bluuebunny/crossref_metadata_2025 huggingface dataset:
Protein structure validation by generalized linear model root‐mean‐square deviation prediction
Authors: Bagaria Anurag , Jaravine Victor , Huang Yuanpeng J. , Montelione Gaetano T. , Güntert Peter
Published: November 2011

Large‐scale initiatives for obtaining spatial protein structures by experimental or computational means have accentuated the need for the critical assessment of protein structure determination and prediction methods. These include blind test projects such as the critical assessment of protein structure prediction (CASP) and the critical assessment of protein structure determination by nuclear magnetic resonance (CASD‐NMR). An important aim is to establish structure validation criteria that can reliably assess the accuracy of a new protein structure. Various quality measures derived from the coordinates have been proposed. A universal structural quality assessment method should combine multiple individual scores in a meaningful way, which is challenging because of their different measurement units. Here, we present a method based on a generalized linear model (GLM) that combines diverse protein structure quality scores into a single quantity with intuitive meaning, namely the predicted coordinate root‐mean‐square deviation (RMSD) value between the present structure and the (unavailable) “true” structure (GLM‐RMSD). For two sets of structural models from the CASD‐NMR and CASP projects, this GLM‐RMSD value was compared with the actual accuracy given by the RMSD value to the corresponding, experimentally determined reference structure from the Protein Data Bank (PDB). The correlation coefficients between actual (model vs. reference from PDB) and predicted (model vs. “true”) heavy‐atom RMSDs were 0.69 and 0.76, for the two datasets from CASD‐NMR and CASP, respectively, which is considerably higher than those for the individual scores (−0.24 to 0.68). The GLM‐RMSD can thus predict the accuracy of protein structures more reliably than individual coordinate‐based quality scores.
Finite departure from convective quasi‐equilibrium: periodic cycle and discharge–recharge mechanism
Authors: Yano Jun‐Ichi , Plant Robert
Published: November 2011

A simple self‐contained theory is proposed for describing the life cycles of convective systems as a discharge–recharge process.

A closed description is derived for the dynamics of an ensemble of convective plumes based on an energy cycle. The system consists of prognostic equations for the cloud work function and the convective kinetic energy. The system can be closed by introducing a functional relationship between the convective kinetic energy and the cloud‐base mass flux.

The behaviour of this system is considered under a bulk simplification. Previous cloud‐resolving models as well as bulk statistical theories for ensemble convective systems suggest that a plausible relationship would be to assume that the convective kinetic energy is linearly proportional to the cloud‐base mass flux.

As a result, the system reduces to a nonlinear dynamical system with two dependent variables, the cloud‐base mass flux and the cloud work function. The fully nonlinear solution of this system always represents a periodic cycle regardless of the initial condition under constant large‐scale forcing. Importantly, the inclusion of energy dissipation in this model does not in itself lead the system into equilibrium. Copyright © 2011 Royal Meteorological Society
Nanoscale imaging in DNA nanotechnology
Authors: Jungmann Ralf , Scheible Max , Simmel Friedrich C.
Published: November 2011

DNA nanotechnology has developed powerful techniques for the construction of precisely defined molecular structures and machines, and nanoscale imaging methods have always been crucial for their experimental characterization. While initially atomic force microscopy (AFM) was the most widely employed imaging method for DNA‐based molecular structures, in recent years a variety of other techniques were adopted by researchers in the field, namely electron microscopy (EM), super‐resolution fluorescence microscopy, and high‐speed AFM. EM is now typically applied for the characterization of compact nanoobjects and three‐dimensional (3D) origami structures, as it offers better resolution than AFM and can be used for 3D reconstruction from single‐particle analysis. While the small size of DNA nanostructures had previously precluded the application of fluorescence microscopic methods, the development of super‐resolution microscopy now facilities the application of fast and powerful optical methods also in DNA nanotechnology. In particular, the observation of dynamical processes associated with DNA nanoassemblies—e.g., molecular walkers and machines—requires imaging techniques that are both fast and allow observation under native conditions. Here single‐molecule fluorescence techniques and high‐speed AFM are beginning to play an increasingly important role. WIREs Nanomed Nanobiotechnol 2012, 4:66–81. doi: 10.1002/wnan.173

This article is categorized under:

Nanotechnology Approaches to Biology > Nanoscale Systems in Biology
Atorvastatin reduces vascular endothelial growth factor (VEGF) expression in human non‐small cell lung carcinomas (NSCLCs) via inhibition of reactive oxygen species (ROS) production
Authors: Chen Jie , Liu Bing , Yuan Jiayi , Yang Jie , Zhang Jingjie , An Yu , Tie Lu , Pan Yan , Li Xuejun
Published: November 2011

