bluuebunny/crossref_metadata_2025 huggingface dataset:
Three-dimensional structure of the buffer/absorber interface in CdS/CuGaSe2 based thin film solar cells
Authors: Rusu M. , Bär M. , Lehmann S. , Sadewasser S. , Weinhardt L. , Kaufmann C. A. , Strub E. , Röhrich J. , Bohne W. , Lauermann I. , Jung Ch. , Heske C. , Lux-Steiner M. Ch.
Published: October 2009

The chemical structure of the CdS/CuGaSe2 chalcopyrite solar cell buffer/absorber interface is investigated by combining element depth profiling using elastic recoil detection analysis and surface-near bulk sensitive x-ray emission spectroscopy. Significant Cd and S concentrations (≥0.1 at. %) are found deep in the absorber bulk. The determined high Cd and S diffusion coefficient values at 333 K of 3.6 and 3.4×10−12 cm2/s, respectively, are attributed to diffusion along CuGaSe2 grain boundaries. As a result, a three-dimensional buffer/absorber interface geometry is proposed.
Two-dimensional growth of SrTiO3 thin films on (001) MgO substrates using pulsed laser deposition and reflection high energy electron diffraction
Authors: McMitchell S. R. C. , Tse Y. Y. , Bouyanfif H. , Jackson T. J. , Jones I. P. , Lancaster M. J.
Published: October 2009

Two-dimensional epitaxial growth of SrTiO3 is achieved on MgO, a substrate presenting a large lattice mismatch of 7.9%. In situ reflection high energy electron diffraction (RHEED) is used to monitor and control the growth. An interval deposition technique is implemented to force the two-dimensional growth. It is necessary to deposit a single atomic layer of TiO2 before SrTiO3 to prevent the formation of high energy SrO/MgO interfaces and so allow the film to completely wet the substrate surface. Defect formation is inhibited. The resulting film exhibits a similar surface to the substrate and shows a streaky RHEED pattern.
Scanning tunneling microscopy with single crystalline W[001] tips: High resolution studies of Si(557)5×5 surface
Authors: Chaika A. N. , Semenov V. N. , Glebovskiy V. G. , Bozhko S. I.
Published: October 2009

Single crystalline [001]-oriented tungsten tips have been applied for high resolution scanning tunneling microscopy (STM) studies of a Si(557) surface consisting of triple steps and 5×5-reconstructed Si(111) terraces. High stability of the W[001] tips allowed us to measure atomically resolved images of this unusual Si(557) reconstruction at various tunneling parameters and propose a model of its atomic structure. STM experiments show that even for nonideal probe geometry a realistic apex configuration can be drawn from the known crystallographic orientation and the tip behavior.
Relaxation and emittance growth of a thermal charged-particle beam
Authors: Teles Tarcísio N. , Pakter Renato , Levin Yan
Published: October 2009

We present a theory that allows us to accurately calculate the distribution functions and the emittance growth of a thermal charged-particle beam after it relaxes to equilibrium. The theory can be used to obtain the fraction of particles, which will evaporate from the beam to form a halo. The calculated emittance growth is found to be in excellent agreement with the simulations.
Effects of hydration levels on the bandwidth of microwave resonant absorption induced by confined acoustic vibrations
Authors: Liu Tzu-Ming , Chen Hung-Pin , Yeh Shih-Chia , Wu Chih-Yu , Wang Chung-Hsiung , Luo Tang-Nian , Chen Yi-Jan , Liu Shen-Iuan , Sun Chi-Kuang
Published: October 2009

We found the hydration levels on the capsid surface of viruses can affect the bandwidth of microwave resonant absorption (MRA) induced by the confined acoustic vibrations (CAV). By decreasing the pH value of solution down to 5.2 or inactivating the capsid proteins, we enhanced the surface hydrophilicity and increased the magnitude of surface potentials. Both of these surface manipulations raised the surface affinity to water molecules and narrowed the bandwidths of CAV-induced MRA. Our results validate the viscoelastic transition of hydration shells.
Charge-transfer induced surface conductivity for a copper based inorganic-organic hybrid
Authors: Arkenbout Anne H. , Uemura Takafumi , Takeya Jun , Palstra Thomas T. M.
Published: October 2009

Inorganic-organic hybrids are receiving increasing attention as they offer the opportunity to combine the robust properties of inorganic materials with the versatility of organic compounds. We have studied the electric properties of an inorganic-organic hybrid with the chemical formula: CuCl4(C6H5CH2CH2NH3)2. This material is a ferromagnetic insulator that can easily be processed from solution. We show that the surface conductivity of the hybrid can be increased by five orders of magnitude by covering the surface with an organic electron donor. This constitutes a novel method to dope perovskite-based materials and study their charge transport properties.
Spatial updating in the great grand canonical ensemble
Authors: Orkoulas G. , Noon Daniel P.
Published: October 2009

