bluuebunny/crossref_metadata_2025 huggingface dataset:
Geometric Models for Quantum Statistical Inference
Authors: Brody Dorje C , Hughston Lane P
Published: November 2023

Our purpose here is to draw attention to an interesting relationship that can be shown to hold between (a) information geometry, and (b) quantum geometry. By ‘information geometry’, we mean the natural geometry associated with families of probability distributions. This is a subject that goes back more than half a century to the pioneering work of Rao (1945), who showed that the Fisher information matrix associated with a parametrised family of probability dis tributions gives rise to a natural Riemannian metric on the parameter space. This then allows one to speak in a precise way of the ‘distance’ between two probability distributions, an idea that turns out to be useful in problems of statistical inference. An extensive literature has thus developed, following this line of enquiry, on applications of differential geometry to statistics (see, e.g., Amari (1985), Barndorff-Nielsen et al. (1986), Murray and Rice (1993)). By ‘quantum geometry’, on the other hand, we mean the geometry of the manifold of states associated with a given quantum mechanical system. In particular, we consider the manifold of ‘pure’ states associated with a given complex Hilbert space. This is the space of ‘rays’ through the origin in the Hilbert space, which has the structure of a complex projective space. It is known that the usual rules of quantum mechanics allow one to construct a natural metric on this space, namely the Fubini-Study metric, the specification of which is equivalent to all the familiar structure associated with ordinary quantum mechanics.
The Sen Conjecture for Distinct Fundamental Monopoles
Authors: Gibbons Gary
Published: November 2023

I review some recent progress in understanding the interactions of BPS monopoles for higher rank groups. S-duality predicts the existence of a middle-dimensional square integrable harmonic form on the moduli space of distinct fundamental BPS monopoles of an arbitrary Lie group. These harmonic forms are exhibited and their uniqueness is discussed. The properties of distinct fundamental monopoles are contrasted with those of identical SU(2) monopoles.
Wilson statistics
Authors: Giacovazzo Carmelo
Published: November 2023

This chapter deals with the statistical properties of the structure factor. Owing to the relevant contributions of A. J. C. Wilson we have called this chapter ‘Wilson statistics’. This chapter mostly considers small molecules; specific problems presented by protein structures will be described in Chapters 14-16.
Direct methods and real space properties
Authors: Giacovazzo Carmelo
Published: November 2023

Crystal structures can be solved by Patterson or by direct methods. Bothe determine the atomic positions starting from the intensities: the first ‘seeks their way’ in direct space, the second in reciprocal space.
The probabilistic estimation of qnartet invariants
Authors: Giacovazzo Carmelo
Published: November 2023

Hauptman’s and Giacovazzo’s approaches differ principally on two points: Hauptman regards the reciprocal lattice vectors as the primitive random variables, while Giacovazzo considers the atomic positional vectors as the primitive random variables; different mathematical techniques are used. Giacovazzo (1977J) showed that Hauptman’s results may be obtained from (5.15) and (5.18) no matter whether the atomic positional vectors or the reciprocal lattice vectors are the primitive random variables.
Probabilistic determinantal approaches
Authors: Giacovazzo Carmelo
Published: November 2023

In Chapter 4, where direct methods were explicitly related to real space properties, we dedicated Sections 4.7-4.9 to Karie-Hauptman matrices. In particular we showed that the positiveness of the Karie-Hauptman determinants is caused by the positivity of the electron density, we studied their algebraic properties, and we argued about their possible connection with the probabilistic approach.
Introduction
Authors: Gray Jeremy
Published: November 2023

The rich series of developments described in this book raises historical, mathematical, scientific and philosophical issues. Some of these naturally concern classical electromagnetic theory which itself, as it was created, raised questions about the relationship between mathematics and physics and about the role of geometry. Current historial scholarship also points up interesting differences in the ways in which the history of mathematics and the history of science are conducted. I shall consider the historiographic question first. It has been aptly said that it is the historian ‘s task to give back to the past its sense of the future. The ways in which historians of science and historians of mathematics attempt to do this differ among themselves, and it would seem that there are significant differences in approach between the two groups. To some extent, this may reflect a difference between doing mathematics and doing science that may also be worth thinking about. This difference is apparent even when only those historians of science are considered who write history of science with the science left in (I shall say nothing of the fashion for history of science with the science left out, nor of the previous vogue for the history of mathematics or science with the history left out).
Einstein, Poincaré, and the testability of geometry
Authors: Miller Arthur
Published: November 2023

The topic of the testability of geometry as it was approached by Henri Poincare and Albert Einstein requires that we go back to their views on the origins of this subject. By origins scientists like Poincare and Einstein meant the psychological as well as scientific. For Poincare the problem of the origins of geometry was of particular importance because from it came the philosophical view with which he has become associated, conventionalism. I will focus more on Poincare for two reasons: Can there be non-Euclidean geometries? This problem had been bandied about ever since Euclid ‘s codification of geometry in about 300 B.C. (if not before see Toth, 1967). All inquiries focused on Euclid ‘s fifth postulate, or axiom, which we can state in two equivalent forms. (I) Consider a straight line and a point outside of this line; then only one line can be drawn through that point which is parallel to the already drawn line.
The library
Authors: Freer Stephen
Published: November 2023

