bluuebunny/crossref_metadata_2025 huggingface dataset:
Wind and temperature effects on thermosphere mass density response to the November 2004 geomagnetic storm
Authors: Lei Jiuhou , Thayer Jeffrey P. , Burns Alan G. , Lu Gang , Deng Yue
Published: May 2010

A unique conjunction of the Thermosphere Ionosphere Mesosphere Energetics and Dynamics (TIMED) and the Challenging Minisatellite Payload (CHAMP) satellites provided simultaneous columnar neutral composition, ΣO/N2, and thermosphere density observations, enabling a novel study of thermospheric response to the 7–9 November 2004 geomagnetic storm. Both ΣO/N2 and mass density showed profound response to this severe geomagnetic storm, but their latitudinal and temporal structures differed markedly. In particular, high‐latitude depletion and low‐latitude enhancement in ΣO/N2 were observed throughout the storm period, especially during the main phase. In contrast, neutral density at 400 km altitude increased from pole to pole shortly after the storm, with strongest enhancement of order 200%–400% during the main phase. Comparisons of observed thermosphere response with simulations from the National Center for Atmospheric Research Thermosphere‐Ionosphere‐Electrodynamics General Circulation Model (TIEGCM) were carried out to interpret the observed contrasting characteristics of thermosphere composition and mass density in response to this geomagnetic storm. The TIEGCM simulations show that the contrasting characteristics occur not only in ΣO/N2 and mass density at a constant altitude at 400 km, but also in O/N2 and mass density on a constant‐pressure surface. At an altitude of 400 km (CHAMP altitude), storm‐time mass densities significantly increase due to an increase in scale height throughout the vertical column between the heat source and satellite altitude. For a given increase in scale height, the more scale height increments separating the heat source from the satellite altitude, the greater is the mass density response. It is shown that scale height change is caused partly by storm‐time neutral temperature enhancements due to heating and partly by changes in mean molecular weight due to winds. These findings indicate that wind effects can cause significant deviations from a mass density pattern resulting solely from neutral temperature changes by altering the mean molecular weight, particularly at high latitudes.
Spatial and temporal variability of the remotely sensed chlorophyll a signal associated with Rossby waves in the South Atlantic Ocean
Authors: Gutknecht E. , Dadou I. , Charria G. , Cipollini P. , Garçon V.
Published: May 2010

The present study focuses on the spatial and temporal variability of interactions between physics and biogeochemistry during the Rossby wave passage in the South Atlantic Ocean. The Rossby wave signature in sea level anomalies (SLA) and surface chlorophyll a concentration anomalies (CHLA) is analyzed using remotely sensed data from 1997 to 2006. Wavelengths between 400 and 1100 km, with westward propagating speeds up to 7.5 cm.s−1, are observed. Using a theoretical model, three processes (meridional advection of surface chlorophyll a concentrations, uplifting of subsurface chlorophyll a maximum, and upwelling of nutrients) are likely to explain the chlorophyll a Rossby wave signature. A statistical assumption allows quantifying the relative importance of each process. Three zones are identified. The Subtropical Gyre is the only area where the contribution of the uplifting process reaches 20%. North and south of this gyre, the meridional advection process is responsible for an important part (around 60%) of the observed chlorophyll a signals. The temporal variability of this dominant process is studied using the phase relationships between CHLA and SLA and the surface meridional chlorophyll a gradient. A seasonal meridional shift (4°) is shown on both data sets on the area of negative meridional gradient. At 30°S–31°S, a clear seasonal cycle is observed in both data sets for the whole studied period, except in 2003 and 2004 where both data sets do not follow the usual seasonal cycle. These particular years can be related to anomalies in large scale atmospheric circulation over the South Atlantic Ocean.
Insights into hydrological regime of Lake Vostok from differential behavior of deuterium and oxygen‐18 in accreted ice
Authors: Ekaykin A. A. , Lipenkov V. Y. , Petit J. R. , Johnsen S. , Jouzel J. , Masson‐Delmotte V.
Published: May 2010

We use isotopic data (deuterium and oxygen‐18) of the recently recovered deepest Vostok ice core section (down to 3650 m depth) to study processes leading to the formation of lake ice and the hydrological regime of subglacial Lake Vostok. The significant variability of the lake ice isotopic content implies fluctuations in physical conditions of ice formation (mainly, volume and/or growth rate of frazil ice crystals) as well as variations of the isotope composition of the freezing water. The latter implies a poor mixing of the source waters (glacier melt and hydrothermal water) with the water of the main lake body. Poor mixing within the lake may have important consequences for the lake's chemical and gas balance and, particularly, for its microbiological content. A poorly mixed lake may provide ecological niches where microbial life can hide from high oxygen concentrations likely typical for the lake. We also show that the isotopic content of the main lake's input (meltwater) significantly differs from that of the output (lake ice), which can be explained by the contribution of an additional (hydrothermal) source. This latter conclusion is supported by the observed noncovariant behavior of deuterium and oxygen‐18 isotopes in the lake ice.
Magnitude estimation using the covered areas of strong ground motion in earthquake early warning
Authors: Lin Ting‐Li , Wu Yih‐Min
Published: May 2010