In spatial updating grand canonical Monte Carlo, particle transfers are implemented by examining the local environment around a point in space. In the present work, these algorithms are extended to very high densities by allowing the volume to fluctuate, thus forming a great grand canonical ensemble. Since fluctuations are unbounded, a constraint must be imposed. The constrained ensemble may be viewed as a superposition of either constant-pressure or grand canonical ensembles. Each simulation of the constrained ensemble requires a set of weights that must be determined iteratively. The outcome of a single simulation is the density of states in terms of all its independent variables. Since all extensive variables fluctuate, it is also possible to estimate absolute free energies and entropies from a single simulation. The method is tested on a system of hard spheres and the transition from the fluid to a face-centered cubic crystal is located with high precision.
Anomalous scaling during glancing angle deposition
Authors: Mukherjee S. , Gall D.
Published: October 2009

Metallic nanorods grown by glancing angle deposition at Ts=300–1123 K exhibit self-affine scaling, where the average rod width w increases with height h according to w∝hp. The growth exponent p for the investigated metals (Ta, Nb, and Cr) varies with temperature and material but collapses onto a single curve when plotted against the homologous temperature θ=Ts/Tm. It decreases from p=0.5 at θ=0 to 0.39 at θ=0.22, consistent with reported theoretical predictions, but exhibits a transition to an anomalous value of p=0.7 at θ=0.26, followed by a decrease to 0.33 at θ=0.41. The cause for the anomalous scaling at 0.24≤θ≤0.34 is unknown but may be due to a gradual transition from two-dimensional to three-dimensional surface island growth.
Social-Activity Travel: Do the ‘Strong-Tie Relationships’ of a Person Exist in the Same Community? The Case of Switzerland
Authors: Ohnmacht Timo
Published: October 2009

In the relatively new field of social-activity travel behavior research, it has often been stated that social relationships have become increasingly physically dispersed in various contemporary societies. If so, this dynamic has enormous consequences on both travel behavior and social support. More explicitly, people have to travel some distance in order to meet, they need to plan their social activities further ahead of time, and, sociologically speaking, they are at risk of weakening their relationships to friends, immediate family, relatives, etc due to spatial distance. In this paper a binominal logit model was used to examine the characteristics of Swiss citizens who had named nonlocal strong-tie relationships in a nationwide representative survey. The empirical findings show various characteristics that increase the likelihood of having strong-tie relationships outside one's community, such as one-person households, higher education, younger cohorts, long-distance commuting, and, interestingly, people who want to spend more time with friends. I elaborate a discussion of these findings as they concern recent debates in the field of social-activity travel behavior.
Cognitive Process Model of Individual Choice Behaviour Incorporating Principles of Bounded Rationality and Heterogeneous Decision Heuristics
Authors: Zhu Wei , Timmermans Harry
Published: October 2009

Although the principle of bounded rationality seems more realistic for formulating formal models of individual choice behaviour than traditional decision-outcome-based discrete choice models, existing studies have some limitations: (1) applications focus on the noncompensatory nature of the models and largely ignore the factor-selection process; (2) heterogeneity of heuristics in reaching a decision is insufficiently studied; (3) the choice of decision strategy is rarely modeled formally. A modeling approach that simultaneously deals with these issues is suggested. Factor thresholds are used as the mechanism for factor selection and representation, resulting in a set of activated and nonactivated factor states. Under the assumption of stochastic contextual effects, the model automatically generates heterogeneous decision heuristics, including the conjunctive, disjunctive, and lexicographic rule. Mental effort and risk perception are assumed to influence the evaluation and choice of heuristics. The concept of preference tolerance is used to predict the probability of selecting a particular heuristic under different decision contexts. The modeling approach is illustrated using the go-home decision of pedestrians in a shopping street in China as an example.
Rewarding Responsibility? Long-Term Unemployed Men and the Welfare-to-Work Agenda
Authors: Ray Kathryn , Hoggart Lesley , Taylor Rebecca , Vegeris Sandra , Campbell-Barr Verity
Published: October 2009

In this paper we explore the responses of a group of long-term unemployed men to chronic labour market insecurity and ‘active’ labour market policies promoting individual responsibility for employability. We draw from an evaluation of a recent pilot scheme: the UK Employment Retention and Advancement Demonstration. We identify a range of responses, shaped through experiences which reflect gender, class, and age divisions. Despite significant labour market disadvantage, some of the men responded by proactively engaging with the employability agenda. Drawing on qualitative longitudinal data, we follow the trajectories of the men in work, examining how they fared in insecure, precarious labour markets. We conclude by looking at the strengths and limitations of the current policy agenda, suggesting that more creative ways need to be found to engage some of the most disadvantaged in the reskilling agenda and that employers are currently a ‘weak link’ in the package of support provided.
A Multidimensional Evaluation of the Effectiveness of Business Incubators: An Application of the PROMETHEE Outranking Method
Authors: Schwartz Michael , Göthner Maximilian
Published: October 2009

Considerable public resources are devoted to the establishment and operation of business incubators (BIs), which are seen as catalysts for the promotion of entrepreneurship, innovation activities, and regional development. Despite the vast amount of research that focused on the effectiveness of incubator initiatives and how to measure incubator performance, there is still a lack of understanding of how to determine which incubators are more effective than others. On the basis of data from 410 graduate firms, we concentrate on this crucial question and compare the long-term effectiveness of five BIs in Germany by applying the multicriteria outranking technique ‘preference ranking organization method for enrichment evaluation’ (PROMETHEE). in particular, we investigate whether PROMETHEE is a well-suited methodological approach for evaluation and comparison in the specific context of business incubation.
In the Absence of Practice
Authors: Harrison Paul
Published: October 2009

