bluuebunny/crossref_metadata_2025 huggingface dataset:
The electric field manipulation of magnetization in La1−xSrxCoO3/Pb(Mg1/3Nb2/3)O3-PbTiO3 heterostructures
Authors: Zhang Q. M. , Li Q. , Gao R. L. , Zhou W. P. , Wang L. Y. , Yang Y. T. , Wang D. H. , Lv L. Y. , Du Y. W.
Published: April 2014

La1−xSrxCoO3 (x = 0.18, 0.33, and 0.5) films were grown epitaxially on piezoelectric Pb(Mg1/3Nb2/3)O3-PbTiO3 substrates by pulsed laser deposition. The magnetization of these films varies with the external electric field, showing the magnetoelectric effect. With different doping content of Sr2+ ions, the change of magnetization for these films show different behaviors with increasing temperature, which can be attributed to the competition between electric-field-induced changes of spin state and double exchange interaction. This work presents an alternative mechanism to investigate the electric field control of magnetism in magnetoelectric heterostructure by tuning the spin state.
Tunable effective nonlinear refractive index of graphene dispersions during the distortion of spatial self-phase modulation
Authors: Wang Gaozhong , Zhang Saifeng , Umran Fadhil A. , Cheng Xin , Dong Ningning , Coghlan Darragh , Cheng Ya , Zhang Long , Blau Werner J. , Wang Jun
Published: April 2014

Spatial self-phase modulation (SSPM) was observed directly when a focused He-Ne laser beam at 633 nm went through liquid-phase-exfoliated graphene dispersions. The diffraction pattern of SSPM was found to be distorted rapidly right after the incident beam horizontally passing through the dispersions, while no distortion for the vertically incident geometry. We show that the distortion is originated mainly from the non-axis-symmetrical thermal convections of the graphene nanosheets induced by laser heating, and the relative change of nonlinear refractive index can be determined by the ratio of the distortion angle to the half-cone angle. Therefore, the effective nonlinear refractive index of graphene dispersions can be tuned by changing the incident intensity and the temperature of the dispersions.
Realizing InGaN monolithic solar-photoelectrochemical cells for artificial photosynthesis
Authors: Dahal R. , Pantha B. N. , Li J. , Lin J. Y. , Jiang H. X.
Published: April 2014

InGaN alloys are very promising for solar water splitting because they have direct bandgaps that cover almost the whole solar spectrum. The demonstration of direct solar-to-fuel conversion without external bias with the sunlight being the only energy input would pave the way for realizing photoelectrochemical (PEC) production of hydrogen by using InGaN. A monolithic solar-PEC cell based on InGaN/GaN multiple quantum wells capable to directly generate hydrogen gas under zero bias via solar water splitting is reported. Under the irradiation by a simulated sunlight (1-sun with 100 mW/cm2), a 1.5% solar-to-fuel conversion efficiency has been achieved under zero bias, setting a fresh benchmark of employing III-nitrides for artificial photosynthesis. Time dependent hydrogen gas production photocurrent measured over a prolonged period (measured for 7 days) revealed an excellent chemical stability of InGaN in aqueous solution of hydrobromic acid. The results provide insights into the architecture design of using InGaN for artificial photosynthesis to provide usable clean fuel (hydrogen gas) with the sunlight being the only energy input.
Theoretical study of defect formation during the initial stages of native-oxide growth on GaSb (001)
Authors: Bermudez V. M.
Published: April 2014

The formation of defects during the initial stages of native-oxide growth on the GaSb (001)-α(4 × 3) surface has been studied computationally using spin-unrestricted density functional theory. It is found that insertion into a Ga-Sb adatom dimer to form a peroxo Ga-O-O-Sb bridge is the most energetically favorable process with insertion into Ga-Sb back-bonds being somewhat less so. A Ga-O-O-Ga bridge between dimers is also favorable, but Sb-O-O-Sb bridges show little if any stability. In the course of analyzing molecular adsorption, a particularly reactive site has been identified that leads to O2 dissociation with little or no barrier. This process is initiated in the vicinity of an Sb-Sb dimer in the terminating layer and leads to sub-surface Ga and Sb defect sites (i.e., coordinatively unsaturated atoms) and to strained Ga-Sb bonds that may be susceptible to further O2 attack. However, the defects formed in these reactions do not produce states in the gap.
Ferroelectric modulation on resonant tunneling through perovskite double-barriers
Authors: Du Ruifang , Qiu Xiangbiao , Li Aidong , Wu Di
Published: April 2014

The negative differential resistance (NDR) due to resonance tunneling is achieved at room temperature in perovskite double-barrier heterostructures composed of a 10 unit-cell-thick SrTiO3 quantum well sandwiched in two 10 unit-cell-thick LaAlO3 barriers. The NDR occurs at 1.2 V and does not change with voltage cycling. When the paraelectric SrTiO3 quantum well is replaced by a ferroelectric BaTiO3, the onset of the NDR can be modulated by polarization switching in the ultrathin BaTiO3. A polarization pointing to the collector lowers the NDR voltage but a polarization pointing to the emitter increases it. The shift of the NDR voltage is ascribed to reversal of the extra electric field in the quantum well due to the polarization switching.
Strain-driven fractional spontaneous exchange bias in ferromagnetic/antiferromagnetic thin films with composition-graded ferromagnetic layer
Authors: Phuoc Nguyen N. , Ong C. K.
Published: April 2014

