bluuebunny/crossref_metadata_2025 huggingface dataset:
Infinitesimal Legendre symmetry in the Geometrothermodynamics programme
Authors: García-Peláez D. , López-Monsalvo C. S.
Published: August 2014

The work within the Geometrothermodynamics programme rests upon the metric structure for the thermodynamic phase-space. Such structure exhibits discrete Legendre symmetry. In this work, we study the class of metrics which are invariant along the infinitesimal generators of Legendre transformations. We solve the Legendre-Killing equation for a K-contact general metric. We consider the case with two thermodynamic degrees of freedom, i.e., when the dimension of the thermodynamic phase-space is five. For the generic form of contact metrics, the solution of the Legendre-Killing system is unique, with the sole restriction that the only independent metric function – Ω – should be dragged along the orbits of the Legendre generator. We revisit the ideal gas in the light of this class of metrics. Imposing the vanishing of the scalar curvature for this system results in a further differential equation for the metric function Ω which is not compatible with the Legendre invariance constraint. This result does not allow us to use Quevedo's interpretation of the curvature scalar as a measure of thermodynamic interaction for this particular class.
Evidence of slippage breakdown for a superhydrophobic microchannel
Authors: Bolognesi G. , Cottin-Bizonne C. , Pirat C.
Published: August 2014

A full characterization of the water flow past a silicon superhydrophobic surface with longitudinal micro-grooves enclosed in a microfluidic device is presented. Fluorescence microscopy images of the flow seeded with fluorescent passive tracers were digitally processed to measure both the velocity field and the position and shape of the liquid-air interfaces at the superhydrophobic surface. The simultaneous access to the meniscus and velocity profiles allows us to put under a strict test the no-shear boundary condition at the liquid-air interface. Surprisingly, our measurements show that air pockets in the surface cavities can sustain non-zero interfacial shear stresses, thereby hampering the friction reduction capabilities of the surface. The effects of the meniscus position and shape as well as of the liquid-air interfacial friction on the surface performances are separately assessed and quantified.
Phase-locking of magnetic islands diagnosed by ECE-imaging
Authors: Tobias B. , Grierson B. A. , Muscatello C. M. , Ren X. , Domier C. W. , Luhmann N. C. , Zemedkun S. E. , Munsat T. L. , Classen I. G. J.
Published: August 2014

Millimeter-wave imaging diagnostics identify phase-locking and the satisfaction of 3-wave coupling selection criteria among multiple magnetic island chains by providing a localized, internal measurement of the 2D power spectral density, S(ω, kpol). In high-confinement tokamak discharges, these interactions impact both plasma rotation and tearing stability. Nonlinear coupling among neoclassical tearing modes of different n-number, with islands not satisfying the poloidal mode number selection criterion ⟨m, m′, m − m′⟩, contributes to a reduction in core rotation and flow shear in the vicinity of the modes.
An ultra-small three dimensional computational microscope
Authors: Kim Ganghun , Menon Rajesh
Published: August 2014

We present a computational approach that allows one to create microscopic images in 3D through a miniature, rigid cannula. Light rays propagate from one end of the cannula to the other resulting in a complex intensity distribution. This distribution is unique to the position of the source of the rays. By applying appropriate calibration and utilizing a nonlinear optimization algorithm, we computationally reconstructed images of objects with a minimum feature size of ∼5 μm. Preliminary experiments indicate that the sensitivity of the imaging technique can be as small as 100 nm in the transverse plane and ∼1 μm in the longitudinal direction. Since the cannula is only 14.7 mm long and 200 μm in diameter, this allows for highly miniaturized microscopes that utilize no optics and no scanning. Furthermore, since the images are obtained with just a single frame (no scanning), fast image acquisition is also feasible.
Voltage controlled modification of flux closure domains in planar magnetic structures for microwave applications
Authors: Parkes D. E. , Beardsley R. , Bowe S. , Isakov I. , Warburton P. A. , Edmonds K. W. , Campion R. P. , Gallagher B. L. , Rushforth A. W. , Cavill S. A.
Published: August 2014

Voltage controlled modification of the magnetocrystalline anisotropy in a hybrid piezoelectric/ferromagnet device has been studied using Photoemission Electron Microscopy with X-ray magnetic circular dichroism as the contrast mechanism. The experimental results demonstrate that the large magnetostriction of the epitaxial Fe81Ga19 layer enables significant modification of the domain pattern in laterally confined disc structures. In addition, micromagnetic simulations demonstrate that the strain induced modification of the magnetic anisotropy allows for voltage tuneability of the natural resonance of both the confined spin wave modes and the vortex motion. These results demonstrate the possibility for using voltage induced strain in low-power voltage tuneable magnetic microwave oscillators.
Effect of the q-nonextensive electron velocity distribution on a magnetized plasma sheath
Authors: Safa N. Navab , Ghomi H. , Niknam A. R.
Published: August 2014

In this work, a sheath model has been developed to investigate the effect of the q-nonextensive electron velocity distribution on the different characteristics of a magnetized plasma. By using Segdeev potential method, a modified Bohm criterion for a magnetized plasma with the nonextensive electron velocity distribution is derived. The sheath model is then used to analyze numerically the sheath structure under different q, the parameter quantifying the nonextensivity degree of the system. The results show that as the q-parameter decreases, the floating potential becomes more negative. The sheath length increases at the lower values of the q-parameter due to the increase in the electron population at the high-energy tail of the distribution function. As q-parameter decreases, the effective temperature of the electrons increases which results in a more extended plasma sheath. The ion velocity and density profiles for the different nonextensivity degrees of the system reflect the gyro-motion of the ions in the presence of the magnetic field. Furthermore, the results coincide with those given by the Maxwellian electron distribution function, when q tends to 1.
Absorption of surface acoustic waves by topological insulator thin films
Authors: Li L. L. , Xu W.
Published: August 2014

