bluuebunny/crossref_metadata_2025 huggingface dataset:
Do falling planets cause stellar spin-up?
Authors: Brown D. J. A. , Cameron A. Collier , Hall C. , Hebb L.
Published: November 2011

We investigate the tidal interactions between hot Jupiter extra-solar planets and their host stars in an effort to characterise the effects of such interactions on stellar rotation. We study the WASP-18 and WASP-19 systems, showing that in both cases tidal interactions cause the eventual spiral in of the the planet towards the Roche limit. We find that for both systems this process will cause significant spin up of the host star, independent of the precise value for the tidal quality factors. By fitting tidal evolution models to observed parameters, we are able to determine that WASP-19 b is currently spiralling in, and that it has a very short remaining lifetime ~ 3 Myr.
Orbital migration models under test
Authors: Kley Wilhelm
Published: November 2011

Planet-disk interaction predicts a change in the orbital elements of an embedded planet. Through linear and fully hydrodynamical studies it has been found that migration is typically directed inwards. Hence, this migration process gives natural explanation for the presence of the ’hot’ planets orbiting close to the parent star, and it plays a mayor role in explaining the formation of resonant planetary systems.

However, standard migration models for locally isothermal disks indicate a too rapid inward migration for small mass planets, and a large number of massive planets are found very far away from the star. Recent studies, including more complete disk physics, have opened up new paths to slow down or even reverse migration. The new findings on migration are discussed and connected to the observational properties of planetary systems.
New Worlds, New Horizons and NASA's approach to the next decade of exoplanet discoveries
Authors: Boss Alan P. , Hudgins Douglas M. , Traub Wesley A.
Published: November 2011

Every ten years the astronomy and astrophysics community in the United States undertakes a survey intended to prioritize plans for major ground- and space-based astronomical facilities for the coming decade. New Worlds, New Horizons (NWNH) was released in August 2010 and represents the community's advice to the United States' funding agencies about the top priorities for 2010-2020. Here we focus on the recommendations of NWNH for space-based exoplanet missions to be considered by NASA, and on the plans developed to date for how NASA will respond to the science goals and missions set out for them by NWNH.
Science with EPICS, the E-ELT planet finder
Authors: Gratton Raffaele , Kasper Markus , Vérinaud Christophe , Bonavita Mariangela , Schmid Hans M.
Published: November 2011

EPICS is the proposed planet finder for the European Extremely Large Telescope. EPICS is a high contrast imager based on a high performing extreme adaptive optics system, a diffraction suppression module, and two scientific instruments: an Integral Field Spectrograph (IFS) for the near infrared (0.95-1.65 μm), and a differential polarization imager (E-POL). Both these instruments should allow imaging and characterization of planets shining in reflected light, possibly down to Earth-size. A few high interesting science cases are presented.
Observations and modelling of earth's transmission spectrum through lunar eclipses: A window to transiting exoplanet characterization
Authors: Pallé E. , Muñoz Antonio García , Osorio Maria R. Zapatero , Montañés-Rodríguez Pilar , Barrena Rafael , Martín Eduardo L.
Published: November 2011

Recently we were able to retrieve the Earth's transmission spectrum through lunar eclipse observations. This spectrum showed that the depth of most molecular species was stronger than models had anticipated. The presence of other atmospheric signatures, such as atmospheric dimers, were also present in the spectrum. We have been developing a radiative transfer code able to reproduce the Earth's transmission spectra at different depths into the penumbra and umbra, and taking into account transmission, refraction, and multiple scattering. Here we discuss the results to date and the work ahead.
Characterisation of SPH noise in simulations of protoplanetary discs
Authors: Arena Serena E. , Gonzalez Jean-François , Crespe Elisabeth
Published: November 2011

The effects of turbulence on the dynamics of dust grains in protoplanetary discs is of relevant importance in the study of pre-planetesimal formation. The complex interplay between gas and dust and the modelling of turbulence require numerical simulations.

A statistical study of the noise in SPH simulations of gas-only protoplanetary accretion discs is performed in order to determine if it could mimic turbulence and to what extent.
Planet candidates from the SARG visual binary survey
Authors: Carolo Elena , Desidera Silvano , Gratton Raffaele , Fiorenzano Aldo Martinez , Endl Michael , Cosentino Rosario , Barbieri Mauro , Bonavita Mariangela , Cecconi Massimo , Claudi Riccardo , Marzari Francesco , Scuderi Salvo
Published: November 2011

We present preliminary results of the radial velocity survey on going at TNG targeting binaries with similar components.
Influence of growth on dust settling and migration in protoplanetary discs
Authors: Crespe Elisabeth , Gonzalez Jean-Francois , Laibe Guillaume , Maddison Sarah T. , Fouchet Laure
Published: November 2011

To form meter-sized pre-planetesimals in protoplanetary discs, dust aggregates have to decouple from the gas at a distance far enough from the central star so they are not accreted. Dust grains are affected by gas drag, which results in a vertical settling towards the mid-plane, followed by radial migration. To have a better understanding of the influence of growth on the dust dynamics, we use a simple grain growth model to determine the dust distribution in observed discs. We implement a constant growth rate into a gas+dust hydrodynamics SPH code and vary the growh rate to study the resulting effect on dust distribution. The growth rate allows us to determine the relative importance between friction and growth.We show that depending on the growth rate, a range of dust distribution can result. For large enough growth rates, grains can decouple from the gas before being accreted onto the central star, thus contributing as planetary building rocks.
3D global simulations of proto-planetary disk with dynamically evolving outer edge of dead zone
Authors: Dzyurkevich Natalia , Turner Neal J. , Kley Willy , Klahr Hubert , Henning Thomas
Published: November 2011

