stochastic feature of stepped leader propagation were investigated in this paper. The charge density along the leader channel and the charge in the leader tip for each lightning branch were approximated by introducing branch correlation coefficients. In combination with geometric characteristics of natural lightning discharge, a stochastic stepped leader propagation model was presented based on the fractal theory. By comparing simulation results with the statistics of natural lightning discharges, it was found that the fractal dimension of lightning trajectory in simulation was in the range of that observed in nature and the calculation results of electric field at ground level were in good agreement with the measurements of a negative flash, which shows the validity of this proposed model. Furthermore, a new equation to estimate the lightning striking distance to flat ground was suggested based on the present model. The striking distance obtained by this new equation is smaller than the value estimated by previous equations, which indicates that the traditional equations may somewhat overestimate the attractive effect of the ground.
In-situ characterization of trapped charges in amorphous semiconductor films during plasma-enhanced chemical vapor deposition
Authors: Nunomura S. , Sakata I.
Published: September 2014

The subband-gap absorption current in a hydrogenated amorphous silicon film has been measured during plasma-enhanced chemical vapor deposition. The current is probed by a near-infrared laser while photoexcited carriers are generated under visible laser illumination. The trapped charge density is determined from the magnitude of current under the assumption of carrier generation and recombination kinetics. The result indicates that trapped charges are distributed uniformly in the film during growth, and they are reduced after the growth. The trapped charge density is minimized at a growth temperature of ≈ 473 K.
Spin filtering in a δ-doped magnetic-electric-barrier nanostructure
Authors: Li Shuai , Lu Mao-Wang , Jiang Ya-Qing , Chen Sai-Yan
Published: September 2014

We report a theoretical study on spin-polarized transport in a δ-doped magnetic-electric-barrier nanostructure, which can be realized in experiments by depositing two ferromagnetic stripes on top and bottom of a semiconductor heterostructure under an applied voltage and by using atomic layer doping technique. The spin-polarized behavior of the electron in this device is found to be quite sensitive to the δ-doping. One can conveniently tune the degree of the electron spin polarization by adjusting the weight and/or position of the δ-doping. Thus, the involved nansosystem can be employed as a controllable spin filter, which may be helpful for exploiting new spin-polarized source for spintronics applications.
Fabrication and characterization of germanium-on-insulator through epitaxy, bonding, and layer transfer
Authors: Lee Kwang Hong , Bao Shuyu , Chong Gang Yih , Tan Yew Heng , Fitzgerald Eugene A. , Tan Chuan Seng
Published: September 2014

A scalable method to fabricate germanium on insulator (GOI) substrate through epitaxy, bonding, and layer transfer is reported. The germanium (Ge) epitaxial film is grown directly on a silicon (Si) (001) donor wafer using a “three-step growth” approach in a reduced pressure chemical vapour deposition. The Ge epilayer is then bonded and transferred to another Si (001) wafer to form the GOI substrate. The Ge epilayer on GOI substrate has higher tensile strain (from 0.20% to 0.35%) and rougher surface (2.28 times rougher) compared to the Ge epilayer before transferring (i.e., Ge on Si wafer). This is because the misfit dislocations which are initially hidden along the Ge/Si interface are now flipped over and exposed on the top surface. These misfit dislocations can be removed by either chemical mechanical polishing or annealing. As a result, the Ge epilayer with low threading dislocations density level and surface roughness could be realized.
Communication: High precision sub-Doppler infrared spectroscopy of the HeH+ ion
Authors: Perry Adam J. , Hodges James N. , Markus Charles R. , Kocheril G. Stephen , McCall Benjamin J.
Published: September 2014

The hydrohelium cation, HeH+, serves as an important benchmark for ab initio calculations that take into account non-adiabatic, relativistic, and quantum electrodynamic effects. Such calculations are capable of predicting molecular transitions to an accuracy of ∼300 MHz or less. However, in order to continue to push the boundaries on these calculations, new measurements of these transitions are required. Here we measure seven rovibrational transitions in the fundamental vibrational band to a precision of ∼1 MHz using the technique of Noise Immune Cavity Enhanced Optical Heterodyne Velocity Modulation Spectroscopy. These newly measured transitions are included in a fit to the rotation-vibration term values to derive refined spectroscopic constants in the v = 0 and v = 1 vibrational states, as well as to calculate rotation-vibration energy levels with high precision.
Anomalous junctions characterized by Raman spectroscopy in SixGe1−x nanowires with axially degraded components
Authors: Xia Minggang , Han Jinyun , Cheng Zhaofang , Liang Chunping , Zhang Shengli
Published: September 2014

