bluuebunny/crossref_metadata_2025 huggingface dataset:
Structural stability of linear random dynamical systems
Authors: Cong Nguyen Dinh
Published: October 2010

In this paper, structural stability of discrete-time linear random dynamical systems is studied. A random dynamical system is called structurally stable with respect to a random norm if it is topologically conjugate to any random dynamical system which is sufficiently close to it in this norm. We prove that a discrete-time linear random dynamical system is structurally stable with respect to its Lyapunov norms if and only if it is hyperbolic.
Admissible subgroups of full ergodic groups
Authors: Fedorov Andrey , Rubshtein Ben-Zion
Published: October 2010

Let G be a countable group of automorphisms of a Lebesgue space (X, m) and let [G] be the full group of G. For a pair of countable ergodic subgroups H1 and H2 of [G], the following problem is considered: when are the full subgroups [H1] and [H2] conjugate in the normalizer N[G] = {g ∈ Aut X: g[G]g-1 = [G]} of [G]. A complete solution of the problem is given in the case when [G] is an approximately finite group of type II and [H] is admissible, in the sense that there exists an ergodic subgroup [H0] of [G] and a countable subgroup Γ ⊂ N[H0] consisting of automorphisms which are outer for [H0], such that [H0] ⊂ [G] and the full subgroup [Ho, Γ] generated by [H0] and Γ coincides with [G].
Rational maps whose Fatou components are Jordan domains
Authors: Pilgrim Kevin M.
Published: October 2010

We prove: If f(z) is a critically finite rational map which has exactly two critical points and which is not conjugate to a polynomial, then the boundary of every Fatou component of f is a Jordan curve. If f(z) is a hyperbolic critically finite rational map all of whose postcritical points are periodic, then there exists a cycle of Fatou components whose boundaries are Jordan curves. We give examples of critically finite hyperbolic rational maps f with a Fatou component ω satisfying f(ω) = ω and f|∂ω not topologically conjugate to the dynamics of any polynomial on its Julia set.
The complexity of the collection of measure-distal transformations
Authors: Beleznay Ferenc , Foreman Matthew
Published: October 2010

It is shown that the collection of measure-distal transformations is a complete co-analytic set and that the Furstenberg order is a -norm. Various other results about skew products are also shown.
IP-sets and polynomial recurrence
Authors: Bergelson Vitaly , Furstenberg Hillel , McCutcheon Randall
Published: October 2010

We combine recurrence properties of polynomials and IP-sets and show that polynomials evaluated along IP-sequences also give rise to Poincaré sets for measure-preserving systems, that is, sets of integers along which the analogue of the Poincaré recurrence theorem holds. This is done by applying to measure-preserving transformations a limit theorem for products of appropriate powers of a commuting family of unitary operators.
Simulation of shock waves in flyer plate impact experiments
Authors: Neff S. , Presura R.
Published: October 2010

In this paper we present a newly developed one-dimensional hydrodynamic simulation code and use it to determine the shock evolution in flyer plate impact experiments. The code is Lagrangian with artificial viscosity and uses shock Hugoniot data in its equation-of-state calculations instead of SESAME data tables. First shock calculations for transparent targets show a good agreement with theoretical predictions, making the code suitable for designing future flyer impact experiments at the Nevada Terawatt Facility.
Plasma-filled diode in the electron accelerator on base of a pulsed linear transformer
Authors: Kovalchuk B.M. , Zherlitsyn A.A. , Pedin N.N.
Published: October 2010

Technique of a linear transformer allows now to build the generators of high power nanosecond pulses with the current rise time of ~100 ns without intermediate power compression stages. This technique is being examined for use in high current high voltage pulsed accelerators. Plasma-filled diode has several advantages over standard vacuum diode that allow to improve the accelerators parameters. In this paper, plasma-filled diode experiments are described on generation of e-beam in the linear transformer accelerator. Possibility of use in the diode of isolated parallel plasma channels has been proven for the e-beam generation with cross-sectional area up to 50 cm2. The beam with current of 100 kA at voltage more than 400 kV was generated in the plasma-filled diode. Energy transmission efficiency from primary storage into a beam is about 54%.
Localization of a high-speed mobile robot using global features
Authors: Cho Seungkeun , Lee Jangmyung
Published: October 2010

A new localization algorithm is proposed for a fast moving mobile robot, which utilizes only one beacon and the global features of the differential-driving mobile robot. It takes a relatively long time to localize a mobile robot with active beacon sensors, since the distance to the beacon is measured based on the traveling time of the ultrasonic signal. When the mobile robot is moving slowly, the measurement time does not yield a high error. At a higher speed, however, the localization error becomes too large for the mobile robot to be located accurately. Therefore, in high-speed mobile robot operations, instead of using two or more active beacons, only one active beacon and the global features of the mobile robot are used to localize the mobile robot. The two global features are the radius and center of the rotational motion for the differential-driving mobile robot, which generally describe the motion of, and are used for the trace prediction of, a mobile robot. In high-speed operations, the localizer finds the intersection point of this predicted trace and the circle, which is centered at the beacon whose radius is the distance between the mobile robot and the beacon. This new approach overcomes the large localization error caused by the high speed of the mobile robot. The performance of the new localization algorithm is verified through experiments with a high-speed mobile robot.
A Typed Feature-based Grammar of Danish
Authors: Underwood Nancy L.
Published: October 2010