3D global MHD simulations of magneto-driven turbulence are performed for the disk of 100 AU with reduced amount of 10μm fluffy dust grains. We use X-ray and cosmic ray ionization, as well as simplified treatment of recombination on dust grains. The ionization of gas and charging of dust grains are dynamically evolving during the simulation, making the zone of high magnetic dissipation (’dead’ zone) variable. In our simulations, the jump in MRI-driven turbulent viscosity inside and outside of dead zone is insignificant. We find no hard edge, but rather a smooth transition between active and dead zone. Subsequently, there is no visible pressure bump at outer edge of the dead zone.
Planetary systems formation and the diversity of extrasolar systems
Authors: Miguel Yamila , Guilera Octavio M. , Brunini Adrián
Published: November 2011

With the end of answer questions as, how common are planetary systems like our own in the Universe? and What is the diversity of planetary systems that we could find in the universe?, we develop a semi-analytical model for computing planetary systems formation and consider different initial conditions for generating a large sample of planetary systems, which is analysed statistically. We explore the effects in the planetary system architecture of assuming different initial disc profiles and planetary migration rates.
The effect of opacity on the evolution of giant planets
Authors: Vazan Allona , Kovetz Attay , Podolak Morris
Published: November 2011

We use an improved version of the planetary evolution code described in Helled et al. (2006) to model the effect of opacity on the evolution of giant planets in the disk instability scenario. We find that changing the opacity law can cause significant changes in the evolutionary path of a protoplanet. Sufficiently high opacities cause oscillatory behavior that delays the final collapse. Peak luminosities just before collapse can exceed 10−5L⊙.
Constraining planetary interiors with the Love number k2
Authors: Kramm Ulrike , Nettelmann Nadine , Redmer Ronald
Published: November 2011

For the solar sytem giant planets the measurement of the gravitational moments J2 and J4 provided valuable information about the interior structure. However, for extrasolar planets the gravitational moments are not accessible. Nevertheless, an additional constraint for extrasolar planets can be obtained from the tidal Love number k2, which, to first order, is equivalent to J2. k2 quantifies the quadrupolic gravity field deformation at the surface of the planet in response to an external perturbing body and depends solely on the planet's internal density distribution. On the other hand, the inverse deduction of the density distribution of the planet from k2 is non-unique. The Love number k2 is a potentially observable parameter that can be obtained from tidally induced apsidal precession of close-in planets (Ragozzine & Wolf 2009) or from the orbital parameters of specific two-planet systems in apsidal alignment (Mardling 2007). We find that for a given k2, a precise value for the core mass cannot be derived. However, a maximum core mass can be inferred which equals the core mass predicted by homogeneous zero metallicity envelope models. Using the example of the extrasolar transiting planet HAT-P-13b we show to what extend planetary models can be constrained by taking into account the tidal Love number k2.
Exoplanet transit spectro-photometry with SOFIA
Authors: Angerhausen Daniel , Krabbe Alfred , Zinnecker Hans
Published: November 2011

We present the prospects of observing extrasolar planets with the Stratospheric Observatory for Infrared Astronomy (SOFIA). Our analysis shows that optical and near-infrared photometric and spectrophotometric follow-up observations during planetary transits and\break eclipses will be feasible with SOFIA's instrumentation, especially with the HIPO-FLITECAM optical/NIR instruments. SOFIA has unique advantages in comparison to ground- and space-based observatories in this field of research which will be outlined.
Detection of small-size planetary candidates with CoRoT data
Authors: Bonomo Aldo S. , Chabaud Pierre-Yves , Deleuil Magali , Moutou Claire , Bordé Pascal
Published: November 2011

With the discovery of CoRoT-7b, the first transiting super-Earth, the CoRoT space mission has shown the capability to detect short-period rocky planets around solar-like stars. By performing a blind test with real CoRoT light curves, we want to establish the detection threshold of small-size planets in CoRoT data. We investigate the main obstacles to the detection of transiting super-Earths in CoRoT data, notably the presence of short-time scale variability and hot pixels.
A microvariability study of nearby M dwarfs from the Western Italian Alps: Status update
Authors: Damasso Mario , Bernagozzi Andrea , Bertolini Enzo , Calcidese Paolo , Giacobbe Paolo , Lattanzi Mario G. , Perdoncin Matteo , Sozzetti Alessandro , Smart Richard , Toso Giorgio
Published: November 2011

Small ground-based telescopes can effectively be used to look for transiting rocky planets around nearby low-mass M stars, as recently demonstrated for example by the MEarth project. Since December 2009 at the Astronomical Observatory of the Autonomous Region of Aosta Valley (OAVdA) we are monitoring photometrically a sample of red dwarfs with accurate parallax measurements. The primary goal of this ‘pilot study’ is the characterization of the photometric microvariability of each target over a typical period of approximately 2 months. This is the preparatory step to long-term survey with an array of identical small telescopes, with kick-off in early 2011. Here we discuss the present status of the study, describing the stellar sample, and presenting the most interesting results obtained so far, including the aggressive data analysis devoted to the characterization of the variability properties of the sample and the search for transit-like signals.
Stellar noise and planet detection. II. Radial-velocity noise induced by magnetic cycles
Authors: Dumusque Xavier , Lovis Cristophe , Udry Stephane , Santos Nuno C.
Published: November 2011

