bluuebunny/crossref_metadata_2025 huggingface dataset:
The non-cell-autonomous component of ALS: new in vitro models and future challenges
Authors: Ferraiuolo Laura
Published: September 2014

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder affecting the motor nerves. At present, there is no effective therapy for this devastating disease and only one Food and Drug Administration (FDA)-approved drug, riluzole, is known to moderately extend survival. In the last decade, the field of ALS has made a remarkable leap forward in understanding some of the genetic causes of this disease and the role that different cell types play in the degenerative mechanism affecting motor neurons. In particular, astrocytes have been implicated in disease progression, and multiple studies suggest that these cells are valuable therapeutic targets. Recent technological advancements have provided new tools to generate astrocytes from ALS patients either from post-mortem biopsies or from skin fibroblasts through genetic reprogramming. The advent of induced pluripotent stem cell (iPSC) technology and the newly developed induced neural progenitor cells (iNPCs) have created unprecedented exciting opportunities to unravel the mechanisms involved in neurodegeneration and initiate high-throughput drug screenings.
WIPI2b and Atg16L1: setting the stage for autophagosome formation
Authors: Wilson Michael I. , Dooley Hannah C. , Tooze Sharon A.
Published: September 2014

The double-membraned autophagosome organelle is an integral part of autophagy, a process that recycles cellular components by non-selectively engulfing and delivering them to lysosomes where they are digested. Release of metabolites from this process is involved in cellular energy homoeostasis under basal conditions and during nutrient starvation. Selective engulfment of protein aggregates and dysfunctional organelles by autophagosomes also prevents disruption of cellular metabolism. Autophagosome formation in animals is crucially dependent on the unique conjugation of a group of ubiquitin-like proteins in the microtubule-associated proteins 1A/1B light chain 3 (LC3) family to the headgroup of phosphatidylethanolamine (PE) lipids. LC3 lipidation requires a cascade of ubiquitin-like ligase and conjugation enzymes. The present review describes recent progress and discovery of the direct interaction between the PtdIns3P effector WIPI2b and autophagy-related protein 16-like 1 (Atg16L1), a component of the LC3-conjugation complex. This interaction makes the link between endoplasmic reticulum (ER)-localized production of PtdIns3P, triggered by the autophagy regulatory network, and recruitment of the LC3-conjugation complex crucial for autophagosome formation.
Chemical intervention tools to probe phosphoinositide-dependent signalling
Authors: Woscholski Rudiger
Published: September 2014

Chemical intervention tools have been beneficial to many investigations elucidating signalling networks and interactions. The present review summarizes the current status of chemical tools to probe phosphoinositide metabolism and signalling. In particular, phosphoinositide-targeting tools are compared with protein-targeting tools with respect to their unique advantages and possible applications.
Layer‐based RED‐FEC (L‐RED‐FEC) method for wireless scalable video streaming
Authors: Ha H. , Yim C.
Published: September 2014

A layer‐based random early detection (RED) forward error correction (FEC) method for scalable video streaming over wireless networks is proposed. The proposed method determines the FEC rate in accordance with the layer‐based error propagation effect as well as network traffic load. Furthermore, a packet importance model based on layer information of scalable video coding (SVC) has been developed for efficient FEC assignment considering the video quality. Simulation results show that the proposed method achieves higher peak signal‐to‐noise ratio (PSNR) values compared with the conventional FEC schemes under various network conditions.
Energy‐efficient sub‐DAC merging scheme for variable resolution SAR ADC
Authors: Srinivasan S.R. , Balsara P.T.
Published: September 2014

An energy‐efficient capacitive digital‐to‐analogue converter (DAC) switching method for a reconfigurable successive‐approximation register (SAR) analogue‐to‐digital converter (ADC) is proposed. The proposed method can achieve a variable resolution starting from 1 bit with 1 bit resolution increments. The proposed method achieves the energy savings due to the fact that the binary‐weighted capacitors are merged with the main‐DAC, as and when required. When sized for the same thermal noise as the traditional SAR ADC, the proposed method achieves 96.9% reduction in switching energy and a factor of 2 improvement in static linearity performance. If sized for the same static linearity as the conventional SAR ADC, the DAC area could be reduced by a factor of 4, which further improves the switching energy savings to 99.2%.
Generation of orange pulse laser in waterproof fluoride glass fibre with graphene thin film
Authors: Fujimoto Y. , Suzuki T. , Ochante R.A.M. , Hirayama T. , Murakami M. , Shiraga H. , Yoshida M. , Ishii O. , Yamazaki M.
Published: September 2014

Orange laser pulses were successfully generated in a Pr‐doped waterproof fluoride glass fibre (Pr:WPFGF) using a graphene thin film as a saturable absorber (SA). Two pulse generation modes were observed: a continuous mode with 0.47 µs pulse duration with a 2.61 µs repetition period and a single giant pulse mode with 9.7 ns pulse duration. The peak wavelength was 603 nm. This result shows that a graphene thin film can be effective as an SA in the visible region, and in the future a visible ultra‐short pulse laser with a modelocking technique may be demonstrated.
Electrostatic contribution from solvent in modulating single-walled carbon nanotube association
Authors: Ou Shu-Ching , Patel Sandeep
Published: September 2014

