bluuebunny/crossref_metadata_2025 huggingface dataset:
Narrow-band optical transmission of metallic nanoslit arrays
Authors: Sun Zhijun , Yang Ying , Zuo Xiaoliu
Published: October 2012

Metallic nanoslit arrays usually demonstrate wide transmission bands for transverse-magnetic-polarized incidence light. Here, we show that by introducing multi-dielectric layers underneath the metallic structure layer on the substrate, a narrow peak is formed, whose bandwidth can be down to a few nanometers. Three types of resonance modes in the region under the metal layer are identified responsible for the formation of the peak, i.e., a two-dimensional cavity resonance mode, which supports optical transmission, and two in-plane hybrid surface plasmon resonance modes locating on both sides of the peak that suppresses the transmission. Such structures can be applied in advanced photonic devices.
Three-dimensional peculiarities in an avalanche transistor provide a broadened range of amplitudes and durations of the generated pulses
Authors: Duan Guoyong , Vainshtein Sergey , Kostamovaara Juha
Published: October 2012

It has been shown that the same avalanche transistor can generate both short (8A/2 ns) and longer high-current pulses (90 A/7 ns), but the operating perimeter length self-organized by the transistor is much smaller in the first case (∼0.1 mm) than in the second (1.6 mm). Since the two-dimensional approach failed to explain this experimental fact, we present here an interpretation using quasi-three-dimensional modelling. Spatial triggering inhomogeneity should not exceed ∼5% for the transistor to survive when generating long pulses, while the same moderate inhomogeneity ensures short-pulsing operation because powerful current filamentation quenches the switching in the rest of the perimeter.
Communication: A vibrational study of propargyl cation using the vacuum ultraviolet laser velocity-map imaging photoelectron method
Authors: Gao Hong , Lu Zhou , Yang Lei , Zhou Jingang , Ng C. Y.
Published: October 2012

By employing the vacuum ultraviolet (VUV) laser velocity-map imaging photoelectron (VUV-VMI-PE) method, we have obtained a vibrationally resolved photoelectron spectrum of gaseous propargyl radical [C3H3(X2B1)] in the energy range of 0-4600 cm−1 above its ionization energy. The cold C3H3 radicals were produced from a supersonically cooled radical beam source based on 193 nm ArF photodissociation of C3H3Cl. The VUV-VMI-PE spectrum of C3H3 thus obtained reveals a Franck-Condon factor (FCF) pattern with a highly dominant origin band along with weak vibrational progressions associated with excitations of the C–C ν5+(a1) and C≡C ν3+(a1) symmetric stretching modes and the CCH ν7+(b1) out-of-plane bending mode of C3H3+(X1A1). The ν5+(a1) vibrational frequency of 1120 cm−1 determined in the present study is lower than the value deduced from the recent Ar-tagged infrared photodissociation study by 102 cm−1, confirming the highly accurate vibrational frequency predictions obtained by the most recent state-of-the-art ab initio quantum calculations. The observation of the FCF disallowed ν7+(b1) mode is indicative of vibronic interactions. The discrepancy observed between the FCF pattern determined in the present study and that predicted by a recent high-level quantum theoretical investigation can be taken as evidence that the potential energy surfaces used in the latter theoretical study are in need of improvement in order to provide a reliable FCF prediction for the C3H3/C3H3+ photoionization system.
Control of Schottky barrier heights by inserting thin dielectric layers
Authors: Lin L. , Li H. , Robertson J.
Published: October 2012

The insertion of ultra-thin dielectric layers to lower n-type Schottky barrier heights is shown to partly involve the creation of a net interfacial dipole as well as unpinning of the Fermi level by suppression of metal-induced gap states. The existence of a net dipole requires a lack of cancellation of dipoles at the two interfaces. This requires a different metal(Ge)-O bond density at the two interfaces, in general requiring differing oxygen chemical potentials. This would need the inserted dielectric to be a diffusion barrier, not just able to create dipoles, favoring the use of Al2O3-based or nitrided dielectrics.
Very high remnant polarization and phase-change electromechanical response of BiFeO3-PbTiO3 at the multiferroic morphotropic phase boundary
Authors: Amorín H. , Correas C. , Ramos P. , Hungría T. , Castro A. , Algueró M.
Published: October 2012

We have investigated the occurrence of phase-change functional responses in the BiFeO3-PbTiO3 perovskite solid solution, analogous to those anticipated by a recent first-principles study of BiFeO3-BiCoO3. Like the former system, BiFeO3-PbTiO3 shows a morphotropic phase boundary (MPB) between multiferroic polymorphs of rhombohedral and tetragonal symmetries. MPB BiFeO3-PbTiO3 is a high temperature ferroelectric with the phase transition around 900 K, and a room temperature square-shape hysteresis loop with remnant polarization as high as 62 μC cm−2. Strain under the electric field was studied, and a phase-change response was found. Analogous magnetoelectric effects are expected from the multiferroic nature of this MPB.
Scaling of equivalent oxide thickness of atomic layer deposited HfO2 film using RuO2 electrodes suppressing the dielectric dead-layer effect
Authors: Kyeom Kim Hyo , Yu Il-Hyuk , Lee Jae Ho , Park Tae Joo , Seong Hwang Cheol
Published: October 2012

