bluuebunny/crossref_metadata_2025 huggingface dataset:
Direct imaging of the magnetization reversal in microwires using all-MOKE microscopy
Authors: Stupakiewicz A. , Chizhik A. , Tekielak M. , Zhukov A. , Gonzalez J. , Maziewski A.
Published: October 2014

We report a method of imaging of the magnetization reversal process using analysis of real-time images of magnetic domain structures in cylindrically shaped microwires. This method uses wide-field polarizing optical microscopy and is based on the magneto-optical Kerr effect (MOKE). The aperture diaphragm in MOKE microscope was used to control the incident angles of the light rays that reached the non-planar surface of the microwire and also determined the MOKE geometries. The movement of the non-central position of the hole in this diaphragm leads to a change in the orientation of the plane of incidence of the light along the perpendicular or the parallel direction to the axial direction of the wire. The visualization of the surface magnetic domain structures is obtained using polar and longitudinal MOKE geometries. The hysteresis loops were obtained by plotting the averaged image contrast as a function of the external magnetic field. The separation of the all-magnetization components is performed using different MOKE geometries in a microscope. We demonstrate the use of vector magnetometry to analyze the orientation of the magnetization in a cylindrically shaped microwire under the influence of an external magnetic field.
Multidimensional free energy surface of unfolding of HP-36: Microscopic origin of ruggedness
Authors: Ghosh Rikhia , Roy Susmita , Bagchi Biman
Published: October 2014

The protein folding funnel paradigm suggests that folding and unfolding proceed as directed diffusion in a multidimensional free energy surface where a multitude of pathways can be traversed during the protein's sojourn from initial to final state. However, finding even a single pathway, with the detail chronicling of intermediates, is an arduous task. In this work we explore the free energy surface of unfolding pathway through umbrella sampling, for a small globular α-helical protein chicken-villin headpiece (HP-36) when the melting of secondary structures is induced by adding DMSO in aqueous solution. We find that the unfolding proceeds through the initial separation or melting of aggregated hydrophobic core that comprises of three phenylalanine residues (Phe7, Phe11, and Phe18). This separation is accompanied by simultaneous melting of the second helix. Unfolding is found to be a multistage process involving crossing of three consecutive minima and two barriers at the initial stage. At a molecular level, Phe18 is observed to reorient itself towards other hydrophobic grooves to stabilize the intermediate states. We identify the configuration of the intermediates and correlate the intermediates with those obtained in our previous works. We also give an estimate of the barriers for different transition states and observe the softening of the barriers with increasing DMSO concentration. We show that higher concentration of DMSO tunes the unfolding pathway by destabilizing the third minimum and stabilizing the second one, indicating the development of a solvent modified, less rugged pathway. The prime outcome of this work is the demonstration that mixed solvents can profoundly transform the nature of the energy landscape and induce unfolding via a modified route. A successful application of Kramer's rate equation correlating the free energy simulation results shows faster rate of unfolding with increasing DMSO concentration. This work perhaps presents the first systematic theoretical study of the effect of a chemical denaturant on the microscopic free energy surface and rates of unfolding of HP-36.
Thermophobicity of liquids: Heats of transport in mixtures as pure component properties—The case of arbitrary concentration
Authors: Hartmann S. , Wittko G. , Schock F. , Groß W. , Lindner F. , Köhler W. , Morozov K. I.
Published: October 2014

We have measured Soret coefficients of a large number of binary mixtures of 23 different organic solvents. The present analysis is based on 77 equimolar mixtures and strongly supports the thermophobicity concept previously developed for the heats of transport of originally 10 different substances [S. Hartmann, G. Wittko, W. Köhler, K. I. Morozov, K. Albers, and G. Sadowski, Phys. Rev. Lett. 109, 065901 (2012)]. Among the investigated compounds, cis-decalin is the most thermophobic, hexane the most thermophilic one. In addition to the equimolar mixtures, we have also analyzed the composition dependence of the Soret coefficients and the heats of transport for 22 selected binary mixtures. Both the interpretation of the heats of transport in equimolar mixtures as pure component thermophobicities and the composition dependence of the Soret coefficient can be understood on the basis of the thermodiffusion theory developed by Morozov [Phys. Rev. E 79, 031204 (2009)], according to which the composition dependence is determined by the excess volume of mixing.
Weighted-density functionals for cavity formation and dispersion energies in continuum solvation models
Authors: Sundararaman Ravishankar , Gunceler Deniz , Arias T. A.
Published: October 2014

Continuum solvation models enable efficient first principles calculations of chemical reactions in solution, but require extensive parametrization and fitting for each solvent and class of solute systems. Here, we examine the assumptions of continuum solvation models in detail and replace empirical terms with physical models in order to construct a minimally-empirical solvation model. Specifically, we derive solvent radii from the nonlocal dielectric response of the solvent from ab initio calculations, construct a closed-form and parameter-free weighted-density approximation for the free energy of the cavity formation, and employ a pair-potential approximation for the dispersion energy. We show that the resulting model with a single solvent-independent parameter: the electron density threshold (nc), and a single solvent-dependent parameter: the dispersion scale factor (s6), reproduces solvation energies of organic molecules in water, chloroform, and carbon tetrachloride with RMS errors of 1.1, 0.6 and 0.5 kcal/mol, respectively. We additionally show that fitting the solvent-dependent s6 parameter to the solvation energy of a single non-polar molecule does not substantially increase these errors. Parametrization of this model for other solvents, therefore, requires minimal effort and is possible without extensive databases of experimental solvation free energies.
The static response function in Kohn-Sham theory: An appropriate basis for its matrix representation in case of finite AO basis sets
Authors: Kollmar Christian , Neese Frank
Published: October 2014

