bluuebunny/crossref_metadata_2025 huggingface dataset:
Valence band offset at interfaces between CuI and indium sulfides
Authors: Konovalov Igor , Makhova Liudmila
Published: May 2008

The energy differences between In 3d5/2, In 4d5/2, and S 2p3/2 core levels are almost the same in β-In2S3, CuIn5S8, AgIn5S8, CuInS2, In6S7, and InS semiconductors. The system of these core levels provides a reference energy that can be used to put the valence band edges of these materials on a common energy scale. The experimental study shows that this common energy scale remains valid within ±0.2 eV for prediction of valence band discontinuities at heterointerfaces between these (and potentially other) indium sulfides and CuI. CuI/CuIn5S8 heterojunction showed no valence band offset and it may be interesting for applications as a diode.
Stress wave attenuation in ceramic plates
Authors: Naik N. K. , Goel Rahul , Kulkarni Mandar D.
Published: May 2008

Studies on planar longitudinal stress wave attenuation in thin ceramic plates are presented using a wave tracking algorithm. The results are also experimentally validated. Ceramic plates consist of grains and grain boundaries. Elastic modulus and density of the grain boundaries are less than those of the grains. When the planar longitudinal stress wave encounters an interface between the grain and the grain boundary, reflection and transmission of the incident stress wave take place because of the impedance mismatch at the interface. It is observed that this leads to attenuation in stress wave intensity. This behavior is represented by stress wave attenuation coefficient. It is observed that the stress wave attenuation coefficient is a material property.
Defects and transport in complex oxide thin films
Authors: Ohnishi Tsuyoshi , Shibuya Keisuke , Yamamoto Takahisa , Lippmaa Mikk
Published: May 2008

Epitaxial oxide thin films are at the heart of new “oxide electronic” applications, such as excitonic ultraviolet light-emitting diodes and resistive switching memories. Complex oxide films are often grown by pulsed laser deposition (PLD) because the technique is believed to be material agnostic. Here, we show that one of the fundamental premises used to justify the use of PLD, that material is transferred from an ablation target to the film without stoichiometry deviations, is incorrect even when no volatile elements are involved. Even more importantly, the commonly used solution of increasing the laser energy density above a material-specific threshold value to obtain stoichiometric films cannot be used in the case of low carrier density systems such as SrTiO3, where even minute 1018 cm−3 order cation nonstoichiometry can have a dramatic effect on transport. Lattice parameter deviations in oxide films, which are often incorrectly ascribed to oxygen loss, correlate very well with cation nonstoichiometry. We show that proper simultaneous choice of ablation laser fluence and ablation area is essential and often more important than the growth temperature and oxygen pressure for obtaining bulklike properties in oxide heterostructures.
Photoelectron spectroscopic investigation of nitrogen chemical states in ZnO: (N,Ga) thin films
Authors: Wang H. , Ho H. P. , Xu J. B.
Published: May 2008

Fabrication of high quality p-type ZnO is the main challenge in recent ZnO research that prevents the practical application of ZnO-based devices in optoelectronics. The mechanism behind is thought to be due to self-compensation of native defects and/or dopant-induced donors. In this report, we investigated the chemical bonding states of nitrogen doped ZnO films under monodoping, codoping, and cluster doping with Ga. It was found that the N/Ga flux ratio in the doping process has a critical influence on the chemical bonding of nitrogen in ZnO. By tuning the N/Ga doping ratio, it is expected to create appropriate chemical environments to enhance the formation of desired dopant species: Ga–N2O2 (codoping), Ga–N3O and Ga–N4 (cluster doping) for p-type ZnO.
Manipulation of quantum interference effects in La0.39Pr0.28Ca0.33MnO3−δ by p-n junction at high temperature
Authors: Wang C. , Yang Y. , Li Z. F. , Chen X. S. , Shen S. C. , Lu W. , Liu J. M.
Published: May 2008

Manipulation of the magnetoresistance mechanism-quantum interference effects (QIEs) is achieved by controlling the hole density in a La0.39Pr0.28Ca0.33MnO3−δ depletion layer with the application of different biases to the La0.39Pr0.28Ca0.33MnO3−δ/SrNbTiO3 p-n junction. The positive magnetoresistance (PMR) induced by QIEs has been tuned up to tenfold with a suitable bias voltage applied to this manganite/titanate p-n junction. Compared to the recent breakthrough achieved on Fe1−xCoxSi [N. Manyala et al., Nature (London) 404, 581 (2000)], the working temperature for QIEs has been increased from 30 to 150 K, and the maximal PMR ratio has been enhanced from 10% to 96% under 1 T at 25 K. The maximal PMR can be obtained by tuning the hole density via the bias voltage within 2 V. It is clearly demonstrated that the carrier density strongly affects the QIEs in the manganites.
Equation of motion for a domain wall movement under a nonuniform transverse magnetic field
Authors: You Chun-Yeol
Published: May 2008