The influences of RuO2 metal gate on the dielectric performance of high-k HfO2 film on Si substrate were examined. The equivalent oxide thickness (EOT) of HfO2 film can be scaled down by ∼0.5 nm in the EOT range from 0.8 to 2.5 nm compared with the standard Pt gate case. This was attributed to the suppression of the dielectric dead-layer effect at the HfO2/RuO2 interface due to the possible ionic polarization of RuO2 within the screening length of the electrode. The estimated work function of RuO2 on HfO2 is ∼5.0 eV suggesting the appropriateness of RuO2 for p-transistor.
Light propagation in an optically active plate with topological charge
Authors: Wang Yicheng , Zhang Huaijin , Yu Haohai , Wang Zhengping , Wang Jiyang
Published: October 2012

We propose the optical zero-spin-to-orbital angular momentum and linear-to-vector polarization conversion realization by an optically active plate with a topological charge. By the geometric phase, the zero spin will also contribute to the orbital optical angular momentum and induce the optical spin-to-orbital angular momentum conversion. Moreover, the proposed angular momentum converter can convert the polarization from linear to radial or azimuthal with high efficiency. We believe that the proposed efficient converter will find potential applications in the study of quantum information conversion, generation and interaction of vector fields, phase and polarization singularities, etc.
Nanocrystalline diamond photonics platform with high quality factor photonic crystal cavities
Authors: Checoury X. , Néel D. , Boucaud P. , Gesset C. , Girard H. , Saada S. , Bergonzo P.
Published: October 2012

We demonstrate a diamond photonics platform with integrated suspended waveguide-cavity structures and two dimensional photonic crystal (PhC) cavities. PhC cavities with quality factors exceeding 2800 have been fabricated using a top-down approach from thin nanocrystalline diamond films. The developed technological process allows one to access these cavities in a fully planar geometry, including light injection and collection from the outside using lensed-fibers. This diamond platform opens the road to large scale fabrication of photonics devices including optical sensor chips.
Bulk silica-based luminescent materials by sol-gel processing of non-conventional precursors
Authors: Rodríguez J. A. , Fernández-Sánchez C. , Domínguez C. , Hernández S. , Berencén Y.
Published: October 2012

The sol-gel synthesis of bulk silica-based luminescent materials using innocuous hexaethoxydisilane and hexamethoxydisilane monomers, followed by one hour thermal annealing in an inert atmosphere at 950 °C–1150 °C, is reported. As-synthesized hexamethoxydisilane-derived samples exhibit an intense blue photoluminescence band, whereas thermally treated ones emit stronger photoluminescence radiation peaking below 600 nm. For hexaethoxydisilane-based material, annealed at or above 1000 °C, a less intense photoluminescence band, peaking between 780 nm and 850 nm that is attributed to nanocrystalline silicon is observed. Mixtures of both precursors lead to composed spectra, thus envisaging the possibility of obtaining pre-designed spectral behaviors by varying the mixture composition.
Characterization of a quantum phase transition in Dirac systems by means of the wave-packet dynamics
Authors: Romera E. , Torres J. J.
Published: October 2012

We study the signatures of phase transitions in the time evolution of wave-packets by analyzing two simple model systems: a graphene quantum dot model in a magnetic field and a Dirac oscillator in a magnetic field. We have characterized the phase transitions using the autocorrelation function. Our work also reveals that the description in terms of Shannon entropy of the autocorrelation function is a clear phase transition indicator.
Squirrel gliders use roadside glide poles to cross a road gap
Authors: Taylor Brendan D. , Goldingay Ross L.
Published: October 2012

Tall wooden poles placed along roadsides may enable road crossing by gliding mammals. We investigated the use of 12-m-high roadside glide poles at one location in Brisbane. Camera traps on roadside poles detected squirrel gliders (Petaurus norfolcensis) on one or both poles on 60 of 310 operational nights including at least 16 confirmed crossings during 125 nights when both roadside cameras operated concurrently. This provides definitive evidence that squirrel gliders will readily use tall wooden poles to make glide-crossings of two-lane roads. This is consistent with other investigations of glide poles and suggests that poles should be installed more broadly to reconnect habitat for gliding mammals.
Anatomy and essential oils from aerial organs in three species of Aldama (Asteraceae - Heliantheae) that have a difficult delimitation
Authors: Bombo Aline Bertolosi , De Oliveira Tuane Santos , De Oliveira Adriana Da Silva Santos , Rehder Vera Lúcia Garcia , Magenta Mara Angelina Galvão , Appezzato-Da-Glória Beatriz
Published: October 2012

Recently, molecular analysis caused the South American Viguiera Kunth species to be transferred to Aldama La Llave. However, the circumscription has not been established for certain of the South American species, including Aldama filifolia (Sch.Bip. ex Baker) E.E.Schill. & Panero, A. linearifolia (Chodat) E.E.Schill. & Panero and A. trichophylla (Dusén) Magenta (comb. nov.), which had previously been treated as synonyms because of their high similarity. Therefore, the present study aimed to evaluate the anatomy of the aerial organs, and the yield and chemical composition of the essential oils from these three species, to determine the differences among them and thereby assist in species distinction. The anatomical analysis identified characteristics unique to each species, which are primarily related to the position and occurrence of secretory structures. Histochemical analysis demonstrated that the glandular trichomes and the canals secrete lipophilic substances, which are characterised by the presence of essential oils. The analysis of these essential oils identified monoterpenes as their major constituent and allowed for the recognition of chemical markers for each species. The anatomical and chemical characteristics identified by the present study confirmed that the studied samples belong to three distinct taxa.
The public library and the social entrepreneur
Authors: Taylor Darren
Published: October 2012

