bluuebunny/crossref_metadata_2025 huggingface dataset:
Hole conduction and electro-mechanical properties of Na0.5Bi2.5Ta2O9-based piezoelectric ceramics with the Li+/Ce3+/Sc3+ modification
Authors: Long Changbai , Fan Huiqing , Wu Yun , Li Yinghong
Published: August 2014

Na0.5Bi2.5Ta2O9-based piezoelectric ceramics, Na0.5-xBi0.5-xLixCexBi2Ta2-xScxO9-x (NBTO-x, x = 0–0.05), were synthesized by using a solid-state reaction process, and their electro-mechanical properties and electrical conduction behaviors were investigated in detail. The Li+/Ce3+/Sc3+ modification improved the electro-mechanical properties of the ceramics effectively, whereas further N2 or O2 annealing led to no obvious increase in piezoelectric coefficient (d33). The composition x = 0.03 ceramic with high temperature stability had a Curie point (Tc) of 784 °C and a d33 of 25.8 pC/N, and its electromechanical coupling factors, kp and kt, were 11.8% and 20.7%, respectively. Variable-atmosphere (air, O2 and N2) impedance data suggested that the NBTO-x ceramics were mainly p-type materials contributing from the bulk response, and the conducting species were holes (h•). Therefore, lower bulk resistivity (ρ) and lower activation energy (Ea) were associated with the treatment with higher PO2 (oxygen partial pressure). In addition, the O2 atmosphere had stronger impact on the conductivity of the pure NBTO than those of the acceptor NBTO-x, and the grain and grain boundary contributed to its resistivity together.
New insights into self-heating in double-gate transistors by solving Boltzmann transport equations
Authors: Thu Trang Nghiêm T. , Saint-Martin J. , Dollfus P.
Published: August 2014

Electro-thermal effects become one of the most critical issues for continuing the downscaling of electron devices. To study this problem, a new efficient self-consistent electron-phonon transport model has been developed. Our model of phonon Boltzmann transport equation (pBTE) includes the decay of optical phonons into acoustic modes and a generation term given by electron-Monte Carlo simulation. The solution of pBTE uses an analytic phonon dispersion and the relaxation time approximation for acoustic and optical phonons. This coupled simulation is applied to investigate the self-heating effects in a 20 nm-long double gate MOSFET. The temperature profile per mode and the comparison between Fourier temperature and the effective temperature are discussed. Some significant differences occur mainly in the hot spot region. It is shown that under the influence of self-heating effects, the potential profile is modified and both the drain current and the electron ballisticity are reduced because of enhanced electron-phonon scattering rates.
Rapid motion of liquid mercury column in carbon nanotubes driven by temperature gradient
Authors: Zhang Zhong-Qiang , Dong Xin , Ye Hong-Fei , Cheng Guang-Gui , Ding Jian-Ning , Ling Zhi-Yong
Published: August 2014

The liquid mercury column can be rapidly transported from high temperature region to low temperature region in single walled carbon nanotubes (SWCNTs) driven by the temperature gradient. Interestingly, the total force acting on the mercury column keeps constant during the temperature gradient-driven process. The motion acceleration of the mercury column is linearly dependent on the magnitude of the temperature gradient. The meniscuses of the hydrophobic mercury column confined in SWCNTs do not appreciably affect the motion behaviors of the mercury column in our proposed model. The influences of the column length and the CNT diameter on the motion behaviors of the mercury column are considered to clarify the mechanism of the size effect. The motion acceleration of the mercury column nonlinearly decreases with increasing the column length and the CNT diameter. The overall oscillation of the SWCNTs plays the dominant role in rapid motion of mercury column for short-length mercury columns and small-diameter SWCNTs.
Engineering of silicon/HfO2 interface by variable energy proton irradiation
Authors: Maurya Savita , Tribedi L. C. , Maringanti Radhakrishna
Published: August 2014

Surfaces and interfaces between materials are of paramount importance for various phenomena, such as painting a house, catalyst driven chemical reactions, intricate life processes, corrosion of materials, and fabrication of various semiconductor devices. Interface of silicon or other such substrates with any of the oxides has profound effect on the performance of metal oxide field effect transistors and other similar devices. Since a surface is an abrupt termination of a periodic crystal, surface atoms will have some unsaturated valence electrons and these unsaturated bonds at the semiconductor surface make it chemically highly reactive. Other than annealing, there is not much that can be done to manage these unsaturated bonds. This study was initiated to explore the possibility of repairing these unsaturated dangling bonds that are formed at the silicon and oxide interface during the deposition of oxide layer above silicon, by the use of proton irradiation. In order to improve the interface characteristics, we present a method to modify the interface of silicon and hafnium dioxide after its fabrication, through proton irradiation. Results of the study are promising and probably this method might be used along with other methods such as annealing to modify the interface, after its fabrication.
Growth and characterization of dilute nitride GaNxP1−x nanowires and GaNxP1−x/GaNyP1−y core/shell nanowires on Si (111) by gas source molecular beam epitaxy
Authors: Sukrittanon S. , Kuang Y. J. , Dobrovolsky A. , Kang Won-Mo , Jang Ja-Soon , Kim Bong-Joong , Chen W. M. , Buyanova I. A. , Tu C. W.
Published: August 2014

