bluuebunny/crossref_metadata_2025 huggingface dataset:
Theory of Chemical ProcessingUsing Pulsed Precipitators
Authors: Lowke JJ , Morrow R
Published: June 2013

A theoretical analysis is given, using methods of gaseous electronics and plasma chemistry, of the removal of S02 and nitrogen oxides from flue gases by use of pulsed electrical corona. Calculations indicate that the rate coefficients in a typical flue gas for the electron dissociation of nitrogen, oxygen and water vapour only become appreciable for values of E/N greater than about 80 Td; E is electric field strength and N the gas number density. Chemical calculations using these data indicate that 802 is removed by conversion to sulphuric acid by reactions with OH radicals, and that oxides of nitrogen are removed largely by reduction from N atoms. To attain these high values of E / N, it is necessary to use pulsed voltages of pulse width r-v1 us in order to avoid electrical breakdown. The maximum pulse widths allowable to avoid breakdown is estimated by requiring the total energy input to be less than that which heatsthe gas by 104 K.
Measurement of Electrical Discharge Parameters Using Optical Fibres
Authors: Everett V , Jones KT , Scelsi GB , Woolsey GA
Published: June 2013

A consequence of the development of optical fibre technology for communications has been the application of optical fibres to the sensing of a wide range of physical and chemical parameters. Many of the properties of fibres that are important for communications' are significant for sensing: these include their insulating nature, their small dimensions, and their immunity to high voltage and electromagnetic radiation. These attributes are particularly significant for sensing electrical discharges, and this review presents a discussion of the potential of optical fibre sensing for discharge parameters, the results of some recent optical fibre measurements made on corona and glow discharges, and suggestions for other discharge. probing approaches using optical fibres.
Interferometers with Internal and External Phase Modulation: Experimental and Analytical Comparison
Authors: J Stevenson Andrew , B Gray Malcolm , C Harb Charles , E McClelland David , Bachor Hans-A
Published: June 2013

Optical intensity noise in a light source easily degrades the sensitivity of a shot-noise-limited interferometer which is directly detecting low frequency phase or displacement variations. In this paper we describe and compare two experimental methods in which we use high frequency optical phase modulation to shift low frequency phase signals in an interferometer to a shot noise limited region of the photocurrent spectrum. This phase modulation is applied either within the interferometer arms-internal modulation-or in a local oscillator beam tapped off the main interferometer and coherently recombined with the interferometer output-external modulation. he photocurrent is mixed electronically with the high frequency modulating waveform to extract the signal information free from laser intensity noise. In our experiments, we have been able to detect interferometrically low frequency signals with true shot-noise-limited sensitivity. We find, theoretically and experimentally, that the interferometric sensitivity achievable in each scheme depends critically on non-ideal factors, such as imperfect interferometric fringe contrast and electronic noise in the detectors or amplifiers. This paper examines the relative merits and operating requirements of both modulation schemes in practical interferometers.
Oscillating Apparent Horizons in Numerically Generated Spacetimes
Authors: Anninos Peter , Bemstein David , Brandt Steve , Hobill David , Seidel Ed , Smarr Larry
Published: June 2013

We investigate the evolution of the apparent horizon in three families of numerically generated spacetimes: the 'black hole plus Brill wave' spacetimes of Bernstein et al., the non-time symmetric generalisation of this by Brandt, and the Misner two black hole spacetime. Various measures of the curvature and shape of the horizon are shown as a function of coordinate time at infinity and it is found that the horizon oscillates at the lowest quasinormal mode frequency of the hole. In addition, in the spacetimes with angular momentum the total angular momentum of the final hole can be read off from the oscillations of the horizon directly without having to extract it from the gravitational radiation emitted by the hole.
Electronic Structure from Polarised Neutron Diffraction
Authors: Chandler GS , Jayatilaka D , Wolff SK
Published: June 2013

The polarised neutron diffraction experiment is described and the nature of the information obtained is outlined. In many cases interpretation of the experiment assumes that the crystal is made up of non-interacting molecular or ionic units. The soundness of this assumption is examined in the case of copper Tutton salt. Polarised neutrons are scattered by the crystal magnetisation density which has a contribution from the orbital motion of electrons. A method for including the spin-orbit contribution to this effect is described for the particular example of the CoCI24− ion.
Close-coupling Formalism for Electron/PositronAtom Systems and Underlying Scattering Theory
Authors: T Stelbovics Andris , Berge Lindsay
Published: June 2013

The close-coupling method for electron/positronatom scattering promises to give a complete description of the scattering process provided the space of target states is properly spanned. This paper will discuss the structure of the equations, emphasising questions of stability associated with the expansions over sets of target states. For electronatom scattering, the character of the solution is discussed and a simple example is given to illustrate the non-convergence of the half-shell T-matrix. This lack of convergence can be fixed by application of the symmetrisation boundary condition, leading to new forms of the equations. For positronatom scattering, the standard equations yield convergent half-shell T-matrices for all but the largest calculations.
Core-hole Electronic Structure Studies on Molecules using Synchrotron Radiation
Authors: P Larkins Frank
Published: June 2013

