bluuebunny/crossref_metadata_2025 huggingface dataset:
Mechanisms of the electron paramagnetic resonance line broadening in La1−xCaxMnO3
Authors: Auslender M. , Rozenberg E. , Shames A. I. , Mukovskii Ya. M.
Published: March 2013

A complex theoretical approach, summarizing ions-ions, ions-carries, and carriers-lattice couplings, is proposed for modeling and analyzing the electron paramagnetic resonance line broadening in doped manganites. Fitting the above model to the experimental data supports the applicability of our approach. The results obtained on single crystals and ceramics of prototypical La1−xCaxMnO3 system in a wide interval of Ca-dopant concentration (0 ≤ x ≤ 0.7) evidence that depending on x (i.e., on magnetic ground state and carriers' content and mobility) the discussed effect is governed by different mechanisms—mainly ions-ions and/or carriers-lattice spin relaxation.
Electronic states, conical intersections, and spin-rovibronic spectroscopy of the nitrogen oxide sulfide radical
Authors: Yazidi Ounaies , Houria Adel Ben , Francisco Joseph S. , Hochlaf Majdi
Published: March 2013

Highly correlated ab initio methods are used to investigate the lowest electronic states of doublet and quartet spin multiplicities for SNO. One-dimensional cuts of the three-dimensional potential energy surfaces (3D-PESs) of these electronic states along the stretch and bend coordinate are calculated. Several avoided crossings and conical intersections are located for bent and linear configurations. The dynamics on the excited electronic states of SNO are very complex, and suggest that multi-step mechanisms should occur to populate the ground state via radiationless processes or lead to predissociation. In addition, our calculations show that the ground ($\tilde X$X̃2A′) and the first excited ($\tilde A$Ã2A″(Π)) states of this radical form a linear-bent Renner–Teller system. They correlate to the SNO(12Π) state at linearity. Systematic studies of both components are performed using standard coupled cluster approaches, explicitly correlated coupled cluster technique, and multi-configurational methods in connection with large basis sets. Core-valence and scalar relativistic effects are examined. For both electronic states, the 3D-PESs are mapped in internal coordinates at the RCCSD(T)-F12b/cc-pVTZ-F12 level. The analytical representations of these potential energy surfaces are incorporated later into perturbative and variational treatments of the nuclear motions. A set of spectroscopic parameters and spin-rovibronic levels calculated variationally are presented. Strong anharmonic resonances are found. These new results allow for the reassignment of earlier experimental IR bands of SNO trapped in cooled argon matrices.
An XPS study on the chemical bond structure at the interface between SiOxNy and N doped polyethylene terephthalate
Authors: Ding Wanyu , Li Li , Zhang Lina , Ju Dongying , Peng Shou , Chai Weiping
Published: March 2013

The super-thin silicon oxynitride (SiOxNy) films were deposited onto the N doped polyethylene terephthalate (PET) surface. Varying the N doping parameters, the different chemical bond structures were obtained at the interface between the SiOxNy film and the PET surface. X-ray photoelectron spectra results showed that at the initial stage of SiOxNy film growth, the C=N bonds could be broken and C–N–Si crosslink bonds could be formed at the interface of SiOxNy/PET, which C=N bonds could be formed onto the PET surface during the N doping process. At these positions, the SiOxNy film could be crosslinked well onto the PET surface. Meanwhile, the doped N could crosslink the [SiO4] and [SiN4] tetrahedrons, which could easily form the dense layer structure at the initial stage of SiOxNy film growth, instead of the ring and/or chain structures of [SiO4] tetrahedrons crosslinked by O. Finally, from the point of applying SiOxNy/PET complex as the substrate, the present work reveals a simple way to crosslink them, as well as the crosslink model and physicochemical mechanism happened at the interface of complex.
Laser direct writing of GaN-based light-emitting diodes—The suitable laser source for mesa definition
Authors: Moser Rüdiger , Goßler Christian , Kunzer Michael , Köhler Klaus , Pletschen Wilfried , Brunne Jens , Schwarz Ulrich T. , Wagner Joachim
Published: March 2013

