bluuebunny/crossref_metadata_2025_split huggingface dataset:
What can phylogenetic patterns tell us about the evolutionary processes generating biodiversity?
Authors: Harvey Paul H , Rambaut Andrew , Nee Sean 
Published: November 2023

Abstract
What can the structure of molecular phylogenies tell us about the evolutionary processes responsible for their genesis? Remarkably little attention has been paid to answering this question, despite the rapid accumulation of molecular sequence data which allows the construction of ever more precise phylogenetic trees. Our goal in this chapter is to provide research groups examining particular taxa with a set of routine procedures for extracting the footprints of the past that may lie hidden in their sequence data. Elsewhere, we have presented illustrative examples showing the types of conclusions that we believe can or cannot be derived from molecular phylogenies. It is not our intention to go over the same ground here, although we shall summarise some relevant points of this previous work insofar as they are relevant to our immediate aim.
Phylogenetic trees based on molecular data can tell us when, on absolute or relative time scales, independently evolving lineages last shared common ancestry. The footprint of the past, which we wish to interpret, consists of the relationships among the times between the nodes in the tree (Fig. 3.1).
Biodiversity of parasites in relation to their life-cycles
Authors: Morand Serge 
Published: November 2023

Abstract
Parasites with simple life-cycles (SLC) require a single host individual in their development, whereas complex life-cycle (CLC) parasites need several hosts. Several groups of parasites are composed entirely of complex life-cycle species (CLC) with at least one intermediate host and one definitive host, as in the case of digenous trematodes, cestodes and acanthocephalans. Although the intermediate host can serve as the site of parasite reproduction, it can also shelter infesting stages and be a prey for the definitive host, with the parasite then becoming an integral part of a predator-prey network.
Few studies have tried to understand the evolution and maintenance of complex life-cycles (Dobson 1989; Dobson and Merenlender 1991; Esch and Fernandez 1993), or the influence of CLC parasites on the dynamics of a multi-species system. Recently, Freeland and Boulton (1992) argued that CLC parasites may predominate parasitic associations and that they may stabilize multi-species systems.
Causes of developmental instability. Environmental factors
Authors: Møller Anders Pape , Swaddle John P 
Published: November 2023

Abstract
A large number of environmental factors can result in a reduction of developmental stability and increased levels of fluctuating asymmetry in bilateral traits. The list of factors is almost endless and the review given here is not exhaustive but merely a representation of the kinds of factors that researchers have thought important in explaining the variations in fluctuating asymmetry that they have observed. These may be tied to the natural ecology of the species studied, or limited to the laboratory equipment through which the investigator can manipulate the developmental conditions of the study organism.
The energetics of pteropodid bats
Authors: Mcnab Brian K , Bonaccorso Frank J 
Published: November 2023

Abstract
The temperature regulation and energetics of pteropodid bats are highly variable. Their thermoregulation is effective in species that weigh more than 60 g, but smaller species often exhibit imprecise regulation at cool environmental temperatures. The smallest nectarivores usually maintain a small temperature differential with the environment, especially at low altitudes. Nectarivores either regulate body temperature at high altitudes or are limited in distribution to lowlands. Basal rate in pteropodids varies with body size, with the propensity to enter torpor and with the size of the island on which pteropodids are found. The low rates of metabolism found in small-island Pteropus, produced directly or by a reduction in body mass, reduce resource use in an environment characterized by limited resources. A lower rate of metabolism is also found in species of Dobsonia endemic to small islands, compared with mainland Dobsonia of the same size, and in the genus Melonycteris, which is endemic to small islands, compared with the equally sized Eonycteris from Borneo. Large Pteropus reduce heat loss at low environmental temperatures, probably through peripheral vasoconstriction, thereby permitting rate of metabolism to fall without compromising the maintenance of a high core temperature. We conclude that the evolution of specialized nectarivory, which appears to have occurred independently at least five times in the Pteropodidae, is usually associated with a reduction _in both mass and rate of metabolism, a combination that leads to a variable body temperature.
Dispersal and philopatry in colonial animals: the case of Miniopterus schreibersii
Authors: Palmeirim Jorge M , Rodrigues Luisa 
Published: November 2023

