bluuebunny/crossref_metadata_2025 huggingface dataset:
The Biology of Bacteria
Authors: Sefton Armine
Published: November 2020

Bacterial infections and infestations of man can be caused by both microbes and non-microbes. Microbes include bacteria, viruses, fungi, and protozoa. Non-microbes include worms, insects, and arachnids. This chapter concentrates on the basic biology of bacteria. A pathogen is an organism that is able to cause disease in its host and the pathogenicity of any organism is its ability to produce disease. Microbes express their pathogenicity by means of their virulence. The virulence of any pathogen is determined by any of its structural, biochemical, or genetic features that enable it to cause disease in the host. The relationship between a host and a potential pathogen is non- static; the likelihood of any pathogen causing disease in its host depends both on the virulence of the pathogen and the degree of resistance or susceptibility of the host, due mainly to the effectiveness of the host’s defence mechanisms. Two of the main factors influencing a bacteria’s pathogenicity are its ability to invade and it ability to produce toxins—either exotoxins or endotoxins. Bacteria are unicellular prokaryotic micro-organisms, unlike human cells, which are eukaryotic. Fungi, protozoa, helminths, and arthropods are also eukaryotic. Prokaryotic organisms contain both DNA and RNA, but their genetic material exists unbound in the cytoplasm of the cell as, unlike eukaryotic cells, they have no nuclear membrane. Sometimes bacteria contain additional smaller circular DNA molecules, called plasmids. The main features of a bacterium are the cell wall, cytoplasm, and cell membrane. However, some bacteria have additional features such as spores, capsules, fimbriae (pili), and flagellae. The construction of the cell wall is different in different bacteria, but all cell walls contain peptidoglycan. The structure of the cell wall determines the staining characteristics when stained using the Gram stain. Although its first use was over a hundred and fifty years ago, is still the standard method for primary classification of bacteria. Occasionally, bacteria do not have a cell wall. Gram staining of a fixed smear of bacteria is used to separate bacteria into Gram positive or Gram negative, and also to demonstrate their shape. Bacteria with a thick peptidoglycan layer but with no outer membrane stain purple and are called Gram positive.
The Biology of Viruses
Authors: Jeffery-Smith Anna , William Tong C. Y.
Published: November 2020

In order to be classified as a virus, certain criteria have to be fulfilled. Viruses must ● Be only capable of growth and multiplication within living cells, i.e. obligate intracellular parasite. Host cells could include humans, animals, insects, plants, protozoa, or even bacteria. ● Have a nucleic acid genome (either RNA or DNA, but not both) surrounded by a protein coat (capsid). ● Have no semipermeable membrane, though some have an envelope formed of phospholipids and proteins. ● Be inert outside of the host cell. Enveloped viruses are susceptible to inactivation by organic solvents such as alcohol. ● Perform replication by independent synthesis of components followed by assembly (c.f. binary fission in bacteria). Viruses are considered as a bundle of genetic programmes encoded in nucleic acids and packaged with a capsid +/ - envelope protein, which can be activated on entry into a host cell (compare this with computer viruses packaged in an enticing way in order to infect and take over control of your PC). Although they share some similarities in their properties, mycoplasma and chlamydia are true bacteria. The virion (assembled infectious particle) consists of viral nucleic acid and capsid. The nucleic acid of a virus can either be ribonucleic acid (RNA) or deoxyribonucleic acid (DNA), and the amount of genetic material varies widely, with some viruses able to encode a few proteins and others having genetic material that encodes hundreds of proteins. In association with the nucleic acid there may be non- structural viral proteins, such as a viral polymerase. The nucleic acid and non- structural proteins are protected by a surrounding layer of capsid proteins. The capsid includes proteins which can attach to host cell receptors. The proteins and the cell receptors to which they bind determine a virus’ tropism, i.e., the ability to bind to and enter different cell types. The term nucleocapsid refers to the nucleic acid core surrounded by capsid protein. Some viruses also have an envelope made up of phospholipids and proteins surrounding the nucleocapsid. This envelope can be formed by the host cell membrane during the process of a virus budding from a cell during replication.
The Use of the Laboratory in the Investigation, Management, and Prevention of Infection
Authors: Rosmarin Caryn
Published: November 2020

