bluuebunny/crossref_metadata_2025 huggingface dataset:
An enthalpy-based hybrid lattice-Boltzmann method for modelling solid–liquid phase transition in the presence of convective transport
Authors: CHAKRABORTY SUMAN , CHATTERJEE DIPANKAR
Published: November 2007

An extended lattice Boltzmann model is developed for simulating the convection–diffusion phenomena associated with solid–liquid phase transition processes. Macroscopic hydrodynamic variables are obtained through the solution of an evolution equation of a single-particle density distribution function, whereas, the macroscopic temperature field is obtained by solving auxiliary scalar transport equations. The novelty of the present methodology lies in the formulation of an enthalpy-based approach for phase-change modelling within a lattice-Boltzmann framework, in a thermodynamically consistent manner. Thermofluidic aspects of phase transition are handled by means of a modified enthalpy–porosity formulation, in conjunction with an appropriate enthalpy-updating closure scheme. Lattice-Boltzmann simulations of melting of pure gallium in a rectangular enclosure, Rayleigh–Bénard convection in the presence of directional solidification in a top-cooled cavity, and crystal growth during solidification of an undercooled melt agree well with the numerical and experimental results available in the literature, and provide substantial evidence regarding the upscaled computational economy provided by the present methodology.
Preservation of statistical properties in large-eddy simulation of shear turbulence
Authors: GUALTIERI P. , CASCIOLA C. M. , BENZI R. , PIVA R.
Published: November 2007

We discuss how large-eddy simulation (LES) can be properly employed to predict the statistics of the resolved velocity fluctuations in shear turbulence. To this purpose ana posterioricomparison of LES data against filtered direct numerical simulation (DNS) is used to establish the necessary conditions that the filter scaleLFmust satisfy to achieve the preservation of the statistical properties of the resolved field. In this context, by exploiting the physical role of the shear scaleLS, the Kármán–Howarth equation allows for the assessment of LES data in terms of scale-by-scale energy production, energy transfer and subgrid energy fluxes. Even higher-order statistical properties of the resolved scales such as the probability density function of longitudinal velocity increments are well reproduced, provided the relative position of the filter scale with respect to the shear scale is properly selected. We consider here the homogeneous shear flow as the simplest non-trivial flow which fully retains the basic mechanism of turbulent kinetic energy production typical of any shear flow, with the advantage that spatial homogeneity implies a well-defined value of the shear scale while numerical difficulties related to resolution requirements in the near wall region are avoided.
Optimal growth of the Batchelor vortex viscous modes
Authors: HEATON C. J.
Published: November 2007

We present calculations of optimal linear growth in the Batchelor (or q) vortex. The level of transient growth is used to quantify the effect of the viscous centre modes found at large Reynolds number and large swirl. The viscous modes compete with inviscid-type transients, which are seen to provide faster growth at short times. Following a smooth transition, the viscous modes emerge as dominant in a different regime at later times. A comparison is drawn with two-dimensional shear flows, such as boundary layers, in which weak instability modes (Tollmien–Schlichting waves) also compete with inviscid transients (streamwise streaks). We find the competition to be more evenly balanced in the Batchelor vortex, because the inviscid transients are damped faster in a swirling jet than a two-dimensional shear flow, so that despite their weak growth rates the viscous modes may be relevant in some situations.
The physics of vortex merger and the effects of ambient stable stratification
Authors: BRANDT LAURA K. , NOMURA KEIKO K.
Published: November 2007

The merging of a pair of symmetric, horizontally oriented vortices in unstratified and stably stratified viscous fluid is investigated. Two-dimensional numerical simulations are performed for a range of flow conditions. The merging process is resolved into four phases of development and key underlying physics are identified. In particular, the deformation of the vortices, explained in terms of the interaction of vorticity gradient, ∇ω, and rate of strain, S, leads to a tilt in ω contours in the vicinity of the center of rotation (a hyperbolic point). In the diffusive/deformation phase, diffusion of the vortices establishes the interaction between ∇ω and mutually induced S. During the convective/deformation phase, induced flow by filaments and, in stratified flow, baroclinically generated vorticity (BV), advects the vortices thereby modifying S, which, in general, may enhance or hinder the development of the tilt. The tilting and diffusion of ω near the center hyperbolic point causes ω from the core region to enter the exchange band where it is entrained. In the convective/entrainment phase, the vortex cores are thereby eroded and ultimately entrained into the exchange band, whose induced flow becomes dominant and transforms the flow into a single vortex. The critical aspect ratio, associated with the start of the convective/entrainment phase, is found to be the same for both the unstratified and stratified flows. In the final diffusive/axisymmetrization phase, the flow evolves towards axisymmetry by diffusion. In general, the effects of stratification depend on the ratio of the diffusive time scale (growth of cores) to the turnover time (establishment of BV), i.e. the Reynolds number. A crossover Reynolds number is found, above which convective merging is accelerated with respect to unstratified flow and below which it is delayed.
Swapping trajectories: a new wall-induced cross-streamline particle migration mechanism in a dilute suspension of spheres
Authors: ZURITA-GOTOR M. , BŁAWZDZIEWICZ J. , WAJNRYB E.
Published: November 2007

