bluuebunny/crossref_metadata_2025 huggingface dataset:
How do we select perceptions and actions? Human brain imaging studies
Authors: Rees Geraint , Frith Christopher D
Published: November 2023

The selective nature of human perception and action implies a modulatory interaction between sensorimotor processes and attentional processes. This chapter explores the use of functional imaging in humans to explore the mechanisms of perceptual selection and the fate of irrelevant stimuli that are not selected. Experiments with positron emission tomography show that two qualitatively different patterns of modulation of cerebral blood flow can be observed in experiments where non-spatial visual attention and auditory attention are manipulated. These patterns of modulation of cerebral blood flow modulation can be described as gain control and bias signal mechanisms. In visual and auditory cortex, the dominant change in cerebral blood flow associated with attention to either modality is related to a bias signal. The relation of these patterns of modulation to attentional effects that have been observed in single neurons is discussed. The existence of mechanisms for selective perception raises the more general question of whether irrelevant ignored stimuli are nevertheless perceived. Lavie’s theory of attention proposes that the degree to which ignored stimuli are processed varies depending on the perceptual load of the current task. Evidence from behavioural and functional magnetic resonance imaging studies of ignored, visual-motion processing is presented in support of this proposal.
Oligodendrocyte Development
Authors: Richardson W D
Published: November 2023

Oligodendrocytes, like other neural cells in the central nervous system (CNS), develop from the neuroepithelial precursors that line the lumen of the spinal cord and the ventricles of the brain—the so-called ventricular zone (VZ). Although myelinating oligodendrocytes are one of the last cell types to differentiate in the CNS—accumulating mainly after birth in rodents—their progenitors are present in the VZ much earlier. In the rat spinal cord, for example, the first overt oligodendrocyte precursors appear in the VZ around embryonic day 14 (El4) or even earlier (conception is E0, birth ∽E21). Soon after this, they undergo a morphological transition, detach from the epithelium and migrate away from the VZ through the developing CNS (Levine and Goldman, 1988; Reynolds and Wilkin, 1988).
Structure and formation of the Node of Ranvier
Authors: Ellisman M , Deerinck T , Bennett V
Published: November 2023

Nodes of Ranvier are the sites on myelinated axons, first discovered by the French pathologist Louis-Antoine Ranvier (1874), where insulating layers of myelin are interrupted and where the ion fluxes occur which are required for propagation of action potentials. Myelinated axons and their nodes of Ranvier are an important evolutionary advance of vertebrates that permit rapid, saltatory propagation of action potentials without an increase in axonal diameter. This physiological achievement is based on adaptations at a molecular level, resulting in an elegant cooperation between glial cells and nerve axons. Nodes of Ranvier include two adjacent specializations of the axonal plasma membrane characterized by high local concentrations of voltage-regulated ion channels: a paranodal region underlying the paranodal processes of glial cells which contains voltage-sensitive potassium channels, and a nodal axon segment between paranodes which is enriched in voltage-dependent sodium channels (Ellisman and Levinson, 1982; Waxman and Ritchie, 1993). The paranodal domain of axons is tightly opposed to paranodal loops of either Schwann cells in the peripheral nervous system (PNS) or oligodendrocytes in the central nervous system (CNS). The nodal axon segment of adult axons is in close contact with specialized microvilli of Schwann cells in the PNS (Berthold and Rydmark, 1995) or in contact with astrocytes in the CNS (Black et al., 1995).
Myelin-specific Genes and their Mutations in the Mouse
Authors: Nave K -A
Published: November 2023

An important function of glial cells in the mammalian nervous system is the assembly of myelin, a specialized cellular organelle and a structural prerequisite for rapid saltatory impulse conduction. Myelin is elaborated differently in the central nervous system (CNS) and peripheral nervous system (PNS)—by oligodendrocytes and Schwann cells, respectively—which provides the opportunity to compare how this function is mastered by two cell types that utilize overlapping but not identical sets of genes. Recent evidence suggests that at least some of the myelin proteins are expressed at a low level in non-glial cells and may have been ‘recruited’ as structural components for the myelin sheath.
Control of Gene Expression by Oligodendrocytes
Authors: Hudson L D
Published: November 2023

Two interlaced events distinguish the oligodendrocyte from other cell types in vertebrates, and the transcriptional controls that underly these events are likely to be unique for oligodendrocytes. The first is the specification of oligodendrocytes from stem cells in the CNS, following a series of signaling events (reviewed in Chapters 2 and 6) that culminate in the expression of the first wave of ‘oligodendrocyte-promoting’ transcription factors. It is reasonable to expect that both the types of transcription factors expressed at this stage and the relative concentrations of these factors are characteristic of cells destined to travel the oligodendrocyte pathway. A priori, none of these transcription factors need be found exclusively in cells of the oligodendrocyte lineage. Indeed, Nature’s way of maximizing the diversity of gene regulation with minimal effort is to combine a relatively small set of players (transcription factors), -∽5% of the total number of genes in Caenorhabditis elegans (Clarke and Berg, 1998; Ruvkun and Hobert, 1998), with multiple copies of their targets (small DNA-binding sites) distributed among the ∽60 000 expressed genes in the genome. A particular gene is then activated or repressed depending on (i) which combination of these target DNA-binding sites it possesses; (ii) what transcription factors are present in the nucleus for binding to these sites; and (iii) whether sufficient amounts of these transcription factors are available for binding to their targets.
Astrocytes are Dynamic Participants in Central Nervous System Development and Injury Responses
Authors: Fitch M T , Silver J
Published: November 2023

