bluuebunny/crossref_metadata_2025 huggingface dataset:
Supersymmetric quantum mechanics: Engineered hierarchies of integrable potentials and related orthogonal polynomials
Authors: Balondo Iyela Daddy , Govaerts Jan , Hounkonnou M. Norbert
Published: September 2013

Within the context of supersymmetric quantum mechanics and its related hierarchies of integrable quantum Hamiltonians and potentials, a general programme is outlined and applied to its first two simplest illustrations. Going beyond the usual restriction of shape invariance for intertwined potentials, it is suggested to require a similar relation for Hamiltonians in the hierarchy separated by an arbitrary number of levels, N. By requiring further that these two Hamiltonians be in fact identical up to an overall shift in energy, a periodic structure is installed in the hierarchy which should allow for its resolution. Specific classes of orthogonal polynomials characteristic of such periodic hierarchies are thereby generated, while the methods of supersymmetric quantum mechanics then lead to generalised Rodrigues formulae and recursion relations for such polynomials. The approach also offers the practical prospect of quantum modelling through the engineering of quantum potentials from experimental energy spectra. In this paper, these ideas are presented and solved explicitly for the cases N = 1 and N = 2. The latter case is related to the generalised Laguerre polynomials, for which indeed new results are thereby obtained. In the context of dressing chains and deformed polynomial Heisenberg algebras, some partial results for N ⩾ 3 also exist in the literature, which should be relevant to a complete study of the N ⩾ 3 general periodic hierarchies.
Consistency problem of the solutions of the space fractional Schrödinger equation
Authors: Bayın Selçuk Ş.
Published: September 2013

Recently, consistency of the infinite square well solution of the space fractional Schrödinger equation has been the subject of some controversy. Hawkins and Schwarz [J. Math. Phys. 54, 014101 (2013)]10.1063/1.4772533 objected to the way certain integrals are evaluated to show the consistency of the infinite square well solutions of the space fractional Schrödinger equation [S. S. Bayin, J. Math. Phys. 53, 042105 (2012)10.1063/1.4705268; S. S. Bayin, J. Math. Phys. 53, 084101 (2012)]10.1063/1.4739758. Here, we show for general n that as far as the integral representation of the solution in the momentum space is concerned, there is no inconsistency. To pinpoint the source of a possible inconsistency, we also scrutinize the different representations of the Riesz derivative that plays a central role in this controversy and show that they all have the same Fourier transform, when evaluated with consistent assumptions.
Communication: Determining the lowest-energy isomer of Au8: 2D, or not 2D
Authors: Hansen Jared A. , Piecuch Piotr , Levine Benjamin G.
Published: September 2013

A parallel numerical derivative code, combined with parallel implementation of the coupled-cluster method with singles, doubles, and non-iterative triples (CCSD(T)), is used to optimize the geometries of the low-energy structures of the Au8 particle. The effects of geometry relaxation at the CCSD(T) level and the combined effects of the basis set and core-valence correlations are examined and the results are compared with the corresponding second-order Møller-Plesset perturbation theory calculations. The highest-level computations, in which the single-point CCSD(T) calculations employing the correlation-consistent basis set of the cc-pVTZ quality and the associated relativistic effective core potential (ECP), both optimized for gold, and correlating the 5d106s1 valence and 5s25p6 semi-core electrons, are combined with the geometrical information obtained with the corresponding CCSD(T)/cc-pVDZ/ECP approach, favor the planar configuration, with the next three non-planar structures separated by 4–6 kcal/mol. In agreement with the earlier work, smaller-basis set CCSD(T) computations provide unreliable results for the relative energetics, even when the geometries are optimized at the CCSD(T) level.
Quadrature phase interferometer for high resolution force spectroscopy
Authors: Paolino Pierdomenico , Aguilar Sandoval Felipe A. , Bellon Ludovic
Published: September 2013

In this article, we present a deflection measurement setup for Atomic Force Microscopy (AFM). It is based on a quadrature phase differential interferometer: we measure the optical path difference between a laser beam reflecting above the cantilever tip and a reference beam reflecting on the static base of the sensor. A design with very low environmental susceptibility and another allowing calibrated measurements on a wide spectral range are described. Both enable a very high resolution (down to \documentclass[12pt]{minimal}\begin{document}$2.5 \times 10^{-15}\,{\rm m}/\sqrt{\rm Hz}$\end{document}2.5×10−15m/ Hz ), illustrated by thermal noise measurements on AFM cantilevers. They present an excellent long-term stability and a constant sensitivity independent of the optical phase of the interferometer. A quick review shows that our precision is equaling or out-performing the best results reported in the literature, but for a much larger deflection range, up to a few μm.
Optical breakdown threshold in nanosecond high repetition second harmonic generation by periodically poled Mg-doped LiTaO3 crystal
Authors: Louchev Oleg A. , Hatano Hideki , Wada Satoshi , Kitamura Kenji
Published: September 2013

Our study shows that a local temperature increase of ≈1 K in the crystal lattice caused by second harmonic generation (SHG) and two-photon absorption of 532 nm radiation at the rear of periodically poled stoichiometric LiTaO3 crystal by changing spontaneous polarization induces a pyroelectric field ≈10 kV/cm, accelerating free electrons to an energy of ≈10 eV, followed by optical breakdown and crystal damage. Theoretical analysis leads to an explicit expression for the threshold laser fluence of optical breakdown giving ≈1.2 J/cm2 for 1064 nm input radiation in 6.8 kHz pulsed SHG operation, agreeing well with the experimentally found value ≈1.32 J/cm2.
One kilometer (1 km) electric solar wind sail tether produced automatically
Authors: Seppänen Henri , Rauhala Timo , Kiprich Sergiy , Ukkonen Jukka , Simonsson Martin , Kurppa Risto , Janhunen Pekka , Hæggström Edward
Published: September 2013

