bluuebunny/crossref_metadata_2025 huggingface dataset:
Introduction
Authors: Lesk Arthur M.
Published: September 2023

This introductory chapter presents the major components of bioinformatics: DNA and protein sequences and structures, genomes and proteomes, databases and information retrieval, the World Wide Web, and computer programming. Before the advent of modern technologies and the internet, biological observations were fundamentally anecdotal and fragmentary. In recent generations, the data have become not only much more quantitative, but also more precise and comprehensive. Biological databases have recently supplemented the archives of nucleic acid sequences, amino acid sequences of proteins, and structures of proteins and protein–nucleic acid complexes. Given the data streams, analysis has become ever more challenging. Not only has bioinformatics developed powerful tools, but its methods are becoming more deeply integrated into the biomedical enterprise.
Artificial intelligence and machine learning
Authors: Lesk Arthur M.
Published: September 2023

This chapter addresses the topics of artificial intelligence and machine learning. The idea of artificial intelligence is that a computer is doing something that, at least casually, can be regarded as ‘thinking’. However, the sophistication of the program might be a translation of some aspect of the intelligence of the programmer. Machine learning goes beyond this; for machine learning, the program has to take the initiative to improve the performance of the algorithm. The chapter then looks at the difference between classification and clustering, as well as between supervised learning and unsupervised learning. The Receiver Operating Characteristic (ROC) curves reveal how the quality of a prediction depends on the choice of separation threshold. The chapter also considers the structure and activity of artificial neurons, and how they can be combined into artificial neural networks; decision trees; and support vector machines.
Vertebrate development I: life cycles and experimental techniques
Authors: Wolpert Lewis , Tickle Cheryll , Arias Alfonso Martinez , Lawrence Peter , Locke James
Published: September 2023

This chapter explores similarities and differences in the development of frogs, birds, fish, and mammals. It also looks into experimental approaches which investigate vertebrate development using Xenopus, zebrafish, chick, and mouse as models. The chapter refers here to transgenic techniques which are used to produce mutations with specific genes as an example. Additionally, the chapter notes how all vertebrates have a similar basic body plan with defining structures such as the spinal cord and skull. It shows the similarity between a mouse and a human in terms of early development. The chapter also links approaches used in investigating human embryonic development. Techniques for interfering with development can be broadly divided between experimental embryological techniques and genetics-based techniques.
Why am I reading this book?
Authors: Hawkins Dawn
Published: September 2023

This chapter provides an overview of the skills required in handling bioscience data. The answers to many questions in the biosciences require a simple description of the natural world—these are called descriptive questions. Getting answers to descriptive questions is the first of two rounds of the scientific process in which the data handling and analysis techniques introduced in this book are used. The answers to descriptive questions will frequently lead us to ask further questions. Scientists then go through a particular series of stages called the hypothetico-deductive approach to answer questions about a cause, mechanism, or function. The first stage of this approach is to generate a research hypothesis. The chapter then differentiates between the two main categories of statistical technique: descriptive statistics and inferential statistics. Descriptive statistics are used to organize, summarize, and describe data while inferential statistics are used to assess patterns in data.
Getting to grips with the basics
Authors: Hawkins Dawn
Published: September 2023

This chapter presents an introduction to key ideas in understanding, performing, and communicating data analyses in biosciences. A population is the entire set of observations relevant to a research question. Since it is usually impractical or impossible to take records from every item in a population, scientists normally work with a subset of observations, known as a sample. The chapter then explains the sampling process, looking at three important issues associated with this process: sample size, pseudoreplication, and bias. It also studies variation and variables, differentiating between dependent and independent variables. A variable is a characteristic that varies between items in a sample while a constant is a characteristic that does not vary between items in a sample. Finally, the chapter considers the process of understanding the relatedness of data and levels of measurement, as well as statistical formulae.
Overview of null hypothesis significance testing
Authors: Hawkins Dawn
Published: September 2023

This chapter assesses the concepts and procedures common to all statistical tests within null hypothesis significance testing (NHST). In brief, NHST is a procedure used to make a decision about whether chance alone can account for apparent patterns in the data. There are four steps to follow when conducting a statistical test: firstly, construct a (statistical) null hypothesis; secondly, choose a critical significance level; thirdly, calculate a statistic; and, finally, reject or accept the (statistical) null hypothesis. The chapter then compares parametric and nonparametric statistics and one- and two-tailed tests. It also introduces effect size and the difference between statistical and biological significance. Finally, the chapter explains the types of error (I and II) and power in NHST before offering guidance on interpreting the results of NHST.
Tests of difference: two unrelated samples
Authors: Hawkins Dawn
Published: September 2023