Some recent developments in the study of core-hole photoabsorption, photoionisation, X-ray emission, Auger electron decay and photofragmentation processes for molecules are discussed. The emphasis is on the interpretation of experimental data obtained from synchrotron radiation studies. New insights which are being obtained through theoretical investigations into the electronic and nuclear properties of excited and ionised states of simple molecules are reviewed.
Electron Collisions with Metastable Helium
Authors: Jacka Marcus , Kelly Jennifer , Lohmann Birgit , Buckman Stephen
Published: June 2013

Measurements and theoretical studies of electron scattering from the metastable 21,3S excited states of helium are briefly reviewed. An apparatus developed for the study of low energy differential scattering from metastable excited states is discussed in detail and the first results of angular distributions for electrons superelastically scattered from the 21,3S states at incident energies of 5, 10 and 30 eV are presented.
Manipulating Beams of Ultra-cold Atoms with a Static Magnetic Field
Authors: Rowlands WJ , Lau DC , Opat GI , Sidorov AI , McLean RJ , Hannaford P
Published: June 2013

We report preliminary results on the deflection of a beam of ultra-cold atoms by a static magnetic field. Caesium atoms trapped in a magneto-optical trap (MOT) are cooled using optical molasses, and then fall freely under gravity to form a beam of ultra-cold atoms. The atoms pass through a static inhomogeneous magnetic field produced by a single current-carrying wire, and are deflected by a force ▽(µB) dependent on the magnetic substate of the atom. The population of atoms in various magnetic substates can be altered by using resonant laser radiation to optically pump the atoms.
Introduction to the Views of Distant Objects in Kerr - Newman Spacetimes
Authors: E Metzenthen William
Published: June 2013

Gravitational effects cause the visual appearance of the external universe to be distorted to observers near a Kerr–Newman black hole. This paper introduces the problem and presents some computer-generated pictures which show how the 'sky' appears to an observer near a Kerr black hole.
Carbon Monoxide Adsorption on a Cu3Pt(111) Single Crystal Alloy
Authors: Shen YG , O'Connor DJ , MacDonald RJ
Published: June 2013

The adsorption of CO on CU3Pt(111) was investigated by low energy He+ ion scattering. The alloy surface was characterised by low energy electron diffraction (LEED) and work function change (Δφ) measurements. No surface ordering of the alloy was evidenced by LEED. The CO induced work function changes were small. Under normal incidence of the beam, only the scattered He+ ions from 0, Cu and Pt were detected, indicating the orientation of the CO molecule with 0 facing away from the surface. In the initial stages of CO adsorption at 200 K, the Pt intensity in a Cu-rich surface was not detectable at an exposure of ~5 L CO, indicating that all the Pt atoms were covered by CO. At a saturation coverage of CO, the Pt intensity in a Pt-rich surface, however, fell to ~12% of its clean surface intensity. This observation strongly suggested that not all the Pt sites were covered by the CO molecules. These results are discussed in relation with the structure and composition of the surface and compared to data for CO adsorption on Pt(111).
Introduction
Authors: Walls and Jason Twamley Dan
Published: June 2013

The Workshop on Atom Optics was held at the University of Adelaide in September 1995. It was attended by pproximately 40 physicists from Australia and New Zealand. The venue for the workshop was the new Institute for Theoretical Physics at the University of Adelaide which provided excellent facilities for lectures and discussion. Atom optics is a field which has grown rapidly since its beginning approximately five years ago. There are now several groups in Australia and New Zealand pursuing research activities in both theoretical and experimental aspects of atom optics.
Reflection and Diffraction of Atomic de Broglie Waves by Evanescent Laser Waves - Bare-state Method
Authors: Feng Xiao-Ping , Witte NS , CL Hollenberg Lloyd , I Opat Geoffrey
Published: June 2013

We present two results in an investigation of reflection and diffraction of atoms by gratings formed either by standing or travelling evanescent laser waves. Both results use the bare-state rather than dressed-state picture. One is based on the Born series, whereas the other is based on the Laplace transformation of the coupled differential equations. The two solutions yield the same theoretical expressions for reflected and diffracted atomic waves in the whole space, including the interaction and the asymptotic regions.
Virtual Compton Scattering from the Proton and the Properties of Nucleon Excited States
Authors: Liu GQ , Thomas AW , Guichon PAM
Published: June 2013

We calculate the N * contributions to the generalised polarisabilities of the proton in virtual Compton scattering. The following nucleon excitations are included: N * (1535), N * (1650), N * (1520), N * (1700), Δ * (1232), Δ * (1620) and Δ * (1700). The relationship between nucleon structure parameters, N *  properties and the generalised polarisabilities of the proton is illustrated.
Effective Charge Effect in 2·0 - 7·0 MeV Partially Stripped Fq+ -  Helium Collisions
Authors: Cai X , Liu ZY , Chen XM , Shen ZY , Ma XW , Liu HP , Hou MD
Published: June 2013

The ratio of the double ionisation cross section to that of the single ionisation of helium was measured for 2�0–7�0 MeV Fq+ (q = 1,2,3,4) bombardment. The effective charge effect in partially stripped Fq+ – helium collisions is studied. It is found that the effective charge qeff increases as the impinging energy increases and that qeff shows almost no dependence upon the projectile charge state in the present energy range.
Guided Propagation of the Alfvén Wave in a Tokamak
Authors: Borg GG
Published: June 2013

