bluuebunny/crossref_metadata_2025 huggingface dataset:
Nitrogen supply controls vegetative growth, biomass and nitrogen allocation for grapevine (cv. Shiraz) grown in pots
Authors: Metay Aurélie , Magnier Jessica , Guilpart Nicolas , Christophe Angélique
Published: September 2014

Maintaining grapevine productivity with limited inputs is crucial in Mediterranean areas. Apart from water, nitrogen (N) is also an important limiting factor in grape growing. The effects of N deficiency on grapevine growth were investigated in this study. Two-year-old Vitis vinifera L.cv. Shiraz plants grafted on 110 R were grown in pots placed outside and exposed to various N supplies (0, 0.6, 1.2, 2.4 and 12 g plant–1) under well-watered conditions. At veraison, plants were harvested and organs separately dried, weighed and analysed for N. During plant growth, the length of the primary and secondary axes and the number of leaves on them were recorded. The N content of leaves was also analysed at three phenological stages (flowering, bunch closure and veraison). All growth processes were inhibited by N deficiency in an intensity-dependent manner. Quantitative relationships with N supply were established. Vegetative growth responded negatively to N stress when comparing control N supply with no N supply: primary axis elongation (–61%), leaf emergence on the primary axis (–47%), leaf emergence on the secondary axis (–94%) and lamina area expansion (–45%). Significant differences on the plant N status were observed from flowering onwards which might be useful for managing fertilisation.
Seed coating reduces respiration losses and affects sugar metabolism during germination and early seedling growth in cereals
Authors: Gorim Linda , Asch Folkard
Published: September 2014

Seed germination and the successful establishment of young seedlings is an important aspect of plant life. Seed coats are used to improve stand establishment and early seedling vigour. Seedlings growing from hydro-absorber coated barley, rye and wheat with coat-shares greater than 75% of the average seed have been shown to promote better seedling growth compared with those seedlings growing from uncoated seeds. We investigated how and why these seedlings performed better by analysing the proportion of grain reserves mobilised for growth and respiration as well as how both sucrose and glucose available in the embryo translated into seedling growth in the presence or absence of seed coats containing hydro-absorber gel. We found that mobilisation efficiency was higher, resulting in higher biomass in these cereals when they were coated. The relationship between sucrose and glucose available to the seedling as well as its correlation with early seedling growth indicate a switch in the enzymatic cleavage of embryonic sucrose from invertase to sucrose synthase. This in turn indicates that in coated seeds, embryonic tissue must be hypoxic leading to a more efficient use of glucose and thus reduced respiration losses during germination.
Decreased expression of aquaporin 2 is associated with impaired endometrial receptivity in controlled ovarian stimulation
Authors: Zhang Dan , Xu Gufeng , Zhang Runju , Zhu Yimin , Gao Huijuan , Zhou Caiyun , Sheng Jianzhong , Huang Hefeng
Published: September 2014

Recently, there has been evidence of decreased implantation rates with in vitro fertilisation and embryo transfer due to controlled ovarian stimulation (COS). The aim of this study was to investigate the effect of COS on embryo implantation and the role of aquaporin 2 (AQP2). We recruited eight patients who underwent COS and 40 matched controls. Endometrial samples were collected on Day 4~8 after injection of human chorionic gonadotrophin in the COS group and in the mid-secretory phase in the control group. Human endometrial morphological changes after COS were examined and expression of AQP2, leukaemia inhibitory factor (LIF) and integrin B3 (ITGB3) were determined by quantitative polymerase chain reaction, western blotting and immunohistochemistry in human endometrium and Ishikawa cells. Attachment rates were obtained using the embryo attachment test. The results showed that endometrial epithelial cells from the COS group were disrupted and lacked pinopodes. Messenger RNA and protein levels of AQP2, LIF and ITGB3 decreased in endometrial samples from the COS group. Knockdown of AQP2 resulted in reduced expression of LIF and ITGB3 and reduced embryo attachment rates. In conclusion, impaired endometrial receptivity in patients who underwent COS is correlated with a decreased expression of AQP2.
Automatic semantic encoding in verbal short-term memory: Evidence from the concreteness effect
Authors: Campoy Guillermo , Castellà Judit , Provencio Violeta , Hitch Graham J. , Baddeley Alan D.
Published: September 2014

The concreteness effect in verbal short-term memory (STM) tasks is assumed to be a consequence of semantic encoding in STM, with immediate recall of concrete words benefiting from richer semantic representations. We used the concreteness effect to test the hypothesis that semantic encoding in standard verbal STM tasks is a consequence of controlled, attention-demanding mechanisms of strategic semantic retrieval and encoding. Experiment 1 analysed the effect of presentation rate, with slow presentations being assumed to benefit strategic, time-dependent semantic encoding. Experiments 2 and 3 provided a more direct test of the strategic hypothesis by introducing three different concurrent attention-demanding tasks. Although Experiment 1 showed a larger concreteness effect with slow presentations, the following two experiments yielded strong evidence against the strategic hypothesis. Limiting available attention resources by concurrent tasks reduced global memory performance, but the concreteness effect was equivalent to that found in control conditions. We conclude that semantic effects in STM result from automatic semantic encoding and provide tentative explanations for the interaction between the concreteness effect and the presentation rate.
The equality case of the Penrose inequality for asymptotically flat graphs
Authors: Huang Lan-Hsuan , Wu Damin
Published: September 2014