It gives information about discoveries, events, proceedings, locations, and method. The botanist must know which authors he should consult about the plant that is the subject of his enquiry. European [vegetables]. C. Bauhin (with systematic [arrangement]) Ray 3, Vaillant. Alpine. Ray, Linnaeus, Haller, Gmelin. Authors who are famous for any work (5) on vegetables, whether they are botanists or amateurs of botany are called PHYTOLOGISTS .
Synonyms
Authors: Freer Stephen
Published: November 2023

Synonyms are variant names given to the same plant by phytologists ([6]), and they refer to genera (VII), species (VIII), and varieties (IX). The fathers, Section 9, mostly agreed on the names of plants, content with those of the genera only. The commentators, Section 10, owing to he lack of descriptions and figures in the writings of the fathers, have applied their names to plants in various ways. The describers, Sections 11 and 12, discovered a greater number of plants, and gave them names arbitrarily. Caspar Bauhin, in a labour of forty years, put together the names given by his predecessors and reduced them to 6,000 species in his Pinax of 1622. The meticulous, Section 14, have doubled the number of plants, by finding new ones on all sides.
Sketches
Authors: Freer Stephen
Published: November 2023

The method of demonstration proposed in [my] Systema naturae [ed.] 6. p.222. establishes the order according to which the history of a plant ought to be put together. A sketch must contain everything that is relevant to the history of the plant, such as its names, marks, appearance, nature, and use. A complete description should not be satisfied, in the usual manner, with the root, stem, leaves and fruit-body, but must take proper notice of the petioles, peduncles, stipules, bracts, glands, hairs, buds, the foliation, and the whole habit. RICINUS with shield-shaped, saw-toothed leaves, and petioles bearing glands. [My] Hortus Cliffortianus 450. Root branchy and fibrous.
Deterministic Dynamical Systems
Authors: Cong Nguyen Dinh
Published: November 2023

In the late nineteenth century Henri Poincaré created a new field of research in mathematics—the theory of dynamical systems—by publishing his famous memoir [129] on the qualitative theory of differential equations. Now, as a result of rapid development over the last four decades, the theory of dynamical systems has become a major branch of mathematics which interacts with almost all other branches of mathematics and finds application in many other sciences, such as physics, chemistry, biology, engineering, and so on.
Combinatorial tools
Authors: Karpinski Marek , Rytter Wojciech
Published: November 2023

Recall that MatchNum(G) is the size (number of edges) of a maximum cardinality matching of a graph G = (V, E) and a perfect matching is a matching of size IVl/2. There are two basic combinatorial tools needed to compute this number: augmenting paths (to construct a matching of a maximal size k);  witness sets (to provide an NC-proof that there is no matching of size larger thank). Almost all efficient sequential algorithms use augmenting paths, contrary to NC¬ algorithms. On the other hand witness sets are not used frequently in sequential computations but they are needed in parallel randomized computations. If an algorithm returns a matching of cardinality k then we are not certain if this cardinality is the maximum possible, even if there is a very small probability of failure. Our algorithm is a Monte Carlo algorithm. A better situation occurs when the algorithm provides a maximum cardinality matching and an easy (checkable in NC) proof that it is maximum. In this case the algorithm becomes the so-called Las Vegas algorithm. If a matching is perfect then it gives the optimality proof by itself.
Four easy subclasses of graphs
Authors: Karpinski Marek , Rytter Wojciech
Published: November 2023

In this chapter we consider three easy cases of matchings in special graphs: trees, dense graphs and regular bipartite graphs. They are easy in the sense of possessing simple NC-algorithms for the matching problem. Usually efficient sequential algorithms for trees also have quite efficient parallel implementations. Regular bipartite and dense graphs are among the few known families of graphs which possess perfect matchings. A tree is an undirected connected graph without cycles. Assume we choose a vertex called a root and direct all edges top down. The root is the topmost vertex. The leaves are degree 1 vertices (except the root). A tree can have no perfect matching, even if the number of vertices is even. For example, K1,n has only one edge in the maximum cardinality matching. Our approach to construct an NC-algorithm for trees is to ca greedy sequential algorithm in parallel.
Parallelization of sequential algorithms
Authors: Karpinski Marek , Rytter Wojciech
Published: November 2023

In this chapter we show several implementations of sequential algorithms. Unfortunately in the case of parallel matchings such an approach does not usually give NC-algorithms for general graphs, though a reasonable parallel speed-up can be achieved. In some special cases (e.g. expander graphs, approximations) the implementation of sequential algorithms leads to NC-algorithms. We have already shown an application of maximal matchings to maximum matchings in the construction of an NC-algorithm for maximum matchings in dense graphs. In this chapter we show yet another application of NC-algorithms for maximal matchings: the sublinear time computation of maximum matchings in bipartite graphs. Denote by NC_Maxima_Match(G) an NC-function returning any maximal matching of a given graph G. Any of the algorithms presented in Chapter 7 can be used as a function NC_Maxima_Match(G) returning a maximal matching and working in polylogarithmic time with a linear number of processors. A parallel version of Hopcroft-Karp algorithm will be presented using NC_Maxima_Match as the main subroutine in the crucial operation Disjoint_Paths.
Comparison With Rectifiability
Authors: David Guy , Semmes Stephen
Published: November 2023

