bluuebunny/crossref_metadata_2025 huggingface dataset:
Strain-induced polarity switching of magnetic vortex in Fe1−xGax alloys with different compositions
Authors: Li Gui-ping , Wang Jie , Shimada Takahiro , Fang Hui , Kitamura Takayuki
Published: May 2014

The strain-induced polarity switching of magnetic vortex in the Fe1−xGax nanodots with different compositions is demonstrated by a real-space phase-field model, which explicitly includes the cross-coupling between magnetization and mechanical strain. The composition of Fe1−xGax nanodots has significant influence on the critical shear strain that induces the polarity switching of magnetization vortex. The critical shear strain in the Fe71Ga29 nanodot is one order of magnitude smaller than that of the Fe19Ga81 nanodot, which makes the polarity switching much easier under a mechanical shear strain. In addition, we elucidate that both the magnetostrictive coefficient and exchange stiffness that changes with compositions play the decisive role in the critical behavior; the higher magnetostrictive coefficient (or lower exchange stiffness) decreases critical shear strain.
Extracting the effective mass of electrons in transparent conductive oxide thin films using Seebeck coefficient
Authors: Wang Yaqin , Zhu Junhao , Tang Wu
Published: May 2014

A method is proposed that combines Seebeck coefficient and carrier concentration to determine the electron effective mass of transparent conductive oxide (TCO) thin films. Experiments were conducted to test the validity of this approach on the transparent conductive Ga-doped ZnO thin films deposited by magnetron sputtering. An evident agreement of the calculated electron effective mass of the films is observed between the proposed approach and the previous studies. Besides, the optical carrier concentration and mobility derived from the calculated electron effective mass and spectroscopic ellipsometry using a complex dielectric function are consistent with those from direct Hall-effect measurement. The agreements suggest that Seebeck coefficient can serve as an alternative tool for extracting the effective mass of electrons in TCO films.
Competition between pressure effects and airflow influence for the performance of plasma actuators
Authors: Kriegseis J. , Barckmann K. , Frey J. , Tropea C. , Grundmann S.
Published: May 2014

The present work addresses the combined influence of pressure variations and different airflow velocities on the discharge intensity of plasma actuators. Power consumption, plasma length, and discharge capacitance were investigated systematically for varying pressure levels (p = 0.1–1 bar) and airflow velocities (U∞=0−100 m/s) to characterize and quantify the favorable and adverse effects on the discharge intensity. In accordance with previous reports, an increasing plasma actuator discharge intensity is observed for decreasing pressure levels. At constant pressure levels, an adverse airflow influence on the electric actuator performance is demonstrated. Despite the improved discharge intensity at lower pressure levels, the seemingly improved performance of the plasma actuators is accompanied with a more pronounced drop of the relative performance. These findings demonstrate the dependency of the (kinematic and thermodynamic) environmental conditions on the electric performance of plasma actuators, which in turn affects the control authority of plasma actuators for flow control applications.
Imperfect relativistic mirrors in the quantum regime
Authors: Mendonça J. T. , Serbeto A. , Galvão R. M. O.
Published: May 2014

The collective backscattering of intense laser radiation by energetic electron beams is considered in the relativistic quantum regime. Exact solutions for the radiation field are obtained, for arbitrary electron pulse shapes and laser intensities. The electron beams act as imperfect nonlinear mirrors on the incident laser radiation. This collective backscattering process can lead to the development of new sources of ultra-short pulse radiation in the gamma-ray domain. Numerical examples show that, for plausible experimental conditions, intense pulses of gamma-rays, due to the double Doppler shift of the harmonics of the incident laser radiation, can be produced using the available technology, with durations less than 1 as.
Optical imaging of objects in turbid media using heterodyned optical Kerr gate
Authors: Zhan Pingping , Tan Wenjiang , Si Jinhai , Xu Shichao , Tong Junyi , Hou Xun
Published: May 2014

In this paper, we demonstrated optical imaging of objects hidden behind highly turbid media with a femtosecond heterodyned optical Kerr gate (HOKG). The experimental results showed that when compared with traditional optical Kerr gated (OKG) imaging, the HOKG imaging system provided higher image sharpness and higher spatial resolution. In traditional OKG imaging system, low pass filtering due to a photoinduced soft aperture decreased the image sharpness. When the HOKG was used, the high spatial frequency components of the object could be effectively compensated.
Quantification of the solid-state charge mobility in a model radical polymer
Authors: Baradwaj Aditya G. , Rostro Lizbeth , Alam Muhammad A. , Boudouris Bryan W.
Published: May 2014

We establish that an oft-used radical polymer, poly(2,2,6,6-tetramethylpiperidinyloxy methacrylate) (PTMA), has a solid-state hole mobility value on the order of 10−4 cm2 V−1 s−1 in a space charge-limited device geometry. Despite being completely amorphous and lacking any π-conjugation, these results demonstrate that the hole mobility of PTMA is comparable to many well-studied conjugated polymers [e.g., poly(3-hexylthiophene)]. Furthermore, we show that the space charge-limited charge carrier mobility of these macromolecules is only a weak function of temperature, in contrast to many thermally-activated models of charge transport in polymeric materials. This key result demonstrates that the charge transport in radical polymers is inherently different than that in semicrystalline, conjugated polymers. These results establish the mechanism of solid-state charge transport in radical polymers and provide macromolecular design principles for this emerging class of organic electronic materials.
Three-dimensional folding of pre-strained polymer sheets via absorption of laser light
Authors: Liu Ying , Miskiewicz Matthew , Escuti Michael J. , Genzer Jan , Dickey Michael D.
Published: May 2014