We experimentally demonstrate that the stress-induced magnetic anisotropy in composition-graded ferromagnetic NiFeTa layers can be employed to trigger exchange bias in NiFeTa/IrMn bilayers without using any deposition field or field cooling procedure. In particular, we found that the NiFeTa/IrMn bilayers exhibit double-shifted loops being composed of both negative and positive exchange biases when the deposition angle is low. As the deposition angle is increased, the magnetization curves change into a single-shifted loop with spontaneous exchange bias aligned along negative or positive direction. The results can be explained by the formation of magnetic domain state under the presence of a strong stress-induced magnetic anisotropy and this domain state is pinned upon the deposition of an antiferromagnetic layer. We also studied the dynamic permeability spectra of the films with respect to temperature and discussed the results in relation with the static magnetic properties.
Elastic properties of graphene nanomeshes
Authors: Carpenter Corinne , Christmann Augusto M. , Hu Lin , Fampiou Ioanna , Muniz Andre R. , Ramasubramaniam Ashwin , Maroudas Dimitrios
Published: April 2014

We study the elastic response of graphene nanomeshes based on molecular-statics and molecular-dynamics simulations of uniaxial tensile deformation tests. Elastic properties are determined as a function of the nanomesh architecture, namely, the lattice arrangement of the pores, pore morphology, material density (ρ), and pore edge passivation, and scaling laws for the density dependence of the elastic modulus M, M(ρ), are established. We find that, for circular unpassivated pores, M scales with the square of ρ. Deviations from quadratic scaling are most strongly influenced by pore morphology and, to a lesser extent, by pore edge passivation and temperature.
Terahertz and infrared transmission of an organic/inorganic hybrid thermoelectric material
Authors: Heyman J. N. , Alebachew B. A. , Kaminski Z. S. , Nguyen M. D. , Coates N. E. , Urban J. J.
Published: April 2014

We report terahertz and infrared transmission measurements of a high-performance thermoelectric material containing tellurium nanowires in a conducting polymer poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) matrix. The DC electrical conductivity of the hybrid material (41 S/cm) is approximately one hundred times that of pure PEDOT:PSS and more than 400 times that of a film of pure tellurium nanowires, while the terahertz-frequency (THz) conductivity of PEDOT:PSS and the hybrid material are comparable at f ∼ 2THz. A frequency-dependent conductivity model indicates that the increased DC conductivity of the hybrid material results from an increase in the DC charge mobility rather than in the free charge density. We suggest that the increased DC conductivity of the hybrid material results from an increase in linkage between PEDOT domains by the tellurium nanowires.
The Effect of Stimulus Size on Stereoscopic Fusion Limits and Response Criteria
Authors: Grove Philip M , Finlayson Nonie J , Ono Hiroshi
Published: April 2014

The stereoscopic fusion limit denotes the largest binocular disparity for which a single fused image is perceived. Several criteria can be employed when judging whether or not a stereoscopic display is fused, and this may be a factor contributing to a discrepancy in the literature. Schor, Wood, and Ogawa (1984 Vision Research, 24, 661–665) reported that fusion limits did not change as a function of bar width, while Roumes, Plantier, Menu, and Thorpe (1997 Human Factors, 39, 359–373) reported higher fusion limits for larger stimuli than for smaller stimuli. Our investigation suggests that differing criteria between the studies could contribute to this discrepancy. In experiment 1 we measured horizontal and vertical disparity fusion limits for thin bars and for the edge of an extended surface, allowing observers to use the criterion of either diplopia or rivalry when evaluating fusion for all stimuli. Fusion limits were equal for thin bars and extended surfaces in both horizontal and vertical disparity conditions. We next measured fusion limits for a range of bar widths and instructed observers to indicate which criterion they employed on each trial. Fusion limits were constant across all stimulus widths. However, there was a sharp change in criterion from diplopia to rivalry when the angular extent of the bar width exceeded about twice the fusion limit, expressed in angular terms. We conclude that stereoscopic fusion limits do not depend on stimulus size in this context, but the criterion for fusion does. Therefore, the criterion for fusion should be clearly defined in any study measuring stereoscopic fusion limits.
Reversing the Reversed Contrast
Authors: Agostini Tiziano , Murgia Mauro , Galmonte Alessandra
Published: April 2014

Galmonte and Agostini (1998 Investigative Ophthalmology & Visual Science, 39(4), S158), Agostini and Galmonte (2002 Psychological Science, 13, 89–93), Bressan (2001 Perception, 30, 1031–1046), and Gilchrist and Annan (2002 Perception, 31, 141–150) reported three different lightness contrast configurations in which grouping factors make a gray target totally surrounded by black appear darker than an equal gray target surrounded by white, reversing the classical contrast effect. In this paper we demonstrate that the three configurations known as ‘reversed contrast’ are based on different mechanisms. Sixteen participants judged the lightness of the gray targets of the original and modified versions of the three configurations. Our results highlight that the Agostini and Galmonte effect is reversed when the global grouping factors are removed, while in a number of variations of Bressan's and Gilchrist and Annan's displays the direction of the effect does not change, even in absence of global grouping factors. Our results indicate that the factors determining the Agostini and Galmonte effect are different from those acting on the other two configurations, in which the lightness change is also due to factors other than belongingness.
Pointing to Azimuths and Elevations of Targets: Blind and Blindfolded-Sighted
Authors: Wnuczko Marta , Kennedy John M
Published: April 2014

