bluuebunny/crossref_metadata_2025 huggingface dataset:
Geometry, kinematics and fracture pattern of the Bangestan anticline, Zagros, SW Iran
Authors: TAVANI STEFANO , STORTI FABRIZIO , SOLEIMANY BAHMAN , FALLAH MOHAMMAD , MUÑOZ JOSEP A. , GAMBINI ROBERTO
Published: April 2011

Thrust-related anticlines in the Zagros Simply Folded Belt provide excellent exposed analogue structures for fractured reservoirs located in the more external sectors of the belt. In these structures it is possible to study the fracture network attributes and understand their relationships to the folding process, thus gathering fundamental information for fracture modelling in reservoirs. In this work we analyse the mesoscopic deformation pattern of the NW–SE-trending Bangestan anticline (SW Zagros, Iran) and discuss its relationship to the kinematic evolution of the hosting structure. The deformation pattern mostly includes extensional structures and pressure solution cleavages striking parallel to the fold axial trend (i.e. longitudinal), transversal extensional structures, and N–S- and E–W-striking extensional structures (oriented oblique to the fold axis). With the aid of deep wells and a transversal reflection seismic profile, we constructed a balanced cross-section of the anticline and propose a kinematic evolution pathway constrained by the mesoscopic deformation pattern. Longitudinal and transversal deformation structures developed before and/or in the very early stages of fold growth. During this stage, the Bangestan anticline grew as a set of unconnected décollement anticlines involving the Cambrian to Pliocenic sedimentary cover. In a later stage, inherited basement faults were reactivated with a right-lateral strike-slip component and the previously developed anticlines propagated laterally up to their complete linkage and thrust breakthrough. This produced the right-lateral strike-slip reactivation of longitudinal joints and the development of N–S- and E–W-striking extensional structures, which were also frequently reworked as strike-slip faults.
Middle-Ground Ethics: Can One Be Politically Realistic Without Being a Political Realist?
Authors: Nardin Terry
Published: April 2011

Thinking about international affairs has oscillated between idealism and realism throughout the modern period. Moralists continue to search for a way to combine what is reasonable in each in an ethically defensible middle between those extremes. Such efforts often yield a soft version of political realism: an ethics of compromise between moral ideals and real-world interests. But this resolution fails to escape an awkward dichotomy between “morality” and “reality,” as if moral considerations were not real and interests never illusory. It also rests on a simplistic conception of politics. Politics is distinguished from other activities in being concerned with obligations prescribed and enforced within a legal order, and those who make political decisions cannot ignore these obligations. Political decision-making must therefore take account of law, which is distinct from both morality and interest. Law may have its ultimate justification in moral principle, but it provides reasons for acting that are distinct from moral reasons. This is true of law at any level, including international law. Law also has material as well as normative force as part of the world in which decisions are made. A more nuanced middle-ground ethics, then, would take account of law as making demands of its own. If we bring law into the picture, we discover limits to action that are grounded on neither morality nor interest.
Portfolio allocation for public pension funds
Authors: PENNACCHI GEORGE , RASTAD MAHDI
Published: April 2011

This paper presents a model of a public pension fund's choice of portfolio risk. Optimal portfolio allocations are derived when pension fund management maximize the utility of wealth of a representative taxpayer or when pension fund management maximize their own utility of compensation. The model's implications are examined using annual data on the portfolio allocations and plan characteristics of 125 state pension funds over the 2000–2009 period. Consistent with agency behavior by public pension fund management, we find evidence that funds chose greater overall asset – liability portfolio risk following periods of relatively poor investment performance. In addition, pension plans that select a relatively high rate with which to discount their liabilities tend to choose riskier portfolios. Moreover, consistent with a desire to gamble for higher benefits, pension plans take more risk when they have greater representation by plan participants on their Boards of Trustees.
The steeply subducting edge of the Cocos Ridge: Evidence from receiver functions beneath the northern Talamanca Range, south‐central Costa Rica
Authors: Dzierma Y. , Rabbel W. , Thorwart M. M. , Flueh E. R. , Mora M. M. , Alvarado G. E.
Published: April 2011

The deep structure of the south‐central Costa Rican subduction zone has not been studied in great detail so far because large parts of the area are virtually inaccessible. We present a receiver function study along a transect of broadband seismometers through the northern flank of the Cordillera de Talamanca (south Costa Rica). Below Moho depths, the receiver functions image a dipping positive conversion signal. This is interpreted as the subducting Cocos Plate slab, compatible with the conversions in the individual receiver functions. In finite difference modeling, a dipping signal such as the one imaged can only be reproduced by a steeply (80°) dipping structure present at least until a depth of about 70–100 km; below this depth, the length of the slab cannot be determined because of possible scattering effects. The proposed position of the slab agrees with previous results from local seismicity, local earthquake tomography, and active seismic studies, while extending the slab location to greater depths and steeper dip angle. Along the trench, no marked change is observed in the receiver functions, suggesting that the steeply dipping slab continues until the northern flank of the Cordillera de Talamanca, in the transition region between the incoming seamount segment and Cocos Ridge. Considering the time predicted for the establishment of shallow angle underthrusting after the onset of ridge collision, the southern Costa Rican subduction zone may at present be undergoing a reconfiguration of subduction style, where the transition to shallow underthrusting may be underway but still incomplete.
Downscaling precipitation using regional climate models and circulation patterns toward hydrology
Authors: Bárdossy András , Pegram Geoffrey
Published: April 2011

