bluuebunny/crossref_metadata_2025 huggingface dataset:
Riot, regeneration and reaction: Spain in the aftermath of the 1898 Disaster
Authors: Balfour Sebastian
Published: July 2011

The crisis of legitimacy following Spain's loss of empire in 1898 combined with the effects of a longer-term crisis of modernization to undermine efforts to reform the political system and regenerate the social and economic life of Spain. Rising social agitation, middle-class movements for national regeneration, Catalan bourgeois nationalism and military reaction all interacted to block the development of a modernizing alternative to the Restoration regime. As a result, the gap between the established order and society grew wider and the potential for peaceful change diminished. Events in the first decade of the century thus established the pattern of conflict that was to dominate Spanish politics until the Civil War.
Earnings Management Surrounding Seasoned Bond Offerings: Do Managers Mislead Ratings Agencies and the Bond Market?
Authors: Caton Gary L. , Chiyachantana Chiraphol N. , Chua Choong-Tze , Goh Jeremy
Published: July 2011

We study earnings management (EM) efforts surrounding seasoned bond offerings using discretionary current accruals. We find that issuers tend to inflate earnings performance prior to an offering. In order for EM efforts to effectively mislead ratings agencies and the bond market, they must lead to inflated bond ratings and decreased offering yields. Regression results indicate the opposite; aggressive EM efforts are associated with lower initial ratings and higher offering yields. We also find a statistically lower proportion of subsequent downgrades for firms with the most aggressive EM efforts, which is inconsistent with these firms’ inflated initial ratings. While some firms may attempt to mislead ratings agencies and market participants by window-dressing earnings, these efforts appear to be counterproductive.
Dimensional synthesis of the Delta robot using transmission angle constraintsDimensional synthesis of the Delta robot using transmission angle constraints
Authors: Zhang LiMin , Mei JiangPing , Zhao XueMan , Huang Tian
Published: July 2011

This paper deals with dynamic dimensional synthesis of the Delta robot using the pressure/transmission angle constraints. Two types of pressure/transmission angles are defined, with which the direct and indirect singularities can be identified in a straightforward manner. Two novel global dynamic metrics are proposed for minimisation, which are associated respectively with the inertial and centrifuge/Coriolis components of the driving torque. Various geometrical and performance constraints are taken into account in terms of workspace/machine volume ratio, pressure/transmission angles, etc. The effects of pressure/transmission angle constraints on the feasible domain of design variables are investigated in depth via an example, and a set of optimised dimensional parameters is obtained for achieving a good kinematic and dynamic performance throughout the entire task workspace.
Unified analysis of statics of some limited-DOF parallel manipulators
Authors: Hu Bo , Lu Yi , Zhang Xiuli , Yu Jianping
Published: July 2011

An observation approach is proposed for determining the poses of the active/constrained wrench and the unified statics of some limited-DOF parallel manipulators (PMs) are studied systematically. First, a general PM model is constructed, and the unified inverse displacement is analyzed. Second, various types of acceptable legs are synthesized; the poses of the active/constrained wrench exerted on the various acceptable legs are determined by the observation approach. Third, a unified 6 × 6 Jacobina matrix and a unified statics equation are derived for solving active/constrained wrench of many limited-DOF PMs. Finally, two PMs are presented to illustrate this approach.
Du verbe de perception visuelle au marqueur parenthétique ‘tu vois’: Grammaticalisation et changement linguistique
Authors: BOLLY CATHERINE
Published: July 2011

L'objectif de cet article est de montrer comment le marqueur parenthétiquetu voiss'est pragmaticalisé au cours des siècles. Afin de déterminer s'il existe une corrélation entre l'émergence de contextes syntaxiques et l'apparition de sens nouveaux pour ce marqueur, nous avons adopté une méthode d'analyse, en diachronie, de données de corpus pseudo-orales. Après avoir mis en exergue les résultats d'analyse en termes de déplacement sémantique et de complexification syntaxique, l'article montrein fineen quoi le recours à la grammaticalisation semble insuffisant pour expliquer l'évolution des parenthétiques et propose d'inscrire ce processus dans la perspective plus large du changement linguistique.
Zen and the art of formalisation
Authors: ASPERTI ANDREA , AVIGAD JEREMY
Published: July 2011

N. G. de Bruijn, now professor emeritus of the Eindhoven University of Technology, was a pioneer in the field of interactive theorem proving. From 1967 to the end of the 1970's, his work on the Automath system introduced the architecture that is common to most of today's proof assistants, and much of the basic technology. But de Bruijn was a mathematician first and foremost, as evidenced by the many mathematical notions and results that bear his name, among them de Bruijn sequences, de Bruijn graphs, the de Bruijn–Newman constant, and the de Bruijn–Erdös theorem. The quotation above is thus interesting not because it is a reflection on his expertise in formal verification, but, rather, of his convictions as a working mathematician.
A formal proof of Pick's Theorem
Authors: HARRISON JOHN
Published: July 2011

Pick's Theorem relates the area of a simple polygon with vertices at integer lattice points to the number of lattice points in its inside and boundary. We describe a formal proof of this theorem using the HOL Light theorem prover. As sometimes happens for highly geometrical proofs, the formalisation turned out to be more work than initially expected. The difficulties arose mostly from formalising the triangulation process for an arbitrary polygon.
A formal study of Bernstein coefficients and polynomials
Authors: BERTOT YVES , GUILHOT FRÉDÉRIQUE , MAHBOUBI ASSIA
Published: July 2011

Bernstein coefficients provide a discrete approximation of the behaviour of a polynomial inside an interval. This can be used, for example, to isolate the real roots of polynomials. We prove formally a criterion for the existence of a single root in an interval and the correctness of the de Casteljau algorithm for computing Bernstein coefficients efficiently.
Formalising Overlap Algebras in Matita
Authors: SACERDOTI COEN CLAUDIO , TASSI ENRICO
Published: July 2011

We describe some formal topological results, formalised in Matita 1/2, presented in predicative intuitionistic logic and in terms of Overlap Algebras.