Abstract
The dispersal behaviour of Miniopterus schreibersii, a colonial cave-dwelling bat, was studied with data obtained by recovery of animals ringed in the eight maternity colonies known in Portugal. The results showed that this species has a strictly philopatric behaviour during the nursing season; females return to give birth in the colony where they were born and very seldom change maternity colony during their lifetime. Males also showed a high level of attachment to their birth site, although during the nursing season most of them roosted in other locations with nonbreeding females. This strictly philopatric behaviour is due to strong imprinting, rather than to lack of knowledge of alternative roosts. Imprinting to maternity colonies takes place during the first weeks of life, and not during the first breeding season.
Does energy or calcium availability constrain reproduction by bats?
Authors: Barclay Robert M R 
Published: November 2023

Abstract
Bats are unusual mammals in being small but having long lives and small litters (typically only one or two young). I hypothesize that litter size is constrained by the need to raise young to near adult size before they can be independent. Our studies, and those of others, on a variety of species of bats indicate that juveniles typically start to fly at over 70% of adult mass and over 95% of adult skeletal size. This constraint appears to be associated with flight in vertebrates, since young birds also do not fly until fully grown. This means that each young is very costly and restricts the number that can be raised. Although energetic demands may be the proximate constraint, I argue that calcium is more important. For bats, calcium demand on reproductive females is high and calcium availability in most diets (insects, fruit, pollen) is low. Birds can at least partially overcome this by supplementing their diet with calcium-rich inanimate objects that are unavailable to bats because of their inability to forage on the ground and detect such items. This may help to explain why the reproductive output of birds exceeds that of bats. If the hypothesis is correct, bat foraging strategies may be based on the calcium content of prey in addition to energy content, and female and male foraging strategies may be based on different currencies. Vertebrate-pollinated and seed-dispersed plants may attract bats by offering high calcium rewards. In addition, however, it would mean that flight could only have evolved in bats in association with long lifespans, thereby constraining the possible life histories available to these mammals.
The trophic niches of sympatric sibling Myotis myotis and M. blythii: do mouse-eared bats select prey?
Authors: Arlettaz Raphael , Perrin Nicolas 
Published: November 2023

Abstract
The two sibling species Myotis myotis and M. blythii, while sympatric in the Swiss Alps, exhibit highly distinct and narrow trophic niches. Does this differ entiation arise purely from the use of distinct feeding habitats or, alternatively, do the species exert active prey selection within their feeding habitats? To answer this question, we compared the distribution of prey in the species’ diets with that in their respective feeding habitats, looking for discrepancies with respect to taxon and/or size. Although the general correlation is fairly good, some local discrepancies arise: (1) M. myotis underexploited small prey items (&lt;0.05 g dry weight), and (2) M. blythii overexploited cockchafers (Melolontha melolontha) and underexploited ground arthropods. We argue, however, that these discrepancies do not result from active prey selection, but from (1) the low availability of some categories of prey (due to either low detectability or low accessibility) and (2) the opportunistic exploitation of atypical feeding habitats. In fact, our results do not falsify the parsimonious hypothesis that the two species exert no active prey selection within their feeding habitats. We are furthermore not aware of any paper from the bat literature that provides definite support for active prey selection among insectivorous vespertilionids. Their echolocation system may actually preclude it.
MS/MS instrumentation
Authors: Jennings Keith R 
Published: November 2023