For the 451 stars of the HARPS high precision program, we study correlations between the radial-velocity (RV) variation and other parameters of the Cross Correlated Function (CCF). After a careful target selection, we found a very good correlation between the slope of the RV-activity index (log(R'HK)) correlation and the Teff for dwarf stars. This correlation allow us to correct RV from magnetic cycles given the activity index and the Teff.
Space interferometry beyond exoplanetology: Can interdisciplinary collaboration contribute to the future of this technique?
Authors: Gabor Pavel
Published: November 2011

Although a formation-flying space interferometer designed for exoplanet spectroscopy is feasible in principle, the novelty and cost of such an instrument is likely to remain daunting unless the scientific benefits of this technology are demonstrated by intermediary, precursor missions. Such instruments would represent intermediary steps in the real-life testing of the technology, and therefore, by the very reason of being intermediary, they may not have the resolving or collecting power needed for the study of the objects where biomarkers could be hoped to be detected, i.e., exo-Earths in the habitable zone of their stars. This paper examines the potential applications of such intermediary instruments. The direct line of thought focuses on exoplanetology (gas giants, protoplanetary discs, Neptunes, super-Earths, etc.); what we would like to stimulate is an exercise in lateral thinking, looking at what might an intermediary interferometric mission contribute to other fields of astrophysical research (galaxies, supernova precursors, planetary nebulae, molecular clouds, etc.). The paper raises the question of collaboration with astrophysicists studying areas other than exoplanets and its potential gains for the future of space interferometry.
Practical suggestions on detecting exomoons in exoplanet transit light curves
Authors: Szabó Gyula M. , Simon A. E. , Kiss Laszlo L. , Regály Zsolt
Published: November 2011

The number of known transiting exoplanets is rapidly increasing, which has recently inspired significant interest as to whether they can host a detectable moon. Although there has been no such example where the presence of a satellite was proven, several methods have already been investigated for such a detection in the future. All these methods utilize post-processing of the measured light curves, and the presence of the moon is decided by the distribution of a timing parameter. Here we propose a method for the detection of the moon directly in the raw transit light curves. When the moon is in transit, it puts its own fingerprint on the intensity variation. In realistic cases, this distortion is too little to be detected in the individual light curves, and must be amplified. Averaging the folded light curve of several transits helps decrease the scatter, but it is not the best approach because it also reduces the signal. The relative position of the moon varies from transit to transit, the moon's wing will appear in different positions on different sides of the planet's transit. Here we show that a careful analysis of the scatter curve of the folded light curves enhances the chance of detecting the exomoons directly.
Radar observations of mesoscale circulations induced by a small lake under varying synoptic‐scale flows
Authors: Asefi‐Najafabady Salvi , Knupp Kevin , Mecikalski John R. , Welch Ronald M.
Published: November 2011

This paper examines Doppler radar observations of springtime lake breeze (LB) circulations produced by a small reservoir (mean width of ∼2 km), Wheeler Lake, on the Tennessee River in northern Alabama. The analysis allows for the formation of a general understanding of the flow structures as a composite of many LB circulation events. It is found that LB circulation, once formed, is robust and persistent over a range of background or synoptic‐scale wind flows despite the small size of Wheeler Lake and the relatively small differences between land and lake temperature (often a few degrees Celsius) that drive the LB circulation. The formation, location, strength, and inland penetration of the Wheeler Lake breeze are highly sensitive to the background wind speed and direction with respect to the lakeshore, resulting in complex spatial and temporal variations in the LB characteristics. The LB front is most prominent as a radar fine line when the ambient flow is offshore (opposing the LB background wind) and perpendicular to the orientation (120°–300°) of the lake. For wind speeds <4–5 m s−1, a radar‐detectable thin line delineating the LB front appears primarily on the upwind side of the lake, either to the north or south, while synoptic‐scale winds stronger than ∼5 m s−1 tend to destroy the breeze front entirely. If the background wind is parallel to lake orientation and the wind is ≤4 m s−1, the LB circulations often develop on both sides of the lake. The radar fine line often appears patchy and broad for low‐wind conditions near 2 m s−1. Overall, the findings of this study show that small lakes can generate persistent local circulations that follow similar patterns of behavior and respond to the synoptic flow as large lakes or sea breezes.
The energy–diversity relationship of complex bacterial communities in Arctic deep-sea sediments
Authors: Bienhold Christina , Boetius Antje , Ramette Alban
Published: November 2011

The availability of nutrients and energy is a main driver of biodiversity for plant and animal communities in terrestrial and marine ecosystems, but we are only beginning to understand whether and how energy–diversity relationships may be extended to complex natural bacterial communities. Here, we analyzed the link between phytodetritus input, diversity and activity of bacterial communities of the Siberian continental margin (37–3427 m water depth). Community structure and functions, such as enzymatic activity, oxygen consumption and carbon remineralization rates, were highly related to each other, and with energy availability. Bacterial richness substantially increased with increasing sediment pigment content, suggesting a positive energy–diversity relationship in oligotrophic regions. Richness leveled off, forming a plateau, when mesotrophic sites were included, suggesting that bacterial communities and other benthic fauna may be structured by similar mechanisms. Dominant bacterial taxa showed strong positive or negative relationships with phytodetritus input and allowed us to identify candidate bioindicator taxa. Contrasting responses of individual taxa to changes in phytodetritus input also suggest varying ecological strategies among bacterial groups along the energy gradient. Our results imply that environmental changes affecting primary productivity and particle export from the surface ocean will not only affect bacterial community structure but also bacterial functions in Arctic deep-sea sediment, and that sediment bacterial communities can record shifts in the whole ocean ecosystem functioning.
The Western English Channel contains a persistent microbial seed bank
Authors: Caporaso J Gregory , Paszkiewicz Konrad , Field Dawn , Knight Rob , Gilbert Jack A
Published: November 2011