The high metastatic potential of non‐small cell lung cancers (NSCLCs) is closely correlated with the elevated expression of vascular endothelial growth factor (VEGF) and resultant tumor angiogenesis. However, no effective strategies against VEGF expression have been available in NSCLCs therapy. This study demonstrated that elevated reactive oxygen species (ROS) levels derived from both mitochondria and NADPH oxidase were required for VEGF expression in NSCLC cells. Atorvastatin administration could significantly inhibit VEGF expression both in vitro and in vivo via inhibition of ROS production. Atorvastatin inhibited ROS generation partly through suppression of Rac1/NADPH oxidase activity. Specifically, atorvastatin could upregulate the activity of glutathione peroxidase (GPx) and catalase, which are responsible for elimination of hydrogen peroxide (H2O2) in the mitochondria and peroxisomes, respectively. Thus, inhibition of ROS production by concomitant suppression of Rac1/NADPH oxidase activity and upregulation of the activity of GPx and catalase contributes critically to atorvastatin‐reduced VEGF expression in NSCLCs. Atorvastatin may be a potential alternative against VEGF expression and angiogenesis in NSCLCs therapy.
Premodifiers in English
Authors: Feist Jim
Published: November 2011

The order and behaviour of the premodifier (an adjective, or other modifying word that appears before a noun) has long been a puzzle to syntacticians and semanticists. Why can we say 'the actual red ball', but not 'the red actual ball'? And why, conversely, do some other premodifiers have free variation in sentences; for example we can say both 'German and English speakers' and 'English and German speakers'? Why do some premodifiers change the meaning of a phrase in some contexts; for example 'young man', can mean 'boyfriend', rather than 'man who is young'? Drawing on a corpus of over 4,000 examples of English premodifiers from a range of genres such as advertising, fiction and scientific texts, and across several varieties of English, this book synthesises research into premodifiers and provides a new explanation of their behaviour, order and use.
Growth and Decline in Colchester, 1300-1525
Authors: Britnell R. H.
Published: November 2011

This is a study of one of England's principal cloth towns during the late Middle Ages. It draws extensively upon unpublished records in Colchester and elsewhere, and is the first history of a medieval English town to analyse in conjunction the relationships between overseas trade, urban development and changes in rural society. First it describes Colchester in the earlier fourteenth century, its trade, its agricultural setting and its form of government. The book then shows how cloth-making grew in Colchester after the Black Death and how the population increased until about 1414. The implications of this for the government of the borough and for the town's role in the local economy are discussed. The last section shows that Colchester's growth was not sustained through the fifteenth century, and examines some of the causal links between economic contraction, institutional change in the borough and agrarian depression in the surrounding countryside.
The Theory of Classical Dynamics
Authors: Griffiths J. B.
Published: November 2011

This textbook describes in detail the classical theory of dynamics, a subject fundamental to the physical sciences, which has a large number of important applications. The author's aim is to describe the essential content of the theory, the general way in which it is used, and the basic concepts that are involved. No deep understanding can be obtained simply by examining theoretical considerations, so Dr Griffiths has included throughout many examples and exercises. This then is an ideal textbook for an undergraduate course for physicists or mathematicians who are familiar with vector analysis.
Young Thomas More and the Arts of Liberty
Authors: Wegemer Gerard B.
Published: November 2011

What does it mean to be a free citizen in times of war and tyranny? What kind of education is needed to be a 'first' or leading citizen in a strife-filled country? And what does it mean to be free when freedom is forcibly opposed? These concerns pervade Thomas More's earliest writings, writings mostly unknown, including his 280 poems, declamation on tyrannicide, coronation ode for Henry VIII and his life of Pico della Mirandola, all written before Richard III and Utopia. This book analyzes those writings, guided especially by these questions: Faced with generations of civil war, what did young More see as the causes of that strife? What did he see as possible solutions? Why did More spend fourteen years after law school learning Greek and immersed in classical studies? Why do his early works use vocabulary devised by Cicero at the end of the Roman Republic?
Ideas of Power in the Late Middle Ages, 1296–1417
Authors: Canning Joseph
Published: November 2011

Through a focused and systematic examination of late medieval scholastic writers - theologians, philosophers and jurists - Joseph Canning explores how ideas about power and legitimate authority were developed over the 'long fourteenth century'. The author provides a new model for understanding late medieval political thought, taking full account of the intensive engagement with political reality characteristic of writers in this period. He argues that they used Aristotelian and Augustinian ideas to develop radically new approaches to power and authority, especially in response to political and religious crises. The book examines the disputes between King Philip IV of France and Pope Boniface VIII and draws upon the writings of Dante Alighieri, Marsilius of Padua, William of Ockham, Bartolus, Baldus and John Wyclif to demonstrate the variety of forms of discourse used in the period. It focuses on the most fundamental problem in the history of political thought - where does legitimate authority lie?
Through South Africa
Authors: Stanley Henry Morton
Published: November 2011

