bluuebunny/crossref_metadata_2025 huggingface dataset:
Stochastic models in kinetic theory
Authors: Wagner Wolfgang
Published: March 2011

The paper is concerned with some aspects of stochastic modeling in kinetic theory. First, an overview of the role of particle models with random interactions is given. These models are important both in the context of foundations of kinetic theory and for the design of numerical algorithms in various engineering applications. Then, the class of jump processes with a finite number of states is considered. Two types of such processes are studied, where particles change their states either independently of each other (monomolecular processes) or via binary interactions (bimolecular processes). The relationship of these processes with corresponding kinetic equations is discussed. Equations are derived both for the average relative numbers of particles in a given state and for the fluctuations of these numbers around their averages. The simplicity of the models makes several aspects of the theory more transparent.
Low-noise Monte Carlo simulation of the variable hard sphere gas
Authors: Radtke Gregg A. , Hadjiconstantinou Nicolas G. , Wagner Wolfgang
Published: March 2011

We present an efficient particle simulation method for the Boltzmann transport equation based on the low-variance deviational simulation Monte Carlo approach to the variable-hard-sphere gas. The proposed method exhibits drastically reduced statistical uncertainty for low-signal problems compared to standard particle methods such as the direct simulation Monte Carlo method. We show that by enforcing mass conservation, accurate simulations can be performed in the transition regime requiring as few as ten particles per cell, enabling efficient simulation of multidimensional problems at arbitrarily small deviation from equilibrium.
Influence of Pt as Mn diffusion barrier on the distribution of blocking temperature in Co/(Pt)/IrMn exchange biased layers
Authors: Baltz V. , Dieny B.
Published: March 2011

Many spintronic devices such as thermally-assisted magnetic random access memories take advantage of the ferromagnetic(F)/antiferromagnetic(AF) interaction to pin the magnetization of a reference layer. However, they suffer from detrimental blocking temperatures distributions from memory cell to memory cell. A low-temperature contribution to the distribution was ascribed to spin-glass like regions which are randomly spread over the film. We report on an attempt to reduce the amount of these spin-glass like regions due to interdiffusion of species by adding a diffusion barrier at the F/AF interface.
Flow structure and momentum transport for buoyancy driven mixing flows in long tubes at different tilt angles
Authors: Znaien J. , Moisy F. , Hulin J. P.
Published: March 2011

Buoyancy driven mixing of fluids of different densities (ρ1 and ρ2) in a long circular tube is studied experimentally at the local scale as a function of the tilt angle from vertical (15°≤θ≤60°) and of the Atwood number [10−3≤At=(ρ2−ρ1)/(ρ2+ρ1)≤10−2]. Particle Image Velocimetry (PIV) and Laser Induced Fluorescence (LIF) measurements in a vertical diametral plane provide the velocity and the relative concentration (and, hence, density) fields. A map of the different flow regimes observed as a function of At and θ has been determined: as At increases and θ is reduced, the regime varies from laminar to intermittent destabilizations and, finally, to developed turbulence. In the laminar regime, three parallel stable layers of different densities are observed; the velocity profile is linear and well predicted from the density profile. The thickness of the intermediate layer can be estimated from the values of At and θ. In the turbulent regime, the density varies slowly with z in the core of the flow: there, transverse turbulent momentum transfer is dominant. As At decreases and θ increases, the density gradient β in the core (and, hence, the buoyancy forces) becomes larger, resulting in higher extremal velocities and indicating a less efficient mixing. While the mean concentration varies with time in the turbulent regime, the mean velocity remains constant. In the strong turbulent regime (highest At and lowest θ values), the transverse gradient of the mean concentration and the fluctuations of concentration and velocity remain stationary, whereas they gradually decay with time when turbulence is weaker.
Microscopic mechanism of nanocrystal formation from solution by cluster aggregation and coalescence
Authors: Hassan Sergio A.
Published: March 2011

Solute-cluster aggregation and particle fusion have recently been suggested as alternative routes to the classical mechanism of nucleation from solution. The role of both processes in the crystallization of an aqueous electrolyte under controlled salt addition is here elucidated by molecular dynamics simulation. The time scale of the simulation allows direct observation of the entire crystallization pathway, from early events in the prenucleation stage to the formation of a nanocrystal in equilibrium with concentrated solution. The precursor originates in a small amorphous aggregate stabilized by hydration forces. The core of the nucleus becomes crystalline over time and grows by coalescence of the amorphous phase deposited at the surface. Imperfections of ion packing during coalescence promote growth of two conjoint crystallites. A parameter of order and calculated cohesive energies reflect the increasing crystalline order and stress relief at the grain boundary. Cluster aggregation plays a major role both in the formation of the nucleus and in the early stages of postnucleation growth. The mechanism identified shares common features with nucleation of solids from the melt and of liquid droplets from the vapor
Effect of temperature and time on properties of spark plasma sintered NiCuZn: Co ferrite
Authors: Zehani K. , Mazaleyrat F. , Loyau V. , Labouré E.
Published: March 2011