Binary encounters between spherical particles in shear flow are studied for a system bounded by a single planar wall or two parallel planar walls under creeping flow conditions. We show that wall proximity gives rise to a new class of binary trajectories resulting in cross-streamline migration of the particles. The spheres on these new trajectories do not pass each other (as they would in free space) but instead they swap their cross-streamline positions. To determine the significance of the wall-induced particle migration, we have evaluated the hydrodynamic self-diffusion coefficient associated with a sequence of uncorrelated particle displacements due to binary particle encounters. The results of our calculations quantitatively agree with the experimental value obtained by Zarraga & Leighton (Phys. Fluids, vol. 14, 2002, p. 2194) for the self-diffusivity in a dilute suspension of spheres undergoing shear flow in a Couette device. We thus show that the wall-induced cross-streamline particle migration is the source of the anomalously large self-diffusivity revealed by their experiments.
Three-dimensional Floquet stability analysis of the wake in cylinder arrays
Authors: KEVLAHAN N. K.-R.
Published: November 2007

Three-dimensional stability of the periodic wake of tightly packed rotated and inline cylinder arrays is investigated for 60 ≤ Re ≤ 270. Results are compared with existing numerical and experimental studies for an isolated cylinder. Numerical Floquet analysis shows that the two-dimensional wakes of the rotated and inline arrays with spacing P/D = 1.5 become unstable at Rec = 64 ± 0.5 and Rec = 132 ± 1 respectively. Two-dimensional vortex shedding flow is unlikely in practice for such flows. The dominant spanwise wavelength is λ/D = 0.9 ± 0.1 for the rotated array at Re = 100 and λ/D = 3.0 ± 0.1 for the inline array at Re = 200. Three-dimensional simulations show excellent agreement with the Floquet analysis for the rotated case, and reasonable agreement for the inline case. The instability mechanism appears to be similar to Mode A for an isolated cylinder, although the structure of the three-dimensional vorticity is different due to the spatial periodicity of the flow. Unlike the isolated cylinder, both array flows are unstable as λ → ∞ (like a thin shear layer). This is the first investigation of three-dimensional wake instability in cylinder arrays, a problem of significant practical and theoretical interest.
Aldhelm's rejection of the Muses and the mechanics of poetic inspiration in early Anglo-Saxon England
Authors: Thornbury Emily V.
Published: November 2007

In the metrical preface to his Enigmata, Aldhelm of Malmesbury denies that he has had anything to do with the Muses. While this gesture connects him to his Christian Latin predecessors (and, less directly, to the pagan poets as well), the unique elements of Aldhelm's poem suggest that he is also drawing upon a native tradition of poetry that valued technical skill above lofty subject-matter. By portraying the Muses within this Germanic framework as useless, rather than dangerous, Aldhelm's rejection enabled his successors to employ the Muses, and other Classical allusions, as harmless decorative elements in their verse.
Epistemic verbs and zero complementizer
Authors: KEARNS KATE
Published: November 2007

This article addresses the question of why certain epistemic verbs, particularly (I) think, have very high rates of zero complementizer in their clausal complements. I consider and reject the influential proposal from Thompson & Mulac (1991b) that the occurrence of zero complementizer in these contexts is associated with syntactic reanalysis of the epistemic verb and its subject to an adverbial-like epistemic phrase. Instead, I propose that zero complementizer signals a shift in the informational structure of the utterance, in which the embedded clause conveys the main assertion, but the syntactic structure of the sentence need not be altered. Further routinization is evident with I think but not with other epistemic verbs. Results from a study of newspaper prose are presented in support of the analysis.
A history of hyper-rhoticity in English
Authors: BRITTON DEREK
Published: November 2007

This article investigates the history of what Wells (1982), in his account of present-day accents of English, calls ‘hyper-rhoticity’. That is, the appearance, in rhotic accents, of epenthetic, unetymological rhyme-/r/, usually taking the form of /r/-colouring in modern accents. It is attested most commonly in final unstressed syllables, but may also occur in syllable rhymes after a long, stressed vowel. The article traces the history of this phenomenon and attempts to show that Early Modern English data which have hitherto been interpreted as evidence for loss of /r/ in such contexts are better attributed to hyper-rhoticity. It is also argued here, in an addendum, that not to accept claims for early /r/-loss in unstressed syllables has wider implications for the history of English phonology. That is, to reject theories of loss of /r/ in final unstressed syllables demands rejection of the notion of early articulatory weakening of /r/ in this context, which has been seen as a prelude to the spread of weakening to other contexts, leading ultimately to loss of rhoticity.
Indefinite possessive NPs and the distinction between determining and nondetermining genitives in English
Authors: WILLEMSE PETER
Published: November 2007