Astrocytes are glial cells found throughout the central nervous system (CNS) that are identified by their stereotypical stellate shape and their characteristic intracellular expression of the intermediate filament glial fibrillary acidic protein (GFAP) (Bignami et al., 1972; Bignami and Dahl, 1974). While glial cells of the astrocyte lineage have been appreciated as an integral framework for neuronal migration and axon growth during development of the nervous system (Silver et al., 1993; Rakic, 1995), astrocytes are much more than merely a passive substrate for other cells to interact with. Astrocytes are involved in neurotransmitter transport (Schousboe and Westergaarde, 1995), establishing and maintaining the endothelial blood-brain barrier (Wolburg and Risau, 1995), ion homeostasis (see Chapter 6), immune recognition (Burudi et al., 1999), metabolic functions within nervous tissue (see Chapter 5), the regulation of axon growth during development (Silver et al., 1993) and the responses of the adult CNS to injury (Fitch and Silver, 1999). This chapter will discuss the active role of astrocytes that provide a dynamic framework of glial boundaries in the CNS during development and following traumatic injury.
Genetic and Cellular Mechanisms of Schwann Cell Tumor Formation: Neurofibromatosis type 1 and Neurofibromatosis type 2
Authors: Ratner N , Daston M M
Published: November 2023

Neurofibromatosis type 1 (NFl; von Recklinghausen disease) and neurofibromatosis type 2 (NF2) are inherited human diseases in which affected individuals are predisposed to develop Schwann cell tumors. NFl and NF2 arise from mutations in different genes, each of which plays a key role in regulating Schwann cell function. The NFl gene on human chromosome 17 encodes an intracellular signaling molecule that functions as a GTPase-activating protein for Ras proteins, while the NF2 gene on human chromosome 22 encodes a cytoskeletal-membrane linking protein. Patients with NFl and NF2 typically present with different types of benign Schwann cell tumors. We describe the symptoms and genetics of NFl and NF2, what has been learned about the roles of the NFl and NF2 gene products in peripheral nerve function, and how loss of these proteins might contribute to formation of Schwann cell tumors.
The Neuropathology of Multiple Sclerosis
Authors: Lucchinetti C , Lassmann H
Published: November 2023

Multiple sclerosis (MS) is an inflammatory relapsing or progressive central nervous system (CNS) disorder characterized by focal areas of myelin destruction associated with astroglial scar formation (Figure 18.1). These lesions are scattered throughout the CNS with a predilection for the optic nerves, brainstem, spinal cord and periventricular white matter. The initial pathological descriptions of MS were reported in the first half of the 19th century (Cruveilhier, 1835; Carswell, 1838; Charcot, 1868). Later studies revealed that the classical clinico-pathological pattern of MS described in these early studies represented only one member of a family of closely related idiopathic inflammatory demyelinating diseases (IIDDs) (Weinshenker and Lucchinetti, 1998). These include fulminant demyelinating disorders such as the acute Marburg variant, Balo’s concentric sclerosis and acute disseminated encephalomyelitis (ADEM); the monosymptomatic IIDDs such as transverse myelitis or isolated optic neuritis or brainstem demyelination; and the recurrent disorders with a restricted topographical distribution including Devic’s neuromyelitis optica and relapsing myelitis. The literature is confusing with respect to the classification of these syndromes. Some studies emphasize specific clinical or pathological features to distinguish between these syndromes. However, there are examples of transitional cases which defy a specific terminology. For example, the typical concentric lesions ofBalo’s concentric sclerosis can be adjacent to more typical MS plaques (Marburg, 1906). In addition, there are patients with lesions demonstrating histological features of both ADEM and MS (Krucke, 1973). The presence of these transitional forms suggests a spectrum of inflammatory diseases which may share a pathogenetic relationship.
Restoring CNS Myelin by Glial Cell Transplantation
Authors: Blakemore W F , Franklin R J M , Noble M
Published: November 2023

Persistent demyelination is the major pathology of multiple sclerosis (MS) and the leukody-strophies, and is also a feature of spinal cord trauma where there is evidence that it contributes to the functional deficit (Bunge et al., 1993; Shi et al., 1997). There are potentially two approaches to achieve remyelination in a situation where it fails: enhancement of the inherent remyelinating capacity of the central nervous system (CNS), or transplantation of an exogenous source of myelin-forming cells. This chapter will focus on the second of these two approaches since this is the one closest to clinical application, not least as a result of the recent progress in manipulating human embryonic and neural stem cells in vitro and the demonstration of their myelinating and remyelinating potential in vivo (see Chapter 20).
Design considerations
Authors: Diggle Peter J , Heagerty Patrick J , Liang Kung-yee. , Zeger Scott L
Published: November 2023