The aim of this paper is to define a method for determining reasonable estimates of rainfall modeled by global circulation models (GCMs) coupled with regional climate models (RCMs). The paper describes and uses two new procedures designed to give confidence in the interpretation of such rainfall estimates. The first of these procedures is the use of circulation patterns (CPs) to define quantile‐quantile (Q‐Q) transforms between observed and RCM‐estimated rainfall (the CPs were derived from sea level pressure (SLP) fields obtained from reanalysis of historical daily weather in a previous study). The Q‐Q transforms are derived using two downscaling techniques during a 20 year calibration period and were validated during a 10 year period of observations. The second novel procedure is the use of a double Q‐Q transform to estimate the rainfall patterns and amounts from GCM‐RCM predictions of SLP and rainfall fields during a future period. This procedure is essential because we find that the CP‐dependent rainfall frequency distributions on each block are unexpectedly different from the corresponding historical distributions. The daily rainfall fields compared are recorded on a 25 km grid over the Rhine basin in Germany; the observed daily data are averaged over the grid blocks, and the RCM values have been estimated over the same grid. Annual extremes, recorded on each block during the validation period, of (1) maximum daily rainfall and (2) the lowest 5% of filtered rainfall were calculated to determine the ability of RCMs to capture rainfall characteristics which are important for hydrological applications. The conclusions are that (1) RCM outputs used here are good at capturing the patterns and rankings of CP‐dependent rainfall; (2) CP‐dependent downscaling, coupled with the double Q‐Q transform, gives good estimates of the rainfall during the validation period; (3) because the RCMs offer future CP‐dependent rainfall distributions that are different from the observed distributions, it is judged that these predictions, once modified by the double Q‐Q transforms, are hydrologically reasonable; and (4) the climate in the Rhine basin in the future, as modeled by the RCMs, is likely to be wetter than in the past. The results suggest that such future projections may be used with cautious confidence.
Neutrophils sustain effective CD8+ T‐cell responses in the respiratory tract following influenza infection
Authors: Tate Michelle D , Brooks Andrew G , Reading Patrick C , Mintern Justine D
Published: April 2011

Neutrophils have an important role in early host protection during influenza A virus infection. Their ability to modulate the virus‐specific adaptive immune response is less clear. Here, we have used a mouse model to examine the impact of neutrophils on CD8+ T‐cell responses during influenza virus infection. CD8+ T‐cell priming, expansion, migration, cytokine secretion and cytotoxic capacity were investigated in the virus‐infected airways and secondary lymphoid organs. To do this, we utilised a Ly6G‐specific monoclonal antibody (mAb; 1A8) that specifically depletes neutrophils in vivo. Neutrophil depletion early after infection with influenza virus strain HKx31 (H3N2) did not alter influenza virus‐derived antigen presentation or naïve CD8+ T‐cell expansion in the secondary lymphoid organs. Trafficking of virus‐specific CD8+ T cells into the infected pulmonary airways was also unaltered. Instead, early neutropenia reduced both the overall magnitude of influenza virus‐specific CD8+ T cells, together with impaired cytokine production and cytotoxic effector function. Therefore, neutrophils are important participants in anti‐viral mechanisms that sustain effective CD8+ T‐cell responses in the respiratory tract of influenza virus‐infected mice.
The Politics of Next Generation Research Democratizing Research-Centred Computational Networks
Authors: Dutton William H
Published: April 2011

Research on information technology has been focused primarily on the worlds of IT and management systems for business and government to the relative neglect of research on the digital and institutional infrastructures that underpin the research enterprise itself. When digital research is studied, the emphasis has been on the diffusion of technological innovations, rather than the social and political dynamics shaping the design and role of technologies in research. However, what researchers know, and with whom they collaborate, could be transformed through the strategic use of advances designed to support research, defined here as ‘research-centred computational networks’. This article presents a framework for conceptualizing the social and technological choices shaping the next generation of research in ways that could open – democratize – key aspects of the research process that move well beyond academic publication. The framework highlights the limited scope of innovation to date, and identifies a variety of factors that maintain and enhance institutional control over the research process, at the risk of losing the creative and productive bottom-up participation by networked researchers and citizen researchers among the public at large. Conceptualizing, prioritizing and advancing study of next generation research is one of the most significant but difficult challenges facing scholars of information technology.
Geometrical interpretation and curvature distribution in nanocarbons
Authors: Gupta Sanju , Saxena Avadh
Published: April 2011