This article tries to fill a descriptive gap in the literature on English possessive NPs by offering a systematic description of indefinite possessive NPs (e.g. a friend's house, a widow's pension, men's suits). Specifically, two descriptive issues are dealt with. Firstly, the different types of determining indefinite genitives are discussed. It is shown that indefinite determiner genitives can have specific reference, generalized reference or generic reference. Moreover, it is argued that in all of these cases, the indefinite genitive specifies a reference point (Langacker 1993) for the identification of the ‘possessee’ and functions as a grounding predication. It is also proposed that subsective gradience (Aarts 2004, 2007) can be diagnosed for determining genitives, i.e. that more central and more peripheral members can be distinguished within this category. Secondly, the distinction between determining and nondetermining, classifying genitives (e.g. a [woman's magazine] ‘a magazine for women’) is re-examined. This distinction is relevant to the description of indefinite possessive NPs, since they have been considered as evidence for a fuzzy boundary between determining and nondetermining genitives (Taylor 1996, Rosenbach 2006). It is argued, against such an analysis, that the two functions of the genitive can be clearly distinguished, even in ‘bridging contexts’ (Evans & Wilkins 2000), i.e. contexts in which both a determining and a nondetermining reading are supported. Consequently, there is no intersective gradience (Aarts 2004, 2007) between determining and nondetermining genitives on the level of the constructional semantics.
Regional Advocacy Networks and the Protocol on the Rights of Women in Africa
Authors: Adams Melinda , Kang Alice
Published: November 2007

While there has been a significant amount of research on transnational feminist activism at the global level, many feminist transnational advocacy networks are mobilizing within world regions. The lack of attention to the regional level has created a considerable imbalance in research on transnational activism. This article's first objective is to define regional advocacy networks (RANs) as a collection of individuals and organizations from the same world region working together toward a common goal. The article's second objective is to explore the conditions under which RANs are influential. We investigate conditions for RAN success through a case study of an African network that helped create one of the world's most progressive treaties on women's rights, the African Union Protocol to the Charter on Human and People's Rights on the Rights of Women in Africa. From an analysis of primary sources and interviews with key participants, we suggest that three factors are crucial for network success: whether a RAN builds alliances with key politicians and civil servants, whether a RAN is able to participate in the decision-making process, and whether a RAN's goals overlap with the target institution's priorities. The broader implication of our study is that scholars seeking to understand the creation of women's rights commitments, the diffusion of women's rights norms, and compliance with women's rights treaties need to look beyond the international and domestic levels of action to include the regional level in their analyses.
Alienation of Affection Torts: Love ’Em or Leave ’Em?
Authors: Gordon Elizabeth Ellen
Published: November 2007

The alienation of affection tort, which allows a plaintiff to sue a third party for interfering with the plaintiff's marriage, has been disparaged by many as a relic of women's former status as their husband's property. Despite its archaic roots, the tort as it operates today is in many ways quite modern and addresses some of the problems, expectations, and obstacles of modern American marriage. Furthermore, it fits in with developments in tort law toward more actions for nontangible, nonfinancial damages. Given the tort's history, one might assume that it benefits men, but women also benefit from and use this tort, as demonstrated in a case study of North Carolina, a jurisdiction where the tort is frequently pursued. In its current form, the alienation tort can be reconciled with feminist theory and with women's interests, and should not be abolished without reconsideration.

“Those whom God hath joined together let no man put asunder.”

Book of Common Prayer 1789
The Challenge of Diversity: The Evolution of Women's Policy Agencies in Britain
Authors: Squires Judith
Published: November 2007

Britain's use of state agencies to address gender relations has evolved significantly over the past 30 years and is currently entering a new phase, characterized by a commitment to a generic equalities, or “diversity,” approach in which multiple equality strands are to be addressed via a single equalities body, the Commission for Equality and Human Rights (CEHR). The CEHR will replace three existing equality commissions that focus on gender, race, and disability, respectively. This shift appears to involve the demise of a singular focus on gender equality and with it the justification for separate women's policy agencies.
Lessons for human rights and humanitarian law in the war on terror: comparing Hamdan and the Israeli Targeted Killings case
Authors: Milanovic Marko
Published: November 2007

The article examines and compares two recent judgments which provide some of the most valuable examples of the difficulties surrounding the application of international humanitarian law to the phenomenon of terrorism: the Hamdan judgment of the Supreme Court of the United States, and the Targeted Killings judgment of the Supreme Court of Israel. Both judgments deal with the thresholds of applicability of the law of armed conflict, as well as with the concept of unlawful combatancy and the relationship between human rights law and humanitarian law. Both judgments are at times inconsistent and lacking in analysis, with the Hamdan judgment in particular misinterpreting the relevant international authorities, including the Commentaries on the Geneva Conventions. Despite these flaws, or because of them, both of these judgments remain instructive. The purpose of this article is to present the lessons for the future that these two decisions might bring to ongoing debates on the impact of global terrorism on the law of armed conflict.
Lessons learned? Disasters, rapid change and globalization
Authors: Dombrowsky Wolf R.
Published: November 2007

Comparing the two tsunamis of Lisbon in 1775 and of Asia in 2004, the article analyses the different paradigmatic interpretations of “Western” religious and secular causality. Based on the rational concept of risk making and risk taking, the need to accept failures and their consequences is discussed, as well as the responsibility to develop human strategies for disaster prevention and to foster living conditions which may avoid large-scale suffering.
Who will assist the victims of use of nuclear, radiological, biological or chemical weapons – and how?
Authors: Loye Dominique , Coupland Robin
Published: November 2007

