bluuebunny/crossref_metadata_2025 huggingface dataset:
Reduction of long‐term bedrock incision efficiency by short‐term alluvial cover intermittency
Authors: Lague D.
Published: May 2010

Fluctuations of the sediment volume stored in mountain channels are driven by stochastic variations of discharge and sediment supply and can inhibit bedrock incision if sediment thickness is too large. Here, I study how this short‐term stochasticity propagates into the long‐term reduction of bedrock incision efficiency (the cover effect) at geological time scales. I introduce a new numerical model that resolves sediment transport and bedrock incision at daily time scales, and is run for thousands of years. It incorporates (1) a transport threshold and daily stochastic variations in water discharge and sediment supply, (2) a freely evolving channel width and slope, and (3) an explicit treatment of alluvial thickness variations and corresponding bed incision reduction. For typical mountain river conditions the model predicts that alluvial cover oscillates between complete and negligible incision reduction. In this intermittent regime the long‐term cover effect is mainly set by the fraction of time spent in full cover, and the present‐day extent of alluvial cover is not representative of long‐term dynamics. The long‐term integrated cover effect law differs strongly from proposed theoretical and experimental models, and it is controlled by sediment supply stochasticity rather than the details of cover development at the hydraulic time scale. Model results also suggest that steady state channel configuration always depends on sediment supply rate, while being never limited by transport capacity or strictly detachment limited. These results point out that discharge and sediment supply stochasticity should not be considered less important than the intricate details of incision laws to model long‐term bedrock channel dynamics.
Properties of the thermal ion plasma near Rhea as measured by the Cassini plasma spectrometer
Authors: Wilson R. J. , Tokar R. L. , Kurth W. S. , Persoon A. M.
Published: May 2010

Rhea is the second largest Saturnian satellite orbiting at 8.74 Saturn radii within the magnetosphere's near corotating thermal plasma. Rhea's orbital speed is less than the corotation speed, so the thermal plasma forms a wake in the direction of Rhea's orbital motion. During 26 November 2005, Cassini passed within 500 km of Rhea and through this wake, with a subsequent flyby an order of magnitude higher on 30 August 2007. The thermal plasma moments during these encounters are investigated here utilizing the Ion Mass Spectrometer (IMS) sensor of Cassini and analyzed by a forward model technique. Owing to the brevity of flybys, IMS is only able to sample a single slice of phase space at high time resolution throughout, rather than actuating to allow sampling of a variety of pitch angles but only providing a few data points. Even with this restriction, the moments before/after the encounter are in good agreement with other nonflyby actuating calculated moments. It is found that the plasma is dominated by water ions, with plasma velocities ≈30% slower than would be expected by rigid corotation, and local plasma densities decrease when passing through the wake. During the encounters, the results show that on the Saturn side of Rhea, there is no radial component of plasma flow, yet there is a radial component of ≈10 km/s outward on the anti‐Saturn side.
Simulated wave number 4 structure in equatorial F‐region vertical plasma drifts
Authors: Ren Zhipeng , Wan Weixing , Xiong Jiangang , Liu Libo
Published: May 2010

This article investigates the wave number 4 longitudinal structure in equatorial vertical E × B plasma drifts (V⊥), using the Theoretical Ionospheric Dynamo Model, Institute of Geology and Geophysics, Chinese Academy of Sciences, Version II model and the DE3 tide wind from the Thermosphere Ionosphere Mesosphere Energetics and Dynamics (TIMED)/TIMED Doppler interferometer (TIDI) observations. We simulate this longitudinal structure and examine its intra‐annual variations and the effect of different DE3 tide components and of different current components on it. We find that this longitudinal structure shows obvious intra‐annual variation, being strongest in northern summer and autumn and weakest in northern winter. This result is consistent with the intra‐annual variation observed by Ren et al. (2009b). Our simulations also suggest that the eastward propagation of the DE3 tide can cause the eastward shift of the wave number 4 structure in V⊥. The wave number 4 structures in V⊥ are mainly driven by a zonal wind component of DE3 tide, which contributes much more than the meridional wind component of DE3 tide to the wave number 4 structure in V⊥. With the influence of the coupling of ionospheric electric fields along the highly conducting magnetic field lines, the symmetric wind component of DE3 tide plays a more important role in the wave number 4 structure in V⊥ than the antisymmetric component does. The intra‐annual variations of the wave number 4 structure in V⊥ are mainly controlled by the symmetric wind component of DE3 tide. Our simulations also suggest that the wave number 4 structures in V⊥ are mainly driven by the Hall current.
Study of variation in the lower ionospheric reflection height with polar day length at Antarctic station Maitri: Estimated with tweek atmospherics
Authors: Saini Shailendra , Gwal A. K.
Published: May 2010

