bluuebunny/crossref_metadata_2025_split huggingface dataset:
Observation of possible topological in-gap surface states in the Kondo insulator SmB6 by photoemission
Authors: Jiang J. , Li S. , Zhang T. , Sun Z. , Chen F. , Ye Z.R. , Xu M. , Ge Q.Q. , Tan S.Y. , Niu X.H. , Xia M. , Xie B.P. , Li Y.F. , Chen X.H. , Wen H.H. , Feng D.L. 
Published: December 2013

AbstractSmB6, a well-known Kondo insulator, exhibits a transport anomaly at low temperature. This anomaly is usually attributed to states within the hybridization gap. Recent theoretical work and transport measurements suggest that these in-gap states could be ascribed to topological surface states, which would make SmB6 the first realization of topological Kondo insulator. Here by performing angle-resolved photoemission spectroscopy experiments, we directly observe several dispersive states within the hybridization gap of SmB6. These states show negligible kz dependence, which indicates their surface origin. Furthermore, we perform photoemission circular dichroism experiments, which suggest that the in-gap states possess chirality of the orbital angular momentum. These states vanish simultaneously with the hybridization gap at around 150 K. Together, these observations suggest the possible topological origin of the in-gap states.
Early urban impact on Mediterranean coastal environments
Authors: Kaniewski David , Van Campo Elise , Morhange Christophe , Guiot Joël , Zviely Dov , Shaked Idan , Otto Thierry , Artzy Michal 
Published: December 2013

AbstractA common belief is that, unlike today, ancient urban areas developed in a sustainable way within the environmental limits of local natural resources and the ecosystem's capacity to respond. This long-held paradigm is based on a weak knowledge of the processes underpinning the emergence of urban life and the rise of an urban-adapted environment in and beyond city boundaries. Here, we report a 6000-year record of environmental changes around the port city of Akko (Acre), Israel, to analyse ecological processes and patterns stemming from the emergence and growth of urban life. We show that early urban development deeply transformed pre-existing ecosystems, swiftly leading to an urban environment already governed by its own ecological rules and this, since the emergence of the cities.
Surface topography regulates wnt signaling through control of primary cilia structure in mesenchymal stem cells
Authors: McMurray R. J. , Wann A. K. T. , Thompson C. L. , Connelly J. T. , Knight M. M. 
Published: December 2013

AbstractThe primary cilium regulates cellular signalling including influencing wnt sensitivity by sequestering β-catenin within the ciliary compartment. Topographic regulation of intracellular actin-myosin tension can control stem cell fate of which wnt is an important mediator. We hypothesized that topography influences mesenchymal stem cell (MSC) wnt signaling through the regulation of primary cilia structure and function. MSCs cultured on grooves expressed elongated primary cilia, through reduced actin organization. siRNA inhibition of anterograde intraflagellar transport (IFT88) reduced cilia length and increased active nuclear β-catenin. Conversely, increased primary cilia assembly in MSCs cultured on the grooves was associated with decreased levels of nuclear active β-catenin, axin-2 induction and proliferation, in response to wnt3a. This negative regulation, on grooved topography, was reversed by siRNA to IFT88. This indicates that subtle regulation of IFT and associated cilia structure, tunes the wnt response controlling stem cell differentiation.
Covalent EGFR inhibitor analysis reveals importance of reversible interactions to potency and mechanisms of drug resistance
Authors: Schwartz Phillip A. , Kuzmic Petr , Solowiej James , Bergqvist Simon , Bolanos Ben , Almaden Chau , Nagata Asako , Ryan Kevin , Feng Junli , Dalvie Deepak , Kath John C. , Xu Meirong , Wani Revati , Murray Brion William 
Published: December 2013

