bluuebunny/crossref_metadata_2025 huggingface dataset:
Absence of splash singularities for surface quasi-geostrophic sharp fronts and the Muskat problem
Authors: Gancedo Francisco , Strain Robert M.
Published: December 2013

Significance

The formation of singularities for the evolution of the interphase between fluids with different characteristics is a fundamental problem in mathematical fluid mechanics. These contour dynamics problems are given by fundamental fluid laws such as Euler’s equation, Darcy’s law, and surface quasi-geostrophic (SQG) equations. This work proves that contours cannot intersect at a single point while the free boundary remains smooth—a “splash singularity”—for either the sharp front SQG equation or the Muskat problem. Splash singularities have been shown for water waves. The SQG equation has seen numerical evidence of single pointwise collapse with curvature blow-up. We prove that maintaining control of the curvature will remove the possibility of pointwise interphase collapse, confirming the numerical experiments.
2 Introduction to Lagrangian Mechanics
Authors: Johns Oliver Davis
Published: December 2013

This chapter argues that modern analytical mechanics began with the work of the eighteenth-century mathematicians who elaborated Newton's ideas. Without changing Newton's fundamental principles, Euler, Laplace, and Lagrange developed elegant computational methods for the increasingly complex problems to which Newtonian mechanics was being applied. The Lagrangian formulation of mechanics is merely an abstract way of writing Newton's second law. When simple Cartesian coordinates are replaced by the most general variables capable of describing the system adequately, the Lagrange equations do not change. The vector methods fail when a mechanical system is described by systems of coordinates much more general than the standard curvilinear ones. The Lagrangian method frees one from the task of keeping track of the components of force vectors and the identities of the particles upon which they act.
4 Introduction to Hamiltonian Mechanics
Authors: Johns Oliver Davis
Published: December 2013

This chapter argues that Hamiltonian mechanics is a much better base from which to build more advanced methods. The Hamilton equations have an elegant symmetry that the Lagrange equations lack. The Hamiltonian function is also used to write the Schroedinger equation of quantum mechanics. The differences between the Lagrange and Hamilton equations result mainly from the different variable sets in which they act. The Lagrangian variable set is the set of generalised coordinates and velocities, whereas the Hamiltonian set is the set of generalised coordinates and momenta. The transformation from Lagrange to Hamilton equations is a Legendre transformation, in which the Lagrangian function of the Lagrangian variable set is to be replaced by the Hamiltonian function of the phase-space variable set.
The Calculus of Variations
Authors: Johns Oliver Davis
Published: December 2013

This chapter introduces the calculus of variations in the context of finite-dimensional configuration spaces. Mastery of this relatively simple form of the theory will provide the background required to study more advanced topics such as the variations of fields in the complex spaces of quantum field theory. The presentation of the calculus of variations here uses the so-called General Parametric Method. In it, a path is specified parametrically, by letting each of its coordinates be a function of some monotonically varying, but initially unspecified, parameter. This method contrasts with some other textbooks in which one of the coordinates is used as the parameter, and the other variables are made functions of it. The two methods are compared in detail in the sections that follow.
11 Central Force Motion
Authors: Johns Oliver Davis
Published: December 2013

This chapter applies a combination of vector mechanics and Lagrangian mechanics to the general system of two point masses interacting by a central force depending only on their separation. The special case of an inverse square central force reproduces Newton's achievement in modern notation. Newton's Principia presented proof that elliptical orbits are a natural consequence of an inverse square gravitational attraction between the sun and the planets, and launched the topic of discussion in this chapter. The central force problem is thus central to the early history of analytical mechanics. An inverse square central force is also found between charged particles in electrodynamics. The orbital motion of an electron around a proton underlies both the Bohr model of the hydrogen atom and the old quantum theory that was superseded by Schroedinger's quantum mechanics.
Scattering
Authors: Johns Oliver Davis
Published: December 2013

This chapter considers a class of experiments in which the event of interest is the scattering, or deflection, of initial velocity into some final velocity, of the beam particles into a range of directions. A classical accelerator experiment directs a beam of particles, idealised here as having uniform particle volume density and velocity across the beam, into a target region where interaction between beam particles and target particles produces an outcome event of interest. The rate of occurrence of such events is then measured. An experiment often has a number of mutually exclusive outcome events. Partial events are still reported as ‘cross sections’, and in most cases, ‘cross sections’ are merely numbers that are conventionally used to report the results of experiments and serve as a common interface between theory and experiment.
14 Hamiltonian Mechanics with Time as a Coordinate
Authors: Johns Oliver Davis
Published: December 2013

