bluuebunny/crossref_metadata_2025 huggingface dataset:
Spin relaxation
Authors: Hore P.J
Published: September 2023

This chapter focuses on two relaxation processes—spin–lattice relaxation and spin–spin relaxation—which cause nuclear spins to return to equilibrium following some disturbance. Spin–lattice relaxation drives the populations of energy levels towards equilibrium, while spin–spin relaxation results in nuclear magnetic resonance (NMR) line broadening. Spin relaxation is caused by the modulation of spin interactions by molecular motions. Dipolar coupling, rendered time-dependent by molecular tumbling, is a common source of spin relaxation. It also causes cross relaxation which leads to the nuclear Overhauser effect. Meanwhile, quadrupolar nuclei often relax very rapidly. The spin–lattice and spin–spin relaxation times, as well as the nuclear Overhauser effect, give information on molecular structure and motion.
Drug Synthesis
Authors: Patrick Graham L.
Published: September 2023

This chapter looks intofocuses on the process of drug synthesis. It notes the role of organic synthesis in the drug design and development process alongside the structure structural features affecting the ease of synthesis. Additionally, the chapter explores the significance of coupling reactions and functional groups in the process of synthesis. It also explains how protection groups are needed as some functional groups tend to be more reactive than others before listing the ideal features of a protecting group. Moreover, the chapter discusses case studies focusing on the synthesis of dofetilide and salbutamol. It uses diagrams to showcase the process of synthesis for multiple examples as well.
Quinolones and fluoroquinolones
Authors: Patrick Graham L.
Published: September 2023

The chapter discusses quinolone and fluoroquinolone. These antibacterial agents which are fully synthetic structures that are particularly useful in the treatment of urinary tract infections and infections which prove other resistant to established antibacterial agents. It looks intoThe chapter considers their mechanism of action in relation to the function of topoisomerases and the inhibition of fluoroquinolones. Nalidixic acid was the first therapeutically useful agent in this class of compounds to be synthesisedsynthesized. Additionally, the chapter explores different methods for the syntheses of quinolones and fluoroquinolones, including which involved syntheses usinga Friedel-Crafts acylation, syntheses involving the nucleophilic substitution of an aryl halide, and tricyclic ring systems. It notes using that quinolones can be used as scaffolds for other targets, such as in the antiviral agent elvitegravir used for the treatment of AIDS.
Multiple variables
Authors: Currell Graham
Published: September 2023

This chapter explores situations in which the investigation produces several measured variables. As the ability to measure and record multiple variables with greater ease and accuracy continues to increase, we are being faced with very large data sets from which we wish to draw out hidden information. A general type of approach is to investigate whether different groups of variables provide related information and then whether it is possible to represent the actions of many variables with a small number of composite variables. The chapter then develops techniques of data reduction through principal component analysis, and data modelling through cluster analysis and multiple regression. It also takes the example of questionnaire data, which could also represent multiple experimental measurements, and identifies a wide range of possible analytical techniques, together with specific references to analyses developed previously.
Project data analysis
Authors: Currell Graham
Published: September 2023

This chapter focuses on project data analysis. It begins by detailing the initial steps in reviewing data and objectives, understanding the source of data uncertainties, and transforming the data into a format suitable for software analysis. For electronic records, the original data should be saved in a secure memory store before copying the data into a new file, and all subsequent analysis should only be carried out on the duplicate data set. The chapter then presents examples of methods to identify experimental characteristics that are suitable for analysis. It also reviews the techniques and issues involved in transforming the data into a format required to match the analytical technique. Finally, the chapter discusses the relevance of normality and equality of variance for many analytical techniques and develops the approach, tests, and transformations that may be involved.
The Inheritance of Multiple Genes
Authors: Meneely Philip , Hoang Rachel Dawes , Hoang Rachel Dawes , Okeke Iruka N. , Heston Katherine
Published: September 2023

This chapter analyses the inheritance pattern of eukaryotic genes, which follows the laws recognized by Gregor Mendel regarding the processes that occur during meiosis in eukaryotes. It considers the more complicated phenotypic ratios that can arise in multiple unlinked genes, when alleles interact in unexpected ways, and when additional inputs from the environment influence the phenotype. It also describes how individual contributing genes always follow the fundamental patterns of single-gene inheritance that arise from meiosis. The chapter looks at the determination of the origins of unexpected phenotypes by working with laboratory organisms, although the same situations prevail in natural environments and affect evolutionary processes. It addresses the question of what happens with two different genes, located on two different chromosomes.
The Locations of Genes on Chromosomes: Linkage and Genetic Maps
Authors: Meneely Philip , Hoang Rachel Dawes , Hoang Rachel Dawes , Okeke Iruka N. , Heston Katherine
Published: September 2023