In this chapter we contrast cross-sectional and longitudinal studies from the design perspective. As discussed in Chapter 1, the major advantage of a longitudinal study is its ability to distinguish the cross-sectional and longitudinal relationships between the explanatory variables and the response. The price associated with this advantage is the potential higher cost incurred by repeated sampling of individuals. At the design stage, we can benefit from guestimates of the potential size of bias from a cross-sectional study and the increase in precision of inferences from a longitudinal study. This information can then be weighed either formally or informally against the additional cost of repeated sampling. Then if a longitudinal study is selected, we must choose the number of persons and number of measurements on each.
Kinetic analysis of enzyme mutants for identification of catalytic residues
Authors: Wei Yansheng , Luo Lusong , Zhang Wenhai , Mariano Debra Dunaway
Published: November 2023

This article will provide a guide for the experimentalist who wishes to define the specific roles of active site residues in catalysis by the enzyme that he or she is studying. This guide is based on the authors’ own experience in analysing the catalytic residues of Pseudomonas sp. strain CBS-3 4-chlorobenzoyl-CoA dehalogenase using a site-directed mutagenesis-transient kinetic analysis based approach. General methods that one might apply to any enzyme will be illustrated with experiments carried out with the dehalogenase.
Recollections and Perspectives
Authors: Boffi Giandomenico , Buchsbaum David A
Published: November 2023

This chapter is neither a collection of results which we assume to be known nor the place to prove some results probably unknown to the reader, but needed in the following. Although it resembles a little of both things, it is essentially a selection of topics, some elementary, some more advanced, which we feel are adequate, or even necessary, to prepare the ground for the material of the chapters to come. Since it is almost impossible to tell which “basic” material is truly universally known, and which is not, we can only assure the reader that those terms in this chapter which are unfamiliar can be easily found in the book by D. Eisenbud, [41].
Evolution: insects and plants forever in combat
Authors: Schoonhoven Louis M , Loon Joop J A van , Dicke Marcel
Published: November 2023

Ehrlich and Raven put forward their theory on the coevolution of insects and plants.43 The resulting discussion was intense and ample new investigations have been initiated so that our concept of how insect-plant interactions evolve is evolving as well. In this Chapter we present the state of the art of this ongoing debate that deals with specialization, speciation, and evolution of insect-plant interactions.
Early studies of brain anatomy in schizophrenia
Authors: Johnston Eve C , Owens David G C
Published: November 2023

Emil Kraepelin (1856–1927) is generally considered to have defined the disease concept that came to be known as schizophrenia. In defining dementia praecox, he drew together hebephrenic, as described by Hecker (1871), catatonia, as described by Kahlbaum (1874), and his own dementia paranoids, as he regarded them all as manifestations of the same disorder, which typically had its onset in early adult life and had a poor outcome (Kraepelin 1896). Kraepelin was working shortly after the first academic department of psychiatry in Europe had been sent up in Berlin in 1865, the first Chair being held by Wilhelm Griesinger, whose statement ‘mental illness is a somatic illness of the brain’ (Griesinger 1861) is often quoted. Investigations relating neuro-pathology to mental disorder were conducted in his department.
Diffusion tensor magnetic resonance imaging
Authors: Bastin Mark E , Lawrie Stephen M
Published: November 2023

A large body of evidence from in vivo imaging and post-mortem studies suggests that the brains of patients with schizophrenia are both structurally and functionally compromised. The most replicated gross morphometric findings from magnetic resonance (MR) imaging studies are enlarged lateral ventricles and reduced cerebral volume, specifically temporal lobe and amygdala/hippocampal complex, compared with age- and gender-matched controls (Lawrie and Abukmeil 1998). Segmentation studies suggest that these volume deficits occur more often in cortical grey matter than white (Zipursky et al. 1992; Schlaepfer et al. 1994). However, while abnormalities of white matter volume are not as widely reported (Wright et al. 2000), there are compelling data from other types of imaging to suggest that white matter function may also be substantially affected in schizophrenia.
Neuroreceptor mapping with PET and SPECT
Authors: Bantick R A , Montgomery A J , Grasby P M
Published: November 2023

Neurochemical techniques can help to identify the underlying biochemical mechanisms involved in schizophrenia and its pharmacological treatment. Post-mortem neuro-chemistry, although highly sensitive, is limited by tissue changes after death, additional pathologies that have led to death and the use of generally elderly subjects who have had lengthy durations of illness and treatment. In contrast, neurochemical imaging, in addition to permitting comparisons of patients (including the drug na;ve) and controls, also enables a wealth of within-subject comparisons (see below). The modalities of in vivo neuroreceptor imaging comprise positron emission tomography (PET), single-photon emission computerized tomography (SPECT) and magnetic resonance spectroscopy (MRS). PET and SPECT enable specific and highly sensitive (nanomolar to picomolar) delineation of in vivo neurochemistry. MRS is less sensitive (millimolar to micromolar) but non-invasive and without the exposure to ionizing radiation that limits subjects’ involvement in PET/SPECT studies. All three techniques have expanding applications within schizophrenia research.
Hierarchical Multivariate CAR Models for Spatio-Temporally Correlated Survival Data
Authors: Carlin Bradley P , Banerjee Sudipto
Published: November 2023