Let d and n be integers, 0 < d < n, fixed. Definition 3.1 (Rectifiable sets)  A subset E of Rn is said to be rectifiable if there exists a sequence of subsets {Ej} of E, each bilipschitz equivalent to a subset of Rd, such that Hd (E\L⋃j Ej) = 0. Strictly speaking we should say something like “rectifiable of dimension d” , but it is simpler to let the dimension be understood implicitly.
Stronger Self-Similarity For Bpi Spaces
Authors: David Guy , Semmes Stephen
Published: November 2023

Roughly speaking, the BPI condition requires that the space have pieces all around that look like each other. There is an annoying ambiguity here; not only might these pieces be small, but a priori they might behave quite differently from place to place. We would be much happier to say that all the pieces look like each other. It turns out that we can always do this, at least to some extent. Let us begin with a couple of definitions.
Sets Made From Nested Cubes
Authors: David Guy , Semmes Stephen
Published: November 2023

In this chapter we shall look at sets constructed in the manner of Section 2.5. These sets provide a nice “universe” in which to work. They behave well and simply in terms of compactness and weak tangents. We would like to understand the geometric and combinatorial conditions under which there are regular mappings between sets of this type, or bilipschitz mappings or Lipschitz mappings with nontrivial image, but we are far from having definitive answers to these questions. We shall provide some observations about these matters, using the notion of “blocking” sets, and related forms of quantitative topology.
Big Pieces of Bilipschitz Mappings
Authors: David Guy , Semmes Stephen
Published: November 2023

Definition 14.1Let (M,d(·,·))and (N,p(·,·))be metric spaces, and suppose that f :M →N is Lipschitz. We say that f has a big bilipschitz pieceif there is a closed subset E of M such that the restriction off to E is bilipschitz and if H  κ  (E) > 0,where κis the Hausdorff dimension of M. Of course the restriction to closed sets comes for free, since a Lipschitz mapping which is bilipschitz on a subset is also bilipschitz on the closure.
Uniformly Disconnected Spaces
Authors: David Guy , Semmes Stephen
Published: November 2023

Roughly speaking, we are asking that there be an isolated “island” inM at any point and with practically arbitrary diameter whose distance to the rest ofM is at least a fixed multiple of its diameter. Basic examples include our usual self similar Cantor sets, as in Section 2.3. Later, when we discuss doubling measures, we shall discuss some amusing ways to deform the geometry of a Cantor set. For the moment let us merely point out that the set described in Section 11.6 is also uniformly disconnected.
Convergence Analysis for Iterative Domain Decomposition Algorithms
Authors: Quarteroni Alfio , Valli Alberto
Published: November 2023

In this chapter we present some abstract theorems that are useful for proving the convergence of iteration-by-subdomain methods. The main part of our analysis will cover the case of substructuring procedures (for disjoint subdomains). The convergence analysis of the Schwarz method for overlapping partitions will be addressed in the last section of this chapter. For a complete analysis of Schwarz methods we refer to Dryja and Widlund (1990, 1995), J. Xu (1992) and Smith et al. (1996).
Advection-Diffusion Equations
Authors: Quarteroni Alfio , Valli Alberto
Published: November 2023

This chapter deals with a class of elliptic equations that are not symmetric, due to the presence of first-order terms in the differential operator. These operators describe advection –diffusion processes, and typically arise in fluid dynamics. Our emphasis is on the case in which the transport phenomena, driven by the advective terms, are dominant with respect to the diffusive ones, which are related to the principal second-order part of the operator. The case of a non-symmetric advection –diffusion equation with dominant diffusion was considered in Section 5.1.
Diffraction-line broadening analysis of dislocation configurations
Authors: Vermeulen A C , Delhez R , Keijser Th.H de , Mittemeijer E J
Published: November 2023

In order to understand the properties of polycrystalline solids, one must be aware of the concerted action of all dislocations in all crystals. Hence, it is desired to characterize the dislocation configuration. The analysis of diffraction-line broadening provides a powerful means for such a characterization in a statistically justified way. Until now, an interpretation of diffraction-line broadening by solids containing dislocations has not been performed in a detailed way. Normally, only some ‘overall’ dislocation density value is presented, which is obtained by applying a questionable formalism (see Section 11.2). This chapter provides a new interpretation of line broadening in terms of densities of the types of dislocations present on all possible slip systems in all groups of crystals; in the solid a group contains all crystals that have the same dislocation configuration. The subdivision of the specimen in groups of crystals may be dictated by, for example, the presence of preferred orientation, the imposition of a state of macroscopic stress, etc. (see Sections 11.4 and 11.5).
Effect of planar defects in crystals on the position and profile of powder diffraction lines
Authors: Ustinov A I
Published: November 2023