The characterization of junctions in nanowires by high-resolution transmission electron microscopy with spherical aberration correction is tricky and tedious. Many disadvantages also exist, including rigorous sample preparation and structural damage inflicted by high-energy electrons. In this work, we present a simple, low-cost, and non-destructive Raman spectroscopy method of characterizing anomalous junctions in nanowires with axially degraded components. The Raman spectra of SixGe1−x nanowires with axially degraded components are studied in detail using a confocal micro-Raman spectrometer. Three Raman peaks (νSi–Si = 490 cm−1, νSi–Ge = 400 cm−1, and νGe–Ge = 284 cm−1) up-shift with increased Si content. This up-shift originates in the bond compression induced by a confined effect on the radial direction of nanowire. The anomalous junctions in SixGe1−x nanowires with axially degraded components are then observed by Raman spectroscopy and verified by transmission electron microscopy energy-dispersive X-ray spectroscopy. The anomalous junctions of SixGe1−x nanowires with axially degraded components are due to the vortex flow of inlet SiH4 and GeH4 gas in their synthesis. The anomalous junctions can be used as raw materials for fabricating devices with special functions.
Migration and vascular lumen formation of endothelial cells in cancer cell spheroids of various sizes
Authors: Patra Bishnubrata , Peng Yu-Sheng , Peng Chien-Chung , Liao Wei-Hao , Chen Yu-An , Lin Keng-Hui , Tung Yi-Chung , Lee Chau-Hwang
Published: September 2014

We developed a microfluidic device to culture cellular spheroids of controlled sizes and suitable for live cell imaging by selective plane illumination microscopy (SPIM). We cocultured human umbilical vein endothelial cells (HUVECs) within the spheroids formed by hepatocellular carcinoma cells, and studied the distributions of the HUVECs over time. We observed that the migration of HUVECs depended on the size of spheroids. In the spheroids of ∼200 μm diameters, HUVECs migrated outwards to the edges within 48 h; while in the spheroids of ∼250 μm diameters, there was no outward migration of the HUVECs up to 72 h. In addition, we studied the effects of pro-angiogenic factors, namely, vascular endothelial growth factor (VEGF) and fibroblast growth factor (β-FGF), on the migration of HUVECs in the carcinoma cell spheroid. The outward migration of HUVECs in 200 μm spheroids was hindered by the treatment with VEGF and β-FGF. Moreover, some of the HUVECs formed hollow lumen within 72 h under VEGF and β-FGF treatment. The combination of SPIM and microfluidic devices gives high resolution in both spatial and temporal domains. The observation of HUVECs in spheroids provides us insight on tumor vascularization, an ideal disease model for drug screening and fundamental studies.
Highly uniform, multi-stacked InGaAs/GaAs quantum dots embedded in a GaAs nanowire
Authors: Tatebayashi J. , Ota Y. , Ishida S. , Nishioka M. , Iwamoto S. , Arakawa Y.
Published: September 2014

We demonstrate a highly uniform, dense stack of In0.22Ga0.78As/GaAs quantum dot (QD) structures in a single GaAs nanowire (NW). The size (and hence emission energy) of individual QD is tuned by careful control of the growth conditions based on a diffusion model of morphological evolution of NWs and optical characterization. By carefully tailoring the emission energies of individual QD, dot-to-dot inhomogeneous broadening of QD stacks in a single NW can be as narrow as 9.3 meV. This method provides huge advantages over traditional QD stack using a strain-induced Stranski-Krastanow growth scheme. We show that it is possible to fabricate up to 200 uniform QDs in single GaAs NWs using this growth technique without degradation of the photoluminescence intensity.
Insights into Elastic and Thermodynamics Properties of Binary Intermetallics in Ni-Al Alloys under Extreme Condition: Full-Electronic Quasi-Harmonic Study
Authors: Luo Yong-song , Cang Yu-ping , Chen Dong
Published: September 2014