Three groups of observers pointed to target circles in a path on the ground, in two parallel rows. Participants in one group viewed the circles and then pointed blindfolded. Those in a second group were blindfolded and then touched the circles with a stick while walking past them. Volunteers in the third group were blind adults, a diverse group, who also used a stick to detect the circles. For all three groups, as distance to the circles increased, pointing azimuths shrank and elevations increased. We suggest that directions to targets on major environmental surfaces may be appreciated similarly by the blind and sighted. We challenge the assumption that the principle of convergence to the horizon, available through vision because of the way in which visual angle decreases on the retina, is not available through touch.
Time-to-Contact Estimation Modulated by Implied Friction
Authors: Yamada Yuki , Sasaki Kyoshiro , Miura Kayo
Published: April 2014

The present study demonstrated that friction cues for target motion affect time-to-contact (TTC) estimation. A circular target moved in a linear path with a constant velocity and was gradually occluded by a static rectangle. The target moved with forward and backward spins or without spin. Observers were asked to respond at the time when the moving target appeared to pass the occluder. The results showed that TTC was significantly longer in the backward spin condition than in the forward and without-spin conditions. Moreover, similar results were obtained when a sound was used to imply friction. Our findings indicate that the observer's experiential knowledge of motion coupled with friction intuitively modulated their TTC estimation.
Portfolio careers for medical graduates: implications for postgraduate training and workforce planning
Authors: Eyre Harris A. , Mitchell Rob D. , Milford Will , Vaswani Nitin , Moylan Steven
Published: April 2014

Portfolio careers in medicine can be defined as significant involvement in one or more portfolios of activity beyond a practitioner’s primary clinical role, either concurrently or in sequence. Portfolio occupations may include medical education, research, administration, legal medicine, the arts, engineering, business and consulting, leadership, politics and entrepreneurship. Despite significant interest among junior doctors, portfolios are poorly integrated with prevocational and speciality training programs in Australia. The present paper seeks to explore this issue. More formal systems for portfolio careers in Australia have the potential to increase job satisfaction, flexibility and retention, as well as diversify trainee skill sets. Although there are numerous benefits from involvement in portfolio careers, there are also risks to the trainee, employing health service and workforce modelling. Formalising pathways to portfolio careers relies on assessing stakeholder interest, enhancing flexibility in training programs, developing support programs, mentorship and coaching schemes and improving support structures in health services. What is known about the topic? Portfolio careers are well understood as a career structure in general business. However, in medicine little is known about the concept of portfolio careers, their drivers, benefits and risks. There are significant issues faced by the Australian junior medical workforce such as a need for diversified skill-sets (e.g. increased involvement in research, public health and leadership), low job satisfaction for junior doctors and an increasing emphasis of work-life balance and mental well-being. What does this paper add? This paper critically analyses the concept of portfolio careers in the postgraduate setting by critiquing literature on the international and national experiences in this field. This paper outlines potential benefits of portfolio careers requiring further research, such as a diversification in the workforce and improved job satisfaction. Risks include reducing the health service provision capacity of junior doctors and drawing doctors away from a medical career. What are the implications for practitioners? This paper has substantial educational and workforce implications for medical students, junior doctors and medical managers. For medical students and junior doctors this paper frames the possibilities in a medical career, as well as benefits and risks of aiming for a portfolio career in medicine. For medical managers, this paper suggests strategies for further research, enhancing workforce job satisfaction and potential pitfalls of increasing opportunities for medical portfolio careers.
A Critical Investigation on the Existence of Selective Microwave Absorption in the Synthesis of CdSe Quantum Dots
Authors: Moghaddam Mojtaba Mirhosseini , Kappe C. Oliver
Published: April 2014

The existence of selective microwave absorption phenomena in the synthesis of CdSe quantum dots has been investigated. These types of microwave effects involving selective microwave absorption by specific reagents have recently been proposed in the microwave-assisted synthesis of various nanoparticles. In the present study, the microwave synthesis of CdSe quantum dots was investigated according to a protocol published by Washington and Strouse to clarify the presence of selective microwave heating. Importantly, control experiments involving conventional conductive heating were executed under otherwise (except for the heating mode) identical conditions, ensuring the same heating and cooling profiles, stirring rates, and reactor geometries. Comparison of powder X-ray diffraction, UV-vis, photoluminescence, and transmission electron microscopy data of the obtained CdSe quantum dots reveals that identical types of nanoparticles are obtained independently of the heating mode. Therefore, no evidence for a selective microwave absorption phenomenon could be obtained.
Substitution of starch for palm oil during gestation: impact on offspring survival and hepatic gene expression in the pig
Authors: Almond K. L. , Fainberg H. P. , Lomax M. A. , Bikker P. , Symonds M. E. , Mostyn A.
Published: April 2014