Overlap Algebras are new algebraic structures designed to ease reasoning about subsets in an algebraic way within intuitionistic logic. We find that they also ease the formalisation of formal topological results in an interactive theorem prover.

Our main result is the existence of a functor between two categories of ‘generalised topological spaces’, one with points (Basic Pairs) and the other point-free (Basic Topologies). This formalisation is part of a wider scientific collaboration with the inventor of the theory, Giovanni Sambin. His goal is to verify in what sense his theory is ‘implementable’, and to discover what problems may arise in the process. We check that all intermediate constructions respect the stringent size requirements imposed by predicative logic. The formalisation is quite unusual, since it has to make explicit size information that is often hidden.

We found that the version of Matita used for the formalisation was largely inappropriate. The formalisation drove several major improvements of Matita that will be integrated in the next major release (Matita 1.0). We show some motivating examples, taken directly from the formalisation, for these improvements. We also describe a possibly sub-optimal solution in Matita 1/2, which is exploitable in other similar systems. We briefly discuss a better solution available in Matita 1.0.
A pluralist approach to the formalisation of mathematics
Authors: ADAMS ROBIN , LUO ZHAOHUI
Published: July 2011

We present a programme of research forpluralist formalisations, that is, formalisations that involve proving results in more than one foundation.

A foundation consists of two parts: a logical part, which provides a notion of inference, and a non-logical part, which provides the entities to be reasoned about. An LTT is a formal system composed of two such separate parts. We show how LTTs may be used as the basis for a pluralist formalisation.

We show how different foundations may be formalised as LTTs, and also describe a new method for proof reuse. If we know that a translation Φ exists between two logic-enriched type theories (LTTs)SandT, and we have formalised a proof of a theorem α inS, we may wish to make use of the fact that Φ(α) is a theorem ofT. We show how this is sometimes possible by writing a proof scriptMΦ. For any proof scriptMαthat proves a theorem α inS, if we changeMαso it first importsMΦ, the resulting proof script will still parse, and will be a proof of Φ(α) inT.

In this paper, we focus on the logical part of an LTT-framework and show how the above method of proof reuse is done for four cases of Φ: inclusion, the double negation translation, theA-translation and the Russell–Prawitz modality. This work has been carried out using the proof assistant Plastic.
Improved early results with cavopulmonary connections
Authors: Mott Antonio R. , Spray Thomas L. , Gaynor J. William , Godinez Rodolfo I. , Nicolson Susan C. , Steven James M. , DeCampli William M. , Schears Gregory J. , Wernovsky Gil
Published: July 2011

Background: We describe the recent results in a large cohort of patients with functionally single ventricle who underwent various modifications of cavopulmonary connections.Methods: Using the database at our institution, we identified all children who underwent cavopulmonary connection operations between June 1995 and June 1997. Demographic data, surgical history, and perioperative course were reviewed.Results: We performed 130 consecutive operations in 113 patients. The procedures included superior cavopulmonary connections in the form of the HemiFontan procedure in 45 instances, and bidirectional Glenn procedures in 11, and bilateral superior cavopulmonary connections in 7. The median age of these patients was 7.0 months. We completed Fontan operations using a fenestrated lateral tunnel on 47 occasions, and using an extracardiac conduit 9 times, 5 of which were fenestrated. A lateral tunnel without fenestration was constructed inone patient. The median age for these procedures was 19.5 months. In the remaining 10 instances, we revised Fontan procedures at a median age of 8 years. Diagnoses included hypoplastic left heart syndrome in 43 patients, double outlet right ventricle in 22, heterotaxy in 13, tricuspid atresia in 13, and a miscellaneous group accounting for the other 22. One death (0.7%) occurred within 30 days of surgery. Clinical seizures occurred in 7 children (5.3%), 6 had no residual neurologic deficits. Atrial pacing was needed in 14 children (10.7%) because of transient junctional rhythm, and 2 received treatment for supraventricular tachycardia. Pleural effusions were diagnosed radiographically after 31 of 130 (24%) procedures. Diuretic therapy resolved the effusion in 21 of these, with only 6 children requiring thoracostomy catheter drainage, and 4 undergoing thoracentesis alone. The median length of stay on the intensive care unit was 2 days, with a range from 1 to 30 days, and median stay in hospital was 6 days, with a range from 3 to 58 days.Conclusion: Mortality and perioperative morbidity after cavopulmonary connections have decreased dramatically in the current era. The long-term results of staged reconstruction for functionally single ventricle, nonetheless, await ongoing study.
Coagulation profile, hepatic function, and hemodynamics following Fontan-type operations
Authors: Tomita Hideshi , Yamada Osamu , Ohuchi Hideo , Ono Yasuo , Arakaki Yoshio , Yagihara Toshikatsu , Echigo Shigeyuki
Published: July 2011

