bluuebunny/crossref_metadata_2025 huggingface dataset:
Synthesis of a potential anti-obesity agent
Authors: Lee Stan , Robinson Graham
Published: September 2023

This chapter examines ICI D7114, which was developed as a possible treatment for obesity and non-insulin dependent diabetes. It looks at animal studies that showed how ICI D7114 acts by stimulating β3-receptors in brown fat tissue and leads to an increase in resting the metabolic rate. It also mentions research routes and processes which suffered from major disadvantages, for example, the overall yield from hydroquinone was only 1.1% and the resolution step was inefficient as it required recrystallizations. The chapter elaborates why hydroquinone and ethylene dibromide are a poor choice as starting materials, since both have the potential for reacting twice. It highlights the easiest way of alkylating phenol with ethylene dibromide, which used a two-phase system that contains a phase-transfer catalyst.
Reactions of the anomeric centre Part I
Authors: Davis Benjamin G. , Fairbanks Antony J.
Published: September 2023

This chapter explains the chemical and structural relationship between carbonyls, hemiacetals, and acetals. It reviews the mechanisms of acetal formation and their application to the Fischer glycosidation reaction. It also discusses the anomeric effect of electronegative anomeric substituents which are more stable in an axial orientation and examines the underlying reasons and consequences of the effect. The chapter describes the process of mutarotation. This process is subject to general acid/base catalysis. The chapter then analyses mechanisms for the inter-conversion of α and β anomers, furanose, and pyranose forms of sugars via open-chain aldehydes. It looks at the rationalization of relative proportions of α/β and furanose/pyranose forms present at equilibrium for glucose in aqueous solution.
Bonding schemes for transition metal clusters
Authors: Housecraft Catherine E.
Published: September 2023

This chapter deals with bonding schemes that treat polyhedral skeleton as a single unit or as an assembly of condensed units. These require a defined number of bonding electrons. It uses the isolobal principle to draw analogies between the transition of metal carbonyl and borane clusters. It also explores the application of the polyhedral skeletal electron pair theory (PSEPT) to metal carbonyl clusters, which provides a rationalization of geometry of the cluster core. The chapter mentions the Wade approach. This determines the number of electrons that a metal-based fragment provides for cluster bonding and rationalizes the structures of transition metal carbonyl clusters that are analogous of boranes and derived anions. It reviews condensed polyhedral structures that are prevalent amongst transition metal carbonyl clusters.
Metal carbonyl dimers and clusters with organic ligands
Authors: Housecraft Catherine E.
Published: September 2023

This chapter examines compounds that contain π-bonded organic ligands and reactions between carbonyl clusters, alkenes, and alkynes. It talks about clusters which contain alkylidyne and related ligands in which a CR group caps a metal triangle. It also describes the M3-triangle and M4-butterfly as metal frameworks which are featured regularly in organometallic cluster chemistry. This is due to their relationship to available sites on metal surfaces, illustrating the occurrences of a triangular M3-site on a flat surface and a butterfly M4-site on a stepped surface. The chapter explains the absorption of small molecules onto a metal surface, which can lead to dissociation and is driven by the formation of M-H and M-C bonds. It points out the key roles played by adsorbed molecular fragments during heterogeneous catalytic processes.
Aldehydes and ketones
Authors: G. Denis Meakins
Published: September 2023

This chapter talks about the carbon-oxygen double bond or carbonyl group, which is the most common group in organic chemistry. It examines keto and enol forms from the carbonyl group, the oxidation and reduction of carbonyl compounds, reactions of keto and enol forms and enolate anions, and aldol and related condensations. It also describes a polarization that can be expressed in terms of electronic effects or of resonance in which the outcome is the same. The chapter refers to carbonyl compounds that exhibit tautomerism, which is a tautomeric compound that consists of an equilibrium mixture of two or more structural isomers under stable conditions. It emphasizes that simple carbonyl compounds contain only very small amounts of the enolic forms, elaborating that the interconversion between keto and enol forms is slow in a solution free from impurities.
Photophysics
Authors: Wayne Carol E. , Wayne Richard P.
Published: September 2023

This chapter examines photophysics. Several of the pathways for loss of electronic excitation do not lead to any chemical change. Instead, the energy is used in a physical process such as the emission of light as luminescence, or it becomes lost by quenching. Alternatively, the excitation energy can populate a new level in the same or a different molecule by intramolecular or intermolecular energy transfer; the new state of the new molecule excited by the energy transfer process can, of course, emit its own radiation. Luminescence, quenching, and the two types of energy transfer are important aspects of photophysics. Luminescent emission provides some of the most reliable information about the nature of primary photochemical processes. The chapter also looks at fluorescence, phosphorescence, and chemiluminescence.
Crystal defects
Authors: Mingos D.M.P.
Published: September 2023