The role of the static Kohn-Sham (KS) response function describing the response of the electron density to a change of the local KS potential is discussed in both the theory of the optimized effective potential (OEP) and the so-called inverse Kohn-Sham problem involving the task to find the local KS potential for a given electron density. In a general discussion of the integral equation to be solved in both cases, it is argued that a unique solution of this equation can be found even in case of finite atomic orbital basis sets. It is shown how a matrix representation of the response function can be obtained if the exchange-correlation potential is expanded in terms of a Schmidt-orthogonalized basis comprising orbitals products of occupied and virtual orbitals. The viability of this approach in both OEP theory and the inverse KS problem is illustrated by numerical examples.
In situ calibration of an infrared imaging video bolometer in the Large Helical Device
Authors: Mukai K. , Peterson B. J. , Pandya S. N. , Sano R.
Published: October 2014

The InfraRed imaging Video Bolometer (IRVB) is a powerful diagnostic to measure multi-dimensional radiation profiles in plasma fusion devices. In the Large Helical Device (LHD), four IRVBs have been installed with different fields of view to reconstruct three-dimensional profiles using a tomography technique. For the application of the measurement to plasma experiments using deuterium gas in LHD in the near future, the long-term effect of the neutron irradiation on the heat characteristics of an IRVB foil should be taken into account by regular in situ calibration measurements. Therefore, in this study, an in situ calibration system was designed.
Synthesis and in vacuo deposition of iron oxide nanoparticles by microplasma-assisted decomposition of ferrocene
Authors: Schaefer Michael , Kumar Ajay , Mohan Sankaran R. , Schlaf Rudy
Published: October 2014

Microplasma-assisted gas-phase nucleation has emerged as an important new approach to produce high-purity, nanometer-sized, and narrowly dispersed particles. This study aims to integrate this technique with vacuum conditions to enable synthesis and deposition in an ultrahigh vacuum compatible environment. The ultimate goal is to combine nanoparticle synthesis with photoemission spectroscopy-based electronic structure analysis. Such measurements require in vacuo deposition to prevent surface contamination from sample transfer, which can be deleterious for nanoscale materials. A homebuilt microplasma reactor was integrated into an existing atomic layer deposition system attached to a surface science multi-chamber system equipped with photoemission spectroscopy. As proof-of-concept, we studied the decomposition of ferrocene vapor in the microplasma to synthesize iron oxide nanoparticles. The injection parameters were optimized to achieve complete precursor decomposition under vacuum conditions, and nanoparticles were successfully deposited. The stoichiometry of the deposited samples was characterized in situ using X-ray photoelectron spectroscopy indicating that iron oxide was formed. Additional transmission electron spectroscopy characterization allowed the determination of the size, shape, and crystal lattice of the particles, confirming their structural properties.
Direct measurements of ion dynamics in collisional magnetic presheaths
Authors: Siddiqui M. Umair , Jackson Cory D. , Kim Justin F. , Hershkowitz Noah
Published: October 2014

Ion velocities and temperatures are measured in the presheath of a grounded plate downstream from an argon helicon plasma source using laser-induced fluorescence (Prf≈450→750 W, Te=2.5→5 eV, Ti=0.1→0.6 eV, n0≈1×1012cm−3, pn=1→6.5 mTorr, λ=0.3→2 cm, ρi≈ 0.5 cm). The plate is held 16°→60° relative to the 1 kG background axial magnetic field. The velocity profiles are compared to a 1D fluid model similar to those presented by Riemann [Phys. Plasmas 1, 552 (1994)] and Ahedo [Phys. Plasmas 4, 4419 (1997)] for the 1 mTorr dataset and are shown to agree well. The model is sensitive to parameters such as collision and ionization frequencies and simplified models, such one presented by Chodura [Phys. Fluids 25, 1628 (1982)], are shown to be inaccurate. E→×B→ flows as large as 40% of cs at the sheath edge are inferred. Definitions for the term “magnetic presheath” and implications for ion flow to tokamak divertors and Hall thruster walls are discussed.
Interaction of high intensity laser with non-uniform clusters and enhanced X-ray emission
Authors: Liu C. S. , Tripathi V. K. , Kumar Manoj
Published: October 2014

Laser irradiated clusters with non-uniform density variation are shown to broaden surface plasmon resonance very significantly. As the clusters get heated and expand hydro-dynamically, the Bremsstrahlung X-ray emission yield passes through a maximum in time. The maximum yield decreases with increase in non-uniformity in the electron density inside the clusters. At higher laser intensity, the nonlinearity in laser cluster interaction may arise even prior to electron heating, via the relativistic mass variation and the nonlinear restoration force on electrons. For clusters with radius less than one tenth of the laser wavelength, the restoration force nonlinearity dominates.
Electronic and structural properties of ultrathin tungsten nanowires and nanotubes by density functional theory calculation
Authors: Sun Shih-Jye , Lin Ken-Huang , Ju Shin-Pon , Li Jia-Yun
Published: October 2014

