bluuebunny/crossref_metadata_2025 huggingface dataset:
Synthesis of lead compounds
Authors: Patrick Graham L.
Published: September 2023

This chapter looks intofocuses on the synthesis of lead compounds. A lead compound is a molecule that shows some activity or, property of interest, and thus has the potential to be developed into a useful drug. The chapter narrates outlines the characteristics of a lead compound, such as its molecular skeleton and functional groups. It also looks intocovers scaffolds, which is define the size and shape of the structures present in a combinatorial library, and distinguishes different types of scaffolds: linear scaffolds and cyclic scaffolds. Additionally, the chapter lists the types of scaffolds by referencing linear scaffolds and cyclic scaffolds. It notes discusses how molecular modelling can be utilised utilized to identify the number of pharmacophores represented in different structures. Then, the chapter discusses the synthesis of a compound library as it is vital which scaffold will be usedand the necessary step of choosing a scaffold for this library. It also tackles the de novo drug design, in which used the SPROUT software programs such as SPROUT are used to design potential lead compoundsme.
Synthesis of isotopically labelled compounds
Authors: Patrick Graham L.
Published: September 2023

This chapter focuses on the synthesis of isotopically labelled compounds. It notes defines isotopes as an elements that differ in the number of neutrons they have in their nucleus and which can be categorised categorized as stable isotopes or radioactive isotopes. The chapter highlights the importance of isotopically labelled compounds in terms of drug metabolism, determination of biosynthetic pathways, binding assays, and radioactive anticancer drugs. It notes considers the radioisotopes used in labelling compounds. Additionally, the chapter mentions the use of labelled drugs in drug metabolism studies and biosynthetic studies alongside the use of radiolabelled compounds in pharmacological assays. AdditionallyMoreover, the chapter explores isotopically labelled drugs and their links to radioactive drugs.
Design and synthesis of tetracyclines
Authors: Patrick Graham L.
Published: September 2023

This chapter explores the design and synthesis of tetracyclines. Tetracyclines are clinically vital broad-spectrum antibacterial agents from whose name derives from the tetracyclic ring system that all of them share. The chapter then mentions how cChlorotetracycline was the first of the tetracyclines to be isolated. TAdditionally, the chapter explains structure activity relationships in relation to early analogues of natural tetracyclines. It also considersnotes the synthesis of tetracyclines and semi-synthetic tetracyclines as well. The chapter, then, highlights how the effectiveness of tetracyclines has declineds due to the appearance of resistant bacterial strains. Novel synthetic approaches are now allowing the full synthesis of a new generation of tetracyclines.
Frequency data
Authors: Currell Graham
Published: September 2023

This chapter focuses on frequency data. It develops techniques which analyse the frequencies and probabilities of observed events. The chapter begins by presenting analyses relevant to single samples of categorical data, e.g. data descriptions and 'goodness of fit' test. It then develops the statistics of the contingency table and the use of cross-tabulation to generate the table from individual observations. Finally, the chapter looks at the analysis of binary systems using logistic regression and the description of probabilities using receiver operating characteristics (ROC) plots. The name 'receiver operating characteristics' derives from its early use to describe the properties of signal detectors in recording either a true or false signal.
Evolution, Genomes, and Genetics
Authors: Meneely Philip , Hoang Rachel Dawes , Hoang Rachel Dawes , Okeke Iruka N. , Heston Katherine
Published: September 2023

This chapter introduces a recent study of the genomes of Charles Darwin’s finches, which identified genes that contribute to the differences in beak shape among the species. It links one of the most important and familiar examples of natural selection among Darwin’s finches with the underlying genetic and genomic basis for the differences observed among the birds. It also uses Darwin’s finches to discuss DNA, molecules, phenotypes, species, and evolution in a community of organisms. The chapter explores the current availability of genomic information from many species of bacteria, plants, and animals. It highlights how evolution has shaped DNA sequences, genes, and genomes throughout biology.
Human Genetic Mapping, Genome-wide Association Studies, and Complex Traits
Authors: Meneely Philip , Hoang Rachel Dawes , Hoang Rachel Dawes , Okeke Iruka N. , Heston Katherine
Published: September 2023

This chapter brings together fundamental concepts of genetics and genomes on complex traits and genome-wide association studies, which focus primarily on human traits and diseases. It explores genome-wide association studies in order to build upon the basic principles that identify contributing genes and causative mutations. It provides an approach that shows how genome-wide associations integrate genomic variation, complex phenotypes, and evolutionary history. The chapter mentions the Human Genome Project, which made it possible to identify hundreds of individual genes that affect disease phenotypes. It focuses on human genetic diseases and provides an analysis of the human genome, which allowed a much deeper understanding of many aspects of the overall biology of Homo sapiens.
Metagenomes: Genome Analysis of Communities
Authors: Meneely Philip , Hoang Rachel Dawes , Hoang Rachel Dawes , Okeke Iruka N. , Heston Katherine
Published: September 2023

