bluuebunny/crossref_metadata_2025 huggingface dataset:
Off-axis electron holography of ferromagnetic multilayer nanowires
Authors: Akhtari-Zavareh Azadeh , Carignan L. P. , Yelon A. , Ménard D. , Kasama T. , Herring R. , Dunin-Borkowski R. E. , McCartney M. R. , Kavanagh K. L.
Published: July 2014

We have used electron holography to investigate the local magnetic behavior of isolated ferromagnetic nanowires (NWs) in their remanent states. The NWs consisted of periodic magnetic layers of soft, high-saturation magnetization CoFeB alloys, and non-magnetic layers of Cu. All NWs were fabricated by pulsed-potential electrodeposition in nanoporous alumina membranes. The NW composition and layer thicknesses were measured using scanning transmission electron microscopy and energy dispersive spectroscopy. The magnetization of individual NWs depended upon the thicknesses of the layers and the direction of an external magnetic field, which had been applied in situ. When the CoFeB was thicker than the diameter (50 nm), magnetization was axial for all external field directions, while thinner layers could be randomized via a perpendicular field. In some cases, magnetization inside the wire was detected at an angle with respect to the axis of the wires. In thinner Cu/CoFeB (<10 nm each) multilayer, magnetic field vortices were detected, associated with opposing magnetization in neighbouring layers. The measured crystallinity, compositions, and layer thicknesses of individual NWs were found to be significantly different from those predicted from calibration growths based on uniform composition NWs. In particular, a significant fraction of Cu (up to 50 at. %) was present in the CoFeB layers such that the measured magnetic induction was lower than expected. These results will be used to better understand previously measured effective anisotropy fields of similar NW arrays.
Synthesis of mono-dispersed nanofluids using solution plasma
Authors: Heo Yong Kang , Bratescu Maria Antoaneta , Ueno Tomonaga , Saito Nagahiro
Published: July 2014

Small-sized and well-dispersed gold nanoparticles (NPs) for nanofluidics have been synthesized by electrical discharge in liquid environment using termed solution plasma processing (SPP). Electrons and the hydrogen radicals are reducing the gold ions to the neutral form in plasma gas phase and liquid phase, respectively. The gold NPs have the smallest diameter of 4.9 nm when the solution temperature was kept at 20 °C. Nucleation and growth theory describe the evolution of the NP diameter right after the reduction reaction in function of the system temperature, NP surface energy, dispersion energy barrier, and nucleation rate. Negative charges on the NPs surface during and after SPP generate repulsive forces among the NPs avoiding their agglomeration in solution. Increasing the average energy in the SPP determines a decrease of the zeta potential and an increase of the NPs diameter. An important enhancement of the thermal conductivity of 9.4% was measured for the synthesized nanofluids containing NPs with the smallest size.
Dynamic plasmonic beam shaping by vector beams with arbitrary locally linear polarization states
Authors: Man Zhongsheng , Du Luping , Min Changjun , Zhang Yuquan , Zhang Chonglei , Zhu Siwei , Paul Urbach H. , Yuan X.-C.
Published: July 2014

Vector beams, which have space-variant state of polarization (SOP) comparing with scalar beams with spatially homogeneous SOP, are used to manipulate surface plasmon polarizations (SPPs). We find that the excitation, orientation, and distribution of the focused SPPs excited in a high numerical aperture microscopic configuration highly depend on the space-variant polarization of the incident vector beam. When it comes to vector beam with axial symmetry, multi-foci of SPPs with the same size and uniform intensity can be obtained, and the number of foci is depending on the polarization order n. Those properties can be of great value in biological sensor and plasmonic tweezers applications.
Prediction of pulse-to-pulse intensity fluctuation characteristics of high power ultrafast fiber amplifiers
Authors: Gürel K. , Elahi P. , Budunoğlu L. , Şenel Ç. , Paltani P. , Ilday F. Ö.
Published: July 2014

We report on the experimental characterization and theoretical prediction of pulse-to-pulse intensity fluctuations, namely, intensity noise, for ultrafast fiber amplifiers. We present a theoretical model with which the intensity noise of a Yb-doped fiber amplifier can be predicted with high accuracy, taking into account seed and pump noise, as well as generation of amplified spontaneous emission. Transfer of pump and seed signal modulations to the amplified output during fiber amplification are investigated thoroughly. Practically, our model enables design and optimization of fiber amplifiers with regards to their intensity noise performance. As a route to reducing noise imparted by pump diodes in a double-clad amplifier, we show the use of multiple, low-power diodes is more beneficial compared to a single, high-power diode due to the largely uncorrelated nature of their individual noise contributions.
Power and efficiency analysis of a realistic resonant tunneling diode thermoelectric
Authors: Agarwal Akshay , Muralidharan Bhaskaran
Published: July 2014

