bluuebunny/crossref_metadata_2025 huggingface dataset:
Linear differential equations in general
Authors: Guest Martin A
Published: November 2023

In this chapter we start again from the beginning, independently of quantum cohomology. Our objective is to set up some terminology from the algebraic theory of overdetermined systems of partial differential equations, that is, the theory of holonomic D-modules. While the general theory of D-modules is very technical, we only need some basic concepts, which we shall introduce gradually.
Likelihood Calculation in Molecular Phylogenetics
Authors: Bryant David , Galtier Nicolas , Poursat Marie-Anne
Published: November 2023

Likelihood estimation is central to many areas of the natural and physical sciences and has had a major impact on molecular phylogenetics. In this chapter we provide a concise review of some of the theoretical and computational aspects of likelihood-based phylogenetic inference. We outline the basic probabilistic model and likelihood computation algorithm, as well as extensions to more realistic models and strategics of likelihood optimization. We survey several of the theoretical underpinnings of the likelihood framework, reviewing research on consistency, identifiability, and the effect of model mis-specification, as well as advantages, and limitations, of likelihood ratio tests.
Reconstructing the Duplication History of Tandemly Repeated Sequences
Authors: Gascuel Olivier , Bertrand, Denis , Elernento Olivier
Published: November 2023

Tandemly repeated sequences can be found in all genomes that have been sequenced so far. However, their evolution is only beginning to be understood. In this chapter, we present state-of-the-art mathematical concepts and approaches for studying tandemly repeated sequences, from an evolutionary perspective. We describe a tandem duplication model for representing the evolution of these sequences, and shows that it has strong biological support. Then, we provide extensive mathematical and combin-atorial characterization of tandem duplication trees and describe several algorithms for inferring tandem duplication trees from aligned and ordered sequences. We finally compare these algorithms using computer simulations and discuss directions for further research.
The Inversion Distance Problem
Authors: Bergeron Anne , Mixtacki, .Iulia , Stoye Jens
Published: November 2023

Among the many genome rearrangement operations, signed inversions stand out for many biological and computational reasons. Inversions, also known as reversals, are widely identified as one of the common rearrangement operations on chromosomes, they are basic to the understanding of more complex operations such as translocations, and they offer many com-putational challenges. From the first formulation of the inversion distance problem, ca. 1992, to its first polynomial solution in 1995, to the several simplifications of the solution in recent years, there is not yet a simple, complete, and elementary treatment of the subject. ‘l’his is the goal of this chapter.
Scale and island ecological theory: towards a new synthesis
Authors: Whittaker Robert J , Fernández-Palacios José María
Published: November 2023

In the previous two chapters we have reviewed island ecological theories from both macroecological and ecological-biogeographical perspectives, tracing the development of ideas following the appearance of the seminal work of MacArthur and Wilson (1963, 1967). We return again to their equilibrium theory at the outset of this chapter. The exploration of these ideas by ecologists has produced many insights, sometimes consistent with the original models, sometimes inconsistent. Departures from predicted behaviours are in many respects of greatest interest, as they show how the models need to be modified. As a research programme, this body of work is characterized by a general assumption that the systems can be characterized as dynamic and equilibrial: indeed we might consider this paradigmatic. Yet, as we know, this assumption may not be supported in all cases. Accordingly, we will consider the alternatives in the present chapter. In so doing we hope to reconcile the apparently conflicting lessons from 40 years of research and to suggest where island ecological theory might be heading.
Anthropogenic losses and threats to island ecosystems
Authors: Whittaker Robert J , Fernández-Palacios José María
Published: November 2023

Throughout our discussions of island ecology and evolution, we have mostly set to one side the significance of humans as shapers of island biogeography. As this chapter will show, this is a questionable practice, as human societies have had a profound influence on island biodiversity in both recent historical and prehistorical time (Morgan and Woods 1986; Johnson and Stattersfield 1990; Groombridge 1992; Pimm et al. 1995). This influence has been manifested in many ways, but the most profound must surely be the extinction of numerous island races and species. Of all the species that have ever lived on the Earth, only a small fraction are alive today. Natural catastrophes, such as volcanic eruptions, meteorite impacts, climate changes, marine transgressions and regressions, in combination with biotic forcing, have been key agents of species extinction in the past. Extinction rates have varied through time, with five phases recognized as particularly intense and widespread events in the fossil record, the so
The brain—gambler and logician
Authors: Berthoz Alain
Published: November 2023

Is the brain a calculator that uses probability theory to make decisions [1] ?The basic principles of probability theory were first hammered out in an exchange of letters between Blaise Pascal and Pierre de Fermat on the subject of gambling. Pascal suggested that when in doubt, one should bet that God exists because that way there is everything to gain—life everlasting—and nothing to lose. After all, if God does not exist, neither does anything else. But the modern concept of probability is the brainchild of Jakob Bernoulli, who in 1713 set forth in Ars conjectandi a general theory for making rational decisions in uncertain circumstances.
Walking and balance
Authors: Berthoz Alain
Published: November 2023

