bluuebunny/crossref_metadata_2025 huggingface dataset:
How does a thermal binary crystal break under shear?
Authors: Horn Tobias , Löwen Hartmut
Published: December 2014

When exposed to strong shearing, the particles in a crystal will rearrange and ultimately, the crystal will break by forming large nonaffine defects. Even for the initial stage of this process, only little effort has been devoted to the understanding of the breaking process on the scale of the individual particle size for thermalized mixed crystals. Here, we explore the shear-induced breaking for an equimolar two-dimensional binary model crystal with a high interaction asymmetry between the two different species such that the initial crystal has an intersecting square sublattice of the two constituents. Using Brownian dynamics computer simulations, we show that the combination of shear and thermal fluctuations leads to a characteristic hierarchical breaking scenario where initially, the more strongly coupled particles are thermally distorted, paving the way for the weakly coupled particles to escape from their cage. This in turn leads to mobile defects which may finally merge, proliferating a cascade of defects, which triggers the final breakage of the crystal. This scenario is in marked contrast to the breakage of one-component crystals close to melting. Moreover, we explore the orientational dependence of the initial shear direction relative to the crystal orientation and compare this to the usual melting scenario without shear. Our results are verifiable in real-space experiments of superparamagnetic colloidal mixtures at a pending air-water interface in an external magnetic field where the shear can be induced by an external laser field.
Self-standing elastomeric composites based on lithium ferrites and their dielectric behavior
Authors: Soreto Teixeira S. , Graça M. P. F. , Dionisio M. , Ilcíkova M. , Mosnacek J. , Spitalsky Z. , Krupa I. , Costa L. C.
Published: December 2014

Lithium ferrite (LiFe5O8) is an attractive material for technological applications due to its physical properties, which are significantly dependent on the preparation method and raw materials. In this work, LiFe5O8 crystallites were obtained by controlled heat-treatment process at 1100 °C, of a homogeneous mixture of Li2O-Fe2O3 powders, prepared by wet ball-milling and using lithium and iron nitrates as raw materials. The main goal was the preparation of a flexible and self-standing tick composite film by embedding lithium ferrite particles in a polymeric matrix, taking advantage of the good mechanical properties of the polymer and of the electrical and dielectric properties of the ferrite. The selected polymer matrix was styrene-b-isoprene-b-styrene copolymer. To prepare the composites, the lithium ferrite particles were chemically modified in order to functionalize their surface. To analyse the influence of the particles surface modification, different composites were made, with modified and unmodified particles. The structure of the obtained composites was studied by FTIR, XRD, TGA, and DSC techniques. The dielectric properties were analysed, in the frequency range between 10 Hz and 1 MHz and in function of temperature in the range between −73 °C and 127 °C. These properties were related with the structure and concentration of the particles in the matrix network. The composites with the modified particles present higher dielectric constant, maintaining values of loss tangent sufficiently low (<10−2) that can be considered interesting for technological applications.
Charge density stabilised local electron spin pair states in insulating polymers
Authors: Serra S. , Montanari G. C. , Dissado L. A.
Published: December 2014

A model is presented that addresses the energy stability of localized electron states in insulating polymers with respect to delocalized free electron-like states at variable charge densities. The model was derived using an effective Hamiltonian for the total energy of electrons trapped in large polarons and spin-paired bipolarons, which includes the electrostatic interaction between charges that occurs when the charge density exceeds the infinite dilution limit. The phase diagram of the various electronic states with respect to the charge density is derived using parameters determined from experimental data for polyethylene, and it is found that a phase transition from excess charge in the form of stable polarons to a stable state of bipolarons with charge = 2 and spin number S = 0 is predicted for a charge density between 0.2 C/m3 and ∼2 C/m3. This transition is consistent with a change from low mobility charge transport to charge transport in the form of pulses with a mobility orders of magnitude higher that has been observed in several insulating polymers.
MgSe/ZnSe/CdSe coupled quantum wells grown on InP substrate with intersubband absorption covering 1.55 μm
Authors: Chen Guopeng , De Jesus Joel , Tamargo Maria C. , Shen Aidong
Published: December 2014

The authors report the observation of intersubband (ISB) transitions in the optical communication wavelength region in MgSe/ZnSe/CdSe coupled quantum wells (QWs). The coupled QWs were grown on InP substrates by molecular beam epitaxy. By inserting ZnSe layers to compensate the strain, samples with high structural quality were obtained, as indicated by well resolved satellite peaks in high-resolution x-ray diffraction. The observed ISB transition energies agree well with the calculated values.
Lasing behaviors upon phase transition in solution-processed perovskite thin films
Authors: Kao Tsung Sheng , Chou Yu-Hsun , Chou Chun-Hsien , Chen Fang-Chung , Lu Tien-Chang
Published: December 2014