This chapter refers to genes located near each other on the same chromosome that are not inherited independently of one another but are likely to be inherited together or linked. It highlights linked genes or linked combinations of alleles that are not always inherited together, as crossing over during meiosis creates new combinations of the alleles. It also describes the frequency of recombination that provides an indication of how closely located the genes are on the chromosome, creating the basis for a genetic map of a chromosome. The chapter highlights maps of the genome based on recombination that geneticists use, including other types of maps that can be made as the DNA of genomes can be sequenced. It describes the linkage between genes as an inevitable by-product of the behaviour of chromosomes at meiosis.
Genetic Analysis of Cellular Processes
Authors: Meneely Philip , Hoang Rachel Dawes , Hoang Rachel Dawes , Okeke Iruka N. , Heston Katherine
Published: September 2023

This chapter reviews the tools of genetic analysis, beginning with George Beadle and Edward Tatum’s experiments in Neurospora and François Jacob and Jacques Monod’s work with lac mutants. It looks at recent genetic screens for the identification of genes essential to embryonic development in Drosophila. It also explores the principles of genetics which can be applied to identify the underlying genetic basis of complex cellular processes, which often start with a genetic screen for mutations in the genome that disrupt the process of interest. The chapter describes shared evolutionary histories which enable many findings from the study of one species to be applied more broadly to other species, providing insights into the underlying workings of many cellular processes. It deals with the underlying logic of the methodology behind genetic screens, utilizing a few informative examples to illustrate key features of a well-designed genetic analysis.
The Dynamic Genome
Authors: Bell Graham
Published: September 2023

This chapter studies the genome itself, which is the source of all the hereditary information underlying the adaptation of organisms to their environment. The evolution of the genome is naturally one of the most pressing issues in evolutionary biology. Why are many genomes much larger than they need to be? How does the gain and loss of genes contribute to evolution? How do new genes come into being? Molecular genetics is beginning to provide answers to fundamental questions like these, and the answers have turned out to depend on the Darwinian rules that govern genome dynamics. The chapter then considers how evolving genomes diverge, how genes are modified at different rates, how eukaryotic genomes have evolved novel features, and how genetic elements may evolve cooperation or conflict.
Orthomyxoviruses: influenza A, B, C
Authors: Oxford John , Kellam Paul , Collier Leslie
Published: September 2023

This chapter covers influenza. The name itself refers to the ancient belief that the virus was caused by a malign and supernatural influence. In Florence during the time of the Renaissance, astrologers linked a curious juxtaposition of stars with an outbreak of infection in the city and attributed it to the influence of the stars, hence, influenza. It describes influenza as the last great uncontrolled plague of mankind and shows how the property of causing epidemics and even pandemics is related directly to the ability of these causal viruses to undergo antigenic variation or massive genetic reassortment. The virus is a so-called emergent virus because originally, at the time of the Ice Age 10,000 years ago, it crossed the species barrier from birds to humans. The chapter highlights influenza as an avian virus that spread silently around the world by migrating geese and ducks.
Arenaviruses: Lassa and haemorrhagic fevers
Authors: Oxford John , Kellam Paul , Collier Leslie
Published: September 2023

This chapter discusses the family of arenaviruses. These cause widespread haemorrhagic fevers in tropical countries, especially in Africa and South America. There is an animal reservoir and periodically the viruses jump the species barrier to infect humans, often agricultural workers. The chapter considers arenaviruses as unusual negative-stranded RNA viruses with two ambisense single-stranded RNA segments, L(ong) and S(hort), meaning that protein-coding open reading frames are present in both directions 5’ to 3’ and 3’ to 5’ of the virus RNA segments. The genome segments have complementary termini and can form pan-handle structures by base pairing. The chapter looks at S RNA, which encodes for the virus glycoprotein in the 5’ to 3’ direction and the nucleoprotein on the opposite strand in a 3’ to 5’ direction.
Paramyxoviruses: measles, RSV, mumps, parainfluenza, metapneumovirus, and the zoonotic henipaviruses
Authors: Oxford John , Kellam Paul , Collier Leslie
Published: September 2023

This chapter investigates the Paramyxoviridae, which cause a variety of diseases involving the respiratory tract in humans, birds, and other animals. In humans, they include measles, respiratory infections caused by Respiratory Syncytial Virus (RSV), parainfluenza viruses, and metapneumovirus, and the more innocuous salivary gland infection of mumps. The chapter discusses the worldwide distribution of paramyxoviruses, which cause respiratory disease in all age groups and are responsible for a number of economically important infections in domestic and farm animals. The henipaviruses Nipah and Hendra are pathogenic zoonotic members of the family and are transmitted by airborne droplets or hand contact, and spread is rapid among children in institutions. The chapter describes members of the family Paramyxoviridae as enveloped, negative-stranded ssRNA viruses.
Papillomaviruses
Authors: Oxford John , Kellam Paul , Collier Leslie
Published: September 2023