Spark plasma sintering is a powerful method to produce fine grain dense ferrite at low temperature. However the process, usually conducted in neutral atmosphere in a carbon die, yields carbon surface deposition and the reduction of Fe3+ into Fe2+. It is shown that subsequent annealing in air can remove carbon and under some conditions produce complete oxidation of Fe2+ ions. Regular values of the resistivity and permittivity (resp., 1 MΩm, 13 ε0) are recovered for most samples annealed at temperatures not higher than 750  °C. A relatively high value of the permeability (up to 240) and a high merit factor (μs×fr>5 GHz) have been achieved.
Microstructural evolution of triple junction and grain boundary phases of a Nd-Fe-B sintered magnet by post-sintering annealing
Authors: Kim Tae-Hoon , Lee Seong-Rae , Kim Dong-Hwan , Nam-Kung Seok , Jang Tae-Suk
Published: March 2011

The microstructural evolution of Nd-rich grain boundary phases (GBP) in connection with triple junction phases (TJP) during post-sintering annealing (PSA) was investigated. The Cu-rich TJP in the as-sintered sample was mostly a fcc-NdO phase but the GBP were a mixture of h-Nd2O3 and Nd phases. The fcc-NdO of the TJP in the as-sintered state gradually transformed to h-Nd2O3 during the first and the second PSA steps. However, it transformed to a C-Nd2O3 phase as both a massive form such as TJP and a thin GBP after the modified second PSA step. This suggests that the mechanism for the formation of metastable C-Nd2O3 may not be solely the interface energy. In contrast, the mixture of h-Nd2O3 and Nd of the GBP in the as-sintered state gradually transformed to C-Nd2O3 which is embedded in the amorphous matrix as the PSA goes from the first to second or modified second PSA step. The formation of the C-Nd2O3 GBP with an amorphous phase is the main factor for increasing the coercivity (from 21.8 to 30.4 kOe) after the second or modified second PSA step.
The probability analysis of opening of DNA
Authors: Srivastava Shikha , Singh Navin
Published: March 2011

We have studied the separation of a double stranded DNA (dsDNA), which is driven by either the temperature or force. By monitoring the probability of opening of entire base pairs along the chain, we show that the opening of a dsDNA depends not only on the sequence but also on the constraints on the chain in the experimental setups. Our results clearly demonstrate that the force-induced melting of dsDNA, whose one of the ends is constrained, is significantly different from the thermal melting, when both ends are free.
Properties of model atomic free-standing thin films
Authors: Shi Zane , Debenedetti Pablo G. , Stillinger Frank H.
Published: March 2011

We present a computational study of the thermodynamic, dynamic, and structural properties of free-standing thin films, investigated via molecular dynamics simulation of a glass-forming binary Lennard-Jones mixture. An energy landscape analysis is also performed to study glassy states. At equilibrium, species segregation occurs, with the smaller minority component preferentially excluded from the surface. The film's interior density and interface width depend solely on temperature and not the initialization density. The atoms at the surface of the film have a higher lateral diffusivity when compared to the interior. The average difference between the equilibrium and inherent structure energies assigned to individual particles, as a function of the distance from the center of the film, increases near the surface. A minimum of this difference occurs in the region just under the liquid–vapor interface. This suggests that the surface atoms are able to sample the underlying energy landscape more effectively than those in the interior, and we suggest a possible relationship of this observation to the recently reported formation of stable glasses by vapor phase deposition.
Boundary conditions at the vapor-liquid interface
Authors: Frezzotti Aldo
Published: March 2011

The paper aims at presenting a review of kinetic theory applications to evaporation condensation problems. The main results for monatomic and polyatomic gases and mixtures are described. The role of boundary conditions at the vapor-liquid interface is discussed and a description of molecular dynamics studies aimed at formulating vapor-liquid interaction models is given.
Multireference coupled-cluster theory: The easy way
Authors: Musiał Monika , Perera Ajith , Bartlett Rodney J.
Published: March 2011

The multi-ionization equation-of-motion coupled-cluster (CC) method is developed for multireference (MR) problems. It is operationally single reference, depending upon a formal matrix diagonalization step to define the coefficients in the wavefunction in an unbiased way that allows for important MR character. The method is illustrated for the autoisomerization of cyclobutadiene, which has a very large multireference effect and compared to other MR-CC results. The newly implemented methods are also used to obtain the vertical double ionization (DI) potentials of several small molecules (H2O, CO, C2H2, C2H4). Also, the performance of the new methods is analyzed by plotting the potential energy curve for twisted ethylene as a function of a dihedral angle between two methylenes. Evaluation of the total molecular energy via MR-DI-CC calculations makes it possible to avoid an unphysical cusp.
Response to “Comment on ‘A smooth, nonsingular, and faithful discretization scheme for polarizable continuum models: The switching/Gaussian approach’” [J. Chem. Phys. 134, 117101 (2011)]
Authors: Lange Adrian W. , Herbert John M.
Published: March 2011

In response to the Comment by Scalmani and Frisch, we clarify certain claims made in the context of our “switching/Gaussian” discretization procedure. Furthermore, an explanation is proposed to explain observed similarities between this technique and the “continuous surface charge” method introduced by Scalmani and Frisch.
GaAs nanoneedles grown on sapphire
Authors: Chuang Linus C. , Moewe Michael , Ng Kar Wei , Tran Thai-Truong D. , Crankshaw Shanna , Chen Roger , Ko Wai Son , Chang-Hasnain Connie
Published: March 2011