Robust seasonal dynamics in microbial community composition have previously been observed in the English Channel L4 marine observatory. These could be explained either by seasonal changes in the taxa present at the L4 site, or by the continuous modulation of abundance of taxa within a persistent microbial community. To test these competing hypotheses, deep sequencing of 16S rRNA from one randomly selected time point to a depth of 10 729 927 reads was compared with an existing taxonomic survey data covering 6 years. When compared against the 6-year survey of 72 shallow sequenced time points, the deep sequenced time point maintained 95.4% of the combined shallow OTUs. Additionally, on average, 99.75%±0.06 (mean±s.d.) of the operational taxonomic units found in each shallow sequenced sample were also found in the single deep sequenced sample. This suggests that the vast majority of taxa identified in this ecosystem are always present, but just in different proportions that are predictable. Thus observed changes in community composition are actually variations in the relative abundance of taxa, not, as was previously believed, demonstrating extinction and recolonization of taxa in the ecosystem through time.
Exenatide as a Weight‐Loss Therapy in Extreme Pediatric Obesity: A Randomized, Controlled Pilot Study
Authors: Kelly Aaron S. , Metzig Andrea M. , Rudser Kyle D. , Fitch Angela K. , Fox Claudia K. , Nathan Brandon M. , Deering Mary M. , Schwartz Betsy L. , Abuzzahab M. Jennifer , Gandrud Laura M. , Moran Antoinette , Billington Charles J. , Schwarzenberg Sarah J.
Published: November 2011

The objective of this pilot study was to evaluate the effects of exenatide on BMI (primary endpoint) and cardiometabolic risk factors in nondiabetic youth with extreme obesity. Twelve children and adolescents (age 9–16 years old) with extreme obesity (BMI ≥1.2 times the 95th percentile or BMI ≥35 kg/m2) were enrolled in a 6‐month, randomized, open‐label, crossover, clinical trial consisting of two, 3‐month phases: (i) a control phase of lifestyle modification and (ii) a drug phase of lifestyle modification plus exenatide. Participants were equally randomized to phase‐order (i.e., starting with control or drug therapy) then crossed‐over to the other treatment. BMI, body fat percentage, blood pressure, lipids, oral glucose tolerance tests (OGTT), adipokines, plasma biomarkers of endothelial activation, and endothelial function were assessed at baseline, 3‐, and 6‐months. The mean change over each 3‐month phase was compared between treatments. Compared to control, exenatide significantly reduced BMI (−1.7 kg/m2, 95% confidence interval (CI) (−3.0, −0.4), P = 0.01), body weight (−3.9 kg, 95% CI (−7.11, −0.69), P = 0.02), and fasting insulin (−7.5 mU/l, 95% CI (−13.71, −1.37), P = 0.02). Significant improvements were observed for OGTT‐derived insulin sensitivity (P = 0.02) and β‐cell function (P = 0.03). Compliance with the injection regimen was excellent (≥94%) and exenatide was generally well‐tolerated (the most common adverse event was mild nausea in 36%). These preliminary data suggest that exenatide should be evaluated in larger, well‐controlled trials for its ability to reduce BMI and improve cardiometabolic risk factors in youth with extreme obesity.
Molecular dynamical investigation on dislocation near twist-grain boundary of Ni under compression
Authors: Chen Jun-Liang , Hsieh Jin-Yuan , Chang Jee-Gong , Lin Hong-Chang , Chiang Hsing-Jung , Huang Huang-Kai , Hwang Chi-Chuan
Published: November 2011

The dislocations and the strength of a nickel bicrystal are investigated in present study. There are three kinds of crystalline orientations of the nickel bicrystal, namely (100), (110), and (111). Misfit dislocations are presented on the interface between two nickel grains when a compression process is utilized on the bicrystal. The misfit dislocations on a Ni(100) interface form a square-latticed network and those on a Ni(111) form a triangle-latticed network. When a large twist angle is applied to the Ni bicrystal, the square- and triangle-latticed unit of the misfit dislocation networks will shrink or even disappear. Thus, a plane defects distribute over the interface. If the bicrystal is compressed further, dislocations within each grain are developed from the defects on the interface between grains. The configuration of the dislocations within grains is more regular when the applied twist angle is smaller. A Ni(111) bicrystal owns the largest amount of maximal stress no matter what the twist angle is. Those of a Ni(110) bicrystal is the second and of a Ni(100) bicrystal is the smallest.
Determination of the instantaneous forces on flapping wings from a localized fluid velocity field
Authors: Minotti F. O.
Published: November 2011

