bluuebunny/crossref_metadata_2025 huggingface dataset:
About the collapse of the 3.3 μm CH stretching band with ionization in polycyclic aromatic hydrocarbons: Configuration interaction and quantum Monte Carlo studies of the CH fragment
Authors: Pauzat Françoise , Pilmé Julien , Toulouse Julien , Ellinger Yves
Published: August 2010

The puzzling difference between the IR spectra of polycyclic aromatic hydrocarbons (PAHs) and those of the corresponding positive ions (PAHs+) is a well documented fact, although the basic reason for it is far from clear. In this report, the CH fragment, in its neutral and ionized forms is taken as a case study for investigating the collapse of the CH stretching vibration with ionization. A comprehensive study of the dipole moment function around the equilibrium geometries of the fragments using large scale configuration interaction and quantum Monte Carlo methods shows very different variations with the CH distance: a marked decrease for neutral CH(Π2) and a perfect stability for ionized CH+(Σ1+). These results are consistent with strong/weak intensities of the CH vibrations in the neutral/ionized PAHs, the key point being the presence, or not, of a hole in the π shell. A topological analysis of the electronic densities shows that the collapse of the CH stretching with ionization is directly linked to the compensation between the internal charge transfer contribution and the distortion of the electronic density within the CH bond.
High current densities in a highly photoluminescent organic single-crystal light-emitting transistor
Authors: Sawabe Kosuke , Takenobu Taishi , Bisri Satria Zulkarnaen , Yamao Takeshi , Hotta Shu , Iwasa Yoshihiro
Published: August 2010

We report the improvement of electron transport in 5,5″-bis(biphenylyl)-2,2′:5′,2″-terthiophene (BP3T) single crystals on a field-effect transistor configuration by systematically investigating the effects of device aging under pure nitrogen and optimizing the organic dielectric layer-fabrication process. We reduced the effect of electron traps and achieved extremely high current densities up to 10 kA/cm2, which is one or two orders of magnitude greater than the current densities achieved in previous devices.
Evolution of the isotropic to nematic phase transition in binary mixtures of octylcyanobiphenyl and n-hexane
Authors: Sigdel K. P. , Iannacchione G. S.
Published: August 2010

High-resolution calorimetry has been performed to study the effect of dilution by a nonmesogenic, low-molecular weight solvent (linear n-hexane) on the isotropic-nematic (I-N) phase transition in the liquid crystal (LC) octylcyanobiphenyl (8CB) as a function of n-hexane concentration. Numerous temperature scans were performed without continuous mixing for pure 8CB and all mixture samples of n-hexane mole fraction ranging from xhex=0.02 to 0.12. The I-N specific heat peak remains first-order for all samples and shifts toward lower temperature nonlinearly while the two-phase I+N coexistence width broadens linearly with increasing xhex. Multiple heating and cooling scans are reproducible and indicate phase separation, if it occurs, must be on very short length scales and is reversible. These results may be a consequence of a competition between random dilution effects and the tendency to phase separate. It is shown that solvent dilution of a LC, if miscible and depending on solvent structure, can lead to a controlled altering of the intermolecular potentials and softening of the LC viscoelastic properties.
On the paradoxical relation between the melting temperature and forbidden energy gap of nanoparticles
Authors: Nanda K. K.
Published: August 2010

We comment on the paradox that seems to exist about a correlation between the size-dependent melting temperature and the forbidden energy gap of nanoparticles. By analyzing the reported expressions for the melting temperature and the band gap of nanoparticles, we conclude that there exists a relation between these two physical quantities. However, the variations of these two quantities with size for semiconductors are different from that of metals.
Aqueous-based synthesis of atomic gold clusters: Geometry and optical properties
Authors: Rath S. , Nozaki S. , Palagin D. , Matulis V. , Ivashkevich O. , Maki S.
Published: August 2010

Gold clusters synthesized by the solution-based growth technique have exhibited ultraviolet (UV) light emission with nearly zero Stokes shift. Atomic arrangement decided optical properties of the Au microclusters have been studied extensively. In addition to the time-of-flight mass spectra, the comparison of experimental and theoretical emission and absorption spectra confirms the presence of Au8 clusters with the planar hexagon+1-shaped geometry. The observed UV emission is attributed to the transition from the highest occupied to the lowest unoccupied molecular orbitals of the hexagon+1 structured Au8 clusters.
A test cassette for x-ray-exposure experiments at the National Ignition Facility
Authors: Fournier K. B. , Celeste J. , Rekow V. , Bopp D. R. , May M. J. , Fisher J. H. , Horton R. , Newlander C. D. , Jenkins P. , Trautz K.
Published: August 2010

We present the design and operation of a test cassette for exposure of samples to radiation environments at the National Ignition Facility. The cassette provides options for square and round samples and exposure areas; the cassette provides for multiple levels of filtration on a single sample, which allows dynamic range in experiments. The samples had normal lines of sight to the x-ray source in order to have uniform x-ray illumination. The incident x-radiation onto the samples was determined by the choice of filter thicknesses and materials. The samples were held at precise locations, accurate to within a few hundred microns, in the target chamber in order to have a known fluence incident. In the cassette, the samples were held in place in such a way that a minimal “line contact” allows them to have the maximal mechanical response to the x-ray load. We present postshot images of the debris found on films used for filters, and pre- and postexposure specimens.
Low voltage operation of plasma focus
Authors: Shukla Rohit , Sharma S. K. , Banerjee P. , Das R. , Deb P. , Prabahar T. , Das B. K. , Adhikary B. , Shyam A.
Published: August 2010