In the present paper investigations are made on the lower ionosphere with the help of observed tweek atmospherics at the Indian Antarctic research station Maitri during the second half of austral summer (January–March of 2003 and 2005). The variations in the lower ionospheric reflection height are found to be in correspondence with the sunrise and sunset at Maitri. The results indicate that the tweek atmospherics are helpful in tracking the changes taking place in the lower ionospheric height through the day‐night boundary. The ionospheric reflection height estimated using the cutoff frequency of fundamental (first‐harmonic or first‐mode) tweek atmospherics ranges from ∼64 to ∼79 km with a maximum calculated error of ±2.7 km. The recordings were carried out from 1800 to 0600 UTC. The analysis shows that the average cutoff frequency for the fundamental tweek atmospherics and hence the ionospheric reflection height varies from the months of January to March in accordance with the sunrise and sunset.
Role of initial stress rotations in rupture dynamics and ground motion: A case study with implications for the Wenchuan earthquake
Authors: Duan Benchun
Published: May 2010

Motivated by observations in the 2008 Mw 7.9 Wenchuan earthquake, we study effects of systematic changes in the principal stress orientation along the fault strike on rupture dynamics and ground motion using a 3‐D finite‐element method. Based on Anderson's theory of faulting, we set up the initial stress field with rotations in stress orientations along strike for a dynamic rupture model of a shallow dipping fault. We find that initial stress rotations along strike can cause dramatic changes in rupture speed and produce distinct patterns in slip distribution and peak ground motion. When a mismatch (unfavorable for faulting) between fault geometry and initial stress orientations is encountered, rupture can spontaneously stop. Some first‐order features in the Wenchuan event may be partially caused by rotations in the principal stress orientation along strike, such as the rupture arrest at the northeast end and two severe destruction zones in the observed seismic intensity distribution. These results may have important implications for assessing seismic hazards imposed by faults with changes in the initial stress field along strike worldwide.
Physical controls on the seasonal migration of the North Pacific transition zone chlorophyll front
Authors: Ayers Jennifer M. , Lozier M. Susan
Published: May 2010

The large seasonal migration of the transition zone chlorophyll front (TZCF) is of interest because a number of marine fauna, both commercial and endangered, appear to track it. Herein we examine the physical dynamics driving this seasonal migration of the TZCF. Vertical processes, traditionally viewed as controlling the dynamical supply of nutrients to surface waters, prove insufficient to explain seasonal variations in nutrient supply to the transition zone. Instead, we find that the horizontal Ekman transport of nutrients from higher latitudes drives the TZCF's southward migration. The estimated horizontal transport of nitrate supports up to 40% of new primary productivity in the region annually and nearly all of new primary productivity in the winter. The significance of horizontal advection to the North Pacific transition zone supports revising the paradigm that nutrients are supplied to surface waters from below.
Intraseasonal response of mixed layer temperature and salinity in the Bay of Bengal to heat and freshwater flux
Authors: Parampil Sindu Raj , Gera Anitha , Ravichandran M. , Sengupta Debasis
Published: May 2010

Buoy and satellite data show pronounced subseasonal oscillations of sea surface temperature (SST) in the summertime Bay of Bengal. The SST oscillations are forced mainly by surface heat flux associated with the active break cycle of the south Asian summer monsoon. The input of freshwater (FW) from summer rain and rivers to the bay is large, but not much is known about subseasonal salinity variability. We use 2002–2007 observations from three Argo floats with 5 day repeat cycle to study the subseasonal response of temperature and salinity to surface heat and freshwater flux in the central Bay of Bengal. About 95% of Argo profiles show a shallow halocline, with substantial variability of mixed layer salinity. Estimates of surface heat and freshwater flux are based on daily satellite data sampled along the float trajectory. We find that intraseasonal variability of mixed layer temperature is mainly a response to net surface heat flux minus penetrative radiation during the summer monsoon season. In winter and spring, however, temperature variability appears to be mainly due to lateral advection rather than local heat flux. Variability of mixed layer freshwater content is generally independent of local surface flux (precipitation minus evaporation) in all seasons. There are occasions when intense monsoon rainfall leads to local freshening, but these are rare. Large fluctuations in FW appear to be due to advection, suggesting that freshwater from rivers and rain moves in eddies or filaments.
Winter interactions between aerosols and weather regimes in the North Atlantic European region
Authors: Ménégoz M. , Guemas V. , Salas y Melia D. , Voldoire A.
Published: May 2010

This study aims at understanding the winter interactions between aerosols and weather regimes in the North Atlantic European region. As a first step, a 6 year simulation of sulfate, black carbon (BC), and dust is performed with a Chemical Transport Model (CTM), forced by the meteorological data issued from the European Centre for Medium‐range Weather Forecast Integrated Forecast System model. The CTM uses the emissions inventory of aerosols and precursor gases provided by the AERosol Comparison between Observations and Models project. In this experiment, atmospheric dynamical processes associated with the different regimes can impact by up to 25% the burden of sulfate and BC and by up to 80% the burden of mineral dust, through the modification of deposition, transport, and chemistry processes. As a second step, the patterns of aerosol anomalies induced by each weather regime are used to force experiments performed with an Atmosphere General Circulation Model. The mean persistence of the negative phase of the North Atlantic Oscillation (NAO–) and the zonal regime is reduced by 1.78 and 0.88 days, respectively, when the atmosphere is forced with the patterns of aerosols induced by the zonal regime and the blocking regime, respectively. This suggests that the interaction between the atmosphere and its aerosol concentration could destabilize the NAO– regime that occurs after a zonal episode. The same conclusion can be set out for a zonal regime that occurs after a blocking episode.
Impact of East Asian summer monsoon on the air quality over China: View from space
Authors: Zhao Chun , Wang Yuhang , Yang Qing , Fu Rong , Cunnold Derek , Choi Yunsoo
Published: May 2010