Significance
Covalent kinase inhibition strategies are reemerging, but critical gaps in the understanding of molecular determinants of potency still persist. A kinetic approach is developed to describe the components of overall inhibitor potency (reversible binding and chemical reactivity). Detailed kinetic descriptions of EGFR covalent drugs are provided. Reversible interactions of covalent inhibitors are found to be essential to biochemical and cellular potency. A dynamic linkage between available affinity and necessary reactivity is proposed. Cysteine oxidation is an emerging type of posttranslational modification. Specific oxidation of the EGF receptor cysteine nucleophile causes highly variable effects on inhibitor potency. Two mechanisms of drug resistance are identified (reversible cysteine–inhibitor warhead interactions and specific cysteine oxidation) as well as a rational framework for understanding and designing covalent inhibitors.
Divisors, line bundles and Jacobians
Authors: Donaldson Simon 
Published: December 2013

Abstract
This chapter first examines cohomology and line bundles, covering sheaves and cohomology, line bundles and projective embeddings, and divisors and unique factorisation. It then turns to Jacobians of Riemann surfaces, covering the Abel-Jacobi Theorem; abstract theory; and the geometry of symmetric products. It concludes by examining the special case when Σ has genus 2, so that Jac(Σ) is a complex surface and there is a surjective map j : Sym2( Σ) → Jac.
Surfaces, interfaces and reflectivity
Authors: Sivia D. S. 
Published: December 2013

Abstract
This chapter focuses on the case of specular reflectivity as an example of elastic scattering. This type of experiment is used in the study of layered materials, and is a good starting point because it simplifies to a one-dimensional problem. The geometrical setup for specular reflectivity comprises a beam of X-rays, or neutrons, of wavelength impinges at a grazing angle on a planar sample, and the fraction that bounce back with the same attributes is ascertained. These measurements are repeated for different angles at a given wavelength, or the other way around with a multichromatic source, and yield the reflectivity curve R(Q). An example presented here involves three alternating layers of two materials deposited on a substrate. For simplicity, all the thicknesses have been made the same. Rather than relating the corresponding reflectivity curve to the SLD depth profile analytically, it is understood qualitatively through the help of the physical insight into Fourier transforms.
Particle collisions
Authors: Galitski Victor , Karnakov Boris , Kogan Vladimir , Galitski, Jr. Victor 
Published: December 2013

Abstract
This chapter looks at problems that deal with the Born approximation; scattering theory (partial-wave analysis); low-energy scattering (resonant scattering); scattering of fast particles (Eikonal approximation); scattering of particles with spin; analytic properties of the scattering amplitude; and scattering of composite quantum particles (inelastic collisions).
The Grand Unified Theory of Computation
Authors: Cristopher Moore 
Published: December 2013

AbstractThis chapter explores a universal notion of computation, first by describing Charles Babbage's vision of a mechanical device that can perform any calculation as well as David Hilbert's dream of a mechanical procedure capable of proving or refuting any mathematical claim. It then considers the universality of modern computers and the undecidability of certain problems, explores diagonalization and the Halting Problem, and discusses Kurt Gödel's Incompleteness Theorem. It also looks at the three models of computation proposed in the early twentieth century — partial recursive functions, the lambda-calculus, and Turing machines — and show that they are all equivalent to each other and can carry out any conceivable computation. The chapter concludes by considering universal computation and undecidability in tilings of the plane, products of fractions, and the motions of a chaotic system.
Memory, Paths, and Games
Authors: Moore Cristopher , Mertens Stephan 
Published: December 2013

AbstractBoth time and memory are limited resources in the real world, but a fundamental difference between the two is that the latter can be reused. The gap between determinism and nondeterministic computation — that is, between finding a solution and checking one — is considerably smaller with memory than it is with time. This chapter explores how various amounts of memory can be used to solve complexity classes of problems either deterministically or nondeterministically. It shows how these classes highlight the difficulty of finding a path through an enormous graph, or finding a winning strategy against a clever opponent. It illustrates computational complexity in mazes, wooden puzzles, and board games thousands of years old. The chapter first discusses the computer's state space, the relationship between space-bounded computation and reachability, paths, and symmetric space. It then examines how nondeterminism works in the space-bounded case and proves that reachability is NL-complete. It also considers middle-first search and nondeterministic space, along with the word game Geography and the Asian game of Go.
Physical-chemical environment of microbes
Authors: Kirchman David L. 
Published: December 2013