Patterned light from a laser can induce rapid self-folding of pre-strained polymer sheets. Black ink coated on the sheet absorbs the light, which converts the photon energy into thermal energy that heats the sheet locally; the temperature of the sheet is highest at the surface where the light impinges on the sheet and decreases through the sheet thickness. The gradient of temperature induces a gradient of strain relaxation through the depth of the sheet, which causes folding within seconds of irradiation. The pattern of laser light that irradiates the compositionally homogeneous two-dimensional (2D) substrate dictates the resulting three-dimensional (3D) shape. Unlike most approaches to self-folding, the methodology described here requires no patterning of pre-defined hinges. It opens up the possibility of using a patterning technique that is inherently 2D to form 3D shapes. The use of lasers also enables systematic control of key process parameters such as power, intensity, and the pattern of light (i.e., beam width and shape). The rate of folding and folding angle measured with respect to these parameters provide an indirect quantification of heat loss in the sample and thereby identify the threshold power and power intensity that must be delivered to the hinge for folding to occur.
Light-controlled electric Freedericksz threshold in dye doped liquid crystals
Authors: Lucchetti L. , Catani L. , Simoni F.
Published: May 2014

We report the results of measurements of the threshold of Freedericksz transition in a nematic liquid crystal doped by Methyl-red. We show that in case of dc field the threshold voltage can decrease or increase depending on the light dose, due to the light-induced desorption and adsorption of charge complexes from and on the irradiated surface, that has been recently demonstrated. This effect has the potential to be exploited in optical devices such as liquid crystal microlenses and spatial light modulators.
New variables for gyrokinetic electromagnetic simulations
Authors: Mishchenko Alexey , Cole Michael , Kleiber Ralf , Könies Axel
Published: May 2014

A new approach to electromagnetic gyrokinetic simulations based on modified gyrokinetic theory is described. The method is validated using a particle-in-cell code. The Toroidal Alfvén Eigenmode at low perpendicular mode numbers, the so-called “magnetohydrodynamical limit,” has been successfully simulated using this method.
Dynamic nanomagnetism characterization of individual magnetic nanoparticles by frequency-modulated magnetic force microscopy
Authors: Li Xiang , Li Zhenghua , Pan Deng , Yoshimura Satoru , Saito Hitoshi
Published: May 2014

In this study, stroboscopic imaging of an alternating magnetic field (AC magnetic field) from individual superparamagnetic Fe3O4 nanoparticles was achieved using the developed frequency modulated-magnetic force microscopy (FM-MFM) technique, which enables the imaging of the vector signals of AC magnetic fields, such as a combination of in-phase and quadrature signals or that of amplitude and phase signals. FM-MFM uses the frequency modulation of cantilever oscillation, caused by the application of an off-resonant AC magnetic field to a mechanically oscillated cantilever, and visualises the vector signals of the AC magnetic field by adding a frequency demodulator and a lock-in amplifier to a conventional magnetic force microscope. Stroboscopic imaging of an AC magnetic field was carried out by varying the phase of the measured in-phase and quadrature signals via a signal processing technique. For the superparamagnetic Fe3O4 nanoparticles, stroboscopic imaging of the time-variable AC magnetic field, caused by the rotation of the magnetic moments within the particles, was demonstrated. This article describes the present status of FM-MFM technology, with particular attention to the feasibility of detecting magnetic moments of individual nanoparticles, and the possible application of FM-MFM in biological imaging.
Robust red-emission spectra and yields in firefly bioluminescence against temperature changes
Authors: Mochizuki Toshimitsu , Wang Yu , Hiyama Miyabi , Akiyama Hidefumi
Published: May 2014

We measured the quantitative spectra of firefly (Photinus pyralis) bioluminescence at various temperatures to investigate the temperature dependence of the luciferin-luciferase reaction at 15–34 °C. The quantitative spectra were decomposed very well into red (1.9 eV), orange (2.0 eV), and green (2.2 eV) Gaussian components. The intensity of the green component was the only temperature sensitive quantity that linearly decreased as the temperature increased at pH 7 and 8. We found the quantitative bioluminescence spectra to be robust below 2.0 eV against temperature and other experimental conditions. The revealed robustness of the red emissions should be useful for quantitative applications such as adenosine-5′-triphosphate detection.
Strain engineering of Dirac cones in graphyne
Authors: Wang Gaoxue , Si Mingsu , Kumar Ashok , Pandey Ravindra
Published: May 2014

6,6,12-graphyne, one of the two-dimensional carbon allotropes with the rectangular lattice structure, has two kinds of non-equivalent anisotropic Dirac cones in the first Brillouin zone. We show that Dirac cones can be tuned independently by the uniaxial compressive strain applied to graphyne, which induces n-type and p-type self-doping effect, by shifting the energy of the Dirac cones in the opposite directions. On the other hand, application of the tensile strain results into a transition from gapless to finite gap system for the monolayer. For the AB-stacked bilayer, the results predict tunability of Dirac-cones by in-plane strains as well as the strain applied perpendicular to the plane. The group velocities of the Dirac cones show enhancement in the resistance anisotropy for bilayer relative to the case of monolayer. Such tunable and direction-dependent electronic properties predicted for 6,6,12-graphyne make it to be competitive for the next-generation electronic devices at nanoscale.
Extreme waves induced by strong depth transitions: Fully nonlinear results
Authors: Viotti Claudio , Dias Frédéric
Published: May 2014