This chapter addresses tests of difference on two samples of unrelated data, considering the parametric t-test and the nonparametric Mann—Whitney U test. Neither the t-test nor the Mann—Whitney U test work if the data in the samples are measured at a nominal-level. The minimum level of measurement needed for the dependent variable is ordinal for a Mann—Whitney U test and scale for a t-test. The independent variable can be measured at any level provided that it only distinguishes two categories. Both the t-test and the Mann—Whitney U test are used to look for differences between two samples. The chapter offers guidance on what sample sizes to use when planning to collect data for use in these tests; demonstrates how to perform each test by hand and with SPSS using real data sets; and illustrates how to identify and report the key results of both tests.
More on the generalized linear model: logistic and loglinear models
Authors: Hawkins Dawn
Published: September 2023

This chapter discusses sub-frameworks of the generalized linear model (GLZM) which can be used for nominal-level data with two categories (binary logistic model) and scale data in the form of counts (loglinear model). It examines how they can be used to assess the relative effects of multiple explanatory (independent) variables on a single response (dependent) variable. The binary logistic model uses the binomial distribution while the loglinear model uses the Poisson distribution and is useful if the response variable is count data. For explanatory variables, it is the same for the binary logistic and loglinear models as it was for the general linear model: one can have one or more categorical or continuous explanatory variable(s), or indeed a mixture. The chapter then demonstrates how to perform both analyses with SPSS using real data sets, and illustrates how to identify and report the key results of both analyses.
Identifying and classifying mutants
Authors: Meneely Philip
Published: September 2023

This chapter explains the process of genetic analysis beginning with a mutant phenotype. It looks at finding the mutation, characterizing the phenotype of the mutation, assigning mutations to genes via complementation tests, and classifying the defect in each mutation depending on its effect on the function. The chapter acknowledges that the overall process depends on the organism and its mutant phenotypes. The chapter clarifies the laboratory procedure of mutant analysis and shows that this is rarely a linear process. It looks into the genetic selections being used to search for mutagenized strains. It highlights the importance of mapping genes amongst mutations. The chapter points out that the assignment of mutants to genes helps us to understand genetic activities as they contribute to the biological processes.
Handling quantities: mass, volume, and concentration
Authors: Blann Andrew D.
Published: September 2023

This chapter highlights important aspects of chemistry central to biomedical science practice, such as the Système International (SI) convention. It describes the structure of the atom and key features of the periodic table. It also reviews the concepts of atomic number, atomic mass, acids, bases, and buffers, including the determination of the mole and molarity. The chapter introduces tools in the field of chemistry that are used for measuring and characterizing different substances. These have central importance to laboratory-based diagnosis. Finally, it discusses electrophoresis, ion-specific electrodes, colorimetry, and high-performance liquid chromatography.
Quality, audit, and good laboratory practice
Authors: Blann Andrew D.
Published: September 2023

This chapter outlines important aspects of the laboratory, including how to ensure that the quality of the product and results of the laboratory are correct. It considers why laboratory procedures are constantly being checked as being fit for purpose and audit. It also clarifies the need for formal data analysis and explains why audit is a continuous process, covering the key features of horizontal audit, vertical audit, and self-audit. The chapter details a set of criteria that ensure the efficient performance of a laboratory and its staff so that it runs at a particularly high quality. It talks about standard operating procedures (SOP) as the crucial part of good laboratory practice as this provides written instructions that ensure that staff carry out complex and routine operations that guarantee the quality of the result.
Research 1: Setting the scene
Authors: Blann Andrew D.
Published: September 2023

This chapter highlights two types of research: one that extends the knowledge of the pathophysiology of human disease and the other that improves patient outcome which is typically called clinical research. It reviews important concepts in both types of research and the different forms that a hypothesis may take. It shows how to determine the sample size and also explains probability, which is the major feature of statistics, and describes basic research design for clinical and laboratory purposes. The chapter details how research is designed and the permissions/approvals that are required. It emphasizes the need for high standards of care in data collection and transfer to a spreadsheet.
Research 3: Large data sets
Authors: Blann Andrew D.
Published: September 2023

This chapter focuses on the testing of complex hypotheses with an increased sample size of hundreds of data points. Situations such as these require more complicated methods, such as multivariate regression analysis. It looks at situations where the index of interest has a continuous variation, and linear analysis is used. It also refers to the index of interest which has a categorical distribution and requires logistic analysis. The chapter discusses certain studies that are designed to answer important questions regarding health care, which often call for analyses over a long period of time, such as the monitoring of the outcome of a group of patients randomized to different treatments. It explores the realm of epidemiology, which is the study of patterns of health and disease within large populations. This sort of study often comprises of hundreds thousands of people.
Climate Change
Authors: Behrens Paul , Niles Meredith T.
Published: September 2023

