bluuebunny/crossref_metadata_2025_split huggingface dataset:
Three-dimensional structures of the MMPs and TIMPs
Authors: Woessner J Frederick , Nagase Hideaki 
Published: November 2023

Abstract
The first three-dimensional (3D) structure of a metalloendopeptidase was reported for the thermophilic bacterial metalloproteinase thermolysin in 1972 by Mateukaryotic metalloendopeptidase was notthews et al. [1390]. The 3D structure of a eukaryotic metalloendopeptidase was not resolved until 1992 when Bode et al. [1347] reported the crystal structure of astacin from cray fish. The structure of astacin revealed that the topology around the catalytic zinc of the active site in this metalloproteinase can be superimposed on that of thermolysin, although the overall amino acid sequences of the two enzymes do not show a significant similarity [1347). Recent pro gress in determining the 3D structures of a number of metalloproteinases has revealed that the overall C”-backbone structure of astacin [19, 123, 1347] has a high degree of similarity with those of members of the other metalloproteinase families, i.e. snake venom metalloproteinases ada malysin II [1369, 1370) and atrolysin C [1421) in the reprolysin subfamily, MMPs in the matrixin subfamily (see below), and Pseudomonas aeruginosa alkaline proteinase [1342] and Serratia proteinase [1341] in the serralysin subfamily. Common structural elements are four parallel (sl, sII, s111, sV) and one antiparallel (slV) ,3-strands and three long a-helices (hA, hB, hC), which are arranged in an identical order (Fig. 4).
Changing Doxastic States: Two Complementary Perspectives
Authors: Rott Hans 
Published: November 2023

Abstract
In the last chapter we have seen how the analysis of knowledge may lead to the problem of belief revision. What one knows at a specific time instant does not only relate to what one believes at that instant, but also to a great variety of potential changes of the agent’s current beliefs. The relevance of the revision of beliefs to problems of epistemology provides an important reason for studying it.
In Chapter 1 we attended to what I called internal problems of belief. This has meant the task of drawing the right inferences on the basis of given information and expectations. If the task is successfully carried out, then the agent reaches a state of cognitive or reflective equilibrium. The present chapter is about problems caused by external interference. The influences from outside the doxastic system that we are going to consider come in two basic types. Agents may either learn new things or become doubtful about things that they used to think are true. Interaction with the world or with other agents may induce them to accept new items of belief, or to cease to accept old items of belief. In accordance with established terminology, I will say that doxastic states, as far as they are represented by belief bases or belief sets, are to be revised and/or contracted in response to new information. External influences are represented by discrete pieces of input to the doxastic system, which will in turn be represented by single input sentences of a given object language. Whether truth-conducive or not, such input first of all means a perturbation to a system that has previously been coherent. The addition of new beliefs frequently leads to a violation of the ideal of consistency, the subtraction of new beliefs violates the ideal of inferential closure.
Molecular biology databases
Authors: Kanehisa Minoru 
Published: November 2023

Abstract
The current state of biology is arguably comparable to seventeenth century physics in terms of the stage of formulating the science. Biology is still an empirical discipline with little formulation of basic principles that can be used in a deductive way to predict various biological phenomena. The technologies of genetics and cell biology, started in the nineteenth century, and of molecular biology, started in the twentieth century, have finally made it possible to gather fundamental observables in biology. It is expected that empirical rules similar to Kepler s laws and basic principles similar to Newton s theory will come along. This is where the computerized databases play critical roles as the basis of our expanding knowledge in biology.
Land of the Rising Sun
Authors: Hamilton W D 
Published: November 2023

Abstract
On a high hill top that overlooks Kyoto city, ancient capital of Japan, I watched free-living Japanese macaques for the first time. One of a crowd of scientific tourists, I had poured from a bus onto the flat, gravelled open space surrounding a kiosk and cafe that crown the hill and found the monkeys all around me. They gave us brief glances and moved quietly out of the way if we came near but much more they seemed to be watching the kiosk. Obviously they were free-living on this hilltop but right in this place could not be called exactly wild; however, the steep slopes over the edge of the small plateau were densely wooded and possibly the troupe obtained most of its food from there.
Cited but Little Read
Authors: Hamilton W D 
Published: November 2023

Abstract
Now comes a two-chapter break from disease and sex and a return to the topics that largely made up Volume 1 of Narrow Roads of Gene Land; but the present one is a very slight chapter. Sometimes it has seemed to me that the challenge to species and group-benefiting evolution issued in my first three papers has brought harpies to follow me ever since. Social behaviour, the topic of this and the next chapter, had been a four-year absolute obsession to me as I wrote the papers in the early 1960s—I was deeply immersed in it, a monomaniac, could do almost nothing else.
Two-Dimensional Problems Of Steady Motion
Authors: Hill R 
Published: November 2023