This chapter investigates crystal defects. The types of defects which are commonly observed can be classified as intrinsic, which are integral to the crystal, and extrinsic, which are created by the insertion of foreign ions into the lattice. The chapter first looks at defects which maintain the same formula (stoichiometry). In an ionic crystalline material, the removal of either a cation or an anion would leave a residual charge on the crystal. If oppositely charged ions are removed in a pairwise fashion, then the crystal stays electroneutral. The two vacancies created in the lattice are described as Schottky defects. Alternatively, an ion may migrate from its regular lattice site into an alternative site in the lattice which is not usually occupied. These defects are described as Frenkel defects. The chapter then considers defects which result in changes in the formula.
UV-visible spectroscopy
Authors: Brisdon Alan K.
Published: September 2023

This chapter evaluates UV–visible spectroscopy. Within inorganic chemistry, the field of study often associated with UV–visible spectroscopy is that of the coloured transition metal complexes. The energies associated with transitions between different arrangements of valence electrons falls within the ultraviolet (UV) and visible region of the electromagnetic spectrum. Just as the most popular form of vibrational spectroscopy is usually referred to by the region it occurs in—the infrared—so the most popular form of electronic spectroscopy is usually known as UV-visible spectroscopy and is in essence the study of the transitions involved in the rearrangements of valence electrons. The chapter then looks at metal–metal transitions, charge-transfer transitions, and ligand-centred transitions.
Putting it all together
Authors: Brisdon Alan K.
Published: September 2023

This chapter presents some worked problems where a number of spectroscopic techniques are brought to bear on the same problem. It is rarely sensible, and frequently not possible, to rely on a single spectroscopic method to provide an unambiguous answer to the identity of an unknown product. Usually, the more techniques that are used, the more confident one can be in assigning the identity of a compound and its potential structure. One problem concerns the identification of a gaseous product which results from the reaction of (Me2HSi)2S with methanol. The presence of a variety of protons makes nuclear magnetic resonance (NMR) spectroscopy a likely candidate, provided one can find a solvent in which this gas is soluble. For a solid sample, it is possible to try and obtain the molecular composition by elemental analysis. For a volatile sample, mass spectrometry is more straightforward.
Changing the reactivity of catalytic surfaces
Authors: Bowker Michael
Published: September 2023

This chapter examines the process of changing the reactivity of catalytic surfaces. If we consider any particular reaction then, in principle, it is possible to manipulate the properties of a catalyst for that reaction by any process that alters the properties of its surface. The chapter then looks at the effects of engineering the active phase of the material by placing additives at the surface. In practice, most industrial processes have additives that act as modifiers to the chemistry at the surface. Promoters can be classed as substances which, when added to a catalyst as a minor component, improve one or more of the properties of the material with respect to product formation. Meanwhile, poisons tend to be electronegative elements. At the simplest level, they block sites on the surface and so reduce the total number of centres of activity. The chapter then discusses the process of alloying.
Raw materials and their conversion
Authors: Bowker Michael
Published: September 2023

This chapter addresses raw materials and their conversion. The major volume sources of chemicals are coal, oil, and natural gas. The chapter then details the pattern of feedstock conversion and the products formed. If we begin with the main carbon source for the petrochemical industry, crude oil, then the first process is separation of the fractions of light molecules, intermediates (naphtha), and heavier fractions. This is achieved by fractional distillation. The most useful molecules for chemical synthesis and for fuel are produced by catalytic cracking of the higher chain length alkenes. Ultimately, synthesis gas is obtained which can be used for a wide range of products.
Heat Transfer
Authors: Winterton R. H. S.
Published: September 2023

Heat Transfer follows a classical approach with main chapters on conduction, forced convection, natural convection, and radiation. Practical problems do not normally divide neatly into purely conduction problems, purely forced convection and so on, although other texts often assume this. To help overcome this, it has been recognised in examples and problems that more than one aspect of heat transfer may be needed to solve a single practical problem.
Complexes
Authors: Mark J. Winter
Published: September 2023

This chapter looks at the concept of d-block metal complexes, which are composed of a central metal atom or ion bound to a discrete number of charged or uncharged molecules or atoms called ligands. It provides a brief historical perspective on ligand types and some factors affecting the strength of metal–ligand interactions. It also mentions Alfred Werner's primary valency, which is referred to as the oxidation number, while the secondary valency is called the coordination number. The chapter explains how Werner recognized that the most common coordination number for d-block metal compounds is six but that four-coordination is also important. The chapter refers to ligands which coordinate to the central metal through the donation of lone pairs of electrons to the metal.
Nuclear Magnetic Resonance
Authors: Hore P. J.
Published: September 2023

Nuclear Magnetic Resonance begins with an introduction to what nuclear magnetic resonance (NMR) is and how it is used in various areas of science. It then moves on to look at chemical shifts. Next, it examines spin-spin coupling. There follows a chapter on chemical exchange. The next chapter is concerned with spin relaxation. The final chapter covers nuclear magnetic resonance (NMR) experiments.
Spin–spin coupling
Authors: Hore P.J
Published: September 2023