We perform all-atom molecular dynamics simulations to compute the potential of mean force (PMF) between two (10,10) single-walled carbon nanotubes solvated in pure nonpolarizable SPC/E and polarizable TIP4P-FQ water, at various temperatures. In general, the reversible work required to bring two nanotubes from a dissociated state (free energy reference) to contact state (free energy minimum) is more favorable and less temperature-dependent in TIP4P-FQ than in SPC/E water models. In contrast, molecular properties and behavior of water such as the spatially-resolved water number density (intertube, intratube, or outer regions), for TIP4P-FQ are more sensitive to temperature than SPC/E. Decomposition of the solvent-induced PMF into different spatial regions suggests that TIP4P-FQ has stronger temperature dependence; the opposing destabilizing/stabilizing contributions from intertube water and more distal water balance each other and suppress the temperature dependence of total association free energy. Further investigation of hydrogen bonding network in intertube water reveals that TIP4P-FQ retains fewer hydrogen bonds than SPC/E, which correlates with the lower water number density in this region. This reduction of hydrogen bonds affects the intertube water dipoles. As the intertube volume decreases, TIP4P-FQ dipole moment approaches the gas phase value; the distribution of dipole magnitude also becomes narrower due to less average polarization/perturbation from other water molecules. Our results imply that the reduction of water under confinement may seem trivial, but underlying effects to structure and free energetics are non-negligible.
A computational and experimental study of the linear and nonlinear response of a star polymer melt with a moderate number of unentangled arms
Authors: Fitzgerald Barry W. , Lentzakis Helen , Sakellariou Georgios , Vlassopoulos Dimitris , Briels Wim J.
Published: September 2014

We present from simulations and experiments results on the linear and nonlinear rheology of a moderate functionality, low molecular weight unentangled polystyrene (PS) star melt. The PS samples were anionically synthesized and close to monodisperse while their moderate functionality ensures that they do not display a pronounced core effect. We employ a highly coarse-grained model known as Responsive Particle Dynamics where each star polymer is approximated as a point particle. The eliminated degrees of freedom are used in the definition of an appropriate free energy as well as describing the transient pair-wise potential between particles that accounts for the viscoelastic response. First we reproduce very satisfactorily the experimental moduli using simulation. We then consider the nonlinear response of the same polymer melts by implementing a start-up shear protocol for a wide range of shear rates. As in experiments, we observe the development of a stress overshoot with increasing shear rate followed by a steady-state shear stress. We also recover the shear-thinning nature of the melt, although we slightly overestimate the extent of shear-thinning with simulations. In addition, we study relaxations upon the removal of shear where we find encouraging agreement between experiments and simulations, a finding that corroborates our agreement for the linear rheology.
Suppressing light reflection from polycrystalline silicon thin films through surface texturing and silver nanostructures
Authors: Akhter Perveen , Huang Mengbing , Kadakia Nirag , Spratt William , Malladi Girish , Bakhru Hassarum
Published: September 2014

This work demonstrates a novel method combining ion implantation and silver nanostructures for suppressing light reflection from polycrystalline silicon thin films. Samples were implanted with 20-keV hydrogen ions to a dose of 1017/cm2, and some of them received an additional argon ion implant to a dose of 5 × 1015 /cm2 at an energy between 30 and 300 keV. Compared to the case with a single H implant, the processing involved both H and Ar implants and post-implantation annealing has created a much higher degree of surface texturing, leading to a more dramatic reduction of light reflection from polycrystalline Si films over a broadband range between 300 and 1200 nm, e.g., optical reflection from the air/Si interface in the AM1.5 sunlight condition decreasing from ∼30% with an untextured surface to below 5% for a highly textured surface after post-implantation annealing at 1000 °C. Formation of Ag nanostructures on these ion beam processed surfaces further reduces light reflection, and surface texturing is expected to have the benefit of diminishing light absorption losses within large-size (>100 nm) Ag nanoparticles, yielding an increased light trapping efficiency within Si as opposed to the case with Ag nanostructures on a smooth surface. A discussion of the effects of surface textures and Ag nanoparticles on light trapping within Si thin films is also presented with the aid of computer simulations.
Graphene vertical hot-electron terahertz detectors
Authors: Ryzhii V. , Satou A. , Otsuji T. , Ryzhii M. , Mitin V. , Shur M. S.
Published: September 2014