The development of a process chain allowing for rapid prototyping of GaN-based light-emitting diodes (LEDs) is presented, which does not rely on photolithography. Structuring of the epitaxial layers is realized by direct-writing laser ablation, allowing a flexible chip layout that can be changed rapidly and at low cost. Besides contact metallization and trench formation, mesa definition is the most critical processing step. For mesa formation and to expose the n-GaN contact layer, the epitaxial grown p-GaN layer together with the active region has to be removed completely without forming cracks or crystal defects in the n-GaN layer or the mesa sidewalls, which would cause sidewall leakage currents. In developing an appropriate laser ablation process that meets these requirements, three different laser systems have been employed in a comparative study. These are a frequency-tripled picosecond (ps) Nd:YVO4 laser emitting at a wavelength of 355 nm and a pulse length of 10 ps and two 20 nanosecond (ns) pulse length laser systems, operating at a wavelength of 248 nm (Excimer laser) and 355 nm (frequency-tripled Nd:YVO4 laser), respectively. First, the laser sources are compared regarding the morphological properties of the resulting laser trenches. Due to band filling effects resulting in optical bleaching of the GaN material when irradiating with ps-laser pulses at 355 nm, the resulting ablation process suffers from cracking. Laser ablation using ns-pulses at both 355 nm and 248 nm leads to crack-free material removal up to a well-defined depth. To keep reverse-bias leakage currents at a level comparable to that of conventional dry-etched mesa-LEDs, subsequent wet etching is essential to remove residues in the mesa-trenches irrespective of the laser source used. Besides wet etching, an additional annealing step has to be applied to mesa-trenches fabricated using ns- and ps-laser pulses at a wavelength of 355 nm. Due to the larger penetration depth at 355 nm, defects causing an increased leakage current are generated in the quantum well region during laser irradiation, which manifest themselves by a spectrally broad defect luminescence. To separate and quantify the contributions from the mesa sidewall leakage and from the areal leakage through the p-n-junction, a series of LEDs have been fabricated and analyzed for which the mesa perimeter length was varied while keeping the mesa area constant. In this way, it is shown that laser ablation with ns-pulses at 248 nm results in the lowest sidewall leakage current as well as forward bias voltage-current and output power-current characteristics very similar to those of conventionally dry etched reference LEDs.
Nano-structuring in SiGe by oxidation induced anisotropic Ge self-organization
Authors: Long Ethan , Galeckas Augustinas , Yu Kuznetsov Andrej , Ronda Antoine , Favre Luc , Berbezier Isabelle , Radamson Henry H.
Published: March 2013

The present study examines the kinetics of dry thermal oxidation of (111), (110), and (100) silicon-germanium (SiGe) thin epitaxial films and the redistribution of Ge near the oxidation interface with the aim of facilitating construction of single and multi-layered nano-structures. By employing a series of multiple and single step oxidations, it is shown that the paramount parameter controlling the Ge content at the oxidation interface is the oxidation temperature. The oxidation temperature may be set such that the Ge content at the oxidation interface is increased, kept static, or decreased. The Ge content at the oxidation interface is modeled by considering the balance between Si diffusion in SiGe and the flux of Si into the oxide by formation of SiO2. The diffusivity of Si in SiGe under oxidation is determined for the three principal crystal orientations by combining the proposed empirical model with data from X-ray diffraction and variable angle spectroscopic ellipsometry. The orientation dependence of the oxidation rate of SiGe was found to follow the order: (111)>(110)>(100). The role of crystal orientation, Ge content, and other factors in the oxidation kinetics of SiGe versus Si are analyzed and discussed in terms of relative oxidation rates.
On the similarity of equilibrium and critical clusters in atomic vapors
Authors: Napari Ismo , Vehkamäki Hanna
Published: March 2013

In a previous paper [I. Napari, J. Julin, and H. Vehkamäki, J. Chem. Phys. 131, 244511 (2009)10.1063/1.3279127] we compared sizes of critical and equilibrium clusters in Lennard-Jones vapors using various geometrical clusters definitions. In particular, we found that the critical and equilibrium clusters were of the same size if each constituent atom in the cluster was required to have at least five neighboring atoms (ten Wolde-Frenkel cluster) but the critical clusters were much larger if only one neighboring atom was sufficient to fulfill the cluster definition (Stillinger cluster). The conclusion was that the critical clusters at high vapor densities have more ramified structure than the corresponding equilibrium clusters. In this study we have performed new molecular dynamics simulations to enlighten this matter. It is found that the surprising conclusion of the earlier work can be traced to the mean first passage time method which was used to obtain critical cluster sizes from simulations. When a certain sized Stillinger cluster first appears in the simulation, the cluster tends to have a more ramified structure than Stillinger clusters of that size observed later in the simulation. However, for the latter clusters the ratio of Stillinger and ten Wolde-Frenkel sizes in the vapor is the same as in the equilibrium simulations, implying similar structure of critical and equilibrium clusters.
A generation/recombination model assisted with two trap centers in wide band-gap semiconductors
Authors: Yamaguchi Ken , Kuwabara Takuhito , Uda Tsuyoshi
Published: March 2013

A generation/recombination (GR) model assisted with two trap centers has been proposed for studying reverse current on pn junctions in wide band-gap semiconductors. A level (Et1) has been assumed to be located near the bottom of the conduction band and the other (Et2) to be near the top of the valence band. The GR model has been developed by assuming (1) a high-electric field; F, (2) a short distance; d, between trap centers, (3) reduction in an energy-difference; Δeff = |Et1 – Et2| – eFd, and (4) hopping or tunneling conductions between trap centers with the same energy-level (Δeff ≈ 0). The GR rate has been modeled by trap levels, capture cross-sections, trap densities, and transition rate between trap centers. The GR rate, about 1010 greater than that estimated from the single-level model, has been predicted on pn junctions in a material with band-gap of 3.1 eV. Device simulations using the proposed GR model have been demonstrated for SiC diodes with and without a guard ring. A reasonable range for reverse current at room temperature has been simulated and stable convergence has been obtained in a numerical scheme for analyzing diodes with an electrically floating region.
Characterization of as-synthesized FeCo magnetic nanoparticles by coprecipitation method
Authors: Kim Jinu , Kim Jinbae , Kim Jongryoul , Hyeon Kim Ki
Published: March 2013