We present a theoretical study on the absorption of the surface acoustic waves (SAWs) by Dirac electrons in topological insulator (TI) thin films (TITFs). We find that due to momentum and energy conservation laws, the absorption of the SAWs in TITFs can only be achieved via intra-band electronic transitions. The strong absorption can be observed up to sub-terahertz frequencies. With increasing temperature, the absorption intensity increases significantly and the cut-off frequency is blue-shifted. More interestingly, we find that the absorption of the SAWs by the TITFs can be markedly enhanced by the tunable subgap in the Dirac energy spectrum of the TI surface states. Such a subgap is absent in conventional two-dimensional electron gases (2DEGs) and in the gapless Dirac 2DEG such as graphene. This study is pertinent to the exploration of the acoustic properties of TIs and to potential application of TIs as tunable SAW devices working at hypersonic frequencies.
Highly efficient organic multi-junction solar cells with a thiophene based donor material
Authors: Meerheim Rico , Körner Christian , Leo Karl
Published: August 2014

The efficiency of organic solar cells can be increased by serial stacked subcells even upon using the same absorber material. For the multi-junction devices presented here, we use the small molecule donor material DCV5T-Me. The subcell currents were matched by optical transfer matrix simulation, allowing an efficiency increase from 8.3% for a single junction up to 9.7% for a triple junction cell. The external quantum efficiency of the subcells, measured under appropriate light bias illumination, is spectrally shifted due to the microcavity of the complete stack, resulting in a broadband response and an increased cell current. The increase of the power conversion efficiency upon device stacking is even stronger for large area cells due to higher influence of the resistance of the indium tin oxide anode, emphasizing the advantage of multi-junction devices for large-area applications.
Percolation mechanism through trapping/de-trapping process at defect states for resistive switching devices with structure of Ag/SixC1−x/p-Si
Authors: Liu Yanhong , Gao Ping , Jiang Xuening , Li La , Zhang Jialiang , Peng Wei
Published: August 2014

Pure SixC1−x (x > 0.5) and B-containing SixC1−x (x > 0.5) based resistive switching devices (RSD) with the structure of Ag/SixC1−x/p-Si were fabricated and their switching characteristics and mechanism were investigated systematically. Percolation mechanism through trapping/ de-trapping at defect states was suggested for the switching process. Through the introduction of B atoms into SixC1−x, the density of defect states was reduced, then, the SET and RESET voltages were also decreased. Based on the percolation theory, the dependence of SET/RESET voltage on the density of defect states was analyzed. These results supply a deep understanding for the SiC-based RSD, which have a potential application in extreme ambient conditions.
Luminescence quenching of conductive Si nanocrystals via “Linkage emission”: Hopping-like propagation of infrared-excited Auger electrons
Authors: Ishii Masashi , Crowe Iain F. , Halsall Matthew P. , Knights Andrew P. , Gwilliam Russell M. , Hamilton Bruce
Published: August 2014

Phosphorus (P) is an n-type dopant for conductive silicon nanocrystals (Si-nc's), the electrical activation of which may be monitored through a non-radiative Auger recombination process that quenches the Si-nc luminescence. We investigated this quenching mechanism through electrical measurements of Si-nc's. Infrared-excited Auger electron emission as the non-radiative process was directly probed and the dynamics of the process are determined from a frequency response analysis. To explain the dynamics, we propose a model in which Auger electrons with a low kinetic energy establish a local inter-nanocrystal conductance and the repetition of this local conductance results in a constant photocurrent (“linkage emission”). This emission becomes significant by electron filling in the Si-nc's owing to the electrical activation of P, which is consistent with observed luminescence quenching behavior. We found that the IR photo-excited emission is distinct from the thermally induced hopping conduction and show that confined, rather than trapped, charges are the source of the Auger electrons. Thus, the process consumes both confined charges and the recombination energy for Auger emission, which explains the luminescence quenching mechanism of Si-nc:P.
Induced electronic anisotropy in bismuth thin films
Authors: Liao Albert D. , Yao Mengliang , Katmis Ferhat , Li Mingda , Tang Shuang , Moodera Jagadeesh S. , Opeil Cyril , Dresselhaus Mildred S.
Published: August 2014

We use magneto-resistance measurements to investigate the effect of texturing in polycrystalline bismuth thin films. Electrical current in bismuth films with texturing such that all grains are oriented with the trigonal axis normal to the film plane is found to flow in an isotropic manner. By contrast, bismuth films with no texture such that not all grains have the same crystallographic orientation exhibit anisotropic current flow, giving rise to preferential current flow pathways in each grain depending on its orientation. Extraction of the mobility and the phase coherence length in both types of films indicates that carrier scattering is not responsible for the observed anisotropic conduction. Evidence from control experiments on antimony thin films suggests that the anisotropy is a result of bismuth's large electron effective mass anisotropy.
Hybrid density functional theory study of Cu(In1−xGax)Se2 band structure for solar cell application
Authors: Chen Xu-Dong , Chen Lin , Sun Qing-Qing , Zhou Peng , Zhang David Wei
Published: August 2014

