bluuebunny/crossref_metadata_2025 huggingface dataset:
Squirrel monkey
Authors: Kirkwood James K , Stathatos Katherine
Published: November 2023

Thorington (1985) classified animals in the genus Saimiri into two species; Saimiri sciureus, of which he proposed there are four subspecies: S.s.  sciureus, S.s. cassiguarensis, S.s. boliviensis, and S.s. oerstedii, and S. madeirae. However, research on the taxonomy of Saimiri is continuing (for example, Van de Berg et al. 1987). These animals are found in wet and dry tropical forests (Baldwin 1985) of the Amazon Basin and surrounding lands (Brazil, Peru, Bolivia, Colombia, and Guyana), but there is also a population in Panama and Costa Rica (Thorington 1985). The latter, which are S.s. oerstedii, are listed as endangered (Mittermeier 1986; IUCN 1990).
Proboscis monkey
Authors: Kirkwood James K , Stathatos Katherine
Published: November 2023

There are no subspecies according to the ISIS classification. The species is found in Borneo (Medway 1970; Hrdy 1977) and on two small islands close to its north-eastern coast: Berhala and Sebatik (Wolfheim 1983). It is a forest species most commonly found in riverine or coastal areas (Kawabe and Mano 1972; Happel et al. 1987).
Biological structures obtained by X-ray diffraction methods
Authors: Waller David A , Dodson Guy G
Published: November 2023

1.1 Introduction

This article is aimed at biochemists and molecular biologists without crystallographic training who wish to learn about the structural determination of macromolecules by X-ray analysis. Examples are taken mainly from the crystallography of proteins. X-ray analysis has had an immense impact on biochemistry and biological science. Our knowledge of the three-dimensional structure of proteins, nucleic acids, viruses, and other macro­ molecular assemblies has come almost entirely through this technique.

The first high-resolution protein structure determined by X-ray crystallography, myoglobin (Kendrew et al. 1960), gave an initial impression of great complexity. On further study it was revealed that the structure was composed of eight helices arranged around the haem group. The conformation of the a-helices agreed with the predictions of Pauling and Corey (1951). This first protein structure was found to contain a core of predominantly non-polar residues with polar residues distributed over its surface. The separation of non-polar side-chains into the interior and polar side-chains onto the exterior of the protein explained many of its physical and chemical properties and gave a reliable structural basis to direct future chemical and biochemical research.
Biopolymers: an NMR survey
Authors: Wuthrich Kurt
Published: November 2023

During the last decade a method for the determination of the complete three­dimensional structure of proteins was developed, which uses nuclear magnetic resonance (NMR) spectroscopy for the data collection and distance geometry, or possibly other mathematical techniques, for the structural interpretation of the NMR data (W üthrich et al. 1982; W üthrich 1986). NMR is the only approach, in addition to diffraction techniques with single crystals, that is available for protein structure determination at atomic resolution. The structural information obtained by NMR is in many ways complementary to that from X-ray crystallography, thus widening our view of protein molecules with regard to a better grasp of the relations between structure and function. The NMR method can be applied with closely similar strategies to other biopolymers, such as DNA, RNA, and polysaccharides. However, since the potentialities of the method are intimately linked with the intrinsic structural properties of the molecules studied, the information on the molecular conformation obtainable with these other classes of com­ pounds may be more limited than with proteins. Much interest of the NMR approach is also focused on studies of intermolecular aggregates between proteins and other small or large molecules.
Evolution of the Genetic Code
Authors: Osawa Syozo
Published: November 2023

The genetic code was deciphered experimentally around 1966 and for a number of years scientists considered it to be "universal" for all forms of life. In 1981 researchers shocked the scientific community with the discovery that the code differed in mitochondria and certain other organisms, evidence that the genetic code was still evolving. This book discusses the distribution and origin of the non-universal codes and examines the possible mechanisms of code changes, making it essential reading for all those interested in evolutionary genetics.
Catalytic Additions of Carbon Dioxide Adducts to Alkynes: Selective Synthesis of Carbamates, Ureas, and Carbonates
Authors: Bruneau Christian , Dixneuf Pierre H
Published: November 2023

CO2 is the meeting point of several idealistic criteria for the functionalization of organic substrates: abundance, low cost, nontoxicity, and reusable carboxylation carbon unit. Its potential wide-range utilization is actually limited by its high stability, but motivates the search for general activation processes. One of the best uses of CO2 is the carboxylation of organic halides via Grignard reagents. However, the overall reaction cost implies loss of the halide and oxidation of magnesium (eqn (1)). In contrast, new generation carboxylation processes should involve the direct coupling with hydrocarbons and the use of a more easily reducible metal catalyst.
Carbon Dioxide as an Organic Building Block. Mechanisms of its Activation by Electron Transfer and Transition-Metal Complexes
Authors: Amatore Christian , Jutand Anny , Nielsen Merete F
Published: November 2023