Increasingly the focus of social analysis and explanation is falling upon doings, on actions and practices, insofar as they are understood to be the origin rather than the effect of signification and meaning. This paper offers a sympathetic critique of such ‘ontologisation’ of practice, asking what is presumed about the human and the social when practice is taken as the primary social ‘thing’. The critique works by outlining, somewhat tentatively, a ‘phenomenology’ of dreamless sleep; a situation and a state in which a subject cannot be said to be doing anything at all. The figures that will be discussed below lie flat out; for the moment they have no bearing or gait, no focused or dispersed attention, no reflexive, deliberative or tacit understanding. This discussion is developed through a reading of Tim Ingold's (2000) landmark essay “The temporality of the landscape” (in The Perception of the Environment Routledge), here taken as exemplary of a broad range of practice based approaches. While looking specifically at issues around skill, place, and sociality, the overarching claim of the paper is that thinking about sleep and about being a being which sleeps provides a way of touching on the susceptibility and finitude of corporeal existence. A susceptibility and a finitude which, I suggest, are the very condition of possibility of practice and action.
Estimation of grassland biophysical parameters using hyperspectral reflectance for fire risk map prediction
Authors: Gianelle D. , Vescovo L. , Mason F.
Published: October 2009

In remote sensing, the reflectance of vegetation has been successfully used for the assessment of grassland biophysical parameters for decades. Several studies have shown that vegetation indices that are based on narrow spectral bands significantly improve the prediction of vegetation biophysical characteristics. In this work, we analyse the relationships between the biophysical parameters of grasslands and the high-spatial-resolution hyperspectral reflectance values obtained from helicopter platform data using both a spectral vegetation index and a regression approach. The regression approach was favoured as it had optimal results with respect to producing higher R2 values than the spectral index approach (water content, 0.91 v. 0.90; leaf-area index, 0.88 v. 0.61; and green ratio, 0.90 v. 0.83). These three parameters were selected to obtain a fire risk map for the Bosco della Fontana grassland areas. The extreme spatial variability of the fire risk confirmed the hypotheses regarding the importance of obtaining scale-appropriate biophysical maps to model fire risk in fragmented landscapes and ecosystems. More studies are needed in order to investigate both the limits and the opportunities of high-spatial-resolution sensors in highly fragmented landscapes for the remote detection of fire risk and to generalise the obtained results to other grassland vegetation types.
A surface fuel classification for estimating fire effects
Authors: Lutes Duncan C. , Keane Robert E. , Caratti John F.
Published: October 2009

We present a classification of duff, litter, fine woody debris, and logs that can be used to stratify a project area into sites with fuel loading that yield significantly different emissions and maximum soil surface temperature. Total particulate matter smaller than 2.5 μm in diameter and maximum soil surface temperature were simulated using the First Order Fire Effects Model. Simulation results were clustered into 10 Effects Groups using an agglomerative routine where each Effects Group defined a unique range of soil temperature and emissions. Classification tree analysis was used to estimate the critical duff, litter, fine woody debris, and log loadings associated with the soil temperature and emissions of each Effects Group. The resulting 21 fuel classes are called Fuel Loading Models and classified the study dataset with an ~34% misclassification rate. The classification can be used to describe fuel loadings for a plot or stand, or as map units for mapping fuel loadings across large regions. The classification process can be used to develop finer-scale fuel classifications for specific regions or ecosystems.
Factors influencing the pattern of fire severities in a large wildfire under extreme meteorological conditions in the Mediterranean basin
Authors: Oliveras Imma , Gracia Marc , Moré Gerard , Retana Javier
Published: October 2009

In Mediterranean ecosystems, large fires frequently burn under extreme meteorological conditions, but they are usually characterized by a spatial heterogeneity of burn severities. The way in which such mixed-severity fires are a result of fuels, topography and weather remains poorly understood. We computed fire severity of a large wildfire that occurred in Catalonia, Spain, as the difference between the post- and pre-fire Normalized Difference Vegetation Index (NDVI) values obtained through Landsat images. Fuel and topographic variables were derived from remote sensing, and fire behavior variables were obtained from an exhaustive reconstruction of the fire. Results showed that fire severity had a negative relationship with percentage of canopy cover, i.e. green surviving plots were mainly those with more forested conditions. Of the topographic variables, only aspect had a significant effect on fire severity, with higher values in southern than in northern slopes. Fire severity was higher in head than in flank and back fires. The interaction of these two variables was significant, with differences between southern and northern aspects being small for head fires, but increasing in flank and back fires. The role of these variables in determining the pattern of fire severities is of primary importance for interpreting the current landscapes and for establishing effective fire prevention and extinction policies.
Burn-scar patterns and their effect on regional burnt-area mapping in insular South-East Asia
Authors: Miettinen Jukka , Liew Soo Chin
Published: October 2009