Atomistic modeling based on the accurate first-principles method is used to investigate the lattice parameter, elastic constant, elastic modulus including bulk modulus (B) and shear modulus (G), Poisson's ratio, and elastic anisotropy of Al, NiAl and Ni3Al under extreme condition. The elastic constants obtained from calculations meet their mechanical stability criteria. Both NiAl and Ni3Al exhibit ductile behavior due to their high bulk mudulus to shear modulus ratios of B/G ratios. Through the full-electronic quasi-harmonic approximation, in which the mobile electrons are considered, we successfully obtain the thermo-physical properties including the thermal expansion coefficient, bulk modulus, heat capacity and entropy at simultaneously high temperatures and high pressures. The calculated quantities agree well with the available results. Some silent results are also interpreted. Several interesting features in the thermodynamic properties can also be observed.
Self-assembly of Binary Particles with Electrostatic and van der Waals Interactions
Authors: Li Yan , Li Hua-ping , He Xue-hao
Published: September 2014

Nanoparticles with competitive interactions in solution can aggregate into complex structures. In this work, the synergistic self-assembles of binary particles with electrostatic and van der Waals interactions are studied with the particle Langevin dynamics simulation using a simple coarse-grained particle model. Various aggregations such as spherical, stacking-disk and tube structures are observed by varying the particles size and the interaction strength. The aggregation structures are explained with the packing theories of amphiphilic molecules in solution and dibolck copolymers in bulk. When the opposite ions are introduced into solution, the distribution of structures in the phase diagram appears an obvious offset. The simulation result is helpful to deeply understand the formation mechanism of complex nanostructures of multicomponent particles in solution.
Exchange Bias Effect in Phase Separated La0.33Pr0.34Ca0.33MnO3 Thin Films
Authors: Li Hui , Li Lin , Cheng Long , Liang Hai-xing , Zeng Chang-gan
Published: September 2014

Exchange bias effect is observed in the phase separated La0.33Pr0.34Ca0.33MnO3 thin films. High exchange bias field of about 1 kOe is achieved at 4 K. The exchange bias effect in La0.33Pr0.34Ca0.33MnO3 thin films might originate from the intrinsic phase separation of the La0.33Pr0.34Ca0.33MnO3 or surface effect. The dependence of exchange bias effect on temperature, cooling field, and thickness is also investigated. This work would open an avenue to the application in the magnetic memory devices based on the phase separated manganites.
Kinetics Study on O2 Adsorption and OHad Desorption at Pt(111), Its Implication to Oxygen Reduction Reaction Kinetics
Authors: Yang Fan , Liao Ling-wen , Li Ming-fang , Mei Dong , Chen Yan-xia
Published: September 2014

Kinetics of dissociative O2 adsorption, OHad desorption, and oxygen reduction reaction (ORR) at Pt(111) electrode in 0.1 mol/L HClO4 has been investigated. Reversible OHad adsorption/desorption occurs at potentials from 0.6 V to 1.0 V (vs. RHE) with the exchange current density of ca. 50 mA/cm2 at 0.8 V, the fast kinetics of OHad desorption indicates that it should not be the rate determining step for ORR. In the kinetic- or kinetic-mass transport mix controlled potential region, ORR current at constant potential displays slight decrease with reaction time. ORR current in the positive-going potential scan is slightly larger than that in the subsequent negative-going scan with electrode rotation speed (>800 r/min) and slow potential scan rate (<100 mV/s). The open circuit potential of Pt/0.1 mol/L HClO4 interface increases promptly from 0.9 V to 1.0 V after switch from O2 free- to O2-saturated solution. The increase of open circuit potential as well as ORR current decays under potential control due to the accumulation of OHad from dissociative adsorption of O2. It indicates that at Pt(111) the net rate for O2 decomposition to OHad is slightly faster than that for OHad removal, one cannot simply use the assumption of rate determining step to discuss ORR kinetics. Instead, the ORR kinetics is determined by both the kinetics for O2 decomposition to OHad as well as the thermo-equilibrium of OHad+H++e ⇌H2O.
Regulatory Uncertainty and Corporate Pollution Control Strategies: An Empirical Study of the ‘Pay for Permit’ Policy in the Tai Lake Basin
Authors: Zhang Bing , Fei Hanxun , Zhang Yongjing , Liu Beibei
Published: September 2014