This chapter introduces the relatively new field of metagenomics, in which genomic information is extracted directly from communities of organisms living in their natural environments and reveals evidence for their interdependence and co-evolution. It demonstrates how genome analysis can be extended beyond individuals or single populations to study entire communities. It considers metagenomics that analyse genome information extracted directly from organisms living in their native environments to address questions of biodiversity and community structure. The chapter refers to the study on metagenomes, which provides a powerful lens through which to view the otherwise invisible world of many microbial communities. It also mentions how metagenomics involve the interplay of the Five Great Ideas of Biology and many more connections that are likely to be found by subsequent experimentation.
The Ancestry of Life
Authors: Bell Graham
Published: September 2023

This chapter details the evolutionary history of the modern groups discussed in the previous chapter and describes their ancient ancestors. The age of a group of organisms can be estimated from the age of the rocks in which the earliest fossils belonging to this group have been found. However, this is only the minimum age of the group because still earlier representatives may not have fossilized or their fossils may not have been found yet. If the rate of neutral mutation were constant over genes and lineages, DNA sequences could also be used to estimate absolute ages, independently of fossils. Ultimately, any given clade descends (to the exclusion of all other clades) from a most recent common ancestor that lived at some time in the past. The chapter considers the ancestry of Homo sapiens, Hominoidea, Primates, Eutheria, Mammalia, Amniota, Tetrapoda, Sarcopterygii, Osteichthyes (bony fishes), Gnathostomata, Chordata, Deuterostomia, Bilateria, Metazoa, Unikonta, and Eukaryota.
Viruses and the community: the science and practice of epidemiology
Authors: Oxford John , Kellam Paul , Collier Leslie
Published: September 2023

This chapter examines the ways in which viruses affect whole communities. This is the province of epidemiology, a word of Greek derivation meaning upon the people. The corresponding term for disease in animal communities is epizootology. The chapter highlights the way in which microbes and other parasites affect communities as one of a constantly shifting balance of power between parasite and host, both of which evolve quite elaborate means of attack and defence. The results of such battles determine the effects of microbes on individuals and outcomes of a highly complex interplay of factors. The chapter talks about American epidemiologist John Paul, who summarized the effects of microbes under the headings of seed, soil, and climate.
Togaviruses: mosquito-borne Chikungunya and teratogenic rubella
Authors: Oxford John , Kellam Paul , Collier Leslie
Published: September 2023

This chapter examines the family Togaviridae, which derives its name from the closely fitting envelope surrounding the virions. The Togaviridae includes two genera: Alphavirus and Rubivirus. The Rubivirus genus has a single virus and it is not arthropod-borne, but causes rubella and foetal infections, while the Alphavirus genus has 28 viruses divided into 7 complexes, most of which are spread by mosquitoes. The chapter refers to Old World alphaviruses, such as Ross River, Sindbis, Semliki Forest, and Chikungunya. These cause febrile illnesses, displayed in the form of a rash and arthralgia. The chapter also covers New World viruses, such as Western equine encephalitis (WEE), Eastern equine encephalitis (EEE), and Venezuelan equine encephalitis (VEE). These are neurovirulent and cause headaches and encephalitis.
Bunyaviruses: Hanta, phlebo and nairo
Authors: Oxford John , Kellam Paul , Collier Leslie
Published: September 2023

This chapter highlights bunyaviruses, a family which takes its name from the prototype Bunyamwera virus, named after the place where it was first isolated in Uganda. This family of some 350 viruses was first established in 1975 and has five genera, of which four are arboviruses pathogenic for humans and other animals: Orthobunyavirus, Phlebovirus, Nairovirus, and Hantavirus. The chapter reviews laboratory studies of these viruses, which are carried out at high containment level 4 in order to obviate aerosol infection of staff. Some of these haemorrhagic fevers are classified as emerging human pathogens and are spread via mosquitos, sand flies, and ticks–with the exception of hantaviruses, which are spread through aerosols of the urine of mice and rats. The chapter clarifies how the bunyaviruses amplify by persistent infection in mosquitoes, midges, sand flies, and ticks, and spread by vertical transmission in the egg or venereally.
Polyomaviruses
Authors: Oxford John , Kellam Paul , Collier Leslie
Published: September 2023