Henry Morton Stanley (1841–1904), the Welsh-born explorer famous for his 1871 meeting with the missionary David Livingstone, travelled widely in Africa. First published in 1898, this is a compendium of letters written by Stanley during his travels to Bulawayo, Johannesburg and Pretoria, which lend a unique insight into colonial South Africa in the late nineteenth century. Focusing on the country's culture and commercial development, he recalls his impressions of industries such as railways, farms and gold mines, social issues such as immigration and poverty, and the contentious relations between the Boer peoples and the British colonists which led to the Second Boer War. Through his passionate exposition, we learn of his adversity towards President Kruger's policies, and his compassion for the people who he claims were left to starve because the government's priorities were military. His memoirs provide a revealing snapshot of an important period in South Africa's history.
An Engineer's Alphabet
Authors: Petroski Henry
Published: November 2011

Written by America's most famous engineering storyteller and educator, this abecedarium is one engineer's selection of thoughts, quotations, anecdotes, facts, trivia and arcana relating to the practice, history, culture and traditions of his profession. The entries reflect decades of reading, writing, talking and thinking about engineers and engineering, and range from brief essays to lists of great engineering achievements. This work is organized alphabetically and more like a dictionary than an encyclopedia. It is not intended to be read from first page to last, but rather to be dipped into, here and there, as the mood strikes the reader. In time, it is hoped, this book should become the source to which readers go first when they encounter a vague or obscure reference to the softer side of engineering.
Travels through Canada and the United States of North America in the Years 1806, 1807, and 1808
Authors: Lambert John
Published: November 2011

In the opening decades of the nineteenth century, the writings of John Lambert renewed the British public's fascination with the landscapes, peoples, flora, and fauna of the Canadian colonies and the United States. First published in 1811, and ultimately running into four editions, this two-volume work is packed with closely-observed descriptions, facts and figures about colonial life, as well as lively anecdotes. The 'corrected and improved' second edition reissued here was published in 1814, towards the end of the Napoleonic Wars. It promised to 'enable the British reader to form a just opinion of the Canadian colonies, and to appreciate the character of the neighbouring enemies who threaten their existence'. A trained painter, Lambert illustrated his account with lithographs based on his own watercolours. Volume 2 contrasts the excitement of New York, Charleston and Boston, bustling with markets, hotels and pleasure gardens, with the conditions endured by plantation slaves.
Measures of RSA Suppression, Attentional Control, and Negative Affect Predict Self-Ratings of Executive Functions
Authors: Healy Brian , Treadwell Aaron , Reagan Mandy
Published: November 2011

The current study was an attempt to determine the degree to which the suppression of respiratory sinus arrhythmia (RSA) and attentional control were influential in the ability to engage various executive processes under high and low levels of negative affect. Ninety-four college students completed the Stroop Test while heart rate was being recorded. Estimates of the suppression of RSA were calculated from each participant in response to this test. The participants then completed self-ratings of attentional control, negative affect, and executive functioning. Regression analysis indicated that individual differences in estimates of the suppression of RSA, and ratings of attentional control were associated with the ability to employ executive processes but only when self-ratings of negative affect were low. An increase in negative affect compromised the ability to employ these strategies in the majority of participants. The data also suggest that high attentional control in conjunction with attenuated estimates of RSA suppression may increase the ability to use executive processes as negative affect increases.
Trait Mindfulness Predicts Attentional and Autonomic Regulation of Alcohol Cue-Reactivity
Authors: Garland Eric L.
Published: November 2011

The trait of mindfulness varies among meditation-naïve individuals and is associated with attentional and autonomic regulation, two neurocognitive functions that become impaired in addiction. It was hypothesized that alcohol dependent inpatients with comparatively high levels of trait mindfulness would exhibit significant autonomic recovery from stress-primed alcohol cues mediated by greater attentional disengagement from such cues. Fifty-eight alcohol dependent inpatients participated in affect-modulated psychophysiological cue-reactivity protocol and a spatial cueing task designed to assess alcohol attentional bias (AB). Associations between trait mindfulness, alcohol AB, and an index of autonomic activity, high-frequency heart rate variability (HFHRV), were examined via multivariate path analysis. Higher trait mindfulness was significantly associated with less difficulty resisting the urge to drink and greater HFHRV recovery from stress-primed alcohol cues. After statistically controlling for the correlation of mindfulness and perceived difficulty resisting drinking urges, the association between mindfulness and HFHRV recovery was partially mediated by attentional disengagement from alcohol cues (model R2 = .30). Alcohol dependent inpatients higher in mindfulness are better able to disengage attention from alcohol cues, which in turn predicts the degree of HFHRV recovery from such cues. Trait mindfulness may index cognitive control over appetitive responses reflected in superior attentional and autonomic regulation of stress-primed alcohol cue-reactivity.
Vicarious Belongingness
Authors: Kneer Julia , Hemme Inna , Bente Gary
Published: November 2011