The analysis of spatially referenced data has been an increasingly active area of both methodological and applied statistical research. As with many fields, advances in computing and software have been largely responsible. Modern database engines, often widely and publicly available to anyone with a web browser, provide an enormous supply of georeferenced data. Sophisticated computer programs known as geographic information systems (GISs) have revolutionized the analysis and display of such data sets, through their ability to “layer” multiple data sources over a common study area. Finally, Markov chain Monte Carlo (MCMC) algorithms enable the fitting of complex hierarchical models in a Bayesian framework, permitting full posterior inference for underlying parameters in even complex model settings (e.g., those involving data that are highly multivariate, temporally correlated, and perhaps even spatially or temporally misaligned).
A Bayesian Analysis of Smooth Transitions in Trend
Authors: Zheng Pjngping , Marriott John M
Published: November 2023

Many real time series exhibit changes in trend. However, because the observed changes are frequently not abrupt, models that specify step changes do not adequately represent the observed behavior. Smooth transition models allow for a smooth change from one linear regime to the next. This paper is concerned with parameter estimation and prediction for a linear trend model with a smooth transition in both the intercept and slope. The smooth transition is modelled using a logistic transition function. We present a Bayesian approach to inference for this model that allows for an autocorrelated error structure and uses the exact likelihood. We develop a slice sampler for the analysis.We apply the analysis to a published macroeconomic data set which exhibits a slowly changing time trend.
What is probability?
Authors: Haigh John
Published: November 2023

Whatever it is, you cannot ignore it. The insurance premium for your house, car, or life reflects the probability the insurers will have to pay out, and how much. Should you have a vaccination against winter flu? You must balance the risks of side-effects or possible reaction to the vaccination against the consequences of declining the protection. Members of a criminal jury are asked to convict only if they believe guilt is established ‘beyond reasonable doubt’. In a civil case, the relevant criterion may be ‘on the balance of probabilities’. You buy, or do not buy, tickets for the National Lottery partly on impulse or for fun, but also partly on your assessment, however vague, of your chance of winning a substantial sum. In card games such as poker or bridge, you expect to play better if you can make a realistic judgement of the likelihood that an opponent holds certain cards.
Dice
Authors: Haigh John
Published: November 2023

Dice have been used in gaming and recreation for thousands of years. They were used in board games in Egypt over 5000 years ago, and in various games of chance invented during the Trojan Wars to relieve the boredom of the soldiers. The Roman emperors played: Augustus wrote to Tiberius about his experiences, and Claudius had a board fitted to his carriage so that he could continue to play while driving. In Games, Gods and Gambling, F. N. David notes that in hoofed animals, the astralagus, or ankle bone, is fairly symmetrical, because of the way a foot takes up the strain placed on it. Dice from ancient times were often constructed from this solid and robust bone.
Anisotropies in the Microwave Sky
Authors: Weinberg Steven
Published: November 2023

We will now return to the theory of anisotropies in the cosmic microwave background, introduced in Section 2.6. In Section 7.1 we derive general formulas for the observed temperature fluctuation. Then in Sections 7.2 and 7.3 we combine these results with the analysis of cosmic evolution in Chapter 6 and introduce a series of approximations that simplify the evaluation of the multipole coefficients for scalar and tensor modes, respectively. Section 7.4 deals with the polarization of the microwave background.
Experiences good and bad: an introduction to psychopathology, classification, and diagnosis for philosophers
Authors: Fulford K W M , Thornton Tim , Graham George
Published: November 2023

The chapter has two aims. The first is to give philosophers (or anyone with no background practical experience of mental distress and disorder) a taste of the more formal aspects of psy- chopathology and the classifications of mental disorder used by professionals working in mental health. The materials in this chapter, it should be said straight away, are perhaps more characteristic of medical, nursing, and psychological professional work, than, say, social work. The mater- ials, it is true, are the result of over a hundred years of careful observation and development of ideas (covered in detail in Parts II and III). All the same, just as the concept of mental disorder remains subject to widely different interpretations (the various ‘models’ we explored in Chapter 2), so the classification of these disorders—the particular ‘symptoms’ identified, the groups and classes and clusters into which they are drawn together—remain much debated. The whole enterprise of classification of mental distress and disorder is indeed challenged by some (see, e.g. Kutchins and Kirk, 1997). As with all the materials in this book, then, this chapter is presented, not as a reflection of a settled or final view, but as a focus for critical engagement and collegial development of ideas.
A Brief History of Mental Disorder
Authors: Fulford K W M , Thornton Tim , Graham George
Published: November 2023