We produced a 1 km continuous piece of multifilament electric solar wind sail tether of μm-diameter aluminum wires using a custom made automatic tether factory. The tether comprising 90 704 bonds between 25 and 50 μm diameter wires is reeled onto a metal reel. The total mass of 1 km tether is 10 g. We reached a production rate of 70 m/24 h and a quality level of 1‰ loose bonds and 2‰ rebonded ones. We thus demonstrated that production of long electric solar wind sail tethers is possible and practical.
On the measurement of laser-induced plasma breakdown thresholds
Authors: Brieschenk Stefan , Kleine Harald , O'Byrne Sean
Published: September 2013

The breakdown threshold of a gas exposed to intense laser-radiation is a function of gas and laser properties. Breakdown thresholds reported in the literature often vary greatly and these differences can partially be traced back to the method that is typically used to determine breakdown thresholds. This paper discusses the traditional method used to determine breakdown thresholds and the potential errors that can arise using this approach, and presents an alternative method which can yield more accurate data especially when determining breakdown thresholds as functions of gas pressure.
Ultrabroadband generation of multiple concurrent nonlinear coherent interactions in random quadratic media
Authors: Mateos Luis , Molina Pablo , Galisteo-López Juan F. , López Cefe , Bausá Luisa E. , Ramírez Mariola O
Published: September 2013

Triply coincident nonlinear second harmonic interactions continuously tunable in an extremely large spectral range (800–1400 nm) are demonstrated in strontium barium niobate random quadratic crystal. The spectral dependence of the triple process is in agreement with a first order quasi-phase-matching collinear interaction. The analysis of the polarization states of the generated beams reveals mutually coherent interactions between different processes simultaneously contributing to the total intensity. The results constitute a necessary step in the implementation of ultra-broadband entangled photon pairs from randomly poled structures and are relevant to a wide range of applications, for which broadband polarization controlled light is required.
Can nitrogen-based cobalt pnictides exist?
Authors: O'Hara Andrew , Demkov Alexander A.
Published: September 2013

Using density functional theory in the local density approximation with a Hubbard correction U, we explore theoretically the possibility of synthesizing nitrogen-based 122 pnictides. By way of example, we consider SrCo2N2, isoelectronically analogues to BaFe2As2, the parent compound of the 122 FeAs superconductors. We analyze the chemical and lattice stability of SrCo2N2, investigate the nature of its bonding, and compare SrCo2N2 to BaFe2As2 and 122 rare-earth cobalt phosphides. Our results strongly suggest that it may indeed be possible to synthesize SrCo2N2 as it is dynamically stable with a ferromagnetic ground state exhibiting a magnetic moment 0.72 μB per cobalt.
Feasibility of an active-read approach for spin-torque switched magnetic tunnel junctions in a random access memory
Authors: Sun Jonathan Z. , DeBrosse John , Wang Pokang
Published: September 2013

The circuit element behavior during an active read-out approach is analyzed for the detection of the bit-state of a spin-transfer-torque (STT) switchable magnetic tunnel junction (MTJ) as a storage bit in a random access memory. Fundamentally, such read-out schemes detect the presence or absence of a hysteresis in the current-voltage characteristic of the MTJ depending on its magnetic configuration and the bias direction. A quantitative assessment is given in terms of the range of threshold distribution to be expected, and the read-out time one can achieve as it depends on various device parameters. The quantitative results given are based on an approximate macrospin model for the STT-switched MTJ.
The effect of laser wavelength on laser-induced carbon plasma
Authors: Moscicki T. , Hoffman J. , Szymanski Z.
Published: September 2013

The effect of laser wavelength on parameters of laser-ablated carbon plume is studied. A theoretical model is applied, which describes the target heating and formation of the plasma and its expansion, and calculations are made for the fundamental and third harmonic of a Nd:YAG laser. The calculated distributions of plasma temperature and electron density in the early phase of expansion show that plasma temperatures are higher in the case of 1064 nm but the electron densities are higher in the case of 355 nm, which is in agreement with experimental findings. It has been shown that while a higher plasma temperature in the case of 1064 nm is the result of stronger plasma absorption, the greater ablation rate in the case of 355 nm results in larger mass density of the ablated plume and hence, in higher electron densities. An additional consequence of a higher ablation rate is slower expansion and smaller dimensions of the plume.
Magnetization of bilayer graphene with interplay between monovacancy in each layer
Authors: Rostami M. , Faez R. , Rabiee Golgir H.
Published: September 2013