This chapter uses the traditional Hamilton equations as the basis for an extended Hamiltonian theory in which time is treated as a coordinate. The traditional Hamilton equations, including the Hamiltonian form of the generalised energy theorem, will be combined into one set of extended Hamilton equations. The extended Hamilton theory developed in the chapter is of fundamental importance for the more advanced topics in mechanics. It is used to write the relativistically covariant Hamiltonian, which is then used to derive the Klein-Gordon equation of relativistic quantum mechanics. The extended Hamilton equations also provide the basis for the discussion of canonical transformations. The objective of extended Hamiltonian theory is to write the equations of motion in terms of an extended set of phase-space variables.
17 Fourvectors and Operators
Authors: Johns Oliver Davis
Published: December 2013

This chapter develops techniques that allow relativistically covariant calculations to be done in an elegant manner, and introduces fourvectors. These are analogous to the familiar vectors in three-dimensional Cartesian space – which will now be referred to as threevectors. The difference is that, in addition to the three spatial components, fourvectors will have an additional zeroth component associated with time which allows one to deal with the fact that the Lorentz transformation of special relativity transforms time as well as spatial coordinates. The theory of fourvectors and operators is presented using an invariant notation. Rather than considering a fourvector to be a set of components in some basis, it is considered to be something that models some physical property of the experiment under study and is independent of the choice of coordinate system.
18 Relativistic Mechanics
Authors: Johns Oliver Davis
Published: December 2013

This chapter discusses the modified version of Newton's laws of motion. The relativistically modified mechanics is presented and then recast into a fourvector form that demonstrates its consistency with special relativity. Traditional Lagrangian and Hamiltonian mechanics can incorporate these modifications, but the transition to a manifestly covariant Lagrangian and Hamiltonian mechanics requires use of the extended Lagrangian and Hamiltonian methods. The traditional Lagrange and Hamilton equations derived here are covariant in the sense that they reproduce the relativistically modified equations of motion. However, it is advantageous to write Lagrangian and Hamiltonian mechanics in a manifestly covariant form in which only invariants and fourvectors appear in the equations. The consistency with special relativity is then apparent by inspection.
Basic definitions
Authors: Donaldson Simon
Published: December 2013

This chapter presents definitions of Riemann surfaces and holomorphic maps, and provides examples, including algebraic curves and quotients.
Elliptic functions and integrals
Authors: Donaldson Simon
Published: December 2013

This chapter examines Riemann surfaces of genus 1. The constructions give an important model for the more general theory to be developed in Part III. The constructions also involve classical topics in mathematics, which relate the abstractions of Riemann surface theory to their origin in concrete calculus problems.
Orbital angular momentum
Authors: Galitski Victor , Karnakov Boris , Kogan Vladimir , Galitski, Jr. Victor
Published: December 2013

This chapter analyzes issues that deal with the general properties of angular momentum; angular momentum, l = 1; the addition of angular momenta; and tensor formalism in angular momentum theory.
Time-dependent quantum mechanics
Authors: Galitski Victor , Karnakov Boris , Kogan Vladimir , Galitski, Jr. Victor
Published: December 2013

This chapter analyzes problems related to the Schrödinger representation (the motion of wave packets); time-dependent observables (constants of motion); time-dependent unitary transformations (the Heisenberg picture of motion); the time-dependent Green function; and quasi-stationary and quasi-energy states (the Berry phase).
The Nature of Computation
Authors: Moore Cristopher , Mertens Stephan
Published: December 2013

Computational complexity is one of the most beautiful fields of modern mathematics, and it is increasingly relevant to other sciences ranging from physics to biology. However, this beauty is often buried underneath layers of unnecessary formalism, and exciting recent results such as interactive proofs, phase transitions, and quantum computing are usually considered too advanced for the typical student. This book bridges these gaps by explaining the deep ideas of theoretical computer science in a clear fashion, making them accessible to non-computer scientists and to computer scientists who finally want to appreciate their field from a new point of view. It starts with a lucid explanation of the P vs. NP problem, explaining why it is so fundamental, and so hard to resolve. It then leads the reader through the complexity of mazes and games; optimisation in theory and practice; randomised algorithms, interactive proofs, and pseudorandomness; Markov chains and phase transitions; and the outer reaches of quantum computing. At every turn, it uses a minimum of formalism, providing explanations that are both deep and accessible.
The Basics
Authors: Moore Cristopher , Mertens Stephan
Published: December 2013

This chapter discusses the complexity of a problem by thinking about the best possible algorithm, or computer program, that solves it. It shows that computational complexity theory is not about how to write better programs, but about understanding the underlying structure of different problems as well as asking fundamental questions about them. The chapter first explains problems and solutions by considering a Eulerian path and a Hamiltonian path. It then examines Euclid's algorithm, time and space, and the notion of scaling in physics. It also analyzes the distinction between polynomial functions of n and exponential ones, why this distinction is very important, and why it is so robust with respect to changes in the definition of computation. Finally, the chapter looks at the tractability and mathematical insight into a problem's structure.
The Deep Question: P vs. NP
Authors: Moore Cristopher , Mertens Stephan
Published: December 2013