This paper presents an overview of the first broad coverage grammatical description of Danish in a Typed Feature Structure (TFS) based unification formalism inspired by HPSG. These linguistic specifications encompass phenomena within inflectional morphology, phrase structure and predicate argument structure, and have been developed with a view to implementation. The emphasis on implementability and re-usability of the specifications has led to the adoption of a rather leaner formal framework than that underlying HPSG. However, the paper shows that the adoption of such a framework does not lead to a loss of expressibility, but in fact enables certain phenomena, such as the interface between morphology and syntax and local discontinuities, to be treated in a simple and elegant fashion.
Danish Motion Verbs: Syntactic Alternations and the Hypothesis of Semantic Determination
Authors: Pederson Bolette Sanford
Published: October 2010

Danish motion verbs provide a good candidate for testing the hypothesis of semantic determination on Danish, a hypothesis most recently discussed by Levin (1993) in her description of English verb classes and alternations. A set of core meaning components for motion verbs is identified and a taxonomy of Danish motion verbs is produced. With the basic assumption that a word's meaning determines its syntactic potential, this paper gives an account of the syntactic alternations that Danish motion verbs can undergo, and exposes a more or less transparent relation between their syntax and semantics.
On the Proper Treatment of Proper Names
Authors: Thomsen Hanne Erdman
Published: October 2010

The present paper is a discussion of the syntactic and semantic treatment of proper names in the generalized quantifier framework, and supports the view that the semantic value of proper names is of the same kind as that of other nouns – sets of individuals, whereas unique individuals are assigned as the value of the NP-level. Furthermore, it i s argued that the set denoted by a name contains the individuals name-related to the expression in question, i.e. the individuals bearing the name. In other uses (e.g. the museum bought a Picasso) the name denotes the extension of an ad hoc predicate. Finally, the relation between th e proposed analysis and Saussure's concept of the linguistic sign is briefly discussed.
Locative Case Adjuncts in Finnish: Notes on Syntactico-Semantic Interface
Authors: Nikanne Urpo
Published: October 2010

This paper discusses Finnish depictive and resultative secondary predicates. The analysis is based on a condition of licensing which can be seen as a version of the principle of Full Interpretation: “A well-formed syntactic structure is licensed only if it can be linked to a well-formed conceptual structure.” The suggested non-trivial theory of the interface between syntax and semantics allows us to avoid unnecessary complexity in syntax, such as small clause and PRO, in secondary predicate adjuncts.
From Manner to Subject Modification: Adverbialization in English
Authors: Swan Toril
Published: October 2010

The paper discusses the process of adverbialization in English, focusing on one type of adverb, subject-modifier adverbs such assadly, thoughtfullyandpinkly. It is also shown that the -lysuffix in English (unlike its cognates in the other Germanic languages) has become an extremely versatile adverb suffix. Finally, it is argued that in English, the manner adverb category is prototypical, whereas other adverb types, notably subject-modifier adverbs, are less central adverbs.
Case Competition in Finnish
Authors: Nelson Diane
Published: October 2010

In this article, the traditional analysis of grammatical case in Finnish - in which the form of the object depends on the presence of an overt subject — is reworked within a formal syntactic framework. Within the Case competition model adopted here, the role of argument structure in case assignment, captured by Burzio's Generalization, plays a vital role in the underlying mechanisms of the case system: only when a verb governs two arguments, one of them Caseless, may it also license accusative case. This dependency is subsumed under universal syntactic relations, including government, binding and the ECP. It is also argued that Finnish incorporates active case subsystems within a main nominative-accusative system. These facts receive a natural account within the adopted framework.
Argument Interpretations in the Ditransitive Construction
Authors: Zhang Niina Ning
Published: October 2010

An indirect object can be interpreted as a Provider or as a Recipient. The evidence considered in this article suggests that the two interpretations can be morphologically analytic in Chinese and typologically parametrized for certain natural classes of verbs in English and Chinese. Two VP projections are proposed for the ditransitive construction. The head of the lower VP can be phonologically realized or null. The content of the null verb is parametrized across languages. The contrasts in indirect object interpretations in these languages are explained in terms of the lexical meanings of the null verb. The contrasts in verb occurrence restrictions in these languages are accounted for by the interpretable feature compatibilities in head adjunction from the lower to the higher VP.
Factors associated with social contacts in four communities during the 2007–2008 influenza season
Authors: DeSTEFANO F. , HABER M. , CURRIVAN D. , FARRIS T. , BURRUS B. , STONE-WIGGINS B. , McCALLA A. , GULED H. , SHIH H. , EDELSON P. , WETTERHALL S.
Published: October 2010

Mathematical models of influenza pandemics are sensitive to changes in contact rates between individuals. We conducted population-based telephone surveys in four North Carolina counties to determine the number of social interactions between individuals during the 2007–2008 influenza season. Influenza activity was monitored through sentinel medical practices. Among 3845 adults, the number of social contacts varied with age, was lower on weekends than on weekdays, and further decreased during school holiday periods. Adults with influenza-like illnesses had fewer social contacts. Adults' contacts in the community setting increased during periods of peak influenza activity. Among 290 children, potential contacts (i.e. other people in the same location) were lowest among preschool-age children and decreased on weekends and during school holidays. In adjusted analyses, children's potential social contacts did not change during periods of peak influenza activity. These results should be useful for modelling influenza epidemics and pandemics and in planning mitigation and response strategies.
Optimal investment strategies and performance sharing rules for pension schemes with minimum guarantee
Authors: PÉZIER JACQUES , SCHELLER JOHANNA
Published: October 2010

