bluuebunny/crossref_metadata_2025 huggingface dataset:
Photoionization efficiency spectroscopy and density functional theory investigations of RhHo2On (n=–2) clusters
Authors: Gentleman Alexander S. , Addicoat Matthew A. , Dryza Viktoras , Gascooke Jason R. , Buntine Mark A. , Metha Gregory F.
Published: April 2009

The experimental and theoretical adiabatic ionization energies (IEs) of the rhodium-holmium bimetallic clusters RhHo2On (n=0–2) have been determined using photoionization efficiency spectroscopy and density functional theory (DFT) calculations. Both sets of data show the IE of RhHo2O to be significantly lower than the values for RhHo2 and RhHo2O2, which are found to be similar. This indicates that there are significant changes in electronic properties upon sequential addition of oxygen atoms to RhHo2. The DFT investigations show that the lowest energy neutral structures are a C2v triangle for RhHo2, a C2v planar structure for RhHo2O where the O atom is doubly bridged to the Ho–Ho bond, and a C2v nonplanar structure for RhHo2O2, where the O2 is dissociative and each O atom is doubly bridged to the Ho–Ho bond in the cluster above and below the RhHo2 trimer plane. Good correlation between the experimental and computational IE data imply that the lowest energy neutral structures calculated are the most likely isomers ionized in the molecular beam. In particular, the theoretical adiabatic IE for the dissociative RhHo2O2 structure is found to compare better with the experimentally determined value than the corresponding lowest energy O2 associative structure.
Nanopositioning of a diamond nanocrystal containing a single nitrogen-vacancy defect center
Authors: van der Sar T. , Heeres E. C. , Dmochowski G. M. , de Lange G. , Robledo L. , Oosterkamp T. H. , Hanson R.
Published: April 2009

Precise control over the position of a single quantum object is important for many experiments in quantum science and nanotechnology. We report on a technique for high-accuracy positioning of individual diamond nanocrystals. The positioning is done with a home-built nanomanipulator under real-time scanning electron imaging, yielding an accuracy of a few nanometers. This technique is applied to pick up, move, and position a single nitrogen-vacancy (NV) defect center contained in a diamond nanocrystal. We verify that the unique optical and spin properties of the NV center are conserved by the positioning process.
Analysis of optical emission spectroscopy in a dual-frequency capacitively coupled CHF3 plasma
Authors: Huang Xiao-Jiang , Xin Yu , Yang Lei , Ye Chao , Yuan Qiang-Hua , Ning Zhao-Yuan
Published: April 2009

The characteristics of a capacitively coupled CHF3 plasma driven by dual-frequency sources (41 MHz/2 MHz) are experimentally investigated by using optical emission spectroscopy technique. The dependences of relative densities of F and H, the ratio of F/CF2, and the excitation temperature, as well as neutral gas rotational temperature on the low or high frequency (LF or HF) power, have been analyzed. It is found that the increment rate of the gas dissociation rate, the ratio of F/CF2, the excitation temperature. and the neutral gas temperature with increasing LF power are larger than that of HF power. The relative densities of F and H, the ratio of F/CF2, and the excitation temperature decrease while the neutral gas temperature increases with increasing gas pressure.
Site-dependent photodissociation of vibrationally excited CD3NH2
Authors: Marom Ran , Weiss Tal , Rosenwaks Salman , Bar Ilana
Published: April 2009

The N–H and C–D bond fission in partially deuterated methylamine, CD3NH2, has been investigated using vibrationally mediated photodissociation. Jet-cooled action spectra and Doppler profiles of the H and D photofragments were monitored following ∼243.1 nm photodissociation of the parent pre-excited to two, three or four N–H stretch quanta. The action spectra were analyzed in terms of simplified local mode/normal mode (LM/NM) and NM models, allowing band assignment and determination of the strong resonances involved in the coupling. The Doppler profiles show that the released H and D photofragments have low translational energy content and that the H is the dominant product, although its yield decreases as higher pre-excited N–H vibrational states are dissociated. The dynamics of the site-dependent bond fission in CD3NH2 is discussed.
Free energy analysis for adsorption-induced lattice transition of flexible coordination framework
Authors: Watanabe Satoshi , Sugiyama Hayato , Adachi Hirobumi , Tanaka Hideki , Miyahara Minoru T.
Published: April 2009

We conduct grand canonical Monte Carlo simulations and free energy analysis for a gate adsorption phenomenon, which is experimentally observed in flexible frameworks of porous coordination polymers. Our calculations demonstrate that the stabilization provided by the guest adsorption drives the structural transition, surmounting the energy cost in creating the adsorption space due to the movement of the host framework. Furthermore, the existence of an energy barrier between two local minima in the free-energy landscape is found to result in hysteretic adsorption.
Structures and magnetic properties of SinMn (n=1–15) clusters
Authors: Li Jian-rong , Wang Guang-hou , Yao Chang-hong , Mu Yue-wen , Wan Jian-guo , Han Min
Published: April 2009

