bluuebunny/crossref_metadata_2025 huggingface dataset:
Visible light detection using single-walled carbon nanotube film and gold nanoparticles or nanorods
Authors: Liu Ji , He Weiwei , Hu Lijun , Liu Zheng , Zhou Haiqing , Wu Xiaochun , Sun Lianfeng
Published: May 2010

Visible light sensing devices using single-walled carbon nanotube (SWNT) film and gold nanoparticles or nanorods were reported. In the devices, half of the SWNT film was decorated with gold nanoparticles or nanorods. When visible light is incident on the device, a temperature difference can be built up between the SWNT film with and without gold nanoparticles (nanorods) due to surface plasmon resonance. As a result, an open circuit voltage can be obtained. The Voc induced and responsivities of these devices are closely related to the wavelength and the intensity of the incident light, indicating the application in visible light detecting.
The effect of rotation and viscous heating on the interpretation of experimental heat diffusivities in the edge pedestal
Authors: Stacey Weston M.
Published: May 2010

A formalism is presented for evaluating the effect of plasma rotation, via viscous heating, on the interpretation of thermal conductivities from measured temperature and density gradients in the edge pedestal. An application to a H-mode DIII-D [J. Luxon, Nucl. Fusion 42, 614 (2002)] discharge indicates that the effect could be significant.
Nanograss and nanostructure formation on silicon using a modified deep reactive ion etching
Authors: Mehran M. , Mohajerzadeh S. , Sanaee Z. , Abdi Y.
Published: May 2010

Silicon nanograss and nanostructures are realized using a modified deep reactive ion etching technique on both plane and vertical surfaces of a silicon substrate. The etching process is based on a sequential passivation and etching cycle, and it can be adjusted to achieve grassless high aspect ratio features as well as grass-full surfaces. The incorporation of nanostructures onto vertically placed parallel fingers of an interdigital capacitive accelerometer increases the total capacitance from 0.45 to 30 pF. Vertical structures with features below 100 nm have been realized.
Improved interfacial state density in Al2O3/GaAs interfaces using metal-organic chemical vapor deposition
Authors: Cheng Cheng-Wei , Fitzgerald Eugene A.
Published: May 2010

In situ deposition of Al2O3 on GaAs was performed by chemical-vapor-deposition (CVD) with trimethyaluminum and isopropanol as precursors. A gallium-rich region in the Al2O3 thin film above the interface was spontaneously formed via the in situ CVD process. Ga-enrichment of the interface was observed using secondary ion mass spectrometry (SIMS) depth profile measurement. X-ray photoelectron spectroscopy (XPS) results show that the gallium-rich region consists of Al2O3 and Ga2O3, but no As2O3 was observed. The Ga2O3–Al2O3 layer above the oxide/GaAs interface reduces the frequency dispersion as measured with capacitance-voltage (C-V) characteristics and lowers the interfacial state density as compared to atomic-layer-deposition *(ALD) deposited films which do not display this gallium enrichment above the interface.
Strongly suppressed 1/f noise and enhanced magnetoresistance in epitaxial Fe–V/MgO/Fe magnetic tunnel junctions
Authors: Herranz D. , Bonell F. , Gomez-Ibarlucea A. , Andrieu S. , Montaigne F. , Villar R. , Tiusan C. , Aliev F. G.
Published: May 2010

Alloying Fe electrodes with V, through reduced FeV/MgO interface mismatch in epitaxial magnetic tunnel junctions with MgO barriers, notably suppresses both nonmagnetic (parallel) and magnetic (antiparallel) state 1/f noise and enhances tunneling magnetoresistance. A comparative study of the room temperature electron transport and low frequency noise in Fe1−xVx/MgO/Fe and Fe/MgO/Fe1−xVx magnetic tunnel junctions with 0≤x≤0.25 reveals that V doping of the bottom electrode for x<0.1 reduces in nearly two orders of magnitude the normalized nonmagnetic and magnetic 1/f noise. We attribute the enhanced TMR and suppressed 1/f noise to strongly reduced misfit and dislocation density.
A flexible cold microplasma jet using biocompatible dielectric tubes for cancer therapy
Authors: Kim Jae Young , Kim Sung-O , Wei Yanzhang , Li Jinhua
Published: May 2010

This paper describes a flexible microplasma jet device using a Tygon® S-54-HL tube as a biocompatible tube and its potential in developing cancer therapies. The optical and physical properties of the plasma jets and preliminary apoptosis data of cultured murine tumor cells and nontumor fibroblast cells treated with these plasma jets are presented. Microplasma jets were observed to induce apoptosis in cultured murine cells in a dose-dependent manner. The murine melanoma tumor cells were more sensitive to plasma treatment than fibroblast cells. These features allow the direct and precise application of this microplasma jet device to tumor cells.
An Experiential Approach to Research in Planning
Authors: Straatemeier Thomas , Bertolini Luca , te Brömmelstroet Marco , Hoetjes Perry
Published: May 2010