There is a potential conflict of interest between a pension fund sponsor and future pensioners when they share unequally in the pension fund performance. Thus, when a scheme offers a yearly guaranteed minimum return to pensioners, as is presently the case with German Pensionskassen, the sponsors cannot afford to invest in risky assets and consequently, pensioners end up with safe but very low expected returns. We examine optimal investment strategies for sponsors under alternative performance sharing rules and seek the rules that are most beneficial to pensioners. We find that the current yearly performance sharing rule imposed on Pensionskassen could be tilted in favor of sponsors without impairing the welfare of pensioners. We also find that the welfare of pensioners would be greatly enhanced if the guaranteed minimum return were applied to the cumulative return since inception of the scheme rather than to yearly returns. The ensuing credit risk taken by pensioners on sponsors could be kept to a minimum by proper regulation; this would induce sponsors to adopt safe constant proportionality portfolio insurance (CPPI) style investment strategies.
High‐Ca boninites from the active Tonga Arc
Authors: Cooper Lauren B. , Plank Terry , Arculus Richard J. , Hauri Erik H. , Hall Paul S. , Parman Stephen W.
Published: October 2010

We report the first known occurrence of high‐Ca boninites within an active submarine island arc, at Volcano A within the Tonga Arc. Both the whole rock and a population of melt inclusions (in Fo86–92 olivines) from a dredged satellite cone have compositions classified as high‐Ca boninite. All samples from Volcano A, however, may be related to parental boninites, given the similarity in their rare earth element patterns and their coherency along a similar liquid line of descent. The primary high‐Ca boninite liquids were generated in the mantle wedge by high cumulative degrees of melting (>∼24%) at typical mantle wedge temperatures (<1300°C) driven by an influx of slab‐derived fluid (>4 wt % H2O in primary liquids). We propose a two‐stage model for generating primary boninite liquids at Volcano A: (1) melting of fertile peridotite within the Lau back‐arc basin, followed by (2) remelting of this residual peridotite with slab‐derived fluid beneath the Tonga Arc. The occurrence of high‐Ca boninites at Volcano A is related to the relative location and duration of back‐arc spreading. Here, the Eastern Lau Spreading Center has been processing mantle for ∼1 Ma, and corner flow circulation brings mantle from the back‐arc melting regime into the arc melting regime at a rate that is a significant fraction (>30%) of the convergence rate. On the basis of Si6.0 and Ti6.0 relationships, we argue that a significant portion of the central Tonga Arc near Volcano A, as well as several other arc volcanoes with active back‐arc basins, are also erupting basaltic andesites with boninite parentage.
A likely universal model of fracture scaling and its consequence for crustal hydromechanics
Authors: Davy P. , Le Goc R. , Darcel C. , Bour O. , de Dreuzy J. R. , Munier R.
Published: October 2010

We argue that most fracture systems are spatially organized according to two main regimes: a “dilute” regime for the smallest fractures, where they can grow independently of each other, and a “dense” regime for which the density distribution is controlled by the mechanical interactions between fractures. We derive a density distribution for the dense regime by acknowledging that, statistically, fractures do not cross a larger one. This very crude rule, which expresses the inhibiting role of large fractures against smaller ones but not the reverse, actually appears be a very strong control on the eventual fracture density distribution since it results in a self‐similar distribution whose exponents and density term are fully determined by the fractal dimension D and a dimensionless parameter γ that encompasses the details of fracture correlations and orientations. The range of values for D and γ appears to be extremely limited, which makes this model quite universal. This theory is supported by quantitative data on either fault or joint networks. The transition between the dilute and dense regimes occurs at about a few tenths of a kilometer for faults systems and a few meters for joints. This remarkable difference between both processes is likely due to a large‐scale control (localization) of the fracture growth for faulting that does not exist for jointing. Finally, we discuss the consequences of this model on the flow properties and show that these networks are in a critical state, with a large number of nodes carrying a large amount of flow.
Cross‐shore surfzone tracer dispersion in an alongshore current
Authors: Clark David B. , Feddersen Falk , Guza R. T.
Published: October 2010