Heterogeneous integration of dissimilar single crystals is of intense research interests. Lattice mismatch has been the most challenging bottleneck which limits the growth of sufficient active volume for functional devices. Here, we report self-assembled, catalyst-free, single crystalline GaAs nanoneedles grown on sapphire substrates with 46% lattice mismatch. The GaAs nanoneedles have a 2–3 nm tip, single wurtzite phase, excellent optical quality, and dimensions scalable with growth time. The needles have the same sharp, hexagonal pyramid shape from ∼100 nm (1.5 min growth) to ∼9 μm length (3 h growth).
Tunneling magnetoresistance in epitaxial discontinuous Fe/MgO multilayers
Authors: García-García A. , Pardo J. A. , Štrichovanec P. , Magén C. , Vovk A. , De Teresa J. M. , Kakazei G. N. , Pogorelov Y. G. , Morellón L. , Algarabel P. A. , Ibarra M. R.
Published: March 2011

Epitaxial discontinuous Fe/MgO multilayers have been grown by pulsed laser deposition on MgO(001) single-crystal substrates. The multilayers with 0.6 nm nominal Fe layers thickness are superparamagnetic and demonstrate tunneling magnetoresistance (TMR) in the current-in-plane configuration. Increasing deposition temperature causes an improvement in crystal quality and is accompanied by higher TMR ratios. The maximum value (9.2% TMR at room temperature and 18 kOe magnetic field) trebles that of polycrystalline samples deposited simultaneously on glass substrates. A model formula for TMR ratio that includes both spin-dependent tunneling and spin-filtering effect is proposed to explain these results.
A simple but fully nonlocal correction to the random phase approximation
Authors: Ruzsinszky Adrienn , Perdew John P. , Csonka Gábor I.
Published: March 2011

The random phase approximation (RPA) stands on the top rung of the ladder of ground-state density functional approximations. The simple or direct RPA has been found to predict accurately many isoelectronic energy differences. A nonempirical local or semilocal correction to this direct RPA leaves isoelectronic energy differences almost unchanged, while improving total energies, ionization energies, etc., but fails to correct the RPA underestimation of molecular atomization energies. Direct RPA and its semilocal correction may miss part of the middle-range multicenter nonlocality of the correlation energy in a molecule. Here we propose a fully nonlocal, hybrid-functional-like addition to the semilocal correction. The added full nonlocality is important in molecules, but not in atoms. Under uniform-density scaling, this fully nonlocal correction scales like the second-order-exchange contribution to the correlation energy, an important part of the correction to direct RPA, and like the semilocal correction itself. For the atomization energies of ten molecules, and with the help of one fit parameter, it performs much better than the elaborate second-order screened exchange correction.
Comprehensive study of the resistance switching in SrTiO3 and Nb-doped SrTiO3
Authors: Chen X. G. , Ma X. B. , Yang Y. B. , Chen L. P. , Xiong G. C. , Lian G. J. , Yang Y. C. , Yang J. B.
Published: March 2011

We have demonstrated that the resistance switching (RS) effect can be controlled by the modification of the electrode configurations and the carrier densities in the Ag/SrTiO3 and Ag/Nb-doped SrTiO3(Nb:STO) structures. The elimination of the Schottky junction in the metal/Nb:STO completely destroys the RS effect, which suggests that the RS effect originates from the modification of Schottky-like barrier formed at the interface of metal/Nb:STO. The rectifying I-V curves revealed that the change in resistance was attributed to the trapping or detrapping carriers at the interface. The carrier density plays an important role in the determination of RS effect. The presence of the RS in SrTiO3 requires an appropriate doping level to provide conditions for trapping carriers at the interface.
Controlling elastic waves with isotropic materials
Authors: Chang Zheng , Hu Jin , Hu Gengkai , Tao Ran , Wang Yue
Published: March 2011

Design of functional devices with isotropic materials has significant advantages, as regards easy fabrication and broadband application. In this letter, we present a method to derive isotropic transformation material parameters for elastodynamics under local conformal transformation. The transformed material parameters are then applied to design a beam bender, a four-beam antenna and an approximate carpet cloak for elastic wave with isotropic materials, validated by the numerical simulations.
Characterization of the gate oxide of an AlGaN/GaN high electron mobility transistor
Authors: Holzworth M. R. , Rudawski N. G. , Pearton S. J. , Jones K. S. , Lu L. , Kang T. S. , Ren F. , Johnson J. W.
Published: March 2011

A subnanometer thick interfacial oxide layer present between the Ni/Au gate metal stack and semiconducting epilayers of an AlGaN/GaN high electron mobility transistor was characterized using high-angle annular dark-field scanning transmission electron microscopy and laser-assisted atom probe tomography. It was revealed that the oxide is composed of distinct Ni-oxide-rich and Al-oxide-rich layers with no Ga-oxide detected. The results provide information that is of potential importance in determining failure mechanisms and improving reliability of AlGaN/GaN high electron mobility transistors.
Au/CuPc interface: A valence band photoemission investigation
Authors: Lozzi Luca , Santucci Sandro
Published: March 2011