FeCo nanoparticles were synthesized by a coprecipitation method without any post treatments. The structure, morphology, and magnetic properties of the FeCo nanoparticles formed at different sodium borohydride reaction times (5, 10, 20, and 30 min) were examined. X-ray diffraction revealed the representative α-FeCo peaks in all samples. The mean crystalline sizes slightly decreased from 31 nm to 21 nm with increasing reducing agent reaction time. A maximum saturation magnetization of 204 emu/g at 300 K was obtained in the sample with a reaction time of 5 min.
Reconfigurable microfluidics combined with antibody microarrays for enhanced detection of T-cell secreted cytokines
Authors: Chen Arnold , Vu Tam , Stybayeva Gulnaz , Pan Tingrui , Revzin Alexander
Published: March 2013

Cytokines are small proteins secreted by leukocytes in blood in response to infections, thus offering valuable diagnostic information. Given that the same cytokines may be produced by different leukocyte subsets in blood, it is beneficial to connect production of cytokines to specific cell types. In this paper, we describe integration of antibody (Ab) microarrays into a microfluidic device to enable enhanced cytokine detection. The Ab arrays contain spots specific to cell-surface antigens as well as anti-cytokine detection spots. Infusion of blood into a microfluidic device results in the capture of specific leukocytes (CD4 T-cells) and is followed by detection of secreted cytokines on the neighboring Ab spots using sandwich immunoassay. The enhancement of cytokine signal comes from leveraging the concept of reconfigurable microfluidics. A three layer polydimethylsiloxane microfluidic device is fabricated so as to contain six microchambers (1 mm × 1 mm × 30 μm) in the ceiling of the device. Once the T-cell capture is complete, the device is reconfigured by withdrawing liquid from the channel, causing the chambers to collapse onto Ab arrays and enclose cell/anti-cytokine spots within a 30 nl volume. In a set of proof-of-concept experiments, we demonstrate that ∼90% pure CD4 T-cells can be captured inside the device and that signals for three important T-cell secreted cytokines, tissue necrosis factor-alpha, interferon-gamma, and interleukin-2, may be enhanced by 2 to 3 folds through the use of reconfigurable microfluidics.
Communication: An efficient analytic gradient theory for approximate spin projection methods
Authors: Hratchian Hrant P.
Published: March 2013

Spin polarized and broken symmetry density functional theory are popular approaches for treating the electronic structure of open shell systems. However, spin contamination can significantly affect the quality of predicted geometries and properties. One scheme for addressing this concern in studies involving broken–symmetry states is the approximate projection method developed by Yamaguchi and co–workers. Critical to the exploration of potential energy surfaces and the study of properties using this method will be an efficient analytic gradient theory. This communication introduces such a theory formulated, for the first time, within the framework of general post–self consistent field (SCF) derivative theory. Importantly, the approach taken here avoids the need to explicitly solve for molecular orbital derivatives of each nuclear displacement perturbation, as has been used in a recent implementation. Instead, the well–known z–vector scheme is employed and only one SCF response equation is required.
Auger recombination as the dominant recombination process in indium nitride at low temperatures during steady-state photoluminescence
Authors: Seetoh I. P. , Soh C. B. , Fitzgerald E. A. , Chua S. J.
Published: March 2013

Auger recombination in InN films grown by metal-organic chemical vapor deposition was studied by steady-state photoluminescence at different laser excitation powers and sample temperatures. It was dominant over radiative recombination and Shockley-Read-Hall recombination at low temperatures, contributing to the sub-linear relationship between the integrated photoluminescence intensity and laser excitation power. Auger recombination rates increased gradually with temperature with an activation energy of 10–17 meV, in good agreement with values from transient photoluminescence reported in literature. As the Auger recombination rates were independent of material quality, they may form an upper limit to the luminous efficiency of InN.
The success of GPS collar deployments on mammals in Australia
Authors: Matthews Alison , Ruykys Laura , Ellis Bill , FitzGibbon Sean , Lunney Daniel , Crowther Mathew S. , Glen Alistair S. , Purcell Brad , Moseby Katherine , Stott Jenny , Fletcher Don , Wimpenny Claire , Allen Benjamin L. , Van Bommel Linda , Roberts Michael , Davies Nicole , Green Ken , Newsome Thomas , Ballard Guy , Fleming Peter , Dickman Christopher R. , Eberhart Achim , Troy Shannon , McMahon Clive , Wiggins Natasha
Published: March 2013

Global Positioning System (GPS) wildlife telemetry collars are being used increasingly to understand the movement patterns of wild mammals. However, there are few published studies on which to gauge their general utility and success. This paper highlights issues faced by some of the first researchers to use GPS technology for terrestrial mammal tracking in Australia. Our collated data cover 24 studies where GPS collars were used in 280 deployments on 13 species, including dingoes or other wild dogs (Canis lupus dingo and hybrids), cats (Felis catus), foxes (Vulpes vulpes), kangaroos (Macropus giganteus), koalas (Phascolarctos cinereus), livestock guardian dogs (C. l. familiaris), pademelons (Thylogale billardierii), possums (Trichosurus cunninghami), quolls (Dasyurus geoffroii and D. maculatus), wallabies (Macropus rufogriseus and Petrogale lateralis), and wombats (Vombatus ursinus). Common problems encountered were associated with collar design, the GPS, VHF and timed-release components, and unforseen costs in retrieving and refurbishing collars. We discuss the implications of collar failures for research programs and animal welfare, and suggest how these could be avoided or improved. Our intention is to provide constructive advice so that researchers and manufacturers can make informed decisions about using this technology, and maximise the many benefits of GPS while reducing the risks.
Koala habitat use and population density: using field data to test the assumptions of ecological models
Authors: Ellis William , FitzGibbon Sean , Melzer Alistair , Wilson Robbie , Johnston Steve , Bercovitch Fred , Dique David , Carrick Frank
Published: March 2013