We investigate the dynamics of the domain wall in a nonuniform field driven domain wall motion memory concept. The equation of motion for a transverse Néel-type domain wall under a nonuniform transverse magnetic field is obtained with a collective coordinate approach. The validity of the equation of the motion is confirmed with micromagnetic simulations. We find that the domain wall velocity depends on the domain wall width, Gilbert damping parameter α, saturation magnetization, and the gradient of the field. The domain wall velocity of ∼100m∕s is obtained with typical material as Permalloy with a moderate field gradient (100Oe∕μm). It has promising results for memory applications.
W. H. Fitton's Geology of Australia's Coasts, 1826
Authors: Branagan D. F. , Moore D. T.
Published: May 2008

In an appendix to Phillip Parker King's 1826 book Narrative of a Survey of the ... Coasts of Australia..., W. H. Fitton attempted, largely on the basis of the rock specimens collected on King's and earlier expeditions, to summarize the geological (mainly lithological) character of Australia's coastal regions. We have examined and identified the specimens, preserved in the Natural History Museum, London, in terms of modern concepts, indicating their stratigraphic affinities. Fitton realized the limitations of his work and, wishing to encourage better knowledge, appended 'Instructions for collecting geological specimens', stressing the need to understand not only the materials, but the order of formation. Fitton was indicating that a sense of stratigraphy was essential to the progress of geology. Despite its deficiencies, Fitton's paper was an important step towards understanding the geology of an almost unknown continent.
Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection
Authors: Keele Brandon F. , Giorgi Elena E. , Salazar-Gonzalez Jesus F. , Decker Julie M. , Pham Kimmy T. , Salazar Maria G. , Sun Chuanxi , Grayson Truman , Wang Shuyi , Li Hui , Wei Xiping , Jiang Chunlai , Kirchherr Jennifer L. , Gao Feng , Anderson Jeffery A. , Ping Li-Hua , Swanstrom Ronald , Tomaras Georgia D. , Blattner William A. , Goepfert Paul A. , Kilby J. Michael , Saag Michael S. , Delwart Eric L. , Busch Michael P. , Cohen Myron S. , Montefiori David C. , Haynes Barton F. , Gaschen Brian , Athreya Gayathri S. , Lee Ha Y. , Wood Natasha , Seoighe Cathal , Perelson Alan S. , Bhattacharya Tanmoy , Korber Bette T. , Hahn Beatrice H. , Shaw George M.
Published: May 2008

The precise identification of the HIV-1 envelope glycoprotein (Env) responsible for productive clinical infection could be instrumental in elucidating the molecular basis of HIV-1 transmission and in designing effective vaccines. Here, we developed a mathematical model of random viral evolution and, together with phylogenetic tree construction, used it to analyze 3,449 complete
env
sequences derived by single genome amplification from 102 subjects with acute HIV-1 (clade B) infection. Viral
env
genes evolving from individual transmitted or founder viruses generally exhibited a Poisson distribution of mutations and star-like phylogeny, which coalesced to an inferred consensus sequence at or near the estimated time of virus transmission. Overall, 78 of 102 subjects had evidence of productive clinical infection by a single virus, and 24 others had evidence of productive clinical infection by a minimum of two to five viruses. Phenotypic analysis of transmitted or early founder Envs revealed a consistent pattern of CCR5 dependence, masking of coreceptor binding regions, and equivalent or modestly enhanced resistance to the fusion inhibitor T1249 and broadly neutralizing antibodies compared with Envs from chronically infected subjects. Low multiplicity infection and limited viral evolution preceding peak viremia suggest a finite window of potential vulnerability of HIV-1 to vaccine-elicited immune responses, although phenotypic properties of transmitted Envs pose a formidable defense.
The potential for genomics in potato improvement.
Authors: Duguay J. L. , Li XiuQing Li XiuQing , Regan S.
Published: May 2008

Demand for the potato, the fourth most consumed food crop in the world, is steadily increasing. In order to meet the rising demands on the industry, researchers and breeders have been working to better all aspects of potato production, including improvements to the tuber itself. This review will highlight the potential for genomics-assisted advancements, paying particular attention to the genomics tools and resources that are available, and the translation of this information into potato improvements. Immense amounts of genomic data have been generated from expressed sequence tag library construction, molecular linkage maps and microarray expression analyses. This information is helping to clarify the genetic components underlying many of the traits that are important for the continued success of the potato, including increased yields, processing quality traits and disease/pest resistance. Natural genetic resources, such as wild potato varieties and germplasm collections contain valuable genetic variation that, when combined with genomics-assisted breeding techniques such as marker-assisted selection and polymorphism identification, hold great potential for future improvements. With the continued integration of genomics tools and information with rapidly developing technologies such as proteomics and metabolomics, improvements to potato health and quality characteristics will be achieved in an expedited manner with full knowledge and understanding of the genetics involved. Moreover, as the technology advances, the potential exists for the production of potatoes with improved environmental and economic impacts, thus ensuring the sustainability of the industry for future generations.
EU regulations on the traceability and detection of GMOs: difficulties in interpretation, implementation and compliance.
Authors: Davison J. , Bertheau Y.
Published: May 2008