This study aimed to deepen understanding on the limits imposed by burn-scar patterns and size distribution on regional burnt-area mapping with medium to coarse resolution (250–1000 m) satellite imagery in insular South-East Asia. Burnt-area maps based on 16 high-resolution SPOT 4 HRVIR and 5 HRG images were analysed in combination with land-cover and soil maps. Although the number of small burn scars (<25ha) was high throughout the region, the proportion of total burnt-area found in small scars varied remarkably (from 3 to 97%) between study sites. Unlike land cover, soil type was found to be a good indicator for usability of medium to coarse-resolution burnt-area mapping owing to the high occurrence of large burn scars on peatland and other wetland areas. A medium-resolution burnt-area mapping simulation (where 500 × 500-m grid cells containing ≥50% burnt area were considered detectable) resulted in 86% detected burnt area in wetlands (peat and alluvial soils) as opposed to only 33% in non-wetland areas. We thereby conclude that burn scar patterns and size distribution permit reliable regional burnt-area mapping with medium to coarse-resolution satellite imagery in the wetlands of insular South-East Asia, whereas alternative methods may need to be used in non-wetland areas.
Urban cat (Felis catus) movement and predation activity associated with a wetland reserve in New Zealand
Authors: Morgan S. A. , Hansen C. M. , Ross J. G. , Hickling G. J. , Ogilvie S. C. , Paterson A. M.
Published: October 2009

Context. House cats are increasingly suggested as having major ecological impacts in semiurban environments. Information on the activity of house cats is relatively scarce, especially in habitats such as wetlands. Aims. This study examines the movement and foraging behaviour of house cats living on the periphery of a wetland reserve in Christchurch city, New Zealand. Methods. Twenty-one domestic cats living in a suburban residential area were studied using radiotelemetry to determine home-range size, mean and maximum distances travelled into the adjacent wetland, and the proportion of time spent in the wetland over a 12-month period. Surveys of prey retrieval for 88 cats were also carried out by cat owners over the same 12-month period. Key results. Cat age and the distance of the cat’s home from the periphery of the wetland were highly correlated with cat movement and hunting activity. These movements were not markedly influenced by season or time of day. Younger cats (<6 years of age) living on the periphery of the wetland had larger home-range sizes, moved significantly further into the wetland and spent a significantly greater proportion of time in the wetland. Cats living close to the wetland also brought a greater diversity and a greater total number of prey items to their home-site. Rates of predation were not significantly influenced by sex or whether the cat was wearing a bell. The most common prey items were introduced rodents and birds; however, 172 of 981 prey items were identified as a native common skink. Conclusions.Consequently, cats living in households on the wetland periphery currently pose a predation risk for the wetland species, and the impact of cats on the native skink population warrants further investigation. Implications. This study suggests that domestic cats will exploit wild habitats but that their potential impact will have both positive (predation of introduced pest species) and negative (occasional direct predation) effects on native wildlife.
Global mapping of Al, Cu, Fe, and Zn in-use stocks and in-ground resources
Authors: Rauch Jason N.
Published: October 2009

Human activity has become a significant geomorphic force in modern times, resulting in unprecedented movements of material around Earth. An essential constituent of this material movement, the major industrial metals aluminium, copper, iron, and zinc in the human-built environment are mapped globally at 1-km nominal resolution for the year 2000 and compared with the locations of present-day in-ground resources. While the maps of in-ground resources generated essentially combine available databases, the mapping methodology of in-use stocks relies on the linear regression between gross domestic product and both in-use stock estimates and the Nighttime Lights of the World dataset. As the first global maps of in-use metal stocks, they reveal that a full 25% of the world's Fe, Al, Cu, and Zn in-use deposits are concentrated in three bands: (
i
) the Eastern seaboard from Washington, D.C. to Boston in the United States, (
ii
) England, Benelux into Germany and Northern Italy, and (
iii
) South Korea and Japan. This pattern is consistent across all metals investigated. In contrast, the global maps of primary metal resources reveal these deposits are more evenly distributed between the developed and developing worlds, with the distribution pattern differing depending on the metal. This analysis highlights the magnitude at which in-ground metal resources have been translocated to in-use stocks, largely from highly concentrated but globally dispersed in-ground deposits to more diffuse in-use stocks located primarily in developed urban regions.
Indirect costs of a nontarget pathogen mitigate the direct benefits of a virus-resistant transgene in wild
Cucurbita
Authors: Sasu Miruna A. , Ferrari Matthew J. , Du Daolin , Winsor James A. , Stephenson Andrew G.
Published: October 2009