A large amount of work has been devoted to the reductive activation of carbon dioxide (for earlier reviews see Darensbourg and Kudarovski 1983; Silvestri 1987; Behr 1988; Braustein et al.1988; Silvestri et al.1990), since this molecule represents an abundant and low-cost potential source of carbon for the production of organic chemicals. Under its natural form, viz.CO2, this is a rather stable molecule, inert to most organic reagents except strong nucleophiles. Conversely, its reductive activation, either by direct electron transfer (outer sphere activation) or by ligation to an electron-rich metal centre (inner-sphere activation) considerably increases its reactivity, especially in view of allowing a facile creation of carbon-carbon bonds. Since several other chapters of this book (see for example Chapters 7-9, 13) are already devoted to the discussion of several of these synthetic perspectives, here the focus is on some mechanistic aspects relevant to the reductive activation of carbon dioxide, in view of its use as a Cl building block in organic chemistry. The first section of this chapter is devoted to the mechanism of electron-transfer activation of CO2, as it occurs upon its electrochemical reduction at inert electrodes. In the second section we will discuss some of the mechanistic subtleties introduced by the combined use of electrochemical and transition metal activation of carbon dioxide, with respect to the formation of carbon-carbon bonds with organic substrates.
Oncogenes and tumour-suppressor genes
Authors: Piris M A , Sanchez-Beato M , Villuendas R , Martinez J C
Published: November 2023

The process of oncogenesis at the cellular level appears to be related to disorders in the control of cell proliferation, differentiation, and programmed cell death. These processes in higher organisms are regulated by multiple mechanisms involving intracellular and extracellular loops of control. Most, if not all, cancer cells contain multiple genetic aberrations that appear to contribute to tumorigenesis by perturbing these pathways. Two basic types of genetic damage are encountered frequently in cancer cells, dominant with targets known as proto-oncogenes, and recessive with targets known as tumour-suppressor genes. The genetic events affecting proto-oncogenes often result in a gain of stimulatory function, whilst that affecting tumour-suppressor genes may cause loss of inhibitory function. Early insights into the molecular control of tumour formation came from studies on RNA tumour retroviruses which lead to the discovery of viral oncogenes. These are segments of the viral genome which induce neoplastic cell transformation in vitro (characterized by loss of adhesion to surfaces, anchorage independent growth, lowered requirement for growth factors, and tumorigenity in nude mice), and contribute to the pathogenesis of virus-induced tumours in vivo. Similar sequences were identified in the genome of most eukaryotic cells displaying remarkable evolutionary conservation between the various species suggesting that they were essential for basic cellular functions. It has also been demonstrated that DNA extracted from tumour cells and introduced into normal cells in culture may induce neoplastic transformation. The genes responsible for this effect have been identified. The homologues of all these viral and cellular transforming genes present in normal cells are called proto-oncogenes, implying that they are potentially oncogenic. Most of these encode proteins involved in the transmission of external growth and differentiation signals from the cell surface to the cytoplasm and nucleus. They modulate multiple biochemical pathways which control gene expression, cytoskeletal architecture, and cellular metabolism, which in turn regulate the progression of the cell cycle and the unfolding of cellular differentiation programmes (1). This implies that the effect of any particular oncogene on cell proliferation may not be independent of, and separable from, its effect on differentiation. Indeed, in general, the proliferative capacity decreases as cells differentiate (2). In other words, increased cell proliferation induced by any particular oncogene may not represent a direct effect on cell cycle regulation, but may be consequential to a decrease in the differentiation potential of the cell.
Oncogenes and tumoursuppressor genes as prognostic indicators in the development of human tumours
Authors: Field J K , Spandidos D A
Published: November 2023

The advent of the development molecular techniques has expanded the field of new prognostic indicators in cancer research. The discovery of oncogenes during the 1980s and tumour-suppressor genes in the early 1990s has provided new data for scientists and clinicians to determine the molecular development and progression of cancer. However, the clinical correlations with the molecular progression of the disease has relied on clinical and histological staging systems that have been used for many years and which have many limitations. The reliance on these staging systems, for example, clinical staging (TNM size of tumour, nodes and metastasis based on the UICC system) and histological (level of differentiation), will in time be replaced by the introduction of molecular staging systems for each cancer. This era has arrived in so far as it is now possible to identify a predisposing genetic aberration in certain familial cancers and identify individuals at risk. Within the next IO years it can be envisaged that molecular markers, such as oncogenes and tumour-suppressor genes, may be used to identify potentially malignant lesions and progressive and terminal stages of neo plasia. As this ideal situation has not yet been attained, this chapter provides an overview of the current state of the art and highlights achievements and limitations of our present understanding of oncogenes and tumour-suppressor genes as being useful prognostic markers in human cancers. The current concept of normal cell proliferation involves the counterbalance of growth-promoting proto-oncogene regulation with the growth-constraining regulations of tumour-suppressor genes. Amplification, translocation mutations, and overexpression of oncogenes have all been implicated in aberrant cell control, resulting in malignant transformation and tumour development. The constraining effects of tumour-suppressor genes are inactivated by gene mutation, deletions, and allele loss, resulting in loss of control and thus unrestrained growth of cancer cells (1).
Epidemic models and propagation of infectious diseases
Authors: Shigesada Nanako , Kawasaki Kohkichi
Published: November 2023