Effects of introducing two monovacancies in bilayer graphene are investigated by using spin-polarized density functional theory. Each layer of bilayer graphene has a monovacancy. Two different classifications are studied, namely, AA and AB. In AA category, vacancies in upper layer and lower layer are chosen from the same sublattices (A or B). However, in AB category, vacancies are selected from the different sublattices (A and B). Two different structures of every classification are examined in order to investigate the effects of two monovacancies on structural, electronic, and magnetic properties of bilayer graphene. Structural optimization reveals that introducing a monovacancy in every layer of bilayer graphene does not significantly change the C–C bonds length around the vacancy domain. It is also found that both AA and AB structures are metallic with the shift of the Fermi level downward. Importantly, AA structures result in magnetic moment of 0.33 μB, but AB ones remain nonmagnetic.
Large anisotropic Fe orbital moments in perpendicularly magnetized Co2FeAl Heusler alloy thin films revealed by angular-dependent x-ray magnetic circular dichroism
Authors: Okabayashi Jun , Sukegawa Hiroaki , Wen Zhenchao , Inomata Koichiro , Mitani Seiji
Published: September 2013

Perpendicular magnetic anisotropy (PMA) in Heusler alloy Co2FeAl thin films sharing an interface with a MgO layer is investigated by angular-dependent x-ray magnetic circular dichroism. Orbital and spin magnetic moments are deduced separately for Fe and Co 3d electrons. In addition, the PMA energies are estimated using the orbital magnetic moments parallel and perpendicular to the film surfaces. We found that PMA in Co2FeAl is determined mainly by the contribution of Fe atoms with large orbital magnetic moments, which are enhanced at the interface between Co2FeAl and MgO. Furthermore, element specific magnetization curves of Fe and Co are found to be similar, suggesting the existence of ferromagnetic coupling between Fe and Co PMA directions.
Enhancing high-temperature thermoelectric properties of PtAs2 by Rh doping
Authors: Kudo Kazutaka , Nakano Seiya , Mizukami Tasuku , Takabatake Toshiro , Nohara Minoru
Published: September 2013

The effects of Rh doping on the thermoelectric properties of Pt1−xRhxAs2 (x = 0, 0.005, and 0.01) with pyrite structure were studied by conducting measurements of electrical resistivity ρ, Seebeck coefficient S, and thermal conductivity κ. The sample with x = 0.005 exhibited large S and low ρ, resulting in a maximum power factor (S2/ρ) of 65 μW/cmK2 at 440 K. The peculiarly shaped “corrugated flat band” predicted for PtSb2 might explain the enhanced thermoelectric properties of doped PtAs2.
A non-iterative technique for determination of solar cell parameters from the light generated I-V characteristic
Authors: Kumar Gaurav , Panchal Ashish K.
Published: September 2013

Accurate information about electrical parameters of a photovoltaic (PV) cell is many times essential for evaluating the performance of the cell when delivering power at its full capacity. This paper presents a technique for determining the cell parameters from the light generated current–voltage (I-V) characteristic with a valid assumption for any kind of cells. The technique neither involves any initial approximations nor iteration processes. The technique is employed for various PV cell technologies such as silicon, copper indium gallium selenide, organic, dye sensitized solar cell, and organic tandem cells, previously available in the literatures. Obtained I-V characteristics for the cells using the present technique are in well agreement with those of reported in the literature. The technique is further extended for the analysis of a silicon cell and a silicon module tested in the laboratory and the results obtained are very close to those of the experimental data.
The role of ZrN capping layer deposited on ultra-thin high-k Zr-doped yttrium oxide for metal-gate metal–insulator–semiconductor applications
Authors: Juan Pi-Chun , Mong Fan-Chen , Huang Jen-Hung
Published: September 2013

Metal-gate MIS structures with and without ZrN capping layer on high-k Y2O3:Zr/Y2O3 stack were fabricated. The binding energies and depth profiles were investigated by x-ray photoelectron spectroscopy (XPS). The x-ray diffraction (XRD) patterns were compared. It is found that Ti out-diffusion into Zr-based high-k dielectric becomes lesser with the insertion of ZrN capping layer. The electrical properties of current-voltage (I-V) and capacitance-voltage (C-V) characteristics were measured in the postannealing temperature range of 550–850 °C. According to the defect reaction model, Zr cation vacancies are associated with the concentration of Ti ion by a transition from +3 to +2 states. The amount of Zr cation vacancies is quantified and equal to a half of Ti substitution amount at Zr site. The reduction in cation vacancies at high temperatures can well explain the decrease in ΔVFB for samples with ZrN layer. In contrast, an excess of Ti outdiffusion will produce the interstitial defects in high-k films without ZrN capping.
Three-dimensional evaluation of gettering ability of Σ3{111} grain boundaries in silicon by atom probe tomography combined with transmission electron microscopy
Authors: Ohno Yutaka , Inoue Kaihei , Tokumoto Yuki , Kutsukake Kentaro , Yonenaga Ichiro , Ebisawa Naoki , Takamizawa Hisashi , Shimizu Yasuo , Inoue Koji , Nagai Yasuyoshi , Yoshida Hideto , Takeda Seiji
Published: September 2013

Three-dimensional distribution of impurities (boron, phosphorus, oxygen, and copper) at Σ3{111} grain boundaries was determined in a Czochralski-grown silicon single crystal by laser-assisted atom probe tomography (APT) combined with transmission electron microscopy, with a detection limit as low as the order of 0.001 at. %. The location of a boundary was determined by APT even when the boundary was not contaminated. Unlike the boundaries in multicrystalline silicon grown by the casting method, the impurities did not segregate at the boundaries even when the impurity concentrations were high. The gettering ability of the boundaries was discussed.
Optical design of low-cost polarizer without chromatic fringe pattern
Authors: Kim Bong Choon , Jin Lim Young , Hee Lee Seung , Lee Gi-Dong
Published: September 2013