Experimental observations are presented of the magnetically guided Alfvén wave excited directly by a small dipole loop antenna located in the scrape-off layer of a tokamak plasma. This wave is excited most efficiently by antenna current elements aligned along the magnetic field and measurements indicate that, at all frequencies below the ion cyclotron frequency, the wave propagates for several transits around the machine with a high degree of localization about magnetic field lines intersecting the antenna. Along the field, the wave has both a slowly varying amplitude and phase with predominantly radial electric and azimuthal magnetic field components. These experiments demonstrate that the Alfvén wave can propagate as a magnetically guided TEM mode in plasmas which are highly inhomogeneous. We also present a simplified mathematical description of the wave.
Positron-acoustic Waves in an Electron - Positron Plasma with an Electron Beam
Authors: Nejoh YN
Published: June 2013

The nonlinear wave structures of large-amplitude positron-acoustic waves are studied in an electron–positron plasma with an electron beam. We present the region where positron-acoustic waves exist by analysing the structure of the pseudopotential. The region depends sensitively on the positron density, the positron temperature and the electron beam temperature. It is shown that the maximum amplitude of the wave decreases as the positron temperature increases, and the region of positron-acoustic waves spreads as the positron . Temperature increases. The present theory is applicable to analysing hirge-amplitude positron-acoustic waves associated with positrons which may occur in interplanetary space.
De-excitation Gamma-ray Technique for Improved Resolution in Intermediate Energy Photonuclear Reactions
Authors: Kuzin A , Rassool R , Thompson MN
Published: June 2013

Use of residual-state decay γ-rays could be a powerful tool in the study of photonuclear reactions. The practicality of this technique in a tagged-photon experiment is demonstrated for the first time with data on the 12C(γ,p) reaction.
Positron Annihilation Study of Deformation in a Two-phase (α+β) Cu - Zn Alloy
Authors: Tang CQ , Yu LH
Published: June 2013

Positron lifetimes have been measured as a function of the degree of deformation ε in a two-phase (α+τ) Cu–Zn alloy. In this alloy the increase of the mean positron lifetime τm with ε is slower and the saturation effect occurs at a larger deformation than that in most simple metals and alloys. With increasing ε the positron lifetime parameters τ1 Ι1 and Ι2 exhibit a rise or fall near ε ≈ 4% and 35%, and they change slowly for 4% < ε < 35%. These results are explained by the special structure of the α and β phases and the particular deformation mechanism in this alloy.
The Motion of Rapidly Rotating Curling Rocks
Authors: Shegelski Mark R. A. , Niebergall Ross
Published: June 2013

We present a physical model that accounts for the motion of rapidly rotating
curling rocks. By rapidly rotating we mean that the rotational speed of the
contact annulus of the rock about the centre of mass is large compared with
the translational speed of the centre of mass. The principal features of the
model are: (i ) that the kinetic friction induces
melting of the ice, with the consequence that there exists a thin film of
liquid water lying between the contact annulus of the rock and the ice;
(ii ) that the curling rock drags some of the thin
liquid film around the rock as it rotates, with the consequence that the
relative velocity between the rock and the thin liquid film is significantly
different to the relative velocity between the rock and the underlying solid
ice surface. Since it is the former relative velocity which dictates the
nature of the motion of the curling rock, our model predicts some interesting
differences between the motions of slowly versus rapidly rotating rocks. Of
principal note is that our model predicts, and observations confirm, that
rapidly rotating curling rocks stop moving translationally well before
rotational motion ceases. This is in sharp contrast to the usual case of slow
rotation, where both rotational and translational motion cease at the same
instant. We have verified this and other predictions of our model by careful
comparison with the motion of actual curling rocks.
Paul Trap Promotion of Electrons in Atomic Collisions
Authors: Oppen G. von , Tschersich M. , Drozdowski R. , Busch M.
Published: June 2013

Electron promotion on rotating potential saddles is proposed as an important
and efficient excitation mechanism taking place in atomic collisions at
intermediate energies. Measurements on the excitation of atoms by positively
charged particles, in particular, excitation of He I states in p–He
collisions provides experimental evidence for this ‘Paul trap’
promotion in two-centre Coulomb potentials.
The Dynamics of Two-electron Atoms
Authors: Briggs John S.
Published: June 2013

Since the first attempts to calculate the helium ground state in the early
days of Bohr–Sommerfeld quantisation, two-electron atoms have posed a
series of challenges to theoretical physics. Despite the seemingly simple
problem of three charged particles with known interactions it took more than
half a century after quantum mechanics was established to describe spectra of
two-electron atoms satisfactorily. The evolution of the understanding of
correlated two-electron dynamics and its importance for
doubly excited resonance states is described in this overview.
Quadratic Solitons: New Possibility for All-optical Switching
Authors: Buryak A. V. , Steblina V. V.
Published: June 2013

We discuss potential applications of quadratic optical solitons for
all-optical switching in bulk quadratic nonlinear media. Among the major
phenomena investigated are soliton scattering, spiralling, fusion, and also
power exchange between the colliding solitons.
Cosmological Particle Production and Causal Thermodynamics
Authors: Mak M. K. , Harko T.
Published: June 2013