In principle, conservation planning relies on long-term data; in reality, conservation decisions are apt to be based upon limited data and short-range goals. For the koala (Phascolarctos cinereus), frequently reliance is made on the assumption that indirect signs can be used to indicate behavioural preferences, such as diet choice. We examined the relationship between the use of trees by koalas and the presence of scats beneath those trees. Tree use was associated with scat presence on 49% of occasions when koalas were radio-tracked in both central Queensland (n = 10 koalas) and south-east Queensland (n = 5 koalas), increasing to 77% of occasions when trees were rechecked the following day. Koala densities were correlated with scat abundance at sites with koala density between ~0.2 and 0.6 koalas per hectare. Our results confirm that scat searches are imprecise indicators of tree use by koalas, but demonstrate that these searches can be used, with caveats, to estimate koala population densities. We discuss how errors in estimating or applying predictive model parameters can bias estimates of occupancy and show how a failure to validate adequately the assumptions used in modelling and mapping can undermine the power of the products to direct rational conservation and management efforts.
Gout-causing Q141K mutation in ABCG2 leads to instability of the nucleotide-binding domain and can be corrected with small molecules
Authors: Woodward Owen M. , Tukaye Deepali N. , Cui Jinming , Greenwell Patrick , Constantoulakis Leeza M. , Parker Benjamin S. , Rao Anjana , Köttgen Michael , Maloney Peter C. , Guggino William B.
Published: March 2013

The multidrug ATP-binding cassette, subfamily G, 2 (ABCG2) transporter was recently identified as an important human urate transporter, and a common mutation, a Gln to Lys substitution at position 141 (Q141K), was shown to cause hyperuricemia and gout. The nature of the Q141K defect, however, remains undefined. Here we explore the Q141K ABCG2 mutation using a comparative approach, contrasting it with another disease-causing mutation in an ABC transporter, the deletion of Phe-508 (ΔF508) in the cystic fibrosis transmembrane conductance regulator (CFTR). We found, much like in ΔF508 CFTR, that the Q141K mutation leads to instability in the nucleotide-binding domain (NBD), a defect that translates to significantly decreased protein expression. However, unlike the CFTR mutant, the Q141K mutation does not interfere with the nucleotide-binding domain/intracellular loop interactions. This investigation has also led to the identification of critical residues involved in the protein–protein interactions necessary for the dimerization of ABCG2: Lys-473 (K473) and Phe-142 (F142). Finally, we have demonstrated the utility of using small molecules to correct the Q141K defect in expression and function as a possible therapeutic approach for hyperuricemia and gout.
Design and pharmacology of a highly specific dual FMS and KIT kinase inhibitor
Authors: Zhang Chao , Ibrahim Prabha N. , Zhang Jiazhong , Burton Elizabeth A. , Habets Gaston , Zhang Ying , Powell Ben , West Brian L. , Matusow Bernice , Tsang Garson , Shellooe Rafe , Carias Heidi , Nguyen Hoa , Marimuthu Adhirai , Zhang Kam Y. J. , Oh Angela , Bremer Ryan , Hurt Clarence R. , Artis Dean R. , Wu Guoxian , Nespi Marika , Spevak Wayne , Lin Paul , Nolop Keith , Hirth Peter , Tesch Greg H. , Bollag Gideon
Published: March 2013

Inflammation and cancer, two therapeutic areas historically addressed by separate drug discovery efforts, are now coupled in treatment approaches by a growing understanding of the dynamic molecular dialogues between immune and cancer cells. Agents that target specific compartments of the immune system, therefore, not only bring new disease modifying modalities to inflammatory diseases, but also offer a new avenue to cancer therapy by disrupting immune components of the microenvironment that foster tumor growth, progression, immune evasion, and treatment resistance. McDonough feline sarcoma viral (v-fms) oncogene homolog (FMS) and v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog (KIT) are two hematopoietic cell surface receptors that regulate the development and function of macrophages and mast cells, respectively. We disclose a highly specific dual FMS and KIT kinase inhibitor developed from a multifaceted chemical scaffold. As expected, this inhibitor blocks the activation of macrophages, osteoclasts, and mast cells controlled by these two receptors. More importantly, the dual FMS and KIT inhibition profile has translated into a combination of benefits in preclinical disease models of inflammation and cancer.
Antibody deficiency associated with an inherited autosomal dominant mutation in TWEAK
Authors: Wang Hong-Ying , Ma Chi A. , Zhao Yongge , Fan Xiying , Zhou Qing , Edmonds Pamela , Uzel Gulbu , Oliveira Joao Bosco , Orange Jordan , Jain Ashish
Published: March 2013