This chapter considers the consequences of the possibility that P is equal to NP. It examines why it is extremely difficult to prove that P is not equal to NP by focusing on a set of ‘metatheorems’ which show the inadequacy of most of the proof techniques that have been proposed thus far. It also looks at the internal structure of NP and highlights its subclasses that capture various types of mathematical proof. The chapter demonstrates that, unless P is equal to NP, problems float in limbo between P and NP-completeness. Moreover, it describes several situations in which lower bounds can be proven and shows that a problem is outside a certain complexity class, or that one class is strictly more powerful than another. It also proves that polynomial time is less powerful than exponential time. Finally, it explores loopholes that might exist in the P vs. NP question and explains why it will eventually be resolved.
Interaction and Pseudorandomness
Authors: Moore Cristopher , Mertens Stephan
Published: December 2013

Although randomness can yield simple, efficient, and beautiful algorithms, it affects computation in many other ways. In NP problems, a ‘yes’ answer can be proven by the Prover to the Verifier. NP problems may be viewed as conversations between the Prover and the Verifier, in which the latter asks for a proof and the former responds with one. This chapter focuses on the Verifier and Prover in the form of Arthur and Merlin, whereby the former tries to convince the latter that two graphs are topologically different. It demonstrates how Arthur can keep Merlin honest by asking him random questions. It also considers the PCP Theorem, which shows that it is possible to check proofs for NP problems by looking at just a few bits. In addition, it examines whether randomised algorithms can be derandomised. It describes pseudorandomness and derandomisation before concluding by looking at the general connection between hardness and randomness.
Random Walks and Rapid Mixing
Authors: Moore Cristopher , Mertens Stephan
Published: December 2013

Random sampling is a technique for dealing with possible states or solutions having an exponentially large space. The best method of random sampling generally involves a random walk or a Markov chain. A Markov chain requires a number of steps to approach equilibrium, and thus provide a good random sample of the state space. This number of steps is called mixing time, which can be calculated by thinking about how quickly its choices overwhelm the system’s memory of its initial state, the extent to which one part of a system influences another, and how smoothly probability flows from one part of the state space to another. This chapter explores random walks and rapid mixing, first by considering a classic example from physics: a block of iron. It then discusses transition matrices, ergodicity, coupling, spectral gap, and expanders, as well as the role of conductance and the spectral gap in rapid mixing. It concludes by showing that temporal mixing is closely associated with spatial mixing.
Introduction to geomicrobiology
Authors: Kirchman David L.
Published: December 2013

Geomicrobiology, the marriage of geology and microbiology, is about the impact of microbes on subsurface environments in terrestrial systems or sediments. A distinguishing feature of geomicrobiology is the long time scale. Even the slow growth and low activity of microbes in subsurface environments have big effects when added up over millennia. After reviewing the basics of bacteria–surface interactions, this chapter discusses biomineralization, which is the microbially mediated formation of solid minerals from soluble ions. The role of microbes can vary from merely providing passive surfaces for mineral formation to active control of the entire precipitation process. The formation of carbonate-containing minerals by coccolithophorids and other marine organisms is especially important because of the role of these minerals in the carbon cycle. Iron minerals can be formed by chemolithoautotrophic bacteria, which gain a small amount of energy from Fe (II) oxidation. Similarly, manganese-rich minerals are formed during Mn(II) oxidation, although how this reaction benefits microbes is unclear. These minerals and others give geologists and geomicrobiologists clues about early life on earth. In addition to forming minerals, microbes help to dissolve them, a process called weathering. They contribute to weathering and mineral dissolution through several mechanisms: production of protons (acidity) or hydroxides that dissolve minerals; production of ligands which chelate metals in minerals and thereby break up the solid phase; and direct reduction of mineral-bound metals to more soluble forms. The chapter ends with some comments about the role of microbes in degrading oil and other fossil fuels.
Primate census and survey techniques
Authors: Plumptre Andrew J. , Sterling Eleanor J. , Buckland Stephen T.
Published: December 2013

This chapter provides an overview of the current methods used to survey primate populations in various habitat types and for various species. Written by two primatologists with extensive experience in using many of the methods in primate surveys and by one of the world’s experts in line transect analyses and co-developer of the free software DISTANCE, it summarizes the options available for estimating primate numbers. The chapter highlights some of the latest techniques, such as genetic capture-recapture methods, lure and cue counts, and occupancy estimation, as well as the more traditional methods of line transect sampling, distance estimation, and total count methods. A special section on nocturnal primate population estimation methods offers advice for overcoming the difficulties of assessing primate population size and density for nocturnal and other rare primate populations.
Behavior within groups
Authors: Kaplin Beth A. , William Apollinaire
Published: December 2013

