bluuebunny/crossref_metadata_2025 huggingface dataset:
Synchronous rotation of the set of double pendula: Experimental observations
Authors: Strzalko J. , Grabski J. , Wojewoda J. , Wiercigroch M. , Kapitaniak T.
Published: December 2012

We study the occurrence of the synchronous rotation of a set of four uncoupled nonidentical double pendula arranged into a cross structure mounted on a vertically excited platform. Under the excitation, the pendula can rotate in different directions (counter-clockwise or clockwise). It has been shown that after a transient, many different types of synchronous configurations with the constant phase difference between pendula can be observed. The experimental results qualitatively agree with the numerical simulations.
The three-dimensional dynamics of the die throw
Authors: Kapitaniak M. , Strzalko J. , Grabski J. , Kapitaniak T.
Published: December 2012

A three-dimensional model of a die throw which considers the die bounces with dissipation on the fixed and oscillating table has been formulated. It allows simulations of the trajectories for dice with different shapes. Numerical results have been compared with the experimental observation using high speed camera. It is shown that for the realistic values of the initial energy the probabilities of the die landing on the face which is the lowest one at the beginning is larger than the probabilities of landing on any other face. We argue that non-smoothness of the system plays a key role in the occurrence of dynamical uncertainties and gives the explanation why for practically small uncertainties in the initial conditions a mechanical randomizer approximates the random process.
Periodic orbits near onset of chaos in plane Couette flow
Authors: Kreilos Tobias , Eckhardt Bruno
Published: December 2012

We track the secondary bifurcations of coherent states in plane Couette flow and show that they undergo a periodic doubling cascade that ends with a crisis bifurcation. We introduce a symbolic dynamics for the orbits and show that the ones that exist fall into the universal sequence described by Metropolis, Stein and Stein for unimodal maps. The periodic orbits cover much of the turbulent dynamics in that their temporal evolution overlaps with turbulent motions when projected onto a plane spanned by energy production and dissipation.
Particle filtering in high-dimensional chaotic systems
Authors: Lingala Nishanth , Sri Namachchivaya N. , Perkowski Nicolas , Yeong Hoong C.
Published: December 2012

We present an efficient particle filtering algorithm for multiscale systems, which is adapted for simple atmospheric dynamics models that are inherently chaotic. Particle filters represent the posterior conditional distribution of the state variables by a collection of particles, which evolves and adapts recursively as new information becomes available. The difference between the estimated state and the true state of the system constitutes the error in specifying or forecasting the state, which is amplified in chaotic systems that have a number of positive Lyapunov exponents. In this paper, we propose a reduced-order particle filtering algorithm based on the homogenized multiscale filtering framework developed in Imkeller et al. “Dimensional reduction in nonlinear filtering: A homogenization approach,” Ann. Appl. Probab. (to be published). In order to adapt the proposed algorithm to chaotic signals, importance sampling and control theoretic methods are employed for the construction of the proposal density for the particle filter. Finally, we apply the general homogenized particle filtering algorithm developed here to the Lorenz'96 [E. N. Lorenz, “Predictability: A problem partly solved,” in Predictability of Weather and Climate, ECMWF, 2006 (ECMWF, 2006), pp. 40–58] atmospheric model that mimics mid-latitude atmospheric dynamics with microscopic convective processes.
Fabrication of large-grained thin polycrystalline silicon films on foreign substrates by titanium-assisted metal-induced layer exchange
Authors: Antesberger T. , Wassner T. A. , Kashani M. , Scholz M. , Lechner R. , Matich S. , Stutzmann M.
Published: December 2012

Metal-induced layer exchange (MILE) is a well-known method to grow large-grained high quality polycrystalline silicon on foreign substrates. We have modified the commonly used layer stack by an additional titanium interfacial layer (substrate/metal/titanium/oxide/amorphous silicon). The resulting layer exchange process is called titanium-assisted metal-induced layer exchange (Ti.MILE). For the investigated metals, Al (Ti.ALILE) and Ag (Ti.AgILE), the additional Ti layer does not affect the overall layer exchange process but results in a strong enlargement of the grains in the resulting polycrystalline silicon layer up to 250 μm. We have investigated the influence of the titanium interfacial layer on the process dynamics and grain growth. Furthermore, the structural and optical properties of the resulting polycrystalline silicon layer are investigated by means of different analysis methods.
Construction of Lax connections by exponentiation
Authors: Beisert Niklas , Lücker Florian
Published: December 2012

We propose a method for constructing the Lax connection of two-dimensional relativistic integrable sigma models on coset spaces by means of exponentiation of a suitable operator. We derive a simple quadratic relation that this operator must satisfy for an entire one-parameter family of connections to be flat.
Multiple solutions for semilinear resonance elliptic problems with nonconstant coefficients at infinity
Authors: Cheng Rong , Hu Jianhua , Wang Zhiyong
Published: December 2012

In this paper, we study a class of semilinear elliptic equations which are completely resonant with nonconstant coefficients at origin and at infinity. By applying Morse theory and Minimax method, we obtain the existence of multiple nontrivial solutions for the equations.
Global solvability and asymptotic behavior of a free boundary problem for the one-dimensional viscous radiative and reactive gas
Authors: Jiang Jie , Zheng Songmu
Published: December 2012