Mutations in the TNF family of proteins have been associated with inherited forms of immune deficiency. Using an array-based sequencing assay, we identified an autosomal-dominant deficiency in TNF-like weak inducer of apoptosis (TWEAK; TNFSF12) in a kindred with recurrent infection and impaired antibody responses to protein and polysaccharide vaccines. This mutation occurs in the sixth exon of
TWEAK
and results in the amino acid substitution R145C within the conserved TNF-homology domain of the full-length protein. TWEAK mutant protein formed high molecular weight aggregates under nonreducing conditions, suggesting an increased propensity for intermolecular interactions. As a result, mutant TWEAK associated with B-cell–activating factor (BAFF) protein and down-regulated the BAFF-mediated activation of the noncanonical NF-κB pathway through inhibition of p100 processing to p52, resulting in inhibition of BAFF-dependent B-cell survival and proliferation. As BAFF mediates T-cell–independent isotype switching and B-cell survival, our data implicate
TWEAK
as a disease-susceptibility gene for a humoral immunodeficiency.
Unique mechanistic insights into the beneficial effects of soluble epoxide hydrolase inhibitors in the prevention of cardiac fibrosis
Authors: Sirish Padmini , Li Ning , Liu Jun-Yan , Lee Kin Sing Stephen , Hwang Sung Hee , Qiu Hong , Zhao Cuifen , Ma Siu Mei , López Javier E. , Hammock Bruce D. , Chiamvimonvat Nipavan
Published: March 2013

Tissue fibrosis represents one of the largest groups of diseases for which there are very few effective therapies. In the heart, myocardial infarction (MI) resulting in the loss of cardiac myocytes can culminate in adverse cardiac remodeling leading to eventual heart failure. Adverse cardiac remodeling includes myocyte hypertrophy, fibrosis, and electrical remodeling. We have previously demonstrated the beneficial effects of several potent soluble epoxide hydrolase inhibitors (sEHIs) in different models of cardiac hypertrophy and failure. Here, we directly determine the molecular mechanisms underlying the beneficial effects of sEHIs in cardiac remodeling post-MI. Treatment with a potent sEHI, 1-trifluoromethoxyphenyl-3-(1-propionylpiperidine-4-yl)urea (TPPU), which was started 1 wk post-MI in a murine model, results in a significant improvement in cardiac function. Importantly, treatment with TPPU results in a decrease in cardiac fibrosis as quantified using histological and immunostaining techniques. Moreover, single-cell–based assays demonstrate that treatment with TPPU results in a significant decrease not only in the percentages but also the proliferative capacity of different populations of cardiac fibroblasts as well as a reduction in the migration of fibroblasts into the heart from the bone marrow. Our study provides evidence for a possible unique therapeutic strategy to reduce cardiac fibrosis and improve cardiac function post-MI.
Role for lysosomal phospholipase A2 in iNKT cell-mediated CD1d recognition
Authors: Paduraru Crina , Bezbradica Jelena S. , Kunte Amit , Kelly Robert , Shayman James A. , Veerapen Natacha , Cox Liam R. , Besra Gurdyal S. , Cresswell Peter
Published: March 2013

Invariant natural killer T (iNKT) cells recognize self lipid antigens presented by CD1d molecules. The nature of the self-antigens involved in the development and maturation of iNKT cells is poorly defined. Lysophospholipids are self-antigens presented by CD1d that are generated through the action of phospholipases A1 and A2. Lysosomal phospholipase A2 (LPLA2, group XV phospholipase A2) resides in the endocytic system, the main site where CD1d antigen acquisition occurs, suggesting that it could be particularly important in CD1d function. We find thatLpla2−/−mice show a decrease in iNKT cell numbers that is neither the result of a general effect on the development of lymphocyte populations nor of effects on CD1d expression. However, endogenous lipid antigen presentation by CD1d is reduced in the absence of LPLA2. Our data suggest that LPLA2 plays a role in the generation of CD1d complexes with thymic lipids required for the normal selection and maturation of iNKT cells.
Fray Felipe Arroyo de la Cuesta’s Work on California’s Native Languages
Authors: Fountain Catherine
Published: March 2013

This article describes the linguistic work of Felipe Arroyo de la Cuesta (1780–1840), a Franciscan missionary from Spain who lived and worked in the missions of Alta California for some 32 years. He was the most prolific chronicler of the indigenous languages of Alta California during the mission period, writing a vocabulary and grammar of the Costanoan/Ohlone language Mutsun, taking notes on a Yokuts language he called Nopthrinthres, and compiling shorter word lists and religious texts in numerous other languages. The present work seeks to bring together and analyze what information is available about Arroyo de la Cuesta’s life and writings and place these within the broader field of missionary linguistics.
Vygotsky, Cognitive Development and Language
Authors: Christy T. Craig
Published: March 2013