This chapter examines the magnetic interactions between nuclei, known variously as spin–spin couplings, scalar couplings, or J-couplings. Spin–spin couplings (J-couplings) give rise to multiplets in liquid-state nuclear magnetic resonance (NMR) spectra. They usually occur via chemical bonds and are generally small when the nuclei are more than three bonds apart. J-couplings give information on bonding networks in molecules. However, J-couplings within a group of magnetically equivalent spins do not produce multiplet splittings. Strongly coupled spins have more complex spectra than weakly coupled spins. Meanwhile, dipolar couplings occur through space and normally do not lead to multiplets in liquid-state NMR spectra.
An Introduction to Drug Synthesis
Authors: Patrick Graham L.
Published: September 2023

An Introduction to Drug Synthesis explores the central role that organic synthesis plays in the process of drug design and development. Part A of the book introduces major concepts and begins by outliningfirstly looks at the drug discovery process. Other chapters in the first part of the text then examines topics such as drug synthesis, retrosynthesis, cycliccycle systems in drug synthesis, and the synthesis of chiral drugs. There is also a chapter on combinational and parallel synthesis. Part B of the book moves on to consider the applications of drug synthesis in the drug development process and. This includes chapters on the synthesis of lead compounds, analogue synthesis in drug design, synthesis of natural products, chemical and process development, and synthesis of isotopically labelled compounds. The final partPart C, the final part of the text, looks at the design and synthesis of selected antibacterial agents.
The synthesis of chiral drugs
Authors: Patrick Graham L.
Published: September 2023

This chapter focuses on the synthesis of chiral drugs. Chiral drugs are asymmetric compounds that can exist as two non-superimposable mirror images known as enantiomers. The chapter defines asymmetric molecules as chiral, while symmetrical molecules are known as achiral. It highlights the significance of chirality in the pharmaceutical industry. Preferential crystallisationcrystallization, forming the formation of diastereomeric derivatives, kinetic resolution, and chromatography could can solve resolve racemic mixtures in relation to asymmetric synthesisinto their two constituent enantiomers. Additionally, the chapter looks into at the asymmetric synthesises of propranolol, asymmetric syntheses from a chiral starting material, and asymmetric syntheses involving an asymmetric reactions. It explores the asymmetric reactions to enzymes as well. In addition, asymmetric reactions using enzymesboth natural and genetically modified onesare discussed. The chapter then considersnotes the examples of asymmetric syntheses by referencing modafinil, armodafinil, and eslicarbazepine acetate as examples of asymmetric syntheses.
Chemical and process development
Authors: Patrick Graham L.
Published: September 2023

This chapter explores focuses onthe chemical and process developments. Process development aims to ensure the number of reactions in the synthetic route and integrate the individual stages, whileC chemical development is the large-scale synthesis of a drug candidate, and process development aims to ensure that the number of reactions used in the synthetic route is as small as possible and the individual stages in the process are integrated in a way that ensures maximum efficiency on a production scale. The chapter looks intoalso looks at green chemistry and its twelve principles of designing processes that are environmentally friendly, energy efficient, and economical with respect to solvents and raw materials. It explores the chemical and process developmental process in relation to temperature, pressure, reaction times, solvents, reagents, catalysts, promoters, and avoiding impurities. Moreover, the chapter notes theconsiders experimental procedures and operational procedures alongside on the large scale, as well as the process of crystallizationcrystallisation. The chapter concludes with a case study illustrating the development of a commercial synthesis of sildenafil.
Statistical concepts
Authors: Currell Graham
Published: September 2023

This chapter develops some underlying statistical concepts from the perspective of experimental data, emphasizing the link between experimental variability and the role of statistics in quantifying and managing this variability. It begins by introducing the value of visualizing experimental data through a variety of graphs, including the boxplot for raw data and the interval plot for calculated mean values. The chapter then reviews the key terminology used to describe the factors and variables that influence the scientific system being analysed, before using the histogram to describe data variations and looking at important standard distributions. It also discusses the uncertainty and error in measurement and develops the mathematics for combining experimental uncertainties. Finally, the chapter develops statistics for analysing data samples and their application in the interpretation of experimental results, before outlining the generic issues associated with hypothesis testing.
Single response variable
Authors: Currell Graham
Published: September 2023

This chapter assesses the techniques used to analyse the effect that one or more factors may have on a single response variable. The data can be described as univariate and may be either interval or ordinal data. The chapter begins by presenting analyses relevant to single samples of replicate data (e.g. the Wilcoxon test), before looking at two data samples, which is essentially a special case of a one factor analysis with just two levels. It then considers investigations that test, or measure, the effect of just one factor, but with more than two levels (e.g. one-way ANOVA, the Kruskal–Wallis test, and repeated measures). Finally, the chapter develops investigations of more than one factor together with possible interactions. The general linear model is used as a flexible approach for conducting ANOVA calculations, and the effect of a covariate term is addressed through the ANCOVA (analysis of covariance).
The Evolution of Life
Authors: Bell Graham
Published: September 2023