The simulated annealing basin-hopping method incorporating the penalty function was used to predict the lowest-energy structures for ultrathin tungsten nanowires and nanotubes of different sizes. These predicted structures indicate that tungsten one-dimensional structures at this small scale do not possess B.C.C. configuration as in bulk tungsten material. In order to analyze the relationship between multi-shell geometries and electronic transfer, the electronic and structural properties of tungsten wires and tubes including partial density of state and band structures which were determined and analyzed by quantum chemistry calculations. In addition, in order to understand the application feasibility of these nanowires and tubes on nano-devices such as field emitters or chemical catalysts, the electronic stability of these ultrathin tungsten nanowires was also investigated by density functional theory calculations.
The molecular structure of the interface between water and a hydrophobic substrate is liquid-vapor like
Authors: Willard Adam P. , Chandler David
Published: October 2014

With molecular simulation for water and a tunable hydrophobic substrate, we apply the instantaneous interface construction [A. P. Willard and D. Chandler, “Instantaneous liquid interfaces,” J. Phys. Chem. B 114, 1954–1958 (2010)] to examine the similarity between a water-vapor interface and a water-hydrophobic surface interface. We show that attractive interactions between a hydrophobic surface and water affect capillary wave fluctuations of the instantaneous liquid interface, but these attractive interactions have essentially no effect on the intrinsic interface. The intrinsic interface refers to molecular structure in terms of distances from the instantaneous interface. Further, the intrinsic interface of liquid water and a hydrophobic substrate differs little from that of water and its vapor. The same is not true, we show, for an interface between water and a hydrophilic substrate. In that case, strong directional substrate-water interactions disrupt the liquid-vapor-like interfacial hydrogen bonding network.
High quality factor metallic glass cantilevers with tunable mechanical properties
Authors: Kanik Michael , Bordeenithikasem Punnathat , Kumar Golden , Kinser Emily , Schroers Jan
Published: October 2014

The resonant properties of bulk metallic glass (BMG) microcantilevers were studied. Pt57.5Cu14.7Ni5.3P22.5 BMG was used to fabricate the cantilevers, on the wafer scale, using a thermoplastic forming technique. The resonant behaviors of the cantilevers were then measured in air and various vacuum levels and annealing conditions. The quality factors increase predictably after annealing at temperatures below the glass transition temperature (Tg) for different times. The increase of quality factor of annealed cantilevers is attributable to the decrease in internal friction of the BMG due to thermally activated structural relaxation. Annealing above Tg resets the quality factor to values comparable to that of the as-formed cantilever. Therefore, the quality factor and mechanical properties of a cantilever could be tuned by the selection of suitable annealing temperatures and times. The measured quality factors are in excess of 2000 in air and 8100 in vacuum.
Diamond Schottky diodes with ideality factors close to 1
Authors: Fiori A. , Teraji T. , Koide Y.
Published: October 2014

The stabilization by vacuum annealing of tungsten carbide/p-diamond Schottky barrier diodes (SBDs) has been investigated. The Schottky barrier height (ϕB) and ideality factor (n), at high temperature, were consistently estimated by employing a vertical SBD structure. An exponential drop of ϕB in time at 600 K and its stabilization at 1.46 eV after 90 min were reported. The lowest n among SBDs examined was close to 1.0 at 600 K. A linear relation between ϕB and n in a statistical electrical characterization suggests a ϕB inhomogeneity.
Influence of strain induced by AlN nucleation layer on the electrical properties of AlGaN/GaN heterostructures on Si(111) substrate
Authors: Christy Dennis , Watanabe Arata , Egawa Takashi
Published: October 2014

The crack-free metal-organic chemical vapor deposition (MOCVD) grown AlGaN/GaN heterostructures on Si substrate with modified growth conditions of AlN nucleation layer (NL) and its influence on the electrical and structural properties of conductive GaN layer are presented. From the Hall electrical measurements, a gradual decrease of two-dimensional electron gas (2DEG) concentration near heterointerface as the function of NL thickness is observed possibly due to the reduction in difference of piezoelectric polarization charge densities between AlGaN and GaN layers. It also indicates that the minimum tensile stress and a relatively less total dislocation density for high pressure grown NL can ensure a 20 % increment in mobility at room temperature irrespective of the interface roughness. The thickness and pressure variations in NL and the subsequent changes in growth mode of AlN contributing to the post growth residual tensile stress are investigated using X-ray diffraction and Raman scattering experiments, respectively. The post growth intrinsic residual stress in top layers of heterostructures arises from lattice mismatches, NL parameters and defect densities in GaN. Hence, efforts to reduce the intrinsic residual stress in current conducting GaN layer give an opportunity to further improve the electrical characteristics of AlGaN/GaN device structures on Si.
Temperature-dependent gate-swing hysteresis of pentacene thin film transistors
Authors: Lin Yow-Jon , Lin Yu-Cheng
Published: October 2014