The full linear causal Israel–Stewart–Hiscock theory of bulk
viscous processes in relativistic cosmological fluids is reformulated as an
effective phenomenological theory for describing particle production processes
in the early universe. Explicit expressions for the particle balance law and
particle production rates are obtained that relate the particle creation rate
to the bulk viscous (creation) pressure. The general formalism is applied to
the case of a full causal cosmological fluid with bulk viscosity coecient
proportional to the Hubble function. In this case the general solution of the
gravitational field equations can be expressed in an exact parametric form.
For an appropriate choice of the physical parameters, the dynamics of the
universe can be modelled as starting from a vacuum quasi-Minkowskian geometry,
followed by an inflationary period but ending in a non-inflationary phase. The
influence of the matter creation processes on the evolution of the universe
and the behaviour of the energy density, temperature and entropy are
investigated.
Discretisation Errors in Landau Gauge on the Lattice
Authors: Bonnet Frederic D. R. , Bowman Patrick O. , Leinweber Derek B. , Williams Anthony G. , Richards David G.
Published: June 2013

Lattice discretisation errors in the Landau gauge condition are examined. An
improved gauge fixing algorithm in which
?(a2) errors are removed is
presented. ?(a2) improvement
of the gauge fixing condition improves comparison with the continuum Landau
gauge in two ways: (1) through the elimination of
?(a2) errors and (2) through a
secondary effect of reducing the size of higher-order errors. These results
emphasise the importance of implementing an improved gauge fixing condition.
Global human appropriation of net primary production doubled in the 20th century
Authors: Krausmann Fridolin , Erb Karl-Heinz , Gingrich Simone , Haberl Helmut , Bondeau Alberte , Gaube Veronika , Lauk Christian , Plutzar Christoph , Searchinger Timothy D.
Published: June 2013

Global increases in population, consumption, and gross domestic product raise concerns about the sustainability of the current and future use of natural resources. The human appropriation of net primary production (HANPP) provides a useful measure of human intervention into the biosphere. The productive capacity of land is appropriated by harvesting or burning biomass and by converting natural ecosystems to managed lands with lower productivity. This work analyzes trends in HANPP from 1910 to 2005 and finds that although human population has grown fourfold and economic output 17-fold, global HANPP has only doubled. Despite this increase in efficiency, HANPP has still risen from 6.9 Gt of carbon per y in 1910 to 14.8 GtC/y in 2005, i.e., from 13% to 25% of the net primary production of potential vegetation. Biomass harvested per capita and year has slightly declined despite growth in consumption because of a decline in reliance on bioenergy and higher conversion efficiencies of primary biomass to products. The rise in efficiency is overwhelmingly due to increased crop yields, albeit frequently associated with substantial ecological costs, such as fossil energy inputs, soil degradation, and biodiversity loss. If humans can maintain the past trend lines in efficiency gains, we estimate that HANPP might only grow to 27–29% by 2050, but providing large amounts of bioenergy could increase global HANPP to 44%. This result calls for caution in refocusing the energy economy on land-based resources and for strategies that foster the continuation of increases in land-use efficiency without excessively increasing ecological costs of intensification.
Rhythmic alternating patterns of brain activity distinguish rapid eye movement sleep from other states of consciousness
Authors: Chow Ho Ming , Horovitz Silvina G. , Carr Walter S. , Picchioni Dante , Coddington Nate , Fukunaga Masaki , Xu Yisheng , Balkin Thomas J. , Duyn Jeff H. , Braun Allen R.
Published: June 2013

Rapid eye movement (REM) sleep constitutes a distinct “third state” of consciousness, during which levels of brain activity are commensurate with wakefulness, but conscious awareness is radically transformed. To characterize the temporal and spatial features of this paradoxical state, we examined functional interactions between brain regions using fMRI resting-state connectivity methods. Supporting the view that the functional integrity of the default mode network (DMN) reflects “level of consciousness,” we observed functional uncoupling of the DMN during deep sleep and recoupling during REM sleep (similar to wakefulness). However, unlike either deep sleep or wakefulness, REM was characterized by a more widespread, temporally dynamic interaction between two major brain systems: unimodal sensorimotor areas and the higher-order association cortices (including the DMN), which normally regulate their activity. During REM, these two systems become anticorrelated and fluctuate rhythmically, in reciprocally alternating multisecond epochs with a frequency ranging from 0.1 to 0.01 Hz. This unique spatiotemporal pattern suggests a model for REM sleep that may be consistent with its role in dream formation and memory consolidation.
Regulatory interplay of Cockayne syndrome B ATPase and stress-response gene
ATF3
following genotoxic stress
Authors: Kristensen Ulrik , Epanchintsev Alexey , Rauschendorf Marc-Alexander , Laugel Vincent , Stevnsner Tinna , Bohr Vilhelm A. , Coin Frédéric , Egly Jean-Marc
Published: June 2013