This chapter discusses the major topics one needs to know about within-group primate behaviour research. It begins by defining the primate group and reviewing the array of social units identified. Primate groups can be described in terms of their social organization, mating system, and social structure; these attributes are discussed, along with group size, cohesion, sex ratios, and costs-benefits of group living. The habituation process, which can vary from a few months to a year or more depending on species and group history, is reviewed. This is followed by a discussion of standard sampling techniques for behavioural data. The authors explore several key within-group attributes including activity budgets, foraging behaviour, competition, aggression, and cooperation. Geographic Information Systems (GIS) is an invaluable tool for with-group behaviour studies, and the authors review the various ways it has been used. Social network analysis is a relatively new approach in primate behavioural studies with great potential. The chapter concludes with the contributions that behavioural studies can make to primate conservation.
Experiments in primatology: from the lab to the field and back again
Authors: Janson Charles H. , Brosnan Sarah F.
Published: December 2013

This chapter discusses how studies of field and captive (both laboratory and free-ranging captive) populations can provide complementary insights into the function and mechanisms of primate behaviours. In both arenas, experiments and observations play a role, although the ease of adopting each approach differs depending on the context, and they each have distinct kinds of strengths and constraints. Studies in captivity generally emphasize experiments on psychological mechanisms or development of behaviour, whereas field studies are best used to document the natural contexts in which functions are evident. Studies in captivity often reveal cognitive capacities that are only documented much later in the wild (e.g., tool use in capuchin monkeys) or that challenge us to discover the adaptive context in which they make sense (e.g., ability to count by chimpanzees). Studies in the wild may reveal behaviours that may not develop easily in confined lab environments (e.g., large-space navigational ability) or suggest explanations for species differences in cognitive abilities found in captivity (e.g., spatial vs. temporal discounting among tamarin species).
Demography, life histories, and population dynamics
Authors: Montenegro Olga L.
Published: December 2013

This chapter reviews the main field and analytical techniques used for demography, life history, and population dynamics research in primates. These methods are mainly used in free-ranging primates, although reference to captive animals is also provided. Topics discussed include the determination of demographic parameters, such as sex and age, population sex ratio, operational sex ratio, and estimation of population vital rates; methods for examining life history characteristics; population dynamics dealing with life tables and matrix population models, including sensitivity and elasticity analysis; and risk assessment methods used for primate conservation.
Captive breeding and ex situ conservation
Authors: Gibson Dean , McCann Colleen
Published: December 2013

Primates began the arduous journey out of their native countries and into captive collections in the late nineteenth century. However, their survival was severely limited by a lack of natural history knowledge and husbandry requirements. In the decades to follow, primate survivorship and propagation in zoos greatly increased. By the 1980s, captive breeding for most primates was routinely successful, but maintaining genetic diversity became the new impediment to population sustainability in zoos. This can be remedied in part by the inception of regional cooperative breeding programs focused on maintaining genetically and demographically robust populations. Many of today’s zoos have emerged as conservation organizations and have the potential to play an important role in species’ recovery and conservation.
Primates in trade
Authors: Linder Joshua M. , Sawyer Sarah , Brashares Justin S.
Published: December 2013

The wildlife trade is a multi-billion dollar business that satisfies demand for a wide range of products including live animals, trophies, ornaments, ingredients for traditional medicines and ceremonies, and meat. The wildlife trade represents one of the greatest threats to animal species across taxonomic groups, especially the primates. It is critical that studies are conducted to understand the biological and socioeconomic dimensions of the wildlife trade to help effectively track, regulate, and mitigate its impacts. The most commonly used methods for studying the wildlife trade include hunter, household, and market surveys, and analyses of official trade data collected by national governments and international organizations. This chapter describes the techniques used within each of these methods and refers to a growing body of research that has employed these techniques to examine the wildlife trade.
Introduction
Authors: Richmond Peter , Mimkes Jürgen , Hutzler Stefan
Published: December 2013

This chapter defines physics as the only science that takes it upon itself to explore those areas of the universe where the fundamental laws are unknown. It is often a surprise to many that physicists are applying their subject to finance and economics. Many colleagues of physicists who are currently looking at problems in economics, finance, and sociology still sometimes comment that these subjects do not fall within the domain of physics. However, history shows otherwise. While Aristotle, Copernicus, Newton, Huygens, Pascal, and Halley are all well known for their studies of natural phenomena, they are also remembered for important contributions that led to greater understanding and advances in economics and finance. The Renaissance brought with it independent thinking and a break from the passive belief that the future was a whim of the Gods. Risk was something that had to be understood, and the physicists described here made seminal contributions to the topic at a time when it was emerging as a serious subject.
Reading financial data
Authors: Richmond Peter , Mimkes Jürgen , Hutzler Stefan
Published: December 2013