Tropospheric O3 columns retrieved from Ozone Monitoring Instrument and Microwave Limb Sounder measurements, CO columns retrieved from Measurements of Pollution in the Troposphere, and tropospheric O3 and CO concentrations retrieved from the Tropospheric Emission Spectrometer from May to August in 2006 are analyzed using the Regional Chemical and Transport Model to investigate the impact of the East Asian summer monsoon on the air quality over China. The observed and simulated migrations of O3 and CO are in good agreement, demonstrating that the summer monsoon significantly affects the air quality over southeastern China, and this influence extends to central East China from June to July. Enhancements of CO and O3 over southeastern China disappear after the onset of the summer monsoon and reemerge in August after the monsoon wanes. The premonsoon high O3 concentrations over southern China are due to photochemical production from pollutant emissions and the O3 transport from the stratosphere. In the summer monsoon season, the O3 concentrations are relatively low over monsoon‐affected regions because of the transport of marine air masses and weak photochemical activity. We find that the monsoon system strongly modulates the pollution problem over a large portion of East China in summer, depending on its strength and tempo‐spatial extension. Model results also suggest that transport from the stratosphere and long‐range transport from East China and South/central Asia all make significant contributions to O3 enhancements over West China. Satellite observations provide valuable information for investigating the monsoon impact on air quality, particularly for the regions with limited in situ measurements.
Daily tropical cyclone intensity response to solar ultraviolet radiation
Authors: Elsner J. B. , Jagger T. H. , Hodges R. E.
Published: May 2010

An inverse relationship between hurricane activity over the Caribbean and the number of sunspots has recently been identified. Here we investigate this relationship using daily observations and find support for the hypothesis that changes in ultraviolet (UV) radiation rather than changes in other concomitant solar and cosmic variations are the cause. The relationship is statistically significant after accounting for annual variation in ocean heat and the El Niño cycle. A warming response in the upper troposphere to increased solar UV forcing as measured by the Mg II index (core‐to‐wing ratio) decreases the atmosphere's convective available potential energy leading to a weaker cyclone. The response amplitude at a cyclone intensity of 44 m s−1is 6.7 ± 2.56 m s−1per 0.01 Mg II units (s.d.), which compares with 4.6 m s−1estimated from the heat‐engine theory using a temperature trend derived from observations. The increasing hurricane response sensitivity with increasing strength is found in the observations and in an application of the theory.
Understanding and predicting the dynamics of tokamak discharges during startup and rampdown
Authors: Jackson G. L. , Politzer P. A. , Humphreys D. A. , Casper T. A. , Hyatt A. W. , Leuer J. A. , Lohr J. , Luce T. C. , Van Zeeland M. A. , Yu J. H.
Published: May 2010

Understanding the dynamics of plasma startup and termination is important for present tokamaks and for predictive modeling of future burning plasma devices such as ITER. We report on experiments in the DIII-D tokamak that explore the plasma startup and rampdown phases and on the benchmarking of transport models. Key issues have been examined such as plasma initiation and burnthrough with limited inductive voltage and achieving flattop and maximum burn within the technical limits of coil systems and their actuators while maintaining the desired q profile. Successful rampdown requires scenarios consistent with technical limits, including controlled H-L transitions, while avoiding vertical instabilities, additional Ohmic transformer flux consumption, and density limit disruptions. Discharges were typically initiated with an inductive electric field typical of ITER, 0.3 V/m, most with second harmonic electron cyclotron assist. A fast framing camera was used during breakdown and burnthrough of low Z impurity charge states to study the formation physics. An improved “large aperture” ITER startup scenario was developed, and aperture reduction in rampdown was found to be essential to avoid instabilities. Current evolution using neoclassical conductivity in the CORSICA code agrees with rampup experiments, but the prediction of the temperature and internal inductance evolution using the Coppi–Tang model for electron energy transport is not yet accurate enough to allow extrapolation to future devices.
Dynamics of thermally driven capillary waves for two-dimensional droplets
Authors: Tüzel Erkan , Pan Guoai , Kroll Daniel M.
Published: May 2010

Capillary waves have been observed in systems ranging from the surfaces of ordinary fluids to interfaces in biological membranes and have been one of the most studied areas in the physics of fluids. Recent advances in fluorescence microscopy and imaging enabled quantitative measurements of thermally driven capillary waves in lipid monolayers and bilayers, which resulted in accurate measurements of the line tension in monolayer domains. Even though there has been a considerable amount of work on the statics and dynamics of capillary waves in three dimensions, to the best of our knowledge, there is no detailed theoretical analysis for two-dimensional droplet morphologies. In this paper, we derive the dynamic correlation function for two-dimensional fluid droplets using linear response theory and verify our results using a novel particle-based simulation technique for binary mixtures.
Envelope ion-acoustic solitary waves in a plasma with positive-negative ions and nonthermal electrons
Authors: Elwakil S. A. , El-Shewy E. K. , Abdelwahed H. G.
Published: May 2010