Infectious diseases have had major impacts on human society throughout its history. Many medieval European cities are known to have declined in the end because of infectious diseases. The number of deaths caused by infectious diseases far exceeds that of all wars in the past. For instance, bubonic plague that swept over Europe in the 14th century took the lives of a quarter of the total population of 100 million. In the Aztec Empire of Central America, smallpox which was brought over by the Europeans reduced the population by half from about 3.5 million originally present in 1520. In this century, a strain of influenza known as Spanish flu broke out at the end of the First World War and caused the death of 20 million people around the world in 1919 (Anderson and May, 1991).
Discovery of the birds of paradise and history of their study
Authors: Frith Clifford B , Beehler Bruce M , Cooper William T , Mcguire Michael
Published: November 2023

The history of the discovery and study of birds of paradise is as colourful as the birds themselves. It has included the lives (and sometimes the deaths) of monarchs and other eminent persons, famous and infamous explorers, traders and collectors, and some of the great evolutionists, zoologists, and ornithologists. Recent decades have seen all manner of people spend significant parts of their lives involved with these magnificent birds. American, Australian, and British self-made, and some knighted, millionaires, academics interested in the theoretical potential of the birds, and enthusiastic but near penniless young birdwatchers have suffered the extreme discomforts of New Guinea for a glimpse of avian paradise. Errol Flynn, before gaining Hollywood fame, had an eye to the bird of paradise plume trade as a possible back-up venture when in New Guinea in search of gold (Flynn 1960; Fuller 1995).
Evolution and biogeography of the birds of paradise
Authors: Frith Clifford B , Beehler Bruce M , Cooper William T , Mcguire Michael
Published: November 2023

As have most traditional treatments (Mayr 1941a; Bock 1963; Gilliard 1969; Diamond 1972; Cooper and Forshaw 1977), we consider the birds of paradise monophylctic-a single evolutionary lineage constituting the family Paradisaeidae. As may become clear from our systematic analysis that appears later in this chapter, proof of the evolutionary cohesiveness (e.g. monophyly) of the various genera here treated as birds of paradise is built on a rather slim dataset, and yet it remains the most parsimonious treatment of this assemblage of genera. Resolution of some of the thornier questions related to the systematics of the group may come once molecular analyses (see, for example, Christidis and Schodde 1992; Nunn and Cracraft 1996) are performed on a complete range of the species in the family.
Conservation
Authors: Frith Clifford B , Beehler Bruce M , Cooper William T , Mcguire Michael
Published: November 2023

During the first decade of the twentieth century, hundreds of thousands of skins of adult male birds of paradise were exported from the island of New Guinea. They were destined to adorn the hats of European and American women and head-dresses of sultans and other Asian aristocracy (Gilliard 1969; Swadling 1996). The millinery trade was booming, no respectable person appeared in public without a hat, and no fashionable woman wished to be seen on the street without a hat sporting aigrettes, plumes, or even whole birds (especially the brilliantly-metallic male hummingbirds of the neotropics).
Family PARADISAEIDAE: the birds of paradise
Authors: Frith Clifford B , Beehler Bruce M , Cooper William T , Mcguire Michael
Published: November 2023

The family Paradisaeidae comprises 42 species of oscinine songbirds with a global distribution restricted to the forests of eastern Australia, New Guinea and its satellite islands, and the north Moluccas (Fig. 1. I, Plates 4-12). All spp. inhabit humid (mostly tropical) forest. A few spp. also range into woodland savanna, and one ranges southward into the Australian subtropics. New Guinea is the centre of generic diversity and sp. richness, and this may be where the group evolved.
Evolution of adaptive polymorphism in spatially heterogeneous environments
Authors: Beaumont Mark A , Meeûs Thierry de , Renaud François
Published: November 2023

The genesis and maintenance of biological diversity can be studied at many levels from molecular biology to community ecology. One of these different, but complementary, levels is genetic diversity. Genetic polymorphism for protein structure has been found to be more extensive than previously thought (e.g. Lewontin and Hubby 1966) and, as a consequence, evolutionary biologists have debated several important questions concerning the maintenance of genetic polymorphism:

(1) How can selection maintain polymorphism?

(2) What is the role played by environmental heterogeneity?

(3) What role can habitat selection play?

(4) What can we infer from polymorphism to understand the process of speciation?
The population dynamics of single host-multiparasitoid interactions
Authors: Jones T Hefin , Hassell Michael P
Published: November 2023

Insect parasitoids and their hosts are an integral part of the complex web of multispecies interactions in which insects exist. Although some insect species are host to a complex of 20 or more parasitoid species, a large number are attacked by only one or two species (Askew and Shaw 1986; Hawkins and Lawton 1987, 1988). Many parasitoid species are polyphagous to some degree, and their populations are thus buffered from fluctuations in abundance of any one of their host species (Southwood and Comins 1976).