Piglet neonatal mortality rates are high (~20%), so nutritional strategies to reduce this are highly desirable. Maternal fat substitution (FS) may promote the preweaning survival of piglets by improving their energy status. Therefore, the aim of the present study was to investigate the effects of FS throughout pregnancy on offspring viability, together with the gene expression of stress-related markers in the liver. Sixteen pregnant sows were randomly allocated to one of two isocaloric diets, control (C) or FS in the form of palm oil, fed from 0 to 110 days gestation. Glucose tolerance was examined on Day 108. Median and low birthweight offspring were allocated to tissue sampling at either 7 days or 6 months postnatal age. In response to a glucose tolerance test, FS sows exhibited a raised glucose area under the curve with no change in basal glucose. Average piglet mortality (up to Day 28) was increased fourfold in the FS group, with surviving median-sized piglets exhibiting significantly lower fatty acid binding protein 1 (FABP1) expression at 7 days. There were no effects on the abundance of any other stress- or metabolic-related genes examined. Thus, this study demonstrates that maternal FS throughout gestation causes maternal glucose intolerance that may be linked to the observed increase in piglet mortality. However, the surviving offspring do not exhibit any detectable differences in postnatal growth or hepatic gene profile in later life.
Extinction in Eden: identifying the role of climate change in the decline of the koala in south-eastern NSW
Authors: Lunney Daniel , Stalenberg Eleanor , Santika Truly , Rhodes Jonathan R.
Published: April 2014

Context
Reviews of climate change in Australia have identified that it is imposing additional stresses on biodiversity, which is already under threat from multiple human impacts.

Aims
The present study aimed to determine the contributions of several factors to the demise of the koala in the Eden region in south-eastern New South Wales and, in particular, to establish to what extent climate change may have exacerbated the decline.

Methods
The study built on several community-based koala surveys in the Eden region since 1986, verified through interviews with survey respondents. Historical records as far back as the late 19th century, wildlife databases and field-based surveys were used to independently validate the community survey data and form a reliable picture of changes in the Eden koala population. Analysis of the community survey data used a logistic model to assess the contribution of known threats to koalas, including habitat loss measured as changes in foliage projective cover, fire, increases in the human population and climate change in the form of changes in temperature and rainfall, to the regional decline of this species.

Key results
We found a marked, long-term shrinkage in the distribution of the koala across the Eden region. Our modelling demonstrated that a succession of multiple threats to koalas from land use (human population growth and habitat loss) and environmental change (temperature increase and drought) were significant contributors to this decline.

Conclusions
Climate change, particularly drought and rising temperatures, has been a hitherto hidden factor that has been a major driver of the decline of the koala in the Eden region.

Implications
Development of strategies to help fauna adapt to the changing climate is of paramount importance, particularly at a local scale.
Renormalization of myoglobin–ligand binding energetics by quantum many-body effects
Authors: Weber Cédric , Cole Daniel J. , O’Regan David D. , Payne Mike C.
Published: April 2014

Significance

Heme-based metalloproteins play a central role in respiration by transporting and storing oxygen, a function that is inhibited by carbon monoxide. Density-functional theory has been unable to provide a complete description of the binding of these ligands to heme's central iron atom, predicting an unrealistically high relative affinity for carbon monoxide. Here, we solve this problem using dynamical mean-field theory in combination with linear-scaling density-functional theory, thus allowing for a simultaneous description of crucial quantum entanglement and protein discrimination effects in the ground-state of the oxygen-heme complex. By simulating the binding process within a 1,000-atom quantum-mechanical model of the myoglobin metalloprotein, we obtain a significantly improved description of its spectroscopic and energetic observables.
Fusion of an intact secretory protein permits a misfolded protein to exit from the endoplasmic reticulum in yeast
Authors: Suyama Kengo , Hori Mizue , Gomi Katsuya , Shintani Takahiro
Published: April 2014

Upon exit from the endoplasmic reticulum (ER), the nascent polypeptides of secretory proteins undergo sorting events. If properly folded, they are directly or indirectly recognized by the coat proteins of budding vesicles for forward transport, while unfolded or misfolded proteins are retained in the ER by a quality control mechanism. To gain insight into the interplay between ER export and ER quality control, we fused a secretory protein invertase to the C-terminus of mutated carboxypeptidase Y (CPY*), a model ER-associated degradation (ERAD) substrate in Saccharomyces cerevisiae. This substrate, designated CPY*-Inv, was largely exported from the ER, although it was fully recognized by the ERAD-related lectin, Yos9, and hence degraded by the ERAD when it remained in the ER. CPY*-Inv relied primarily on the p24 complex, a putative ER export receptor for invertase, for escape from ERAD, suggesting that the ERAD and the ER export of soluble secretory proteins are competitive.
Initiation of protein association in tofu formation by metal ions
Authors: Arii Yasuhiro , Takenaka Yasuyuki
Published: April 2014