This chapter talks about papillomaviruses, giving particular attention to the human papilloma virus (HPV), which is the most common sexually transmitted infection in the USA, with millions of new cases each year. Oncogenic HPV types are responsible for 2535% of oral cancers, 90% of anal cancers, and 40% of penile cancers in the USA. The chapter describes papillomaviruses as non-enveloped small icosahedral viruses that are 5255 nm in diameter. The papillomavirus genome is a double-stranded circular DNA that is 8 kbp in length and encodes for 910 ORFs depending on the virus. The chapter emphasizes that papillomaviruses have a strong tropism for squamous epithelial cells and that the replication of the virus is intrinsically linked to the differentiation state of the epithelial cell.
Retroviruses: HIV-1 and -2 and HTLV
Authors: Oxford John , Kellam Paul , Collier Leslie
Published: September 2023

This chapter recounts the first discovery of a retrovirus. This was made as long ago as 1910 by Peyton Rous, who worked at the Rockefeller Institute for Medical Research in New York. This agent, avian sarcoma virus, induced tumours in muscle, bone, and other tissues of chickens. The chapter highlights the discovery of other retroviruses which caused tumours in the 1930s. However, these viruses were regarded as laboratory curiosities until the description of feline leukaemia virus, a gammaretrovirus, which was first discovered in the 1960s and appeared to spread naturally in household cats. The chapter mentions the Visna Virus of sheep, discovered in 1954. This was shown to persistently infect sheep and could lead to ovine progressive pneumonia. The discovery if HIV-1, which causes AIDS, led to a surge of interest in this previously understudied family of viruses, and the chapter examines the properties as well as the clinical and pathological aspects of HIV in detail.
Control of viral diseases by immunization
Authors: Oxford John , Kellam Paul , Collier Leslie
Published: September 2023

This chapter focuses on the control of viral diseases by immunization. It discusses the germ theory of disease, which was accepted in the late nineteenth century and led to the development of concepts of immunity, which made it possible to develop the scientific framework for the practice of immunization against microbial diseases. Vaccines contain what in modern terminology are virus proteins with antigenic areas called epitopes, which induce both B-cell and T-cell immunity. The chapter refers to vaccine-induced immunity that may last several years or a lifetime and explains that the ability to make these long-term responses is mediated by memory cells. The first vaccines to be prepared in the laboratory were those against smallpox and rabies. The chapter reviews other milestones of virus vaccine development, such as the attenuated yellow fever (YF) vaccine manufactured from infected chick embryos.
Protein structure
Authors: Lesk Arthur M.
Published: September 2023

This chapter explores the structures of proteins in more detail than thus far in this text. Building on the basic structural and physical chemistry of amino acids and protein conformations, it examines the features that stabilize native states. Proteins combine the unity of a common and repetitive mainchain with the variety available from a sequence of sidechains individual to each protein. The sequence of sidechains both determines the three-dimensional structure of the protein (including its overall folding pattern in general and the structure of the active site in particular), and provides the chemistry required for function. The twenty standard amino acids contain groups of several physicochemical types and are adequate for many but not all purposes. In addition to amino acids, many proteins bind prosthetic groups—ions or small organic molecules—that stabilize or modify the structure, and/or participate in catalysis. They also serve regulatory purposes.
Species, populations, and individuals
Authors: Rowe Graham , Sweet Michael , Beebee Trevor J. C.
Published: September 2023

This chapter discusses the importance of species. It looks into the possibility of solving the species problem using the concepts of biological species, morphological species, phylogenetic species, and the operational taxonomic unit. Speciation is the process resulting in the formation of new species and accounts for biological diversity which is then divided between anagenesis and cladogenesis. The chapter also explores the concept of hybrids, hybrid zones, environmental DNA, and ancient DNA techniques. It includes molecular markers which it states are delivering new insights into the nature of species and boundaries. Spatial differences are emphasized for studying speciation mechanisms alongside investigating the balance of local adaptation and gene flow.
Phylogeography
Authors: Rowe Graham , Sweet Michael , Beebee Trevor J. C.
Published: September 2023

This chapter explains the concept of phylogeography which is focused on the principles and processes of the geographical distribution of genealogical lineages. First, it expounds on the molecular markers of phylogeography. It specifically looks at mitochondrial DNA (MtDNA). MtDNA is often the marker of choice as it showcases a relatively simple pattern of maternal inheritance without recombination. The chapter looks into coalescent theory. This theory aims to interpret the distribution of times to a gene tree's common ancestry in terms of various evolutionary forces. The chapter adds the genetic variation in geographic space and time while referencing Bayesian inference in phylogeography. Moreover, it considers the phylogeography of microorganisms.
Microbial ecology and metagenomics
Authors: Rowe Graham , Sweet Michael , Beebee Trevor J. C.
Published: September 2023