In this paper, we study a Neumann and free boundary problem for the one-dimensional viscous radiative and reactive gas. We prove that under rather general assumptions on the heat conductivity κ, for any arbitrary large smooth initial data, the problem admits a unique global classical solution. Our global existence results improve those results by Umehara and Tani [“Global solution to the one-dimensional equations for a self-gravitating viscous radiative and reactive gas,” J. Differ. Equations 234(2), 439–463 (2007)10.1016/j.jde.2006.09.023; Umehara and Tani “Global solvability of the free-boundary problem for one-dimensional motion of a self-gravitating viscous radiative and reactive gas,” Proc. Jpn. Acad., Ser. A: Math. Sci. 84(7), 123–128 (2008)]10.3792/pjaa.84.123 and by Qin, Hu, and Wang [“Global smooth solutions for the compressible viscous and heat-conductive gas,” Q. Appl. Math. 69(3), 509–528 (2011)].10.1090/S0033-569X-2011-01218-0 Moreover, we analyze the asymptotic behavior of the global solutions to our problem, and we prove that the global solution will converge to an equilibrium as time goes to infinity. This is the result obtained for this problem in the literature for the first time.
Progress in the mathematical theory of quantum disordered systems
Authors: Wreszinski Walter F.
Published: December 2012

We review recent progress in the mathematical theory of quantum disordered systems: the Anderson transition, including some joint work with Marchetti, the (quantum and classical) Edwards-Anderson (EA) spin-glass model and return to equilibrium for a class of spin-glass models, which includes the EA model initially in a very large transverse magnetic field.
Cantilever anemometer based on a superconducting micro-resonator: Application to superfluid turbulence
Authors: Salort J. , Monfardini A. , Roche P.-E.
Published: December 2012

We present a new type of cryogenic local velocity probe that operates in liquid helium (1 K < T < 4.2 K) and achieves a spatial resolution of ≈ 0.1 mm. The operating principle is based on the deflection of a micro-machined silicon cantilever which reflects the local fluid velocity. Deflection is probed using a superconducting niobium micro-resonator sputtered on the sensor and used as a strain gauge. We present the working principle and the design of the probe, as well as calibration measurements and velocity spectra obtained in a turbulent helium flow above and below the superfluid transition.
A macroscopic non-destructive testing system based on the cantilever-sample contact resonance
Authors: Fu Ji , Lin Lizhi , Zhou Xilong , Li Yingwei , Li Faxin
Published: December 2012

Detecting the inside or buried defects in materials and structures is always a challenge in the field of nondestructive testing (NDT). In this paper, enlightened by the operation principle of the contact resonance force microscopy or atomic force acoustic microscopy (AFAM), we proposed a macroscopic NDT system based on contact resonance of the cantilever-sample surface to detect the local stiffness variations in materials or structures. We fabricated a piezoelectric unimorph with the dimension typically of 150 mm × 8 mm × 2 mm to act as a macroscopic cantilever, whose flexural mode vibration was driven by a wideband power amplifier together with a signal generator. The vibration signal of the macroscopic cantilever is detected by a high sensitive strain gauge bonded on the cantilever surface which is much more stable than the laser diode sensor in AFAM, thus making it very suitable for outdoor operations. Scanning is realized by a three-dimensional motorized stage with the Z axis for pressing force setting. The whole system is controlled by a LabVIEW-based homemade software. Like the AFAM, this NDT system can also work in two modes, i.e., the single-frequency mode and the resonance-tracking mode. In the latter mode, the contact stiffness at each pixel of the sample can be obtained by using the measured contact resonance frequency and a beam dynamics model. Testing results of this NDT system on a grid structure with an opaque panel show that in both modes the prefabricated defect beneath the panel can be detected and the grid structures can be clearly “seen,” which indicates the validity of this NDT system. The sensitivity of this NDT system was also examined.
A levitation instrument for containerless study of molten materials
Authors: Nordine Paul C. , Merkley Dennis , Sickel Jeffrey , Finkelman Steve , Telle Rainer , Kaiser Arno , Prieler Robert
Published: December 2012

A new aero-acoustic levitation instrument (AAL) has been installed at the Institute for Mineral Engineering at RWTH University in Aachen, Germany. The AAL employs acoustically stabilized gas jet levitation with laser-beam heating and melting to create a contact-free containerless environment for high temperature materials research. Contamination-free study of liquids is possible at temperatures in excess of 3000 °C and of undercooled liquids at temperatures far below the melting point. Digital control technology advances the art of containerless experiments to obtain long-term levitation stability, allowing new experiments in extreme temperature materials research and to study operation of the levitation instrument itself. Experiments with liquid Al2O3 at temperatures more than 3200 °C, 1200 °C above the melting point, and with liquid Y3Al5O12 far below the melting point are reported. Fast pyrometry and video recording instruments yield crystallization rates in undercooled liquid Al2O3 as a function of temperature. Levitation of dense liquid HfO2 at temperatures above 2900 °C is demonstrated. Capabilities are described for resonant frequency matching in the three-axis acoustic positioning system, acoustic control of sample spin, and position control of standing wave nodes to stabilize levitation under changing experimental conditions. Further development and application of the levitation technology is discussed based on the results of experiments and modeling of instrument operations.
The impact of wind power on power system transient stability based on probabilistic weighting method
Authors: Ayodele T. R. , Jimoh A. A. , Munda J. L. , Agee J. T.
Published: December 2012