The temperature-dependent hysteresis-type transfer characteristics of pentacene-based organic thin film transistors (OTFTs) were researched. The temperature-dependent transfer characteristics exhibit hopping conduction behavior. The fitting data for the temperature-dependent off-to-on and on-to-off transfer characteristics of OTFTs demonstrate that the hopping distance (ah) and the barrier height for hopping (qϕt) control the carrier flow, resulting in the hysteresis-type transfer characteristics of OTFTs. The hopping model gives an explanation of the gate-swing hysteresis and the roles played by qϕt and ah.
Phase diagram and incommensurate antiferroelectric structure in (Pb1−1.5xLax)(Zr0.42Sn0.40Ti0.18)O3 ceramics discovered by band-to-band optical transitions
Authors: Ding X. J. , Xu L. P. , Hu Z. G. , Chen X. F. , Wang G. S. , Dong X. L. , Chu J. H.
Published: October 2014

Optical properties and phase transitions of (Pb1−1.5xLax)(Zr0.42Sn0.40Ti0.18)O3 (PLZST 100x/42/40/18) ceramics with different compositions have been investigated by temperature dependent spectroscopic ellipsometry. Two interband critical points (Ecp1 and Ecp2) located at about 3.9 and 5.1 eV can be obtained by fitting standard line shapes to the second derivatives of the complex dielectric functions. Based on the band-to-band transitions, the phase diagram of PLZST ceramics can be well presented. Moreover, a peculiar incommensurate antiferroelectric state has been found to exist above the temperature of the normal commensurate antiferroelectric tetragonal structure. It can be stable below Curie temperature, evolving slowly with decreasing temperature towards the commensurate structure, which is due to strong pinning of incommensurate domain walls. The phenomena can result from a competition between ferroelectric ordering and antiferroelectric ordering caused by the lanthanum modification.
Spin valve effect of the interfacial spin accumulation in yttrium iron garnet/platinum bilayers
Authors: Jin Lichuan , Zhang Dainan , Zhang Huaiwu , Tang Xiaoli , Bai Feiming , Zhong Zhiyong , Fan Xin , Xiao John Q.
Published: October 2014

We report the spin valve effect in yttrium iron garnet/platinum (YIG/Pt) bilayers. The spin Hall effect (SHE) generates spin accumulation at the YIG/Pt interface and can be opened/closed by magnetization switching in the electrical insulator YIG. The interfacial spin accumulation was measured in both YIG/Pt and YIG/Cu/Pt structures using a planar Hall configuration. The spin valve effect remained, even after a 2 nm thick Cu layer was inserted between the YIG and Pt layers, which aimed to exclude the induced magnetization at the YIG/Pt interface. The transverse Hall voltage and switching field were dependent on the applied charge current density. The origin of this behavior can be explained by the SHE induced torque exerted on the domain wall, caused by the transfer of the spin angular momentum from the spin-polarized current to the YIG magnetic moment.
Reproducible strain measurement in electronic devices by applying integer multiple to scanning grating in scanning moiré fringe imaging
Authors: Kim Suhyun , Jung Younheum , Kim Joong Jung , Lee Sunyoung , Lee Haebum , Kondo Yukihito
Published: October 2014

Scanning moiré fringe (SMF) imaging by high-angle annular dark field scanning transmission electron microscopy was used to measure the strain field in the channel of a transistor with a CoSi2 source and drain. Nanometer-scale SMFs were formed with a scanning grating size of ds at integer multiples of the Si crystal lattice spacing dl (ds ∼ ndl, n = 2, 3, 4, 5). The moiré fringe formula was modified to establish a method for quantifying strain measurement. We showed that strain fields in a transistor measured by SMF images were reproducible with an accuracy of 0.02%.
Photoluminescence lineshape of ZnO
Authors: Ullrich Bruno , Singh Akhilesh K. , Bhowmick Mithun , Barik Puspendu , Ariza-Flores David , Xi Haowen , Tomm Jens W.
Published: October 2014

The merger of the absorption coefficient dispersion, retrieved from transmission by the modified Urbach rule introduced by Ullrich and Bouchenaki [Jpn. J. Appl. Phys. 30, L1285, 1991], with the extended Roosbroeck-Shockley relation reveals that the optical absorption in ZnO distinctively determines the photoluminescence lineshape. Additionally, the ab initio principles employed enable the accurate determination of the carrier lifetime without further specific probing techniques.
Improving the mechanical properties of Zr-based bulk metallic glass by controlling the activation energy for β-relaxation through plastic deformation
Authors: Adachi Nozomu , Todaka Yoshikazu , Yokoyama Yoshihiko , Umemoto Minoru
Published: October 2014

The mechanism of plastic deformation in bulk metallic glasses (BMGs) is widely believed to be based on a shear transformation zone (STZ). This model assumes that a shear-induced atomic rearrangement occurs at local clusters that are a few to hundreds of atoms in size. It was recently postulated that the potential energy barrier for STZ activation, WSTZ, calculated using the cooperative shear model, is equivalent to the activation energy for β-relaxation, Eβ. This result suggested that the fundamental process for STZ activation is the mechanically activated β-relaxation. Since the Eβ value and the glass transition temperature Tg of BMGs have a linear relation, that is, because Eβ ≈ 26RTg, the composition of the BMG determines the ease with which the STZ can be activated. Enthalpy relaxation experiments revealed that the BMG Zr50Cu40Al10 when deformed by high-pressure torsion (HPT) has a lower Eβ of 101 kJ/mol. The HPT-processed samples accordingly exhibited tensile plastic elongation (0.34%) and marked decreases in their yield strength (330 MPa). These results suggest that mechanically induced structural defects (i.e., the free volume and the anti-free volume) effectively act to reduce WSTZ and increase the number of STZs activated during tensile testing to accommodate the plastic strain without requiring a change in the composition of the BMG. Thus, this study shows quantitatively that mechanically induced structural defects can overcome the compositional limitations of Eβ (or WSTZ) and result in improvements in the mechanical properties of the BMG.
Minorities: Methodological Questions in Relation to Slovenes in Carinthia
Authors: Čuješ Rudolf P.
Published: October 2014