A detailed quantitative understanding of the dynamics of species within such complex communities is rarely feasible. Instead, in an attempt to determine what factors are promoting the persistence of interacting species, the search has been more for broad patterns of community organisation (May 1981). This has frequently involved developing models that are either tailored to specific questions, or attempt to describe particular systems (Kareiva 1989; Jones et al. 1994). It is possible ‘that interactions between relatively few keystone members of complex communities determine the overall state of the system, with the dynamics of many of the other species influenced by, but not influencing the keystone species’ (Memmott and Godfray 1994).
The Antarctic Cheilostomatida
Authors: Hayward P J
Published: November 2023

The Cheilostomatida comprises the majority of living species of marine bryozoans. With the exception of certain estuarine habitats, and Northern Hemisphere intertidal seaweed habitats, where species of Ctenostomatida may predominate, the cheilostomates everywhere outnumber the heavily calcified Cyclostomatida and the non-calcified ctenostomates. Cheilostomate colonies exhibit an immensely wide diversity of form, and, while colony form may be characteristic for a family or genus, it is only rarely so at the species level. The taxonomy of the group is largely founded on the characters of the constituent zooids of the colony.
Evolution of colony characteristics
Authors: Crozier Ross H , Pamilo Pekka
Published: November 2023

Colony life with a reproductive division of labour is the hallmark of the eusocial insects. In earlier chapters we have presented simple family models in which the colony is headed by one reproductive female, and in most cases we have assumed that she has mated with a single male. This gives the simplest possible colonial structure that results in the typically high sister relatednesses in hymenopteran species. Even though some social insect colonies do have such a simple familial composition, many (probably most) species have genetically more complex colonies. In many species females mate with several males and a colony can have more than one reproductive female. Either several to many queens reproduce in a single colony or workers can compete with the queen and lay haploid eggs that develop into males. Colonies can also be subdivided into several physically separate nests that exchange individuals. Such complex colonial structures pose new problems to evolutionary theory: what is the functional unit and what is the unit of selection (cf. Table 1.6)? When a colony has many reproductives in it and the worker fom! can be divided into different kin groups (patrilines and matrilines), we can also ask whether individuals can distinguish between various levels of kinship and direct their behaviours in favour of closely related nest-mates. We can also wonder how much the genetic heterogeneity of a colony can increase before its social harmony breaks down. These are the questions we deal with in this chapter.
Intra-colony conflicts over sex-allocation
Authors: Crozier Ross H , Pamilo Pekka
Published: November 2023

The relatedness asymmetries to which social Hymenoptera are prone lead inevitably to a conflict of interest over the basic function of the colony: the reproduction of the genetic material. The queens and workers will be selected to favour different patterns of investments between the new queens and males, and colony maintenance. Factors affecting the relatedness structure of colonies and of populations will inevitably affect the results of this conflict. Such factors include whether or not the workers produce any of the males (thus affecting relatedness structure) and whether queenless colonies contribute significantly to male-production (thus devaluing males for the queen-right colonies). The sex ratio among reproductives is not the only arena of conflict between queens and workers: the question of the division of resources actually involves a three-way split, in that resources have to be allocated not only to queens and males but also to colony maintenance (further workers). In those species whose colonies reproduce by splitting ( ‘fission ‘), there: will also be the potential for disagreement over the timing of this event, and the relative investment in males and the daughter colonies. The central problem of social insect sex allocation is thus ‘Who wins? ‘ in the evolutionary struggle between queens and workers.
The comparative ecophysiology of water balance in microchiropteran bats
Authors: Webb Peter I
Published: November 2023

Aspects of water balance were studied in the three species of bat commonly found in north-east Scotland: Plecotus auritus, Myotis daubentonii and Pipistrellus pipistrellus. One of these species (M. daubentonii) has a close association with open water in the wild, while one (P. pipistrellus) has a much lower mean body mass (c. 6 g) than the other two (c. 10 g). Faecal water content and maximum urine-concentrating ability were not significantly different between P. auritus and M. daubentonii. However, urine loss was higher (by c. 140 µI/day) and resting evaporative water loss lower (also by

c. 140 µI/day) in M. daubentonii than in P. auritus. In free-flying captive colonies of bats, total water intake was highest in M. daubentonii, intermediate in P. auritus and lowest in P. pipistrellus. It seems possible that M. daubentonii demonstrate high water flux outside the day roost and compensate through a low water flux within the day roost. A low rate of water intake in captive P. pipistrellus may simply be a function of small body size.
Characterization of mitochondrial DNA variability within the microchiropteran genus Pipistrellus: approaches and applications
Authors: Barratt E M , Bruford M w. , Burland T M , JONES G , Racey P A , Wayne R K
Published: November 2023