The pre-analytical stage is broadly classified into four elements: 1. Appropriate selection and use of diagnostic tests; 2. Proper filling in of request forms (paper or electronic); 3. Collection and transport of specimens; and 4. Checks made when the specimen and request form reach the laboratory to ensure the correct patient, sample, and request have been made. A large part of the laboratory role is to advise on the collection of appropriate samples in order to ensure the best chance of diagnosing a suspected infection syndrome or specific pathogen. This requires having a working knowledge of the range and processes of tests available in the laboratory for each clinical syndrome, and the ability to appreciate their strengths and weaknesses, sensitivities and specificities. In addition, advice on the sampling technique may need to be provided regarding the timing of the sample, the type of sample, number or volume of samples, and optimal storage and transport conditions that are required for the specific test. Failure to take sufficient amount of the correct sample, at the correct time, and using the correct container, or storing it in a suboptimal manner, may lead to falsely negative or positive results. Most laboratories have manuals for guidance on sampling details and the tests performed. It is vital that this information is available to clinical staff. Microbiologists and virologists contribute to this guide and assist in ensuring it is communicated to the clinicians taking the samples. This is particularly important for precious samples that cannot easily be repeated, e.g surgical biopsies, CSF from lumbar punctures. Ensuring the correct completion of the request form is vital. Important clinical details should be included on the request to help guide the most appropriate tests. Examples of important information to be documented on the request include travel history, antibiotic history, immune status, underlying diseases, and site of suspected infection. The analytical stage consists of the actual testing of the sample. Examples of common tests performed in this stage include microscopy, culture, sensitivity testing, serology, and molecular detection, as well as more novel techniques such as mass spectrometry, bioinformatics, and sequencing.
Cardiovascular Infections
Authors: Wani Robert Serafino , Das Satya
Published: November 2020

Infective endocarditis (IE) is inflammation of the endothelial lining of the heart valves due to infective causes. IE is a rare condition with an incidence rate of three to nine cases per 100,000 population with a male to female ratio of 2:1. The rate is higher in people with unrepaired cyanotic congenital heart disease, prosthetic heart valves and previous endocarditis. Other risk factors for IE include: rheumatic fever (now accounts for < 10% of IE cases in developed countries), degenerative conditions of heart valves, intravenous drug abuse, diabetes, and HIV infection. One third of the cases are now healthcare associated infection (HCAI), particularly with haemodialysis, cardiac surgery, implantable cardiac devices, intravascular lines, and urinary catheters. In the past decade Staphylococcus aureus has replaced viridans streptococci as the leading cause of IE, the rate of enterococcal (mostly E. faecalis) and Bartonella IE has increased, while that of culture negative endocarditis has decreased. Untreated IE is a uniformly fatal condition, but the mortality rate can be reduced to 5–40% with appropriate treatment. There are two important prerequisite steps to the development of IE: 1. A damaged endothelium due to high pressure gradient and turbulent blood flow around a heart valve or septal defect. Fibrin and platelet deposition occur on the roughened endothelium forming a non-infective thrombus or vegetation. 2. Bacteraemia due to endocarditis-prone organisms resulting from trauma to mucous membranes (e.g. oral cavity, urinary, and gastrointestinal tract) or other colonized tissue or foreign body, which is not cleared by host defence mechanisms. Micro-organisms then attach to the damaged endothelium through a specific ligand-receptor interaction (hence the predilection for certain organisms to cause endocarditis, e.g. viridans streptococci from the mouth), colonize the thrombus, and grow and multiply within it to give rise to a mature/infective vegetation, which is the pathological hallmark of IE. Virulent organisms, classically S. aureus, can apparently infect a healthy endocardium. Damage to the endothelium results in valvular incompetence/regurgitation and symptoms and signs of heart failure and when severe, it is a potentially fatal condition that requires urgent valve surgery, even if the infection has fully responded to antimicrobial therapy.
Gastro-intestinal, Hepatic, Pancreatic, and Biliary Infections
Authors: Riddell Anna , William Tong C. Y.
Published: November 2020