This chapter explores microbial ecology and metagenomics. It notes the role of microbial communities in nature in line with outstanding issues in microbial ecology such as species identification, population dynamics, and community structure. Moreover, the chapter explains immunological and genomic approaches to microbial ecology. An example of which would be antibody identification. The chapter also discusses metagenomics in relation to ribosomal sequences and microbial ecology. The chapter looks at the genetic variability of bacteria species. It also discusses the phylogeography of viruses, bacteria, and fungi. DNA hybridization methods based on DNA microarray technology offer great promise on microbial identification and community analysis, especially where it is necessary to resolve closely related operational taxonomic units (OTU).
Genomes
Authors: Rowe Graham , Sweet Michael , Beebee Trevor J. C.
Published: September 2023

This chapter focuses on genomes. The genome is recognized to be the complete set of an organism's DNA. The chapter discusses the history of the first genome sequences. It gives an overview of notable genomes and their date of publication. The chapter highlights the Human Genome Project in line with competing sequencing strategies for eukaryotic genomes and comparative genomics. It notes that whole genome shotgun (WGS) and next generation sequencing (NGS) are used to sequence genomes. Genome reassembly is the major challenge of sequencing a large eukaryotic genome. In addition, the chapter explains microbiomes being used in metabarcoding and metagenomics approaches. It also explores genome annotation.
Algebra IV
Authors: Monk Paul , Munro Lindsey J.
Published: September 2023

This chapter focuses on fractions and percentages. A fraction involves one quantity divided by another. The part of the fraction above the solidus line is called the numerator, and the part below the denominator. The denominator sometimes represents the total number possible, and the numerator represents the overall proportion under scrutiny. We can simplify many fractions by cancelling portions of the numerator and denominator. Another way to simplify a fraction is turning it into a decimal. We obtain a numerical value of a fraction by dividing the value of the numerator by the value of the denominator. Long division is thus the first method of converting a fraction into a decimal. The chapter then explains the process of multiplying, adding, subtracting, and dividing fractions. It also considers the concept of a percentage, which relates to the hundredth part of a thing.
Algebra VI
Authors: Monk Paul , Munro Lindsey J.
Published: September 2023

This chapter addresses the process of multiplying brackets and factorizing. The acronym BODMAS tells us that brackets have the highest priority in rearrangements and algebra. The correct way to multiply out a bracket is to multiply each term within the bracket by the factor positioned outside it. When two brackets are positioned side by side, we multiply them term by term. The chapter then looks at the process of squaring a bracket by multiplying it with itself, as well as squaring larger brackets and obtaining coefficients using Pascal's triangle. The term ‘perfect square’ refers to the product of a bracket multiplied by itself. Finally, the chapter details the process of factorizing simple expressions, the difference between two squares, by completing a square, quadratic equations, and by using ‘the quadratic formula’.
Advanced BODMAS
Authors: Monk Paul , Munro Lindsey J.
Published: September 2023

This chapter illustrates the process of performing simple rearrangement using the BODMAS rule. When rearranging, we identify the presenting function and perform its inverse. The chapter then looks at rearrangements involving brackets. A bracket is the collection of algebraic terms sandwiched between symmetrical symbols. It contains more than one term because it makes no sense to use bracket symbols to ‘group together’ a single term. We cannot move any of the content from within the bracket. Rather, we move the entire bracket as a complete and whole unit. Indeed, we treat everything grouped between the bracket symbols as a self-contained whole. The chapter also considers the process of rearranging exponentials and logarithms, as well as rearrangements involving powers, roots, and trigonometry.
Integration III
Authors: Monk Paul , Munro Lindsey J.
Published: September 2023

This chapter addresses the process of integration by parts, by substitution, with power series, and using published tables. We try integration by parts if the integral is a product and one term of the product gives a constant when differentiated (one or more times). Integration by parts allows us to integrate products that cannot be integrated more straightforwardly. Occasionally, we need to integrate by parts more than once; we call this procedure ‘successive reduction’. Meanwhile, we try integration by substitution if the integral is a function of a function. We can also check if the integral is a standard function available from published tables or can be rearranged to give such an integral.
Matrices II
Authors: Monk Paul , Munro Lindsey J.
Published: September 2023