Eco Computer Systems has been authorised by Lewisham Council to take over three of its five libraries, Sydenham, Crofton Park and Grove Park. Each library has a self-issue system and is run by volunteers guided by policy formulated by steering groups of local organisations and local people. Darren Taylor, the founder and owner of Eco Computer Systems, explains the motivation.
Estimating the economic value of libraries
Authors: Saxena Shishir , McDougall Andrew
Published: October 2012

The authors are economists working for the Australian consultancy, SGS Economics & Planning in Melbourne. In 2011, the company produced a report for the State Library of Victoria on the value of libraries. Shishir Saxena and Andrew McDougall were responsible for the research that went into this report.
Environmental complexity and stakeholder theory in formal research network evaluations
Authors: Wixted Brian , Holbrook J.
                      Adam
Published: October 2012

Governments in OECD countries are turning more and more towards creating networked entities as a means of organising cross-sector and multidisciplinary research. Yet, there is little discussion of how such networks operate and how they differ in evaluation terms from other research entities (individuals and organisations). This particularly relates to the policy objectives of networks. In this paper, we use the literature on evaluation, impact and value as a lens through which to focus on the nature and benefits of formal research networks. This paper seeks to refine our concepts of research networks and, in defining the concept of formal research networks, to map the policy issues in evaluating networks. We argue that, to do this, it is important that two extant literatures (stakeholder theory and organisational environments) be introduced into the analysis of network operations. We focus particularly on the significance of environmental complexity for network evaluation.
Rebuilding Pakistan in the Aftermath of the Floods: Disaster Relief as Conflict Prevention
Authors: Arai Tatsushi
Published: October 2012

In July and August 2010, Pakistan faced floods on an unprecedented scale that affected some 20 million people. Focus group interviews conducted in severely affected communities demonstrated a decline in the availability of accessible renewable resources to the point of increasing the potential for civil violence. These manifestations of environmental scarcity included strained landlord-tenant relations and other forms of structural inequity that magnified the devastating socio-economic effects of the floods. The article concludes with recommendations for conflict-sensitive measures to facilitate post-disaster recovery and defines humanitarian relief as an integral part of national security and conflict prevention in Pakistan.
Heeding Women's Voices: Breaking Cycles of Conflict and Deepening the Concept of Peacebuilding
Authors: Noma Emiko , Aker Dee , Freeman Jennifer
Published: October 2012

This article highlights the gap between institutional approaches to peacebuilding – which narrowly focus on post-conflict reconstruction of formal state institutions – and the lived experiences of grassroots peacebuilders. It analyses the documented stories of participants in the Women PeaceMakers 1 Program at the Joan B. Kroc Institute for Peace & Justice at the University of San Diego, demonstrating that peacebuilding does not occur simply after conflict, but at all phases of peace processes. The article and its three case studies – developed with three women peacemakers from the Philippines, Guatemala and South Africa – contend that this expands and deepens the practical and academic definitions of peacebuilding. Without this evolved understanding of the concept, women's actions to build peace will continue to be overlooked and underfunded.
Infidel Brands: Unveiling Alternative Meanings of Global Brands at the Nexus of Globalization, Consumer Culture, and Islamism
Authors: Izberk-Bilgin Elif
Published: October 2012

Religion and ideology are prominent forces shaping consumption. While consumer researchers have studied both topics considerably, examinations of religious ideology remain scant. Notably lacking is research on how religion, myths, and ideology intertwine in the marketplace, informing attitudes toward brands. This ethnography investigates how the religious ideology of Islamism informs brand meanings among low-income Turkish consumers and identifies three discourses that construct global brands as infidels. Informants use the infidel parable to characterize market societies as devoid of social equality, morality, and justice. Their critique culminates in a consumer jihad against global brands. Through the consumer jihad, informants accommodate and protest the social crises posed by modernity and globalization as they seek to recreate the Golden Age of Islam. Exploring the relationships among economic means, cultural capital, and religious ideology helps this study bridge related domains of research on religiosity, ideology, and brand meanings that are often investigated separately.
Commitment and Behavior Change: Evidence from the Field
Authors: Baca-Motes Katie , Brown Amber , Gneezy Ayelet , Keenan Elizabeth A. , Nelson Leif D.
Published: October 2012

Influencing behavior change is an ongoing challenge in psychology, economics, and consumer behavior research. Building on previous work on commitment, self-signaling, and the principle of consistency, a large, intensive field experiment (N = 2,416) examined the effect of hotel guests' commitment to practice environmentally friendly behavior during their stay. Notably, commitment was symbolic—guests were unaware of the experiment and of the fact that their behavior would be monitored, which allowed them to exist in anonymity and behave as they wish. When guests made a brief but specific commitment at check-in, and received a lapel pin to symbolize their commitment, they were over 25% more likely to hang at least one towel for reuse, and this increased the total number of towels hung by over 40%. This research highlights how a small, carefully planned intervention can have a significant impact on behavior. Theoretical and practical implications for motivating desired behavior are discussed.
Tip of the Hat, Wag of the Finger: How Moral Decoupling Enables Consumers to Admire and Admonish
Authors: Bhattacharjee Amit , Berman Jonathan Z. , Reed Americus
Published: October 2012