Frequent adjustments of environmental regulations usually cause business and investment risks, resulting in significant challenges for policy effectiveness. This paper examines how regulatory uncertainty affects decision making through an empirical study of the ‘Pay for Permit’ policy in the Tai Lake Basin in China. The results show that firms' willingness to decrease pollution is positively influenced by their perceived attitudes, social pressure, and perceived behavioural control. In addition, perceived regulatory uncertainty has significant impacts on social pressure and attitudes toward pollution control. Firms that perceive less regulatory uncertainty are more inclined to adopt antipollution strategies under the Pay for Permit policy. To reduce regulatory uncertainty, China's policy makers should maintain a consistent level of environmental regulations, set clear and reliable long-term policy targets, and strengthen policy enforcement.
Deliberative Decarbonisation? Assessing the Potential of an Ethical Governance Framework for Low-Carbon Energy through the Case of Carbon Dioxide Capture and Storage
Authors: Mabon Leslie , Shackley Simon , Vercelli Samuela , Anderlucci Jonathan , Boot Kelvin
Published: September 2014

In this paper we explore the potential of a framework of ethical governance for low-carbon energy. Developing mainly in the field of information and communications technology, ethical governance is concerned with the marginalisation of ethical and moral issues during development and deployment of new technologies. Focusing on early carbon dioxide capture and storage (CCS) projects, we argue that a focus on technical arguments in the governance of low-carbon energy similarly risks sidelining deeper issues such as fairness, justice, and values. We believe an ethical governance approach does have potential for low-carbon energy technologies like CCS, but also that climate change mitigation technologies pose particular challenges for the implementation of ethical governance.
Interactions between the superb lyrebird (Menura novaehollandiae) and fire in south-eastern Australia
Authors: Nugent Daniel T. , Leonard Steven W. J. , Clarke Michael F.
Published: September 2014

Context
The superb lyrebird Menura novaehollandiae is thought to be an important ecosystem engineer that, through its foraging, accelerates the decomposition of litter in Eucalyptus forests. Lyrebird foraging is therefore likely to affect forest fuel loads and hence fire behaviour in these fire-prone forests. In turn, fire is likely to reduce the abundance and influence the distribution of lyrebirds.

Aims
Our goal was to determine the impacts of a major bushfire on the habitat and food sources for the superb lyrebird and the effects of foraging activities of lyrebirds on litter fuel and potential fire behaviour in gullies of herb-rich foothill forests.

Methods
The effect of fire on lyrebirds and their habitat in the post-fire environment was examined at the landscape-scale, 2 years after fire; and at the patch-scale, 3 years after fire. Paired exclusion and control plots were also used over a 9-month period to assess the effects of foraging by the lyrebird on litter accumulation and fuel connectivity. Fire-behaviour models were used to determine the potential influence of lyrebird scratchings on fire behaviour.

Key results
At the landscape scale, lyrebirds were present in both unburnt and ground-burnt sites, but not in canopy-burnt sites. Within patchily burnt sites, lyrebirds favoured foraging in unburnt patches. On average, lyrebird foraging reduced litter fuel loads by 25% (1.66 t ha–1) in plots in which they were free to forage, compared with plots from which they were excluded, over a 9-month period. Fire-behaviour modelling showed that lyrebird foraging led to a lower likelihood of fire occurring and less intense fire.

Conclusions
Distinctly different vegetation structure and composition between burnt and unburnt patches appears to influence both the foraging patterns and distribution of lyrebirds. Additionally, foraging by lyrebirds reduces surface fuel loads and fuel connectivity such that fire spread is likely to be inhibited.

Implications
We propose that alternative stable states may emerge in Eucalyptus forests as a result of feedback mechanisms among lyrebirds, vegetation and fuel accumulation. Therefore, the ecological role of lyrebirds is an important consideration in forest fuel management and conservation in these extensive, fire-prone forests in south-eastern Australia.
Invariant natural killer T cells act as an extravascular cytotoxic barrier for joint-invading Lyme
Borrelia
Authors: Lee Woo-Yong , Sanz Maria-Jesus , Wong Connie H. Y. , Hardy Pierre-Olivier , Salman-Dilgimen Aydan , Moriarty Tara J. , Chaconas George , Marques Adriana , Krawetz Roman , Mody Christopher H. , Kubes Paul
Published: September 2014