A lot of theoretical and experimental work (Landau, 1937; Wilson, 1941; Hendricks and Teller, 1942; Jagodzinski, 1949a–c; Kakinoki and Komura, 1952, 1954; Gevers, 1952, 1954a,b; Warren, 1959; Alegra, 1964) has demonstrated that planar defects, stacking faults, twin boundaries, antiphase boundaries, etc., influence both the location and profiles of diffraction peaks. It is important to take the potential planar defects in a crystal into account in cases when the intensity distribution in a peak is utilized for determination of other real crystal characteristics [size of coherent scattering units (crystallites), stress value in a crystal, lattice period, atom locations, etc.].
Effect of stacking disorder on the profile of the powder diffraction line
Authors: Weiss Z , Čapková P
Published: November 2023

Among the different types of defects in layer structures, translation stacking faults are particularly frequent in natural and synthetic materials alike. This disorder is due to an irregular translation of the layers, parallel to their own planes. The occurrence of translation stacking faults is not limited to metal elements (such as cobalt), or simple structures like ZnS, CdS, SiC, which are based on close-packed layer structures. More complicated layer structures, such as phyllosilicates or high Tcsuperconductors, also exhibit translation stacking faults. Stacking faults play an important role in the solid-state transformations and in the formation of polytype structures.
Restoration and preprocessing of physical profiles from measured data
Authors: Cernansky Marian
Published: November 2023

Profiles of diffraction lines contain important information about the real structure of polycrystalline materials, e.g. about crystallite size and lattice strains (Langford and Louer, 1996). However, the physical interpretation is related to pure or physical diffraction profiles, f,which in most cases cannot be measured directly and are obtained from really measured profiles, h,by removing the instrumental distortion described by the instrumental function, g.This function includes both geometrical factors (finite width of source and slits, divergence of beams, flat-specimen surface, its transparency and displacement, imperfect focusing, etc.) and spectral factors, e.g. the finite wavelength interval of the primary radiation (see, for example, Stokes, 1955; Wilson, 1963; Azaroff et al.,1974; Klug and Alexander, 1974; Jenkins, 1989a). The instrumental function, g,is obtained in practice by the measurement of a suitable standard without diffraction broadening-an ideal standard. The case of a non-ideal standard was discussed by de Keijser and Mittemeijer (1978, 1980) and Delhez et al.(1980, 1982).
Crystal size and distortion parameters in fibres using Wide-Angle X-ray Scattering (WAXS)
Authors: Somashekar R
Published: November 2023

Crystal size and paracrystalline disorder of the lattice, which exist in polymer crystals, contribute to the width of the diffraction peaks. Methods have been proposed for obtaining both quantities from the intensity profile (Hosemann and Bagchi, 1962; Guinier, 1963; Vainshtein, 1966). An excellent review of Fourier methods and integral breadth methods is given by Klug and Alexander (1974). The treatments used to estimate crystal size and distortion parameters are based on the Fourier analysis of line profiles (Warren and Averbach, 1952) or on variance analysis (Wilson, 1962b, 1963, 1968; Langford, 1965, 1968). A comparison of these two methods has been given by Balzar and Ledbetter (1993a). In fact, size-strain analysis in the case of high temperature superconductors has been carried out using these methods (Balzar, 1992; Petersen et al.,1992). Fourier methods that can be used with the profile of a single reflection have been proposed (Gangulee, 1974; Mignot and Rondot, 1975; Zocchi, 1980; Nandi et al.,1984), but these again rely heavily on low order coefficients. The integral breadth methods (Ramarao and Anantharaman, 1965; Nandi and Sen Gupta, 1978; de Keijser et al.,1982) are based on the assumption that the Cauchy function determines size and that the Gaussian function gives strain. The most widely used method of de Keijser et al.(1982) gives size and strain parameters from Cauchy and Gaussian parts of the Voigt function. It has been pointed out by Balzar and Ledbetter (1993b) that the Warren-Averbach method gives surface-weighted domain sizes and a mean square strain averaged over the same distance perpendicular to the diffracting planes, whereas integral breadth gives volume-weighted domain sizes and an upper limit of strain. Several attempts have also been made to estimate crystal size distribution using the statistical approximation method (Benedetti et al.,1988; Bonetto et al.,1990; Nicolae and Emil, 1990; Espinat et al.,1993). The extent of amorphous scattering in polymer fibres has been estimated by Narten et al.(1991) casting doubts on the accuracy of existing methods of crystal size determinations. Murthy and Minor (1990) and Dokter et al.(1994, 1995) have given general procedures for evaluating amorphous scattering from X-ray diffraction scans of semi-crystalline polymers. Recently, Lee et al.(1995) have estabilished the one-to-one relationship between the structure and property of fibres using wide-angle X-ray scattering studies.
Homogeneous Turbulence Approaching a Wavy Surface
Authors: Sajjadi S G , Hunt J C R , Wong H
Published: November 2023

An unidirectional turbulent shear flow over a wavy surface affects the turbulence by means of two mechanisms. First, the no-slip condition at the surface produces a mean velocity gradient which interacts with the velocity and the vorticity of the turbulence. Second, the velocity fluctuations of the turbulence must be zero at the wavy wall.
Mutual Transformation of Waves in Smooth Shear Flows
Authors: Rogava A D , Tevzadze A G
Published: November 2023