Past systematic studies of the genus Pipistrellus have used either morphological or karyological characters to reconstruct phylogenetic relationships. We provide a new molecular perspective on the relationships of Pipistrellus species through a phylogenetic analysis of mitochondrial cytochrome b DNA sequence data. We have used the polymerase chain reaction to amplify DNA of individuals from both living populations and museum collections. Our results show that Pipistrellus is a diphyletic grouping, containing two distinct clades that differ by about 12% in mitochondrial DNA sequence. Surprisingly, we find that genotypes from the UK population of P. pipistrellus are found in both clades. Three possible explanations for this observation are (1) that hybridization has occurred between species from both clades, (2) that two distinct ancestral lineages have been retained in the species, or (3) that the lineages comprise separate species.
Mitochondrial diversity and heteroplasmy in two European populations of the large mouse-eared bat, Myotis myotis
Authors: Petri Barbara , Neuweiler Gerhard , Paabo Svante
Published: November 2023

A total of 101 animals were sampled from three nursery colonies of Myotis myotis in Portugal and in Bavaria, southern Germany. A segment of the triple-stranded part of the mitochondrial control region ranging from 400 bp to 800 bp was amplified via PCR and analysed by gel electrophoresis. Substantial length variation was found among different animals and 33% of the bats were heteroplasmic for up to six different size classes. When the DNA sequence of the heteroplasmic segment was determined, the length variation was found to be due to a variable number of tandemly repeated motifs of 82 bp, as has also been described for the American evening bat, Nycticeius humeralis. Heteroplasmy, as well as homoplasmy, were stably inherited in 25 mother-pup pairs. Mechanisms for the generation of length and sequence heteroplasmy are thought to be slippage mutations caused by the D-loop replication procedures and to a lesser degree by biparental inheritance of mitochondrial DNA.
Ionization methods
Authors: Esmans E L
Published: November 2023

In recent years a number of ionization methods differing from the traditional electron impact technique (EI), have been introduced in mass spectrometry (MS). Field ionization (FI) and field desorption (FD) (Lattimer and Schulten 1989) were two of the pioneering alternative ionization techniques used, but have nowadays been superseded in popularity by techniques such as fast atom bombardment (FAB) or liquid secondary ion mass spectrometry (LSIMS), plasma desorption (PD), laser desorption (LD), matrix assisted laser desorption (MALDI), and electrospray/ionspray (ES/IS) techniques (Trainor and Derrick 1992).
Characterization of proteins by mass spectrometry: from primary structure to conformational studies*
Authors: Forest Eric , Buzy Armelle , Guy Philippe , Halgand Frederic , Jaquinod Michel
Published: November 2023

Proteins are the object of intense investigation, justified by the major role they play in most cellular mechanisms and by their potential applications in the fields of pharmacy, diagnosis, plant biotechnology, chemistry, and the environment. In order to understand the functioning mechanisms of these macromolecules, it is necessary to characterize their structure precisely. Nuclear magnetic resonance, circular dichroism, as well as X-ray crystallography have been the most common techniques used to probe the threedimensional conformation of proteins. Mass spectrometry (MS), which has proved to be a powerful technique to study the primary structure of proteins, has been used only recently to probe conformational properties. In this article the results concerning the primary structure of the four proteins of the glycine decarboxylase complex from pea leaf mitochondria will be presented. Then, localization of disulphide bridges which represent a first element of the three-dimensional structure, will be illustrated with proteins from spider, scorpion, and wheat seed. Lastly, results and projects concerning conformational studies of bacterial cytochromes c and of a plant enzyme, which is a potential target of herbicides, will be presented.
Mass spectrometric studies on flavonoid glycosides
Authors: Claeys M , Li Q M , Van Den Heuvel H , Dillen L
Published: November 2023

Mass spectrometric methods based on the combined use of fast atom bombardment (FAB), collisionally-induced dissociation (CID) of positive ions, and tandem mass spectrometric techniques have been developed for the structural characterization of flavonoid glycosides containing aglycone moieties of the flavone or flavonol type. With respect to the characterization of flavonoid 0- glycosides, mass spectrometric methods involving low-energy CID yield information on: (1) the carbohydrate sequence; (ii) the aglycone moiety; and (iii) the glycosylation position. The characterization offlavonoid C-glycosides is addressed by high-energy CID, which enables differentiation between isomeric mono-6-C- and 8-C-glycosides, and isomeric di-6,8-C-glycosides. The structural elucidation offlavone O,C-diglycosides is accomplished by resorting to lowand high-energy CID; low-energy CID allows the determination of the type of the terminal O-linked carbohydrate residue, whereas high-energy CID enables identification of the type and the linkage position of the C-linked carbohydrate.
Introduction
Authors: Evans Martin J
Published: November 2023

This book, a practical handbook for researchers using embryonic stem (ES) cells, may be thought of as a cookbook. Some cooks reading a cookbook will just slavishly copy a recipe or two whereas others will learn from it, use it as a sourcebook, and provide their own interpretations resulting in novel dishes. It is hoped that you, the scientists using this volume, will emulate the adventurous chefs and use the protocols and ideas presented here as a stimulus for your own original studies and developments, which should take the field forward and fulfil its great potential.
Production of ES cell-derived mice
Authors: Kato Yoko , Tsunoda Yukio
Published: November 2023