Significance

Invariant natural killer T cells (iNKT) have been found primarily patrolling inside blood vessels in the liver, where they respond to bacterial glycolipids presented by CD1d on liver macrophages. We show joint iNKT cells are localized outside of blood vessels and respond directly to the joint-homing pathogen,
Borrelia burgdorferi
, which causes Lyme borreliosis using multichannel spinning-disk intravital microscopy. These iNKT cells interacted with
B. burgdorferi
at the vessel wall and disrupted its dissemination attempts into joints. Successful penetrance of
B. burgdorferi
out of the vasculature and into the joint tissue was met by a lethal attack by extravascular iNKT cells through a granzyme-dependent pathway. These results suggest a critical extravascular iNKT cell immune surveillance in joints that functions as a cytotoxic barrier.
Single-molecule correlated chemical probing of RNA
Authors: Homan Philip J. , Favorov Oleg V. , Lavender Christopher A. , Kursun Olcay , Ge Xiyuan , Busan Steven , Dokholyan Nikolay V. , Weeks Kevin M.
Published: September 2014

Significance

RNA molecules function as the central conduit of information transfer in biology. To do this, they encode information both in their sequences and in their higher-order structures. Understanding the higher-order structure of RNA remains challenging. In this work we devise a simple, experimentally concise, and accurate approach for examining higher-order RNA structure by converting widely used massively parallel sequencing into an easily implemented single-molecule experiment for detecting through-space interactions and multiple conformations. We then use this experiment to analyze higher-order RNA structure, detect biologically important hidden states, and refine accurate three-dimensional structure models.
Evolved tooth gain in sticklebacks is associated with acis-regulatory allele ofBmp6
Authors: Cleves Phillip A. , Ellis Nicholas A. , Jimenez Monica T. , Nunez Stephanie M. , Schluter Dolph , Kingsley David M. , Miller Craig T.
Published: September 2014

Significance

How body pattern evolves in nature remains largely unknown. Although recent progress has been made on the molecular basis of losing morphological features during adaptation to new environments (regressive evolution), there are few well worked out examples of how morphological features may be gained in natural species (constructive evolution). Here we use genetic crosses to study how threespine stickleback fish have increased their tooth number in a new freshwater environment. Genetic mapping and gene expression experiments suggest regulatory changes have occurred in the gene for a bone morphogenetic signaling molecule, leading to increased expression in the freshwater fish that have more teeth. Our studies suggest that changes in gene regulation may underlie both gain and loss traits during vertebrate evolution.
Metabolic programming of mesenchymal stromal cells by oxygen tension directs chondrogenic cell fate
Authors: Leijten Jeroen , Georgi Nicole , Moreira Teixeira Liliana , van Blitterswijk Clemens A. , Post Janine N. , Karperien Marcel
Published: September 2014

Significance

Multipotent cells, such as mesenchymal stromal cells (MSCs), have the capacity to differentiate into cartilage-forming cells. Chondrocytes derived from MSCs obtain an epiphyseal cartilage-like phenotype, which turns into bone upon implantation via endochondral ossification. Here, we report that the chondrogenic fate of MSCs can be metabolically programmed by low oxygen tension to acquire an articular chondrocyte-like phenotype via mechanisms that resemble natural development. Our study identifies metabolic programming of stem cells by oxygen tension as a powerful tool to control cell fate, which may have broad applications for the way in which stem cells are now prepared for clinical use.
PreImplantation factor promotes neuroprotection by targeting microRNA let-7
Authors: Mueller Martin , Zhou Jichun , Yang Lihua , Gao Yuan , Wu Fuju , Schoeberlein Andreina , Surbek Daniel , Barnea Eytan R. , Paidas Michael , Huang Yingqun
Published: September 2014

Significance

Secreted from viable embryos into the maternal circulation, PreImplantation factor (PIF) has long been implicated in modulating maternal immune tolerance and promoting embryo implantation. Recent evidence also suggests its possible therapeutic use in CNS disorders. However, the molecular signal-transduction pathways driving PIF-mediated effects are unclear. Using murine cell culture combined with a rat hypoxic-ischemic brain injury model, we show that synthetic PIF (sPIF) inhibits microRNA let-7 biogenesis by destabilizing the key microRNA-processing protein, KH-type splicing regulatory protein, in a Toll-like receptor 4–dependent manner. This regulation, together with its induced upregulation of the anti-inflammatory cytokine IL-10, may contribute to sPIF-mediated neuroprotection in vivo and also may underlie PIF's physiological role in maternal immune modulation and embryo implantation.
Vacuum arc under axial magnetic fields: experimental and simulation research
Authors: Jia Shenli , Shi Zongqian , Wang Lijun
Published: September 2014