This paper reports on the influence of wind power on transient stability of a power system taking into consideration the stochastic nature of a disturbance to the network. Traditionally, transient stability is evaluated using the deterministic method. This technique is usually considered for a single operating condition so called the worst case scenario. However, factors that affect the transient stability of a power system such as types of disturbance and its location, the clearing time, and even the pre-disturbance system state are all random processes. A probabilistic method using conditional probability is used in analysing the effects of wind generator technologies, wind power location, and wind power penetration level on the transient stability of a power system. The indices for probability of stability are established; comparison is made between the probabilistic and deterministic techniques in the evaluation of risk of instability of a power system consisting wind generators. DigSilent power factory 14.0 and matlab™ are employed in the analysis. Some of the key results show that wind power has both positive and negative influences on the transient stability of a power system depending on the location of the wind farm and the penetration level of the wind power. The deterministic approach gives a high pessimistic result compared to the probabilistic method. The probabilistic technique has the ability to quantify the level of instability in a power system.
Housing Inequalities under Market Deepening: The Case of Guangzhou, China
Authors: Li Si-Ming
Published: December 2012

Escalating housing prices in China's major metropolises have brought widespread discontents. There is a general impression that housing inequality is rising, and that housing has become increasingly out of reach of ordinary households. Yet, much of the literature on urban housing in China is based on data generated in the early reform period. Very little has been written about what has happened since the 1998 housing reform when both the production and the consumption of housing became primarily market based. The present paper aims to address this deficiency with reference to surveys conducted in Guangzhou in 1996, 2001, and 2005. Quality-adjusted inequality indices including the Gini coefficient and the Theil index are computed to compare housing inequality before and after the ending of welfare allocation of housing at the turn of the century. Quite unexpectedly, the results show only a modest increase in inequality in housing consumption.
Asymmetrical Integration: Public Finance Deprivation in China's Urbanized Villages
Authors: Po Lanchih
Published: December 2012

China's unprecedented urbanization since the 1978 economic reform has left many rural villages engulfed by expanding urban jurisdictions. Because of the collective ownership of land, these villages have not vanished over night. On the contrary, they have maneuvered to bypass planning and construction codes and rebuilt themselves into high-density neighborhoods, housing millions of migrants in the cities. This paper analyzes the continued survival of the collective economy of these villages-in-the-city ( chengzhongcun) from the perspective of public finance. Urbanized villages remain financially responsible for public services within their jurisdictions, including infrastructure, sanitation, policing, social welfare, and even education. Neither the problem of urban—rural disparities, nor the consequent lack of adequate public services has been resolved by the integration of these villages into urban areas. These villages have had to find new ways to cope with rapid population growth, finance an urbanized community, and at the same time, bear the burden of their stigmatization as a cancerous growth within otherwise ‘modern’ cities. Using the rapidly urbanized Pearl River Delta region as an empirical case, this paper explores how the urban villages are asymmetrically integrated within the cities: they contribute to the city's growth, but receive little or no public support. In contrast with the common sense that incorporation into an urban jurisdiction will bring about rising fiscal investment, in China, it is the rural villages that are financing the growth of cities.
Two Waves of Gentrification and Emerging Rights Issues in Guangzhou, China
Authors: He Shenjing
Published: December 2012

Since the late 1980s two waves of gentrification have occurred in Guangzhou, China and brought about dramatic transformations of cityscape and sociospatial configuration in the central city. Accordingly, the emphasis of urban policy has shifted from fighting the ‘blight’ to eliminating the ‘obsolescence’, which signifies the rise of neoliberal urban policies. The first wave of gentrification started in the late 1980s and paused in 1999 and was mainly in the form of sporadic housing redevelopment justified by city betterment and infrastructure improvement. The second wave surged around 2005, featuring an ambitious urban upgrading scheme with the aim of building a world-class city. While the first wave of gentrification was a modest experiment of marketised operation, the second wave of gentrification is at the core of the local government's growth-seeking and city reimaging neoliberal urban strategy. Defending the right to appropriation has been a major struggle for residents affected in both waves of gentrification, although in the first wave there was very little room left for rights claiming. In the second wave, rights conflicts have gone deeper and been more fierce, and struggles for a right to participation started to rise. Buttressed by local media, academics, activists, and volunteers, local residents have made modest progress in defending their rights. Yet, it is still far from seriously challenging the power structure in urban decision-making and the trajectory of (re)urbanisation dominated by the elite class and vested interest groups.
Rethinking Social Power and the Right to the City Amidst China's Emerging Urbanism
Authors: Qian Junxi , He Shenjing
Published: December 2012