This chapter studies symmetry operations and elements. All chemical species are fluxional at temperatures above absolute zero: their bond lengths and angles change continually as these species vibrate and move. They undergo dynamic changes that cause some or all their component atoms to move between symmetry-equivalent positions. Ultimately, all orbitals and many molecules are symmetrical. The chapter develops a systematic way of describing their symmetry, looking at the concepts of symmetry planes and reflections; centres of symmetry and inversion operations; and rotation operations. The chapter then considers mathematical ways of using matrices to describe the symmetry operations that underpin a vast array of chemistry-related techniques such as spectroscopy.
Fixation and specimen handling
Authors: Muskett David
Published: September 2023

This chapter investigates the way in which biopsies and resections are first handled in the laboratory. Once specimens arrive in the laboratory, they follow a process to the point of diagnosis. The process for most specimens remains the same until the first slide has been viewed for diagnosis. The chapter begins by looking at specimen collection. Specimens need to be transported from the operating theatres and clinical areas to the laboratory; this should be done safely, in appropriate environmental conditions, and in a timely manner. The chapter then explains the need for accurate specimen reception, the principles of specimen fixation, the need for specimen decalcification and the means by which this can be achieved, and the need for accurate patient details supplied with samples.
Mohs procedures
Authors: Orchard Guy , Shams Mohammad
Published: September 2023

This chapter assesses the process and procedures involved in Mohs techniques. Mohs has a growing application for the surgical removal of cancers. Indeed, its main application has been in the use of surgical removal of skin cancers. Mohs procedures have the benefits of offering unparalleled accuracy for the total skin clearance of tumours without recurrence. The chapter then looks at the applications of Mohs in modern histopathology laboratories and the benefits it can bring to patient care. It also explains what slow Mohs is and when its application is appropriate, before considering the role of rapid immunocytochemical staining to aid in the assessment of frozen and paraffin sections in Mohs procedures.
Analytical immunocytochemistry
Authors: Orchard Guy , Muskett David , Warren Anne
Published: September 2023

This chapter describes how immunocytochemistry (ICC) can be employed in the investigation of pathological states. It begins by explaining malignancy, which is defined by a change in the normal cell biology of cells. It results in an abnormal growth or tumour that can then spread (metastasize) to other body sites. Within histopathology, there are recognized key malignant tumour groups, including carcinoma, lymphoma, melanoma, mesothelioma, and sarcoma. The chapter then looks at the key antibodies used in ICC, before focusing on the investigation of breast cancer, lung cancer, and prostate cancer. It also discusses the use of ICC in the investigation of lymphoma; how ICC can contribute to the identification of tumours of an unknown primary malignancy, the role of ICC in the investigation of autoimmune skin disease, and the role of ICC in the strategy of patient management targeted therapies.
Molecular diagnostics in action
Authors: Taniere Philippe
Published: September 2023

This chapter identifies the mission of a molecular diagnostic service involved in solid tumour testing. Molecular tests add information on diagnosis, prognosis, and prediction to therapy; targets are chromosomes, genes, or proteins. In routine practice, molecular pathology diagnostic services need to be able to offer the whole range of techniques needed for the patient's management. Nature and number of tests per tumour are guided by clinical relevance. Ultimately, pathologists play a key role in the prescription of the relevant tests and their final interpretation. Appropriate management of tissue is crucial; molecular tests are performed following the diagnostic procedure which includes immunocytochemistry. The chapter then looks at mutation testing, multiplex gene testing, and protein assessment.
Introduction: a glance at the past, a glimpse of the future
Authors: Shambayati Behdad
Published: September 2023

This chapter states how cytology became accepted as a valuable diagnostic tool, almost a hundred years after Johannes Mueller's 1845 publication on the microscopic appearance of malignant cells. It looks at George Papanicolaou's work which contributed to the field of cervical cytology and helped form the basis of successful cervical screening programmes around the world. It also highlights advances in diagnostic procedures that are combined with developments in cytology sampling devices and methods. The chapter discusses the adoption of liquid-based cytology (LBC) methodology, which has enhanced cytological diagnosis and reduced the need for repeated sampling in all areas of cytology. It includes special staining, immunocytochemistry, and molecular techniques that have added refinement to the cytological diagnosis.
Preparation techniques
Authors: Evered Andrew , Shambayati Behdad
Published: September 2023

This chapter emphasizes the importance of a proper collection of specimens by a well-trained clinician, explaining that it is the first step towards a clinically useful cytological diagnosis. It explores the group of techniques for specimen collection that take advantage of the tendency of neoplasms to shed cells and aid cell collection: exfoliative methods or aspiration methods. It refers to a sampling error, which is the failure to collect a sufficient quantity of diagnostically relevant cells that leads to the problem of false negative reporting. The chapter explains fixation as the process by which cells and their constituents are chemically changed to preserve their morphology and to facilitate subsequent demonstration techniques. It covers specimen processing that maximizes the chances of making clinically useful cytological diagnoses.
Normal cervical cytology
Authors: Evered Andrew
Published: September 2023