It is uncertain who will assist the victims of use of nuclear, radiological, biological or chemical weapons if an international response is required, and how this assistance can be provided without undue risk to those providing it. The use of such weapons or any other release of the materials of which they are composed cannot be considered as presenting a uniform risk. There are a variety of risks, each with its own implications for getting help to the people affected and for the health and security of those bringing that help. The political implications are serious and complex. This brief review shows the difficulties inherent in assisting the victims or potential victims of use of nuclear, radiological, biological and chemical weapons.
Visualizing, Summarizing, and Comparing Odds Ratio Structures
Authors: de Rooij Mark , Anderson Carolyn J.
Published: November 2007

Abstract. The odds ratio is one of the main measures of association in 2 × 2 tables. For larger tables, summary measures of association have been proposed as well as modeling strategies, where the odds ratios can be deduced from the parameters of a model. We propose a computationally simple scaling methodology, which gives a summary measure of association and a visualization of the odds ratio structure. Different variants of the methodology are discussed and compared, both theoretically and empirically. The methodology is also generalized to multiple tables, where not only the structure of each table is important, but also comparisons among tables.
Are There Test Administrator Effects in Large-Scale Educational Assessments?
Authors: Lüdtke Oliver , Robitzsch Alexander , Trautwein Ulrich , Kreuter Frauke , Ihme Jan Marten
Published: November 2007

Abstract. In large-scale educational assessments such as the Third International Mathematics and Sciences Study (TIMSS) or the Program for International Student Assessment (PISA), sizeable numbers of test administrators (TAs) are needed to conduct the assessment sessions in the participating schools. TA training sessions are run and administration manuals are compiled with the aim of ensuring standardized, comparable, assessment situations in all student groups. To date, however, there has been no empirical investigation of the effectiveness of these standardizing efforts. In the present article, we probe for systematic TA effects on mathematics achievement and sample attrition in a student achievement study. Multilevel analyses for cross-classified data using Markov Chain Monte Carlo (MCMC) procedures were performed to separate the variance that can be attributed to differences between schools from the variance associated with TAs. After controlling for school effects, only a very small, nonsignificant proportion of the variance in mathematics scores and response behavior was attributable to the TAs (< 1%). We discuss practical implications of these findings for the deployment of TAs in educational assessments.
A global inventory of the soil CH4 sink
Authors: Dutaur Laure , Verchot Louis V.
Published: November 2007

Methane uptake by soils is a small but important flux in the global budget of atmospheric methane, and could be susceptible to changes in land use and climate. Estimates of this sink vary between 20 and 45 Tg yr−1. We propose to develop a better constrained estimate using a mechanistic understanding of the biogeochemical controls of soil CH4 uptake. We reviewed over 120 published papers reporting field measurements of CH4 uptake and made over 318 annual estimates of CH4 uptake for various types of ecosystems. We collected data from these papers for a number of parameters that are known to influence the magnitude of the sink including climatic zone, ecosystem, latitude, annual mean rainfall, annual mean temperature, and the soil texture. Regression analyses with the continuous variables (latitude, rainfall, and temperature) yielded results with poor predictive ability and no significant relationship. Stratification by class variables such as climatic zone, ecosystem type and soil texture provided better predictive ability (R2 = 0.29, P < 0.0001). The mean largest uptake rates were observed in temperate forests with coarse soil texture, but the variance within this stratum was also large. Without any stratification, we estimate that the global soil CH4 sink is 36 ± 23 Tg yr−1. With stratification, the best current estimate of the global soil uptake of CH4 is 22 ± 12 Tg yr−1. The ecosystem type accounted for the largest part of the variation in the global data set. This inventory showed that ecosystem type, geographic zone, and soil texture strongly control CH4 uptake. Inventory methods that take into account underlying factors that control the process provide better estimates of sink strength.
Separating the effects of albedo from eco‐physiological changes on surface temperature along a successional chronosequence in the southeastern United States
Authors: Juang Jehn‐Yih , Katul Gabriel , Siqueira Mario , Stoy Paul , Novick Kimberly
Published: November 2007

In the southeastern United States (SE), the conversion of abandoned agricultural land to forests is the dominant feature of land‐cover change. However, few attempts have been made to quantify the impact of such conversion on surface temperature. Here, this issue is explored experimentally and analytically in three adjacent ecosystems (a grass‐covered old‐field, OF, a planted pine forest, PP, and a hardwood forest, HW) representing a successional chronosequence in the SE. The results showed that changes in albedo alone can warm the surface by 0.9°C for the OF‐to‐PP conversion, and 0.7°C for the OF‐to‐HW conversion on annual time scales. However, changes in eco‐physiological and aerodynamic attributes alone can cool the surface by 2.9 and 2.1°C, respectively. Both model and measurements consistently suggest a stronger over‐all surface cooling for the OF‐to‐PP conversion, and the reason is attributed to leaf area variations and its impacts on boundary layer conductance.
Hydrological responses to climate change and irrigation in the Aral Sea drainage basin
Authors: Shibuo Yoshihiro , Jarsjö Jerker , Destouni Georgia
Published: November 2007