Recently, polyethylene terephthalate (PET) has been considered as a substitute material for a protection film in a polarizer in order to reduce the cost. However, PET film exhibits high retardation intrinsically due to the stretching process, which induces a chromatic fringe pattern so called a color mura in oblique viewing angle directions, associated with a strong wavelength dispersion. Based on simulation and experimental results, placing an optic axis of PET film in plane can suppress the color mura without the need to use any compensation films; the film thus exhibits high performance as well as low cost.
Origin of stress and enhanced carrier transport in solution-cast organic semiconductor films
Authors: Cour Ishviene , Chinta Priya V. , Schlepütz Christian M. , Yang Yongsoo , Clarke Roy , Pindak Ron , Headrick Randall L.
Published: September 2013

Molecular packing in laterally directed solution deposition is a strong function of variables such as printing speed, substrate temperature, and solution concentration. Knowledge of the ordering mechanisms impacts on the development of new processes and materials for improved electronic devices. Here, we present real-time synchrotron x-ray scattering results combined with optical video microscopy, revealing the stages of ordering during the deposition of organic thin films via hollow capillary writing. Limited long range ordering is observed during the initial crystallization, but it gradually develops over 3–4 s for a range of deposition conditions. Buckling of thin films is typically observed for deposition above room temperature. We infer that compressive stress originates from thermal transients related to solvent evaporation on timescales similar to the development of long range ordering. Under optimized conditions, elimination of cracks and other structural defects significantly improves the average charge carrier mobility in organic field-effect transistors.
Specific heat determination and simulation of metastable ternary Ni80Cu10Si10 alloy melt
Authors: Ma X. B. , Wang H. P. , Zhou K. , Chang J. , Hong Z. Y.
Published: September 2013

Specific heat of undercooled liquid alloys is a critical material property for studies in metastable thermodynamics and heat transfer. Here, the specific heat of Ni80Cu10Si10 alloy was experimentally determined by a levitation technique, and the results were compared with the molecular dynamics simulation data. The maximum experimental undercooling was achieved at 263 K, whereas the simulation showed an undercooling of 607 K. Both the measured and simulated results suggest that the specific heat remains almost constant at the metastable liquid state of Ni80Cu10Si10 alloy. As the undercooling is increased from 100 K to 263 K, the Gibbs free energy difference is raised by 274%.
Effects of dietary xylanase and liquid feeding on growth performance and nutrient digestibility of weaner pigs fed diets high in millrun (wheat by-product)
Authors: l'Anson Katie A. , Choct Mingan , Brooks Peter H.
Published: September 2013

The viability of including millrun (a byproduct of wheat milling) in diets for weaned pigs was assessed in two 26-day feeding experiments, the first using 48 and the second 128 individually housed, entire male pigs (Large White × Landrace) weaned at 28 days (average weight 7.4 kg). In Experiment 1, millrun included in iso-energy, iso-lysine diets at 0, 12.5, 25, 37.5, and 50% had no effect on performance or digestibility. Therefore, in Experiment 2, pigs received diets containing 50% millrun in a 2 × 4 factorial design. The two factors were: (1) feed form (dry or liquid) and (2) enzyme supplementation (0 or 300 μg/g of a xylanase primarily targeting soluble non-starch polysaccharide (sNSP), 400 μg/g of a xylanase targeting only insoluble NSP, or both xylanases. The inclusion of NSP-degrading enzymes had no significant effect on pig performance or diet digestibility. Feed conversion ratio (FCR) was improved by 0.10 ± 0.02 in liquid-fed pigs (P < 0.05). Apparent digestible energy and faecal gross energy (GE) digestibility were not affected by treatment, but ileal GE and crude protein (CP) digestibility were, respectively, 9.0 ± 3.4 and 2.5 ± 0.65 percentage units higher in pigs fed liquid diets (P < 0.05). Dietary treatment significantly affected the concentrations of sugar, starch, total NSP, and sNSP in digesta from different segments of the gut, without affecting pig performance. In conclusion, weaner pigs can be fed appropriately formulated diets containing 50% millrun without loss of performance. The FCR and CP digestibility were improved by liquid feeding, but not by the addition of NSP-degrading enzymes.
Interactions between waterlogging and ray blight in pyrethrum
Authors: Javid Muhammad , Zhang Pingjie , Taylor Paul W. J. , Pethybridge Sarah J. , Groom Tim , Nicolas Marc E.
Published: September 2013

The effects of waterlogging, alone and combined with ray blight disease (caused by Stagonosporopsis tanaceti), on pyrethrum (Tanacetum cinerariifolium) plant growth were quantified in glasshouse trials. Six pyrethrum cultivars were initially studied for their response to 6 days of waterlogging and their recovery from waterlogging during 26 days post-waterlogging. Waterlogging caused substantial root death and leaf wilting and accelerated senescence in all cultivars. Root growth was 80% more reduced than shoot growth. Cultivar ‘F’ showed significantly higher root porosity and growth following waterlogging than other cultivars. In contrast, cv. ‘C’ had the greatest growth reduction from waterlogging and poor root-system recovery after waterlogging. Plants of cvv. C and F inoculated with S. tanaceti and then waterlogged were more significantly affected than were those exposed to waterlogging only. For both cultivars, shoot growth under the combined treatment, relative to initial growth, recovered up to 25%, but root growth suffered irreversible damage. The combined treatment decreased the number of stems by 39% compared with waterlogging alone after the post-waterlogging period. In conclusion, pyrethrum cultivars showed differential reactions to waterlogging; but growth in all cultivars was seriously affected by a combination of waterlogging and infection by ray blight.
Short-term effects of fire on small rodents in the Brazilian Cerrado and their relation with feeding habits
Authors: Vieira Emerson M. , Briani Denis C.
Published: September 2013