Europe has probably the strictest GMO regulation in the world. Its objectives are to give maximum protection of public health and the environment, while at the same time providing a science-based regulatory structure where biotechnology can flourish. In contrast to the situation in the USA, European opinion on the health and environmental biosafety of GMOs has been highly polarized, with the result that the public has expressed the desire of having an informed choice in what they are eating. Consequently, the European Union has introduced legislation on the traceability and detection of GMOs, including labelling of food and feed containing GMOs, or derived products thereof, above a defined threshold of fortuitous presence. This review article summarizes EC regulations, directives and recommendations on traceability and labelling, and discusses the practical problems involved in their implementation. These include the definition of the labelling threshold and the units of measure, sampling of large cargos, mixtures of GMOs, stacked genes, unauthorized GMOs, unknown GMOs and asynchronous approval. The ways in which the EC integrated project Co-Extra is contributing to the resolution of these problems are also discussed.
AgBase: a tool for systems biology in agricultural species.
Authors: Nanduri B. , McCarthy F. M.
Published: May 2008

Genome sequences are available for several agriculturally important species (both eukaryotic and prokaryotic) and genome sequences and '-omics' technologies show promise for translating genomics data into increased production efficiency, sustainable agriculture and advances for the bio-economy. However, predictive and preventative systems modelling depends on biological information and not just genomics data. Systems biology approaches allow the integration of various '-omics' data to produce valuable models to understand complex biological systems. The two approaches for doing systems biology are bottom-up modelling and top-down modelling. We focus on top-down systems biology, which entails four fundamental and overlapping steps: the enumeration of the system's parts, elucidation of interactions between these parts, modelling regulation of these interaction networks and generating predictive and dynamic models. Systems biology in agriculturally important species is truly possible only when all the elements required for systems biology become available for these species. The AgBase databases provide critical components for systems biology modelling in agriculture as they provide experimentally based structural annotation of genomic sequences and highly curated functional annotations of gene products using Gene Ontology (GO). The GO underpins network analysis and can also be used to model physiological function in biological systems. Like the '-omics' data being modelled, agricultural databases (and agricultural researchers) need to be better integrated to support the multidisciplinary research required for systems biology.
Bovine venereal campylobacteriosis: an overview.
Authors: Mshelia G. D. , Singh J. , Amin J. D. , Woldehiwet Z. , Egwu G. O. , Murray R. D.
Published: May 2008

Campylobacter fetus
is a well-recognized pathogen of animals and humans. The organism has been divided into two subspecies,
C. fetus
subsp.
venerealis
and
C. fetus
subsp.
fetus
, that are highly related phenotypically and genotypically. Due to this relatedness, it has become imperative to differentiate these two subspecies in order to avoid misdiagnosis and highlight clonal origins geographically. The principal phenotypic differentiating test at the moment is the growth of
C. fetus
subsp.
fetus
in the presence of 1% glycine, but glycine-tolerant variants of
C. fetus
subsp.
venerealis
have also been described. Molecular tools such as polymerase chain reaction (PCR), amplified fragment length polymorphism (AFLP), numerical analysis of pulsed-field gel electrophoresis (PFGE)-DNA profiles and gene sequence analysis amongst others have been used to differentiate
C. fetus
subspecies; and they seem to hold promise for the future.
C. fetus
subsp.
fetus
colonize the intestines of cattle and sheep and is associated with sporadic abortions and enteritis, while,
C. fetus
subsp.
venerealis
is highly adapted to the genital tracts of cattle and is the causative agent of bovine venereal campylobacteriosis (BVC). This disease has a worldwide distribution and is of major economic concern to cattle industries in various parts of the world. The prevalence of the disease is highest in the developing countries where natural breeding in cattle is widely practiced. BVC is associated with lowered fertility, embryo mortality and abortion; other clinical features of the disease include many services per conception, poor pregnancy rates, long calving intervals, stillbirths and birth of weak calves that may eventually die. Vaccines have been shown to be useful in the protection of cattle against the menace of BVC, but commercial vaccines are only available in some parts of the world where advanced agricultural practices have limited its occurrence. The continued presence of this disease in the developing world poses a threat to sustainable cattle production efforts in these countries. Previous reviews highlighted the epidemiology, pathogenesis and diagnosis of the disease; in this review the clinical features of BVC, advances in diagnosis, treatment and prevention, as well as the geographic distribution of the disease have been reviewed. To achieve faster results worldwide, the need for collaborative research on BVC between investigators in developing countries and their counterparts in the developed countries has been recommended.
Applications of radio frequency identification (RFID) in meat production: two case studies.
Authors: Townsend A. , Mennecke B.
Published: May 2008

Radio frequency identification (RFID) is of increasing importance in the meat industry because of the increasing need to manage information about animal products as these products progress through the value chain. Broader industry trends driven by retailers such as Wal-Mart as well as US government initiatives from the Department of Defense (DOD) and US Department of Agriculture (USDA) have pushed RFID to the forefront as a vital technology for enabling supply chain product traceability, location intelligence and product tracking. Because of the increasing importance of this topic in various segments of the meat supply chain, it is critical that stakeholders in the meat industry develop greater knowledge about RFID capabilities and limitations. To address this need, we review the important features of RFID and discuss its application in managing and creating intelligence about meat product status in the value chain. We also illustrate the value of RFID in meat production by presenting two case studies showing how it can be used to bring value to specific segments of the meat industry.
How useful is sustainability as a paradigm to shape agriculture.
Authors: Pearson C. J.
Published: May 2008