Abstract
Many physical-chemical properties affecting microbes are familiar to ecologists examining large organisms in our visible world. This chapter starts by reviewing the basics of these properties, such as temperature effects and the importance of water for microbes in soils. Another important property – pH – has direct effects on organisms and indirect effects via how hydrogen ions determine the chemical form of key molecules and compounds in nature. Oxygen content is also critical, as it essential to the survival of all but a few eukaryotes. Light is used as an energy source by phototrophs, but it can have deleterious effects on microbes, especially ultraviolet light. In addition to these familiar factors, the small size of microbes sets limits on their physical world. Microbes are said to live in a ‘low Reynolds number environment’. When the Reynolds number is smaller than about one, viscous forces dominate over inertial forces. For a macroscopic organism like us, moving in a low Reynolds number environment would seem like swimming in molasses. The chapter also provides an overview of the physical environment of aquatic and terrestrial habitats, and ends with a discussion of how the physical-chemical environment of microbes in biofilms is quite different from that of free-living organisms.
Microbial primary production and phototrophy
Authors: Kirchman David L. 
Published: December 2013

Abstract
This chapter focuses on the most important process in the biosphere – primary production – the turning of carbon dioxide into organic material by higher plants and algae. While higher plants dominate terrestrial ecosystems, photosynthetic microbes account for nearly all of primary production in the oceans. After reviewing basic physiology of photosynthesis, the chapter discusses approaches to measuring gross and net primary production, and how these processes affect fluxes of oxygen and carbon dioxide into and out of aquatic ecosystems. It then points out that terrestrial plants have high biomass but relatively low growth, while the opposite is the case for aquatic algae. In spite of these fundamental differences, each ends up contributing roughly 50 percent of total primary production in the biosphere. But primary production varies greatly with the seasons in temperate ecosystems, punctuated by the spring bloom, when the biomass of one algal type, diatoms, reaches a maximum. Other abundant algal types include coccolithophorids in the oceans and filamentous cyanobacteria in freshwaters. After the bloom, small algae take over and out-compete larger forms for limiting nutrients because of superior uptake kinetics. Abundant types of small algae include two coccoid cyanobacteria – Synechococcus and Prochlorococcus – the latter said to be the most abundant photoautotroph on the planet because of its large numbers in oligotrophic oceans. Other algae, often dinoflagellates, are toxic. Many algae also can graze on other microbes, probably to obtain limiting nitrogen or phosphorus. Still other microbes are mainly heterotrophic, but are capable of harvesting light energy.
Microbial growth, biomass production, and controls
Authors: Kirchman David L. 
Published: December 2013

Abstract
Soon after the discovery that bacteria are abundant in natural environments, the question arose as to whether or not they were active. Although the plate count method suggested that they were dormant if not dead, other methods indicated that a large fraction of bacteria and fungi are active, as discussed in this chapter. The chapter describes fundamental equations for exponential growth and logistic growth, as well as phases of growth in batch cultures, continuous cultures, and chemostats. In contrast to measuring growth in laboratory cultures, it is difficult to measure it in natural environments for complex communities with co-occurring mortality. Among many methods that have been suggested over the years, the most common one for bacteria is the leucine approach; for fungi it is the acetate-in-ergosterol method. These methods indicate that the growth rate of the bulk community is on the order of days for bacteria in natural environment. It is faster in aquatic habitats than in soils: bacteria grow faster than fungi in soils. But bulk rates for bacteria appear to be slower than those for phytoplankton. All of these rates for natural communities are much slower than rates measured for most microbes in the laboratory. Some of the factors limiting heterotrophic bacteria and fungi include temperature and inorganic nutrients, but the supply of organic compounds is perhaps most important in most environments.
Physiology and energetics
Authors: Schmid Jutta 
Published: December 2013