Expressions are derived to relate the instantaneous pressure force on a flapping wing to the velocity field on a plane at the trailing edge and on a highly localized region around and near the wing, valid when the vortex sheet is thin. In its more practical version, the formalism is applicable to wings with close to two-dimensional geometry and has the advantage of not using spatial derivatives, but only a time derivative of a surface integral of the velocity. In the purely two-dimensional case, the expression obtained is used to justify a much simpler one that only requires the evaluation of the time derivative of the wing circulation. A comparison with a numerical simulation in a two-dimensional case shows a good representation of the forces, even with the most simplified expression, when the condition of a thin wake is met. Other examples are shown in which the wake is not thin in order to explore the limitations of the formalism. It is found in these cases that the thrust is sometimes not so well reproduced, with a tendency to be overestimated, while the lift is generally better reproduced. Remarkably, the simpler expression reproduces rather acceptably the phase and amplitude of both thrust and lift in all cases.
Stress release phenomena in chromia scales formed on NiCr-30 alloys: Influence of metallurgical parameters
Authors: Guerain M. , Goudeau P. , Grosseau-Poussard J. L.
Published: November 2011

Stress release phenomena are studied for α-Cr2O3 thermal oxide films grown on NiCr-30 alloys. The influence of specific metallurgical parameters, such as cooling rate and initial surface roughness, is investigated thanks to Raman spectroscopy. Systematic correlations are established between the residual stress level in the scales and the damage rate resulting from a delamination process by buckling. Different buckling morphologies are characterized mainly according to the cooling rate range.
Enhancing the visibility of graphene on GaAs
Authors: Peters K. , Tittel A. , Gayer N. , Graf A. , Paulava V. , Wurstbauer U. , Hansen W.
Published: November 2011

We present a method to enhance the visibility of graphene on GaAs. Therefore the samples are spin-coated with e-beam resist of well defined thickness. For determination of the optimal thickness, the optical contrast is calculated taking into account thicknesses and refractive indices of the layers as well as the sensitivity of the human eye. The visibility studies of single-layer graphene on GaAs are accompanied by Raman spectroscopy and magnetotransport measurements. We demonstrate that it is possible to detect graphene flakes by optical microscopy and determine the number of graphene layers by measuring the Raman signal through the resist layer.
Simple relations among the elastic moduli of the polycrystalline intermetallic compounds LaMxNi5−x (M = Al,Sn)
Authors: Yeheskel O. , Leisure R. G.
Published: November 2011

An examination of the elastic moduli of a number of the polycrystalline intermetallic compounds LaMxNi5−x (M = Al,Sn) reveals a simple relation between the shear modulus, G, and Young’s modulus, E. The results, for a wide range of x, show that the ratio G/E is approximately constant. Further, this constant for these hexagonal close packed (hcp) structures is almost the same as that found many years ago for a large number of hcp polycrystalline metallic elements. This result is shown to be useful for estimating other moduli from the knowledge of only the shear modulus.
Renormalization, resonance bifurcation, and phase contrast in dynamic atomic force microscopy
Authors: Cantrell Sean A. , Cantrell John H.
Published: November 2011

Renormalization of the model describing dynamic atomic force microscopy is shown to provide a simple and robust interpretation of cantilever dynamics as a single spring and mass with frequency-dependent cantilever stiffness and damping parameters. Renormalization predicts a bifurcation in the free-space cantilever resonance that leads to the occurrence of multiple stable resonance modes experimentally observed during cantilever-sample “contact.” The bifurcation results from the coupling of the cantilever modes via the nonlinearity of the tip-sample interaction force and the running of the cantilever parameters with frequency. The effective interaction force is represented by a polynomial expansion with coefficients Fij (i,j = 0, 1, 2, …) that account for cantilever-to-sample energy transfer in a single system model. The effective cantilever spring constant obtained from F10 and the interaction force energy transfer factor obtained from F01 are used to show that phase contrast in the linear regime of operation can be expressed in terms of conservative or dissipative force parameters alone when operating in constant amplitude control near the free-space resonance frequency of the cantilever. The model predicts that dissipative force parameters dominate phase contrast at low drive frequencies, while conservative force parameters dominate phase contrast at sufficiently high drive frequencies for appropriate values of F10.
Seroprevalence and correlates of hepatitis A among HIV-negative American men who have sex with men
Authors: Bialek Stephanie R. , Barry Vaughn , Bell Beth P. , Valleroy Linda A. , Behel Stephanie , MacKellar Duncan A. , Secura Gina , Thiede Hanne , McFarland Willi , Ford Wesley L. , Bingham Trista A. , Shehan Douglas A. , Celentano David D. , for the Young Men’s Survey Study Group
Published: November 2011

Background Hepatitis A outbreaks are well documented among men who have sex with men (MSM). This analysis examines characteristics associated with hepatitis A virus (HAV) infection among a large group of young adult MSM from five USA cities. Methods: The Young Men’s Survey was a cross-sectional prevalence study of HIV infection and related behavioural risk factors among MSM aged 15–29 years during 1994–2000. Serum specimens from HIV-negative participants were retrospectively tested for antibodies to HAV (anti-HAV). Data were stratified by ethnicity and analysed with logistic regression. Results: Overall anti-HAV prevalence was 18.4% among the 2708 participants, and varied by ethnicity from 6.9 to 45.3% and was highest among Hispanic and Asian men (P < 0.001). Prevalence increased with age across all racial/ethnic groups. Among white men, anti-HAV positivity was associated with having 20 or more lifetime male sex partners for those aged 15–22 years (adjusted odds ratio (AOR) = 2.1, 95% confidence interval (CI) = 1.0–4.1) and ever having had unprotected anal sex for those aged 23–29 years (AOR = 2.4, 95% CI = 1.2–4.5). Conclusions: Factors associated with a history of HAV infection among MSM in non-outbreak settings are probably similar to those among non-MSM. MSM are still at risk for HAV infection as a result of outbreaks occurring in MSM communities. Additional studies of hepatitis A vaccination coverage are needed to determine if strategies to vaccinate MSM are adequate.
Recruitment of OCRL and Inpp5B to phagosomes by Rab5 and APPL1 depletes phosphoinositides and attenuates Akt signaling
Authors: Bohdanowicz Michal , Balkin Daniel M. , De Camilli Pietro , Grinstein Sergio
Published: November 2011