This chapter describes the characteristics of financial data, and the general way in which it may be analysed. It then briefly describes the two different styles or approaches to investing. Financial transactions have been recorded on a daily basis since the nineteenth century, and since 1984, the sampling rate of transaction values has been made on a minute-by-minute basis. Companies now publish financial information in the form of accounts, with reporting periods varying from country to country. The data within company reports is concerned with the fundamental health of a company and spans income from sales, expenditure on salaries, capital investment, overall profit or earning, dividend payouts to shareholders, and transfers to the company reserves. These reports, together with periodic meetings with company directors, are the greatest concern of fundamental investors, as opposed to technical traders, who rely more on the asset price movements over time than on fundamental data.
7 Generalized diffusion processes and the Fokker‐Planck equation
Authors: Richmond Peter , Mimkes Jürgen , Hutzler Stefan
Published: December 2013

This chapter discusses the Chapman-Kolmogorov equation, but limits the scope to Markov processes. It is shown here how it can be reduced to the Fokker-Planck partial differential equation, using the concept of n-th order diffusion constants. These diffusion constants find applications, for example, when computing the evolution of the average of a random variable, and it is illustrated to obtain the average price of a Brownian asset as a function of time. Finally, the chapter introduces a more general Langevin equation than the one previously discussed, in order to study functions of random variables. It should be noted that the chapter forms the basis of the discussion on options and more realistic models of asset fluctuations, with an approach which essentially follows that by Lax et al. (2006).
Asset fluctuations and scaling
Authors: Richmond Peter , Mimkes Jürgen , Hutzler Stefan
Published: December 2013

This chapter first discusses the notion of stable distributions and shows that the consequence of this assumption is that the characteristic function of the corresponding distribution function has a particular form. In a special limit, this yields a Gaussian distribution. More generally, the probability distribution conforms to the Levy stable function, which has particular scaling properties. It has been noticed some years previously that asset prices did not follow Gaussian statistics. Bachelier himself questioned whether real assets actually followed the Gaussian law. The dilemma he faced was a lack of data that would have allowed him to properly assess the matter. Benoit Mandelbrot in 1963 also found that the Gaussian distribution did not fit empirical data. His study of asset prices, which suggested that asset price fluctuations conform to stable Levy distributions with fat tails, rather than Gaussian distributions, had profound implications for financial mathematics.
18 Production and economic growth
Authors: Richmond Peter , Mimkes Jürgen , Hutzler Stefan
Published: December 2013

This chapter adapts and exploits the concept of the Carnot cycle within our physical economics methodology to understand the mechanisms of economic production and finance. Proposed by the French engineer Nicolas Carnot in 1824 and developed by Benoit Clapeyron, another French engineer, during the period 1830–50, the Carnot cycle is a theoretical concept that forms the basis for understanding the operation of engines and heat pumps or refrigerators. It can be shown to be the most efficient route for the conversion of thermal energy into work or creating and maintaining a temperature difference. In order to move forward, an ‘economic’ Carnot cycle should be considered. If by some means the system is moved through a series of different states and finally returns to its initial state, it can be said that an economic cycle has occurred.
19 Economics and entropy
Authors: Richmond Peter , Mimkes Jürgen , Hutzler Stefan
Published: December 2013

This chapter considers details of the microstructure of an economic system, formulating what is known as physical macroeconomics. At the macroeconomic level, this can seem a somewhat mysterious quantity. This approach, however, has introduced a new state function, the economic entropy. A proper understanding of entropy is only possible by considering the system microstructure. It can be said that entropy measures the total number of microstates a system may adopt that are consistent with the macrostate. As a result of evolution of the dynamical variables, the system will, over a sufficient time, visit all possible points in the system phase space. Following the definition of Boltzmann entropy, it can be said that in economics, the entropy is similarly a measure of the total number of available ‘economic’ states, whereas the energy measures the probability that any particular state in this ‘economic’ phase space will be realised.
Temporal and Spatial Changes in the Pea Black Spot Disease Complex in Western Australia
Authors: Tran Hieu Sy , Li Yu Pin , You Ming Pei , Khan Tanveer N. , Pritchard Ian , Barbetti Martin J.
Published: December 2013

Black spot (also referred to as Ascochyta blight, Ascochyta foot rot and black stem, and Ascochyta leaf and pod spot) is a devastating disease of pea (Pisum sativum) caused by one or more pathogenic fungi, including Didymella pinodes, Ascochyta pisi, and Phoma pinodella. Surveys were conducted across pea-growing regions of Western Australia in 1984, 1987, 1989, 1996, 2010, and 2012. In total, 1,872 fungal isolates were collected in association with pea black spot disease symptoms. Internal transcribed spacer regions from representative isolates, chosen based on morphology, were sequenced to aid in identification. In most years and locations, D. pinodes was the predominant pathogen in the black spot complex. From 1984 to 2012, four new pathogens associated with black spot symptoms on leaves or stems (P. koolunga, P. herbarum, Boeremia exigua var. exigua, and P. glomerata) were confirmed. This study is the first to confirm P. koolunga in association with pea black spot symptoms in field pea in Western Australia and show that, by 2012, it was widely present in new regions. In 2012, P. koolunga was more prevalent than D. pinodes in Northam and P. pinodella in Esperance. P. herbarum and B. exigua var. exigua were only recorded in 2010. Although A. pisi was reported in Western Australia in 1912 and again in 1968 and is commonly associated with pea black spot in other states of Australia and elsewhere, it was not recorded in Western Australia from 1984 to 2012. It is clear that the pathogen population associated with the pea black spot complex in Western Australia has been dynamic across time and geographic location. This poses a particular challenge to development of effective resistance against the black spot complex, because breeding programs are focused almost exclusively on resistance to D. pinodes, largely ignoring other major pathogens in the disease complex. Furthermore, development and deployment of effective host resistance or fungicides against just one or two of the pathogens in the disease complex could radically shift the make-up of the population toward pathogen species that are least challenged by the host resistance or fungicides, creating an evolving black spot complex that remains ahead of breeding and other management efforts.
Separate enrichment analysis of pathways for up- and downregulated genes
Authors: Hong Guini , Zhang Wenjing , Li Hongdong , Shen Xiaopei , Guo Zheng
Published: December 2013