Significance

Genotoxic attack results in temporary arrest of RNA synthesis. Mutations in the DNA repair factor Cockayne syndrome B gene product (CSB) that are responsible for the Cockayne syndrome phenotype lead to clinical features such as developmental and neurodegenerative defects and photosensitivity. In UV-irradiated CSB-deficient CS1AN cells, certain genes remain permanently repressed by the activating transcription factor 3, the product of a stress-response gene, which cannot be removed from promoter by the transcription machinery. We suggest that transcriptional defects observed in UV-irradiated CSB-deficient cells result from the permanent transcriptional repression of certain genes as well as from defects in DNA repair.
Unphosphorylated STAT5A stabilizes heterochromatin and suppresses tumor growth
Authors: Hu Xiaoyu , Dutta Pranabananda , Tsurumi Amy , Li Jinghong , Wang Jingtong , Land Hartmut , Li Willis X.
Published: June 2013

Tumor suppressors known to date impede cancer growth by arresting the cell cycle or promoting apoptosis. Here we show that unphosphorylated human STAT5A functions as a tumor suppressor capable of repressing multiple oncogenes via heterochromatin formation. Unphosphorylated STAT5A binds to heterochromatin protein 1α (HP1α) and stabilizes heterochromatin. Expressing unphosphorylated STAT5A or HP1α inhibits colon cancer growth in mouse xenograft models. Transcriptome profiling shows that expressing an unphosphorylatable STAT5A has similar effects to overexpressing HP1α in global gene expression. Notably, the majority of the genes commonly repressed by unphosphorylated STAT5A and HP1α have been implicated in cancer development. Finally, down-regulation, somatic mutations, and deletions of STAT5 genes are found in certain human cancers. These results suggest that unphosphorylated STAT5A may epigenetically suppress tumor growth by promoting heterochromatin formation.
Isotopic evidence of early hominin diets
Authors: Sponheimer Matt , Alemseged Zeresenay , Cerling Thure E. , Grine Frederick E. , Kimbel William H. , Leakey Meave G. , Lee-Thorp Julia A. , Manthi Fredrick Kyalo , Reed Kaye E. , Wood Bernard A. , Wynn Jonathan G.
Published: June 2013

Carbon isotope studies of early hominins from southern Africa showed that their diets differed markedly from the diets of extant apes. Only recently, however, has a major influx of isotopic data from eastern Africa allowed for broad taxonomic, temporal, and regional comparisons among hominins. Before 4 Ma, hominins had diets that were dominated by C3resources and were, in that sense, similar to extant chimpanzees. By about 3.5 Ma, multiple hominin taxa began incorporating13C-enriched [C4or crassulacean acid metabolism (CAM)] foods in their diets and had highly variable carbon isotope compositions which are atypical for African mammals. By about 2.5 Ma,Paranthropusin eastern Africa diverged toward C4/CAM specialization and occupied an isotopic niche unknown in catarrhine primates, except in the fossil relations of grass-eating geladas (Theropithecus gelada). At the same time, other taxa (e.g.,Australopithecus africanus) continued to have highly mixed and varied C3/C4diets. Overall, there is a trend toward greater consumption of13C-enriched foods in early hominins over time, although this trend varies by region. Hominin carbon isotope ratios also increase with postcanine tooth area and mandibular cross-sectional area, which could indicate that these foods played a role in the evolution of australopith masticatory robusticity. The13C-enriched resources that hominins ate remain unknown and must await additional integration of existing paleodietary proxy data and new research on the distribution, abundance, nutrition, and mechanical properties of C4(and CAM) plants.
High-resolution structures of the IgM Fc domains reveal principles of its hexamer formation
Authors: Müller Roger , Gräwert Melissa A. , Kern Thomas , Madl Tobias , Peschek Jirka , Sattler Michael , Groll Michael , Buchner Johannes
Published: June 2013

IgM is the first antibody produced during the humoral immune response. Despite its fundamental role in the immune system, IgM is structurally only poorly described. In this work we used X-ray crystallography and NMR spectroscopy to determine the atomic structures of the constant IgM Fc domains (Cµ2, Cµ3, and Cµ4) and to address their roles in IgM oligomerization. Although the isolated domains share the typical Ig fold, they differ substantially in dimerization properties and quaternary contacts. Unexpectedly, the Cµ4 domain and its C-terminal tail piece are responsible and sufficient for the specific polymerization of Cµ4 dimers into covalently linked hexamers of dimers. Based on small angle X-ray scattering data, we present a model of the ring-shaped Cµ4 structure, which reveals the principles of IgM oligomerization.
Emergence of the advancing neuromechanical phase in a resistive force dominated medium
Authors: Ding Yang , Sharpe Sarah S. , Wiesenfeld Kurt , Goldman Daniel I.
Published: June 2013

Undulatory locomotion, a gait in which thrust is produced in the opposite direction of a traveling wave of body bending, is a common mode of propulsion used by animals in fluids, on land, and even within sand. As such, it has been an excellent system for discovery of neuromechanical principles of movement. In nearly all animals studied, the wave of muscle activation progresses faster than the wave of body bending, leading to an advancing phase of activation relative to the curvature toward the tail. This is referred to as “neuromechanical phase lags” (NPL). Several multiparameter neuromechanical models have reproduced this phenomenon, but due to model complexity, the origin of the NPL has proved difficult to identify. Here, we use perhaps the simplest model of undulatory swimming to predict the NPL accurately during sand-swimming by the sandfish lizard, with no fitting parameters. The sinusoidal wave used in sandfish locomotion, the friction-dominated and noninertial granular resistive force environment, and the simplicity of the model allow detailed analysis, and reveal the fundamental mechanism responsible for the phenomenon: the combination of synchronized torques from distant points on the body and local traveling torques. This general mechanism should help explain the NPL in organisms in other environments; we therefore propose that sand-swimming could be an excellent system with which to generate and test other neuromechanical models of movement quantitatively. Such a system can also provide guidance for the design and control of robotic undulatory locomotors in complex environments.
Structure of the archaeal head-tailed virus HSTV-1 completes the HK97 fold story
Authors: Pietilä Maija K. , Laurinmäki Pasi , Russell Daniel A. , Ko Ching-Chung , Jacobs-Sera Deborah , Hendrix Roger W. , Bamford Dennis H. , Butcher Sarah J.
Published: June 2013