We analyzed retrospectively the relationship between coagulation profile, and either hepatic function or hemodynamics, in patients who had undergone a Fontan-type procedure, comparing them, first, with a control group of 12 patients without significant hemodynamic abnormality, and, second, with a group of 14 patients who had not undergone a Fontan procedure, but whose mean right atrial pressure exceeded 8 mmHg. Follow-up catheterization had been performed in all 30 patients submitted to the Fontan-type operation. Prothrombin time, and factor XIII, were significantly lower in those who had undergone the Fontan procedure than in the other groups. Those submitted to the Fontan operation also had lower levels of protein C than controls, and their levels of plasminogen were lower than the patients with high right atrial pressure. Both aspartate aminotransferase and alanine aminotransferase were higher in those undergoing the Fontan procedure than in the other groups, while gamma-glutamyltranspeptidase in these patients was higher than in the control group. Mean right atrial pressure was highest in those under-going the Fontan procedure, while cardiac index was lowest. Prothrombin time was correlated to some extent with aspartate aminotransferase, mean right atrial pressure, and cardiac index. Protein C correlated with both aspartate aminotransferase and mean right atrial pressure, while factor XIII correlated with alanine aminotransferase, mean right atrial pressure, and cardiac index. Aspartate aminotransferase, alanine aminotransferase, and gamma-glutamyltranspeptidase, parameters of hepatic function, correlated significantly with mean right atrial pressure. In those who had undergone the Fontan procedure, decreased synthesis of pro-and anti-coagulant factors is a risk factor for both thrombosis and bleeding. Abnormal hemodynamics, in the absence of a right sided pumping chamber, may predispose to subclinical hepatic dysfunction, leading to selective disturbances of protein synthesis.
Unusual totally anomalous pulmonary venous connection in right isomerism and functionally univentricular heart
Authors: Chowdhury Ujjwal K. , Kothari Shyam S. , Airan Balram
Published: July 2011

We report a rare variation in the pattern of totally anomalous pulmonary venous connection in that two vertical veins drained into the left brachiocephalic vein from a common pulmonary venous confluence. The child had associated right isomerism and functionally univentricular heart. Awareness of this possibility may avoid a reoperation or even death.
Successful occlusion of a coronary arteriovenous fistula using an Amplatzer™ duct occluder
Authors: Sadiq Masood , Wilkinson James L , Qureshi Shakeel A
Published: July 2011

In an 11-year old boy with a large coronary arteriovenous fistula between the left coronary artery and the right atrium, we achieved successful closure using a 10–8 Amplatzer Duct Occluder introduced from the right internal jugular vein. Angiography 6 weeks later showed complete occlusion of the fistula, with normal opacification of the left coronary arterial system. This technique may be used as an alternative to coils and surgery in selected patients.
Rupture of pulmonary aneurysms in association with long-standing Waterston shunts
Authors: Hull Dearbhla A. , Shinebourne Elliot , Gerlis Leon , Nicholson Andrew G. , Sheppard Mary N.
Published: July 2011

Anastomosis of the ascending aorta to the right pulmonary artery, the so-called Waterston shunt, was undertaken as a palliative procedure for children with cyanotic congenital heart disease due to obstruction of the pulmonary outflow tract with reduced pulmonary blood flow. We present the clinico-pathological correlations in two patients who underwent construction of Waterston shunts as neonates, and subsequently died of ruptured pulmonary aneurysms in adult life. Rupture should, therefore, be recognized as a late complication of this procedure, and be considered in the long-term follow-up of such patients, especially when the shunted lung is hypertensive.
Open-domain textual question answering techniques
Authors: HARABAGIU SANDA M. , MAIORANO STEVEN J. , PAŞCA MARIUS A.
Published: July 2011

Textual question answering is a technique of extracting a sentence or text snippet from a document or document collection that responds directly to a query. Open-domain textual question answering presupposes that questions are natural and unrestricted with respect to topic. The question answering (Q/A) techniques, as embodied in today's systems, can be roughly divided into two types: (1) techniques for Information Seeking (IS), which localize the answer in vast document collections; and (2) techniques for Reading Comprehension (RC) that answer a series of questions related to a given document. Although these two types of techniques and systems are different, it is desirable to combine them for enabling more advanced forms of Q/A. This paper discusses an approach that successfully enhanced an existing IS system with RC capabilities. This enhancement is important because advanced Q/A, as exemplified by the ARDA AQUAINT program, is moving towards Q/A systems that incorporate semantic and pragmatic knowledge enabling dialogue-based Q/A. Because today's RC systems involve a short series of questions in context, they represent a rudimentary form of interactive Q/A which constitutes a possible foundation for more advanced forms of dialogue-based Q/A.
Statins and myocardial remodelling: cell and molecular pathways
Authors: Porter Karen E. , Turner Neil A.
Published: July 2011