Axial magnetic field (AMF) technology is a most important control method of vacuum arc, particularly for high-current vacuum arcs in vacuum interrupters. In this paper, a review of the state of current research on vacuum arcs under AMF is presented. The major aspects of vacuum arc in an AMF such as arc voltage, the motion of cathode spots, and anode activities are discussed, and the most recent progress both of experimental and simulation research is presented.
Influence of the inter-electrode distance on the production of nanoparticles by means of atmospheric pressure inert gas dc glow discharge
Authors: Hontañón Esther , Palomares Jose María , Guo Xiaoai , Engeln Richard , Nirschl Hermann , Kruis Frank Einar
Published: September 2014

This work is aimed at investigating the influence of the inter-electrode spacing on the production rate and size of nanoparticles generated by evaporating a cathode on an atmospheric pressure dc glow discharge. Experiments are conducted in the configuration of two vertically aligned cylindrical electrodes in upward coaxial flow with copper as a consumable cathode and nitrogen as a carrier gas. A constant current of 0.5 A is delivered to the electrodes and the inter-electrode distance spanned from 0.5 to 10 mm. Continuous stable nanoparticle production is attained by optimal coaxial flow convection cooling of the cathode. Both the particle production rate and the primary particle size increase with the inter-electrode spacing up to nearly 5 mm and strongly decrease with an increasing inter-electrode distance beyond 5 mm. Production rates in the range of 1 mg h−1 of very small nanoparticles (<10 nm) are attained by a micro glow discharge (<1 mm); while glow discharges of intermediate sizes (<5 mm) result in production rates of up to 10 mg h−1 and primary particles of sizes between 10 and 20 nm. No correlation is found between the measured spatially averaged plasma parameters and nanoparticle production. Since the latter is largely determined by the properties of the cathode surface, spatially resolved spectrometric measurements are needed to discern between the positive column and the cathode region of the glow discharge plasma.
Epitaxy from the liquid phase: tuning metastable phases in Fe–Pd thin films by laser-assisted rapid solidification on substrates
Authors: Arabi-Hashemi A , Ehrhardt M , Lorenz P , Hirsch D , Zimmer K , Mayr S G
Published: September 2014

Epitaxy by crystallization of thin liquid films on suitable substrates constitutes an alternative approach to molecular beam epitaxy, particularly if metastable phases are required. Employing laser-assisted rapid solidification, we demonstrate for the example of the body-centred-cubic, body-centred-tetragonal, face-centred-tetragonal and face-centred-cubic phases of Fe7Pd3 thin films, how the interplay of cooling rate and substrate-assisted nucleation affects the resulting metastable crystal phase and epitaxial relationship. Exemplarily employing lanthanum strontium aluminium tantalum oxide, MgO, and Si single crystals as substrates, this is experimentally demonstrated by an x-ray diffraction study and pole figure measurements. The underlying solidification kinetics are clarified using finite element calculations on the resulting time–temperature profile. Employing secondary ion mass spectroscopy we additionally demonstrate that the absence of interdiffusion is a central requirement for successful application.
The graceful sigmoid: Johan Hjort's contribution to the theory of rational fishing
Authors: Holt Sidney J.
Published: September 2014

This historical essay describes the theory behind, and implications of, models of optimum yield from an exploited animal population (in particular for whaling) formulated by Johan Hjort and his colleagues, Per Ottestad and Gunnar Jahn, in the 1930s. The essay places the evolution of fishery science during the 1930s–1940s into context.
Stress-induced DNA damage: a case study in diffuse large B-cell lymphoma
Authors: Nicasio-Collazo Luz Adriana , Delgado-González Alexandra , Castañeda-Priego Ramón , Hernández-Lemus Enrique
Published: September 2014

DNA damage is one of the mechanisms of mutagenesis. Sequence integrity may be affected by the action of thermal changes, chemical agents, both endogenous and exogenous, and other environmental issues. Abnormally high mutation rates are referred to asgenomic instability: a phenomenon closely related to the onset of cancer. Mutant genotypes may be able to confer some kind of selective advantage on subclonal cell populations, leading them to multiply until dominance in a localized tissue environment that later becomes the tumour. Cellular stress, especially that of oxidative and ionic nature, is a recognized trigger for DNA-damaging processes. A physico-chemical model has shown that high hysteresis rates in DNA denaturation curves may be indicative of dissipative processes inducing DNA damage, thus potentially leading to uncontrolled mutagenesis and genome instability. We here study selectively to what extent this phenomenon may occur by analysing the sequence length and composition effects on the thermodynamic behaviour and the presence of hysteresis in pressure-driven DNA denaturation; pronounced hysteresis in the denaturation/renaturation curves may indicate thermal susceptibility to DNA damage. In particular, we consider highly mutated regions of the genome characterized in diffuse large B-cell lymphoma on a recent whole exome next-generation sequencing effort.
Theoretical and experimental evidence of non-symmetric doubly localized rogue waves
Authors: He Jingsong , Guo Lijuan , Zhang Yongshuai , Chabchoub Amin
Published: September 2014