Abstract
Primates and many other mammalian species exhibit a wide range of physiological and behavioural adaptations that enable them to cope with fluctuations in climate and energy availability. Measures of energy demands are indispensable to understanding how animals organize their annual cycles and how individuals and populations respond to climate-induced changes in thermal and ecological stressors. Thus, understanding the behavioural responses and physiological consequences of primates is a useful tool for conservation planning for endangered species. This chapter describes different methodologies of studying energy expenditure that can be applied to primates, and details how to measure body temperature of primates using different types of sensory systems. It also outlines practical details that must be considered before using a particular technique and elucidates the advantages and disadvantages that attend their use.
Population genetics, molecular phylogenetics, and phylogeography
Authors: Blair Mary E. , Morales-Jimenez Alba L. 
Published: December 2013

Abstract
This chapter provides a synthesis and evaluation of molecular techniques in the study of primate ecology, evolution, and conservation. It discusses how to obtain, preserve, and transport samples for genetic analysis; laboratory techniques for DNA extraction, genotyping, and sequencing; and data analyses relevant to research questions at the species- and population-level, including population genetics, molecular phylogenetics, and phylogeography. The chapter also highlights new and emerging approaches, including next-generation sequencing and landscape genetics. Discussed throughout is the relevance of these methods to various research questions related to primate conservation as well as ecology and evolution. In particular, molecular approaches allow research questions to not only address patterns, but also the ecological and evolutionary processes behind those patterns, enabling the conservation of natural populations that are capable of coping with continued environmental change.
Basics of probability
Authors: Richmond Peter , Mimkes Jürgen , Hutzler Stefan 
Published: December 2013

AbstractThis chapter focuses on a large variety of random systems that encompass the world. It shows the outcome of a sequence of throws of a six-sided die, the simulated motion of a Brownian particle, and the temporal fluctuations of the Coca Cola stock price as examples of random fluctuations. In principle, everything could be calculated from first principles if only one knew the initial conditions, the nature of the dynamical laws, and the values of the parameters within these equations. However, tiny errors would rapidly grow and lead to an erroneous solution. Fortunately, random or stochastic systems can be analysed in a different manner, offering more general information. The key is to calculate sensible quantities. The central concept in the analysis of all stochastic systems is the random variable. While it is not possible to compute the particular outcome of a stochastic event, it may be possible to compute the probability that the random variable takes on a certain value.
4 Time dependent processes and the Chapman‐Kolmogorov equation
Authors: Richmond Peter , Mimkes Jürgen , Hutzler Stefan 
Published: December 2013

AbstractThis chapter examines the statistical dynamics associated with the random motion of the change of the price of an asset. If the price of an asset is assumed to be analogous to the position of a particle, it could be imagined that some kind of Newtonian dynamics could apply to this system. A better analogy, however, would be with the random or stochastic motion of a Brownian particle, since the change of the price of an asset is a stochastic or random process. It can be seen here that the process involves a hierarchy of equations that are generally intractable. However, invoking the particular assumption that the process is Markovian, i.e. that it has a very short-term memory, it is possible to reduce this hierarchy down to a simple closed form, represented by the Chapman-Kolmogorov integral equation.
8 Derivatives and options
Authors: Richmond Peter , Mimkes Jürgen , Hutzler Stefan 
Published: December 2013

AbstractThis chapter traces the origins of the use of derivatives to the era of Mesopotamian farmers and compares it to similar transactions widely used by businesses today. Mesopotamian farmers routinely sold the following year's grain harvest due for delivery at the time of harvesting at a ‘future’ price, agreed today. The actual future price went up and down according to the market. Today, for a fee, an agreement is made to engage, at some point in the future, in a trade at a fixed price. The fee is the price of the so-called derivative contract that clearly should depend in some way on the price of the underlying asset. All businesses seek to reduce uncertainty in the financial state of their businesses by trying to fix the price of the underlying commodity. As a result, they are all natural buyers and sellers of derivative contracts.
Models of asset fluctuations
Authors: Richmond Peter , Mimkes Jürgen , Hutzler Stefan 
Published: December 2013