The purpose of this report is to outline a new linear mechanism of mutual transformations of waves in smooth shear flows. The mechanism is closely related to non-normality of linear dynamics of waves in shear flows and is best interpreted in the framework of a nonmodal approach- by tracing of evolution of spatial Fourier harmonics (SFH’s) of waves in time. The core of the phenomenon may be specified as follows: Wave frequency is a certain function (specified by its’ dispersion) of the wave numbers. Mean flow velocity shear results (even in linear approximation) the variation of a wave number(s) of each SFH in time, due to the effect of the shearing background on the wave crest. With this variation it follows that the frequency of SFH varies in time - it “slides along” the dispersion curve of the wave mode. As a result, for definite parameters of the system, if the dispersion curves of the wave modes pass nearby one another, wave frequencies will be closely related in a limited time interval. It is this fact which causes the mutual transformation of the waves in case of a slow variation of waves frequencies. Phenomenon of linear transformation of waves should be realized in a wide variety of terrestrial and astrophysical shear flows and grant significant diversity to processes taking place in these flows.
Application of System Identification Techniques in Wind Wave Modelling
Authors: Cieślikiewicz Witold , Graff Jerzy
Published: November 2023

In this paper the development of a parametric transformation linking the meteorological conditions with the sea response for the southern North Sea region is presented. The method of empirical orthogonal functions and system identification procedures are used to develop the parameterisation. The method of empirical orthogonal functions is applied to the wind velocity field and it is shown that the wind field time history can be adequately represented by the first few principal components. These wind field principal components are used to synthesise the meteorological input for system identification. The system identification procedures are then applied to develop a new efficient form of parametric model linking spatial meteoro logical data with the wind wave field response.
Effects of Waves in both the Surface and Bottom Boundary Layers
Authors: Davies A M , Jones J E , Kwong S C M , Xing J
Published: November 2023

A brief overview is presented of the influence of turbulence due to wind wave breaking upon wind induced surface currents. The sensitivity of computed surface currents to the parameterization of surface turbulence is initially illustrated using simulations of the wind induced movement of the Ebro plume off the coast of southern Spain, where an experiment is planned to measure surface currents using HF Radar. Subsequently the storm which occurred in the region of the Shetland Islands at the time of the Braer Oil spill, is used to examine surface currents during major storms. The role of wind waves in enhancing bottom stress in shallow water regions, and the effect on the near shore circulation, is illustrated using a high resolution three dimensional model of the Eastern Irish Sea.
Strong Turbulence at a Free Surface
Authors: Brocchini1 M , Peregrine D H
Published: November 2023

The behaviour of a free surface which is affected by strong turbulence is being studied. We summarise some of the salient points of our work. These include a derivation of averaged boundary conditions which include mass and momentum flows in the surface layer and the transfer to the bulk liquid. There is description of the various free surface regimes that occur and which need to be considered in order to determine suitable closures for the averaged terms.
A naïve introduction to ┌-convergence
Authors: Braides Andrea , Defranceschi Anneliese
Published: November 2023

This property is clearly the fundamental requirement for a good variational convergence. The equality above can be seen as a ‘Weierstrass theorem along the sequence (fj)’, where replaces f in Theorem 1.9.
The fundamental estimate
Authors: Braides Andrea , Defranceschi Anneliese
Published: November 2023

It is convenient to highlight some properties from which it is possible to guarantee that the r-limits define inner regular increasing set functions. In this section p≥2 L
Homogenization with non-standard growth Conditions
Authors: Braides Andrea , Defranceschi Anneliese
Published: November 2023

In this chapter we prove a homogenization result for functionals whose integrands satisfy some ‘non-standard growth conditions ‘, thanks to an accurate use of Rellich ‘s Theorem and a careful generalization of the direct methods of ┌-convergence.
Homogenization of multi-dimensional structures
Authors: Braides Andrea , Defranceschi Anneliese
Published: November 2023

In this chapter we describe some homogenization processes that may model the macroscopic properties of media whose microscopic behaviour takes lower dimensional or multi-dimensional structures into account. We will show that the method for homogenization described in Chapter 14 can be adapted to the asymptotic analysis of these functionals. In addition to this study, we also have to face the problem of the choice of a proper description of the small-scale functionals themselves, whose natural domain is not the usual Sobolev-space setting. In Sections 24.1 and 24.2 we deal with energies defined on lower-dimensional structures whose homogenization gives rise to integral functionals defined on full dimensional domains. We are going to describe two different and, to some extent, complementary approaches to this problem. We remark that while the limit analysis will be performed in detail, the description of the energies at length scale e is only outlined, leaving some details to the reader. In Section 24.3 we consider energies which describe structures as rods, plates or thin films, where one or more dimensions are negligible with respect to the others. These lower-dimensional energies are obtained by a ┌-limit procedure from (normalized) energies defined on full-dimensional domains contracting to lower-dimensional ones. We treat the case when the full dimensional structures possess in addition a (periodic) cellular structure. For the sake of illustration, we only deal with the simplified case when the period and the ‘thickness ‘ of the structure are on a comparable scale.
Cathepsin H (EC 3.4.22.16)
Authors: Kirschke Heidrun , Barrett Alan J , Rawlings Neil D
Published: November 2023