The advent of statins has revolutionised the treatment of patients with raised plasma cholesterol and increased cardiovascular risk. However, the beneficial effects of this class of drugs are far greater than would be expected from lowering of cholesterol alone, and they appear to offer cardiovascular protection at multiple levels, primarily as a result of their pleiotropic activity. Indeed, their favourable effects on the heart seem to be mediated in part through reduced prenylation and subsequent inhibition of small GTPases, particularly those of the Rho family. Such statin-mediated effects are manifested by reduced onset of heart failure and improvements in cardiac dysfunction and remodelling in heart failure patients. Experimental studies have shown that statins mediate their effects on the two major resident cell types of the heart–cardiomyocytes and cardiac fibroblasts–and thus facilitate improvement of adverse remodelling of ischaemic or non-ischaemic aetiology. This review examines evidence for the cellular effects of statins in the heart, and discusses the underlying molecular mechanisms at the level of the cardiomyocyte (hypertrophy, cell death and contractile function) and the cardiac fibroblast (differentiation, proliferation, migration and extracellular matrix synthesis). The prospects for future therapies and ongoing clinical trials are also summarised.
High power density SiGe millimeter-wave power amplifiers
Authors: Farmer Thomas J. , Darwish Ali , Huebschman Benjamin , Viveiros Edward , Zaghloul Mona E.
Published: July 2011

This paper presents measured results for two-stage and three-stage high-voltage/high-power (HiVP) amplifiers implemented in a commercial 0.12 μm silicon germanium (SiGe) heterojunction bipolar transistor (HBT) bipolar Complementary Metal Oxide Semiconductor (BiCMOS) process at millimeter wave. The HiVP configuration provides a new tool for millimeter-wave silicon designers to achieve large output voltage swings, high output power density, customizable bias, and a way to minimize, if not eliminate, matching circuitry at millimeter-wave frequencies. The two-stage amplifier has achieved a PSAT = 5.41 dBm with a power added efficiency (PAE) of 8.06% at center frequency 30 GHz. The three-stage amplifier has achieved a PSAT = 8.85 dBm with a PAE of 11.35% with a total chip area of 0.068 mm2 at center frequency 30 GHz. Simulation, layout, fabrication, and measurement results are presented in this paper.
Accurate modeling and optimization of microwave circuits and devices using adaptive neuro-fuzzy inference system
Authors: Harkouss Youssef
Published: July 2011

In this paper, an accurate neuro-fuzzy-based model is proposed for efficient computer-aided design (CAD) modeling and optimization of microwave circuits and devices. The adaptive neuro-fuzzy inference system (ANFIS) approach is used to determine the scattering parameters of a microstrip filter and is applied to the optimization design of this microstrip filter. The ANFIS has the advantages of expert knowledge of fuzzy inference system and learning capability of artificial neural networks. The neuro-fuzzy model has been trained and tested with different sets of input/output data. Finally, different results, which confirm the validity of the proposed model, are reported.
Design and characterization of an active recovering mechanism for high-performance RF MEMS redundancy switches
Authors: Solazzi Francesco , Tazzoli Augusto , Farinelli Paola , Faes Alessandro , Mulloni Viviana , Margesin Benno , Meneghesso Gaudenzio
Published: July 2011

This paper presents the design and characterization of an active push/pull toggle RF micro-electro-mechanical systems (MEMS) switch for satellite redundancy networks. The actively controlled pull-up mechanism allows for extended restoring capabilities of the switch in case of ON-state stiction. As a proof of concept an active push/pull MEMS capacitive switch was modeled, designed, and manufactured in shunt configuration on a 50 Ω coplanar transmission line. RF measurement results show a return loss better than 15 dB in the 0.1–40 GHz range and an insertion loss better than 0.5 dB over the same range. The restoring capability of the switch was experimentally proved up to 9 h, and a predictive model was proposed for the estimation of the switch time to failure.
Sensitivity of the Northern Humboldt Current System nearshore modeled circulation to initial and boundary conditions
Authors: Echevin Vincent , Colas Francois , Chaigneau Alexis , Penven Pierrick
Published: July 2011

The influence of the eastern Paciﬁc equatorial circulation on the dynamics of the Northern Humboldt Current System is studied using an eddy‐resolving regional circulation model forced by boundary conditions from three distinct ocean general circulation models. The seasonal variability of the modeled nearshore circulation and the mesoscale activity are contrasted in order to evaluate the role of the density forcing. The seasonal variability of the surface and subsurface alongshore currents strongly depends on the amplitude and timing of the seasonal eastward propagating equatorial waves. The equatorward flow and upwelling intensity are also impacted by nonlinear processes, such as the seasonal generation of nearshore mesoscale eddies, which create alongshore pressure gradients modulating the surface current. Boundary conditions affect differently the intensity and phase of the eddy kinetic energy, as baroclinic instability is triggered by coastal waves during austral summer and fall, whereas it is sustained by the wind‐driven upwelling during austral winter.
Comparative analysis of bed resistance partitioning in high‐gradient streams
Authors: David Gabrielle C. L. , Wohl Ellen , Yochum Steven E. , Bledsoe Brian P.
Published: July 2011