If, on a beautiful summer afternoon, it pleases you to take a leisurely stroll through the Luxembourg Gardens, reading the poems of Verlaine, it is unlikely you will be making many strategic cognitive decisions. Still, watch out for the child who suddenly comes looking for his ball between your dreamer’s legs and trips you! But if you play for a French football, rugby, or basketball team, if you are a mountain hiker, a police officer chasing a thief, a roofer on the top of a five-storey building, it’s a completely different matter. You can choose to go quickly or slowly, to walk or run, to jump from one foot to the other, or with both feet together.
Sensory conflict: perception of movement
Authors: Berthoz Alain
Published: November 2023

Imagine you are sitting in a train. The train on the track beside you departs.Watching it move out your window, you have the illusion that your train is the one leaving. This illusion can also be felt on a bridge, looking at a river. The movement of a visual scene may be due either to movement of the body, or to movement of the world, in that case, with the body remaining still. How do we decide which interpretation is correct? We are in the same situation as Solomon, except that we cannot cut the solution in two.

Sometimes, a conflict is the result of several simultaneous movements in the visual world. For example, in the train, if you look out the window and a blizzard is raging, the clouds race by. The visual field consists of several contradictory movements: that of the environment in a sense contrary to the train, of the snowflakes, of the cloudshow does the brain decide that some elements of the environment are moving and others not? This decision is complex [2].
Music and how we became human—a view from cognitive semiotics Exploring imaginative hypotheses
Authors: Brandt Per Aage
Published: November 2023

On the evidence from palaeontology, our species, Homo sapiens, was biologically stable and physiologically modern 160,000 years ago (Stringer 2003). When glaciation stopped 150,000 years later, agriculture, writing, and history emerged—cultural life based on a symbolically represented shared past. Somewhere in the middle of this long period, perhaps about 50,000 years ago, humans apparently began to ‘make sense’ together—to symbolize, paint, speak, and form kinship systems that held communities together—and, according to the scenario I propose, perhaps first made music.
Voices of shared emotion and meaning: Young infants and their mothers in Scotland and Japan
Authors: Powers Niki , Trevarthen Colwyn
Published: November 2023

A journey of cultural discovery has already begun when an infant is born—from the inborn powers of human expression and experience within the growing Self toward mastery of habits that have been cultivated by generations of forebears; they who have learned and taught their knowledge and skills so that their children may assimilate a history of many Others’ lives and meanings (Gomes-Pedro 2002). To discover what other people know, a child has to participate in feelings with them, not just exchange information about the world they are in together (Halliday 1975; Jahoda and Lewis 1988; Bruner 1996; Rogoff 2003; Rogoff et al. 2003).
The effects of maternal depression on the ‘musicality’ of infant-directed speech and conversational engagement
Authors: Marwick Helen , Murray Lynne
Published: November 2023

In this chapter, we look at the effect of the mental illness of depression on the ‘musicality’ of a mother’s voice as she talks with her young infant, and discuss the possible impact of this on the infant’s emotional and cognitive development. The term musicality has been used to capture fundamental characteristics of human vocal communication—the shared expressiveness in timing, phrasing, intonation and voice quality. All of these dimensions can be identified in the earliest caregiver–infant talk and play.We first summarize the characteristics of musicality—timing and expression—in human communication in general, and then consider its special place in the vocal expressiveness of adults talking to infants, and on the part of infants themselves. Finally, we review findings on the impact of depression on maternal expressiveness, their implications for how we should understand conversational engagements between depressed mothers and their infants, and the significance for diagnosis and therapy.
Between communicative musicality and collaborative musicing: A perspective from community music therapy
Authors: Pavlicevic Mercédès , Ansdell Gary
Published: November 2023

The marriage between communicative musicality and improvisational music therapy was ostensibly made in heaven. Music therapists in search of a new explanatory and legitimating theory came back from conferences in the 1980s with the fruits of Trevarthen and Stern’s work. They felt their search had ended. We, too, are among the many music therapists to admire the elegant synthesis Malloch and Trevarthen subsequently made in their theory of communicative musicality, which they described as ‘a foundation for a theory of music therapy’ (Trevarthen and Malloch 2000, p. 5) based on the belief that ‘Communicative Musicality is the source of the music therapeutic experience and its effects’ (p. 3).
Biology And Molecular Neuropathology Of β-Amyloid Protein
Authors: Lee Edward B , Lee Virginia M -Y
Published: November 2023

A century ago, Alois Alzheimer described the post-mortem neuropathological findings from a woman who suffered from the disease which now bears his name (Alzheimer 1907). In addition to profound neuron loss, he found two major lesions in the cortex and hippocampus, now known as senile plaques and neurofibrillary tangles. Until the biochemical purification of the building blocks of these two pathological lesions, the mechanisms underlying the pathogenesis of Alzheimer‘s disease (AD) were difficult to ascertain. Eight decades after the initial description of AD, the molecular era of AD research was ushered in with the isolation of the AP peptide, initially from cerebrovascular amyloid (Glenner and Wong 1984) and subsequently from senile plaques (Masters et al. 1985 ).
Presenilins
Authors: Vetrivel Kulandaivelu S , Thinakaran Gopal
Published: November 2023