In this paper we engage with a theoretical reflection on the concept of the right to the city amidst China's emerging urbanism. In particular, we conceptualize the right to the city as embedded within the complex geometries of power relations throughout the production process of China's urban modernity; and in this sense assert the right to urban life is inevitably entangled with a social project of altering dominant power structures. We suggest that the rights of three social groups—namely socialist workers in work units, rural migrants, and urban redevelopment displacees—to the modern Chinese city is situated within the uneven distribution of social power and corresponding infrastructures of social control, which contribute to these social groups' structural marginality in the process of urban social formation. In some cases, these social groups may be endowed with substantial rights to social welfare but the dominant power structure is left unquestioned and unchallenged, resulting in latent forms of social vulnerability. Therefore, the concept of the right to the city needs to be captured as a combination of the distribution of things (social welfare) and the mobilization of process (structural change). In this sense, a Hegelian teleology of linear social development to comprehend the rights issue amid China's emerging urbanism must be called into question.
Becoming Urban: Sitework from a Moss-Eye View
Authors: Gabrys Jennifer
Published: December 2012

Discussing an urban walking event, “Moss-eye view”, held in the City of London, this paper considers the ways in which cities may be understood from the view of more-than-human processes and incorporations. The walk explores how distinct insights emerge into ways of ‘becoming urban’ by attending to organisms, environments, and forms of sitework that are not typically foregrounded in the usual economies of the City of London. Moss incorporates the material effects of urban ecologies across time and space, and thus forms a process of bio-indication in the city, capturing pollutants and making resources available for other organisms. Mosses in the city might be studied as sentient, more-than-human exchangers of and participants in urban energies, and as in-between and peripheral organisms that connect up sites by working across material, affective, political, socionatural, and imaginative registers. It is argued that the “Moss-eye view” walking event is a form of research that opens up infra-urban practices for understanding cities through alternative associations and incorporations of urban life.
Multidimensional Diversity in Two European Cities: Thinking beyond Ethnicity
Authors: Piekut Aneta , Rees Philip , Valentine Gill , Kupiszewski Marek
Published: December 2012

This paper shifts discussion on social diversity from ethnic diversity to broader social diversity. We explore spatial social diversity and assess opportunities to encounter diversity in an urban context. In doing so, we prepared a description of diversity in the residential communities of two cities, Leeds and Warsaw, using census data for small areas (UK 2001, Poland 2002). Selected variables were used to represent the key social dimensions of difference: demographic, socioeconomic, ethnic, and disability. A cluster analysis using a k-means algorithm was implemented for each city separately and for the two cities combined using harmonized indicators. We selected eight cluster solutions for each city which had different profiles and spatial distributions. A combined cluster analysis showed that there was little overlap in community types across the two cities. The paper illustrates that Leeds and Warsaw residents experience very different opportunities to encounter difference which need to be taken into account when local diversity policies are implemented.
Structural Evaluation of Institutional Bias in China's Urban Housing: The Case of Guangzhou
Authors: Chen Guo
Published: December 2012

Institutional bias is an important topic in social justice and the presence of institutional bias is widely recognized in China's urban housing sector. This paper proposes a new framework for measuring and assessing institutional bias in China's urban housing system based on structural equation modeling and the Pratt index of relative importance for linear regression. The proposed framework analyzes the structural pathways through which nonmarket institutional forces affect housing, and provides quantitative measures to evaluate both the direct and the indirect effects of biased institutions on housing outcomes. A case study of Guangzhou is presented to demonstrate the proposed ideas and methods using first-hand household survey data collected in 2009. The results of the case study show the dominance of institutional effects over market effects on housing outcomes through direct and indirect pathways. The results also show that, although institutional forces affect most subjective and objective measures of housing outcomes, they induce the largest effects on homeownership attainment and physical housing conditions. This suggests that, at this stage, property ownership and material housing well-being are two potential central areas of China's housing justice.
The Rewards of Individual Engagement in Volunteering: A Missing Dimension of the Big Society
Authors: Nichols Geoff , Ralston Rita
Published: December 2012

This paper examines the experience of volunteering in relation to the latent functions of paid work identified by social psychologists. In-depth interviews with fourteen volunteers illustrate the considerable rewards of volunteering, especially in terms of personal status and identity. The common rewards of volunteering and employment challenge the traditional dichotomy between paid and unpaid work. However, the experience of volunteering is context specific, and for some the lack of material benefits will limit its ability to substitute for employment. The promotion of volunteering within the UK Big Society policy could acknowledge its personal benefits, while being mindful that their ability to contribute to a satisfying life is moderated by the individual's circumstances and attitude towards the opportunities volunteering offers.
Differential Urbanisation Trends in South Africa—Regional and Local Equivalents
Authors: Geyer Hermanus S , Geyer Hermanus S , du Plessis Danie J , van Eeden Amanda
Published: December 2012