We collected the strong‐motion accelerograms with peak ground acceleration (PGA) larger than 100 Gal (1 Gal = 1.0 cm/s2) from large crustal earthquakes in Taiwan recorded by the Taiwan Strong Motion Instrumentation Program (TSMIP) stations to find an empirical relationship between the area of high PGA and the corresponding earthquake magnitude. We found that the logarithms of the areas inside the PGA contours have a linear relation to the corresponding earthquake magnitudes. We propose that this relationship might be able to rapidly define the earthquake magnitude while providing sufficient seismic station coverage and might have practical application in earthquake early warning (EEW) and rapid reporting systems. The proposed magnitude estimation method is directly related to the level of strong surface shaking and is inherently suitable for the purpose of the EEW and rapid reporting systems.
Electron beams as the source of whistler‐mode auroral hiss at Saturn
Authors: Kopf A. J. , Gurnett D. A. , Menietti J. D. , Schippers P. , Arridge C. S. , Hospodarsky G. B. , Kurth W. S. , Grimald S. , André N. , Coates A. J. , Dougherty M. K.
Published: May 2010

Over the last three years, the Cassini spacecraft has been in a series of high inclination orbits, allowing investigation and measurements of Saturnian auroral phenomena. During this time, the Radio and Plasma Wave Science (RPWS) Investigation on Cassini detected low frequency whistler mode emissions propagating upward along the auroral field lines, much like terrestrial auroral hiss. Comparisons of RPWS data with Cassini Plasma Spectrometer (CAPS) plasma measurements during a high‐latitude pass on 17 October 2008, show that intense upward moving electron beams with energies of a few hundred eV were associated with auroral hiss emissions. In this paper we show that these beams produce large growth rates for whistler‐mode waves propagating along the resonance cone, similar to the generation of auroral hiss at Earth.
Map model for synchronization of systems of many coupled oscillators
Authors: Barlev Gilad , Girvan Michelle , Ott Edward
Published: May 2010

Synchronization of many coupled oscillators is a generic issue in a wide variety of natural situations. We consider a discrete time map model for the study of such problems. Issues addressed include the effects of noise, oscillation frequency diversity, and network topology, particularly community structure.
Strong stabilization of the Rayleigh–Taylor instability by material strength at megabar pressures
Authors: Park Hye-Sook , Remington B. A. , Becker R. C. , Bernier J. V. , Cavallo R. M. , Lorenz K. T. , Pollaine S. M. , Prisbrey S. T. , Rudd R. E. , Barton N. R.
Published: May 2010

Experimental results showing significant reductions from classical in the Rayleigh–Taylor (RT) instability growth rate due to high pressure effective lattice viscosity in metal foils are presented. Stabilization of RT instability (RTI) by ablation and density gradients has been studied for decades. The regime of stabilized RTI due to material strength at high pressure is new. On the Omega Laser in the Laboratory for Laser Energetics, University of Rochester, target samples of polycrystalline vanadium are compressed and accelerated quasi-isentropically at ∼1 Mbar pressures, while maintaining the samples in the solid-state. Provided strong shocks are avoided, the higher the applied peak pressure, the higher the predicted foil strength, and hence, the higher the degree of strength stabilization of RTI. Several experiments were conducted where the amount of RT growth is measured by face-on radiography. The vanadium samples are probed by a laser driven He-α x-ray backlighter which produced 5.2 keV radiation. Comparison of the results with constitutive models for solid state strength under these conditions show that the measured RT growth is substantially lower than predictions using existing models that work well at low pressures and long time scales. High pressure, high strain rate data can be explained by the enhanced strength due to a phonon drag mechanism, creating a high effective lattice viscosity.
Large deviations for the stochastic quasigeostrophic equation with multiplicative noise
Authors: Yang Desheng , Duan Jinqiao
Published: May 2010

This paper proves a large deviation principle for the stochastic quasigeostrophic equation with multiplicative noise. The proof is based on the Laplace principle and on weak convergence methods. We also give a rigorous mathematical result on the existence of a strong solution and uniqueness of mild solutions to the stochastic quasigeostrophic equation in the dimension d=2,3. Finally, large deviations for short time are considered.
Cell patterning using microstructured ferromagnetic thin films
Authors: Lai Mei-Feng , Chen Chia-Yi , Lee Chiun-Peng , Huang Hao-Ting , Ger Tzong-Rong , Wei Zung-Hang
Published: May 2010

Magnetic cell patterning is demonstrated through controlling the micromagnetic states in microstructured ferromagnetic thin films. The number of magnetic nanoparticles entering the cells by endocytosis can be determined by magnetophoresis experiment and is found to be dependent of the cocultured extracellular magnetic nanoparticles concentrations. In zigzag magnetic films the effects of cell patterning differ for magnetic films at as-deposited state and at remanent states after applying fields in different directions. Remanent states of concentric rings are proposed for cell patterning. Cells can be arranged at any positions in sequence by selectively changing the magnetic field directions.
Ironless transducer for measuring the mechanical properties of porous materials
Authors: Doutres Olivier , Dauchez Nicolas , Genevaux Jean-Michel , Lemarquand Guy , Mezil Sylvain
Published: May 2010