Cu(In1−xGax)Se2 (CIGS) alloy based thin film photovoltaic solar cells have attracted more and more attention due to its large optical absorption coefficient, long term stability, low cost and high efficiency. However, the previous theoretical investigation of this material with first principle calculation cannot fulfill the requirement of experimental development, especially the accurate description of band structure and density of states. In this work, we use first principle calculation based on hybrid density functional theory to investigate the feature of CIGS, with B3LYP applied in the CuIn1−xGaxSe2 stimulation of the band structure and density of states. We report the simulation of the lattice parameter, band gap and chemical composition. The band gaps of CuGaSe2, CuIn0.25Ga0.75Se2, CuIn0.5Ga0.5Se2, CuIn0.75Ga0.25Se2 and CuInSe2 are obtained as 1.568 eV, 1.445 eV, 1.416 eV, 1.275 eV and 1.205 eV according to our calculation, which agree well with the available experimental values. The band structure of CIGS is also in accordance with the current theory.
Rhizobium-induced elevation in xylem cytokinin delivery in pigeonpea induces changes in shoot development and leaf physiology
Authors: Yong Jean W. H. , Letham D. Stuart , Wong S. Chin , Farquhar Graham D.
Published: August 2014

Inoculation with Rhizobium strain IC3342 induces in pigeonpea (Cajanus cajan (L) Millsp.) a leaf curl syndrome and elevated cytokinin levels in the xylem sap. High nitrogen (N) nutrition was found to inhibit onset of the syndrome which could then be induced by N-free nutrient after development of seven trifoliate leaves. This provided a new system to study the role of xylem cytokinin in shoot development and yielded plants suitable for determining the rate of delivery of xylem cytokinin to the shoot which for IC3342-inoculated plants was found to be three times that of control plants. Relative to leaves of control plants, the non-curled leaves of these IC3342 plants exhibited higher nitrogen and chlorophyll content and greater photosynthetic rate and stomatal conductance. Induction of the syndrome increased leaf thickness in developing leaves but not in expanded leaves already formed. Diameter of stems and number of laterals were also increased markedly by IC3342 inoculation which in addition induced leaf hyponasty. Exogenous cytokinins when applied directly to control leaves induced leaf curl and increased leaf thickness. The present studies are discussed in relation to the role of xylem cytokinins in plant development and especially the release of lateral buds from apical dominance.
Effect of fire on small mammals: a systematic review
Authors: Griffiths Anthony D. , Brook Barry W.
Published: August 2014

Fire is a natural disturbance that exerts an important influence on global ecosystems, affecting vegetation distribution and structure, the carbon cycle and climate. However, human-induced changes to fire regimes may affect at-risk species groups such as small mammals. We examine the effect of fire on small mammals and evaluate the relative sensitivity to fire among different groups using a systematic review methodology that included critiquing the literature with respect to survey design and statistical analysis. Overall, small mammal abundance is slightly higher, and demographic parameters more favourable, in unburnt sites compared to burnt sites. This was more pronounced in species with body size range of 101–1000g and with habitat requirements that are sensitive to fire (e.g. dense ground cover): in 66.6 and 69.7% of pairwise comparisons, abundance or a demographic parameter were higher in unburnt than burnt sites. This systematic review demonstrates that there remains a continued focus on simple shifts in abundance with regards to effect of fire and small mammals, which limits understanding of mechanisms responsible for change. Body size and habitat preference were most important in explaining variation in small mammal species’ responses to fire.
Molecular pathogenesis of congenital diaphragmatic hernia revealed by exome sequencing, developmental data, and bioinformatics
Authors: Longoni Mauro , High Frances A. , Russell Meaghan K. , Kashani Alireza , Tracy Adam A. , Coletti Caroline M. , Hila Regis , Shamia Ahmed , Wells Julie , Ackerman Kate G. , Wilson Jay M. , Bult Carol J. , Lee Charles , Lage Kasper , Pober Barbara R. , Donahoe Patricia K.
Published: August 2014

Significance

Congenital diaphragmatic hernia (CDH) is a common birth defect associated with high morbidity and mortality. Focusing on the coding sequence of 51 genes, discovered in human studies and in mouse models, we studied 275 CDH patients and identified multiple variants in CDH-causing genes. Information on gene expression in embryonic mouse diaphragms and protein interactions allowed us to prioritize additional compelling CDH-associated genes. We believe that an improved understanding of the genetics of CDH will be important to design new therapeutic strategies for patients with diaphragmatic defects.
Calcineurin determines toxic versus beneficial responses to α-synuclein
Authors: Caraveo Gabriela , Auluck Pavan K. , Whitesell Luke , Chung Chee Yeun , Baru Valeriya , Mosharov Eugene V. , Yan Xiaohui , Ben-Johny Manu , Soste Martin , Picotti Paola , Kim Hanna , Caldwell Kim A. , Caldwell Guy A. , Sulzer David , Yue David T. , Lindquist Susan
Published: August 2014

Significance

Ca
2+
homeostasis is indispensable for the well being of all living organisms. Ca
2+
homeostasis is disrupted by α-synuclein (α-syn), whose misfolding plays a major role in neurodegenerative diseases termed synucleinopathies, such as Parkinson disease. We report that α-syn can induce sustained and highly elevated levels of cytoplasmic Ca
2+
, thereby activating a calcineurin (CN) cascade that results in toxicity. CN is a highly conserved Ca
2+
–calmodulin (CaM)-dependent phosphatase critical for sensing Ca
2+
concentrations and transducing that information into cellular responses. Limiting, but not eliminating, the availability of CaM, CN and/or CN substrates directly with genetic or pharmacological tools shifts the α-syn–induced CN cascade to a protective mode. This has mechanistic implications for CN's activity and provides a therapeutic venue for the treatment of synucleinopathies.
Episodic star formation in a group of LAEs at z = 5.07
Authors: Rodríguez Espinosa J. M. , González-Martín O. , Castro Rodríguez N. , Pérez-González P. G. , Mas-Hesse J.M. , Muñoz-Tuñón C. , Cava A. , Cardiel N. , Cabrera Lavers A. , Gallego J. , Hernán Caballero A. , Herrera Ruiz N. , Ramírez Olivencia N.
Published: August 2014