What reasoning processes do consumers use to support public figures who act immorally? Existing research emphasizes moral rationalization, whereby people reconstrue improper behavior in order to maintain support for a transgressor. In contrast, the current research proposes that people also engage in moral decoupling, a previously unstudied moral reasoning process by which judgments of performance are separated from judgments of morality. By separating these judgments, moral decoupling allows consumers to support a transgressor's performance while simultaneously condemning his or her transgressions. Five laboratory studies demonstrate that moral decoupling exists and is psychologically distinct from moral rationalization. Moreover, because moral decoupling does not involve condoning immoral behavior, it is easier to justify than moral rationalization. Finally, a field study suggests that in discussions involving public figures’ transgressions, moral decoupling may be more predictive of consumer support (and opposition) than moral rationalization.
On a new class of abstract impulsive differential equations
Authors: Hernández Eduardo , O’Regan Donal
Published: October 2012

In this note we introduce a new class of abstract impulsive differential equations for which the impulses are not instantaneous. We introduce the concepts of mild and classical solution and we establish some results on the existence of these types of solutions. An example involving a partial differential equation is presented.
Tor1 regulates protein solubility in Saccharomyces cerevisiae
Authors: Peters Theodore W. , Rardin Matthew J. , Czerwieniec Gregg , Evani Uday S. , Reis-Rodrigues Pedro , Lithgow Gordon J. , Mooney Sean D. , Gibson Bradford W. , Hughes Robert E.
Published: October 2012

Accumulation of insoluble protein in cells is associated with aging and aging-related diseases; however, the roles of insoluble protein in these processes are uncertain. The nature and impact of changes to protein solubility during normal aging are less well understood. Using quantitative mass spectrometry, we identify 480 proteins that become insoluble during postmitotic aging in Saccharomyces cerevisiae and show that this ensemble of insoluble proteins is similar to those that accumulate in aging nematodes. SDS-insoluble protein is present exclusively in a nonquiescent subpopulation of postmitotic cells, indicating an asymmetrical distribution of this protein. In addition, we show that nitrogen starvation of young cells is sufficient to cause accumulation of a similar group of insoluble proteins. Although many of the insoluble proteins identified are known to be autophagic substrates, induction of macroautophagy is not required for insoluble protein formation. However, genetic or chemical inhibition of the Tor1 kinase is sufficient to promote accumulation of insoluble protein. We conclude that target of rapamycin complex 1 regulates accumulation of insoluble proteins via mechanisms acting upstream of macroautophagy. Our data indicate that the accumulation of proteins in an SDS-insoluble state in postmitotic cells represents a novel autophagic cargo preparation process that is regulated by the Tor1 kinase.
Calcineurin-dependent cofilin activation and increased retrograde actin flow drive 5-HT–dependent neurite outgrowth inAplysiabag cell neurons
Authors: Zhang Xiao-Feng , Hyland Callen , Van Goor David , Forscher Paul
Published: October 2012

Neurite outgrowth in response to soluble growth factors often involves changes in intracellular Ca2+; however, mechanistic roles for Ca2+in controlling the underlying dynamic cytoskeletal processes have remained enigmatic. Bag cell neurons exposed to serotonin (5-hydroxytryptamine [5-HT]) respond with a threefold increase in neurite outgrowth rates. Outgrowth depends on phospholipase C (PLC) → inositol trisphosphate → Ca2+→ calcineurin signaling and is accompanied by increased rates of retrograde actin network flow in the growth cone P domain. Calcineurin inhibitors had no effect on Ca2+release or basal levels of retrograde actin flow; however, they completely suppressed 5-HT–dependent outgrowth and F-actin flow acceleration. 5-HT treatments were accompanied by calcineurin-dependent increases in cofilin activity in the growth cone P domain. 5-HT effects were mimicked by direct activation of PLC, suggesting that increased actin network treadmilling may be a widespread mechanism for promoting neurite outgrowth in response to neurotrophic factors.
AffyRNADegradation: control and correction of RNA quality effects in GeneChip expression data
Authors: Fasold Mario , Binder Hans
Published: October 2012

Motivation: Gene expression experiments aim to accurately quantify thousands of transcripts in parallel. Factors posterior to RNA extraction can, however, impair their accurate representation. RNA degradation and differences in the efficiency of amplification affect raw intensity measurements using Affymetrix expression arrays. The positional intensity decay of specifically hybridized probes along the transcript they intend to interrogate is used to estimate the RNA quality in a sample and to correct probe intensities for the degradation bias. This functionality, for which no previous software solution is available, is implemented in the R/Bioconductor package AffyRNADegradation presented here.