This paper presents a measurement setup for determining the mechanical properties of porous materials at low and medium frequencies by extending toward higher frequencies the quasistatic method based on a compression test. Indeed, classical quasistatic methods generally neglect the inertia effect of the porous sample and the coupling between the surrounding fluid and the frame; they are restricted to low frequency range (<100 Hz) or specific sample shape. In the present method, the porous sample is placed in a cavity to avoid a lateral airflow. Then a specific electrodynamic ironless transducer is used to compress the sample. This highly linear transducer is used as actuator and sensor; the mechanical impedance of the porous sample is deduced from the measurement of the electrical impedance of the transducer. The loss factor and the Young’s modulus of the porous material are estimated by inverse method based on the Biot’s model. Experimental results obtained with a polymer foam show the validity of the method in comparison with quasistatic method. The frequency limit has been extended from 100 Hz to 500 Hz. The sensitivity of each input parameter is estimated in order to point out the limitations of the method.
Electric field induced microstructures in thin films on physicochemically heterogeneous and patterned substrates
Authors: Srivastava Samanvaya , Reddy P. Dinesh Sankar , Wang Cindy , Bandyopadhyay Dipankar , Sharma Ashutosh
Published: May 2010

We study by nonlinear simulations the electric field induced pattern formation in a thin viscous film resting on a topographically or chemically patterned substrate. The thin film microstructures can be aligned to the substrate patterns within a window of parameters where the spinodal length scale of the field induced instability is close to the substrate periodicity. We investigate systematically the change in the film morphology and order when (i) the substrate pattern periodicity is varied at a constant film thickness and (ii) the film thickness is varied at a constant substrate periodicity. Simulations show two distinct pathway of evolution when the substrate-topography changes from protrusions to cavities. The isolated substrate defects generate locally ordered ripplelike structures distinct from the structures on a periodically patterned substrate. In the latter case, film morphology is governed by a competition between the pattern periodicity and the length scale of instability. Relating the thin film morphologies to the underlying substrate pattern has implications for field induced patterning and robustness of inter-interface pattern transfer, e.g., coding-decoding of information printed on a substrate.
Phases of modified Stockwell transforms and instantaneous frequencies
Authors: Guo Qiang , Molahajloo Shahla , Wong M. W.
Published: May 2010

The phase of a signal is analyzed using the Stockwell transform. In particular, the relationships between the instantaneous frequencies of a signal in polar form and the phase of the corresponding Stockwell transform are given. The corresponding results using a reciprocal Morlet wavelet transform are given for comparisons.
Graphene-like silicon nanoribbons on Ag(110): A possible formation of silicene
Authors: Aufray Bernard , Kara Abdelkader , Vizzini Sébastien , Oughaddou Hamid , Léandri Christel , Ealet Benedicte , Le Lay Guy
Published: May 2010

Scanning tunneling microscopy (STM) and ab initio calculations based on density functional theory (DFT) were used to study the self-aligned silicon nanoribbons on Ag(110) with honeycomb, graphene-like structure. The silicon honeycombs structure on top of the silver substrate is clearly observed by STM, while the DFT calculations confirm that the Si atoms adopt spontaneously this new silicon structure.
Multiscale modelling and nonlinear finite element analysis as clinical tools for the assessment of fracture risk
Authors: Christen David , Webster Duncan James , Müller Ralph
Published: May 2010

The risk of osteoporotic fractures is currently estimated based on an assessment of bone mass as measured by dual-energy X-ray absorptiometry. However, patient-specific finite element (FE) simulations that include information from multiple scales have the potential to allow more accurate prognosis. In the past, FE models of bone were limited either in resolution or to the linearization of the mechanical behaviour. Now, nonlinear, high-resolution simulations including the bone microstructure have been made possible by recent advances in simulation methods, computer infrastructure and imaging, allowing the implementation of multiscale modelling schemes. For example, the mechanical loads generated in the musculoskeletal system define the boundary conditions for organ-level, continuum-based FE models, whose nonlinear material properties are derived from microstructural information. Similarly microstructure models include tissue-level information such as the dynamic behaviour of collagen by modifying the model's constitutive law. This multiscale approach to modelling the mechanics of bone allows a more accurate characterization of bone fracture behaviour. Furthermore, such models could also include the effects of ageing, osteoporosis and drug treatment. Here we present the current state of the art for multiscale modelling and assess its potential to better predict an individual's risk of fracture in a clinical setting.
In silicodesign of treatment strategies in wound healing and bone fracture healing
Authors: Geris L. , Schugart R. , Van Oosterwyck H.
Published: May 2010

Wound and bone fracture healing are natural repair processes initiated by trauma. Over the last decade, many mathematical models have been established to investigate the healing processesin silico, in addition to ongoing experimental work. In recent days, the focus of the mathematical models has shifted from simulation of the healing process towards simulation of the impaired healing process and thein silicodesign of treatment strategies. This review describes the most important causes of failure of the wound and bone fracture healing processes and the experimental models and methods used to investigate and treat these impaired healing cases. Furthermore, the mathematical models that are described address these impaired healing cases and investigate various therapeutic scenariosin silico. Examples are provided to illustrate the potential of thesein silicoexperiments. Finally, limitations of the models and the need for and ability of these models to capture patient specificity and variability are discussed.
Trabecular bone remodelling simulation considering osteocytic response to fluid-induced shear stress
Authors: Adachi Taiji , Kameo Yoshitaka , Hojo Masaki
Published: May 2010