The structure, electronic, magnetic properties of SinMn clusters up to n=15 are systematically investigated using the density functional theory within the generalized gradient approximation. In the most stable configurations of SinMn clusters, the equilibrium site of Mn atom gradually moves from convex, to a surface, and to a concave site as the number of Si atoms varying from 1 to 15. Starting from n=11, the Mn atom completely falls into the center of the Si outer frame, forming Mn-encapsulated Si cages. Maximum peaks of second-order energy difference are found at n=6, 8, 10, and 12, indicating that these clusters possess relatively higher stability. The electronic structures and magnetic properties of SinMn clusters are discussed. The magnetic moment of SinMn clusters mainly is located on Mn atom. The 3d electrons in Mn atom play a dominant role in the determination of the magnetism of Mn atom in SinMn clusters. Furthermore, the moment of Mn atom in SinMn clusters exhibits oscillatory behavior and are quenched at n>7 except for n=12, mainly due to the charge transfer, strong hybridization between Mn 4s, 3d, 4p and Si 3s, 3p states.
Spectral response design of hydrogenated amorphous silicon p-i-n diodes for ambient light sensing
Authors: Tan S. S. , Liu C. Y. , Jiang Yeu-Long , Lin Der-Yu , Hsu Klaus Y. J.
Published: April 2009

For the applications involving ambient light sensing, the spectral response of photodetectors is required to mimic that of human eyes and the cost must be low. This paper discusses the layer structure design of human-eye-like hydrogenated amorphous silicon (a-Si:H) p-i-n photodiodes. The resultant sample devices are insensitive to infrared light and have a normal spectral response in the light band ranging between 400 nm wavelength and 740 nm wavelength. The spectrum peak locates around 560 nm wavelength, similar to the case of human eyes. The devices are suitable for low-cost ambient light sensing applications.
Beta value at separatrix of field-reversed configuration
Authors: Ikeyama Taeko , Hiroi Masanori , Nogi Yasuyuki , Ohkuma Yasunori
Published: April 2009

A pressure profile inside and outside a separatrix of a field-reversed configuration is determined by comparing three types of assumed pressure profiles with the radial profile of bremsstrahlung. It is found that the pressure profile is flatter near the field null than the rigid rotor profile. Edge-layer parameters as beta value at the separatrix, separatrix radius, and edge-layer width are determined from the pressure profile. The reliability of those parameters is confirmed by a magnetic method measuring an excluded flux radius.
On the physical interpretation of Malyshkin’s (2008) model of resistive Hall magnetohydrodynamic reconnection
Authors: Uzdensky Dmitri A.
Published: April 2009

A simple Sweet–Parker-like model for the electron current layer in resistive Hall magnetohydrodynamic reconnection is presented, with the focus on the small-resistivity limit. The derivation readily recovers the main results obtained recently by Malyshkin [Phys. Rev. Lett. 101, 225001 (2008)], but is much quicker and more physically transparent. In particular, it highlights the role of resistive drag in determining the electron outflow velocity. The principal limitations of any such approach are discussed.
Waveguide mode imaging and dispersion analysis with terahertz near-field microscopy
Authors: Mitrofanov Oleg , Tan Thomas , Mark Paul R. , Bowden Bradley , Harrington James A.
Published: April 2009

Propagation of terahertz waves in hollow metallic waveguides depends on the waveguide mode. Near-field scanning probe terahertz microscopy is applied to identify the mode structure and composition in dielectric-lined hollow metallic waveguides. Spatial profiles, relative amplitudes, and group velocities of three main waveguide modes are experimentally measured and matched to the HE11, HE12, and TE11 modes. The combination of near-field microscopy with terahertz time-resolved spectroscopy opens the possibility of waveguide mode characterization in the terahertz band.
Delta-doped LaAlO3/SrTiO3 interfaces
Authors: Fix T. , MacManus-Driscoll J. L. , Blamire M. G.
Published: April 2009

The quasi-two-dimensional electron gases formed at the interface between insulators such as SrTiO3/LaAlO3 are predicted to arise from an interfacial electronic reconstruction, but the extent to which oxygen vacancies within the substrate contribute to the conduction remains unclear. We show that delta-doping the interface with transition metal cations dramatically alters the properties and supports the model of a highly two-dimensional charge sheet.
Enhanced terahertz emission from coherent longitudinal optical phonons in a quantum well structure under applied bias
Authors: Mizoguchi Kohji , Kanzawa Yusuke , Saito Shingo , Sakai Kiyomi , Nakayama Masaaki
Published: April 2009

We report on the characteristics of terahertz waves emitted from coherent longitudinal optical (LO) phonons in a GaAs/AlAs multiple quantum well structure under an applied electric field. It is found that the intensity of the terahertz wave from the coherent LO phonon is resonantly enhanced in comparison with the intensity in a low electric-field region, under the condition that an intersubband energy is tuned to the LO-phonon energy of GaAs. The pump-energy dependence of the terahertz-wave intensity indicates that the enhancement originates from the double resonances in the Raman scattering process.
Surface-plasmon resonance of a planar lollipop near-field transducer
Authors: Peng Chubing
Published: April 2009

Surface-plasmon resonance of a lollipop near-field transducer integrated in a planar solid immersion mirror for heat-assisted magnetic recording has been studied by pump-probe photothermal measurement and recording on a phase-change medium. Lollipops of 190 nm in disk diameter and 20-nm-thick were found to exhibit two resonant modes in 710–950 nm. Recording on a phase-change medium showed that the wavelength at the short resonant mode is not sensitive to the presence of a medium, while the resonance at the long wavelength exhibits significant redshift. On resonance, the plasmon efficiency enables the pronounced near-field optical recording.
Thermal expansion of RuFe alloys and its relationship to the high pressure phase of Fe
Authors: Qadri Syed B. , Keller Teddy M. , Laskoski Matt , Skelton E. F. , Husz A. , Mahadik N. A.
Published: April 2009