Alzheimer‘s disease (AD) is the leading cause of dementia in the elderly. While the vast majority of AD occurs as an age-associated disorder, autosomal dominant inheritance of mutant genes APP, PSENl, or PSEN2, which encode the amyloid precursor protein (APP), presenilin 1 (PSl), or presenilin 2 (PS2), respectively, cause early-onset AD in several families (familial Alzheimer‘s disease (FAD)). Mutations in PSENl and PSEN2 account for the majority of cases of FAD. Since the first discovery of a genetic link between PSENl and PSEN2 with AD, several research groups have sought to unravel how pathogenic mutations in PSEN genes cause dysfunction of select populations of neurons in the brain leading to AD pathogenesis. PSl and PS2 are polytopic membrane proteins which function as the catalytic subunit of an enzyme complex, termed y-secretase.
Current Pharmacological Approaches To Treating Alzheimer‘s Disease
Authors: Wilcock Gordon K , Dawbarn David
Published: November 2023

Pharmacological approaches to the treatment of Alzheimer‘s disease (AD) can be broadly grouped into those that aim for symptomatic treatment, those that attempt to modify the disease process, and those that may lower the risk or delay the onset of AD. The distinction between these approaches is not clear cut, as will become apparent. Symptomatic treatments have mainly centred on neurotransmitter systems. The well established deficits in the cholinergic system in AD provided an obvious focus for phar macological research, and led to the development of the first drugs to be licensed for the treatment of AD. However, numerous other neurotransmitter systems are affected in AD, including the noradrenergic, serotonergic, glutaminergic, and dopaminergic systems. These systems have physiological roles in normal cognitive functioning, and multiple neurotransmitter deficits probably contribute to the cognitive decline in AD.
Future Directions: The A Amyloid Pathway As The Target For Diagnosing, Preventing, Or Treating Alzheimer‘s Disease*
Authors: Masters Colin L
Published: November 2023

Future research into Alzheimer‘s disease (AD) will continue to be dominated by efforts to develop rational therapeutic strategies based on our progressive understanding of the molecular basis of synaptic degeneration in AD. In this chapter, the current status of dis covering targets and developing drugs for use in the amyloid precursor protein/amyloid beta (APP/AP) pathway (Fig. 18.1) is reviewed. The 2005-2006 literature is surveyed, which includes several useful reviews (Benson 2005; Bloom et al. 2005; Golde 2005; Higuchi et al. 2005; Pangalos et al. 2005; Selkoe 2005; Hilbush et al. 2005; Wisniewski and Frangione 2005). Also reviewed are two public data bases of clinical trials which enumer ate the current status of clinical activity in this area (Novartis International, maintained by Herrling and colleagues (Kwon and Herrling 2005) and the Clinical Trials registry sponsored by the NIH .
Sex, Sexes and Selfish Elements
Authors: Hurst Laurence D
Published: November 2023

It was a chance conversation that led to me doing a DPhil (as they call their PhDs in Oxford) under Bill ’s supervision. In the summer of 1986, just prior to my final undergraduate year studying Zoology at Cambridge, I happened to talk to Nick Davies, our lecturer in behavioural ecology. We chatted about what I found interesting. The idea that male birds show off their parasite status to females was a really fascinating idea, I remarked. He suggested that I should therefore do a DPhil with Bill Hamilton in Oxford. Nick kindly wrote a letter of introduction and, sometime later that year, I found myself in Bill ’s office in the Zoology department, being interviewed by him and Alan Grafen for a DPhil position that they would jointly supervise.
Hamilton And Gaia (A preface to ‘Spora and Gaia: How microbes fly with their clouds ‘)
Authors: Lenton Tim
Published: November 2023

The story of my work with Bill unfolds with the spring of 1997, and I will tell it in his written words, where possible. I was in the third year of my PhD studies at the University of East Anglia in Norwich, and had been absorbed in an effort to reconcile what I was learning about the planetary effects of life and what I knew about the mechanism of natural selection. This was summarized in a review article I had written and (rather optimistically) submitted to Nature (eventually to be published as ‘Gaia and natural selection ‘1). I was eager to resolve what I saw as some long-held misunderstandings between ‘Gaiaists ‘, as Bill called them, and evolutionary biologists. I was aware of Bill ’s interest in Gaia from things he ’d written and through my friendship with Jim Lovelock. The two met in January 1997 and ‘a bit unhappy about the way the discussion ended, seemingly in deadlock ’, Bill then wrote Jim a long letter clarifying his views on Gaia.
Who Was Left Out? Exclusions, refusals, and drop-outs
Authors: Simon Stephen D
Published: November 2023

Research studies often have a narrow focus, but sometimes it can be too narrow. When too many patients are left out, those who remain may not be representative of the types of patients you will encounter.
Mountain or Molehill? The Clinical Importance of the Results
Authors: Simon Stephen D
Published: November 2023