Cross‐shore surfzone tracer dispersion in a wave driven alongshore current is examined over a range of wave and current conditions with 6 continuous dye releases, each roughly 1–2 hours in duration, at Huntington Beach, California. Fluorescent dye tracer released near the shoreline formed shore parallel plumes that were sampled on repeated cross‐shore transects with a jet ski mounted fluorometer. Ensemble averaged cross‐shore tracer concentration profiles are generally shoreline attached (maximum at or near the shoreline), with increasing cross‐shore widths and decreasing peak values with downstream distance. More than a few 100 m from the source, tracer is often well mixed across the surfzone (i.e., saturated) with decreasing tracer concentrations farther seaward. For each release, cross‐shore surfzone absolute diffusivities are estimated using a simple Fickian diffusion solution with a no‐flux boundary at the shoreline, and range from 0.5–2.5 m2 s−1. Surfzone diffusivity scalings based on cross‐shore bore dispersion, surfzone eddy mixing length, and undertow driven shear dispersion are examined. The mixing‐length scaling has correlation r2 = 0.59 and the expected best‐fit slope <1, indicating that horizontal rotational motions are important for cross‐shore tracer dispersion in the surfzone.
Impact of Asian dust and continental pollutants on cloud chemistry observed in northern Taiwan during the experimental period of ABC/EAREX 2005
Authors: Wang Sheng‐Hsiang , Lin Neng‐Huei , OuYang Chang‐Feng , Wang Jia‐Lin , Campbell James R. , Peng Chi‐Ming , Lee Chung‐Te , Sheu Guey‐Rong , Tsay Si‐Chee
Published: October 2010

Observations of particulate matter (PM), vertical cloud and aerosol structure and cloud water chemistry in northern Taiwan were conducted during the ABC/EAREX 2005 period. Five Asian continental outflow regimes reaching Taiwan were identified. One was coupled with a dust storm observed not only at Gosan, Korea, but also over Taiwan, suggesting the scope of its regional impact. The arrival of the dust event was determined by lidar, cloud water, and surface PM measurements. When continental outflow events correspond to the presence of significant dust concentrations, air quality can be drastically worsened due to high levels of PM. PM10 (PM with aerodynamic diameters < 10 μm), pH, conductivity, and ion concentrations of cloud water increased drastically near the dissipating stage of the frontal passage/cloud event for the dust case. Cloud water may have become acidified by pollution from industrial and urban regions along the coast of eastern China. Nevertheless, abundant Ca2+ contributed to the neutralization of acidic cloud water during the dust stage. The much higher aerosol and chemical loading injected into these clouds caused an enrichment effect in the cloud water, which can double the cloud loading of total ions, when Ca2+ increases by approximately 7 times.
Within‐shell variations in carbon and oxygen isotope compositions of two modern brachiopods from a subtropical shelf environment off Amami‐o‐shima, southwestern Japan
Authors: Yamamoto Kazuyuki , Asami Ryuji , Iryu Yasufumi
Published: October 2010

This study examines the fidelity of carbon (δ13C) and oxygen (δ18O) isotope compositions of two modern brachiopod species (Kikaithyris hanzawai and Basiliola lucida) to use as proxies of δ13C values of total dissolved inorganic carbon and temperature and/or δ18O values of seawater, respectively. Well‐preserved shells of K. hanzawai and living individuals of B. lucida were collected from a subtropical shelf environment off Amami‐o‐shima, southwestern Japan. Some portions of the shells are in isotopic equilibrium with the ambient seawater, while other portions are not. The degree of disequilibrium differs between the two species and between different portions of each shell. Statistically significant positive correlations are recognized between the δ13C and δ18O values of these samples, which can be ascribed to a kinetic fractionation effect. Far from the posterior shell edge and along the axis of shell growth, the δ18O values of the secondary shell layer of K. hanzawai mostly fall within the expected range of equilibrium calcite. The δ13C values from the inner surface of the secondary shell layer in both species are relatively constant and are equivalent to or very close to equilibrium calcite. Therefore, these portions of the shells are most suitable for collecting reliable environmental proxy data. Although the δ13C and δ18O values of modern brachiopod shells are predominantly controlled by a kinetic fractionation effect, the appropriate selection of species and shell portions that reflect the isotopic composition of ambient seawater can facilitate the reconstruction of secular variations in oceanic δ13C or δ18O values.
Calibrating a long‐term meteoric 10Be accumulation rate in soil
Authors: Reusser Lucas , Graly Joseph , Bierman Paul , Rood Dylan
Published: October 2010

Using 13 samples collected from a 4.1 meter profile in a well‐dated and stable New Zealand fluvial terrace, we present the first long‐term accumulation rate for meteoric 10Be in soil (1.68 to 1.72 × 106 at/(cm2·yr)) integrated over the past ∼18 ka. Site‐specific accumulation data, such as these, are prerequisite to the application of meteoric 10Be in surface process studies. Our data begin the process of calibrating long‐term meteoric 10Be delivery rates across latitude and precipitation gradients. Our integrated rate is lower than contemporary meteoric 10Be fluxes measured in New Zealand rainfall, suggesting that long‐term average precipitation, dust flux, or both, at this site were less than modern values. With accurately calibrated long‐term delivery rates, such as this, meteoric 10Be will be a powerful tool for studying rates of landscape change in environments where other cosmogenic nuclides, such as in situ 10Be, cannot be used.
A whole atmosphere model simulation of the impact of a sudden stratospheric warming on thermosphere dynamics and electrodynamics
Authors: Fuller‐Rowell Tim , Wu Fei , Akmaev Rashid , Fang Tzu‐Wei , Araujo‐Pradere Eduardo
Published: October 2010