Ru 1 − x Fe x alloys crystallize in a hexagonal-close-packed structure for x<0.70 with a space group of P63/mmc, the same phase as that of a high pressure phase of iron, ε-Fe. Thermal expansion coefficients of Ru1−xFex alloys of various compositions were determined over a temperature range of 300–530 K using high resolution x-ray diffraction measurements. The coefficients of linear thermal expansion for hexagonal phase along the c and a axes showed a linear dependence on the composition. These results when extrapolated showed direct relationship to the thermoelastic properties of ε-Fe. This study also demonstrates that high pressure and high temperature phases can be simulated and engineered to exist at ambient conditions with proper choice of alloying.
In Pursuit of Scarcity: Transnational Students, ‘Employability’, and the MBA
Authors: Waters Johanna L
Published: April 2009

‘Credential inflation’ is perhaps one of the more contentious consequences of the recent expansion of higher education. Concerns over the effects of credential inflation have spawned a number of debates around concepts of ‘employability’ and postgraduate learning. In the contemporary knowledge-based economy, it is argued, the employability of young graduates is increasingly dependent upon their ability to maintain ‘positional advantage’ in a labour market characterised by ‘boundaryless careers’. I examine these debates in the context of East Asia. Here, young people's positional advantage is sought, firstly, through the acquisition of an international first degree, obtained at an overseas institution. However, with more and more middle-class students going abroad for their education before returning to seek work, the ‘overseas degree’ is also increasingly subject to devaluation through credential inflation. I highlight the significance of postgraduate education and particularly the Masters of Business Administration (MBA) for young, overseas-educated, graduates in Hong Kong. I argue that the MBA is now seen as a vital supplement to an overseas undergraduate education and as part of an extended temporal and spatial process of study, in the face of prevalent discourses of ‘employability’, individual responsibility, and the need for the continual upgrading of skills.
‘Stepping in Time’: Walking, Time, and Space in the City
Authors: Middleton Jennie
Published: April 2009

There is a well-documented emphasis within transport policy on speed and efficiency, with the benefits of transport schemes frequently assessed in these terms. The focus on reducing journey times is also evident in pedestrian policy, with the ‘time-saving’ attributes of walking often promoted. However, this emphasis on speed within the transport policy arena reflects linear understandings of time as nothing more than ‘clock time’ passing. In contrast, this paper explores the multiple forms of temporality and spatiality that emerge out of and shape urban pedestrian movement. The discussion draws upon in-depth interview and diary data from fieldwork undertaken in London, and in so doing provides a ‘timely’ empirical engagement with theoretical understandings of time and space. Within this examination of the multiple temporalities of urban walking, it is suggested that people become aware of the experiential dimensions of time when they are made to wait. The paper moves on to explore the issues of physical mobility difficulties in the context of highlighting the multiple spatialities of walking, and attention is also drawn to how people use temporal and spatial concerns to frame their identities as to who they are in relation to others. It is suggested that notions of rhythm provide a productive means for engaging with how time, space, and identity interrelate as people walk.
Inclusion under the Law as Exclusion from the City: Negotiating the Spatial Limitation of Citizenship in Seattle
Authors: Carr John , Brown Elizabeth , Herbert Steve
Published: April 2009

We use this paper to argue that the contemporary tendency of urban governments to exclude a host of ‘undesirables' from the city—such as the homeless, teens of color, and prostitutes—must be seen as part of a broader process by which the law includes, weighs, and assesses all urban denizens. We use three case studies from Seattle to demonstrate how the law enacts a vision of urban form which reflects and spatially enforces core normative liberal identities, even when the state seeks to render the city more inclusive, fair, and just. In so doing, we underscore how the incorporation of these identities into state processes not only solidifies and reinforces the exclusion of undesirable or disorderly ‘others’, but also spatially sorts all urban dwellers along a variety of identity lines.
Migration, Hukou Status, and Labor-Market Segmentation: The Case of High-Tech Development in Dalian
Authors: Fan Chuncui Velma , Hall Peter V , Wall Geoffrey
Published: April 2009

This paper examines the relationship between migration and labor-market segmentation in the northeastern Chinese city of Dalian. Several authors have stressed the importance of institutional arrangements in shaping the opportunity structures confronting migrants to China's urban areas. In particular, the ‘insider status' defined by the differential hukou or household registration status has been implicated in differential access to housing, schooling, health, and other benefits, as well as employment. The examination of the role of the hukou system in shaping employment outcomes in three high-tech industrial sectors of Dalian does not challenge this general finding; however, important variations among the software, biotech, and digital manufacturing industries are found. In these industries, the increasingly decentralized decision making of local economic development policy and shortages of skilled workers are leading to a selective relaxation of the hukou system—at least for some migrants. The implications of these changes for labor-market outcomes and urban development are highlighted.
The Geographies of Student Migration in the UK
Authors: Duke-Williams Oliver
Published: April 2009