Recent studies on free-surface gravity waves over uneven bathymetries have shown that “rogue” waves can be triggered by strong depth variations. This phenomenon is here studied by means of spectral simulations of the free-surface Euler equations. We focus on the case of a random, one-directional wave field with prescribed statistics propagating over a submerged step, and consider different depth variations, up to an almost deep-to-shallow transition (kpH ≈ 1.8 − 0.78, where kp is the characteristic wavenumber and H the water depth). Strongly non-Gaussian statistics are observed in a region localized around the depth transition, beyond which they settle rapidly on the steady statistical state of finite-depth random wave fields. Extreme fluctuations are enhanced by stronger depth variations. Freak-wave formation is interpreted as a general signature of out-of-equilibrium dynamics, associated with the spectral settling from the deep-water to the finite-depth equilibrium. We also document that during such a transition the wave spectrum shows remarkable similarity with Phillips ω−5-law for the strongest depth variations considered.
Supercooling transition in phase separated manganite thin films: An electrical transport study
Authors: Singh Sandeep , Kumar Pawan , Siwach P. K. , Tyagi Pawan Kumar , Singh H. K.
Published: May 2014

The impact of variation in the relative fractions of the ferromagnetic metallic and antiferromagnetic/charge ordered insulator phases on the supercooling/superheating transition in strongly phase separated system, La5/8−yPryCa3/8MnO3 (y ≈ 0.4), has been studied employing magnetotransport measurements. Our study clearly shows that the supercooling transition temperature is non-unique and strongly depends on the magneto-thermodynamic path through which the low temperature state is accessed. In contrast, the superheating transition temperature remains constant. The thermo-magnetic hysteresis, the separation of the two transitions and the associated resistivity, all are functions of the relative fraction of the coexisting phases.
Gyrokinetic particle-in-cell simulations of Alfvén eigenmodes in presence of continuum effects
Authors: Mishchenko Alexey , Könies Axel , Hatzky Roman
Published: May 2014

First-principle gyrokinetic particle-in-cell simulations of a global Toroidal Alfvén Eigenmode (TAE) are undertaken in the presence of a strong coupling with the continuum. Effects of the bulk plasma temperature on the interplay between the TAE and Kinetic Alfvén Waves (KAWs) are investigated. A global TAE-KAW structure is identified which appears to be more unstable with respect to the fast ions than a simple (fluid-like) TAE mode.
Unexpected Pyrolytic Behaviour of Substituted Benzo[c]thiopyran and Thieno[2,3-c]thiopyran S,S-dioxides
Authors: Aitken R. Alan , Hauduc Clémence , Hossain M. Selim , McHale Emily , Schwan Adrian L. , Slawin Alexandra M. Z. , Stewart Colin A.
Published: May 2014

Flash vacuum pyrolysis (FVP) of benzo[c]thiopyran S,S-dioxide (1) results in formation of indene and 2-vinylbenzaldehyde as previously described. A range of eight analogues with various substitution patterns are found to behave differently. In general, there is no extrusion of SO2 to give products analogous to indene, but unsaturated carbonyl products analogous to 2-vinylbenzaldehyde are formed in most cases by way of ring expansion to a 7-membered ring sultine, extrusion of SO, and intramolecular hydrogen atom transfer. Other processes observed include formation of anthracene via an isomeric 7-membered sultine with loss of SO, CO and methane or butane, and formation of 4-ethylidene-4,5-dihydrocyclobuta[b]thiophenes by way of SO loss, a radical rearrangement, and extrusion of acetone. The analogues with a halogen substituent at position 8 on the benzene ring require a higher temperature to react and give naphthalene resulting from net elimination of HX and SO2. The X-ray crystal structure of 1 is also reported.
Crop-available water and agronomic management, rather than nitrogen supply, primarily determine grain yield of commercial chickpea in northern New South Wales
Authors: Elias N. V. , Herridge D. F.
Published: May 2014