Availability: The package is available via Bioconductor at the URL http://bioconductor.org/packages/release/bioc/html/AffyRNA Degradation.html

Contact:  Fasold@izbi.uni-Leipzig.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Movements and site fidelity of harbour seals (Phoca vitulina) in Kattegat, Denmark, with implications for the epidemiology of the phocine distemper virus
Authors: Dietz Rune , Teilmann Jonas , Andersen Signe M. , Rigét Frank , Olsen Morten T.
Published: October 2012

Dietz, R., Teilmann, J., Andersen S. M. Rigét, F., and Olsen, M. T. 2013. Movements and site fidelity of harbour seals (Phoca vitulina) in Kattegat, Denmark, with implications for the epidemiology of the phocine distemper virus. – ICES Journal of Marine Science, 70:186–195. Twenty-seven harbour seals were caught and tagged at the island of Anholt in central Kattegat, Denmark, the epicentre of the phocine distemper virus (PDV) outbreaks in 1988 and 2002 that killed 50–60% of the populations. The satellite tagging shows that harbour seals from Anholt moved widely across Kattegat with a maximum distance of 249 km from the tagging haul-out site. Overall, females travelled over a wider area compared with males [90% kernel home range (KHR) females, 5189 km2; males, 3293 km2). KHR calculated for yearlings (6414 km2) is larger than for subadults (2534 km2), which again is larger than for adult seals (1713 km2), showing a strong site fidelity, indicating limited gene flow between haul-out sites. Distances moved and home range sizes increased across autumn, peaked in February–March, and decreased through spring. During the breeding season in spring, all seals were very stationary around Anholt. The onset of the PDV epizootics in 1988 and 2002 took place when the Anholt harbour seals congregate on the Island during April. Anholt seal were also documented to have contact with infected seal locations at Hesselø, Læsø, and the Swedish west coast, although this contact takes place during winter prior to the documented summer outbreaks.
In the presence of IL-21 human cord blood T cells differentiate to IL-10-producing Th1 but not Th17 or Th2 cells.
Authors: Doganci Aysefa , Birkholz Julia , Gehring Stephan , Puhl Alexander G. , Zepp Fred , Meyer Claudius U.
Published: October 2012

IL-21, a member of the IL-2 cytokine family, is mainly produced by activated CD4+ T cells and controls the activity of immune and also non-immune cells. As a pleiotropic cytokine, IL-21 acts on both innate and adaptive immune responses, suggesting that IL-21 may be a master regulator of the T-cell-dependent adaptive immune response. Although IL-21 is described as mostly promoting inflammation, evidence also suggests inhibitory effects of IL-21. However, its role, particularly in the human neonatal immune system, has not been detailed so far. Here, we assessed the effect of IL-21 in the specific context of the neonatal immune response and delineated differences between the human newborn and adult immune response. In umbilical cord blood, we demonstrated that IL-21 polarized naive CD4+ T cells into Th1 cells, producing IL-10, a key negative regulator during certain infections and autoimmunity. Furthermore, IL-21 stimulation increased IFNγ secretion and inhibited the development of Th2 and Th17 cells and molecules associated with their function. Thus, in neonates, known to show limitations in establishing Th1 responses, IL-21 played a clear role in supporting Th1 responses in vitro, while appearing irrelevant for the adult immune response. Overall, we demonstrated the capability of IL-21 to induce the immunosuppressive cytokine IL-10 and outlined its potential to compensate the restricted Th1 response in human newborns and consequently to reduce the susceptibility for infectious diseases in the first period of life.
Evidence of Muller’s ratchet in herpes simplex virus type 1
Authors: Jaramillo Nacarí , Domingo Esteban , Muñoz-Egea María Carmen , Tabarés Enrique , Gadea Ignacio
Published: October 2012

Population bottlenecks can have major effects in the evolution of RNA viruses, but their possible influence in the evolution of DNA viruses is largely unknown. Genetic and biological variation of herpes simplex virus type 1 (HSV-1) has been studied by subjecting 23 biological clones of the virus to 10 plaque-to-plaque transfers. In contrast to large population passages, plaque transfers led to a decrease in replicative capacity of HSV-1. Two out of a total of 23 clones did not survive to the last transfer in 143 TK–cells. DNA from three genomic regions (DNA polymerase, glycoprotein gD and thymidine kinase) from the initial and passaged clones was sequenced. Nucleotide substitutions were detected in the TK and gD genes, but not in the DNA polymerase gene. Assuming a uniform distribution of mutations along the genome, the average rate of fixation of mutations was about five mutations per viral genome and plaque transfer. This value is comparable to the range of values calculated for RNA viruses. Four plaque-transferred populations lost neurovirulence for mice, as compared with the corresponding initial clones. LD50values obtained with the populations subjected to serial bottlenecks were 4- to 67-fold higher than for their parental clones. These results equate HSV-1 with RNA viruses regarding fitness decrease as a result of plaque–to-plaque transfers, and show that population bottlenecks can modify the pathogenic potential of HSV-1. Implications for the evolution of complex DNA viruses are discussed.
Intratypic changes of the E1 gene and the long control region affect ori function of human papillomavirus type 18 variants
Authors: Amador-Molina Alfredo , González-Montoya José Luis , García-Carrancá Alejandro , Mohar Alejandro , Lizano Marcela
Published: October 2012

A persistent infection with high-risk human papillomavirus (HPV) constitutes the main aetiological factor for cervical cancer development. HPV16 and 18 are the most prevalent types found in cervical cancer worldwide. It has been proposed that HPV intratype variations may result in differences in biological behaviour. Three different HPV18 variants belonging to the Asian Amerindian (AsAi), European (E) and African (Af) branches have been associated with specific histological types of cervical cancer with different relative prognoses, suggesting that HPV18 genomic variations might participate in disease evolution. The E1 viral protein plays a critical role in controlling viral replication and load, requiring interaction with the E2 protein to bind to the long control region (LCR). In this work, we analysed if intratype variations in the LCR and E1 and E2 genes of HPV18 impact ori replication. While the changes found in E2 genes of the tested variants were irrelevant in replication, we found that variations in E1 and LCR in fact affect ori function. It was demonstrated that nucleotide differences in the LCR variants impact ori function. Nevertheless, HPV18 E1 Af gene was mainly involved in the highest ori replication, compared with the E and AsAi E1 variants. Immunofluorescence analysis showed increased levels of Af E1 in the nucleus, correlating with the enhanced ori function. Site-directed mutagenesis revealed that at least two positions in the N-terminal domain of E1 could impact its nuclear accumulation.
Mucosal transmission and pathogenesis of chronic wasting disease in ferrets
Authors: Perrott Matthew R. , Sigurdson Christina J. , Mason Gary L. , Hoover Edward A.
Published: October 2012