We propose and analyze the concept of the vertical hot-electron terahertz (THz) graphene-layer detectors (GLDs) based on the double-GL and multiple-GL structures with the barrier layers made of materials with a moderate conduction band off-set (such as tungsten disulfide and related materials). The operation of these detectors is enabled by the thermionic emissions from the GLs enhanced by the electrons heated by incoming THz radiation. Hence, these detectors are the hot-electron bolometric detectors. The electron heating is primarily associated with the intraband absorption (the Drude absorption). In the frame of the developed model, we calculate the responsivity and detectivity as functions of the photon energy, GL doping, and the applied voltage for the GLDs with different number of GLs. The detectors based on the cascade multiple-GL structures can exhibit a substantial photoelectric gain resulting in the elevated responsivity and detectivity. The advantages of the THz detectors under consideration are associated with their high sensitivity to the normal incident radiation and efficient operation at room temperature at the low end of the THz frequency range. Such GLDs with a metal grating, supporting the excitation of plasma oscillations in the GL-structures by the incident THz radiation, can exhibit a strong resonant response at the frequencies of several THz (in the range, where the operation of the conventional detectors based on A3B5 materials, in particular, THz quantum-well detectors, is hindered due to a strong optical phonon radiation absorption in such materials). We also evaluate the characteristics of GLDs in the mid- and far-infrared ranges where the electron heating is due to the interband absorption in GLs.
Adaptive fuzzy dynamic surface control for the chaotic permanent magnet synchronous motor using Nussbaum gain
Authors: Luo Shaohua
Published: September 2014

This paper is concerned with the problem of adaptive fuzzy dynamic surface control (DSC) for the permanent magnet synchronous motor (PMSM) system with chaotic behavior, disturbance and unknown control gain and parameters. Nussbaum gain is adopted to cope with the situation that the control gain is unknown. And the unknown items can be estimated by fuzzy logic system. The proposed controller guarantees that all the signals in the closed-loop system are bounded and the system output eventually converges to a small neighborhood of the desired reference signal. Finally, the numerical simulations indicate that the proposed scheme can suppress the chaos of PMSM and show the effectiveness and robustness of the proposed method.
Electrical modeling of InAs/GaSb superlattice mid-wavelength infrared pin photodiode to analyze experimental dark current characteristics
Authors: Delmas Marie , Rodriguez Jean-Baptiste , Christol Philippe
Published: September 2014

Dark current characteristics of 7 Monolayers (ML) InAs/ 4 ML GaSb SL pin photodiodes are simulated using ATLAS software. Using appropriate models and material parameters, we obtain good agreement between the simulated and the experimental dark current curves of photodiodes grown by molecular beam epitaxy. The n-type non-intentionally-doped (nid) SL samples exhibit a dependence of the lifetime with temperature following the T−12 law, signature of Shockley-Read-Hall (SRH) Generation-Recombination current. We also studied the dependence of the dark current with the absorber doping level. It appears that the absorber doping level must not exceed a value of 2 × 1015 cm−3, above this value the dark current is increasing with increased doping level. However for this doping value, a dark current as low as 5 × 10−9 A/cm2, at 50 mV reverse bias at 77 K can be obtained.
A theoretical study of the thermodynamic properties of YMgX4 (X=Co, Ni, Cu) compounds
Authors: Li Ruizi , Shen Jiang , Tian Fuyang
Published: September 2014

The stability, electronic structures, elastic and thermal properties of the ternary YMgX4 (X=Co, Ni, Cu) compounds are investigated by first principle calculations in combination with the quasi-harmonic Debye model. The three compounds are predicted to be stable according to the formation enthalpies (ΔH), elastic constants (cij) and phonon dispersion models. The elastic constants and polycrystalline elastic moduli reveal the relatively low anisotropy of these compounds. The electronic structures and bonding characters are analyzed by the electron densities of states and difference charge densities in the (110) plane. The comparisons between the phonon density of state and the quasi-harmonic Debye model imply the heat capacities (Cv) and vibrational entropies (S) are close for YMgCo4 and YMgCu4, whereas large deviation for YMgNi4. A possible reason is that YMgNi4 has the slightly strong directional bondings, relative to YMgCo4 and YMgCu4.
A Barium Vanadium(V) Selenite Hydrate, Ba(VO2)2(SeO3)2·H2O: A Novel 3D Polymer of Cross-Linked Sheets with Embedded ···V–O–V··· 21 Helices
Authors: Kilminster Kieryn L. , Lincoln Francis J. , Skelton Brian W. , White Allan H.
Published: September 2014

The characterisation, by a single-crystal X-ray study at ~150 K, of brown acicular crystals of barium(ii) bis(dioxovanadium(v)) bis(selenite(iv)) monohydrate, BaSe2V2O10·H2O, obtained as a minor product of the synthesis of the previously reported ‘Ba(VO)2(SeO3)2(HSeO3)2’, is recorded. Crystals are monoclinic, P21/c, a = 10.803(2), b = 5.1126(8), c = 17.905(3) Å, β = 92.048(2)°, V = 988.3(3) Å3, 2456 independent diffractometer reflections refining to R1 = 0.032, wR2 = 0.084. A single BaV2Se2O11H2 formula unit, devoid of crystallographic symmetry, comprises the asymmetric unit of the structure, which is a three-dimensional polymer, with component sheets parallel to the crystallographic b axis, containing pentavalent vanadium atoms, one five-, the other six-coordinate, linked by selenite pyramids.
Whorfian effects on colour memory are not reliable
Authors: Wright Oliver , Davies Ian R. L. , Franklin Anna
Published: September 2014