The reintroduction of mouse ES (mES) cells into an embryonic environment allows expression of their pluripotency, as defined by the capacity to contribute to all tissue and cell types, including the germ cells (1, 2). This most powerful feature of mES cells has led to their exploitation in transgenic research, providing a direct route for the insertion of genetic modifications into the germline of fertile animals. Techniques for generating chimeric mice using mES cells – specifically, blastocyst injection and morula aggregation – are now standard worldwide (3); and recent refinements to those techniques have increased the efficiency of production of mice that are derived entirely – rather than partially – from the introduced mES cells, that is ‘mES cell-derived mice’. These refinements include the use of host embryos that have been rendered tetraploid (4), and which in consequence are incompetent to undergo fetal development; and the hyperthermic treatment of host embryos selectively to kill their inner cell masses (ICMs) (5). To compromise the viability of the host embryo’s ICM by either of these means favours its reconstitution by exogenously added mES cells, and consequently the production of mES cell-derived fetuses and offspring. In addition, mES cell-derived mice may be cloned by the technique of nuclear transfer using mES cells as the donor cells, or ‘karyoplasts’ (6). In this chapter we provide our current methods for producing mES cell-derived mice by embryo reconstitution (morula aggregation and blastocyst injection) using tetraploid and hyperthermically treated host embryos, and by nuclear transfer. Owing to space limitations, the reader is referred to primary texts for comprehensive coverage of supplementary methods in mouse husbandry, embryo micromanipulation, and surgical transfer (7).
Isolation and characterization of human ES cells
Authors: Pera Martin F , Laslett Andrew , Hawes Susan M , Tellis Irene , Koh Karen , Nguyen Lihn
Published: November 2023

This chapter will describe methods for the isolation and characterization of human embryonic stem (hES) cell lines from preimplantation blastocysts. The first derivation of hES cells was reported in 1998 (1), and since that time a number of groups have successfully established other, similar cell lines with the key features of primate pluripotent stem cells (2). There have been some significant improvements to the original culture system for hES cell propagation, and some refinements in the methodology for characterization of the cells. However, the mechanisms that regulate hES cell proliferation and differentiation are still poorly understood; there are practical limitations to existing culture methodology; and detailed, multicentre comparisons to assess the properties of hES cell isolates derived under different conditions and from different laboratories have not yet been carried out. Thus, while the current methodology is certainly adequate to support derivation and expansion of hES cells, the techniques and approaches described herein are likely to undergo substantial modification in the next several years.
ES cell lines from the cynomolgus monkey (Macaca fascicularis)
Authors: Suemori Hirofumi , Sasai Yoshiki , Umeda Katsutsugu , Nakatsuji Norio
Published: November 2023

Human ES (hES) cells hold great promise as an unlimited source of functional cells and tissues for transplantation therapy and regenerative medicine, owing to their pluripotency and capacity for indefinite proliferation in vitro. However, the realization of this goal demands not only robust methods for establishing and maintaining the undifferentiated hES cells, and for inducing their differentiation into specific cell types: animal model systems are both requisite and timely for testing the efficacy and safety of ES cell-based transplantation procedures. The use of monkey ES cells and transplantation models offers considerable advantages over murine systems: Strong similarities in the biology of human and monkey ES cells, and clear differences between primate (specifically, human and monkey) and murine ES cells, are emerging.
Paul P. Ewald—the German period
Authors: Hildebrandt G
Published: November 2023

This chapter treats mainly Ewald’s working life in the years between 1910 and 1937, beginning with the year when Ewald began his thesis and ending with the year when he left Germany. A few reminiscences will be added to touch on some important events for which Ewald returned to his native country after the Second World War.
Paul Ewald and the dynamical theory of electron scattering
Authors: Cowley J M , Moodie A F
Published: November 2023

It is one of the marks of the great scientist that with the passage of time specific aspects of his work extend and branch and, not infrequently, emerge in fields unknown at the time of the original discoveries. Examples of this can be found throughout the work of Paul Ewald, but few of these can be more striking than that afforded by his two-beam approximation with its celebrated coupled pendulum solution and its vivid geometry.
Ewald’s optical extinction theorem
Authors: Bullough R K , Hynne R
Published: November 2023

In his commentary on Ewald’s fundamental papers (1916a,b, 1917, 1937) in Chapter 11, Hellmut Juretschke draws attention to the elegant way in which P.P. Ewald solved the boundary problem for the propagation of electromagnetic (e.m.) waves in a crystal. He describes how by using a half-space (with a boundary) Ewald was able to show that the incident e.m. field (the field incident upon the crystal from outside) was extinguished inside the crystal and replaced by another e.m. field with different wave number. Similar considerations were independently developed more macroscopically by C.W. Oseen (1915) and the extinction process gained the name of the ‘extinction theorem’ (or the ‘optical extinction theorem’ in the sense of ‘optics’) of Ewald-Oseen. This chapter reanalyses the action of this ‘extinction theorem’ in an amorphous optical dielectric rather than a crystal and traces some of the subsequent history of the extinction theorem and its various applications in this context.
Introduction to the Dynamical Theory of X-Ray Diffraction
Authors: Ewald P P
Published: November 2023