Sealing of phagosomes is accompanied by the disappearance of phosphatidylinositol (4,5)-bisphosphate (PtdIns(4,5)P2) from their cytoplasmic leaflet. Elimination of PtdIns(4,5)P2, which is required for actin remodeling during phagosome formation, has been attributed to hydrolysis by phospholipase C and phosphorylation by phosphatidylinositol 3-kinase. We found that two inositol 5-phosphatases, OCRL and Inpp5B, become associated with nascent phagosomes. Both phosphatases, which are Rab5 effectors, associate with the adaptor protein APPL1, which is recruited to the phagosomes by active Rab5. Knockdown of APPL1 or inhibition of Rab5 impairs association of OCRL and Inpp5B with phagosomes and prolongs the presence of PtdIns(4,5)P2and actin on their membranes. Even though APPL1 can serve as an anchor for Akt, its depletion accentuated the activation of the kinase, likely by increasing the amount of PtdIns(4,5)P2available to generate phosphatidylinositol (3,4,5)-trisphosphate. Thus, inositol 5-phosphatases are important contributors to the phosphoinositide remodeling and signaling that are pivotal for phagocytosis.
The kinase activity of human Rio1 is required for final steps of cytoplasmic maturation of 40S subunits
Authors: Widmann Barbara , Wandrey Franziska , Badertscher Lukas , Wyler Emanuel , Pfannstiel Jens , Zemp Ivo , Kutay Ulrike
Published: November 2011

RIO proteins form a conserved family of atypical protein kinases. Humans possess three distinct RIO kinases—hRio1, hRio2, and hRio3, of which only hRio2 has been characterized with respect to its role in ribosomal biogenesis. Here we show that both hRio1 and hRio3, like hRio2, are associated with precursors of 40S ribosomal subunits in human cells. Furthermore, we demonstrate that depletion of hRio1 by RNA interference affects the last step of 18S rRNA maturation and causes defects in the recycling of several trans-acting factors (hEnp1, hRio2, hLtv1, hDim2/PNO1, and hNob1) from pre-40S subunits in the cytoplasm. Although the effects of hRio1 and hRio2 depletion are similar, we show that the two kinases are not fully interchangeable. Moreover, rescue experiments with a kinase-dead mutant of hRio1 revealed that the kinase activity of hRio1 is essential for the recycling of the endonuclease hNob1 and its binding partner hDim2 from cytoplasmic pre-40S. Kinase-dead hRio1 is trapped on pre-40S particles containing hDim2 and hNob1 but devoid of hEnp1, hLtv1, and hRio2. These data reveal a role of hRio1 in the final stages of cytoplasmic pre-40S maturation.
Three-dimensional structure of the radial spokes reveals heterogeneity and interactions with dyneins inChlamydomonasflagella
Authors: Barber Cynthia F. , Heuser Thomas , Carbajal-González Blanca I. , Botchkarev Vladimir V. , Nicastro Daniela
Published: November 2011

Radial spokes (RSs) play an essential role in the regulation of axonemal dynein activity and thus of ciliary and flagellar motility. However, few details are known about the complexes involved. Using cryo–electron tomography and subtomogram averaging, we visualized the three-dimensional structure of the radial spokes in Chlamydomonas flagella in unprecedented detail. Unlike many other species, Chlamydomonas has only two spokes per axonemal repeat, RS1 and RS2. Our data revealed previously uncharacterized features, including two-pronged spoke bases that facilitate docking to the doublet microtubules, and that inner dyneins connect directly to the spokes. Structures of wild type and the headless spoke mutant pf17 were compared to define the morphology and boundaries of the head, including a direct RS1-to-RS2 interaction. Although the overall structures of the spokes are very similar, we also observed some differences, corroborating recent findings about heterogeneity in the docking of RS1 and RS2. In place of a third radial spoke we found an uncharacterized, shorter electron density named “radial spoke 3 stand-in,” which structurally bears no resemblance to RS1 and RS2 and is unaltered in the pf17 mutant. These findings demonstrate that radial spokes are heterogeneous in structure and may play functionally distinct roles in axoneme regulation.
MR-Tandem: parallel X!Tandem using Hadoop MapReduce on Amazon Web Services
Authors: Pratt Brian , Howbert J. Jeffry , Tasman Natalie I. , Nilsson Erik J.
Published: November 2011

Summary: MR-Tandem adapts the popular X!Tandem peptide search engine to work with Hadoop MapReduce for reliable parallel execution of large searches. MR-Tandem runs on any Hadoop cluster but offers special support for Amazon Web Services for creating inexpensive on-demand Hadoop clusters, enabling search volumes that might not otherwise be feasible with the compute resources a researcher has at hand. MR-Tandem is designed to drop in wherever X!Tandem is already in use and requires no modification to existing X!Tandem parameter files, and only minimal modification to X!Tandem-based workflows.