We have demonstrated self-catalyzed GaNxP1−x and GaNxP1−x/GaNyP1−y core/shell nanowire growth by gas-source molecular beam epitaxy. The growth window for GaNxP1−x nanowires was observed to be comparable to that of GaP nanowires (∼585 °C to ∼615 °C). Transmission electron microscopy showed a mixture of cubic zincblende phase and hexagonal wurtzite phase along the [111] growth direction in GaNxP1−x nanowires. A temperature-dependent photoluminescence (PL) study performed on GaNxP1−x/GaNyP1−y core/shell nanowires exhibited an S-shape dependence of the PL peaks. This suggests that at low temperature, the emission stems from N-related localized states below the conduction band edge in the shell, while at high temperature, the emission stems from band-to-band transition in the shell as well as recombination in the GaNxP1−x core.
Whispering gallery micro-global positioning system for nanoparticle sizing in real time
Authors: Keng D. , Tan X. , Arnold S.
Published: August 2014

We have devised a simple means for determining the size of a nanoparticle in one binding event (i.e., real time) by utilizing two polar modes of a slightly eccentric Whispering Gallery Mode (WGM) spheroidal resonator. The ratio of shifts of these modes locates the absolute latitude angle at which a nano-particle binds. From this location, the size of the nanoparticle is calculated using the reactive sensing principle. Although our latitude-only micro-global positioning scheme is applied to nanoparticle sizing using slightly eccentric spheroids in aqueous solution, this approach can be applied to WGM micro-resonators having a variety of shapes.
Shewanella oneidensis
MR-1 nanowires are outer membrane and periplasmic extensions of the extracellular electron transport components
Authors: Pirbadian Sahand , Barchinger Sarah E. , Leung Kar Man , Byun Hye Suk , Jangir Yamini , Bouhenni Rachida A. , Reed Samantha B. , Romine Margaret F. , Saffarini Daad A. , Shi Liang , Gorby Yuri A. , Golbeck John H. , El-Naggar Mohamed Y.
Published: August 2014

Significance

Bacterial nanowires from
Shewanella oneidensis
MR-1 were previously shown to be conductive under nonphysiological conditions. Intense debate still surrounds the molecular makeup, identity of the charge carriers, and cellular respiratory impact of bacterial nanowires. In this work, using in vivo fluorescence measurements, immunolabeling, and quantitative gene expression analysis, we demonstrate that
S. oneidensis
MR-1 nanowires are extensions of the outer membrane and periplasm, rather than pilin-based structures, as previously thought. We also demonstrate that the outer membrane multiheme cytochromes MtrC and OmcA localize to these membrane extensions, directly supporting one of the two models of electron transport through the nanowires; consistent with this, production of bacterial nanowires correlates with an increase in cellular reductase activity.
Genetic diversity of seed storage proteins in diploid, tetraploid and hexaploid Avena species
Authors: Yan Honghai , Baum B. R. , Zhou Pingping , Zhao Jun , Wei Yuming , Ren Changzhong , Xiong Fangqiu , Liu Gang , Zhong Lin , Zhao Gang , Peng Yuanying
Published: August 2014

Genetic diversities of 106 Avena accessions, including diploid, tetraploid and hexaploid species, derived from different countries were characterized based on seed storage proteins polymorphism using SDS-PAGE. A total of 24 protein bands and 72 protein patterns were detected in all 106 accessions. The genetic similarity value varied from 0.50 to 1.00. The seed storage protein patterns were largely independent of environmental fluctuation. Accessions of the same species or with identical genome constitutions had the same or similar protein patterns. Relatively lower within-species variations were observed compared with among-species variations. The AACCDD genome hexaploid species and the AA genome diploid species were more divergent than other species, with percentages of polymorphic bands of 85.7% and 61.1% respectively. In the AA genome diploid species, the AsAs genome diploids displayed higher variations than the modified AA genome diploid species. Clustering results showed a close relationship between the hexaploid species and the AACC genome tetraploid species. The AABB genome tetraploid species were similar to the AsAs genome diploid species, with the exception of the species A. agadiriana with AABB genome constitution, which showed a close relationship with the AcAc genome diploid species A. canariensis and the polyploid species carrying the A and C genomes.
Comparison of total energy expenditure assessed by two devices in controlled and free‐living conditions
Authors: Rousset Sylvie , Fardet Anthony , Lacomme Philippe , Normand Sylvie , Montaurier Christophe , Boirie Yves , Morio Béatrice
Published: August 2014

The objective of this study was to evaluate the validity of total energy expenditure (TEE) provided by Actiheart® and Armband®. Normal‐weight adult volunteers wore both devices either for 17 hours in a calorimetric chamber (CC, n = 49) or for 10 days in free‐living conditions (FLC) outside the laboratory (n = 41). The two devices and indirect calorimetry or doubly labelled water, respectively, were used to estimate TEE in the CC group and FLC group. In the CC, the relative value of TEE error was not significant (p > 0.05) for Actiheart® but significantly different from zero for Armband®, showing TEE underestimation (−4.9%, p < 0.0001). However, the mean absolute values of errors were significantly different between Actiheart® and Armband®: 8.6% and 6.7%, respectively (p = 0.05). Armband® was more accurate for estimating TEE during sleeping, rest, recovery periods and sitting–standing. Actiheart® provided better estimation during step and walking. In FLC, no significant error in relative value was detected. Nevertheless, Armband® produced smaller errors in absolute value than Actiheart® (8.6% vs. 12.8%). The distributions of differences were more scattered around the means, suggesting a higher inter‐individual variability in TEE estimated by Actiheart® than by Armband®. Our results show that both monitors are appropriate for estimating TEE. Armband® is more effective than Actiheart® at the individual level for daily light‐intensity activities.
Loss of γ-cytoplasmic actin triggers myofibroblast transition of human epithelial cells
Authors: Lechuga Susana , Baranwal Somesh , Li Chao , Naydenov Nayden G. , Kuemmerle John F. , Dugina Vera , Chaponnier Christine , Ivanov Andrei I.
Published: August 2014