This chapter discusses polyomaviruses, which have been the object of intense study investigating how cells become transformed into tumour cells and also other basic parameters of cellular RNA and DNA synthesis. Like papillomaviruses, the viruses of this family are widespread in the community, but unlike papillomaviruses, their disease impact is very small. The chapter highlights the polyomavirus genomes, which have compact regulatory regions and a number of overlapping genes to compensate for the small size of the genome, which is only 5.3kb coding for 68 proteins. The three regions of the genome are the non-coding region (NCCR), which contains the origin of replication (ori), and the early and late coding regions. The chapter details how polyomaviruses bind to sialic acid-containing glycoproteins and gangliosides, and enter cells by endocytosis of specialized vesicles called caveolae.
Proteins as catalysts: enzyme structure, kinetics, and mechanism
Authors: Lesk Arthur M.
Published: September 2023

This chapter evaluates the role of proteins as catalysts, focusing on enzymes. Cells produce thousands of enzymes. Most act intracellularly, to catalyze a network of metabolic reactions, and the replication, transcription, translation, and repair of DNA. A smoothly integrated operation of the metabolic network requires control mechanisms. The chapter begins by looking at the crucial features of enzymes: catalysis, specificity with respect to substrate and reaction, and ability to be regulated. It then considers the general ideas of enzyme kinetics, including the Michaelis–Menten model, and the measurement and interpretation of the Michaelis constant KM and the maximum velocity (under conditions of saturation of enzyme by substrate) Vmax. The chapter also studies the idea of an enzyme mechanism, the different types of enzyme inhibitors, the mechanism of blood coagulation, motor proteins, and the principles of membrane transport and allosteric change.
Conservation genetics
Authors: Rowe Graham , Sweet Michael , Beebee Trevor J. C.
Published: September 2023

The chapter looks into conservation genetics as a method used to mitigate extinction. It explains how molecular genetics is used in conservation biology. Molecular systemics are great assets in wildlife forensic investigations. PCR technology enables genetic studies to be conducted on rare species. The chapter notes careful evaluation is needed as neutral estimates of genetic diversity sometimes differ from measures of adaptive variation. Next, the chapter explores the basis and impact of inbreeding and captive breeding in relation to the genetic load of smaller populations. The chapter expounds on the concept of plant and animal conservations as well. De-extinction, meanwhile, is regarded as only a movie concept.
Algebra VII
Authors: Monk Paul , Munro Lindsey J.
Published: September 2023

This chapter describes the process of solving simultaneous linear equations. ‘Linear’ means the equations have variables of the form x and y associated with a straight line rather than curved lines — finding the common value when one or more of the lines is curved requires a different procedure. Solving simultaneous linear equations involves elimination and substitution. We can achieve elimination by subtracting like terms from between the two equations. The chapter then looks at the situation in which there are two equations and two unknowns. It considers the process of solving simultaneous linear equations graphically, with algebra, with negative coefficients, with factors, and with generalized equations.
Powers I
Authors: Monk Paul , Munro Lindsey J.
Published: September 2023

This chapter explores powers, starting with the basic nomenclature relating to base, power, index, and exponent. The number on the power tells us the number of times the base has been multiplied by itself. However, it is difficult to visualize the power if it is not an integer. The chapter then looks at negative indices. A negative index indicates a fraction, while a larger index equates to a smaller number. The chapter also considers the special cases of the indices of one and zero. Anything expressed with a power of one is the thing itself, while anything expressed with a power of zero has a value of one. Finally, the chapter explains the algebra of indices — detailing the first, second, and third law of powers — before examining fractional indices and roots.
Powers II
Authors: Monk Paul , Munro Lindsey J.
Published: September 2023

This chapter studies exponential functions and logarithms. Mathematically, one of the simplest exponential equations is y = ax where a is a constant, x is the controlled variable, and y is the observed variable. The chapter then looks at exponential graphs, which follow general shapes called growth or decay. The crucial difference between these two types of graphs is the sign of the argument and the sign before the exponential. The chapter also considers logarithms as the inverse of exponential functions and in bases other than e. It explains the laws of logarithms, the relationship between ln and log, and numerical calculations with logarithms. Multiplication and division problems are simplified when using the first and second laws of logarithms, respectively. Meanwhile, the third law of logarithms allows for a simple, alternative approach to calculate roots.
Differentiation I
Authors: Monk Paul , Munro Lindsey J.
Published: September 2023

This chapter provides an introduction to differentiation, defining tangents, chords, and gradients of curves. A gradient is a rate of change. The term ‘rate of change’ means that an observed variable changes in response to our changing a different, controlled variable. A positive gradient means the line goes up the page as we move from left to right, while a negative gradient means the line goes down the page as we move from left to right. When we determine the gradient of a curve, we first draw a tangent. A tangent is defined as a straight line that touches the curve at a single point and never crosses it. The chapter then looks at the process of differentiation from first principles and by rule.
Differentiation V
Authors: Monk Paul , Munro Lindsey J.
Published: September 2023