Most planning research seeks to understand how current planning practices influence (and are influenced by) the processes and institutional contexts of decision making and the transformation of spaces. Typically, analytical methods borrowed from other social sciences are employed for this purpose. However, if one wants to know how new planning practices can be generated, a different research approach seems to be needed. Relevant innovations do not originate in an academic vacuum, but have to be developed in coproduction with intended users and in the context of their intended use. Only then can a reciprocal learning process between research and practice be activated in which original hypotheses about possible planning innovations are developed through iterative testing, reflection, and adaptation. In our opinion, carrying out research into possible planning innovations thus requires a different type of research methodology from the one typically applied. Because of its static nature, a traditional comparative case-study analysis—as often used in planning research—does not allow for such an iterative, evolutionary process. In this paper we propose a new methodology, which we have labelled ‘experiential case-study analysis’. In this approach each case study provides learning experiences that fuel theory building, but also serve as input for the next case study. We have used this approach to develop and test different planning innovations in three case studies in the field of transport and urban planning in The Netherlands.
Assessing Wind Comfort in Urban Planning
Authors: Reiter Sigrid
Published: May 2010

There are increasing concerns regarding the quality of urban public spaces. Wind is one important environmental factor that influences pedestrians' comfort and safety. In modern cities there are increasing numbers of high constructions and complex forms which can involve problems of significant wind discomfort around these buildings. Architects and town planners need guidelines and simple design tools to take account of wind in their projects. This paper reports the progress made in using computational fluid dynamics (CFD) simulations for assessing wind comfort in urban planning. Fluent software was validated for wind studies in urban environments by comparing CFD simulation results with published wind-tunnel tests. This validation shows that mean wind velocities around buildings can be simulated numerically with a very high degree of accuracy. On the basis of the results of a large number of CFD simulations, a methodology and simple graphical tools were developed to quantify critical wind speeds around buildings. In practice these should help architects and town planners when designing our built environment. Moreover, this study shows how numerical modelling is now a high-performance tool for developing useful guidelines and simple design tools for urban planners.
Lock-in and its Influence on the Project Performance of Large-Scale Transportation Infrastructure Projects: Investigating the Way in Which Lock-in Can Emerge and Affect Cost Overruns
Authors: Cantarelli Chantal C , Flyvbjerg Bent , van Wee Bert , Molin Eric J E
Published: May 2010

Lock-in, the escalating commitment of decision makers to an ineffective course of action, has the potential to explain the large cost overruns in large-scale transportation infrastructure projects. Lock-in can occur both at the decision-making level (before the decision to build) and at the project level (after the decision to build) and can influence the extent of overruns in two ways. The first involves the ‘methodology’ of calculating cost overruns according to the ‘formal decision to build’. Due to lock-in, however, the ‘real decision to build’ is made much earlier in the decision-making process and the costs estimated at that stage are often much lower than those that are estimated at a later stage in the decision-making process, thus increasing cost overruns. The second way that lock-in can affect cost overruns is through ‘practice’. Although decisions about the project (design and implementation) need to be made, lock-in can lead to inefficient decisions that involve higher costs. Sunk costs (in terms of both time and money), the need for justification, escalating commitment, and inflexibility and the closure of alternatives are indicators of lock-in. Two case studies, of the Betuweroute and the High Speed Link-South projects in the Netherlands, demonstrate the presence of lock-in and its influence on the extent of cost overruns at both the decision-making and project levels. This suggests that recognition of lock-in as an explanation for cost overruns contributes significantly to the understanding of the inadequate planning process of projects and allows development of more appropriate means.
Flesh, Metal, Road: Tracing the Machinic Geographies of Race
Authors: Swanton Dan
Published: May 2010

By approaching the road as a contact zone, I develop novel insights into the turbulent multiculture of a northern mill town in England. Through a montage of encounters with taxis and ‘flash’ cars on the streets of Keighley, West Yorkshire, I illustrate how social differentiation is performed on the road as human difference is sorted and judged through assemblages of flesh, metal, and road. I develop recent debates on the social construction of race, arguing for a perspective that foregrounds what race does in social interaction. And so I offer a reconsideration of race as a technology of differentiation at work in interaction that is allied to what I call the ‘racism of assemblages’, which traces how loose racial summaries distributed across bodies, things, and spaces become the basis for perception, judgment, and action. In the process, I also assemble perspectives on multiculture from below, which disrupt talk of segregation and ‘parallel lives' in northern mill towns, and question arguments that more interaction and community cohesion are the answer to living with difference.
Natural Visual-Field Features Enhance Vection
Authors: Bubka Andrea , Bonato Frederick
Published: May 2010

When a large optic-flow pattern is viewed, induced self-motion perception (vection) can result even for observers who are stationary relative to Earth. Vection is common in optokinetic drums, large-screen cinemas, vehicle simulators, and other virtual environments. However, not all optic-flow patterns are equally effective in producing vection. We hypothesized that visual-field characteristics that typically accompany self-motion are likely to facilitate vection. The two characteristics tested in the current study were color and global visual-field movement consistent with head bob and sway that occurs when a person walks or runs. Stationary observers viewed first-person perspective video clips on a rear-projection screen that depicted forward self-motion. Vection onset and magnitude were measured with a computer-interfaced slide device. In experiment 1, either a grayscale or color video was presented. In experiment 2, the video was shot either from a smooth rolling cart or with a hand-held camera that yielded gait information in addition to global expansion. Vection onset was found to be faster, and stronger in magnitude, when videos containing color and gait movements were viewed. These results suggest that visual-field features that are common during actual self-motion can enhance vection in a virtual environment, resulting in a more realistic experience for viewers.
Molecules match morphology: mitochondrial DNA supports Bayer's Lytreia - Bebryce - Heterogorgia (Alcyonacea : Octocorallia) clade hypothesis
Authors: Vargas Sergio , Eitel Michael , Breedy Odalisca , Schierwater Bernd
Published: May 2010