Plasma foci of compact sizes and operating with low energies (from tens of joules to few hundred joules) have found application in recent years and have attracted plasma-physics scientists and engineers for research in this direction. We are presenting a low energy and miniature plasma focus which operates from a capacitor bank of 8.4 μF capacity, charged at 4.2–4.3 kV and delivering approximately 52 kA peak current at approximately 60 nH calculated circuit inductance. The total circuit inductance includes the plasma focus inductance. The reported plasma focus operates at the lowest voltage among all reported plasma foci so far. Moreover the cost of capacitor bank used for plasma focus is nearly 20 U.S. dollars making it very cheap. At low voltage operation of plasma focus, the initial breakdown mechanism becomes important for operation of plasma focus. The quartz glass tube is used as insulator and breakdown initiation is done on its surface. The total energy of the plasma focus is approximately 75 J. The plasma focus system is made compact and the switching of capacitor bank energy is done by manual operating switch. The focus is operated with hydrogen and deuterium filled at 1–2 mbar.
Valley filter in strain engineered graphene
Authors: Fujita T. , Jalil M. B. A. , Tan S. G.
Published: August 2010

We propose a simple, yet highly efficient and robust device for producing valley polarized current in graphene. The device comprises of two distinct components; a region of uniform uniaxial strain, adjacent to an out-of-plane magnetic barrier configuration formed by patterned ferromagnetic stripes. We show that when the amount of strain, magnetic field strength, and Fermi level are properly tuned, the output current can be made to consist of only a single valley contribution. Perfect valley filtering is achievable within experimentally accessible parameters.
Magnetic behavior of SnO2 nanosheets at room temperature
Authors: Wang Cen , Ge Mingyuan , Jiang J. Z.
Published: August 2010

Magnetic behavior of SnO2 nanosheets has been investigated both experimentally and theoretically. It is found that SnO2 nanosheets with a thickness of 1.5–13 nm show ferromagnetic state at ambient temperature. First-principles calculations reveal that oxygen atoms at O-terminated surface in SnO2 sheet are spin polarized, resulting in magnetic moment of 1.6 μB for pure SnO2 nanosheet while Sn atoms just beneath the O-terminated surface contribute only −0.082 μB. This study will stimulate more investigations for understanding the origin of ferromagnetic TM-doped SnO2 (TM=3d transition metals) in particular case and TM-doped semiconductor oxides in general at ambient temperature and trigger further studies for magnetic behavior of low-dimensional systems which are nonmagnetic in bulk state.
Oxygen vacancy estimation of high k metal gate using thermal dynamic model
Authors: Chang H. L. , Liang M. S.
Published: August 2010

Oxygen vacancies are electronic defects in materials. In a metal oxide system, the distribution of such vacancies is determined by the oxygen affinity. This study predicts the oxygen vacancy concentration in a high-k/metal gate system using a developed thermal dynamic model. A system with Ti:N=2 has a 200 mV lower flat band voltage than an N rich metal. The Gibbs free energy of formation of oxygen vacancies, ∼0.5 eV, is derived from flab band voltage shifts and created neutral oxygen vacancy. The oxygen vacancy model based on estimating thermal dynamics is proposed.
Tuning carrier type and density in Bi2Se3 by Ca-doping
Authors: Wang Zhiyong , Lin Tao , Wei Peng , Liu Xinfei , Dumas Randy , Liu Kai , Shi Jing
Published: August 2010

The carrier type and density in Bi2Se3 single crystals are systematically tuned by introducing a calcium (Ca) dopant. A carrier density of ∼1×1017 cm−3 which corresponds to ∼25 meV in the Fermi energy is obtained in both n- and p-type materials. Electrical transport properties show that the insulating behavior is achieved in low carrier density crystals. In addition, both the band gap and reduced effective mass of carriers are determined.
Matching effect and dynamic phases of vortex matter in Bi2Sr2CaCu2O8 nanoribbon with a periodic array of holes
Authors: Avci S. , Xiao Z. L. , Hua J. , Imre A. , Divan R. , Pearson J. , Welp U. , Kwok W. K. , Crabtree G. W.
Published: August 2010

We report investigations on the dynamics of vortex matter with periodic pinning in crystalline Bi2Sr2CaCu2O8 nanoribbons containing an array of nanoscale holes. We found that the matching effect is enhanced near the melting field and persists to higher fields beyond the melting line. We attribute this enhancement to the existence of a soft-solid phase and a mixture of solid-liquid phases near the melting line, enabling the vortices to pin more effectively. We observed distinct regions in the voltage-current curves attributed to transitions of various dynamic phases which also account for the driving current dependent appearance of the matching effect.
Space charges and size effects in semiconducting ferroelectric BaTiO3/SrTiO3 superlattices
Authors: Liu Y. Y. , Li J. Y.
Published: August 2010