We are undertaking a search for high-redshift low-luminosity Lyman Alpha sources in the SHARDS (Survey for High-z Absorption Red and Dead Sources) survey. Among the pre-selected Lyman Alpha sources two candidates were spotted, located 3.19 arcsec apart, and tentatively at the same redshift. Here, we report on the spectroscopic confirmation with Gran Telescopio Canarias of the Lyman Alpha emission from this pair of galaxies at a confirmed spectroscopic redshifts of z=5.07. Furthermore, one of the sources is interacting/merging with another close companion that looks distorted. Based on the analysis of the spectroscopy and additional photometric data, we infer that most of the stellar mass of these objects was assembled in a burst of star formation 100 Myr ago. A more recent burst (2 Myr old) is necessary to account for the measured Lyman Alpha flux. We claim that these two galaxies are good examples of Lyman Alpha sources undergoing episodic star formation. Besides, these sources very likely constitute a group of interacting Lyman Alpha emitters (LAEs).
The Novel Monocot-Specific 9-Lipoxygenase ZmLOX12 Is Required to Mount an Effective Jasmonate-Mediated Defense Against Fusarium verticillioides in Maize
Authors: Christensen Shawn A. , Nemchenko Andriy , Park Yong-Soon , Borrego Eli , Huang Pei-Cheng , Schmelz Eric A. , Kunze Susan , Feussner Ivo , Yalpani Nasser , Meeley Robert , Kolomiets Michael V.
Published: August 2014

Fusarium verticillioides is a major limiting factor for maize production due to ear and stalk rot and the contamination of seed with the carcinogenic mycotoxin fumonisin. While lipoxygenase (LOX)-derived oxylipins have been implicated in defense against diverse pathogens, their function in maize resistance against F. verticillioides is poorly understood. Here, we functionally characterized a novel maize 9-LOX gene, ZmLOX12. This gene is distantly related to known dicot LOX genes, with closest homologs found exclusively in other monocot species. ZmLOX12 is predominantly expressed in mesocotyls in which it is strongly induced in response to F. verticillioides infection. The Mutator transposon-insertional lox12-1 mutant is more susceptible to F. verticillioides colonization of mesocotyls, stalks, and kernels. The infected mutant kernels accumulate a significantly greater amount of the mycotoxin fumonisin. Reduced resistance to the pathogen is accompanied by diminished levels of the jasmonic acid (JA) precursor 12-oxo phytodienoic acid, JA-isoleucine, and expression of jasmonate-biosynthetic genes. Supporting the strong defense role of jasmonates, the JA-deficient opr7 opr8 double mutant displayed complete lack of immunity to F. verticillioides. Unexpectedly, the more susceptible lox12 mutant accumulated higher levels of kauralexins, suggesting that F. verticillioides is tolerant to this group of antimicrobial phytoalexins. This study demonstrates that this unique monocot-specific 9-LOX plays a key role in defense against F. verticillioides in diverse maize tissues and provides genetic evidence that JA is the major defense hormone against this pathogen.
Quick and Accurate Detection and Quantification of Magnaporthe oryzae in Rice Using Real-Time Quantitative Polymerase Chain Reaction
Authors: Sun Geng , Liu Jinliang , Li Guihua , Zhang Xianghui , Chen Tingting , Chen Jingyuan , Zhang Hao , Wang Dongping , Sun Fengjie , Pan Hongyu
Published: August 2014

Rice blast, caused by Magnaporthe oryzae, is one of the most severe fungal diseases in rice worldwide. In this study, we developed methods to quickly and accurately detect and quantify M. oryzae in the pure cultures of the fungus, rice plants, and rice seed by using SYBR Green I of the real-time quantitative polymerase chain reaction (qPCR). Results of absolute qPCR show that Magnaporthe oryzae can be detected at as low as 6.9 × 10−5 ng of genomic DNA. Results also show that all 10 varieties of rice seed examined in this study contain this fungus, indicating that M. oryzae is generally widespread in rice seed. We report the quantification of DNA of M. oryzae in rice leaves collected in the field, instead of in the lab, using relative qPCR by using rice actin gene as a housekeeping gene. Our results show great practical significance because we would know the potential fungal infection even before planting.
First Report of Xanthomonas euvesicatoria Causing Bacterial Spot Disease in Pepper in Northwestern Nigeria
Authors: Jibrin M. O. , Timilsina S. , Potnis N. , Minsavage G. V. , Shenge K. C. , Akpa A. D. , Alegbejo M. D. , Beed F. , Vallad G. E. , Jones J. B.
Published: August 2014