In bone functional adaptation by remodelling, osteocytes in the lacuno-canalicular system are believed to play important roles in the mechanosensory system. Under dynamic loading, bone matrix deformation generates an interstitial fluid flow in the lacuno-canalicular system; this flow induces shear stress on the osteocytic process membrane that is known to stimulate the osteocytes. In this sense, the osteocytes behave as mechanosensors and deliver mechanical information to neighbouring cells through the intercellular communication network. In this study, bone remodelling is assumed to be regulated by the mechanical signals collected by the osteocytes. From the viewpoint of multi-scale biomechanics, we propose a mathematical model of trabecular bone remodelling that takes into account the osteocytic mechanosensory network system. Based on this model, a computational simulation of trabecular bone remodelling was conducted for a single trabecula under cyclic uniaxial loading, demonstrating functional adaptation to the applied mechanical loading as a load-bearing construct.
Effect of fatigue on force fluctuations in knee extensors in young adults
Authors: Singh Navrag B. , Arampatzis Adamantios , Duda Georg , Heller Markus O. , Taylor William R.
Published: May 2010

This study investigated the hypothesis that fatiguing exercises led to increased force fluctuations during submaximal isometric knee extensions and to decreased accuracy and steadiness in the time and frequency domains. Sixteen young adults (eight males, eight females) were tested, in a seated posture with 90° knee flexion, to assess their ability to reproduce target extensor torques set at 15 per cent and 20 per cent of their maximum voluntary isometric contraction, both before and after fatiguing exercises. Normalized mean (NMAE) and peak (NPAE) of the absolute error were both used to quantify accuracy, whereas normalized standard deviation of the absolute error (NSAE) was used to quantify steadiness of the torque trials in the time domain. Mean and median power frequencies (MnPF, MdPF) and normalized peak power (NPkP) were used to assess the spectral structure of the torque signals. NMAE, NSAE and NPAE all showed excellent intra- as well as intersession reliabilities (intraclass correlation values greater than 0.75 and low standard error of measurement values), demonstrating repeatability of the test set-up. NMAE, NSAE and NPAE increased significantly post-fatigue (greater than 42%), together with a shift towards higher frequency (MnPF and MdPF) components, indicating that the set-up was sensitive enough to detect the decreased force accuracy and steadiness of the musculature after fatigue. Increased force variability in both the time and frequency domains could therefore explain decreased steadiness after fatigue.
Influence of fatigue on the simulated relation between the amplitude of the surface electromyogram and muscle force
Authors: Dideriksen Jakob L. , Farina Dario , Enoka Roger M.
Published: May 2010

A linear relation between surface electromyogram (EMG) amplitude and muscle force is often assumed and used to estimate the contributions of selected muscles to various tasks. In the presence of muscle fatigue, however, changes in the properties of muscle fibre action potentials and motor unit twitch forces can alter the relation between surface EMG amplitude and force. A novel integrative model of motor neuron control and the generation of muscle fibre action potentials was used to simulate surface EMG signals and muscle force during three fatigue protocols. The change in the simulated relation between surface EMG amplitude and force depended on both the level of fatigue and the details of the fatiguing contraction. In general, surface EMG amplitude overestimated muscle force when fatigue was present. For example, surface EMG amplitudes corresponding to 60 per cent of the amplitude obtained at maximal force without fatigue corresponded to forces in the range 10–40% of the maximal force across three representative fatigue protocols. The results indicate that the surface EMG amplitude cannot be used to predict either the level of muscle activation or the magnitude of muscle force when the muscle exhibits any fatigue.
Local variation and parallel evolution: morphological and genetic diversity across a species complex of neotropical crater lake cichlid fishes
Authors: Elmer Kathryn R. , Kusche Henrik , Lehtonen Topi K. , Meyer Axel
Published: May 2010

The polychromatic and trophically polymorphic Midas cichlid fish species complex (Amphilophuscf.citrinellus) is an excellent model system for studying the mechanisms of speciation and patterns of phenotypic diversification in allopatry and in sympatry. Here, we first review research to date on the species complex and the geological history of its habitat. We analyse body shape variation from all currently described species in the complex, sampled from six crater lakes (maximally 1.2–23.9 kyr old) and both great lakes in Nicaragua. We find that Midas cichlid populations in each lake have their own characteristic body shape. In lakes with multiple sympatric species of Midas cichlid, each species has a distinct body shape. Across the species complex, most body shape change relates to body depth, head, snout and mouth shape and caudal peduncle length. There is independent parallel evolution of an elongate limnetic species in at least two crater lakes. Mitochondrial genetic diversity is higher in crater lakes with multiple species. Midas cichlid species richness increases with the size and age of the crater lakes, though no such relationship exists for the other syntopic fishes. We suggest that crater lake Midas cichlids follow the predicted pattern of an adaptive radiation, with early divergence of each crater lake colonization, followed by intralacustrine diversification and speciation by ecological adaptation and sexual selection.
Speciation inFicedulaflycatchers
Authors: Qvarnström Anna , Rice Amber M. , Ellegren Hans
Published: May 2010