We prove the equality case of the Penrose inequality in all dimensions for asymptotically flat hypersurfaces. It was recently proven by G. Lam that the Penrose inequality holds for asymptotically flat graphical hypersurfaces in Euclidean space with non-negative scalar curvature and with a minimal boundary. Our main theorem states that if the equality holds, then the hypersurface is a Schwarzschild solution. As part of our proof, we show that asymptotically flat graphical hypersurfaces with a minimal boundary and non-negative scalar curvature must be mean convex, using the argument that we developed in our paper, Hypersurfaces with non-negative scalar curvature (J. Differential Geom., vol. 95 (2013), pp. 249–278). This enables us to obtain the ellipticity for the linearized scalar curvature operator and to establish the strong maximum principles for the scalar curvature equation.
An improvement on eigenfunction restriction estimates for compact boundaryless Riemannian manifolds with nonpositive sectional curvature
Authors: Chen Xuehua
Published: September 2014

Let

(
M
,
g
)

(M,g)

be an

n
n

-dimensional compact boundaryless Riemannian manifold with nonpositive sectional curvature. Then our conclusion is that we can give improved estimates for the

L
p

L^p

norms of the restrictions of eigenfunctions of the Laplace-Beltrami operator to smooth submanifolds of dimension

k
k

, for

p
>

2
n

n
−
1

p>\dfrac {2n}{n-1}

when

k
=
n
−
1

k=n-1

and

p
>
2

p>2

when

k
≤
n
−
2

k\leq n-2

, compared to the general results of Burq, Gérard and Tzvetkov. Earlier, Bérard gave the same improvement for the case when

p
=
∞

p=\infty

, for compact Riemannian manifolds without conjugate points for

n
=
2

n=2

, or with nonpositive sectional curvature for

n
≥
3

n\geq 3

and

k
=
n
−
1

k=n-1

. In this paper, we give the improved estimates for

n
=
2

n=2

, the

L
p

L^p

norms of the restrictions of eigenfunctions to geodesics. Our proof uses the fact that the exponential map from any point in

x
∈
M

x\in M

is a universal covering map from

R

2

⋍

T

x

M

\mathbb {R}^2\backsimeq T_{x}M

to

M
M

, which allows us to lift the calculations up to the universal cover

(

R

2

,

g
~

)

(\mathbb {R}^2,\tilde {g})

, where

g
~

\tilde {g}

is the pullback of

g
g

via the exponential map. Then we prove the main estimates by using the Hadamard parametrix for the wave equation on

(

R

2

,

g
~

)

(\mathbb {R}^2,\tilde {g})

, the stationary phase estimates, and the fact that the principal coefficient of the Hadamard parametrix is bounded, by observations of Sogge and Zelditch. The improved estimates also work for

n
≥
3

n\geq 3

, with

p
>

4
k

n
−
1

p>\frac {4k}{n-1}

. We can then get the full result by interpolation.
The Nori fundamental gerbe of a fibered category
Authors: Borne Niels , Vistoli Angelo
Published: September 2014

We extend Nori’s theory of the fundamental group scheme to a theory of the fundamental gerbe, which applies to schemes, algebraic stacks, and more general fibered categories, even in the absence of a rational point. We give a Tannakian interpretation of the fundamental gerbe in terms of essentially finite bundles, extending Nori’s correspondence for complete varieties with a rational point. We also show how our formalism allows a natural formulation of Grothendieck’s Section Conjecture in arbitrary characteristic.
TBC1D9B functions as a GTPase-activating protein for Rab11a in polarized MDCK cells
Authors: Gallo Luciana I. , Liao Yong , Ruiz Wily G. , Clayton Dennis R. , Li Min , Liu Yong-Jian , Jiang Yu , Fukuda Mitsunori , Apodaca Gerard , Yin Xiao-Ming
Published: September 2014

Rab11a is a key modulator of vesicular trafficking processes, but there is limited information about the guanine nucleotide-exchange factors and GTPase-activating proteins (GAPs) that regulate its GTP-GDP cycle. We observed that in the presence of Mg2+(2.5 mM), TBC1D9B interacted via its Tre2-Bub2-Cdc16 (TBC) domain with Rab11a, Rab11b, and Rab4a in a nucleotide-dependent manner. However, only Rab11a was a substrate for TBC1D9B-stimulated GTP hydrolysis. At limiting Mg2+concentrations (<0.5 mM), Rab8a was an additional substrate for this GAP. In polarized Madin–Darby canine kidney cells, endogenous TBC1D9B colocalized with Rab11a-positive recycling endosomes but less so with EEA1-positive early endosomes, transferrin-positive recycling endosomes, or late endosomes. Overexpression of TBC1D9B, but not an inactive mutant, decreased the rate of basolateral-to-apical IgA transcytosis—a Rab11a-dependent pathway—and shRNA-mediated depletion of TBC1D9B increased the rate of this process. In contrast, TBC1D9B had no effect on two Rab11a-independent pathways—basolateral recycling of the transferrin receptor or degradation of the epidermal growth factor receptor. Finally, expression of TBC1D9B decreased the amount of active Rab11a in the cell and concomitantly disrupted the interaction between Rab11a and its effector, Sec15A. We conclude that TBC1D9B is a Rab11a GAP that regulates basolateral-to-apical transcytosis in polarized MDCK cells.
The role of Sec3p in secretory vesicle targeting and exocyst complex assembly
Authors: Luo Guangzuo , Zhang Jian , Guo Wei
Published: September 2014