In 1976 Kirschke and co-workers [169] named a lysosomal peptidase cathepsin H. This enzyme was termed L20C21 in 1972 by the same authors [340] and later cathepsin B3 [ 343], because of similarities to cathepsin B (then known as cathepsin B1). Histochemical demonstration by Sylven in 1968 [718] of a thiol-dependent lysosomal enzyme active against Leu-NHNap is now attributable to cathepsin H. In 1975 Davidson and Poole [1372] partially purified an enzyme hydrolysing Bz-Arg-NHNap, but different from cathepsin B, from rat liver lysosomes. This enzyme obviously was cathepsin H. A BANA hydrolase from rat skin described by Jarvinen and Hopsu-Havu in 1975 [1385] was identified in 1985 by immunological methods as cathepsin H [1009]. A benz!ijlarginine-/3-naphthylamide hydrolase isolated from rabbit lung by Singh and Kalnitsky in 1978 [392] was reported to degrade collagen [264] and in 1983 was named cathepsin I by Kalnitsky et al. [1261]. However, in later work by Kirschke and co-workers in 1986 [171], preparations of this enzyme from rabbit lung and rat lung did not show collagenolytic activity, but showed high cross-reactivity with an antibody to cathepsin H from rat liver. There was therefore no reason to retain the name cathepsin I for the enzyme from rabbit lung. The name cathepsin H (EC 3.4.22.16) was recommended by the nomenclature committee of IUB in 1981.
Cathepsin S (EC 3.4.22.27)
Authors: Kirschke Heidrun , Barrett Alan J , Rawlings Neil D
Published: November 2023

In 1975 the name cathepsin S was given to a cysteine peptidase purified from bovine lymph nodes by Turnsek and co-workers [402] and in 1981 from spleen by Locnikar et a!. [355]. The enzyme showed similarities to cathepsin L, but differed in a number of respects, including pl, Mn pH stability, activity against synthetic substrates and sensitivity to inhibitors, as shown by Kirschke and Bromme and co-workers, 1984-1989 [93, 170, 172, 346]. In 1991 studies on the

amino acid sequences by Ritonja et al. and \'viederanders and co-workers [1190, 1213] confirmed that cathepsins S and L are different enzymes. The name cathepsin S (EC 3.4.22.27) was recommended by the nomenclature committee of International Cnion of Biochemistry and Molecular Biology (IUBMB) in 1992.

Cathepsin S is one of the lysosomal cysteine proteinases known so far to show a restricted tissue distribution. The highest levels have been detected in spleen, sessile lung macrophages and heart [34, 172,295,346, 1141, 1195], but the occurrence of the enzyme has also been described in ileum, brain, thyroid and ovary [1180].

Cathepsin S has been shown to be preferentially expressed in cells of mononuclear-phagocytic origin [1710] and overexpressed in cortical neurones and glia in samples of brain from patients with Alzheimer's disease [1684]. Cells doubly transfected with both p-amyloid precursor protein and cathepsin S, but not with the other cathepsins, secreted high levels of amyloid p-peptides, indicating a function of cathepsin S in the pathogenesis of Alzheimer's disease [1337]. Cathepsin S was also shown to be essential in B cells for effective proteolysis of the invariant chain necessary to render class II molecules competent for binding peptides [1345].
Legumain (EC 3.4.22.34)
Authors: Kirschke Heidrun , Barrett Alan J , Rawlings Neil D
Published: November 2023

It has been known since the initial discovery of Csoma and Polgar in 1984 [1292] that the seeds of several legumes and other plants contain an endopeptidase specific for the hydrolysis of asparaginyl bonds. The enzyme has been termed asparagi!!JI endopeptidase [1259] and vacuolar processing enzyme [1305], but the name recommended by the nomenclature committee of the IUBMB is legumain. Kembhavi et al. [1389] in 1993 isolated legumain from moth bean (Vigna aconitifo!ia) and described a convenient fluorimetric assay in which the substrate was Z-Ala-Ala-Asn-NHMec. The cloning and sequencing of legumain from castor bean [1381] revealed some sequence identities with the 'haemoglobinase', from the blood fluke, Schistosoma mansoni. The parasite enzyme has now been shown also to be an asparaginyl endopeptidase and termed Schistosoma legumain [1638]. In reviewing the cysteine peptidases, Rawlings and Barrett [1187] assigned the number Cl 3 to the peptidase family containing the legume asparaginyl endopeptidase and the Schistosoma endopeptidase. This family shows no relationship to the papain family, Cl, to which all the other lysosomal cysteine proteinases belong. During 1995, the publication of human EST sequences made it clear that the human genome contains a form of legumain. This prompted Barrett and co-workers in 1997 [1783] to clone and sequence the cDNA for human legumain and to isolate and characterize the enzyme from pig kidney, using the assay that they had introduced earlier for the moth bean enzyme. The properties of the mammalian enzyme were so similar to those of the plant and Schistosoma forms that it seems appropriate to retain the same name, leJ,umain, for the mammalian enzyme.
Introduction
Authors: Acheson David
Published: November 2023

In August 1684 the astronomer Edmund Halley travelled to Cambridge, anxious to seek Newton’s advice on the key scientific problem of the day, which concerned planetary motion.
Artefact
Authors: Dudai Yadin
Published: November 2023