Methodology can be defined as “the principles of organized investigation.” It deals primarily with the question how to arrive at substantive knowledge about the subject under investigation. It is an indispensable tool for scientific work without which the quality of the acquired knowledge would be at the best haphazardous and at worst erroneous.
Humanism in the Slovene Lands∗
Authors: Lencek Rado L.
Published: October 2014

The question whether a Slovene cultural historian is warranted and justified to speak of a “Slovene Humanism period,” was in Slovene historiography seriously raised in the thirties. Asked in a dispute over a suggestion that a number of scholars, by provenience Inner Austrian Slovenes, who between 1450 and 1525 paved the way for Italian Renaissance Humanism at the University of Vienna, belong to Slovene cultural tradition, the question was answered with the proposition that in the Slovene lands of the fifteenth and sixteenth centuries an atmosphere of interests and activities existed which indeed might be understood as a “Slovene Humanism.” In the discussion which followed and which is even today far from terminated, the concept “humanism” has been, of course, understood in very loose and broad terms, so that soon even such Protestant Reformers as Primož Trubar (1508-1586) could be proclaimed “Humanist writers.” What I propose to do in this paper is to reexamine this question; in addition, I hope to be able to show that the proposition I wish to develop in relation to a period in Slovene cultural history, may be applicable to the cultural and social history of Slavic nations in general.
Manifestations of Nationalism in the Baltic Republics
Authors: Forgus Silvia P.
Published: October 2014

The occupation of the Baltic States by the Soviet Union in 1940 failed to extinguish feelings of nationalism and patriotism among the native Estonian, Latvian, and Lithuanian peoples; on the contrary, foreign occupation strengthened their national spirit. Dwelling on the successes and memories of their former independence, Estonian, Latvian, and Lithuanian nationalists continue to denounce the Soviet occupation and resist the policies of communization and Russification practiced by the Soviet regime.
Phyllosomata associated with large gelatinous zooplankton: hitching rides and stealing bites
Authors: O'Rorke Richard , Lavery Shane D. , Wang Miao , Gallego Ramón , Waite Anya M. , Beckley Lynnath E. , Thompson Peter A. , Jeffs Andrew G.
Published: October 2014

During a zooplankton survey 350 km off the coast of Western Australia, we captured a large and robust zooid of a salp (Thetys vagina), to which six late stage larvae (phyllosomata) of the western rock lobster (Panulirus cygnus) were attached. High-throughput sequencing analyses of DNA extracts from midgut glands of the larvae confirmed that each phyllosoma had consumed mainly salp tissue (x¯ = 64.5% ± 15.9 of DNA reads). These results resolve long-standing conjecture whether spiny lobster phyllosomata attach to large gelatinous hosts to feed on them.
A review of the past, the present, and the future of fishers' knowledge research: a challenge to established fisheries science
Authors: Hind Edward J.
Published: October 2014

Fishers' knowledge research is an approach to fisheries research that has a relatively long history, yet has generally failed to become integrated into the fisheries science mainstream alongside approaches that rely primarily on the knowledge of professional scientists. Its continued position on the margins of fisheries science has not however stopped fishers' knowledge researchers from publishing an expanding literature, which they often use to advocate for the greater consideration of fishers' knowledge by fisheries scientists and managers. They believe that the unique and often highly qualitative knowledge of fishers could inform better decision-making, resulting in improved socio-ecological outcomes for fisheries. This review first outlines the scope of the fishers' knowledge literature, before outlining five waves of fishers' knowledge research that have developed over the last century. For each wave, the nature of the fishers' knowledge documented during it is noted, as is the research and dissemination approach taken by its practitioners. The impact of that wave on mainstream fisheries science is then assessed. Overall, it is found that only one wave of fishers' knowledge research is beginning to have consistent success integrating with mainstream fisheries science, a wave that omits the research of many of the unique elements of fishers' knowledge. Other waves have died out, or are in danger of dying out, either because they have failed to be noticed by mainstream fisheries scientists or because mainstream fisheries scientists have not welcomed their outputs. It is summarized that fishers' knowledge research will only continue as a productive activity if mainstream fisheries scientists begin to open their discipline to other knowledge cultures and if fishers' knowledge researchers facilitate this action by disseminating their research so that it is more accessible to these scientists.
Movements of female lumpfish (Cyclopterus lumpus) around Iceland
Authors: Kennedy James , Jónsson Sigurður Þ. , Kasper Jacob M. , Ólafsson Halldór G.
Published: October 2014