The formation of the metal–organic interface depositing gold, by thermal evaporation in ultrahigh vacuum conditions, onto a copper phthalocyanine film has been studied by means of ultraviolet photoemission spectroscopy. The evolution of the valence band spectra and in particular of the highest occupied molecular orbitals (HOMO) and of the Au upper states has been followed as a function of gold film thickness. The HOMO peak position is strongly influenced by the Au deposition, suggesting an n-doping process of the organic film. The gold 6s state behavior indicates the formation of small metal clusters whose size increases as a function of the gold deposited. The doping of the organic film determines a strong reduction of the film ionization energy.
Conservation management of rivers and wetlands under climate change - a synthesis
Authors: Kingsford Richard T.
Published: March 2011

Dams, diversion of water, invasive species, overharvesting and pollution are degrading rivers and wetlands. Climate change may exacerbate impacts of these threats through predicted reductions in rainfall and increased temperature, decreasing flow and altering timing and variability of flow regimes. Papers in this special issue identify conservation-management strategies for wetlands and rivers through recovery of flow regimes, alteration of dam operations, protected-area management and improved governance and adaptive management. On most regulated rivers, flow regimes should be recovered by increasing environmental flows. Alteration of dam operations can also improve river health through structures on dams (e.g. fishways, multi-level offtakes), reinstating floodplains and improving flow delivery. Further, time-limited licensing for dams and accompanying regular assessments of safety and of environmental and socioeconomic impacts could improve operations. Protected areas remain the core strategy for conservation, with recent improvements in their identification and management, supported by analytical tools that integrate across large spatial and temporal scales. Finally, effective conservation requires good governance and rigorous adaptive management. Conservation management of rivers and wetlands can be significantly improved by adopting these strategies although considerable challenges remain, given increasing human pressures on freshwater resources, compounded by the impacts of climate change.
Embryo transfer in the dromedary camel (Camelus dromedarius) using non-ovulated and ovulated, asynchronous progesterone-treated recipients
Authors: Skidmore J. A. , Billah M.
Published: March 2011

The aim of the present study was to investigate the use of exogenous progesterone and equine chorionic gonadotrophin (eCG) in non-ovulated and ovulated, asynchronous dromedary camel recipients being prepared for an embryo transfer programme. The uteri of 12 mated donor camels were flushed non-surgically 7 days after ovulation and 42 embryos were recovered. In Experiment 1, 16 embryos were transferred non-surgically to recipients on Day 3 or 4 after ovulation (ov+3 and ov+4, respectively). Each recipient received a daily dose of 75 mg, i.m., progesterone-in-oil from 2 days before embryo transfer until 6 days after ovulation. Thereafter, the progesterone dose was reduced to 50 mg on Day 7 and finally to 25 mg day–1 on Days 8 and 9. Nine of 16 recipients (56%; ov+3, n = 4; ov+4, n = 5) became pregnant compared with none of eight non-progesterone treated controls, into which embryos were transferred on Day 4 after ovulation. In Experiment 2, 18 non-ovulated recipients received 75 mg, i.m., progesterone-in-oil daily from 3 days before until 12 days after non-surgical transfer of a Day 7 blastocyst, at which time pregnancy was diagnosed by ultrasonography. All pregnant recipients continued to receive 75 mg progesterone-in-oil daily for a further 6 days, when each camel received 2000 IU, i.m., eCG. Progesterone treatment was then reduced to 50 mg day–1 and, when a follicle(s) ≥1.3 cm in diameter were present in the ovaries, each animal received 20 μg buserelin to induce ovulation. Once the corpora lutea had developed, progesterone treatment was reduced to 25 mg day–1 for a final 3 days. Fourteen of 18 recipients (78%) became pregnant and seven of these (50%) remained pregnant after eCG treatment. Of the seven pregnancies that were lost, two were lost before eCG treatment, two did not respond to eCG treatment and three responded to eCG treatment and ovulated, but lost their pregnancies 6–8 days after the last progesterone injection.
Polycomb purification by in vivo biotinylation tagging reveals cohesin and Trithorax group proteins as interaction partners
Authors: Strübbe Gero , Popp Christian , Schmidt Alexander , Pauli Andrea , Ringrose Leonie , Beisel Christian , Paro Renato
Published: March 2011

The maintenance of specific gene expression patterns during cellular proliferation is crucial for the identity of every cell type and the development of tissues in multicellular organisms. Such a cellular memory function is conveyed by the complex interplay of the Polycomb and Trithorax groups of proteins (PcG/TrxG). These proteins exert their function at the level of chromatin by establishing and maintaining repressed (PcG) and active (TrxG) chromatin domains. Past studies indicated that a core PcG protein complex is potentially associated with cell type or even cell stage-specific sets of accessory proteins. In order to better understand the dynamic aspects underlying PcG composition and function we have established an inducible version of the biotinylation tagging approach to purify Polycomb and associated factors from
Drosophila
embryos. This system enabled fast and efficient isolation of Polycomb containing complexes under near physiological conditions, thereby preserving substoichiometric interactions. Novel interacting proteins were identified by highly sensitive mass spectrometric analysis. We found many TrxG related proteins, suggesting a previously unrecognized extent of molecular interaction of the two counteracting chromatin regulatory protein groups. Furthermore, our analysis revealed an association of PcG protein complexes with the cohesin complex and showed that Polycomb-dependent silencing of a transgenic reporter depends on cohesin function.
A competitive network theory of species diversity
Authors: Allesina Stefano , Levine Jonathan M.
Published: March 2011