The Whorfian hypothesis suggests that differences between languages cause differences in cognitive processes. Support for this idea comes from studies that find that patterns of colour memory errors made by speakers of different languages align with differences in colour lexicons. The current study provides a large-scale investigation of the relationship between colour language and colour memory, adopting a cross-linguistic and developmental approach. Colour memory on a delayed matching-to-sample (XAB) task was investigated in 2 language groups with differing colour lexicons, for 3 developmental stages and 2 regions of colour space. Analyses used a Bayesian technique to provide simultaneous assessment of two competing hypotheses (H1–Whorfian effect present, H0–Whorfian effect absent). Results of the analyses consistently favoured H0. The findings suggest that Whorfian effects on colour memory are not reliable and that the importance of such effects should not be overestimated.
Mental fixation and metacognitive predictions of insight in creative problem solving
Authors: Storm Benjamin C. , Hickman Michelle L.
Published: September 2014

Five experiments examined the influence of exposure to fixating information on metacognitive judgements of insight in creative problem solving. Participants were briefly presented with a series of Remote Associates Test problems and were asked to predict the likelihood of solving the problems at a later time. Before making predictions, however, participants were exposed to cue–response pairs designed to induce fixation. Although participants solved fewer problems in this fixation condition than in a baseline condition, when it came to making predictions, participants were just as confident in their ability to solve problems in the fixation condition as they were in the baseline condition. In fact, in some experiments, participants were significantly more confident in the fixation condition than in the baseline condition. These results suggest that people may not take into account the fixating effects of nontarget information when making judgements about their ability to solve problems.
Verb position in early Germanic main clauses
Authors: Walkden George
Published: September 2014

This chapter represents an attempt to put the methodology for syntactic reconstruction outlined in the previous chapter into practice. The focus throughout is on the position of the finite verb in declarative main clauses. Section 3.2 focuses particularly on the V2/V3 alternation that has often been observed, arguing that it is information-structurally conditioned and can be reconstructed for Proto-Northwest Germanic. In section 3.3 it considers V1 main clauses. section 3.4 it discusses ‘verb-late’ main clauses, which have so far resisted insightful analysis. After demonstrating the presence of such clauses in all the early West Germanic languages, it proposes an account based on the discourse status of these clauses. Section 3.5 is an attempt to integrate Gothic into the picture.
Null arguments in early Germanic
Authors: Walkden George
Published: September 2014

This chapter discusses the occurrence of null arguments in early Germanic. In 5.2 it presents data on the occurrence of null arguments from five key early Germanic languages, including new quantitative studies of Gothic, Old Norse, Old English, and Old Saxon. Section 5.3 analyses these data within a generative framework, assessing the applicability of different theories. It argues that the theory of identification of null subjects by rich verbal agreement is not sufficient to explain the range of null arguments attested in early Germanic; a topic-drop analysis is also ruled out. It is argued the early Northwest Germanic languages were ‘partial’ null argument languages. In 5.4 these languages are looked at from a diachronic perspective, and it is argued that the restriction to main clauses found in Northwest Germanic is an innovation, and that we can tentatively reconstruct Proto-Germanic (like Gothic) as a canonical null subject language.
Introduction: The C Word
Authors: Ran Hirschl
Published: September 2014

From its beginnings as a relatively obscure and exotic subject studied by a devoted few, comparative constitutionalism has developed into one of the more fashionable subjects in contemporary legal scholarship, and has become a cornerstone of constitutional jurisprudence and constitution-making in an increasing number of countries worldwide. Despite this tremendous renaissance, the “comparative” aspect of comparative constitutional law, as a method and a project, remains blurry and under-theorized. The introduction sets out the main arguments and structure of the book. The intellectual history and analytical underpinnings of comparative constitutional inquiry are charted and the various types, aims, and methodologies of engagement with the constitutive laws of others through the ages are probed. The introduction also surveys in a nutshell arguments developed in the book as to how and why comparative constitutional inquiry has been, and perhaps ought to be more extensively, pursued by academics and jurists worldwide.
6 Case Selection and Research Design in Comparative Constitutional Studies
Authors: Ran Hirschl
Published: September 2014

Comparative constitutional law’s methodological matrix is fuzzy and amorphous. A close look at social science methods suggests a toolkit of considerations to be addressed in conducting comparative constitutional inquiry, thus supporting various types of comparative constitutional studies. The meanings, purposes, and modes of comparative inquiry in contemporary comparative constitutional studies are identified; some basic principles of case selection and research design employed in inference-oriented small-N studies are presented; and the emerging world of multivariate, large-N studies is explored. It is argued that no research method enjoys an a priori advantage over another without taking into account the scope and nature of the studied phenomenon or the question the research purports to address. Thus, attempts to outline an “official” comparative method are not only unrealistic but also unwise. Comparative constitutionalists should settle instead on a set of several more sensible guiding principles, common rules of casuality, and a multi-method approach.
Expressive Performance in Contemporary Concert Music
Authors: Clarke Eric , Doffman Mark
Published: September 2014