Lev Vygotsky’s (1896–1934) views of the genesis of language and its relation to thought, illustrated here by his account of the origin of the pointing gesture, can be seen as anticipating current research in socially constituted cognition, pragmatics, developmental psychology and grammaticalization, in all of which the importance of contextual and pragmatic factors looms large. His conceptualization of the evolution of communication from action to semiosis has bearing on, and is illuminated by, recent developments in neurobiology, developmental psychology, primatology, and grammaticalization theory. Specifically, recently discovered mirror neuron systems may offer a neurophysiological platform for the evolution of language from gesture and imitation, for the transition from action to sign, from referential to relational meaning, an evolution in which the establishment of joint attention is pivotal. With his emphasis on the dynamic, socially constructed nature of signs, Vygotsky shares Humboldt’s view of language asenergeia, as a system in a perpetual state of emergence, a view consistent with Condillac’s ‘language of action’, in which spontaneous vocalizations and gestures give rise to sign functions. Research of the grammaticalization pathways associated with demonstratives and modal particles also offers new perspectives on the process and hypothesized unidirectionality of grammaticalization, including the plausible claim that demonstratives represent a second and separate source of candidates for grammaticalization. Integrating grammaticalization research with findings from relevant social and natural sciences holds out the prospect of underwriting significant advances in understanding the origin of language and the emergence of grammar.
Counterfactual conditionals in focus
Authors: Hobæk Haff Marianne
Published: March 2013

This article is a comparative exploration of counterfactual conditionals introduced by the conjunction ‘if’ in French and Norwegian, a topic which has not been studied before. My analyses are based on examples from monolingual and multilingual corpora, complemented by two questionnaires, in French and Norwegian, respectively. Both languages have two main patterns corresponding to (A) [‘if’ + imperfect + conditional simple] and (B) [‘if’ + pluperfect + conditional perfect], but their use is somewhat different in the two languages. Regarding counterfactual present, both have two patterns at their disposal. In French, however, pattern (A) seems preferred whereas Norwegian displays a clear preference for pattern (B). When confronted with examples of counterfactual future, both groups of informants initially hesitated, but ultimately considered pattern (B) as an acceptable solution in many cases. Not only the tenses but also the type of verb, eventual temporal adjuncts and the context are important for the interpretations. Neither French nor Norwegian grammars present the issue satisfactorily and therefore need to be revised.
The logic of failures of the cinematic imagination
Authors: Fulda Joseph S.
Published: March 2013

This piece is intended to explicate – by providing a precising definition of – the common cinematic figure which I term “the failure of the cinematic imagination,” while presenting a logical puzzle and its solution within a simple Gricean framework.
Effects of Soil Resources on Species Composition, Plant Diversity, and Plant Biomass in an Alpine Meadow, Qinghai-Tibetan Plateau
Authors: Wang Changting , Long Ruijun , Wang Qilan , Jing Zengchun , Du Yangong , Cao Guangmin
Published: March 2013

We investigated the effects of soil resources on species composition, plant diversity, and plant biomass in four alpine Kobresia meadow communities. Species diversity was lower in the Kobresia tibetica swamp meadow community than in the other three communities, but this community was characterized by the highest aboveground and belowground biomass and soil nutrients. Aboveground biomass was positively correlated with soil organic matter and soil total nitrogen in all four alpine meadow communities. The proportion of light fraction organic carbon (LFOC) was positively correlated with soil total organic carbon in all types of grassland. In alpine meadows, belowground biomass mostly occurred at 0-10 cm soil, as did soil nutrients. Community differences in plant species composition were reflected in biomass distribution. The highest total biomass (13,759 ± 497 g/m2) including above- and belowground biomass appeared in the sedge-dominated Kobresia tibetica swamp meadow community. Intermediate biomass (3,235 ± 142 g/m2, 2,645 ± 16 g/m2) was found in the Kobresia pygmaea swamp meadow and Potentilla fruticosa shrubs meadow community, dominated by forbs, sedges, and woody plants. The lowest biomass (2,433 ± 162 g/m2) was observed in the Kobresia humilis meadow, mainly dominated by forbs and grasses. The results indicated that fertility of the vegetation caused a decrease in plant species, increase in plant biomass, and also changes in species composition. Species traits (such as ability to respond to higher nutrient levels) as well as competitive interaction may determine ecosystem function (e.g., productivity). Plants with higher competitive ability would then have access to a greater proportion of available resources, leading to increased total resource uptake by roots, lower nutrient losses from the ecosystems, and increased aboveground and belowground biomass. The distribution of aboveground and belowground biomass is largely influenced by the plant species and growth forms within spatial gradients in soil moisture and edaphic conditions.
Evolution of Tre-2/Bub2/Cdc16 (TBC) Rab GTPase-activating proteins
Authors: Gabernet-Castello Carme , O'Reilly Amanda J. , Dacks Joel B. , Field Mark C.
Published: March 2013

Rab GTPases serve as major control elements in the coordination and definition of specific trafficking steps and intracellular compartments. Rab activity is modulated in part by GTPase-activating proteins (GAPs), and many RabGAPs share a Tre-2/Bub2/Cdc16 (TBC)–domain architecture, although the majority of TBC proteins are poorly characterized. We reconstruct the evolutionary history of the TBC family using ScrollSaw, a method for the phylogenetic analysis of pan-eukaryotic data sets, and find a sophisticated, ancient TBC complement of at least 10 members. Significantly, the TBC complement is nearly always smaller than the Rab cohort in any individual genome but also suggests Rab/TBC coevolution. Further, TBC-domain architecture has been well conserved in modern eukaryotes. The reconstruction also shows conservation of ancestral TBC subfamilies, continuing evolution of new TBCs, and frequent secondary losses. These patterns give additional insights into the sculpting of the endomembrane system.
First Report of Brown Rot on Crataegus pinnatifida var. major Caused by Monilia yunnanensis in China
Authors: Zhao Y. Z. , Wang D. , Liu Z. H.
Published: March 2013