Nonhierarchical competition between species has been proposed as a potential mechanism for biodiversity maintenance, but theoretical and empirical research has thus far concentrated on systems composed of relatively few species. Here we develop a theory of biodiversity based on a network representation of competition for systems with large numbers of competitors. All species pairs are connected by an arrow from the inferior to the superior. Using game theory, we show how the equilibrium density of all species can be derived from the structure of the network. We show that when species are limited by multiple factors, the coexistence of a large number of species is the most probable outcome and that habitat heterogeneity interacts with network structure to favor diversity.
Pointing gesture in young children
Authors: Cochet Hélène , Vauclair Jacques
Published: March 2011

This paper provides an overview of recent studies that have investigated the development of pointing behaviors in infants and toddlers. First, we focus on deictic gestures and their role in language development, taking into account the different hand shapes and the different functions of pointing, and examining the cognitive abilities that may or may not be associated with the production of pointing gestures. Second, we try to demonstrate that when a distinction is made between pointing gestures and manipulative activities, the study of children’s hand preference can help to highlight the development of speech-gesture links.
Discourse presentation in Early Modern English writing
Authors: McIntyre Dan , Walker Brian
Published: March 2011

In this article we report on a pilot project investigating the presentation of speech, writing and thought in Early Modern English prose fiction and news writing. The aim of the project is to determine whether discourse presentation changes diachronically and what the function of the various discourse presentation categories were in the Early Modern period. To study this we have built and annotated a small corpus of Early Modern English writing using the model of speech, writing and thought presentation outlined in Semino & Short (2004). We are thus able to compare our findings against those of Semino and Short for Present Day English writing. The quantitative results of our pilot study and our initial qualitative analyses lead to a number of hypotheses which we suggest are suitable for testing on a larger corpus of data.
Useful wild tree resources of southern Sudan: a review
Authors: Robinson Jonathan
Published: March 2011

Southern Sudan has a rich tree flora. Trees are important in the livelihoods of the numerous tribes of the region, who use them for shelter, fuel, food, fodder, medicine and income generation. The gallery and depression forests contain valuable timber trees. Other species provide non-timber forest products that are potentially tradable outside Sudan, particularly in African countries that have over-exploited their own forest resources. As the carrying capacity of the western and central areas of Sudan decreases, the pressure on the natural resources of the higher rainfall southern areas will increase. This in itself might initiate conflict, as various tribes compete over a relatively rich resource base. The recent peace established between the north and south could result in depletion of the forest resources of the south through commercial exploitation. This paper details and discusses the wild tree resources of southern Sudan, including many already threatened species.
The Voice of Dramatherapy: Fragments of Voice Work with a Group of Dramatherapists According to the Sesame Approach
Authors: Natan Eran
Published: March 2011

The integration of voice as part of dramatherapy, following the model of the Sesame approach to Drama and Movement Therapy, can help clients express themselves and form communication with others creatively. This paper presents an experimental voice group which I led with a group of dramatherapists in order to encourage them to enable the voice to become a more essential component of their dramatherapeutic practice. The paper describes the sessions the voice group has undergone, including brief introductions which present the central vocal theme of each session. These themes include breathing, the authentic voice, the child archetype, voice and feeling, stories, the hunter archetype and chants and songs. The author gives some practical suggestions for voice activities that can be embedded in therapeutic intervention. Finally, this article presents the participants' impressions of the voice work, derived from a questionnaire they filled in. According to their feedback, this article concludes that more voice should be integrated in dramatherapy as a therapeutic tool. The author supplies different methods that may be used in order to encourage dramatherapists and their clients to integrate voice more naturally with movement, drama, story, play and touch, the main elements of the Sesame approach to dramatherapy.
Distinguishing published scholarly content with CrossMark
Authors: MEYER Carol Anne
Published: March 2011

The landscape of scholarly communication is complicated by multiple versions of the same documents, available from different sources. What happens if changes need to be made to published documents when scholars tap so many sources? How can important changes be communicated to readers so that they do not rely on outdated or, worse, repudiated research? This article explores the issues and describes the CrossMark service as a possible solution.
Librarians' use of usage statistics for journals and e‐books
Authors: COX Laura
Published: March 2011

In September 2010 MPS Limited undertook a short survey of librarians, addressing their use of usage statistics. Over 300 librarians responded. This article covers the findings. 97% of the librarians surveyed use usage statistics in some way. As would be expected, they find COUNTER‐compliant usage statistics invaluable and place their importance above non‐COUNTER‐compliant usage data. They also rely on this information as a major part of the decision‐making process when it comes to purchase and cancellation decisions.
Evaluating the influence of a medical journal using Google Scholar
Authors: SANNI S.A. , ZAINAB A.N.
Published: March 2011