There is empirical evidence that mortality salience (MS) influences effects of advertisements. For instance, mere exposure to high-value goods can enhance cultural worldview and self-esteem and thus act as a buffer against existential anguish. Besides cultural worldview and self-esteem, close relationships can help to reduce existential anguish. Drawing upon terror management theory (TMT), the current study addressed the question of whether MS combined with emotional commercials influences perception of the ads as well as further behavior. We compared the effects of socioemotional versus informational ads after MS induction, measuring perceived emotionality of the ads, evaluation of ads and products, recall, and buying intention. Significant effects were found in all outcome variables, except for recall, supporting the hypothesis that under MS induction, commercials with a socioemotional content can enhance advertisement impact.
The Impact of Transaction Utility on Consumer Decisions
Authors: Muehlbacher Stephan , Kirchler Erich , Kunz Angelika
Published: November 2011

In consumption decisions, Thaler (1985) distinguishes acquisition and transaction utility. Whereas acquisition utility stands for the pleasure from obtaining a good, transaction utility denominates the value consumers derive from the deal itself. Transaction utility depends on a comparison of actual prices with reference to other prices such as the regular price. The present article reports two experimental studies demonstrating the effect of transaction utility on purchase decisions. In Experiment 1 (N = 90), on the basis of prospect theory (Kahneman & Tversky, 1979), it is expected that negative transaction utility affects purchase decisions to a higher degree than its positive counterpart. Results support this hypothesis. In Experiment 2 (N = 121) it is hypothesized that acquisition utility moderates the effect of transaction utility, that is, transaction utility becomes less important if a product is desired primarily for its actual value. Though both forms of utility affected purchase intentions, no support for the moderation hypothesis was observed.
Mortality Salience and Worldview Affirmation Strengthen Support for Foreign Products
Authors: Sullivan Daniel , Jonas Eva , Jodlbauer Barbara
Published: November 2011

Research in terror management theory shows that, when reminded of their own death, people experience an elevated need to feel secure in their cultural worldview. This effect has consequences for consumer behavior. One unexplored possibility is that a worldview-affirming prime will buffer anxiety and actually increase willingness to purchase products representative of a foreign worldview after a death reminder. In our study, we first induced mortality or failure salience in 137 Austrian residents. Participants then read a diary entry about a holiday spent either in the mountains of Austria or in foreign countries. Finally, we measured willingness to pay a higher price for a local (“Fair Milk”) versus a foreign product (“fair trade”). Analyses showed that following mortality salience (compared to failure salience) the worldview-affirming prime (a diary entry about Austrian culture) uniquely increased willingness to pay higher prices for foreign products.
When Imagery Influences Spending Decisions
Authors: Kamleitner Bernadette
Published: November 2011

Consumers who think about spending money on a product may do so by engaging in different processing modes. Previous research has shown that imagery processing is particularly likely to lead to persuasion. This paper sheds further light on why this may happen. It argues that imagery spontaneously leads to the simulation of ownership and that the resulting sense of ownership mediates the effect of imagery on consumer behavior. Two studies support the proposed relation between imagery processing, psychological ownership, and consumer behavior. Psychological ownership mediates the effect of imagery and affects consumer reactions beyond imagery. Consumers’ mental projection into an ownership-like-state seems to be a key factor driving product acquisition.
Consumer Decisions as a Central Research Topic in Economic Psychology
Authors: Hoelzl Erik , Kirchler Erich
Published: November 2011

This section outlines the increasing interest of the scientific community in economic psychology and behavioral economics as a means to answer questions about human decision making in an economic/consumer context. It gives a quick overview of the activities of important societies in the field, such as the International Association for Research in Economic Psychology and the Society for the Advancement of Behavioral Economics, as well as periodicals devoted to psycho-economic research, including a categorization of papers published in the Journal of Economic Psychology in the period 1981–2010.
Connecting the terrestrial gamma‐ray flash source strength and observed fluence distributions
Authors: Carlson B. E. , Gjesteland T. , Østgaard N.
Published: November 2011

Terrestrial gamma‐ray flashes (TGFs) as observed by satellites have a broad fluence distribution. This fluence distribution is not trivially related to the source strength distribution, since even a very strong TGF may still be observed at low fluence if the source is far from the satellite. In this paper we connect the source strength distribution with the observed fluence distribution by calculating the effective size and probability of detection of TGFs as a function of their source strength. For sources at a single altitude, power law distributions of source strength give softer power law distributions in observed fluence with especially pronounced softening for very hard source power law indices. This result holds even with broad source altitude distributions in regions of the fluence distribution away from the peak fluence since such regions tend to be dominated by TGFs produced in a relatively narrow range of higher altitudes.
Involvement of interleukin‐1β mediated nuclear factor κB signalling pathways to down‐regulate prostate‐specific antigen and cell proliferation in LNCaP prostate cancer cells
Authors: Bouraoui Yosra , Rais Nawfel Ben , Culig Zoran , Oueslati Ridha
Published: November 2011