Abstract
In this and the two following chapters the ideas and techniques of Chapter VI a.re applied to the solution of a variety of problems of plane strain. We begin with problems of steady motion, in which the stress and velocitydo not vary at anyfixed point (referred to some coordinate system which may be at rest or moving uniformly). This condition is fulfilled in continuous processes of shaping metals, for example rolling, drawing, and extrusion. The approximation by the plastic-rigid body is likely to be good since the strains are usually large; the error due to the neglect of work-hardening can be largely removed by a simple correction factor, as we shall see. While the two-dimensional theory is strictly valid only for wide blocks or sheets, as in strip-rolling, it gives a useful qualitative picture of the deformation in such processes as the drawing of wire or the extrusion of rod; it will be shown, too, that the theoretical results, suitably modified, frequently provide a. close estimate of the energy consumption.
Mathematical Preliminaries
Authors: Chandrasekhar S 
Published: November 2023

Abstract
In this chapter, we shall provide an account of the analytical methods that lie at the base of much of the developments that are to be described in this book. These consist of Cartan’s calculus of differential forms and the tetrad and the Newman-Penrose formalisms. While none of these matters are novel in themselves, they cannot all be found in a coherent treatment in one place; and the account is included to make the book as self-contained as is possible. The presentation of the elements of differential geometry in §§2-6 is, however, not intended to replace the standard accounts of the subject available elsewhere: the presentation is confined to the barest essentials leading to Cartan’s equations of structure.
The Reissner-Nordstrom Solution
Authors: Chandrasekhar S 
Published: November 2023

Abstract
A spherically symmetric solution of the coupled equations of Einstein and of Maxwell is that of Reissner and Nordstrom. It represents a black hole with a mass M and a charge Q. Since one does not expect any macroscopic body to possess a net charge, the consideration of a charged black-hole would appear to be outside the realm of reality. Nevertheless, the study of the Reissner-Nordstrom solution contributes to our understanding of the nature of space and time. Thus, we shall find that the scattering of incident electromagnetic and gravitational waves by the Reissner-Nordstrom black hole is described by a symmetric unitary scattering-matrix of order four and allows for the partial conversion of energy of one kind (electromagnetic or gravitational) into energy of the other kind. Besides, the Reissner-Nordstrom solution provides a more general framework for the many surprising analytical features which we encountered in the study of the Schwarzschild solution in Chapter 4. And finally, the fact that the Reissner-Nordstrom solution has two horizons,
The Kerr Metric
Authors: Chandrasekhar S 
Published: November 2023

Abstract
In this chapter, we begin the study of the Kerr solution. It represents, as we have stated in the Prologue, the unique solution which the general theory of relativity provides for the description of all black holes that can occur in the astronomical universe by the gravitational collapse of stellar masses; and it is the only instance of a physical theory providing an exact description of a macroscopic object. In large measure, the preceding chapters are but preludes to the study we now begin.
Simple cases of electrification
Authors: Maxwell James Clerk 
Published: November 2023

Abstract
124.] We shall consider, in the first place, two parallel plane conducting surfaces of infinite extent, at a distance c from each other, maintained respectively at potentials A and B.
It is manifest that in this case the potential V will be a function of the distance z from the plane A, and will be the same for all points of any parallel plane between A and B, except near the boundaries of the electrified surfaces, which by the supposition are at an infinitely great distance from the point considered.
Confocal Quadric Surfaces*
Authors: Maxwell James Clerk 
Published: November 2023

Abstract
147.] Let the general equation of a confocal system be
(1)
where, λ is a variable parameter, which we shall distinguish by a suffix for the species of quadric, viz. we shall take λ.1 for the hyperboloids of two sheets, ‘A.2 for the hyperboloids of one sheet, and λ.3 for the ellipsoids. The quantities
Theory of conjugate functions in two dimensions,
Authors: Maxwell James Clerk 
Published: November 2023

Abstract
The number of independent cases in which the problem of electrical equilibrium has been solved is very small. The method of spherical harmonics has been employed for spherical conductors, and the methods of electrical images and of inversion are still more powerful in the cases to which they can be applied. The case of surfaces of the second degree is the only one, as far as I know, in which both the equipotential surfaces and the lines of force are known when the lines of force are not plane curves.
Electrolysis
Authors: Maxwell James Clerk 
Published: November 2023

Abstract
255.] I Have already stated that when an electric current in any part of its circuit passes through certain compound substances called Electrolytes, the passage of the current is accompanied by a certain chemical process called Electrolysis, in which the substance is resolved into two components called Ions, of which one, called the Anion, or the electronegative component, appears at the Anode, or place where the current enters the electrolyte, and the other, called the Cation, appears at the Cathode, or the place where the current leaves the electrolyte.
Conduction In Three Dimensions
Authors: Maxwell James Clerk 
Published: November 2023