Recent research on studentification in the UK has examined the ways in which significant growth in student numbers over the last twenty years or so have led to marked change in the nature of the parts of cities in which clusters of students live. Yet these changes do not happen in isolation: the students are also associated with major migration flows into and out of studentified parts of cities. I examine the migration flows associated with a set of wards selected on the basis of having a high concentration of students. Examination of the age profiles of migrants into and out of these wards supports an argument that assumptions can be made that, for most of the selected wards, in-migrants are predominantly new students entering the system, whilst out-migrants are predominantly recently graduated students leaving the system. The specific origins from which new students arrive, and destinations to which former students depart, are examined and mapped, and the role of higher education as a mechanism through which the South East of England gains qualified workers is considered.
Problems with Sb analysis of environmentally relevant samples
Authors: Hjortenkrans David S. T. , Mänsson Nina S. , Bergbäck Bo G. , Häggerud Agneta V.
Published: April 2009

Environmental context. Reliable results of chemical analysis are crucial for a proper environmental risk assessment. The recovery of antimony concentrations in environmentally relevant samples is here shown to be most dependent on the extraction method chosen. A reported low antimony concentration in present or historical samples may be misleading for decision-makers.
Abstract. Antimony is found in elevated concentrations in the roadside environment, industrial sites and generally in urban areas. An extended use of multielement analysis has produced more concentration data for metals in the environment. However, volatilisation of elements in the digestion step may be a problem as some of the certified and recommended digestion methods are performed in open vessels. The aim of the current study was to focus on wet digestion-derived problems for the analysis of volatile elements, with specific reference to Sb. Both soils and products, namely tyres and brake linings, were sampled. The samples were digested using different methods with variations in temperature, acid mix, and the use of open or closed vessels. For some methods, the recovery was <10%, indicating a need for revision of certified and recommended digestion procedures. For a multielement analysis, a closed vessel method must be used. If the aim is to study only Sb, a wet-digestion method optimised for Sb is the natural choice. This may be valuable to consider when handling environmentally relevant samples such as soils contaminated with Sb from point or diffuse sources.
Ecological threshold concentrations for antimony in water and soil
Authors: Oorts Koen , Smolders Erik
Published: April 2009

Environmental context. Antimony (Sb) is a natural trace element with several industrial applications and anthropogenic emissions can increase Sb concentrations in the environment. In order to assess the potential risks of elevated antimony concentrations to aquatic and terrestrial organisms, toxicity thresholds must be known and environmental criteria defined. Setting such criteria for antimony is not straightforward because the Sb speciation in the standard toxicity test is likely to differ from that in the environment.
Abstract. Ecologically relevant threshold concentrations for antimony are required in order to assess the potential risks of anthropogenic emissions of Sb to the environment. The present paper reports a summary of the ecotoxicity data available for various Sb substances and discusses the derivation of ecological threshold concentrations for Sb in freshwater and soils. It was concluded that data from tests with SbCl3 are useful for calculation of Sb toxicity thresholds in water. The results from SbCl3 in soil toxicity tests have little relevance because of demonstrated confounding factors of pH and salinity. The derivation of Sb threshold concentrations in soil was, therefore, based on toxicity tests in soils amended with the sparingly soluble Sb2O3 with correction for incomplete dissolution during the duration of the toxicity tests. The lowest chronic toxicity thresholds are 1.1 mg Sb L–1 in water and 370 mg Sb kg–1 dry weight for soil. These concentrations are more than 100-fold larger than typical natural background concentrations.
Retention of radio tags in golden perch (Macquaria ambigua), silver perch (Bidyanus bidyanus) and carp (Cyprinus carpio)
Authors: O'Connor J. P. , Koehn J. D. , Nicol S. J. , O'Mahony D. J. , McKenzie J. A.
Published: April 2009

Radio tagging and tracking are widely used to study freshwater fish; however, details of fish survival or tag retention rates are rarely reported. The results from five independent tagging trials associated with different tag attachment methods are reported in the present study. Implanted peritoneal cavity tags were trialled for two native Australia freshwater fish species (golden perch and silver perch) and introduced carp. Oesophageal and external tags were also trialled on silver perch. The results from the peritoneal cavity implantation trials in golden perch, silver perch and carp achieved an overall success rate of 81% (after 315 days), 18% (after 200 days) and 43% (after 323 days) respectively. The external attachment of radio tags to silver perch had limited success with all fish either rejecting their tags or dying before 256 days. Silver perch trialled with oesophageal tags had an overall success rate of 25% after 200 days. The trials indicate that internal tagging is suitable for longer-term radio tracking of golden perch, but further developments are required for longer-term applications to silver perch and carp. Tag rejection rates are unlikely to be constant between species or through time and this variability should be incorporated into the study design to prevent bias.
Transgenic multivitamin corn through biofortification of endosperm with three vitamins representing three distinct metabolic pathways
Authors: Naqvi Shaista , Zhu Changfu , Farre Gemma , Ramessar Koreen , Bassie Ludovic , Breitenbach Jürgen , Perez Conesa Dario , Ros Gaspar , Sandmann Gerhard , Capell Teresa , Christou Paul
Published: April 2009