Transdifferentiation of epithelial cells into mesenchymal cells and myofibroblasts plays an important role in tumor progression and tissue fibrosis. Such epithelial plasticity is accompanied by dramatic reorganizations of the actin cytoskeleton, although mechanisms underlying cytoskeletal effects on epithelial transdifferentiation remain poorly understood. In the present study, we observed that selective siRNA-mediated knockdown of γ-cytoplasmic actin (γ-CYA), but not β-cytoplasmic actin, induced epithelial-to-myofibroblast transition (EMyT) of different epithelial cells. The EMyT manifested by increased expression of α-smooth muscle actin and other contractile proteins, along with inhibition of genes responsible for cell proliferation. Induction of EMyT in γ-CYA–depleted cells depended on activation of serum response factor and its cofactors, myocardial-related transcriptional factors A and B. Loss of γ-CYA stimulated formin-mediated actin polymerization and activation of Rho GTPase, which appear to be essential for EMyT induction. Our findings demonstrate a previously unanticipated, unique role of γ-CYA in regulating epithelial phenotype and suppression of EMyT that may be essential for cell differentiation and tissue fibrosis.
Failure of cell cleavage induces senescence in tetraploid primary cells
Authors: Panopoulos Andreas , Pacios-Bras Cristina , Choi Justin , Yenjerla Mythili , Sussman Mark A. , Fotedar Rati , Margolis Robert L.
Published: August 2014

Tetraploidy can arise from various mitotic or cleavage defects in mammalian cells, and inheritance of multiple centrosomes induces aneuploidy when tetraploid cells continue to cycle. Arrest of the tetraploid cell cycle is therefore potentially a critical cellular control. We report here that primary rat embryo fibroblasts (REF52) and human foreskin fibroblasts become senescent in tetraploid G1 after drug- or small interfering RNA (siRNA)-induced failure of cell cleavage. In contrast, T-antigen–transformed REF52 and p53+/+ HCT116 tumor cells rapidly become aneuploid by continuing to cycle after cleavage failure. Tetraploid primary cells quickly become quiescent, as determined by loss of the Ki-67 proliferation marker and of the fluorescent ubiquitination-based cell cycle indicator/late cell cycle marker geminin. Arrest is not due to DNA damage, as the γ-H2AX DNA damage marker remains at control levels after tetraploidy induction. Arrested tetraploid cells finally become senescent, as determined by SA-β-galactosidase activity. Tetraploid arrest is dependent on p16INK4a expression, as siRNA suppression of p16INK4a bypasses tetraploid arrest, permitting primary cells to become aneuploid. We conclude that tetraploid primary cells can become senescent without DNA damage and that induction of senescence is critical to tetraploidy arrest.
The actin regulators Enabled and Diaphanous direct distinct protrusive behaviors in different tissues duringDrosophiladevelopment
Authors: Nowotarski Stephanie H. , McKeon Natalie , Moser Rachel J. , Peifer Mark
Published: August 2014

Actin-based protrusions are important for signaling and migration during development and homeostasis. Defining how different tissues in vivo craft diverse protrusive behaviors using the same genomic toolkit of actin regulators is a current challenge. The actin elongation factors Diaphanous and Enabled both promote barbed-end actin polymerization and can stimulate filopodia in cultured cells. However, redundancy in mammals and Diaphanous’ role in cytokinesis limited analysis of whether and how they regulate protrusions during development. We used two tissues driving Drosophila dorsal closure—migratory leading-edge (LE) and nonmigratory amnioserosal (AS) cells—as models to define how cells shape distinct protrusions during morphogenesis. We found that nonmigratory AS cells produce filopodia that are morphologically and dynamically distinct from those of LE cells. We hypothesized that differing Enabled and/or Diaphanous activity drives these differences. Combining gain- and loss-of-function with quantitative approaches revealed that Diaphanous and Enabled each regulate filopodial behavior in vivo and defined a quantitative “fingerprint”—the protrusive profile—which our data suggest is characteristic of each actin regulator. Our data suggest that LE protrusiveness is primarily Enabled driven, whereas Diaphanous plays the primary role in the AS, and reveal each has roles in dorsal closure, but its robustness ensures timely completion in their absence.
Cdc42 controls the dilation of the exocytotic fusion pore by regulating membrane tension
Authors: Bretou Marine , Jouannot Ouardane , Fanget Isabelle , Pierobon Paolo , Larochette Nathanaël , Gestraud Pierre , Guillon Marc , Emiliani Valentina , Gasman Stéphane , Desnos Claire , Lennon-Duménil Ana-Maria , Darchen François
Published: August 2014