The majority of recent empirical research on performance has focused on material from common practice repertoires, rather than on contemporary music, much of which is marked by radical changes in compositional style, greater flexibility in performance, and increased uncertainty for listeners. This chapter examines how the perceptuo-motor organization of expression may be disturbed or compromised by complex musical materials, but moves beyond a purely psychological approach to consider the influence of histories and style, suggesting ways in which often radical features of notation, composition, and performance practice participate in changing attitudes and approaches to expression. It also examines the significance of developments such as extended techniques and electro-acoustic music in considering what it means to be technically accomplished and expressively appropriate in contemporary performance, and it suggests some implications and future directions for the empirical investigation of expression in new music.
Expressiveness in Jazz Performance
Authors: Bauer William R.
Published: September 2014

This chapter focuses on the ways performers use jazz as an immediate, dynamic communicative medium, and personalize elements of a stylistic vocabulary by manipulating them to form expressive gestures. Featuring passages in which Louis Armstrong achieves heightened emotional expression, the case studies illustrate schemata and techniques that individual soloists use to convey meaning to experienced listeners and dancers. Two salient features of jazz performance practice are highlighted—a particular variety of swing that results from cross-tempo, and oral–syntactical phrasing, through which soloists generate large-dimension narratives out of recurrent “multiforms” and their variation. Jazz’s rich history and prehistory continue to inform current performance practices, and historical sources show that defining elements of instrumental practices, such as swing and phrasing, pre-existed in African-American vocal practices. In key respects, these correlate with deeply embedded African musical and linguistic practices, which early jazz musicians enculturated to African-American oral traditions extended.
Audience Response and Expressive Pitch Inflections in a Live Recording of Legendary Singer Kesar Bai Kerkar
Authors: van der Meer Wim
Published: September 2014

This chapter examines several “snapshots” from a recording by the legendary singer Kesar Bai Kerkar (1892–1977), in which the customary audience response to a concert of classical Hindustani music, in the form of appreciative verbal interjections, is clearly audible. These responses identify “special” moments in the performance, which can be considered particularly expressive. Praat software was used to generate pitch-lines, which elucidate what is happening in the performance at these selected moments. The analyses must be understood within the framework of the music being performed and the ideas about aesthetics of expression. A brief outline of expressivity in the context of Hindustani music is given. The recording is from one genre, a particular period, and one school, and the introductory sketch about expression of emotion and the role of raga in the context of Hindustani music is necessarily a brief synopsis of a vast subject.
Quantitative Methods
Authors: Goebl Werner , Dixon Simon , Schubert Emery
Published: September 2014

This chapter introduces the reader to developing and state-of-the-art tools for measuring musical expressivity. It summarizes recent quantitative measurement and analysis techniques of three domains of musical expressiveness: body motion, musical sound, and listeners’ continuous response to musical sound. It outlines computational methods to quantitatively assess expressive aspects of the body movements of the performing musicians, to extract expressive information from the musical sound itself, and to examine the perception of expressiveness through self-report continuous response methods. The chapter highlights the critical philosophical implications of making measurements of expressiveness, specifically in distinguishing between the measurement of physical aspects, such as motion and musical characteristics, and experiential aspects—the actual sensation of expressiveness experienced by the perceiver. The key philosophical point that unifies the chapter is that each of these aspects is understood through the world of ideas, definitions, and, most importantly, instruments for measuring physical and psychometric signals.
Implications for Music Studies
Authors: Cook Nicholas
Published: September 2014

To speak of the expressivity of music is to refocus attention from musical artefacts such as scores towards the experience of music as performed: rather than the expressivity of the performance adding to that of the work, the listener's concern is with the total expressiveness of what is heard. This refocusing of attention represents a radical reconstruction of the object of musical study—one that does not entail forgetting about scores, but rather seeking to understand the role that they play in the culture of music as performance. Seen in this perspective, musicology is able to draw on the tradition of cross-disciplinary research, ranging from cultural to computational perspectives. It might indeed become the first field to deliver on the potential for productive interaction between traditional and digital approaches to the humanities.
Implications for Empirical Expressive Music Performance Research
Authors: Davidson Jane W.
Published: September 2014

This chapter explores the implications of the issues discussed in the current volume for future empirical expressive music performance enquiry. It argues for the continued development of diverse approaches to capture quantifiable as well as qualitative factors leading to the generation of musical expression, acknowledging that such research is not easy, but is necessary to balance previous work that adopted a predominantly cognitive stance, ignoring socio-cultural context.  Inevitably, mixed methods involve techniques such as juxtaposing objective measurements of one variable (e.g. the degree of bodily movement according to an intended expressive intention) against observed qualitative data that may seems less justifiable within the more scientific framework of quantitative techniques, but which offer rich interpretation and inference. Prospects for the future involve finding methodological and theoretical paradigms to extend and deepen current empirical findings and to maintain a sense of critical reflection on what remains to be understood.
Introduction: Why Should We Care?
Authors: Cook Roy T
Published: September 2014