Chickpea (Cicer arietinum L.) is considered an effective rotation crop in Australia’s northern grains region; however, concerns exist that grain yields of commercial crops are reduced because of nitrogen (N) deficiency related to inadequate nodulation and N2 fixation. As part of a program to address these issues, we report on the monitoring of 22 commercial fields around Moree, northern NSW, during 2005–07 that were designated for chickpea, and an associated farmer survey (81 respondents). Our objectives were to determine whether the monitored crops were limited by N and to develop recommendations that would optimise productivity for farmers growing chickpeas. In 2005, only soil water and nitrate data were collected from the six fields designated for chickpea. In 2006 and 2007, almost complete datasets were assembled from the 16 chickpea fields or crops, including soil water and nitrate at sowing, row spacing, plant density, plant height, stubble cover, weed density and composition, shoot biomass, grain yield, nodulation and N2 fixation (%N derived from the atmosphere (%Ndfa) and total crop N fixed). The associated survey provided insights into farmer knowledge of, and practices related to, inoculation.
Field monitoring indicated moderate–high levels of soil nitrate at sowing (averages 114, 126 and 110 kg N ha–1 to 1.2 m depth for 2005, 2006 and 2007, respectively) and generally low plant nodulation (0.11–1.16 g fresh wt plant–1) and N2 fixation (0–62%Ndfa and 0–87 kg N ha–1). Grain yield varied between 0.53 and 2.91 t ha–1 across the 14 monitored crops, with averages of 1.89 t ha–1 in 2006 and 1.02 t ha–1 in 2007. Although total crop N and grain yields were highly correlated with total (i.e. soil + fixed) N supply, there was no evidence that the monitored chickpea crops were N-limited. Rather, we conclude that soil N and biologically fixed N were complementary in supplying N to the crops, the grain yields of which were primarily determined by the supply of plant-available water (PAW) and water-use efficiency (WUE). Simple and multivariate regression analyses showed that stubble cover during the fallow (positively correlated with sowing PAW) and sowing date (positively correlated with crop WUE) were significant determinants of grain yield. We conclude that farmers could improve inoculation practice by ensuring the time between seed inoculation and sowing is always <24 h.
Opportunities and challenges in Australian grasslands: pathways to achieve future sustainability and productivity imperatives
Authors: Bell Lindsay W. , Hayes Richard C. , Pembleton Keith G. , Waters Cathy M.
Published: May 2014

Grassland production systems contribute 40% to Australia’s gross agricultural production value and utilise >50% of its land area. Across this area, diverse systems exist, but these can be broadly classified into four main production systems: (i) pastoral grazing, mainly of cattle at low intensity (i.e. <0.4 dry sheep equivalents/ha) on relatively unimproved native rangelands in the arid and semi-arid regions of northern and central Australia; (ii) crop–livestock systems in the semi-arid zone where livestock graze a mixture of pastures and crops that are often integrated; (iii) high-rainfall, permanent pasture zone in the coastal hinterland and highlands; and (iv) dairy systems covering a broad range of environments and production intensities. A notable trend across these systems has been the decline in sheep numbers and the proportion of income from wool, with beef cattle or sheep meat increasingly important. Although there is evidence that most of these systems have lifted production efficiencies over the past 30 years, total factor productivity growth (i.e. change in output relative to inputs) has failed to match the decline in terms of trade. This has renewed attention on how research and development can help to increase productivity. These industries also face increasing scrutiny to improve their environmental performance and develop sustainable production practices. In order to improve the efficiency and productivity of grassland production systems, we propose and explore in detail a range of practices and innovations that will move systems to new or improved states of productivity or alter efficiency frontiers. These include: filling gaps in the array of pastures available, either through exploring new species or improving the adaptation and agronomic characteristics of species currently sown; overcoming existing and emerging constraints to pasture productivity; improving livestock forage-feed systems; and more precise and lower cost management of grasslands. There is significant scope to capture value from the ecological services that grasslands provide and mitigate greenhouse gas emissions from livestock production. However, large reductions in pasture research scientist numbers (75–95%) over the past 30 years, along with funding limitations, will challenge our ability to realise these potential opportunities.
Phylogeny, biogeography and description of Ameripassalus, a new Mesoamerican genus of Passalidae (Coleoptera)
Authors: Jimऻnez-Ferbans Larry , Reyes-Castillo Pedro
Published: May 2014

Ameripassalus, gen. nov., is described as the first genus of Passalini with a distribution restricted to Mesoamerica. The species include A. guatemalensis (Kaup, 1869), comb. nov. from Passalus Fabricius, A. difficilis, sp. nov. and A. tamaulipensis, sp. nov. from Mexico, and A. jacki, sp. nov. and A. nigritus, sp. nov. from Guatemala. A matrix of 46 morphological characters, including the species from Ameripassalus, gen. nov. and 13 species of the genera Paxillus MacLeay, Ptichopus Kaup, Heliscus Zang, Veturius Kaup, Spasalus Kaup, Passipassalus Fonseca & Reyes-Castillo, Passalus Fabricius and Leptaulax Kaup were analysed. Only a single most parsimonious tree was found; in this Ameripassalus is retrieved as a monophyletic group. Ameripassalus difficilis, sp. nov. is shown as the sister group of the rest of the species in the genus. The species with the southernmost distribution (A. guatemalensis (A. nigritus, sp. nov. + A. jacki, sp. nov.)) form a nested clade within the species with the northernmost distribution. Keys to identify adults of the genera of Passalini and to the species of Ameripassalus are provided.
Molecular and morphological systematics of neustonic nudibranchs (Mollusca : Gastropoda : Glaucidae : Glaucus), with descriptions of three new cryptic species
Authors: Churchill Celia K. C. , Valdés Ángel , Ó Foighil Diarmaid
Published: May 2014