Virus-resistant transgenic squash are grown throughout the United States and much of Mexico and it is likely that the virus-resistant transgene (VRT) has been introduced to wild populations repeatedly. The evolutionary fate of any resistance gene in wild populations and its environmental impacts depend upon trade-offs between the costs and benefits of the resistance gene. In a 3-year field study using a wild gourd and transgenic and nontransgenic introgressives, we measured the effects of the transgene on fitness, on herbivory by cucumber beetles, on the incidence of mosaic viruses, and on the incidence of bacterial wilt disease (a fatal disease vectored by cucumber beetles). In each year, the first incidence of zucchini yellow mosaic virus occurred in mid-July and spread rapidly through the susceptible plants. We found that the transgenic plants had greater reproduction through both male and female function than the susceptible plants, indicating that the VRT has a direct fitness benefit for wild gourds under the conditions of our study. Moreover, the VRT had no effect on resistance to cucumber beetles or the incidence of wilt disease before the spread of the virus. However, as the virus spread through the fields, the cucumber beetles became increasingly concentrated upon the healthy (mostly transgenic) plants, which increased exposure to and the incidence of wilt disease on the transgenic plants. This indirect cost of the VRT (mediated by a nontarget herbivore and pathogen) mitigated the overall beneficial effect of the VRT on fitness.
Hydrodynamic gene delivery of baboon trypanosome lytic factor eliminates both animal and human-infective African trypanosomes
Authors: Thomson Russell , Molina-Portela Pilar , Mott Helen , Carrington Mark , Raper Jayne
Published: October 2009

Several species of African trypanosomes cause fatal disease in livestock, but most cannot infect humans due to innate trypanosome lytic factors (TLFs). Human TLFs are pore forming high-density lipoprotein (HDL) particles that contain apolipoprotein L-I (apoL-I) the trypanolytic component, and haptoglobin-related protein (Hpr), which binds free hemoglobin (Hb) in blood and facilitates the uptake of TLF via a trypanosome haptoglobin-hemoglobin receptor. The human-infective
Trypanosoma brucei rhodesiense
escapes lysis by TLF by expression of serum resistance-associated (SRA) protein, which binds and neutralizes apoL-I. Unlike humans, baboons are not susceptible to infection by
T. b. rhodesiense
due to previously unidentified serum factors. Here, we show that baboons have a TLF complex that contains orthologs of Hpr and apoL-I and that full-length baboon apoL-I confers trypanolytic activity to mice and when expressed together with baboon Hpr and human apoA-I, provides protection against both animal infective and the human-infective
T. brucei rhodesiense
in vivo. We further define two critical lysines near the C terminus of baboon apoL-1 that are necessary and sufficient to prevent binding to SRA and thereby confer resistance to human-infective trypanosomes. These findings form the basis for the creation of TLF transgenic livestock that would be resistant to animal and human-infective trypanosomes, which would result in the reduction of disease and the zoonotic transmission of human infective trypanosomes.
The comparative genomics of viral emergence
Authors: Holmes Edward C.
Published: October 2009

RNA viruses are the main agents of emerging and re-emerging diseases. It is therefore important to reveal the evolutionary processes that underpin their ability to jump species boundaries and establish themselves in new hosts. Here, I discuss how comparative genomics can contribute to this endeavor. Arguably the most important evolutionary process in RNA virus evolution, abundant mutation, may even open up avenues for their control through “lethal mutagenesis.” Despite this remarkable mutational power, adaptation to diverse host species remains a major adaptive challenge, such that the most common outcome of host jumps are short-term “spillover” infections. A powerful case study of the utility of genomic approaches to studies of viral evolution and emergence is provided by influenza virus and brought into sharp focus by the ongoing epidemic of swine-origin H1N1 influenza A virus (A/H1N1pdm). Research here reveals a marked lack of surveillance of influenza viruses in pigs, coupled with the possibility of cryptic transmission before the first reported human cases, such that the exact genesis of A/H1N1pdm (where, when, how) is uncertain.
A chemical-genetic approach to study G protein regulation of β cell function in vivo
Authors: Guettier Jean-Marc , Gautam Dinesh , Scarselli Marco , de Azua Inigo Ruiz , Li Jian Hua , Rosemond Erica , Ma Xiaochao , Gonzalez Frank J. , Armbruster Blaine N. , Lu Huiyan , Roth Bryan L. , Wess Jürgen
Published: October 2009

Impaired functioning of pancreatic β cells is a key hallmark of type 2 diabetes. β cell function is modulated by the actions of different classes of heterotrimeric G proteins. The functional consequences of activating specific β cell G protein signaling pathways in vivo are not well understood at present, primarily due to the fact that β cell G protein-coupled receptors (GPCRs) are also expressed by many other tissues. To circumvent these difficulties, we developed a chemical-genetic approach that allows for the conditional and selective activation of specific β cell G proteins in intact animals. Specifically, we created two lines of transgenic mice each of which expressed a specific designer GPCR in β cells only. Importantly, the two designer receptors differed in their G protein-coupling properties (G
q/11
versus G
s
). They were unable to bind endogenous ligand(s), but could be efficiently activated by an otherwise pharmacologically inert compound (clozapine-N-oxide), leading to the conditional activation of either β cell G
q/11
or G
s
G proteins. Here we report the findings that conditional and selective activation of β cell G
q/11
signaling in vivo leads to striking increases in both first- and second-phase insulin release, greatly improved glucose tolerance in obese, insulin-resistant mice, and elevated β cell mass, associated with pathway-specific alterations in islet gene expression levels. Selective stimulation of β cell G
s
triggered qualitatively similar in vivo metabolic effects. Thus, this developed chemical-genetic strategy represents a powerful approach to study G protein regulation of β cell function in vivo.
Cloning human herpes virus 6A genome into bacterial artificial chromosomes and study of DNA replication intermediates
Authors: Borenstein Ronen , Frenkel Niza
Published: October 2009