Availability and implementation: MR-Tandem is implemented as a lightly modified X!Tandem C++ executable and a Python script that drives Hadoop clusters including Amazon Web Services (AWS) Elastic Map Reduce (EMR), using the modified X!Tandem program as a Hadoop Streaming mapper and reducer. The modified X!Tandem C++ source code is Artistic licensed, supports pluggable scoring, and is available as part of the Sashimi project at http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/trans_proteomic_pipeline/extern/xtandem/. The MR-Tandem Python script is Apache licensed and available as part of the Insilicos Cloud Army project at http://ica.svn.sourceforge.net/viewvc/ica/trunk/mr-tandem/. Full documentation and a windows installer that configures MR-Tandem, Python and all necessary packages are available at this same URL.

Contact:  brian.pratt@insilicos.com
Using Poisson mixed-effects model to quantify transcript-level gene expression in RNA-Seq
Authors: Hu Ming , Zhu Yu , Taylor Jeremy M. G. , Liu Jun S. , Qin Zhaohui S.
Published: November 2011

Motivation: RNA sequencing (RNA-Seq) is a powerful new technology for mapping and quantifying transcriptomes using ultra high-throughput next-generation sequencing technologies. Using deep sequencing, gene expression levels of all transcripts including novel ones can be quantified digitally. Although extremely promising, the massive amounts of data generated by RNA-Seq, substantial biases and uncertainty in short read alignment pose challenges for data analysis. In particular, large base-specific variation and between-base dependence make simple approaches, such as those that use averaging to normalize RNA-Seq data and quantify gene expressions, ineffective.

Results: In this study, we propose a Poisson mixed-effects (POME) model to characterize base-level read coverage within each transcript. The underlying expression level is included as a key parameter in this model. Since the proposed model is capable of incorporating base-specific variation as well as between-base dependence that affect read coverage profile throughout the transcript, it can lead to improved quantification of the true underlying expression level.

Availability and implementation: POME can be freely downloaded at http://www.stat.purdue.edu/~yuzhu/pome.html.

Contact:  yuzhu@purdue.edu; zhaohui.qin@emory.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Common Spear Rot of Oil Palm in Indonesia
Authors: Suwandi  , Akino Seishi , Kondo Norio
Published: November 2011

Common spear rot (CSR), which is also known as crown disease, was first reported in Indonesia in the 1920s. It has caused considerable losses in young oil palm plantings, and yet the pathogenic agent has remained elusive. Symptomatic spear leaves were collected from oil palm plantations and farm plots in South Sumatra, North Sumatra, and Bangka-Belitung, Indonesia. Of the 14 different fungi isolated, Fusarium incarnatum, F. solani, an undescribed Fusarium sp., and Ceratocystis paradoxa were isolated most frequently from diseased leaf tissue. F. incarnatum and the undescribed Fusarium sp. were also frequently isolated from healthy leaf tissue, along with Pestalotiopsis microspora and Curvularia affinis. Ceratocystis paradoxa was never isolated from healthy leaf tissue. Koch's postulate experiments showed that C. paradoxa was able to infect wounded oil palm leaves causing a symptom of extensive rotting similar to that found in the field. Although isolated less frequently and less virulent than C. paradoxa, F. sacchari was also capable of causing lesions on succulent wounded, inoculated leaves. For both C. paradoxa and F. sacchari, the disease severity index was greater when the oil palm leaves appeared to have more succulent growth. Likewise, other Fusarium species and other nonfusarial fungi that were usually not pathogenic were weakly virulent on palms with more succulent growth. These findings confirm that C. paradoxa is one pathogen that is associated with CSR of oil palm in Indonesia.
JC virus promoter/enhancers contain TATA box-associated Spi-B-binding sites that support early viral gene expression in primary astrocytes
Authors: Marshall Leslie J. , Moore Lisa D. , Mirsky Matthew M. , Major Eugene O.
Published: November 2011

JC virus (JCV) is the aetiological agent of the demyelinating disease progressive multifocal leukoencephalopathy, an AIDS defining illness and serious complication of mAb therapies. Initial infection probably occurs in childhood. In the working model of dissemination, virus persists in the kidney and lymphoid tissues until immune suppression/modulation causes reactivation and trafficking to the brain where JCV replicates in oligodendrocytes. JCV infection is regulated through binding of host factors such as Spi-B to, and sequence variation in the non-coding control region (NCCR). Although NCCR sequences differ between sites of persistence and pathogenesis, evidence suggests that the virus that initiates infection in the brain disseminates via B-cells derived from latently infected haematopoietic precursors in the bone marrow. Spi-B binds adjacent to TATA boxes in the promoter/enhancer of the PML-associated JCV Mad-1 and Mad-4 viruses but not the non-pathogenic, kidney-associated archetype. The Spi-B-binding site of Mad-1/Mad-4 differs from that of archetype by a single nucleotide, AAAAGGGAAGGGA to AAAAGGGAAGGTA. Point mutation of the Mad-1 Spi-B site reduced early viral protein large T-antigen expression by up to fourfold. Strikingly, the reverse mutation in the archetype NCCR increased large T-antigen expression by 10-fold. Interestingly, Spi-B protein binds the NCCR sequence flanking the viral promoter/enhancer, but these sites are not essential for early viral gene expression. The effect of mutating Spi-B-binding sites within the JCV promoter/enhancer on early viral gene expression strongly suggests a role for Spi-B binding to the viral promoter/enhancer in the activation of early viral gene expression.
Tax1-expressing feline 8C cells are useful to monitor the life cycle of human T-cell leukemia virus type I
Authors: Mori Takahisa , Shimizu Nobuaki , Jinno-Oue Atsushi , Tanaka Atsushi , Shinagawa Masahiko , Tokizawa Shigemi , Akagi Tsuyoshi , Hoshino Hiroo
Published: November 2011