Chronic wasting disease (CWD) of cervids is almost certainly transmitted by mucosal contact with the causative prion, whether by direct (animal-to-animal) or indirect (environmental) means. Yet the sites and mechanisms of prion entry remain to be further understood. This study sought to extend this understanding by demonstrating that ferrets exposed to CWD via several mucosal routes developed infection, CWD prion protein (PrPCWD) amplification in lymphoid tissues, neural invasion and florid transmissible spongiform encephalopathy lesions resembling those in native cervid hosts. The ferrets developed extensive PrPCWD accumulation in the nervous system, retina and olfactory epithelium, with lesser deposition in tongue, muscle, salivary gland and the vomeronasal organ. PrPCWD accumulation in mucosal sites, including upper respiratory tract epithelium, olfactory epithelium and intestinal Peyer’s patches, make the shedding of prions by infected ferrets plausible. It was also observed that regionally targeted exposure of the nasopharyngeal mucosa resulted in an increased attack rate when compared with oral exposure. The latter finding suggests that nasal exposure enhances permissiveness to CWD infection. The ferret model has further potential for investigation of portals for initiation of CWD infection.
Detection of rhabdovirus viral RNA in oropharyngeal swabs and ectoparasites of Spanish bats
Authors: Aznar-Lopez Carolina , Vazquez-Moron Sonia , Marston Denise A. , Juste Javier , Ibáñez Carlos , Berciano Jose Miguel , Salsamendi Egoitz , Aihartza Joxerra , Banyard Ashley C. , McElhinney Lorraine , Fooks Anthony R. , Echevarria Juan
Published: October 2012

Rhabdoviruses infect a variety of hosts, including mammals, birds, reptiles, fish, insects and plants. As bats are the natural host for most members of the genus Lyssavirus, the specificity of the amplification methods used for active surveillance is usually restricted to lyssaviruses. However, the presence of other rhabdoviruses in bats has also been reported. In order to broaden the scope of such methods, a new RT-PCR, able to detect a diverse range of rhabdoviruses, was designed. The method detected 81 of 86 different rhabdoviruses. In total, 1488 oropharyngeal bat swabs and 38 nycteribiid samples were analysed, and 17 unique rhabdovirus-related sequences were detected. Phylogenetic analysis suggested that those sequences detected in bats did not constitute a monophyletic group, even when originating from the same bat species. However, all of the sequences detected in nycteribiids and one sequence obtained from a bat did constitute a monophyletic group with Drosophila melanogaster sigma rhabdovirus.
PrP-associated resistance to scrapie in five highly infected goat herds
Authors: Corbière Fabien , Perrin-Chauvineau Cécile , Lacroux Caroline , Costes Pierrette , Thomas Myriam , Brémaud Isabelle , Martin Samuel , Lugan Séverine , Chartier Christophe , Schelcher François , Barillet Francis , Andreoletti Olivier
Published: October 2012

The PrP gene polymorphisms at codons 142 (I/M), 154 (R/H), 211 (R/Q), 222 (Q/K) and 240 (S/P) and their association with susceptibility to classical scrapie infection were investigated in five French goat herds displaying a high disease prevalence (>10 %). On the basis of PrPSc detection in the central nervous system and in various lymphoid tissues, 301 of 1343 goats were found to be scrapie infected. The statistical analyses indicated that while P240 mutation had no direct impact on scrapie infection risk, the H154, Q211 and K222 mutations were associated with high resistance to scrapie. The M142 mutated allele was associated with a limited protection level against the disease. These results further reinforce the view that, like in sheep, the control and eradication of classical scrapie through the selection of certain PrP alleles could be envisaged in commercial goat population.
An Ancient Duplication of Apple MYB Transcription Factors Is Responsible for Novel Red Fruit-Flesh Phenotypes
Authors: Chagné David , Lin-Wang Kui , Espley Richard V. , Volz Richard K. , How Natalie M. , Rouse Simon , Brendolise Cyril , Carlisle Charmaine M. , Kumar Satish , De Silva Nihal , Micheletti Diego , McGhie Tony , Crowhurst Ross N. , Storey Roy D. , Velasco Riccardo , Hellens Roger P. , Gardiner Susan E. , Allan Andrew C.
Published: October 2012