Total flow resistance can be partitioned into its components of grain (ffgrain), form (ffstep), wood (ffwood), and spill (ffspill) resistance. Methods for partitioning flow resistance developed for low‐gradient streams are commonly applied to high‐gradient systems. We examined the most widely used methods for calculating each component of resistance, along with the limitations of these methods, using data gathered from 15 high‐gradient (0.02 < S0 < 0.195) step‐pool, cascade, and plane‐bed reaches in Fraser Experimental Forest. We calculated grain resistance using three equations that relate relative submergence (R/Dm) to ffgrain as well as using an additive drag approach. The drag approach was also used for calculating ffwood and ffstep. The ffgrain contributed the smallest amount toward all reaches at all flows, although the value varied with the method used. The Parker and Peterson (1980) equation using D90 best represented ffgrain at high flows, whereas the Keulegan (1938) equation using D50 best characterized ffgrain at base flows, giving a lower bound for grain resistance. This suggests that ffgrain may be better represented if two grain sizes are used to calculate this component of resistance. The drag approach, which is used to calculate wood resistance, overestimated the significance of individual logs in the channel. The contribution of ffspill was reduced at higher flows when form drag around the step is accounted for at higher flows. We propose a method for evaluating the contribution of ffstep that accounts for form drag around the steps once they are submerged at higher flows. We evaluated the potential sources of error for the estimation of each component of resistance. Determination of the drag coefficient was one of the major sources of error when calculating drag around wood, steps, or boulders.
Nonparametric error model for a high resolution satellite rainfall product
Authors: Gebremichael Mekonnen , Liao Gong‐Yi , Yan Jun
Published: July 2011

Characterization of the error distribution of satellite rainfall product has important benefits in practical applications such as rainfall‐runoff modeling. Most operational satellite rainfall products are, however, still deterministic and lack any estimate of their uncertainty. Given a high resolution satellite rainfall estimate, it is of interest to know the distribution of the actual rainfall. We develop a new nonparametric model that generates the distribution of actual rainfall values for any given satellite rainfall estimate. The model handles the conditional distribution as the mixture of a positive continuous distribution and a point mass at zero. We fitted and validated the model using rain gauge‐adjusted ground‐based radar rainfall (representing actual rainfall) and CMORPH satellite rainfall estimates (representing high‐resolution satellite rainfall), available at a resolution of 0.25° × 0.25° and 3‐hourly, over a domain of 6.25° × 6.25° in the southern United States where the radar rainfall products are considered to be of high quality. The modeling approach can be replicated in other regions.
‘The Molecular Biology of the Hamburger’
Authors: Jacobs Howy
Published: July 2011

McDonald's Corporation has entered the higher education marketplace by sponsoring a university course in England. Inspired by this development, Howy proposes his own spiced‐up degree course in fast‐food biotechnology.
Treasure our rarities
Authors: van Helden Paul
Published: July 2011

When scientists sift through data or make experimental observations they often filter out odd results. Yet, these outliers can actually be the most interesting data points, which lead to new insights.
The association of phosphoinositide 3‐kinase enhancer A with hepatic insulin receptor enhances its kinase activity
Authors: Chan Chi Bun , Liu Xia , He Kunyan , Qi Qi , Jung Dae Y , Kim Jason K , Ye Keqiang
Published: July 2011

Dysfunction of hepatic insulin receptor tyrosine kinase (IRTK) causes the development of type 2 diabetes. However, the molecular mechanism regulating IRTK activity in the liver remains poorly understood. Here, we show that phosphoinositide 3‐kinase enhancer A (PIKE‐A) is a new insulin‐dependent enhancer of hepatic IRTK. Liver‐specific Pike‐knockout (LPKO) mice display glucose intolerance with impaired hepatic insulin sensitivity. Specifically, insulin‐provoked phosphoinositide 3‐kinase/Akt signalling is diminished in the liver of LPKO mice, leading to the failure of insulin‐suppressed gluconeogenesis and hyperglycaemia. Thus, hepatic PIKE‐A has a key role in mediating insulin signal transduction and regulating glucose homeostasis in the liver.
Our microbial selves: what ecology can teach us
Authors: Gonzalez Antonio , Clemente Jose C , Shade Ashley , Metcalf Jessica L , Song Sejin , Prithiviraj Bharath , Palmer Brent E , Knight Rob
Published: July 2011

Advances in DNA sequencing have allowed us to characterize microbial communities—including those associated with the human body—at a broader range of spatial and temporal scales than ever before. We can now answer fundamental questions that were previously inaccessible and use well‐tested ecological theories to gain insight into changes in the microbiome that are associated with normal development and human disease. Perhaps unsurprisingly, the ecosystems associated with our body follow trends identified in communities at other sites and scales, and thus studies of the microbiome benefit from ecological insight. Here, we assess human microbiome research in the context of ecological principles and models, focusing on diversity, biological drivers of community structure, spatial patterning and temporal dynamics, and suggest key directions for future research that will bring us closer to the goal of building predictive models for personalized medicine.
A general model of continuous character evolution
Authors: Boettiger Carl
Published: July 2011

I present a general model for continuous character evolution, review some of the common challenges that emerge in such complex methods and review strategies for handling them.
The trapping of N2 molecules and the reduction in its bonding length in Ge(001) due to N2+ ion implantation
Authors: Lee Young Mi , Yun Won Seok , Hong Soon Cheol , Jung Min-Cherl
Published: July 2011