This study shows how a journal's influence can be calculated by using citations obtained from Google Scholar and other methods even though the journal is not covered by any citation databases. Influence is measured in terms of foreign contributions, ‘equivalent’ immediacy scores of recent articles, and the calculation of citations and ‘equivalent’ impact factor. A total of 580 articles published in the Medical Journal of Malaysia (MJM) between 2004 and 2008 served as the sample. Very few foreign authors contributed to MJM (12.5%), implying its low regional acceptance as a channel for research communication. Immediacy scores for each year indicate citations were received by recently published articles. A total of 1,164 citations were received by 446 of the 580 articles and the main citing sources were journals (1,083) with reasonable h index and impact factor. Yearly impact scores ranged between 0.367 and 0.616. Higher impact factor scores were obtained by older articles.
Global classical solutions of the Boltzmann equation without angular cut-off
Authors: Gressman Philip , Strain Robert
Published: March 2011

This work proves the global stability of the Boltzmann equation (1872) with the physical collision kernels derived by Maxwell in 1866 for the full range of inverse-power intermolecular potentials,r−(p−1)r^{-(p-1)}withp>2p>2, for initial perturbations of the Maxwellian equilibrium states, as announced in an earlier paper by the authors. We more generally cover collision kernels with parameterss∈(0,1)s\in (0,1)andγ\gammasatisfyingγ>−n\gamma > -nin arbitrary dimensionsTn×Rn\mathbb {T}^n \times \mathbb {R}^nwithn≥2n\ge 2. Moreover, we prove rapid convergence as predicted by the celebrated BoltzmannHH-theorem. Whenγ≥−2s\gamma \ge -2s, we have exponential time decay to the Maxwellian equilibrium states. Whenγ>−2s\gamma >-2s, our solutions decay polynomially fast in time with any rate. These results are completely constructive. Additionally, we prove sharp constructive upper and lower bounds for the linearized collision operator in terms of a geometric fractional Sobolev norm; we thus observe that a spectral gap exists only whenγ≥−2s\gamma \ge -2s, as conjectured by Mouhot and Strain. It will be observed that this fundamental equation, derived by both Boltzmann and Maxwell, grants a basic example where a range of geometric fractional derivatives occur in a physical model of the natural world. Our methods provide a new understanding of the grazing collisions in the Boltzmann theory.
Compounds In Literature (CIL): screening for compounds and relatives in PubMed
Authors: Grüning Björn A. , Senger Christian , Erxleben Anika , Flemming Stephan , Günther Stefan
Published: March 2011

Summary: Searching for certain compounds in literature can be an elaborate task, with many compounds having several different synonyms. Often, only the structure is known but not its name. Furthermore, rarely investigated compounds may not be described in the available literature at all. In such cases, preceding searches for described similar compounds facilitate literature mining. Highlighted names of proteins in selected texts may further accelerate the time-consuming process of literary research. Compounds In Literature (CIL) provides a web interface to automatically find names, structures, and similar structures in over 28 million compounds of PubChem and more than 18 million citations provided by the PubMed service. CIL's pre-calculated database contains more than 56 million parent compound–abstract relations. Found compounds, relatives and abstracts are related to proteins in a concise ‘heat map’-like overview. Compounds and proteins are highlighted in their respective abstracts, and are provided with links to PubChem and UniProt.

Availability: An easy-to-use web interface with detailed descriptions, help and statistics is available from http://cil.pharmaceutical-bioinformatics.de.

Contact:  stefan.guenther@pharmazie.uni-freiburg.de
Customizable views on semantically integrated networks for systems biology
Authors: Weile Jochen , Pocock Matthew , Cockell Simon J. , Lord Phillip , Dewar James M. , Holstein Eva−Maria , Wilkinson Darren , Lydall David , Hallinan Jennifer , Wipat Anil
Published: March 2011

Motivation: The rise of high-throughput technologies in the post-genomic era has led to the production of large amounts of biological data. Many of these datasets are freely available on the Internet. Making optimal use of these data is a significant challenge for bioinformaticians. Various strategies for integrating data have been proposed to address this challenge. One of the most promising approaches is the development of semantically rich integrated datasets. Although well suited to computational manipulation, such integrated datasets are typically too large and complex for easy visualization and interactive exploration.

Results: We have created an integrated dataset for Saccharomyces cerevisiae using the semantic data integration tool Ondex, and have developed a view-based visualization technique that allows for concise graphical representations of the integrated data. The technique was implemented in a plug-in for Cytoscape, called OndexView. We used OndexView to investigate telomere maintenance in S. cerevisiae.

Availability: The Ondex yeast dataset and the OndexView plug-in for Cytoscape are accessible at http://bsu.ncl.ac.uk/ondexview.

Contact:  anil.wipat@ncl.ac.uk

Supplementary information:  Supplementary data is available at Bioinformatics online.
AStream: an R package for annotating LC/MS metabolomic data
Authors: Alonso Arnald , Julià Antonio , Beltran Antoni , Vinaixa Maria , Díaz Marta , Ibañez Lourdes , Correig Xavier , Marsal Sara
Published: March 2011

Summary: AStream, an R-statistical software package for the curation and identification of feature peaks extracted from liquid chromatography mass spectrometry (LC/MS) metabolomics data, is described. AStream detects isotopic, fragment and adduct patterns by identifying feature pairs that fulfill expected relational patterns. Data reduction by AStream allows compounds to be identified reliably and subsequently linked to metabolite databases. AStream provides researchers with a fast, reliable tool for summarizing metabolomic data, notably reducing curation time and increasing consistency of results.