A Whole Atmosphere Model (WAM) has been used to explore the possible physical connection between a sudden stratospheric warming (SSW) and the dynamics and electrodynamics of the lower thermosphere. WAM produces SSWs naturally without the need for external forcing. The classical signatures of an SSW appear in the model with a warming of the winter polar stratosphere, a reversal of the temperature gradient, and a breakdown of the stratospheric polar vortex. Substantial changes in the amplitude of stationary planetary wave numbers 1, 2, and 3 occur as the zonal mean zonal wind evolves. The simulations also show a cooling in the mesosphere and a warming in the lower thermosphere consistent with observations. The magnitude of this particular SSW is modest, belonging to the category of minor warming. In the lower thermosphere the amplitude of diurnal, semidiurnal, and terdiurnal, eastward and westward propagating tidal modes change substantially during the event. Since the magnitude of the warming is minor and the tidal interactions with the mean flow and planetary waves are complex, the one‐to‐one correspondence between tidal amplitudes in the lower thermosphere and the zonal mean and stationary waves in the stratosphere is not entirely obvious. The increase in the magnitude of the terdiurnal tide (TW3) in the lower thermosphere has the clearest correlation with the SSW, although the timing appears delayed by about three days. The fast group velocity of the long vertical wavelength TW3 tide would suggest a faster onset for the direct propagation of the tide from the lower atmosphere. It is possible that changes in the magnitude of the diurnal and semidiurnal tides, with their slower vertical propagation, may interact in the lower thermosphere to introduce a terdiurnal tide with a longer delay. An increase in TW3 in the lower thermosphere would be expected to alter the local time variation of the electrodynamic response. The day‐to‐day changes in the lower thermosphere winds from WAM are shown to introduce variability in the magnitude of dayside low latitude electric fields, with a tendency during the warming for the dayside vertical drift to be larger and occur earlier, and for the afternoon minimum to be smaller. The numerical simulations suggest that it is quite feasible that a major SSW, with a magnitude seen in January 2009, could cause large changes in lower thermosphere electrodynamics and hence in total electron content.
ENSO‐induced tropical convection variability over the Indian and western Pacific oceans during the northern winter as revealed by a self‐organizing map
Authors: Sakai Kumi , Kawamura Ryuichi , Iseri Yoshihiko
Published: October 2010

The dominant low‐frequency patterns of outgoing longwave radiation over the tropical Indian and western Pacific oceans in response to El Niño‐Southern Oscillation (ENSO) during the northern winter are investigated using the nonlinear classification method of the self‐organizing map (SOM), additionally aided by an empirical orthogonal function (EOF) analysis. There are at least two different air‐sea coupled phenomena in the tropical Indian Ocean, i.e., the Indian Ocean Dipole (IOD) mode in late summer and fall and the Wind‐Evaporation‐Sea surface temperature (WES) feedback‐driven mode in the winter and spring. The SOM results exhibit that the phase of WES becomes positive (negative) at the El Niño (La Niña) phase, which indicates a linear linkage of WES with ENSO. In contrast, few combined patterns of the negative IOD and the La Niña event can be extracted although the reversed pattern is prominent, suggesting a nonlinear‐like relationship between IOD and ENSO. Since the ENSO‐induced convective forcing over the tropical Indian and western Pacific oceans has strong asymmetric features with respect to the ENSO phase, the remote response of the East Asian winter monsoon to ENSO becomes complicated. At the El Niño event, the monsoon circulation in the southern part of East Asia tends to be attenuated in late winter through the dominance of the western North Pacific anticyclone in the lower troposphere, but at the La Niña event, the monsoon circulation over Korea and Japan is enhanced in early winter through the downstream development of stationary Rossby wave packets along the South Asian waveguide.
High rates of denitrification and nitrate removal in cold seep sediments
Authors: Bowles Marshall , Joye Samantha
Published: October 2010

We measured denitrification and nitrate removal rates in cold seep sediments from the Gulf of Mexico. Heterotrophic potential denitrification rates were assayed in time-series incubations. Surficial sediments inhabited by Beggiatoa exhibited higher heterotrophic potential denitrification rates (32 μm N reduced day−1) than did deeper sediments (11 μm N reduced day−1). Nitrate removal rates were high in both sediment horizons. These nitrate removal rates translate into rapid turnover times (<1 day) for the nitrate pool, resulting in a faster turnover for the nitrate pool than for the sulfate pool. Together, these data underscore the rigorous nature of internal nitrogen cycling at cold seeps and the requirement for novel mechanisms to provide nitrate to the sediment microbial community.
Standardization in UniProtKB/Swiss-Prot
Authors: Ferro Rojas Serenella , Morgat Anne , Consortium UniProt
Published: October 2010

Within the UniProt consortium, the UniProtKB/Swiss-Prot knowledge base provides the international community with a stable, comprehensive, fully classified, richly and accurately annotated protein sequence database that is fully operable with other databases. Annotation relates to function(s) of the protein (their catalytic activity and the corresponding metabolic pathway(s) in which the protein may be involved), their cellular location, their interactions with other cellular components, etc. It is challenging to unify the way we annotate proteins, to ensure consistency and to describe data unambiguously. It is also highly valuable both for querying the database and for analyzing high-throughput data (expression data for instance). Because it is of fundamental importance to use standardized nomenclatures, annotations in UniProtKB/Swiss-Prot are progressively moving towards controlled vocabularies (CVs) and ontologies. Controlled vocabulary - or terminology - provides a list of concepts and text descriptions of their meaning. Concepts in a CV are often organized in a hierarchy. Ontology provides a formal representation of knowledge with definitions of concepts, their attributes and relations between them.As an illustration, we will describe the processes used to produce SUBCELLULAR and PATHWAY annotation sections in UniProtKB/Swiss-Prot. The CVs used in these two sections are based on in-house resources, UniProt subcell^1^ and UniPathway^2^ respectively. The links between these resources and other existing resources will be presented too, with a specific focus on Gene Ontology^3^ as we envisage using it extensively in order to describe protein functions or other biological processes.
Automatisation in UniProtKB / Swiss-Prot Annotation: New Rules and Tools
Authors: Team The HAPMAP , Team The PROSITE , de Castro Edouard , Bridge Alan , Consortium UniProt
Published: October 2010