In this paper, the temperature dependent lasing characteristics of solution-processed organic-inorganic halide perovskite CH3NH3PbI3 films have been demonstrated. The lasing temperature can be sustained up to a near room temperature at 260 K. Via the temperature dependent photoluminescence (PL) measurements, an emerged phase-transition band can be observed, ascribing to the crystalline structures changed from the orthorhombic to tetragonal phase states in the perovskites as a function of a gradual increase in the ambient temperature. The optical characteristics of the PL emission peaks and the anomalous shifts of the peak intensities are highly correspondent with the phase states in perovskites at different temperatures, showing a low-threshold lasing behavior at the phase transition. The laser cavities may be formed under multiple random scattering provided by the polycrystalline grain boundary and/or phase separation upon the phase transition. Since the threshold gain is potentially high in the random cavities, the large material gain exhibited by the solution-processed perovskite would be very promising in making practical laser devices.
GeSn p-i-n waveguide photodetectors on silicon substrates
Authors: Peng Yu-Hsiang , Cheng H. H. , Mashanov Vladimir I. , Chang Guo-En
Published: December 2014

We report an investigation on GeSn p-i-n waveguide photodetectors grown on a Ge-buffered Si wafer. In comparison with a reference Ge detector, the GeSn detector shows an enhanced responsivity in the measured energy range, mainly attributed to the smaller bandgap caused by Sn-alloying. Analysis of the quantum efficiency indicates that increasing the Sn content in the active layers can significantly shorten the required device length to achieve the maximum efficiency. The present investigation demonstrates the planar photodetectors desired for monolithic integration with electronic devices.
A large-area hemispherical perforated bead microarray for monitoring bead based aptamer and target protein interaction
Authors: Choi Jong Seob , Bae Sunwoong , Kim Kyung Hoon , Seo Tae Seok
Published: December 2014

Herein, we present a large-area 3D hemispherical perforated microwell structure for a bead based bioassay. Such a unique microstructure enables us to perform the rapid and stable localization of the beads at the single bead level and the facile manipulation of the bead capture and retrieval with high speed and efficiency. The fabrication process mainly consisted of three steps: the convex micropatterned nickel (Ni) mold production from the concave micropatterned silicon (Si) wafer, hot embossing on the polymer matrix to generate the concave micropattened acrylate sheet, and reactive ion etching to make the bottom holes. The large-area hemispherical perforated micropatterned acrylate sheet was sandwiched between two polydimethylsiloxane (PDMS) microchannel layers. The bead solution was injected and recovered in the top PDMS microchannel, while the bottom PDMS microchannel was connected with control lines to exert the hydrodynamic force in order to alter the flow direction of the bead solution for the bead capture and release operation. The streptavidin-coated microbead capture was achieved with almost 100% yield within 1 min, and all the beads were retrieved in 10 s. Lysozyme or thrombin binding aptamer labelled microbeads were trapped on the proposed bead microarray, and the in situ fluorescence signal of the bead array was monitored after aptamer-target protein interaction. The protein-aptamer conjugated microbeads were recovered, and the aptamer was isolated for matrix assisted laser desorption/ionization time-of-flight mass spectrometry analysis to confirm the identity of the aptamer.
Label-free detection of protein-protein interactions on multi-scale micro-well arrays using spatial light modulator
Authors: Cho Eikhyun , Shin Ryung , Shim Jongmyeong , Jung Hyo-il , Kang Shinill
Published: December 2014

A mass production method of label-free protein microarray integrated with micro-well structures for the use of miniaturized multi-parallel scanning system was investigated. The geometrical parameters of biosensing structure were designed by rigorous coupled wave analysis simulation, and micro-well structures were designed considering the detection and material delivery system. The protein microarray with micro-well structures was fabricated by one-step UV nanoimprinting process using an electroformed multi-scale metallic stamp. Finally, microarray scanning was achieved using optical modulation without applying any motorized system and the feasibility of proposed protein microarray and scanning system was demonstrated by verifying the bio-molecular interactions.
Distinct magnetic signatures of fractional vortex configurations in multiband superconductors
Authors: da Silva R. M. , Milošević M. V. , Domínguez D. , Peeters F. M. , Aguiar J. Albino
Published: December 2014

Vortices carrying fractions of a flux quantum are predicted to exist in multiband superconductors, where vortex core can split between multiple band-specific components of the superconducting condensate. Using the two-component Ginzburg-Landau model, we examine such vortex configurations in a two-band superconducting slab in parallel magnetic field. The fractional vortices appear due to the band-selective vortex penetration caused by different thresholds for vortex entry within each band-condensate, and stabilize near the edges of the sample. We show that the resulting fractional vortex configurations leave distinct fingerprints in the static measurements of the magnetization, as well as in ac dynamic measurements of the magnetic susceptibility, both of which can be readily used for the detection of these fascinating vortex states in several existing multiband superconductors.
Prediction and analysis of infra and low-frequency noise of upwind horizontal axis wind turbine using statistical wind speed model
Authors: Lee Gwang-Se , Cheong Cheolung
Published: December 2014