Abstract
285.] At any point let an element of area dS be taken normal to the axis of x, and let Q units of electricity pass across this area from the negative to the positive side in unit of time, then, if becomes ultimately equal to u when dS is indefinitely diminished, u is said to be the Component of the electric current in the direction of x at the given point.
In the same way we may determine v and w, the components of the current in the directions of y and z respectively.
Conduction in dielectrics
Authors: Maxwell James Clerk 
Published: November 2023

Abstract
325.] We have seen that when electromotive force acts on a dielectric medium it produces in it a state which we have called electric polarization, and which we have described as consisting of electric displacement within the medium in a direction which, in isotropic media, coincides with that of the electromotive force, combined with a superficial charge on every element of volume into which we may suppose the dielectric divided, which is negative on the side towards which the force acts, and positive on the side from which it acts.
Conditional implications and non-monotonic consequence
Authors: Gabbay Dov M 
Published: November 2023

Abstract
Gabbay put forward his case for his system 𝕔 using proof-theoretic considerations. Makinson [1989] proposed a semantics for Gabbay’s logic and showed completeness. Makinson also studied the properties of the consequence relations associated with many well-known non-monotonic systems. Kraus et al [1990] used the preferential semantics of Shoham [1987; 1988] to give semantics for a family of axiomatic extensions of Gab- bay’s C logic for the language of classical logic. Thus a new area of research activity has emerged, namely the syntactic and semantic study of non-monotonic logics through their consequence relations.
combining temporal logic systems
Authors: Gabbay Dov M 
Published: November 2023

Abstract
In this chapter we are interested in describing systems in which two distinct temporal ‘points of view’ coexist. Descriptions of temporal systems under a single point of view, i.e. one-dimensional temporal systems, abound in the literature. These one-dimensional temporal logics differ from each other in several ways. They differ in the form the logic is presented, whether a proof theoretical, model theoretical or algebraic presentation. They differ in the ontology of time adopted, whether time is to be represented as a set of points, intervals or events. They can also differ in the properties assigned to flows of time, whether linear or branching time, discrete or dense, continuous or allowing for gaps. In this chapter we consider both proof- and model-theoretical presentations of temporal logics on a point-based ontology. Most of the results presented assume that the flow of time is linear.
Fibring implication logics
Authors: Gabbay Dov M 
Published: November 2023

Abstract
The proof-theoretical side of our investigations into fibred semantics can be formulated as follows: how can we combine different proof systems into more general ones, possibly preserving the desirable properties of the originals? We expect semantically based methods, e.g. semantic tableau methods, to play a crucial role in developing suitable proof methods based on fibred semantics.
Fibring modal tableaux
Authors: Gabbay Dov M 
Published: November 2023

Abstract
In the previous chapter we studied under which conditions proof systems are well suited for fibring, and we argued that labelled tableaux are calculi of this kind. In Chapters 14 and 15 we have shown how D‘Agostino and Mondadori ‘s 1994 classical proof system KE, a combination of tableaux and natural deduction inference rules which allows for a restricted (‘analytic‘) use of the cut rule, can be extended to deal with fibred logics, in particular for a combination of modal and substructural logics and the combination of different fragment of substructural implications.
Fibring labelled deductive systems
Authors: Gabbay Dov M 
Published: November 2023

Abstract
We saw in previous chapters how fibring can be done with the instrumental use of labels. This chapter applies our fibring ideas to labelled deductive systems (LDS). LDS (see [Gabbay, 1996b]) is a general methodology for presenting and studying logical systems. It unifies many areas of logic and has extensive applications.
Lattice Gas Cellular Automata
Authors: Succi Sauro 
Published: November 2023

Abstract
Digital arithmetic is to scientific computing as collisions of molecules are to fluid mechanics: crucial to the implementation, but irrelevant to most scientific questions . L. N. Trefehen, ‘Maxims about numerical mathematics, computer science and life’, SIAM News , Jan/Feb, 1998. In 1986, Uriel Frisch, Brosl Hasslacher and Yves Pomeau produced their wonderful bombshell: a simple cellular automaton obeying nothing but conservation laws at a microscopic level was able to reproduce the complexity of real fluid flows [18]. This discovery caused great excitement in the fluid dynamics community. The prospects were promising: a round-off free, intrinsically parallel computational paradigm for fluid flows, perhaps, even more, the analogue of the Ising model for turbulence! However, a few serious problems were quickly recognized and addressed with great intensity in the following years.
Lbe Flows In Disordered Media
Authors: Succi Sauro 
Published: November 2023