The Evolution of Life provides an introduction to the central issue of evolutionary biology—adaptation through natural selection—in six sections. The first section looks at the basics, covering the evidence and engine of evolution. The second part looks at the history of evolution, examining the tree of life, the diversity of life, and ancestry of life. The next section focuses on the origins of variation, species, and innovation. Then the text moves on to adaptation and includes an evaluation of the dynamic genome. Section 5 focuses on selection and covers artificial selection, experimental evolution, and selection in natural populations. The final section considers sexual selection, cooperation and conflict, and symbiosis and struggle.
Rabies: zoonotic rabies
Authors: Oxford John , Kellam Paul , Collier Leslie
Published: September 2023

This chapter examines rabies, a devastating disease of animals that is comparatively rarely transmitted to humans and has been recognized since the dawn of history. It appeared in the Babylonian Eshnunna Code before 2300 bc. The infection spread to Europe and then to the world both by natural migration and colonial activity. The chapter mentions Aulus Cornelius Celsius, who first described hydrophobia in ad 100 and recommended cautery of animal bites with a hot iron. This remained the treatment of rabid animal bites until 1884, when Louis Pasteur introduced his famous human rabies vaccine. There have been 24,000 human deaths in Africa alone, almost all contracting rabies from dogs, and the burden in Asia is even larger. The chapter considers rabies a neglected enzootic disease that presents a serious public health threat in developing countries.
Adenovirus: respiratory, eye, and gastroenteritis viruses
Authors: Oxford John , Kellam Paul , Collier Leslie
Published: September 2023

This chapter focuses on adenoviruses, which were first isolated from human adenoids. They cause widespread disease that ranges from colds to pneumonia and diarrhoea to bladder infections. Adenoviruses infect the eye, gut, and respiratory tree. The chapter looks at the study of adenovirus replication, which led to important discoveries of messenger RNA splicing. Members of the family Adenoviridae are icosahedral, non-enveloped linear dsDNA viruses of which some are 80 nm in diameter. The chapter highlights the five recognized genera of the adenoviruses: Mastadenovirus, isolated from mammals and humans; Aviadenovirus, isolated from birds; Atadenovirus, isolated from birds, mammals, and reptiles; Ichtadenovirus, isolated from fish; and Siadenovirus, isolated from reptiles and birds.
Hepadnaviruses: hepatitis B and D
Authors: Oxford John , Kellam Paul , Collier Leslie
Published: September 2023

This chapter discusses the hepadnaviruses and considers the estimation of WHO that two billion people have been exposed to and 350 million people worldwide are chronically infected by hepatitis B. In some countries more than 10% of the population is afflicted, and surveys of the global burden of disease HBV rank it as the tenth leading cause of death, which makes it a major public health priority. The chapter mentions that there are excellent recombinant vaccines. Over 180 countries of the world have started a Universal Vaccination Campaign for neonates to blunt the clinical effect of the virus. New Directly Acting Antivirals (DAAs) are used in combination therapy, and the transmission routes of the virus are extremely well defined. The chapter discusses the scientific viewpoint that the virus has the most compact and unique genome and shares with HIV the use of reverse transcriptase (RT) as a key step in the replication cycle.
The clinical virology laboratory
Authors: Oxford John , Kellam Paul , Collier Leslie
Published: September 2023

This chapter considers the clinical virology laboratory and reviews the use of virus genome detection for clinical diagnosis, which has increased dramatically. In general, virus genome detection is more rapid and sensitive than cell-culture and can be used before a detectable antibody response has developed. The chapter traces the discovery of potent antivirals for hepatitis C, hepatitis B, HIV, and influenza, wherein there is a huge demand for the diagnostic laboratory to monitor levels of virus in the appropriate clinical sample of the patient using rapid molecular tests. These tests can also give the first indication of drug-resistant virus mutants, which could compromise antiviral therapy. The chapter covers the collection and transport of clinical specimens to the laboratory, different rapid diagnostic methods, the isolation of viruses in cell cultures, and the detection of antiviral antibodies.
Protein structure determination
Authors: Lesk Arthur M.
Published: September 2023

This chapter discusses protein structure determinations, which involve experimental and computational methods, and combined applications of both. For many years, X-ray crystallography and fibre diffraction were the only methods for determining the positions of individual atoms in macromolecular structures. A companion appeared in the 1980s, when K. Wüthrich, R.R. Ernst, and their coworkers developed methods for solving protein structures by nuclear magnetic resonance (NMR) spectroscopy. With a third technique, cryo-electron microscopy (cryo-EM), it has been possible to determine structures of large aggregates, including viral capsids, large protein complexes, and intact ribosomes. Cryo-EM of large multiprotein complexes plus X-ray crystal structures of individual components has proved a powerful combination. The chapter also considers protein structure prediction and modelling.
Bioinformatics of protein sequence and structure
Authors: Lesk Arthur M.
Published: September 2023