The paper analyses trends in the location of commercial, industrial, and different residential land uses in the four largest metropolitan cities of South Africa over the past decade. Recent development patterns show strong decentralisation trends of away from core cities to the metropolitan fringes despite proactive containment policies. Elements of the differential urbanisation model are used to explain heterogeneous migration patterns within a rapidly urbanising South African population. Indications are that strong centrifugal patterns in the cities are linked to both local decentralisation and deflected urbanisation at the regional level. This results in continuing social stratification in all four agglomerations and the continuation of the ‘post-apartheid city.’ The persistent movement of populations and commercial and industrial land uses to the urban fringe has resulted in the strengthening of the multicentric urban framework of the four metropolitan cities.
The Dimensionality of ‘Place Attachment’ for Older People in Rural Areas of South West England and Wales
Authors: Burholt Vanessa
Published: December 2012

Previously I have used qualitative data to develop a four-domain (physical, social, temporal, and psychological) model of attachment to place for older people in rural areas. Drawing on data for 920 older people (60+ years) living in rural areas of South West England and Wales, and utilising items developed from the initial qualitative analysis to represent each domain empirically, this paper uses exploratory factor analysis to identify the underlying factor structure of place attachment for older people in these rural areas. It examines the match between the resulting factor structure and an a priori conceptualisation of place attachment. I develop subscales and an overall scale of place attachment and tests for reliability and rating scaling assumptions (content validity). Using principal axis factoring three factors are identified: social attachment, aesthetic attachment, and appropriateness of resources and the environment. The three factors account for 23.5%, 11.6%, and 6.4% of the variance and good internal reliability is demonstrated (Cronbach's α 0.71, 0.72, and 0.72). The analysis suggests that this is a psychometrically reliable and valid instrument fit for the purpose of measuring attachment to place for older people in rural areas. However, further psychometric evaluations with other samples are required to confirm the model structure, and to develop a fourth domain representing an historical attachment to place.
Barriers to the Acquisition of Urban Hukou in Chinese Cities
Authors: Zhang Li , Tao Li
Published: December 2012

The hukou system is one of the most enduring legacies of the 20th-century Chinese socialist control instruments. The hukou in the Chinese context is an official identity of residency rights in a given geographic unit. Cities use the hukou policy to impede the urban hukou of migrants who are deemed unworthy in terms of socioeconomic attributes. Based on policy documents and data collected from forty-five sample cities, this paper offers statistical measures and explanations for barriers to urban hukou nationwide. The paper introduces the city's entry barrier (CEB) index to rank the degree of difficulty of acquiring urban hukou and performs factor analysis to identify the key determinants that significantly explain the various levels of the CEB index across cities. Our empirical findings suggest that a more developed city tends to develop a higher entry barrier to its hukou. The intention of city governments to impose barriers to urban hukou is enshrined largely in their progrowth mentality and their metaphors on the political economy of urbanization.
The ‘Mainstream Muslim’ Opposing Islamophobia: Self-Representations of American Muslims
Authors: McGinty Anna Mansson
Published: December 2012

This paper explores the public self-representations of Muslim American leaders from major Muslim organizations in the United States as articulated in a local community engagement. I argue that the prevalent self-representations of the ‘mainstream Muslim’ and ‘American Islam’ have become politicized terms in an effort to construct a political and religious constituency in resistance to rampant Islamophobic expressions. By stressing compatibility and reconciliation with American political and social life, a counternarrative of citizenship and belonging emerges. Hence, the self-representations also shed important light on how Muslims as a minority group negotiate and perform politics of belonging and inclusion in the United States through the appropriation of powerful notions of what represents ‘the mainstream’. As any religious definition, ‘American Islam’ has to be understood as a particular discursive product specific to time and place. While highlighting hybridity and fluidity, as well as the flexibility of the religious faith with respect to interpretation, ‘American Islam’—a definition used by activists as well as scholars—also has essentializing tendencies overlooking particular voices and geographies within the Muslim community in the USA.
The Economic Impact of Greening Urban Vacant Land: A Spatial Difference-In-Differences Analysis
Authors: Heckert Megan , Mennis Jeremy
Published: December 2012

Vacant land is a serious problem in many cities, and cities have recently begun to explore greening as a management strategy to reduce the negative influence of vacancy. The city of Philadelphia, Pennsylvania pioneered the use of a simple greening treatment—removal of debris coupled with planting grass and trees—as a means of improving blighted communities. Though they are becoming more popular, the actual economic impact of these programs is not well understood. This paper details the use of a spatial difference-in-differences approach for measuring the impact of Philadelphia's innovative vacant land greening program on nearby residential property values. This approach compares observed changes in property values surrounding treated vacant lots with observed changes around control lots—lots which might have been treated but were not. While property values throughout the city increased during the study period, properties surrounding greened vacant lots had a greater increase in value than properties surrounding nongreened vacant lots. By developing both global and local versions of the model, we also explore spatial variation in the impacts of the program—offering insight into which kinds of neighborhoods might derive the greatest economic benefit from vacant land greening programs.
Why older people engage in physical activity: an exploratory study of participants in a community-based walking program
Authors: Capalb Darren J. , O'Halloran Paul , Liamputtong Pranee
Published: December 2012