Do the research results add up to something important or are the results trivial? For the results to be important, the study needs to have a narrow focus, it has to measure the right outcomes, and the change in the outcome has to be large from a clinical perspective.
Where Is the Evidence? Searching for Information
Authors: Simon Stephen D
Published: November 2023

In a book like this, it would be difficult to give a comprehensive overview of how to search the published literature to find all the research studies associated with a particular treatment or a particular disease. You should discuss any serious literature search with a professional librarian.
Introduction
Authors: Bertuglia Cristoforo Sergio , Vaio Franco
Published: November 2023

In our picture of reality, we almost always focus our attention on the description of the evolution over time of objects that we identify with respect to their surrounding environment and which we call systems, mostly in an attempt to predict their future behaviour. Systems are objects with varying degrees of complexity, although they are always acknowledged as containing different elements that interact with one other. Various kinds of relations may also exist between the system and the external environment, but these are either of a different nature or of a lesser intensity with respect to those that are encountered inside what we identify as ‘system’ and that contribute to its definition.
Linearity in models
Authors: Bertuglia Cristoforo Sergio , Vaio Franco
Published: November 2023

A vast quantity of different system dynamics can be found in both natural and social sciences. However, they all have several common characteristics which enable them to be described in fairly simple and, above all, very general mathematical terms. We are referring to the dynamic processes typical of systems close to a configuration of stable equilibrium. Such systems tend towards equilibrium by means of a process that, to a good approximation, can be described by a so-called linear model. In other words, we can approximate the description of the evolution of these systems towards equilibrium by means of a calculable evolutive trajectory, if we know the initial conditions, using a law of motion expressed in the form of an extremely simple differential equation: a linear differential equation.
Dynamical systems and the phase space
Authors: Bertuglia Cristoforo Sergio , Vaio Franco
Published: November 2023

Let us reconsider a point that was introduced in chapter 2, but specifying the terms better: we want to define what is meant by dynamical system. When we describe the evolution of a system we use several state variables, i.e. a set of magnitudes, chosen appropriately, functions of time, the values of which define everything we know about the system completely and unambiguously; let us indicate them, just to be clear, with x;(t). Thus the evolution of a system is given by the evolution of the set of n state variables, each of which evolves according to a specific deterministic law. In this sense, we can speak of a dynamical system, identifying a system of this nature with the system of equations that defines the evolution of all of the state variables.
The chaotic pendulum
Authors: Bertuglia Cristoforo Sergio , Vaio Franco
Published: November 2023

In this part we have discussed oscillations at some length. Whether we are examining a pendulum or a mass connected to a spring, an electrical current in a specific circuit or a wave broadcast by an antenna, economic cycles (real or assumed) or the listing of a stock, or further still, in a more general and abstract sense, the condition of dynamic equilibrium of a system that is interacting with other systems, the mathematical model of oscillations represents a basic schema that can be adapted, by making the appropriate corrections, to fit the case in question. A wide number of variants of the model of motion of an oscillating system can be constructed. These depend not so much on the nature of the specific system being studied, but rather on the different external conditions in which the system finds itself, or, to put it better, that we wish to be taken into account. The oscillations described by a linear model, for example, can be applied to the dynamics of a pendulum as well as to a mass attached to a spring, a current in an electric circuit, etc., as long as the disturbances to the state of stable equilibrium are smal1. This is precisely what the model does: it abstracts the common characteristics, in this case the dynamics of the motion close to the condition of stable equilibrium, ignoring the other characteristics that define the specific oscillating system. If the dynamics envisaged by the linear model do not successfully adapt to the description of the oscillations observed, this may be due to the fact that the oscillating system is not close to its stable equilibrium, or even that the oscillating system is so disturbed that it cannot find a stable equilibrium. In this case a new model of nonlinear oscillations, one of the many variants that can be conceived starting from the basic model of the harmonic oscillator, must be used to provide an acceptable description of the dynamics observed.
Linear models in social processes: the case of two interacting populations
Authors: Bertuglia Cristoforo Sergio , Vaio Franco
Published: November 2023

After having presented, in the paragraphs above, several versions of one of the simplest and most important models in mathematical physics, the model of the oscillator, which has served as a basis for developments and extensions into other sectors, we will now look at another example of modelling that has become a classic theme in social science: the case of a system of two interacting populations. A number of different theories have been adopted in the approach to this subject which have given rise to a numerous family of models. In general these are models that are essentially of theoretical interest: they do not represent anything more than an initial attempt to model extremely complex phenomena such as social ones (in this context, naturally, the term social is intended in a broad sense, referring to any group of individuals, identifiable according to certain parameters, that interact with another group of individuals).
Chaos in real systems and in mathematical models
Authors: Bertuglia Cristoforo Sergio , Vaio Franco
Published: November 2023