To find the cause of N2 → N + N dissociation in Ge(001) at low temperature, the N2+ ion implantation process was carried out on a Ge(001) substrate, followed by rapid thermal annealing (RTA). After N2+ ion implantation, the presence of N2 molecules and the chemical states of GeNx were determined using near-edge x-ray absorption of fine structure (NEXAFS) and high-resolution x-ray photoelectron spectroscopy with synchrotron radiation, respectively. Rapid thermal annealing was performed at 600 °C, after which a change in chemical state from the chemically meta-stable state of GeNx to the stable state of Ge3N4 was observed. In addition, the intensity of the N2 vibration mode peak in NEXAFS was decreased, although it did not completely disappear. To explain the N2 →N + N dissociation at the low temperature, a first-principle calculation for N2 bonding length was performed in both vacuum and Ge(001) states. We confirmed that implantation resulted in the trapping of N2 molecules in Ge(001), and their bonding length was changed from 1.117 to 1.205 Å at a difference energy of 2.529 eV. It was assumed that the relaxed change in the N2 bonding length originated from the dissociation of N2 molecules at low temperature.
Numerical simulation of fluid flow around a vertical-axis turbine
Authors: Abraham J. P. , Mowry G. S. , Plourde B. P. , Sparrow E. M. , Minkowycz W. J.
Published: July 2011

A novel, vertical-axis turbine has been designed to meet a specific power-generation need. It is intended that the turbine will provide local electricity to off-grid cellular communication towers. It is intended that the turbine will reduce or eliminate the use of diesel-power generation for these towers and result in a reduction of operating costs and greenhouse gas emissions. The design effort has had two main stages. First, a prototype turbine blade was designed and tested in a large-scale wind tunnel. The initial design was based on available literature information. Subsequently, numerical simulations of the fluid flow patterns around the turbine blade were used to create improvements to the design. These improvements include the use of venting apertures in the turbine blade to reduce negative drag and thrust loading and the use of caps to improve power-generation efficiency. Through numerical modeling, significant improvements in performance were achieved resulting in a viable turbine design.
Upgrades to the Auburn linear experiment for instability studies
Authors: Eadon A. C. , Tejero E. , DuBois A. , Thomas E.
Published: July 2011

The Auburn linear experiment for instability studies (ALEXIS) is a laboratory plasma physics experiment that is designed to investigate the role of spatially non-uniform E × B drifts using a magnetized cylindrical plasma column. This paper discusses the recent upgrades to the ALEXIS device, including improvements to the plasma source, gas management systems, and diagnostic suite.
Predictive modelling for EAST divertor operation
Authors: Chen YiPing
Published: July 2011

The predictive modelling study of the divertor operation in EAST tokamak [B. Wan et al., Nucl. Fusion 49, 104011 (2009)] with double null (DN) configuration is carried out by using the two-dimensional edge plasma code B2.5-SOLPS5.0 [D. P. Coster, X. Bonnin et al., J. Nucl. Mater. 337–339, 366 (2005)]. The modelling study includes the particle and power balance in the scrape-off-layer (SOL), the operation parameters of plasma density, temperature and plasma heat fluxes at the separatrix, the target plates and the wall, and the effect of the gas puffing, drifts, and vertical target plate on the divertor operation. The fluid model for the edge plasma is applied using the real magnetohydrodynamic (MHD) equilibrium from the MHD equilibrium code EFIT [L. L. Lao et al., Nucl. Fusion 25, 1611 (1985)] and the real divertor geometry in the device. Before EAST tokamak starts its experimental programme of divertor operation, the modelling plays an important role in the design of its experimental programme and the optimization of the divertor operation parameters. Based on the modelling results, EAST divertor can operate over a large wide of plasma parameters with different regimes. For a heating power of 8 MW and an edge density at core-SOL interface Nedge = 0.8 × 10191/m3 and Nedge = 1.3 × 10191/m3, the EAST divertor begins access to the high recycling operation regime at the outer and inner target plates, respectively, where the plasma temperature and the heat fluxes at the target plates decrease. The gas puffing can increase the plasma density at the separatrix and trigger the transition from the high recycling operation into detachment at the target plates. When E × B and B × ▿B drifts are taken into account, the asymmetry of plasma parameters and heat fluxes between up-down SOLs can be found. The vertical target plate in EAST divertor can reduce the peak values of heat fluxes at the target plate and enables detachment at lower plasma density. The divertor with the vertical target plate can be considered as a possible option for EAST divertor upgrade in the future.
Global Hall-MHD simulations of magnetorotational instability in a plasma Couette flow experiment
Authors: Ebrahimi F. , Lefebvre B. , Forest C. B. , Bhattacharjee A.
Published: July 2011

Global MHD and Hall-MHD numerical simulations relevant to the Madison plasma Couette flow experiment (MPCX) have been performed using the extended MHD code NIMROD. The MPCX has been constructed to study the magnetorotational instability (MRI) in a plasma. The two-fluid Hall effect, which is relevant to some astrophysical situations such as protostellar disks, is also expected to be important in the MPCX. Here, we first derive the local Hall dispersion relation including viscosity, extending earlier work by Balbus and Terquem [Astrophys. J. 552, 235 (2001)]. The predictions of the local analysis are then compared with nonlocal calculations of linear stability of the MRI for a parameter range relevant to the MPCX. It is found that the MHD stability limit and mode structure are altered by the Hall term, and nonlocal analysis is necessary to obtain quantitatively reliable predictions for MPCX. Two-fluid physics also significantly changes the nonlinear evolution and saturation of the axisymmetric MRI. Both the Reynolds and Maxwell stresses contribute significantly to momentum transport. In the Hall regime, when the magnetic field is parallel to the rotation axis, the Maxwell stress is larger than the Reynolds stress (similar to the MHD regime). However, when the magnetic field is antiparallel to the rotation axis in the Hall regime, the Reynolds stress is much larger than the Maxwell stress. To further study the role of non-axisymmetric modes, we have also carried out fully nonlinear MHD computations. Non-axisymmetric modes play an increasingly important role as the magnetic Reynolds number increases and grow to large amplitudes in a saturated turbulent state.
The characterization of nitrogen doped TiO2 photoanodes and its application in the dye sensitized solar cells
Authors: Zhang Jing , Sun Qiang , Zheng Jun , Zhang Xueni , Cui Yanzheng , Wang Peiqing , Li Weiping , Zhu Yuejin
Published: July 2011