This chapter discusses how the human food systems contributes to climate change and some solutions to reduce its impact. The discussion starts with an explanation of the climate processes, reviewing the concepts of the greenhouse effect, the carbon cycle, and the global warming potential. Then it looks at how humans are impacting these processes, resulting in anthropogenic climate change. The chapter explains that the presence of extra greenhouse gases in the atmosphere results in the trapping of more energy (in the form of heat) in the Earth's different systems, predominantly the oceans and the atmosphere. This, in turn, results in changes in our climate, including more extreme weather events such as droughts, floods, hurricanes, and fires. Furthermore, the chapter presents case studies to show how complicated some food choices are. Lastly, it tackles how climate change will impact food systems as the environment changes.
Collective Action
Authors: Ehrhardt David , Bosker Thijs , Archambault Caroline
Published: September 2023

This chapter discusses how collective action problems hinder the transition to sustainable food systems. It explains the concept of competing incentives, cost-benefit analysis, and bounded rationality. It also differentiates between private goods, club goods, public goods, and common goods. This classification of goods is used as an important piece in the puzzle of collective action problems in food sustainability. The chapter introduces the tragedy of the commons, which describes the general human tendency to abuse non-excludable goods and presents different social-scientific models to explain it: the discrepancy between individual costs and collective benefits, the problem of free-riding, and the model of the prisoner's dilemma. Furthermore, the discussion covers Ostrom's eight principles for community-based natural resource management. Finally, the chapter outlines a range of institutionalist solutions to collective action problems.
A pantheon of pathogens 1: Bacteria, fungi, and viruses
Authors: Fullick William
Published: September 2023

This chapter discusses three types of pathogens: bacteria, fungi, and viruses. Bacteria may be grouped taxonomically, or according to shape, oxygen dependence, or staining. Many bacteria do not cause infectious diseases in humans; those which do cause disease may lead to mild, localized infections or severe, life-threatening ones. Meanwhile, fungi are grouped taxonomically. They rarely cause infections in humans with functioning immune systems, but can take advantage of individuals with lowered immunity to cause severe symptoms of disease. Finally, viruses have a variety of methods for infiltrating their host's cells, but cannot reproduce without using the organelles within these cells, making them obligate parasites. They will often damage or destroy the cell once they have replicated. Viruses tend to be classified either using classical taxonomic methods or by the Baltimore classification.
Haemopoiesis and the bone marrow
Authors: Blann Andrew
Published: September 2023

This chapter outlines the origin and development of blood cells, which is the process of haemopoiesis. It explains that haemopoiesis is the regulated development of blood cells as they progress from being precursor stem cells in the bone marrow to fully functioning mature cells found in the blood. It also stresses the importance of learning about haemopoiesis as it is the key to understanding several pathological processes, including anaemia, autoimmunity, and leukaemia. The chapter lists the major components of bone marrow and describes the mechanisms of haemopoiesis, including the significance of growth factors. It explores the complex nature of the molecular genetics of blood cell development and the value of the analysis of bone marrow.
Anaemia 2: Haemolysis
Authors: Blann Andrew , Marwah Sukhjinder
Published: September 2023

This chapter focuses on the destruction of red blood cells, called haemolysis. It explains that haemolysis can be classified as an external factor acting on essentially healthy red cells, or as the destruction of red cells with defects of haemoglobin, the cell membrane, or in metabolic enzymes. It lists the different causes of the inappropriate destruction of red blood cells and clarifies the relationship between gene mutation and anaemia. The chapter describes the major features of the haemoglobinopathies and outlines how mutations in genes for membrane components and enzymes can lead to anaemia. It also highlights haemolytic anaemias, which are generally caused by a shortening of the lifespan of the red cell and failure of the bone marrow to be able to compensate for this reduced lifespan.
The laboratory investigation of haematological malignancies
Authors: Knight Gavin
Published: September 2023

This chapter introduces the laboratory investigation of haematological malignancy, which includes being ‘hands on’ in the examination of blood films and other laboratory-generated data. It clarifies how the results of the laboratory investigation have an important bearing on the patient's management as it has a profound impact on patient care. It also recognizes the important role that the haematology laboratory plays in the diagnosis of haematological malignancies as it contributes to patient investigation and diagnosis. The chapter describes some of the most common presenting symptoms associated with malignancies, putting them into a biological and physiological context. It covers a range of molecular biological and cytogenetic investigations essential for the diagnosis and classification of haematological malignancies.
Bleeding disorders and their laboratory investigation
Authors: Moore Gary , Gurney David
Published: September 2023