Magnesium and calcium ions are important factors in making tofu. However, the molecular role of these ions remains unclear in tofu formation. We have previously shown that magnesium chloride concentration-dependent produced silken tofu-like (SP) and regular tofu-like (RP) precipitates, but was an inconsequential factor for the retention of tofu. We investigated in this present study, the effect of various metal chlorides on the metal chloride concentration-dependent changes in tofu formation. These changes occurred in a similar manner to that of the magnesium ion, in which SP formation was followed by RP formation. It is interesting that the midpoint concentration for the formation of SP and RP represented a good correlation with the stability constant of EDTA. This correlation demonstrated the possibility that metal ions would interact with the carboxyl groups of soy proteins. We consider from these results that metal ions were the initiators of protein association in tofu formation.
Exploration of polar lipid accumulation profiles in Euglena gracilis using LipidBlast, an MS/MS spectral library constructed in silico
Authors: Ogawa Takumi , Furuhashi Takeshi , Okazawa Atsushi , Nakai Rai , Nakazawa Masami , Kind Tobias , Fiehn Oliver , Kanaya Shigehiko , Arita Masanori , Ohta Daisaku
Published: April 2014

A rapid protocol for polar lipid profiling was applied to Euglena gracilis lipid metabolism by LipidBlast, an MS/MS spectral similarity search tool. The similarity search results suggested anoxia-induced polar lipid metabolism in Euglena characterized by the accumulation of differential lipid classes, carbon chain lengths, and unsaturated bond numbers. The informatics-supported MS spectral search provides an alternative option for global lipid profiling studies.
The Jim Crow Craze in London's Press and Streets, 1836–39
Authors: Scriven Tom
Published: April 2014

In 1836, American actor Thomas D. Rice first arrived in Great Britain to tour the creation that had made him famous in the USA, Jim Crow. This blackface depiction of a raggedy, runaway slave, with his infectious songs, eccentric dancing and demotic appeal soon took London by storm. The Jim Crow craze lasted for three years, with Rice finding fame, fortune and success and his imitators becoming ubiquitous in the capital's theatres and on its streets. Although the act and its character have been acknowledged as a precursor to the evolution of British minstrelsy and blackface traditions throughout the Victorian period, the craze itself has not been substantially studied in its British context. This essay will look beyond Rice's act and the performance of Jim Crow in the theatres to look instead at Jim Crow's appropriation in print satire and street performance. It will argue that these requisitions of Jim Crow illustrate how Georgian traditions of carnival and grotesque humour were redeveloped for the early Victorian context. In print, Jim Crow was widely utilized in caustic bodily humour that attacked insincere politicians. On the streets, this same humour was seen as obscene and was repressed and contained, paving the way for the respectable, mainstream Victorian blackface act. However, integral to both appropriations of Jim Crow was the figure of the black buffoon, and the act rapidly provided an archetype for the belittling and persecution of London's black population.
Effect of speed on local dynamic stability of locomotion under different task constraints in running
Authors: Mehdizadeh Sina , Arshi Ahmed Reza , Davids Keith
Published: April 2014

A number of studies have investigated effects of speed on local dynamic stability of walking, although this relationship has been rarely investigated under changing task constraints, such as during forward and backward running. To rectify this gap in the literature, the aim of this study was to investigate the effect of running speed on local dynamic stability of forward and backward running on a treadmill. Fifteen healthy male participants took part in this study. Participants ran in forward and backward directions at speeds of 80%, 100% and 120% of their preferred running speed. The three‐dimensional motion of a C7 marker was recorded using a motion capture system. Local dynamic stability of the marker was quantified using short‐ and long‐term largest finite‐time Lyapunov exponents (LyE). Results showed that short‐term largest finite‐time LyE values increased with participant speed meaning that local dynamic stability decreased with increasing speed. Long‐term largest finite‐time LyEs, however, remained unaffected as speed increased. Results of this study indicated that, as in walking, slow running is more stable than fast running. These findings improve understanding of how stability is regulated when constraints on the speed of movements is altered. Implications for the design of rehabilitation or sport practice programmes suggest how task constraints could be manipulated to facilitate adaptations in locomotion stability during athletic training.
NeuroD1 mediates nicotine-induced migration and invasion via regulation of the nicotinic acetylcholine receptor subunits in a subset of neural and neuroendocrine carcinomas
Authors: Osborne Jihan K. , Guerra Marcy L. , Gonzales Joshua X. , McMillan Elizabeth A. , Minna John D. , Cobb Melanie H.
Published: April 2014

Cigarette smoking is a major risk factor for acquisition of small cell lung cancer (SCLC). A role has been demonstrated for the basic helix-loop-helix transcription factor NeuroD1 in the pathogenesis of neural and neuroendocrine lung cancer, including SCLC. In the present study we investigate the possible function of NeuroD1 in established tumors, as well as actions early on in pathogenesis, in response to nicotine. We demonstrate that nicotine up-regulates NeuroD1 in immortalized normal bronchial epithelial cells and a subset of undifferentiated carcinomas. Increased expression of NeuroD1 subsequently leads to regulation of expression and function of the nicotinic acetylcholine receptor subunit cluster of α3, α5, and β4. In addition, we find that coordinated expression of these subunits by NeuroD1 leads to enhanced nicotine-induced migration and invasion, likely through changes in intracellular calcium. These findings suggest that aspects of the pathogenesis of neural and neuroendocrine lung cancers may be affected by a nicotine- and NeuroD1-induced positive feedback loop.
Streptococcus pneumoniaedetects and responds to foreign bacterial peptide fragments in its environment
Authors: Hathaway Lucy J. , Bättig Patrick , Reber Sandra , Rotzetter Jeannine U. , Aebi Suzanne , Hauser Christoph , Heller Manfred , Kadioglu Aras , Mühlemann Kathrin
Published: April 2014