It has been proposed that viruses can be divided into a small number of structure-based viral lineages. One of these lineages is exemplified by bacterial virus Hong Kong 97 (HK97), which represents the head-tailed dsDNA bacteriophages. Seemingly similar viruses also infect archaea. Here we demonstrate using genomic analysis, electron cryomicroscopy, and image reconstruction that the major coat protein fold of newly isolated archaeal
Haloarcula sinaiiensis
tailed virus 1 has the canonical coat protein fold of HK97. Although it has been anticipated previously, this is physical evidence that bacterial and archaeal head-tailed viruses share a common architectural principle. The HK97-like fold has previously been recognized also in herpesviruses, and this study expands the HK97-like lineage to viruses from all three domains of life. This is only the second established lineage to include archaeal, bacterial, and eukaryotic viruses. Thus, our findings support the hypothesis that the last common universal ancestor of cellular organisms was infected by a number of different viruses.
Wolbachiauses a host microRNA to regulate transcripts of a methyltransferase, contributing to dengue virus inhibition inAedes aegypti
Authors: Zhang Guangmei , Hussain Mazhar , O’Neill Scott L. , Asgari Sassan
Published: June 2013

The endosymbiontWolbachiais common among insects and known for the reproductive manipulations it exerts on hosts as well as inhibition of virus replication in their hosts. Recently, we showed thatWolbachiauses host microRNAs to manipulate host gene expression for its efficient maintenance in the dengue mosquito vector,Aedes aegypti. Cytosine methylation is mediated by a group of proteins called DNA (cytosine-5) methyltransferases, which are structurally and functionally conserved from prokaryotes to eukaryotes. The biological functions of cytosine methylation include host defense, genome stability, gene regulation, developmental promotion of organs, and lifespan regulation.Ae. aegyptihas only one DNA methyltransferase gene (AaDnmt2) belonging to the cytosine methyltransferase family 2, which is the most deeply conserved and widely distributed gene among metazoans. Here, we show that in mosquitoes the introduced endosymbiont,Wolbachia, significantly suppresses expression ofAaDnmt2, but dengue virus induces expression ofAaDnmt2. Interestingly, we found that aae-miR-2940 microRNA, which is exclusively expressed inWolbachia-infected mosquitoes, down-regulates the expression ofAaDnmt2. Reversely, overexpression of AaDnmt2 in mosquito cells led to inhibition ofWolbachiareplication, but significantly promoted replication of dengue virus, suggesting a causal link between thisWolbachiamanipulation and the blocking of dengue replication inWolbachia-infected mosquitoes. In addition, our findings provide an explanation for hypomethylation of the genome inWolbachia-infectedAe. aegypti.
What’s your problem? And how might we deepen it?
Authors: Boyd Brian
Published: June 2013

Literary studies need not always incorporate evolution but should always be at least compatible with the most powerful theory for explaining life. Evolution can open up new questions (like: why are we art-making, storytelling, versifying animals?), suggest new principles (like: always take into consideration the costs and benefits of creating or engaging in literary works), and offer new explanations of the life art represents and the effects it elicits (in sociality or emotion, say). These insights need not be restricted to human universals – evolutionary anthropology and evolutionary personality psychology investigate societal and individual differences – and can help explain at multiple levels, the global, the local, the individual, the work or the detail. Evolutionary considerations should not be required a priori but incorporated on a case-by-case basis, where they can almost always add explanatory depth.
The fluency of spoilers
Authors: D. Leavitt Jonathan , Christenfeld Nicholas J.S.
Published: June 2013

Spoilers, despite their name, seem to increase enjoyment of stories. This could be because readers enjoy reading expected endings, because knowing the ending allows them to appreciate aesthetic elements instead of guessing what will happen, or because knowing the ending increases fluency by enabling readers to correctly interpret clues and events. We conducted three experiments to test these hypotheses. Experiment 1 collected ratings at the midpoints of anthologized stories, and determined that readers experience greater pleasure even before reading the end of spoiled stories. This spoiler benefit was mediated by processing fluency, and not by appreciation of aesthetic elements. Experiment 2 found that spoilers similar to those in Experiment 1 do not increase ease of reading — or pleasure — for very-easy-to-read stories. Experiment 3 found, however, that very simple spoilers could increase the pleasure of easy-to-read stories.
A novel pathway spatiotemporally activates Rac1 and redox signaling in response to fluid shear stress
Authors: Liu Yunhao , Collins Caitlin , Kiosses William B. , Murray Ann M. , Joshi Monika , Shepherd Tyson R. , Fuentes Ernesto J. , Tzima Ellie
Published: June 2013