A continuum theory is developed to investigate the effects of space charges and size on ferroelectric superlattices, treating the ferroelectric perovskites as wide band-gap semiconductors instead of insulators, making it possible to couple the distribution of polarization and space charges through Maxwell’s equation. It is found that the space charges tend to accumulate near the superlattice interface, resulting in large electric field near the interface, and thus enhanced polarization and asymmetric hysteresis loop. It also eliminates the uniform polarization that would exist in the superlattice in the absence of space charges. The effect of superlattice thickness is also investigated, and good agreements with experiments are observed.
Potential micrometeoroid and orbital debris protection system using a gradient magnetic field and magnetic flux compression
Authors: Giffin A. , Shneider M. N. , Miles R. B.
Published: August 2010

A system for using a magnetic field in conjunction with conventional shielding configurations to protect against micrometeoroid and orbital debris is presented. Analytical, numerical, and experimental studies of a conductor moving through a gradient magnetic field have been performed. The results show that in the high magnetic Reynolds number regime a conducting object will experience large forces that tend to deform it while moving through the gradient field. Additionally a configuration using magnetic flux compression is introduced to act as a magnetic shock absorber. Separately or together, this technology may augment or replace current protection designs for space systems.
Cobalt dependence of the magneto-optical response in magnetoplasmonic nanodisks
Authors: González-Díaz J. B. , Sepúlveda B. , García-Martín A. , Armelles G.
Published: August 2010

In this work, we study the plasmon-mediated enhancement of the magneto-optical (MO) activity in the case of Au/Co/Au nanodisks as a function of the Co content. We show that both the spectral shape and amplitude of the complex polar Kerr rotation are modified by the relative amount of gold (diamagnetic) and cobalt (ferromagnetic). We demonstrate that such shape modification is dictated by the predominance of the absorptive or dispersive part of the MO constant in each material, which is intimately related to the origin of their MO activity.
Carrier hopping in disordered semiconducting polymers: How accurate is the Miller–Abrahams model?
Authors: Vukmirović Nenad , Wang Lin-Wang
Published: August 2010

We performed direct calculations of carrier hopping rates in strongly disordered conjugated polymers based on the atomic structure of the system, the corresponding electronic states and their coupling to all phonon modes. We found that the dependence of hopping rates on distance and the dependence of the mobility on temperature are significantly different than the ones stemming from the simple Miller–Abrahams model, regardless of the choice of the parameters in the model. A model that satisfactorily describes the hopping rates in the system and avoids the explicit calculation of electron–phonon coupling constants was then proposed and verified. Our results indicate that, in addition to electronic density of states, the phonon density of states and the spatial overlap of the wave functions are the quantities necessary to properly describe carrier hopping in disordered conjugated polymers.
Strong coupling between on chip notched ring resonator and nanoparticle
Authors: Wang S. , Broderick K. , Smith H. , Yi Y.
Published: August 2010

We have demonstrated a new photonic structure to achieve strong optical coupling between nanoparticle and photonic molecule by utilizing a notched microring resonators. By creating a notch in the ring resonator and putting a nanoparticle inside the notch, large spectral shifts and splittings at nanometer scale can be achieved, compared to only picometer scale observed by fiber tip evanescently coupled to the surface of microsphere, thereby significantly lowered the quality factor requirement for single nanoparticle detection. The ability for sorting the type of nanoparticles due to very different mode shift and splitting behavior of dielectric and metallic nanoparticles is also emphasized.
Quantum well saturable absorber mirror with electrical control of modulation depth
Authors: Liu Xiaomin , Rafailov Edik U. , Livshits Daniil , Turchinovich Dmitry
Published: August 2010

We demonstrate a quantum well (QW) semiconductor saturable absorber mirror (SESAM) comprising low-temperature grown InGaAs/GaAs QWs incorporated into a p-i-n structure. By applying the reverse bias voltage in the range 0–2 V to the p-i-n structure, we were able to change the SESAM modulation depth in the range 2.5–0.5%, as measured by nonlinear reflectivity of 450 fs long laser pulses with 1065 nm central wavelength, in the pump fluence range 1.6–26.7 μJ/cm2. This electrical control of the modulation depth is achieved by controlling the small-signal loss of the SESAM via quantum-confined Stark effect in the QWs.
Photonic crystal nanobeam lasers
Authors: Zhang Y. , Khan M. , Huang Y. , Ryou J. , Deotare P. , Dupuis R. , Lončar M.
Published: August 2010

Photonic crystal lasers operating at room temperature based on high Q/V nanobeam cavities have been demonstrated. We reported a large spontaneous emission factor (β∼0.97) by fitting the L-L curve with the rate equations.
Self-assembled GaAs islands on Si by droplet epitaxy
Authors: Somaschini C. , Bietti S. , Koguchi N. , Montalenti F. , Frigeri C. , Sanguinetti S.
Published: August 2010