While older people experience substantial physical and mental health benefits from regular physical activity, participation rates among older people are low. There is a need to gather more information about why older people do and do not engage in physical activity. This paper aims to examine the reasons why older men and women chose to engage in a community-based physical activity program. Specific issues that were examined included reasons why older people who had been involved in a community-based program on a regular basis: commenced the program; continued with the program; and recommenced the program after they had dropped out. Ten participants (eight females and two males) aged between 62 and 75 years, who had been participating in a community-based physical activity program for a minimum of 6 months, were individually interviewed. Thematic analysis was used to analyse the data. Three major themes emerged, including ‘time to bond: social interaction’ with sub-themes ‘bona fide friendships’ and ‘freedom from being isolated’; ‘I want to be healthy: chronic disease management’; and ‘new lease on life’. Two of the primary reasons why older people both commenced and recommenced the program were the promise of social interaction and to be able to better manage their chronic conditions.
Specification of skeletal muscle differentiation by repressor element-1 silencing transcription factor (REST)-regulated Kv7.4 potassium channels
Authors: Iannotti Fabio Arturo , Barrese Vincenzo , Formisano Luigi , Miceli Francesco , Taglialatela Maurizio
Published: December 2012

Changes in the expression of potassium (K+) channels is a pivotal event during skeletal muscle differentiation. In mouse C2C12 cells, similarly to human skeletal muscle cells, myotube formation increased the expression of Kv7.1, Kv7.3, and Kv7.4, the last showing the highest degree of regulation. In C2C12 cells, Kv7.4 silencing by RNA interference reduced the expression levels of differentiation markers (myogenin, myosin heavy chain, troponinT-1, and Pax3) and impaired myotube formation and multinucleation. In Kv7.4-silenced cells, the differentiation-promoting effect of the Kv7 activator N-(2-amino-4-(4-fluorobenzylamino)-phenyl)-carbamic acid ethyl ester (retigabine) was abrogated. Expression levels for the repressor element-1 silencing transcription factor (REST) declined during myotube formation. Transcript levels for Kv7.4, as well as for myogenin, troponinT-1, and Pax3, were reduced by REST overexpression and enhanced upon REST suppression by RNA interference. Four regions containing potential REST-binding sites in the 5′ untranslated region and in the first intron of the Kv7.4 gene were identified by bioinformatic analysis. Chromatin immunoprecipitation assays showed that REST binds to these regions, exhibiting a higher efficiency in myoblasts than in myotubes. These data suggest that Kv7.4 plays a permissive role in skeletal muscle differentiation and highlight REST as a crucial transcriptional regulator for this K+ channel subunit.
A genome-wide transcriptional analysis of morphology determination inCandida albicans
Authors: Carlisle Patricia L. , Kadosh David
Published: December 2012

Candida albicans, the most common cause of human fungal infections, undergoes a reversible morphological transition from yeast to pseudohyphal and hyphal filaments, which is required for virulence. For many years, the relationship among global gene expression patterns associated with determination of specific C. albicans morphologies has remained obscure. Using a strain that can be genetically manipulated to sequentially transition from yeast to pseudohyphae to hyphae in the absence of complex environmental cues and upstream signaling pathways, we demonstrate by whole-genome transcriptional profiling that genes associated with pseudohyphae represent a subset of those associated with hyphae and are generally expressed at lower levels. Our results also strongly suggest that in addition to dosage, extended duration of filament-specific gene expression is sufficient to drive the C. albicans yeast-pseudohyphal-hyphal transition. Finally, we describe the first transcriptional profile of the C. albicans reverse hyphal-pseudohyphal-yeast transition and demonstrate that this transition involves not only down-regulation of known hyphal-specific, genes but also differential expression of additional genes that have not previously been associated with the forward transition, including many involved in protein synthesis. These findings provide new insight into genome-wide expression patterns important for determining fungal morphology and suggest that in addition to similarities, there are also fundamental differences in global gene expression as pathogenic filamentous fungi undergo forward and reverse morphological transitions.
Caenorhabditis elegansreveals a FxNPxY-independent low-density lipoprotein receptor internalization mechanism mediated by epsin1
Authors: Kang Yuan-Lin , Yochem John , Bell Leslie , Sorensen Erika B. , Chen Lihsia , Conner Sean D.
Published: December 2012

Low-density lipoprotein receptor (LDLR) internalization clears cholesterol-laden LDL particles from circulation in humans. Defects in clathrin-dependent LDLR endocytosis promote elevated serum cholesterol levels and can lead to atherosclerosis. However, our understanding of the mechanisms that control LDLR uptake remains incomplete. To identify factors critical to LDLR uptake, we pursued a genome-wide RNA interference screen using Caenorhabditis elegans LRP-1/megalin as a model for LDLR transport. In doing so, we discovered an unanticipated requirement for the clathrin-binding endocytic adaptor epsin1 in LDLR endocytosis. Epsin1 depletion reduced LDLR internalization rates in mammalian cells, similar to the reduction observed following clathrin depletion. Genetic and biochemical analyses of epsin in C. elegans and mammalian cells uncovered a requirement for the ubiquitin-interaction motif (UIM) as critical for receptor transport. As the epsin UIM promotes the internalization of some ubiquitinated receptors, we predicted LDLR ubiquitination as necessary for endocytosis. However, engineered ubiquitination-impaired LDLR mutants showed modest internalization defects that were further enhanced with epsin1 depletion, demonstrating epsin1-mediated LDLR endocytosis is independent of receptor ubiquitination. Finally, we provide evidence that epsin1-mediated LDLR uptake occurs independently of either of the two documented internalization motifs (FxNPxY or HIC) encoded within the LDLR cytoplasmic tail, indicating an additional internalization mechanism for LDLR.
PKD controls mitotic Golgi complex fragmentation through a Raf–MEK1 pathway
Authors: Kienzle Christine , Eisler Stephan A. , Villeneuve Julien , Brummer Tilman , Olayioye Monilola A. , Hausser Angelika
Published: December 2012