We present determinant expressions for vector rogue wave (RW) solutions of the Manakov system, a two-component coupled nonlinear Schrödinger (NLS) equation. As a special case, we generate a family of exact and non-symmetric RW solutions of the NLS equation up to third order, localized in both space and time. The derived non-symmetric doubly localized second-order solution is generated experimentally in a water wave flume for deep-water conditions. Experimental results, confirming the characteristic non-symmetric pattern of the solution, are in very good agreement with theory as well as with numerical simulations, based on the modified NLS equation, known to model accurately the dynamics of weakly nonlinear wave packets in deep water.
The dynamics of mergers and acquisitions: ancestry as the seminal determinant
Authors: Viegas Eduardo , Cockburn Stuart P. , Jensen Henrik J. , West Geoffrey B.
Published: September 2014

Understanding the fundamental mechanisms behind the complex landscape of corporate mergers and acquisitions is of crucial importance to economies across the world. Adapting ideas from the fields of complexity and evolutionary dynamics to analyse business ecosystems, we show here that ancestry, i.e. the cumulative sum of historical mergers across all ancestors, is the key characteristic to company mergers and acquisitions. We verify this by comparing an agent-based model to an extensive range of business data, covering the period from the 1830s to the present day and a range of industries and geographies. This seemingly universal mechanism leads to imbalanced business ecosystems, with the emergence of a few very large, but sluggish ‘too big to fail’ entities, and very small, niche entities, thereby creating a paradigm where a configuration akin to effective oligopoly or monopoly is a likely outcome for free market systems.
Swelling-induced and controlled curving in layered gel beams
Authors: Lucantonio A. , Nardinocchi P. , Pezzulla M.
Published: September 2014

We describe swelling-driven curving in originally straight and non-homogeneous beams. We present and verify a structural model of swollen beams, based on a new point of view adopted to describe swelling-induced deformation processes in bilayered gel beams, that is based on the split of the swelling-induced deformation of the beam at equilibrium into two components, both depending on the elastic properties of the gel. The method allows us to: (i) determine beam stretching and curving, once assigned the characteristics of the solvent bath and of the non-homogeneous beam, and (ii) estimate the characteristics of non-homogeneous flat gel beams in such a way as to obtain, under free-swelling conditions, three-dimensional shapes. The study was pursued by means of analytical, semi-analytical and numerical tools; excellent agreement of the outcomes of the different techniques was found, thus confirming the strength of the method.
Social affiliation matters: both same-sex and opposite-sex relationships predict survival in wild female baboons
Authors: Archie Elizabeth A. , Tung Jenny , Clark Michael , Altmann Jeanne , Alberts Susan C.
Published: September 2014

Social integration and support can have profound effects on human survival. The extent of this phenomenon in non-human animals is largely unknown, but such knowledge is important to understanding the evolution of both lifespan and sociality. Here, we report evidence that levels of affiliative social behaviour (i.e. ‘social connectedness’) with both same-sex and opposite-sex conspecifics predict adult survival in wild female baboons. In the Amboseli ecosystem in Kenya, adult female baboons that were socially connected to either adult males or adult females lived longer than females who were socially isolated from both sexes—females with strong connectedness to individuals of both sexes lived the longest. Female social connectedness to males was predicted by high dominance rank, indicating that males are a limited resource for females, and females compete for access to male social partners. To date, only a handful of animal studies have found that social relationships may affect survival. This study extends those findings by examining relationships to both sexes in by far the largest dataset yet examined for any animal. Our results support the idea that social effects on survival are evolutionarily conserved in social mammals.
Nest fidelity is driven by multi-scale information in a long-lived seabird
Authors: Robert Alexandre , Paiva Vítor H. , Bolton Mark , Jiguet Frédéric , Bried Joël
Published: September 2014