Bacterial spot (BS) has been reported as an important disease on pepper in Nigeria (4). Xanthomonas campestris pv. vesicatoria was identified as the causal agent using phenotypic and pathogenicity tests; however, X. campestris pv. vesicatoria is a synonym for two genetically distinct groups that have been elevated to the species X. euvesicatoria and X. vesicatoria (2). Furthermore, the latter two species and X. gardneri cause similar diseases on pepper (2). In order to determine the species associated with BS on pepper, leaves with irregular, dark brown lesions were collected from pepper plants in fields from northwestern Nigeria, and isolations were made on nutrient agar (NA). Yellow, mucoid colonies typical of Xanthomonas were isolated. Six strains isolated from pepper were determined to be non-amylolytic. For race determinations, bacterial suspensions of the pepper strains, derived from 24-h cultures grown on NA at 28°C, were adjusted to 108 CFU/ml and infiltrated into leaves of tomato and pepper differential genotypes (5). The six pepper strains elicited HRs on the tomato differential genotypes. The strains produced a susceptible reaction on all pepper differentials and were designated as pepper race 6 (5). Multilocus sequence analysis (MLSA) using six housekeeping genes (fusA, lacF, gyrB, gltA, gapA, and lepA) was used to further analyze the strains (1) (GenBank Accession Nos. KJ938585 to KJ938587, KJ938592 to KJ938594, KJ938599 to KJ938601, KJ938606 to KJ938608, KJ938633 to KJ938635, and KJ938640 to KJ938642). A partial sequence of hrpB2 was also sequenced since the four Xanthomonas species associated with BS can be differentiated based on sequence divergence (3) (KJ938622 to KJ938627). The housekeeping gene sequences were aligned along with other Xanthomonas sequences imported from the NCBI database using muscle tool from MEGA software, 5.2.2. Maximum likelihood phylogenetic trees constructed for the six housekeeping gene sequences individually and in concatenation revealed that the Nigerian pepper strains were identical to the X. euvesicatoria reference strain 85-10. Although BS is common in Nigeria, to our knowledge, this represents the first report for this pepper pathogen in Nigeria.

References: (1) N. F. Almeida et al. Phytopathology 100:208, 2010. (3) J. B. Jones et al. System Appl. Microbiol. 27:755, 2004. (4) A. Obradovic et al. Eur. J. Plant Pathol. 88:736, 2004. (2) E. U. Opara and F. J. Odibo. J. Mol. Gen. 1:35, 2009. (5) R. E. Stall et al. Ann. Rev. Phytopathol. 47:265, 2009.
New Insights into Mango Malformation Disease Epidemiology Lead to a New Integrated Management Strategy for Subtropical Environments
Authors: Freeman Stanley , Shtienberg Dani , Maymon Marcel , Levin Adolfo G. , Ploetz Randy C.
Published: August 2014

Mango (Mangifera indica) is regarded as the king of fruits in India, where it has been cultivated for at least 4,000 years and has great cultural and religious significance. Many Indian mango cultivars originated in the fifteenth century when the best selections of mango seedlings were propagated by grafting and planted in large orchards, in some cases numbering 100,000 trees. With the arrival of voyagers to India from Europe, mango was soon established throughout the tropics and subtropics. Mango malformation disease (MMD) is one of the most important and destructive diseases of this crop. It affects inflorescences and vegetative portions of the plant. Although trees are not killed, the vegetative phase of the disease impedes canopy development and the floral phase reduces fruit yield dramatically; substantial economic losses can occur since malformed inflorescences do not bear fruit. Significant advances have been made in understanding the etiology of MMD, which is caused by more than one agent. However, until recently little progress had been made on the epidemiology of this disease. The results that are discussed in this article are only for MMD caused by F. mangiferae.
Adapting to a changing environment: non-obvious thresholds in multi-scale systems
Authors: Perryman Clare , Wieczorek Sebastian
Published: August 2014

Many natural and technological systems fail to adapt to changing external conditions and move to a different state if the conditions vary too fast. Such ‘non-adiabatic’ processes are ubiquitous, but little understood. We identify these processes with a new nonlinear phenomenon—an intricate threshold where a forced system fails to adiabatically follow a changing stable state. In systems with multiple time scales, we derive existence conditions that show such thresholds to be generic, but non-obvious, meaning they cannot be captured by traditional stability theory. Rather, the phenomenon can be analysed using concepts from modern singular perturbation theory: folded singularities and canard trajectories, including composite canards. Thus, non-obvious thresholds should explain the failure to adapt to a changing environment in a wide range of multi-scale systems including: tipping points in the climate system, regime shifts in ecosystems, excitability in nerve cells, adaptation failure in regulatory genes and adiabatic switching in technology.
Simiduia curdlanivorans sp. nov., a curdlan-degrading bacterium isolated from the junction between the ocean and a freshwater spring, and emended description of the genus Simiduia
Authors: Park Sooyeon , Kim Soo-In , Jung Yong-Taek , Yoon Jung-Hoon
Published: August 2014

A Gram-stain-negative, aerobic, non-spore-forming, non-flagellated and rod-shaped bacterial strain, designated DMCK3-4T, was isolated from the zone where the ocean and a freshwater spring meet at Jeju island, South Korea. Strain DMCK3-4T grew optimally at 30 °C, at pH 7.0–8.0 and in the presence of 2.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain DMCK3-4T clustered with the strains of three members of the genus

Simiduia

, with which it exhibited 97.0–99.0 % sequence similarity. Sequence similarities to the type strains of the other species with validly published names were less than 92.2 %. Strain DMCK3-4T contained Q-8 as the predominant ubiquinone and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C17 : 1ω8c, C16 : 0, C17 : 0 and C18 : 1ω7c as the major fatty acids. The major polar lipids of strain DMCK3-4T were phosphatidylethanolamine, phosphatidylglycerol, two unidentified glycolipids, one unidentified lipid and one unidentified aminolipid. The DNA G+C content of strain DMCK3-4T was 51.8 mol% and its mean DNA–DNA relatedness values with

Simiduia agarivorans

KCTC 23176T,

Simiduia areninigrae

KCTC 23293T and Simiduia litorea NRIC 0917T were 23–34 %, respectively. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain DMCK3-4T is distinct from other species of the genus

Simiduia

. On the basis of the data presented, strain DMCK3-4T is considered to represent a novel species of the genus

Simiduia

, for which the name Simiduia curdlanivorans sp. nov. is proposed. The type strain is DMCK3-4T ( = KCTC 42075T = CECT 8570T). An emended description of the genus