During membrane trafficking, vesicular carriers are transported and tethered to their cognate acceptor compartments before soluble N-ethylmaleimide–sensitive factor attachment protein (SNARE)-mediated membrane fusion. The exocyst complex was believed to target and tether post-Golgi secretory vesicles to the plasma membrane during exocytosis. However, no definitive experimental evidence is available to support this notion. We developed an ectopic targeting assay in yeast in which each of the eight exocyst subunits was expressed on the surface of mitochondria. We find that most of the exocyst subunits were able to recruit the other members of the complex there, and mistargeting of the exocyst led to secretion defects in cells. On the other hand, only the ectopically located Sec3p subunit is capable of recruiting secretory vesicles to mitochondria. Our assay also suggests that both cytosolic diffusion and cytoskeleton-based transport mediate the recruitment of exocyst subunits and secretory vesicles during exocytosis. In addition, the Rab GTPase Sec4p and its guanine nucleotide exchange factor Sec2p regulate the assembly of the exocyst complex. Our study helps to establish the role of the exocyst subunits in tethering and allows the investigation of the mechanisms that regulate vesicle tethering during exocytosis.
Cbx2 stably associates with mitotic chromosomes via a PRC2- or PRC1-independent mechanism and is needed for recruiting PRC1 complex to mitotic chromosomes
Authors: Zhen Chao Yu , Duc Huy Nguyen , Kokotovic Marko , Phiel Christopher J. , Ren Xiaojun
Published: September 2014

Polycomb group (PcG) proteins are epigenetic transcriptional factors that repress key developmental regulators and maintain cellular identity through mitosis via a poorly understood mechanism. Using quantitative live-cell imaging in mouse ES cells and tumor cells, we demonstrate that, although Polycomb repressive complex (PRC) 1 proteins (Cbx-family proteins, Ring1b, Mel18, and Phc1) exhibit variable capacities of association with mitotic chromosomes, Cbx2 overwhelmingly binds to mitotic chromosomes. The recruitment of Cbx2 to mitotic chromosomes is independent of PRC1 or PRC2, and Cbx2 is needed to recruit PRC1 complex to mitotic chromosomes. Quantitative fluorescence recovery after photobleaching analysis indicates that PRC1 proteins rapidly exchange at interphasic chromatin. On entry into mitosis, Cbx2, Ring1b, Mel18, and Phc1 proteins become immobilized at mitotic chromosomes, whereas other Cbx-family proteins dynamically bind to mitotic chromosomes. Depletion of PRC1 or PRC2 protein has no effect on the immobilization of Cbx2 on mitotic chromosomes. We find that the N-terminus of Cbx2 is needed for its recruitment to mitotic chromosomes, whereas the C-terminus is required for its immobilization. Thus these results provide fundamental insights into the molecular mechanisms of epigenetic inheritance.
Molecular counting by photobleaching in protein complexes with many subunits: best practices and application to the cellulose synthesis complex
Authors: Chen Yalei , Deffenbaugh Nathan C. , Anderson Charles T. , Hancock William O.
Published: September 2014

The constituents of large, multisubunit protein complexes dictate their functions in cells, but determining their precise molecular makeup in vivo is challenging. One example of such a complex is the cellulose synthesis complex (CSC), which in plants synthesizes cellulose, the most abundant biopolymer on Earth. In growing plant cells, CSCs exist in the plasma membrane as six-lobed rosettes that contain at least three different cellulose synthase (CESA) isoforms, but the number and stoichiometry of CESAs in each CSC are unknown. To begin to address this question, we performed quantitative photobleaching of GFP-tagged AtCESA3-containing particles in living Arabidopsis thaliana cells using variable-angle epifluorescence microscopy and developed a set of information-based step detection procedures to estimate the number of GFP molecules in each particle. The step detection algorithms account for changes in signal variance due to changing numbers of fluorophores, and the subsequent analysis avoids common problems associated with fitting multiple Gaussian functions to binned histogram data. The analysis indicates that at least 10 GFP-AtCESA3 molecules can exist in each particle. These procedures can be applied to photobleaching data for any protein complex with large numbers of fluorescently tagged subunits, providing a new analytical tool with which to probe complex composition and stoichiometry.
Measuring fast gene dynamics in single cells with time-lapse luminescence microscopy
Authors: Mazo-Vargas Anyimilehidi , Park Heungwon , Aydin Mert , Buchler Nicolas E.
Published: September 2014