Lumpfish (Cyclopterus lumpus) migrate from their offshore feeding areas to the coastal areas of Iceland during March and April where they remain for several months before spawning. Their movements during this time are poorly documented. Using the results of an extensive tag-recapture study (the largest documented for lumpfish) which took place between 2008 and 2014, the movement of female lumpfish around Iceland was investigated and the implications for fisheries management were considered. Of 9710 female fish tagged, 880 were recaptured and 82 of these were recaptured after more than 250 days at liberty (DAL). There was a negative relationship between length at tagging and recapture rate indicating that between 2008 and 2014, the fishery was selecting for smaller fish. Lumpfish showed extensive movements with fish tagged in coastal areas being recaptured up to 587 km from their tagging location and were capable of swimming up to 49 km day−1. Fish were most frequently caught in the area in which they were tagged; however, movement between areas was common. There were indications of homing behaviour with 75% of the fish, which were recaptured after 250 DAL, caught within 80 km of their tagging location. Fish which were tagged offshore before the fishing season showed no clear pattern of where they would be recaptured. These extensive movements and homing behaviour are discussed in the context of the management of the lumpfish fishery.
Multi-model ensemble projections of climate change effects on global marine biodiversity
Authors: Jones Miranda C. , Cheung William W. L.
Published: October 2014

Species distribution models (SDMs) are important tools to explore the effects of future global changes in biodiversity. Previous studies show that variability is introduced into projected distributions through alternative datasets and modelling procedures. However, a multi-model approach to assess biogeographic shifts at the global scale is still rarely applied, particularly in the marine environment. Here, we apply three commonly used SDMs (AquaMaps, Maxent, and the Dynamic Bioclimate Envelope Model) to assess the global patterns of change in species richness, invasion, and extinction intensity in the world oceans. We make species-specific projections of distribution shift using each SDM, subsequently aggregating them to calculate indices of change across a set of 802 species of exploited marine fish and invertebrates. Results indicate an average poleward latitudinal shift across species and SDMs at a rate of 15.5 and 25.6 km decade−1 for a low and high emissions climate change scenario, respectively. Predicted distribution shifts resulted in hotspots of local invasion intensity in high latitude regions, while local extinctions were concentrated near the equator. Specifically, between 10°N and 10°S, we predicted that, on average, 6.5 species would become locally extinct per 0.5° latitude under the climate change emissions scenario Representative Concentration Pathway 8.5. Average invasions were predicted to be 2.0 species per 0.5° latitude in the Arctic Ocean and 1.5 species per 0.5° latitude in the Southern Ocean. These averaged global hotspots of invasion and local extinction intensity are robust to the different SDM used and coincide with high levels of agreement.
A novel function of interferon regulatory factor-1: inhibition of Th2 cells by down-regulating theIl4gene duringListeriainfection
Authors: Maruyama Saho , Kanoh Makoto , Matsumoto Akira , Kuwahara Makoto , Yamashita Masakatsu , Asano Yoshihiro
Published: October 2014

Infection with certain pathogens induces a shift of the Th subset balance to a Th1 dominant state. This, in turn, results in the suppression of Th2 responses. We focused on the involvement of interferon regulatory factor-1 (IRF-1) in the suppression of Th2 cells during Listeria infection. We found that the inhibition of IL-4 production by Th2 cells is mediated by a soluble factor (LmSN) produced by Listeria-infected antigen-presenting cells. The inhibition is not observed with T cells from Irf1 gene-targeted mice. IRF-1 suppresses transcription of the Il4 gene in Th2 cells. Under the influence of the LmSN, IRF-1 binds to the 3ʹ untranslated region (UTR) region of the Il4 gene and down-regulates Il4 gene transcription. Finally, we identified IL-1α and IL-1β as the mediator of the LmSN activity. Signaling through IL-1R induces the stabilization and/or nuclear translocation of IRF-1. We propose that IRF-1 functions to induce the T-cell subset shift via a novel mechanism. Under the influence of IL-1, IRF-1 translocates into the nucleus and acts on the 3ʹUTR region of the Il4 gene, thus inhibiting its transcription in Th2 cells. As a result, the immune system shifts predominantly to a Th1 response during Listeria infection, resulting in effective protection of the host.
Images in Anesthesiology: Bedside Lung Ultrasonography
Authors: Barbara David W.
Published: October 2014

Supplemental Digital Content is available in the text.
Biological Effects of Anti-Granulocyte-Macrophage Colony-Stimulating Factor (GM-CSF) Antibody Formation in Patients Treated With GM-CSF (Sargramostim) as Adjuvant Therapy of Melanoma
Authors: Spitler Lynn E. , Cao Huynh , Piironen Timo , Whiteside Theresa L. , Weber Robert W. , Cruickshank Scott
Published: October 2014

Objectives:

We investigated the development of binding and neutralizing antibodies to granulocyte-macrophage colony-stimulating factor (GM-CSF) in patients receiving prolonged therapy with GM-CSF as adjuvant therapy of melanoma and the impact of these antibodies on biological effects.

Methods:

Fifty-three patients with high-risk melanoma that had been surgically excised were treated with GM-CSF, 125 μg/m2 daily for 14 days every 28 days for 1 year after surgical resection of disease. Serum samples for antibodies to GM-CSF were measured before treatment and on study days 155 and 351. Blood draws for testing biological effects were keyed to GM-CSF administration: days 0 (before), 15 (after 14 d on GM-CSF), 29 (after 14 d off GM-CSF), 155, and 351 (after 14 d on GM-CSF in the sixth and 13th cycle of treatment).