Speciation in animals often requires that population divergence goes through three major evolutionary stages, i.e. ecological divergence, development of sexual isolation and the build-up of genetic incompatibility. There is theoretical consensus regarding favourable conditions required for speciation to reach its final and irreversible stage, but empirical tests remain rare. Here, we review recent research on processes of speciation, based on studies in hybrid zones between collared (Ficedula albicollis) and pied flycatchers (Ficedula hypoleuca). A major advantage of this study system is that questions concerning all three major sources of reproductive isolation and their interconnections can be addressed. We conclude that (i) ecological divergence is caused by divergence in life-history traits, (ii) females prefer mates of their own species based on differences in both plumage and song characteristics, (iii) male plumage characteristics have diverged but their song has converged in sympatry, (iv) there is genetic incompatibility in accordance with Haldane's rule, and (v) the Z-chromosome appears to be a hotspot for genes involved in sexual isolation and genetic incompatibility. We discuss how identification of the genes underlying the three major sources of reproductive isolation can be used to draw conclusions about links between the processes driving their evolution.
Group selection and the development of the biological species concept
Authors: Mallet James
Published: May 2010

The development of what became known as the biological species concept began with a paper by Theodosius Dobzhansky in 1935, and was amplified by a mutualistic interaction between Dobzhansky, Alfred Emerson and Ernst Mayr after the second world war. By the 1950s and early 1960s, these authors had developed an influential concept of species as coadapted genetic complexes at equilibrium. At this time many features of species were seen as group advantages maintained by selection to avoid breakdown of beneficial coadaptation and the ‘gene pool’. Speciation thus seemed difficult. It seemed to require, more so than today, an externaldeus ex machina, such as allopatry or the founder effect, rather than ordinary within-species processes of natural selection, sexual selection, drift and gene flow.

In the mid-1960s, the distinctions between group and individual selection were clarified. Dobzhansky and Mayr both understood the implications, but their views on species changed little. These group selectionist ideas now seem peculiar, and are becoming distinctly less popular today. Few vestiges of group selectionism and species-level adaptationism remain in recent reviews of speciation. One wonders how many of our own cherished views on evolution will seem as odd to future biologists.
Removal of Spindly from microtubule-attached kinetochores controls spindle checkpoint silencing in human cells
Authors: Gassmann Reto , Holland Andrew J. , Varma Dileep , Wan Xiaohu , Çivril Filiz , Cleveland Don W. , Oegema Karen , Salmon Edward D. , Desai Arshad
Published: May 2010

The spindle checkpoint generates a “wait anaphase” signal at unattached kinetochores to prevent premature anaphase onset. Kinetochore-localized dynein is thought to silence the checkpoint by transporting checkpoint proteins from microtubule-attached kinetochores to spindle poles. Throughout metazoans, dynein recruitment to kinetochores requires the protein Spindly. Here, we identify a conserved motif in Spindly that is essential for kinetochore targeting of dynein. Spindly motif mutants, expressed following depletion of endogenous Spindly, target normally to kinetochores but prevent dynein recruitment. Spindly depletion and Spindly motif mutants, despite their similar effects on kinetochore dynein, have opposite consequences on chromosome alignment and checkpoint silencing. Spindly depletion delays chromosome alignment, but Spindly motif mutants ameliorate this defect, indicating that Spindly has a dynein recruitment-independent role in alignment. In Spindly depletions, the checkpoint is silenced following delayed alignment by a kinetochore dynein-independent mechanism. In contrast, Spindly motif mutants are retained on microtubule-attached kinetochores along with checkpoint proteins, resulting in persistent checkpoint signaling. Thus, dynein-mediated removal of Spindly from microtubule-attached kinetochores, rather than poleward transport per se, is the critical reaction in checkpoint silencing. In the absence of Spindly, a second mechanism silences the checkpoint; this mechanism is likely evolutionarily ancient, as fungi and higher plants lack kinetochore dynein.
Polycomb group genes Psc and Su(z)2 restrict follicle stem cell self-renewal and extrusion by controlling canonical and noncanonical Wnt signaling
Authors: Li Xinghua , Han Yue , Xi Rongwen
Published: May 2010