Anthocyanin accumulation is coordinated in plants by a number of conserved transcription factors. In apple (Malus × domestica), an R2R3 MYB transcription factor has been shown to control fruit flesh and foliage anthocyanin pigmentation (MYB10) and fruit skin color (MYB1). However, the pattern of expression and allelic variation at these loci does not explain all anthocyanin-related apple phenotypes. One such example is an open-pollinated seedling of cv Sangrado that has green foliage and develops red flesh in the fruit cortex late in maturity. We used methods that combine plant breeding, molecular biology, and genomics to identify duplicated MYB transcription factors that could control this phenotype. We then demonstrated that the red-flesh cortex phenotype is associated with enhanced expression of MYB110a, a paralog of MYB10. Functional characterization of MYB110a showed that it was able to up-regulate anthocyanin biosynthesis in tobacco (Nicotiana tabacum). The chromosomal location of MYB110a is consistent with a whole-genome duplication event that occurred during the evolution of apple within the Maloideae family. Both MYB10 and MYB110a have conserved function in some cultivars, but they differ in their expression pattern and response to fruit maturity.
Production of Diploid Male Gametes in Arabidopsis by Cold-Induced Destabilization of Postmeiotic Radial Microtubule Arrays
Authors: De Storme Nico , Copenhaver Gregory P. , Geelen Danny
Published: October 2012

Whole-genome duplication through the formation of diploid gametes is a major route for polyploidization, speciation, and diversification in plants. The prevalence of polyploids in adverse climates led us to hypothesize that abiotic stress conditions can induce or stimulate diploid gamete production. In this study, we show that short periods of cold stress induce the production of diploid and polyploid pollen in Arabidopsis (Arabidopsis thaliana). Using a combination of cytological and genetic analyses, we demonstrate that cold stress alters the formation of radial microtubule arrays at telophase II and consequently leads to defects in postmeiotic cytokinesis and cell wall formation. As a result, cold-stressed male meiosis generates triads, dyads, and monads that contain binuclear and polynuclear microspores. Fusion of nuclei in binuclear and polynuclear microspores occurs spontaneously before pollen mitosis I and eventually leads to the formation of diploid and polyploid pollen grains. Using segregation analyses, we also found that the majority of cold-induced dyads and triads are genetically equivalent to a second division restitution and produce diploid gametes that are highly homozygous. In a broader perspective, these findings offer insights into the fundamental mechanisms that regulate male gametogenesis in plants and demonstrate that their sensitivity to environmental stress has evolutionary significance and agronomic relevance in terms of polyploidization.
Diagnosis and therapy of pancreas divisum by ERCP: A single center experience
Authors: Rustagi Tarun , Golioto Michael
Published: October 2012

Objective

The aim of this study was to determine the diagnosis and endoscopic management of pancreas divisum with results from long‐term experience at our institution.

Methods

A prospectively collected database of all patients who underwent endoscopic retrograde cholangiopancreatography (ERCP) with the diagnosis of pancreas divisum at our institution from January 2001 to April 2010 was retrospectively analyzed.

Results

A total of 45 patients were identified with pancreas divisum with 62 ERCP procedures. The major indication for ERCP included pancreatitis in 33 patients (73.3%), of whom 18 had idiopathic recurrent acute pancreatitis, 8 had recurrent pancreatic‐type pain and 7 had chronic pancreatitis. The median size of the incision of sphincterotomy was 5 mm (range 3–8 mm). In all 37 patients (82.2%) underwent placement of stent into the dorsal pancreatic duct, with a median stent size of 5 Fr by 7 cm (range 3–10 Fr by 3–12 cm). The overall response rate was 75.8%.

Conclusions

The frequency of finding pancreas divisum during ERCP varies among institutions and is low compared with the autopsy series, given that many patients may remain asymptomatic or might not undergo ERCP even if the symptoms develop. Our study is the first to describe specific procedure‐related details during therapeutic endoscopy for pancreas divisum.
Effect of recombinant Lactobacillus casei expressing interleukin‐10 in dextran sulfate sodium‐induced colitis mice
Authors: Qiu Zhi Bing , Chen Jian , Chen Jia Jie , Rong Lan , Ding Wei Qun , Yang Hai Jing , Zhong Liang
Published: October 2012

Objective

To study the effect of recombinant Lactobacillus casei (L.casei) expressing interleukin (IL)‐10 combined with 5‐aminosalicylic acid (5‐ASA) in dextran sulfate sodium (DSS)‐induced colitis mice.

Methods

Recombinant L. casei CECT 5276, which can secrete IL‐10, was constructed. The length of colon tissue, disease activity index (DAI) and histological score (HS) of the mice were determined to evaluate the modeling and the effectiveness of L. casei. Real‐time polymerase chain reaction (PCR), Western blot and ELISA were used to determine the levels of nuclear factor kappa‐light‐chain‐enhancer of activated B cells (NF‐κB), peroxisome proliferator‐activated receptor (PPAR)‐γ, interferon (IFN)‐γ, transforming growth factor (TGF)‐β and IL‐10.

Results

Recombinant L. casei expressing IL‐10 combined with 5‐ASA was more effective than L. casei with 5‐ASA. Among the three different concentrations of the recombinant L. casei, the highest concentration group (2 × 109 colony‐forming units/mL) had the best effectiveness.