Low-dimensional systems with sharp features in the density of states have been proposed as a means for improving the efficiency of thermoelectric devices. Quantum dot systems, which offer the sharpest density of states achievable, however, suffer from low power outputs while bulk (3-D) thermoelectrics, while displaying high power outputs, offer very low efficiencies. Here, we analyze the use of a resonant tunneling diode structure that combines the best of both aspects, that is, density of states distortion with a finite bandwidth due to confinement that aids the efficiency and a large number of current carrying transverse modes that enhances the total power output. We show that this device can achieve a high power output (∼0.3 MW∕m2) at efficiencies of ∼40% of the Carnot efficiency due to the contribution from these transverse momentum states at a finite bandwidth of kT∕2. We then provide a detailed analysis of the physics of charge and heat transport with insights on parasitic currents that reduce the efficiency. Finally, a comparison between the resonant tunneling diode and a quantum dot device with comparable bandwidth reveals that a similar performance requires ultra-dense areal quantum dot densities of ∼1012/cm2.
Enhanced open voltage of BiFeO3 polycrystalline film by surface modification of organolead halide perovskite
Authors: Zhao Pengjun , Bian Liang , Wang Lei , Xu Jinbao , Chang Aimin
Published: July 2014

Inorganic-organolead halide perovskite CH3NH3PbI3 modified BiFeO3 polycrystalline film has been established. The composite photoelectrode presents much larger open voltage and several magnitudes superior photoelectric conversion performance in comparison to the ordinary BiFeO3 polycrystalline film. The I-V curve shows that the short-circuit current (Jsc) is 1.74 mA·cm−2 and open-circuit voltage (Voc) is 1.62 V, the device's photon to current efficiency is over 1%. The large open voltage and high photovoltaic efficiency is believed to attributed to the spontaneous polarization of composite perovskite induced by BiFeO3 lattice and modified reduced work function of the modified BiFeO3 surface. Our results clearly show that the present BiFeO3-CH3NH3PbI3 planar device is capable to generate a large voltage in macro scale under visible light, leading an approach to further applications on photodetectors and optoelectronic switch.
Simulation and thermal imaging of the 2006 Esperanza Wildfire in southern California: application of a coupled weather–wildland fire model
Authors: Coen Janice L. , Riggan Philip J.
Published: July 2014

The 2006 Esperanza Fire in Riverside County, California, was simulated with the Coupled Atmosphere–Wildland Fire Environment (CAWFE) model to examine how dynamic interactions of the atmosphere with large-scale fire spread and energy release may affect observed patterns of fire behaviour as mapped using the FireMapper thermal-imaging radiometer. CAWFE simulated the meteorological flow in and near the fire, the fire’s growth as influenced by gusty Santa Ana winds and interactions between the fire and weather through fire-induced winds during the first day of burning. The airflow was characterised by thermally stratified, two-layer flow channelled between the San Bernardino and San Jacinto mountain ranges with transient flow accelerations driving the fire in Cabazon Peak’s lee. The simulation reproduced distinguishing features of the fire including its overall direction and width, rapid spread west-south-westward across canyons, spread up canyons crossing its southern flank, splitting into two heading regions and feathering of the fire line. The simulation correctly depicted the fire’s location at the time of an early-morning incident involving firefighter fatalities. It also depicted periods of deep plume growth, but anomalously described downhill spread of the head of the fire under weak winds that was less rapid than observed. Although capturing the meteorological flow was essential to reproducing the fire’s evolution, fuel factors including fuel load appeared to play a secondary role.
Catalytic strategy used by the myosin motor to hydrolyze ATP
Authors: Kiani Farooq Ahmad , Fischer Stefan
Published: July 2014

Significance

Biomolecular motor proteins like myosin generate mechanical force from the chemical energy of ATP. Like gas engines, they have different parts (protein domains) that run through a well-defined cycle of motions, consuming one ATP per cycle. Because ATP is very stable, motor proteins catalyze its breakdown (hydrolysis). The catalytic mechanism is at the core of understanding how these motors work, because the activation of the catalytic ATPase-function coordinates the motion of the different domains. Identifying which protein groups are essential for catalysis allows one to understand how the precise coupling between ATPase activation and mechanical motion is achieved. Moreover, ATPases are involved in most biochemical processes and are expected to have a catalytic strategy very similar to the one reported here.
The
Legionella
effector SidC defines a unique family of ubiquitin ligases important for bacterial phagosomal remodeling
Authors: Hsu FoSheng , Luo Xi , Qiu Jiazhang , Teng Yan-Bin , Jin Jianping , Smolka Marcus B. , Luo Zhao-Qing , Mao Yuxin
Published: July 2014

Significance

Legionella pneumophila
, the Legionnaires’ disease-causing bacterial pathogen, translocates a myriad of bacterial proteins, called effectors, into host cells. These proteins exploit normal host cellular functions to facilitate bacterial intracellular growth. To identify the functions of these bacterial effectors has been a major challenge. Here, we determined the structure of one such effector, substrate of Icm/Dot transporter (SidC), which was previously thought to be a vesicle-tethering factor for recruiting endoplasmic reticulum (ER) vesicles to the bacterial vacuoles. Surprisingly, our data uncovered a canonical catalytic triad resembling that of cysteine proteases. We further demonstrated that SidC possesses ubiquitin ligase activity, which is required for the enrichment of ER proteins and ubiquitin conjugates to bacterial vacuoles. Collectively, our data on SidC define a unique family of ubiquitin ligases.
Covalent agonists for studying G protein-coupled receptor activation
Authors: Weichert Dietmar , Kruse Andrew C. , Manglik Aashish , Hiller Christine , Zhang Cheng , Hübner Harald , Kobilka Brian K. , Gmeiner Peter
Published: July 2014