Vitamin deficiency affects up to 50% of the world's population, disproportionately impacting on developing countries where populations endure monotonous, cereal-rich diets. Transgenic plants offer an effective way to increase the vitamin content of staple crops, but thus far it has only been possible to enhance individual vitamins. We created elite inbred South African transgenic corn plants in which the levels of 3 vitamins were increased specifically in the endosperm through the simultaneous modification of 3 separate metabolic pathways. The transgenic kernels contained 169-fold the normal amount of β-carotene, 6-fold the normal amount of ascorbate, and double the normal amount of folate. Levels of engineered vitamins remained stable at least through to the T3 homozygous generation. This achievement, which vastly exceeds any realized thus far by conventional breeding alone, opens the way for the development of nutritionally complete cereals to benefit the world's poorest people.
Can language prime culture in Hispanics? The differential impact of self‐construals in predicting intention to use a condom
Authors: Lechuga Julia , Wiebe John S.
Published: April 2009

The highly influential theory of planned behavior suggests that norms and attitudes predict an important antecedent of behavior: intention. Cross‐cultural research suggests that culturally influenced self‐construals can be primed and differentially affect behaviors that are influenced by norms and attitudes. The purpose of this experiment was twofold: (1) To investigate whether language functions as a prime for culture in Hispanics, and (2) if so, if norms and attitudes differentially predict condom use intention. Fluent English–Spanish bilingual participants (N = 145) of Mexican descent were randomly assigned to answer questionnaires in English and Spanish. Subjective norms and private evaluations towards condom use were assessed and their relative strength in predicting condom use intention was evaluated. Results suggest that language can prime culture and affect the relative accessibility of culture‐relevant norms and self‐construals in Hispanics. Moreover, consistent with our expectations, norms and attitudes differentially predicted condom use intention.
Sentence comprehension affects the dynamics of bimanual coordination: Implications for embodied cognition
Authors: Olmstead Anne J. , Viswanathan Navin , Aicher Karen A. , Fowler Carol A.
Published: April 2009

Recent work in embodied cognition has demonstrated that language comprehension involves the motor system (e.g., Glenberg & Kaschak, 2002). Such findings are often attributed to mechanisms involving simulations of linguistically described events (Barsalou, 1999; Fischer & Zwaan, 2008). We propose that research paradigms in which simulation is the central focus need to be augmented with paradigms that probe the organization of the motor system during language comprehension. The use of well-studied motor tasks may be appropriate to this endeavour. To this end, we present a study in which participants perform a bimanual rhythmic task (Kugler & Turvey, 1987) while judging the plausibility of sentences. We show that the dynamics of the bimanual task differ when participants judge sentences describing performable actions as opposed to sentences describing events that are not performable. We discuss the general implications of our results for accounts of embodied cognition.
Lattices, rafts, and scaffolds: domain regulation of receptor signaling at the plasma membrane
Authors: Lajoie Patrick , Goetz Jacky G. , Dennis James W. , Nabi Ivan R.
Published: April 2009

The plasma membrane is organized into various subdomains of clustered macromolecules. Such domains include adhesive structures (cellular synapses, substrate adhesions, and cell–cell junctions) and membrane invaginations (clathrin-coated pits and caveolae), as well as less well-defined domains such as lipid rafts and lectin-glycoprotein lattices. Domains are organized by specialized scaffold proteins including the intramembranous caveolins, which stabilize lipid raft domains, and the galectins, a family of animal lectins that cross-link glycoproteins forming molecular lattices. We review evidence that these heterogeneous microdomains interact to regulate substratum adhesion and cytokine receptor dynamics at the cell surface.
Myeloid heme oxygenase–1 regulates innate immunity and autoimmunity by modulating IFN-β production
Authors: Tzima Sotiria , Victoratos Panayiotis , Kranidioti Ksanthi , Alexiou Maria , Kollias George
Published: April 2009

Heme oxygenase–1 (HO-1) is a key cytoprotective, antioxidant, and antiinflammatory molecule. The pathophysiological functions of HO-1 have been associated with its enzymatic activities in heme catabolism. We have examined the immune functions of HO-1 by its conditional ablation in myeloid cells (HO-1M-KO mice). We demonstrate that myeloid HO-1 is required for the activation of interferon (IFN) regulatory factor (IRF) 3 after Toll-like receptor 3 or 4 stimulation, or viral infection. HO-1–deficient macrophages show reduced expression of IFN-β and of primary IRF3 target genes encoding RANTES, IP-10 and MCP-1. In the presence of polyI:C, myeloid HO-1 knockout mice infected with Listeria monocytogenes, a model dependent on IFN-β production, showed enhanced bacterial clearance and survival, whereas control mice succumbed to infection. Moreover, after induction of experimental autoimmune encephalomyelitis, mice with myeloid-specific HO-1 deficiency developed a higher incidence and an exacerbated, nonremitting clinical disease correlating with persistent activation of antigen-presenting cells, enhanced infiltration of Th17 cells, and a nonregressing myelin-specific T cell reactivity. Notably, these defects were rectified by exogenous administration of IFN-β, confirming that HO-1 functions directly upstream of this critical immune pathway. These results uncover a novel direct function for myeloid HO-1 in the regulation of IFN-β production, establishing HO-1 as a critical early mediator of the innate immune response.
A Challenge to Goliath
Authors: Rossner Mike
Published: April 2009

Megapublishers obligate librarians to buy hundreds of journals they do not need in order to access the journals their constituents actually read. The time has come to challenge this business model, which is unsustainable for the libraries.
Steady-state solutions for Gierer-Meinhardt type systems with Dirichlet boundary condition
Authors: Ghergu Marius
Published: April 2009