A recent molecular phylogenetic study on Glaucus, a genus of neustonic aeolid nudibranchs, revealed undescribed cryptic diversity. Glaucus atlanticus is sister to the traditional species Glaucus marginatus, which is a complex of four genetically distinct cryptic species (Informal clade ‘Marginatus’). The present paper revises the systematics of Glaucus and provides formal descriptions for three new species in the informal clade ‘Marginatus’ substantiated by species delimitation analyses. Molecular and morphological evidence confirms that the type species of Glaucus, Glaucus atlanticus, has a cosmopolitan subtropical distribution and is characterised by having a uniseriate ceratal arrangement, a penial spine and a longitudinal, medial silver stripe on the sole of the foot. Examination of type material indicates that the name G. marginatus should be retained for the most widespread of these species, found in the Indian and Pacific Oceans. This species is characterised by molecular diagnostic characters as well as the presence of a bursa copulatrix. Glaucus marginatus is sister to the undescribed species Glaucus bennettae, sp. nov., which is found in the South Pacific Ocean and lacks a bursa copulatrix. The other two undescribed species, Glaucus thompsoni, sp. nov. and Glaucus mcfarlanei, sp. nov. are only known from the North Pacific Ocean, and are characterised by molecular diagnostic characters as well as possessing and lacking a bursa copulatrix, respectively. Because sister species of Glaucus differ in their reproductive anatomy, we hypothesise that mating behaviour has played a role in cladogenesis in this group.
ZooBank Publication code: http://zoobank.org/References/E352E264-A440-4AF1-8565-B57B7EEE25BC
Usefulness of two bioeconomic frameworks for evaluation of community-initiated species conservation projects
Authors: Jones Christopher , McNamara Les
Published: May 2014

Context
Community-based conservation managers and their funding providers must apportion limited resources to potential projects that provide varying biodiversity benefits. Funding applicants must demonstrate that proposed projects are likely to provide positive conservation returns on investments.

Aims
We investigated the practical usefulness of two bioeconomic frameworks, the Project Prioritisation Protocol and the Investment Framework for Environmental Resources (INFFER) in guiding community-based conservation funding decisions and the benefits and challenges to community groups in evaluating projects using the tools.

Methods
We evaluated four species-based community-led conservation projects in New Zealand using the tools, and assessed the quality, relevance and potential impact of the frameworks to community conservation, including users’ perceptions of their usefulness.

Key results
Benefit–cost metrics from both tools indicated that all four projects would provide a low return on investment. However, both tools were highly sensitive to key assumptions about the values of conservation assets (species) being managed and the values of predicted differences made by projects. Both tools scored well against criteria used to assess their technical ‘quality’. INFFER had greater flexibility for use in different situations, but its use by community groups may be constrained by the time demands of completing a full project evaluation. Both tools can help users define problems and formulate innovative solutions through assessment of success and risk factors and the identification of project efficiencies.

Conclusions
Although both tools provide quantitative, transparent processes for the relative evaluation and ranking of competing projects, their sensitivities to species and/or asset valuation and benefit estimates mean that users should not accept scores and project rankings uncritically. For community groups, evaluation frameworks are likely to be useful to document costs, conservation benefits and risk factors accurately and transparently, and can encourage applicants to develop more robust approaches to project management, including the development of specific and measurable management objectives.

Implications
Adoption of more transparent and standardised assessment of funding applications by agencies, despite some of the drawbacks of currently available tools, would facilitate more transparent prioritisation of competing funding bids and would encourage community groups to develop a more robust approach to project design and management.
Existing cardiomyocytes generate cardiomyocytes at a low rate after birth in mice
Authors: Ali Shah R. , Hippenmeyer Simon , Saadat Lily V. , Luo Liqun , Weissman Irving L. , Ardehali Reza
Published: May 2014

Significance

The nature of postnatal cardiomyogenesis in mammals remains in dispute. Here, we provide cell-level evidence for the birth of cardiomyocytes in newborn and adult mice. Our clonal analysis, based on the mosaic analysis with double markers mouse model, shows that cardiomyocytes are the parent cell of origin of cardiomyocytes that are generated postnatally. Our findings confirm that limited, symmetric division of cardiomyocytes is a rare phenomenon in the mouse heart after birth.
Facile synthesis of the cyclohexane fragment of enacloxins, a series of antibiotics isolated from Frateuria sp. W-315
Authors: Saito Aki , Igarashi Wataru , Furukawa Hiroyuki , Yamada Teiko , Kuwahara Shigefumi , Kiyota Hiromasa
Published: May 2014

An efficient and good yield synthesis of the cyclohexane moiety of enacyloxins, a series of antibiotics isolated from Frateuria sp. W-315, was achieved from d-quinic acid using a successive Barton–McCombie deoxygenation.
The role of familiarity in associative recognition of unitized compound word pairs
Authors: Ahmad Fahad N. , Hockley William E.
Published: May 2014

This study examined the effect of unitization and contribution of familiarity in the recognition of word pairs. Compound words were presented as word pairs and were contrasted with noncompound word pairs in an associative recognition task. In Experiments 1 and 2, yes–no recognition hit and false-alarm rates were significantly higher for compound than for noncompound word pairs, with no difference in discrimination in both within- and between-subject comparisons. Experiment 2 also showed that item recognition was reduced for words from compound compared to noncompound word pairs, providing evidence of the unitization of the compound pairs. A two-alternative forced-choice test used in Experiments 3A and 3B provided evidence that the concordant effect for compound word pairs was largely due to familiarity. A discrimination advantage for compound word pairs was also seen in these experiments. Experiment 4A showed that a different pattern of results is seen when repeated noncompound word pairs are compared to compound word pairs. Experiment 4B showed that memory for the individual items of compound word pairs was impaired relative to items in repeated and nonrepeated noncompound word pairs, and Experiment 5 demonstrated that this effect is eliminated when the elements of compound word pairs are not unitized. The concordant pattern seen in yes–no recognition and the discrimination advantage in forced-choice recognition for compound relative to noncompound word pairs is due to greater reliance on familiarity at test when pairs are unitized.
A response to Jon Mills' paper, ‘Jung's Metaphysics’
Authors: Saban Mark
Published: May 2014