Despite extensive research on microscopic structure and physical property characterization of advanced nanocarbon systems, they have not been viewed as topologically distinct nanoscale materials with various geometries (curvature). This work is motivated by our recent work [S. Gupta and A. Saxena, J. Raman Spectrosc. 40, 1127 (2009)] where we introduced the notion of “global” topology for novel nanocarbons and provided systematic trends by monitoring the phonon spectra via resonance Raman spectroscopy, which led to the paradigm of curvature/topology → property → functionality relationship in these materials. Here we determined the distribution of the mean (H) and Gaussian (K) curvatures as pertinent observables for geometric characterization taking into account the observed geometrical parameters, that is, radius, polar, azimuthal, or conical angle associated with tubular (single, double-, and multi-walled nanotubes; K = 0), spherical (hypo- and hyperfullerenes; K > 0) and complex (helical nanoribbons and nanotori/nanorings; K < 0) nanocarbon geometries to quantify the interplay of intrinsic surface curvature and topology, wherein global topology of the overall sp2-bonded carbon (sp2C) constrains local topology of the constituent carbon rings. We also studied various other structures such as catenoid and saddle-shaped surfaces as interesting nanocarbons. We compared these results with highly oriented pyrolytic graphite and monolayer graphene as layered and planar systems, respectively. Moreover, nanocarbons discussed herein are their derivatives. Curvature leads to nonlinearity that manifests itself in some form of symmetry breaking which can be extrapolated to topological variation due to nanoscale defects. Thus it may either close/open the bandgap leading to the introduction of new Raman spectroscopy signatures and optical absorption peaks, changes in mechanical properties, electrical behavior, and electronic density of states and possibly inducing magnetism. Finally, we elucidate the role of curved geometry in Casimir forces arising in carbon nanostructures.
Understanding junction breakdown in multicrystalline solar cells
Authors: Breitenstein Otwin , Bauer Jan , Bothe Karsten , Kwapil Wolfram , Lausch Dominik , Rau Uwe , Schmidt Jan , Schneemann Matthias , Schubert Martin C. , Wagner Jan-Martin , Warta Wilhelm
Published: April 2011

Extensive investigations on industrial multicrystalline silicon solar cells have shown that, for standard 1 Ω cm material, acid-etched texturization, and in absence of strong ohmic shunts, there are three different types of breakdown appearing in different reverse bias ranges. Between −4 and −9 V there is early breakdown (type 1), which is due to Al contamination of the surface. Between −9 and −13 V defect-induced breakdown (type 2) dominates, which is due to metal-containing precipitates lying within recombination-active grain boundaries. Beyond −13 V we may find in addition avalanche breakdown (type 3) at etch pits, which is characterized by a steep slope of the I-V characteristic, avalanche carrier multiplication by impact ionization, and a negative temperature coefficient of the reverse current. If instead of acid-etching alkaline-etching is used, all these breakdown classes also appear, but their onset voltage is enlarged by several volts. Also for cells made from upgraded metallurgical grade material these classes can be distinguished. However, due to the higher net doping concentration of this material, their onset voltage is considerably reduced here.
Kinetic simulations of a deuterium-tritium Z pinch with >1016 neutron yield
Authors: Welch D. R. , Rose D. V. , Thoma C. , Clark R. E. , Mostrom C. B. , Stygar W. A. , Leeper R. J.
Published: April 2011

Fully kinetic, collisional, and electromagnetic simulations of the time evolution of an imploding and burning Z pinch plasma have been performed. Using the implicit particle-in-cell (PIC) code, multidimensional (1D and 3D) simulations of deuterium and deuterium-tritium Z pinches provide insight into the mechanisms of neutron production. The PIC code allows non-Maxwellian particle distributions, simulates finite mean-free-path effects, performs self-consistent calculations of anomalous resistivity, and permits charge separation. At low pinch current, neutron production is dominated by high energy ions driven by instabilities. The instabilities produce a power-law ion-energy distribution function in the distribution tail. At higher currents with deuterium-tritium fuel, the vast majority of the neutrons is thermonuclear in origin and neutron yield follows an I4 neutron yield scaling with current. High-current, multidimension simulations (up to 40 MA with > 1016 neutron yield) suggest that the fraction of thermonuclear neutrons increases with current and the strong dependence of neutron yield with current will continue at still higher currents. Scenarios for fusion breakeven and possible ignition in the 40–80 MA regime are discussed.
Magnetocapacitance in Ca3CoMnO6
Authors: Kaushik S. D. , Rayaprol S. , Saha J. , Mohapatra N. , Siruguri V. , Babu P. D. , Patnaik S.
Published: April 2011

Magnetocapacitance (MC) measurements—that is, measuring capacitance as a function of temperature at constant magnetic field—has been carried out on a quasi-1D compound, Ca3CoMnO6. MC reveals the presence of a magnetodielectric effect (MDE), which in turn signals the presence of magnetoelectric coupling below the magnetic ordering temperature, TN ( = 15 K). We also observed the sign reversal of the MDE as the temperature increased from 3 to 20 K. The MDE is positive at 3 K and negative between 3 and 15 K, and it saturates to a near zero value above 15 K. The sign change of the MDE is explained in terms the spin-pair correlation of neighboring spins of Co/Mn at a given applied magnetic field H. A negative MDE signifies antiferromagnetic ordering, and a positive MDE signifies ferromagnetic/paramagnetic ordering. Neutron diffraction study reveals changes in the magnetic structure in the temperature range of 2 to 10 K. The present work brings out the possible correlation between the magnetic structure and the dielectric properties of Ca3CoMnO6.
Direct current effects on 1/f noise in patterned Permalloy films
Authors: Zhang Hanqiao , Li Chaojiang , Pearson L. Wilson , Wang Pingshan
Published: April 2011