This chapter examines bioinformatics, a new field which is a hybrid of biology and computer science. Biology, especially high-throughput data streams such as DNA sequencing and structural genomics projects, provides its input. Computer science permits the effective use of information-processing equipment to support research based on these data. Databases organize knowledge and make it accessible. Algorithms then allow analysis of the information, thereby producing additional data streams to be incorporated into the repository. The chapter then looks at the concept of sequence alignment, the methods for aligning sequences, and facilities for sequence database searching based on them, notably BLAST (Basic Local Alignment Search Tool) and PSI-BLAST. It also considers the characteristics of pairwise sequence alignment, multiple sequence alignment, and structural alignment.
Evolution of protein structure and function
Authors: Lesk Arthur M.
Published: September 2023

This chapter looks at the evolution of protein structure and function. Protein evolution is characterized by the exploration by a set of genomes of the space of amino acid sequences in search of selectively advantageous variants. Evolution acts at the level of protein functions, in a feedback cycle that selects gene sequences. Two or more proteins are homologous if they are descended from a common ancestor. The chapter then distinguishes between two types of homologues: orthologues and paralogues. Orthologues are homologous proteins in different species, descended from a single ancestral protein, while paralogues are homologues in the same species arising from gene duplication, and their descendants. The chapter also looks at evolutionary variations in protein families, including globins, NAD-binding domains, serine proteases, and opsins. Finally, it explores how proteins can develop new functions during evolution: the mechanisms, pathways, and limitations.
Molecular biology for ecologists
Authors: Rowe Graham , Sweet Michael , Beebee Trevor J. C.
Published: September 2023

This chapter focuses on molecular biology. It notes that nucleic acids constitute the genetic information of living organisms as DNA and RNA are recognized as polymers of nucleotides. Moreover, the chapter explores the structure and modifications of RNA and DNA. It also refers to polymerase chain reaction (PCR). The chapter discusses genome organization and genomics wherein the eukaryotic genome structure, non-coding DNA, and other functional genomic sequences are explained. Also, it looks into proteins like antibodies, gene expression, transcriptome, and proteome. It explains epigenetic modifications of DNA and looks at how histone proteins can change gene expressions and create phenotypic differences. In addition, the chapter explains how mutations generate genetic diversity through point mutation, large deletions and insertions, and polymerase slippage.
Behavioural ecology
Authors: Rowe Graham , Sweet Michael , Beebee Trevor J. C.
Published: September 2023

This chapter looks into behavioural ecology. Sexual selection, which is a form of natural selection, helps explain the distinct sexual dimorphism in the secondary sexual characteristics between the sexes alongside kin selection. The chapter recognizes five basic types of animal mating systems: monogamy, polygyny, polyandry, polygynandry, and promiscuity. It notes how molecular techniques have been used to examine dispersal behaviour and enabled dietary analysis. The chapter highlights behaviour playing as a key part in reproductive success in terms of speciation. It mentions how epigenetic modifications of the genome and transgenerational epigenetic inheritance influenced modifications in animal behaviour.
Serous effusions and peritoneal washings
Authors: Shambayati Behdad
Published: September 2023

This chapter covers the cytopathology of serous cavities, which are commonly involved in cancer. It outlines the important clinical implications of the reporting of malignant cells in serous fluids as patients with a malignant effusion will have an advanced disease and will require appropriate management. It also examines malignant cells in serous fluids, which are more commonly due to metastatic malignancy than to mesothelioma, that is, primary malignant tumour of the mesothelium. The chapter describes cells from a malignant mesothelioma, which show diverse cytological features. It is noted that immunocytochemistry can be helpful in confirming the mesothelial nature of the cells once a diagnosis of malignancy has been established. The chapter also discusses the finding of malignant cells in peritoneal washings, which is used to stage ovarian, fallopian tube, and peritoneal cancers.
Cytology of the head and neck
Authors: Cross Paul , Shambayati Behdad
Published: September 2023

This chapter explains the basic anatomy of the head and neck areas in the body. The terms head and neck cover the oral cavity, salivary glands, thyroid gland, and lymph nodes. There are also many major blood vessels and nerves here. In practice, it is difficult to separate these as discrete and separate entities in the area. As a result of the easy access of the organs in this part of the body, cytology is used, along with radiology, for clinical investigation. The chapter looks at the main organs and normal tissue types of those areas. It then moves on to consider the pathologies of the tissues of the head and neck. Next, it describes the role of cytology in the diagnosis and management of head and neck lesions. Finally, the chapter notes that rapid on-site assessment by trained biomedical scientists can considerably improve the quality of FNA sampling for head and neck lesions.
Advances in cytopathology
Authors: Ping Bruno
Published: September 2023