This chapter argues for the importance of the Yablo paradox, and motivates the chapters to follow. Particular attention is paid to the thought that our theorizing, up to now, regarding semantic paradox has been somewhat narrow in that it has focused for the most part on the manifestly circular Liar paradox, and that as a result new insights and lessons can be obtained by focusing on other sorts of construction— the Yablo paradox being a central, and promising, such example.
Origins and Mathematics
Authors: Cook Roy T
Published: September 2014

This chapter presents the origin, history, and mathematics of the Yablo paradox. Careful formulations of the paradox within both arithmetic and a pointer semantics-based language are presented, as well as a number of formal results and philosophical observations that will be critical in the chapters to follow (e.g. the fact that the Yablo paradox, formulated in Peano arithmetic with a truth predicate, is not inconsistent, but merely ω-inconsistent). This chapter also provides a partial solution to the Characterization Problem (for the pointer semantics language) and shows how this problem is equivalent to an outstanding problem in the theory of directed graphs— that of determining whether a directed graph has a kernel.
Generalizing the Yablo Paradox
Authors: Cook Roy T
Published: September 2014

This chapter addresses the Generalizability Question, focusing on Roy Sorensen’s idea that the pattern found in the Yablo paradox will allow for a general purge of self-reference by providing us with a non-circular version of every well-known circular paradox. After examining the most promising method for carrying our such a purge— unwindings— and showing that the project looks somewhat promising for the case of the pointer semantics developed in Chapter 1, the chapter concludes by showing that the answer to the Generalizability Question must in the end be 𠄜no𠄝, since unwindings in more expressively rich contexts, such as arithmetic, tend to collapse into infinite sequences of sentences that are, in fact, circular.
The Curry Generalization
Authors: Cook Roy T
Published: September 2014

This short concluding chapter examines the connections between the Yablo paradox, the Liar paradox involving negation, and the Curry paradox involving the material conditional. A Yablo–Curry hybrid is presented that incorporates the interesting and problematic aspects of the Yablo and Curry paradoxes into a single construction. The chapter concludes with a discussion of the difficulties facing any detailed examination similar to the one undertaken in previous chapters using graph theory and related techniques, of this more general Curry–Yablo construction (and variants and generalizations of it).
The Poisson Equation
Authors: Elman Howard C. , Silvester David J. , Wathen Andrew J.
Published: September 2014

This chapter concerns the statement of the Poisson equation and its weak formulation. This is followed by a description of finite element discretization and properties of the discrete problem.
Solution of discrete Poisson 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.
The Stokes equations
Authors: Stuart A. M. , Söli E.
Published: September 2014

This chapter concerns the statement of the Stokes equations, a model of incompressible flows. It presents the weak formulation. This is followed by a description of finite element discretization and properties of the discrete problem. It includes discussion of inf–sup stability of both the continuous and discrete problems.
The Navier–Stokes Equations
Authors: Elman Howard C. , Silvester David J. , Wathen Andrew J.
Published: September 2014

This chapter concerns the statement and properties of the steady Navier–Stokes equations and the corresponding weak formulation. This includes discussion of stability theory, bifurcation and nonlinear iteration. This is followed by a description of finite element discretization and error analysis of discrete solutions.
Quantum logic gates in superconducting qubits
Authors: Martinis J. M.
Published: September 2014

This chapter emphasizes the importance of the fidelity of quantum logic gates in quantum processing systems. It presents a processing architecture developed at the University of California at Santa Barbara in which the tuning capability of the phase qubit is used to shuttle information between different cavities.
Exploring quantum matter with ultracold atoms
Authors: Bloch I.
Published: September 2014

The course summarized in this chapter gave a basic introduction to the physics of ultracold quantum gases in optical lattices, describing their generation, properties (especially many-body effects), and possible applications.
Quantum error correction
Authors: Chuang I. L.
Published: September 2014

This chapter treats the subject of quantum error correction and fault-tolerant quantum computation. In particular, it presents the various representations of open-system quantum dynamics, insisting on the indistinguishability between different unravelings. Quantum error correction with discrete gates reacting to discrete error syndromes obtained from projective measurement can be seen as a form of quantum feedback that stabilizes a whole manifold of quantum states rather than a single one. The chapter gives a useful general introduction to the theory of stabilizers, which is key to the understanding of error correcting codes. It explains in full detail the principles behind the size of the overhead needed to make the entire quantum processor fault-tolerant, not just its memory.
Exploring the quantum world with photons trapped in cavities and Rydberg atoms
Authors: Raimond J.-M.
Published: September 2014