Abstract
The study of transport phenomena in disordered media is a subject of wide interdisciplinary concern, with many applications in fluid mechanics, condensed matter, and life and environmental sciences as well. Flows through grossly irregular (porous) media is a specific fluid mechanical application of great practical value in applied science and engineering. It is arguably also one of the applications of choice of the LBE (and LGCA) methods. The dual field–particle character of LBE shines brightly here: the particle-like nature of LBE (populations move along specific particle trajectories) permits a transparent treatment of grossly irregular geometries in terms of elementary mechanical events, such as mirror and bounce-back reflections. On the other hand, the field-like nature of LBE (populations carry smooth, hydrodynamic information) permits achievement of fluid dynamic behavior also in tiny interstitial regions of the flow which are hardly accessible to the macroscopic approach. These assets were quickly recognized by researchers in the field, and still make of LBE (and LGCA) an excellent numerical tool for microhydrodynamic flows in porous media.
Functional roles of microsatellites and minisatellites
Authors: Kashi Yechezkel , Soller Morris 
Published: November 2023

Abstract
A number of lines of evidence are reviewed showing that microsatellite and minisatellite sequences serve as functional coding and regulatory elements in the eukaryote genome. These include the presence of homopolymeric amino acid tracts in numerous proteins, conservation of microsatellites in relation to coding sequences, and ability of microsatellites to bind proteins and to serve as enhancer elements in expression constructs. Variation in microsatellite repeat number is found to have pronounced effects on their regulatory and coding functions, and is associated with phenotypic variation at both the biochemical and organismic levels. The combination of high mutation rate and regulatory/coding function raises the possibility that microsatellites are a major source of eukaryotic genetic variation.
Minisatellites and mutation processes in tandemly repetitive DNA
Authors: Armour John A L , Alegre Santos Alonso , Miles Sue , Williams Louise J , Badge Richard M 
Published: November 2023

Abstract
Detailed analysis of mutational processes at some human minisatellite loci is possible because of the very high rates of germline mutation and the presence of internal structural variation. This variation in the distribution of variant repeat units can be used both to survey allelic variation across populations and to define the structural basis of length change mutations. More recently, the fidelity with which minisatellite alleles can be amplified by PCR (even from the single molecule level) has allowed direct assays of germ line mutation from sperm DNA samples. The unexpected features of minisatellite mutation include polarity, recombinational exchanges between alleles, and mutation rate variation between alleles. The implications of these studies for our view of microsatellite mutation and evolution will be discussed.
Statistics of microsatellite loci: estimation of mutation rate and pattern of population expansion
Authors: Chakraborty Ranajit , Kimmel Marek 
Published: November 2023

Abstract
Applications of microsatellite loci in evolutionary studies are based on examination of the expectations of summary statistics of genetic variation at these loci, under a model for mutation and genetic drift. Usually, the single-step stepwise mutation model with unrestricted allelic states is assumed, and the effect of genetic drift is studied by assuming that the population size is constant over time. In this chapter, we illustrate the effects of relaxing both of these assumptions. We show that an expansion or contraction of population size over time leaves a signature on the genetic variation that can be detected by estimating the composite parameter (the product of population size and the mutation rate) from heterozygosity and allele size variance. Allele size restrictions also produce an imbalance between heterozygosity and allele size variance. These two statistics are insensitive to directional (expansion/contraction) bias of mutations if allele-size constraints are absent. Further, the feature that microsatellite alleles can be ordered by their sizes allows estimation of relative mutation rates of loci grouped by their biological properties. Applications of these principles to microsatellite data from several human populations indicate that the mutation rates are inversely related to the motif size, and the African populations exhibit indications of the most ancient human bottleneck.
Integrable Systems and Twistors
Authors: Richard Ward , Martin Speigh 
Published: November 2023

AbstractFor the purpose of this chapter, integrable systems are special kinds of non-linear differential equations (although one should note that there are also integrable difference equations, and the study of these is increasingly prominent). For essentially any system of differential equations, one has local existence theorems, so existence of solutions is not the issue. The question, rather, is what the solutions are like. For a non-linear differential equation chosen at random, one has no hope of writing down explicit solutions in terms of known functions. The classification of a function as ‘known’ may seem artificial, having more to do with what we’ve bothered to learn than the function itself; but in fact there is more to it than that. The known functions (e.g. trigonometric functions or elliptic functions) are known because they have nice properties, and can be defined using only a finite amount of information. The functions involved in the solutions of a generic nonlinear differential equation are so awful as to be literally indescribable in any but a tautological way (that is, one can really only define them as solutions of the differential equation). An extreme example of this is chaotic systems.