Several studies attempting to clarify the taxonomy and systematics of Octocorallia have highlighted the important role of molecular characters in corroborating or rejecting previous hypotheses based on morphological variation. One such hypothesis is that of a close phylogenetic relationship between the genera Lytreia, Bebryce and Heterogorgia proposed by Bayer based on morphological studies of the genera. Herein, we tested Bayer’s hypothesis using the mitochondrial marker mshI. We deduced a molecular phylogeny including members of the families Gorgoniidae and ‘Paramuriceidae’ that corroborated the existence of Bayer’s Lytreia–Bebryce–Heterogorgia clade. In addition, we provide a morphological assessment of the three genera as well as diagnoses for each of them. We also discuss, based on the phylogenetic results obtained, the evolution of sclerite morphology within Bayer’s Lytreia–Bebyce–Heterogorgia clade. Finally, we propose a Tethyan origin for the Lytreia–Bebryce–Heterogorgia clade.
Systematic revision, cladistics and biogeography of the genus Neogutierrezia Martínez (Coleoptera:Scarabaeidae) and its phylogenetic placement in Rutelinae based on structural alignment of 28S rDNA sequences
Authors: Ocampo Federico C. , Ruiz-Manzanos Eider , E. Marvaldi Adriana
Published: May 2010

The Argentinean endemic genus Neogutierrezia Martínez, 1953 (Scarabaeidae : Rutelinae) is revised and seven new species are described: N. bicolor Ocampo & Ruiz-Manzanos, sp. nov., N. chelii Ocampo & Ruiz-Manzanos, sp. nov., N. galileoi Ocampo & Ruiz-Manzanos, sp. nov., N. lagosae Ocampo & Ruiz-Manzanos, sp. nov., N. payuniensis Ocampo & Ruiz-Manzanos, sp. nov., N. scutata Ocampo & Ruiz-Manzanos, sp. nov. and N. variabilis Ocampo & Ruiz-Manzanos, sp. nov. Species status is proposed for N. affinis Martínez stat. nov., which was formerly considered as subspecies of N. mirabilis Martínez. The genus Neogutierrezia now includes 10 species distributed in the Monte biogeographic province in Argentina. In order to clarify the systematic placement of the genus Neogutierrezia, a molecular phylogenetic analysis was performed using structurally aligned 28S rDNA sequences (expansion segments D2 and D3) from 23 taxa in Scarabaeoidea, including two representative species of Neogutierrezia. This is the first report of an annotated secondary structure alignment of the D2 and D3 segments of 28S rRNA that spans a wide sample of scarabaeoids, providing a useful homology template for further phylogenetic reconstruction in these and closely related beetles. Results of the molecular parsimony analysis strongly indicate that the genus is closely related to members of the Rutelinae (Scarabaeidae), and thus Neogutierrezia Martínez is transferred from Melolonthinae: Pachydemini to Rutelinae, new placement. A morphological cladistic analysis of the genus was also undertaken, including all the 10 known species in the genus plus two outgroup taxa in Rutelinae, and based on 53 adult characters. The most-parsimonious cladogram provides evidence for the monophyly of the genus, which shows three main clades, distributed in Central Monte and Southern Monte. The adult morphology of the 10 species is described and a key is provided, along with illustrations of the diagnostic characters. The biogeography of species in the genus is discussed.
Hypotheses from mitochondrial DNA: congruence and conflict between DNA sequences and morphology in Dolichopodinae systematics (Diptera:Dolichopodidae)
Authors: Pollet Marc , Germann Christoph , Tanner Samuel , Bernasconi Marco Valerio
Published: May 2010

The molecular phylogeny of the subfamily Dolichopodinae (Diptera : Dolichopodidae) is reconstructed based on 79 species of 7 dolichopodine genera as ingroup, and 10 non-dolichopodine species from different genera as outgroup. A Bayesian analysis based on a mitochondrial DNA dataset consisting of 1702 characters (COI : 810; 12S : 366; 16S : 526) was carried out. Genital and non-genital morphological characters from a hitherto unpublished data matrix (based on 57 Dolichopodidae species) were used to explain and support the lineages hypothesised by our molecular phylogenetic analysis. The monophyly of the subfamily Dolichopodinae, and of the genera Dolichopus and Gymnopternus, was confirmed. The molecular analysis yielded nine species groups in Dolichopus that were proposed in previous studies using COI and Cyt-b. No evidence was found to support a clade including Dolichopus, Ethiromyia, and Gymnopternus. The genus Hercostomus proved polyphyletic with respect to Poecilobothrus, Sybistroma, and Gymnopternus. The following lineages were represented by strongly supported clades: Hercostomus germanus species group, H. vivax species group, H. nigrilamellatus species group, H. plagiatus species group, H. longiventris species group, H. fulvicaudis species group, and Poecilobothrus, Gymnopternus, Tachytrechus and Sybistroma (including Hercostomus nanus and H. parvilamellatus). Two clades that were previously established on the basis of morphology were confirmed in our phylogenetic analysis: (i) Poecilobothrus and the flower-feeding Hercostomus germanus species group, and (ii) the H. longiventris lineage and Sybistroma. In most cases, the groups identified in the molecular analysis could be supported and explained by morphological characters. Species of the Hercostomus germanus species group, Poecilobothrus, the Hercostomus longiventris species group, and a Sybistroma subclade have a similar microhabitat affinity.
The Rhynchoproctinae, a south-east Asiatic subfamily of giant millipedes: cladistic analysis, classification, four new genera and a deviating new species from north-west Thailand (Diplopoda:Spirostreptida:Harpagophoridae)
Authors: Pimvichai Piyatida , Enghoff Henrik , Panha Somsak
Published: May 2010