Modulation instability of ion-acoustic waves is investigated in a plasma composed of positive and negative ions as well as nonthermal electrons. For this purpose, a linear dispersion relation and a nonlinear Schrödinger equation are derived. The latter admits localized envelope solitary wave solutions of bright-(pulses) and dark-(holes, voids) type. The envelope soliton depends on the intrinsic plasma parameters. It is found that modulation instability of ion-acoustic waves is significantly affected by the presence of nonthermal electrons. The present model is used to investigate the solitary excitations in the (H+,O2−) and (H+,H−) plasmas, where they are presented in the D-region and F-region of the Earth’s ionosphere. The findings of this investigation should be useful in understanding the stable electrostatic wave packet acceleration mechanisms in positive-negative ion plasmas, and also enhance our knowledge on the occurrence of instability associated to the propagation of the envelope ion-acoustic solitary waves in space and in laboratory plasmas where two distinct groups of ions and non-Boltzmann distributed electrons are present.
Time-resolved photoelectron imaging of ultrafast S2→S1 internal conversion through conical intersection in pyrazine
Authors: Suzuki Yoshi-Ichi , Fuji Takao , Horio Takuya , Suzuki Toshinori
Published: May 2010

A nonadiabatic electronic transition through a conical intersection was studied by pump-probe photoelectron imaging spectroscopy with a 22 fs time resolution in the benchmark polyatomic molecule of pyrazine and deuterated pyrazine. The lifetimes of the S2 state of pyrazine and deuterated pyrazine were determined to be 22±3 fs by the global fitting of the time-energy maps of photoelectron kinetic energy (PKE) distributions. The lifetime of S3 was determined to be 40–43 fs. Two-dimensional maps of photoelectron distributions were obtained for time (t) and PKE, and individual PKE distributions upon ionization from S2 and S1 were extracted. Quantum beat with an approximately 50 fs period was observed after the S2→S1 internal conversion, which was attributed to the totally symmetric vibration ν6a in S1.
Adsorption and thermal decomposition of acetic acid on Si(111)7×7 studied by vibrational electron energy loss spectroscopy
Authors: Venugopal V. , Chatterjee A. , Ebrahimi M. , He Z. H. , Leung K. T.
Published: May 2010

Vibrational electron energy loss spectroscopy (EELS) has been used to characterize the adsorption of acetic acid on Si(111)7×7 at room temperature and as a function of annealing temperature. At room temperature, acetic acid is found to undergo OH dissociative adsorption to form predominantly unidentate adstructure. The equilibrium geometry and the corresponding characteristic vibrational wavenumbers of the adstructures were obtained by density functional theory calculations and are found to be in good accord with the vibrational EELS data. Annealing the sample near 473 K marked the onset of CO dissociation of the acetate adstructure with the emergence of SiOSi vibrational modes at 720 and 1020 cm−1. Further annealing to 673 K caused a marked intensity reduction in the CC stretch at 930 cm−1 and in the CH3 vibrational features at 1360 and 2990 cm−1, suggesting further dissociation of the adstructures. The complete removal of the blueshifted SiH stretching mode at 2275 cm−1 upon further annealing to 773 K is consistent with the recombinative desorption of H2 from Si monohydrides expected in this temperature range. The emergence of the SiC stretching mode at 830 cm−1 at 873 K is in good accord with the formation of SiC. Similar thermal evolution of the vibrational features have also been observed for acetic acid adsorption on a sputtered Si(111) surface.
Bubble entrapment through topological change
Authors: Thoroddsen S. T. , Takehara K. , Etoh T. G.
Published: May 2010

When a viscous drop impacts onto a solid surface, it entraps a myriad of microbubbles at the interface between liquid and solid. We present direct high-speed video observations of this entrapment. For viscous drops, the tip of the spreading lamella is separated from the surface and levitated on a cushion of air. We show that the primary mechanism for the bubble entrapment is contact between this precursor sheet of liquid with the solid and not air pulled directly through cusps in the contact line. The sheet makes contact with the solid surface, forming a wetted patch, which grows in size, but only entraps a bubble when it meets the advancing contact line. The leading front of this wet patch can also lead to the localized thinning and puncturing of the liquid film producing strong splashing of droplets.
A shape theorem for Riemannian first-passage percolation
Authors: LaGatta T. , Wehr J.
Published: May 2010

Riemannian first-passage percolation is a continuum model, with a distance function arising from a random Riemannian metric in Rd. Our main result is a shape theorem for this model, which says that large balls under this metric converge to a deterministic shape under rescaling. As a consequence, we show that smooth random Riemannian metrics are geodesically complete with probability of 1.
Amplification of SPPS150 and Salmonella typhi DNA with a high throughput oscillating flow polymerase chain reaction device
Authors: Sugumar D. , Ismail Asma , Ravichandran Manickam , Aziah Ismail , Kong L. X.
Published: May 2010