This chapter begins by examining higher-order differentials. We differentiate a derivative to obtain a rate of a rate. The first derivative tells us the gradient which is itself a rate, while the second derivative tells us the rate at which the gradient itself changes. We obtain the second derivative of a function by differentiating twice; we obtain higher-order derivatives by differentiating a function repeatedly. The chapter then considers turning points, looking at maxima, minima, and inflections. If a graph has an inflection, the gradient at the turning point does not change sign, but merely decreases to zero then increases again. The chapter finally explains the process of determining the coordinates of a turning point and using a second derivative to find a turning point.
Matrices I
Authors: Monk Paul , Munro Lindsey J.
Published: September 2023

This chapter explores matrices, which are rectangular collections of data that obey the rules of mathematics called matrix algebra. A matrix is a way of presenting a large amount of information in a small amount of space. Matrices are particularly useful in quantum mechanics and are readily compatible with modern electronic computational devices. The chapter then looks at the process of adding, subtracting, and multiplying matrices. Adding and subtracting matrices requires that the matrices have the same order. Meanwhile, multiplying a matrix with a simple factor involves multiplying each element in turn by the factor. The chapter also considers the determinant, eigenvalues, transpose, and inverse of a matrix. Finally, it discusses the process of using matrices to solve simultaneous linear equation.
Statistics I
Authors: Monk Paul , Munro Lindsey J.
Published: September 2023

This chapter addresses averages and simple data analysis. Physical scientists deal with three different kinds of data: nominal, ordinal, and scale data. Statistics analyses only scale data. The chapter then explains the concepts of a data distribution. Many examples in chemistry follow a normal distribution with data grouping symmetrically round a central value with no bias toward the left or to the right. One of the simplest ways of obtaining a final result is to take the average of the data in a series. The word ‘average’ can mean one of three distinct types of calculation: the mean, the mode, or the median. Finally, the chapter considers sample size, the standard deviation, and the Q-test.
Statistics IV
Authors: Monk Paul , Munro Lindsey J.
Published: September 2023

This chapter studies variance testing with two or more nominal variables, introducing the statistical tool of ANOVA. We can employ ANOVA in three conceptual ways. These are called one-way ANOVA, two-way ANOVA, and N-way ANOVA. We use one-way ANOVA when we want to test three or more groups to see if there is a difference between them. The two-way ANOVA extends the one-way approach and analyses situations that are more complicated and can only be defined with two independent variables. An N-way ANOVA is the obvious extension of the two-way ANOVA but looks at the influence of N independent nominal variables on the measured variable. The chapter then looks at one-way ANOVA analysis using F-tests, as well as omnibus ANOVA tests.
Histopathology reporting
Authors: Orchard Guy , Ward Chris , Pritchard Susan
Published: September 2023

This chapter discusses the process and content of a histopathology report, including the supplementary report. As well as containing all the patient demographical information, the report is divided into specific sections. A histopathology report is a verified document that contains a diagnosis, which is determined following the examination of cells, tissues, and sometimes foreign or infectious agents under the microscope. The chapter then looks at the key microscopic observations seen in the two key areas of histopathology – inflammation and cancer. It highlights the use of diagnostic datasets and the role of tissue pathways in histopathology, as well as the value of molecular/genetic information in histopathology reports.
Patterns in the Marine Environment
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 major patterns in marine organisms and their biology. Doing so gives a strong insight into the processes that determine success and evolution of life on Earth. The chapter shows how the wide expanse of the oceanscape changes dramatically, from undersea mountain ranges to sediment plains and coral reefs to forests of kelp. Patterns of organisms, so obvious at the shore, are also evident from the poles to the tropics, from coasts to ocean centres, from the shallows to the deep abyss, and from millions of years ago to the present day. Patterns occur in species richness, abundance, ancientness, or size, all of which are indicators of powerful changes on the planet surface over time and space. Oceans have widened or been compressed, risen and fallen, heated and cooled, and remain dynamic as a habitat for life.
Marine Microbial Secondary Production
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 how oceanic microbes play a dominant role in cycling of matter and energy in the ocean and introduces the key organism groups in marine microbial food webs. The viruses, bacteria, and archaea that comprise the microbial community are introduced, together with a discussion of their relative abundances and interactions with other organisms. The latest techniques to measure the abundance, diversity, and activity of micro-organisms in the oceans are discussed. The origins, production, and composition of dissolved and particulate organic matter fuelling microbial production and basic metabolic processes are also explored. The ecological context into which these micro-organisms are embedded is developed, leading to a final discussion of the seasonal cycle of production and consumption in temperate waters, as well as the roles of marine microbes in the global carbon cycle and climate system.
Conservation
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 highlights the development and drivers of marine conservation; the ways in which conservation issues are identified and prioritized; and some of the ways in which marine conservation has sought to find a way to accommodate the short-term needs, aspirations, and expectations of humans. It also describes how conservation policy is developed and implemented, and gives some examples of successes and failures of conservation initiatives. In dealing with issues of conservation and sustainable development, the marine ecologist enters a wide arena, where practice and policy are swayed by ethical, cultural, political, social, and economic values. But this is also a challenging and rewarding arena, where science can play a role in making a difference to the future state of the seas and oceans as well as to the people depending on them. As the chapter shows, practicing marine scientists can contribute to conservation and management in various ways.
Sea and Society
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 deals with how humans function within marine ecosystems. Humans harvest a wide range of marine renewable and non-renewable resources, and the ocean is a recipient of the products of human activities on land. Understanding the value of marine ecosystems to mankind both in pure economic terms and in terms of the services provided is important in evaluating how best to manage human activities so that the provision of marine goods and services is maintained or enhanced. Economic approaches have provided a better understanding of fisher behaviour and show how smart incentives can be used to reduce environmental impacts while maintaining food production. Consumer buying-power is used to reward more sustainable behaviour through ecolabelling of seafood products. People are better informed about the importance of the marine environment than ever before, and this has stimulated engagement with citizen science projects run through social media and mobile platform technologies.
The perfect gas
Authors: Atkins Peter , Paula Julio de , Smith David
Published: September 2023