Artefact stems from the Latin ‘something made with skill’, but occasionally, in science, the major skill at stake is how to distinguish an artefact from a natural to boring conclusions gain immortality in obscure journals. But if the news is smashing, for example, that specific memories can be transferred from one individual to another in brain extracts (Babich et al. 1965; Ungar and Oceguera-Navarro 1965), the scientific community does its best to sort the facts out, even if the causes of the artefact, or at least what appears to be an artefact to the contemporary eye, do not always become clear in the process (Byrne et al. 1966; Nicholls et al. 1967; Smalheiser et al. 2001).
Capacity
Authors: Dudai Yadin
Published: November 2023

Pondering the capacity of our memory carries with it the risk of being enslaved to the common *metaphor of memory as a static storehouse (Roediger 1980). This misconception should be avoided at the outset. Furthermore, in the case of the nervous system, even the definition itself evokes cardinal issues: What is the meaning of ‘store’ (definition 1)? Are *internal representations stored as such, reactivated, or reconstructed anew each time they are *retrieved?1 If memory is reconstructed, then the capacity of the system should involve the ability to decompress and recreate information; however, something must eventually be stored as, clearly, the brain does not reconstruct memories from void.
Clever Hans
Authors: Dudai Yadin
Published: November 2023

Hans was purchased by a retired German schoolteacher, Wilhelm von Osten, in 1900 with the aim of reproducing the remarkable behaviour originally noted by von Osten in an earlier Hans. Soon the feats of Hans II over-shadowed those of his predecessor, endowed him with the respectable title ‘Clever Hans’ (Pfungst 1911), and earned him an honourable position in the history of experimental psychology.
Context
Authors: Dudai Yadin
Published: November 2023

constant in the course of the experiment, and is hence synonymous with apparatus, environment, and background stimuli (e.g. Lubow and Gewirtz 1995). In *real-life, the background often varies significantly from one moment to another, but still is not usually considered the target of learning or *retrieval. The information about the time and place in which the target was acquired is referred to as ‘source information’. The context itself could, however, become the experimental variable. This is illustrated in a study by Godden and Baddeley (1975), in which divers were instructed to learn word lists both on land and underwater, and subsequently *recall the lists either on land or underwater. After learning on land, recall was better on land, and after learning underwater, recall was better underwater (Figure 20).
Controls
Authors: Dudai Yadin
Published: November 2023

In the Middle Ages ‘control’ meant a ‘duplicate register’, or ‘duplicate roll’ (contra–rotulus in Latin). Rolls were the standard material for writing administrative and financial records (Clanchy 1993), and the duplicate rolls were used by one officer of the law to check upon the rolls of another officer. The transition from the language of bureaucracy and commerce to that of scientific *culture has its roots in the Methods of experimentalinquiry proposed by the British philosopher John Stuart Mill.
Cue
Authors: Dudai Yadin
Published: November 2023

‘Cue’ originated in the medieval theatre, and is the spelled name of the letter q, the abbreviation of quand -o, Latin for ‘when’. For a while it was also spelled qu or cu. It meant a signal that prompts another event in the performance, such as the entrance of an actor (Harrison 1998). Cues fulfil fundamental roles in all the paradigms and assays of learning and memory.
Culture
Authors: Dudai Yadin
Published: November 2023

Culture in Latin meant tilling and husbandry, and cultor was a planter, inhabitant, and worshipper of gods (Cassell’s Concise Latin dictionary 1966). In modern society, the agricultural connotations of culture are largely gone, but the sense of belonging to a physical or virtual niche remains; some kind of worshipping, be it religious or secular, is also often retained. So versatile are the uses and implications of ‘culture’, that dictionaries give up on defining it in a comprehensive manner. ‘Culture’ is widely discussed from different points of views in anthropology, sociology, archaeology, history, political science, critical theory and aesthetics, philosophy, ethology, and socio-biology (Kroeber and Kluckhohn 1963).
Declarative memory
Authors: Dudai Yadin
Published: November 2023

The term ‘declarative memory’, depending on the *context of the discussion, refers to a faculty and experience of memory (definition 1), the material stored and *retrieved (definition 2), and the relevant brain system(s) (definition 3). That part of our memory is directly accessible to conscious recollection but part is not, was first explicitly stated by philosophers (e.g. de Biran 1804; Bergson 1908). Ryle (1949) formulated it as the distinction between ‘knowing that’ and ‘knowing how’. ‘Knowing how’ refers to *skills and procedures, ‘knowing that’ to information that can be ‘declared’, i.e. declarative memory.
Dementia
Authors: Dudai Yadin
Published: November 2023

The common feature of all the dementias is multiple cognitive deficits that include severe memory impairment, and at least one of the following cognitive disturbances: aphasia (deterioration of language function); apraxia (impaired ability to execute motor activities despite intact sensorimotor function); agnosia (failure to identify objects despite intact sensory function); or disturbance in executive function (the ability to reason, *plan and execute complex behaviour) (DSM-IV 1994). Severe memory impairment in the absence of other cognitive disturbances is *amnesia.
Dimension
Authors: Dudai Yadin
Published: November 2023