The subfamily Rhynchoproctinae is revised at the generic level. Four new genera and a remarkable new species are described: Alienostreptus, gen. nov. from Vietnam, Armatostreptus, gen. nov., Heptischius, gen. nov., and Heptischius lactuca, sp. nov. from Thailand, and Prominulostreptus, gen. nov. from China. Agaricogonopus Zhang & Zhang, 1997, is removed from synonymy with Junceustreptus Demange, 1961. All 14 genera of the subfamily share three diagnostic gonopodal characters: the posterior surface of the anterior coxal fold forms a deep concavity, there is a mesal flap on the gonopod coxa, and the posterior coxal fold is very low. A cladistic analysis based on morphological data supports monophyly of Rhynchoproctinae and the distincness of the newly described genera. A dichotomous key to the genera is included.
'Moa's Ark' or 'Goodbye Gondwana': is the origin of New Zealand's terrestrial invertebrate fauna ancient, recent or both?
Authors: Giribet Gonzalo , Boyer Sarah L.
Published: May 2010

Evaluating the hypothesis of New Zealand’s total submersion during the Oligocene requires the strictest tests, including sound phylogenetic data and dating of phylogenies. Although New Zealand has been traditionally considered to host ancient biota that originated by vicariance after it separated from Australia ~80 Mya, the ancient origins of its biota have been recently questioned, with some authors even suggesting that all current land organisms had to arrive to the islands after it re-emerged from the ocean 22 million years ago. Here we examine examples of short-range endemic soil-dwelling invertebrates and find compelling evidence that at least some of them are the result of old lineages that diversified in New Zealand before the hypothesised submersion event 22 million year ago. We conclude that New Zealand indeed has old lineages as well as recently diversified lineages and compare this situation with that of other more stable areas of the Neotropics.
Aurora A contributes to p150glued phosphorylation and function during mitosis
Authors: Romé Pierre , Montembault Emilie , Franck Nathalie , Pascal Aude , Glover David M. , Giet Régis
Published: May 2010

Aurora A is a spindle pole–associated protein kinase required for mitotic spindle assembly and chromosome segregation. In this study, we show that Drosophila melanogaster aurora A phosphorylates the dynactin subunit p150glued on sites required for its association with the mitotic spindle. Dynactin strongly accumulates on microtubules during prophase but disappears as soon as the nuclear envelope breaks down, suggesting that its spindle localization is tightly regulated. If aurora A's function is compromised, dynactin and dynein become enriched on mitotic spindle microtubules. Phosphorylation sites are localized within the conserved microtubule-binding domain (MBD) of the p150glued. Although wild-type p150glued binds weakly to spindle microtubules, a variant that can no longer be phosphorylated by aurora A remains associated with spindle microtubules and fails to rescue depletion of endogenous p150glued. Our results suggest that aurora A kinase participates in vivo to the phosphoregulation of the p150glued MBD to limit the microtubule binding of the dynein–dynactin complex and thus regulates spindle assembly.
The Cdc42 GEF Intersectin 2 controls mitotic spindle orientation to form the lumen during epithelial morphogenesis
Authors: Rodriguez-Fraticelli Alejo E. , Vergarajauregui Silvia , Eastburn Dennis J. , Datta Anirban , Alonso Miguel A. , Mostov Keith , Martín-Belmonte Fernando
Published: May 2010

Epithelial organs are made of tubes and cavities lined by a monolayer of polarized cells that enclose the central lumen. Lumen formation is a crucial step in the formation of epithelial organs. The Rho guanosine triphosphatase (GTPase) Cdc42, which is a master regulator of cell polarity, regulates the formation of the central lumen in epithelial morphogenesis. However, how Cdc42 is regulated during this process is still poorly understood. Guanine nucleotide exchange factors (GEFs) control the activation of small GTPases. Using the three-dimensional Madin–Darby canine kidney model, we have identified a Cdc42-specific GEF, Intersectin 2 (ITSN2), which localizes to the centrosomes and regulates Cdc42 activation during epithelial morphogenesis. Silencing of either Cdc42 or ITSN2 disrupts the correct orientation of the mitotic spindle and normal lumen formation, suggesting a direct relationship between these processes. Furthermore, we demonstrated this direct relationship using LGN, a component of the machinery for mitotic spindle positioning, whose disruption also results in lumen formation defects.
Ethnicity and Culture and Their Relationship to Health Care
Authors: Dogra Nisha
Published: May 2010

This paper focuses on recognizing the concepts of ethnicity, culture and diversity and how care can be delivered with the principle of equality to diverse communities. The learning outcomes and contents are listed in Box 1 . Much of this paper is likely to refresh existing knowledge rather than be new information for health care providers. However, I hope the perspective given enables you to challenge yourself and reflect on your own practice.
Promoting Equality and Valuing Diversity for Lesbian, Gay, Bisexual and Trans Patients
Authors: Fish Julie
Published: May 2010

Equality and diversity lie at the heart of current UK health priorities. They are important subjects for everyone who works in the National Health Service (NHS). This is particularly the case for the GP, whose role is located at the interface between the NHS and the community he or she serves. The patient-doctor relationship is crucial to the health status and health care experiences of local people; a number of whom are likely to be lesbian, gay, bisexual or trans (LGBT) people. To achieve the optimal outcomes from such encounters, the skilled GP understands the social context in which LGBT people live their lives, is knowledgeable about LGBT health concerns, is a skilled communicator with LGBT patients and has developed attitudes which value diversity. This article examines current evidence about the health needs of LGBT communities and identifies ways to support GPs to promote equality and value diversity for LGBT patients.
Gender, Health and Disease
Authors: Shiner Alice , Simon Chantal , Howe Amanda
Published: May 2010