Streptococcus pneumoniaeis an important cause of bacterial meningitis and pneumonia but usually colonizes the human nasopharynx harmlessly. As this niche is simultaneously populated by other bacterial species, we looked for a role and pathway of communication between pneumococci and other species. This paper shows that two proteins of non-encapsulatedS. pneumoniae, AliB-like ORF 1 and ORF 2, bind specifically to peptides matching other species resulting in changes in the pneumococci. AliB-like ORF 1 binds specifically peptide SETTFGRDFN, matching 50S ribosomal subunit protein L4 of Enterobacteriaceae, and facilitates upregulation of competence for genetic transformation. AliB-like ORF 2 binds specifically peptides containing sequence FPPQS, matching proteins ofPrevotellaspecies common in healthy human nasopharyngeal microbiota. We found that AliB-like ORF 2 mediates the early phase of nasopharyngeal colonizationin vivo. The ability ofS. pneumoniaeto bind and respond to peptides of other bacterial species occupying the same host niche may play a key role in adaptation to its environment and in interspecies communication. These findings reveal a completely new concept of pneumococcal interspecies communication which may have implications for communication between other bacterial species and for future interventional therapeutics.
Estimating Phylogeny from microRNA Data: A Critical Appraisal
Authors: Thomson Robert , Plachetzki David , Mahler Luke , Moore Brian
Published: April 2014

Recent progress in resolving the tree of life continues to expose relationships that resist resolution, which drives the search for novel sources of information to solve these difficult phylogenetic problems. A recent example, the presence and absence of microRNA families, has been vigorously promoted as an ideal source of phylogenetic data and has been applied to several perennial phylogenetic problems. The utility of such data for phylogenetic inference hinges critically both on developing stochastic models that provide a reasonable description of the process that give rise to these data, and also on the careful validation of those models in real inference scenarios. Remarkably, however, the statistical behavior and phylogenetic utility of microRNA data have not yet been rigorously characterized. Here we explore the behavior and performance of microRNA presence/absence data under a variety of evolutionary models and reexamine datasets from several previous studies. We find that highly heterogeneous rates of microRNA gain and loss, pervasive secondary loss, and sampling error collectively render microRNA-based inference of phylogeny difficult. Moreover, our reanalyses fundamentally alter the conclusions for four of the five studies that we reexamined. Our results indicate that the capacity of miRNA data to resolve the tree of life has been overstated, and we urge caution in their application and interpretation.
MixMir: microRNA motif discovery from gene expression data using mixed linear models
Authors: Diao LIYANG , Marcais Antoine , Norton Scott , Chen Kevin C.
Published: April 2014

MicroRNAs (miRNAs) are a class of ~22nt non-coding RNAs that potentially regulate over 60% of human protein-coding genes. MiRNA activity is highly specific, differing between cell types, developmental stages and environmental conditions, so the identification of active miRNAs in a given sample is of great interest. Here we present a novel computational approach for analyzing both mRNA sequence and gene expression data, called MixMir. Our method corrects for 3' UTR background sequence similarity between transcripts, which is known to correlate with mRNA transcript abundance. We demonstrate that after accounting for kmer sequence similarities in 3' UTRs, a statistical linear model based on motif presence/absence can effectively discover active miRNAs in a sample. MixMir utilizes fast software implementations for solving mixed linear models which are widely-used in genome-wide association studies (GWAS). Essentially we use 3' UTR sequence similarity in place of population cryptic relatedness in the GWAS problem. Compared to similar methods such as miREDUCE, Sylamer and cWords, we found that MixMir performed better at discovering true miRNA motifs in Dicer knockout CD4+ T-cells, as well as protein and mRNA expression data obtained from miRNA transfection experiments in human cell lines. MixMir can be freely downloaded from https://github.com/ldiao/MixMir.
Predicting the virulence of MRSA from its genome sequence
Authors: Laabei Maisem , Recker Mario , Rudkin Justine K. , Aldeljawi Mona , Gulay Zeynep , Sloan Tim J. , Williams Paul , Endres Jennifer L. , Bayles Kenneth W. , Fey Paul D. , Yajjala Vijaya Kumar , Widhelm Todd , Hawkins Erica , Lewis Katie , Parfett Sara , Scowen Lucy , Peacock Sharon J. , Holden Matthew , Wilson Daniel , Read Timothy D. , van den Elsen Jean , Priest Nicholas K. , Feil Edward J. , Hurst Laurence D. , Josefsson Elisabet , Massey Ruth C.
Published: April 2014