We investigated the short-term (up to 60 days) fire effects on small rodents and their relation to feeding habitats in the fire-prone Cerrado of central Brazil, the most species-rich savanna in the world. We conducted prescribed-fire experiments with pre- and post-fire simultaneous sampling in burned and unburned areas to investigate the hypothesis that the effects of fire on the abundance of small rodents is related to changes in food availability and consequently the feeding habits of the animals. The findings revealed a higher availability of invertebrates in just-burned areas compared with plant resources. Stomach analyses indicated that invertebrate consumption increased after fire for the four most common rodents, but Calomys tener and especially Calomys expulsus, consumed more invertebrates in the burned areas than Necromys lasiurus or Cerradomys scotti. These Calomys rodents were also the post-fire dominant species. Thus, even within the group of rodents that are generalist feeders, distinctive short-term responses to fire were associated with changes in resource availability and with resultant differences in the abundance of plant matter and invertebrates in the rodent diets.
Letter counting
Authors: Ycart Bernard
Published: September 2013

Counting letters in written texts is a very ancient practice. It has accompanied the development of cryptology, quantitative linguistics, and statistics. In cryptology, counting frequencies of the different characters in an encrypted message is the basis of the so called frequency analysis method. In quantitative linguistics, the proportion of vowels to consonants in different languages was studied long before authorship attribution. In statistics, the alternation vowel-consonants was the only example that Markov ever gave of his theory of chained events. A short history of letter counting is presented. The three domains, cryptology, quantitative linguistics, and statistics, are then examined, focusing on the interactions with the other two fields through letter counting. As a conclusion, the eclecticism of the scholars of past centuries, their background in humanities, and their familiarity with cryptograms, are identified as contributing factors to the mutual enrichment process which is described here.
A Bayesian approach to finding groups in a food web
Authors: Solow Andrew R. , Solow Andrew R.
Published: September 2013

A food web describes the feeding links between species in a community. The species in many food webs are organized into groups of highly linked species that are weakly linked to species in other groups. A Bayesian approach to identifying such groups in an observed food web is described. This approach extends a previous non-Bayesian one that does not exploit information about the relatively high density of links within groups and relatively low density between groups. Under the new approach, this information is encoded through prior distributions for within- and between-group link densities. The approach is shown to work well on simulated food webs. Results are presented of the application of the method to the Coachella Valley desert food web.
Identification of human CCR8 as a CCL18 receptor
Authors: Islam Sabina A. , Ling Morris F. , Leung John , Shreffler Wayne G. , Luster Andrew D.
Published: September 2013

The CC chemokine ligand 18 (CCL18) is one of the most highly expressed chemokines in human chronic inflammatory diseases. An appreciation of the role of CCL18 in these diseases has been hampered by the lack of an identified chemokine receptor. We report that the human chemokine receptor CCR8 is a CCL18 receptor. CCL18 induced chemotaxis and calcium flux of human CCR8-transfected cells. CCL18 bound with high affinity to CCR8 and induced its internalization. Human CCL1, the known endogenous CCR8 ligand, and CCL18 competed for binding to CCR8-transfected cells. Further, CCL1 and CCL18 induced heterologous cross-desensitization of CCR8-transfected cells and human Th2 cells. CCL18 induced chemotaxis and calcium flux of human activated highly polarized Th2 cells through CCR8. Wild-type but not Ccr8-deficient activated mouse Th2 cells migrated in response to CCL18. CCL18 and CCR8 were coexpressed in esophageal biopsy tissue from individuals with active eosinophilic esophagitis (EoE) and were present at markedly higher levels compared with esophageal tissue isolated from EoE patients whose disease was in remission or in normal controls. Identifying CCR8 as a chemokine receptor for CCL18 will help clarify the biological role of this highly expressed chemokine in human disease.
Knowledge as a Mental Episode
Authors: Matilal Bimal Krishna
Published: September 2013

Perception yields knowledge. More generally, perception, in the sense of ‘sensing’, is regarded as an important source of knowledge. Or, to put it in the Indian terminology, it is a primary ‘means’ of knowing. One cannot get a clear idea of perception in the Indian context unless one is sure as to what counts as knowledge or a knowing event in traditional Indian philosophy. This chapter tries to introduce the notion of a knowing event. This leads to discussion of many issues related to the notion of a mental event, for a knowing event is treated here as a species of mental event. The discussion looks at doubting, mental acts, mental episodes, intentionality, psychologism, and logical theories.
Imagination, Perception, and Language
Authors: Matilal Bimal Krishna
Published: September 2013

The parable of the magician and the tiger's bone has been used in the Buddhist canons to show how proliferations of conceptual and linguistic snares capture man, who in fact is himself the creator of this labyrinth of concepts in the first place. Man objectifies the concepts only to be entangled by them. Language distorts reality by proliferating false concepts and images. This is a well-known pan-Buddhist theme, and it is often woven around such notions as prapānca, vikalpa, and kalpanā. The chapter first explains these notions, and leads to deeper problems of perception, language, and meaning. It considers perception, verbal proliferation, imagination, prelinguistic perception, immediate and mediate perception, construction, and conception-free awareness.
Universals
Authors: Matilal Bimal Krishna
Published: September 2013