Significance

Protein crystallography has greatly contributed to our understanding of the structure and function of G protein-coupled receptors (GPCRs). Recent success in the structural investigation of active GPCR conformations was guided by the application of high-affinity agonists and G proteins or G protein mimetic nanobodies. However, poor affinities of agonists prevent the formation of diffraction-quality crystals and hamper the generation of state-specific nanobodies. To overcome this limitation, we present a general approach to covalently binding molecular tools for the construction of stable ligand-receptor complexes capable of G protein activation. Besides the promotion of structural studies, tethered agonist-GPCR complexes may find application in biochemical and biophysical experiments that require reliable labeling of distinct receptor populations, underlining the versatility of covalent agonists for studying GPCR activation.
Radial bone size and strength indices in male road cyclists, mountain bikers and controls
Authors: McVeigh Joanne A. , Meiring Rebecca , Cimato Alessandra , Micklesfield Lisa K. , Oosthuyse Tanja
Published: July 2014

Mountain biking (MB), unlike road cycling (RC) involves exposure to ground impact bone strain and requires upper‐body muscle forces to maintain stability over uneven terrain and therefore may have differential effects on radial bone structure and strength. This study aimed to compare serum bone turnover marker concentration, 1‐repetition maximum muscle strength and the radial proximal (diaphysis) and distal (metaphysis) bone structure [bone mineral content, total and cortical area (CoA), density and thickness, diameter and circumference], strength strain indices and muscle cross‐sectional area (MCSA) using peripheral quantitative computed tomography (pQCT) between 30 male cyclists (18–34 years) MB (n = 10), RC (n = 10) and non‐athletes controls (CON, n = 10). Differences were assessed by ANOVA and an ANCOVA (adjusting for body mass and height) where appropriate. MB radii were characterised by significantly stronger (14–16%), denser (9–27%) and larger (10%) metaphyses and stronger (22–23%) and larger (11–13%) diaphyses compared to RC and CON. RC had significantly 7% higher strength indices and 4% greater CoA and thickness than CON at the diaphysis, with no differences for other bone measurements. Serum C‐terminal telopeptides of type‐1 collagen concentration (bone resorption marker) was higher in RC than MB (p < 0.05) and above the age‐reference range. MCSA and strength were greater in MB than RC (p < 0.05). Muscle forces generated during RC appear to produce an osteogenic stimulus to increase radial bone strength indices with minimal improvement in bone structure. However greater resorptive activity in RC suggests inadequate loading to support bone maintenance. In conclusion, bone loading, muscle size and strength of MB are superior to RC.
Hypoxia-induced Bmi1 promotes renal tubular epithelial cell–mesenchymal transition and renal fibrosis via PI3K/Akt signal
Authors: Du Rui , Xia Lin , Ning Xiaoxuan , Liu Limin , Sun Wenjuan , Huang Chen , Wang Hanmin , Sun Shiren
Published: July 2014

Hypoxia is an important microenvironmental factor in the development of renal fibrosis; however, the underlying mechanisms are not well elucidated. Here we show that hypoxia induces Bmi1 mRNA and protein expression in human tubular epithelial cells. We further demonstrate that Bmi1 expression might be directly regulated by hypoxia-inducible factor-1a (HIF-1a) under low oxygen. Moreover, chromatin immunoprecipitation and reporter gene assay studies reveal cooperative transactivation of Bmi1 by HIF-1α and Twist. Enforced Bmi1 expression induces epithelial–mesenchymal transition (EMT), whereas silencing endogenous Bmi-1 expression reverses hypoxia-induced EMT. Up-regulation of Bmi1 leads to stabilization of Snail via modulation of PI3K/Akt signaling, whereas ablation of PI3K/Akt signaling partially rescues the phenotype of Bmi1-overexpressing cells, indicating that PI3K/Akt signaling might be a major mediator of Bmi1-induced EMT. In a rat model of obstructive nephropathy, Bmi1 expression increases in a time-dependent manner. Furthermore, we demonstrate that increased levels of Bmi1, correlated with HIF-1α and Twist, are associated with patients with chronic kidney disease. We provide in vitro and in vivo evidence that activation of HIF-1a/Twist-Bmi1 signaling in renal epithelial cells is associated with the development of chronic renal disease and may promote fibrogenesis via modulation of PI3K/Akt/Snail signaling by facilitating EMT.
Discovery of a Thorne–Żytkow object candidate in the Small Magellanic Cloud
Authors: Levesque Emily M. , Massey Philip , Żytkow Anna N. , Morrell Nidia
Published: July 2014

Thorne–Żytkow objects (TŻOs) are a theoretical class of star in which a compact neutron star is surrounded by a large, diffuse envelope. Supergiant TŻOs are predicted to be almost identical in appearance to red supergiants (RSGs). The best features that can be used at present to distinguish TŻOs from the general RSG population are the unusually strong heavy-element and Li lines present in their spectra, products of the star's fully convective envelope linking the photosphere with the extraordinarily hot burning region in the vicinity of the neutron star core. Here, we present our discovery of a TŻO candidate in the Small Magellanic Cloud. It is the first star to display the distinctive chemical profile of anomalous element enhancements thought to be unique to TŻOs. The positive detection of a TŻO will provide the first direct evidence for a completely new model of stellar interiors, a theoretically predicted fate for massive binary systems, and never-seen-before nucleosynthesis processes that would offer a new channel for Li and heavy-element production in our Universe.
Evidence for varying social strategies across the day in chacma baboons
Authors: Sick Claudia , Carter Alecia J. , Marshall Harry H. , Knapp Leslie A. , Dabelsteen Torben , Cowlishaw Guy
Published: July 2014