Detailed investigations of 1/f noise were performed in patterned Permalloy films. The gold bridges for the four probe measurement setup were deposited on a quartz substrate. Pattern geometry, bias current, and transverse magnetostatic field effects on the material’s 1/f noise were studied. The normalized Hooge parameter and frequency slope were analyzed in the framework of the empirical Hooge relation. Different dependences of the noise versus bias current generated Oersted field and the magnetostatic field were observed. The normalized Hooge parameter and frequency slope were pattern width and field configuration dependent.
Enhanced magnetic properties of Bi-substituted cobalt ferrites
Authors: Franco A. , Machado F. L. A. , Zapf V. S. , Wolff-Fabris F.
Published: April 2011

In this paper we present a magnetic study of Co1−xBixFe2O4 nanoparticles obtained by applying magnetic fields up to 14 T and for temperatures in the range of 5 to 340 K. Hysteresis loops yield a saturation magnetization (Ms), coercive field (Hc), and remanent magnetization (Mr) that vary significantly with temperature and bismuth content. The T-dependence of Ms obtained for H = 5 T presents a maximum at 150 K and a minimum at 25 K that are also dependent on the value of x. However, for H = 14 T, this anomalous behavior disappears and the magnetization smoothly approaches saturation down to 5 K. The magnetic cubic anisotropy constant for different Bi contents, determined by a “law of approach” to saturation, was found to be smaller than those values for pure cobalt ferrite nanoparticles and strongly dependent on temperature. A discussion on the implications of the anomalous behavior in the determination of the anisotropy constant in these sample materials is also presented.
Temperature dependent magnetic properties of Co nanowires and nanotubes prepared by electrodeposition method
Authors: Ahmad Naeem , Chen J. Y. , Iqbal Javed , Wang W. X. , Zhou W. P. , Han X. F.
Published: April 2011

Co nanowires (NWs) and nanotubes (NTs) with same length and different diameter have been deposited in anodized aluminum oxide templates by electrodeposition method at the room temperature. The Co NWs show hcp structure while Co NTs show poor crystalline with no strong texture. The spontaneous magnetization of the Co NWs was found to be parallel to the nanowires, while Co NTs have a transverse spontaneous magnetization. Magnetization reversal occurs by curling mode in Co nanotubes while nucleation mode in Co nanowires. Temperature dependent magnetic properties show that the thermal energy decreases at low temperature causing an increase in coercivity and saturation magnetization. The dominance of shape anisotropy in case of Co NWs is manifested by the weak temperature dependence of the enhanced coercive field. Magnetostatic interactions and magnetocrystalline anisotropy is found dominant in case of Co NTs due to their distinct geometry.
Flux- and gradient-driven global gyrokinetic simulation of tokamak turbulence
Authors: Görler Tobias , Lapillonne Xavier , Brunner Stephan , Dannert Tilman , Jenko Frank , Aghdam Sohrab Khosh , Marcus Patrick , McMillan Ben F. , Merz Florian , Sauter Olivier , Told Daniel , Villard Laurent
Published: April 2011

The Eulerian gyrokinetic turbulence code gene has recently been extended to a full torus code. Moreover, it now provides Krook-type sources for gradient-driven simulations where the profiles are maintained on average as well as localized heat sources for a flux-driven type of operation. Careful verification studies and benchmarks are performed successfully. This setup is applied to address three related transport issues concerning nonlocal effects. First, it is confirmed that in gradient-driven simulations, the local limit can be reproduced—provided that finite aspect ratio effects in the geometry are treated carefully. In this context, it also becomes clear that the profile widths (not the device width) may constitute a more appropriate measure for finite-size effects. Second, the nature and role of heat flux avalanches are discussed in the framework of both local and global, flux- and gradient-driven simulations. Third, simulations dedicated to discharges with electron internal barriers are addressed.
Experimental study of a drop bouncing on a liquid surface
Authors: Zou Jun , Wang Peng Fei , Zhang Ting Rong , Fu Xin , Ruan Xiaodong
Published: April 2011

The behavior of millimetric drops bouncing on a gas-liquid interface is studied using a high-speed video camera. The bounce time is found to be not dependent on the impact velocity of the drop over a wide range of velocities and is linear with the 1.5th power of the drop diameter. The success probability of drop bounce becomes sensitive to the depth of target liquid once the depth is shallower than five times depth of the maximum crater size, and when the depth is the same as the maximum crater depth, the success probability is greatest. However, the bounce time is insensitive to the liquid depth. The coefficient of restitution is compared to previous experiments done for drops smaller than 1 mm.
Engineering of magnetostriction in Fe3Pt1−xIrx by controlling the Ir concentration
Authors: Odkhuu Dorj , Yun Won Seok , Rhim S. H. , Hong Soon Cheol
Published: April 2011

A tremendous change in both the sign and magnitude of magnetostriction (λ001) in Fe3Pt1−xIrx (x=0–1.0) was discovered through a first-principles study using the highly precise full-potential linearized augmented plane wave method. The obtained λ001 values span a wide range from −1050 (x=0) to +2670 ppm (x=0.25), a significantly large enhancement over the λ001 values attained for Galfenol, a widely investigated material. Further analysis confirmed that this large effect originates mainly from the nonmagnetic Ir and Pt with induced moments, of which the 5d orbital has larger spin–orbit coupling than the 3d orbital of Fe.
Highly air-stable electrical performance of graphene field effect transistors by interface engineering with amorphous fluoropolymer
Authors: Shin Woo Cheol , Seo Sunae , Cho Byung Jin
Published: April 2011