Involvement of NF‐κB (nuclear factor κB) mediated by IL‐1β (interleukin‐1β) on cell proliferation and PSA (prostate‐specific antigen) production of LNCaP prostate cell lines and the possible cross‐talk with Akt (also known as protein kinase B) signalling pathway has been investigated. NF‐κB and Akt were analysed by Western blotting from LNCaP cells treated by IL‐1β before proliferation and PSA production were measured. IL‐1β inhibited proliferation and decreased PSA production. The Akt pathway was not sensitive, whereas NF‐κB phosphorylation occurred as a result of treatment. PSA production and proliferation of LNCaP cells were down‐regulated by NF‐κB mediated by IL‐1β promoting anti‐apoptotic signalling and co‐suppressor factors of PSA expression. IL‐1β through NF‐κB activation provides a rationale for therapeutic approaches in the anticancer treatment of prostate.
Symmetry principles in quantum systems theory
Authors: Zeier Robert , Schulte-Herbrüggen Thomas
Published: November 2011

General dynamic properties such as controllability and simulability of spin systems, fermionic and bosonic systems are investigated in terms of symmetry. Symmetries may be due to the interaction topology or due to the structure and representation of the system and control Hamiltonians. In either case, they obviously entail constants of motion. Conversely, the absence of symmetry implies irreducibility and provides a convenient necessary condition for full controllability much easier to assess than the well-established Lie-algebra rank condition. We give a complete lattice of irreducible simple subalgebras of \documentclass[12pt]{minimal}\begin{document}$\mathfrak {su}(2^n)$\end{document}su(2n) for up to n = 15 qubits. It complements the symmetry condition by allowing for easy tests solving homogeneous linear equations to filter irreducible representations of other candidate algebras of classical type as well as of exceptional types. Moreover, here we give the first single necessary and sufficient symmetry condition for full controllability. The lattice of irreducible simple subalgebras given also determines mutual simulability of dynamic systems of spin or fermionic or bosonic nature. We illustrate how controlled quadratic fermionic (and bosonic) systems can be simulated by spin systems and in certain cases also vice versa.
Information storage and retrieval for probe storage using optical diffraction patterns
Authors: van Honschoten Joost W. , de Jong Henri W. , Koelmans Wabe W. , Parnell Thomas P. , Zaboronski Oleg
Published: November 2011

A method for fast information retrieval from a probe storage device is considered. It is shown that information can be stored and retrieved using the optical diffraction patterns obtained by the illumination of a large array of cantilevers by a monochromatic light source. In thermo-mechanical probe storage, the information is stored as a sequence of indentations on the polymer medium. To retrieve the information, the array of probes is actuated by applying a bending force to the cantilevers. Probes positioned over indentations experience deflection by the depth of the indentation, probes over the flat media remain un-deflected. Thus the array of actuated probes can be viewed as an irregular optical grating, which creates a data-dependent diffraction pattern when illuminated by laser light. We develop a low complexity modulation scheme, which allows the extraction of information stored in the pattern of indentations on the media from Fourier coefficients of the intensity of the diffraction pattern. We then derive a low-complexity maximum-likelihood sequence detection algorithm for retrieving the user information from the Fourier coefficients. The derivation of both the modulation and the detection schemes is based on the Fraunhofer formula for data-dependent diffraction patterns. The applicability of Fraunhofer diffraction theory to the optical set-up relevant for probe storage is established both theoretically and experimentally. We confirm the potential of the optical readout technique by demonstrating that the impairment characteristics of probe storage channels (channel noise, global positioning errors, small indentation depth) do not lead to an unacceptable increase in data recovery error rates. We also show that for as long as the Fresnel number F ≤ 0.1, the optimal channel detector derived from Fraunhofer diffraction theory does not suffer any significant performance degradation.
The two-stage dynamics in the Fermi-Pasta-Ulam problem: From regular to diffusive behavior
Authors: Ponno A. , Christodoulidi H. , Skokos Ch. , Flach S.
Published: November 2011

A numerical and analytical study of the relaxation to equilibrium of both the Fermi-Pasta-Ulam (FPU) α-model and the integrable Toda model, when the fundamental mode is initially excited, is reported. We show that the dynamics of both systems is almost identical on the short term, when the energies of the initially unexcited modes grow in geometric progression with time, through a secular avalanche process. At the end of this first stage of the dynamics, the time-averaged modal energy spectrum of the Toda system stabilizes to its final profile, well described, at low energy, by the spectrum of a q-breather. The Toda equilibrium state is clearly shown to describe well the long-living quasi-state of the FPU system. On the long term, the modal energy spectrum of the FPU system slowly detaches from the Toda one by a diffusive-like rising of the tail modes, and eventually reaches the equilibrium flat shape. We find a simple law describing the growth of tail modes, which enables us to estimate the time-scale to equipartition of the FPU system, even when, at small energies, it becomes unobservable.
Response to “Comment on ‘Cosmic ray diffusion: Detailed investigation of a recent model’” [Phys. Plasmas 18, 114701 (2011)]
Authors: Lerche Ian , Tautz R. C.
Published: November 2011