Simiduia

is also proposed.
Flavobacterium oryzae sp. nov., isolated from a flooded rice field, and emended descriptions of Flavobacterium flevense, Flavobacterium yonginense and Flavobacterium myungsuense
Authors: Chen Wen-Ming , Chen Jhen-Ci , Sheu Shih-Yi
Published: August 2014

A bacterial strain, designated Jyi-05T, was isolated from a flooded rice field and characterized using a polyphasic taxonomic approach. Cells of strain Jyi-05T were Gram-stain-negative, strictly aerobic, bright-yellow-pigmented rods that were motile by gliding. Growth occurred at 10–30 °C (optimum 30 °C), at pH 6.5–7.5 (optimum pH 7.0) and with 0–2 % (w/v) NaCl (optimum 1 %, w/v, NaCl). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Jyi-05T belonged to the genus

Flavobacterium

and was most closely related to

Flavobacterium flevense

DSM 1076T with sequence similarity of 97.6 %. Strain Jyi-05T contained iso-C15 : 0 (16.6 %), anteiso-C15 : 0 (10.8 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c; 10.3 %), iso-C17 : 0 3-OH (9.2 %), C16 : 0 (7.3 %) and iso-C15 : 0 3-OH (7.2 %) as the predominant fatty acids. The major isoprenoid quinone was MK-6. The polar lipid profile consisted of phosphatidylethanolamine and several uncharacterized aminophospholipids and phospholipids. The major polyamine was homospermidine. The genomic DNA G+C content of strain Jyi-05T was 34.2 mol%. The DNA–DNA relatedness of strain Jyi-05T with respect to recognized species of the genus

Flavobacterium

was less than 70 %. On the basis of the phylogenetic inference and phenotypic data, strain Jyi-05T should be classified as a novel species, for which the name Flavobacterium
oryzae sp. nov. is proposed. The type strain is Jyi-05T ( = BCRC 80522T = LMG 27292T = KCTC 32240T). Emended descriptions of

Flavobacterium flevense

,

Flavobacterium yonginense

and

Flavobacterium myungsuense

are also presented.
Brevundimonas denitrificans sp. nov., a denitrifying bacterium isolated from deep subseafloor sediment
Authors: Tsubouchi Taishi , Koyama Sumihiro , Mori Kozue , Shimane Yasuhiro , Usui Keiko , Tokuda Maki , Tame Akihiro , Uematsu Katsuyuki , Maruyama Tadashi , Hatada Yuji
Published: August 2014

A novel Gram-stain-negative, aerobic, heterotrophic, stalked and capsulated bacterium with potential denitrification ability, designated strain TAR-002T, was isolated from deep seafloor sediment in Japan. Colonies lacked lustre, and were viscous and translucent white. The ranges of temperature, pH and salt concentration for growth were 8–30 °C, pH 6.0–10.0 and 1–3 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences confirmed that strain TAR-002T belongs to the genus

Brevundimonas

of the class

Alphaproteobacteria

. Levels of similarity between the 16S rRNA gene sequence of strain TAR-002T and those of the type strains of species of the genus

Brevundimonas

were 93.5–98.9 %; the most closely related species was

Brevundimonas basaltis

. In DNA–DNA hybridization assays between strain TAR-002T and its phylogenetic neighbours,

Brevundimonas lenta

DS-18T,

B. basaltis

J22T,

Brevundimonas subvibrioides

ATCC 15264T and

Brevundimonas alba

DSM 4736T, mean hybridization levels were 6.4–27.7 %. The G+C content of strain TAR-002T was 70.3 mol%. Q-10 was the major respiratory isoprenoid quinone. The major fatty acids were C18 : 1ω7c and C16 : 0, and the presence of 1,2-di-O-acyl-3-O-[d-glucopyranosyl-(1→4)-α-d-glucopyranuronosyl]glycerol (DGL) indicates the affiliation of strain TAR-002T with the genus

Brevundimonas

. On the basis of biological characteristics and 16S rRNA gene sequence comparisons, strain TAR-002T is considered to represent a novel species of the genus

Brevundimonas

, for which the name Brevundimonas denitrificans sp. nov. is proposed; the type strain is TAR-002T ( = NBRC 110107T = CECT 8537T).
Loktanella ponticola sp. nov., isolated from seawater
Authors: Jung Yong-Taek , Park Sooyeon , Park Ji-Min , Yoon Jung-Hoon
Published: August 2014

A Gram-reaction-negative, aerobic, non-flagellated and coccoid, ovoid or rod-shaped bacterial strain, designated W-SW2T, was isolated from seawater in the South Sea of South Korea. The novel strain grew optimally at pH 7.0–8.0, at 25 °C and in the presence of approximately 2 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that strain W-SW2Tfell within the clade comprising the type strains of species of the genusLoktanella, clustering and sharing the highest sequence similarity value (96.3 %) with the type strain ofLoktanella koreensis. The 16S rRNA gene sequence similarity values between strain W-SW2Tand the type strains of the other species of the genusLoktanellawere in the range 93.1–96.0 %. The DNA G+C content of strain W-SW2Twas 55.9 mol%. Strain W-SW2Tcontained Q-10 as the predominant ubiquinone and C18 : 1ω7cas the predominant fatty acid. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, one unidentified aminolipid and one unidentified lipid. Differential phenotypic properties, together with the phylogenetic distinctiveness, revealed that strain W-SW2Tis separated phylogenetically from other species of the genusLoktanella. On the basis of the data presented, strain W-SW2Tis considered to represent a novel species of the genusLoktanella, for which the nameLoktanella ponticolasp. nov. is proposed. The type strain is W-SW2T( = KCTC 42133T = NBRC 110409T).
Resistance behaviour of inducible clindamycin-resistant staphylococci from clinical samples and aquatic environments
Authors: Heß Stefanie , Gallert Claudia
Published: August 2014