Excellent stability on the electrical characteristics of graphene field effect transistors in an air ambient is achieved by inserting an amorphous fluoropolymer between the graphene channel and SiO2 gate dielectric. The interface engineering exploits the highly water repellent property of the fluoropolymer stemming from high hydrophobicity and low moisture permeation, and results in negligible hole doping of graphene from absorption of water molecules. In addition, the graphene field effect transistors with the fluoropolymer/SiO2 gate dielectric shows superior performances including negligible VDirac hysteresis and highly stable carrier mobility, which are important characteristics for analog rf device applications.
Dual gate indium-gallium-zinc-oxide thin film transistor with an unisolated floating metal gate for threshold voltage modulation and mobility enhancement
Authors: Zan Hsiao-Wen , Chen Wei-Tsung , Yeh Chung-Cheng , Hsueh Hsiu-Wen , Tsai Chuang-Chuang , Meng Hsin-Fei
Published: April 2011

In this study, we propose a floating dual gate (FDG) indium-gallium-zinc-oxide (IGZO) thin film transistor (TFT) with a floating metal back gate that is directly contact with IGZO without a dielectric layer. The floating back gate effect is investigated by changing the work function (ϕ) of the back gate. The FDG IGZO TFT exhibits an improved field-effect mobility (μ), unchanged subthreshold swing (SS), high on/off current ratio, and a tunable threshold voltage ranged (Vth) from −5.0 to +7.9 V without an additional back gate power supply.
Silicon diffusion in aluminum for rear passivated solar cells
Authors: Urrejola Elias , Peter Kristian , Plagwitz Heiko , Schubert Gunnar
Published: April 2011

We show that the lateral spread of silicon in a screen-printed aluminum layer increases by (1.50±0.06) μm/°C, when increasing the peak firing temperature within an industrially applicable range. In this way, the maximum spread limit of diffused silicon in aluminum is predictable and does not depend on the contact area size but on the firing temperature. Therefore, the geometry of the rear side pattern can influence not only series resistance losses within the solar cell but the process of contact formation itself. In addition, too fast cooling lead to Kirkendall void formations instead of an eutectic layer.
The Psychometrics of Photographic Cropping: The Influence of Colour, Meaning, and Expertise
Authors: McManus I Christopher , Zhou Fanzhi Anita , l'Anson Sophie , Waterfield Lucy , Stöver Katharina , Cook Richard
Published: April 2011

Cropping is the central act of photography, the viewfinder of a camera being used to crop a portion of the visual world which is then surrounded with a frame. Six studies are described which show that the act of cropping is carried out reliably and confidently by both expert and non-expert participants. Two studies confirm that some croppers are better croppers than others, their cropped images being preferred aesthetically over the croppings of less-good croppers. Colour had little impact on cropping decisions, whereas thresholded monochrome images (‘Mooney images’) dramatically altered crop positions. That suggests that cropping can be driven top – down, by the meaning of objects in photographs, but the fact that the Mooneyised images are still cropped consistently, suggests that image structure, perhaps in the form of low-level image properties, may still be important. Experts crop pictures differently from non-experts, and they take longer, viewing a wider range of possible crops, pausing longer to assess crops, and using more formal terminology when reflecting on their cropping decisions. Experts' crops are not, however, preferred more, either by non-expert viewers or by expert viewers. Cropping, it is suggested, is an ideal paradigm for experimental aesthetics, allowing precise experimental control with Fechner's Method of Production, a technique which normally is not easy to use.
Aesthetic Preferences in the Size of Images of Real-World Objects
Authors: Linsen Sarah , Leyssen Mieke H R , Sammartino Jonathan , Palmer Stephen E
Published: April 2011

Konkle and Oliva (in press, Journal of Experimental Psychology: Human Perception and Performance) found that the preferred (‘canonical’) visual size of a picture of an object within a frame is proportional to the logarithm of its known physical size. They used within-participants designs on several tasks, including having participants adjust the object's size to ‘look best’. We examined visual size preference in 2AFC tasks with explicit aesthetic instructions to choose: “which of each pair you like best”. We also used both within- and between-participants conditions to investigate the possible role of demand characteristics. In experiments 1 and 2, participants saw all possible image pairs depicting the same object at six different sizes for twelve real-world objects that varied in physical size. Significant effects of known physical size were present, regardless of whether participants made judgments about a single object (the between-participants design) or about all objects intermixed (the within-participants design). Experiment 3 showed a reduced effect when the amount of image detail present at different visual sizes was kept constant by posterizing the images. The results are discussed in terms of ecological biases on aesthetic preferences.
Natural history of the common tree snake, Dendrelaphis punctulatus (Serpentes:Colubridae), in the wet - dry tropics of north Queensland
Authors: Fearn S. , Trembath D. F.
Published: April 2011