Results:

Of 53 patients enrolled, 43 were evaluable for the development of anti-GM-CSF antibodies. Of these, 93% developed binding antibodies and 42% developed both binding and neutralizing antibodies. The increase in the white blood cell count, percent eosinophils, or neopterin levels engendered by GM-CSF administration was abrogated or markedly decreased in patients with neutralizing antibodies but not in patients who developed only binding antibodies.

Conclusions:

Ninety-three percent of patients with melanoma treated with GM-CSF as adjuvant therapy develop antibodies to GM-CSF. In those with neutralizing antibodies, a diminution of the biological effects of GM-CSF was observed. The development of neutralizing antibodies might also abrogate the potential clinical benefit of this treatment and should be considered in the design of future clinical trials.
Serratia myotis sp. nov. and Serratia vespertilionis sp. nov., isolated from bats hibernating in caves
Authors: García-Fraile P. , Chudíčková M. , Benada O. , Pikula J. , Kolařík M.
Published: October 2014

During the study of bacteria associated with bats affected by white-nose syndrome hibernating in caves in the Czech Republic, we isolated two facultatively anaerobic, Gram-stain-negative bacteria, designated strains 12T and 52T. Strains 12T and 52T were motile, rod-like bacteria (0.5–0.6 µm in diameter; 1–1.3 µm long), with optimal growth at 20–35 °C and pH 6–8. On the basis of the almost complete sequence of their 16S rRNA genes they should be classified within the genus

Serratia

; the closest relatives to strains 12T and 52T were

Serratia quinivorans

DSM 4597T (99.5 % similarity in 16S rRNA gene sequences) and

Serratia ficaria

DSM 4569T (99.5 % similarity in 16S rRNA gene sequences), respectively. DNA–DNA relatedness between strain 12T and

S. quinivorans

DSM 4597T was only 37.1 % and between strain 52T and

S. ficaria

DSM 4569T was only 56.2 %. Both values are far below the 70 % threshold value for species delineation. In view of these data, we propose the inclusion of the two isolates in the genus

Serratia

as representatives of Serratia myotis sp. nov. (type strain 12T = CECT 8594T = DSM 28726T) and Serratia
vespertilionis sp. nov. (type strain 52T = CECT 8595T = DSM 28727T).
Comparison of genes required for H2O2 resistance in Streptococcus gordonii and Streptococcus sanguinis
Authors: Xu Yifan , Itzek Andreas , Kreth Jens
Published: October 2014

Hydrogen peroxide (H2O2) is produced by several members of the genusStreptococcusmainly through the pyruvate oxidase SpxB under aerobic growth conditions. The acute toxic nature of H2O2raises the interesting question of how streptococci cope with intrinsically produced H2O2, which subsequently accumulates in the microenvironment and threatens the closely surrounding population. Here, we investigate the H2O2susceptibility of oralStreptococcus gordoniiandStreptococcus sanguinisand elucidate potential mechanisms of how they protect themselves from the deleterious effect of H2O2. Both organisms are considered primary colonizers and occupy the same intraoral niche making them potential targets for H2O2produced by other species. We demonstrate thatS. gordoniiproduces relatively more H2O2and has a greater ability for resistance to H2O2stress. Functional studies show that, unlike inStreptococcus pneumoniae, H2O2resistance is not dependent on a functional SpxB and confirms the important role of the ferritin-like DNA-binding protein Dps. However, the observed increased H2O2resistance ofS. gordoniioverS. sanguinisis likely to be caused by an oxidative stress protection machinery present even under anaerobic conditions, whileS. sanguinisrequires a longer period of time for adaptation. The ability to produce more H2O2and be more resistant to H2O2might aidS. gordoniiin the competitive oral biofilm environment, since it is lower in abundance yet manages to survive quite efficiently in the oral biofilm.
Inference of evolutionary forces acting on human biological pathways
Authors: Daub J.T. , Dupanloup I. , Robinson-Rechavi M. , Excoffier L.
Published: October 2014

Because natural selection is likely to act on multiple genes underlying a given phenotypic trait, we study here the potential effect of ongoing and past selection on the genetic diversity of human biological pathways. We first show that genes included in gene sets are generally under stronger selective constraints than other genes and that their evolutionary response is correlated. We then introduce a new procedure to detect selection at the pathway level based on a decomposition of the classical McDonald-Kreitman test extended to multiple genes. This new test, called 2DNS, detects outlier gene sets and takes into account past demographic effects as well as evolutionary constraints specific to gene sets. Selective forces acting on gene sets can be easily identified by a mere visual inspection of the position of the gene sets relative to their 2D null distribution. We thus find several outlier gene sets that show signals of positive, balancing, or purifying selection, but also others showing an ancient relaxation of selective constraints. The principle of the 2DNS test can also be applied to other genomic contrasts. For instance, the comparison of patterns of polymorphisms private to African and non-African populations reveals that most pathways show a higher proportion of non-synonymous mutations in non-Africans than in Africans, potentially due to different demographic histories and selective pressures.
Phinch: An interactive, exploratory data visualization framework for –Omic datasets
Authors: Bik Holly M. ,   Pitch Interactive Inc.
Published: October 2014