This chapter considers the microscopic examination of epithelial cells derived from the cervix as an important part of the repertoire of cytology laboratories around the world. It begins with a description of the normal anatomy, physiology, and histology of the female genital tract, which is important for gaining a complete understanding of the spectrum of microscopic features seen in cervical samples. It also looks at the cytology of normal epithelial cells and the morphological changes that occur during inflammation, infections, metaplasia, and various medical interventions. The chapter covers several types of microorganisms that can be identified in cervical samples that can be determined by the clinician, not the cytologist. It highlights hormonal variations, metaplasia, inflammation, iatrogenesis, and non-epithelial cells, which can confound the microscopical interpretation of cells.
Quality issues in cervical screening and cytology
Authors: Crossley John , Cross Paul
Published: September 2023

This chapter discusses quality in the context of cervical screening and cytology. It explains that quality assurance is designed to prevent errors from occurring while quality control is designed to identify errors which occur despite quality assurance measures. The chapter outlines procedures that are undertaken and areas that are assessed to assure and control the quality of services within cytology and cervical screening. It covers cytology primary screening and HPV primary screening, and triage in relation to both of these types of screening. The chapter emphasizes that the protection from developing cancer is provided by the sensitivity of screening, while the specificity ensures the minimum amount of unnecessary intervention and harm. The specificity of a cervical screening programme is dependent on the method of triaging the cases that test positive at primary screening and the quality measures used to assure and control the triage process. It is highlighted that the delivery of high-quality screening programmes depends on appropriate training, education, and professional development of staff and continuous auditing of services..
Lower respiratory tract cytology
Authors: Shambayati Behdad
Published: September 2023

This chapter delves into the cytology of the lower respiratory tract, particularly as it relates to the diagnosis of lung cancer. It points out that respiratory cytology is heavily dependent on good sample preparation, which is why it is crucial to involve an appropriately trained cytologist during sample collection at bronchoscopy or FNA procedures to ensure sample adequacy. The chapter explains that infective agents, such as the herpes simplex virus, Pneumocystis jiroveci, and Aspergillus, are occasionally encountered in cytological samples. The chapter highlights that there are two main types of lung cancer, non-small cell and small cell lung cancer, which require different treatment. Therefore, achieving an accurate cytological diagnosis is crucial. Light microscopy of respiratory samples, when combined with appropriate immunocytochemical markers, provides the clinician with a highly accurate diagnostic modality that can be used for identifying the right treatment of the patient.
Data analysis in cytopathology
Authors: Evered Andrew
Published: September 2023

This chapter starts off by exploring the kinds of data that interest cytologists, and how these data can be summarized and displayed in meaningful ways. It then introduces simple calculations that can help cytologists understand how well cytology performs at individual, laboratory, and national levels. These are so-called audit activities, providing important information about past and current performance and how cytology services can be continually improved. The chapter later explores how to collate and analyse data collected from research activities. Unlike audit, cytology research creates generalizable new knowledge that can be valid in a wide range of scientific and clinical applications. Research is therefore different from audit, the results of which are only valid locally. Interpretation of research data can be challenging work and may involve unconventional and specialized types of analysis. Finally, the chapter deals only with the most commonly used analytical techniques.
Rocky and Sandy Shores
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 explores rocky and sandy shores. The biodiversity of the shore is exceptionally high compared to that of land, with all major taxonomic groups represented. Ecological research on shores has underpinned much of present-day marine ecology and has strongly influenced mainstream ecology. In addition, shores are of increasing concern to governmental policy-makers because of their recognized provision of goods and services for humans, such as coastal defence, recreation, and fisheries products. Shorelines around the world are experiencing major impacts caused by human population pressure, and there is a necessity to defend our economic and social investment in coastal development from the effects of accelerated sea-level rise. Understanding how shores function ecologically is therefore important not simply for intellectual reasons, but for practical purposes if their full value is to be maintained.
Pelagic Ecosystems
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 turns to the pelagic realm. The pelagic environment encompasses the entire water column of the world's seas and oceans. It extends from the sea surface to the abyssal depths and from the tropics to the polar regions, and is a highly heterogeneous and dynamic three-dimensional habitat. It is, in fact, the most voluminous habitat on Earth. The pelagic environment is home to some of the most revered and reviled marine inhabitants, and great whales and jellyfish alike are all subject to the consequences of pelagic ecosystem variability. The chapter shows how physical processes in the pelagic exert major control on biological activity, leading to substantial geographic variability in primary and secondary production-and hence in fisheries potential. Knowledge of biophysical interactions is thus essential for understanding ecological patterns and processes in the pelagic environment.
The Deep Sea
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 explores the deep sea, which represents the largest, yet least-known, biome on earth. The environment is remarkably constant across the ocean floor: cold, dark water overlying soft, deep mud. While the high hydrostatic pressure is the most obvious physical feature of the deep, it is food supply from the surface that is the limiting factor for life on the abyssal plain. In temperate areas, the food input can be seasonal, providing cues for reproductive cycles. Due to the lack of food, the community of animals in the deep sea is at much lower densities than in shallow waters. Potentially there are millions of species inhabiting the deep-sea benthos; the main groups of large, mobile organisms are echinoderms, decapod crustaceans, and fish. Recent exploration using submersibles has revealed exciting 'island' habitats in the deep sea with a level of production and diversity higher than their surrounding environments.
Pollution, Disturbance, and Environmental Monitoring
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 considers the role of human activities in causing ecological disturbance. The significance of human activities is gauged against the scale and frequency of natural sources of disturbance. Human activities modify the marine environment, both through the removal of biomass and habitats and via the addition of contaminants and physical structures. To understand the ecological importance of human activities in the marine environment, one must be able to detect changes in measured ecological characteristics using appropriate observational or experimental techniques. An understanding of the scale at which ecological processes operate should underpin the ultimate selection of metrics chosen for study (e.g. diversity, abundance, biomass). Hence, the chapter discusses the relevance of a selection of measures and the importance of developing appropriate experimental designs.
Ecological Indicators
Authors: Goodenough Anne E. , Hart Adam G.
Published: September 2023