Sustainability meets the criteria of a paradigm. Agricultural research oriented to sustainability has risen since 1975 to about 3500 publications per year. A working definition of a sustainable agricultural system is one that maintains or improves the environmental, human (social) and economic capitals of part or preferably all the food chain involving farm inputs, on-farm activities and transfers to the consumer. This review asks three questions to evaluate whether the paradigm is having a major influence in shaping agriculture. To what extent has it altered the nature of agricultural research? To what extent has it become embedded in rural development? And has its rise coincided with the solving of some obvious large-scale problems of non-sustainability? It appears that in the majority of government extension programmes and the scientific literature there is a gap between the professed generic goal of sustainability and the recommended innovations, practices or suggested monitoring, if any. Organically certified systems are the best example of operationalizing the paradigm. To increase the impact of the paradigm in shaping agriculture will require the essence of sustainable systems to be described simply and more rigorous analysis of the impact of an innovation in terms of some measures, or sampling, of all three (human, social and economic) capitals.
Virus-induced gene silencing and its applications.
Authors: Senthil-Kumar M. , Anand A. , Uppalapati S. R. , Mysore K. S.
Published: May 2008

Virus-induced gene silencing (VIGS) is an efficient tool for plant functional genomics. Our current understanding about the phenomenon of post-transcriptional gene silencing (PTGS) in plant defence against viruses has enabled us to modify virus genomes for VIGS in different plant species. In this review, we provide a comprehensive update on the application of VIGS. We have attempted to cover the following topics in this review: different VIGS vectors available to date; VIGS as a tool to identify novel genes involved in various aspects of plant biology; VIGS in different plant species; utility of VIGS in different plant organs; VIGS for deciphering cellular functions of known genes; and future application of VIGS in modern plant biology.
Potential role of tillage to increase soil organic carbon sequestration.
Authors: Chan K. Y.
Published: May 2008

The importance of soil organic carbon (SOC) in maintaining soil quality is well recognized and more recently there has been much interest in the role of soil as a carbon (C) sink for combating climate change. The impact of tillage on SOC sequestration is reviewed in the context of current knowledge of SOC stabilization mechanisms and soil structure relationships. The current tendency to make comparisons between no-tillage (NT) and conventional tillage of the surface soil, with the latter often ill-defined, is an oversimplification and neglects the potential role of tillage in increasing SOC storage. Research is needed to develop tillage practices that avoid/minimize SOC losses and increase the potential of SOC sequestration in protected forms, particularly in the subsoil layers. To advance this, the development of novel tillage implementation and practices in the context of managing SOC storage of whole soil profile are needed.
Heat stress in feedlot cattle.
Authors: Brown-Brandl T. M.
Published: May 2008

Heat stress in feedlot cattle is a common summertime occurrence in cattle-producing parts of the world (USA, Australia, Brazil, etc.). The impact of heat stress on feedlot animals is quite varied: from little to no effect in a brief exposure; to causing reductions in feed intake, growth, and well-being of the cattle in a moderate event; to death of vulnerable animals during an extreme event. The level of heat stress an animal experiences can be broken down into three primary factors: animal susceptibility, environmental conditions and management strategies. Each of these factors can also be broken down into different elements. This paper describes the physical and physiological processes that describe homeostasis along with factors affecting animal susceptibility, methods of summarizing environmental conditions and some management strategies that can be used to relieve stress.
Assessment and maintenance of soil fertility in temperate organic agriculture.
Authors: Watson C. A. , Stockdale E. A. , Rees R. M.
Published: May 2008

The maintenance of soil fertility is a key tenet of organic farming and can be broadly defined as the ability of the soil to support the productivity of the system. The central concept of soil fertility in these systems is the use of legume-based multi-annual rotations together with the judicious use of on-farm manures. Rotations provide the opportunity for nutrient elements to be replenished, usually within a grass-clover ley phase with inputs of carbon and nitrogen (by the biological processes of photosynthesis and nitrogen fixation). We review evidence that shows that this 'building phase' of the rotations is also associated with increased biological activity and changes to the soil's physical characteristics. The sequence of crops within a rotation is designed to utilize changing levels of fertility and optimize the utilization of nutrient resources over the period of the rotation. Crops with high nutrient demand would therefore normally be placed at a point following the incorporation of a nutrient-rich ley phase. In some circumstances cover crops or undersown vegetation are appropriate to conserve nutrients and reduce losses at particular times within the cropping sequence. Where necessary, a small range of carefully controlled external inputs are allowed. The best methods of assessing soil fertility in organic farming depend upon longer-term and integrative assessments of the system such as crop yields or long-term changes in soil quality and organic matter rather than snapshot measurements of individual nutrient pools.
Transgenic approaches to mastitis.
Authors: Maga E. A.
Published: May 2008