Using environmental sequencing approaches, we now have the ability to deeply characterize biodiversity and biogeographic patterns in understudied, uncultured microbial taxa (investigations of bacteria, archaea, and microscopic eukaryotes using 454/Illumina sequencing platforms). However, the sheer volume of data produced from these new technologies requires fundamentally different approaches and new paradigms for effective data analysis. Scientific visualization represents an innovative method towards tackling the current bottleneck in bioinformatic workflows. In addition to giving researchers a unique approach for exploring large datasets, it stands to empower biologists with the ability to conduct powerful analyses without requiring a deep level of computational knowledge. Here we present Phinch, an interactive, browser-based visualization framework that can be used to explore and analyze biological patterns in high-throughput -Omic datasets. This project takes advantage of standard file formats from computational pipelines in order to bridge the gap between biological software (e.g. microbial ecology pipelines) and existing data visualization capabilities (harnessing the flexibility and scalability of technologies such as HTML5).
Fitting the Balding-Nichols model to forensic databases
Authors: Rohlfs Rori V. , Aguiar Vitor R. C. , Lohmueller Kirk E. , Castro Amanda M. , Ferreira Alessandro C. S. , Almeida Vanessa C. O. , Louro Iuri D. , Nielsen Rasmus
Published: October 2014

Large forensic databases provide an opportunity to compare observed empirical rates of genotype matching with those expected under forensic genetic models. A number of researchers have taken advantage of this opportunity to validate some forensic genetic approaches, particularly to ensure that estimated rates of genotype matching between unrelated individuals are indeed slight overestimates of those observed. However, these studies have also revealed systematic error trends in genotype probability estimates. In this analysis, we investigate these error trends and show how the specific implementation of the Balding-Nichols model must be considered when applied to database-wide matching. Specifically, we show that in addition to accounting for increased allelic matching between individuals with recent shared ancestry, studies must account for relatively decreased allelic matching between individuals with more ancient shared ancestry.
Ongoing worldwide homogenization of human pathogens
Authors: Poisot T , Nunn C , Morand S
Published: October 2014

Background

Infectious diseases are a major burden on human population, especially in low- and middle-income countries. The increase in the rate of emergence of infectious outbreaks necessitates a better understanding of the worldwide distribution of diseases through space and time.

Methods

We analyze 100 years of records of diseases occurrence worldwide. We use a graph-theoretical approach to characterize the worldwide structure of human infectious diseases, and its dynamics over the Twentieth Century.

Findings

Since the 1960s, there is a clear homogenizing of human pathogens worldwide, with most diseases expanding their geographical area. The occurrence network of human pathogens becomes markedly more connected, and less modular.

Interpretation

Human infectious diseases are steadily expanding their ranges since the 1960s, and disease occurrence has become more homogenized at a global scale. Our findings emphasize the need for international collaboration in designing policies for the prevention of outbreaks.

Funding

T.P. is funded by a FRQNT-PBEE post-doctoral fellowship, and through a Marsden grant from the Royal Academy of Sciences of New-Zealand. Funders had no input in any part of the study.
A continuum of specialists and generalists in empirical communities
Authors: Poisot Timothée , Kéfi Sonia , Morand Serge , Stanko Michal , Marquet Pablo , Hochberg Michael
Published: October 2014

Understanding the persistence of specialists and generalists within ecological communities is a topical research question, with far-reaching consequences for the maintenance of functional diversity. Although theoretical studies indicate that restricted conditions may be necessary to achieve co-occurrence of specialists and generalists, analyses of larger empirical (and species-rich) communities reveal the pervasiveness of coexistence. In this paper, we analyze 175 ecological bipartite networks of three interaction types (animal hosts-parasite, plant-herbivore and plant-pollinator), and measure the extent to which these communities are composed of species with different levels of specificity in their biotic interactions. We find a continuum from specialism to generalism. Furthermore, we demonstrate that diversity tends to be greatest in networks with intermediate connectance, and argue this is because of physical constraints in the filling of networks.
DevoWorm: differentiation waves and computation in C. elegans embryogenesis
Authors: Alicea Bradly , McGrew Steven , Gordon Richard , Larson Stephen , Warrington Tim , Watts Mark
Published: October 2014

Development is a complex process that, under normal circumstances, proceeds in a stable and patterned fashion. Developmental morphogenesis (called embryogenesis) can tell us a great deal about the function and structure of an adult organism. One of the most important aspects of development to understand is the progression of cell division and differentiation in what will become an adult worm. This is where the DevoWorm project can both address multiple outstanding theoretical issues and provide graphical clarity to the embryogenetic process. As a representative of mosaic development,C. elegansembryogenesis is both tractable in terms of cell number and relatively well-characterized. In this paper, we will lay out a theoretical re-interpretation of embryogenesis in addition to developing an RDF-based computational framework for visualizing the results of this theoretical effort. Our theoretical efforts will ultimately involve the construction of a differentiation tree and data analyses that support the concept of differentiation waves acting to coordinate cellular differentiation and embryonic form. The differentiation tree will also feature a means to perturb development in a manner that mimics phenotypic mutagenesis. This will allow us to understand the selective variability that is inherent in biological development, but that remains so poorly understood. In tandem, these developments will allow us to construct a conceptual and computational framework which can be applied to both mosaic and regulative development.