Mills' paper tackles an important question for Jungian studies: what are the underlying metaphysical assumptions behind analytical psychology? However, his attempt to pursue this inquiry is undermined by a strong but unsupportable insistence by Mills that Jung intended to present himself primarily as an ontologist. I also argue that various further inaccuracies and misreadings lead Mills into a fundamental misunderstanding of the intentions and aims that characterise Jung's psychology.
Unpacking the glocalization of organization: from term, to theory, to analysis
Authors: Drori Gili S. , Höllerer Markus A. , Walgenbach Peter
Published: May 2014

Over the past two decades, the notion of ‘glocalization’ came to stand for more than what the term literally encompasses. Not only does it refer to the mutually constitutive character of the global and the local; rather, it spearheads the challenge to the numerous dichotomies that have dominated previous discussions of globalization, and points to the dualities of similarity and variation as well as universalism and particularism. In this short essay, we make an attempt to specify the dimensions of complexity and multidimensionality inherent in the notion of glocalization of organization and management. We propose three sets of analytic conceptualizations. First, we identify three axes of glocalization: vertical, horizontal, and temporal. Second, we extract three core themes of glocalization: the ‘what’, ‘who’, and ‘how’. Last, we name several sequenced components of glocalization: abstraction, construction of equivalency, and adoption and adaptation. Laced together, these conceptualizations are the basis for description and analysis of glocalization. We argue that the important principle of such an analytic approach to the multidimensionality of glocalization is the intersection, or conjuncture, among these three sets of conceptualizations.
‘The weaker-willed, the craven-hearted’: the decline of One Nation Conservatism
Authors: Dorey Peter , Garnett Mark
Published: May 2014

For most of the period from 1945 until the 1970s, the official policy of the Conservative Party reflected a ‘One Nation’ approach to politics. Dominating the higher echelons of the party, representatives of this tradition prided themselves on a pragmatic outlook which enabled them to accept much of the policy framework bequeathed by the 1945–1951 Labour Governments led by Clement Attlee: the public ownership of several major industries (such as coal and the railways), the pursuit of full employment, a universal welfare state ‘from cradle to grave’ and partnership with the trade unions. After the election of Margaret Thatcher as party leader in 1975, however, this approach fell rapidly from favour, and almost four decades later the chances of a revival still look remote. A full explanatory account of the demise of the One Nation Tradition in Britain's Conservative Party, and its supplanting by Thatcherism, lies beyond the scope of a single article. Here we examine the main factors – relating to changes within the party and the British electorate as a whole, as well as individual failings and ‘events’ both at home and abroad – behind a development which has played a central role in British politics over recent decades.
CAVER Analyst 1.0: graphic tool for interactive visualization and analysis of tunnels and channels in protein structures
Authors: Kozlikova Barbora , Sebestova Eva , Sustr Vilem , Brezovsky Jan , Strnad Ondrej , Daniel Lukas , Bednar David , Pavelka Antonin , Manak Martin , Bezdeka Martin , Benes Petr , Kotry Matus , Gora Artur , Damborsky Jiri , Sochor Jiri
Published: May 2014

Summary: The transport of ligands, ions or solvent molecules into proteins with buried binding sites or through the membrane is enabled by protein tunnels and channels. CAVER Analyst is a software tool for calculation, analysis and real-time visualization of access tunnels and channels in static and dynamic protein structures. It provides an intuitive graphic user interface for setting up the calculation and interactive exploration of identified tunnels/channels and their characteristics.

Availability and Implementation: CAVER Analyst is a multi-platform software written in JAVA. Binaries and documentation are freely available for non-commercial use at http://www.caver.cz .

Contact:  jiri@chemi.muni.cz or sochor@fi.muni.cz

Supplementary information:  Supplementary data are available at Bioinformatics online.
Asian Versus Non-Asian Outcomes in Nasopharyngeal Carcinoma: A North American Population-based Analysis
Authors: Hamilton Sarah N. , Ho Cheryl , Laskin Janessa , Zhai Yongliang , Mak Paul , Wu Jonn
Published: May 2014

Objectives:

The effect of ethnicity on nasopharyngeal cancer (NPC) outcomes is unclear. This retrospective analysis examines survival and the impact of concurrent chemoradiation (chemoRT) among Asian and non-Asian patients.

Methods:

Subjects included 380 consecutive patients with NPC treated at a Canadian institution from 2000 to 2009. Five-year Kaplan-Meier progression-free survival (PFS), disease-specific survival (DSS), and overall survival (OS) were compared between Asian (n=279) and non-Asian (n=101) subjects. Multivariable analysis was performed using Cox regression modeling. Two-variable interaction terms with concurrent chemoRT were used to examine whether concurrent chemoRT conferred different effects among subgroups.