Abstract
Since mass spectrometers became widely available commercially about 40 years ago, they have proved of considerable value in the determination of the structures of many classes of pure compounds. When used in conjunction with separation techniques such as gas chromatography (GC) and highperformance liquid chromatography (HPLC), they have proved to be equally useful in identifying components of complex mixtures. In each type of application, it is assumed that the ionization process will give rise to a significant number of fragment ions from which structural information may be deduced. As the polarity of the sample increases, thereby reducing its volatility, the applicability of ionization techniques such as electron ionization and chemical ionization decreases and ionization must be effected by using one of several desorption ionization methods. Although these have the advantage that they considerably extend the mass range of samples that may be ionized, they normally give rise to very few fragment ions. They are therefore primarily of use in helping one determine the relative molecular mass (RMM) of samples, but when used in conjunction with a standard type of mass spectrometer they give little structural information.
Mass spectrometry of fatty acid derivatives
Authors: Christie William W 
Published: November 2023

Abstract
The potential of mass spectrometry (MS) for the identification of fatty acids of natural origin has been evident for many years. However, until relatively recently there were few reports of structural analyses on real samples containing unsaturated fatty acids as opposed to model compounds. The topic has been the subject of several reviews (Minnikin 1978; Schmitz and Klein 1986; Jensen and Gross 1987; Murphy 1993). The main problem has been the location of double bonds, although there have also been difficulties with ring structures or branch-points. There are three general approaches to the location of double bonds in unsaturated fatty acids by MS: (i) they can be ‘fixed’ by preparation of specific chemical adducts, which give distinctive fragmentation patterns; (ii) tandem MS techniques can, in some circumstances, give valuable structural information; and (iii) specific amide or ester derivatives, which, following ionization, stabilize the charge on a nitrogen atom remote from the double bonds, can be prepared. With this last approach, radical-induced cleavage predominates in the mass spectrometer and distinctive fragmentations are achieved according to double-bond position. In particular, the use first of pyrrolidine (reviewed by Andersson 1978) and more recently of picolinyl ester or 2-alkenyl-4, 4-dimethyloxazoline (DMOX) derivatives (Fig. 13.1) (reviewed by Harvey 1922) of fatty acids permits gas chromatography (GC)-MS to be employed in a simple manner for the simultaneous separation and characterization of these compounds from natural lipid extracts.
New brassinosteroids from Ornithopus sativus and Apium graveolens
Authors: Schmidt J , Spengler B , Voigt B , Adam G 
Published: November 2023

Abstract
Brassinosteroids represent a class of naturally occurring phytohormones with plant growth stimulating and antistress activity (Cutler et al. 1991; Sakurai and Fujioka 1993; Adam and Petzold 1994). In the course of our investigations concerning the occurrence of brassinosteroids in European cultivated plants we have investigated both seeds and young shoots of the legume Ornithopus sativus (Serradella) as well as seeds of the umbellifer Apium graveolens (celery). GC-EI MS is a very sensitive and valuable method for the identification of brassinosteroids because of the low content of these compounds in plant material (ng- to µg-level/kg plant material) (Ikekawa and Takatsuto 1984). The most suitable and common brassinosteroid derivatives used for the GC-MS analysis are the methaneboronates and the methaneboronates/trjmethylsilyl ether (Takatsuto et al. 1982).
Generating animal models of human mitochondrial genetic disease using mouse ES cells
Authors: MacGregor Grant R , Wei Wei Fan , Waymire Katrina G , Wallace Douglas C 
Published: November 2023

Abstract
The use of mouse ES (mES) cells to generate transgenic animals has revolutionized the study of gene action in vivo, and has provided animal models for studying the pathophysiology of human genetic disease and therapies thereof. Since the discovery that inherited mitochondrial DNA (mtDNA) mutations can cause age-related degenerative diseases (1), it has been realized that inherited mtDNA mutations are also associated with human adaptation to different environments, a broad spectrum of degenerative diseases, and with cancer. Somatic mtDNA mutations can accumulate during the lifetime of the individual, and have been implicated in the onset and progression of age-related diseases, and of ageing and cancer. Indeed, the importance of somatic mtDNA mutations in ageing has been affirmed by the expression in mice of a mutant form of mtDNA polymerase γ subunit A, which contains a D257A mutation that inactivates the 3 ′−5 ′ endonuclease. These animals have an increased mtDNA mutation rate and age prematurely (2). These findings highlight the pressing need for animal models of mitochondrial disease to better understand the role of the mitochondrion in the pathophysiology of disease, and in human genetics.
In vitro differentiation of mouse ES cells into pancreatic and hepatic cells
Authors: Blyszczuk Przemyslaw , Kania Gabriela , Wobus Anna M 
Published: November 2023