This paper is concerned with the following Gierer-Meinhardt type systems subject to Dirichlet boundary conditions:\[<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="StartLayout Enlarged left-brace 1st Row 1st Column normal upper Delta u minus alpha u plus StartFraction u Superscript p Baseline Over v Superscript q Baseline EndFraction plus rho left-parenthesis x right-parenthesis equals 0 comma u greater-than 0 comma 2nd Column a m p semicolon in normal upper Omega comma 2nd Row 1st Column normal upper Delta v minus beta v plus StartFraction u Superscript r Baseline Over v Superscript s Baseline EndFraction equals 0 comma v greater-than 0 comma 2nd Column a m p semicolon in normal upper Omega comma 3rd Row 1st Column u equals 0 comma v equals 0 2nd Column a m p semicolon on partial-differential normal upper Omega comma EndLayout">{Δu−αu+upvq+ρ(x)=0,u>0,amp;in Ω,Δv−βv+urvs=0,v>0,amp;in Ω,u=0,v=0amp;on ∂Ω,\begin {cases} \Delta u - \alpha u + \frac {u^p}{v^q} + \rho (x) = 0,\; u > 0, & \text {in $\Omega $},\\ \Delta v - \beta v + \frac {u^r}{v^s} = 0,\; v > 0, & \text {in $\Omega $}, \\ u=0,\; v=0 & \text {on $\partial \Omega $}, \end {cases}\]whereΩ⊂RN\Omega \subset \mathbb {R}^N(N≥1N\geq 1) is a smooth bounded domain,ρ(x)≥0\rho (x)\geq 0inΩ\Omegaandα,β≥0\alpha ,\beta \geq 0. We are mainly interested in the case of different source terms, that is,(p,q)≠(r,s)(p,q)\neq (r,s). Under appropriate conditions on the exponentsp,q,rp,q,randsswe establish various results of existence, regularity and boundary behavior. In the one dimensional case a uniqueness result is also presented.
Towards a combinatorial classification of skew Schur functions
Authors: McNamara Peter , van Willigenburg Stephanie
Published: April 2009

We present a single operation for constructing skew diagrams whose corresponding skew Schur functions are equal. This combinatorial operation naturally generalises and unifies all results of this type to date. Moreover, our operation suggests a closely related condition that we conjecture is necessary and sufficient for skew diagrams to yield equal skew Schur functions.
Every sum system is divisible
Authors: Izumi Masaki
Published: April 2009

We show that every sum system is divisible. Combined with B. V. R. Bhat and R. Srinivasan’s result, this shows that every product system arising from a sum system (and every generalized CCR flow) is either of type I or type III. A necessary and sufficient condition for such a product system to be of type I is obtained.
Collapsing manifolds obtained by Kummer-type constructions
Authors: Paternain Gabriel , Petean Jimmy
Published: April 2009

We construct

F

\mathcal {F}

-structures on a Bott manifold and on some other manifolds obtained by Kummer-type constructions. We also prove that if

M
=
E
#
X

M=E\# X

, where

E
E

is a fiber bundle with structure group

G
G

and a fiber admitting a

G
G

-invariant metric of non-negative sectional curvature and

X
X

admits an

F

\mathcal {F}

-structure with one trivial covering, then one can construct on

M
M

a sequence of metrics with sectional curvature uniformly bounded from below and volume tending to zero (i.e.

Vol
K

⁡
(
M
)
=
0

\operatorname {Vol}_K(M)=0

). As a corollary we prove that all the elements in the Spin cobordism ring can be represented by manifolds

M
M

with

Vol
K

⁡
(
M
)
=
0

\operatorname {Vol}_K (M)=0

.
Log canonical models for the moduli space of curves: The first divisorial contraction
Authors: Hassett Brendan , Hyeon Donghoon
Published: April 2009

In this paper, we initiate our investigation of log canonical models for

(

M

¯

g

,
α
δ
)

(\overline {\mathcal {M}}_g,\alpha \delta )

as we decrease

α
\alpha

from 1 to 0. We prove that for the first critical value

α
=
9

/

11

\alpha = 9/11

, the log canonical model is isomorphic to the moduli space of pseudostable curves, which have nodes and cusps as singularities. We also show that

α
=
7

/

10

\alpha = 7/10

is the next critical value, i.e., the log canonical model stays the same in the interval

(
7

/

10
,
9

/

11
]

(7/10, 9/11]

. In the appendix, we develop a theory of log canonical models of stacks that explains how these can be expressed in terms of the coarse moduli space.
GeneRegionScan: a Bioconductor package for probe-level analysis of specific, small regions of the genome
Authors: Folkersen Lasse , Diez Diego , Wheelock Craig E. , Haeggström Jesper Z. , Goto Susumu , Eriksson Per , Gabrielsen Anders
Published: April 2009

Summary: Whole-genome microarrays allow us to interrogate the entire transcriptome of a cell. Affymetrix microarrays are constructed using several probes that match to different regions of a gene and a summarization step reduces this complexity into a single value, representing the expression level of the gene or the expression level of an exon in the case of exon arrays. However, this simplification eliminates information that might be useful when focusing on specific genes of interest. To address these limitations, we present a software package for the R platform that allows detailed analysis of expression at the probe level. The package matches the probe sequences against a target gene sequence (either mRNA or DNA) and shows the expression levels of each probe along the gene. It also features functions to fit a linear regression based on several genetic models that enables study of the relationship between gene expression and genotype.