Despite increasing concern about low-frequency noise of modern large horizontal-axis wind turbines (HAWTs), few studies have focused on its origin or its prediction methods. In this paper, infra- and low-frequency (the ILF) wind turbine noise are closely examined and an efficient method is developed for its prediction. Although most previous studies have assumed that the ILF noise consists primarily of blade passing frequency (BPF) noise components, these tonal noise components are seldom identified in the measured noise spectrum, except for the case of downwind wind turbines. In reality, since modern HAWTs are very large, during rotation, a single blade of the turbine experiences inflow with variation in wind speed in time as well as in space, breaking periodic perturbations of the BPF. Consequently, this transforms acoustic contributions at the BPF harmonics into broadband noise components. In this study, the ILF noise of wind turbines is predicted by combining Lowson’s acoustic analogy with the stochastic wind model, which is employed to reproduce realistic wind speed conditions. In order to predict the effects of these wind conditions on pressure variation on the blade surface, unsteadiness in the incident wind speed is incorporated into the XFOIL code by varying incident flow velocities on each blade section, which depend on the azimuthal locations of the rotating blade. The calculated surface pressure distribution is subsequently used to predict acoustic pressure at an observing location by using Lowson’s analogy. These predictions are compared with measured data, which ensures that the present method can reproduce the broadband characteristics of the measured low-frequency noise spectrum. Further investigations are carried out to characterize the IFL noise in terms of pressure loading on blade surface, narrow-band noise spectrum and noise maps around the turbine.
Ab initio structural and vibrational properties of GaAs diamondoids and nanocrystals
Authors: Abdulsattar Mudar Ahmed , Hussein Mohammed T. , Hameed Hadeel Ali
Published: December 2014

Gallium arsenide diamondoids structural and vibrational properties are investigated using density functional theory at the PBE/6-31(d) level and basis including polarization functions. Variation of energy gap as these diamondoids increase in size is seen to follow confinement theory for diamondoids having nearly equiaxed dimensions. Density of energy states transforms from nearly single levels to band structure as we reach larger diamondoids. Bonds of surface hydrogen with As atoms are relatively localized and shorter than that bonded to Ga atoms. Ga-As bonds have a distribution range of values due to surface reconstruction and effect of bonding to hydrogen atoms. Experimental bulk Ga-As bond length (2.45 Å) is within this distribution range. Tetrahedral and dihedral angles approach values of bulk as we go to higher diamondoids. Optical-phonon energy of larger diamondoids stabilizes at 0.037 eV (297 cm-1) compared to experimental 0.035 eV (285.2 cm-1). Ga-As force constant reaches 1.7 mDyne/Å which is comparable to Ga-Ge force constant (1.74 mDyne/Å). Hydrogen related vibrations are nearly constant and serve as a fingerprint of GaAs diamondoids while Ga-As vibrations vary with size of diamondoids.
Multi-scale simulation studies on interaction between anionic surfactants and cations
Authors: Meng Siwei , Zhang Jin , Ma Yue , Li Xiaotong , Zhang Rong , Liu Bing , Zhang Fei , Hou Tengfei , Lu Guiwu
Published: December 2014

In this paper, a dissipative particle dynamics (DPD) simulation method was used to investigate the impact of cations on the rheological properties of dodecyl sulfonate surfactant solutions. In order to obtain reasonable interaction between head groups of the surfactant, the geometric structure and interaction between dodecyl sulfonate and cations are optimized using density function theory (DFT) at the B3LYP/6-31G level. The DFT calculated results indicate that α-methylene nearest the head group can be classified as a part of the polar head. After binding, the charge on polar head decreases, thus greatly reduces the repulsion between the head groups. It is found that the presence of counterions is one of induction factors on the formation of wormlike micelles, thus greatly enhances the viscosity of surfactant solution. With the increasing in shear strengthen, the wormlike micelles are gradually oriented in the x direction and then broken up into small spherical micelles. This process is also shown by the decrease of viscosity, which decreases quickly at the low shear rates, then keeps almost a constant at the moderate shear rates and at last decreases again at the shear rates larger than a critical value. Compared with monovalent cations, divalent cations have a stronger effect on the rheological properties of dodecyl sulfonate solutions.
Optically tunable acoustic wave band-pass filter
Authors: Swinteck N. , Lucas P. , Deymier P. A.
Published: December 2014

The acoustic properties of a hybrid composite that exhibits both photonic and phononic behavior are investigated numerically with finite-element and finite-difference time-domain simulations. The structure is constituted of a periodic array of photonic resonant cavities embedded in a background superlattice. The resonant cavities contain a photo-elastic chalcogenide glass that undergoes atomic-scale structural reorganization when irradiated with light having energy close to its band-gap. Photo-excitation of the chalcogenide glass changes its elastic properties and, consequently, augments the acoustic transmission spectrum of the composite. By modulating the intensity of light irradiating the hybrid photonic/phononic structure, the position and spectral width of phonon passing-bands can be controlled. This demonstration offers the technological platform for optically-tunable acoustic wave band-pass filters.
Electrooptical properties of hybrid liquid crystalline systems containing CdSe quantum dots
Authors: Dradrach K. , Bartkiewicz S. , Miniewicz A.
Published: December 2014

In this paper, we present electrooptical properties of hybrid liquid crystalline systems, which contained CdSe quantum dots (QDs). We have shown by experiments of degenerated two-wave mixing and transverse conductivity measurements that liquid crystal cells filled with nematic and doped with semiconductor nanoparticles exhibit photorefractive effect associated with photoconductivity appearing in the system. We also present the mathematical model, which explains the relationship between the photoconductivity of the layer on which the QDs reside and the generation of holographic gratings. Our research may help to develop better understanding of processes observed in such systems and create more efficient materials for holographic data storage.
Effect of van der Waals forces on thermal conductance at the interface of a single-wall carbon nanotube array and silicon
Authors: Feng Ya , Zhu Jie , Tang Dawei
Published: December 2014