Membrane fusion underlies multiple processes, including exocytosis of hormones and neurotransmitters. Membrane fusion starts with the formation of a narrow fusion pore. Radial expansion of this pore completes the process and allows fast release of secretory compounds, but this step remains poorly understood. Here we show that inhibiting the expression of the small GTPase Cdc42 or preventing its activation with a dominant negative Cdc42 construct in human neuroendocrine cells impaired the release process by compromising fusion pore enlargement. Consequently the mode of vesicle exocytosis was shifted from full-collapse fusion to kiss-and-run. Remarkably, Cdc42-knockdown cells showed reduced membrane tension, and the artificial increase of membrane tension restored fusion pore enlargement. Moreover, inhibiting the motor protein myosin II by blebbistatin decreased membrane tension, as well as fusion pore dilation. We conclude that membrane tension is the driving force for fusion pore dilation and that Cdc42 is a key regulator of this force.
Person endings in the old Italian verb system
Authors: Vanelli Laura
Published: August 2014

This chapter offers a contrastive account of the systems of verbal inflection in thirteenth-century Florentine (also known as old Italian) and in the modern language. The old Italian system is characterized, in particular, a) by a high degree of allotropy, that is to say of alternant realizations of the same cell in the paradigm, and b) by the nature of the endings in which we find those which are etymologically to be expected co-existing with the innovations which will in due course yield the modern system. The analysis of the old Italian system thus allows us to investigate the mechanisms and dynamics of morphological change by which one system has given way to the other. Of central importance here is the interaction of the principles of isomorphism and iconicity in determining the eventual outcome of the changing system
Kind-defining relative clauses in the diachrony of Italian
Authors: Beninca Paola , Cinque Guglielmo
Published: August 2014

Within the larger class of relative clauses, we isolate the subclass of relative clauses which modify a nominal predicate, as in Gianni è un uomo che non si dà mai per vinto (It.), ‘Gianni is a man that never surrenders’. This type of relative clause is shown to belong to a larger class of kind-defining relatives, in which other kinds of verbs incorporate a stage-level predicate. Their properties in varieties of Italian and English, and their evolution in the history of Italian are considered. Comparing old Florentine with other medieval and modern Italian varieties, it is clear that the diachronic change is very limited; the distinctive features that set this class apart are present in all of these linguistic areas. It is proposed their special properties can be related to the fact that, in opposition to restrictives, the DP in predicate position is not truly referential.
Looking Forward: Njal’s Prescience: Chapters 22–3
Authors: Miller William Ian
Published: August 2014

What of a strange chapter narrated in the future tense? This chapter is a discussion of the limits of Njal’s prescience and the constraints on it, which are quite substantial, his so-called prescience being more often what we would call sophistication regarding human behaviour. Njal also scripts some of his predictions; he does not read the future so much as make it. The discussion distinguishes among advice giving, prediction, persuasion, and prophecy, all of which readily use the future tense to tell ‘stories’ yet to happen. The role of Fate in the saga and in the literature on the sagas is criticized, and there is some discussion of the interpretive problems that arise, depending on the level of foreknowledge we attribute to Njal.
The Burning: Chapters 124–32
Authors: Miller William Ian
Published: August 2014

What are Njal’s motives in counselling to defend from inside the farmhouse? Skarphedin knows that it is lethal counsel, yet her defers, being intent on not marring his final scene by squabbling with his father. The chapter discusses in detail the sublime realization of the Burning: the triple meaning of Njal’s taking to his bed to die, Skarphedin’s launching of Kari, and the contrasting ‘miracles’ of Njal’s radiant corpse and Skarphedin’s never going down without lower legs and feet to stand on. It also discusses the complex character of Flosi, his losing a game of ‘chicken’ with Ingjald of Keldur. There is a formal farewell and evaluation of Skarphedin, his inability to escape his father’s control, and his ironical coming into his inheritance only as he and it are burning around him.
The Trial of Flosi and the Battle: Chapters 135, 141–5
Authors: Miller William Ian
Published: August 2014

This chapter deals extensively with the saga’s treatment of law, the limits of law, some procedural matters that may trouble the reader, the nature of legal expertise, and the portraits of three men of law: the wonderful Thorhall Asgrimsson, Mord, and Eyjolf, and their roles prior to and during the Battle at the Althing. It has been an unfortunate common critical response to read the saga as an indictment of the law. That is far from the case. The law functions well within appropriate limits, but the core feud of the saga comes to expand to something approaching law, and then is simply beyond the law’s competence, any law’s. The saga gives a remarkable astute analysis of just where the limits of law’s competence lie.
A Conclusion: Justice and Exits
Authors: Miller William Ian
Published: August 2014

A discussion of some troubling exits and non-exits of characters: primarily Mord and Hallgerd. Why is the latter just forgotten and dropped without a thought; why does the former suffer no sanction for his putative ill-doings? The writer is too given to realism and refusing easy moralizing. People like Mord tend to land on their feet because at some level they know their limits. Hallgerd’s revenge is appreciated for its utter non-utility, it being purely aesthetic, artfully accomplished, the moral and the aesthetic merging in refusal not to pay back what she owes. The sublimity of the author/narrator’s first person pronoun farewell is evoked.
Hindu Theology in Early Modern South Asia
Authors: Okita Kiyokazu
Published: August 2014