The development of next generation sequencing technologies promises a massive increase in the rate of submission of new protein sequences to sequence databases such as the Universal Protein Resource Knowledge Base, UniProtKB. At UniProtKB/Swiss-Prot we propose to meet this challenge by continuing to expand and develop systems for the automatic propagation of existing annotation to newly submitted protein sequences. These developments will promote the standardization of ortholog annotation both across and within kingdoms and significantly enhance our ability to accurately annotate new protein sequences which are being produced at an ever increasing rate.
Data Curation in Biology - Past, Present and Future
Authors: Thornton Janet
Published: October 2010

Data curation has been critical in the development of biology from Darwin and Linnaeus to UniProt, the careful collection and organisation of data has been the spring from which new hypotheses and understanding have emerged. In this presentation, I will describe how we have used data curation in my own research group - and also present an overview of curation at the EBI. With new technical developments and the move towards the semantic web, the role of curation in the future needs to develop to take advantage of these new opportunities. This will be discussed.
Internalized Societal Attitudes Moderate the Impact of Weight Stigma on Avoidance of Exercise
Authors: Vartanian Lenny R. , Novak Sarah A.
Published: October 2010

Experiences with weight stigma negatively impact both psychological outcomes (e.g., body dissatisfaction, depression) and behavioral outcomes (e.g., dieting, exercise). However, not everyone is equally affected by experiences with weight stigma. This study examined whether internalized societal attitudes about weight moderated the impact of weight stigma. Adult participants (n = 111) completed measures of experiences with weight stigma, as well as two indexes of internalized societal attitudes (the moderators): Internalized anti‐fat attitudes and internalization of societal standards of attractiveness. Psychological outcomes included self‐esteem, body dissatisfaction, drive for thinness, and bulimic symptoms; behavioral outcomes included avoidance of exercise and self‐reported exercise behavior. Weight stigma was positively correlated with body dissatisfaction, drive for thinness, and bulimic symptoms, and was negatively correlated with state and trait self‐esteem. Both indexes of internalized attitudes moderated the association between weight stigma and avoidance of exercise: Individuals high in anti‐fat attitudes and high in internalization of societal standards of attractiveness were more motivated to avoid exercise if they also experienced a high degree of weight stigma; individuals low in anti‐fat attitudes and low in internalization were relatively unaffected. Avoidance of exercise was negatively correlated with self‐reported strenuous exercise. These findings suggest that weight stigma can negatively influence motivation to exercise, particularly among individuals who have internalized societal attitudes about weight. Reducing internalization might be a means of minimizing the negative impact of weight stigma and of facilitating healthy weight management efforts.
Contribution of Adipose Tissue to Plasma 25‐Hydroxyvitamin D Concentrations During Weight Loss Following Gastric Bypass Surgery
Authors: Lin Edward , Armstrong‐Moore Dereka , Liang Zhe , Sweeney John F. , Torres William E. , Ziegler Thomas R. , Tangpricha Vin , Gletsu‐Miller Nana
Published: October 2010

Roux‐en‐y gastric bypass (RYGB) surgery is associated with dramatic improvements in obesity‐related comorbidity, but also with nutritional deficiencies. Vitamin D concentrations are depressed in the severely obese, but the impact of weight loss via RYGB is unknown. We determined associations between adiposity and systemic 25‐hydroxyvitamin D (25(OH)D) during weight loss and the immediate and longer‐term effects of RYGB. Plasma 25(OH)D concentrations and fat mass (FAT) were determined by immunoassay and air displacement plethysmography, respectively, at 0 (before RYGB surgery), and at 1, 6, and 24 months in severely obese white and African American (AA) women (n = 20). Decreases in adiposity were observed at 1, 6, and 24 months following RYGB (P < 0.05). Plasma 25(OH)D concentrations increased at 1 month (P = 0.004); a decreasing trend occurred over the remainder months after surgery (P = 0.02). Despite temporary improvement in vitamin D status, a high prevalence of vitamin D insufficiency was observed (76, 71, 67, and 82%, at baseline, 1, 6, and 24 months, respectively), and plasma 25(OH)D concentrations were lower in AA compared to white patients (P < 0.05). Strong positive baseline and 1 month cross‐sectional correlations between FAT and plasma 25(OH)D were observed, which remained after adjustment for age and race subgroup (β = 0.76 and 0.61, respectively, P = 0.02). In conclusion, 25(OH)D concentrations increased temporarily and then decreased during the 24 months following RYGB. The acute increase and the positive associations observed between adipose tissue mass and systemic 25(OH)D concentrations suggest storage in adipose tissue and release during weight loss.
Weight Reduction in Obese Adolescents With and Without Binge Eating
Authors: Bishop‐Gilyard Chanelle T. , Berkowitz Robert I. , Wadden Thomas A. , Gehrman Christine A. , Cronquist Joanna L. , Moore Reneé H.
Published: October 2010