Availability and implementation: The software is implemented as a platform-independent R package available through the Bioconductor repository at http://www.bioconductor.org/. It is licensed as GPL 2.0.

Contact:  lasse.folkersen@ki.se

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Mixtures of Polya trees for flexible spatial frailty survival modelling
Authors: Zhao Luping , Hanson Timothy E. , Carlin Bradley P.
Published: April 2009

Mixtures of Polya trees offer a very flexible nonparametric approach for modelling time-to-event data. Many such settings also feature spatial association that requires further sophistication, either at the point level or at the lattice level. In this paper, we combine these two aspects within three competing survival models, obtaining a data analytic approach that remains computationally feasible in a fully hierarchical Bayesian framework using Markov chain Monte Carlo methods. We illustrate our proposed methods with an analysis of spatially oriented breast cancer survival data from the Surveillance, Epidemiology and End Results program of the National Cancer Institute. Our results indicate appreciable advantages for our approach over competing methods that impose unrealistic parametric assumptions, ignore spatial association or both.
Control of specific growth rate in Saccharomyces cerevisiae
Authors: Snoep J. L. , Mrwebi M. , Schuurmans J. M. , Rohwer J. M. , Teixeira de Mattos M. J.
Published: April 2009

In this contribution we resolve the long-standing dispute whether or not the Monod constant (KS), describing the overall affinity of an organism for its growth-limiting substrate, can be related to the affinity of the transporter for that substrate (KM). We show how this can be done via the control of the transporter on the specific growth rate; they are identical if the transport step has full control. The analysis leads to the counter-intuitive result that the affinity of an organism for its substrate is expected to be higher than the affinity of the enzyme that facilitates its transport. Experimentally, we show this indeed to be the case for the yeastSaccharomyces cerevisiae, for which we determined a KMvalue for glucose more than two times higher than the KSvalue in glucose-limited chemostat cultures. Moreover, we calculated that at glucose concentrations of 0.03 and 0.29 mM, the transport step controls the specific growth rate at 78 and 49 %, respectively.
Glyceraldehyde-3-phosphate dehydrogenase of Xanthomonas campestris pv. campestris is required for extracellular polysaccharide production and full virulence
Authors: Lu Guang-Tao , Xie Jia-Ri , Chen Lei , Hu Jiang-Ru , An Shi-Qi , Su Hui-Zhao , Feng Jia-Xun , He Yong-Qiang , Jiang Bo-Le , Tang Dong-Jie , Tang Ji-Liang
Published: April 2009

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) plays an important role in glucose catabolism, converting glyceraldehyde 3-phosphates to 1,3-bisphosphoglycerates. Open reading frame (ORF)XC_0972in the genome ofXanthomonas campestrispv.campestris(Xcc) strain 8004 is the only ORF in this strain annotated to encode a GAPDH. In this work, we have demonstrated genetically that this ORF encodes a unique GAPDH inXccstrain 8004, which seems to be constitutively expressed. A GAPDH-deficient mutant could still grow in medium with glucose or other sugars as the sole carbon source, and no phosphofructokinase activity was detectable in strain 8004. These facts suggest thatXccmay employ the Entner–Doudoroff pathway, but not glycolysis, to utilize glucose. The mutant could not utilize pyruvate as sole carbon source, whereas the wild-type could, implying that the GAPDH ofXccis involved in gluconeogenesis. Furthermore, inactivation of theXccGAPDH resulted in impairment of bacterial growth and virulence in the host plant, and reduction of intracellular ATP and extracellular polysaccharide (EPS). This reveals that GAPDH is required for EPS production and full pathogenicity ofXcc.
Impact of lgt mutation on lipoprotein biosynthesis and in vitro phenotypes of Streptococcus agalactiae
Authors: Bray Beverley A. , Sutcliffe Iain C. , Harrington Dean J.
Published: April 2009

Although Streptococcus agalactiae, the group B Streptococcus, is a leading cause of invasive neonatal disease worldwide the molecular basis of its virulence is still poorly understood. To investigate the role of lipoproteins in the physiology and interaction of this pathogen with host cells, we generated a mutant S. agalactiae strain (A909ΔLgt) deficient in the Lgt enzyme and thus unable to lipidate lipoprotein precursors (pro-lipoproteins). The loss of pro-lipoprotein lipidation did not affect the viability of S. agalactiae or its growth in several different media, including cation-depleted media. The processing of two well-characterized lipoproteins, but not a non-lipoprotein, was clearly shown to be aberrant in A909ΔLgt. The mutant strain was shown to be more sensitive to oxidative stress in vitro although the molecular basis of this increased sensitivity was not apparent. The inactivation of Lgt also resulted in changes to the bacterial cell envelope, as demonstrated by reduced retention of both the group B carbohydrate and the polysaccharide capsule and a statistically significant reduction (P=0.0079) in A909ΔLgt adherence to human endothelial cells of fetal origin. These data confirm that failure to process lipoproteins correctly has pleiotropic effects that may be of significance to S. agalactiae colonization and pathogenesis.
Mitochondrial nucleoids from the yeast Candida parapsilosis: expansion of the repertoire of proteins associated with mitochondrial DNA
Authors: Miyakawa Isamu , Okamuro Akira , Kinsky Slavomir , Visacka Katarina , Tomaska Lubomir , Nosek Jozef
Published: April 2009