AbstractThis chapter aims to construct analytical models of asset fluctuations using the framework of Fokker-Planck equations, together with the generalised diffusion constants, and shows that simple trial forms for D 1 and D 2 result in a distribution function of returns which has a power law tail. However, while the model captures the exponential decay of the linear autocorrelation function of returns, it fails to reproduce the long-range correlations exhibited by square returns. The chapter generalises the approach using a trial time dependent function for the density distribution. This provides a more successful route to the characterisation of the long- and short-time nature of both autocovariance functions. Finally, using the Fokker-Plank equations, it is shown how this approach, which accounts for the fat tails in the distribution functions, may be applied to the computation of option prices.
Risk
Authors: Richmond Peter , Mimkes Jürgen , Hutzler Stefan 
Published: December 2013

AbstractThis chapter introduces the statistics associated with extreme events and then goes on to discuss how these ideas have been used to construct portfolios where the risk is minimized. While extreme events can take asset prices in a positive as well as a negative direction, risk generally refers to negative or adverse outcomes. The chapter develops the ideas of the efficient portfolio proposed by the economist Harry Markowitz in the 1950s. A specific return can be expected through the acceptance of a specific risk. An increase in expected return comes at the expense of increased risk. The following sections show that assets are generally correlated, and these correlations should be taken into account when computing optimum portfolios. Two techniques, whose applications originate from physics, are introduced, namely minimum spanning trees and an analysis based on random matrices.
Two non‐financial markets
Authors: Richmond Peter , Mimkes Jürgen , Hutzler Stefan 
Published: December 2013

AbstractThis chapter presents recent findings concerning online betting markets and house markets. Traditionally, if one wanted to bet on a certain outcome of an event, such as a horserace or a soccer match, the bet would be placed with a bookmaker. The bookmaker sets the odds deemed appropriate for the expected probability of the outcome and the customer can place bets against those odds. If a bet is offered, or laid, with odds for example at three to one, the customer who backs the bet can expect to win three times the money he or she placed on the bet with a probability of 1/4. The bookmaker will consequently keep the placed money with a probability of 3/4. Bookmakers can expect to make profits in the long run by providing odds to their customers which slightly overestimate the true probabilities of that given outcome.
16 Markets
Authors: Richmond Peter , Mimkes Jürgen , Hutzler Stefan 
Published: December 2013

AbstractThis chapter argues that a slowly changing economy will not alter the dither of a country by much and, empirically, it can be observed that the foreign exchange rates can often be fairly stable over long periods of time. This was the position with many countries within the European Union during the latter part of the twentieth century, and probably the reason why politicians thought they were able to introduce a common currency. In effect, they supposed fluctuations were Gaussian and did not exhibit power law tails. However, what is becoming clear is that the lack of control of spending within parts of this new common currency area during periods of low interest rates has given rise to unsustainable levels of debt within some of these countries. Politicians argue that only with greater central control and coordination of individual member countries can the situation be stabilised.
20 Approaches to non‐equilibrium economics
Authors: Richmond Peter , Mimkes Jürgen , Hutzler Stefan 
Published: December 2013

AbstractThis chapter shows that, in economics, a statistical mechanics in which the allowable states of the system are associated with a constant dither, leading to free energies that are proportional to the logarithm of a partition function, is not sufficient to describe fully economic systems. At the very least, a gradient in the dither in either time or space, which supports Carnot type processes, is required. Ultimately, it can be expected that this is associated with human behaviour and the response to economic situations. Different people can be expected to react in different ways, depending on their access to information, their ability to process said information, and their general attitude to risk and so on. Furthermore, any one person may not react in the same way at different times. The main point is that the dither in social systems is a self-generated phenomenon, and to assume it is constant for an agent may not always be appropriate.