Cloning of large viral genomes into bacterial artificial chromosomes (BACs) facilitates analyses of viral functions and molecular mutagenesis. Previous derivations of viral BACs involved laborious recombinations within infected cells. We describe a single-step production of viral BACs by direct cloning of unit length genomes, derived from circular or head-to-tail concatemeric DNA replication intermediates. The BAC cloning is independent of intracellular recombinations and DNA packaging constraints. We introduced the 160-kb human herpes virus 6A (HHV-6A) genome into BACs by digesting the viral DNA replicative intermediates with the Sfil enzyme that cleaves the viral genome in a single site. The recombinant BACs contained also the puromycin selection gene, GFP, and LoxP sites flanking the BAC sequences. The HHV-6A-BAC vectors were retained stably in puromycin selected 293T cells. In the presence of irradiated helper virus, supplying most likely proteins enhancing gene expression they expressed early and late genes in SupT1 T cells. The method is especially attractive for viruses that replicate inefficiently and for viruses propagated in suspension cells. We have used the fact that the BAC cloning “freezes” the viral DNA replication intermediates to analyze their structure. The results revealed that HHV-6A-BACs contained a single direct repeat (DR) rather than a DR-DR sequence, predicted to arise by circularization of parental genomes with a DR at each terminus. HHV-6A DNA molecules prepared from the infected cells also contained DNA molecules with a single DR. Such forms were not previously described for HHV-6 DNA.
Household actions can provide a behavioral wedge to rapidly reduce US carbon emissions
Authors: Dietz Thomas , Gardner Gerald T. , Gilligan Jonathan , Stern Paul C. , Vandenbergh Michael P.
Published: October 2009

Most climate change policy attention has been addressed to long-term options, such as inducing new, low-carbon energy technologies and creating cap-and-trade regimes for emissions. We use a behavioral approach to examine the reasonably achievable potential for near-term reductions by altered adoption and use of available technologies in US homes and nonbusiness travel. We estimate the plasticity of 17 household action types in 5 behaviorally distinct categories by use of data on the most effective documented interventions that do not involve new regulatory measures. These interventions vary by type of action and typically combine several policy tools and strong social marketing. National implementation could save an estimated 123 million metric tons of carbon per year in year 10, which is 20% of household direct emissions or 7.4% of US national emissions, with little or no reduction in household well-being. The potential of household action deserves increased policy attention. Future analyses of this potential should incorporate behavioral as well as economic and engineering elements.
Not the average view of adipogenesis
Authors: Short Ben
Published: October 2009

Study on cell heterogeneity offers a surprising twist to adipocyte differentiation.
Ana3 is a conserved protein required for the structural integrity of centrioles and basal bodies
Authors: Stevens Naomi R. , Dobbelaere Jeroen , Wainman Alan , Gergely Fanni , Raff Jordan W.
Published: October 2009

Recent studies have identified a conserved “core” of proteins that are required for centriole duplication. A small number of additional proteins have recently been identified as potential duplication factors, but it is unclear whether any of these proteins are components of the core duplication machinery. In this study, we investigate the function of one of these proteins, Drosophila melanogaster Ana3. We show that Ana3 is present in centrioles and basal bodies, but its behavior is distinct from that of the core duplication proteins. Most importantly, we find that Ana3 is required for the structural integrity of both centrioles and basal bodies and for centriole cohesion, but it is not essential for centriole duplication. We show that Ana3 has a mammalian homologue, Rotatin, that also localizes to centrioles and basal bodies and appears to be essential for cilia function. Thus, Ana3 defines a conserved family of centriolar proteins and plays an important part in ensuring the structural integrity of centrioles and basal bodies.
γ-Tubulin ring complexes regulate microtubule plus end dynamics
Authors: Bouissou Anaïs , Vérollet Christel , Sousa Aureliana , Sampaio Paula , Wright Michel , Sunkel Claudio E. , Merdes Andreas , Raynaud-Messina Brigitte
Published: October 2009

γ-Tubulin is critical for the initiation and regulation of microtubule (MT) assembly. In Drosophila melanogaster, it acts within two main complexes: the γ-tubulin small complex (γ-TuSC) and the γ-tubulin ring complex (γ-TuRC). Proteins specific of the γ-TuRC, although nonessential for viability, are required for efficient mitotic progression. Until now, their role during interphase remained poorly understood. Using RNA interference in Drosophila S2 cells, we show that the γ-TuRC is not critical for overall MT organization. However, depletion of any component of this complex results in an increase of MT dynamics. Combined immunofluorescence and live imaging analysis allows us to reveal that the γ-TuRC localizes along interphase MTs and that distal γ-tubulin spots match with sites of pause or rescue events. We propose that, in addition to its role in nucleation, the γ-TuRC associated to MTs may regulate their dynamics by limiting catastrophes.
Lateral transport of Smoothened from the plasma membrane to the membrane of the cilium
Authors: Milenkovic Ljiljana , Scott Matthew P. , Rohatgi Rajat
Published: October 2009