This chapter discusses the ‘perfect gas’, which is an idealized version of a gas. Its equation of state may be assembled from the experimental observations summarized by Boyle's law, Charles's law, and Avogadro's principle. Boyle's law implies that if a fixed amount of gas is compressed (that is, its volume is reduced) at constant temperature into half its original volume, then its pressure will double. Meanwhile, Charles's law states that at constant pressure, the volume of a fixed amount of gas is proportional to the absolute temperature. Finally, according to Avogadro's principle, at a given temperature and pressure, equal volumes of gas contain the same numbers of molecules. The chapter then looks at two elementary applications of the perfect gas equation of state, before considering Dalton's law.
Standard potentials
Authors: Atkins Peter , Paula Julio de , Smith David
Published: September 2023

This chapter examines standard potentials. Although the contribution of a single electrode to the potential difference cannot be measured absolutely, a scheme can be devised for establishing the contributions relative to a standard. These standard potentials are of great importance for predicting equilibrium constants, for discussing the ability of one species to reduce another, for the determination of pH, and for the determination of thermodynamic data. The standard potential of a couple is the standard cell potential in which it forms the right-hand electrode and a hydrogen electrode is on the left. The chapter then looks at the electrochemical series, which is a table of relative reducing powers of couples.
Reactions in solution
Authors: Atkins Peter , Paula Julio de , Smith David
Published: September 2023

This chapter explains that most chemical reactions take place in solution, and so it is important to understand what controls their rates. The concept of the rate-determining step plays an important role for reactions in solution where it leads to the distinction between ‘diffusion control’ and ‘activation control’. In the diffusion-controlled limit, the condition for the encounter rate to be rate-determining is not that it is the slowest step, but that the reaction rate of the encounter pair is much greater than the rate at which the pair breaks up without reacting. In the activation-controlled limit, the condition for the rate of energy accumulation to be rate-determining is a competition between the rate of reaction of the pair and the rate at which the pair breaks up, and all three rate constants control the overall rate. The chapter then looks at Fick's first law of diffusion and Fick's second law of diffusion.
Homogeneous catalysis
Authors: Atkins Peter , Paula Julio de , Smith David
Published: September 2023

This chapter explores homogeneous catalysis. A catalyst lowers the activation energy of a reaction, thereby accelerating it, by providing an alternative path that avoids the slow, rate-determining step of the uncatalysed reaction. A homogeneous catalyst is a catalyst in the same phase as the reaction mixture. Enzymes are very selective homogeneous catalysts that regulate the rates of biological processes. One of the earliest descriptions of the action of enzymes is the Michaelis–Menten mechanism. The chapter then considers how an inhibitor supresses the action of an enzyme. In competitive inhibition, the inhibitor competes for the active site and reduces the ability of the enzyme to bind the substrate. In non-competitive inhibition, the inhibitor attaches to another part of the enzyme molecule, thereby distorting it and reducing its ability to bind the substrate.
Heterogeneous catalysis
Authors: Atkins Peter , Paula Julio de , Smith David
Published: September 2023