In this paper, a novel oscillating flow polymerase chain reaction (PCR) device was designed and fabricated to amplify SPPS150 and salmonella typhi. In this new design, the samples are shuttled (oscillating flow) inside a microfluidic chip to three different temperature zones required for DNA amplification. The amplification cycle time has markedly been reduced as the reagent volume used was only about 25% of that used in conventional PCRs. Bubble formation and adsorption issues commonly associated to chip based PCR were also eliminated. Based on the performance evaluated, it is demonstrated that this oscillating flow PCR has the advantages of both the stationary chamber and continuous flow PCR devices.
Nondestructive depth-resolved spectroscopic investigation of the heavily intermixed In2S3/Cu(In,Ga)Se2 interface
Authors: Bär M. , Barreau N. , Couzinié-Devy F. , Pookpanratana S. , Klaer J. , Blum M. , Zhang Y. , Yang W. , Denlinger J. D. , Schock H.-W. , Weinhardt L. , Kessler J. , Heske C.
Published: May 2010

The chemical structure of the interface between a nominal In2S3 buffer and a Cu(In,Ga)Se2 (CIGSe) thin-film solar cell absorber was investigated by soft x-ray photoelectron and emission spectroscopy. We find a heavily intermixed, complex interface structure, in which Cu diffuses into (and Na through) the buffer layer, while the CIGSe absorber surface/interface region is partially sulfurized. Based on our spectroscopic analysis, a comprehensive picture of the chemical interface structure is proposed.
Integrating size-structured assessment and bioeconomic management advice in Australia's northern prawn fishery
Authors: Punt André E. , Deng Roy A. , Dichmont Catherine M. , Kompas Tom , Venables William N. , Zhou Shijie , Pascoe Sean , Hutton Trevor , Kenyon Rob , van der Velde Tonya , Kienzle Marco
Published: May 2010

Punt, A. E., Deng, R. A., Dichmont, C. M., Kompas, T., Venables, W. N., Zhou, S., Pascoe, S., Hutton, T., Kenyon, R., van der Velde, T., and Kienzle, M. 2010. Integrating size-structured assessment and bioeconomic management advice in Australia's northern prawn fishery. – ICES Journal of Marine Science, 67: 1785–1801. Three species in Australia's northern prawn fishery (Penaeus semisulcatus, P. esculentus, and Metapenaeus endeavouri) are assessed using a size-structured population model that operates on a weekly time-step. The parameters of this multispecies population model are estimated using data on catches, catch rates, length frequency data from surveys and the fishery, and tag release–recapture data. The model allows for the technical interaction among the three species. The results from the multispecies stock assessment are used to calculate the time-series of catches and levels of fishing effort that maximize net present value. The bioeconomic model takes into account costs which are proportional to catches and those which are proportional to fishing effort, as well as fixed costs. The sensitivity of the results is examined by changing the assumptions regarding the values for the economic parameters of the bioeconomic model as well as those on which the assessment are based. The results suggest that fishing effort needs to be reduced in the short term to achieve economic goals, although most stocks are estimated currently to be above the stock size corresponding to maximum sustainable yield. Short-term catches and effort levels are sensitive to model assumptions, and in particular, to trends in prices and costs.
Mechanical testing of bones: the positive synergy of finite–element models andin vitroexperiments
Authors: Cristofolini Luca , Schileo Enrico , Juszczyk Mateusz , Taddei Fulvia , Martelli Saulo , Viceconti Marco
Published: May 2010

Bone biomechanics have been extensively investigated in the past both within vitroexperiments and numerical models. In most cases either approach is chosen, without exploiting synergies. Both experiments and numerical models suffer from limitations relative to their accuracy and their respective fields of application.In vitroexperiments can improve numerical models by: (i) preliminarily identifying the most relevant failure scenarios; (ii) improving the model identification with experimentally measured material properties; (iii) improving the model identification with accurately measured actual boundary conditions; and (iv) providing quantitative validation based on mechanical properties (strain, displacements) directly measured from physical specimens being tested in parallel with the modelling activity. Likewise, numerical models can improvein vitroexperiments by: (i) identifying the most relevant loading configurations among a number of motor tasks that cannot be replicatedin vitro; (ii) identifying acceptable simplifications for thein vitrosimulation; (iii) optimizing the use of transducers to minimize errors and provide measurements at the most relevant locations; and (iv) exploring a variety of different conditions (material properties, interface, etc.) that would require enormous experimental effort. By reporting an example of successful investigation of the femur, we show how a combination of numerical modelling and controlled experiments within the same research team can be designed to create a virtuous circle where models are used to improve experiments, experiments are used to improve models and their combination synergistically provides more detailed and more reliable results than can be achieved with either approach singularly.
A vision and strategy for the virtual physiological human in 2010 and beyond
Authors: Hunter Peter , Coveney Peter V. , de Bono Bernard , Diaz Vanessa , Fenner John , Frangi Alejandro F. , Harris Peter , Hose Rod , Kohl Peter , Lawford Pat , McCormack Keith , Mendes Miriam , Omholt Stig , Quarteroni Alfio , Skår John , Tegner Jesper , Randall Thomas S. , Tollis Ioannis , Tsamardinos Ioannis , van Beek Johannes H. G. M. , Viceconti Marco
Published: May 2010