Phase space, orbit, basin of attraction and attractor are all mathematical concepts and as such are abstract; this means that they relate more to the abstract models that we construct of the processes observed, rather than to the processes themselves. In a certain sense, we imagine attractors and dynamical orbits on the basis of our mathematization of phenomena (when we succeed in doing so). But the passage from the real system, that we assume to be deterministic, despite the fact that its evolution might seem unpredictable to us, to the mathematical mode] that describes it, from a certain viewpoint, is an arbitrary passage, because a real system and its mathematical model are conceptually found in two completely different spheres. The correspondence between the two is based only on the fact that very often the mode] created ‘works well’ in predicting the behaviour of the real system, as we have already seen. The differential equations of the mode] are nonlinear (in general) and deterministic, so much so that often we call them the law that controls the real corresponding process; they give rise to deterministic chaos that seems to do a good job of reproducing the phenomenology observed. But it is still the chaos of a model, i.e. a chaos of a mathematical nature; the problem is linking this with the chaos observed. This passage, however, is not always easy to make.
The problem of measuring chaos in real systems
Authors: Bertuglia Cristoforo Sergio , Vaio Franco
Published: November 2023

In the previous sections we have mostly talked about the stability and chaos of dynamical processes in mathematical models. Now we would like to look at the problem of the stability and chaos (if any) in observed dynamical processes, i.e. referring to the analysis of historic data series observed in real systems. Definition (18.9) of the Lyapunov exponents does not have only a theoretical meaning, but can be used in important applications to real cases. The problem we are faced with is how to use a series of data in order to be able to calculate quantities such as Lyapunov exponents and to identify the presence, if any, of an attractor and its dimension (fractional or integer). This would enable us to establish, in particular, if the historic series of data is produced by a system that functions’ according to a deterministic law, regardless of whether we have chaos or not, or if the data observed are stochastic, i.e. if they are the result not of a law, but of that which is commonly ca11ed ‘chance’, and follow a probability distribution. The problem is anything but easy, in particular for systems in whose dynamics it is difficult, if not impossible, to observe regularities, as usuaUy happens in social sciences.
Some thoughts on the meaning of ‘doing mathematics’
Authors: Bertuglia Cristoforo Sergio , Vaio Franco
Published: November 2023

In this Chapter and in Chapter 32 and 33, to conclude the book, we would like to reflect for a moment on the fact that, as we have said on many an occasion, at the moment there is no formalization of complexity that enables it to overcome its current, rather confused state, which for now is known as the ‘complexity approach’, and to achieve the objective of first becoming a method and then a bona fide scientific theory. The complexity approach that has recently appeared in modern scientific circles is generally still limited to an empirical phase in which the concepts are not abundantly clear and the methods and techniques are noticeably lacking. This can lead to the abuse of the term ‘complexity’ which is sometimes used in various contexts, in senses that are very different from one another, or at times even erroneously, to describe situations in which the system does not even display complex characteristics.
Digression into the main interpretations of the foundations of mathematics
Authors: Bertuglia Cristoforo Sergio , Vaio Franco
Published: November 2023

In this section, we will be making a digression from the main theme of the book, to take a brief look at the main interpretations that scientific thought has given, at least in the last century and a half, to the foundations of mathematics, and more generally, to the meaning of working with mathematics. A reflection on the actual meaning that is attributed to mathematics and its limitations, in fact, is necessary in order to attempt to clarify the question of the applicability of mathematics (and of which mathematics) to complexity, i.e. if and in what way could it be possible to formulate mathematical laws to describe the complex phenomenology.
Felix Hausdorff’s Considered Empiricism
Authors: Epple Moritz
Published: November 2023

1 Introduction

This chapter presents some of the epistemological views of a rather unconventional mathematician, philosopher, and writer of the period around 1900, Felix Hausdorff. Hausdorff was born in 1868, and together with his wife, Lotte Hausdorff, née Goldschmidt, and her sister, he took his own life on 26th of January 1942 in order to avoid being sent to a concentration camp.Today, Hausdorff is mostly known for his ground-breaking monograph on set theory, the Grundzüge der Mengenlehre, published in 1914, shortly before the outbreak of World War I. Among other things, this monograph contained the first extended discussion of the notion of a topological space. In the interwar period that followed, Hausdorff’s Grundzüge and its successor, simply entitled Mengenlehre and published in 1927, became probably the most often cited book in this area of mathematics.
H. Weyl’s mature view of mathematical knowledge
Authors: Scholz Erhard
Published: November 2023

Introduction

Hermann Weyl’s views of mathematical knowledge went through various transformations. He described most of them himself in his retrospective (Weyl 1954). In 1905, at the beginning of his university studies, he was thrown (by Hilbert’s views on the foundations of geometry) from a youthful and naive Kantianism to a ‘positivism’ in the sense of H. Poincaré and E. Mach. Five years later, he came under the influence of Husserl’s phenomenology and turned away from positivism. At Zürich he came into close contact with F. Medicus, an expert in the philosophy of post-Kantian German idealism and an editor of J. G. Fichte’s works. After Weyl came back from service in the German army in 1916, his philosophical outlook turned radically towards realism in the sense of German idealist philosophy, formed under the impression of his way of reading Fichte and, a little later, under the personal influence of L.E.J. Brouwer. In 1926 he had the chance to rework his philosophical outlook when he wrote his contribution Philosophie der Mathematik und Naturwissenschaften for the handbook of philosophy edited by M. Schröter and A. Bumler (Weyl 1927a). During this work Weyl became more closely acquainted with Leibniz’ philosophy, among others. He broadened and refined his philosophical views and started to reconsider his earlier exaggerated rejection of Hilbert’s formalist views in the foundations of mathematics.
Hints and solutions for starred exercises and problems
Authors: Stirzaker David
Published: November 2023