Abstract
In mammalian development, both the pancreas and liver originate from the definitive endoderm. The pancreas develops from dorsal and ventral regions of the foregut, and the liver from the foregut adjacent to the ventral pancreas compartment (1, 2). At present, the lack of available methods for enriching either pancreatic or hepatic progenitor cells from their respective organ in vitro is a major obstacle for the efficient generation of selected, pure populations of derivative cells. Moreover, the progenitor cells of the liver and pancreas are not yet clearly defined. Nestin-positive cells deriving from pancreatic islets, and generated after in vitro culture, are suggested to represent pancreatic progenitor cells (3); and oval cells are regarded as hepatic stem/progenitor cells (4). However, cells residing in the pancreatic (5) and hepatic (6) ductal epithelium and expressing cytokeratin 19 also have been proposed as pancreatic and hepatic stem or progenitor cells in vivo.
The significance of Ewald’s dynamical theory of diffraction
Authors: Kato Norio 
Published: November 2023

Abstract
Professor Ewald passed away at the age of 97, on 22 August 1985 at Ithaca, the university town for Cornell where he spent the last period of his life. When I received the news, I fell into deep grief. After a year or so, however, considering his age in particular, I began to think more about his scientific achievements themselves and what we could do to develop them. It was very natural, therefore, that a ‘microsymposium’ with this aim had been planned in the 1987 Congress of the IUCr (International Union of Crystallography) at Perth, Australia.
Paul P. Ewald–a personal appreciation
Authors: Juretschke Hellmut J 
Published: November 2023

Abstract
Most of the other contributions to this volume deal eloquently with the various primarily scientific ideas and accomplishments of Paul Ewald himself or flowing out of his work. I would like to fill in some more of the background of his numerous broader public contributions to crystallography. At the same time, I would also like to remember him as a friend and colleague, and to touch upon how I saw him in more private roles.
X-ray topography
Authors: Authier A , Capelle B 
Published: November 2023

Abstract
In the theory of dispersion [... ] an important role is played by the reciprocity theorem. That is to say, if you have a ray falling in one direction and generating a secondary ray in another direction, then, if you let the incident ray take the direction of the secondary one, the primary ray will also be generated again. So this showed that you cannot consider a single wave but you have to consider a whole bundle of waves or, as we now say, a wave field propagating in the crystal, instead of a single wave which is sufficient in Optics. P.P. Ewald (from a lecture given at the International School on X-ray Topography and Dynamical Theory, Limoges, August 1975).
Computing for High Resolution Images and Diffraction Patterns
Authors: Barry J 
Published: November 2023

Abstract
The computation of images and diffraction patterns is necessary because electrons interact strongly with matter. Even for a crystal of less than 100 A thickness, the transmitted electrons undergo multiple elastic scattering. Because of the strong multiple scattering, the amplitudes and phases of the resultant Bragg beams cannot be directly related to the structure factors. In order to solve the structure fom a given diffraction pattern of an unknown structure, it is necessary to compute diffraction patterns for a trial structure, and compare with the experimental results. For high resolution lattice images the need for computation is even more imperative because of the additional effects of objective lens defocus and microscope resolution.
Identification of Unknowns in Electron Diffraction
Authors: Carr M J , Lyman C E , Cowley J M 
Published: November 2023