We presented an innovative fabrication technique for the self-assembly of GaAs islands on Si substrates by droplet epitaxy. The islands show highly tunable density (from 107 to some 109 islands/cm2) and size (from 75 to 250 nm), and small size dispersion (below 10%). The islands, made by single relaxed crystals with lattice parameters close to the GaAs bulk, show well defined shapes, with a high aspect ratio. The low thermal budget required for the island self-assembly, together with the high scalability of the process, make these islands good candidates for local artificial substrates or local strain sources with the required lattice parameters, band alignment, and crystalline quality as now required for the implementation of high quality devices on Si.
The Mythical Forest, the Becoming-Desert: Environmental Knowledge Production and the Iconography of Destruction in the Gran Sabana, Venezuela
Authors: Sletto Bjørn
Published: August 2010

Landscape managers increasingly draw on indigenous practices of controlled burning to develop vegetation heterogeneity and reduce fuel loads, thereby avoiding extensive and destructive fires. However, anthropogenic fire is also commonly represented as a primary driver of environmental change, which in some places has led to an emphasis on heavy-handed fire suppression rather than fire management. These contradictions in global fire management are an example of the complex articulations between the social production of tropical landscapes and the processes of environmental knowledge production. This article draws on constructivist approaches in political ecology and Lacanian psychoanalysis to analyze a conflict between state agencies and indigenous people surrounding fire management in the Gran Sabana, Venezuela. Iconic features of this cultural landscape operate as signifiers in institutional discourse, informing the ways in which environmental knowledge is appropriated and produced and in turn shaping the subjectivities and practices of state fire managers.
Xeriscape People and the Cultural Politics of Turfgrass Transformation
Authors: Mustafa Daanish , Smucker Thomas A , Ginn Franklin , Johns Rebecca , Connely Shanon
Published: August 2010

Turfgrass yards dominate the residential landscapes of St Petersburg, Florida, and much of the rest of the urban and suburban United States. Increasingly, alternatives to the resource-intensive turfgrass lawn are the focus of interest among environmentalists, state and county governments, and growing numbers of residents in cities in the water-scarce Southeast and Southwest. Drawing on ethnographic and survey field research on everyday yard practices, resource use, and landscape perceptions, we explore the environmental and cultural dilemmas presented by the choice between conventional turfgrass and the more environmentally benign xeriscaping. We engage with Bourdieu's notions of habitus, field, and distinction to explore how local and personal scale yards, as produced and consumed technonatures, mediate the scales of global environmentalism, national and regional cultural identities, classed aesthetics, and personal and collective security. We find that xeriscaping does not increase proportionate to income. We argue that yards are a display of cultural capital and that xeriscapers are invested in an environmentalist field that operates at an imagined global scale as opposed to the neighborhood and national scale values invoked with the traditional turfgrass lawn. Referring to Bourdieu's work on taste and distinction, we argue that xeriscaped landscapes may entail a more environmentally benign set of landscaping practices but that the adoption of xeriscaping is no less implicated in the reproduction of privilege and distinction than is the traditional turfgrass lawn.
Ecotourism: The Modern Predator? Implications of Gorilla Tourism on Local Livelihoods in Bwindi Impenetrable National Park, Uganda
Authors: Laudati Ann
Published: August 2010

The role of ecotourism as a means of influencing the path of local development or encouraging conservation activities is not unproblematic. Indeed, an increasing body of literature not only challenges the assumed benevolence of ecotourism but critically questions the role of ecotourism in contributing to the greater social and economic justice so often assumed under these programs. This paper seeks to contribute to this growing body of critical literature through an analysis of the impact of ecotourism on the everyday lives of rural villagers adjacent to Bwindi Impenetrable National Park, Uganda, paying particular attention to the social forms of access to and control over the process through which decisions about ecotourism take place. Drawing on a year of ethnographic-based fieldwork, this paper focuses on how the commodification of Bwindi as a product of wilderness, a wild and unspoilt destination marketed to foreign visitors, promotes the external control of conservation spaces by international organizations that ultimately contribute to, rather than alleviate, poverty and dependency in local communities. Beyond providing just another case study, however, this analysis argues that the ‘new’ relations between people and parks created under ecotourism in Bwindi have in actuality created new forms of control and vulnerabilities.
Landscape, Territory, and Civil Society in Catalonia
Authors: Nogué Joan , Wilbrand Stephanie
Published: August 2010

In recent decades intense territorial transformations in European Mediterranean countries have caused radical changes in their landscapes, with a resulting impact on the territorial identity of local societies. Faced with the risk of irreversible loss of sense of place and of local identity, as a result of nonconsensual processes almost always poorly explained by the administration, civil society has recently reacted in an increasingly indignant and organized manner, demanding a new culture of territory. This article analyzes, in the case of Catalonia, the interaction between landscape, territory, and civil society and demonstrates that this interaction, organized in a large number of associations in defence of territorial identity, has shown itself to be extraordinarily vital and dynamic. In this context, landscape has been revealed as the catalyst and unifying element of growing conflicts of a territorial and environmental nature palpable in Catalan society.
Strong and long: Effects of word length on phonological binding in verbal short-term memory
Authors: Jefferies Elizabeth , Frankish Clive , Noble Katie
Published: August 2010