Little is known about binge eating (BE) in adolescents. The primary aim of the present study was to examine the relationship between BE and weight loss in adolescents (BMI ≥95th percentile) enrolled in a randomized controlled trial of behavioral and pharmacologic treatment of obesity. Participants were 82 treatment‐seeking adolescents (BMI = 37.9 ± 3.8 kg/m2; age = 14.1 ± 1.2 years; 67% females; 42% African American, 55% white). Participants completed the Children's Depression Inventory (CDI), the Piers Harris Self‐Esteem Questionnaire, and the Eating Inventory (including cognitive restraint, disinhibition, and hunger scales). BE was assessed by a questionnaire and a confirmatory interview. At baseline, 24% of participants met criteria for BE (N = 13 met full BE disorder (BED) criteria; N = 7 met subthreshold BE). There were no significant differences in percentage reduction in initial BMI between participants with or without BE at month 6 (−7.0 ± 1.6 vs. −6.9 ± 0.9%) or month 12 (−8.8 ± 2.4 vs. −8.3 ± 1.3%) (omnibus main effect BE P = 0.89, interaction BE × time P = 0.84, interaction BE × drug P = 0.61). The rate of BE declined significantly over time from 24% (n = 20) at baseline to 8% (n = 6) at month 6 and 3% (n = 2) at month 12 (P = 0.003). There were significant decreases in hunger and disinhibition as well as an increase in cognitive restraint over time (all P ≤ 0.0001). Findings suggest a combination of behavioral and pharmacologic therapy may produce both weight loss and improvement in BE.
Factors Associated With Tracking of BMI: A Meta‐Regression Analysis on BMI Tracking*
Authors: Bayer Otmar , Krüger Helia , Von Kries Rüdiger , Toschke André M.
Published: October 2010

Stable tracking of body composition is a prerequisite for the long‐term effect of preventive measures against obesity and its harmful effects. As BMI tracking estimates reported by individual studies vary considerably, we performed a meta‐regression analysis to provide a summary estimate and to assess determinants of BMI tracking. Using the Medline and EMBASE databases, a systematic review was conducted to identify publications reporting correlation coefficients as tracking estimates between BMI at baseline and follow‐up measurements and the time interval between these measurements. Additional information recorded included age at baseline measurement, gender, and origin of the studied population. Based on the extracted data, a meta‐regression analysis was performed using mixed effects models to account for multiple measurements of the same cohorts. Data on 55,072 individuals (797,094 person‐years) extracted from 48 publications with follow‐up times between 0.5 and 44 years entered the analysis. The overall estimates for the 1‐year tracking correlation coefficient were strong (r = 0.78–0.86 depending on age at baseline measurement) and gradually decreasing over time (0.67–0.78 after 10 years, and 0.27–0.47 after 30 years). Study origin classified by continent was another significant predictor of BMI tracking whereas gender was not. In conclusion, this meta‐regression analysis showed a high degree of BMI tracking across all age groups investigated and independent of BMI. Successful prevention in weight control is likely to have long term effects at any age, thereby being beneficial with respect to the associated risks of over‐ and underweight.
PMA-induced up-regulation of TBX3 is mediated by AP-1 and contributes to breast cancer cell migration
Authors: Mowla Shaheen , Pinnock Romaney , Leaner Virna D. , Goding Colin R. , Prince Sharon
Published: October 2010

The T-box transcription factor TBX3 provides an important link between embryonic development and cancer. TBX3 mediates limb, mammary gland and heart development and, in humans, mutations resulting in haplo-insufficiency of TBX3 lead to ulnar-mammary syndrome. Importantly, the de-regulation of TBX3 gene expression has been linked to several cancers, where it acts to suppress senescence and promotes proliferation and tumour invasion. Despite the negative impact of de-regulated TBX3 expression as seen by developmental defects and cancer, surprisingly little is known about the regulation of the TBX3 gene. In the present paper, we show that the phorbol ester PMA increases TBX3 protein and mRNA levels in a protein kinase C-dependent manner via the AP-1 (activator protein 1) transcription factors c-Jun and JunB. Furthermore, these AP-1 factors are shown to mediate the activation of the TBX3 gene by binding a non-consensus PMA-response element in the TBX3 promoter in vitro and in vivo. We also demonstrate that TBX3 contributes to the PMA-induced migration previously observed for the MCF-7 breast epithelium cancer cell line. Our present results reveal a previously unidentified pathway that up-regulates TBX3 expression and provides additional evidence that increased levels of TBX3 contribute to metastasis.
In vivo evidence for the iron-binding activity of an iron–sulfur cluster assembly protein IscA in Escherichia coli
Authors: Wang Wu , Huang Hao , Tan Guoqiang , Si Fan , Liu Min , Landry Aaron P. , Lu Jianxin , Ding Huangen
Published: October 2010