The function of primary cilia depends critically on the localization of specific proteins in the ciliary membrane. A major challenge in the field is to understand protein trafficking to cilia. The Hedgehog (Hh) pathway protein Smoothened (Smo), a 7-pass transmembrane protein, moves to cilia when a ligand is received. Using microscopy-based pulse-chase analysis, we find that Smo moves through a lateral transport pathway from the plasma membrane to the ciliary membrane. Lateral movement, either via diffusion or active transport, is quite distinct from currently studied pathways of ciliary protein transport in mammals, which emphasize directed trafficking of Golgi-derived vesicles to the base of the cilium. We anticipate that this alternative route will be used by other signaling proteins that function at cilia. The path taken by Smo may allow novel strategies for modulation of Hh signaling in cancer and regeneration.
Spermatozoa capture HIV-1 through heparan sulfate and efficiently transmit the virus to dendritic cells
Authors: Ceballos Ana , Remes Lenicov Federico , Sabatté Juan , Rodríguez Rodrígues Christian , Cabrini Mercedes , Jancic Carolina , Raiden Silvina , Donaldson Mónica , Agustín Pasqualini Rodolfo , Marin-Briggiler Clara , Vazquez-Levin Mónica , Capani Francisco , Amigorena Sebastián , Geffner Jorge
Published: October 2009

Semen is the main vector for HIV-1 dissemination worldwide. It contains three major sources of infectious virus: free virions, infected leukocytes, and spermatozoa-associated virions. We focused on the interaction of HIV-1 with human spermatozoa and dendritic cells (DCs). We report that heparan sulfate is expressed in spermatozoa and plays an important role in the capture of HIV-1. Spermatozoa-attached virus is efficiently transmitted to DCs, macrophages, and T cells. Interaction of spermatozoa with DCs not only leads to the transmission of HIV-1 and the internalization of the spermatozoa but also results in the phenotypic maturation of DCs and the production of IL-10 but not IL-12p70. At low values of extracellular pH (∼6.5 pH units), similar to those found in the vaginal mucosa after sexual intercourse, the binding of HIV-1 to the spermatozoa and the consequent transmission of HIV-1 to DCs were strongly enhanced. Our observations support the notion that far from being a passive carrier, spermatozoa acting in concert with DCs might affect the early course of sexual transmission of HIV-1 infection.
Risk Factors and Clinical Impact of Klebsiella pneumoniae Carbapenemase-Producing K. pneumoniae
Authors: Gasink Leanne B. , Edelstein Paul H. , Lautenbach Ebbing , Synnestvedt Marie , Fishman Neil O.
Published: October 2009

Background.

Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae is an emerging pathogen with serious clinical and infection control implications. To our knowledge, no study has specifically examined risk factors for KPC-producing K. pneumoniae or its impact on mortality.

Methods.

To identify risk factors for infection or colonization with KPC-producing K. pneumoniae, a case-control study was performed. Case patients with KPC-producing K. pneumoniae were compared with control subjects with carbapenem-susceptible K. pneumoniae. A cohort study evaluated the association between KPC-producing K. pneumoniae and in-hospital mortality.

Results.

Fifty-six case patients and 863 control subjects were identified. In multivariable analysis, independent risk factors for KPC-producing K. pneumoniae were (1) severe illness (adjusted odds ratio [AOR], 4.31; 95% confidence interval [CI], 2.25–8.25), (2) prior fluoroquinolone use (AOR, 3.39; 95% CI, 1.50, 7.66), and (3) prior extended-spectrum cephalosporin use (AOR, 2.55; 95% CI, 1.18, 5.52). Compared with samples from other anatomic locations, K. pneumoniae isolates from blood samples were less likely to harbor KPC (AOR, 0.33; 95% CI, 0.12, 0.86). KPC-producing K. pneumoniae was independently associated with in-hospital mortality (AOR, 3.60; 95% CI, 1.87–6.91).

Conclusions.

KPC-producing K. pneumoniae is an emerging pathogen associated with significant mortality. Our findings highlight the urgent need to develop strategies for prevention and infection control. Limiting use of certain antimicrobials, specifically fluoroquinolones and cephalosporins, use may be effective strategies.
Comprehensive control of resistive wall modes in DIII-D advanced tokamak plasmas
Authors: Okabayashi M. , Bogatu I.N. , Chance M.S. , Chu M.S. , Garofalo A.M. , In Y. , Jackson G.L. , La Haye R.J. , Lanctot M.J. , Manickam J. , Marrelli L. , Martin P. , Navratil G.A. , Reimerdes H. , Strait E.J. , Takahashi H. , Welander A.S. , Bolzonella T. , Budny R.V. , Kim J.S. , Hatcher R. , Liu Y.Q. , Luce T.C.
Published: October 2009