This chapter studies heterogeneous catalysis, in which the catalyst and the reagents are in different phases. A common example is a solid that increases the rate of a gas-phase reaction. The solid provides a surface to which the reactants bind and so facilitates encounters between reactants. In general, heterogeneous catalysts are highly selective and to find an appropriate catalyst each reaction must be investigated individually. Two techniques have revolutionized the study of surfaces in recent years: scanning tunnelling microscopy (STM) and atomic force microscopy (AFM). Ultimately, the key to the operation of a heterogeneous catalyst is the attachment of molecules to a surface by the process called adsorption. The chapter then differentiates between physisorption and chemisorption, before looking at adsorption isotherms. It also considers the mechanisms of surface-catalysed reactions, including the Langmuir–Hinshelwood mechanism and the Eley–Rideal mechanism.
The dynamics of microscopic systems
Authors: Atkins Peter , Paula Julio de , Smith David
Published: September 2023

This chapter discusses the central concepts and equations of quantum theory which demonstrates how particles spread through space like waves and are described mathematically by a wavefunction. It examines how the wavefunction is interpreted and introduces the uncertainty principle, which is one of the most profound departures of quantum mechanics from classical mechanics. It also highlights the dynamical properties of a system that are contained in the wavefunction and are obtained by solving the Schrödinger equation. The chapter reconciles the facts that atoms and molecules can possess only certain energies, that waves exhibit the properties of particles, and that particles exhibit the properties of waves. It reviews the classical concept that have been accommodated by the development of quantum mechanics, in which equations are set up to treat a particle as spread through space like a wave.
Vibration
Authors: Atkins Peter , Paula Julio de , Smith David
Published: September 2023

This chapter introduces the harmonic oscillator, which is a simple but very important model for the description of molecular vibrations. It shows how energies of vibration are restricted to certain values and covers acceptable wavefunctions that show that the oscillator may be found at extensions and compressions that are forbidden by classical physics. It also talks about the energy of a harmonic oscillator which is quantized and may be found at extensions not allowed classically. The chapter considers vibration as a very important type of motion of a molecule when bonds stretch, compress, and bend. It highlights polyatomic molecules with more than one mode of vibration and explores the consequences of the vibration not being harmonic.
The origin of thermodynamic properties
Authors: Atkins Peter , Paula Julio de , Smith David
Published: September 2023

This chapter shows how the molecular partition function is used to calculate and give insight into important thermodynamic functions: internal energy, heat capacity, entropy, and Gibbs energy. It talks about the final step into the calculations of chemically significant expressions when the Gibbs energy is available that shows how equilibrium constants can be calculated from structural and spectroscopic data. It also provides a molecular interpretation of thermodynamic properties that acts as a bridge between spectroscopy and thermodynamics. The chapter reviews how a partition function is used to calculate and interpret thermodynamic properties of systems as small as atoms and as large as biopolymers. It highlights the equilibrium constant, which is related to the distribution of molecules over the available states of a system composed of reactants and products.
Where do I begin?
Authors: Holmes Debbie , Moody Peter , Dine Diana , Trueman Laurence
Published: September 2023

This chapter provides the basic tools to begin research and explains some of the terms we need to be familiar with when designing or reviewing experimental work. First, it discusses how we define an aim and at least one objective. Next comes the decision on what is being measured and whether these measurements (observations) are being collected from the statistical population or a sample. Finally, the chapter argues that we must decide if the data can be analysed by testing hypotheses. There are two main approaches to analysing data. The first is to choose a null hypothesis to test the data against. The other option is to analyse the data to see which of a number of alternative models best fits it (information-theoretic approach).
Selection
Authors: Bromham Lindell
Published: September 2023

This chapter assesses the process of natural selection. The study of heritable variation has provided the building blocks of evolutionary theory. Charles Darwin showed that variation was ubiquitous, and he proposed that cumulative selection of small variants could lead to the formation of phenotypically distinct populations. If some of the heritable variation ever present in populations confers any increased chance of successful reproduction, then, over many generations, we expect those variations to increase in representation in the population. But while the basic process of selection is wonderfully simple, the outcomes of selection plays are complicated by many influences, including the environment, population composition, genetic background, and linkage between alleles. These complicating factors can make fitness of single alleles far from simple to assess. However, not all changes in allele frequencies in populations are driven by selection.
Phylogeny
Authors: Bromham Lindell
Published: September 2023

This chapter studies phylogeny. As populations divide and diverge, their DNA sequences become increasingly different from each other. DNA sequences sampled at the end point of this process carry the historical signal of population divergence. We can use alignments of DNA sequences to draw evolutionary trees that display the similarities between related lineages and the paths of descent of species. Sometimes the patterns in the sequences reveal a hierarchical history of populations dividing again and again. Because of this, we can use patterns of differences between DNA sequences from contemporary populations to reconstruct their evolutionary history. But sometimes the patterns are more complicated, if the historical signal has been erased, or when previously distinct lineages join back together through hybridization or gene transfer. One can represent many different histories in a network diagram.
What is physiology?
Authors: Pocock Gillian , Richards Christopher D. , Richards David A.
Published: September 2023