Hydrological model interpretation of the water flow development in the Aral Sea Drainage Basin (ASDB) indicates that the water diversion and irrigation schemes in this region have considerably increased evapotranspiration and thereby decreased net water flux (precipitation minus evapotranspiration) from the atmosphere to the surface of the ASDB. Increased evapotranspiration cools the irrigated areas, and the decrease of net atmospheric water influx to the ASDB may also have non‐local effects outside the basin. Such effects have previously been estimated by atmospheric modeling, assuming a global average evapotranspiration return flow to the atmosphere of about 40% of irrigation. Our results indicate larger return flows, of nearly 100% of the applied irrigation water in the ASDB, which may also imply considerably larger than previously estimated non‐local water and climate effects of the world's irrigated areas.
Direct numerical simulation of salt sheets and turbulence in a double‐diffusive shear layer
Authors: Kimura Satoshi , Smyth William
Published: November 2007

We describe three‐dimensional direct numerical simulations (DNS) of double‐diffusively stratified flow interacting with inflectional shear. The extreme difference in diffusivity (and thus minimum length scale) between heat, salt and momentum in seawater is replicated for the first time in a three‐dimensional simulation. The primary instability generates salt sheets, which are oriented parallel to the direction of the sheared background flow. Subsequently, two distinct mechanisms of secondary instability combine to lead the flow to a turbulent state. In this state, the effective saline diffusivity is smaller than that calculated by previous investigators for the unsheared case. The Schmidt number is much smaller than unity, indicating that salt sheets are less effective at transporting momentum than is often assumed.
Analytical and numerical investigation of the radiation and scattering from concentric metamaterial cylinders excited by an electric line source
Authors: Arslanagic Samel , Ziolkowski Richard W. , Breinbjerg Olav
Published: November 2007

An antenna configuration consisting of an arbitrarily located electric line source radiating in the presence of a pair of concentric metamaterial cylinders is investigated analytically and numerically. The near‐ and far‐field properties of these structures are analyzed through an investigation of such parameters as the total radiated power, directivity, and total as well as differential scattering cross sections. The results obtained for these metamaterial structures are compared to those for the corresponding structures made of conventional materials. It is shown that electrically small concentric metamaterial structures can be designed to be resonant and to possess advantageous radiation and scattering characteristics in contrast to the corresponding structures made of conventional materials. More specifically, it is shown that metamaterial structures lead to significant enhancements of the total radiated power as well as the total and differential scattering cross sections. Moreover, the feasibility of controlling the directivity pattern of the electrically small metamaterial structures through appropriate locations of the electric line source is demonstrated. The effects of the dispersion and loss present in the metamaterials are taken into account to study the bandwidth properties of these resonant configurations.
Creatine kinase in energy metabolic signaling in muscle
Authors: Kongas Olav , van Beek Johannes
Published: November 2007

There has been much debate on the mechanism of regulation of mitochondrial ATP synthesis to balance ATP consumption during changing cardiac workloads. A key role of creatine kinase (CK) isoenzymes in this regulation of oxidative phosphorylation and in intracellular energy transport had been proposed, but has in the mean time been disputed for many years. It was hypothesized that high-energy phosphoryl groups are obligatorily transferred via CK; this is termed the phosphocreatine shuttle. The other important role ascribed to the CK system is its ability to buffer ADP concentration in cytosol near sites of ATP hydrolysis.

Almost all of the experiments to determine the role of CK had been done in the steady state, but recently the dynamic response of oxidative phosphorylation to quick changes incytosolic ATP hydrolysis has been assessed at various levels of inhibition of CK. Steady state models of CK function in energy transfer existed but were unable to explain the dynamic response with CK inhibited.

The aim of this study was to explain the mode of functioning of the CK system in heart, and in particular the role of different CK isoenzymes in the dynamic response to workload steps. For this purpose we used a mathematical model of cardiac muscle cell energy metabolism containing the kinetics of the key processes of energy production, consumption and transfer pathways. The model underscores that CK plays indeed a dual role in the cardiac cells. The buffering role of CK system is due to the activity of myofibrillar CK (MMCK) while the energy transfer role depends on the activity of mitochondrial CK (MiCK). We propose that this may lead to the differences in regulation mechanisms and energy transfer modes in species with relatively low MiCK activity such as rabbit in comparison with species with high MiCK activity such as rat.

The model needed modification to explain the new type of experimental data on the dynamic response of the mitochondria. We submit that building a Virtual Muscle Cell is not possible without continuous experimental tests to improve the model. In close interaction with experiments we are developing a model for muscle energy metabolism and transport mediated by the creatine kinase isoforms which now already can explain many different types of experiments.
Inhibition ofIhin Striatal Cholinergic Interneurons Early after Transient Forebrain Ischemia
Authors: Deng Ping , Zhang Yuchun , Xu Zao C
Published: November 2007

Striatal cholinergic interneurons are relatively resistant to ischemic insults. These neurons express hyperpolarization-activated cation current ( Ih) that profoundly regulates neuronal excitability. Changes in neuronal excitability early after ischemia may be crucial for determining neuronal injury. Here we report that Ihin cholinergic interneurons was decreased 3 h after transient forebrain ischemia, which was accompanied by a negative shift of the voltage dependence of activation. The inhibition of Ihmight be due to the tonic activation of adenosine A1 receptors, as blockade of A1 receptors significantly increased Ihin postischemic neurons, but had no effect on control neurons. Consistent with the inhibition of Ih, postischemic neurons showed a reduction in both spontaneous firing and hyperpolarization-induced rebound depolarization. These findings indicate that Ihmay play excitatory roles in striatal cholinergic interneurons. Postischemic inhibition of Ihmight be a novel mechanism by which adenosine confers neuronal resistance to cerebral ischemia.
Identification of a conserved motif required for Vps35p/Vps26p interaction and assembly of the retromer complex
Authors: Gokool Suzanne , Tattersall Daniel , Reddy Jonathan V. , Seaman Matthew N. J.
Published: November 2007