This study examined the effects of item length on the contribution of linguistic knowledge to immediate serial recall (ISR). Long words are typically recalled more poorly than short words, reflecting the greater demands that they place on phonological encoding, rehearsal, and production. However, reverse word length effects—that is, better recall of long than short words—can also occur in situations in which phonological maintenance is difficult, suggesting that long words derive greater support from long-term lexical knowledge. In this study, long and short words and nonwords (containing one vs. three syllables) were presented for immediate serial recall in (a) pure lists and (b) unpredictable mixed lists of words and nonwords. The mixed-list paradigm is known to disrupt the phonological stability of words, encouraging their phonemes to recombine with the elements of other list items. In this situation, standard length effects were seen for nonwords, while length effects for words were absent or reversed. A detailed error analysis revealed that long words were more robust to the mixed-list manipulation than short words: Their phonemes were less likely to be omitted and to recombine with phonemes from other list items. These findings support an interactive view of short-term memory, in which long words derive greater benefits from lexical knowledge than short words—especially when their phonological integrity is challenged by the inclusion of nonwords in mixed lists.
From Left to Right: Processing Acronyms Referring to Names of Political Parties Activates Spatial Associations
Authors: van Elk Michiel , van Schie Hein T. , Bekkering Harold
Published: August 2010

In line with previous studies, showing that abstract concepts like “power” or “god” implicitly activate spatial associations, in the present study we hypothesized that spatial associations are coactivated during the processing of acronyms referring to names of political parties as well. In four studies, it was found that the reading of these acronyms was accompanied by the implicit activation of spatial left–right associations. That is, participants responded faster to left-wing parties by means of a left-hand button press and vice versa for right-wing parties (Experiments 1 to 3), and participants responded faster when a political acronym was presented at the side of the screen corresponding to the political orientation of the acronym (Experiment 4). Interestingly, a correlation was observed between the effect size for left-wing parties and participants’ political preferences, suggesting that the reaction time effects reflect the perceived distance of a party to one's own political orientation. Together these findings indicate that spatial representations activated in response to political acronyms do not simply reflect lexical–semantic associations or spatial metaphors, but representations of parties’ political orientation relative to one's own sociopolitical position.
Lesions in the anterior thalamic nuclei of rats do not disrupt acquisition of stimulus sequence learning
Authors: Aggleton John P. , Amin Eman , Jenkins Trisha A. , Pearce John M. , Robinson Jasper
Published: August 2010

Sequence learning and spatial alternation were examined in rats with anterior thalamic lesions or sham surgeries. There was a lesion-induced deficit in spatial alternation but not in sequence learning. During sequence learning, rats discriminated between six different sequentially presented compounds (e.g., reinforce A before B, but not B before A), composed of audio-visual elements. The solution required rats to learn both specific stimulus sequences and the reward contingencies associated with these specific temporal relationships. The failure of anterior thalamic lesions to affect the acquisition of this sequential configural task complements the recent finding that anterior thalamic lesions also spare the acquisition of a configural task involving specific stimulus pairings and their spatial relationships. These findings suggest that such “structural” learning is more reliant on cortico-hippocampal than thalamo-hippocampal interactions.
Development of a vocabulary of object shapes in a child with a very-early-acquired visual agnosia: A unique case
Authors: Funnell Elaine , Wilding John
Published: August 2010

We report a longitudinal study of an exceptional child (S.R.) whose early-acquired visual agnosia, following encephalitis at 8 weeks of age, did not prevent her from learning to construct an increasing vocabulary of visual object forms (drawn from different categories), albeit slowly. S.R. had problems perceiving subtle differences in shape; she was unable to segment local letters within global displays; and she would bring complex scenes close to her eyes: a symptom suggestive of an attempt to reduce visual crowding. Investigations revealed a robust ability to use the gestalt grouping factors of proximity and collinearity to detect fragmented forms in noisy backgrounds, compared with a very weak ability to segment fragmented forms on the basis of contrasts of shape. When contrasts in spatial grouping and shape were pitted against each other, shape made little contribution, consistent with problems in perceiving complex scenes, but when shape contrast was varied, and spatial grouping was held constant, S.R. showed the same hierarchy of difficulty as the controls, although her responses were slowed. This is the first report of a child's visual–perceptual development following very early neurological impairments to the visual cortex. Her ability to learn to perceive visual shape following damage at a rudimentary stage of perceptual development contrasts starkly with the loss of such ability in childhood cases of acquired visual agnosia that follow damage to the established perceptual system. Clearly, there is a critical period during which neurological damage to the highly active, early developing visual–perceptual system does not prevent but only impairs further learning.
Towards a scalable, open-standards service for brokering cross-protocol data transfers across multiple sources and sinks
Authors: Meredith David , Crouch Stephen , Galang Gerson , Jiang Ming , Nguyen Hung , Turner Peter
Published: August 2010