Strong social bonds can make an important contribution to individual fitness, but we still have only a limited understanding of the temporal period relevant to the adjustment of social relationships. While there is growing recognition of the importance of strong bonds that persist for years, social relationships can also vary over weeks and months, suggesting that social strategies may be optimized over shorter timescales. Using biological market theory as a framework, we explore whether temporal variation in the benefits of social relationships might be sufficient to generate daily adjustments of social strategies in wild baboons. Data on grooming, one measure of social relationships, were collected from 60 chacma baboons (Papio ursinus) across two troops over a six month period. Our analyses suggest that social strategies can show diurnal variation, with subordinates preferentially grooming more dominant individuals earlier in the day compared with later in the day. These findings indicate that group-living animals may optimize certain elements of their social strategies over relatively short time periods.
Keep the nest clean: survival advantages of corpse removal in ants
Authors: Diez Lise , Lejeune Philippe , Detrain Claire
Published: July 2014

Sociality increases exposure to pathogens. Therefore, social insects have developed a wide range of behavioural defences, known as ‘social immunity’. However, the benefits of these behaviours in terms of colony survival have been scarcely investigated. We tested the survival advantage of prophylaxis, i.e. corpse removal, in ants. Over 50 days, we compared the survival of ants in colonies that were free to remove corpses with those that were restricted in their corpse removal. From Day 8 onwards, the survival of adult workers was significantly higher in colonies that were allowed to remove corpses normally. Overall, larvae survived better than adults, but were slightly affected by the presence of corpses in the nest. When removal was restricted, ants removed as many corpses as they could and moved the remaining corpses away from brood, typically to the nest corners. These results show the importance of nest maintenance and prophylactic behaviour in social insects.
Age-dependent social learning in a lizard
Authors: Noble Daniel W. A. , Byrne Richard W. , Whiting Martin J.
Published: July 2014

Evidence of social learning, whereby the actions of an animal facilitate the acquisition of new information by another, is taxonomically biased towards mammals, especially primates, and birds. However, social learning need not be limited to group-living animals because species with less interaction can still benefit from learning about potential predators, food sources, rivals and mates. We trained male skinks (Eulamprus quoyii), a mostly solitary lizard from eastern Australia, in a two-step foraging task. Lizards belonging to ‘young’ and ‘old’ age classes were presented with a novel instrumental task (displacing a lid) and an association task (reward under blue lid). We did not find evidence for age-dependent learning of the instrumental task; however, young males in the presence of a demonstrator learnt the association task faster than young males without a demonstrator, whereas old males in both treatments had similar success rates. We present the first evidence of age-dependent social learning in a lizard and suggest that the use of social information for learning may be more widespread than previously believed.
Ice-binding proteins that accumulate on different ice crystal planes produce distinct thermal hysteresis dynamics
Authors: Drori Ran , Celik Yeliz , Davies Peter L. , Braslavsky Ido
Published: July 2014

Ice-binding proteins that aid the survival of freeze-avoiding, cold-adapted organisms by inhibiting the growth of endogenous ice crystals are called antifreeze proteins (AFPs). The binding of AFPs to ice causes a separation between the melting point and the freezing point of the ice crystal (thermal hysteresis, TH). TH produced by hyperactive AFPs is an order of magnitude higher than that produced by a typical fish AFP. The basis for this difference in activity remains unclear. Here, we have compared the time dependence of TH activity for both hyperactive and moderately active AFPs using a custom-made nanolitre osmometer and a novel microfluidics system. We found that the TH activities of hyperactive AFPs were time-dependent, and that the TH activity of a moderate AFP was almost insensitive to time. Fluorescence microscopy measurement revealed that despite their higher TH activity, hyperactive AFPs from two insects (moth and beetle) took far longer to accumulate on the ice surface than did a moderately active fish AFP. An ice-binding protein from a bacterium that functions as an ice adhesin rather than as an antifreeze had intermediate TH properties. Nevertheless, the accumulation of this ice adhesion protein and the two hyperactive AFPs on the basal plane of ice is distinct and extensive, but not detectable for moderately active AFPs. Basal ice plane binding is the distinguishing feature of antifreeze hyperactivity, which is not strictly needed in fish that require only approximately 1°C of TH. Here, we found a correlation between the accumulation kinetics of the hyperactive AFP at the basal plane and the time sensitivity of the measured TH.
Compliant threads maximize spider silk connection strength and toughness
Authors: Meyer Avery , Pugno Nicola M. , Cranford Steven W.
Published: July 2014