Before entering mitosis, the stacks of the Golgi cisternae are separated from each other, and inhibiting this process delays entry of mammalian cells into mitosis. Protein kinase D (PKD) is known to be involved in Golgi-to–cell surface transport by controlling the biogenesis of specific transport carriers. Here we show that depletion of PKD1 and PKD2 proteins from HeLa cells by small interfering RNA leads to the accumulation of cells in the G2 phase of the cell cycle and prevents cells from entering mitosis. We further provide evidence that inhibition of PKD blocks mitotic Raf-1 and mitogen-activated protein kinase kinase (MEK) activation, and, as a consequence, mitotic Golgi fragmentation, which could be rescued by expression of active MEK1. Finally, Golgi fluorescence recovery after photobleaching analyses demonstrate that PKD is crucial for the cleavage of the noncompact zones of Golgi membranes in G2 phase. Our findings suggest that PKD controls interstack Golgi connections in a Raf-1/MEK1–dependent manner, a process required for entry of the cells into mitosis.
Structurally unique interaction of RBD-like and PH domains is crucial for yeast pheromone signaling
Authors: Yerko Volodymyr , Sulea Traian , Ekiel Irena , Harcus Doreen , Baardsnes Jason , Cygler Miroslaw , Whiteway Malcolm , Wu Cunle
Published: December 2012

The Ste5 protein forms a scaffold that associates and regulates the components of the mitogen-activated protein (MAP) kinase cascade that controls mating-pheromone-mediated signaling in the yeast Saccharomyces cerevisiae. Although it is known that the MEK kinase of the pathway, Ste11, associates with Ste5, details of this interaction have not been established. We identified a Ras-binding-domain-like (RBL) region in the Ste11 protein that is required specifically for the kinase to function in the mating pathway. This module is structurally related to domains in other proteins that mediate Ras-MAP kinase kinase kinase associations; however, this RBL module does not interact with Ras, but instead binds the PH domain of the Ste5 scaffold. Structural and functional studies suggest that the key role of this PH domain is to mediate the Ste5–Ste11 interaction. Overall these two evolutionarily conserved modules interact with each other through a unique interface, and thus in the pheromone pathway the structural context of the RBL domain contribution to kinase activation has been shifted through a change of its interaction partner from Ras to a PH domain.
Lamin A tail modification by SUMO1 is disrupted by familial partial lipodystrophy–causing mutations
Authors: Simon Dan N. , Domaradzki Tera , Hofmann Wilma A. , Wilson Katherine L.
Published: December 2012

Lamin filaments are major components of the nucleoskeleton that bind LINC complexes and many nuclear membrane proteins. The tail domain of lamin A directly binds 21 known partners, including actin, emerin, and SREBP1, but how these interactions are regulated is unknown. We report small ubiquitin-like modifier 1 (SUMO1) as a major new posttranslational modification of the lamin A tail. Two SUMO1 modification sites were identified based on in vitro SUMOylation assays and studies of Cos-7 cells. One site (K420) matches the SUMO1 target consensus; the other (K486) does not. On the basis of the position of K486 on the lamin A Ig-fold, we hypothesize the SUMO1 E2 enzyme recognizes a folded structure–dependent motif that includes residues genetically linked to familial partial lipodystrophy (FPLD). Supporting this model, SUMO1-modification of the lamin A tail is reduced by two FPLD-causing mutations, G465D and K486N, and by single mutations in acidic residues E460 and D461. These results suggest a novel mode of functional control over lamin A in cells.
Apolipoprotein(a) stimulates nuclear translocation of β-catenin: a novel pathogenic mechanism for lipoprotein(a)
Authors: Cho Taewoo , Romagnuolo Rocco , Scipione Corey , Boffa Michael B. , Koschinsky Marlys L.
Published: December 2012