My good friend the organizer of this session prepared me to speak to an audience consisting partly of experts in the applications of this theory and partly to people knowing the theory only by name. I shall dwell, therefore, on the method of the theory rather than on results or applications, of which the other papers of this session will contain examples.
A Review ofmy Papers on Crystal Optics 1912 to 1968
Authors: Ewald P P
Published: November 2023

The theory of the diffraction of X-rays by crystals was developed by Ewald as part of a unified study of the interaction of light of all wavelengths with crystals, beginning with the work for his 1912 thesis and extending to his papers in 1968. The formulation of the problem in terms of the interaction of electromagnetic radiation with a periodic array of dipoles is placed in its historical perspective and is compared with Laue’s version based on the assumption of a continuous electron density distribution. The Borrmann effect, hinted at in 1917, is derived readily from consideration of the dispersion surface.
E
Authors: Atkins P W
Published: November 2023

When a mathematical operation (such as multiplication, division, or differentiation) is performed on a function, the result is generally some different function. For instance, differentiation of x2 yields the different function 2x. However, for some combinations of operations and functions the same function is regenerated, but perhaps multiplied by a number (Fig. E.l). Thus differentiation of e2x gives 2e2X, which is the same function multiplied by 2. In such cases, the function is said to be an eigenfunction of the operator (in this case the differential operator d/dx), and the numerical factor (2 in the example) is called the eigenvalue of the operator. (Eigen is the German word meaning ‘own’ or ‘characteristic’.) If an operator Q operates on a function f and produces wf, where w is a number, f is an eigenfunction of Q and w is the corresponding eigenvalue. An expression of the form Qi= wf is called an eigenvalue equation.
H
Authors: Atkins P W
Published: November 2023

Sir William Rowan Hamilton (1805-1865), who was Astronomer Royal of Ireland while still an undergraduate, set up a system of classical mechanics which was to turn out to be ideally suited to reformulation as quantum mechanics. Indeed, it is arguable that he almost discovered quantum mechanics itself, and quite possibly would have done so if experiments had required it during his lifetime. For the systems that concern us, in classical mechanics the hamiltonian, H, of a system is the sum of the kinetic energy, T, and potential energy, V, of all the particles present.
K
Authors: Atkins P W
Published: November 2023

The kinetic energy, T, of a particle is the energy it possesses on account of its motion. In classical mechanics, the kinetic energy is related to the linear momentum p by T= p2 /2m (and by T=½mv2, where v is the velocity). In quantum mechanics the kinetic energy is proportional to the second derivative of the wavefunction (Box K.1). As the wavefunction becomes more sharply curved, so the kinetic energy of the particle increases. Conversely, a particle with a wavefunction that is almost flat everywhere has almost zero kinetic energy.
M
Authors: Atkins P W
Published: November 2023

The most intense transitions in molecules are due to °electric dipole transitions. When these transitions are forbidden by °selection rules other mechanisms may have sufficient strength to cause a transition, but at a much lower intensity.
Q
Authors: Atkins P W
Published: November 2023

An electric multipole is an array of positive and negative point electric charges. An electric monopole is a single point charge. An °electric dipole consists of two equal and opposite point charges (Fig. Q.1) with zero net charge. An electric quadrupole consists of four point charges with overall zero charge and zero dipole moment. It may be pictured as two dipoles arranged so that their dipole moments cancel (Fig. Q.1). Higher multipoles may be constructed in an analogous way. Thus, a 2”-pole consists of 2” point electric charges in an array that has no lower multipole moment (see below). Some multipoles are shown in Fig. Q.l, but alternative arrangements may also be envisaged. Any arbitrary distribution of charge may be expressed as a sum of multipoles.
R
Authors: Atkins P W
Published: November 2023

The energy of an atomic °term depends on the kinetic energies of the electrons, their attractive Coulombic interactions with the positively charged nucleus, and their mutual Coulombic repulsions. The last are very difficult to take into account quantitatively, yet they make an important contribution to the energy of the atom and to the relative energies of its °terms. In particular, the repulsions between the valence electrons of incomplete shells depend on the orbitals the electrons occupy, and hence terms with different total orbital angular momentum have different energies.
Analytical profile fitting of X-ray powder diffraction profiles in Rietveld analysis
Authors: Snyder Robert L
Published: November 2023

The inherent asymmetry of many powder diffraction profiles has been a principal hindrance in extending the application of diffraction techniques. The resurgence of developments in this area in recent years is primarily the result of the availability of general algorithms permitting computer automation of powder diffractometers (Mallory and Snyder 1979). The ability to collect digitized representations of the line profiles and apply numerical methods to their analysis has led to a number of new and exciting applications (Snyder 1983). The most exciting of these has been the continuing development of the whole pattern X-ray refinement method to obtain crystal structure information, begun by Rietveld (1969), who applied it to neutron diffraction (Chapter 2). The mostly symmetric-Gaussian nature of neutron diffraction lines has aided this application of the method to develop to its current rather mature state.
Ab initio structure solution with powder diffraction data
Authors: Cheetham Anthony K
Published: November 2023