The gastro-intestinal tract (GIT) hosts the most numerous and diverse reservoir of microbes in humans. There is increasing interest in the relationship between the GIT microbiome and human health. Obesity, diabetes, allergy, and a number of inflammatory diseases have been linked with the human GIT microbiome. Infections of the GIT arise either as a result of a change in the relationship between the commensal microbes colonizing the GIT (endogenous infection) or entry in to the GIT of a micro-organism which causes disease (exogenous infection). Commensals most commonly invade host tissues as a result of compromised defensive barriers. Disease associated with exogenous infection can be toxin-mediated, or associated with local or systemic invasion of the host. Endogenous infections are usually polymicrobial. In the mouth the aetiology, presentation, and anatomical associations have led to the description of a number of syndromes. Peritonsillar infection with involvement of the internal jugular vein is Lemierre’s syndrome, which is particularly associated with infection with Fusobacterium necrophorum. ‘Trench mouth’ is a severe form of ulcerative gingivitis, so named because in the absence of oral hygiene it was a relatively common diagnosis among those in the trenches during the First World War. Ludwig’s angina is a severe infection of the floor of the mouth which spreads in to the submandibular and sub-lingual space, often following a tooth-related infection. Deep neck infections are more common in children than adults and can involve the parapharyngeal, retropharyngeal, peri-tonsillar, or sub-mandibular spaces. Children with deep neck infections are more likely than adults to present with cough and respiratory distress. Oesophagitis has a wide range of potential aetiologies. Fungi (particularly Candida species) are probably the most common microbial cause of oesophagitis. Fungal infection of the distal oesophagus is thought to play an important role in the pathogenesis of disseminated fungal infection. Risk factors for fungal infection include poor oral intake, exposure to antibiotics, immunocompromise (HIV, steroids, cancer treatments), gastric acid suppressants, and damage to mucosal integrity (naso-gastric tubes, acid reflux, varices). Bacteria (including Mycobacteria, Actinomycetes, Treponemes), parasites, and viruses (herpes simplex, cytomegalovirus) are rarer infectious causes of oesophagitis.
Ocular Infections
Authors: Buchanan Ruaridh , Rosmarin Caryn
Published: November 2020

Pathogens of every type can affect the eye— bacterial, fungal, viral, protozoal, and parasitic. The eye is a complex structure but for the purposes of categorizing infections it can be viewed as a series of layers, which are: ● Conjunctiva ● Cornea ● Vitreous humour ● Retina The bulk of acute conjunctivitis is viral— up to 90% of infection will be due to adenovirus. Enterovirus species can cause acute epidemic haemorrhagic conjunctivitis, e.g. coxsackie A 24 virus, enterovirus 70. Bacterial causes are more common in children than adults and include S. aureus, S. pneumoniae, and H. influenzae. Pseudomonas aeruginosa and other Gram negatives may cause conjunctivitis in contact lens wearers. It is sometimes possible to differentiate viral from bacterial disease clinically. Where viral conjunctivitis usually results in watery eyes and often comes in concert with a more generalized viral illness, bacterial infection usually occurs in the absence of systemic features and is more likely to be associated with purulent discharge or matting of the eyelids. Viral conjunctivitis does not require specific treatment save in the rare instances where herpes simplex virus is the causative agent—topical aciclovir can then be used. Bacterial infections, however, will resolve more rapidly with topical therapy. A wide range of preparations are available but topical chloramphenicol is the mainstay of treatment. Purulent conjunctivitis in the neonate is often a result of congenitally acquired N. gonorrhoeae or Chlamydia trachomatis infection. In these circumstances conjunctivitis can be the herald of systemic infection and it is therefore wise to treat both systemically and topically. Swabs can be sent for PCR and culture to identify the pathogen. Chlamydia can be treated with topical and oral azithromycin; gonococcal infection can be treated with topical chloramphenicol and a systemic cephalosporin chosen based on local sensitivity patterns. Sexually active adults can also occasionally suffer from these infections and should be treated similarly. Herpes simplex virus is a relatively common cause, usually inoculated directly into the eye by contaminated fingers. The classic presentation is with a unilateral dendritic ulcer, easily visualized on fluorescein dye staining. Herpes zoster virus can also affect the cornea—reactivation in the distribution of the ophthalmic branch of the trigeminal nerve (CN V) results in ophthalmic shingles.
Mechanism of Action of Antimicrobial Agents
Authors: Buchanan Ruaridh , Sefton Armine
Published: November 2020