Lipoprotein(a) (Lp(a)) is associated with cardiovascular disease risk. This may be attributable to the ability of Lp(a) to elicit endothelial dysfunction. We previously reported that apolipoprotein(a) (apo(a); the distinguishing kringle-containing component of Lp(a)) elicits cytoskeletal rearrangements in vascular endothelial cells, resulting in increased cellular permeability. These effects require a strong lysine-binding site (LBS) in apo(a). We now report that apo(a) induces both nuclear β-catenin–mediated cyclooxygenase-2 (COX-2) expression and prostaglandin E2 secretion, indicating a proinflammatory role for Lp(a). Apo(a) caused the disruption of VE-cadherin/β-catenin complexes in a Src-dependent manner, decreased β-catenin phosphorylation, and increased phosphorylation of Akt and glycogen synthase kinase-3β, ultimately resulting in increased nuclear translocation of β-catenin; all of these effects are downstream of apo(a) attenuation of phosphatase and tensin homologue deleted on chromosome 10 activity. The β-catenin–mediated effects of apo(a) on COX-2 expression were absent using a mutant apo(a) lacking the strong LBS. Of interest, the normal and LBS mutant forms of apo(a) bound to human umbilical vein endothelial cells in a similar manner, and the binding of neither was affected by lysine analogues. Taken together, our findings suggest a novel mechanism by which apo(a) can induce proinflammatory and proatherosclerotic effects through modulation of vascular endothelial cell function.
Yeast G-proteins mediate directional sensing and polarization behaviors in response to changes in pheromone gradient direction
Authors: Moore Travis I. , Tanaka Hiromasa , Kim Hyung Joon , Jeon Noo Li , Yi Tau-Mu
Published: December 2012

Yeast cells polarize by projecting up mating pheromone gradients, a classic cell polarity behavior. However, these chemical gradients may shift direction. We examine how yeast cells sense and respond to a 180oswitch in the direction of microfluidically generated pheromone gradients. We identify two behaviors: at low concentrations of α-factor, the initial projection grows by bending, whereas at high concentrations, cells form a second projection toward the new source. Mutations that increase heterotrimeric G-protein activity expand the bending-growth morphology to high concentrations; mutations that increase Cdc42 activity result in second projections at low concentrations. Gradient-sensing projection bending requires interaction between Gβγ and Cdc24, whereas gradient-nonsensing projection extension is stimulated by Bem1 and hyperactivated Cdc42. Of interest, a mutation in Gα affects both bending and extension. Finally, we find a genetic perturbation that exhibits both behaviors. Overexpression of the formin Bni1, a component of the polarisome, makes both bending-growth projections and second projections at low and high α-factor concentrations, suggesting a role for Bni1 downstream of the heterotrimeric G-protein and Cdc42 during gradient sensing and response. Thus we demonstrate that G-proteins modulate in a ligand-dependent manner two fundamental cell-polarity behaviors in response to gradient directional change.
RS-WebPredictor: a server for predicting CYP-mediated sites of metabolism on drug-like molecules
Authors: Zaretzki Jed , Bergeron Charles , Huang Tao-wei , Rydberg Patrik , Swamidass S. Joshua , Breneman Curt M.
Published: December 2012

Summary: Regioselectivity-WebPredictor (RS-WebPredictor) is a server that predicts isozyme-specific cytochrome P450 (CYP)-mediated sites of metabolism (SOMs) on drug-like molecules. Predictions may be made for the promiscuous 2C9, 2D6 and 3A4 CYP isozymes, as well as CYPs 1A2, 2A6, 2B6, 2C8, 2C19 and 2E1. RS-WebPredictor is the first freely accessible server that predicts the regioselectivity of the last six isozymes. Server execution time is fast, taking on average 2s to encode a submitted molecule and 1s to apply a given model, allowing for high-throughput use in lead optimization projects.

Availability: RS-WebPredictor is accessible for free use at http://reccr.chem.rpi.edu/Software/RS-WebPredictor/

Contact:  brenec@rpi.edu
Fast and robust optical flow for time-lapse microscopy using super-voxels
Authors: Amat Fernando , Myers Eugene W. , Keller Philipp J.
Published: December 2012

Motivation: Optical flow is a key method used for quantitative motion estimation of biological structures in light microscopy. It has also been used as a key module in segmentation and tracking systems and is considered a mature technology in the field of computer vision. However, most of the research focused on 2D natural images, which are small in size and rich in edges and texture information. In contrast, 3D time-lapse recordings of biological specimens comprise up to several terabytes of image data and often exhibit complex object dynamics as well as blurring due to the point-spread-function of the microscope. Thus, new approaches to optical flow are required to improve performance for such data.

Results: We solve optical flow in large 3D time-lapse microscopy datasets by defining a Markov random field (MRF) over super-voxels in the foreground and applying motion smoothness constraints between super-voxels instead of voxel-wise. This model is tailored to the specific characteristics of light microscopy datasets: super-voxels help registration in textureless areas, the MRF over super-voxels efficiently propagates motion information between neighboring cells and the background subtraction and super-voxels reduce the dimensionality of the problem by an order of magnitude. We validate our approach on large 3D time-lapse datasets of Drosophila and zebrafish development by analyzing cell motion patterns. We show that our approach is, on average, 10 × faster than commonly used optical flow implementations in the Insight Tool-Kit (ITK) and reduces the average flow end point error by 50% in regions with complex dynamic processes, such as cell divisions.

Availability: Source code freely available in the Software section at http://janelia.org/lab/keller-lab.

Contact:  amatf@janelia.hhmi.org or kellerp@janelia.hhmi.org

Supplementary information:  Supplementary data are available at Bioinformatics online.