Results:

Asian subjects presented with earlier stage (P=0.005), were younger, had better performance status, and were less likely smokers (all P<0.001). Survival among Asian versus non-Asian subjects with stage I/II NPC were: PFS 68% versus 59% (P=0.04), DSS 87% versus 77% (P=0.08), and OS 84% versus 74% (P=0.003). Corresponding rates with stage III/IVA/IVB disease were PFS 49% versus 42% (P=0.12), DSS 72% versus 46% (P=0.001), and OS 70% versus 44% (P<0.001). On multivariable analysis, Asian ethnicity, age below 65 years, ECOG performance status 0-1, early stage, staging MRI use, and concurrent chemoRT were associated with improved DSS and OS (P<0.05). On testing interactions with concurrent chemoRT, Asian versus non-Asian ethnicity was significant (hazard ratio 3.9), suggesting that concurrent chemoRT conferred more benefit among non-Asian compared with Asian subjects.

Conclusions:

In this population-based study, Asian ethnicity was associated with improved DSS and OS. Concurrent chemoRT conferred more benefit among non-Asian compared with Asian subjects.
Flavihumibacter solisilvae sp. nov., isolated from forest soil
Authors: Lee Hyo Jung , Jeong Sang Eun , Cho Myong-Suk , Kim SeonHee , Lee Sang-Suk , Lee Byoung-Hee , Jeon Che Ok
Published: May 2014

A Gram-stain-positive, strictly aerobic, yellow colony-forming bacterium, designated strain 3-3T, was isolated from forest soil of Bac Kan Province in Vietnam. Cells were non-motile rods without gliding motility, showing oxidase- and catalase-positive reactions. Growth was observed at 20–37 °C (optimum, 28 °C) and pH 5.5–9.5 (optimum, pH 7.5). The major cellular fatty acids were iso-C15 : 0, iso-C15 : 1 G and summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c). Strain 3-3T contained phosphatidylethanoamine, three unidentified aminolipids and three unidentified lipids. The G+C content of the genomic DNA was 49.5 mol% and the only isoprenoid quinone detected was menaquinone 7 (MK-7). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 3-3T formed a tight phylogenetic lineage with

Flavihumibacter petaseus

T41T with a bootstrap value of 100 %. Strain 3-3T was related most closely to

F. petaseus

T41T with 97.3 % 16S rRNA gene sequence similarity and the level of DNA–DNA relatedness between the two was 9.4±1.2 %. Based on phenotypic, chemotaxonomic and molecular features, strain 3-3T represents a novel species of the genus

Flavihumibacter

, for which the name Flavihumibacter solisilvae sp. nov. is proposed. The type strain is 3-3T ( = KACC 17917T = JCM 19891T).
miRNA modulation of SOCS1 using an influenza A virus delivery system
Authors: Izzard Leonard , Ye Siying , Jenkins Kristie , Xia Yingju , Tizard Mark , Stambas John
Published: May 2014

Difficulties associated with efficient delivery and targeting of miRNAs to cells is hampering the real world application of miRNA technology. This study utilized an influenza A-based delivery system to express miR-155 in order to knockdown SOCS1 mRNA. Using qPCR and dual luciferase technology we show that miR-155 delivery resulted in a significant increase in cellular miR-155 which facilitated a downregulation of SOCS1 gene expression and a functional increase in IL-6 and IFN-β cytokines.
Higher gene expression variability in the more aggressive subtype of chronic lymphocytic leukemia
Authors: Ecker Simone , Pancaldi Vera , Rico Daniel , Valencia Alfonso
Published: May 2014

Background

Chronic Lymphocytic Leukemia (CLL) presents two subtypes which have drastically different clinical outcomes. So far, these two subtypes are not associated to clear differences in gene expression profiles. Interestingly, recent results have highlighted important roles for heterogeneity, both at the genetic and at the epigenetic level in CLL progression.

Results

We propose to use gene expression variability across patients to investigate differences between the two CLL subtypes. We find that the most aggressive type of this disease shows higher variability of gene expression across patients and we elaborate on this observation to produce a method that classifies patients into clinical subtypes. Finally, we find that, overall, genes that show higher variability in the aggressive subtype are related to cell cycle, development and inter-cellular communication, probably related to faster progression of this disease subtype.

Conclusions

There are strong relations between disease subtype and gene expression variability linking significantly increased expression variability to phenotypes such as aggressiveness and resistance to therapy in CLL.
Practopoiesis: Or how life fosters a mind
Authors: Nikolić Danko
Published: May 2014

The mind is a biological phenomenon. Thus, biological principles of organization should also be the principles underlying mental operations. Practopoiesis states that the key for achieving intelligence through adaptation is an arrangement in which mechanisms laying a lower level of organization, by their operations and interaction with the environment, enable creation of mechanisms lying at a higher level of organization. When such an organizational advance of a system occurs, it is called a traverse. A case of traverse is when plasticity mechanisms (at a lower level of organization), by their operations, create a neural network anatomy (at a higher level of organization). Another case is the actual production of behavior by that network, whereby the mechanisms of neuronal activity operate to create motor actions. Practopoietic theory explains why the adaptability of a system increases with each increase in the number of traverses. With a larger number of traverses, a system can be relatively small and yet, produce a higher degree of adaptive/intelligent behavior than a system with a lower number of traverses. The present analyses indicate that the two well-known traverses—neural plasticity and neural activity—are not sufficient to explain human mental capabilities. At least one additional traverse is needed, which is named anapoiesis for its contribution in reconstructing knowledge e.g., from long-term memory into working memory. The conclusions bear implications for brain theory, the mind-body explanatory gap, and developments of artificial intelligence technologies.
Cancer-associated recurrent mutations in RNase III domains of DICER1
Authors: Arman Aksoy Bülent , Jacobsen Anders , Fieldhouse Robert J. , Lee William , Demir Emek , Ciriello Giovanni , Schultz Nikolaus , Marks Debora S. , Sander Chris
Published: May 2014