Simply take the expected value of each side of the inequality, which is preserved.
Parameter estimation I
Authors: Sivia D S
Published: November 2023

Parameter estimation is a common data analysis problem. Like Laplace, for example, we may be interested in knowing the mass of Saturn; or, like Millikan, the charge of the electron. In the simplest case, we are only concerned with the value of a single parameter; such elementary examples are the focus of this chapter. They serve as a good introduction to the use of Bayes ‘ theorem, and allow for a discussion of error-bars and confidence intervals.

Let us begin with the analysis of data from a simple coin-tossing experiment. Suppose I told you that I had been to Las Vegas for my holidays, and had come across a very strange coin in one of the casinos; given that I had observed 4 heads in 11 flips, do you think it was a fair coin? By fair, we mean that we would be prepared to lay an even 50 : 50 bet on the outcome of a flip being a head or a tail. In ascribing the property of fairness (solely) to the coin we are, of course, assuming that the coin-tosser was not skilled enough to be able to control the initial conditions of the flip (such as the angular and linear velocities).
Non-parametric estimation
Authors: Sivia D S
Published: November 2023

In Chapters 2 and 3, we dealt with problems which entailed the estimation of the values of a few well-defined parameters; the analysis was then extended, in Chapter 4, to cover the case where there was some doubt as to their optimal number. Now let ‘s move on to the most difficult situation, in which we want to draw inferences about an object of interest but don ‘t have enough information, or confidence, to be able to characterize it by a specific type of functional model. This is a rather open-ended question that requires us to think of both a suitable description and any weak constraints which might be appropriate for a flexible ‘free-form ‘ solution.
Molecular cytogenetics of cancer
Authors: Sheer Denise , Shipley Janet M
Published: November 2023

Cancer arises from the accumulation of genetic changes which confer a selective advantage to the cells in which they occur. These changes consist of mutations, and numerical and structural chromo- some aberrations. They usually occur in somatic cells, but certain genetic changes can be inherited and cause a predisposition to cancer (Lengauer et al., 1998; Balmain et al., 2003; see also Chapter 3). Recurrent and sometimes highly specific chromosome aberrations are present in different types of cancer. Molecular genetic analysis of these aberrations has identified numerous genes which contribute to tumorigenesis, opening new avenues of research into regulatory pathways in the cell. Chromosome aberrations are increasingly playing a role in clinical management of cancer patients, since they can provide critical diagnostic and prognostic information.
Cytokines and cancer
Authors: Szlosarek Peter W , Balkwill Frances R
Published: November 2023

Complex multicellular organisms maintain cellular homeostasis at the local tissue level via a diverse array of secreted low-molecular weight mediators collectively called cytokines. These include tumour necrosis factor-a (TNF-a), interleukins (ILs), interferons (IFNs), colony-stimulating factors, chemokines, angiogenic factors, and growth factors. Unlike classical endocrine hormones, these proteins act in an autocrine, paracrine, and/or juxtacrine fashion on a variety of cells, ranging from stem cells to those that are fully differentiated. Cytokines act within an informational network consisting of ligands and their respective cell- surface receptors and downstream intracellular signalling pathways, enabling cells to participate in a range of processes including cell activation (survival, growth, and differentiation), cell death (apoptosis), cell motility, inflammation, and immunity (see Table 14.1).
Stem cells, haemopoiesis, and leukaemia
Authors: Greaves Mel
Published: November 2023

The leukaemias, and related diseases lymphoma and myeloma, are all blood cell cancers. Because of the accessibility of this tissue, the relative ease of cell culture, and the availability of model systems with animal cells, knowledge of the cellular and molecular basis of these forms of cancer has often led the way and provided paradigms for cancer research in general. Leukaemias are different from other cancers in so far as their evolution and dissemination does not require architectural disruption and metastatic processes that are critically involved in most other cancers.
Immunotherapy of cancer
Authors: Jackson Andrew M , Porte Joanne
Published: November 2023

Immunotherapy has the potential not only to destroy tumours but also to engender life-long immunity. Furthermore for a small proportion of tumours with viral ethiology, it may be possible to prevent malignancy by prophylactic vaccination. Immunotherapy is a most important and rapidly growing area in applied cancer research and is no longer at the fringe of biological science or restricted to in vitro and pre-clinical systems. Rather, immunotherapy is now being explored as a clinical option for all malignancies, and for some diseases it is already the front-line therapy of choice.
Developmental constraints on or developmental structure in brain evolution?
Authors: Finlay Barbara L , Cheung Desmond Tak-Ming , Darlington Richard B
Published: November 2023