IscA is a key member of the iron–sulfur cluster assembly machinery in prokaryotic and eukaryotic organisms; however, the physiological function of IscA still remains elusive. In the present paper we report the in vivo evidence demonstrating the iron-binding activity of IscA in Escherichia coli cells. Supplement of exogenous iron (1 μM) in M9 minimal medium is sufficient to maximize the iron binding in IscA expressed in E. coli cells under aerobic growth conditions. In contrast, IscU, an iron–sulfur cluster assembly scaffold protein, or CyaY, a bacterial frataxin homologue, fails to bind any iron in E. coli cells under the same experimental conditions. Interestingly, the strong iron-binding activity of IscA is greatly diminished in E. coli cells under anaerobic growth conditions. Additional studies reveal that oxygen in medium promotes the iron binding in IscA, and that the iron binding in IscA in turn prevents formation of biologically inaccessible ferric hydroxide under aerobic conditions. Consistent with the differential iron-binding activity of IscA under aerobic and anaerobic conditions, we find that IscA and its paralogue SufA are essential for the iron–sulfur cluster assembly in E. coli cells under aerobic growth conditions, but not under anaerobic growth conditions. The results provide in vivo evidence that IscA may act as an iron chaperone for the biogenesis of iron–sulfur clusters in E. coli cells under aerobic conditions.
A 130 point Nd:YAG Thomson scattering diagnostic on MAST
Authors: Scannell R. , Walsh M. J. , Dunstan M. R. , Figueiredo J. , Naylor G. , O’Gorman T. , Shibaev S. , Gibson K. J. , Wilson H.
Published: October 2010

A Thomson scattering diagnostic designed to measure both edge and core physics has been implemented on MAST. The system uses eight Nd:YAG lasers, each with a repetition rate of 30 Hz. The relative and absolute timing of the lasers may be set arbitrarily to produce fast bursts of measurements to suit the time evolution of the physics being studied. The scattered light is collected at F/6 by a 100 kg six element lens system with an aperture stop of 290 mm. The collected light is then transferred to 130 polychromators by 130 independent fiber bundles. The data acquisition and processing are based on a distributed computer system of dual core processors embedded in 26 chassis. Each chassis is standalone and performs data acquisition and processing for five polychromators. This system allows data to be available quickly after the MAST shot and has potential for real-time operations.
Mechanism for spontaneous growth of nanopillar arrays in ultrathin films subject to a thermal gradient
Authors: Dietzel Mathias , Troian Sandra M.
Published: October 2010

Several experimental groups have reported spontaneous formation of periodic pillar arrays in molten polymer nanofilms confined within closely spaced substrates held at different temperatures. These formations have been attributed to a radiation pressure instability caused by interface reflection of acoustic phonons. We demonstrate here how variations in thermocapillary stress at the air/polymer interface can produce significant periodic protrusions in any viscous film no matter how small the transverse thermal gradient. The linear stability analysis of the interface evolution equation corresponds to an extreme limit of Bénard–Marangoni flow peculiar to films of nanoscale dimensions—deformation amplitudes are small in comparison to the pillar spacing and hydrostatic forces are negligible. Finite element simulations of the full nonlinear equation provide estimates of the array pitch and growth rates beyond the linear regime. Results of the Lyapunov free energy as a function of time also confirm that pillarlike elongations are energetically preferred in nanofilms, in contrast to cellular instabilities in macroscopically thick films. If not mass limited, fluid elongations continue to grow until contact with the cooler substrate is achieved. These predictions should facilitate the fabrication of extended arrays for nanoscale optical, photonic, and biological applications.
Mechanisms of high quality i-ZnO thin films deposition at low temperature by vapor cooling condensation technique
Authors: Lee Hsin-Ying , Xia Shang-Da , Zhang Wei-Ping , Lou Li-Ren , Yan Jheng-Tai , Lee Ching-Ting
Published: October 2010

A comparative mechanism investigation on the structural and optoelectronic properties of i-ZnO thin films, deposited on the silicon substrates at various temperatures were conducted. The experimental results verified that the i-ZnO films deposited at a low temperature have better quality over the conventional high temperature deposited ones. This low temperature deposition by using vapor cooling condensation technique has been successfully used to fabricate optoelectronic devices, such as UV light-emitting diodes and UV photodetectors. The mechanisms responsible for the fact that the low temperature deposited samples had better quality were analyzed in terms of the adsorption/desorption and diffusion of ZnO particles in the growth process.
A comparative evaluation of Al2O3 coated low heat rejection diesel engine performance and emission characteristics using fuel as rice bran and pongamia methyl ester
Authors: Musthafa M. Mohamed , Sivapirakasam S. P. , Udayakumar M.
Published: October 2010

In this study, for the first time, a nanoceramic Al2O3 was used as a coating material in the low heat rejection engine concept. Experiments were conducted on single cylinder, four stroke, water cooled, and direct injection diesel engine. First, the engine was tested at different load conditions without coating. Then, combustion chamber surfaces (cylinder head, cylinder liner, valves, and piston crown face) were coated with nanoceramic material of Al2O3 using plasma spray method. Comparative evaluation on performance and emission characteristics using fuel as rice bran methyl ester, pongamia methyl ester, and biodiesel/diesel fuel mixtures was studied in the ceramic coated and uncoated engines under the same running conditions. An increase in engine power and a decrease in specific fuel consumption, as well as significant improvements in exhaust gas emissions (except NOx) and smoke density, were observed in the ceramic coated engines compared with those of the uncoated engine.