Mutations in the RNase IIIb domain of DICER1 are known to disrupt processing of 5p-strand pre-miRNAs and these mutations have previously been associated with cancer. Using data from the Cancer Genome Atlas project, we show that these mutations are recurrent across four cancer types and that a previously uncharacterized recurrent mutation in the adjacent RNase IIIa domain also disrupts 5p-strand miRNA processing. Analysis of the downstream effects of the resulting imbalance 5p/3p shows a statistically significant effect on the expression of mRNAs targeted by major conserved miRNA families. In summary, these mutations in DICER1 lead to an imbalance in miRNA strands, which has an effect on mRNA transcript levels that appear to contribute to the oncogenesis.
Role of LDB1 in the transition from chromatin looping to transcription activation
Authors: Krivega Ivan , Dale Ryan K. , Dean Ann
Published: May 2014

Many questions remain about how close association of genes and distant enhancers occurs and how this is linked to transcription activation. In erythroid cells, lim domain binding 1 (LDB1) protein is recruited to the β-globin locus via LMO2 and is required for looping of the β-globin locus control region (LCR) to the active β-globin promoter. We show that the LDB1 dimerization domain (DD) is necessary and, when fused to LMO2, sufficient to completely restore LCR–promoter looping and transcription in LDB1-depleted cells. The looping function of the DD is unique and irreplaceable by heterologous DDs. Dissection of the DD revealed distinct functional properties of conserved subdomains. Notably, a conserved helical region (DD4/5) is dispensable for LDB1 dimerization and chromatin looping but essential for transcriptional activation. DD4/5 is required for the recruitment of the coregulators FOG1 and the nucleosome remodeling and deacetylating (NuRD) complex. Lack of DD4/5 alters histone acetylation and RNA polymerase II recruitment and results in failure of the locus to migrate to the nuclear interior, as normally occurs during erythroid maturation. These results uncouple enhancer–promoter looping from nuclear migration and transcription activation and reveal new roles for LDB1 in these processes.
miR824-Regulated AGAMOUS-LIKE16 Contributes to Flowering Time Repression in Arabidopsis
Authors: Hu Jin-Yong , Zhou Yue , He Fei , Dong Xue , Liu Liang-Yu , Coupland George , Turck Franziska , de Meaux Juliette
Published: May 2014

The timing of flowering is pivotal for maximizing reproductive success under fluctuating environmental conditions. Flowering time is tightly controlled by complex genetic networks that integrate endogenous and exogenous cues, such as light, temperature, photoperiod, and hormones. Here, we show that AGAMOUS-LIKE16 (AGL16) and its negative regulator microRNA824 (miR824) control flowering time in Arabidopsis thaliana. Knockout of AGL16 effectively accelerates flowering in nonvernalized Col-FRI, in which the floral inhibitor FLOWERING LOCUS C (FLC) is strongly expressed, but shows no effect if plants are vernalized or grown in short days. Alteration of AGL16 expression levels by manipulating miR824 abundance influences the timing of flowering quantitatively, depending on the expression level and number of functional FLC alleles. The effect of AGL16 is fully dependent on the presence of FLOWERING LOCUS T (FT). Further experiments show that AGL16 can interact directly with SHORT VEGETATIVE PHASE and indirectly with FLC, two proteins that form a complex to repress expression of FT. Our data reveal that miR824 and AGL16 modulate the extent of flowering time repression in a long-day photoperiod.
Bipolar Plasma Membrane Distribution of Phosphoinositides and Their Requirement for Auxin-Mediated Cell Polarity and Patterning inArabidopsis
Authors: Tejos Ricardo , Sauer Michael , Vanneste Steffen , Palacios-Gomez Miriam , Li Hongjiang , Heilmann Mareike , van Wijk Ringo , Vermeer Joop E.M. , Heilmann Ingo , Munnik Teun , Friml Jiří
Published: May 2014

Cell polarity manifested by asymmetric distribution of cargoes, such as receptors and transporters, within the plasma membrane (PM) is crucial for essential functions in multicellular organisms. In plants, cell polarity (re)establishment is intimately linked to patterning processes. Despite the importance of cell polarity, its underlying mechanisms are still largely unknown, including the definition and distinctiveness of the polar domains within the PM. Here, we show in Arabidopsis thaliana that the signaling membrane components, the phosphoinositides phosphatidylinositol 4-phosphate (PtdIns4P) and phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P2] as well as PtdIns4P 5-kinases mediating their interconversion, are specifically enriched at apical and basal polar plasma membrane domains. The PtdIns4P 5-kinases PIP5K1 and PIP5K2 are redundantly required for polar localization of specifically apical and basal cargoes, such as PIN-FORMED transporters for the plant hormone auxin. As a consequence of the polarity defects, instructive auxin gradients as well as embryonic and postembryonic patterning are severely compromised. Furthermore, auxin itself regulates PIP5K transcription and PtdIns4P and PtdIns(4,5)P2 levels, in particular their association with polar PM domains. Our results provide insight into the polar domain–delineating mechanisms in plant cells that depend on apical and basal distribution of membrane lipids and are essential for embryonic and postembryonic patterning.