Time-lapse fluorescence microscopy is an important tool for measuring in vivo gene dynamics in single cells. However, fluorescent proteins are limited by slow chromophore maturation times and the cellular autofluorescence or phototoxicity that arises from light excitation. An alternative is luciferase, an enzyme that emits photons and is active upon folding. The photon flux per luciferase is significantly lower than that for fluorescent proteins. Thus time-lapse luminescence microscopy has been successfully used to track gene dynamics only in larger organisms and for slower processes, for which more total photons can be collected in one exposure. Here we tested green, yellow, and red beetle luciferases and optimized substrate conditions for in vivo luminescence. By combining time-lapse luminescence microscopy with a microfluidic device, we tracked the dynamics of cell cycle genes in single yeast with subminute exposure times over many generations. Our method was faster and in cells with much smaller volumes than previous work. Fluorescence of an optimized reporter (Venus) lagged luminescence by 15–20 min, which is consistent with its known rate of chromophore maturation in yeast. Our work demonstrates that luciferases are better than fluorescent proteins at faithfully tracking the underlying gene expression.
Inhibition of ESCRT-II–CHMP6 interactions impedes cytokinetic abscission and leads to cell death
Authors: Goliand Inna , Nachmias Dikla , Gershony Ofir , Elia Natalie
Published: September 2014

Recently the ESCRT-III filamentous complex was designated as the driving force for mammalian cell abscission, that is, fission of the intercellular membrane bridge connecting daughter cells at the end of cytokinesis. However, how ESCRT-III is activated to set on abscission has not been resolved. Here we revisit the role of the upstream canonical ESCRT players ESCRT-II and CHMP6 in abscission. Using high-resolution imaging, we show that these proteins form highly ordered structures at the intercellular bridge during abscission progression. Furthermore, we demonstrate that a truncated version of CHMP6, composed of its first 52 amino acids (CHMP6-N), arrives at the intercellular bridge, blocks abscission, and subsequently leads to cell death. This phenotype is abolished in a mutated version of CHMP6-N designed to prevent CHMP6-N binding to its ESCRT-II partner. Of interest, deleting the first 10 amino acids from CHMP6-N does not interfere with its arrival at the intercellular bridge but almost completely abolishes the abscission failure phenotype. Taken together, these data suggest an active role for ESCRT-II and CHMP6 in ESCRT-mediated abscission. Our work advances the mechanistic understanding of ESCRT-mediated membrane fission in cells and introduces an easily applicable tool for upstream inhibition of the ESCRT pathway in live mammalian cells.
Syntactic Reconstruction and Proto-Germanic
Authors: Walkden George
Published: September 2014

This book investigates methods, possibilities, and limitations in the reconstruction of syntax in a framework which holds that the object of enquiry is knowledge of language and which acknowledges that the transmission of that knowledge is discontinuous. The main objections to syntactic reconstruction raised in the literature are assessed, and it is argued that the reconstruction of syntax is qualitatively different from lexical-phonological reconstruction due to the so-called ‘correspondence problem’ it is also suggested that other objections to syntactic reconstruction based on assumed lack of parallel between syntax and phonology, such as the supposed absence of directional tendencies and inability to identify contact influence, are either illusory or reduce to the correspondence problem. It is argued that the approach taken in current Minimalist theories of syntactic variation, in which all such variation is attributed to the properties of lexical items, sheds light on the problem of syntactic reconstruction by enabling a clear comparison between syntactic and phonological variation, and opens the door for syntactic reconstruction as lexical reconstruction. Practical solutions for circumventing the correspondence problem are also discussed, in particular the use of both distributional properties of lexical items and the phonological forms of such items in order to establish cognacy. The bulk of the book is devoted to case studies from the early Germanic languages intended to illustrate this methodology, dealing with verb position in main clauses, the syntax of the wh-system, and the (non-)occurrence of null pronominal subjects and objects.
Introduction
Authors: Walkden George
Published: September 2014

This chapter outlines the aims of the book in more detail. It presents the approach to history that will be taken, as well as details of the syntactic theory adopted, and some discussion of the five main languages investigated: Gothic, Old Norse, Old English, Old High German, and Old Saxon. The chapter argues for a constructivist approach to history, and couples this with a syntactic framework of the kind developed in recent Minimalist theorizing. The texts and corpora that are used as empirical basis for the individual case studies are also discussed.
A methodology for syntactic reconstruction
Authors: Walkden George
Published: September 2014

This chapter lays out a framework for the reconstruction of syntax. Section 2.2 is dedicated to the question of syntactic variation: it defends an implementation of Principles & Parameters theory against the criticisms of Newmeyer (2004). Section 2.3 addresses the question of syntactic change, arguing that it is desirable to reduce ‘language’ to individual grammars as assumed within the generative tradition, and that the task of diachronic linguistics then becomes to investigate the historical relationships between these grammars, mediated by transmission and acquisition. In section 2.4 an attempt is made to draw parallels between lexical-phonological and syntactic reconstruction, and, where these fail, to work around them as far as possible.
The wh-system of early Germanic
Authors: Walkden George
Published: September 2014

This chapter capitalizes on the intuition that syntactic reconstruction is lexical reconstruction in order to reconstruct aspects of the early Germanic wh-system. This chapter gives an overview and analysis of constituent order in the wh-system. The following sections are devoted to more detailed examinations of individual wh-elements. Section 4.3 analyses attested cases of underspecification of reflexes of *hwat in the early Germanic languages; section 4.4 discusses the forms *hwaþeraz/*hweþeraz and their reflexes. A theme of this chapter is that comparative work on the grammars of living languages can inform work on historically attested languages and on reconstruction.
Philosophical Reflections on Expressive Music Performance
Authors: Doğantan-Dack Mine
Published: September 2014