In this study, the species diversity of staphylococci with inducible resistance to macrolides, lincosamides and streptogramin B (MLSB) isolated from clinical samples, sewage and river water was investigated. Inducible clindamycin resistance was tested using a D-test and macrodilution assays. Inducible cross-resistance (iMLSBphenotype) was examined by PCR ofermgene classesA,B,C,F,G,Q,Tand43. AlthoughermCwas the most frequently detected resistance gene in iMLSBphenotypes of environmental staphylococci (61.2 %), resistance genes encoding iMLSBwere more diverse than in staphylococci from hospital samples. In 22.4 % of iMLSBstaphylococci from aquatic environments, none of the eight testedermgenes was found. Those isolates anderm43-expressingStaphylococcus lentusdisplayed low erythromycin MICs (3–16 µg ml−1) compared withermC-positive environmental staphylococci (≥256 µg ml−1). In contrast to clinical isolates with clearly defined resistance behaviour, resistance patterns against MLSBand MICs for clindamycin of environmental isolates were more diverse. Although the abundance of iMLSBstaphylococci in the aquatic environment was lower than in staphylococci from hospital samples, the diversity of resistance genes encoding this phenotype seemed to be higher. Oleandomycin is the best marker to correlate iMLSBphenotype and the respectiveermgene. The phenotypical behaviour of environmental isolates may differ from the resistance pattern of clinical iMLSBstaphylococci expressingermAorermC, and this should be considered for successful treatment of infections.
Two C4-sterol methyl oxidases (Erg25) catalyse ergosterol intermediate demethylation and impact environmental stress adaptation in Aspergillus fumigatus
Authors: Blosser Sara J. , Merriman Brittney , Grahl Nora , Chung Dawoon , Cramer Robert A.
Published: August 2014

The human pathogenAspergillus fumigatusadapts to stress encountered in the mammalian host as part of its ability to cause disease. The transcription factor SrbA plays a significant role in this process by regulating genes involved in hypoxia and low-iron adaptation, antifungal drug responses and virulence. SrbA is a direct transcriptional regulator of genes encoding key enzymes in the ergosterol biosynthesis pathway, includingerg25Aanderg25B, and ΔsrbAaccumulates C4-methyl sterols, suggesting a loss of Erg25 activity [C4-sterol methyl oxidase (SMO)]. Characterization of the two genes encoding SMOs inAspergillus fumigatusrevealed that both serve as functional C4-demethylases, with Erg25A serving in a primary role, as Δerg25Aaccumulates more C4-methyl sterol intermediates than Δerg25B. Single deletion of these SMOs revealed alterations in canonical ergosterol biosynthesis, indicating that ergosterol may be produced in an alternative fashion in the absence of SMO activity. A Δerg25Astrain displayed moderate susceptibility to hypoxia and the endoplasmic reticulum stress-inducing agent DTT, but was not required for virulence in murine or insect models of invasive aspergillosis. Inducing expression oferg25Apartially restored the hypoxia growth defect of ΔsrbA. These findings implicatedAspergillus fumigatusSMOs in the maintenance of canonical ergosterol biosynthesis and indicated an overall involvement in the fungal stress response.
Growth of Primary and Lateral Roots of Vicia faba L. in the Solution of Calcium Sulfate
Authors: Pyshnov Michael
Published: August 2014

The presence of calcium sulfate in cultivating solution prevents bacterial contamination, browning/lignification and the death of the roots. There is no need for surface sterilization of seeds. No other ingredients, beside calcium sulfate, are needed for the healthy growth of the primary and lateral roots. There is no need to change the solution for several weeks when up to 60 lateral roots per seed can appear.

A modification of the two-stage growing technique where the seeds are first suspended in moist air over the cultivating solution to grow primary roots, and then, the primary roots are covered with the cultivating solution to grow lateral roots, was used.

The hypothesis is put forward that primary roots actually need water as a liquid to expel air, as the air is probably preventing the appearance of lateral roots.
Dynamics of Carbon-Concentrating Mechanism Induction and Protein Relocalization during the Dark-to-Light Transition in Synchronized Chlamydomonas reinhardtii
Authors: Mitchell Madeline C. , Meyer Moritz T. , Griffiths Howard
Published: August 2014

In the model green alga Chlamydomonas reinhardtii, a carbon-concentrating mechanism (CCM) is induced under low CO2 in the light and comprises active inorganic carbon transport components, carbonic anhydrases, and aggregation of Rubisco in the chloroplast pyrenoid. Previous studies have focused predominantly on asynchronous cultures of cells grown under low versus high CO2. Here, we have investigated the dynamics of CCM activation in synchronized cells grown in dark/light cycles compared with induction under low CO2. The specific focus was to undertake detailed time course experiments comparing physiology and gene expression during the dark-to-light transition. First, the CCM could be fully induced 1 h before dawn, as measured by the photosynthetic affinity for inorganic carbon. This occurred in advance of maximum gene transcription and protein accumulation and contrasted with the coordinated induction observed under low CO2. Between 2 and 1 h before dawn, the proportion of Rubisco and the thylakoid lumen carbonic anhydrase in the pyrenoid rose substantially, coincident with increased CCM activity. Thus, other mechanisms are likely to activate the CCM before dawn, independent of gene transcription of known CCM components. Furthermore, this study highlights the value of using synchronized cells during the dark-to-light transition as an alternative means of investigating CCM induction.
The ABC Transporter ABCG1 Is Required for Suberin Formation in Potato Tuber Periderm
Authors: Landgraf Ramona , Smolka Ulrike , Altmann Simone , Eschen-Lippold Lennart , Senning Melanie , Sonnewald Sophia , Weigel Benjamin , Frolova Nadezhda , Strehmel Nadine , Hause Gerd , Scheel Dierk , Böttcher Christoph , Rosahl Sabine
Published: August 2014