This chapter covers bleeding disorders that arise from hereditary or acquired abnormalities of coagulation factors, von Willebrand factor (VWF), platelets, and blood vessels. It reviews the main laboratory tests available to biomedical scientists in order to identify and characterize bleeding disorders. It also describes the principles and interpretation of coagulation screening tests, platelet function analysis, factor assays and raw data assessment, and inhibitor screening and measurement. The chapter explains that bleeding disorders occur when components of haemostasis are deficient to an extent that confers a tendency to bleed excessively. It emphasizes how the type, site, and severity of haemorrhage can give important clues to whether a haemostatic disorder is present and the areas of haemostasis that are affected.
Thrombophilia
Authors: Moore Gary , Jennings Ian
Published: September 2023

This chapters defines thrombophilia, looks at the causes, and discusses the methods used to identify the defects that may be involved. It explains that the term thrombophilia literally translates to ‘clot-loving’, which is caused by defects or deficiencies of the anticoagulant system that lead to a predisposition to thrombosis. It also considers thrombophilia as either hereditary or acquired as some defects that are thought to cause the condition are of uncertain aetiology. The chapter talks about the deficiency of the natural anticoagulants antithrombin, protein C, and protein S, which may be the result of a mutation that causes a reduced concentration of the normally functioning protein in the circulation. It defines antithrombin as a naturally occurring inhibitor of several components of the procoagulant system, including thrombin, FIXa, FXa, FXIa, and FVIIa–tissue factor (TF) complex.
Acquired disorders of haemostasis
Authors: Moore Gary
Published: September 2023

This chapter covers non-hereditary causes of bleeding and thrombosis, which are referred to as acquired disorders that arise as a consequence of another primary disorder that may be hereditary or acquired. It names a number of acquired haemostatic disorders and describes their causes. It also discusses how acquired disorders of haemostasis can affect routine coagulation screening tests and how routine and specialist haemostasis assays can be employed to diagnose acquired disorders of haemostasis. The chapter explains that acquired bleeding disorders occur more frequently than inherited forms and are more common in hospitalized patients. It mentions disseminated intravascular coagulation (DIC), which results from excessive activation of coagulation exacerbated by loss of regulatory and localization mechanisms.
Haemostasis and anticoagulation
Authors: Moore Gary , Needham Jane
Published: September 2023

This chapter outlines the reasons for anticoagulant therapy, mode of action and use of therapeutic agents, laboratory assays for monitoring treatment, and associated clinical services for patient care. It highlights the importance of anticoagulant management and associated clinical risks, and it demonstrates how to monitor anticoagulant therapy in the laboratory. It also promotes awareness for hereditary or acquired conditions that can influence treatment outcomes, including interacting drugs and models of clinical services. The chapter outlines the risks associated with having an inherited or acquired thrombophilia defect, medical conditions that can lead to thrombosis, and events or environment that lead to blood stasis. It highlights important differences between causes and treatment for arterial and venous thrombosis.
Fungi and Fungus-like Organisms
Authors: Beales Paul
Published: September 2023

This chapter looks at the fungi and protist kingdoms. These contain a diverse group of organisms and comprise of between 1.5 and 5 million species, although only around 100 000 species have been described. The chapter points out that only 10 per cent of fungi and protists are actually plant pathogens, while the remainder live as saprophytes or in a symbiotic relationship with their host plant. It also explores some of the best-known plant pathogens in the fungi and protist kingdoms. The chapter clarifies that fungi are eukaryotic, heterotrophic organisms that depend upon external organic carbon sources which are broken down by secreted fungal enzymes and absorbed as dissolved molecules by the fungus. It discusses how fungi can't make their own food by photosynthesis as plants do; instead the fungus secretes enzymes that break down and digest other organisms outside of its body.
Analytical chemistry
Authors: Burrows Andrew , Holman John , Lancaster Simon , Overton Tina , Parsons Andrew , Pilling Gwen , Price Gareth
Published: September 2023

This chapter talks about analytical chemistry, which is concerned with determining which substances are in a sample (qualitative analysis) and how much of each substance is present (quantitative analysis). A great deal of interesting and exciting scientific discovery has gone into advancing analytical chemistry and the chapter brings together a number of topics from across all branches of the subject. The chapter describes the chemical principles behind a range of analytical methods and show how they can be used. It lists some of the methods used in analytical chemistry, such as titrations and gravimetric analysis. It deals with instrumental chemical analysis and shows how this covers a wide range of concentrations. It also shows how to calculate the concentrations of analyte solutions given the appropriate calibration data using calibration curves or the standard addition method as appropriate.
Chemical equilibrium
Authors: Burrows Andrew , Holman John , Lancaster Simon , Overton Tina , Parsons Andrew , Pilling Gwen , Price Gareth
Published: September 2023