Molecular dynamics simulations are performed to evaluate the effect of van der Waals forces among single-wall carbon nanotubes (SWNTs) on the interfacial thermal conductance between a SWNT array and silicon substrate. First, samples of SWNTs vertically aligned on silicon substrate are simulated, where both the number and arrangement of SWNTs are varied. Results reveal that the interfacial thermal conductance of a SWNT array/Si with van der Waals forces present is higher than when they are absent. To better understand how van der Waals forces affect heat transfer through the interface between SWNTs and silicon, further constructs of one SWNT surrounded by different numbers of other ones are studied, and the results show that the interfacial thermal conductance of the central SWNT increases with increasing van der Waals forces. Through analysis of the covalent bonds and vibrational density of states at the interface, we find that heat transfer across the interface is enhanced with a greater number of chemical bonds and that improved vibrational coupling of the two sides of the interface results in higher interfacial thermal conductance. Van der Waals forces stimulate heat transfer at the interface.
Anisotropic elasticity and abnormal Poisson’s ratios in super-hard materials
Authors: Huang Chuanwei , Li Rongpeng , Chen Lang
Published: December 2014

We theoretically investigated the variable mechanical properties such as Young’s modulus, Poisson’s ratios and compressibility in super-hard materials. Our tensorial analysis reveals that the mechanical properties of super-hard materials are strongly sensitive to the anisotropy index of materials. In sharp contrast to the traditional positive constant as thought before, the Poisson’s ratio of super-hard materials could be unexpectedly negative, zero, or even positive with a value much larger than the isotropic upper limit of 0.5 along definite directions. Our results uncover a correlation between compressibility and hardness, which offer insights on the prediction of new super-hard materials.
The Impact of Stereoscopic Depth on the Munker-White Illusion
Authors: Kavšek Michael
Published: December 2014

The current study investigated the impact of stereoscopic depth information on adults' perception of a coloured version of the Munker–White illusion. In one half of the illusory figure red patches were embedded in black stripes and flanked by yellow stripes. In the other half of the illusory figure red patches were embedded in yellow stripes and flanked by black stripes. The red patches either remained in the same depth plane as the black and yellow inducing stripes (zero horizontal disparity condition) or were shifted into the foreground (crossed horizontal disparity condition) or into the background (uncrossed horizontal disparity condition). According to the results, the illusory effect was robust across all viewing conditions. The illusion mainly consisted of a subjective darkening of the red patches superimposed on the yellow stripes, a perceived hue shift of the red patches superimposed on the black stripes toward yellow, and a subjective saturation decrease in both kinds of red patches. Moreover, the study established a partial confirmation of Anderson's scission theory, according to which the Munker–White illusion should be largest in the crossed horizontal disparity condition, intermediate in the zero horizontal disparity condition, and smallest in the uncrossed horizontal disparity condition.
Effect of climate change on crustose coralline algae at a temperate vent site, White Island, New Zealand
Authors: Brinkman T. J. , Smith A. M.
Published: December 2014

Natural CO2 vents allow study of the effects of climate change on marine organisms on a different scale from laboratory-based studies. This study outlines a preliminary investigation into the suitability of natural CO2 vents near White Island, Bay of Plenty, New Zealand (37°31.19′S, 117°10.85′E) for climate change research by characterising water chemistry from two vent and three control locations on a seasonal basis, as well as examining their effects on skeletons of the local calcifying crustose coralline algae. pH measurements at vent sites, calculated from dissolved inorganic carbon and alkalinity, showed reduced mean pH levels (7.49 and 7.85) relative to background levels of 8.06, whereas mean temperatures were between 0.0 and 0.4°C above control. Increases in sulfur and mercury at sites near White Island were probably a result of volcanic unrest. Crustose coralline algae did not show significant variability in skeletal Mg-calcite geochemistry, but qualitative comparisons of calcite skeletons under scanning electron microscopy saw greater deformation and dissolution in coralline algae calcite crystals from vent sites compared to controls. Although additional monitoring of pH fluctuations and hydrogen sulphides is still needed, the low pH and increased temperatures indicate potential for studying multistressor effects of projected climate changes in a natural environment.
Bnip3 mediates doxorubicin-induced cardiac myocyte necrosis and mortality through changes in mitochondrial signaling
Authors: Dhingra Rimpy , Margulets Victoria , Chowdhury Subir Roy , Thliveris James , Jassal Davinder , Fernyhough Paul , Dorn Gerald W. , Kirshenbaum Lorrie A.
Published: December 2014

Significance

We provide new, exciting evidence for a previously unidentified signaling pathway that mechanistically links mitochondrial respiratory chain defects to necrosis and heart failure induced by the chemotherapy agent doxorubicin (DOX). We specifically show that DOX disrupts protein complexes between the key respiratory chain proteins, including uncoupling protein 3 and cytochrome
c
oxidase, resulting in abnormal mitochondrial respiration and necrosis through a mechanism contingent on Bcl-2-like 19kDa-interacting protein 3 (Bnip3). Perhaps most compelling is our finding that inhibiting Bnip3 completely abrogated the cardiotoxic effects of DOX. These exciting findings have important clinical implications not only for preventing heart failure by targeting Bnip3 in cancer patients undergoing chemotherapy, but also for understanding the pathogenesis of other diseases in which mitochondrial function is compromised.
Patterns of text reuse in a scientific corpus
Authors: Citron Daniel T. , Ginsparg Paul
Published: December 2014