The more we discover about the basic structure of vertebrate and invertebrate evolution, the more impressive the evidence of its conservative nature becomes. Evidence for commonalities versus special adaptations in brain evolution, with particular attention to rules for the proliferation of the cortex will be discussed. Conserved developmental rules that produce highly predictable brain organization seem best described as rules that produce generic, optimal organization rather than limiting constraints.
Applications
Authors: Cameron Peter J
Published: November 2023

One of the most famous applications of coding theory occurred in the exploration of the outer planets of the solar system by unmanned space probes. These probes carried scientific equipment and cameras. The information about temperatures, magnetic fields, and so on was very important to astronomers, but the pictures of Jupiter, Saturn, and their moons made us all aware of the existence of other worlds with their distinctive characters.
Quasi-isometries and quasisymmetric maps
Authors: Fletcher A , Markovic V
Published: November 2023

Quasiconformal maps of the upper half-plane H to itself extend to the boundary R. We show what conditions such mappings R R must satisfy, and conversely that every such mapping extends to a quasiconformal mapping of H. Such self-mappings of R are called quasisymmetric. We investigate properties of quasisymmetric maps and illustrate two ways of extending quasisymmetric maps to quasiconformal maps, the Beurling–Ahlfors extension and the conformally natural Douady–Earle extension. We also define the notion of a quasi-isometry and show that all quasiconformal maps are quasi-isometric.
The Beltrami differential equation
Authors: Fletcher A , Markovic V
Published: November 2023

The solution of the Beltrami differential equation is a quasiconformal mapping, and all quasiconformal mappings arise in this way, giving a correspondence between quasiconformal mappings and Beltrami differentials.
Current perspectives on high-level groupings of protists
Authors: Simpson Alastair G B , Patterson David J
Published: November 2023

Most of the major branches of eukaryotic diversification are protistan. The modern understanding of protistan diversity and evolutionary relationships is based on morphological studies, especially by transmission electron microscopy, and on molecular phylogenetic studies, initially dominated by small subunit ribosomal RNA but increasingly involving multigene datasets. Morphological studies define approximately 60 robust lineages of eukaryotes. Current syntheses, primarily based on molecular phylogenetic studies, place these lineages in six to eight ‘‘supergroups’’. However, this catalogue is incomplete as the definition of most supergroups is not clear and their extent and compositions are disputed, and a further 25 lineages, for which there are electron microscopical data and/or molecular data, are not currently assigned to any supergroup.
Ciliate genome evolution
Authors: McGrath C L , Zufall, R A , Katz L A
Published: November 2023

The study of genome evolution in eukaryotic microbes such as ciliates can elucidate trends across the eukaryotic tree of life as well as unique, lineage-specific genome features. Ciliate genomes are unique among eukaryotes in that: (i) two distinct genomes exist in separate nuclei (the ‘‘somatic’’ macronucleus and ‘‘germline’’ micronucleus) within every cell; and (ii) macronuclear genomes undergo developmentally-regulated rearrangements, which can be extensive and lead to the generation of as many as 25 000 000 ‘‘chromosomes’’ in a single ciliate (reviewed in Klobutcher and Herrick 1997; Prescott 1994; Riley and Katz 2001). Ciliates have also been a rich source for the discovery of features found elsewhere across the tree of life, including the existence of self-splicing RNA (Kruger et al. 1982) and telomeres (Blackburn and Gall 1978). This Chapter reviews the basics of ciliate genomes and discusses the implications of genome processing on ciliate evolution.
Cognitive Control Processes And Hypnosis
Authors: Egner Tobias , Raz Amir
Published: November 2023

The striking changes in perception and conscious awareness that can be achieved with hypnotic induction have fascinated psychologists for many years. How does one account for neurologically healthy subjects who, following hypnotic induction and appropriate suggestions, report to perceive an illusory voice, or negate seeing an object placed right in front of them? To hypnosis researchers, the recent advent of cognitive neuroscience has brought forth great promise, with new techniques such as functional magnetic resonance imaging (fMRI) allowing us to take a peek into the hypnotized brain. However, the benefits of a cross-talk between the fields of hypnosis and cognitive neuroscience research are mutual, for hypnotic suggestions can serve as a rich avenue for the investigation of fundamental brain processes (Raz and Shapiro 2002).
New Paradigms Of Hypnosis Research
Authors: Jamieson Graham A , Hasegawa Harutomo
Published: November 2023

In hypnosis, verbal suggestions, in responsive individuals, can lead to remarkable alterations in subjective experiences. These include atypical changes in perception (positive and negative hallucinations), pain (analgesia), memory (amnesia) and the experience of volition. Some behaviours may appear to occur without volitional control (ideomotor suggestion) whilst others occur despite volitional control (challenge suggestion). The considerable effects of hypnotic suggestion on somatic physiology have been successfully applied to the treatment of a variety of medical disorders, i.e. the effects of hypnosis may be observed in phenomenological, behavioural and physiological data. Historically, research paradigms in hypnosis have emphasized methodologies largely restricted to one or another of these possible data sets.
Time Distortion, And The Nature Of Hypnosis And Consciousness
Authors: Naish Peter LN
Published: November 2023