Two strategies are often adopted for enrichment analysis of pathways: the analysis of all differentially expressed (DE) genes together or the analysis of up- and downregulated genes separately. However, few studies have examined the rationales of these enrichment analysis strategies. Using both microarray and RNA-seq data, we show that gene pairs with functional links in pathways tended to have positively correlated expression levels, which could result in an imbalance between the up- and downregulated genes in particular pathways. We then show that the imbalance could greatly reduce the statistical power for finding disease-associated pathways through the analysis of all-DE genes. Further, using gene expression profiles from five types of tumours, we illustrate that the separate analysis of up- and downregulated genes could identify more pathways that are really pertinent to phenotypic difference. In conclusion, analysing up- and downregulated genes separately is more powerful than analysing all of the DE genes together.
Alignment of crystal orientations of the multi-domain photonic crystals in
Parides sesostris
wing scales
Authors: Yoshioka S. , Fujita H. , Kinoshita S. , Matsuhana B.
Published: December 2013

It is known that the wing scales of the emerald-patched cattleheart butterfly,
Parides sesostris
, contain gyroid-type photonic crystals, which produce a green structural colour. However, the photonic crystal is not a single crystal that spreads over the entire scale, but it is separated into many small domains with different crystal orientations. As a photonic crystal generally has band gaps at different frequencies depending on the direction of light propagation, it seems mysterious that the scale is observed to be uniformly green under an optical microscope despite the multi-domain structure. In this study, we have carefully investigated the structure of the wing scale and discovered that the crystal orientations of different domains are not perfectly random, but there is a preferred crystal orientation that is aligned along the surface normal of the scale. This finding suggests that there is an additional factor during the developmental process of the microstructure that regulates the crystal orientation.
Singular Hopf bifurcation in a differential equation with large state-dependent delay
Authors: Kozyreff G. , Erneux T.
Published: December 2013

We study the onset of sustained oscillations in a classical state-dependent delay (SDD) differential equation inspired by control theory. Owing to the large delays considered, the Hopf bifurcation is singular and the oscillations rapidly acquire a sawtooth profile past the instability threshold. Using asymptotic techniques, we explicitly capture the gradual change from nearly sinusoidal to sawtooth oscillations. The dependence of the delay on the solution can be either linear or nonlinear, with at least quadratic dependence. In the former case, an asymptotic connection is made with the Rayleigh oscillator. In the latter, van der Pol’s equation is derived for the small-amplitude oscillations. SDD differential equations are currently the subject of intense research in order to establish or amend general theorems valid for constant-delay differential equation, but explicit analytical construction of solutions are rare. This paper illustrates the use of singular perturbation techniques and the unusual way in which solvability conditions can arise for SDD problems with large delays.
Energetics of the acrobatic courtship in male golden-collared manakins (Manacus vitellinus)
Authors: Barske J. , Fusani L. , Wikelski M. , Feng N. Y. , Santos M. , Schlinger B. A.
Published: December 2013

In lek mating systems, females choose mates through indicators of quality, which males may exhibit by their performance of courtship displays. In temperate regions, displaying seasons are brief (one to two months), whereas in the tropics courtship seasons may be prolonged. Moreover, in temperate-breeding animals lekking behaviour can be energetically demanding, but little is known about the energy costs of lekking in tropical animals. Daily, over the course of a nearly seven-month-long breeding season, male golden-collared manakins (Manacus vitellinus) of Panamanian rainforests perform acrobatic courtship displays that markedly elevate heart rates, suggesting that they require high energy investment. Typically, animals of tropical lowland forests (such as manakins) exhibit a ‘slow pace of life’ metabolic strategy. We investigated whether male manakin courtship is indeed metabolically costly or whether the birds retain a low daily energy expenditure (DEE), as seen in other tropical species. To assess these questions, we calibrated manakin heart rate against metabolic rate, examined daily lek activity and, using telemetry, obtained heart rates of individual wild, lekking male manakins. Although metabolic rates peak during courtship displays, we found that males actually invest minimal time (only approx. 5 min d−1) performing displays. As a consequence, the DEE of approximately 39 kJ d−1for male manakins is comparable to other lowland tropical species. The short, intense bursts of courtship by these birds make up only approximately 1.2% of their total DEE. Presumably, this cost is negligible, enabling them to perform daily at their arenas for months on end.
Differential replication of two porcine parvovirus strains in bovine cell lines ensues from initial DNA processing and NS1 expression
Authors: Fernandes Sandra , Boisvert Maude , Szelei Jozsef , Tijssen Peter
Published: December 2013