Discussion about the problem of universals usually starts with Plato's theory of forms along with Aristotle's critique of forms and his own doctrine of universals. ln the Indian context the starting-point has always been the early Vaisesika-sūtra discussion of ‘existent-ness’ and ‘generic properties’. The second and third sections of this chapter look briefly at Bharṭrhari's psychological nominalism or holism as well as Diṅnāga's apoha nominalism. Diṅnāga agreed with Bharṭrhari thesis; however, the major disagreement with Bharṭrhari probably lies in Diṅnāga's view that the naked object can be grasped or is grasped by purely sensory awareness, and the pure percept is therefore ineffable and self-cognized. The fourth section discusses mentalism and realism. The last section deals with the ontology and semantics of the discussion on universals and particulars.
An Inverse Demand System for New England Groundfish: Welfare Analysis of the Transition to Catch Share Management
Authors: Lee Min-Yang A. , Thunberg Eric M.
Published: September 2013

The welfare effects of the 2010 transition from Days‐at‐Sea to catch share management in the Northeast U.S. groundfish fishery are examined by combining a model of groundfish demand with a simulation‐based model of supply. Counterfactual supply is constructed based on the Days‐at‐Sea system that was recalibrated to meet mandated conservation goals. Due to the decreases in catch that were required to meet those goals, the 2010 policy undoubtedly resulted in worse outcomes for both producers and consumers compared to 2009. However, the conservation‐equivalent Days‐at‐Sea system would have been far worse for both consumers and producers.
Topoisomerase IV is required for partitioning of circular chromosomes but not linear chromosomes in Streptomyces
Authors: Huang Tzu-Wen , Hsu Chin-Chen , Yang Han-Yu , Chen Carton W.
Published: September 2013

Filamentous bacteria of the genus Streptomyces possess linear chromosomes and linear plasmids. Theoretically, linear replicons may not need a decatenase for post-replicational separation of daughter molecules. Yet, Streptomyces contain parC and parE that encode the subunits for the decatenase topoisomerase IV. The linear replicons of Streptomyces adopt a circular configuration in vivo through telomere–telomere interaction, which would require decatenation, if the circular configuration persists through replication. We investigated whether topoisomerase IV is required for separation of the linear replicons in Streptomyces. Deletion of parE from the Streptomyces coelicolor chromosome was achieved, when parE was provided on a plasmid. Subsequently, the plasmid was eliminated at high temperature, and ΔparE mutants were obtained. These results indicated that topoisomerase IV was not essential for Streptomyces. Presumably, the telomere–telomere association may be resolved during or after replication to separate the daughter chromosomes. Nevertheless, the mutants exhibited retarded growth, defective sporulation and temperature sensitivity. In the mutants, circular plasmids could not replicate, and spontaneous circularization of the chromosome was not observed, indicating that topoisomerase IV was required for decatenation of circular replicons. Moreover, site-specific integration of a plasmid is impaired in the mutants, suggesting the formation of DNA knots during integration, which must be resolved by topoisomerase IV.
Structure of the human telomere in Na+ solution: an antiparallel (2+2) G-quadruplex scaffold reveals additional diversity
Authors: Lim Kah Wai , Ng Veronica Chinn Min , Martín-Pintado Nerea , Heddi Brahim , Phan Anh Tuân
Published: September 2013

Single-stranded DNA overhangs at the ends of human telomeric repeats are capable of adopting four-stranded G-quadruplex structures, which could serve as potential anticancer targets. Out of the five reported intramolecular human telomeric G-quadruplex structures, four were formed in the presence of K+ ions and only one in the presence of Na+ ions, leading often to a perception that this structural polymorphism occurs exclusively in the presence of K+ but not Na+. Here we present the structure of a new antiparallel (2+2) G-quadruplex formed by a derivative of a 27-nt human telomeric sequence in Na+ solution, which comprises a novel core arrangement distinct from the known topologies. This structure complements the previously elucidated basket-type human telomeric G-quadruplex to serve as reference structures in Na+-containing environment. These structures, together with the coexistence of other conformations in Na+ solution as observed by nuclear magnetic resonance spectroscopy, establish the polymorphic nature of human telomeric repeats beyond the influence of K+ ions.
Principles of molecular assemblies leading to molecular nanostructures
Authors: Mali Kunal S. , De Feyter Steven
Published: September 2013

Self-assembled physisorbed monolayers consist of regular two-dimensional arrays of molecules. Two-dimensional self-assembly of organic and metal–organic building blocks is a widely used strategy for nanoscale functionalization of surfaces. These supramolecular nanostructures are typically sustained by weak non-covalent forces such as van der Waals, electrostatic, metal–ligand, dipole–dipole and hydrogen bonding interactions. A wide variety of structurally very diverse monolayers have been fabricated under ambient conditions at the liquid–solid and air–solid interface or under ultra-high-vacuum (UHV) conditions at the UHV–solid interface. The outcome of the molecular self-assembly process depends on a variety of factors such as the nature of functional groups present on assembling molecules, the type of solvent, the temperature at which the molecules assemble and the concentration of the building blocks. The objective of this review is to provide a brief account of the progress in understanding various parameters affecting two-dimensional molecular self-assembly through illustration of some key examples from contemporary literature.
Cationic amphiphilic drugs self-assemble to the core–shell interface of PEGylated phospholipid micelles and stabilize micellar structure
Authors: Wang Jing , Xing Xueqing , Fang Xiaocui , Zhou Chang , Huang Feng , Wu Zhonghua , Lou Jizhong , Liang Wei
Published: September 2013