This chapter explains the concepts behind ecological indicators. Some ecological indicator systems are based on the abundance of a single species. It is said that environmental indicators are founded on the principle of ecological niches and tolerance range. The chapter lists types of ecological indicators, such as surveys and biotic indices, and discusses the theory underpinning environmental indicators. Then, the chapter explicates biological and biodiversity indicators. It also considers the effort of reconstructing historic landscapes known as palaeo-biomonitoring. The chapter highlights the importance of being aware of ecological indicators so that they can be used appropriately and results are correctly interpreted. It also includes an interview with applied ecologist Alice Trevail.
In Situ Conservation
Authors: Goodenough Anne E. , Hart Adam G.
Published: September 2023

This chapter focuses on in situ conservation. First, it defines in situ conservation and explains that it covers numerous active management techniques. The chapter looks at the aims of in situ management, which range from creating, restoring, protecting, and maintaining to improving and connecting. Then it lists active management and custodial management as approaches. The chapter explicates the process of managing habitats and species by citing translocations, insurance population, and reintroductions as examples. In addition, in situ conservation is underpinned by policies such as the Intergovernmental Panel on Climate Change, Biodiversity Action Plans, National Biodiversity Strategy Action Plans, and the Convention on Biological Diversity's implications and frameworks. The chapter includes an interview with applied ecologist Gareth Parry.
1Advanced EPR techniques
Authors: Chechik Victor , Carter Emma , Murphy Damien
Published: September 2023

This chapter explains the basic theory of continuous wave (CW) electron paramagnetic resonance (EPR), illustrating the power of the technique to study a wide range of paramagnetic systems. It cites several experiments based on pulsed techniques similar to those routinely employed in nuclear magnetic resonance (NMR) spectroscopy. It also talks about how Pulse EPR can offer significant advantages over CW methods, such as direct detection of relaxation times and access to longer distances between paramagnetic centres. The chapter talks about the independent control of the electron and nuclear spins via the application of short microwave (MW) and radiofrequency (RF) pulses. It presents the vector model and product operator formalism used in pulse techniques.
The kinetic model of gases
Authors: Atkins Peter , Paula Julio de , Smith David
Published: September 2023

This chapter examines the kinetic model of gases, which illustrates how to build a model that accounts for the observed properties of a perfect gas in terms of assumptions about the behaviour of its molecules. As well as accounting for the gas laws, the model can be used to predict the average speed at which molecules move in a gas and the dependence of that speed on temperature. The model can also be used to predict the spread of molecular speeds and its dependence on molecular mass and temperature. The chapter then looks at the root-mean-square speed of gas molecules, before discussing the Maxwell distribution of speeds. It also considers the processes of diffusion, effusion, and molecular collisions.
Real gases
Authors: Atkins Peter , Paula Julio de , Smith David
Published: September 2023

This chapter investigates the properties of actual gases, so-called ‘real gases’. The deviations from perfect behaviour give insight into the nature of the interactions between molecules. The extent of deviations from perfect behaviour is summarized by introducing the compression factor. Meanwhile, the isotherms of a real gas introduce the concept of vapour pressure and critical behaviour. A gas can be liquefied by pressure alone only if its temperature is at or below its critical temperature. The chapter then looks at the virial equation, which is an empirical extension of the perfect gas equation that summarizes the behaviour of real gases over a range of conditions. It also considers the van der Waals equation, which is a model equation of state for a real gas expressed in terms of two parameters, one corresponding to molecular attractions and the other to molecular repulsions.
Entropy changes
Authors: Atkins Peter , Paula Julio de , Smith David
Published: September 2023