Hemodynamic forces regulate embryonic organ development, hematopoiesis, vascular remodeling, and atherogenesis. The mechanosensory stimulus of blood flow initiates a complex network of intracellular pathways, including activation of Rac1 GTPase, establishment of endothelial cell (EC) polarity, and redox signaling. The activity of the nicotinamide adenine dinucleotide phosphate (NADPH) oxidase can be modulated by the GTP/GDP state of Rac1; however, the molecular mechanisms of Rac1 activation by flow are poorly understood. Here, we identify a novel polarity complex that directs localized Rac1 activation required for downstream reactive oxygen species (ROS) production. Vav2 is required for Rac1 GTP loading, whereas, surprisingly, Tiam1 functions as an adaptor in a VE-cadherin–p67phox–Par3 polarity complex that directs localized activation of Rac1. Furthermore, loss of Tiam1 led to the disruption of redox signaling both in vitro and in vivo. Our results describe a novel molecular cascade that regulates redox signaling by the coordinated regulation of Rac1 and by linking components of the polarity complex to the NADPH oxidase.
The Hippo pathway polarizes the actin cytoskeleton during collective migration of Drosophila border cells
Authors: Lucas Eliana P. , Khanal Ichha , Gaspar Pedro , Fletcher Georgina C. , Polesello Cedric , Tapon Nicolas , Thompson Barry J.
Published: June 2013

Collective migration of Drosophila border cells depends on a dynamic actin cytoskeleton that is highly polarized such that it concentrates around the outer rim of the migrating cluster of cells. How the actin cytoskeleton becomes polarized in these cells to enable collective movement remains unknown. Here we show that the Hippo signaling pathway links determinants of cell polarity to polarization of the actin cytoskeleton in border cells. Upstream Hippo pathway components localize to contacts between border cells inside the cluster and signal through the Hippo and Warts kinases to polarize actin and promote border cell migration. Phosphorylation of the transcriptional coactivator Yorkie (Yki)/YAP by Warts does not mediate the function of this pathway in promoting border cell migration, but rather provides negative feedback to limit the speed of migration. Instead, Warts phosphorylates and inhibits the actin regulator Ena to activate F-actin Capping protein activity on inner membranes and thereby restricts F-actin polymerization mainly to the outer rim of the migrating cluster.
On different extremal bases for ℂ-convex domains
Authors: Nikolov Nikolai , Pflug Peter , Thomas Pascal
Published: June 2013

We provide a counterexample (a strongly convex domain in

C

3

\mathbb {C}^3

) to a statement about certain extremal bases in the papers of J. D. McNeal in 1992 and 1994 which was used to prove estimates for the Bergman kernel and invariant metrics. We also prove that those estimates in fact remain correct for the same bases (other authors had introduced different bases to fix this).
On the volume set of point sets in vector spaces over finite fields
Authors: Vinh Le Anh
Published: June 2013

We show that if

E

\mathcal {E}

is a subset of the

d
d

-dimensional vector space over a finite field

F

q

\mathbb {F}_q

(

d
≥
3

d \geq 3

) of cardinality

|

E

|

≥
(
d
−
1
)

q

d
−
1

|\mathcal {E}| \geq (d-1)q^{d - 1}

, then the set of volumes of

d
d

-dimensional parallelepipeds determined by

E

\mathcal {E}

covers

F

q

\mathbb {F}_q

. This bound is sharp up to a factor of

(
d
−
1
)

(d-1)

, as taking

E

\mathcal {E}

to be a

(
d
−
1
)

(d - 1)

-hyperplane through the origin shows.
Relating genes to function: identifying enriched transcription factors using the ENCODE ChIP-Seq significance tool
Authors: Auerbach Raymond K. , Chen Bin , Butte Atul J.
Published: June 2013

Motivation: Biological analysis has shifted from identifying genes and transcripts to mapping these genes and transcripts to biological functions. The ENCODE Project has generated hundreds of ChIP-Seq experiments spanning multiple transcription factors and cell lines for public use, but tools for a biomedical scientist to analyze these data are either non-existent or tailored to narrow biological questions. We present the ENCODE ChIP-Seq Significance Tool, a flexible web application leveraging public ENCODE data to identify enriched transcription factors in a gene or transcript list for comparative analyses.

Implementation: The ENCODE ChIP-Seq Significance Tool is written in JavaScript on the client side and has been tested on Google Chrome, Apple Safari and Mozilla Firefox browsers. Server-side scripts are written in PHP and leverage R and a MySQL database. The tool is available at http://encodeqt.stanford.edu.