This chapter emphasizes the importance of having a sound knowledge of the structure and function of the body for anyone concerned with medicine or the health sciences. Such a knowledge provides a foundation on which to build strategies for diagnosis, treatment, and prevention of disease. It introduces physiology, which is the study of the functions of living matter and is concerned with how an organism performs its varied activities. The success of physiology in explaining how organisms perform their daily tasks is based on the notion that organisms are intricate and exquisite machines whose operation is governed by the laws of physics and chemistry. The chapter outlines how a full knowledge of human anatomy requires the examination of the human body. This is complemented by modern imaging techniques such as magnetic resonance imaging (MRI), which can visualize the internal structures of the body in life.
The adrenal glands
Authors: Pocock Gillian , Richards Christopher D. , Richards David A.
Published: September 2023

This chapter looks at adrenal glands. These have distinct endocrine functions. For example, the adrenal medulla secretes the catecholamines adrenaline and noradrenaline in response to activation of its sympathetic nerve supply. The chapter looks at how the adrenal medulla acts as part of the sympathetic nervous system. Its hormones are concerned with the body's very rapid responses to acute stress. The adrenal cortex secretes three classes of steroid hormones: glucocorticoid hormones, mineralocorticoid hormones, and sex steroids. The chapter refers to cortisol, the principal glucocorticoid, which has a wide range of metabolic effects, while aldosterone, the principal mineralocorticoid, is crucial to the maintenance of normal body fluid volume and composition. The chapter looks at the important actions of the catecholamines and the adrenal corticosteroid hormones.
Introduction to the cardiovascular system
Authors: Pocock Gillian , Richards Christopher D. , Richards David A.
Published: September 2023

This chapter considers the exchange of nutrients and waste products between the cells and the environment of unicellular organisms and simple animals. Examples include sponges. These can be accomplished by simple diffusion across the cell membranes. The chapter cites diffusion as a random process in three dimensions, the time required for equilibration increases rapidly with increasing distance. In more complex animals, diffusion of nutrients by itself would not suffice to permit adequate exchange of nutrients and waste products, as most cells are separated from the external environment by a considerable distance. The chapter describes the organization of the circulation, its gross anatomy, the structure of the blood vessels, and their innervation. One of the primary functions of the circulatory system is to promote the carriage of oxygen and nutrients to the cells and remove the products of metabolism.
The electrocardiogram
Authors: Pocock Gillian , Richards Christopher D. , Richards David A.
Published: September 2023

This chapter discusses the initiation of the heartbeat which begins with the pacemaker activity of the sinoatrial (SA) node. It demonstrates how a heartbeat spreads across the heart from the right atrium to the left before passing to the ventricles by way of the atrioventricular (AV) node and the bundle of its left and right branches. Since the cardiac myocytes form a syncytium, an electrical disturbance in one region can spread across the whole heart in much the same way as the conduction of the action potential in unmyelinated nerve fibres. The chapter examines how the heart remain depolarized as the wave of excitation proceeds, while other regions are polarized and at rest. Local electrical circuits are established between these regions which permit the flow of small currents through the extracellular fluid.
The physiology of exercise
Authors: Pocock Gillian , Richards Christopher D. , Richards David A.
Published: September 2023

This chapter reviews the interactions between the physiology of the endocrine, circulatory, and respiratory systems in the performance of everyday physical activity as the whole body responds to the stress of exercise. It explores how much energy is expended for different intensities of exercise and what is the source of that energy. It also talks about how the cardiovascular and respiratory systems are adjusted to meet the demands of exercise, and how far performance can be improved by training. The chapter looks at the intensity of exercise that varies from the very mild, such as a gentle stroll, to very severe, such as that encountered in sprinting and other athletic pursuits. It is a matter of everyday experience that the ability to sustain physical activity depends on its intensity.
Acid–base balance
Authors: Pocock Gillian , Richards Christopher D. , Richards David A.
Published: September 2023

This chapter explains how the body continually produces CO2 and non-volatile acids as a result of metabolic activity. The chapter refers to the blood hydrogen ion concentration [H+] which is normally maintained within the relatively narrow range of 40-45 nmol of free hydrogen ions per litre. This corresponds to a blood pH between 7.35 and 7.4, and the extreme limits that are generally held to be compatible with life range from pH 6.8 to pH 7.7. The chapter talks about hydrogen ions which are absorbed by other molecules in a process known as buffering, and acid products are subsequently eliminated from the body via the lungs and kidneys. The concept of acid-base balance refers to the processes that maintain the hydrogen ion concentration of the body fluids within its normal limits.
The skin and thermoregulation
Authors: Pocock Gillian , Richards Christopher D. , Richards David A.
Published: September 2023