Availability: The AStream R package and a study example can be freely accessed at http://www.urr.cat/AStream/AStream.html.

Contact:  smarsal@ir.vhebron.net; ajulia@ir.vhebron.net

Supplementary information:  Supplementary data are available at Bioinformatics online.
Mottness collapse and statistical quantum criticality
Authors: Zaanen J. , Overbosch B. J.
Published: March 2011

We put forward here the case that the anomalous electron states found in cuprate superconductors and related systems are rooted in a deeply non-classical fermion sign structure. The collapse of Mottness, as advocated by Phillips and supported by recent dynamical cluster approximation results on the Hubbard model, sets the necessary microscopic conditions. The crucial insight is due to Weng, who demonstrated that, in the presence of Mottness, the fundamental workings of quantum statistics change, and we will elaborate on the effects of this Weng statistics with an emphasis on characterizing it further using numerical methods. The pseudo-gap physics of the underdoped regime appears as a consequence of the altered statistics and the profound question is how to connect this by a continuous quantum phase transition to the overdoped regime ruled by normal Fermi–Dirac statistics. Proof of principle follows from Ceperley’s constrained path integral formalism, in which states can be explicitly constructed showing a merger of Fermi–Dirac sign structure and scale invariance of the quantum dynamics.
Holographic non-Fermi-liquid fixed points
Authors: Faulkner Tom , Iqbal Nabil , Liu Hong , McGreevy John , Vegh David
Published: March 2011

Techniques arising from string theory can be used to study assemblies of strongly interacting fermions. Via this ‘holographic duality’, various strongly coupled many-body systems are solved using an auxiliary theory of gravity. Simple holographic realizations of finite density exhibit single-particle spectral functions with sharp Fermi surfaces, of a form distinct from those of the Landau theory. The self-energy is given by a correlation function in an infrared (IR) fixed-point theory that is represented by a two-dimensional anti de Sitter space (AdS2) region in the dual gravitational description. Here, we describe in detail the gravity calculation of this IR correlation function.
The role of connexin36 gap junctions in modulating the hypnotic effects of isoflurane and propofol in mice
Authors: Jacobson G. M. , Voss L. J. , Melin S. M. , Cursons R. T. M. , Sleigh J. W.
Published: March 2011

Gap junction blockade is a possible mechanism by which general anaesthetic drugs cause unconsciousness. We measured the sensitivity of connexin36 knockout mice to the hypnotic effects of isoflurane and propofol. The experimental endpoint was recovery of the righting reflex of the anaesthetised animals during 0.2% step‐reductions in isoflurane concentration, or following intraperitoneal injection of propofol (100 mg.kg−1). Connexin36 knockout animals were more sensitive to the hypnotic effects of isoflurane than ‘normal’ wild‐type animals. The half maximal effective concentration (EC50) for recovery of righting reflex was 0.37% for connexin36 knockout vs 0.49% for wild‐type animals (p < 0.001). For propofol, connnexin36 knockout animals showed more rapid loss of righting reflex than wild‐type animals (mean (SD) 2.8 (0.13) vs 3.8 (0.27) min); and young (< 60 days) connexin36 knockout animals remained anaesthetised for longer than young wild‐type mice (47.2 (2.9) vs 30.5 (1.7) min; p < 0.00001). These findings suggest that the hypnotic effects of anaesthetic drugs may be moderately enhanced by gap junction blockade.
Comparison between major histocompatibility complex class II tetramer staining and surface expression of activation markers for the detection of allergen‐specific CD4+ T cells
Authors: Bonvalet M. , Wambre E. , Moussu H. , Horiot S. , Kwok W. W. , Louise A. , Ebo D. , Hoarau C. , Van Overtvelt L. , Baron‐Bodo V. , Moingeon P.
Published: March 2011

Cite this as: M. Bonvalet, E. Wambre, H. Moussu, S. Horiot, W. W. Kwok, A. Louise, D. Ebo, C. Hoarau, L. Van Overtvelt, V. Baron‐Bodo and P. Moingeon, Clinical & Experimental Allergy, 2011 (41) 821–829.

Background
Major histocompatibility complex (MHC) class II tetramers (tetramers) allow to detect allergen‐specific CD4+ T cells at a single‐cell level. Limits to this technology include HLA restriction and the need to identify immunodominant T cell epitopes.

Objective
Assessing the expression of various activation markers following allergen stimulation to replace tetramer staining.

Methods
Peripheral blood mononuclear cells (PBMCs) from 25 birch pollen, grass pollen or house dust mite allergic individuals were stimulated with peptide mixes encompassing immunodominant epitopes from corresponding major allergens. After 2 weeks of in vitro amplification, cells were stained with both the appropriate tetramer and antibodies directed to CD25, CD30, CD39, CD69, CD137, CD154, GITR, HLA‐DR and ICOS, before FACS analysis.