Mastitis is an important disease affecting the dairy industry both in terms of animal welfare and the costs associated with treating the illness. Many mastitis prevention procedures are in place such as teat dipping, line cleaning and dry cow antibiotic treatments, yet mastitis is still common in most herds. The use of antibiotics to treat infected cows also poses concerns of having antibiotic residues in milk and the development of antibiotic resistance. In fact, one of the major mastitis-causing pathogens,
Staphylococcus aureus
, is resistant to treatment. To date, efforts have been focused on producing vaccines to combat mastitis but have yet to be successful. Another approach to fight mastitis is the use of genetic engineering to produce antimicrobial compounds in the mammary gland. Work along this line has been going on since the early 1990s, starting in mouse models and leading to the report of the production of transgenic cattle resistant to
S. aureus
mastitis in 2005. This review will focus on the past and present works conducted with transgenic animals and their potential and hurdles as a novel approach to fight mastitis.
MAPPING EUROPEAN IDEOSCAPES
Authors: Mihelj Sabina , Koenig Thomas , Downey John , Štetka Václav
Published: May 2008

Despite embracing the rhetoric of transnational flows and networks, comparative research on media content continues to fall prey to methodological nationalism. When it comes to empirical measurement, researchers often, despite their best intentions, fall back on techniques that assume that the discourses circulating within particular nationally bounded communicative spaces are homogenous. In this article, we developed a set of propositions and analytical approaches that should help to overcome this impasse, and used them to examine the newspaper debates on the EU Constitutional Treaty in seven European states: the Czech Republic, Germany, France, the Slovak Republic, Slovenia, Switzerland, and the UK. We suggested that instead of focusing solely on comparisons between nationally bounded communicative spheres, we should also look at differences between class-related communicative spaces. By adopting such an approach, we can acknowledge both sub-national segmentations of communicative spaces and transnational linkages, while at the same time not losing sight of the importance of the national. The results support our initial contention that the research on European mass communication ought to move beyond comparisons between national units and the levels of their respective Europeanization, and examine how European issues are conveyed in media catering to different social classes.
Differential regulation of interleukin 12 and interleukin 23 production in human dendritic cells
Authors: Gerosa Franca , Baldani-Guerra Barbara , Lyakh Lyudmila A. , Batoni Giovanna , Esin Semih , Winkler-Pickett Robin T. , Consolaro Maria Rita , De Marchi Mario , Giachino Daniela , Robbiano Angela , Astegiano Marco , Sambataro Angela , Kastelein Robert A. , Carra Giuseppe , Trinchieri Giorgio
Published: May 2008

We analyzed interleukin (IL) 12 and IL-23 production by monocyte-derived dendritic cells (mono-DCs). Mycobacterium tuberculosis H37Rv and zymosan preferentially induced IL-23. IL-23 but not IL-12 was efficiently induced by the combination of nucleotide-binding oligodimerization domain and Toll-like receptor (TLR) 2 ligands, which mimics activation by M. tuberculosis, or by the human dectin-1 ligand β-glucan alone or in combination with TLR2 ligands, mimicking induction by zymosan. TLR2 ligands inhibited IL-12 and increased IL-23 production. DC priming with interferon (IFN) γ strongly increased IL-12 production, but was not required for IL-23 production and inhibited IL-23 production induced by β-glucan. The pattern of IL-12 and IL-23 induction was reflected in accumulation of the IL-12p35 and IL-23p19 transcripts, respectively, but not IL-12/23p40. Although IL-23, transforming growth factor β, and IL-6 contained in the supernatants of activated mono-DCs played a role in the induction of IL-17 by human CD4+ T cells, IL-1β, in combination with one or more of those factors, was required for IL-17 production, and its production determined the differential ability of the stimuli used to elicit mono-DCs to produce soluble factors directing IL-17 production. Thus, the differential ability of pathogens to induce antigen-presenting cells to produce cytokines regulates the immune response to infection.
Constitutive CD40 signaling in B cells selectively activates the noncanonical NF-κB pathway and promotes lymphomagenesis
Authors: Hömig-Hölzel Cornelia , Hojer Caroline , Rastelli Julia , Casola Stefano , Strobl Lothar J. , Müller Werner , Quintanilla-Martinez Leticia , Gewies Andreas , Ruland Jürgen , Rajewsky Klaus , Zimber-Strobl Ursula
Published: May 2008

CD40, a member of the tumor necrosis factor (TNF) receptor family, plays an essential role in T cell–dependent immune responses. Because CD40 is widely expressed on the surface of tumor cells in various B cell malignancies, deregulated CD40 signaling has been suggested to contribute to lymphomagenesis. In this study, we show that B cell-specific expression of a constitutively active CD40 receptor, in the form of a latent membrane protein 1 (LMP1)/CD40 chimeric protein, promoted an increase in the number of follicular and marginal zone B cells in secondary lymphoid organs in transgenic mice. The B cells displayed an activated phenotype, prolonged survival and increased proliferation, but were significantly impaired in T cell-dependent immune responses. Constitutive CD40 signaling in B cells induced selective and constitutive activation of the noncanonical NF-κB pathway and the mitogen-activated protein kinases Jnk and extracellular signal–regulated kinase. LMP1/CD40-expressing mice older than 12 mo developed B cell lymphomas of mono- or oligoclonal origin at high incidence, thus showing that the interplay of the signaling pathways induced by constitutive CD40 signaling is sufficient to initiate a tumorigenic process, ultimately leading to the development of B cell lymphomas.
Resonance between passing fast ions and MHD instabilities both in the tokamak and the RFP configurations
Authors: Gobbin M. , White R.B. , Marrelli L. , Martin P.
Published: May 2008