European funding under framework 7 (FP7) for the virtual physiological human (VPH) project has been in place now for nearly 2 years. The VPH network of excellence (NoE) is helping in the development of common standards, open-source software, freely accessible data and model repositories, and various training and dissemination activities for the project. It is also helping to coordinate the many clinically targeted projects that have been funded under the FP7 calls. An initial vision for the VPH was defined by framework 6 strategy for a European physiome (STEP) project in 2006. It is now time to assess the accomplishments of the last 2 years and update the STEP vision for the VPH. We consider the biomedical science, healthcare and information and communications technology challenges facing the project and we propose the VPH Institute as a means of sustaining the vision of VPH beyond the time frame of the NoE.
An overview of recent applications of computational modelling in neonatology
Authors: Wrobel Luiz C. , Ginalski Maciej K. , Nowak Andrzej J. , Ingham Derek B. , Fic Anna M.
Published: May 2010

This paper reviews some of our recent applications of computational fluid dynamics (CFD) to model heat and mass transfer problems in neonatology and investigates the major heat and mass-transfer mechanisms taking place in medical devices, such as incubators, radiant warmers and oxygen hoods. It is shown that CFD simulations are very flexible tools that can take into account all modes of heat transfer in assisting neonatal care and improving the design of medical devices.
Development of coarse-graining DNA models for single-nucleotide resolution analysis
Authors: Doi Kentaro , Haga Tomoaki , Shintaku Hirofumi , Kawano Satoyuki
Published: May 2010

Recently, analytical techniques have been developed for detecting single-nucleotide polymorphisms in DNA sequences. Improvements of the sequence identification techniques has attracted much attention in several fields. However, there are many things that have not been clarified about DNA. In the present study, we have developed a coarse-graining DNA model with single-nucleotide resolution, in which potential functions for hydrogen bonds and the
π
-stack effect are taken into account. Using Langevin-dynamics simulations, several characteristics of the coarse-grained DNA have been clarified. The validity of the present model has been confirmed, compared with other experimental and computational results. In particular, the melting temperature and persistence length are in good agreement with the experimental results for a wide range of salt concentrations.
Predicting the yield of the proximal femur using high-order finite-element analysis with inhomogeneous orthotropic material properties
Authors: Yosibash Zohar , Tal David , Trabelsi Nir
Published: May 2010

High-order finite-element (FE) analyses with inhomogeneous isotropic material properties have been shown to predict the strains and displacements on the surface of the proximal femur with high accuracy when compared with
in vitro
experiments. The same FE models with inhomogeneous orthotropic material properties produce results similar to those obtained with isotropic material properties. Herein, we investigate the yield prediction capabilities of these models using four different yield criteria, and the spread in the predicted load between the isotropic and orthotropic material models. Subject-specific high-order FE models of two human femurs were generated from CT scans with inhomogeneous orthotropic or isotropic material properties, and loaded by a simple compression force at the head. Computed strains and stresses by both the orthotropic and isotropic FE models were used to determine the load that predicts ‘yielding’ by four different ‘yield criteria’: von Mises, Drucker–Prager, maximum principal stress and maximum principal strain. One of the femurs was loaded by a simple load until fracture, and the force resulting in yielding was compared with the FE predicted force. The surface average of the ‘maximum principal strain’ criterion in conjunction with the orthotropic FE model best predicts both the yield force and fracture location compared with other criteria. There is a non-negligible influence on the predictions if orthotropic or isotropic material properties are applied to the FE model. All stress-based investigated ‘yield criteria’ have a small spread in the predicted failure. Because only one experiment was performed with a rather simplified loading configuration, the conclusions of this work cannot be claimed to be either reliable or sufficient, and future experiments should be performed to further substantiate the conclusions.
Repeated evolution of reproductive isolation in a marine snail: unveiling mechanisms of speciation
Authors: Johannesson Kerstin , Panova Marina , Kemppainen Petri , André Carl , Rolán-Alvarez Emilio , Butlin Roger K.
Published: May 2010

Distinct ecotypes of the snailLittorina saxatilis, each linked to a specific shore microhabitat, form a mosaic-like pattern with narrow hybrid zones in between, over which gene flow is 10–30% of within-ecotype gene flow. Multi-locus comparisons cluster populations by geographic affinity independent of ecotype, while loci under selection group populations by ecotype. The repeated occurrence of partially reproductively isolated ecotypes and the conflicting patterns in neutral and selected genes can either be explained by separation in allopatry followed by secondary overlap and extensive introgression that homogenizes neutral differences evolved under allopatry, or by repeated evolution in parapatry, or in sympatry, with the same ecotypes appearing in each local site. Data from Spain, the UK and Sweden give stronger support for a non-allopatric model of ecotype formation than for an allopatric model. Several different non-allopatric mechanisms can, however, explain the repeated evolution of the ecotypes: (i) parallel evolution by new mutations in different populations; (ii) evolution from standing genetic variation; and (iii) evolution in concert with rapid spread of new positive mutations among populations inhabiting similar environments. These models make different predictions that can be tested using comprehensive phylogenetic information combined with candidate loci sequencing.
The roles of time and ecology in the continental radiation of the Old World leaf warblers (PhylloscopusandSeicercus)
Authors: Price Trevor D.
Published: May 2010