Recently [Phys. Plasmas 18, 082305 (2011)], the otherwise successful unified non-linear transport (UNLT) theory was critically examined. In a comment [Phys. Plasmas 18, 114701 (2011)], it was argued that the deviation from the original UNLT theory is marginal. Here, it is emphasized that the main point was to investigate the basic mathematical properties of the UNLT formulation by showing model approaches rather than deriving complete solutions.
Output-feedback lag-synchronization of time-delayed chaotic systems in the presence of external disturbances subjected to input nonlinearity
Authors: Pourdehi Shabnam , Karimipour Dena , Karimaghaee Paknosh
Published: November 2011

In this paper, an adaptive output error feedback control scheme is proposed for the lag-synchronization of two time-delayed chaotic systems in the presence of channel time-delay, external disturbances and input nonlinearity. Using the Lyapunov theory, stability of the proposed adaptive controller is proved. Lyapunov–Krasovskii approach is used to deal with the existence of time-delay in the system dynamics. Finally, two numerical simulations are presented to illustrate the effectiveness of the developed method.
Chemical-state resolved depth profile and band discontinuity in TiN/HfSiON gate stack structure with AlOx cap layer
Authors: Toyoda S. , Kamada H. , Kumigashira H. , Oshima M.
Published: November 2011

We have investigated chemical-state-resolved depth profiles and band discontinuity for TiN/HfSiON gate stack structure with an AlOx cap layer on a Si substrate using backside angle-resolved photoemission spectroscopy. Depth profiles show that Al atoms diffuse through the high-k layer and are accumulated at the high-k/SiO2 interface during the thermal annealing process. The decrease in relative chemical shift of Si 2p to Hf 4f core-level spectra by inserting the AlOx cap layer can be explained by the lowering of the valence-band discontinuity, which is induced by the modification of the interface dipole of the high-k/SiO2 system.
Micromachined fragment capturer for biomedical applications
Authors: Choi Young-Soo , Lee Dong-Weon
Published: November 2011

Due to changes in modern diet, a form of heart disease called chronic total occlusion has become a serious disease to be treated as an emergency. In this study, we propose a micromachined capturer that is designed and fabricated to collect plaque fragments generated during surgery to remove the thrombus. The fragment capturer consists of a plastic body made by rapid prototyping, SU-8 mesh structures using MEMS techniques, and ionic polymer metal composite (IPMC) actuators. An array of IPMC actuators combined with the SU-8 net structure was optimized to effectively collect plaque fragments. The evaporation of solvent through the actuator's surface was prevented using a coating of SU-8 and polydimethylsiloxane thin film on the actuator. This approach improved the available operating time of the IPMC, which primarily depends on solvent loss. Our preliminary results demonstrate the possibility of using the capturer for biomedical applications.
Force-momentum-based self-guided Langevin dynamics: A rapid sampling method that approaches the canonical ensemble
Authors: Wu Xiongwu , Brooks Bernard R.
Published: November 2011

The self-guided Langevin dynamics (SGLD) is a method to accelerate conformational searching. This method is unique in the way that it selectively enhances and suppresses molecular motions based on their frequency to accelerate conformational searching without modifying energy surfaces or raising temperatures. It has been applied to studies of many long time scale events, such as protein folding. Recent progress in the understanding of the conformational distribution in SGLD simulations makes SGLD also an accurate method for quantitative studies. The SGLD partition function provides a way to convert the SGLD conformational distribution to the canonical ensemble distribution and to calculate ensemble average properties through reweighting. Based on the SGLD partition function, this work presents a force-momentum-based self-guided Langevin dynamics (SGLDfp) simulation method to directly sample the canonical ensemble. This method includes interaction forces in its guiding force to compensate the perturbation caused by the momentum-based guiding force so that it can approximately sample the canonical ensemble. Using several example systems, we demonstrate that SGLDfp simulations can approximately maintain the canonical ensemble distribution and significantly accelerate conformational searching. With optimal parameters, SGLDfp and SGLD simulations can cross energy barriers of more than 15 kT and 20 kT, respectively, at similar rates for LD simulations to cross energy barriers of 10 kT. The SGLDfp method is size extensive and works well for large systems. For studies where preserving accessible conformational space is critical, such as free energy calculations and protein folding studies, SGLDfp is an efficient approach to search and sample the conformational space.
Coercivity control in finite arrays of magnetic particles
Authors: Yang Bo , Zhao Yang
Published: November 2011

Micromagnetic simulation has been performed for two-dimensional arrays of single-domain magnetic particles using the Landau-Lifshitz equation of motion and an energy minimization method. Effects of array anisotropy and spin positional disorder on the hysteresis loop and coercivity of the particle systems are investigated. Simulation results show that the hysteresis loop can be largely modified by breaking geometric symmetry of square arrays, and coercivity in general is found to increase with array disorder. Magnetic hysteresis is strongly affected by disorder when the array contains only a few particles.
Pulsed terahertz emission from GaN/InN heterostructure
Authors: Reklaitis Antanas
Published: November 2011