Common tree snakes, Dendrelaphis punctulatus, are medium to large colubrid snakes that are relatively common in the eastern and northern parts of tropical Australia. The only previous study on this species involved museum specimens from across the taxon’s range. During a seven-year period we collected data on 131 field-caught specimens from a melanotic population in the Townsville district of north Queensland. Dendrelaphis punctulatus was found to be primarily diurnal, with a peak in activity centred around the reproductive period during the transition from dry to wet seasons. Females were larger than males with respect to all measured parameters, including mass and head size. Reproduction in females was strongly seasonal and clutch size was related to maternal body size. Prey items consisted of frogs, lizards and locusts.
Follistatin-like 1 (Fstl1) is a bone morphogenetic protein (BMP) 4 signaling antagonist in controlling mouse lung development
Authors: Geng Yan , Dong Yingying , Yu Mingyan , Zhang Long , Yan Xiaohua , Sun Jingxia , Qiao Long , Geng Huixia , Nakajima Masahiro , Furuichi Tatsuya , Ikegawa Shiro , Gao Xiang , Chen Ye-Guang , Jiang Dianhua , Ning Wen
Published: April 2011

Lung morphogenesis is a well orchestrated, tightly regulated process through several molecular pathways, including TGF-β/bone morphogenetic protein (BMP) signaling. Alteration of these signaling pathways leads to lung malformation. We investigated the role of Follistatin-like 1 (Fstl1), a secreted follistatin-module–containing glycoprotein, in lung development. Deletion of
Fstl1
in mice led to postnatal lethality as a result of respiratory failure. Analysis of the mutant phenotype showed that Fstl1 is essential for tracheal cartilage formation and alveolar maturation. Deletion of the
Fstl1
gene resulted in malformed tracheal rings manifested as discontinued rings and reduced ring number.
Fstl1
-deficient mice displayed septal hypercellularity and end-expiratory atelectasis, which were associated with impaired differentiation of distal alveolar epithelial cells and insufficient production of mature surfactant proteins. Mechanistically, Fstl1 interacted directly with BMP4, negatively regulated BMP4/Smad1/5/8 signaling, and inhibited BMP4-induced surfactant gene expression. Reducing BMP signaling activity by Noggin rescued pulmonary atelectasis of
Fstl1
-deficient mice. Therefore, we provide in vivo and in vitro evidence to demonstrate that Fstl1 modulates lung development and alveolar maturation, in part, through BMP4 signaling.
Stability of hydrocarbons at deep Earth pressures and temperatures
Authors: Spanu Leonardo , Donadio Davide , Hohl Detlef , Schwegler Eric , Galli Giulia
Published: April 2011

Determining the thermochemical properties of hydrocarbons (HCs) at high pressure and temperature is a key step toward understanding carbon reservoirs and fluxes in the deep Earth. The stability of carbon-hydrogen systems at depths greater than a few thousand meters is poorly understood and the extent of abiogenic HCs in the Earth mantle remains controversial. We report ab initio molecular dynamics simulations and free energy calculations aimed at investigating the formation of higher HCs from dissociation of pure methane, and in the presence of carbon surfaces and transition metals, for pressures of 2 to 30 GPa and temperatures of 800 to 4,000 K. We show that for T≥2,000 K and P≥4 GPa HCs higher than methane are energetically favored. Our results indicate that higher HCs become more stable between 1,000 and 2,000 K and P≥4 GPa. The interaction of methane with a transition metal facilitates the formation of these HCs in a range of temperature where otherwise pure methane would be metastable. Our results provide a unified interpretation of several recent experiments and a detailed microscopic model of methane dissociation and polymerization at high pressure and temperature.
Anti–ErbB-2 mAb therapy requires type I and II interferons and synergizes with anti–PD-1 or anti-CD137 mAb therapy
Authors: Stagg John , Loi Sherene , Divisekera Upulie , Ngiow Shin Foong , Duret Helene , Yagita Hideo , Teng Michele W. , Smyth Mark J.
Published: April 2011

Trastuzumab, a monoclonal antibody targeting human epidermal growth factor receptor-2 (HER2/ErbB-2), has become the mainstay of treatment for HER2-positive breast cancer. Nevertheless, its exact mechanism of action has not been fully elucidated. Although several studies suggest that Fc receptor-expressing immune cells are involved in trastuzumab therapy, the relative contribution of lymphocyte-mediated cellular cytotoxicity and antitumor cytokines remains unknown. We report here that anti–ErbB-2 mAb therapy is dependent on the release of type I and type II IFNs but is independent of perforin or FasL. Our study thus challenges the notion that classical antibody-dependent, lymphocyte-mediated cellular cytotoxicity is important for trastuzumab. We demonstrate that anti–ErbB-2 mAb therapy of experimental tumors derived from MMTV-ErbB-2 transgenic mice triggers MyD88-dependent signaling and primes IFN-γ–producing CD8+ T cells. Adoptive cell transfer of purified T cell subsets confirmed the essential role of IFN-γ–producing CD8+ T cells. Notably, anti–ErbB-2 mAb therapy was independent of IL-1R or IL-17Ra signaling. Finally, we investigated whether immunostimulatory approaches with antibodies against programmed death-1 (PD-1) or 41BB (CD137) could be used to capitalize on the immune-mediated effects of trastuzumab. We demonstrate that anti–PD-1 or anti-CD137 mAb can significantly improve the therapeutic activity of anti–ErbB-2 mAb in immunocompetent mice.
Quantification of receptor tyrosine kinase transactivation through direct dimerization and surface density measurements in single cells
Authors: Swift Jody L. , Godin Antoine G. , Doré Kim , Freland Laure , Bouchard Nathalie , Nimmo Chelsea , Sergeev Mikhail , De Koninck Yves , Wiseman Paul W. , Beaulieu Jean-Martin
Published: April 2011