In many ways, lives of men and women have become more similar over recent years, as more and more women have entered the labour market. Despite this, differences remain. These, in turn, affect both patients' experiences of health and disease and the health services required.
Meeting the Health Care Needs of People with Learning Disabilities
Authors: Vahabzadeh Arshya B. N. , Delaffon Vijay , Biswas Asit B.
Published: May 2010

This article aims to highlight the delivery of health care to people with learning disabilities (PWLD) in the context of new Department of Health guidance and implementation of the Mental Capacity Act (2005). We seek to identify a myriad of barriers to health care delivery in this population and look at strategies to tackle these barriers. We will also consider the issue of capacity, which is particularly important for PWLD. We will highlight the importance of recognizing this population's enhanced baseline medical morbidity and how a best interests team approach is optimal when targeting interventions.
Fungal Susceptibility at Four Temperature‐Moisture Combinations and Carbon Dioxide Kit Color Reader Evaluation
Authors: Moog D. J. P. , Stroshine R. L. , Seitz L. M.
Published: May 2010

The susceptibility of shelled corn to invasion by storage fungi was assessed using a carbon dioxide (CO2) test kit. Shelled corn samples were rewetted to either 16 or 21% wb moisture content (MC) and incubated ≤80 hr at either 24 or 30°C in sealed glass jars. CO2 concentration in the jars was quantified using the color number (0–5) of an indicator gel, which was determined either by visual comparison to a color card (VR) or using a Digital Color Reader (DCR). Plots of DCR color numbers versus time were smoother than those for VR color numbers. The DCR was better able to distinguish differences among samples, especially when color numbers were <2.0. The highest coefficients of determination (r2) for linear regressions of color number versus ergosterol difference were 0.75 for the DCR readings and 0.73 for the VR readings. Rankings of fungal susceptibility were similar at all four temperature‐MC combinations and many r2 values for linear regressions comparing readings at other conditions with those at 21% MC and 24°C were statistically significant (α ≤ 0.05). Incubation conditions and time of prior storage had a noticeable yet relatively minor effect on which fungi infected the kernels.
Exotic Corn Lines with Increased Resistant Starch and Impact on Starch Thermal Characteristics
Authors: Rohlfing Kim A. , Pollak Linda M. , White Pamela J.
Published: May 2010

Ten parent corn lines, including four mutants (dull sugary2, amylose‐extender sugary2, amylose‐extender dull, and an amylose‐extender with introgressed Guatemalen germplasm [GUAT ae]) and six lines with introgressed exotic germplasm backgrounds, were crossed with each other to create 20 progeny crosses to increase resistant starch (RS) as a dietary fiber in corn starch and to provide materials for thermal evaluation. The resistant starch 2 (RS2) values from the 10 parent lines were 18.3–52.2% and the values from the 20 progeny crosses were 16.6–34.0%. The %RS2 of parents was not additive in the offspring but greater RS2 in parents was correlated to greater RS2 in the progeny crosses (r = 0.63). Differential scanning calorimetry (DSC) measured starch thermal characteristics, revealing positive correlations of peak gelatinization temperature and change in enthalpy with %RS2 (r = 0.65 and r = 0.67, P ≤ 0.05); however, % retrogradation (a measure of RS3) and retrogradation parameters did not correlate with %RS2. The %RS2 and onset temperature increased with the addition of the ae gene, likely because RS delays gelatinization.
Multi-year evolutionary dynamics of West Nile virus in suburban Chicago, USA, 2005–2007
Authors: Amore Giusi , Bertolotti Luigi , Hamer Gabriel L. , Kitron Uriel D. , Walker Edward D. , Ruiz Marilyn O. , Brawn Jeffrey D. , Goldberg Tony L.
Published: May 2010

West Nile virus has evolved in concert with its expansion across North America, but little is known about the evolutionary dynamics of the virus on local scales. We analysed viral nucleotide sequences from mosquitoes collected in 2005, 2006, and 2007 from a known transmission ‘hot spot’ in suburban Chicago, USA. Within this approximately 11 × 14 km area, the viral envelope gene has increased approximately 0.1% yr−1in nucleotide-level genetic diversity. In each year, viral diversity was higher in ‘residential’ sites characterized by dense housing than in more open ‘urban green space’ sites such as cemeteries and parks. Phylodynamic analyses showed an increase in incidence around 2005, consistent with a higher-than-average peak in mosquito and human infection rates that year. Analyses of times to most recent common ancestor suggest that WNV in 2005 and 2006 may have arisen predominantly from viruses present during 2004 and 2005, respectively, but that WNV in 2007 had an older common ancestor, perhaps indicating a predominantly mixed or exogenous origin. These results show that the population of WNV in suburban Chicago is an admixture of viruses that are both locally derived and introduced from elsewhere, containing evolutionary information aggregated across a breadth of spatial and temporal scales.
Methods of modelling viral disease dynamics across the within- and between-host scales: the impact of virus dose on host population immunity
Authors: Steinmeyer Shelby H. , Wilke Claus O. , Pepin Kim M.
Published: May 2010