Data Transfer Service (DTS) is an open-source project that is developing a document-centric message model for describing a bulk data transfer activity, with an accompanying set of loosely coupled and platform-independent components for brokering the transfer of data between a wide range of (potentially incompatible) storage resources as scheduled, fault-tolerant batch jobs. The architecture scales from small embedded deployments on a single computer to large distributed deployments through an expandable ‘worker-node pool’ controlled through message-orientated middleware. Data access and transfer efficiency are maximized through the strategic placement of worker nodes at or between particular data sources/sinks. The design is inherently asynchronous, and, when third-party transfer is not available, it side-steps the bandwidth, concurrency and scalability limitations associated with buffering bytes directly through intermediary client applications. It aims to address geographical–topological deployment concerns by allowing service hosting to be either centralized (as part of a shared service) or confined to a single institution or domain. Established design patterns and open-source components are coupled with a proposal for a document-centric and open-standards-based messaging protocol. As part of the development of the message protocol, a bulk data copy activity document is proposed for the first time.
The design and implementation of a workflow analysis tool
Authors: Curcin Vasa , Ghanem Moustafa , Guo Yike
Published: August 2010

Motivated by the use of scientific workflows as a user-oriented mechanism for building executable scientific data integration and analysis applications, this article introduces a framework and a set of associated methods for analysing the execution properties of scientific workflows. Our framework uses a number of formal modelling techniques to characterize the process and data behaviour of workflows and workflow components and to reason about their functional and execution properties. We use the framework to design the architecture of a customizable tool that can be used to analyse the key execution properties of scientific workflows at authoring stage. Our design is generic and can be applied to a wide variety of scientific workflow languages and systems, and is evaluated by building a prototype of the tool for the Discovery Net system. We demonstrate and discuss the utility of the framework and tool using workflows from a real-world medical informatics study.
Adoption of e-Infrastructure services: configurations of practice
Authors: Voss Alex , Asgari-Targhi Marzieh , Procter Rob , Fergusson David
Published: August 2010

This paper reports findings from a study of researchers and research-computing support staff. It explores examples of the social relations supporting the adoption, adaptation and domestication of e-Research technologies and e-Infrastructures and makes recommendations for funding organizations, technology suppliers, service providers and institutions.
Global hydrology modelling and uncertainty: running multiple ensembles with a campus grid
Authors: Gosling Simon N. , Bretherton Dan , Haines Keith , Arnell Nigel W.
Published: August 2010

Uncertainties associated with the representation of various physical processes in global climate models (GCMs) mean that, when projections from GCMs are used in climate change impact studies, the uncertainty propagates through to the impact estimates. A complete treatment of this ‘climate model structural uncertainty’ is necessary so that decision-makers are presented with an uncertainty range around the impact estimates. This uncertainty is often underexplored owing to the human and computer processing time required to perform the numerous simulations. Here, we present a 189-member ensemble of global river runoff and water resource stress simulations that adequately address this uncertainty. Following several adaptations and modifications, the ensemble creation time has been reduced from 750 h on a typical single-processor personal computer to 9 h of high-throughput computing on the University of Reading Campus Grid. Here, we outline the changes that had to be made to the hydrological impacts model and to the Campus Grid, and present the main results. We show that, although there is considerable uncertainty in both the magnitude and the sign of regional runoff changes across different GCMs with climate change, there is much less uncertainty in runoff changes for regions that experience large runoff increases (e.g. the high northern latitudes and Central Asia) and large runoff decreases (e.g. the Mediterranean). Furthermore, there is consensus that the percentage of the global population at risk to water resource stress will increase with climate change.
Cooperation for direct fitness benefits
Authors: Leimar Olof , Hammerstein Peter
Published: August 2010

Studies of the evolution of helping have traditionally used the explanatory frameworks of reciprocity and altruism towards relatives, but recently there has been an increasing interest in other kinds of explanations. We review the success or otherwise of work investigating alternative processes and mechanisms, most of which fall under the heading of cooperation for direct benefits. We evaluate to what extent concepts such as by-product benefits, pseudo-reciprocity, sanctions and partner choice, markets and the build-up of cross-species spatial trait correlations have contributed to the study of the evolution of cooperation. We conclude that these alternative ideas are successful and show potential to further increase our understanding of cooperation. We also bring up the origin and role of common interest in the evolution of cooperation, including the appearance of organisms. We note that there are still unresolved questions about the main processes contributing to the evolution of common interest. Commenting on the broader significance of the recent developments, we argue that they represent a justified balancing of the importance given to different major hypotheses for the evolution of cooperation. This balancing is beneficial because it widens considerably the range of phenomena addressed and, crucially, encourages empirical testing of important theoretical alternatives.
Apoptosis-promoted tumorigenesis: γ-irradiation-induced thymic lymphomagenesis requires Puma-driven leukocyte death
Authors: Michalak Ewa M. , Vandenberg Cassandra J. , Delbridge Alex R.D. , Wu Li , Scott Clare L. , Adams Jerry M. , Strasser Andreas
Published: August 2010