Stem cells are critical for maintaining tissue homeostasis and are commonly governed by their niche microenvironment, although the intrinsic mechanisms controlling their multipotency are poorly understood. Polycomb group (PcG) genes are epigenetic silencers, and have emerged recently as important players in maintaining stem cell multipotency by preventing the initiation of differentiation programs. Here we describe an unexpected role of specific PcG genes in allowing adult stem cell differentiation and preventing stem cell-derived tumor development. We show that Posterior sex combs (Psc), which encodes a core Polycomb-repressive complex 1 (PRC1) component, functions redundantly with a similar gene, Suppressor of zeste two [Su(z)2], to restrict follicle stem cell (FSC) self-renewal in the Drosophila ovary. FSCs carrying deletion mutations of both genes extrude basally from the epithelium and continue to self-propagate at ectopic sites, leading to the development of FSC-like tumors. Furthermore, we show that the propagation of the mutant cells is driven by sustained activation of the canonical Wnt signaling pathway, which is essential for FSC self-renewal, whereas the epithelial extrusion is mediated through the planar cell polarity pathway. This study reveals a novel mechanism of epithelial extrusion, and indicates a novel role of polycomb function in allowing adult stem cell differentiation by antagonizing self-renewal programs. Given evolutionary conservation of PcG genes from Drosophila to mammals, they could have similar functions in mammalian stem cells and cancer.
Labeling Cytoskeletal F-Actin with Rhodamine Phalloidin or Fluorescein Phalloidin for Imaging: Figure 1.
Authors: Chazotte Brad
Published: May 2010

INTRODUCTION

The eukaryotic cell has evolved to compartmentalize its functions and transport various metabolites among cellular compartments. Therefore, in cell biology, the study of organization and structure/function relationships is of great importance. The cytoskeleton is composed of a series of filamentous structures, including intermediate filaments, actin filaments, and microtubules. Immunofluorescent staining has been most frequently used to study cytoskeletal components. However, it is also possible to fluorescently label isolated cytoskeletal proteins and either microinject them back into the cell or add them to fixed, permeabilized cells. Alternatively, it is possible to use the mushroom-derived fluorescinated toxins, phalloidin or phallacidin, to label F-actin of the cytoskeleton, as is described in this article. Phalloidin is available labeled with different fluorophores. The choice of the specific fluorophore should depend on whether phalloidin labeling for actin is part of a double-label experiment. In most cells, the abundance of actin filaments should provide a very strong signal. In double-label experiments, the fluorophore should be chosen to take this into account. In general, rhodamine labels are more resistant to photobleaching and can be subjected to the longer exposures required for finer structures.
Low-Magnification Live Imaging of Xenopus Embryos for Cell and Developmental Biology: Figure 1.
Authors: Wallingford John B.
Published: May 2010

INTRODUCTION

Biological processes occur dynamically, so dynamic analyses are essential to further our understanding of them. Embryos of the frog Xenopus laevis are an ideal model system for time-lapse imaging of biological processes. Xenopus embryos are especially amenable to in vivo imaging of whole embryos, individual cells, and subcellular processes. Low-magnification imaging of intact Xenopus embryos can be combined effectively with manipulations of gene function and has provided key insights into the control of morphogenetic movements during gastrulation and neural tube closure. The utility of this approach is not limited to tissue movements, but rather extends to studies of cytokinesis, wound healing, and other dynamic events. This protocol describes methods for low-magnification time-lapse imaging of intact Xenopus embryos.
Variance Component Methods for Analysis of Complex Phenotypes
Authors: Almasy Laura , Blangero John
Published: May 2010

INTRODUCTION

Variance component methods have a long history in human quantitative genetics as well as in agricultural genetics and animal breeding. They are designed for genetic analysis of continuously varying quantitative traits such as body mass index (BMI), cholesterol levels, or intelligence quotient. They can be used to assess the strength of genetic effects on a trait, to localize genes influencing a trait through either linkage or association methods, to assess whether associated variants are likely to be the functional variants behind a given localization signal, to explore whether related traits have shared genetic influences in multivariate analyses, and to characterize the genetic effects on a trait through analyses of gene-gene and gene-environment interactions.
Stabilization of Proteins for Storage
Authors: Simpson Richard J.
Published: May 2010

INTRODUCTION

Following isolation and purification, it is often necessary to store proteins and peptides for extended periods of time before performing detailed biophysical, enzymatic, and structural proteomics. Therefore, it is essential that the pure target protein maintain its original biological (or functional) behavior over an extended period of storage which may range from weeks to years. Protein pharmaceuticals must remain viable following extensive shipping and storage, and they must remain devoid of all possible inactivation processes. The shelf life of a protein depends on both the intrinsic nature of the protein and the storage conditions. Proteins (especially enzymes) must be stored at an appropriate temperature and pH range and frequently in the presence of concentrated (~1 M) glycerol, sucrose, or a similar substance, for the proteins to retain activity and prevent aggregation. This article discusses the major causes of protein inactivation and describes a range of measures that can be adopted to maintain the stability and solubility of proteins.
Characterization of an Electric-Pneumatic Hybrid Prismatic Actuator
Authors: Csonka Paul J. , Waldron Kenneth J.
Published: May 2010

Many high performance actuators have been developed in recent years. However, these actuators are generally designed for precise, relatively slow movements, or imprecise dynamic motion, but incapable of generating quasistatic trajectories. This dichotomy arises in part due to thrusting actuation technology that often trades off impulse for precision. A characterization of a bidirectional hybrid actuator developed for use in legged robots is described here. This actuator is capable of precise noncompliant positioning, and storage and rapid release of energy, which makes it equally suitable for static and dynamic positioning applications. Characterizations shown here allow tuning the actuator in future versions to reduce losses and increase efficiency.
Hydrogen Bonds and Kinematic Mobility of Protein Molecules
Authors: Shahbazi Zahra , Ilieş Horea T. , Kazerounian Kazem
Published: May 2010