This chapter talks about a sign of the change in Gibbs energy for a reaction that can be used to predict whether or not the reaction is spontaneous. The size of the Gibbs energy changes allows quantitative predictions about the equilibrium composition of the reaction mixture to be made. The chapter defines and demonstrates how to use the three types of equilibrium constant: Kc, Kp, and the thermodynamic equilibrium constant, including the reaction quotient. It explains how the equilibrium constant and composition change when experimental conditions such as pressure, concentration, and temperature are varied. The application equilibrium thermodynamics to real chemical situations are also covered.
Introducing hormones
Authors: Hinson Joy , Raven Peter
Published: September 2023

This chapter provides an overview of hormones, which constitute a range of different compounds, including peptides and steroids. Oversimplification of information about hormones can lead to some misleading ideas. For example, not all hormones are slow acting as is often assumed. The endocrine and nervous systems are closely connected, and hormones are released by a range of different tissues in the body, not just the 'classical' endocrine organs. Steroid hormones are all made from cholesterol by a process called steroidogenesis, while peptide hormones are made just like any other protein. The effects of hormones are all as a result of the hormone binding to its receptor. These receptors are found in target tissues, and their cellular location depends on the chemical type of hormone. The chapter then looks at negative feedback control, which is the most effective means of regulating blood levels of hormones and their effects.
Periodicity in the properties of s- and p-block atoms
Authors: Norman Nicholas C.
Published: September 2023

This chapter examines the properties of the elements themselves and provides an understanding of the origin of the observed periodic trends. The first, and perhaps most important, point to note is that the p-block is the only part of the periodic table which contains non-metals. Moreover, within the p-block, the metals are found in the bottom left-hand corner while the so-called metalloids or semi-metals lie along a diagonal from top left to bottom right with the non-metals occupying the top right. There is, therefore, a trend from metallic to non-metallic character as we move from bottom left to top right. This pattern correlates precisely with the trend seen for the element electronegativity discussed in the previous chapter. A final point of interest while dealing with the elements themselves concerns the so-called binding energies (or atomization energies), which relate to the magnitude of the interatomic forces which bind the elements together.
Synthetic Biology, Stem Cells, and Regenerative Medicine
Authors: Pollard Steven M.
Published: September 2023

This chapter reviews key features, various sources, and applications of stem cells. It describes the key challenges of differentiating pluripotent stem cells to specific cell and tissue types and explains how synthetic transcription factors can help control stem cell behaviour. It also cites the potential applications of mammalian synthetic biology for new types of tissue repair and regeneration. The chapter discusses how stem cell technologies connect with and use synthetic biology and analyses the various types of stem cell and how the new and emerging toolbox of synthetic biology is unlocking new ways to control and manipulate mammalian stem cells. It demonstrates the new ways experimental tools dissect the molecular processes in controlling cell form and function.
Improving the power of an experiment
Authors: Colegrave Nick , Ruxton Graeme D.
Published: September 2023

This chapter discusses why inherent variation is a challenge to achieving good statistical power and how design decisions can reduce or control the effects of inherent variation. It demonstrates the increase of power by changing the experimental design to increase the strength of the effect that should be detected. It also addresses why increasing sample size increases power and why higher power will be more costly to achieve. The chapter talks about changes to the experiment that increase its power but may incur other costs, which could be felt financially, in terms of increased effort required, or could involve ethical issues. It explores the quantification of power benefits and the costs of different options for an experiment that have a rational basis for choosing the alternative with the most attractive trade-off between power and costs.
How to quantify power by simulation
Authors: Colegrave Nick , Ruxton Graeme D.
Published: September 2023

This chapter focuses on the necessity of being able to make estimates concerning a potential study design to assess its power. It explains how to generate assumptions and convert them into a good estimate of statistical power by conducting a simulation of a potential study in R or in any other programming language. The chapter also shows how to modify one’s approach to compare multiple possible versions of a study to decide which one offers the power that is needed most efficiently. The key aspects involved in estimating power covered in the chapter can be applied to any study. The chapter also introduces basic computational skills which form part of the toolkit that is needed to perform power analyses.
Parasite Genomics
Authors: Chappell Lia , Lindsay Sarah J , Jones Phil , Parkhill Julian , Roberts Jonathan , Holroyd Nancy , Szpak Michal , Gale Francesca
Published: September 2023