Suprathermal ions in fusion plasmas have different confinement properties in tokamak and reversed field pinch (RFP) configurations. These differences are explained in terms of guiding centre drifts by an analytical approach. Magnetic field perturbations and passing fast ions can satisfy resonance conditions which do not hold for thermal or low energy particles. Such a resonance is controlled by a generalization for passing fast ions of the safety factor parameter. Applications to experimental situations show good agreement in predicting the radial position of the resonances in the fast ion phase space. Numerical simulations in RFP devices are qualitatively consistent with the longer confinement times of fast ions, especially in helical regimes.
Swelfe: a detector of internal repeats in sequences and structures
Authors: Abraham Anne-Laure , Rocha Eduardo P. C. , Pothier Joël
Published: May 2008

Summary: Intragenic duplications of genetic material have important biological roles because of their protein sequence and structural consequences. We developed Swelfe to find internal repeats at three levels. Swelfe quickly identifies statistically significant internal repeats in DNA and amino acid sequences and in 3D structures using dynamic programming. The associated web server also shows the relationships between repeats at each level and facilitates visualization of the results.

Availability:  http://bioserv.rpbs.jussieu.fr/swelfe

Contact:  annela@abi.snv.jussieu.fr

Supplementary information:  Supplementary data are available at Bioinformatics online.
Penalized estimation of haplotype frequencies
Authors: Ayers Kristin L. , Lange Kenneth
Published: May 2008

Motivation: Low haplotype diversity and linkage disequilibrium are the rule in short genomic segments. This fact suggests that parsimony should be enforced in estimation of haplotype frequencies. The current article introduces a diversity penalty that automatically discards potential haplotypes with low explanatory power. The standard EM algorithm for haplotype frequency estimation can accommodate the penalty if one passes over to a more general minorize–maximize (MM) scheme for estimation.

Results: Our new MM algorithm converges in fewer iterations, eliminates marginal haplotypes from further consideration and reduces the computational complexity of each iteration. Estimation by the MM algorithm also improves haplotyping and genotype imputation compared to naive application of the EM algorithm. Thus, the MM algorithm is a useful substitute for the EM algorithm. Compared to the most sophisticated current methods of haplotyping and genotype imputation, the MM algorithm is slightly less accurate but at least an order of magnitude faster.

Availability: Our software will be made available in the next release the program Mendel at http://www.genetics.ucla.edu/software/.

Contact:  kayers@ucla.edu
Prerecruit survival and recruitment of northern Gulf of St Lawrence Atlantic cod
Authors: Duplisea Daniel E. , Robert Dominique
Published: May 2008

Duplisea, D. E., and Robert, D. 2008. Prerecruit survival and recruitment of northern Gulf of St Lawrence Atlantic cod. – ICES Journal of Marine Science, 65: 946–952. Recruitment (R) of exploited marine fish populations is usually modelled exclusively as a function of spawning-stock biomass (SSB). A problem arising when modelling over long time-series is that the nature of the R–SSB relationship is unlikely to be stationary. Changes are often interpreted as productivity regime shifts and are linked to alterations in prerecruit survival rate. We examine the role of environment and predation by fish and harp seals as factors affecting the R–SSB relationship in the northern Gulf of St Lawrence cod, by fitting linear models using combinations of covariates to explain cod prerecruit survival. The most parsimonious model (based on a Bayesian Information Criterion, BIC) included cod, mackerel, and temperature, whereas redfish and seals did not appear in any of the best-fit models. Recruitment models derived from this analysis could be used in operating models for management strategy evaluation simulations for northern Gulf cod, so one could develop harvest control rules that are robust to changes in recruitment productivity regimes.
On the stability of lumps and wave collapse in water waves
Authors: Akylas T.R , Cho Yeunwoo
Published: May 2008

In the classical water-wave problem, fully localized nonlinear waves of permanent form, commonly referred to as lumps, are possible only if both gravity and surface tension are present. While much attention has been paid to shallow-water lumps, which are generalizations of Korteweg–de Vries solitary waves, the present study is concerned with a distinct class of gravity–capillary lumps recently found on water of finite or infinite depth. In the near linear limit, these lumps resemble locally confined wave packets with envelope and wave crests moving at the same speed, and they can be approximated in terms of a particular steady solution (ground state) of an elliptic equation system of the Benney–Roskes–Davey–Stewartson (BRDS) type, which governs the coupled evolution of the envelope along with the induced mean flow. According to the BRDS equations, however, initial conditions above a certain threshold develop a singularity in finite time, known as wave collapse, due to nonlinear focusing; the ground state, in fact, being exactly at the threshold for collapse suggests that the newly discovered lumps are unstable. In an effort to understand the role of this singularity in the dynamics of lumps, here we consider the fifth-order Kadomtsev–Petviashvili equation, a model for weakly nonlinear gravity–capillary waves on water of finite depth when the Bond number is close to one-third, which also admits lumps of the wave packet type. It is found that an exchange of stability occurs at a certain finite wave steepness, lumps being unstable below but stable above this critical value. As a result, a small-amplitude lump, which is linearly unstable and according to the BRDS equations would be prone to wave collapse, depending on the perturbation, either decays into dispersive waves or evolves into an oscillatory state near a finite-amplitude stable lump.
Divergent expansion, Borel summability and three-dimensional Navier–Stokes equation
Authors: Costin Ovidiu , Luo Guo , Tanveer Saleh
Published: May 2008