Modeling protein molecules as kinematic chains provides the foundation for developing powerful approaches to the design, manipulation, and fabrication of peptide based molecules and devices. Nevertheless, these models possess a high number of degrees of freedom (DOFs) with considerable computational implications. On the other hand, real protein molecules appear to exhibit a much lower mobility during the folding process than what is suggested by existing kinematic models. The key contributor to the lower mobility of real proteins is the formation of hydrogen bonds during the folding process. In this paper, we explore the pivotal role of hydrogen bonds in determining the structure and function of the proteins from the point of view of mechanical mobility. The existing geometric criteria on the formation of hydrogen bonds are reviewed and a new set of geometric criteria is proposed. We show that the new criteria better correlate the number of predicted hydrogen bonds with those established by biological principles than other existing criteria. Furthermore, we employ established tools in kinematics mobility analysis to evaluate the internal mobility of protein molecules and to identify the rigid and flexible segments of the proteins. Our results show that the developed procedure significantly reduces the DOF of the protein models, with an average reduction of 94%. Such a dramatic reduction in the number of DOF can have enormous computational implications in protein folding simulations.
New Approach to the Dynamic Modeling of Compliant Mechanisms
Authors: Wang Wenjing , Yu Yueqing
Published: May 2010

A new dynamic model of compliant mechanisms is developed based on the pseudo-rigid-body model. The kinetic energy and potential energy of various kinds of compliant segments are derived using numerical methods at first. The dynamic equation of planar compliant mechanisms is then developed based on the Lagrange equation. The natural frequency is obtained in the example of a planar compliant parallel-guiding mechanism. The numerical results show the advantage of the proposed method for the dynamic analysis of compliant mechanisms.
The Analysis of Planetary Gear Trains
Authors: Raghavan Madhusudan
Published: May 2010

The generalized lever is a new tool in gear train representation. It extends the traditional concept of a lever representation of a planetary gear set to 1 that includes negative lever ratios. This allows an exhaustive permutation of the nodes of a lever, thereby leading to all possible topological arrangements of a planetary gear train. Consequently, we achieve a compact representation of large families of planetary gear trains, which would otherwise have to be dealt with on a case-by-case basis.
Toward the Design of a Decoupled, Two-Dimensional, Vision-Based μN Force Sensor
Authors: Cappelleri David J. , Krishnan Girish , Kim Charles , Kumar Vijay , Kota Sridhar
Published: May 2010

In this paper, we present three designs for a decoupled, two-dimensional, vision-based micro-Newton (μN) force sensor for microrobotic applications. There are currently no reliable, multi-axis, commercially-available force sensors to measure forces at this scale that can be easily integrated into standard microrobotic test-beds. In our previous work, we presented a design consisting of a planar, elastic mechanism with known force-deflection characteristics. It was inspired by the designs of pre-existing micro electromechanical system suspension mechanisms. A charge-coupled device camera was used to track the deformation of the mechanism as it was used to manipulate objects in a microscale/mesoscale robotic manipulation test-bed. By observing the displacements of select points on the mechanism, the manipulation forces were estimated. In this work, we have designed a compliant mechanism with decoupled stiffness using the building block approach. By designing mechanisms with circular compliance and stiffness ellipses along with zero magnitude compliance and stiffness vectors, we are able to achieve our design requirements. Validation of this approach through the testing of macroscale prototypes and a scaled design for microrobotic applications are offered, along with a sensitivity analysis, yielding insights for microfabricating such designs.
Imitation Control for Biped Robot Using Wearable Motion Sensor
Authors: Liu Tao , Inoue Yoshio , Shibata Kyoko
Published: May 2010

In conventional imitation control, optical tracking devices have been widely adopted to capture human motion and control robots in a laboratory environment. Wearable sensors are attracting extensive interest in the development of a lower-cost human-robot control system without constraints from stationary motion analysis devices. We propose an ambulatory human motion analysis system based on small inertial sensors to measure body segment orientations in real time. A new imitation control method was developed and applied to a biped robot using data of human joint angles obtained from a wearable sensor system. An experimental study was carried out to verify the method of synchronous imitation control for a biped robot. By comparing the results obtained from direct imitation control with an improved method based on a training algorithm, which includes a personal motion pattern, we found that the accuracy of imitation control was markedly improved and the tri-axial average errors of x-y- and z-moving displacements related to leg length were 12%, 8% and 4%, respectively. Experimental results support the feasibility of the proposed control method.
"SAFER ISLAND CONCEPT" DEVELOPED AFTER THE 2004 INDIAN OCEAN TSUNAMI: A CASE STUDY OF MALDIVES
Authors: RIYAZ MAHMOOD , PARK KYUNG-HO
Published: May 2010

This study deals with the "safer island concept" implemented for the reconstruction and rehabilitation works after the 26 December 2004 Indian Ocean Tsunami in the Maldives. The safer island concept has been developed as an important adaptation strategy for tsunamis as well as the sea-level rise due to climate change. Reconstruction work in Dhuvaafaru Island to rehabilitate the entire population of Kandholhudhoo Island of Raa atoll is chosen as a case study. The appropriateness of the functionality of the redesigned island to provide security and safety for the island communities is evaluated using the digital elevation model.