In Part I of this book, we explored current ideas about mental disorder, the variety and subtlety of descriptive psychopathology (in Chapter 3), and the range of often competing ways in which the concept of mental disorder itself has been understood (Chapters 2, 4, and 6). In this part we will be looking at the historical origins of these ideas.We will be asking such questions as: how have we come to recognize the variety and subtlety of psychopathological concepts? Where have our categories of disorder come from? Who decided which phenomena are ‘symptoms’? And why? Are current classifications the last word on the subject?
From Bioethics to Values-Based Practice in Psychiatric Diagnosis
Authors: Fulford K W M , Thornton Tim , Graham George
Published: November 2023

In Session 1 of Chapter 20, the case of Simon showed that values are inherent in psychiatric diagnosis, not peripherally but at the very heart of traditional psychopathology, in the differential diagnosis of schizophrenia. That value judgements are involved in this differential diagnosis is implicit in ICD. It is explicit in DSM, in the DSM’s additional Criterion B of ‘social/occupational dysfunction’.
Mind, brain, and mental illness: an introduction to the philosophy of mind
Authors: Fulford K W M , Thornton Tim , Graham George
Published: November 2023

Mental health practitioners—users of services and carers, nurses, general practitioners, psychiatrists, psychologists, etc.—claim a spe- cial expertise in the mental. The philosophy of mind should thus be, uniquely, their philosophy. Conversely, mental health practice, given the remarkable range of abnormal mental phenomena with which it is concerned, should be uniquely interesting to philosophers of mind. Yet for much of the twentieth century, the two sides, philoso- phers and practitioners, have studiously avoided each other.
First-order quasilinear systems
Authors: Ockendon John , Howison Sam , Lacey Andrew , Movchan Alexander
Published: November 2023

When we use vector systems of partial differential equations, we can model many more physical situations than when we are restricted to the scalar case. For example, as well as looking at the simple kinematic wave models of Chapter 1, we can study situations which allow simultaneous wave propagation both backwards and forwards. A famous example is that of shallow water waves where gravity and fluid inertia balance each other in a shallow layer of water with a free surface, of depth h(x,t), flowing above a horizontal bed along the x axis (Fig. 2.l(a)). Let the fluid density be a constant p.
Introduction to second-order scalar equations
Authors: Ockendon John , Howison Sam , Lacey Andrew , Movchan Alexander
Published: November 2023

In Chapter 2 we tried to describe, in the simplest possible terms, the only reason ably general framework that exists concerning the solutions of the Cauchy problem for arbitrary partial differential equations. Many pages could now be spent in explaining this framework in more detail, but we will instead devote the next three chapters to a more specialised analysis of three commonly occurring classes of second-order scalar equations. This will enable us not only to illustrate as simply as possible the subtleties that can arise when ‘non-hyperbolic’ equations are being solved, but also to look at the role played by the ideas proposed in Chapter 2 when they are viewed in a more concrete setting.
Elliptic equations
Authors: Ockendon John , Howison Sam , Lacey Andrew , Movchan Alexander
Published: November 2023

In this chapter we will, as usual, begin by discussing some physical situations that are modelled by elliptic equations, as defined in a rather unfocused way in Chapter 3. Most of the examples involve scalar second-order equations, several of which are special cases, such as steady states, of evolution models discussed in Chapters 4 and 6.

The methods we will use in the subsequent analysis of these models are more ad hoc than those used on hyperbolic equations, for the simple reason that we have no general well-posedness statement analogous to that for the Cauchy problem for hyperbolic equations. Moreover, we will find that the influence of the data for elliptic problems, especially singularities in the boundary data, is much less localised and ‘coherent’ than it is for hyperbolic equations, where we recall that many kinds of singularities merely propagate along characteristics.
Non-quasilinear equations
Authors: Ockendon John , Howison Sam , Lacey Andrew , Movchan Alexander
Published: November 2023

Several practical situations give rise to partial differential equations that are not quasilinear. For example, suppose u(x, y) is the elevation of a pile of dry sand that is heaped on a table in limiting equilibrium, so that if any more sand was

poured from above it would slide off. Then the angle between the normal to the surface u = u(x, y) and the vertical (0, 0, 1) is a prescribed constant 1, the angle of friction, so that
Miscellaneous topics
Authors: Ockendon John , Howison Sam , Lacey Andrew , Movchan Alexander
Published: November 2023

Our discussion over the past eight chapters has covered much ground but only scratched the surface of what is known about many methods for special classes of pdes.168 In this miscellany we will attempt to take the reader further into some of the ‘tricks of the trade’. However, before going into detail, we will make some general remarks about some areas of mathematics that are not only germane to the classical theory of pdes, but also so large and important as to warrant their own text books; yet we have scarcely mentioned them thus far.
Hardware for functional MRI
Authors: Glover Gary H
Published: November 2023