The lipid biopolymer suberin plays a major role as a barrier both at plant-environment interfaces and in internal tissues, restricting water and nutrient transport. In potato (Solanum tuberosum), tuber integrity is dependent on suberized periderm. Using microarray analyses, we identified ABCG1, encoding an ABC transporter, as a gene responsive to the pathogen-associated molecular pattern Pep-13. Further analyses revealed that ABCG1 is expressed in roots and tuber periderm, as well as in wounded leaves. Transgenic ABCG1-RNAi potato plants with downregulated expression of ABCG1 display major alterations in both root and tuber morphology, whereas the aerial part of the ABCG1-RNAi plants appear normal. The tuber periderm and root exodermis show reduced suberin staining and disorganized cell layers. Metabolite analyses revealed reduction of esterified suberin components and hyperaccumulation of putative suberin precursors in the tuber periderm of RNA interference plants, suggesting that ABCG1 is required for the export of suberin components.
A novel high-temperature furnace for combinedin situsynchrotron X-ray diffraction and infrared thermal imaging to investigate the effects of thermal gradients upon the structure of ceramic materials
Authors: Robinson James B. , Brown Leon D. , Jervis Rhodri , Taiwo Oluwadamilola O. , Millichamp Jason , Mason Thomas J. , Neville Tobias P. , Eastwood David S. , Reinhard Christina , Lee Peter D. , Brett Daniel J. L. , Shearing Paul R.
Published: August 2014

A new technique combiningin situX-ray diffraction using synchrotron radiation and infrared thermal imaging is reported. The technique enables the application, generation and measurement of significant thermal gradients, and furthermore allows the direct spatial correlation of thermal and crystallographic measurements. The design and implementation of a novel furnace enabling the simultaneous thermal and X-ray measurements is described. The technique is expected to have wide applicability in material science and engineering; here it has been applied to the study of solid oxide fuel cells at high temperature.
Political Performance: A Framework for Analysing Democratic Politics
Authors: Rai Shirin M.
Published: August 2014

This article develops a framework to examine the co-constitutive nature of performance and politics and to suggest that such a framework is critical to promoting an interdisciplinary approach to understanding our complex political world. It does this by disaggregating the component parts of political performance and suggesting how, once these are made visible, we are able to reflect upon more complex processes of its re-aggregation into our analysis of politics. The framework is constituted along two axes – one that maps individual performance, which is nevertheless socially embedded; and the other that charts the political effects of performance. The framework allows us to reflect upon social and political institutions, movements and events and analyse these through the prism of performance and politics. The empirical core of the article is the Indian parliament.
The Imperative of Non-Ideal Theory
Authors: Knight Jack
Published: August 2014

In this review piece I assess the theoretical approach employed by Elizabeth Anderson in her book The Imperative of Integration. Anderson advocates a non-ideal theoretical approach to questions of normative political theory. She uses non-ideal arguments to offer a compelling justification of racial integration as a social policy. I unpack her argument to identify some of the important strengths of non-ideal theory. In doing so, I argue that non-ideal approaches provide insights that are necessary for the development of persuasive answers to normative questions, but that are not achievable with ideal theoretical alternatives.
Acute Fatal Upper Airway Obstruction from an Occult Cavernous Hemangioma of the Larynx
Authors: Kiho Liina , Byard Roger W.
Published: August 2014

A 42‐year‐old previously well man collapsed while holding his throat. Resuscitation was unsuccessful, and at autopsy, the most significant findings were limited to the larynx, pharynx, and anterior mediastinum where there were multinodular dark blue tumors. Within the larynx, the lower border of the tumor was well demarcated, not extending beyond the vocal cords. A separate large polypoidal tumor mass was attached to the right aryepiglottic fold by a thin fibrous stalk. Histologic examination revealed numerous large, thin‐walled cavernous‐type vascular spaces typical of a multifocal cavernous hemangioma. Death was due to asphyxiation from obstruction of the upper airways by a cavernous hemangioma of the larynx. Adult laryngeal hemangiomas are rare and are usually supraglottic. This case demonstrates that pedunculated laryngeal cavernous hemangiomas may remain occult until the initiation of an obstructive episode with sudden collapse and death. In such instances, the diagnosis must rely upon an autopsy examination.
The Use of Decision Trees and Naïve Bayes Algorithms and Trace Element Patterns for Controlling the Authenticity of Free‐Range‐Pastured Hens’ Eggs
Authors: Barbosa Rommel Melgaço , Nacano Letícia Ramos , Freitas Rodolfo , Batista Bruno Lemos , Barbosa Fernando
Published: August 2014

This article aims to evaluate 2 machine learning algorithms, decision trees and naïve Bayes (NB), for egg classification (free‐range eggs compared with battery eggs). The database used for the study consisted of 15 chemical elements (As, Ba, Cd, Co, Cs, Cu, Fe, Mg, Mn, Mo, Pb, Se, Sr, V, and Zn) determined in 52 eggs samples (20 free‐range and 32 battery eggs) by inductively coupled plasma mass spectrometry. Our results demonstrated that decision trees and NB associated with the mineral contents of eggs provide a high level of accuracy (above 80% and 90%, respectively) for classification between free‐range and battery eggs and can be used as an alternative method for adulteration evaluation.