This chapter presents a review of the latest achievements in cavity quantum electrodynamics with Rydberg atoms. In particular, it illustrates an example of quantum feedback, which is the stabilization of a Fock state in the cavity against spontaneous emission. The feedback process involves the rapid measurement of atoms passing through the cavity and performing a quantum nondemolition measurement of its photon number. The information is fed to a processor that in real time computes the right classical signal to send to the cavity to re-pump it in the right way.
SQUID amplifiers
Authors: Clarke J. , Devoret M. H. , Kamal A.
Published: September 2014

This chapter treats the concrete example of the microwave SQUID, a practical quantum-limited amplifier. The appeal of the SQUID is that it is sufficiently sophisticated to be used in a variety of applications, yet sufficiently simple to allow a detailed analysis of the origin of noise and its processing through the active elements of the device. In particular, the noise of the SQUID can be understood as the mixed-down counterpart of the Johnson noise of the SQUID resistors in the vicinity of the Josephson frequency and its harmonics. The ultimate performances of the microwave SQUID amplifier are discussed.
An introduction to laser cooling optomechanical systems
Authors: Harris J. G. E.
Published: September 2014

This chapter treats the cooling of optomechanical resonators in a semiclassical manner, from the point of view of retarded friction.
Tomography schemes for characterizing itinerant microwave photon fields
Authors: Eichler C. , Bozyigit D. , Lang C. , Steffen L. , Fink J. , Wallraff A.
Published: September 2014

This chapter illustrates the analysis of propagating microwave signals by splitters and amplifiers and shows that one can recover enough information to reconstruct the Wigner function of a microwave quantum field emitted by a qubit.
Using a “frictionless” pendulum for quantum measurement
Authors: Siddiqi I.
Published: September 2014

This chapter presents a quantum-limited amplifier based on parametric amplification and bifurcation of a Josephson junction.
A superconducting artificial atom with two internal degrees of freedom
Authors: Buisson O.
Published: September 2014

This chapter describes the construction of a superconducting artificial atom with two internal degrees of freedom by adding a large inductance to a dc-SQUID phase qubit loop, thus decoupling the junctions’ dynamics.
Facial Reconstruction of a Mucormycosis Survivor by Free Rectus Abdominis Muscle Flap, Tissue Expansion, and Ocular Prosthesis
Authors: Silberstein Eldad , Krieger Yuval , Rosenberg Nir , Bogdanov-Berezovsky Alexander , Shoham Yaron , Saphier Oshra , Pagkalos Vasileios A. , Joshua Ben-Zion
Published: September 2014

Invasive sinonasal mucormycosis is a rare fungal infection that usually occurs in immunocompromised or diabetic patients, and it is often fatal. The authors present a case of a woman patient suffering from systemic lupus erythematosus and diabetes mellitus treated with prednisone, presenting with a rapidly progressive rhino-orbital-cerebral mucormycosis. She was successfully treated with combined intravenous antifungal therapy and radical debridement followed by complex defect reconstruction with a free vertical rectus abdominis myocutaneous flap, tissue expander, and ophthalmic prosthesis.
Those Salicylate Cases—How Sweet Are They?
Authors: Lim Christopher S. , Marcelo Christian B. , Bryant Sean M.
Published: September 2014

Owing to the complex metabolism of salicylates, both hyperglycemia and hypoglycemia have been reported with salicylate poisoning. The aim of this study was to characterize this relationship. Data from the Illinois Poison Center were retrospectively queried over a 5-year period (2008–2012), and patients with a salicylate concentration ≥30 mg/dL were included. Hypoglycemia and hyperglycemia were defined as glucose concentrations <55 and >140 mg/dL, respectively. Of the 160 patients included, most were normoglycemic (81%) and 19% were hyperglycemic. No patient experienced hypoglycemia. Our study indicates that hypoglycemia may be a very rare occurrence in the setting of salicylate poisoning. Clinicians must remain vigilant, regardless of the glucose concentration, when entertaining salicylism as an etiology in appropriate patients.
Clostridium huakuii sp. nov., an anaerobic, acetogenic bacterium isolated from methanogenic consortia
Authors: Ruan Zhiyong , Wang Yanwei , Zhang Chi , Song Jinlong , Zhai Yi , Zhuang Yan , Wang Huimin , Chen Xiaorong , Li Yanting , Zhao Bingqiang , Zhao Bin
Published: September 2014