Task-driven changes in neuronal metabolism during a functional magnetic resonance imaging (fMRI) experiment result in relatively small signal modulations, typically only a few per cent at 1.5 Tesla (Ogawa et al. 1990). Analysis of the data generally compares (in a statistical sense) the signal levels resulting from a sensory or cognitive task with those obtained during a baseline condition. Changes in the signal that result from system drift, physiological functions, basal metabolism fluctuations, and other sources add noise to the comparison process and reduce the significance of the results. Because the neuronal signal modulations are small, it is important that the scan technique is optimized to maximize the signal levels and reduce these spurious sources of noise as much as possible.
Selection of the optimal pulse sequence for functional MRI
Authors: Bandettini Peter A
Published: November 2023

Since its inception in 1991, functional MRI (fMRI) has experienced an explosive growth in the number of users and a steady widening in its range of applications. A recent (2000) search of the National Library of Medicine database for articles with ‘fMRI’ or ‘BOLD’ in the title revealed over 1000 citations. The rapid rate of improvement in pulse sequence design, data processing, information content, data interpretation, and paradigm design can be overwhelming to the novice and even to the advanced user. This chapter is written to assist the fMRI user in making an informed decision regarding the choice of functional MRI pulse sequence. A second goal is to present the pulse sequence choices against a wider backdrop of relevant variables, ranging from paradigm timing to available hardware. The hope is to build a broader perspective of what the limits and possibilities of fMRI are.
Extracting brain connectivity
Authors: Buchel Christian , Friston Karl
Published: November 2023

In the late nineteenth century the early investigations of brain function were dominated by the concept of functional segregation. This approach was driven largely by the data available to scientists of that era. Patients with circumscribed lesions were found who were impaired in one particular ability while other abilities remained largely intact. Indeed, descriptions of patients with different kinds of aphasia (an impairment of the ability to use or comprehend words), made at this time, have left a permanent legacy in the contrast between Broca’s and Wernicke’s aphasia. These syndromes were thought to result from damage to anterior or posterior regions of the left hemisphere respectively.
Clinical applications of mapping neurocognitive processes in the human brain with functional MRI
Authors: Thulborn Keith R , Gisbert Antonio
Published: November 2023

The diagnosis and treatment of sensory, motor and cognitive dysfunction is of central importance to medicine yet there are substantial limitations in our strategies for their diagnoses and monitoring. In current medical practice, diseases of the central nervous system (CNS) are broadly categorized into those that are neurological (when a biological basis for the illness is known) and those that are psychiatric (when a specific biological basis has not been determined). This rather arbitrary division is rooted in an emphasis on structural pathology. Functional testing has until recently been very limited. The neurological and psychiatric examinations of traditional medicine interrogate the CNS by testing if specific stimuli elicit expected responses. The assumption made from normal responses is that the CNS is normal.
Basic Examples
Authors: Villegas Fernando Rodriguez
Published: November 2023

In this chapter we will explore some basic examples, introducing mathematical and computational concepts that we will develop further later.
Positive Definite Binary Quadratic Forms
Authors: Villegas Fernando Rodriguez
Published: November 2023

A significant portion of Gauss’s Disquitiones Arithmeticae is about binary quadratic forms. Since then there have been numerous treatments, especially for the positive definite case. The most relevant reference for us will be Cox’s book [26]. Also many of the routines described here have built-in versions in PARI. Nevertheless, because binary forms are so central to number theory, we include this short (and rather sketchy) chapter with the most basic facts and algorithms for the positive definite case.
Sequences
Authors: Villegas Fernando Rodriguez
Published: November 2023

In this chapter we discuss some computational aspects of sequences of numbers by concentrating on the sequence of trinomial numbers. For well-known sequences we give their label in Sloane’s encyclopedia of sequences [86].
Combinatorics
Authors: Villegas Fernando Rodriguez
Published: November 2023

The best way to describe the main algorithmic idea of this chapter is by means of the concept of a stack. A stack is a storage structure in which: we may either place a new object at the top of the stack or we may remove the object currently at the top of the stack.
Polynomials
Authors: Villegas Fernando Rodriguez
Published: November 2023

The measure was introduced by Mahler [61] to give a simple proof of an inequality due to Gelfond. For P Z x we have M(P) 1 with equality if and only if P is monic and all of its non-zero roots are in the unit circle. By a theorem of Kronecker therefore M(P) 1 if and only if P is a product of a power of x and a cyclotomic polynomial.
Solution of Discrete Poisson Problems
Authors: Elman Howard C , Silvester David J , Wathen Andrew J
Published: November 2023

The coefficient matrix of the linear system arising from finite element discretization of the Poisson equation is symmetric positive-definite. For the discretizations discussed in Chapter 1, it is also sparse. That is, only a very small proportion of its entries is nonzero. In this chapter, we discuss effective iterative methods for solving such systems, concentrating on two general approaches, Krylov subspace methods and multigrid methods.
Dependent responses
Authors: Lindsey J K
Published: November 2023

As computers increase in power, more and more data are collected. When large quantities of data are available on the same individuals, they will often be inter­dependent in certain specific ways. Thus, more complex models must be used than those provided in the previous chapters. In an introductory text, I can only present a few of the basic concepts. Generally, one assumes that observations on the same individual may be dependent but that those on different individuals are independent.