Abstract
As is the case for x-ray diffraction, a large proportion of electron diffraction studies have the aim of confirming or revealing the presence in a sample of one or more previously-known phases. This implies the collection from the sample of sufficient information to allow the identification to be made by use of one or more of the existing data-bases. For a phase not previously characterized it may be desirable to carry out a more detailed investigation, and possibly a complete structure analysis, using the techniques outlined in Chapters 6 or 7. However the number of phases which have been adequately characterized is now so great that in most cases the identification of an “unknown” involves only its recognition as a previously “known” phase.
Convergent-Beam Diffraction
Authors: Eades J A 
Published: November 2023

Abstract
In the transmission electron microscope, the intensity transmitted in the direction of the incident beam by a crystalline sample is a complex function of the angle the incident beam makes with the crystal structure. An example of this spectacular variation is given in figure 7.1, which shows, as a function of angle, the intensity of the beam transmitted through gallium arsenide near [100]. There is a comparably complex variation of the intensity of each of the diffracted beams, except that the diffracted beams have intensity only for a range of angles close to the Bragg angle (figure 7.2).
Accurate Structure Factor Amplitude and Phase Determination
Authors: Spence J C H 
Published: November 2023

Abstract
The history of structure factor measurement by transmission electron diffraction may be divided into three areas (i) The study of the three-beam dynamical theory of electron diffraction and its degeneracies, (ii) Improvements in the algorithms and hardware used for dynamical computations, and (iii) Advances in electron microscope design and performance. This chapter reviews developments in each of these areas. A summary of most of the measurements which have been made is given, together with a detailed description of experimental methods. A review of useful results from three-beam theory is also given.
D
Authors: Atkins P W 
Published: November 2023

Abstract
non-zero angular momentum ensures that a d electron never approaches very close to the nucleus: the repulsive centrifugal force of the motion rises more rapidly than the attractive Coulombic force, and the net force is repulsive as r approaches zero. The boundary surfaces of the five real forms of the wave functions of the 3d orbitals are shown in Fig. D.1 (the boundary surfaces of other d orbitals are similar). All the orbitals have two nodal planes. The peculiar shape of the d22 orbital is a result of forming linear combinetions of the °complex forms of the orbitals in order to depict them more simply. Figure D.2 indicates how the five orbitals look when represented as complex wave functions, which is appropriate when we want to identify each orbital with a specific value of m1: now they all look like members of the same family.
L
Authors: Atkins P W 
Published: November 2023

Abstract
The lanthanide contraction is the striking reduction in atomic and ionic radius that occurs across the first row of the f block and which leaves the subsequent elements of Period 6 with smaller radii than would have been expected by extrapolation from previous periods. Similar contractions occur in the d block, and have been named (but apparently not entirely seriously) ‘scandinide contractions’. The origin of the lanthanide contraction is the poor shielding provided by the f electrons. Although the poor shielding is conventionally ascribed to the highly angular character of the orbitals, a closer analysis shows that the true explanation lies in their radial character. First, we should note that the 4f orbitals make only a minor contribution to the electron density in the outer reaches of the atom, so the electron density in the 5s and Sp orbitals determines the atomic radius.
O
Authors: Atkins P W 
Published: November 2023

Abstract
According to quantum mechanics, all the dynamical information about a system is contained in its °wave function. The outcome of an observation of a particular property can be predicted by performing the appropriate mathematical operation on the wave function. Each physical observable is therefore represented by an operator, a mathematical action such as multiplication or differentiation. The operator corresponding to the observable Q is often denoted fi, but we shall not make that distinction here. Different choices of operators for observables correspond to the different representations of quantum mechanics.
U
Authors: Atkins P W 
Published: November 2023

Abstract
Heisenberg’s uncertainty principle states that:
The product of the uncertainties in the simultaneous specifications of two °complementary observables can never be less than a small quantity of the order of h. The precise form of the principle is given in Box U.1. It implies that as one observable is constrained to have a more precise value, so its partner becomes more ill-defined. An experiment designed to measure the two observables simultaneously will be able to determine one precisely only at the expense of losing information about the other (see °duality). The principle was established by Werner Heisenberg in 1927, as a consequence of his formulation of °matrix mechanics.