The retromer complex is a conserved cytoplasmic coat complex that mediates the endosome-to-Golgi retrieval of vacuole/lysosome hydrolase receptors in yeast and mammals. The recognition of cargo proteins by the retromer is performed by the Vps35p/VPS35 (where Vps is vacuolar protein sorting) component, which together with Vps26p/VPS26 and Vps29p/VPS29, forms the cargo-selective subcomplex. In this report, we have identified a highly-conserved region of Vps35p/VPS35 that is essential for the interaction with Vps26p/VPS26 and for assembly of the retromer complex. Mutation of residues within the conserved region results in Vps35p/VPS35 mutants, which cannot bind to Vps26p/VPS26 and are not efficiently targeted to the endosomal membrane. These data implicate Vps26p/VPS26 in regulating Vps35p/VPS35 membrane association and therefore suggest a role for Vps26p/VPS26 in cargo recognition.
Molecular characterization of the thi3 gene involved in thiamine biosynthesis in Zea mays: cDNA sequence and enzymatic and structural properties of the recombinant bifunctional protein with 4-amino-5-hydroxymethyl-2-methylpyrimidine (phosphate) kinase and thiamine monophosphate synthase activities
Authors: Rapala-Kozik Maria , Olczak Mariusz , Ostrowska Katarzyna , Starosta Agata , Kozik Andrzej
Published: November 2007

A thiamine biosynthesis gene, thi3, from maize Zea mays has been identified through cloning and sequencing of cDNA and heterologous overexpression of the encoded protein, THI3, in Escherichia coli. The recombinant THI3 protein was purified to homogeneity and shown to possess two essentially different enzymatic activities of HMP(-P) [4-amino-5-hydroxymethyl-2-methylpyrimidine (phosphate)] kinase and TMP (thiamine monophosphate) synthase. Both activities were characterized in terms of basic kinetic constants, with interesting findings that TMP synthase is uncompetitively inhibited by excess of one of the substrates [HMP-PP (HMP diphosphate)] and ATP. A bioinformatic analysis of the THI3 sequence suggested that these activities were located in two distinct, N-terminal kinase and C-terminal synthase, domains. Models of the overall folds of THI3 domains and the arrangements of active centre residues were obtained with the SWISS-MODEL protein modelling server, on the basis of the known three-dimensional structures of Salmonella enterica serotype Typhimurium HMP(-P) kinase and Bacillus subtilis TMP synthase. The essential roles of Gln98 and Met134 residues for HMP kinase activity and of Ser444 for TMP synthase activity were experimentally confirmed by site-directed mutagenesis.
Molecules incorporating a benzothiazole core scaffold inhibit the N-myristoyltransferase of Plasmodium falciparum
Authors: Bowyer Paul W. , Gunaratne Ruwani S. , Grainger Munira , Withers-Martinez Chrislaine , Wickramsinghe Sasala R. , Tate Edward W. , Leatherbarrow Robin J. , Brown Katherine A. , Holder Anthony A. , Smith Deborah F.
Published: November 2007

Recombinant N-myristoyltransferase of Plasmodium falciparum (termed PfNMT) has been used in the development of a SPA (scintillation proximity assay) suitable for automation and high-throughput screening of inhibitors against this enzyme. The ability to use the SPA has been facilitated by development of an expression and purification system which yields considerably improved quantities of soluble active recombinant PfNMT compared with previous studies. Specifically, yields of pure protein have been increased from 12 μg·l−1 to >400 μg·l−1 by use of a synthetic gene with codon usage optimized for expression in an Escherichia coli host. Preliminary small-scale ‘piggyback’ inhibitor studies using the SPA have identified a family of related molecules containing a core benzothiazole scaffold with IC50 values <50 μM, which demonstrate selectivity over human NMT1. Two of these compounds, when tested against cultured parasites in vitro, reduced parasitaemia by >80% at a concentration of 10 μM.
Structures of the four subfamilies of phosphodiesterase-4 provide insight into the selectivity of their inhibitors
Authors: Wang Huanchen , Peng Ming-Sheng , Chen Yi , Geng Jie , Robinson Howard , Houslay Miles D. , Cai Jiwen , Ke Hengming
Published: November 2007