Brains are considered to have evolved in evolution under pressures that were supposed to lead to the selection of faculties beneficial for survival in a limited niche of the universe.2 It is therefore likely, in spite of occasional sparks of unjustified hubris that claim otherwise, that the individual human brain perceives only limited dimensions of nature, in terms of both properties and magnitude. That segment of our physical ambience that is directly accessible to our senses and has shaped our intuition3 can be dubbed, based on its dimensions, as the ‘mesoworld’.
Engram
Authors: Dudai Yadin
Published: November 2023

The notion that *stimuli produce enduring physical changes in the brain, and that these changes are the basis for memory, has been with us since early times (e.g. see Plato’s etched wax tablets of memory, Theaetetus; *metaphor). About 100 years ago, a German scholar, Richard Semon, termed the material record engraved by a stimulus in living tissue as the ‘engram’ (Semon 1904). The etymological roots of the term are Greek, and it means ‘something converted into writing’. Semon had in mind a rather general theory of experience-experience dependent records in living organisms, which included not only neural but also *developmental and genetic memory in all types of tissue.
Fear conditioning
Authors: Dudai Yadin
Published: November 2023

‘Show me a man who is not a slave; one is a slave to lust, another to greed, another to ambition, and all men are slaves to fear’ (Seneca 63–65). Fear drives fundamental responses to the world in individuals and societies alike (Durkheim 1895; Freud 1908). James (1890), influenced by Darwin (1872), considered fear merely as an instinct. He even thought that the need to exercise this instinct had diminished in evolution, and in a some-what naive burst of trust in the virtues of human kind, remarked: ‘…the progress from brute to man is characterized by nothing so much as by the decrease in frequency of proper occasions for fear’ (James 1890).
Homeostasis
Authors: Dudai Yadin
Published: November 2023

‘Homeostasis’ stems from Greek, meaning same stand or same state. The term was coined by Cannon: ‘…The coordinated physiological processes which maintain most of the steady states in the organism are so complex and so peculiar to living beings … that I have suggested a special designation for these states, homeostasis. The word does not imply something set and immobile, a stagnation. It means a condition—a condition which may vary, but which is relatively constant’ (Cannon 1932). Antecedents of the concept of ‘homeostasis’ can be traced back to ancient Greece (Adolph 1961).
Homo sapiens sapiens
Authors: Dudai Yadin
Published: November 2023

Humans are a very popular species in memory research. Over the years, far more memory experiments have been published on humans than on *monkeys, or on all invertebrate species combined. Only rodents still keep an edge in popularity in labs that specialize in the neurobiology of memory, but this could change, with the widespread availability of *functional neuroimaging. And yet, human beings almost always identify themselves with the side of the experimenter, even in situations in which they themselves suffer the fate of the experimental *subject, be it involuntarily in evolution or disease, or voluntarily in the lab. This raises some additional doubts on whether Homo (from ‘earth’ in Latin, a reminder of old myths) is indeed always sapiens (from ‘to be wise to taste’ in Latin, another reminder of a biblical story).
Honeybee
Authors: Dudai Yadin
Published: November 2023

Humankind has displayed keen interest in bees since the dawn of history. There is no evidence that the opposite was ever true. Cave paintings dating 10 000 years ago already depict bold honey harvesters driving away the stinging bees with smoke (Menzel and Mercer 1987). A few millennia later, when the Almighty led the Israelites from slavery to freedom, he promised ‘a good and large land, a land flowing with milk and honey’ (Exodus 3: 8). To this day, cultivation of the common honeybee, Apis mellifera L. (Rutner 1988), is a significant source of income to some, and a hobby to others; a cult encyclopaedia detailing whatever-you-ever-wanted-to-know-about-bees-and-never-dared-to-ask-them is claimed to have sold over the years more than half a million copies (Root 1972).
Imprinting
Authors: Dudai Yadin
Published: November 2023

When we select a partner, we often proudly consider it to be an epitome of free choice of a mature human being. Well, we may be wrong. Members of many species learn very early in life to restrict their social preferences to a specific class of objects. This acquired*bias comes to restrict the choice of the mate much later on. It is called ‘sexual imprinting’. In other words, there are always traces of one’s parents in one’s spouse. The basic phylogenetic function of sexual imprinting is considered to ensure that in due time, individuals do not waste their energy in courting the wrong species.
Instrumental conditioning
Authors: Dudai Yadin
Published: November 2023

In *classical conditioning the subject learns relations among *stimuli; in instrumental conditioning (also ‘instrumental learning’) it learns the impact of its actions on the world. The scientific interest in this type of learning can be traced to Bain (1859), who,impressed by his experience in the Scottish Highlands, noted ‘association of movement with the effects produced on outward things’ in animals trying to leap over obstacles:‘…spontaneous impulses of locomotion lead them to make attempts … any attempt causing a hurt is desisted from; after a number of trials and failures, the proper adjustment is come to, and finally cemented’.
Metaplasticity
Authors: Dudai Yadin
Published: November 2023

A valuable take-home message from the metaplasticity studies relates to the importance of the history of the experimental *subject or preparation and to the influence of this history on the outcome of the experiment. The investigation of metaplasticity reminds us that individual subjects or preparations, even if *controlled for age, gender, *nutrition, or *context at the time of experiment, etc., could still differ not only in terms of their particular past experience on a specific activity or item of information, but also in their activity dependent *capacity to undergo plastic changes at any particular moment in time.