Although the reproductive success of most organisms depends on factors acting at several spatial scales, little is known about how organisms are able to synthesize multi-scale information to optimize reproduction. Using longitudinal data from a long-lived seabird, Monteiro's storm-petrel, we show that average breeding success is strongly related to oceanic conditions at the population level, and we postulate that (i) individuals use proximal information (their own reproduction outcome in yeart) to assess the qualities of their mate and nest and to decide to retain them or not in yeart+ 1; (ii) the intensity of these responses depends on the quality of the oceanic environment in yeart, which affects the predictability of reproduction outcome in yeart+ 1. Our results confirm that mate and nest fidelities are higher following successful reproduction and that the relationship between the success of a given pair and subsequent nest fidelity is stronger in years with unfavourable oceanic conditions, suggesting that individuals rely on distant information to modulate their use of proximal information and adjust their breeding strategy.
Lack of prosociality in great apes, capuchin monkeys and spider monkeys: convergent evidence from two different food distribution tasks
Authors: Amici Federica , Visalberghi Elisabetta , Call Josep
Published: September 2014

Prosociality can be defined as any behaviour performed to alleviate the needs of others or to improve their welfare. Prosociality has probably played an essential role in the evolution of cooperative behaviour and several studies have already investigated it in primates to understand the evolutionary origins of human prosociality. Two main tasks have been used to test prosociality in a food context. In the Platforms task, subjects can prosocially provide food to a partner by selecting a prosocial platform over a selfish one. In the Tokens task, subjects can prosocially provide food to a partner by selecting a prosocial token over a selfish one. As these tasks have provided mixed results, we used both tasks to test prosociality in great apes, capuchin monkeys and spider monkeys. Our results provided no compelling evidence of prosociality in a food context in any of the species tested. Additionally, our study revealed serious limitations of the Tokens task as it has been previously used. These results highlight the importance of controlling for confounding variables and of using multiple tasks to address inconsistencies present in the literature.
Bradyrhizobium neotropicale sp. nov., isolated from effective nodules of Centrolobium paraense
Authors: Zilli Jerri E. , Baraúna Alexandre C. , da Silva Krisle , De Meyer Sofie E. , Farias Eliane N. C. , Kaminski Paulo E. , da Costa Ismaele B. , Ardley Julie K. , Willems Anne , Camacho Natália N. , Dourado Fernanda dos S. , O’Hara Graham
Published: September 2014

Root nodule bacteria were isolated from Centrolobium paraense Tul. grown in soils from the Amazon region, State of Roraima (Brazil). 16S rRNA gene sequence analysis of seven strains (BR 10247T, BR 10296, BR 10297, BR 10298, BR 10299, BR 10300 and BR 10301) placed them in the genus

Bradyrhizobium

with the closest neighbours being the type strains of

Bradyrhizobium paxllaeri

(98.8 % similarity),

Bradyrhizobium icense

(98.8 %),

Bradyrhizobium lablabi

(98.7 %),

Bradyrhizobium jicamae

(98.6 %),

Bradyrhizobium elkanii

(98.6 %),

Bradyrhizobium pachyrhizi

(98.6 %) and

Bradyrhizobium retamae

(98.3 %). This high similarity, however, was not confirmed by the intergenic transcribed spacer (ITS) 16S–23S rRNA region sequence analysis nor by multi-locus sequence analysis. Phylogenetic analyses of five housekeeping genes (dnaK, glnII, gyrB, recA and rpoB) revealed

Bradyrhizobium iriomotense

EK05T ( = LMG 24129T) to be the most closely related type strain (95.7 % sequence similarity or less). Chemotaxonomic data, including fatty acid profiles [major components being C16 : 0 and summed feature 8 (18 : 1ω6c/18 : 1ω7c)], DNA G+C content, slow growth rate and carbon compound utilization patterns, supported the placement of the novel strains in the genus

Bradyrhizobium

. Results of DNA–DNA relatedness studies and physiological data (especially carbon source utilization) differentiated the strains from the closest recognized species of the genus

Bradyrhizobium

. Symbiosis-related genes for nodulation (nodC) and nitrogen fixation (nifH) placed the novel species in a new branch within the genus

Bradyrhizobium

. Based on the current data, these seven strains represent a novel species for which the name Bradyrhizobium neotropicale sp. nov. is proposed. The type strain is BR 10247T ( = HAMBI 3599T).