This chapter aims to initiate a tradition of philosophizing about expressive music performance, and to draw attention to the immense complexity of the phenomenon. After revisiting Carl Seashore’s definition of performance and teasing apart some of its conceptual and methodological aspects, the chapter discusses some of the epistemological premises that have pervaded psychological research on expressive performance. It then explores the connection between performance expression and emotional expression in an attempt to identify potential universals of expressive music performance. It is argued that the meanings emanating from the sounds of a performance are the reflection of non-sonic factors, of historical–cultural contingencies, and of complex social dynamics that have not been targeted by the mainstream of expressive performance research. Drawing examples from both western and non-western cultural contexts, the chapter argues for the inclusion of philosophical enquiry within the field, so that expressive music performance may be more fully understood.
Heuristics for Expressive Performance
Authors: Leech-Wilkinson Daniel , Prior Helen M.
Published: September 2014

This chapter discusses concepts and terms that professional musicians find useful in preparing for and talking and thinking about expressive performance. An example is “shape,” which, as recent research has shown, is immensely flexible and useful for sharing ideas about how to generate expressive performance without having to specify exactly which sounds might be required. The word is used between musical performers with a high level of mutual understanding, as a way of communicating expressive features that are actually very difficult to articulate in more detail. Further examples of heuristics for musical expression are drawn from a recent interview study of professional musicians, and their implications are discussed. It is argued that this kind of terminology, easily dismissed as superficial or vague, is in fact precisely targeted to the nature of the task and is highly effective in use by musicians.
Commercial Sound Recordings and Trends in Expressive Music Performance
Authors: Fabian Dorottya
Published: September 2014

Sound recordings provide crucial evidence of stylistic changes in music performance, highlighting the strong impact of time and place (i.e. history and culture) on what is regarded as an expressive performance at any given time. This chapter summarizes some of these stylistic differences as pertaining to eighteenth-century baroque and nineteenth-century romantic music—first, by briefly reviewing a broad cross-section of both empirical and historical sources, and secondly, by providing analytical snapshots of commercially recorded performances in tandem with contemporaneous written documents and listeners’ perceptions of technical details and aesthetic effect. It highlights the need for closer collaboration between cognitive music psychologists and historical musicologists to create more sophisticated models and a deeper understanding of the relationship between expressive performance and taste. It also questions the usefulness of linking expressiveness primarily to compositional (and score-based) structures, and argues for more nuanced approaches that engage more with individual difference.
Expressiveness in Historical Perspective
Authors: Milsom David , Da Costa Neal Peres
Published: September 2014

This chapter examines the philosophical and aesthetic underpinnings of nineteenth-century performance, as suggested in contemporary written literature and heard on early recordings, and summarizes them as an almost universal understanding of music in terms of its linguistic and declamatory properties, giving rise to flexibility in the meaning of music notation and basic musical parameters, and being used to justify specific expressive practices. The chapter summarizes the main tenets of such thought as a context for understanding the nature of expressive practices in violin and piano playing, including portamento, vibrato, dislocation, and arpeggiation. The authors discuss their experiences of producing “stylistically reconstructive” recordings, highlighting the challenges and potential for musical expressiveness. The results suggest that any research into cognitive/psychological music performance, particularly of the romantic repertoire, must widen its parameters beyond the modern aesthetics of expressivity, and focus more on the singing and rhetorical devices examined in this chapter.
Temporal Variation in Singing as Interplay between Speech and Music in Estonian Songs
Authors: Lippus Pärtel , Ross Jaan
Published: September 2014

Acoustic syllable durations were measured in Estonian utterances performed in parallel as recited and sung. A systematic effect of phonological syllable length was found irrespective of the group of participants (contemporary or historic). This effect of syllable length was modified by the mode of performance: it was present considerably less in music than in speech. In music, the effect of syllable length was in turn modified by song: it was present in two of the three songs, but absent in one song. The above results suggest that the correspondence between linguistic duration and musical rhythm in a quantity language such as Estonian is loosely defined. The nature of the correspondence between linguistic quantity and musical rhythm may be considered to a certain extent analogous to the tone–tune relationship in tonal languages.
Expressiveness in the Performance of Bedzan Pygmies’ Vocal Polyphonies
Authors: Marandola Fabrice
Published: September 2014

Every performance of the vocal polyphonies of the Bedzan Pygmies demonstrates a subtle balance between the numerous variations performed by each individual singer and the necessity for the choir as a whole to preserve the identity of the piece. The variability of both scale and motivic systems is characteristic of these polyphonies, whose study requires the use of specific methods. This chapter describes how the combination of multitrack recordings, graphic transcriptions, and experiments leads to determination of the nature of the musical system. Based on a limited number of rules, this musical system involves a set of constraints that provide balance and ensure its sustainability, while creating a network of possibilities related to expressiveness at the collective level (scale system, motivic system, identity of the pieces), and at the individual level (intonation of the degrees, choice of the motives, constant interaction).
The Yablo Paradox
Authors: Cook Roy T
Published: September 2014