Microbial virulence is a complex and often multifactorial phenotype, intricately linked to a pathogen’s evolutionary trajectory. Toxicity, the ability to destroy host cell membranes, and adhesion, the ability to adhere to human tissues, are the major virulence factors of many bacterial pathogens, including Staphylococcus aureus. Here, we assayed the toxicity and adhesiveness of 90 MRSA (methicillin resistant S. aureus) isolates and found that while there was remarkably little variation in adhesion, toxicity varied by over an order of magnitude between isolates, suggesting different evolutionary selection pressures acting on these two traits. We performed a genome-wide association study (GWAS) and identified a large number of loci, as well as a putative network of epistatically interacting loci, that significantly associated with toxicity. Despite this apparent complexity in toxicity regulation, a predictive model based on a set of significant single nucleotide polymorphisms (SNPs) and insertion and deletions events (indels) showed a high degree of accuracy in predicting an isolate’s toxicity solely from the genetic signature at these sites. Our results thus highlight the potential of using sequence data to determine clinically relevant parameters and have further implications for understanding the microbial virulence of this opportunistic pathogen.
Two Mitogen-Activated Protein Kinases, MPK3 and MPK6, Are Required for Funicular Guidance of Pollen Tubes in Arabidopsis
Authors: Guan Yuefeng , Lu Jianping , Xu Juan , McClure Bruce , Zhang Shuqun
Published: April 2014

Double fertilization in flowering plants requires the delivery of two immotile sperm cells to the female gametes by a pollen tube, which perceives guidance cues, modifies its tip growth direction, and eventually enters the micropyle of the ovule. In spite of the recent progress, so far, little is known about the signaling events in pollen tubes in response to the guidance cues. Here, we show that MPK3 and MPK6, two Arabidopsis (Arabidopsis thaliana) mitogen-activated protein kinases, mediate the guidance response in pollen tubes. Genetic analysis revealed that mpk3 mpk6 double mutant pollen has reduced transmission. However, direct observation of mpk3 mpk6 mutant pollen phenotype was hampered by the embryo lethality of double homozygous mpk3  –/–  mpk6  –/– plants. Utilizing a fluorescent reporter-tagged complementation method, we showed that the mpk3 mpk6 mutant pollen had normal pollen tube growth but impaired pollen tube guidance. In vivo pollination assays revealed that the mpk3 mpk6 mutant pollen tubes were defective in the funicular guidance phase. By contrast, semi-in vitro guidance assay showed that the micropylar guidance of the double mutant pollen tube was normal. Our results provide direct evidence to support that the funicular guidance phase of the pollen tube requires an in vivo signaling mechanism distinct from the micropyle guidance. Moreover, our finding opened up the possibility that the MPK3/MPK6 signaling pathway may link common signaling networks in plant stress response and pollen-pistil interaction.
Human‐induced biotic invasions and changes in plankton interaction networks
Authors: Kratina Pavel , Mac Nally Ralph , Kimmerer Wim J. , Thomson James R. , Winder Monika
Published: April 2014

Pervasive and accelerating changes to ecosystems due to human activities remain major sources of uncertainty in predicting the structure and dynamics of ecological communities. Understanding which biotic interactions within natural multitrophic communities are weakened or augmented by invasions of non‐native species in the context of other environmental pressures is needed for effective management.

We used multivariate autoregressive models with detailed time‐series data from largely freshwater and brackish regions of the upper San Francisco Estuary to assess the topology, direction and strength of trophic interactions following major invasions and establishment of non‐native zooplankton in the early 1990s. We simultaneously compared the effects of fish and clam predation, environmental temperature and salinity intrusion using time‐series data from >60 monitoring locations spanning more than three decades.

We found changes in the networks of biotic interactions in both regions after the major zooplankton invasions. Our results imply an increased pressure on native herbivores; intensified negative interactions between herbivores and omnivores; and stronger bottom‐up influence of juvenile copepods but weaker influence of phytoplankton as a resource for higher trophic levels following the invasions. We identified salinity intrusion as a primary pressure but showed relatively stronger importance of biotic interactions for understanding the dynamics of entire communities.

Synthesis and applications. Our findings highlight the dynamic nature of biotic interactions and provide evidence of how simultaneous invasions of exotic species may alter interaction networks in diverse natural ecosystems over large spatial and temporal scales. Efforts to restore declining fish stocks may be in vain without fully considering the trophic dynamics that limit the flow of energy to target populations. Focusing on multitrophic interactions that may be threatened by invasions rather than a limited focus on responses of individual species or diversity is likely to yield more effective management strategies.
Development of microsatellite markers for Aquilegia buergeriana var. oxysepala (Ranunculaceae), a vulnerable Japanese herb
Authors: Itagaki Tomoyuki , Kimura Megumi K. , Lian Chunlan , Sakai Satoki
Published: April 2014

Aquilegia buergeriana var. oxysepala is a vulnerable herb, for which 20 microsatellite markers were developed. The applicability of these markers was confirmed by genotyping of 66 individuals collected from four natural populations in Japan. Of the 20 loci, 15 showed polymorphism. For the 15 polymorphic markers, the number of alleles per locus ranged from 2 to 12, and the expected and observed heterozygosities ranged from 0.13 to 0.77 and 0.02 to 0.65, respectively. The markers described here are sufficiently polymorphic and informative to investigate the genetic diversity and population genetic structure of A. buergeriana var. oxysepala.
Drinking cheaply: the demand for basic wine in Italy
Authors: Cembalo Luigi , Caracciolo Francesco , Pomarici Eugenio
Published: April 2014