Porcine parvovirus (PPV) is a small DNA virus with restricted coding capacity. The 5 kb genome expresses three major non-structural proteins (NS1, NS2 and SAT), and two structural proteins (VP1 and VP2). These few viral proteins are pleiotropic and interact with cellular components throughout viral replication. In this regard, very few cell lines have been shown to replicate the virus efficiently. Cell lines were established from a primary culture of bovine cells that allowed allotropic variants of PPV to be distinguished. Three cell lines were differentially sensitive to infection by two prototype PPV strains, NADL-2 and Kresse. In the first cell line (D10), infection was restricted early in the infectious cycle and was not productive. Infection of the second cell line (G11) was 1000 times less efficient with the NADL-2 strain compared with porcine cells, while production of infectious virus of the Kresse strain was barely detectable. Restriction points in these cells were the initial generation of DNA replication intermediates and NS1 production. Infection with chimeras between NADL-2 and Kresse showed that residues outside the previously described allotropic determinant were also partially responsible for the restriction to Kresse replication in G11 cells. F4 cells were permissive to both strains, although genome replication and infectious virus production were lower than in the porcine cells used for comparison. These results highlight the dependent nature of parvovirus tropism on host factors and suggest that cells from a non-host origin can fully support a productive infection by both strains.
Increased dosage of DYRK1A and DSCR1 delays neuronal differentiation in neocortical progenitor cells
Authors: Kurabayashi Nobuhiro , Sanada Kamon
Published: December 2013

Down's syndrome (DS), a major genetic cause of mental retardation, arises from triplication of genes on human chromosome 21. Here we show that DYRK1A (dual-specificity tyrosine-phosphorylated and -regulated kinase 1A) and DSCR1 (DS critical region 1), two genes lying within human chromosome 21 and encoding for a serine/threonine kinase and calcineurin regulator, respectively, are expressed in neural progenitors in the mouse developing neocortex. Increasing the dosage of both proteins in neural progenitors leads to a delay in neuronal differentiation, resulting ultimately in alteration of their laminar fate. This defect is mediated by the cooperative actions of DYRK1A and DSCR1 in suppressing the activity of the transcription factor NFATc. In Ts1Cje mice, a DS mouse model, dysregulation of NFATc in conjunction with increased levels of DYRK1A and DSCR1 was observed. Furthermore, counteracting the dysregulated pathway ameliorates the delayed neuronal differentiation observed in Ts1Cje mice. In sum, our findings suggest that dosage of DYRK1A and DSCR1 is critical for proper neurogenesis through NFATc and provide a potential mechanism to explain the neurodevelopmental defects in DS.
Multiple small RNA pathways regulate the silencing of repeated and foreign genes in C. elegans
Authors: Fischer Sylvia E.J. , Pan Qi , Breen Peter C. , Qi Yan , Shi Zhen , Zhang Chi , Ruvkun Gary
Published: December 2013

Gene segments from other organisms, such as viruses, are detected as foreign and targeted for silencing by RNAi pathways. A deep-sequencing map of the small RNA response to repeated transgenes introduced to Caenorhabditis elegans revealed that specific segments are targeted by siRNAs. Silencing of the foreign gene segments depends on an antiviral response that involves changes in active and silent chromatin modifications and altered levels of antisense siRNAs. Distinct Argonaute proteins target foreign genes for silencing or protection against silencing. We used a repeated transgene in a genome-wide screen to identify gene disruptions that enhance silencing of foreign genetic elements and identified 69 genes. These genes cluster in four groups based on overlapping sets of coexpressed genes, including a group of germline-expressed genes that are likely coregulated by the E2F transcription factor. Many of the gene inactivations enhance exogenous RNAi. About half of the 69 genes have roles in endogenous RNAi pathways that regulate diverse processes, including silencing of duplicated genes and transposons and chromosome segregation. Of these newly identified genes, several are required for siRNA biogenesis or stability in the oocyte-specific ERGO-1 pathway, including eri-12, encoding an interactor of the RNAi-defective protein RDE-10, and ntl-9/CNOT9, one of several CCR4/NOT complex genes that we identified. The conserved ARF-like small GTPase ARL-8 is required specifically for primary siRNA biogenesis or stability in the sperm-specific ALG-3/4 endogenous RNAi pathway.
Platform-based product design and environmental turbulence
Authors: F. Thomas Ellen
Published: December 2013

Purpose

– When competing in a turbulent environment, strategic flexibility can be a competitive advantage. One source of flexibility is the new product development (NPD) process, or more specifically product design. The purpose of this paper is to investigate platform-based product design and its relationship to environmental turbulence, strategic flexibility, and market performance.