This book examines the Yablo paradox—a paradoxical, infinite sequence of sentences, each of which entails the falsity of all others later than it in the sequence—with special attention paid to the idea that this paradox provides us with an example of a semantic paradox that involves no circularity. The three main chapters of the book focus, respectively, on three questions that can be (and have been) asked about the Yablo construction. First, the Characterization Problem: What patterns of sentential reference (circular or not) generate semantic paradoxes? Addressing this problem requires an interesting and fruitful detour through the theory of directed graphs, allowing us to make connections between philosophical problems and purely mathematical ones. Next is the Circularity Question: Is the Yablo paradox genuinely non-circular? Answering this question is complicated: although the original formulation of the Yablo paradox is circular, it turns out that it is not so in any sense that can bear the blame for the paradox. Further, formulations of the paradox using infinitary conjunction provide genuinely non-circular constructions. Finally, we have the Generalizability Question: Can the Yabloesque pattern be used to generate genuinely non-circular variants of other paradoxes, such as epistemic and set-theoretic paradoxes? Although there are general constructions—unwindings—that transform circular constructions into Yablo-like sequences, it turns out that these sorts of construction are not “well-behaved” when transferred from semantic puzzles to puzzles of other sorts. The text concludes with a short discussion of the connections between the Yablo paradox and the Curry paradox.
Solution of Discrete Stokes Problems
Authors: Elman Howard C. , Silvester David J. , Wathen Andrew J.
Published: September 2014

This chapter concerns iterative methods for solution of the discrete Stokes equations. It discusses the preconditioned minimum residual method, preconditioning strategies and multigrid methods, including convergence analysis of these methods.
Optimization with PDE Constraints
Authors: Elman Howard C. , Silvester David J. , Wathen Andrew J.
Published: September 2014

This chapter is an introduction to techniques of optimization with constraints defined by partial differential equations. It discusses optimization and discretization methods together with solution algorithms for the resulting saddle-point problems.
Solution of discrete convection–diffusion problems
Authors: Stuart A. M. , Söli E.
Published: September 2014

This chapter concerns iterative methods for solution of discrete convection–diffusion equations. It discusses Krylov subspace methods, principally the generalized minimum residual method, together with preconditioning strategies and multigrid methods, including convergence analysis of these methods.
Solution of Discrete Navier–Stokes Problems
Authors: Elman Howard C. , Silvester David J. , Wathen Andrew J.
Published: September 2014

This chapter concerns iterative methods for solution of the discrete Navier–Stokes equations. The emphasis is on preconditioning methods tailored to the structure of the linearized differential equations and the impact of boundary conditions on derivation of methods. These ideas are combined with multigrid methods and algorithms for nonlinear iteration.
Circuit QED: superconducting qubits coupled to microwave photons
Authors: Girvin S. M.
Published: September 2014

This chapter introduces the basic concepts of quantum information processing with superconducting quantum circuits. It starts with a demonstration of how,in these electrodynamic systems, both the superconducting gap and the long-range Coulomb interactions contribute to the existence of collective modesthat have extremely low dissipationand that can be quantized. The chapter also gives in-depth coverage of quantum harmonic oscillators in all their glory from various perspectives. Superconducting qubits are then introduced, starting with the fundamental theory of the Josephson effect and moving on to a presentation of the variety of existing superconducting qubits. Particular attention is given to the dispersive readout of qubits through their interaction with a cavity into which flying modes can be scattered. Finally, the opportunities offered for quantum information processing by employing the cavity as a quantum bus are presented.
Quantum optomechanics
Authors: Marquardt F.
Published: September 2014

This chapter provides a general introduction to the basic concepts of quantum optomechanics. It shows how strongly quantum optomechanical systems reduce to a linear interaction between a phonon mode and the mode of the fluctuations of the cavity field. It then presents the effect of light on the response the mechanical system, drawing an analogy with sideband cooling. Homodyne measurement of the position of the mechanical system is described. The chapter ends by explaining how to prepare exotic states of a mechanical oscillator and how the physics of the interaction between light and matter at play in optomechanics may one dayallow investigations of the possible effects of quantum gravity.
Two-electron spin qubits in GaAs: control and dephasing due to nuclear spins
Authors: Yacoby A. , Bluhm H.
Published: September 2014

This chapter presents a review of quantum dots in two-dimensional electron gases. The spin qubits realized in these systems are strongly affected by the surrounding nuclear spins. An elegant demonstration is given that the nuclear spin bath is not as irreversible as one might think. Echo sequences can efficiently undo the dephasing of the qubitbrought about by the motion of nuclear spins.
Superconducting quantum circuits: artificial atoms coupled to 1D modes
Authors: Nakamura Y.
Published: September 2014

This chapter illustrates the special properties of quantum matter-light interaction in one dimension by experiments done on a superconducting artificial atom coupled to photons traveling along a microwave transmission line.
PseKNC-General: a cross-platform package for generating various modes of pseudo nucleotide compositions
Authors: Chen Wei , Zhang Xitong , Brooker Jordan , Lin Hao , Zhang Liqing , Chou Kuo-Chen
Published: September 2014

Summary: The avalanche of genomic sequences generated in the post-genomic age requires efficient computational methods for rapidly and accurately identifying biological features from sequence information. Towards this goal, we developed a freely available and open-source package, called PseKNC-General (the general form of pseudo k-tuple nucleotide composition), that allows for fast and accurate computation of all the widely used nucleotide structural and physicochemical properties of both DNA and RNA sequences. PseKNC-General can generate several modes of pseudo nucleotide compositions, including conventional k-tuple nucleotide compositions, Moreau–Broto autocorrelation coefficient, Moran autocorrelation coefficient, Geary autocorrelation coefficient, Type I PseKNC and Type II PseKNC. In every mode, >100 physicochemical properties are available for choosing. Moreover, it is flexible enough to allow the users to calculate PseKNC with user-defined properties. The package can be run on Linux, Mac and Windows systems and also provides a graphical user interface.