This chapter focuses on parasite genomics. Parasitic infections may have beneficial effects on our immune systems, and the possibility that parasites have the potential to deliver previously unrecognized benefits as well as causing devastating harm makes it even more important to understand their biology. Some protozoan parasites, such as malaria and trypanosomes, use antigenic variation to evade destruction by the mammalian immune system. Genetic engineering can be used to manipulate the genomes of parasites and their vectors, and is a novel way to tackle disease transmission. Genomics can also give major insights into the mechanisms behind drug resistance in parasites. However, a limiting factor in parasite genomics is often the availability of parasite material: parasites can be small and live in places that are hard to access. Animal hosts and specialized environments are often needed to keep and study parasites in the lab.
Solving Tomorrow’s Problems with Natural Products
Authors: Bowater Richard , Bowater Laura , Husband Tom
Published: September 2023

This chapter explains what natural products are and assesses their role as primary and secondary metabolites within cells. Natural products are molecules produced by enzymatic reactions that take place in living organisms. The chapter studies how natural products from plants and microbes have become essential components of modern society and looks at the potential of these molecules to address grand societal challenges, such as food security and human disease. It also addresses how scientists have developed technologies to produce large amounts of natural products in the laboratory and to modify them. Biotechnology relies on either the exploitation of biochemical processes, as seen in bioremediation, or the synthesis of a useful end product, such as ethanol. Finally, the chapter considers some of the ethical issues associated with these scientific breakthroughs.
What’s the Evidence?
Authors: Ingram Neil , Andrews Sylvia Hixson , Still Jane
Published: September 2023

This chapter examines the evidence for evolution that we can see through looking at fossils, anatomy, biochemistry, ecological genetics, and genomics. Fossils are the most familiar evidence for evolution since they gave proof of life in the past geological ages. Anatomy studies the structure of living organisms and its comparison to other groups of organisms gives clues to evolutionary relationships. The science of biochemistry depends on the development of tools and techniques that spark new insights into the natural world. Genomics, on the other hand, showcases the formation of species such as DNA. The chapter also gives an overview of developmental biology which capitalizes on the emergence of genomics.
The opioid analgesics
Authors: Patrick Graham L.
Published: September 2023

This chapter starts by desribing morphine extracted from opium and explains why it is known as one of the oldest drugs used in medicine. It considers morphine as a powerful analgesic that has various side effects, the most serious being respiratory depression, tolerance, and dependence. It also analyzes the important binding groups on morphine, such as the phenol, the aromatic ring, and the ionized amine. The chapter explores different analgesic receptors with which morphine interacts. these require the presence of a pharmacophore because of the need for binding groups. The chapter points out how the ability of opioids to cross the blood–brain barrier plays an important role in analgesic activity.
The design and development of aliskiren
Authors: Patrick Graham L.
Published: September 2023

This chapter talks about aliskiren, which is an antihypertensive agent which inhibits the enzyme that catalyses the initial reaction at the start of the renin-angiotensin-aldosterone system (RAAS). It explains how the inhibition of renin has the effect of blocking the RAAS cascade and preventing the production of a potent vasoconstrictor which increases blood pressure called angiotensin II. The chapter investigates the development of aliskiren which covers a substantial research effort spanning from 1972 to 2007. It demonstrates many of the strategies and methods involved in designing an effective therapeutic agent from a peptide lead compound. It also looks at peptidomimetic strategies that were carried out to produce small structures with a low molecular weight and less peptide character.
The Ocean in Motion
Authors: Kent Michael
Published: September 2023

This chapter discusses the water cycle. Seawater is constantly on the move, escaping into the atmosphere to play an essential role in the water cycle. The most obvious signs of water movement in the sea are surface waves driven mainly by the wind. Tides, the rhythmical rise and fall of sea level, are responsible for dramatic variations in conditions to which intertidal organisms have become adapted. The chapter then explains the ocean circulation system, which consists of surface currents and subsurface currents. Surface currents form an interconnecting series of circulating systems called gyres. Meanwhile, subsurface currents are driven mainly by density changes in the seawater to create a thermohaline circulation. The combined movements of the cool subsurface and warm surface currents form the Ocean Conveyor Belt that interconnects all parts of the global ocean.
Seawater Matters
Authors: Kent Michael
Published: September 2023

This chapter examines the importance of seawater. There are two main theories about the origins of seawater—that the Earth might have captured water from asteroids and comets which collided with it—or that the water was released explosively in huge quantities from inside the Earth itself, during a period of intense volcanic activity. Two basic properties that make seawater special are dipolarity and hydrogen bonding. Other special properties of seawater include its high surface tension; its thermal properties, including its high specific heat capacity, latent heat of vaporization, and its freezing properties; its solvent properties; its relatively high density and viscosity compared to pure water; its high compressibility; the increase in its pressure with depth; and its ability to conduct electricity, and transmit sound waves and solar radiation. The chapter then considers the adaptations of marine organisms to living in seawater. These include adaptations to the thermal environment, to salinity variations, to moving and floating in water, to the photic environment, and to diving from the surface into deep waters.
What Does Marine Biodiversity Do for Us?
Authors: Kent Michael
Published: September 2023