Extremely low infectivity has hampered direct (cell-free) infection studies of human T-cell leukemia virus type I (HTLV-I). In order to break through this barrier, we examined the susceptibility of many kinds of cells to HTLV-I and found a feline kidney cell line, 8C, that is highly susceptible to HTLV-I and produced remarkable amounts of infectious progeny viruses. Tax1 protein encoded by HTLV-I is known as a transcription activator for viral and cellular genes. We found that the 8C cells expressing the Tax1 protein (8C/TaxWT cells) can produce more progeny viruses than 8C cells when the cells were exposed to cell-free HTLV-I. A large number of syncytia were also induced in these cells. Here, we propose 8C/TaxWT cells as a useful tool to study the cell-free HTLV-I infection.
Generation of T-cell receptors targeting a genetically stable and immunodominant cytotoxic T-lymphocyte epitope within hepatitis C virus non-structural protein 3
Authors: Pasetto Anna , Frelin Lars , Brass Anette , Yasmeen Anila , Koh Sarene , Lohmann Volker , Bartenschlager Ralf , Magalhaes Isabelle , Maeurer Markus , Sällberg Matti , Chen Margaret
Published: November 2011

Hepatitis C virus (HCV) is a major cause of severe liver disease, and one major contributing factor is thought to involve a dysfunction of virus-specific T-cells. T-cell receptor (TCR) gene therapy with HCV-specific TCRs would increase the number of effector T-cells to promote virus clearance. We therefore took advantage of HLA-A2 transgenic mice to generate multiple TCR candidates against HCV using DNA vaccination followed by generation of stable T-cell–BW (T-BW) tumour hybrid cells. Using this approach, large numbers of non-structural protein 3 (NS3)-specific functional T-BW hybrids can be generated efficiently. These predominantly target the genetically stable HCV genotype 1 NS31073–1081CTL epitope, frequently associated with clearance of HCV in humans. These T-BW hybrid clones recognized the NS31073peptide with a high avidity. The hybridoma effectively recognized virus variants and targeted cells with low HLA-A2 expression, which has not been reported previously. Importantly, high-avidity murine TCRs effectively redirected human non-HCV-specific T-lymphocytes to recognize human hepatoma cells with HCV RNA replication driven by a subgenomic HCV replicon. Taken together, TCR candidates with a range of functional avidities, which can be used to study immune recognition of HCV-positive targets, have been generated. This has implications for TCR-related immunotherapy against HCV.
Airway challenges in critical care
Authors: Nolan J. P. , Kelly F. E.
Published: November 2011

Airway management in the intensive care unit is more problematic than during anaesthesia. In general, critically ill patients have less physiological reserve and complications are more common, both during the initial airway intervention (which includes risks associated with induction of anaesthesia), and later once the airway has been secured. Despite these known risks, those managing the airway of a critically ill patient, particularly out of hours, may be relatively inexperienced. Solutions to these challenging airway problems include: recognition of those patients with a potential airway problem; implementation of a plan to deal with their airway; immediate availability of a difficult airway trolley; use of capnography for every airway intervention and continuously in all ventilator‐dependent patients; and appropriate training of all intensive care unit staff including use of simulation.
More than meets the eye. Feminist poststructuralism as a lens towards understanding obesity
Authors: Aston Megan , Price Sheri , Kirk Sara Frances Louise , Penney Tarra
Published: November 2011

aston m., price s., kirk s.f.l. & penney t. (2011) More than meets the eye. Feminist poststructuralism as a lens towards understanding obesity. Journal of Advanced Nursing 68(5), 1187–1194.

Aim.  This paper presents a discussion of the application of a feminist poststructuralist‐based theoretical framework as an innovative approach towards understanding and managing the complex health issue of obesity.

Background.  Obesity is often viewed as a lifestyle choice for which the individual is blamed. This individualistic, dichotomous and behavioural perspective only allows for a narrow understanding of obesity and may even lead to misperceptions, stereotypes and marginalization of clients experiencing obesity. Feminist poststructuralism can provide a critical lens to understand the social construction of obesity and the broader environmental and cultural contexts of this health issue.

Data sources.  The theoretical framework draws from the writings of Foucault, Scott, Butler, Cheek, and Powers, published between 1983 and 2005.

Discussion.  The concepts of discourse analysis and power relations are explored and discussed in a clear manner so that nurses can easily apply this framework to their practice as they observe, question, analyse, critique and assess the care experienced by clients who are obese. The concepts of personal and social beliefs, values and stereotypes are also discussed and examples of how to apply them in practice are provided.

Implications.  It is imperative that we continue to question our everyday nursing practices as we work to support clients, especially those who feel marginalized. This focus on power relations and reflective practice can give direction to new possibilities for change in obesity management.