A Gram-staining-positive, spore-forming, obligately anaerobic, acetogenic bacterium, designated LAM1030T, was isolated from methanogenic consortia enriched from biogas slurry collected from the large-scale anaerobic digester of Modern Farming Corporation in Hebei Province, China. Cells of strain LAM1030T were motile, straight or spiral-rod-shaped. Strain LAM1030T could utilize glucose, fructose, maltose, galactose, lactose, sucrose, cellobiose, mannitol, pyruvate, succinic acid and tryptophan as the sole carbon source. Acetic acid, isovaleric acid and butanoic acid were the main products of glucose fermentation. Sodium sulfite was used as an electron acceptor. Growth of strain LAM1030T was completely inhibited by the addition of ampicillin, tetracycline, gentamicin or erythromycin at a concentration of 20 µg ml−1. The main polar lipids of strain LAM1030T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, 11 unknown glycolipids and two unknown phospholipids. No respiratory quinone was detected. The major fatty acids of strain LAM1030T were C16 : 0 (21.1 %), C14 : 0 (10.3 %), summed feature 9 (including C16:0 10-methyl and/or iso-C17:1 ω9c) (11.3% ), summed feature 3 (including C16:1 ω7c and/or C16:1 ω6c) (10.6% ) and iso-C15 : 0 (6.6 %). Analysis of the 16S rRNA gene sequence indicated that strain LAM1030T belonged to the genus

Clostridium

and was most closely related to

Clostridium subterminale

DSM 6970T,

Clostridium thiosulfatireducens

DSM 13105T and

Clostridium sulfidigenes

DSM 18982T, with 97.0, 96.9 and 96.8 % similarity, respectively. The G+C content of the genomic DNA of strain LAM1030T was 31.2±0.3 mol%. On the basis of its phenotypic, phylogenetic and chemotaxonomic characterization, strain LAM1030T is suggested to represent a novel species of the genus

Clostridium

, for which the name Clostridium huakuii sp. nov. is proposed. The type strain is LAM1030T ( = ACCC 00698T = JCM 19186T).
Single molecule-level detection and long read-based phasing of epigenetic variations in bacterial methylomes
Authors: Beaulaurier John , Zhu Shijia , Sebra Robert , Zhang Xue-Song , Rosenbluh Chaggai , Deikus Gintaras , Shen Nan , Munera Diana , Waldor Matthew K. , Blaser Martin , Chess Andrew , Schadt Eric E. , Fang Gang
Published: September 2014

Comprehensive genome-wide analyses of bacterial DNA methylation have not been possible until the recent advent of single molecule, real-time (SMRT) sequencing. This technology enables the direct detection of N6-methyladenine (6mA) and 4-methylcytosine (4mC) at single nucleotide resolution on a genome-wide scale. The distributions of these two major types of DNA methylation, along with 5-methylcytosine (5mC), comprise the bacterial methylome, some rare exceptions notwithstanding. SMRT sequencing has already revealed marked diversity in bacterial methylomes as well as the existence of heterogeneity of methylation in cells in single bacterial colonies, where such ‘epigenetic’ variation can enable bacterial populations to rapidly adapt to changing conditions. However, current methods for studying bacterial methylomes using SMRT sequencing mainly rely on population-level summaries that do not provide the single-cell resolution necessary for dissecting the epigenetic heterogeneity in bacterial populations. Here, we present a novel SMRT sequencing-based framework, consisting of two complementary methods, for single molecule-level detection of DNA methylation and assessment of methyltransferase activity through single molecule-level long read-based epigenetic phasing. Using seven bacterial strains and integrating data from SMRT and Illumina sequencing, we show that our method yields significantly improved resolution compared to existing population-level methods, and reveals several distinct types of epigenetic heterogeneity. Our approach enables new investigations of the complex architecture and dynamics of bacterial methylomes and provides a powerful new tool for the study of bacterial epigenetic control.
Inference of Gorilla demographic and selective history from whole genome sequence data
Authors: McManus Kimberly F. , Kelley Joanna L. , Song Shiya , Veeramah Krishna , Woerner August E. , Stevison Laurie S. , Ryder Oliver A. ,   Great Ape Genome Project, Kidd Jeffrey M. , Wall Jeffrey D. , Bustamante Carlos D. , Hammer Michael F.
Published: September 2014

While population-level genomic sequence data have been gathered extensively for humans, similar data from our closest living relatives are just beginning to emerge. Examination of genomic variation within great apes offers many opportunities to increase our understanding of the forces that have differentially shaped the evolutionary history of hominid taxa. Here, we expand upon the work of the Great Ape Genome Project by analyzing medium to high coverage whole genome sequences from 14 western lowland gorillas (Gorilla gorilla gorilla), 2 eastern lowland gorillas (G. beringei graueri), and a single Cross River individual (G. gorilla diehli). We infer that the ancestors of western and eastern lowland gorillas diverged from a common ancestor ~261 thousand years ago (kya), and that the ancestors of the Cross River population diverged from the western lowland gorilla lineage ~68 kya. Using a diffusion approximation approach to model the genome-wide site frequency spectrum, we infer a history of western lowland gorillas that includes an ancestral population expansion of ~1.4-fold around ~970 kya and a recent ~5.6-fold contraction in population size ~23 kya. The latter may correspond to a major reduction in African equatorial forests around the Last Glacial Maximum. We also analyze patterns of variation among western lowland gorillas to identify several genomic regions with strong signatures of recent selective sweeps. We find that processes related to taste, pancreatic and saliva secretion, sodium ion transmembrane transport, and cardiac muscle function are overrepresented in genomic regions predicted to have experienced recent positive selection.