Significance

In the modern electronic format it is both easier to reuse text and easier to detect reused text. This is the first comprehensive study of patterns of text reuse within the full texts of an important large scientific corpus, covering a 20-y timeframe. It provides an important baseline for what is regarded as standard practice within the affected research communities, a standard somewhat more lenient than that currently applied to journalists, popular authors, and public figures.
Hummingbirds control hovering flight by stabilizing visual motion
Authors: Goller Benjamin , Altshuler Douglas L.
Published: December 2014

Significance

The avian brain has numerous specializations for navigation and processing visual information, but relatively little is known about how flying birds control their position in space. To study the role of vision in controlling hovering flight, we developed a virtual reality environment where visual patterns could be displayed to a freely flying hummingbird. Normal flight could only be performed if the visual background was completely stationary. In contrast, any motion in the background image caused the birds to lose stability. In natural settings, visual motion is constantly produced when objects and observers move relative to each other. This research demonstrates that flying birds are surprisingly sensitive to movements in their visual field and direct flight to respond to those movements.
The birth of a dinosaur footprint: Subsurface 3D motion reconstruction and discrete element simulation reveal track ontogeny
Authors: Falkingham Peter L. , Gatesy Stephen M.
Published: December 2014

Significance

We reconstructed the 3D foot movements of guineafowl traversing a granular substrate from biplanar X-rays, and then incorporated those kinematics into a discrete element simulation. Digital track models permitted visualization of in vivo track formation at the surface and at virtual bedding planes for the first time. Application of these volumetric data to fossil dinosaur tracks uncovered the developmental origin of previously enigmatic features. A “track ontogeny” perspective helps integrate limb and substrate dynamics into the interpretation of track morphology, from which foot anatomy cannot be read directly.
Inflammatory sensitization of nociceptors depends on activation of NMDA receptors in DRG satellite cells
Authors: Ferrari Luiz Fernando , Lotufo Celina Monteiro , Araldi Dionéia , Rodrigues Marcos A. , Macedo Larissa P. , Ferreira Sérgio H. , Parada Carlos Amilcar
Published: December 2014

Significance

The present study provides evidence for a role of glutamate as a neuromodulator of the afferent nociceptive information. Our results show that the nociceptive impulse generated by an inflammatory event in the peripheral tissue is regulated in the dorsal root ganglia (DRG) by a system that involves satellite glial cells and glutamatergic NMDA receptors. To our knowledge, this work is one of the first demonstrations of the involvement of glutamate in a modulatory process in the DRG, a site where there are no synapses, in addition to its classical role as a neurotransmitter.
Site-specific vibrational spectral signatures of water molecules in the magic H
3
O
+
(H
2
O)
20
and Cs
+
(H
2
O)
20
clusters
Authors: Fournier Joseph A. , Wolke Conrad T. , Johnson Christopher J. , Johnson Mark A. , Heine Nadja , Gewinner Sandy , Schöllkopf Wieland , Esser Tim K. , Fagiani Matias R. , Knorke Harald , Asmis Knut R.
Published: December 2014

Significance

Understanding the mechanics underlying the diffuse OH stretching spectrum of water is a grand challenge for contemporary physical chemistry. Water clusters play an increasingly important role in this endeavor, as they allow one to freeze and isolate the spectral behavior of relatively large assemblies with well-defined network morphologies. We exploit recently developed, hybrid instruments that integrate laser spectroscopy with cryogenic ion trap mass spectrometry to capture the H
3
O
+
and Cs
+
ions in cage structures formed by 20 water molecules. Their infrared spectra reveal a pattern of distinct transitions that is unprecedented for water networks in this size range. Theoretical analysis of these patterns then reveals the intramolecular distortions associated with water molecules at various sites in the 3D cages.
Folding kinetics of WW domains with the united residue force field for bridging microscopic motions and experimental measurements
Authors: Zhou Rui , Maisuradze Gia G. , Suñol David , Todorovski Toni , Macias Maria J. , Xiao Yi , Scheraga Harold A. , Czaplewski Cezary , Liwo Adam
Published: December 2014

Significance

In spite of recent advances made in computer simulation techniques, one of the main challenges in the protein-folding field is to bridge microscopic motions and experimental measurements. This paper demonstrates that the physics-based, coarse-grained united-residue (UNRES) force field, which has the ability to simulate folding of small- and midsize proteins in the millisecond timescale, can predict the folding kinetics correctly and bridge theoretical and experimental worlds. The results suggest that the use of the UNRES force field will open a new door to the understanding of protein motions at much longer timescales and help explain the differences between theoretical results and experimental observations.
Hebbian and neuromodulatory mechanisms interact to trigger associative memory formation
Authors: Johansen Joshua P. , Diaz-Mataix Lorenzo , Hamanaka Hiroki , Ozawa Takaaki , Ycu Edgar , Koivumaa Jenny , Kumar Ashwani , Hou Mian , Deisseroth Karl , Boyden Edward S. , LeDoux Joseph E.
Published: December 2014