This chapter focuses on the skin, which is the largest organ in the body, covering the entire outer surface of the body. Together with the hair, nails, and glands, the skin forms an integumentary system. The chapter points out that the thickest skin is found in areas that are subject to abrasion such as the soles of the feet, while the thinnest is found around the eyes. The chapter looks at how a great deal of useful information regarding a person's age, nutritional status, hydration status, circulation, and emotional state can be obtained by careful inspection of the skin. Furthermore, the characteristics and colour of a person's skin can sometimes yield information regarding certain disease states, particularly in those whose skin is pale.
Introduction to the gastrointestinal system
Authors: Pocock Gillian , Richards Christopher D. , Richards David A.
Published: September 2023

This chapter describes the gross anatomical organization of the gastrointestinal system, the internal structure of the gut wall, and its blood supply. It provides an overview of the nervous and hormonal mechanisms that regulate the motility and secretory activity of the gut. It also presents a detailed examination of the structure and functions of the mouth and oesophagus, the stomach, and the small and large intestine, together with the digestive functions of the pancreas. The chapter outlines key aspects of nutrition and energy balance, noting how food is required by the body both for the production of energy and for the growth and repair of tissues. Each day an average adult consumes around 1 kg of solid food and 1-2 litres of fluid. The majority of this material is in a form that first must be broken down into simple molecules.
The physiology of the male and female reproductive systems
Authors: Pocock Gillian , Richards Christopher D. , Richards David A.
Published: September 2023

This chapter discusses reproduction, which is the ability to produce a new generation of individuals of the same species. It explains how genetic material is transmitted from parents to their offspring to ensure that the characteristics of the species are perpetuated. The essential feature of sexual reproduction is the recombination of chromosomes from two separate individuals to produce offspring that differ genetically from their parents. The chapter explores the creation and fusion of the male and female gametes: the spermatozoa (sperm) and ova (eggs). Gametes are specialized sex cells produced by the gonads that provide a link between one generation and the next.
Neuronal control of motor output
Authors: Zupanc Günther K. H.
Published: September 2023

This chapter looks at different model systems that try to explain how coordinated contractions of muscles are controlled at the neural level. These muscle activities are associated with simple reflexes and rhythmic behaviors that often persist over long periods. The chapter reviews the model proposed by Charles Scott at the beginning of the twentieth century, which states that such coordinated activities are the result of a chain of reflexes, coordinated by proprioceptive information, in the spinal cord. The discussion also covers another major model proposed by Thomas Graham Brown, which assumes the existence of an intrinsic oscillator in the spinal cord that drives the coordinated activity of the muscles. Furthermore, the chapter tackles in detail the escape swimming behavior of Xenopus tadpoles relevant to the study of neural mechanisms involved in generating locomotor behavior.
Cellular mechanisms of learning and memory
Authors: Zupanc Günther K. H.
Published: September 2023

This chapter focuses on the cellular mechanisms that underlie the memory stage. It explains amnesia, or the disturbance in long-term memory, manifested by total or partial inability to recall past experiences. The discussion distinguishes between anterograde amnesia and retrograde amnesia. The chapter then describes the two types of memory: explicit and implicit memories. It tackles the sensitization in the marine mollusk Aplysia as a model system to explain the cell biology of an implicit memory system. It discusses the neural circuit of the gill-withdrawal reflex and the molecular biology of both short-term and long-term sensitization. Furthermore, the chapter zooms in on the hippocampus of mammals and birds as a model to study the cell biology of an explicit memory system — explaining the concepts of long-term potentiation and adult neurogenesis.
Drug Synthesis
Authors: Rostron Chris
Published: September 2023

This chapter assesses drug synthesis, which has become an integral component, not only of drug development, but also of drug design. Key to any synthetic method is the nature of the starting materials. Wherever possible, a balance must be achieved between the availability and cost of starting materials and the relative probability of them giving rise to the required final product. In addition to the starting materials, the nature of the chemical reactions involved in the synthetic pathway need to be taken into consideration. The chapter examines the design of drug synthetic pathways, diversity-oriented synthesis, and protecting groups. It also looks at chiral synthesis, partial synthesis of xenobiotics (semi-synthetic drugs), and genetically engineered synthesis.
Optimization of Lead Compounds
Authors: Rostron Chris
Published: September 2023

This chapter addresses the optimization of lead compounds. Once a lead compound has been identified, from whatever source, the next step in the drug design and development process is the optimization of this lead compound. There are two main aspects to this optimization process: improvement in the interaction of the molecule with the appropriate drug target (pharmacodynamics) and improvement in the ability of the molecule to be available to that target (pharmacokinetics). These two processes are carried out simultaneously because it would be pointless identifying a molecule that is highly active at the target only to find that it cannot be absorbed or is very rapidly metabolized. During this improvement process, in vitro (and possibly in vivo) testing will continue on any molecules so produced in order to further inform the optimization process.