Availability and implementation: The package is freely available at: http://lin.uestc.edu.cn/server/pseknc .

Contact:  chenweiimu@gmail.com or lqzhang@vt.edu or kcchou@gordonlifescience.org .

Supplementary information:  Supplementary data are available at Bioinformatics online.
Effect of ocean warming and acidification on a plankton community in the NW Mediterranean Sea
Authors: Maugendre L. , Gattuso J.-P. , Louis J. , de Kluijver A. , Marro S. , Soetaert K. , Gazeau F.
Published: September 2014

The effect of ocean warming and acidification was investigated on a natural plankton assemblage from an oligotrophic area, the bay of Villefranche (NW Mediterranean Sea). The assemblage was sampled in March 2012 and exposed to the following four treatments for 12 days: control (∼360 μatm, 14°C), elevated pCO2 (∼610 μatm, 14°C), elevated temperature (∼410 μatm, 17°C), and elevated pCO2 and temperature (∼690 μatm, 17°C). Nutrients were already depleted at the beginning of the experiment and the concentrations of chlorophyll a (chl a), heterotrophic prokaryotes and viruses decreased, under all treatments, throughout the experiment. There were no statistically significant effects of ocean warming and acidification, whether in isolation or combined, on the concentrations of nutrients, particulate organic matter, chl a and most of the photosynthetic pigments. Furthermore, 13C labelling showed that the carbon transfer rates from 13C-sodium bicarbonate into particulate organic carbon were not affected by seawater warming nor acidification. Rates of gross primary production followed the general decreasing trend of chl a concentrations and were significantly higher under elevated temperature, an effect exacerbated when combined to elevated pCO2 level. In contrast to the other algal groups, the picophytoplankton population (cyanobacteria, mostly Synechococcus) increased throughout the experiment and was more abundant in the warmer treatment though to a lesser extent when combined to high pCO2 level. These results suggest that under nutrient-depleted conditions in the Mediterranean Sea, ocean acidification has a very limited impact on the plankton community and that small species will benefit from warming with a potential decrease of the export and energy transfer to higher trophic levels.
Hepatitis C in Sub-Saharan Africa: Urgent Need for Attention
Authors: Layden Jennifer E. , Phillips Richard , Opare-Sem Ohene , Akere Adegboyega , Salako Babatunde L. , Nelson Kenrad , Dugas Lara , Luke Amy , Tayo Bamidele O. , Cooper Richard S.
Published: September 2014

The hepatitis C virus (HCV), which was not recognized as an infectious agent until the 1980s, is responsible for a worldwide epidemic. The World Health Organization estimates global prevalence at 2.8%, with 185 million persons infected. In contrast to hepatitis B, where successful vaccine campaigns have reduced the disease burden, much less progress has been made toward the control of HCV. Phylogenetic studies suggest that HCV originated in Africa and has been endemic in some regions for at least 500–600 years. However, little is known about the epidemiology, transmission, and clinical course of HCV in Africa. With the advent of highly effective anti-HCV agents, there exists great potential to at least curb the global epidemic. For regions such as sub-Saharan Africa, however, this will require a thorough understanding of the regional population-level epidemiology, risk factors, and transmission mechanisms. Only then can effective treatment and prevention strategies be introduced.
Accurate Estimation of Energy Requirements of Young Patients
Authors: Carpenter Andrea , Pencharz Paul , Mouzaki Marialena
Published: September 2014

The provision of optimal nutritional care is based on accurate estimations of patients' resting energy expenditure. The latter can be calculated with the use of predictive equations or measured with indirect calorimetry (IC). Owing to their ease of use, mathematical equations have largely replaced IC in clinical practice. This article examines the limitations and predictive inaccuracy of commonly used equations in pediatrics, which may contribute to the provision of poor nutritional care and directly affect patient outcomes. In addition, the role of IC is discussed and the physiology of nutrient metabolism, in terms of energy expenditure, is reviewed.
miR‐222 Overexpression May Contribute to Liver Fibrosis in Biliary Atresia by Targeting PPP2R2A
Authors: Dong Rui , Zheng Yijie , Chen Gong , Zhao Rui , Zhou Zhijian , Zheng Shan
Published: September 2014

Objective:

Biliary atresia (BA) is a devastating liver disease in infants. Progressive hepatic fibrosis is often observed in postoperative patients with BA even after a successful Kasai portoenterostomy procedure. MicroRNA‐222 (miRNA) has been linked to the activation of stellate cells and the progression of liver fibrosis.

Methods:

In this study, the miR‐222 expression profile in BA and infants with anicteric choledochal cyst (CC) was determined. The functional effect of miR‐222 inhibition on the growth of the human hepatic stellate cell line LX‐2 was also evaluated. The downstream signaling pathways and target of miR‐222 were determined by coupling gene expression profiling and pathway analysis and by in silico prediction, respectively. In addition, we demonstrated miR‐222 overexpression in patients with BA compared with choledochal cyst controls.

Results:

Inhibition of miR‐222 in the LX‐2 cell line significantly decreased cell proliferation. We also identified protein phosphatase 2A subunit B as a target of miR‐222. The downstream signaling pathway, Akt, was also influenced by miR‐222. A consistent reduction of Akt phosphorylation and Ki67 in the LX‐2 line was shown following miR‐222 suppression.