Significance

The influential Hebbian plasticity hypothesis suggests that an increase in the strength of connections between neurons whose activity is correlated produces memories. Other theories, however, propose that neuromodulatory systems need to be activated together with Hebbian plasticity mechanisms to engage memory formation. The present work provides direct in vivo evidence supporting the idea that a parallel mechanism involving neuromodulation and Hebbian processes is both necessary and sufficient to trigger synaptic strengthening and behavioral associative memory formation. This parallel process may represent a general mechanism used by many learning systems in the brain.
Gill Infection Model for Columnaris Disease in Common Carp and Rainbow Trout
Authors: Declercq A. M. , Chiers K. , Haesebrouck F. , Van den Broeck W. , Dewulf J. , Cornelissen M. , Decostere A.
Published: December 2014

Challenge models generating gill lesions typical for columnaris disease were developed for the fry of both Common Carp Cyprinus carpio and Rainbow Trout Oncorhynchus mykiss by means of an immersion challenge and Flavobacterium columnare field isolates were characterized regarding virulence. Carp inoculated with highly virulent isolates revealed diffuse, whitish discoloration of the gills affecting all arches, while in trout mostly unilateral focal lesions, which were restricted to the first two gill arches, occurred. Light microscopic examination of the gills of carp exposed to highly virulent isolates revealed a diffuse loss of branchial structures and desquamation and necrosis of gill epithelium with fusion of filaments and lamellae. In severe cases, large parts of the filaments were replaced with necrotic debris entangled with massive clusters of F. columnare bacterial cells enwrapped in an eosinophilic matrix. In trout, histopathologic lesions were similar but less extensive and much more focal, and well delineated from apparently healthy tissue. Scanning and transmission electron microscopic observations of the affected gills showed long, slender bacterial cells contained in an extracellular matrix and in close contact with the destructed gill tissue.

This is the first study to reveal gill lesions typical for columnaris disease at macroscopic, light microscopic, and ultrastructural levels in both Common Carp and Rainbow Trout following a challenge with F. columnare. The results provide a basis for research opportunities to examine pathogen–gill interactions.

Received January 10, 2014; accepted July 27, 2014
Thromboxane A2 acts as tonic immunoregulator by preferential disruption of low-avidity CD4+ T cell–dendritic cell interactions
Authors: Moalli Federica , Cupovic Jovana , Thelen Flavian , Halbherr Pascal , Fukui Yoshinori , Narumiya Shuh , Ludewig Burkhard , Stein Jens V.
Published: December 2014

Interactions between dendritic cells (DCs) and T cells control the decision between activation and tolerance induction. Thromboxane A2 (TXA2) and its receptor TP have been suggested to regulate adaptive immune responses through control of T cell–DC interactions. Here, we show that this control is achieved by selectively reducing expansion of low-avidity CD4+ T cells. During inflammation, weak tetramer-binding TP-deficient CD4+ T cells were preferentially expanded compared with TP-proficient CD4+ T cells. Using intravital imaging of cellular interactions in reactive peripheral lymph nodes (PLNs), we found that TXA2 led to disruption of low- but not high-avidity interactions between DCs and CD4+ T cells. Lack of TP correlated with higher expression of activation markers on stimulated CD4+ T cells and with augmented accumulation of follicular helper T cells (TFH), which correlated with increased low-avidity IgG responses. In sum, our data suggest that tonic suppression of weak CD4+ T cell–DC interactions by TXA2–TP signaling improves the overall quality of adaptive immune responses.
Full groups and soficity
Authors: Elek Gábor
Published: December 2014

First, we answer a question of Giordano and Pestov by proving that the full group of a sofic equivalence relation is a sofic group. Then, we give a short proof of the theorem of Grigorchuk and Medynets that the topological full group of a minimal Cantor homeomorphism is LEF. Finally, we show that for certain non-amenable groups all the generalized lamplighter groups are sofic.
A Chat about Insurance: Experimental Results from Rural Bangladesh
Authors: Clarke Daniel , de Nicola Francesca , Vargas Hill Ruth , Kumar Neha , Mehta Parendi
Published: December 2014

Farmers throughout the developing world face multiple sources of uninsured risk to agricultural production and household assets. In this paper, we present results from an experimental demand‐elicitation exercise in rural Bangladesh to shed light on smallholder farmers' interest in formal insurance products. We propose a suite of insurance and savings products, and we randomly vary the price of one insurance option (area‐yield insurance) and the presence of one of the savings options (group savings). Consistent with economic theory, farmers buy more of the insurance products that cover the risks they primarily face. However, because farmers are subject to a variety of risks, they do not focus on only one type of insurance; instead, they evenly split their endowment between life and disability insurance and agricultural insurance. Demand for area‐yield insurance falls with price; we also observe important cross‐price elasticities with other insurance products. The presence of group savings does not alter demand for insurance, though group savings is found to be a particularly popular risk management tool, especially when decisions are made in groups.
Supply Response, Marginal Cost, and Soil Erosion Implications of Stover‐based Biofuels
Authors: Sesmero Juan , Pratt Michelle , Tyner Wallace
Published: December 2014

Existing economic analysis of corn stover as an energy feedstock has not considered potential changes in land use associated with different stover prices. We estimate the response of corn stover supply density to its price driven by changes in land use and examine its implications for a processing plant's pricing strategy and marginal cost, as well as associated changes in soil erosion. We find that plants will exploit the intensive margin as well as the extensive margin to secure additional amounts of stover. Our results show, counterintuitively, that a market for stover may result in lower soil erosion due to reallocations of land to continuous corn with removal, which, combined with no‐till farming, results in lower soil erosion than the baseline without stover removal. Also contrary to expectations, using cover crops with stover removal may result in higher soil erosion due to land use changes within the fuel shed associated with optimal pricing.
Achievements and challenges in structural bioinformatics and computational biophysics
Authors: Samish Ilan , Bourne Philip E. , Najmanovich Rafael J.
Published: December 2014

Motivation: The field of structural bioinformatics and computational biophysics has undergone a revolution in the last 10 years. Developments that are captured annually through the 3DSIG meeting, upon which this article reflects.