The resistive wall mode (RWM) and neoclassical tearing mode (NTM) have been simultaneously suppressed in the DIII-D for durations of over 2 s at beta values 20% above the no-wall limit with modest electron cyclotron current drive and very low plasma rotation. The achieved plasma rotation was significantly lower than reported previously. However, in this regime where stable operation is obtained, it is not unconditionally guaranteed. Various MHD activities, such as edge localized modes (ELMs) and fishbones, begin to couple to the RWM branch near the no-wall limit; feedback has been useful in improving the discharge stability to such perturbations. Simultaneous operation of slow dynamic error field correction and fast feedback suppressed the pile-up of ELM-induced RWM at a series of ELM events. This result implies that successful feedback operation requires not only direct feedback against unstable RWM but also careful control of MHD-induced RWM aftermath, which is the dynamical response to a small-uncorrected error field near the no-wall beta limit. These findings are extremely useful in defining the challenge of control of the RWM and NTM in the unexplored physics territory of burning plasmas in ITER.
Minimal residual disease is a significant predictor of treatment failure in non T‐lineage adult acute lymphoblastic leukaemia: final results of the international trial UKALL XII/ECOG2993
Authors: Patel Bella , Rai Lena , Buck Georgina , Richards Sue M. , Mortuza Yeasmin , Mitchell Wayne , Gerrard Gareth , Moorman Anthony V. , Duke Veronique , Hoffbrand A. Victor , Fielding Adele K. , Goldstone Anthony H. , Foroni Letizia
Published: October 2009

The predictive value of molecular minimal residual disease (MRD) monitoring using polymerase chain reaction amplification of clone‐specific immunoglobulin or T‐cell Receptor rearrangements was analysed in 161 patients with non T‐lineage Philadelphia‐negative acute lymphoblastic leukaemia (ALL) participating in the UK arm of the international ALL trial UKALL XII/Eastern Cooperative Oncology Group (ECOG) 2993. MRD positivity (≥10−4) in patients treated with chemotherapy alone was associated with significantly shorter relapse‐free survival (RFS) at several time‐points during the first year of therapy. MRD status best discriminated outcome after phase 2 induction, when the relative risk of relapse was 8·95 (2·85–28·09)‐fold higher in MRD‐positive (≥10−4) patients and the 5‐year RFS 15% [95% confidence interval (CI) 0–40%] compared to 71% (56–85%) in MRD‐negative (<10−4) patients (P = 0·0002) When MRD was detected prior to autologous stem cell transplantation (SCT), a significantly higher rate of treatment failure was observed [5‐year RFS 25% (CI 0–55%) vs. 77% (95% CI 54–100%) in MRD‐negative/<10−4, P = 0·01] whereas in recipients of allogeneic‐SCT in first complete remission, MRD positivity pre‐transplant did not adversely affect outcome. These data provide a rationale for introducing MRD‐based risk stratification in future studies for the delineation of those at significant risk of treatment failure in whom intensification of therapy should be evaluated.
A taxonomy of political processes in systems development
Authors: Sabherwal Rajiv , Grover Varun
Published: October 2009

Significant resources invested in information system development (ISD) are wasted due to political manoeuvres. Prior research on ISD politics has contributed mainly through theoretical development and case studies. This has enhanced understanding of relevant concepts, political tactics and conditions facilitating politics. However, there is limited understanding of the different processes through which politics unfold. This paper uses 89 ISD projects to develop a taxonomy of political processes in ISD. The taxonomy includes three distinct processes: Tug of War, wherein multiple parties strive to gain project control; Obstacle Race, which involves efforts to resist and pursue the project; and Empire Building, wherein the project is used as an instrument to enhance political or resource bases. The taxonomy is explained using the non‐proponents' view of the project and the balance of power between system's proponents and non‐proponents. We also discuss the emergent taxonomy's implications for how politics can be managed and studied.
Urbanization and the more‐individuals hypothesis
Authors: Chiari Claudia , Dinetti Marco , Licciardello Cinzia , Licitra Gaetano , Pautasso Marco
Published: October 2009

1. Urbanization is a landscape process affecting biodiversity world‐wide. Despite many urban–rural studies of bird assemblages, it is still unclear whether more species‐rich communities have more individuals, regardless of the level of urbanization. The more‐individuals hypothesis assumes that species‐rich communities have larger populations, thus reducing the chance of local extinctions.

2. Using newly collated avian distribution data for 1 km2 grid cells across Florence, Italy, we show a significantly positive relationship between species richness and assemblage abundance for the whole urban area. This richness–abundance relationship persists for the 1 km2 grid cells with less than 50% of urbanized territory, as well as for the remaining grid cells, with no significant difference in the slope of the relationship. These results support the more‐individuals hypothesis as an explanation of patterns in species richness, also in human modified and fragmented habitats.

3. However, the intercept of the species richness–abundance relationship is significantly lower for highly urbanized grid cells. Our study confirms that urban communities have lower species richness but counters the common notion that assemblages in densely urbanized ecosystems have more individuals. In Florence, highly inhabited areas show fewer species and lower assemblage abundance.

4. Urbanized ecosystems are an ongoing large‐scale natural experiment which can be used to test ecological theories empirically.