There is a long and well-established tradition of using powder diffraction methods to study crystal structures. The earliest examples were inevitably concerned with the structures of simple materials such as iron metal (Hull 1917), and although for many decades powder methods were used predominantly as a means of qualitative analysis, a number of structure determinations, e.g. x- and ,G-UF 5 (Zachariasen 1949), were reported. Such studies were largely based upon geometrical considerations and trial-and- error methods, although Zachariasen and Ellinger (1963) were able to solve the monoclinic structure of ,G-plutonium by a manual direct-methods procedure. Nevertheless, powder methods were largely restricted to studies on simple structure types until the advent of the Rietveld method in 1969 (Rietveld 1969) extended their scope to the refinement of complex, low symmetry systems with as many as 50 atoms in the asymmetric unit (Cheetham and Taylor 1977; Hewat 1986). This important development has inevitably led to a re-examination of the methods that are available for the solution of unknown structures, and it is with this exciting challenge that the present chapter is concerned. We stress. however, that the Rietveld method continues to play a vital role in the subsequent refinement, which is necessary in order to complete the structure determination.
Higher-Order Approximations
Authors: Shmueli Uri , Weiss George H
Published: November 2023

We have shown that the central limit theorem can be used to calculate useful approximations to both univariate and multivariate pdfs that are generally easy to evaluate numerically. However, there are circumstances in which Gaussian approximations may be qualitatively inaccurate. Under these circumstances it is obviously desirable to find corrections to the Gaussian approximation or, alternatively, to find representations of the pdfs that are exact and whose numerical implementations are not too difficult. Both approaches to this goal will be discussed, Chapter 4 being largely devoted to approximate correction methods that build on the Gaussian approximation. However, before discussing the nature of these corrections we present an example in which the central limit theorem is shown to lead to a poor approximation to the pdf for the intensity.
Statistical Formulation Of The General Problem
Authors: McComb W D
Published: November 2023

We have seen that fluid turbulence can be regarded as a problem involving a random field ua(x, t). Or, as we also saw in Section 3.3.1, Fourier transformation can provide us with a formulation in terms of many degrees of freedom: that is, the Fourier components ua(k, t). Naturally, this latter interpretation leads us to view the turbulence problem from the point of view of the subject of statistical mechanics. This will be the dominant theme of this chapter, although we shall not entirely neglect the ‘field’ interpretation (still valid in k-space, especially if we take the limit Loo). In the first part of the chapter, we shall attempt to assess the turbulence problem in the context of statistical mechanics. This will be done against the background of a summary treatment of the classical N-body problem. Then we shall give the functional formalism for turbulence, followed by a discussion of the criteria to be satisfied by a theory of isotropic turbulence.
Turbulent Diffusion: The Lagrangian Picture
Authors: McComb W D
Published: November 2023

The ability to disperse and mix added substances is one of the characteristic features of fluid turbulence. It is also an aspect which is of enormous environmental and industrial importance. In this part of the book, our attention will be concentrated mainly on the underlying phenomenon of the diffusive action of turbulence. Indeed, to be more precise, we shall be concerned with the subject of passive scalar convec-tion, where by ‘scalar’ we mean something like temperature or chemical species concentration and by ‘passive’ we mean that the added substance does not change the nature of the fluid to the point where the turbulence is appreciably affected. This subject can be discussed perfectly well in terms of a statistical formulation in adularia (laboratory) coordinate frame, and, in fact, will be treated in just this way in Chapter 13. However, several profound insights have been gained by working in Lagrangian coordinates and, for this reason, we begin by discussing turbulent diffusion from this point of view in the present chapter.
Turbulent Diffusion: The Eulerian Picture
Authors: McComb W D
Published: November 2023

In this chapter we shall treat the diffusive and mixing properties of fluid turbulence in the same way as we have treated the random velocities, that is, by means of Eulerian fields. In this approach the marked fluid point will no longer be quite such a fruitful concept. Instead we shall be interested in the concentration field describing the distribution of the added substance, which is being dispersed from some initial location by the motions of the fluid. For example, we might be interested in the diffusion of heat from, say, a point or line source situated in a flowing gas or liquid, or we might consider the way in which common salt (in aqueous solution) spreads out when injected into a turbulent water flow (or the same problem for helium gas in air). Clearly, there are many such practical examples-indeed, all possible combinations of host liquid, added contaminant, form of source, and geometry of flow!
Three-Dimensional Flows
Authors: Bird G A
Published: November 2023

Homogeneous (or zero-dimensional), one-dimensional, two-dimensional, and axially symmetric flows are idealizations and all real gas flows are threedimensional. In DSMC computations of the idealized flows with restricted dimensions, the other dimension or dimensions may be regarded as being so small that the statistical fluctuations correspond with those in the real gas. This is not possible in a three-dimensional flow and the number of real molecules that are represented by each simulated molecule (the parameter FNUM in the DSMC programs) must be regarded as a computational approximation. While this poses an ideological difficulty, it is the sheer magnitude of the computational task that is the most serious problem associated with DSMC computations of three-dimensional flows.