In this paper, nitrogen doped TiO2 photoanodes were achieved by calcining the mixture of urea and the commercial P25 nanoparticles slurry. Its application in the dye sensitized solar cells was examined. X-ray photoelectron spectroscopy indicated the N substituted the O atoms and formed N-Ti-O bonds. The optical band gap of the doped TiO2 photoanodes was reduced. From the photoelectrochemical experiments, it is known that nitrogen doping introduced new energy states above the valence band of the TiO2 photoanode, which lead to the visible light response and increased electron density. Optimized photo to electric conversion efficiency of the DSSC 6.71% is obtained with short current density (Jsc) of 14.3 mA cm−2, open circuit voltage (Voc) of 0.669 V and fill factor (FF) of 0.706 by the nitrogen doping, compared with 5.31% of the undoped one (Jsc of 13.2 mA cm−2, Voc of 0.638 V and FF of 0.624) at 0.99sun AM1.5, which is mainly due to the energy band structure change and partly the morphology change of the photoanode.
Determination of 3D flame surface density variables from 2D measurements: Validation using direct numerical simulation
Authors: Chakraborty Nilanjan , Hawkes Evatt R.
Published: July 2011

Three-dimensional compressible direct numerical simulation (DNS) data of freely propagating statistically planar turbulent premixed flames have been used to assess the accuracy of the isotropy- derived correction factors, which relate the two-dimensional projections of the different terms of the Reynolds averaged flame-surface density (FSD) transport equation with their corresponding actual three-dimensional counterparts for different values of Karlovitz number Ka, Lewis number Le, heat release parameter τ, and turbulent Reynolds number Ret. It is shown that the isotropic distribution of the surface area weighted probability density function (pdf) of the angle φ between the normal vectors on the measurement plane and on the flame surface provides a simple algebraic relation between the generalised FSDs evaluated in two and three dimensions (i.e., Σ2D and Σ3D), irrespective of the values of Ka,τ,Le, and Ret. Isotropic relations between two-dimensional and three-dimensional counterparts of the surface-averaged curvature and the FSD propagation term are also found to work well for all the values of Ka,τ,Le, and Ret considered in this study. However, the relations between the value obtained from two-dimensional projection and the actual three-dimensional value for the tangential strain rate and curvature terms in the FSD transport equation work well only for the high values of turbulent Reynolds number. The reasons behind the disagreement between the predictions of the relations derived based on isotropy arguments for both the tangential strain rate and curvature terms of the FSD transport equation are explained in detail. It is found that the threshold value of Ret above which the assumption of isotropy yields an accurate relation between two-dimensional projection and three-dimensional values for the tangential strain rate and curvature terms of the FSD transport equation depends on the values of heat release parameter, Lewis number, and the regime of the prevailing combustion process.
Dark and grey compressional dispersive Alfvén solitons in plasmas
Authors: Shukla P. K. , Eliasson B. , Stenflo L.
Published: July 2011

The amplitude modulation of compressional dispersive Alfvén (CDA) waves in a low-β plasma is considered. It is shown that the dynamics of modulated CDA waves is governed by a cubic nonlinear Schrödinger equation, which depicts the formation of a dark/grey envelope CDA soliton.
Effect of nanotube-length on the transport properties of single-file water molecules: Transition from bidirectional to unidirectional
Authors: Su Jiaye , Guo Hongxia
Published: July 2011

We use molecular dynamics (MD) simulations to study the transport of single-file water molecules through carbon nanotubes (CNTs) with various lengths in an electric field. Most importantly, we find that even the water dipoles inside the CNT are maintained along the field direction, a large amount of water molecules can still transport against the field direction for short CNTs, leading to a low unidirectional transport efficiency (η). As the CNT length increases, the efficiency η will increase remarkably, and achieves the maximum value of 1.0 at or exceeding a critical CNT length. Consequently, the transition from bidirectional to unidirectional transport is observed and is found to be relevant to thermal fluctuations of the two reservoirs, which is explored by the interaction between water molecules inside and outside the CNT. We also find that the water flow vs CNT length follows an exponential decay of f  ∼  exp ( − L/L0), and the average translocation time of individual water molecules yields to a power law of τtrans  ∼  Lυ, where L0 and ν are constant and slightly depend on the field strength. We further compare our results with the continuous-time random-walk (CTRW) model and find that the water flow can also be described by a power law of f  ∼  L−μ modified from CTRW. Our results provide some new physical insights into the biased transport of single-file water molecules, which show the feasibility of using CNTs with any length to pump water in an electric field. The mechanism is important for designing efficient nanofluidic apparatuses.
Coil-to-globule transition by dissipative particle dynamics simulation
Authors: Guo Jiayi , Liang Haojun , Wang Zhen-Gang
Published: July 2011