We describe how the Borel summability of a divergent asymptotic expansion can be expanded and applied to nonlinear partial differential equations (PDEs). While Borel summation does not apply for non-analytic initial data, the present approach generates an integral equation (IE) applicable to much more general data.

We apply these concepts to the three-dimensional Navier–Stokes (NS) system and show how the IE approach can give rise to local existence proofs. In this approach, the global existence problem in three-dimensional NS systems, for specific initial condition and viscosity, becomes a problem of asymptotics in the variable
p
(dual to 1/
t
or some positive power of 1/
t
). Furthermore, the errors in numerical computations in the associated IE can be controlled rigorously, which is very important for nonlinear PDEs such as NS when solutions are not known to exist globally.

Moreover, computation of the solution of the IE over an interval [0,
p
0
] provides sharper control of its
p
→∞ behaviour. Preliminary numerical computations give encouraging results.
On the linear stability of Stokes layers
Authors: Blennerhassett P.J , Bassom Andrew P
Published: May 2008

Oscillatory flows occur naturally, with applications ranging across many disciplines from engineering to physiology. Transition to turbulence in such flows is a topic of practical interest and this article discusses some recent work that has furthered our understanding of the stability of a class of time-periodic fluid motions. Our study starts with an examination of the linear stability of a classical flat Stokes layer. Although experiments conducted over many years have demonstrated conclusively that this layer is unstable at a sufficiently large Reynolds number, it has only been relatively recently that rigorous theoretical confirmation of this behaviour has been obtained. The analysis and numerical calculations for the planar Stokes layer were subsequently extended to flows in channels and pipes and for the flow within a torsionally oscillating circular cylinder. We discuss why our predictions for the onset of instability in these geometries are in disappointingly poor agreement with experimental results. Finally, some suggestions for future experimental work are given and some areas for future theoretical analysis outlined.
Palaeoproterozoic ice houses and the evolution of oxygen-mediating enzymes: the case for a late origin of photosystem II
Authors: Kirschvink Joseph L , Kopp Robert E
Published: May 2008

Two major geological problems regarding the origin of oxygenic photosynthesis are (i) identifying a source of oxygen pre-dating the biological oxygen production and capable of driving the evolution of oxygen tolerance, and (ii) determining when oxygenic photosynthesis evolved. One solution to the first problem is the accumulation of photochemically produced H2O2at the surface of the glaciers and its subsequent incorporation into ice. Melting at the glacier base would release H2O2, which interacts with seawater to produce O2in an environment shielded from the lethal levels of ultraviolet radiation needed to produce H2O2. Answers to the second problem are controversial and range from 3.8 to 2.2 Gyr ago. A sceptical view, based on the metals that have the redox potentials close to oxygen, argues for the late end of the range. The preponderance of geological evidence suggests little or no oxygen in the Late Archaean atmosphere (less than 1 ppm). The main piece of evidence for an earlier evolution of oxygenic photosynthesis comes from lipid biomarkers. Recent work, however, has shown that 2-methylhopanes, once thought to be unique biomarkers for cyanobacteria, are also produced anaerobically in significant quantities by at least two strains of anoxygenic phototrophs. Sterane biomarkers provide the strongest evidence for a date 2.7 Gyr ago or above, and could also be explained by the common evolutionary pattern of replacing anaerobic enzymes with oxygen-dependent ones. Although no anaerobic sterol synthesis pathway has been identified in the modern biosphere, enzymes that perform the necessary chemistry do exist. This analysis suggests that oxygenic photosynthesis could have evolved close in geological time to the Makganyene Snowball Earth Event and argues for a causal link between the two.
Methane, oxygen, photosynthesis, rubisco and the regulation of the air through time
Authors: Nisbet Euan G , Nisbet R. Ellen R
Published: May 2008

Rubisco I's specificity, which today may be almost perfectly tuned to the task of cultivating the global garden, controlled the balance of carbon gases and O
2
in the Precambrian ocean and hence, by equilibration, in the air. Control of CO
2
and O
2
by rubisco I, coupled with CH
4
from methanogens, has for the past 2.9 Ga directed the global greenhouse warming, which maintains liquid oceans and sustains microbial ecology.