Millions of years of evolution have adapted spider webs to achieve a range of functionalities, including the well-known capture of prey, with efficient use of material. One feature that has escaped extensive investigation is the silk-on-silk connection joints within spider webs, particularly from a structural mechanics perspective. We report a joint theoretical and computational analysis of an idealized silk-on-silk fibre junction. By modifying the theory of multiple peeling, we quantitatively compare the performance of the system while systematically increasing the rigidity of the anchor thread, by both scaling the stress–strain response and the introduction of an applied pre-strain. The results of our study indicate that compliance is a virtue—the more extensible the anchorage, the tougher and stronger the connection becomes. In consideration of the theoretical model, in comparison with rigid substrates, a compliant anchorage enormously increases the effective adhesion strength (work required to detach), independent of the adhered thread itself, attributed to a nonlinear alignment between thread and anchor (contact peeling angle). The results can direct novel engineering design principles to achieve possible load transfer from compliant fibre-to-fibre anchorages, be they silk-on-silk or another, as-yet undeveloped, system.
Ribosome recycling induces optimal translation rate at low ribosomal availability
Authors: Marshall E. , Stansfield I. , Romano M. C.
Published: July 2014

During eukaryotic cellular protein synthesis, ribosomal translation is made more efficient through interaction between the two ends of the messenger RNA (mRNA). Ribosomes reaching the 3′ end of the mRNA can thus recycle and begin translation again on the same mRNA, the so-called ‘closed-loop’ model. Using a driven diffusion lattice model of translation, we study the effects of ribosome recycling on the dynamics of ribosome flow and density on the mRNA. We show that ribosome recycling induces a substantial increase in ribosome current. Furthermore, for sufficiently large values of the recycling rate, the lattice does not transition directly from low to high ribosome density, as seen in lattice models without recycling. Instead, a maximal current phase becomes accessible for much lower values of the initiation rate, and multiple phase transitions occur over a wide region of the phase plane. Crucially, we show that in the presence of ribosome recycling, mRNAs can exhibit a peak in protein production at low values of the initiation rate, beyond which translation rate decreases. This has important implications for translation of certain mRNAs, suggesting that there is an optimal concentration of ribosomes at which protein synthesis is maximal, and beyond which translational efficiency is impaired.
Influence of inhomogeneous static magnetic field-exposure on patients with erosive gastritis: a randomized, self- and placebo-controlled, double-blind, single centre, pilot study
Authors: Juhász Márk , Nagy Viktor L. , Székely Hajnal , Kocsis Dorottya , Tulassay Zsolt , László János F.
Published: July 2014

This pilot study was devoted to the effect of static magnetic field (SMF)-exposure on erosive gastritis. The randomized, self- and placebo-controlled, double-blind, pilot study included 16 patients of the 2nd Department of Internal Medicine, Semmelweis University diagnosed with erosive gastritis. The instrumental analysis followed a qualitative (pre-intervention) assessment of the symptoms by the patient: lower heartburn (in the ventricle), upper heartburn (in the oesophagus), epigastric pain, regurgitation, bloating and dry cough. Medical diagnosis included a double-line upper panendoscopy followed by 30 min local inhomogeneous SMF-exposure intervention at the lower sternal region over the stomach with peak-to-peak magnetic induction of 3 mT and 30 mT m−1gradient at the target site. A qualitative (post-intervention) assessment of the same symptoms closed the examination. Sham- or SMF-exposure was used in a double-blind manner. The authors succeeded in justifying the clinically and statistically significant beneficial effect of the SMF- over sham-exposure on the symptoms of erosive gastritis, the average effect of inhibition was 56% byp= 0.001,n= 42 + 96. This pilot study was aimed to encourage gastroenterologists to test local, inhomogeneous SMF-exposure on erosive gastritis patients, so this intervention may become an evidence-based alternative or complementary method in the clinical use especially in cases when conventional therapy options are contraindicated.
On the description of subsystems in relativistic hypersurface Bohmian mechanics
Authors: Dürr Detlef , Lienert Matthias
Published: July 2014

A candidate for a realistic relativistic quantum theory is the hypersurface Bohm–Dirac model. Its formulation uses a foliation of space–time into space-like hypersurfaces. In order to apply the theory and to make contact with the usual quantum formalism, one needs a framework for the description of subsystems. The presence of spin together with the foliation renders the subsystem description more complicated than in the non-relativistic case with spin. In this paper, we provide such a framework in terms of an appropriate conditional density matrix and an effective wave function as well as clarify their relation, thereby generalizing previous subsystem descriptions in the non-relativistic case.
When does a physical system compute?
Authors: Horsman Dominic , Stepney Susan , Wagner Rob C. , Kendon Viv
Published: July 2014

Computing is a high-level process of a physical system. Recent interest in non-standard computing systems, including quantum and biological computers, has brought this physical basis of computing to the forefront. There has been, however, no consensus on how to tell if a given physical system is acting as a computer or not; leading to confusion over novel computational devices, and even claims that every physical event is a computation. In this paper, we introduce a formal framework that can be used to determine whether a physical system is performing a computation. We demonstrate how the abstract computational level interacts with the physical device level, in comparison with the use of mathematical models in experimental science. This powerful formulation allows a precise description of experiments, technology, computation and simulation, giving our central conclusion:
physical computing is the use of a physical system to predict the outcome of an abstract evolution
. We give conditions for computing, illustrated using a range of non-standard computing scenarios. The framework also covers broader computing contexts, where there is no obvious human computer user. We introduce the notion of a ‘computational entity’, and its critical role in defining when computing is taking place in physical systems.
Superfluid light in bulk nonlinear media
Authors: Carusotto Iacopo
Published: July 2014