Focusing on the idea of genealogical affiliation (sampradāya), this book explores the interactions between royal power and priestly authority in eighteenth-century north India. Specifically, it examines how the religious policies of Jaisingh II (1688–1743) of Jaipur influenced the self-representation of Gauḍīya Vaiṣṇavas, as articulated by Baladeva Vidyābhūṣaṇa (c.1700–1793). Gauḍīya Vaiṣṇavas centred around the God Kṛṣṇa was initiated by Caitanya (1486–1533) and quickly became one of the most influential Hindu devotional movements in early modern South Asia. In the increasingly volatile late Mughal period, Jaisingh II tried to establish the legitimacy of his kingship by resorting to moral discourse. As a part of this strategy, he demanded that religious traditions in his kingdom conform to what he conceived of as Brahmanically normative. In this context the Gauḍīya school was forced to deal with their lack of clear genealogical affiliation, lack of an independent commentary on the Brahmasūtras, and their worship of Goddess Rādhā and Kṛṣṇa, who, according to the Gauḍīya, were not married. Based on a study of Baladeva’s Brahmasūtra commentary, the book examines how the Gauḍīya responded to the king’s demand, and thereby contributes to (1) genealogical studies; (2) the study of early modern South Asia; (3) Purāṇic studies, and (4) the study of Hindu theology.
The Learned Press: Oriental Languages
Authors: Hamilton Alastair
Published: August 2014

The publications of the Oxford press indicate the growing interest in Eastern languages from the sixteenth through the eighteenth centuries. The earliest publications were in the biblical languages Hebrew and Aramaic, for the study of Hebrew had become an essential part of the humanist tradition in England and two works of Hebrew grammar were published in the 1630s. Even before William Laud established a professorship of Arabic at the university, he acquired oriental types from Holland so that the press collection grew to include Arabic, Syriac, Ethiopic, Coptic, Armenian, Samaritan, and Cyrillic. While composing and proofing in these languages was laborious and expensive, print runs remained small and sales were seldom satisfactory. The Press nevertheless maintained consistently high standards of production and continued to advance oriental studies by supporting important new critical scholarship and commentary.
Models of amino acid and codon substitution
Authors: Yang Ziheng
Published: August 2014

This chapter discusses Markov chain models of amino acid replacement and codon substitution. It then discusses the various methods for estimating the numbers of synonymous and nonsynonymous substitutions (dS and dN) between two protein-coding genes. Both the counting and maximum likelihood methods are included.
Maximum likelihood methods
Authors: Yang Ziheng
Published: August 2014

This chapter describes the pruning algorithm for calculating the likelihood on a tree, as well as extensions under complex substitution models, including the gamma and covarion models of rate variation among sites and lineages. It discusses numerical optimization algorithms for maximum likelihood estimation. It provides a critical assessment of methods for reconstructing ancestral states for both molecular sequences and morphological characters. Finally the chapter discusses model selection in phylogenetics using the likelihood ratio test (LRT) and information criteria such as the Akaike information criterion (AIC) and Bayesian information criterion (BIC).
Comparison of phylogenetic methods and tests on trees
Authors: Yang Ziheng
Published: August 2014

This chapter summarizes the criteria for comparing different tree reconstruction methods, such as consistency and efficiency, as well as computer simulation studies that evaluate the statistical performance of the various methods. It provides a critical examination of the assumptions underlying the parsimony method of phylogeny reconstruction, and its relationships to the likelihood method. It also discusses the differences of the maximum likelihood (ML) method for phylogeny reconstruction from conventional ML for parameter estimation and demonstrates that the ML tree does not have the asymptotic efficiency of a conventional likelihood estimate (MLE). The chapter then discusses the various statistical tests in the Frequentist framework developed to evaluate the significance of the estimated phylogenetic tree, including the bootstrap, K-H test, S-H test, etc..
Bayesian theory
Authors: Yang Ziheng
Published: August 2014

This chapter summarizes the Frequentist–Bayesian controversy in statistics, and introduces the basic theory of Bayesian statistical inference, such as the prior, posterior, and Bayes’ theorem. Classical methods for Bayesian computation, such as numerical integration, Laplacian expansion, Monte Carlo integration, and importance sampling, are illustrated using biological examples.
Molecular clock and estimation of species divergence times
Authors: Yang Ziheng
Published: August 2014

This chapter discusses the hypothesis of the molecular clock and its use to date species divergences. It introduces various tests of the molecular clock as well as strategies to relax the clock in divergence time estimation. Bayesian methods of divergence time estimation are discussed in detail, including different prior models of rate drift such as the correlated-rate model based on the geometric Brownian motion process, and specification of the prior on divergence times incorporating uncertainties in fossil calibrations. The chapter describes the infinite-site and finite-site theories, which characterize the uncertainties in posterior divergence time estimates.
Quantitative genetic approaches to understanding sexual selection and mating system evolution in the wild
Authors: Reid Jane M.
Published: August 2014

Major ambitions in evolutionary biology are to understand the forces that drive the evolution and persistence of mate choice, and of associated primary and secondary sexual traits and emergent mating systems. Particular uncertainty, and hence substantial research interest, concerns the degree to which ongoing evolution of diverse morphological, physiological and behavioural traits and mating systems could be caused or constrained by indirect selection stemming from genetic covariation between such traits and associated mating preferences and fitness components. This chapter highlights the virtues of a quantitative genetic approach to answering such questions, in terms of both deriving pertinent theory and explicitly testing such theory in wild populations experiencing natural genetic and environmental variation. Two case studies are used, which aim to dissect the coevolution of a female mating preference and ornamental male trait in collared flycatchers (Ficedula albicollis) and the evolution of female extra-pair reproduction in song sparrows (Melospiza melodia), to illustrate the opportunities afforded by a wild population quantitative genetic approach to understanding sexual selection and mating system evolution, but also to illustrate the substantial remaining challenges.
Future temporal reference in child language
Authors: Weist Richard M.
Published: August 2014