The wine market has evolved dramatically over the last three decades. The premium wine segment has expanded significantly to the detriment of basic wines. Nevertheless, in traditional wine producing and consuming countries, inexpensive wines still account for a large market share, both in volume and value. Marketing strategies for such wines are changing in an attempt to tap this increasingly crowded market segment. Despite its importance, the basic wine segment has not been studied in‐depth and is often assumed to have no product differentiation. This paper tried to ascertain the existence of a possible degree of heterogeneity within nonpremium wines and to measure, by means of elasticity computation, the relationships among categories of wines aggregated with criteria that go beyond price. A demand system (censored QUAIDS) was estimated, using a statistically representative panel of 6,773 Italian households, to see to what extent, if any, substitution occurs in home consumption of basic wines, which is the main channel of distribution of inexpensive wines in Italy. Although price is an important lever in supply policies, our results also suggest the importance of packaging, such as carton as an alternative to glass.
Aoria rufotestacea Faimaire (Coleoptera: Chrysomelidae) long been confused as Bromius obscurus (Linnaeus) in Korea
Authors: An Seunglak , Hong Chang‐Ki , Kim Seulki , Lee Seongkyun , Cho Soowon
Published: April 2014

Western grape rootworm, Bromius obscurus (Linnaeus) is a well‐known pest of grape vines in Europe and North America. We found that all the Korean specimens that have long been known as B. obscurus turned out to be Aoria rufotestacea Faimaire, showing with only about 83% sequence similarity in COI barcodes. The small puncture patterned specimens of A. rufotestacea were initially confused with A. scutellaris Pic, but confirmed to be A. rufotestacea with genitalic characteristics as well as 100% matched COI barcode sequence. Here we describe and compare the morphologically confusing species, B. obscurus and A. rufotestacea, with description of scutellaris‐like wing variation, in detail with adult images and COI sequences.
The Pleasures of Austerity
Authors: BERRY HELEN
Published: April 2014

This article challenges the paradigm of untrammelled consumer pleasures in the Georgian era by exploring the various motivations for disengagement from the dominant social codes of polite consumption. It examines the use of the terms ‘austere’ and ‘austerity’ in Georgian print culture, and the censure that resulted from being thus described. The religious and philosophical underpinnings of austerity as a stand against dominant modes of Anglicanism are considered, concluding with a case study of the fashionable physician George Cheyne, whose struggle to control his own obesity led to the formulation of a medical and dietary solution to over‐consumption.
New oral anticoagulants: clinical indications, monitoring and treatment of acute bleeding complications
Authors: FENGER‐ERIKSEN C. , MÜNSTER A.‐M. , GROVE E. L.
Published: April 2014

New oral anticoagulants like the direct thrombin inhibitor, dabigatran (Pradaxa®), and factor Xa‐inhibitors, rivaroxaban (Xarelto®) and apixaban (Eliquis®) are available for prophylaxis and treatment of thromboembolic disease. They are emerging alternatives to warfarin and provide equal or better clinical outcome together with reduced need for routine monitoring. Methods for measuring drug concentrations are available, although a correlation between plasma drug concentrations and the risk of bleeding has not been firmly established. Standard laboratory measures like prothrombin time and activated partial thromboplastin time are not sensitive enough to detect thrombin or factor Xa inhibition provided by new oral anticoagulants. Thus, these standard tests may only be used as a crude estimation of the actual anticoagulation status. Further challenges regarding patients receiving new oral anticoagulants who presents with major bleeding or need for emergency surgery pose a unique problem. No established agents are clinically available to reverse the anticoagulant effect, although preclinical data report prothrombin complex concentrate as more efficient than fresh frozen plasma or other prohaemostatic agents.

This review summaries current knowledge on approved new oral anticoagulants and discusses clinical aspects of monitoring, with particular focus on the management of the bleeding patient.
Redundancy in seed dispersal by three sympatric ungulates: a reintroduction perspective
Authors: Polak T. , Gutterman Y. , Hoffman I. , Saltz D.
Published: April 2014

Reintroductions may play an important role in re‐establishing key ecosystem functions and are potentially a valuable ecosystem‐restoration tool. Here, we focus on the role of reintroduced ungulates as seeds dispersers – a key process in shaping plant community structure and dynamics. In a comparative study, we investigated which plant species are dispersed by three sympatric ungulates in the Negev desert, Israel: Arabian oryx Oryx leucoryx, Asiatic wild ass Equus hemionus and dorcas gazelle Gazella dorcas. The oryx and wild ass were locally extirpated and recently reintroduced while the gazelle is the only wide‐ranging ungulate that has existed continuously in the region. We hypothesized that although all three species are ungulates, because of expected differences in diet resulting from the differences in their size and digestive characteristics, there will be little overlap in their role as seed dispersers. In addition, we experimentally tested the importance of ingestion of the seeds of the keystone acacia Acacia raddiana and the presence of dung on germination success and seedlings growth. We found that each of the ungulates dispersed a different assemblage of plant species with little overlap, highlighting the importance of the reintroduction of both species in ecosystem restoration. Oryx were the key dispersers of acacia seeds, and oryx‐ingested seeds planted with oryx pellets had a germination success 250 times higher than non‐ingested seeds planted without pellets. Seedlings from ingested seeds also grew faster than seedlings from non‐ingested seeds. We found little redundancy between ungulates as seed dispersers in this region, highlighting the importance of reintroductions as a restorative process even when other species from the same guild still exist in the wild.