The dynamics of a collapsing polymer under a temperature quench in dilute solution is investigated by dissipative particles dynamics. Hydrodynamic interactions and many-body interaction are preserved naturally by incorporating explicit solvent particles in this approach. Our simulation suggests a four-stage collapse pathway: localized clusters formation, cluster coarsening in situ, coarsening involving global backbone conformation change into a crumpled globule, and compaction of the globule. For all the quench depths and chain lengths used in our study, collapse proceeds without the chain getting trapped in a metastable “sausage” configuration, as reported in some earlier studies. We obtain the time scales for each of the first three stages, as well as its scaling with the quench depths ξ and chain lengths N. The total collapse time scales as τc ∼ ξ−0.46 ± 0.04N0.98 ± 0.09, with the quench depth and degree of polymerization.
Note: Mounting ultra-high vacuum windows with low stress-induced birefringence
Authors: Solmeyer Neal , Zhu Kunyan , Weiss David S.
Published: July 2011

We have developed a way to mount ultra-high vacuum windows onto standard ConFlat® vacuum systems with very low stress-induced birefringence. Each window is sealed to a stainless steel flange with a compressed indium wire, and that flange is connected to a vacuum chamber with another indium seal. We find that deformation of a standard ConFlat flange during indium sealing dominates the stress on the window, so an extra-rigid flange is needed for minimal birefringence. With this mounting scheme, the typical residual birefringence is Δn = 2.3 × 10−7 and is unchanged by a 120 °C bake.
Communication: Linear-expansion shooting techniques for accelerating self-consistent field convergence
Authors: Wang Yan Alexander , Yam Chi Yung , Chen Ya Kun , Chen GuanHua
Published: July 2011

Based on the corrected Hohenberg-Kohn-Sham total energy density functional [Y. A. Zhang and Y. A. Wang, J. Chem. Phys. 130, 144116 (2009)]10.1063/1.3104662, we have developed two linear-expansion shooting techniques (LIST)– direct LIST (LISTd) and indirect LIST (LISTi), to accelerate the convergence of self-consistent field (SCF) calculations. Case studies show that overall LISTi is the most robust and efficient algorithm for accelerating SCF convergence, whereas LISTd is advantageous in the early stage of an SCF process. More importantly, LISTi outperforms Pulay's direct inversion in the iterative subspace (DIIS) [P. Pulay, J. Comput. Chem. 3, 556 (1982)]10.1002/jcc.540030413 and its two recent improvements, energy-DIIS [K. N. Kudin, G. E. Scuseria, and E. Cancès, J. Chem. Phys. 116, 8255 (2002)]10.1063/1.1470195 and augmented Roothaan-Hall energy-DIIS [X. Hu and W. Yang, J. Chem. Phys. 132, 054109 (2010)]10.1063/1.3304922.
ATP-sensitive potassium channel (K
ATP
)–dependent regulation of cardiotropic viral infections
Authors: Eleftherianos Ioannis , Won Sungyong , Chtarbanova Stanislava , Squiban Barbara , Ocorr Karen , Bodmer Rolf , Beutler Bruce , Hoffmann Jules A. , Imler Jean-Luc
Published: July 2011

The effects of the cellular environment on innate immunity remain poorly characterized. Here, we show that in
Drosophila
ATP-sensitive potassium channels (K
ATP
) mediate resistance to a cardiotropic RNA virus, Flock House virus (FHV). FHV viral load in the heart rapidly increases in K
ATP
mutant flies, leading to increased viremia and accelerated death. The effect of K
ATP
channels is dependent on the RNA interference genes
Dcr-2
,
AGO2
, and
r2d2
, indicating that an activity associated with this potassium channel participates in this antiviral pathway in
Drosophila
. Flies treated with the K
ATP
agonist drug pinacidil are protected against FHV infection, thus demonstrating the importance of this regulation of innate immunity by the cellular environment in the heart. In mice, the Coxsackievirus B3 replicates to higher titers in the hearts of
mayday
mutant animals, which are deficient in the Kir6.1 subunit of K
ATP
channels, than in controls. Together, our data suggest that K
ATP
channel deregulation can have a critical impact on innate antiviral immunity in the heart.
Attention during Lectures: Beyond Ten Minutes
Authors: Wilson Karen , Korn James H.
Published: July 2011

Many authors claim that students' attention declines approximately 10 to 15 min into lectures. To evaluate this claim, we reviewed several types of studies including studies of student note taking, observations of students during lectures, and self-reports of student attention, as well as studies using physiological measures of attention. We found that the research on which this estimate is based provides little support for the belief that students' attention declines after 10 to 15 min. Most studies failed to account for individual differences in attention. Our findings indicate that instructors should take into account individual differences in student attention when lecturing and determine whether students are recording the relevant content of the lecture in their notes.
HOMER as an Acronym for the Scientific Method
Authors: Lakin Jessica L. , Giesler R. Brian , Morris Kathryn A. , Vosmik Jordan R.
Published: July 2011

Mnemonic strategies, such as acronyms, effectively increase student retention of course material. We present an acronym based on a popular television character to help students remember the basic steps in the scientific method. Our empirical evaluation of the acronym revealed that students found it to be enjoyable, useful, and worthy of use in future courses.