This chapter investigates the acquisition of future temporal reference in child language within the framework of the emergence of the ‘Event time’ and the ‘Reference time’ temporal systems and within a cross-linguistic perspective. The chapter probes the developmental language–thought relationship between the emergence of the event time and the reference time systems in the child’s language and the child’s capacity for autobiographical memory and ‘episodic future thinking’. An argument for a precocious understanding of the deictic relations of the child’s tense morphology is presented. Further, the chapter explains how children acquire the capacity to establish reference time at relatively remote locations away from speech time creating a complex system of temporal reference. These accomplishments in child language are linked to the conceptual capacity for past and future time travel, re-experiencing and pre-experiencing episodic representations. The potential relevance of the Whorfian hypothesis as it applies to child language and future temporal reference is explored.
On future in commands
Authors: Aikhenvald Alexandra Y.
Published: August 2014

The expression of future time and tense can correlate with sentence types. As predicted by Lyons (1977: 746–7), the most frequently attested grammaticalized time reference in imperatives is that of immediate versus delayed—or future—imperative. This contrasts with a wider range of possibilities for future meanings grammaticalized in declarative clauses. The grammatical distinction of immediate and future imperative is widely attested in North American Indian languages. Future imperatives may have overtones of politeness (as in Epena Pedee, a Chocoan language from Colombia, and in Yup’ik). Some languages distinguish ‘near future’ and ‘remote future’ imperatives (e.g. Koasati, a Muskogean language). An essentially temporal distinction in imperatives may also correlate with spatial distance. This chapter offers a discussion of future meanings expressed in imperatives across the world’s languages (using Aikhenvald 2010: 130–3 as a point of departure).
Future reference and current relevance with the French composed past
Authors: de Saussure Louis
Published: August 2014

This chapter investigates reference to future eventualities with the composed past in French. The French composed past has an ambiguous meaning, corresponding to either a present perfect or a narrative past, while being compatible with future temporal adverbs and has, therefore, a theoretically unexpected future meaning. The chapter argues that a Futurate Composed Past utterance (FCP) expresses a future state resulting from a prior eventuality and suggests that this temporal reference is pragmatically constructed in the search for relevance through a perspectival shift implying a point of view situated by the future adverb, from which the state of affairs is considered true. The difference between FCP and Anterior Future utterances may reside in the fact that the FCP triggers a pragmatic deontic-practical modality—has concrete implications about what to do in the actual present—contrary to what is obtained with the Anterior Future. It is suggested that this is achieved through simulative cognitive processes.
Modeling Commodity Prices with Dynamic Conditional Beta
Authors: Engle Robert
Published: August 2014

The Dynamic Conditional Beta model is applied to the returns on 21 commodities to examine evidence of transitions in the market structure. The econometrics of transition models is examined from the influential perspective of Timo Teräsvirta’s smooth transition models. The betas on the SP500 are estimated dynamically and reveal big increases associated with the financial crisis and the increasing role of mainstream financial traders. Shocks to commodity markets in earlier periods were arguably more likely to be supply shocks that were uncorrelated with broad equity indices, whereas the financial crisis was a demand shock to this sector and increased the correlation and beta on the indices. The hedging value of commodities is clearly reduced but it appears that most commodities still have a role in a minimum variance portfolio.
Solutions of the Navier–Stokes Equations
Authors: Ruban Anatoly I. , Gajjar Jitesh S. B.
Published: August 2014

This chapter describes solutions of the Navier–Stokes equations, starting with simple physical situations where these equations allow exact solutions, i.e. solutions in analytic form. These include Couette flow between two parallel plates, Hagen–Poiseuille flow through a pipe, flow above an impulsively started plate (where the notion of a self-similar solution and the Stokes layer are introduced), dissipation of the potential vortex caused by fluid viscosity, and Kármán flow above an infinite rotating disk. Some numerical solutions of the Navier–Stokes equations are then presented to illustrate various important properties of viscous flows. Flow past a circular cylinder is examined, and it is shown what happens to the separation eddy region behind the cylinder as the Reynolds number increases. The behaviour of flow in a cavity is also discussed, and it is demonstrated how recirculating eddies can multiply as the fluid viscosity decreases.
Elements of Gasdynamics
Authors: Ruban Anatoly I. , Gajjar Jitesh S. B.
Published: August 2014

This chapter deals with inviscid compressible flows of a perfect gas. It starts with an analysis of small perturbations propagating through a gas at rest using piston theory and then turns to integrals of motion, including compressible versions of the Bernoulli equation, entropy conservation law, and Kelvin’s Circulation Theorem. Crocco’s formula, which allows determination of whether a flow is potential in the presence of shock waves, is derived. The theory of characteristics is formulated for two-dimensional potential flows and applied to Prandtl–Meyer flow over a body surface bend and flow past a corner. The formation of shock waves, normal or oblique, is discussed. The shock conditions are deduced and the shock polar, which describes the behaviour of oblique shocks, is introduced. These results are applied to flows past a wedge and a circular cone. Finally, unsteady compressible flows are analysed, in particular shock tubes and blast waves are considered.
OptiType: precision HLA typing from next-generation sequencing data
Authors: Szolek András , Schubert Benjamin , Mohr Christopher , Sturm Marc , Feldhahn Magdalena , Kohlbacher Oliver
Published: August 2014