We study the epidemiology of a viral disease with dose-dependent replication and transmission by nesting a differential-equation model of the within-host viral dynamics inside a between-host epidemiological model. We use two complementary approaches for nesting the models: an agent-based (AB) simulation and a mean-field approximation called the growth-matrix (GM) model. We find that although infection rates and predicted case loads are somewhat different between the AB and GM models, several epidemiological parameters, e.g. mean immunity in the population and mean dose received, behave similarly across the methods. Further, through a comparison of our dose-dependent replication model against two control models that uncouple dose-dependent replication from transmission, we find that host immunity in a population after an epidemic is qualitatively different than when transmission depends on time-varying viral abundances within hosts. These results show that within-host dynamics and viral dose should not be neglected in epidemiological models, and that the simpler GM approach to model nesting provides a reasonable tradeoff between model complexity and accuracy of results.
The virulence–transmission trade-off in vector-borne plant viruses: a review of (non-)existing studies
Authors: Froissart R. , Doumayrou J. , Vuillaume F. , Alizon S. , Michalakis Y.
Published: May 2010

The adaptive hypothesis invoked to explain why parasites harm their hosts is known as the trade-off hypothesis, which states that increased parasite transmission comes at the cost of shorter infection duration. This correlation arises because both transmission and disease-induced mortality (i.e. virulence) are increasing functions of parasite within-host density. There is, however, a glaring lack of empirical data to support this hypothesis. Here, we review empirical investigations reporting to what extent within-host viral accumulation determines the transmission rate and the virulence of vector-borne plant viruses. Studies suggest that the correlation between within-plant viral accumulation and transmission rate of natural isolates is positive. Unfortunately, results on the correlation between viral accumulation and virulence are very scarce. We found only very few appropriate studies testing such a correlation, themselves limited by the fact that they use symptoms as a proxy for virulence and are based on very few viral genotypes. Overall, the available evidence does not allow us to confirm or refute the existence of a transmission–virulence trade-off for vector-borne plant viruses. We discuss the type of data that should be collected and how theoretical models can help us refine testable predictions of virulence evolution.
Pathways to extinction: beyond the error threshold
Authors: Manrubia Susanna C. , Domingo Esteban , Lázaro Ester
Published: May 2010

Since the introduction of the quasispecies and the error catastrophe concepts for molecular evolution by Eigen and their subsequent application to viral populations, increased mutagenesis has become a common strategy to cause the extinction of viral infectivity. Nevertheless, the high complexity of virus populations has shown that viral extinction can occur through several other pathways apart from crossing an error threshold. Increases in the mutation rate enhance the appearance of defective forms and promote the selection of mechanisms that are able to counteract the accelerated appearance of mutations. Current models of viral evolution take into account more realistic scenarios that consider compensatory and lethal mutations, a highly redundant genotype-to-phenotype map, rough fitness landscapes relating phenotype and fitness, and where phenotype is described as a set of interdependent traits. Further, viral populations cannot be understood without specifying the characteristics of the environment where they evolve and adapt. Altogether, it turns out that the pathways through which viral quasispecies go extinct are multiple and diverse.
Gene-specific repression of the p53 target gene PUMA via intragenic CTCF–Cohesin binding
Authors: Gomes Nathan P. , Espinosa Joaquín M.
Published: May 2010

The p53 transcriptional program orchestrates alternative responses to stress, including cell cycle arrest and apoptosis, but the mechanism of cell fate choice upon p53 activation is not fully understood. Here we report that PUMA (p53 up-regulated modulator of apoptosis), a key mediator of p53-dependent cell death, is regulated by a noncanonical, gene-specific mechanism. Using chromatin immunoprecipitation assays, we found that the first half of the PUMA locus (∼6 kb) is constitutively occupied by RNA polymerase II and general transcription factors regardless of p53 activity. Using various RNA analyses, we found that this region is constitutively transcribed to generate a long unprocessed RNA with no known coding capacity. This permissive intragenic domain is constrained by sharp chromatin boundaries, as illustrated by histone marks of active transcription (histone H3 Lys9 trimethylation [H3K4me3] and H3K9 acetylation [H3K9Ac]) that precipitously transition into repressive marks (H3K9me3). Interestingly, the insulator protein CTCF (CCCTC-binding factor) and the Cohesin complex occupy these intragenic chromatin boundaries. CTCF knockdown leads to increased basal expression of PUMA concomitant with a reduction in chromatin boundary signatures. Importantly, derepression of PUMA upon CTCF depletion occurs without p53 activation or activation of other p53 target genes. Therefore, CTCF plays a pivotal role in dampening the p53 apoptotic response by acting as a gene-specific repressor.
Propagation of adipogenic signals through an epigenomic transition state
Authors: Steger David J. , Grant Gregory R. , Schupp Michael , Tomaru Takuya , Lefterova Martina I. , Schug Jonathan , Manduchi Elisabetta , Stoeckert Christian J. , Lazar Mitchell A.
Published: May 2010