Cell signaling involves dynamic changes in protein oligomerization leading to the formation of different signaling complexes and modulation of activity. Spatial intensity distribution analysis (SpIDA) is an image analysis method that can directly measure oligomerization and trafficking of endogenous proteins in single cells. Here, we show the use of SpIDA to quantify dimerization/activation and surface transport of receptor protein kinases—EGF receptor and TrkB—at early stages of their transactivation by several G protein-coupled receptors (GPCRs). Transactivation occurred on the same timescale and was directly limited by GPCR activation but independent of G-protein coupling types. Early receptor protein kinase transactivation and internalization were not interdependent for all receptor pairs tested, revealing heterogeneity between groups of GPCRs. SpIDA also detected transactivation of TrkB by dopamine receptors in intact neurons. By allowing for time and space resolved quantification of protein populations with heterogeneous oligomeric states, SpIDA provides a unique approach to undertake single cell multivariate quantification of signaling processes involving changes in protein interactions, trafficking, and activity.
Genome-wide functional screen identifies a compendium of genes affecting sensitivity to tamoxifen
Authors: Mendes-Pereira Ana M. , Sims David , Dexter Tim , Fenwick Kerry , Assiotis Ioannis , Kozarewa Iwanka , Mitsopoulos Costas , Hakas Jarle , Zvelebil Marketa , Lord Christopher J. , Ashworth Alan
Published: April 2011

Therapies that target estrogen signaling have made a very considerable contribution to reducing mortality from breast cancer. However, resistance to tamoxifen remains a major clinical problem. Here we have used a genome-wide functional profiling approach to identify multiple genes that confer resistance or sensitivity to tamoxifen. Combining whole-genome shRNA screening with massively parallel sequencing, we have profiled the impact of more than 56,670 RNA interference reagents targeting 16,487 genes on the cellular response to tamoxifen. This screen, along with subsequent validation experiments, identifies a compendium of genes whose silencing causes tamoxifen resistance (including
BAP1
,
CLPP
,
GPRC5D
,
NAE1
,
NF1
,
NIPBL
,
NSD1
,
RAD21
,
RARG
,
SMC3
, and
UBA3
) and also a set of genes whose silencing causes sensitivity to this endocrine agent (
C10orf72
,
C15orf55/NUT
,
EDF1
,
ING5
,
KRAS
,
NOC3L
,
PPP1R15B
,
RRAS2
,
TMPRSS2
, and
TPM4
). Multiple individual genes, including
NF1
, a regulator of RAS signaling, also correlate with clinical outcome after tamoxifen treatment.
Sublethal exposure to crude oil during embryonic development alters cardiac morphology and reduces aerobic capacity in adult fish
Authors: Hicken Corinne E. , Linbo Tiffany L. , Baldwin David H. , Willis Maryjean L. , Myers Mark S. , Holland Larry , Larsen Marie , Stekoll Michael S. , Rice Stanley D. , Collier Tracy K. , Scholz Nathaniel L. , Incardona John P.
Published: April 2011

Exposure to high concentrations of crude oil produces a lethal syndrome of heart failure in fish embryos. Mortality is caused by cardiotoxic polycyclic aromatic hydrocarbons (PAHs), ubiquitous components of petroleum. Here, we show that transient embryonic exposure to very low concentrations of oil causes toxicity that is sublethal, delayed, and not counteracted by the protective effects of cytochrome P450 induction. Nearly a year after embryonic oil exposure, adult zebrafish showed subtle changes in heart shape and a significant reduction in swimming performance, indicative of reduced cardiac output. These delayed physiological impacts on cardiovascular performance at later life stages provide a potential mechanism linking reduced individual survival to population-level ecosystem responses of fish species to chronic, low-level oil pollution.
Misacylation of specific nonmethionyl tRNAs by a bacterial methionyl-tRNA synthetase
Authors: Jones Thomas E. , Alexander Rebecca W. , Pan Tao
Published: April 2011

Aminoacyl-tRNA synthetases perform a critical step in translation by aminoacylating tRNAs with their cognate amino acids. Although high fidelity of aminoacyl-tRNA synthetases is often thought to be essential for cell biology, recent studies indicate that cells tolerate and may even benefit from tRNA misacylation under certain conditions. For example, mammalian cells selectively induce mismethionylation of nonmethionyl tRNAs, and this type of misacylation contributes to a cell’s response to oxidative stress. However, the enzyme responsible for tRNA mismethionylation and the mechanism by which specific tRNAs are mismethionylated have not been elucidated. Here we show by tRNA microarrays and filter retention that the methionyl-tRNA synthetase enzyme from
Escherichia coli
(EcMRS) is sufficient to mismethionylate two tRNA species,