Results: An increase in the accessible data, computational resources and methodology has resulted in an increase in the size and resolution of studied systems and the complexity of the questions amenable to research. Concomitantly, the parameterization and efficiency of the methods have markedly improved along with their cross-validation with other computational and experimental results.

Conclusion: The field exhibits an ever-increasing integration with biochemistry, biophysics and other disciplines. In this article, we discuss recent achievements along with current challenges within the field.

Contact:  Rafael.Najmanovich@USherbrooke.ca
Comparison of Serum Hemagglutinin and Neuraminidase Inhibition Antibodies After 2010–2011 Trivalent Inactivated Influenza Vaccination in Healthcare Personnel
Authors: Laguio-Vila Maryrose R. , Thompson Mark G. , Reynolds Sue , Spencer Sarah M. , Gaglani Manjusha , Naleway Allison , Ball Sarah , Bozeman Sam , Baker Steven , Martínez-Sobrido Luis , Levine Min , Katz Jackie , Fry Alicia M. , Treanor John J.
Published: December 2014

Background.  Most inactivated influenza vaccines contain purified and standardized hemagglutinin (HA) and residual neuraminidase (NA) antigens. Vaccine-associated HA antibody responses (hemagglutination inhibition [HAI]) are well described, but less is known about the immune response to the NA.

Methods.  Serum of 1349 healthcare personnel (HCP) electing or declining the 2010–2011 trivalent-inactivated influenza vaccine ([IIV3], containing A/California/7/2009 p(H1N1), A/Perth/16/2009 [H3N2], B/Brisbane/60/2008 strains) were tested for NA-inhibiting (NAI) antibody by a modified lectin-based assay using pseudotyped N1 and N2 influenza A viruses with an irrelevant (H5) HA. Neuraminidase-inhibiting and HAI antibody titers were evaluated approximately 30 days after vaccination and end-of-season for those with polymerase chain reaction (PCR)-confirmed influenza infection.

Results.  In 916 HCP (68%) receiving IIV3, a 2-fold increase in N1 and N2 NAI antibody occurred in 63.7% and 47.3%, respectively. Smaller responses occurred in HCP age >50 years and those without prior 2009–2010 IIV3 nor monovalent A(H1N1)pdm09 influenza vaccinations. Forty-four PCR-confirmed influenza infections were observed, primarily affecting those with lower pre-exposure HAI and NAI antibodies. Higher pre-NAI titers correlated with shorter duration of illness for A(H1N1)pdm09 virus infections.

Conclusions.  Trivalent-inactivated influenza vaccine is modestly immunogenic for N1 and N2 antigens in HCP. Vaccines eliciting robust NA immune responses may improve efficacy and reduce influenza-associated morbidity.
Coeliac Disease Screening Among a Large Cohort of Overweight/Obese Children
Authors: Nenna Raffaella , Mosca Antonella , Mennini Maurizio , Papa Raffaele E. , Petrarca Laura , Mercurio Roberta , Montuori Monica , Piedimonte Alessandra , Bavastrelli Maria , De Lucia Ilaria C. , Bonamico Margherita , Vania Andrea
Published: December 2014

Coeliac disease (CD) is a chronic, gluten‐dependent enteropathy with a prevalence of approximately 1% in Western countries. Up to now, CD has been described only in sporadic cases of obesity. Our study aimed to evaluate retrospectively CD prevalence in a large series of overweight/obese children and adolescents. Among the 1527 overweight/obese children and adolescents consecutively evaluated, 17 (7 boys, 1.11%) were positive for serology and showed villous atrophy. In all of the patients with CD a well‐balanced gluten‐free diet was started, and a loss of weight rapidly obtained. Our study demonstrates that CD prevalence in overweight/obese children is similar to the general paediatric population in Italy.
Ancient population genomics and the study of evolution
Authors: Parks M. , Subramanian S. , Baroni C. , Salvatore M. C. , Zhang G. , Millar C. D. , Lambert D. M.
Published: December 2014