Motivation: The human leukocyte antigen (HLA) gene cluster plays a crucial role in adaptive immunity and is thus relevant in many biomedical applications. While next-generation sequencing data are often available for a patient, deducing the HLA genotype is difficult because of substantial sequence similarity within the cluster and exceptionally high variability of the loci. Established approaches, therefore, rely on specific HLA enrichment and sequencing techniques, coming at an additional cost and extra turnaround time.

Result: We present OptiType, a novel HLA genotyping algorithm based on integer linear programming, capable of producing accurate predictions from NGS data not specifically enriched for the HLA cluster. We also present a comprehensive benchmark dataset consisting of RNA, exome and whole-genome sequencing data. OptiType significantly outperformed previously published in silico approaches with an overall accuracy of 97% enabling its use in a broad range of applications.

Contact:  szolek@informatik.uni-tuebingen.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
GlycoPattern: a web platform for glycan array mining
Authors: Agravat Sanjay B. , Saltz Joel H. , Cummings Richard D. , Smith David F.
Published: August 2014

Summary: GlycoPattern is Web-based bioinformatics resource to support the analysis of glycan array data for the Consortium for Functional Glycomics. This resource includes algorithms and tools to discover structural motifs, a heatmap visualization to compare multiple experiments, hierarchical clustering of Glycan Binding Proteins with respect to their binding motifs and a structural search feature on the experimental data.

Availability and implementation: GlycoPattern is freely available on the Web at http://glycopattern.emory.edu with all major browsers supported.

Contact:  sanjay.agravat@emory.edu
Planet X revamped after the discovery of the Sedna-like object 2012 VP113?
Authors: Iorio L.
Published: August 2014

The recent discovery of the Sedna-like dwarf planet 2012 VP113 by Trujillo and Sheppard has revamped the old-fashioned hypothesis that a still unseen trans-Plutonian object of planetary size, variously dubbed over the years as Planet X, Tyche and Telisto, might lurk in the distant peripheries of the Solar system. This time, the presence of a super-Earth with mass mX =2–15 m⊕ at a distance dX ≈ 200–300 astronomical units (au) has been proposed to explain the observed clustering of the arguments of perihelion ω near ω ≈ 0° but not ω ≈ 180° for Sedna, 2012 VP113 and other minor bodies of the Solar system with perihelion distances q > 30 au and semimajor axes a > 150 au. Actually, such a scenario is strongly disfavoured by the latest constraints $\Delta \dot{\varpi }$ on the anomalous perihelion precessions of some Solar system planets obtained with the INPOP and EPM ephemerides. Indeed, they yield dX ≳ 496–570 au (mX = 2 m⊕) and dX ≳ 970–1111 au (mX = 15 m⊕). Much tighter constraints could be obtained in the near future from the New Horizons mission to Pluto.
The rarity of star formation in brightest cluster galaxies as measured by WISE
Authors: Fraser-McKelvie Amelia , Brown Michael J. I. , Pimbblet Kevin A.
Published: August 2014

We present the mid-infrared star formation rates of 245 X-ray selected, nearby (z < 0.1) brightest cluster galaxies (BCGs). A homogeneous and volume limited sample of BCGs was created by X-ray selecting clusters with Lx > 1 × 1044 erg s− 1. The Wide-Field Infrared Survey Explorer (WISE) All WISE Data Release provides the first measurement of the 12 μm star formation indicator for all BCGs in the nearby Universe. Perseus A and Cygnus A are the only galaxies in our sample to have star formation rates of > 40 M⊙ yr− 1, indicating that these two galaxies are highly unusual at current times. Stellar populations of 99 ± 0.6 per cent of local BCGs are (approximately) passively evolving, with star formation rates of < 10 M⊙ yr− 1. We find that in general, star formation produces only modest BCG growth at the current epoch.
Novel applications of statins for bone regeneration
Authors: Shah Sarita R. , Werlang Caroline A. , Kasper F. Kurtis , Mikos Antonios G.
Published: August 2014

The use of statins for bone regeneration is a promising and growing area of research. Statins, originally developed to treat high cholesterol, are inhibitors of the enzyme 3-hydroxy-3-methylglutaryl, the rate-limiting enzyme of the mevalonate pathway. Because the mevalonate pathway is responsible for the synthesis of a wide variety of important biochemical molecules, including cholesterol and other isoprenoids, the effects of statins are pleiotropic. In particular, statins can greatly affect the process of bone turnover and regeneration via effects on important cell types, including mesenchymal stem cells, osteoblasts, endothelial cells, and osteoclasts. Statins have also been shown to have anti-inflammatory and antimicrobial properties that may be useful since infection can derail normal bone healing. This review will explore the pleiotropic effects of statins, discuss the current use of statins for bone regeneration, particularly with regard to biomaterials-based controlled delivery, and offer perspectives on the challenges and future directions of this emerging area of bone tissue engineering.
Voriconazole-Resistant Penicillium oxalicum: An Emerging Pathogen in Immunocompromised Hosts
Authors: Chowdhary Anuradha , Kathuria Shallu , Agarwal Kshitij , Sachdeva Neelam , Singh Pradeep K. , Jain Sandeep , Meis Jacques F.
Published: August 2014