Results
Following allergen stimulation, percentages of tetramer+ cells among CD4+ CD154+ cells range from 5% to 87%, depending upon donors. As for CD154, a large inter‐individual variability is observed in terms of surface expression for all activation markers tested in allergen‐stimulated PBMCs. T cells reactive with either tetramers (0.4–10.4% CD4+ T cells) or anti‐marker antibodies (2.2–32.7% CD4+ T cells), but not both, are observed, reflecting the presence of anergic as well as non‐specifically activated cells. Tetramer+/marker+, tetramer+/marker− and tetramer−/marker+ cells were compared for their capacity to express cytokines, demonstrating that only the former represent bona fide allergen‐specific activated CD4+ T cells, based upon a higher expression of cytokines or corresponding genes in presence of the allergen.

Conclusion and Clinical Relevance
No strict correlation exists between tetramer staining and the expression of multiple activation markers in stimulated CD4+ T cells. Dual staining allows to discriminate functional tetramer+/marker+ vs. anergic (tetramer+/marker−) allergen‐specific T cells or non‐specifically activated (tetramer−/marker+) T cells. Combining tetramer staining with the detection of activation markers helps understanding patient heterogeneity regarding specific CD4+ T cell responses. This approach has immediate relevance for monitoring immune changes induced during specific immunotherapy.
Multichannel estimation of frequency‐department Q from VSP data1
Authors: Harris P. E. , Kerner C. , White R. E.
Published: March 2011

A Method of estimating attenauation from the first arrivals of VSP data is presented. The motivation is the desire to investigate the effects of scattering on wave propagation, and particularly the apparent attenuation and associated phase delay due to fine layering (the O'Doherty‐Anstey effect).

In order to take account of the frequency dependence of the predicted scattering attenuation, and to provide robust statistics for the estimates, a beam‐forming method is used to measure the attenuation. This simularaneously estimates the slowness and polarization angle of the different wave modes, and results in attenuation measurements which are largely free of interference from reflected and mode‐converted energy. By working in the frequency domain and measuring amplitude decay with depth, the frequency dependence of the attenuation is also accounted for. The beam‐forming algorithm works in two passes, the first of which estimates slownesses and polarization angles over a small depth range, while the second uses the information from the first pass over a larger depth range to estimate attenuation.

An approximate error analysis of the method shows that the standard variance of the estimated Q values is proportional to Q2 and the data quality (measured by its spectral coherence), and inversely proportional to the square of the analysis depth range and the square of the frequency. Hence the depth resolution is traded against the stability of the results.

The method is applied to a zero‐offset three‐component VSP. The data are of good quality, with a bandwidth ranging from 180 Hz in the shallow part to 100 Hz in the deepest part. Stable results were obtained using a 450 m depth range. Above about 50 Hz, there is little evidence of frequency dependence in the attenuation. There is a clear division in depth into layers of higher and lower attenuation, with values of Q typically between 50 and 200. Below 50 Hz, however, attenuation increases rapidly with decreasing frequency throughout the depth range, with values of Q of less than 10 at 15 Hz. This behaviour appears anomalous since on physical grounds we expect very high values of Q at low frequency, and we have no explanation for these observations.
Impacts of multiple extreme winter warming events on sub‐Arctic heathland: phenology, reproduction, growth, and CO2flux responses
Authors: BOKHORST S. , BJERKE J. W. , STREET L. E. , CALLAGHAN T. V. , PHOENIX G. K.
Published: March 2011

Extreme weather events can have strong negative impacts on species survival and community structure when surpassing lethal thresholds. Extreme, short‐lived, winter warming events in the Arctic rapidly melt snow and expose ecosystems to unseasonably warm air (for instance, 2–10 °C for 2–14 days) but upon return to normal winter climate exposes the ecosystem to much colder temperatures due to the loss of insulating snow. Single events have been shown to reduce plant reproduction and increase shoot mortality, but impacts of multiple events are little understood as are the broader impacts on community structure, growth, carbon balance, and nutrient cycling. To address these issues, we simulated week‐long extreme winter warming events – using infrared heating lamps and soil warming cables – for 3 consecutive years in a sub‐Arctic heathland dominated by the dwarf shrubsEmpetrum hermaphroditum, Vaccinium vitis‐idaea(both evergreen) andVaccinium myrtillus(deciduous). During the growing seasons after the second and third winter event, spring bud burst was delayed by up to a week forE. hermaphroditumandV. myrtillus, and berry production reduced by 11–75% and 52–95% forE. hermaphroditumandV. myrtillus, respectively. Greater shoot mortality occurred inE. hermaphroditum(up to 52%),V. vitis‐idaea(51%), andV. myrtillus(80%). Root growth was reduced by more than 25% but soil nutrient availability remained unaffected. Gross primary productivity was reduced by more than 50% in the summer following the third simulation. Overall, the extent of damage was considerable, and critically plant responses were opposite in direction to the increased growth seen in long‐term summer warming simulations and the ‘greening’ seen for some arctic regions. Given the Arctic is warming more in winter than summer, and extreme events are predicted to become more frequent, this generates large uncertainty in our current understanding of arctic ecosystem responses to climate change.