We review how the paraxial approximation naturally leads to a hydrodynamic description of light propagation in a bulk Kerr nonlinear medium in terms of a wave equation analogous to the Gross–Pitaevskii equation for the order parameter of a superfluid. The main features of the many-body collective dynamics of the fluid of light in this propagating geometry are discussed: generation and observation of Bogoliubov sound waves in the fluid of light is first described. Experimentally accessible manifestations of superfluidity are then highlighted. Perspectives in view of realizing analogue models of gravity are finally given.
Insights into the molecular mechanisms underlying diversified wing venation among insects
Authors: Shimmi Osamu , Matsuda Shinya , Hatakeyama Masatsugu
Published: July 2014

Insect wings are great resources for studying morphological diversities in nature as well as in fossil records. Among them, variation in wing venation is one of the most characteristic features of insect species. Venation is therefore, undeniably a key factor of species-specific functional traits of the wings; however, the mechanism underlying wing vein formation among insects largely remains unexplored. Our knowledge of the genetic basis of wing development is solely restricted toDrosophila melanogaster. A critical step in wing vein development inDrosophilais the activation of the decapentaplegic (Dpp)/bone morphogenetic protein (BMP) signalling pathway during pupal stages. A key mechanism is the directional transport of Dpp from the longitudinal veins into the posterior crossvein by BMP-binding proteins, resulting in redistribution of Dpp that reflects wing vein patterns. Recent works on the sawflyAthalia rosae, of the order Hymenoptera, also suggested that the Dpp transport system is required to specify fore- and hindwing vein patterns. Given that Dpp redistribution via transport is likely to be a key mechanism for establishing wing vein patterns, this raises the interesting possibility that distinct wing vein patterns are generated, based on where Dpp is transported. Experimental evidence inDrosophilasuggests that the direction of Dpp transport is regulated by prepatterned positional information. These observations lead to the postulation that Dpp generates diversified insect wing vein patterns through species-specific positional information of its directional transport. Extension of these observations in some winged insects will provide further insights into the mechanisms underlying diversified wing venation among insects.
Does energy availability predict gastropod reproductive strategies?
Authors: McClain Craig R. , Filler Ryan , Auld Josh R.
Published: July 2014

The diversity of reproductive strategies in nature is shaped by a plethora of factors including energy availability. For example, both low temperatures and limited food availability could increase larval exposure to predation by slowing development, selecting against pelagic and/or feeding larvae. The frequency of hermaphroditism could increase under low food availability as population density (and hence mate availability) decreases. We examine the relationship between reproductive/life-history traits and energy availability for 189 marine gastropod families. Only larval type was related to energy availability with the odds of having planktotrophic larvae versus direct development decreasing by 1% with every one-unit increase in the square root of carbon flux. Simultaneous hermaphroditism also potentially increases with carbon flux, but this effect disappears when accounting for evolutionary relationships among taxa. Our findings are in contrast to some theory and empirical work demonstrating that hermaphroditism should increase and planktotrophic development should decrease with decreasing productivity. Instead, they suggest that some reproductive strategies are too energetically expensive at low food availabilities, or arise only when energy is available, and others serve to capitalize on opportunities for aggregation or increased energy availability.
Reflections on the development of health economics in low- and middle-income countries
Authors: Mills Anne
Published: July 2014

Health economics is a relatively new discipline, though its antecedents can be traced back to William Petty FRS (1623–1687). In high-income countries, the academic discipline and scientific literature have grown rapidly since the 1960s. In low- and middle-income countries, the growth of health economics has been strongly influenced by trends in health policy, especially among the international and bilateral agencies involved in supporting health sector development. Valuable and influential research has been done in areas such as cost–benefit and cost-effectiveness analysis, financing of healthcare, healthcare provision, and health systems analysis, but there has been insufficient questioning of the relevance of theories and policy recommendations in the rich world literature to the circumstances of poorer countries. Characteristics such as a country's economic structure, strength of political and social institutions, management capacity, and dependence on external agencies, mean that theories and models cannot necessarily be transferred between settings. Recent innovations in the health economics literature on low- and middle-income countries indicate how health economics can be shaped to provide more relevant advice for policy. For this to be taken further, it is critical that such countries develop stronger capacity for health economics within their universities and research institutes, with greater local commitment of funding.
Symbiotic state influences life-history strategy of a clonal cnidarian
Authors: Bingham Brian L. , Dimond James L. , Muller-Parker Gisèle
Published: July 2014

Along the North American Pacific coast, the common intertidal sea anemone
Anthopleura elegantissima
engages in facultative, flexible symbioses with
Symbiodinium muscatinei
(a dinoflagellate) and
Elliptochloris marina
(a chlorophyte). Determining how symbiotic state affects host fitness is essential to understanding the ecological significance of engaging in such flexible relationships with diverse symbionts. Fitness consequences of hosting
S. muscatinei
,
E. marina
or negligible numbers of either symbiont (aposymbiosis) were investigated by measuring growth, cloning by fission and gonad development after 8.5–11 months of sustained exposure to high, moderate or low irradiance under seasonal environmental conditions. Both symbiotic state and irradiance affected host fitness, leading to divergent life-history strategies. Moderate and high irradiances led to a greater level of gonad development in individuals hosting
E. marina
, while high irradiance and high summer temperature promoted cloning in individuals hosting
S. muscatinei
and reduced fitness of aposymbiotic anemones. Associating with
S. muscatinei
may contribute to the success of
A. elegantissima
as a spatial competitor on the high shore: (i) by offsetting the costs of living under high temperature and irradiance conditions, and (ii) by promoting a high fission rate and clonal expansion. Our results suggest that basic life-history characteristics of a clonal cnidarian can be affected by the identity of the endosymbionts it hosts.
Familiarity affects social network structure and discovery of prey patch locations in foraging stickleback shoals
Authors: Atton N. , Galef B. J. , Hoppitt W. , Webster M. M. , Laland K. N.
Published: July 2014