Thus, dependent observations will arise primarily when several responses are recorded from the same individual. They may involve the same variable or sev­eral different response variables. Such responses may be obtained more or less simultaneously or they may evolve over time. When more than one individual is involved, if the same response variable is being measured several times on each, such observations are called repeated measurements.
A retrospective analysis of the clinical case records of ‘autistic psychopaths’ diagnosed by Hans Asperger and his team at the University Children’s Hospital,
Authors: Hippler Kathrin , Klicpera Christian
Published: November 2023

To date, it is questionable whether the diagnostic criteria for Asperger syndrome (AS) as stated by ICD-10 or DSM-IV still reflect Asperger’s original account of ‘autistic psychopathy’ (AP) from the 1940s. The present study examined 74 clinical case records of children with AP diagnosed by Hans Asperger and his team at the Viennese Children’s Clinic and Asperger’s private practice between 1950 and 1986. The characteristic features of the children are outlined, including reasons for referral, parental background, behavioural problems, cognitive functioning, communication and interests. Results show that the patients of Asperger described in our study represent a subgroup of children with very high intellectual functioning, specific circumscribed interests and talents but impaired social, communication and motor skills. Sixty-eight percent of the sample met ICD-10 criteria for AS, while 25% fulfilled the diagnostic criteria for autism. Implications for the diagnosis of AS are discussed.
The role of the fusiform face area in social cognition: implications for the pathobiology of autism
Authors: Schultz Robert T , Grelotti David J , Klin Ami , Kleinman Jamie , Van der Gaag Christiaan , Marois Rene , Skudlarski Pawel
Published: November 2023

A region in the lateral aspect of the fusiform gyrus (FG) is more engaged by human faces than any other category of image. It has come to be known as the ‘fusiform face area’ (FFA). The origin and extent of this specialization is currently a topic of great interest and debate. This is of special relevance to autism, because recent studies have shown that the FFA is hypoactive to faces in this disorder. In two linked functional magnetic resonance imaging (fMRI) studies of healthy young adults, we show here that the FFA is engaged by a social attribution task (SAT) involving perception of human-like interactions among three simple geometric shapes. The amygdala, temporal pole, medial prefrontal cortex, inferolateral frontal cortex and superior temporal sulci were also significantly engaged. Activation of the FFA to a task without faces challenges the received view that the FFA is restricted in its activities to the perception of faces. We speculate that abstract semantic information associated with faces is encoded in the FG region and retrieved for social computations. From this perspective, the literature on hypoactivation of the FFA in autism may be interpreted as a reflection of a core social cognitive mechanism underlying the disorder.
Farewell to certainty
Authors: Baggott Jim
Published: November 2023

The ‘old’ quantum theory discussed in the last chapter was characterized by the entirely arbitrary imposition of quantum conditions on problems otherwise described in terms of the concepts and theories of classical physics. There was an element of magic about it. To get the exact shape of the curve of spectral density with frequency or wavelength of black-body radiation, one assumed ε= hv without questioning the reasons too closely.To get the Balmer formula from an ‘impossible’ classical picture of a negatively charged electron in a circular orbit around the positively charged hydrogen atomic nucleus, one assumed the orbital angular momentum to be constrained to values nh/2  π, where n is an integer. This was not very satisfactory. A more meaningful theory was needed in which the quantum conditions and their implications in terms of quantum numbers and discontinuous quantum jumps were the result of the theory and not input assumptions.
Bell’s theorem and local reality
Authors: Baggott Jim
Published: November 2023

If we reject the ‘spooky’ action at a distance that seems to be required in the Copenhagen interpretation of quantum theory, and which is highlighted by the EPR thought experiment, we must accept the EPR argument that the theory is somehow incomplete. In essence, this involves the rejection of the first postulate of quantum theory: the state of a quantum mechanical system is not completely described by the wave function or state vector.Einstein had hinted at a statistical interpretation. In his opinion, the squares of the wave functions or state vectors of quantum theory represented statistical probabilities obtained by averaging over a large number of real particles. The Copenhagen interpretation of the EPR experiment insists that the reality of the physical states that can be measured is defined by the nature of the interaction between two quantum particles and the nature of the experimental arrangement. A completely deterministic, locally real version of quantum theory demands that the physical states of the particles be established at the moment of their interaction and that the particles separate as individually real entities in those physical states. The physical states of the particles are prescribed by the physics of their interaction and independent of how we choose to set up the measuring instrument, and so no reference to the nature of the latter is necessary, except to define how the independently real particles interact with it. The instrument thus probes an observer-independent reality.
Quantum non-locality
Authors: Baggott Jim
Published: November 2023

It is probably reasonable to suppose that the derivation, in the late 1960s and early 1970s, of an equation that is demonstrably violated by a quantum theory then over 40 years old should have settled the matter one way or the other, once and for all. Correlated quantum particles are everywhere in physics and chemistry, the simplest and most obvious example being the helium atom, an understanding of the spectroscopy of which had led to the introduction of the Pauli principle in the first place. But it became apparent that the special circumstances under which Bell’s inequality could be subjected to experimental test had never been realized in the laboratory. Suddenly, the race was on to perfect an apparatus that could be used to perform the necessary measurements on pairs of correlated quantum particles.
Understanding the ‘scientific revolution’
Authors: Hodgkin Luke
Published: November 2023