Recently, the study of ancient DNA (aDNA) has been greatly enhanced by the development of second-generation DNA sequencing technologies and targeted enrichment strategies. These developments have allowed the recovery of several complete ancient genomes, a result that would have been considered virtually impossible only a decade ago. Prior to these developments, aDNA research was largely focused on the recovery of short DNA sequences and their use in the study of phylogenetic relationships, molecular rates, species identification and population structure. However, it is now possible to sequence a large number of modern and ancient complete genomes from a single species and thereby study the genomic patterns of evolutionary change over time. Such a study would herald the beginnings of ancient population genomics and its use in the study of evolution. Species that are amenable to such large-scale studies warrant increased research effort. We report here progress on a population genomic study of the Adélie penguin (
Pygoscelis adeliae
). This species is ideally suited to ancient population genomic research because both modern and ancient samples are abundant in the permafrost conditions of Antarctica. This species will enable us to directly address many of the fundamental questions in ecology and evolution.
The ancient Yakuts: a population genetic enigma
Authors: Keyser Christine , Hollard Clémence , Gonzalez Angela , Fausser Jean-Luc , Rivals Eric , Alexeev Anatoly Nikolayevich , Riberon Alexandre , Crubézy Eric , Ludes Bertrand
Published: December 2014

This study is part of an ongoing project aiming at determining the ethnogenesis of an eastern Siberian ethnic group, the Yakuts, on the basis of archaeological excavations carried out over a period of 10 years in three regions of Yakutia: Central Yakutia, the Vilyuy River basin and the Verkhoyansk area. In this study, genetic analyses were carried out on skeletal remains from 130 individuals of unknown ancestry dated mainly from the fifteenth to the nineteenth century AD. Kinship studies were conducted using sets of commercially available autosomal and Y-chromosomal short tandem repeats (STRs) along with hypervariable region I sequences of the mitochondrial DNA. An unexpected and intriguing finding of this work was that the uniparental marker systems did not always corroborate results from autosomal DNA analyses; in some cases, false-positive relationships were observed. These discrepancies revealed that 15 autosomal STR loci are not sufficient to discriminate between first degree relatives and more distantly related individuals in our ancient Yakut sample. The Y-STR analyses led to similar conclusions, because the current Y-STR panels provided the limited resolution of the paternal lineages.
Unravelling the complexity of domestication: a case study using morphometrics and ancient DNA analyses of archaeological pigs from Romania
Authors: Evin Allowen , Flink Linus Girdland , Bălăşescu Adrian , Popovici Dragomir , Andreescu Radian , Bailey Douglas , Mirea Pavel , Lazăr Cătălin , Boroneanţ Adina , Bonsall Clive , Vidarsdottir Una Strand , Brehard Stéphanie , Tresset Anne , Cucchi Thomas , Larson Greger , Dobney Keith
Published: December 2014

Current evidence suggests that pigs were first domesticated in Eastern Anatolia during the ninth millennium cal BC before dispersing into Europe with Early Neolithic farmers from the beginning of the seventh millennium. Recent ancient DNA (aDNA) research also indicates the incorporation of European wild boar into domestic stock during the Neolithization process. In order to establish the timing of the arrival of domestic pigs into Europe, and to test hypotheses regarding the role European wild boar played in the domestication process, we combined a geometric morphometric analysis (allowing us to combine tooth size and shape) of 449 Romanian ancient teeth with aDNA analysis. Our results firstly substantiate claims that the first domestic pigs in Romania possessed the same mtDNA signatures found in Neolithic pigs in west and central Anatolia. Second, we identified a significant proportion of individuals with large molars whose tooth shape matched that of archaeological (likely) domestic pigs. These large ‘domestic shape’ specimens were present from the outset of the Romanian Neolithic (6100–5500 cal BC) through to later prehistory, suggesting a long history of admixture between introduced domestic pigs and local wild boar. Finally, we confirmed a turnover in mitochondrial lineages found in domestic pigs, possibly coincident with human migration into Anatolia and the Levant that occurred in later prehistory.
Screening ancient tuberculosis with qPCR: challenges and opportunities
Authors: Harkins Kelly M. , Buikstra Jane E. , Campbell Tessa , Bos Kirsten I. , Johnson Eric D. , Krause Johannes , Stone Anne C.
Published: December 2014

The field of ancient DNA (aDNA) has rapidly accelerated in recent years as a result of new methods in next-generation sequencing, library preparation and targeted enrichment. Such research is restricted, however, by the highly variable DNA preservation within different tissues, especially when isolating ancient pathogens from human remains. Identifying positive candidate samples via quantitative PCR (qPCR) for downstream procedures can reduce reagent costs, increase capture efficiency and maximize the number of sequencing reads of the target. This study uses four qPCR assays designed to target regions within the
Mycobacterium tuberculosis
complex (MTBC) to examine 133 human skeletal samples from a wide geographical and temporal range, identified by the presence of skeletal lesions typical of chronic disseminated tuberculosis. Given the inherent challenges working with ancient mycobacteria, strict criteria must be used and primer/probe design continually re-evaluated as new data from bacteria become available. Seven samples tested positive for multiple MTBC loci, supporting them as strong candidates for downstream analyses. Using strict and conservative criteria, qPCR remains a fast and effective screening tool when compared with screening by more expensive sequencing and enrichment technologies.
Notification that new names of prokaryotes, new combinations, and new taxonomic opinions have appeared in volume 64, part 9, of the IJSEM
Authors: Oren Aharon , Garrity George M.
Published: December 2014

This listing of names of prokaryotes published in a previous issue of the IJSEM is provided as a service to bacteriology to assist in the recognition of new names and new combinations. This procedure was proposed by the Judicial Commission [Minute 11(ii), Int J Syst Bacteriol 41 (1991), p. 185]. The names given herein are listed according to the Rules of priority (i.e. page number and order of valid publication of names in the original articles).