Both rubisco compensation controls and the danger of greenhouse runaway (e.g. glaciation) put limits on biological productivity. Rubisco may sustain the air in either of two permissible stable states:
either
an anoxic system with greenhouse warming supported by both high methane mixing ratios as well as carbon dioxide,
or
an oxygen-rich system in which CO
2
largely fulfils the role of managing greenhouse gas, and in which methane is necessarily only a trace greenhouse gas, as is N
2
O. Transition from the anoxic to the oxic state risks glaciation. CO
2
build-up during a global snowball may be an essential precursor to a CO
2
-dominated greenhouse with high levels of atmospheric O
2
.

Photosynthetic and greenhouse-controlling competitions between marine algae, cyanobacteria, and terrestrial C3 and C4 plants may collectively set the CO
2
 : O
2
ratio of the modern atmosphere (last few million years ago in a mainly glacial epoch), maximizing the productivity close to rubisco compensation and glacial limits.
SOMNUS, a CCCH-Type Zinc Finger Protein inArabidopsis, Negatively Regulates Light-Dependent Seed Germination Downstream of PIL5
Authors: Kim Dong Hwan , Yamaguchi Shinjiro , Lim Soohwan , Oh Eunkyoo , Park Jeongmu , Hanada Atsushi , Kamiya Yuji , Choi Giltsu
Published: May 2008

Light absorbed by seed phytochromes of Arabidopsis thaliana modulates abscisic acid (ABA) and gibberellic acid (GA) signaling pathways at least partly via PHYTOCHROME-INTERACTING FACTOR3-LIKE5 (PIL5), a phytochrome-interacting basic helix-loop-helix transcription factor. Here, we report a new mutant, somnus (som), that germinates in darkness, independently of various light regimens. SOM encodes a nucleus-localized CCCH-type zinc finger protein. The som mutant has lower levels of ABA and elevated levels of GA due to expressional changes in ABA and GA metabolic genes. Unlike PIL5, however, SOM does not regulate the expression of GA-INSENSITIVE and REPRESSOR OF GA1 (RGA/RGA1), two DELLA genes encoding GA negative signaling components. Our in vivo analysis shows that PIL5 activates the expression of SOM by binding directly to its promoter, suggesting that PIL5 regulates ABA and GA metabolic genes partly through SOM. In agreement with these results, we also observed that the reduced germination frequency of a PIL5 overexpression line is rescued by the som mutation and that this rescue is accompanied by expressional changes in ABA and GA metabolic genes. Taken together, our results indicate that SOM is a component in the phytochrome signal transduction pathway that regulates hormone metabolic genes downstream of PIL5 during seed germination.
Are there genetic influences on addiction: evidence from family, adoption and twin studies
Authors: Agrawal Arpana , Lynskey Michael T.
Published: May 2008

Aims  In this exciting era of gene discovery, we review evidence from family, adoption and twin studies that examine the genetic basis for addiction. With a focus on the classical twin design that utilizes data on monozygotic and dizygotic twins, we discuss support in favor of heritable influences on alcohol, nicotine, cannabis and other illicit drug dependence.

Methods  We review whether these genetic factors also influence earlier stages (e.g. experimentation) of the addictive process and whether there are genetic influences specific to each psychoactive substance.

Results  Converging evidence from these studies supports the role of moderate to high genetic influences on addiction with estimates ranging from 0.30 to 0.70. The changing role of these heritable factors as a function of gender, age and cultural characteristics is also discussed. We highlight the importance of the interplay between genes and the environment as it relates to risk for addiction and the utility of the children‐of‐twins design for emerging studies of gene–environment interaction is presented.

Conclusions  Despite the advances being made by low‐cost high‐throughput whole genome association assays, we posit that information garnered from twin studies, especially extended twin designs with power to examine gene–environment interactions, will continue to form the foundation for genomic research.
Contingency management reduces drug‐related human immunodeficiency virus risk behaviors in cocaine‐abusing methadone patients
Authors: Hanson Tressa , Alessi Sheila M. , Petry Nancy M.
Published: May 2008

Aim  Contingency management (CM) is efficacious in reducing drug use. This study examined whether CM also reduces human immunodeficiency virus (HIV) risk behaviors and if these effects are mediated by longest duration of abstinence achieved during treatment.

Design  Data were analyzed from a subset of participants in a combined data set of three published randomized controlled trials of CM treatments.

Setting  A community‐based methadone maintenance clinic.

Participants  One‐hundred and sixty‐five cocaine‐abusing methadone maintenance patients.

Intervention  Participants received either standard methadone treatment or standard methadone treatment with CM for 3 months.

Measurements  The HIV Risk Behavior Scale (HRBS) was administered prior to randomization to a study condition and 3 months after the study treatments ended. The primary objective indicator of drug use was longest duration of cocaine and opioid abstinence achieved during treatment.

Findings  Relative to those assigned to standard care, participants receiving CM significantly decreased overall HIV risk behaviors and injection drug use risk behaviors. CM participants also achieved longer durations of consecutive cocaine and opioid abstinence during treatment. Duration of abstinence achieved mediated the relationship between treatment condition and HRBS difference scores.

Conclusions  These results suggest that CM treatment reduces HIV drug use risk behaviors in cocaine‐abusing methadone maintenance patients.