Although tumor development requires impaired apoptosis, we describe a novel paradigm of apoptosis-dependent tumorigenesis. Because DNA damage triggers apoptosis through p53-mediated induction of BH3-only proteins Puma and Noxa, we explored their roles in γ-radiation-induced thymic lymphomagenesis. Surprisingly, whereas Noxa loss accelerated it, Puma loss ablated tumorigenesis. Tumor suppression by Puma deficiency reflected its protection of leukocytes from γ-irradiation-induced death, because their glucocorticoid-mediated decimation in Puma-deficient mice activated cycling of stem/progenitor cells and restored thymic lymphomagenesis. Our demonstration that cycles of cell attrition and repopulation by stem/progenitor cells can drive tumorigenesis has parallels in human cancers, such as therapy-induced malignancies.
The epigenome and the mitochondrion: bioenergetics and the environment
Authors: Wallace Douglas C.
Published: August 2010

In the July 15, 2010, issue of Genes & Development, Yoon and colleagues (pp. 1507–1518) report that, in a siRNA knockdown survey of 6363 genes in mouse C2C12 cells, they discovered 150 genes that regulated mitochondrial biogenesis and bioenergetics. Many of these genes have been studied previously for their importance in regulating transcription, protein and nucleic acid modification, and signal transduction. Some notable examples include Brac1, Brac2, Pax4, Sin3A, Fyn, Fes, Map2k7, Map3k2, calmodulin 3, Camk1, Ube3a, and Wnt. Yoon and colleagues go on to validate their observations by extensively documenting the role of Wnt signaling in the regulation of mitochondrial function.
Preparation of Very-High-Yield Recombinant Proteins Using Novel High-Cell-Density Bacterial Expression Methods
Authors: Murray Victoria , Chen Jianglei , Huang Yuefei , Li Qianqian , Wang Jianjun
Published: August 2010

INTRODUCTION

Using bacterial hosts such as Escherichia coli to produce recombinant proteins is a common practice in many laboratories. Here, we describe a protocol for preparing very-high-yield recombinant proteins using novel high-cell-density bacterial expression methods. By combining strictly regulated traditional isopropyl-β-D-thiogalactopyranoside (IPTG) induction with high-cell-density auto-induction, we have developed an efficient bacterial expression method that can be used widely and does not require changing expression vectors or fermentation. Beginning with a newly created bacterial expression vector, we outline the specific steps to determine whether the vector expresses the target protein, select high-expression colonies of the target protein, and optimize expression conditions for very-high-yield protein production. This method routinely produces 15-35 mg of pure protein from 50-mL bacterial cell cultures.
High-Throughput Microscopy Using Live Mammalian Cells
Authors: Terjung Stefan , Walter Thomas , Seitz Arne , Neumann Beate , Pepperkok Rainer , Ellenberg Jan
Published: August 2010

INTRODUCTION

Since the complete sequencing of several genomes, the systematic understanding of protein function and interaction has become one of the most important tasks in current molecular biology. Recent advances in light microscopy equipment regarding automation and acquisition speed offer the possibility to perform hundreds of experiments in parallel to study protein function and interaction in intact cells. In this context, live cell imaging is an excellent tool that may be used to investigate dynamic or rarely occurring cellular processes, to distinguish between primary and secondary phenotypes, and to study the phenotype kinetics. In this article, we present a guideline for high-throughput microscopy for functional screening in living cells. We shall examine each aspect of the general screening process and consider specific examples in the processing of time-lapse experiments. Although this article is largely based on examples from cultured mammalian cells, many of its considerations apply to cultured cells from other species such as Drosophila and to some extent to microscopy-based screening in small organisms such as Caenorhabditis elegans.
Moenkhausia celibela: a new species from the Amazon basin, Brazil (Characiformes: Characidae)
Authors: Marinho M. M. F. , Langeani F.
Published: August 2010

A new species of Characidae, Moenkhausia celibela, is described from the Rio Amazonas at Santarém, Rio Maraú, several localities in the Rio Tapajós, Rio Curuá‐Una, Rio Xingu and Rio Jari, all from the Amazon basin, Brazil. The new species is distinguished from its congeners, except species included in Géry's 1992 Moenkhausia lepidura group, by presenting a dark blotch on the upper caudal‐fin lobe, and the lower lobe is hyaline or light grey. Moenkhausia celibela is distinguished from the species of the M. lepidura group by the absence of a humeral spot and the presence of a roughly triangular and dark spot at the caudal‐fin base, extending posteriorly along the middle caudal‐fin rays, and distinctly separate from the spot on the upper caudal‐fin lobe.
Obtusilactone A and (−)‐sesamin induce apoptosis in human lung cancer cells by inhibiting mitochondrial Lon protease and activating DNA damage checkpoints
Authors: Wang Hui‐Min , Cheng Kuo‐Chen , Lin Cheng‐Jung , Hsu Shu‐Wei , Fang Wei‐Cheng , Hsu Tai‐Feng , Chiu Chien‐Chih , Chang Hsueh‐Wei , Hsu Chun‐Hua , Lee Alan Yueh‐Luen
Published: August 2010