PDE4 (phosphodiesterase-4)-selective inhibitors have attracted much attention as potential therapeutics for the treatment of both depression and major inflammatory diseases, but their practical application has been compromised by side effects. A possible cause for the side effects is that current PDE4-selective inhibitors similarly inhibit isoforms from all four PDE4 subfamilies. The development of PDE4 subfamily-selective inhibitors has been hampered by a lack of structural information. In the present study, we rectify this by providing the crystal structures of the catalytic domains of PDE4A, PDE4B and PDE4D in complex with the PDE4 inhibitor NVP {4-[8-(3-nitrophenyl)-[1,7]naphthyridin-6-yl]benzoic acid} as well as the unliganded PDE4C structure. NVP binds in the same conformation to the deep cAMP substrate pocket and interacts with the same residues in each instance. However, detailed structural comparison reveals significant conformational differences. Although the active sites of PDE4B and PDE4D are mostly comparable, PDE4A shows significant displacements of the residues next to the invariant glutamine residue that is critical for substrate and inhibitor binding. PDE4C appears to be more distal from other PDE4 subfamilies, with certain key residues being disordered. Our analyses provide the first structural basis for the development of PDE4 subfamily-selective inhibitors.
Identification of a region on hypoxia-inducible-factor prolyl 4-hydroxylases that determines their specificity for the oxygen degradation domains
Authors: Villar Diego , Vara-Vega Alicia , Landázuri Manuel O. , Del Peso Luis
Published: November 2007

HIFs [hypoxia-inducible (transcription) factors] are essential for the induction of an adaptive gene expression programme under low oxygen partial pressure. The activity of these transcription factors is mainly determined by the stability of the HIFα subunit, which is regulated, in an oxygen-dependent manner, by a family of three prolyl 4-hydroxylases [EGLN1–EGLN3 (EGL nine homologues 1–3)]. HIFα contains two, N- and C-terminal, independent ODDs (oxygen-dependent degradation domains), namely NODD and CODD, that, upon hydroxylation by the EGLNs, target HIFα for proteasomal degradation. In vitro studies indicate that each EGLN shows a differential preference for ODDs, However, the sequence determinants for such specificity are unknown. In the present study we showed that whereas EGLN1 and EGLN2 acted upon any of these ODDs to regulate HIF1α protein levels and activity in vivo, EGLN3 only acted on the CODD. With the aim of identifying the region within EGLNs responsible for their differential substrate preference, we investigated the activity and binding pattern of different EGLN deletions and chimaeric constructs generated by domain swapping between EGLN1 and EGLN3. These studies revealed a region of 97 residues that was sufficient to confer the characteristic substrate binding observed for each EGLN. Within this region, we identified the minimal sequence (EGLN1 residues 236–252) involved in substrate discrimination. Importantly, mapping of these sequences on the EGLN1 tertiary structure indicates that substrate specificity is determined by a region relatively remote from the catalytic site.
Vitamin E prevents hypobaric hypoxia-induced mitochondrial dysfunction in skeletal muscle
Authors: Magalhães José , Ferreira Rita , Neuparth Maria J. , Oliveira Paulo J. , Marques Franklim , Ascensão António
Published: November 2007

In the present study, the effect of vitamin E (α-tocopherol) on mice skeletal muscle mitochondrial dysfunction and oxidative damage induced by an in vivo acute and severe hypobaric hypoxic insult (48 h at a barometric pressure equivalent to 8500 m) has been investigated. Male mice (n=24) were randomly divided into the following four groups (n=6): control (C), hypoxia (H), vitamin E (VE; 60 mg/kg of body weight intraperitoneally, three times/week for 3 weeks) and hypoxia+VE (HVE). A significant increase in mitochondrial protein CGs (carbonyl groups) was found in the H group compared with the C group. Confirming previous observations from our group, hypoxia induced mitochondrial dysfunction, as identified by altered respiratory parameters. Hypoxia exposure increased Bax content and decreased the Bcl-2/Bax ratio, whereas Bcl-2 remained unchanged. Inner and outer mitochondrial membrane integrity were significantly affected by hypoxia exposure; however, vitamin E treatment attenuated the effect of hypoxia on mitochondrial oxidative phosphorylation and on the levels of CGs. Vitamin E supplementation also prevented the Bax and Bcl-2/Bax ratio impairments caused by hypoxia, as well as the decrease in inner and outer mitochondrial membrane integrity. In conclusion, the results suggest that vitamin E prevents the loss of mitochondrial integrity and function, as well as the increase in Bax content, which suggests that mitochondria are involved in increased cell death induced by severe hypobaric hypoxia in mice skeletal muscle.
Effects of the reaction atmosphere composition on the synthesis of single and multiwalled nitrogen-doped nanotubes
Authors: Ayala P. , Grüneis A. , Kramberger C. , Rümmeli M. H. , Solórzano I. G. , Freire F. L. , Pichler T.
Published: November 2007

Single and multiwalled nitrogen-doped carbon nanotubes were grown by chemical vapor deposition varying the feedstock composition between pure acetonitrile and ethanol/acetonitrile mixtures. The advantage of using C∕N sources that develop close vapor pressure values has been used in order to elucidate the effects of the reaction atmosphere in the synthesis of N-doped nanotubes. Our findings show that the morphology of the nanotube material depends strongly on the composition of the reaction atmosphere. When carrying out the experiments in an atmosphere solely determined by the vapor pressure of the feedstock components, improved homogeneity is achieved with pure C∕N sources or low concentration of the foreign solute. Under these conditions the temperature has strong influence in the diameter distribution.
Random-phase-approximation-based correlation energy functionals: Benchmark results for atoms
Authors: Jiang Hong , Engel Eberhard
Published: November 2007