This chapter considers automated screening and what role it could undertake in a cervical screening programme. It explores the overall impact of HPV testing, the cervical cancer vaccine, and the effect they will have on the future of cervical cytology. Immunocytochemistry (ICC) has been used for a while now. The chapter considers how new markers can be used to give better diagnostic and predictive information. Molecular techniques are emerging as useful tests to be used alongside conventional cytomorphology. Many cancers have an underlying genetic cause; analysis of DNA and RNA at the molecular level is yielding more information and contributing to the diagnosis of disease and subclassification of tumours. The chapter aims to build on existing expertise and extend the use of techniques to help clinicians, surgeons, and oncologists provide better treatment and improve survival rates of patients with cancer.
Expertise in cytopathology
Authors: Evered Andrew
Published: September 2023

This chapter looks back at what has been explored in this book. The book has explained in great detail that the primary task in cytology is the visual interpretation of cells. It is widely assumed that the job requires highly tuned mental skills acquired over a long period of training and practice, but in fact very little is known about the cognitive processes involved in reaching accurate and reliable cytological decisions, how these skills develop, or, importantly, the causes of diagnostic error. These topics are the focus of discussion in this chapter. The chapter starts by looking at the core mental skills of an expert cytologist. It also describes the main features of a response curve diagram. It looks at terms such as discriminability index and criterion. It also considers bias experienced by cytologists. Finally, it looks at the clinical consequences of cytology error and computer-aided detection and diagnosis in cytology.
Continental Shelf Seabed
Authors: Kaiser Michel J. , Attrill Martin J. , Jennings Simon , Thomas David N. , Barnes David K. A. , Brierley Andrew S. , Graham Nicholas A. J. , Hiddink Jan Geert , Howell Kerry L. , Kaartokallio Hermanni
Published: September 2023

This chapter examines systems pertaining to the continental shelf seabed. Continental shelves are the most heavily exploited and utilized areas of the world's oceans and support the greatest level of biological production. The ecology of the shallow shelf areas is strongly influenced by physical processes such as waves, tides, currents, erosion, and inputs of material from the adjacent land mass. These processes generate a great diversity of ecosystems and habitats at regional and local levels. The composition of the seabed and its associated biota are a direct reflection of past geological events and current physical processes that act upon it. The continental shelf seabed varies greatly. Furthermore, the benthic community is a critical link in the transfer of organic material and nutrients from the water column above to the seabed.
Estuaries
Authors: Kaiser Michel J. , Attrill Martin J. , Jennings Simon , Thomas David N. , Barnes David K. A. , Brierley Andrew S. , Graham Nicholas A. J. , Hiddink Jan Geert , Howell Kerry L. , Kaartokallio Hermanni
Published: September 2023

This chapter concerns estuaries. Estuaries represent the great transition between freshwater and marine biomes, and as such they are influenced by both aquatic realms while having a distinct and exceptionally variable environment and ecology of their own. The chapter asserts that the perception of estuaries as low-diversity, muddy, and inhospitable places is misguided and stems from a narrow appreciation of the estuarine system. Despite the incredibly varied conditions present in estuaries, which make them challenging for life, they are inhabited by a wide range of invertebrates, often in very high numbers, and are vital nursery systems for fish and feeding grounds for birds. They have also been referred to as the most degraded habitat type on earth, so they are perhaps the finest example for studying the conflicts between ecology, conservation, and human use.
Mangrove Forests and Seagrass Meadows
Authors: Kaiser Michel J. , Attrill Martin J. , Jennings Simon , Thomas David N. , Barnes David K. A. , Brierley Andrew S. , Graham Nicholas A. J. , Hiddink Jan Geert , Howell Kerry L. , Kaartokallio Hermanni
Published: September 2023

This chapter discusses mangrove forests and seagrass meadows. These represent two of the most valuable marine habitats in the world, important for providing a high level of productivity and physical structure that support a considerable biodiversity of associated animals. However, both systems are remarkable in that they are based on higher plants more generally associated with terrestrial systems, so mangrove trees and seagrasses demonstrate fascinating physical, biological, and life-cycle adaptations that enable survival in the marine realm. Mangrove forests host a unique mix of marine and terrestrial animals, including insects, birds, fish, and particularly crabs, whose activities heavily influence the productivity of mangrove forests. Seagrass beds provide a structural habitat on generally featureless soft-sediment bottoms, and so are utilized by a wide and diverse range of fish and invertebrates, providing a physical home, food supply, and shelter from predation.
Electron Paramagnetic Resonance
Authors: Chechik Victor , Carter Emma , Murphy Damien
Published: September 2023

Electron Paramagnetic Resonance starts off with an overview of electron paramagnetic resonance (EPR) spectroscopy. The first chapter presents the theory of continuous wave (CW) EPR spectroscopy. The text then goes on to look at experimental methods in CW EPR and isotropic EPR spectra of organic radicals. It also examines anisotropic EPR spectra in the solid state and transition metal ions and inorganic radicals. The last few chapters look at systems with multiple unpaired electrons, linewidth of EPR spectra, and advanced EPR techniques.
Theory of continuous wave (CW) EPR spectroscopy
Authors: Chechik Victor , Carter Emma , Murphy Damien
Published: September 2023