Numerous factors affect the fine-scale social structure of animal groups, but it is unclear how important such factors are in determining how individuals encounter resources. Familiarity affects shoal choice and structure in many social fishes. Here, we show that familiarity between shoal members of sticklebacks (Gasterosteus aculeatus) affects both fine-scale social organization and the discovery of resources. Social network analysis revealed that sticklebacks remained closer to familiar than to unfamiliar individuals within the same shoal. Network-based diffusion analysis revealed that there was a strong untransmitted social effect on patch discovery, with individuals tending to discover a task sooner if a familiar individual from their group had previously done so than if an unfamiliar fish had done so. However, in contrast to the effect of familiarity, the frequency with which individuals had previously associated with one another had no effect upon the likelihood of prey patch discovery. This may have been due to the influence of fish on one another's movements; the effect of familiarity on discovery of an empty ‘control’ patch was as strong as for discovery of an actual prey patch. Our results demonstrate that factors affecting fine-scale social interactions can also influence how individuals encounter and exploit resources.
The tropicalization of temperate marine ecosystems: climate-mediated changes in herbivory and community phase shifts
Authors: Vergés Adriana , Steinberg Peter D. , Hay Mark E. , Poore Alistair G. B. , Campbell Alexandra H. , Ballesteros Enric , Heck Kenneth L. , Booth David J. , Coleman Melinda A. , Feary David A. , Figueira Will , Langlois Tim , Marzinelli Ezequiel M. , Mizerek Toni , Mumby Peter J. , Nakamura Yohei , Roughan Moninya , van Sebille Erik , Gupta Alex Sen , Smale Dan A. , Tomas Fiona , Wernberg Thomas , Wilson Shaun K.
Published: July 2014

Climate-driven changes in biotic interactions can profoundly alter ecological communities, particularly when they impact foundation species. In marine systems, changes in herbivory and the consequent loss of dominant habitat forming species can result in dramatic community phase shifts, such as from coral to macroalgal dominance when tropical fish herbivory decreases, and from algal forests to ‘barrens’ when temperate urchin grazing increases. Here, we propose a novel phase-shift away from macroalgal dominance caused by tropical herbivores extending their range into temperate regions. We argue that this phase shift is facilitated by poleward-flowing boundary currents that are creating ocean warming hotspots around the globe, enabling the range expansion of tropical species and increasing their grazing rates in temperate areas. Overgrazing of temperate macroalgae by tropical herbivorous fishes has already occurred in Japan and the Mediterranean. Emerging evidence suggests similar phenomena are occurring in other temperate regions, with increasing occurrence of tropical fishes on temperate reefs.
Live imaging of baculovirus infection of midgut epithelium cells: a functional assay of per os infectivity factors
Authors: Mu Jingfang , van Lent Jan W. M. , Smagghe Guy , Wang Yun , Chen Xinwen , Vlak Just M. , van Oers Monique M.
Published: July 2014

The occlusion-derived viruses (ODVs) of baculoviruses are responsible for oral infection of insect hosts, whereas budded viruses (BVs) are responsible for systemic infection within the host. The ODV membrane proteins play crucial roles in mediating virus entry into midgut epithelium cells to initiate infection and are important factors in host-range determination. For Autographa californica multiple nucleopolyhedrovirus (AcMNPV), seven conserved ODV membrane proteins have been shown to be essential for oral infectivity and are called per os infectivity factors (PIFs). Information on the function of the individual PIF proteins in virus entry is limited, partly due to the lack of a good in vitro system for monitoring ODV entry. Here, we constructed a baculovirus with EGFP fused to the nucleocapsid to monitor virus entry into primary midgut epithelium cells ex vivo using confocal fluorescence microscopy. The EGFP-labelled virus showed similar BV virulence and ODV infectivity as WT virus. The ability to bind and enter host cells was then visualized for WT AcMNPV and viruses with mutations in P74 (PIF0), PIF1 or PIF2, showing that P74 is required for ODV binding, whilst PIF1 and PIF2 play important roles in the entry of ODV after binding to midgut cells. This is the first live imaging of ODV entry into midgut cells and complements the genetic and biochemical evidence for the role of PIFs in the oral infection process.
V genes in primates from whole genome shotgun data
Authors: Olivieri David N. , Gambón-Deza Francisco
Published: July 2014