Many continental sister species are allopatric or parapatric, ecologically similar and long separated, of the order of millions of years. Sympatric, ecologically differentiated, species, are often even older. This raises the question of whether build-up of sympatric diversity generally follows a slow process of divergence in allopatry, initially without much ecological change. I review patterns of speciation among birds belonging to the continental Eurasian Old World leaf warblers (PhylloscopusandSeicercus). I consider speciation to be a three-stage process (range expansions, barriers to gene flow, reproductive isolation) and ask how ecological factors at each stage have contributed to speciation, both among allopatric/parapatric sister species and among those lineages that eventually led to currently sympatric species. I suggest that time is probably the critical factor that leads to reproductive isolation between sympatric species and that a strong connection between ecological divergence and reproductive isolation remains to be established. Besides reproductive isolation, ecological factors can affect range expansions (e.g. habitat tracking) and the formation of barriers (e.g. treeless areas are effective barriers for warblers). Ecological factors may often limit speciation on continents because range expansions are difficult in ‘ecologically full’ environments.
On the origin of species: insights from the ecological genomics of lake whitefish
Authors: Bernatchez Louis , Renaut Sébastien , Whiteley Andrew R. , Derome Nicolas , Jeukens Julie , Landry Lysandre , Lu Guoqing , Nolte Arne W. , Østbye Kjartan , Rogers Sean M. , St-Cyr Jérôme
Published: May 2010

In contrast to the large amount of ecological information supporting the role of natural selection as a main cause of population divergence and speciation, an understanding of the genomic basis underlying those processes is in its infancy. In this paper, we review the main findings of a long-term research programme that we have been conducting on the ecological genomics of sympatric forms of whitefish (Coregonusspp.) engaged in the process of speciation. We present this system as an example of how applying a combination of approaches under the conceptual framework of the theory of adaptive radiation has yielded substantial insight into evolutionary processes in a non-model species. We also discuss how the joint use of recent biotechnological developments will provide a powerful means to address issues raised by observations made to date. Namely, we present data illustrating the potential offered by combining next generation sequencing technologies with other genomic approaches to reveal the genomic bases of adaptive divergence and reproductive isolation. Given increasing access to these new genomic tools, we argue that non-model species studied in their ecological context such as whitefish will play an increasingly important role in generalizing knowledge of speciation.
Evolving entities: towards a unified framework for understanding diversity at the species and higher levels
Authors: Barraclough Timothy G.
Published: May 2010

Current approaches to studying the evolution of biodiversity differ in their treatment of species and higher level diversity patterns. Species are regarded as the fundamental evolutionarily significant units of biodiversity, both in theory and in practice, and extensive theory explains how they originate and evolve. However, most species are still delimited using qualitative methods that only relate indirectly to the underlying theory. In contrast, higher level patterns of diversity have been subjected to rigorous quantitative study (using phylogenetics), but theory that adequately explains the observed patterns has been lacking. Most evolutionary analyses of higher level diversity patterns have considered non-equilibrium explanations based on rates of diversification (i.e. exponentially growing clades), rather than equilibrium explanations normally used at the species level and below (i.e. constant population sizes). This paper argues that species level and higher level patterns of diversity can be considered within a common framework, based on equilibrium explanations. It shows how forces normally considered in the context of speciation, namely divergent selection and geographical isolation, can generate evolutionarily significant units of diversity above the level of reproductively isolated species. Prospects for the framework to answer some unresolved questions about higher level diversity patterns are discussed.
A novel role for 14–3–3σ in regulating epithelial cell polarity
Authors: Ling Chen , Zuo Dongmei , Xue Bin , Muthuswamy Senthil , Muller William J.
Published: May 2010

The loss of epithelial polarity is thought to play an important role during mammary tumor progression. Using a unique transgenic mouse model of ErbB2-induced mammary tumorigenesis, we demonstrated previously that amplification of ErbB2 is frequently accompanied by loss of the 14–3–3σ gene. Here, we demonstrate that ectopic expression of 14–3–3σ results in restoration of epithelial polarity in ErbB2-transformed mammary tumor cells. We further demonstrate that targeted deletion of 14–3–3σ within primary mammary epithelial cells increases their proliferative capacity and adversely affects their ability to form polarized structures. Finally, we show that 14–3–3σ can specifically form complexes with Par3, a protein that is essential for the maintenance of a polarized epithelial state. Taken together, these observations suggest that 14–3–3σ plays a critical role in retaining epithelial polarity.
Argonaute quenching and global changes in Dicer homeostasis caused by a pathogen-encoded GW repeat protein
Authors: Azevedo Jacinthe , Garcia Damien , Pontier Dominique , Ohnesorge Stephanie , Yu Agnes , Garcia Shahinez , Braun Laurence , Bergdoll Marc , Hakimi Mohamed Ali , Lagrange Thierry , Voinnet Olivier
Published: May 2010