This chapter shows how to use the definition of entropy change to calculate the change in entropy when a system undergoes changes of volume and temperature and when a phase transition takes place. It specifically looks at Trouton's rule. The entropy of the system increases when a perfect gas expands isothermally. Entropy also increases with temperature. The chapter then demonstrates how to adapt the definition of entropy change to the calculation of the change in entropy of the surroundings. Ultimately, the change in entropy of the surroundings is calculated from the energy transferred as heat into them regardless of whether the process is reversible or not.
Partial molar quantities
Authors: Atkins Peter , Paula Julio de , Smith David
Published: September 2023

This chapter discusses partial molar quantities. When a substance is a component of a mixture, it makes a contribution to the properties of the mixture that depends on the composition. For a general description of the thermodynamics of mixtures, it is necessary to introduce other ‘partial’ properties. A partial molar property is the contribution (per mole) that a substance makes to an overall property of a mixture. The easiest partial molar property to visualize is the partial molar volume. The chapter then considers how the concept of a partial molar quantity can be applied to other state functions. The most important is the partial molar Gibbs energy, which is the chemical potential of a component. The chapter also looks at spontaneous mixing.
The thermodynamics of reaction
Authors: Atkins Peter , Paula Julio de , Smith David
Published: September 2023

This chapter focuses on the thermodynamics of reaction. The reaction Gibbs energy provides the signpost of spontaneous change and is defined in terms of the chemical potentials that the participants in a reaction have at an arbitrary stage of the reaction. At constant temperature and pressure, a reaction mixture tends to adjust its composition until its Gibbs energy is a minimum. The chapter then introduces the reaction quotient, which is a natural way of expressing the composition of a reaction mixture in a thermodynamic context, and its equilibrium value, the all-important equilibrium constant. It also differentiates between exergonic compound and endergonic compound.
Proton transfer equilibria
Authors: Atkins Peter , Paula Julio de , Smith David
Published: September 2023

This chapter describes proton transfer equilibria. It begins by looking at the Brønsted–Lowry theory of acids and bases, according to which an acid is a proton donor and a base is a proton acceptor. The strength of an acid is reported in terms of its acidity constant and that of a base in terms of its basicity constant. The chapter then considers protonation and deprotonation. It differentiates between a weak acid and a strong acid. A strong acid is commonly regarded as being completely deprotonated in aqueous solution. The chapter also differentiates between a strong base and a weak base.
Acid–base equilibria of salts in water
Authors: Atkins Peter , Paula Julio de , Smith David
Published: September 2023

This chapter studies the acid–base equilibria of salt solutions. The ions that a dissolved salt provide are themselves either acids or bases, sometimes both. Acidity constants can be used to predict the pH of solutions, and that information in turn can be used to account for the variation of pH during the course of a titration. That information is also helpful as a guide to the selection of solutes that stabilize the pH of solutions. The chapter looks at acid–base titrations, explaining how the pH of a mixed solution of a weak acid and its conjugate base is given by the Henderson–Hasselbalch equation. It then considers the buffer action, examining the buffer solution and differentiating between an acid buffer and a base buffer.
Solubility equilibria
Authors: Atkins Peter , Paula Julio de , Smith David
Published: September 2023

This chapter highlights solubility equilibria. A solid dissolves in a solvent until the solution and the solid solute are in equilibrium. At this stage, the solution is said to be saturated, and its molar concentration is the molar solubility of the solid. That the two phases—the solid solute and the solution—are in dynamic equilibrium implies that equilibrium concepts can be used to discuss the composition of the saturated solution. A solubility equilibrium is an example of a heterogeneous equilibrium in which the species are in different phases (the solid solute and the solution). The chapter then looks at the solubility constant before considering the common-ion effect. The common-ion effect is the reduction in solubility of a sparingly soluble salt by the presence of a common ion. The chapter also examines the effect of added salts on solubility.
Rate laws
Authors: Atkins Peter , Paula Julio de , Smith David
Published: September 2023

This chapter details the identification of rate laws, which is the first step in the process of understanding how chemical reactions occur and is an essential step in predicting how the composition of a reaction mixture changes with time. The rate of reaction is often found to be proportional to the molar concentrations of the reactants raised to a simple power. The rate constant is independent of the concentrations of the species taking part in the reaction but depends on the temperature. An experimentally determined equation of this kind is called the ‘rate law’ of the reaction. A rate law provides a basis for the classification of reactions according to their kinetics. The chapter then differentiates between pseudofirst-order and pseudosecond-order rate law, and considers the determination of a rate law through the isolation method and the method of initial rates.