Of all the phenomena and claims that have been linked to hypnosis, such as pain control, memory modification or even enhancement of the immune system (Gruzelier et al. 2002a), it may seem strange to focus upon something as obscure as its effect on timing. In fact, among the alleged effects of hypnosis, time distortion seems to have a rather spe- cial characteristic, making it valuable when trying to understand the nature of hypnosis itself. Before I explain that characteristic, and describe the associated research, I will begin by showing why research on the other phenomena (while valuable for other reasons) may not be best placed to explain the nature of hypnosis.
Minimal Surfaces
Authors: Calegari Danny
Published: November 2023

We here review the theory of minimal surfaces, especially in 3-manifolds. Monotonicity properties of codimension one minimal surfaces, e.g. barrier surfaces, the maximum principle etc. complement the role of monotonicity in the theory of groups of homeomorphisms of 1-manifolds. When we come to study taut foliations in earnest in Chapter 4, we will see that both kinds of monotonicty are tightly entwined, and lead to a rich and beautiful theory.
Essential Laminations
Authors: Calegari Danny
Published: November 2023

This is a short chapter, whose purpose is mainly to introduce the definition and some basic properties and examples of essential laminations and genuine laminations. This is a rich and important theory, but in some ways outside the main focus of this book. We refer the interested reader to the papers [89], [92], [95], [94], [96], [150], [2] for some of the highlights of the theory.
Integrability in classical mechanics
Authors: Dunajski Maciej
Published: November 2023

Integrable systems are non-linear differential equations (DEs) which ‘in principle’ can be solved analytically. This means that the solution can be reduced to a finite number of algebraic operations and integrations. Such systems are very rare – most non-linear DEs admit chaotic behaviour and no explicit solutions can be written down. Integrable systems nevertheless lead to very interesting mathematics ranging from differential geometry and complex analysis to quantum field theory and fluid dynamics. In this chapter we shall introduce the integrability of ordinary differential equations (ODEs). This is a fairly clear concept based on existence of sufficiently many well-behaved first integrals, or, as a physicist would put it, constants of the motion.
Hamiltonian formalism and zero-curvature representation
Authors: Dunajski Maciej
Published: November 2023

We shall make contact with the Definition 1.2.1 of finite-dimensional integrable systems and show that KdV has infinitely many first integrals.
Events and their probabilities
Authors: Grimmett Geoffrey R , Stirzaker David R
Published: November 2023

A fair coin is tossed repeatedly. Show that, with probability one, a head turns up sooner or later. Show similarly that any given finite sequence of heads and tails occurs eventually with probability one. Explain the connection with Murphy’s Law.
Random variables and their distributions
Authors: Grimmett Geoffrey R , Stirzaker David R
Published: November 2023

You wish to ask each of a large number of people a question to which the answer “yes” is embarrassing. The following procedure is proposed in order to determine the embarrassed fraction of the population. As the question is asked, a coin is tossed out of sight of the questioner. If the answer would have been “no” and the coin shows heads, then the answer “yes” is given. Otherwise people respond truthfully.
Discrete random variables
Authors: Grimmett Geoffrey R , Stirzaker David R
Published: November 2023

We toss n coins, and each one shows heads with probability p, independently of each of the others. Each coin which shows heads is tossed again.
Data collection
Authors: Gelman Andrew , Nolan Deborah
Published: November 2023

One way students learn about data collection is actually to collect some data. This teaches some of the principles of experimental design and also gives the students a feel for the practical struggles and small decisions needed in real data gathering. This chapter includes several classroom demonstrations and examples to illustrate key ideas, as well as examples of instructions for longer projects.
Probability
Authors: Gelman Andrew , Nolan Deborah
Published: November 2023

We cover probability around the middle of the semester (see Section 12.3), and by that time a few probability examples have already arisen in class. In covering descriptive statistics (see Chapter 3), we discuss the concepts of one- and two dimensional distributions along with the basic use of the normal distribution. We informally introduce probability calculations in the context of random sampling for data collection (see Section 5.1.1). This chapter has some examples and demonstrations focused specifically on probability. More theoretical probability examples appear in Chapter 15, with some of the easier problems in Section 15.2.
Student activities in survey sampling
Authors: Gelman Andrew , Nolan Deborah
Published: November 2023

The principles of active student participation that we have discussed in the context of an introductory statistics course can also be used in more advanced classes. Part I of this book contains many activities on sampling that we also use in our more advanced courses. For example, Section 8.1 describes a demonstration in which students draw samples of candies from a bag and weigh them. The candies are of different shapes and sizes; the larger ones are easier to grab, which leads to sampling bias. The activity on family size (Section 5.1.6) demonstrates size-biased sampling, and the examples of wacky surveys in the news (Section 5.1.3) offer a variety of examples of bias. Section 10.2 has many examples of selection bias.