This chapter presents a theoretical background on continuous wave (CW) electron paramagnetic resonance (EPR) spectroscopy, focusing on electron Zeeman, nuclear Zeeman, and hyperfine interactions. It discusses electron spin angular momentum and considers the effect of placing the unpaired electron in an external magnetic field from a classical perspective. It also examines the influence of the hyperfine interaction and elaxation mechanism on the EPR spectrum. The chapter regards electrons as negatively charged particles that possess an intrinsic property called spin, which is characterized by the spin angular momentum S. It cites a sample in EPR spectroscopy that contains unpaired electrons, which is irradiated with electromagnetic radiation in the presence of an external field.
Transition metal ions and inorganic radicals
Authors: Chechik Victor , Carter Emma , Murphy Damien
Published: September 2023

This chapter describes transition metal ions (TMI) as isolated dopants in a solid matrix that coordinates an organic ligand in a metal complex. It analyses the unpaired electron confined to metal-based d-orbitals. It also looks at the key difference between the electron paramagnetic resonance (EPR) spectra of TMIs compared to organic radicals, noting that EPR exhibit large anisotropic g values which are no longer close to ge. The chapter presents the EPR linewidths which are often larger compared to organic radicals due to the short relaxation times. It explains why low temperature measurements are required to lengthen the relaxation time sufficiently for EPR spectra to be observable.
Questionnaires, focus groups, and interviews
Authors: Holmes Debbie , Moody Peter , Dine Diana , Trueman Laurence
Published: September 2023

This chapter provides a brief introduction to the use of questionnaires, focus groups, and interviews to gather scientific information. It discusses the design of the questions in relation to the sample size and how the data may be analysed quantitatively. Questionnaires, focus groups, and interviews may allow us to collect both quantitative (numerical) data and qualitative (descriptive) information. Qualitative approaches are based on the notion that reality varies for different people in different contexts; therefore, we cannot use a single scale against which to make measurements. An example of this is people's perception of pain. Qualitative information can be summarized, but here the focus is on how these methods may be used effectively to obtain numerical or quantitative data and how these data may be analysed.
Hypothesis testing: Associations and relationships
Authors: Holmes Debbie , Moody Peter , Dine Diana , Trueman Laurence
Published: September 2023

This chapter takes a look at the second hypothesis that may be tested: a test for an association. An association is where one variable changes in a consistent and similar manner to another variable. There are three groups of statistical tests that can be used: chi-squared tests for association, correlation analysis, and regression analysis. The chapter discusses what is meant by an association and a relationship, and issues relating to limited experimental designs and small sample sizes. Each test is illustrated with an example from undergraduate research. The statistics tests covered in the chapter are: chi-squared test for association; Spearman's rank correlation; Pearson's product moment correlation; coefficient of determination; simple linear regression; linear regression; principal axis regression; and ranged principal axis regression.
Thermodynamics
Authors: Elliott Joanne , Page Elizabeth
Published: September 2023

This chapter explains the system in which the reaction of interest being studied and the surroundings are the rest of the space around the system. It points out that the system that is supplemented by surroundings is called the universe. It also outlines different types of systems that vary according to their transfer of matter and energy and elaborates on how energy can take the form of either heat or work. The transfer of energy as heat arises when there is a difference in temperature. Work is carried out by a reaction when it opposes a force. An example is when gas is produced, and it expands against external pressure. The chapter clarifies how work is done on the system if the atmosphere pushes in on the reaction and compresses any gaseous components.
Workbook in Inorganic Chemistry
Authors: Almond Matthew , Spillman Mark
Published: September 2023

Workbook in Inorganic Chemistry firstly concentrates on topics related to atomic structure. The text then moves on to examine molecular orbitals and structure. Following this is a chapter on periodicity and the chemistry of the s-block and p-block, which are explained in great detail. After this, the text moves on to look at solids. Finally, there is a chapter on the coordination complexes of the d-block metals.
Transfusion and Transplantation Science
Authors: Avent Neil D.
Published: September 2023

Transfusion and Transplantation Science starts with an introduction to basic immunology and techniques. It then looks at human blood-group antigens, haemolytic disease of the fetus and newborn, the clinical use of blood components, and microbiological testing of blood donations. It moves on to discuss human platelet antigens (HPA) and human neutrophil antigens (HNA) and their clinical significance. Also considered are compatibility testing and adverse effects, as well as immune mediated red cell distribution. The text then examines human leucocyte antigens (HLA) and their clinical significance, haematopoietic stem cell transplantation and stem cell plasticity. Finally, it considers tissue banking and quality issues.
An Introduction to Molecular Evolution and Phylogenetics
Authors: Bromham Lindell
Published: September 2023

An Introduction to Molecular Evolution and Phylogenetics first talks the reader through the story of DNA. It then delves into more detail describing DNA as the immortal germline. The text then considers mutation, and also looks at replication, the genome, genes, selection, and drift. The text goes on to consider species and the origin of species. It also describes the role of alignment, phylogeny, and hypotheses. Finally, it looks at rates in terms of tempo and mode and dates in terms of time.
Drift
Authors: Bromham Lindell
Published: September 2023