The study results show that the design enhanced mitigation measures of the island might show some resilience for less frequent natural disasters such as smaller tsunamis, while the implementation of the concept may create greater vulnerability for more frequent disasters, such as flash floods and storms. An integrated approach with appropriate risk assessment of floods, storms, and other physical aspects of the island is recommended for the future development of the safer island concept.
BOUNDARY EXTENSION AND STOP CRITERIA FOR EMPIRICAL MODE DECOMPOSITION
Authors: WU QIN , RIEMENSCHNEIDER SHERMAN D.
Published: May 2010

In this paper, a new idea about the boundary extension has been introduced and applied to the Empirical Mode Decomposition (EMD) algorithm. Instead of the traditional mirror extension on the boundary, we propose a ratio extension on the boundary. We also adopt the stop criteria by Rilling et al. for B-Spline based EMD algorithm. Numerical experiments are used for empirically assessing performance of the modified EMD algorithm. The examples indicate that the ratio boundary extension indeed improves the result of the original EMD.
A NOVEL APPROACH OF EDGE DETECTION VIA A FAST AND ADAPTIVE BIDIMENSIONAL EMPIRICAL MODE DECOMPOSITION METHOD
Authors: BHUIYAN SHARIF M. A. , KHAN JESMIN F. , ADHAMI REZA R.
Published: May 2010

A novel approach of edge detection is proposed that utilizes a bidimensional empirical mode decomposition (BEMD) method as the primary tool. For this purpose, a recently developed fast and adaptive BEMD (FABEMD) is used to decompose the given image into several bidimensional intrinsic mode functions (BIMFs). In FABEMD, order statistics filters (OSFs) are employed to get the upper and lower envelopes in the decomposition process, instead of surface interpolation, which enables fast decomposition and well-characterized BIMFs. Binarization and morphological operations are applied to the first BIMF obtained from FABEMD to achieve the desired edges. The proposed approach is compared with several other edge detection methodologies, which include a combination of classical BEMD and morphological processing, the Canny and Sobel edge detectors, as well as combinations of BEMD/FABEMD and Canny/Sobel edge detectors. Simulation results with real images demonstrate the efficacy and potential of the proposed edge detection algorithm employing FABEMD.
AUTOMATED SLEEP STAGING TECHNIQUE BASED ON THE EMPIRICAL MODE DECOMPOSITION ALGORITHM: A PRELIMINARY STUDY
Authors: DONG JING , LIU DONGDONG , ZHANG CHENG , MA JING , WANG GUANGFA , GUO DAN , LIU YANHUI , ZHONG HUA , ZHANG JUE , PENG CHUNG-KANG , FANG JING
Published: May 2010

An automatic sleep staging method is proposed to score wakefulness and three nonrapid eye movement (NREM) stages S1, S2 and S3, based on the Empirical Mode Decomposition (EMD) algorithm. Patients with sleep disorders were tested using this method. Good agreements between manual and automatic staging results were achieved in terms of their Cohen's Kappa value.
A New Estimation Algorithm from Measurements with Multiple‐Step Random Delays and Packet Dropouts
Authors: Caballero-Águila R. , Hermoso-Carazo A. , Linares-Pérez J.
Published: May 2010

The least‐squares linear estimation problem using covariance
information is addressed in discrete‐time linear stochastic
systems with bounded random observation delays which can lead to
bounded packet dropouts. A recursive algorithm, including the
computation of predictor, filter, and fixed‐point smoother, is
obtained by an innovation approach. The random delays are
modeled by introducing some Bernoulli random variables with known
distributions in the system description. The derivation of the
proposed estimation algorithm does not require full knowledge of
the state‐space model generating the signal to be estimated, but
only the delay probabilities and the covariance functions of the
processes involved in the observation equation.
Stacked Heterogeneous Neural Networks for Time Series Forecasting
Authors: Leon Florin , Zaharia Mihai Horia
Published: May 2010

A hybrid model for time series forecasting is proposed. It is a stacked neural network, containing one normal multilayer perceptron with bipolar sigmoid activation functions, and the other with an exponential activation function in the output layer. As shown by the case studies, the proposed stacked hybrid neural model performs well on a variety of benchmark time series. The combination of weights of the two stack components that leads to optimal performance is also studied.
Point Ordering with Natural Distance Based on Brownian Motion
Authors: Kim Philsu , Kim Hyoungseok
Published: May 2010

We consider a curve reconstruction problem from unorganized point clouds
with noise. In general, the result of curve reconstruction depends on how to select and
order the representative points to resemble the shape of the clouds. We exploit a natural
distance based on a property of one‐dimensional Brownian motion to order sample points,
which simultaneously reflect smoothness and nearness of points, so that our algorithm is
able to reconstruct not only simple curves but also nonsimple curves. Numerous examples
show that this algorithm is effective. The natural distance proposed in this paper is able
to play an important role in a variety of fields of measuring the distance of points with
considering direction.