Crataegus pinnatifida Bge. var. major N. is a time-honored herbal medicine and an important economic fruit that is processed into various foods. Cultivated fields are mostly situated in northern China. In August 2012, a fruit brown rot disease on mature plants was found in Fushun, Liaoning Province, China. This disease reduced the yield and the quality of fruits; the incidence of fruits affected in each tree was between 20% and 35%. The initial stage of infection was marked by regular or irregular light brown spots turning dark brown and gradually supporting many grey fluffy tufts of mycelium. At last, the lesions expanded, causing the fruits to become rotted or withered. The pathogen was isolated from infected fruits by a tissue isolation method (1) and cultured on potato dextrose agar (PDA) at 25°C under 12 h light/12 h dark for 7 days. The colonies reached 60 to 75 mm in diameter after 7 days and were pale green or pale yellow with a neat greyish white margin; the aerial mycelium sometimes formed annulations. The conidia were single, hyaline, lemon-shaped or oval, and 11.3 ± 1.4 (8.0 to 16.5) × 6.4 ± 0.8 (5.1 to 7.6) μm; sporulation was sparse and stromata that formed after 15 days were abundant, black, and spherical to elliptical in shape. Conidiophores were simple or branched, bearing a single conidium on the tip. The internal transcribed spacer (ITS) region of rDNA amplified with primers ITS1 and ITS4 was directly sequenced in both directions. The ITS1-5.8S-ITS2 sequence of rDNA was 100% identical to Monilinia yunnanensis (GenBank Accession No. HQ908788.1), which is distinguished from the closely related M. fructigena (AF150679.1) and M. polystroma (JX315717.1). The pathogen was identified as M. yunnanensis on the basis of morphological characteristics (2) and the ITS sequence of rDNA (2,3). Pathogenicity tests were performed on detached healthy fruits. Four fruits were wounded with a sterilized nail and inoculated by placing a PDA plug of mycelia on upper surfaces of the fruits. Another four fruits treated with sterile PDA plugs served as a control. Fruits were cultured in petri dishes with a 12-h photoperiod at 25°C and 90% relative humidity. The initial symptoms on inoculated fruits were observed after 5 days, while no symptoms showed on the controls. The pathogen was reisolated from the inoculated fruit and identified as M. yunnanensis by the above methods. While M. yunnanensis has been reported to cause brown rot on peach (2), to our knowledge, this is the first report of M. yunnanensis infecting C. pinnatifida Bge. var. major N. in China.

References: (1) Z. D. Fang. Research Methods of Plant Disease, 1998. (2) M. J. Hu et al. Monilinia species causing brown rot of peach in China. PLoS ONE. Online publication. doi:10.1371/journal.pone.0024990, 2011. (3) G. C. M. van Leeuwen et al. Mycol. Res. 106:444, 2002.
Hydrogen Peroxide Accumulation and Transcriptional Changes in Grapevines Recovered from Flavescence Dorée Disease
Authors: Gambino Giorgio , Boccacci Paolo , Margaria Paolo , Palmano Sabrina , Gribaudo Ivana
Published: March 2013

Flavescence dorée (FD) is considered one of the most severe phytoplasma diseases affecting grapevine. The spontaneous, complete, and stable remission of the symptoms of FD (recovery) is a phenomenon that may occur in infected grapevines. The molecular bases of this phenomenon are still unclear, although some works suggest that recovery could be linked to the accumulation of hydrogen peroxide (H2O2). Several genes coding for enzymes involved in H2O2 metabolism, in the ascorbate-glutathione cycle, defense responses, and the biosynthesis of hormones were identified. The H2O2 content was biochemically determined and the expression levels of 44 genes were analyzed through quantitative real-time reverse-transcription polymerase chain reaction in healthy (H), infected by FD-associated phytoplasma (I), and 2-years-recovered (R) plants of Vitis vinifera ‘Barbera’. In tissues of R plants, large amounts of H2O2 were detected, essentially linked to an upregulation of genes involved in the production of H2O2 (germin-like protein and glycolate oxidase); whereas, in I grapevines, the overexpression of some scavenging genes reduced the quantity of H2O2. The recovery state was characterized by the activation of ethylene biosynthesis and of defense genes not linked to salicylic acid (SA) signaling, such as the WRKY2 transcription factor. Conversely, I plants reacted to phytoplasma with SA-mediated signaling, even though this response does not appear to be effective against the pathogen.
Molecular mechanisms creating bistable switches at cell cycle transitions
Authors: Verdugo Anael , Vinod P. K. , Tyson John J. , Novak Bela
Published: March 2013