The transcriptional mechanisms by which temporary exposure to developmental signals instigates adipocyte differentiation are unknown. During early adipogenesis, we find transient enrichment of the glucocorticoid receptor (GR), CCAAT/enhancer-binding protein β (CEBPβ), p300, mediator subunit 1, and histone H3 acetylation near genes involved in cell proliferation, development, and differentiation, including the gene encoding the master regulator of adipocyte differentiation, peroxisome proliferator-activated receptor γ2 (PPARγ2). Occupancy and enhancer function are triggered by adipogenic signals, and diminish upon their removal. GR, which is important for adipogenesis but need not be active in the mature adipocyte, functions transiently with other enhancer proteins to propagate a new program of gene expression that includes induction of PPARγ2, thereby providing a memory of the earlier adipogenic signal. Thus, the conversion of preadipocyte to adipocyte involves the formation of an epigenomic transition state that is not observed in cells at the beginning or end of the differentiation process.
Pleiotropic role forMYCNin medulloblastoma
Authors: Swartling Fredrik J. , Grimmer Matthew R. , Hackett Christopher S. , Northcott Paul A. , Fan Qi-Wen , Goldenberg David D. , Lau Jasmine , Masic Selma , Nguyen Kim , Yakovenko Slava , Zhe Xiao-Ning , Flynn Gilmer Heather C. , Collins Rodney , Nagaoka Mai , Phillips Joanna J. , Jenkins Robert B. , Tihan Tarik , Vandenberg Scott R. , James C. David , Tanaka Kohichi , Taylor Michael D. , Weiss William A. , Chesler Louis
Published: May 2010

Medulloblastoma (MB) is the most common malignant brain tumor of childhood. Sonic Hedgehog (SHH) signaling drives a minority of MB, correlating with desmoplastic pathology and favorable outcome. The majority, however, arises independently of SHH and displays classic or large cell anaplastic (LCA) pathology and poor prognosis. To identify common signaling abnormalities, we profiled mRNA, demonstrating misexpression ofMYCNin the majority of human MB and negligible expression in normal cerebella. We clarified a role in pathogenesis by targetingMYCN(and luciferase) to cerebella of transgenic mice.MYCN-driven MB showed either classic or LCA pathologies, with Shh signaling activated in ∼5% of tumors, demonstrating thatMYCNcan drive MB independently of Shh. MB arose at high penetrance, consistent with a role forMYCNin initiation. Tumor burden correlated with bioluminescence, with rare metastatic spread to the leptomeninges, suggesting roles forMYCNin both progression and metastasis. Transient pharmacological down-regulation ofMYCNled to both clearance and senescence of tumor cells, and improved survival. Targeted expression ofMYCNthus contributes to initiation, progression, and maintenance of MB, suggesting a central role forMYCNin pathogenesis.
Nrf2 establishes a glutathione-mediated gradient of UVB cytoprotection in the epidermis
Authors: Schäfer Matthias , Dütsch Sabine , auf dem Keller Ulrich , Navid Fatemeh , Schwarz Agatha , Johnson Delinda A. , Johnson Jeffrey A. , Werner Sabine
Published: May 2010

Ultraviolet (UV) B irradiation can severely damage the skin and even induce tumorigenesis. It exerts its effects by direct DNA modification and by formation of reactive oxygen species (ROS). We developed a strategy to genetically activate target gene expression of the transcription factor NF-E2-related factor 2 (Nrf2) in keratinocytes in vivo based on expression of a constitutively active Nrf2 mutant. Activation of Nrf2 target genes strongly reduced UVB cytotoxicity through enhancement of ROS detoxification. Remarkably, the protective effect was extended to neighboring cells. Using different combinations of genetically modified mice, we demonstrate that Nrf2 activates the production, recycling, and release of glutathione and cysteine by suprabasal keratinocytes, resulting in protection of basal cells in a paracrine, glutathione/cysteine-dependent manner. Most importantly, we found that endogenous Nrf2 controls selective protection of suprabasal keratinocytes from UVB-induced apoptosis through activation of cytoprotective genes. This finding explains the preferential UVB-induced apoptosis of basal cells, which is important for elimination of mutated stem cells as well as for preservation of skin integrity. Taken together, our results identify Nrf2 as a key regulator in the UV response of the skin.
JMJ14, a JmjC domain protein, is required for RNA silencing and cell-to-cell movement of an RNA silencing signal in Arabidopsis
Authors: Searle Iain R. , Pontes Olga , Melnyk Charles W. , Smith Lisa M. , Baulcombe David C.
Published: May 2010

JMJ14 is a histone H3 Lys4 (H3K4) trimethyl demethylase that affects mobile RNA silencing in an Arabidopsis transgene system. It also influences CHH DNA methylation, abundance of endogenous transposon transcripts, and flowering time. JMJ14 acts at a point in RNA silencing pathways that is downstream from RNA-dependent RNA polymerase 2 (RDR2) and Argonaute 4 (AGO4). Our results illustrate a link between RNA silencing and demethylation of histone H3 trimethylysine. We propose that JMJ14 acts downstream from the Argonaute effector complex to demethylate histone H3K4 at the target of RNA silencing.
Tracheal intubation following training with the GlideScope® compared to direct laryngoscopy
Authors: Ayoub C. M. , Kanazi G. E. , Al Alami A. , Rameh C. , El‐Khatib M. F.
Published: May 2010

Tracheal intubation using direct laryngoscopy has a high failure rate when performed by untrained medical personnel. This study compares tracheal intubation following direct laryngoscopy by inexperienced medical students when initially trained by using either the GlideScope®, a video assisted laryngoscope, or a rigid (Macintosh) laryngoscope. Forty‐two medical students with no previous experience in tracheal intubation were randomly divided into two equal groups to receive training with the GlideScope or with direct laryngoscopy. Subsequently, each medical student performed three consecutive intubations on patients with normal airways that were observed by a anaesthetist who was blinded to the training method. The rates of successful intubation were significantly higher in the Glidescope group after the first (48%), second (62%), and third (81%) intubations compared with the Macintosh group (14%, 14% and 33%; p = 0.043, 0.004 and 0.004, respectively). The mean (SD) times for the first, second, and third successful tracheal intubations were significantly shorter in the Glidescope group (59.3 (4.4) s, 56.6 (7.1) s and 50.1 (4.0) s) than the Macintosh group (70.7 (7.5) s, 73.7 (7.3) s and 67.6 (2.0) s; p = 0.006, 0.003 and 0.0001, respectively). Training with a video‐assisted device such as the GlideScope improves the success rate and time for tracheal intubation in patients with normal airways when this is performed by inexperienced individuals following a short training programme.
Physiological responses of largemouth bass to acute temperature and oxygen stressors
Authors: VANLANDEGHEM M. M. , WAHL D. H. , SUSKI C. D.
Published: May 2010