Philosophy is written in that vast book which stands forever open before our eyes, I mean the universe; but it cannot be read until we have learnt the language and become familiar with the characters in which it is written. It is written in mathematical language, and the letters are triangles, circles and other geometrical figures, without which means it is humanly impossible to comprehend a single word. (Galileo, Il Saggiatore (The Assayer), tr. in Drake 1960, pp. 183–4)
The calculus
Authors: Hodgkin Luke
Published: November 2023

By the help of this new Analysis Mr Newton found out most of the propositions in the Principia Philosophiae. (Newton 1967–1981 8, 598–9) The ‘new Analysis’ was what we now call the calculus; a point in learning mathematics where many students give up, and which many others never reach. Intended to make everything easy, it is still found a stumbling-block.
Geometries and space
Authors: Hodgkin Luke
Published: November 2023

Most people are unaware that around a century and a half ago a revolution took place in the field of geometry that was as scientifically profound as the Copernican revolution in astronomy and, in its impact, as philosophically important as the Darwinian theory of evolution. (Greenberg 1974, p. ix) It is a general conviction that geometry, with all its truths, is valid with unconditioned generality for all men, all times, all peoples, and not merely for all historically factual ones but all conceivable ones.
Land and plantation development
Authors: Evans Julian , Turnbull John W
Published: November 2023

Most tree-planting enterprises, especially industrial plantations, require large areas of land. Therefore, land availability and quality is of first importance in plantation forestry. This chapter considers: Aspects of this topic were introduced in Part I but in considering land and land-use further, it is emphasized that developing the potential of a nation’s land, removing the constraints of inaccessibility, aridity, and other physical or ecological factors, is one of the cornerstones of development.
Clonal plantations
Authors: Evans Julian , Turnbull John W
Published: November 2023

Vegetative propagation is being increasingly used to multiply selected planting material in plantation forestry and agroforestry in the tropics. It is a way of raising planting stock not involving seed and includes cuttings, layering, budding, grafting and, recently, micro propagation. Propagating plants vegetative results in clones, with each clone retaining the genetic characteristics of the tree at the point from which the buds or cuttings were obtained. It must be stressed that vegetative propagation is only a means of multiplying planting material, it is not a breeding method and does not result in genetically improved plants.
Dynamics of stand growth
Authors: Evans Julian , Turnbull John W
Published: November 2023

In the tropics, tree growth and stand development are usually more rapid than under temperate conditions. Therefore, it is important that the influences on stand development available to the forester to modify the quality and quantity of timber produced are understood. Similarly, understanding individual tree-growth patterns can help management of farm and village trees to maximize yield of branch wood or fodder or minimize their competitive effect on other crops and so on. After the establishment period, and provided growth is not impaired by deficiency, disease or other damage, the amount of growing space a tree has dominates its growth and development and the yield of a stand as a whole.
Tree-planting in rural development and agroforestry
Authors: Evans Julian , Turnbull John W
Published: November 2023

Trees, tree-planting, and woodlands are now recognized as an integral part of rural development. Fruit trees planted in home gardens and shelterbelt development are examples of the link between tree-planting and food security (e.g. Falconer and Arnold 1988; Hoskins 1990). Agroforestry can assist soil conservation (Young 1997) and help combat desertification (Baumer 1990). There has been greater recognition of the need for more sustainable agricultural practices and in many countries local people have had their access reduced to shrinking natural forest resources. Tree-planting has been the means many farmers have used to improve the sustainability of their cropping practices and to enable them to place greater reliance on on-farm resources to provide both timber and non-timber tree products.
Recurrent networks with binary neurons
Authors: Coolen A C C , Kühn R , Sollich P
Published: November 2023

We now turn to recurrent networks of binary (Ising) neurons σi ∈ {1, 1} , with fixed synaptic interactions { Jij } and fixed thresholds { 𝓋i} . We still have explicit (stochastic) rules (1.29) that determine the evolution in time of our system, namely
Notes and suggestions for further reading
Authors: Coolen A C C , Kühn R , Sollich P
Published: November 2023

with mathematical tools, took rather a long time to emerge. Neurons were only discovered in 1880 by Ramon y Cajal, using a novel staining method developed byGolgi. Until then there had been two scientific camps: neuronists believed that the brain consisted of interconnected information processing cells, whereas reticularists saw the brain as a continuous uninterrupted network of fibres only. In 1936, Turing [2] contributed significantly to the further demystification of the concept of ‘intelligence’ and proved statements about computability by machines. This more or less marked the start of the field of ‘artifical intelligence’. McCulloch and Pitts [3] were the first to introduce a very simple discrete mathematical neuron model, in 1943, and they subsequently proved its universality. In 1949 the psychologist Hebb [4] introduced the idea that biological neural networks store information in the strengths of their interactions (the synapses).