Contact:  abutte@stanford.edu

Supplementary information:  Supplementary material is available at Bioinformatics online.
Testing the rotating hotspot model using X-ray burst oscillations from 4U 1636−536
Authors: Artigue Romain , Barret Didier , Lamb Frederick K. , Lo Ka Ho , Miller M. Coleman
Published: June 2013

Precise and accurate measurements of neutron star masses and radii would provide valuable information about the still uncertain properties of cold matter at supranuclear densities. One promising approach to making such measurements involves an analysis of the X-ray flux oscillations often seen during thermonuclear (type 1) X-ray bursts. These oscillations are almost certainly produced by emission from hotter regions on the stellar surface modulated by the rotation of the star. One consequence of the rotation is that the oscillation should appear earlier at higher photon energies than at lower energies. Ford found compelling evidence for such a hard lead in the tail oscillations of one type 1 burst from Aql X-1. Subsequently, Muno, Özel & Chakrabarty analysed oscillations in the tails of type 1 bursts observed using the Rossi X-ray Timing Explorer. They found significant evidence for variation of the oscillation phase with energy in 13 of the 51 oscillation trains they analysed and an apparent linear trend of the phase with energy in six of nine average oscillation profiles produced by folding the energy-resolved oscillation waveforms from five stars and then averaging them in groups. In four of these nine averaged energy-resolved profiles, the oscillation appeared to arrive earlier at lower energies than at higher energies. Such a trend is inconsistent with a simple rotating hotspot model of the burst oscillations and, if confirmed, would mean that this model cannot be used to constrain the masses and radii of these stars and would raise questions about its applicability to other stars. We have therefore re-analysed individually the oscillations observed in the tails of the four type 1 bursts from 4U 1636−536 that, when averaged, provided the strongest evidence for a soft lead in the analysis by Muno et al. We have also analysed the oscillation observed during the superburst from this star. We find that the data from these five bursts, treated both individually and jointly, are fully consistent with a rotating hotspot model. Unfortunately, the uncertainties in these data are too large to provide interesting constraints on the mass and radius of this star.
Evolutionary constraints on the planetary hypothesis for transition discs
Authors: Clarke C. J. , Owen J. E.
Published: June 2013

We assume a scenario in which transition discs (i.e. discs around young stars that have signatures of cool dust but lack significant near-infrared emission from warm dust) are associated with the presence of planets (or brown dwarfs). These are assumed to filter the dust content of any gas flow within the planetary orbit and produce an inner ‘opacity hole’. In order to match the properties of transition discs with the largest (∼50 au scale) holes, we place such ‘planets’ at large radii in massive discs and then follow the evolution of the tidally coupled disc–planet system, comparing the system's evolution in the plane of mm flux against hole radius with the properties of observed transition discs. We find that, on account of the high disc masses in these systems, all but the most massive ‘planets’ (100 Jupiter masses) are conveyed to small radii by Type II migration without significant fading at millimetre wavelengths. Such behaviour would contradict the observed lack of mm bright transition discs with small (<10 au) holes. On the other hand, imaging surveys clearly rule out the presence of such massive companions in transition discs. We conclude that this is a serious problem for models that seek to explain transition discs in terms of planetary companions unless some mechanism can be found to halt inward migration and/or suppress mm flux production. We suggest that the dynamical effects of substantial accretion on to the planet/through the gap may offer the best prospect for halting such migration and that further long-term simulations are required to clarify this issue.
Modelling interstellar physics and chemistry: implications for surface and solid-state processes
Authors: Williams David , Viti Serena
Published: June 2013

We discuss several types of regions in the interstellar medium of the Milky Way and other galaxies in which the chemistry appears to be influenced or dominated by surface and solid-state processes occurring on or in interstellar dust grains. For some of these processes, for example, the formation of H
2
molecules, detailed experimental and theoretical approaches have provided excellent fundamental data for incorporation into astrochemical models. In other cases, there is an astrochemical requirement for much more laboratory and computational study, and we highlight these needs in our description. Nevertheless, in spite of the limitations of the data, it is possible to infer from astrochemical modelling that surface and solid-state processes play a crucial role in astronomical chemistry from early epochs of the Universe up to the present day.
Catalytic conversion of acetylene to polycyclic aromatic hydrocarbons over particles of pyroxene and alumina
Authors: Tian M. , Liu B. S. , Hammonds M. , Wang N. , Sarre P. J. , Cheung A. S.-C.
Published: June 2013

Polycyclic aromatic hydrocarbons (PAHs) are known to be present in many astrophysical objects and environments, but our understanding of their formation mechanism(s) is far from satisfactory. In this paper, we describe an investigation of the catalytic conversion reaction of acetylene gas to PAHs over pyroxene and alumina. Crystalline silicates such as pyroxenes (with general formula [Mg, Fe]SiO
3
) and alumina (Al
2
O
3
) are observed astrophysically through their infrared spectra and are likely to promote grain surface chemical reactions. In the experiments reported here, gas-phase PAHs were produced by the catalytic reaction of acetylene over crystalline silicates and alumina using a pulsed jet expansion technique and the gaseous products detected using time-of-flight mass spectrometry. In a separate experiment, the catalytic formation of PAHs from acetylene was further confirmed with acetylene gas at atmospheric pressure flowing continuously through a fixed-bed reactor. The gas effluent and carbonaceous compounds deposited on the catalysts were dissolved separately in dichloromethane and analysed using gas chromatography–mass spectrometry. Among the samples studied, alumina showed higher activity than the pyroxene-type grains for the acetylene reaction. It is proposed that formation of the PAHs relies on the Mg
2+
ions in the pyroxenes and Al
3+
ions in alumina, where these ions act as Lewis acid sites. X-ray diffraction, Fourier transform infrared and high-resolution transmission electron microscopy techniques were used to characterize the structure and physical properties of the pyroxene and alumina samples.