This chapter addresses genetic drift. Not all changes to the genome are driven by selection. Many alleles in a population make no difference to an individual's chances of reproduction. Instead of being removed by negative selection or fixed by positive selection, selectively neutral alleles will fluctuate in frequency over generations, until they are eventually either lost from the population or replace all other alleles at that locus. Neutral theory also allows us to predict the patterns of substitution we expect to see in the absence of selection. We can use this expectation to identify sites that are conserved by negative selection or mutations that have been promoted by positive selection. Neutral theory also provides insight into the way that even complex patterns and traits do not necessarily demand an adaptive explanation.
Alignment
Authors: Bromham Lindell
Published: September 2023

This chapter explores sequence alignment. Descent with modification creates hierarchies of similarities, such that close relatives will be more similar in many respects, including their genomes. As such, a systematic hierarchy based on descent allows prediction of similarity across many different characteristics. Therefore, taxonomic groups should be based on similarity by descent (homologies) not incidental similarities that evolved independently in different lineages (analogies). To use DNA sequences to trace evolutionary past and processes, we must first establish homology through sequence alignment, where sites all originally copied from the same ancestral sequences are compared across lineages to detect evolutionary changes. Indeed, sequence alignment is the process whereby homologies are distinguished from analogies.
Hypotheses
Authors: Bromham Lindell
Published: September 2023

This chapter illustrates how phylogenies can be used to test hypotheses about evolutionary past and processes. There are many possible phylogenies that could explain how we ended up with the DNA sequences we have observed. Phylogenetic analysis is a way of generating and comparing different hypotheses for the evolution of a set of sequences, so requires a criterion for choosing the most plausible history. Most methods compare the plausibility of different phylogenies, using a model of molecular evolution which states the relative probability of different kinds of sequence changes. The strength of support for different possible phylogenies can be compared by asking whether slightly different data, or differences in the analysis, would have produced the same result. Phylogenies can also be used to test hypotheses about evolution by asking what patterns we would expect to see if the hypothesis was true.
Enzymes as Drug Targets
Authors: Rostron Chris
Published: September 2023

This chapter examines enzymes as drug targets. The unique tertiary structure of an enzyme usually results in the formation of a specific active site at which the enzyme selectively interacts with its substrate(s). The chapter then considers two models which attempt to explain enzyme specificity: the ‘lock and key’ model and the induced fit model. Virtually all enzymes are also proteins and act as catalysts for many of the cell's chemical reactions. Enzymes, both human and non-human, are important drug targets. Many drugs act as enzyme inhibitors, hindering or preventing the catalytic activity of the enzymes. Drugs acting as inhibitors may be reversible or irreversible. Reversible inhibition may be competitive or non-competitive. Meanwhile, a number of useful drugs exploit the biochemical differences between humans and invading organisms such as bacteria.
Rate Constants and Equilibria
Authors: Harvey Jeremy
Published: September 2023

This chapter assesses the methods used to study the thermodynamics and kinetics of chemical reactions based on quantum chemistry, molecular mechanics and statistical mechanics. Statistical thermodynamics can be used to calculate thermodynamic properties such as relative free energies based on properties of the potential energy surface V(R). For gas-phase molecules, this can be done by evaluating the quantum mechanical molecular partition function in terms of the translational, rotational, and vibrational properties of the molecules. Combined with accurate quantum chemical calculations, this can yield very accurate free energies. In a similar way, activation free energies as used in transition state theory can be obtained. Meanwhile, statistical thermodynamics for extended systems relies on properties of the classical partition function for the system. While this cannot be explicitly evaluated, it serves as a basis for both direct and biased methods for free energy evaluation.
Hybrid and Multi-Scale Methods
Authors: Harvey Jeremy
Published: September 2023

This chapter addresses hybrid and multi-scale methods. Chemistry of a ‘core’ system is frequently perturbed by the ‘environment’. If the perturbation is weak, as is often the case, it is acceptable to perform calculations on the core part only. The effects of the environment can in many cases be described using continuum models, which can conveniently be coupled to quantum chemical calculations. It is also possible to devise hybrid methods, in which the atoms making up the core and the environment in the model are treated at different levels of theory. One very popular family of hybrid methods treats the core quantum mechanically (QM) and the environment with molecular mechanics (MM), and these methods are referred to as QM/MM methods.
Amines and Amino Acids
Authors: Clugston Michael , Stewart Malcolm , Birembaut Fabrice
Published: September 2023

This chapter describes the mechanisms of amines and amino acids. It also notes the two common naming systems of amines, which are known to be one class of organic compounds with nitrogen atoms. Amines are classified in terms of their general formulas, alkyl group, and hydrogen atoms attached to the nitrogen atom. The Gabriel synthesis is a method of successfully making a primary amine. Amino acids have two function groups: an amino group and a carboxylic acid group. Amino acids also polymerize to construct polypeptides. The chapter discusses the effects of pH and zwitterions as well.