Conclusions:

Our results show that miR‐222 overexpression is common in BA and contributes to LX‐2 cell proliferation by targeting protein phosphatase 2A subunit B and Akt signaling.
Abdominal Circumference or Gastric Residual Volume as Measure of Feed Intolerance in VLBW Infants
Authors: Kaur Avneet , Kler Neelam , Saluja Satish , Modi Manoj , Soni Arun , Thakur Anup , Garg Pankaj
Published: September 2014

Background:

The aim of the study was to compare prefeed abdominal circumference (AC) and gastric residual volume (GRV) as a measure of feed intolerance in very‐low‐birth‐weight infants (VLBW).

Methods:

Eighty VLBW infants were randomized to 2 groups; feed intolerance was monitored by measuring either GRV group or prefeed AC group. The primary outcome was time to full enteral feeds (180 mL · kg−1 · day−1). Other main outcome measures were feed interruption days, duration of parenteral nutrition, incidence of culture positive sepsis, necrotizing enterocolitis, mortality, and duration of hospital stay.

Results:

The median (interquartile range) time to achieve full feeds was 10 (9–13) versus 14 (12–17.5) days in AC and GRV groups, respectively (P < 0.001). Infants in AC group had fewer feed interruption days (0 [0–2] vs 2.0 [1, 5], P < 0.001) and shorter duration of parenteral nutrition (P < 0.001). The incidence of culture‐positive sepsis in AC and GRV groups was 17.5% and 30 %, respectively (P = 0.18). Duration of hospital stay and mortality were comparable in both the groups.

Conclusions:

Prefeed AC as a measure of feed intolerance in VLBW infants may shorten the time taken to achieve full feeds.
Pico Gauges for Minimally Invasive Intracellular Hydrostatic Pressure Measurements
Authors: Knoblauch Jan , Mullendore Daniel L. , Jensen Kaare H. , Knoblauch Michael
Published: September 2014

Intracellular pressure has a multitude of functions in cells surrounded by a cell wall or similar matrix in all kingdoms of life. The functions include cell growth, nastic movements, and penetration of tissue by parasites. The precise measurement of intracellular pressure in the majority of cells, however, remains difficult or impossible due to their small size and/or sensitivity to manipulation. Here, we report on a method that allows precise measurements in basically any cell type over all ranges of pressure. It is based on the compression of nanoliter and picoliter volumes of oil entrapped in the tip of microcapillaries, which we call pico gauges. The production of pico gauges can be accomplished with standard laboratory equipment, and measurements are comparably easy to conduct. Example pressure measurements are performed on cells that are difficult or impossible to measure with other methods.
Accurate atomic displacement parameters from time-of-flight neutron-diffraction data at TOPAZ
Authors: Jørgensen Mads R. V. , Hathwar Venkatesha R. , Sist Mattia , Wang Xiaoping , Hoffmann Christina M. , Briseno Alejandro L. , Overgaard Jacob , Iversen Bo B.
Published: September 2014

Accurate atomic displacement parameters (ADPs) are a good indication of high-quality diffraction data. Results from the newly commissioned time-of-flight Laue diffractometer TOPAZ at the SNS are presented. Excellent agreement is found between ADPs derived independently from the neutron and X-ray data emphasizing the high quality of the data from the time-of-flight Laue diffractometer.
Density functional calculations of polysynthetic Brazil twinning in α-quartz. Corrigenda and addenda
Authors: Grimmer Hans , Delley Bernard
Published: September 2014

Two corrections and a number of additions are made to the article by Grimmer & Delley [Acta Cryst.(2012), A68, 359–365].
Quantitative gas saturation estimation by frequency‐dependent amplitude‐versus‐offset analysis
Authors: Wu Xiaoyang , Chapman Mark , Li Xiang‐Yang , Boston Patrick
Published: September 2014

Seismic amplitudes contain important information that can be related to fluid saturation. The amplitude‐versus‐offset analysis of seismic data based on Gassmann's theory and the approximation of the Zoeppritz equations has played a central role in reservoir characterization. However, this standard technique faces a long‐standing problem: its inability to distinguish between partial gas and “fizz‐water” with little gas saturation. In this paper, we studied seismic dispersion and attenuation in partially saturated poroelastic media by using frequency‐dependent rock physics model, through which the frequency‐dependent amplitude‐versus‐offset response is calculated as a function of porosity and water saturation. We propose a cross‐plotting of two attributes derived from the frequency‐dependent amplitude‐versus‐offset response to differentiate partial gas saturation and “fizz‐water” saturation. One of the attributes is a measure of “low frequency”, or Gassmann, of reflectivity, whereas the other is a measure of the “frequency dependence” of reflectivity. This is in contrast to standard amplitude‐versus‐offset attributes, where there is typically no such separation. A pragmatic frequency‐dependent amplitude‐versus‐offset inversion for rock and fluid properties is also established based on Bayesian theorem. A synthetic study is performed to explore the potential of the method to estimate gas saturation and porosity variations. An advantage of our work is that the method is in principle predictive, opening the way to further testing and calibration with field data. We believe that such work should guide and augment more theoretical studies of frequency‐dependent amplitude‐versus‐offset analysis.