In plants and invertebrates, viral-derived siRNAs processed by the RNaseIII Dicer guide Argonaute (AGO) proteins as part of antiviral RNA-induced silencing complexes (RISC). As a counterdefense, viruses produce suppressor proteins (VSRs) that inhibit the host silencing machinery, but their mechanisms of action and cellular targets remain largely unknown. Here, we show that the Turnip crinckle virus (TCV) capsid, the P38 protein, acts as a homodimer, or multiples thereof, to mimic host-encoded glycine/tryptophane (GW)-containing proteins normally required for RISC assembly/function in diverse organisms. The P38 GW residues bind directly and specifically to Arabidopsis AGO1, which, in addition to its role in endogenous microRNA-mediated silencing, is identified as a major effector of TCV-derived siRNAs. Point mutations in the P38 GW residues are sufficient to abolish TCV virulence, which is restored in Arabidopsis ago1 hypomorphic mutants, uncovering both physical and genetic interactions between the two proteins. We further show how AGO1 quenching by P38 profoundly impacts the cellular availability of the four Arabidopsis Dicers, uncovering an AGO1-dependent, homeostatic network that functionally connects these factors together. The likely widespread occurrence and expected consequences of GW protein mimicry on host silencing pathways are discussed in the context of innate and adaptive immunity in plants and metazoans.
The Hippo–YAP pathway in organ size control and tumorigenesis: an updated version
Authors: Zhao Bin , Li Li , Lei Qunying , Guan Kun-Liang
Published: May 2010

The Hippo signaling pathway is gaining recognition as an important player in both organ size control and tumorigenesis, which are physiological and pathological processes that share common cellular signaling mechanisms. Upon activation by stimuli such as high cell density in cell culture, the Hippo pathway kinase cascade phosphorylates and inhibits the Yes-associated protein (YAP)/TAZ transcription coactivators representing the major signaling output of the pathway. Altered gene expression resulting from YAP/TAZ inhibition affects cell number by repressing cell proliferation and promoting apoptosis, thereby limiting organ size. Recent studies have provided new insights into the Hippo signaling pathway, elucidating novel phosphorylation-dependent and independent mechanisms of YAP/Yki inhibition by the Hippo pathway, new Hippo pathway components, novel YAP target transcription factors and target genes, and the three-dimensional structure of the YAP–TEAD complex, and providing further evidence for the involvement of YAP and the Hippo pathway in tumorigenesis.
The JARID2–PRC2 duality: Figure 1.
Authors: Herz Hans-Martin , Shilatifard Ali
Published: May 2010

Polycomb group proteins (PcG) are required for proper developmental regulation and cell fate commitment in metazoans. Recently, four studies reported the identification of JARID2, a JmjC domain-containing protein, as a component of the Polycomb-repressive complex 2 (PRC2), which is involved in implementing histone H3 Lys 27 methylation and transcriptional repression during development. Here, we discuss the implications of these studies for an improved understanding of PcG function in development.
A viral suppressor protein inhibits host RNA silencing by hooking up with Argonautes: Figure 1.
Authors: Jin Hailing , Zhu Jian-Kang
Published: May 2010

RNA viruses are particularly vulnerable to RNAi-based defenses in the host, and thus have evolved specific proteins, known as viral suppressors of RNA silencing (VSRs), as a counterdefense. In this issue of Genes & Development, Azevedo and colleagues (pp. 904–915) discovered that P38, the VSR of Turnip crinkle virus, uses its glycine/tryptophane (GW) motifs as an ARGONAUTE (AGO) hook to attract and disarm the host's essential effector of RNA silencing. Several GW motif-containing cellular proteins are known to be important partners of AGOs in RNA silencing effector complexes in yeast, plants, and animals. The GW motif appears to be a versatile and effective tool for regulating the activities of RNA silencing pathways, and the use of GW mimicry to compete for and inhibit host AGOs may be a strategy used by many pathogens to counteract host RNAi-based defenses.
Claudin-like protein 24 interacts with the VEGFR-2 and VEGFR-3 pathways and regulates lymphatic vessel development
Authors: Saharinen Pipsa , Helotera Hanna , Miettinen Juho , Norrmen Camilla , D'Amico Gabriela , Jeltsch Michael , Langenberg Tobias , Vandevelde Wouter , Ny Annelii , Dewerchin Mieke , Carmeliet Peter , Alitalo Kari
Published: May 2010

The Claudin-like protein of 24 kDa (CLP24) is a hypoxia-regulated transmembrane protein of unknown function. We show here that clp24 knockdown in Danio rerio and Xenopus laevis results in defective lymphatic development. Targeted disruption of Clp24 in mice led to enlarged lymphatic vessels having an abnormal smooth muscle cell coating. We also show that the Clp24−/− phenotype was further aggravated in the Vegfr2+/LacZ or Vegfr3+/LacZ backgrounds and that CLP24 interacts with vascular endothelial growth factor receptor-2 (VEGFR-2) and VEGFR-3 and attenuates the transcription factor CREB phosphorylation via these receptors. Our results indicate that CLP24 is a novel regulator of VEGFR-2 and VEGFR-3 signaling pathways and of normal lymphatic vessel structure.