Progression through the eukaryotic cell cycle is characterized by specific transitions, where cells move irreversibly from stagei−1 of the cycle into stagei. These irreversible cell cycle transitions are regulated by underlying bistable switches, which share some common features. An inhibitory protein stalls progression, and an activatory protein promotes progression. The inhibitor and activator are locked in a double-negative feedback loop, creating a one-way toggle switch that guarantees an irreversible commitment to move forward through the cell cycle, and it opposes regression from stageito stagei−1. In many cases, the activator is an enzyme that modifies the inhibitor in multiple steps, whereas the hypo-modified inhibitor binds strongly to the activator and resists its enzymatic activity. These interactions are the basis of a reaction motif that provides a simple and generic account of many characteristic properties of cell cycle transitions. To demonstrate this assertion, we apply the motif in detail to the G1/S transition in budding yeast and to the mitotic checkpoint in mammalian cells. Variations of the motif might support irreversible cellular decision-making in other contexts.
Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome
Authors: Fitzsimons Michael S. , Novotny Mark , Lo Chien-Chi , Dichosa Armand E.K. , Yee-Greenbaum Joyclyn L. , Snook Jeremy P. , Gu Wei , Chertkov Olga , Davenport Karen W. , McMurry Kim , Reitenga Krista G. , Daughton Ashlynn R. , He Jian , Johnson Shannon L. , Gleasner Cheryl D. , Wills Patti L. , Parson-Quintana Beverly , Chain Patrick S. , Detter John C. , Lasken Roger S. , Han Cliff S.
Published: March 2013

The majority of microbial genomic diversity remains unexplored. This is largely due to our inability to culture most microorganisms in isolation, which is a prerequisite for traditional genome sequencing. Single-cell sequencing has allowed researchers to circumvent this limitation. DNA is amplified directly from a single cell using the whole-genome amplification technique of multiple displacement amplification (MDA). However, MDA from a single chromosome copy suffers from amplification bias and a large loss of specificity from even very small amounts of DNA contamination, which makes assembling a genome difficult and completely finishing a genome impossible except in extraordinary circumstances. Gel microdrop cultivation allows culturing of a diverse microbial community and provides hundreds to thousands of genetically identical cells as input for an MDA reaction. We demonstrate the utility of this approach by comparing sequencing results of gel microdroplets and single cells following MDA. Bias is reduced in the MDA reaction and genome sequencing, and assembly is greatly improved when using gel microdroplets. We acquired multiple near-complete genomes for two bacterial species from human oral and stool microbiome samples. A significant amount of genome diversity, including single nucleotide polymorphisms and genome recombination, is discovered. Gel microdroplets offer a powerful and high-throughput technology for assembling whole genomes from complex samples and for probing the pan-genome of naturally occurring populations.
Knowledge input for the domain of information science
Authors: Tsay Ming‐yueh
Published: March 2013

Purpose

The aim of this paper is to explore the knowledge input and the subject relationship with other disciplines for the domain of information science through a citation analysis, from the references of each article from 1998 to 2008, of four leading information science journals, Journal of the American Society for Information Science and Technology, Information Processing and Management, Journal of Information Science, and Journal of Documentation.

Design/methodology/approach

The Ulrich's Periodical Directory, Library of Congress Subject Heading, retrieved from the WorldCat and LISA database were used to identify the main class, subclass and subject of cited journals and books. The highly cited journals and books, the main classes and subclasses of cited journals and books in papers of the four journals, the highly cited subjects in journals and books of library and information science were identified and analyzed.

Findings

The study reveals that information science possessing strong self knowledge flow as these four source journals are also the four most cited. The class library science, book industries and trade, general information resources consists of a mainstream of knowledge flow into information science. The highly cited subjects of LIS journals encompass searching, online information retrieval, information work, subject indexing, World Wide Web, technical services, citation analysis, information seeking behavior, etc. The three most cited LCSH subjects on WorldCat of books are information storage and retrieval, information science, human‐computer interaction, etc.

Originality/value

The knowledge inputs for information science include mainly information science itself and social sciences and general science as well. Moreover, there are minor inputs from various subjects.
Italian wines and Asia: policy scenarios and competitive dynamics
Authors: Corsi Armando Maria , Marinelli Nicola , Alampi Sottini Veronica
Published: March 2013

Purpose

The paper aims to analyse the current situation and the perspectives of Italian wine in key Asian export markets – China, Japan, India, Singapore and South Korea. These countries show the highest growing rates in wine consumption and are forecasted to become increasingly more strategic for Italian wine producers.

Design/methodology/approach

A SWOT analysis is applied to the most recent set of secondary data available from the Italian National Institute of Statistics (ISTAT), the Italian National Institute for Foreign Trade (ICE), the International Organisation of Wine and Vine (OIV) and Euromonitor International reports.

Findings

The study reveals that the most interesting markets for Italian wines are China and South Korea. The key strengths are mainly related to high quality products, evoking classic values and being perceived as a status symbol, while the main concerns for Italian wines are mainly related to promotion and distribution issues.

Research limitations/implications

The SWOT analysis can be used to develop a strategy that takes into consideration the potential strengths and opportunities and the impact of weaknesses and threats, but it cannot cover all the possible aspects Italian wineries must know about Asian markets. It offers a base for further and deeper thoughts about the how to succeed in the most dynamic and challenging markets of the next 20 years.

Originality/value

Differently from other studies, which tend to analyse Italian perspectives in Asian markets on a country‐by‐country basis, this work represents the most recent and comprehensive research on Italian wines in Asian markets.