Design/methodology/approach

– A theoretical model is developed and relationships are empirically tested using structural equation modeling. Data were collected from engineering design managers in the US manufacturing industry.

Findings

– The paper found that the higher the level of environmental turbulence the more firms turned to platform product design. Also, the higher the level of platform design the higher the level of market performance, both in the short term and the long term. Finally, the paper showed that strategic flexibility positively and partially mediates the positive relationship between platform design and performance.

Originality/value

– Platform-based product design is a research area noticeably devoid of empirical work. Furthermore, research has called for a better understanding of the different contexts in which platforms are applied stating that platform planning is too often decoupled from NDP strategy resulting in unsatisfactory results.
Detection and prevention of financial abuse against elders
Authors: A. Harries Priscilla , L. Davies Miranda , J. Gilhooly Kenneth , L.M. Gilhooly Mary , Cairns Deborah
Published: December 2013

Purpose

– This paper reports on banking and finance professionals' decision making in the context of elder financial abuse. The aim was to identify the case features that influence when abuse is identified and when action is taken.

Design/methodology/approach

– Banking and finance professionals (n=70) were shown 35 financial abuse case scenarios and were asked to judge how certain they were that the older person was being abused and the likelihood of taking action.

Findings

– Three case features significantly influenced certainty of financial abuse: the nature of the financial problem presented, the older person's level of mental capacity and who was in charge of the client's money. In cases where the older person was more confused and forgetful, there was increased suspicion that financial abuse was taking place. Finance professionals were less certain that financial abuse was occurring if the older person was in charge of his or her own finances.

Originality/value

– The research findings have been used to develop freely available online training resources to promote professionals' decision making capacity (www.elderfinancialabuse.co.uk). The resources have been advocated for use by Building Societies Association as well as CIFAS, the UK's Fraud Prevention Service.
What's normal? Influencing women's perceptions of normal genitalia: an experiment involving exposure to modified and nonmodified images
Authors: Moran C , Lee C
Published: December 2013

Objective

Examine women's perceptions of what is ‘normal’ and ‘desirable’ in female genital appearance.

Design

Experiment with random allocation across three conditions.

Setting

Community.

Sample

A total of 97 women aged 18–30 years.

Methods

Women were randomly assigned to view a series of images of (1) surgically modified vulvas or (2) nonmodified vulvas, or (3) no images. They then viewed and rated ten target images of surgically modified vulvas and ten of unmodified vulvas.

Main outcome measures

Women used a four‐point Likert scale (‘strongly agree’ to ‘strongly disagree’), to rate each target image for ‘looks normal’ and ‘represents society's ideal’. For each woman, we created two summary scores that represented the extent to which she rated the unmodified vulvas as more ‘normal’ and more ‘society's ideal’ than the modified vulvas.

Results

For ratings of ‘normality,’ there was a significant effect for condition (F2,94 = 2.75 P = 0.007,  = 0.082): women who had first viewed the modified images rated the modified target vulvas as more normal than the nonmodified vulvas, significantly different from the control group, who rated them as less normal. For ratings of ‘society's ideal’, there was again a significant effect for condition (F2,92 = 7.72, P < 0.001,  = 0.125); all three groups rated modified target vulvas as more like society's ideal than the nonmodified target vulvas, with the effect significantly strongest for the women who had viewed the modified images.

Conclusions

Exposure to images of modified vulvas may change women's perceptions of what is normal and desirable. This may explain why some healthy women seek labiaplasty.
Myanmar under reform: Emerging pressures on water, energy and food security
Authors: Kattelus Mirja , Rahaman Muhammad Mizanur , Varis Olli
Published: December 2013

Myanmar's water‐related sectors are subject to intensive changes, as the country's abundant land and water resources provide substantial scope for development. Recent steps towards economic reform in Myanmar have led to a surge of foreign investment directed towards intensified natural resource extraction. Both the agricultural and the energy sector are increasingly affected by foreign investments that will impact the status of water, energy and food security in the country. With these on‐going developments, Myanmar's future is largely dependent on how its natural resources are managed and how the benefits from the resource extraction are shared. With various institutional changes and new actors welcomed to the sectors, existing livelihoods and ecosystems dependent on the land and water resources are to face increasing competition for the shared resources, while lacking secured access to them. There are increasing concerns that this sectoral development is occurring at the expense of environmental and social sustainability. As one way to tackle these challenges, the water‐energy‐food nexus approach could help in finding synergies and co‐benefits across sectors by addressing the imbalances along the nexus and externalities derived from the on‐going intensification.