Molecules of mitochondrial DNA (mtDNA) are packed into nucleic acid–protein complexes termed mitochondrial nucleoids (mt-nucleoids). In this study, we analysed mt-nucleoids of the yeastCandida parapsilosis, which harbours a linear form of the mitochondrial genome. To identify conserved as well as specific features of mt-nucleoids in this species, we employed two strategies for analysis of their components. First, we investigated the protein composition of mt-nucleoids isolated fromC. parapsilosismitochondria, determined N-terminal amino acid sequences of 14 proteins associated with the mt-nucleoids and identified corresponding genes. Next, we complemented the list of mt-nucleoid components with additional candidates identified in the complete genome sequence ofC. parapsilosisas homologues ofSaccharomyces cerevisiaemt-nucleoid proteins. Our approach revealed several known mt-nucleoid proteins as well as additional components that expand the repertoire of proteins associated with these cytological structures. In particular, we identified and purified the protein Gcf1, which is abundant in the mt-nucleoids and exhibits structural features in common with the mtDNA packaging protein Abf2 fromS. cerevisiae. We demonstrate that Gcf1p co-localizes with mtDNA, has DNA-binding activityin vitro, and is able to stabilize mtDNA in theS. cerevisiaeΔabf2mutant, all of which points to a role in the maintenance of theC. parapsilosismitochondrial genome. Importantly, in contrast to Abf2p,in silicoanalysis of Gcf1p predicted the presence of a coiled-coil domain and a single high-mobility group (HMG) box, suggesting that it represents a novel type of mitochondrial HMG protein.
Bmh1p (14-3-3) mediates pathways associated with virulence in Candida albicans
Authors: Kelly Michelle N. , Johnston Douglas A. , Peel Bethany A. , Morgan Timothy W. , Palmer Glen E. , Sturtevant Joy E.
Published: April 2009

The ability of the pathogenic fungusCandida albicansto cause disease requires rapid adaptation to changes in the host environment and to an evolving host immune response. The identification of ‘virulence factors’ usingin vitrocharacterization of mutant strains has traditionally relied on a common set of phenotypic and biochemical assays (most often performed at 30 °C) and the subsequent correlation with their corresponding virulence in mouse models of disease. Utilizing a panel of isogenic mutants for the multifunctional signal-modulating 14-3-3 protein (Bmh1p), we have found that specific mutations affect a variety of different pathways currently associated with virulence, including those involved with the formation of filaments, as well as interaction with host immune cells. Surprisingly, our studies revealed that deficiencies in many of these pathways do not always correlate with virulence in a mouse model of disseminated infection. Mutations within the binding pocket of Bmh1p that affect the ability of the protein to efficiently bind ligand had varying effects on the results of a number ofin vitroandin vivoassays. The capability,in vitro, to filament in embedment conditions, and to filament and form chlamydospores under microaerophilic conditions on cornmeal agar, does not correlate with virulence. It is likely that only a subset of hyphal signalling pathways is actually required for the establishment of infection in the disseminated mouse model. Most importantly, our results suggest that the delayed onset of lag-phase growthin vitroat 37 °C, and not at 30 °C, results in an inability of these mutants to rapidly adjust to environmental changesin vivoand may be responsible for their increased clearance and reduced virulence. It is critical, therefore, that futurein vitrostudies of putative virulence factors inC. albicansinclude careful characterization at physiological temperatures.
A rigorous comparison of X-ray diffraction thickness measurement techniques using silicon-on-insulator thin films
Authors: Ying Andrew J. , Murray Conal E. , Noyan I. C.
Published: April 2009

Thickness data from semiconductor-grade silicon-on-insulator thin-film samples determined from high-resolution X-ray diffraction (HRXRD) data using the Scherrer equation, rocking-curve modeling, thickness fringe analysis, Fourier analysis and the Warren–Averbach method, as well as with cross-sectional transmission electron microscopy and X-ray reflectivity measurements, are presented. The results show that the absolute accuracy of thin-film thickness values obtained from HRXRD data is approximately 1 nm for all techniques if all sources of broadening are correctly identified, while their precision is one or two orders of magnitude smaller. The use of multiple techniques is required to determine the various contributions to peak broadening.
Implementation and use of robust refinement in powder diffraction in the presence of impurities
Authors: Stone Kevin H. , Lapidus Saul H. , Stephens Peter W.
Published: April 2009

A modification to the usual least-squares analysis is implemented for the robust refinement of structural parameters from powder diffraction data in the presence of unmodeled impurities. This is accomplished in the programTOPAS-Academicby an iterative reweighting of the data as the model is refined. The method is tested and characterized using mixtures of known materials, acetaminophen and ibuprofen. The technique is also used to refine two previously unknown structures.
A prototype environmental gas cell forin situsmall-molecule X-ray diffraction
Authors: Warren John E. , Pritchard Robin G. , Abram Don , Davies Hazel M. , Savarese Teresa L. , Cash Ryan J. , Raithby Paul R. , Morris Russell , Jones Richard H. , Teat Simon J.
Published: April 2009

This paper reports the development of a prototype environmental gas cell, capable of allowing a single crystal to be exposed to different gas mixtures and/or a vacuum whilstin situon the single-crystal diffractometer. The design and application of the cell to the study of a single crystal in the presence of sulfur dioxide are described.