The adaptive immune system uses V genes for antigen recognition. The evolutionary diversification and selection processes within and across species and orders are poorly understood. Here, we studied the amino acid (AA) sequences obtained of translated in-frame V exons of immunoglobulins (IG) and T cell receptors (TR) from 16 primate species whose genomes have been sequenced. Multi-species comparative analysis supports the hypothesis that V genes in the IG loci undergo birth/death processes, thereby permitting rapid adaptability over evolutionary time. We also show that multiple cladistic groupings exist in the TRA (35 clades) and TRB (25 clades) V gene loci and that each primate species typically contributes at least one V gene to each of these clade. The results demonstrate that IG V genes and TR V genes have quite different evolutionary pathways; multiple duplications can explain the IG loci results, while co-evolutionary pressures can explain the phylogenetic results, as seen in genes of the TR loci. We describe how each of the 35 V genes clades of the TRA locus and 25 clades of the TRB locus must have specific and necessary roles for the viability of the species.
Two ZnIIcoordination complexes assembled by trithiocyanuric acid and two different N-donor auxiliary ligands
Authors: He Xiao-Xiao , Guo Ya-Mei
Published: July 2014

The dipyridyl-type building blocks 4-amino-3,5-bis(pyridin-3-yl)-1,2,4-triazole (3-bpt) and 4,4′-bipyridine (bpy) have been used to assemble with ZnIIin the presence of trithiocyanuric acid (ttcH3) to afford two coordination compounds, namely bis[4-amino-3,5-bis(pyridin-3-yl)-1,2,4-triazole-κN3]bis(trithiocyanurato-κ2N,S)zinc(II), [Zn(C3H2N3S3)2(C12H10N6)2]·2H2O, (1), andcatena-poly[[[bis(trithiocyanurato-κ2N,S)zinc(II)]-μ-4,4′-bipyridine-κ2N:N′] 4,4′-bipyridine monosolvate], {[Zn2(C3H2N3S3)4(C10H8N2)3]·C10H8N2}n, (2). Single-crystal X-ray analysis indicates that complex (1) is a mononuclear structure, while complex (2) presents a one-dimensional chain coordination motif. In both complexes, the central ZnIIcation adopts an octahedral geometry, coordinated by four N- and two S-donor atoms. Notably, trithiocyanurate (ttcH2−) adopts the same bidentate chelating coordination mode in each complex and exists in the thione tautomeric form. The 3-bpt co-ligand in (1) adopts a monodentate coordination mode and serves as a terminal pendant ligand, whereas the 4,4′-bipyridine (bpy) ligand in (2) adopts a bidentate–bridging coordination mode. The different coordination characters of the different N-donor auxiliary ligands lead to structural diversity for complexes (1) and (2). Further analysis indicates that the resultant three-dimensional supramolecular networks for (1) and (2) arise through intermolecular N—H...S and N—H...N hydrogen bonds. Both complexes have been further characterized by FT–IR spectroscopy and elemental analyses.
Niclosamide methanol solvate and niclosamide hydrate: structure, solvent inclusion mode and implications for properties
Authors: Harriss Bethany I. , Wilson Claire , Radosavljevic Evans Ivana
Published: July 2014

Structural studies have been carried out of two solid forms of niclosamide [5-chloro-N-(2-chloro-4-nitrophenyl)-2-hydroxybenzamide, NCL], a widely used anthelmintic drug, namely niclosamide methanol monosolvate, C13H8Cl2N2O4·CH3OH or NCL·MeOH, and niclosamide monohydrate, denoted HA. The structure of the methanol solvate obtained from single-crystal X-ray diffraction is reported for the first time, elucidating the key host–guest hydrogen-bonding interactions which lead to solvate formation. The essentially planar NCL host molecules interactviaπ-stacking and pack in a herringbone-type arrangement, giving rise to channels along the crystallographicaaxis in which the methanol guest molecules are located. The methanol and NCL molecules interactviashort O—H...O hydrogen bonds. Laboratory powder X-ray diffraction (PXRD) measurements reveal that the initially phase-pure NCL·MeOH solvate readily transforms into NCL monohydrate within hours under ambient conditions. PXRD further suggests that the NCL monohydrate, HA, is isostructural with the NCL·MeOH solvate. This is consistent with the facile transformation of the methanol solvate into the hydrate when stored in air. The crystal packing and the topology of guest-molecule inclusion are compared with those of other NCL solvates for which the crystal structures are known, giving a consistent picture which correlates well with known experimentally observed desolvation properties.
On the subgroup structure of the hyperoctahedral group in six dimensions
Authors: Zappa Emilio , Dykeman Eric C. , Twarock Reidun
Published: July 2014

The subgroup structure of the hyperoctahedral group in six dimensions is investigated. In particular, the subgroups isomorphic to the icosahedral group are studied. The orthogonal crystallographic representations of the icosahedral group are classified and their intersections and subgroups analysed, using results from graph theory and their spectra.
Cutaneous lesions of Kikuchi's disease: Evolution of histopathological findings
Authors: Kanno Kyoko , Minami‐Hori Masako , Ishida‐Yamamoto Akemi , Komura Keiji , Oikawa Kensuke , Miyokawa Naoyuki , Iizuka Hajime
Published: July 2014

We report a 38‐year‐old male patient who presented with cutaneous lesions mimicking widespread discoid lupus erythematosus with high‐grade fever, arthralgia and lymphadenopathy. Additional lymph node and skin biopsies, however, revealed karyorrhectic debris without neutrophils and numerous CD68‐positive cells, a characteristic finding of Kikuchi's disease (KD). Comparing skin biopsies on different occasions, we could see different forms of histopathology. The histopathology of skin lesions of KD may vary during the clinical course, which may reflect the stage of the disease.