Abstract  Temperature and oxygen gradients exist in nearly every water body, but anthropogenic activities can subject fish to rapid changes in these important environmental variables. These rapid changes in temperature and oxygen (generally referred to as temperature or oxygen shock) may have sub‐lethal consequences depending upon the magnitude and the fish species. This study quantified physiological changes in largemouth bass, Micropterus salmoides (Lacepède), exposed to two levels of heat and cold shocks and to two levels of hypoxic and hyperoxic shocks. Following a cold shock from 20 °C to 8 °C, plasma cortisol and glucose increased after 1 h and lactate dehydrogenase activity increased after 6 h. Plasma glucose and K+ concentrations increased 1 h after a heat shock from 20 °C to 32 °C but not after 6 h. Bass subjected to a hypoxic shock from 8 to 2 mg O2 L−1 showed decreased plasma K+ and increased plasma glucose and white muscle lactate. No changes in physiological parameters were observed in bass subjected up to 18 mg O2 L−1 hyperoxia. Results from this study suggest that largemouth bass can tolerate a wide range of temperature and oxygen shocks, but temperature decreases of 20 to 8 °C and hypoxia as low as 4 mg O2 L−1 should be avoided to minimise physiological perturbations.
The Mediterranean Sea as a ‘cul‐de‐sac’ for endemic fishes facing climate change
Authors: BEN RAIS LASRAM FRIDA , GUILHAUMON FRANÇOIS , ALBOUY CAMILLE , SOMOT SAMUEL , THUILLER WILFRIED , MOUILLOT DAVID
Published: May 2010

The Mediterranean Sea is a hotspot of biodiversity, and climate warming is expected to have a significant influence on its endemic fish species. However, no previous studies have predicted whether fish species will experience geographic range extensions or contractions as a consequence of warming. Here, we projected the potential future climatic niches of 75 Mediterranean Sea endemic fish species based on a global warming scenario implemented with the Mediterranean model OPAMED8 and a multimodel inference, which included uncertainty. By 2070–2099, the average surface temperature of the Mediterranean Sea was projected to warm by 3.1 °C. Projections for 2041–2060 are that 25 species would qualify for the International Union for the Conservation of Nature and Natural Resources (IUCN) Red List, and six species would become extinct. By 2070–2099, 45 species were expected to qualify for the IUCN Red List whereas 14 were expected to become extinct. By the middle of the 21st century, the coldest areas of the Mediterranean Sea (Adriatic Sea and Gulf of Lion) would act as a refuge for cold‐water species, but by the end of the century, those areas were projected to become a ‘cul‐de‐sac’ that would drive those species towards extinction. In addition, the range size of endemic species was projected to undergo extensive fragmentation, which is a potentially aggravating factor. Since a majority of endemic fishes are specialists, regarding substratum and diet, we may expect a reduced ability to track projected climatic niches. As a whole, 25% of the Mediterranean Sea continental shelf was predicted to experience a total modification of endemic species assemblages by the end of the 21st century. This expected turnover rate could be mitigated by marine protected areas or accelerated by fishing pressure or competition from exotic fishes. It remains a challenge to predict how these assemblage modifications might affect ecosystem function.
Effect of temperature on RNA silencing of a negative‐stranded RNA plant virus: Citrus psorosis virus
Authors: Velázquez K. , Renovell A. , Comellas M. , Serra P. , García M. L. , Pina J. A. , Navarro L. , Moreno P. , Guerri J.
Published: May 2010

Citrus psorosis virus (CPsV), genus Ophiovirus, causes a bark scaling disease of citrus. CPsV virions are kinked filaments with three negative‐stranded RNA molecules (vRNA) and a 48 kDa coat protein. The effect of temperature on symptom expression, virus accumulation and RNA silencing was examined in sweet orange seedlings (Citrus sinensis) graft‐inoculated with three different CPsV isolates and grown in a glasshouse at 26/18°C or 32/26°C (day/night). Most plants kept in the cooler glasshouse showed a shock reaction in the first flush with shoot necrosis, and then moderate to intense chlorotic flecking and spotting in young leaves, whereas plants incubated at 32/26°C did not exhibit shoot necrosis, and young leaf symptoms were milder. Virus titre estimated by ELISA and by northern and dot blot hybridization paralleled symptom intensity, with significantly higher virus accumulation in plants incubated at 26/18°C. The amount of CPsV‐derived small RNAs (CPsV‐sRNAs) slightly increased at 32/26°C, with the ratio of CPsV‐sRNA/vRNA being higher at 32/26°C than at 26/18°C. These results suggest that (i) CPsV infection induces RNA silencing in citrus plants, (ii) symptom intensity is associated with virus accumulation, and (iii) temperature increase enhances the RNA silencing response of citrus plants and decreases virus accumulation.