and

, indicating that tRNA mismethionylation is also present in the bacterial domain of life. We demonstrate that the anticodon nucleotides of these misacylated tRNAs play a critical role in conferring mismethionylation identity. We also show that a certain low level of mismethionylation is maintained for these tRNAs, suggesting that mismethionylation levels may have evolved to confer benefits to the cell while still preserving sufficient translational fidelity to ensure cell viability. EcMRS mutants show distinct effects on mismethionylation, indicating that many regions in this synthetase enzyme influence mismethionylation. Our results show that tRNA mismethionylation can be carried out by a single protein enzyme, mismethionylation also requires identity elements in the tRNA, and EcMRS has a defined structure-function relationship for tRNA mismethionylation.
Quantification of the forces driving self-assembly of three-dimensional microtissues
Authors: Youssef Jacquelyn , Nurse Asha K. , Freund L. B. , Morgan Jeffrey R.
Published: April 2011

In a nonadhesive environment, cells will self-assemble into microtissues, a process relevant to tissue engineering. Although this has been recognized for some time, there is no basis for quantitative characterization of this complex process. Here we describe a recently developed assay designed to quantify aspects of the process and discuss its application in comparing behaviors between cell types. Cells were seeded in nonadhesive micromolded wells, each well with a circular trough at its base formed by the cylindrical sidewalls and by a central peg in the form of a right circular cone. Cells settled into the trough and coalesced into a toroid, which was then driven up the conical peg by the forces of self-assembly. The mass of the toroid and its rate of upward movement were used to calculate the cell power expended in the process against gravity. The power of the toroid was found to be 0.31 ± 0.01 pJ/h and 4.3 ± 1.7 pJ/h for hepatocyte cells and fibroblasts, respectively. Blocking Rho kinase by means of Y-27632 resulted in a 50% and greater reduction in power expended by each type of toroid, indicating that cytoskeletal-mediated contraction plays a significant role in the self-assembly of both cell types. Whereas the driving force for self-assembly has often been viewed as the binding of surface proteins, these data show that cellular contraction is important for cell–cell adhesion. The power measurement quantifies the contribution of cell contraction, and will be useful for understanding the concerted action of the mechanisms that drive self-assembly.
Topology based data analysis identifies a subgroup of breast cancers with a unique mutational profile and excellent survival
Authors: Nicolau Monica , Levine Arnold J. , Carlsson Gunnar
Published: April 2011

High-throughput biological data, whether generated as sequencing, transcriptional microarrays, proteomic, or other means, continues to require analytic methods that address its high dimensional aspects. Because the computational part of data analysis ultimately identifies shape characteristics in the organization of data sets, the mathematics of shape recognition in high dimensions continues to be a crucial part of data analysis. This article introduces a method that extracts information from high-throughput microarray data and, by using topology, provides greater depth of information than current analytic techniques. The method, termed
Progression Analysis of Disease
(
PAD
), first identifies robust aspects of cluster analysis, then goes deeper to find a multitude of biologically meaningful shape characteristics in these data. Additionally, because
PAD
incorporates a visualization tool, it provides a simple picture or graph that can be used to further explore these data. Although
PAD
can be applied to a wide range of high-throughput data types, it is used here as an example to analyze breast cancer transcriptional data. This identified a unique subgroup of
Estrogen Receptor
-positive (
ER
+
) breast cancers that express high levels of
c-MYB
and low levels of innate inflammatory genes. These patients exhibit 100% survival and no metastasis. No supervised step beyond distinction between tumor and healthy patients was used to identify this subtype. The group has a clear and distinct, statistically significant molecular signature, it highlights coherent biology but is invisible to cluster methods, and does not fit into the accepted classification of
Luminal A/B
,
Normal-like
subtypes of
ER
+
breast cancers. We denote the group as
c-MYB
+
breast cancer.
Genes involved in convergent evolution of eusociality in bees
Authors: Woodard S. Hollis , Fischman Brielle J. , Venkat Aarti , Hudson Matt E. , Varala Kranthi , Cameron Sydney A. , Clark Andrew G. , Robinson Gene E.
Published: April 2011

Eusociality has arisen independently at least 11 times in insects. Despite this convergence, there are striking differences among eusocial lifestyles, ranging from species living in small colonies with overt conflict over reproduction to species in which colonies contain hundreds of thousands of highly specialized sterile workers produced by one or a few queens. Although the evolution of eusociality has been intensively studied, the genetic changes involved in the evolution of eusociality are relatively unknown. We examined patterns of molecular evolution across three independent origins of eusociality by sequencing transcriptomes of nine socially diverse bee species and combining these data with genome sequence from the honey bee
Apis mellifera
to generate orthologous sequence alignments for 3,647 genes. We found a shared set of 212 genes with a molecular signature of accelerated evolution across all eusocial lineages studied, as well as unique sets of 173 and 218 genes with a signature of accelerated evolution specific to either highly or primitively eusocial lineages, respectively. These results demonstrate that convergent evolution can involve a mosaic pattern of molecular changes in both shared and lineage-specific sets of genes. Genes involved in signal transduction, gland development, and carbohydrate metabolism are among the most prominent rapidly evolving genes in eusocial lineages. These findings provide a starting point for linking specific genetic changes to the evolution of eusociality.