Since polymeric micelles are promising and have potential in drug delivery systems, people have become more interested in studying the compatibility of polymeric carriers and drugs, which might help them to simplify the preparation method and increase the micellar stability. In this article, we report that cationic amphiphilic drugs can be easily encapsulated into PEGylated phospholipid (PEG–PE) micelles by self-assembly method and that they show high encapsulation efficiency, controllable drug release and better micellar stability than empty micelles. The representative drugs are doxorubicin and vinorelbine. However, gemcitabine and topotecan are not suitable for PEG–PE micelles due to lack of positive charge or hydrophobicity. Using a series of experiments and molecular modelling, we figured out the assembly mechanism, structure and stability of drug-loaded micelles, and the location of drugs in micelles. Integrating the above information, we explain the effect of the predominant force between drugs and polymers on the assembly mechanism and drug release behaviour. Furthermore, we discuss the importance of pKaandto evaluate the compatibility of drugs with PEG–PE in self-assembly preparation method. In summary, this work provides a scientific understanding for the reasonable designing of PEG–PE micelle-based drug encapsulation and might enlighten the future study on drug–polymer compatibility for other polymeric micelles.
Fluorene-based macromolecular nanostructures and nanomaterials for organic (opto)electronics
Authors: Xie Ling-Hai , Yang Su-Hui , Lin Jin-Yi , Yi Ming-Dong , Huang Wei
Published: September 2013

Nanotechnology not only opens up the realm of nanoelectronics and nanophotonics, but also upgrades organic thin-film electronics and optoelectronics. In this review, we introduce polymer semiconductors and plastic electronics briefly, followed by various top-down and bottom-up nano approaches to organic electronics. Subsequently, we highlight the progress in polyfluorene-based nanoparticles and nanowires (nanofibres), their tunable optoelectronic properties as well as their applications in polymer light-emitting devices, solar cells, field-effect transistors, photodetectors, lasers, optical waveguides and others. Finally, an outlook is given with regard to four-element complex devices via organic nanotechnology and molecular manufacturing that will spread to areas such as organic mechatronics in the framework of robotic-directed science and technology.
Proposal to change the name

Rhodoligotrophos

Fukuda et al. 2012, 1947 to Rhodoligotrophus. Request for an Opinion
Authors: Oren Aharon , Garrity George M. , Schink Bernhard
Published: September 2013

In the opinion of the authors, the genus name

Rhodoligotrophos

was formed in violation of Principle 3 and Rule 10a of the International Code of Nomenclature of Prokaryotes which requires that genus names are to be treated as Latin substantives. We therefore propose renaming the genus

Rhodoligotrophos

as Rhodoligotrophus. A Request for an Opinion is submitted to the Judicial Commission of the International Committee on Systematics of Prokaryotes regarding this proposed name change.
Characterization of a cyclophosphamide-induced murine model of immunosuppression to study Acinetobacter baumannii pathogenesis
Authors: Manepalli Swetha , Gandhi Jay A. , Ekhar Vaibhav V. , Asplund Melissa B. , Coelho Carolina , Martinez Luis R.
Published: September 2013

Acinetobacter baumannii is a Gram-negative bacterium that opportunistically infects critically ill hospitalized patients with breaches in skin integrity and airway protection, leading to significant morbidity and mortality. Considering the paucity of well-established animal models of immunosuppression to study A. baumannii pathogenesis, we set out to characterize a murine model of immunosuppression using the alkylating agent cyclophosphamide (CYP). We hypothesized that CYP-induced immunosuppression would increase the susceptibility of C57BL/6 mice to developing A. baumannii-mediated pneumonia followed by systemic disease. We demonstrated that CYP intensified A. baumannii-mediated pulmonary disease, abrogated normal immune cell function and led to altered pro-inflammatory cytokine release. The development of an animal model that mimics A. baumannii infection onset in immunosuppressed individuals is crucial for generating novel approaches to patient care and improving public health strategies to decrease exposure to infection for individuals at risk.
Development and evaluation of a multiplex PCR for eight plasmid-mediated quinolone-resistance determinants
Authors: Ciesielczuk H. , Hornsey M. , Choi V. , Woodford N. , Wareham D. W.
Published: September 2013

The objective of this study was to develop and validate an expanded multiplex PCR assay for the simultaneous detection of eight plasmid-mediated quinolone-resistance determinants inEnterobacteriaceae. Primers were designed to amplify conserved fragments ofqnrABCDS,qepA,oqxABandaac(6′)-Ib-crgenes and were optimized in uniplex and multiplex PCR assays with control template DNA. The assay was used to determine the prevalence of plasmid-mediated quinolone resistance (PMQR) genes in 174 ciprofloxacin-resistant and 43 ciprofloxacin-susceptible extraintestinal pathogenicEscherichia coliisolates. Each resistance gene could be detected alone and in combination. PMQR determinants were detected in 65 ciprofloxacin-resistant isolates (37 %) and one ciprofloxacin-susceptible isolate (2 %). Prevalences of the identified determinants were:aac(6′)-Ib-cr, 34.5 %;qnrS, 1.1 %;qepA, 1.1 %; andoqxAB, 0.6 %. In conclusion, we developed an eight-target multiplex PCR for the accurate detection of PMQR genes and confirmed that PMQR prevalence remains low among humanEscherichia coliclinical isolates in the UK.
Vaccinia virus immune evasion: mechanisms, virulence and immunogenicity
Authors: Smith Geoffrey L. , Benfield Camilla T. O. , Maluquer de Motes Carlos , Mazzon Michela , Ember Stuart W. J. , Ferguson Brian J. , Sumner Rebecca P.
Published: September 2013