Penicillium species are rarely reported agents of infections in immunocompromised patients. We report 3 cases of invasive mycosis caused by voriconazole-resistant Penicillium oxalicum in patients with acute myeloid leukemia, diabetes mellitus, and chronic obstructive pulmonary disease, while on voriconazole therapy. Penicillium oxalicum has not been previously recognized as a cause of invasive mycoses.
Phase II Study of Modified FOLFOX6 With Bevacizumab in Metastatic Gastroesophageal Adenocarcinoma
Authors: Li Jia , Yao Xiaopan , Kortmansky Jeremy S. , Fischbach Neal A. , Stein Stacey , Deng Yanhong , Zhang Yue , Doddamane Indukala , Karimeddini David , Hochster Howard S. , Lacy Jill
Published: August 2014

Background:

The median survival for patients with metastatic gastroesophageal adenocarcinoma is <12 months. Bevacizumab has demonstrated promising activity in metastatic gastroesophageal adenocarcinoma when used in combination with cisplatin-based regimens for patients from the Americas. We conducted a prospective phase II trial to investigate the efficacy of bevacizumab in combination with the oxaliplatin-based regimen, modified FOLFOX6, in patients with metastatic gastroesophageal adenocarcinoma.

Methods:

Patients with untreated metastatic adenocarcinoma of the stomach, gastroesophageal junction, or distal esophagus received mFOLFOX6 (leucovorin 400 mg/m2, fluorouracil 400 mg/m2 bolus and 2400 mg/m2 continuous infusion over 46 h, oxaliplatin 85 mg/m2) and bevacizumab (10 mg/kg) every 2 weeks until disease progression or intolerance. Response by RECIST was evaluated by CT scan every 8 weeks. The primary objective was progression-free survival (PFS); secondary objectives were safety, response rate, and overall survival (OS).

Results:

A total of 39 patients with untreated metastastic gastroesophageal adenocarcinoma were enrolled between September 2008 and June 2012. Median number of cycles administered was 12 (range, 4 to 86). The confirmed response rate was 56.4% (3 complete response and 19 partial response). The median PFS was 7.8 months and median OS was 14.7 months. Three patients remain on treatment, and 11 patients are alive, of whom 6 have survived >24 months. Treatment-related grade 3/4 toxicities included neutropenia (33.3%), neuropathy (20.5%), thromboembolism (VTE) (7.7%), thrombocytopenia (7.7%), anemia (2.6%), hypertension (2.6%), and proteinuria (2.6%). We observed no GI perforations or grade 3/4 GI hemorrhagic events.

Conclusions:

First-line mFOLFOX6 with bevacizumab for metastatic gastroesophageal adenocarcinoma was well tolerated and associated with longer PFS and OS compared with historical data from similar populations treated without bevacizumab. Our results suggest that the addition of bevacizumab to mFOLFOX6 may provide clinical benefit in American patients with metastatic gastroesophageal adenocarcinoma, a finding consistent with previous studies of first-line bevacizumab in combination with chemotherapy for this disease.
Experimental study of the impact of antimicrobial treatments on Campylobacter, Enterococcus and PCR-capillary electrophoresis single-strand conformation polymorphism profiles of the gut microbiota of chickens
Authors: Mourand Gwenaëlle , Jouy Eric , Bougeard Stéphanie , Dheilly Alexandra , Kérouanton Annaëlle , Zeitouni Salman , Kempf Isabelle
Published: August 2014

An experiment was conducted to compare the impact of antimicrobial treatments on the susceptibility of Campylobacter, Enterococcus faecium and Enterococcus faecalis, and on the diversity of broiler microbiota. Specific-pathogen-free chickens were first orally inoculated with strains of Campylobacter and Enterococcus faecium. Birds were then orally treated with recommended doses of oxytetracycline, sulfadimethoxine/trimethoprim, amoxicillin or enrofloxacin. Faecal samples were collected before, during and after antimicrobial treatment. The susceptibility of Campylobacter, Enterococcus faecium and Enterococcus faecalis strains isolated on supplemented or non-supplemented media was studied and PCR-capillary electrophoresis single-strand conformation polymorphism (CE-SSCP) profiles of the gut microbiota were analysed. Enrofloxacin-resistant Campylobacter were selected in the enrofloxacin-treated group and showed the Thr86Ile mutation in the gyrA gene. Acquisition of the tetO gene in Campylobacter coli isolates was significantly more frequent in birds given oxytetracycline. No impact of amoxicillin treatment on the susceptibility of Campylobacter could be detected. Ampicillin- and sulfadimethoxine/trimethoprim-resistant Enterococcus faecium were selected in amoxicillin-treated broilers, but no selection of the inoculated vancomycin-resistant Enterococcus faecium could be detected, although it was also resistant to tetracycline and sulfadimethoxine/trimethoprim. PCR-CE-SSCP revealed significant variations in a few peaks in treated birds as compared with non-treated chickens. In conclusion, antimicrobial treatments perturbed chicken gut microbiota, and certain antimicrobial treatments selected or co-selected resistant strains of Campylobacter and Enterococcus.