This chapter explores how marine biodiversity benefits us all both tangibly and intangibly, considering the concept of ecosystem services. Marine ecosystem services are categorized into four types: supporting services, provisioning services, regulating services, and cultural services. The chapter begins by describing the release of oxygen as a by-product of photosynthesis by marine primary producers. It then considers the sequestration of carbon by marine organisms in relation to climate change; the use of marine model organisms in research to gain insights into the functioning of our own and other species; and the monetary values of goods and services provided by marine biodiversity. Medical products derived from marine organisms show how marine biodiversity benefits physical health. Finally, the chapter focuses on marine ecosystem sentinels, looking at the sperm whale as a prime example of a marine organism that can be used to indicate past and ongoing changes in the global marine ecosystem that might affect human health, before evaluating the benefits of marine biodiversity to human mental health.
What Are We Doing to Marine Biodiversity?
Authors: Kent Michael
Published: September 2023

This chapter identifies current human threats to marine biodiversity, the greatest of which is habitat destruction from activities such as fishing, housing, and industrial development. Habitat destruction is increasing with increases in global human population. Probably the greatest potential threat to marine biodiversity is from anthropogenic climate change. This is linked to ocean warming, ocean deoxygenation, and ocean acidification; ocean warming can lead to coral bleaching and ocean deoxygenation. Climate change is particularly important in slowing down the Atlantic Meridional Overturning Circulation (AMOC). The AMOC is not in imminent danger of stopping, but its slowing down is likely to have significant effects on regional climates and marine biodiversity. Other important threats to marine biodiversity include marine pollution, overfishing, and the introduction of non-native species by human agents. There are many examples of human actions and organizations that help protect marine biodiversity, but well-designed and well-managed Marine Protection Areas are probably the most effective.
Bar charts for qualitative data
Authors: Humphreys Rosalind K. , Ruxton Graeme D.
Published: September 2023

This chapter explains how to use bar charts to express qualitative data or categorical data. Even if bar charts can simultaneously display nominal data and ordinal data, different data types can influence the design of the bar charts themselves. Bar charts are an effective way to display data due to their linear arrangement of bars, their visibility of valued categories, category labels, and easy data set comparison. Moreover, grouped bar charts are ideal for presenting qualitative data on the same categories from across multiple samples. The chapter looks into the advantages and disadvantages of bar chart y-axes at a non-zero value. It also presents the basic code for bar charts when using the R data.
Scatterplots for quantitative data
Authors: Humphreys Rosalind K. , Ruxton Graeme D.
Published: September 2023

This chapter explains how a scatterplot is a good choice for presenting quantitative data. It explains that scatterplots are the most effective way of plotting data points of two variables and determining the relationship between those variables. Time series is a common type of scatterplot when plotting the change in one continuous variable over time through lines. Moreover, univariate scatterplots, also known as strip charts, are useful for one-dimensional quantitative data with a small sample size. The chapter considers the advantages and disadvantages of starting scatterplot y-axes at a non-zero value. It then explains the basic code for scatterplots when using R.
Customizing everything using R: day-to-day
Authors: Humphreys Rosalind K. , Ruxton Graeme D.
Published: September 2023

This chapter discusses the features and functions that concern plotting figures in R code. R has a vast range of customizable graphical parameters that enable people to control the way their figures are displayed. Thus, controlling the way the figures are displayed means that the figures can improve their respective functionality and aesthetic appeal through design components, such as colour, font, points, and lines. The chapter cites the importance of legends, which allows easy interpretation when multiple design features are used in a single figure. It also explains how axes can be used to control in R to express data even more clearly.
Fitting curves; rational and inverse functions
Authors: Reed Martin B
Published: September 2023

This chapter looks at two concepts that can provide functions: the reciprocal of a function and the inverse of a function. It discusses a class of functions called rational functions, which have important applications in the biosciences. It also explores how the functions produced can be used with real data, such as how to use data-points obtained from experiment or observation and how to determine the values of the parameters in the function. The chapter demonstrates how to find the values of the parameters m and c from two data-points, including how to put a best-fit straight line through to more than two data-points. It reviews a technique that can fit general curves to data and reveals how the equation of the best-fit straight line is calculated in MS Excel.
Periodic functions
Authors: Reed Martin B
Published: September 2023