Conclusions

Recombinant L. casei combined with 5‐ASA is effective in the treatment of DSS‐induced colitis. The possible mechanism might be the blocking of the excessive activation of NF‐κB pathway, thus suppressing the release of inflammation‐related factors.
Consequences of increased temperature and acidification on bacterioplankton community composition during a mesocosm spring bloom in the Baltic Sea
Authors: Lindh Markus V. , Riemann Lasse , Baltar Federico , Romero‐Oliva Claudia , Salomon Paulo S. , Granéli Edna , Pinhassi Jarone
Published: October 2012

Despite the paramount importance of bacteria for biogeochemical cycling of carbon and nutrients, little is known about the potential effects of climate change on these key organisms. The consequences of the projected climate change on bacterioplankton community dynamics were investigated in a Baltic Sea spring phytoplankton bloom mesocosm experiment by increasing temperature with 3°C and decreasing pH by approximately 0.4 units via CO2 addition in a factorial design. Temperature was the major driver of differences in community composition during the experiment, as shown by denaturing gradient gel electrophoresis (DGGE) of amplified 16S rRNA gene fragments. Several bacterial phylotypes belonging to Betaproteobacteria were predominant at 3°C but were replaced by members of the Bacteriodetes in the 6°C mesocosms. Acidification alone had a limited impact on phylogenetic composition, but when combined with increased temperature, resulted in the proliferation of specific microbial phylotypes. Our results suggest that although temperature is an important driver in structuring bacterioplankton composition, evaluation of the combined effects of temperature and acidification is necessary to fully understand consequences of climate change for marine bacterioplankton, their implications for future spring bloom dynamics, and their role in ecosystem functioning.
IgE, but not IgG4, antibodies to Ara h 2 distinguish peanut allergy from asymptomatic peanut sensitization
Authors: Hong X. , Caruso D. , Kumar R. , Liu R. , Liu X. , Wang G. , Pongracic J. A. , Wang X.
Published: October 2012

Background

There are no available clinical tests that can accurately predict peanut allergy (PA) and/or anaphylaxis. This study is aimed at evaluating whether the component‐resolved diagnostic (CRD) IgE and IgG4 tests can (i) distinguish PA from asymptomatic peanut sensitization (PS) and (ii) differentiate anaphylactic from nonanaphylactic PA.

Methods

This study included 20 nonatopic controls, 58 asymptomatically peanut‐sensitized children, 55 nonanaphylactic, and 53 anaphylactic PA cases from the Chicago Food Allergy Study. IgE and IgG4 to 103 allergens were measured using the ImmunoCAP ISAC technology and were compared among each group of children. The random forest test was applied to estimate each allergen's ability to predict PA and/or peanut anaphylaxis.

Results

Peanut allergy cases (with or without anaphylaxis) had significantly higher IgE reactivity to Ara h 1–3 (peanut allergens) and Gly m 5–6 (soy allergens) than asymptomatically sensitized children (P < 0.00001). Similar but more modest relationships were found for IgG4 to Ara h 2 (P < 0.01). IgE to Ara h 2 was the major contributor to accurate discrimination between PA and asymptomatic sensitization. With an optimal cutoff point of 0.65 ISU‐E, it conferred 99.1% sensitivity, 98.3% specificity, and a 1.2% misclassification rate in the prediction of PA, which represented a higher discriminative accuracy than IgE to whole peanut extract (P = 0.008). However, none of the IgE and/or IgG4 tests could significantly differentiate peanut anaphylaxis from nonanaphylactic PA.

Conclusions

IgE to Ara h 2 can efficiently differentiate clinical PA from asymptomatic PS, which may represent a major step forward in the diagnosis of PA.
Early response and local control of stage I non‐small‐cell lung cancer after stereotactic radiotherapy: difference by histology
Authors: Miyakawa Akifumi , Shibamoto Yuta , Kosaki Katsura , Hashizume Chisa
Published: October 2012

To investigate the possible influences of various factors on tumor response to radiation, regression speeds and long‐term local control rates of primary adenocarcinoma and squamous cell carcinoma of the lung after stereotactic body radiotherapy were evaluated. Ninety‐one patients (65 men and 26 women) with a median age of 76 years were serially examined using computed tomography at 2, 4 and 6 months after treatment. Tumor histology was adenocarcinoma in 62 patients and squamous cell carcinoma in 29 patients. The prescribed dose was 48 Gy in four fractions given twice a week for T1 tumors (≤3 cm) and 52 Gy in four fractions given twice a week for T2 tumors (3–5 cm). Tumor shrinkage speed and 3‐year local control rates were similar between T1 and T2 tumors and between patients with normal pulmonary function and those with impaired function. Squamous cell carcinomas shrank faster than adenocarcinomas at 2 and 4 months after radiation, but mean relative tumor size at 6 months and local control rates at 3 years did not differ significantly between the two histologies. Tumors in patients with a higher hemoglobin level tended to shrink faster but the control rates were not different. It is concluded that, although squamous cell carcinoma shrinks faster than adenocarcinoma, the two types of lung cancer are of similar radiosensitivity in terms of long‐term control rates. Radiosensitivity should not be evaluated by early tumor response. (Cancer Sci 2013; 104: 130–134)
Motor Origins of Tool Use
Authors: Kahrs Björn A. , Jung Wendy P. , Lockman Jeffrey J.
Published: October 2012

The current study examines the developmental trajectory of banging movements and its implications for tool use development. Twenty (6‐ to 15‐month‐old) infants wore reflective markers while banging a handled cube; movements were recorded at 240 Hz. Results indicated that through the second half‐year, banging movements undergo developmental changes making them ideally suited for instrumental hammering and pounding. Younger infants were inefficient and variable when banging the object: Their hands followed circuitous paths of great lengths at high velocities. By 1 year, infants showed consistent and efficient straight up‐down hand trajectories of smaller magnitude and velocity, allowing for precise aiming and delivering dependable levels of force. The findings suggest that tool use develops gradually from infants' existing manual behaviors.