Dynamics of the electron-hole plasma excited by the femtosecond optical pulse in wurtzite GaN/InN heterostructure is investigated by Monte Carlo simulations. The GaN/InN heterostructure for pulsed terahertz emission is suggested. The results of Monte Carlo simulations show that the power of terahertz emission from the GaN/InN heterostructure exceeds the power of terahertz emission from the surface of InN by one order of magnitude.
Effect of a symmetry breaking layer on the open circuit voltage of conventional bulk-heterojunction solar cells
Authors: Kim Heejoo , Hwa Seo Jung , Cho Shinuk
Published: November 2011

Solution processable titanium suboxide (TiOx) was introduced as an artificial symmetry breaking layer in bulk-heterojunction (BHJ) solar cells comprising a low band gap conjugated polymer, poly[(4,4′-bis(2-ethylhexyl)dithiene[3,2-b:2′,3′-d]silole)-2,6-diyl-alt-(4,7-bis(2-thienyl)-2,1,3-benzothiadiazole)-5,5′-diyl] (Si-PCPDTBT), and a soluble fullerene, [6,6]-phenyl-C71-butyric methyl ester (PC71BM). The inserted TiOx layer obviously extracted the same level of open circuit voltage (Voc) regardless of metal work function. Ultraviolet photoelectron spectroscopy (UPS) results indicated that the formation of the interface dipole between the TiOx symmetry breaking layer and metal electrode successfully modifies the effective work function of the cathode electrode, thereby leading to symmetry breaking in BHJ solar cells.
Communication: Length scale dependent oil-water energy fluctuations
Authors: Underwood Robin , Ben-Amotz Dor
Published: November 2011

Interfacial fluctuations in the cohesive (van der Waals) interaction energy of spherical oil-drops with water provide evidence of a length scale dependent transition from linear to non-linear response behavior. For sub-nanometer oil-drop sizes, energy fluctuations are found to be independent of the van der Waals coupling strength, while nanometer (and larger) size oil drops experience highly non-linear energy fluctuations. The latter behavior is linked to enhanced hydrophobic density fluctuations and the emergence of entropic contributions to oil-water cohesive interaction free energies.
Landscapes of Performance: Stalking as Choreography
Authors: Campbell Elaine
Published: November 2011

Recent advances in nonrepresentational theory (NRT) encourage us to think of landscape as something which is actualised by, in, and through the performativities and affectivities of seeing. While NRT certainly moves us from a static to a more dynamic account of landscape, and along the way introduces an innovative, theoretical vocabulary for talking about and experiencing landscape, it may inhibit more than (or as much as) it facilitates understanding. In this paper, NRT's contribution to the geographical canon will be critically interrogated; in particular, NRT's focus on performance, and its preference for practices and materiality over imagery and the symbolic, will be questioned. This provides the important groundwork for considering the broader utility of NRT, most especially its resonance with the concerns of cultural criminology and its burgeoning interest in ‘criminologies of space’. Using the phenomenon of stalking as an exemplar of a performative practice in late modernity, the paper sets out an understanding of landscape as an intersection of representations, discourses, sensibilities, and material practices. In this way it offers a synthesising, hybridised account of landscape which draws on Foster's notion of choreography to better capture the interrelationalities of the performativity of lived experience(s) and the structuring relations of sociocultural norms, values, and relations of power. Making use of a number of data sources, which include interview material, Hollywood films, and online discussion boards, the paper examines stalking as a choreographic and choreographed process which, amongst other things, engenders a world of imaginary and transgressive landscapes.
Traits associated with drought survival in three Australian tropical rainforest seedlings
Authors: Deines Jillian M. , Hellmann Jessica J. , Curran Timothy J.
Published: November 2011

Drought affects the distribution of plant species in tropical forests and will likely increase under climate change. Future rainforest composition may be determined by species’ abilities to withstand increased drought incidence, particularly at the vulnerable seedling stage. A greenhouse drought survival experiment was conducted on seedlings of three common evergreen tree species from Australia’s Wet Tropics to assess species’ drought survival. This was then related to five functional traits to evaluate the relative importance of desiccation tolerance (ability to persist through drought) and desiccation delay (ability to postpone drought stress) in drought survival. Among the three species examined, delay traits (leaf shedding, root-to-shoot ratio and stem saturated water content) corresponded with experimental drought survival better than tolerance traits (specific leaf area, stem density). Notably, we found differential leaf shedding among these evergreen species and a positive correlation between percent leaf loss and drought survival among individuals across all species (R2 = 0.42). If this pattern holds with greater species replication, it suggests that desiccation delay, particularly via leaf shedding, is important for drought survival even in nominally evergreen species. We suggest that finer classifications of deciduousness such as percent leaf loss under drought stress may be useful in predicting species’ responses to drought conditions.
Gender, peer and partner influences on adolescent HIV risk in rural South Africa
Authors: Harrison Abigail , Smit Jenni , Hoffman Susie , Nzama Thobile , Leu Cheng-Shiun , Mantell Joanne , Stein Zena , Exner Theresa
Published: November 2011