Virus infection of mammalian cells is sensed by pattern recognition receptors and leads to an innate immune response that restricts virus replication and induces adaptive immunity. In response, viruses have evolved many countermeasures that enable them to replicate and be transmitted to new hosts, despite the host innate immune response. Poxviruses, such as vaccinia virus (VACV), have large DNA genomes and encode many proteins that are dedicated to host immune evasion. Some of these proteins are secreted from the infected cell, where they bind and neutralize complement factors, interferons, cytokines and chemokines. Other VACV proteins function inside cells to inhibit apoptosis or signalling pathways that lead to the production of interferons and pro-inflammatory cytokines and chemokines. In this review, these VACV immunomodulatory proteins are described and the potential to create more immunogenic VACV strains by manipulation of the gene encoding these proteins is discussed.
Isolating Nuclei from Cultured Cells for Patch-Clamp Electrophysiology of Intracellular Ca2+ Channels
Authors: Mak Don-On Daniel , Vais Horia , Cheung King-Ho , Foskett J. Kevin
Published: September 2013

Nuclear patch-clamp experiments can be performed with intact nuclei or with nuclei from which the outer nuclear membrane has been removed. This protocol presents procedures for harvesting different types of cultured cells, isolating nuclei, and exposing the inner nuclear membrane by agitating in the presence of sodium citrate. Particulars about obtaining and maintaining the cells of interest in culture are not described here. However, care should be taken not to allow the cells to grow beyond a density of 2–3 × 106 cells/mL because this may decrease both the cell viability and the success rate of detecting active inositol 1,4,5-trisphosphate receptor (InsP3R) channels in nuclear patches.
Creating Transgenic shRNA Mice by Recombinase-Mediated Cassette Exchange
Authors: Premsrirut Prem K. , Dow Lukas E. , Park Youngkyu , Hannon Gregory J. , Lowe Scott W.
Published: September 2013

RNA interference (RNAi) enables sequence-specific, experimentally induced silencing of virtually any gene by tapping into innate regulatory mechanisms that are conserved among most eukaryotes. The principles that enable transgenic RNAi in cell lines can also be used to create transgenic animals, which express short-hairpin RNAs (shRNAs) in a regulated or tissue-specific fashion. However, RNAi in transgenic animals is somewhat more challenging than RNAi in cultured cells. The activities of promoters that are commonly used for shRNA expression in cell culture can vary enormously in different tissues, and founder lines also typically vary in transgene expression due to the effects of their single integration sites. There are many ways to produce mice carrying shRNA transgenes and the method described here uses recombinase-mediated cassette exchange (RMCE). RMCE permits insertion of the shRNA transgene into a well-characterized locus that gives reproducible and predictable expression in each founder and enhances the probability of potent expression in many cell types. This procedure is more involved and complex than simple pronuclear injection, but if even a few shRNA mice are envisioned, for example, to probe the functions of several genes, the effort of setting up the processes outlined below are well worthwhile. Note that when creating a transgenic mouse, one should take care to use the most potent shRNA possible. As a rule of thumb, the sequence chosen should provide >90% knockdown when introduced into cultured cells at single copy (e.g., on retroviral infection at a multiplicity of ≤0.3).
Immunohistochemical Assessment of Immune Cells in Mouse Tumor Tissue
Authors: Bayne Lauren J. , Vonderheide Robert H.
Published: September 2013

This protocol describes a procedure for the evaluation of immune cells at the histological level. This technique preserves tissue architecture, making use of tissues that have been frozen in optimal cutting temperature (OCT) medium immediately after dissection and then cut with a cryostat into thin (∼8 µm) sections. The tissue slices are transferred to microscope slides and, as described here, are fixed with either methanol or formaldehyde. The fixed tissue sections are then stained with antibodies directed against cell surface markers expressed by the immune cells of interest. The antibodies are detected with an avidin–biotin-based peroxidase system, and, after mounting, the sections can be stored and viewed for years.
A Myeloid-Derived Suppressor Cell–Mediated T-Cell Suppression Assay for Functional Evaluation of Immune Cells in Tumor-Bearing Mice
Authors: Bayne Lauren J. , Vonderheide Robert H.
Published: September 2013

This protocol describes a procedure to evaluate the ability of Gr-1+ CD11b+ myeloid-derived suppressor cells (MDSCs) isolated from the spleen or tumor of a tumor-bearing mouse to suppress antigen-specific T-cell proliferation. MDSCs are cultured with responder splenocytes from an OT-1 T-cell receptor transgenic mouse stimulated with cognate peptide (OVA-257 peptide) or with an irrelevant, control peptide. This protocol spans a 4-d period. The readout is T-cell proliferation by 3[H]-thymidine incorporation during an 18-h pulse between Days 3 and 4.