The random phase approximation for the correlation energy functional of the density functional theory has recently attracted renewed interest. Formulated in terms of the Kohn-Sham orbitals and eigenvalues, it promises to resolve some of the fundamental limitations of the local density and generalized gradient approximations, as, for instance, their inability to account for dispersion forces. First results for atoms, however, indicate that the random phase approximation overestimates correlation effects as much as the orbital-dependent functional obtained by a second order perturbation expansion on the basis of the Kohn-Sham Hamiltonian. In this contribution, three simple extensions of the random phase approximation are examined; (a) its augmentation by a local density approximation for short-range correlation, (b) its combination with the second order exchange term, and (c) its combination with a partial resummation of the perturbation series including the second order exchange. It is found that the ground state and correlation energies as well as the ionization potentials resulting from the extensions (a) and (c) for closed subshell atoms are clearly superior to those obtained with the unmodified random phase approximation. Quite some effort is made to ensure highly converged data, so that the results may serve as benchmark data. The numerical techniques developed in this context, in particular, for the inherent frequency integration, should also be useful for applications of random phase approximation-type functionals to more complex systems.
Probability density function modeling of scalar mixing from concentrated sources in turbulent channel flow
Authors: Bakosi J. , Franzese P. , Boybeyi Z.
Published: November 2007

Dispersion of a passive scalar from concentrated sources in fully developed turbulent channel flow is studied with the probability density function (PDF) method. The joint PDF of velocity, turbulent frequency and scalar concentration is represented by a large number of Lagrangian particles. A stochastic near-wall PDF model combines the generalized Langevin model of Haworth and Pope [Phys. Fluids 29, 387 (1986)] with Durbin's [J. Fluid Mech. 249, 465 (1993)] method of elliptic relaxation to provide a mathematically exact treatment of convective and viscous transport with a nonlocal representation of the near-wall Reynolds stress anisotropy. The presence of walls is incorporated through the imposition of no-slip and impermeability conditions on particles without the use of damping or wall-functions. Information on the turbulent time scale is supplied by the gamma-distribution model of van Slooten et al. [Phys. Fluids 10, 246 (1998)]. Two different micromixing models are compared that incorporate the effect of small scale mixing on the transported scalar: the widely used interaction by exchange with the mean and the interaction by exchange with the conditional mean model. Single-point velocity and concentration statistics are compared to direct numerical simulation and experimental data at Reτ=1080 based on the friction velocity and the channel half width. The joint model accurately reproduces a wide variety of conditional and unconditional statistics in both physical and composition space.
Initiation of aluminum wire array on the 1-MA ZEBRA accelerator and its effect on ablation dynamics and x-ray yield
Authors: Sarkisov G. S. , Rosenthal S. E. , Struve K. W. , Cowan T. E. , Presura R. , Astanovitskiy A. L. , Haboub A. , Morozov A.
Published: November 2007

The effect of current prepulse on the initiation of Al wire arrays, ablation dynamics and x-ray production was investigated on the 1-MA ZEBRA accelerator (University of Nevada, Reno). It is shown that increasing the number of wires lowers the temperature of the wire cores at the time of breakdown. Al arrays with cold wire cores demonstrate long and inhomogeneous ablation, and a less intense, wider x-ray pulse. Shortening the current prepulse by a flashover switch causes an increased wire-core temperature, symmetrization and synchronization of the wires’ ablation, and improvement of the amplitude and shape of the x-ray pulse. Application of a vacuum flashover switch can be important for shortening the current prepulse on the upcoming 28-MA ZR-accelerator at Sandia National Laboratories to optimize the x-ray production and shot-to-shot reproducibility from wire-array Z pinches.
Multiferroic properties of polycrystalline Bi1−xCaxFeO3
Authors: Kothari Deepti , Reddy V. Raghavendra , Gupta Ajay , Sathe Vasant , Banerjee A. , Gupta S. M. , Awasthi A. M.
Published: November 2007

It is shown that Ca2+ doping at Bi-site results in the release of weak ferromagnetism in BiFeO3. Structural transformation from rhombohedral to triclinic is observed with 10% Ca doping. Raman measurements show the presence of oxygen vacancies with Ca doping and no evidence of either intermediate valence or the tetravalence of iron is observed from Mössbauer measurements. No significant change in Neel temperature is observed with Ca doping. The observed weak ferromagnetism and ferroelectric nature at room temperature indicates the multiferroic nature of Bi1−xCaxFeO3 (x=5% and 10%) samples.
Electro-optical sampling of ultrashort THz pulses by fs-laser pulses at 530 nm with BaTiO3
Authors: Pradarutti B. , Matthäus G. , Riehemann S. , Notni G. , Limpert J. , Nolte S. , Tünnermann A.
Published: November 2007

Electro-optical sampling (EOS) of ultrabroadband terahertz (THz) radiation with the help of ultrashort 530 nm fs-laser pulses is reported. The THz pulses are generated by exciting a surface emitter (InAs) with a parabolic fiber laser amplifier delivering 100 fs pulses at a repetition rate of 75 MHz and an average power of 10 W at 1060 nm. The pulses are frequency doubled to 530 nm for gating and BaTiO3 is used as the detector crystal.