Background and methods
In preparation for a school-based intervention in KwaZulu-Natal, South Africa, a cross-sectional survey of potential HIV risk factors in youth aged 14–17 (n = 983) was conducted. Results: Boys were significantly more likely than girls to report lifetime sexual activity (37.7% v. 13.8%, P < 0.01). Among boys and girls, 46.1% reported condom use at last sex. Discussion of condom use with a partner was the strongest predictor of condom use (boys, odds ratio (OR) = 7.39; girls, OR = 5.58, P < 0.0001). Age was independently associated with sexual activity for boys (OR = 1.49, P < 0.0001) and girls (OR = 1.74, P = 0.02). For boys, perceptions of male peer behaviour were associated with both ever having participated in sexual activity (OR = 1.48, P < 0.01) and condom use at last sex (OR = 1.79, P < 0.01). Girls who equated condom use with having numerous partners were more likely to use them. Among boys, results challenged some expected gender beliefs: support for girls’ initiative in relationship formation and refusal of sex were significant predictors of sexual activity. Among girls, higher pregnancy risk perception (OR = 1.32, P = 0.02) and knowledge (OR = 4.85, P = 0.055) were associated with sexual activity. Conclusions: Creating more gender equitable norms can reduce HIV risk behaviours. HIV prevention interventions should build on existing gender equitable beliefs, and work to promote others, including sexual communication and negotiation skills, and modelling of positive peer norms.
Entrainment regimes and flame characteristics of wildland fires
Authors: Nelson Ralph M. , Butler Bret W. , Weise David R.
Published: November 2011

This paper reports results from a study of the flame characteristics of 22 wind-aided pine litter fires in a laboratory wind tunnel and 32 field fires in southern rough and litter–grass fuels. Flame characteristic and fire behaviour data from these fires, simple theoretical flame models and regression techniques are used to determine whether the data support the derived models. When the data do not support the models, alternative models are developed. The experimental fires are used to evaluate entrainment constants and air/fuel mass ratios in the model equations. Both the models and the experimental data are consistent with recently reported computational fluid dynamics simulations that suggest the existence of buoyancy- and convection-controlled regimes of fire behaviour. The results also suggest these regimes are delimited by a critical value of Byram’s convection number. Flame heights and air/fuel ratios behave similarly in the laboratory and field, but flame tilt angle relationships differ.
Invisible pair bonds detected by molecular analyses
Authors: Takahashi Tetsumi , Ochi Haruki , Kohda Masanori , Hori Michio
Published: November 2011

A focus on pair bonds between males and females is fundamental to study the evolution of social organization. Because pair bonds are generally identified from direct observations of pairs that maintain physical proximity, pair bonds may have been overlooked in animals that do not exhibit such visible pairs. The Lake Tanganyika cichlid fish
Xenotilapia rotundiventralis
forms schools that consist of mouthbrooding and non-brooding adults in mid-water, and visible pairs are not recognized. A previous study suggested that mouthbrooding females transfer fractions of the young to males when the young become large. However, it remains a mystery whether the mating pairs maintain pair bonds so that the females can transfer the young to their mates. To answer this question, we conducted a parentage analysis using 10 microsatellite markers. The analysis showed that the mouthbrooding adults were most likely genetic fathers and mothers of the young in their mouths. This finding suggests that the female-to-male shift of young takes place between mating partners, and thus the mating pairs maintain pair bonds at least until the shift of young. The present study is the first to detect pair bonds in animals in which physical proximity has not been observed.
Top-down causation: an integrating theme within and across the sciences?
Authors: Ellis George F. R. , Noble Denis , O'Connor Timothy
Published: November 2011

This issue of the journal is focused on ‘top-down (downward) causation'. The words in this title, however, already raise or beg many questions. Causation can be of many kinds. They form our ways of ordering our scientific understanding of the world, all the way from the reductive concept of cause as elementary objects exerting forces on each other, through to the more holistic concept of attractors towards which whole systems move, and to adaptive selection taking place in the context of an ecosystem. As for ‘top’ and ‘down’, in the present scientific context, these are clearly metaphorical, as some of the articles in this issue of the journal make clear. Do we therefore know what we are talking about? The meeting at the Royal Society on which this set of papers is based included philosophers as well as scientists, and some of those (Jeremy Butterfield, Barry Loewer, Alan Love, Samir Okasha and Eric Scerri) have contributed articles to this issue. We would like also to thank those (Claus Kiefer, Peter Menzies, Jerome Feldman and David Papineau) who contributed only to the discussion meeting. Their contributions were also valuable, both at the meeting and by influencing the articles that have been written by others. We include a glossary with this introduction, composed by one of us (O'Connor). The clarification of the use of words and their semantic frames is an important role of philosophy, and this was evident in the discussions at the meeting and is now evident in many of the articles published here. Moreover, philosophical analysis is not limited to the papers by the professional philosophers. The idea of top-down causation is intimately related to concepts of emergence; indeed, it is a key factor in strong theories of emergence.