This chapter deals with periodic functions, which are functions that have a certain basic pattern of behaviour or cycle that repeats. It refers to the basic trigonometric functions: the sine and cosine, which are the most commonly used and relevant periodic functions. It also discusses a simple MS Excel function that can be used to produce periodic graphs with sudden changes in value. The chapter explains that sawtooth functions are used in sound waves created in music synthesizers and are used to describe the horizontal scanning function in cathode-ray-tube televisions and monitors. It considers functions whose graphs are smooth oscillations, wherein the curves are called sinusoidal.
Instantaneous rate of change: the derivative
Authors: Reed Martin B
Published: September 2023

This chapter talks about the mathematical rate-of-change theory, in other words, calculus, which has two branches: differential calculus and integral calculus. It considers differential equation as the most powerful use of calculus in the biosciences as it is an equation involving the derivative of a function and the function itself. It also examines how epidemiologists come up with predictions for the likely course of a new strain of influenza by modelling the instantaneous rate at which the disease is spreading. The chapter clarifies that rate-of-change involves an independent variable and a dependent variable, such as the velocity of a moving object is the rate-of-change of its position. It illustrates this topic using the Michaelis–Menten equation as this describes an enzyme-catalysed biochemical reaction wherein the rate of reaction v depends on the substrate concentration s.
Rules of differentiation
Authors: Reed Martin B
Published: September 2023

This chapter reviews the derivatives of functions and the rules of differentiation. It explains the product and quotient rules as the rules that allow the differentiation of complicated functions, provided they are built up from standard basic functions whose derivatives are known. It also includes problems that differentiate the reciprocal functions: the secant, cosecant, and cotangent. The chapter explores the use of implicit differentiation to find the derivative of the natural logarithm, y = ln x. It describes a curve as continuous if there are no sudden jumps in the function value, and differentiable if there are no sudden changes in the first derivative.
The definite integral
Authors: Reed Martin B
Published: September 2023

This chapter provides a geometric and physical interpretation of the integral, which leads to the concept of the definite integral as a numerical quantity instead of a function. It highlights practical applications of the definite integral, including a powerful method for evaluating definite integrals numerically. It also demonstrates how to calculate a definite integral by working out the indefinite integral F(x)| = (x) dx and omitting the constant of integration. The chapter points out that areas below the x-axis are counted as negative, noting the importance of checking that the function does not cross the x-axis anywhere within the interval. It talks about a concept of the definite integral that is independent of the idea of differentiation, which can be used to define the definite integral mathematically as a process that involves taking the limit called Riemann integration.
Differential equations I
Authors: Reed Martin B
Published: September 2023

This chapter deals with the differential equation, which is an equation involving a derivative and its solution requires finding y as a function of x. It points out that finding solutions for differential equations require basic algebra, the theory of functions, and differential and integral calculus. It also classifies the different types of differential equation, including methods for solving first-order differential equations. The chapter covers solution techniques applied to mathematical models of biological processes and numerical techniques implemented in MS Excel, which produce the solution as a set of data-points that can be graphed. It mentions the main classification of differential equations in terms of their order and the concept of boundary conditions.
Pharmaceuticals and Medicines
Authors: Moynihan Humphrey A. , Crean Abina M.
Published: September 2023

This chapter provides an overview of the essential properties of pharmaceuticals. Pharmaceuticals can be divided into two categories: active pharmaceutical ingredients (APIs) and excipients. APIs are the actual drug substances that give medicines their therapeutic properties. The main classes of APIs are psychopharmacological agents, pharmacodynamic agents, chemotherapeutic agents, and agents acting on metabolic diseases and endocrine function. Meanwhile, excipients are combined with the API to make dosage forms, or medicines, which can deliver the API to the required site of action in the body. The excipients may act as diluents, surfactants, lubricants, disintegrants, viscosity enhancers, or binders. Dosage forms may be administered to the patient by a variety of routes of administration. These include administration by the mouth (oral), by the surface of the body (topical), and by other routes. Delivery may be local or systemic. The choice of dosage form may depend on patient factors and illness factors.
Foundations of Chemical Biology
Authors: Dobson C. M. , Gerrard J.A. , Pratt A.J.
Published: September 2023

Foundations of Chemical Biology begins by stating that chemical biology is born out of a desire to understand the molecular basis of life. It asks: what are the molecules found in cells? How do their intrinsic properties equip them to perform all the complex processes found in cells? This book introduces the fundamental chemistry of the molecules that are essential to all cells. The molecules covered include amino acids and sugar phosphate derivatives, and the macromolecules derived from them (proteins and nucleic acids respectively). This book introduces important concepts concerning their intrinsic chemistry. The aim is to provide insight into the fundamental ideas relating to the chemistry of life that can then be applied to more advanced aspects of chemical biology.