Several compounds from Cinnamomum kotoense show anticancer activities. However, the detailed mechanisms of most compounds from C. kotoense remain unknown. In this study, we investigated the anticancer activity of obtusilactone A (OA) and (−)‐sesamin in lung cancer. Our results show that human Lon is upregulated in non‐small‐cell lung cancer (NSCLC) cell lines, and downregulation of Lon triggers caspase‐3 mediated apoptosis. Through enzyme‐based screening, we identified two small‐molecule compounds, obtusilactone A (OA) and (−)‐sesamin from C. kotoense, as potent Lon protease inhibitors. Obtusilactone A and (−)‐sesamin interact with Ser855 and Lys898 residues in the active site of the Lon protease according to molecular docking analysis. Thus, we suggest that cancer cytotoxicity of the compounds is partly due to the inhibitory effects on Lon protease. In addition, the compounds are able to cause DNA double‐strand breaks and activate checkpoints. Treatment with OA and (−)‐sesamin induced p53‐independent DNA damage responses in NSCLC cells, including G1/S checkpoint activation and apoptosis, as evidenced by phosphorylation of checkpoint proteins (H2AX, Nbs1, and Chk2), caspase‐3 cleavage, and sub‐G1 accumulation. In conclusion, OA and (−)‐sesamin act as both inhibitors of human mitochondrial Lon protease and DNA damage agents to activate the DNA damage checkpoints as well induce apoptosis in NSCLC cells. These dual functions open a bright avenue to develop more selective chemotherapy agents to overcome chemoresistance and sensitize cancer cells to other chemotherapeutics. (Cancer Sci 2010; 101: 2612–2620)
Differential role of repair proteins, BRCA1/NBS1 and Ku70/DNA‐PKcs, in radiation‐induced centrosome overduplication
Authors: Shimada Mikio , Kobayashi Junya , Hirayama Ryoichi , Komatsu Kenshi
Published: August 2010

Centrosomes are important cytoplasmic organelles involved in chromosome segregation, defects in which can result in aneuploidy, and contribute to tumorigenesis. It is known that DNA damage causes the supernumerary centrosomes by a mechanism in which centrosomes continue to duplicate during cell cycle arrest at checkpoints. We show here that ionizing radiation induces the overduplication of centrosomes in a dose‐dependent manner, and that the level of overduplication is pronounced in BRCA1‐ and NBS1‐deficient cells, even though their checkpoint control is abrogated. Conversely, marginal increases in overduplication were observed in Ku70‐ and DNA‐PKcs‐deficient cells, which are intact in checkpoint control. The frequency of radiation‐induced overduplication of centrosomes might be associated with DNA repair, as it was decreased with reduced cell killing after protracted exposures to radiation. As a result, when the frequency of radiation‐induced centrosome overduplication was plotted against radiation‐induced cell killing, similar curves were seen for both protracted and acute exposures in wild‐type cells, Ku70‐deficient, and DNA‐PKcs‐deficient cells, indicating a common mechanism for centrosome overduplication. However, the absence of either BRCA1 or NBS1 enhanced radiation‐induced overduplication frequencies by 2–4‐fold on the basis of the same cell killing. These results suggest that radiation‐induced centrosome overduplication is regulated by at least two mechanisms: a checkpoint‐dependent pathway involved in wild‐type cells, Ku70‐deficient and DNA‐PKcs‐deficient cells; and a checkpoint‐independent pathway as observed in BRCA1‐deficient and NBS1‐deficient cells. (Cancer Sci 2010; 101: 2531–2537)
Mite allergen induces nitric oxide production in alveolar macrophage cell lines via CD14/toll‐like receptor 4, and is inhibited by surfactant protein D
Authors: Liu C.‐F. , Chen Y.‐L. , Chang W.‐T. , Shieh C.‐C. , Yu C.‐K. , Reid K. B. M. , Wang J.‐Y.
Published: August 2010

Background
Previously, we have found that dust mite allergens can directly activate alveolar macrophages (AMs), induce inflammatory cytokines, and enhance T‐helper type 2 cytokine production. A molecule of innate immunity in the lung, surfactant protein D (SP‐D), is able to bind mite allergens and alleviates allergen‐induced airway inflammation.

Objectives
This study was aimed at investigating the activation pathway of mite allergen (Dermatophagoides pteronyassinus, Der p)‐induced nitric oxide (NO) production by AMs, and the role of SP‐D in the modulation of activated AMs by mite allergens.

Methods
Porcine SP‐D was purified from bronchoalveolar lavage fluids of Lan‐Yu mini‐pigs, by affinity chromatography on maltose‐sepharose. NO production, inducible expression of lipopolysaccharides (LPS)‐related binding and responding surface receptors complex, CD14 and toll‐like receptor 4 (TLR4), as well as inducible NO synthase (iNOs) and nuclear factor‐κB activation were studied in two AMs cell lines, MH‐S (BALB/c strain),and AMJ2‐C11 (C57BL/6 strain), and one peritoneal macrophage cell line (RAW264.7), after stimulation with LPS, or Der p.

Results
LPS and Der p elicited different responses of NO production in the different cell lines, and the response might depend upon the expression of the cell surface CD14/TLR4 complex in different genetic backgrounds of macrophage cell lines. Pretreatment of macrophages with SP‐D could inhibit NO production from Der p or LPS‐stimulated alveolar macrophages.

Conclusion
Mite allergen‐induced alveolar macrophage activation is mediated by CD14/TLR4 receptors and can be inhibited by SP‐D; it further supports the concept that SP‐D may be an important modulator of allergen‐induced pulmonary inflammation.