Antibacterial and antifungal agents aim to kill pathogens, or at the very least incapacitate them. To achieve this aim these agents must have a reasonable degree of toxicity at the cellular level. If this toxicity was equally manifest against all cell types then the drugs would be unusable in patients as the side effect profile would be unacceptably severe. Selective toxicity, whereby the agents are orders of magnitude more toxic to bacteria or fungi than human cells, allows for the safe and effective administration of these agents to patients. There are a number of different mechanisms by which an antimicrobial agent can yield selective toxicity: ● Target a cellular structure that exists only in bacteria/fungi—e.g. the cell wall; ● Target a cellular structure that has a significantly different structure in bacteria/ fungi— e.g. the ribosome; the fungal cell membrane; ● Target cellular enzymes that are significantly different in bacteria/fungi e.g. topoisomerase; ● Target a synthetic pathway that exists only in bacteria e.g. folate synthesis. Broadly, antibacterial drugs can be divided into the following categories: ● Agents that target the cell wall; ● Agents that target the cell membrane; ● Agents that inhibit protein synthesis; ● Agents that inhibit DNA replication/ transcription of RNA; ● Agents that target folate synthesis; ● Agents that directly damage intracellular structures. The cell wall is unique to bacteria, and therefore an ideal target. Disrupting the complex cross-linking process required to produce the cell wall leads to loss of bacterial cell integrity and therefore to cell death. The following classes of antibiotics target the cell wall: The first class to be discovered, and still in many cases the most effective, incorporates the four-membered beta-lactam ring—its homology to d-alanyl-d-alanine allows beta-lactam-containing compounds to bind to cell wall peptidoglycans and act as chain terminators. The beta-lactam ring is fused to a five-membered sulphur-containing ring. Variations in side chains account for the differing pharmacokinetics and spectra of action of the different compounds—for example, the addition of an amino group to benzylpenicillin produces ampicillin.
Mechanisms of Antibiotic Resistance
Authors: Buchanan Ruaridh , Wareham David
Published: November 2020

Although antibiotic resistance has come to the fore in the media and clinical practice relatively recently, it is by no means a new issue; Alexander Fleming discussed the risks of penicillin resistance more than sixty years ago, but even he was behind the times. Bacteria have been competing with each other for millions of years, producing compounds which kill or inhibit other species—it is not surprising that bacteria have evolved defence mechanisms. Current major concerns are the rise of pan-drug resistant gram-negative organisms and the spread of multi-drug resistant TB. Bacterial cells turn over rapidly—this rate of reproduction leads to many errors in DNA replication. Many of these mutations are deleterious to the organism, but others confer new properties, such as changing the structure of an enzyme. The application of selection pressure in the form of antimicrobial therapy leads to the survival of mutants that have randomly acquired resistance mechanisms. There are two useful ways to categorize resistance mechanisms: by how bacterial cells acquire them and by the physical mechanism of action. The types of acquisition have important infection control ramifications. Resistance can be subdivided into three separate categories: ● Intrinsic resistance— mechanisms hard coded into all members of a bacterial species at the chromosomal level. If an organism’s antibiogram suggests susceptibility to an agent to which it should be intrinsically resistant, further work should be done to check that the identification is correct. Examples include gram-negative bacteria being resistant to glycopeptides due to the outer cell membrane, anaerobes being resistant to aminoglycosides due to lack of an uptake mechanism, and amoxicillin resistance in Klebsiella due to beta-lactamase production. ● Mutational resistance—resistance that arises randomly due to DNA replication errors in conjunction with selection pressure applied by antimicrobial agents. This is the basis of the majority of the mechanisms detailed in this chapter. ● Transferrable resistance— mutational resistance that is passed horizontally from the bacterium in which it arose to another cell, possibly of a different species entirely. This happens through either transposons (DNA that incorporates into the bacterial chromosome) or plasmids (rings of DNA that replicate independent of the main chromosome).
Outpatient Parenteral Antimicrobial Treatment (OPAT)
Authors: Melzer Mark
Published: November 2020

Outpatient parenteral antimicrobial therapy (OPAT) is the provision of intravenous (IV) antibiotics to patients in the community or an ambulatory care setting. It was first used to treat children with cystic fibrosis in the 1970s but did not become part of adult services in the UK until the 1990s. OPAT facilitates hospital admission avoidance and decreased lengths of inpatient stay. It is associated with high levels of patient satisfaction. Recent clinical guidelines on the provision of OPAT services in the UK and US have recently been published Skin and soft tissue infections (SSTIs), in particular lower limb cellulitis, are the commonest medical conditions referred to OPAT services. Patients are typically treated for three to five days with IV antibiotics but patients with lymphoedema or underlying skin conditions typically require longer courses. Increasingly, multidrug-resistant urinary tract infections (UTIs) may be treated in the community with IV antibiotics, although oral options such as fosfomycin are now available. Patients with bone and joint infection invariably require prolonged parenteral antibiotic courses, whether this be vertebral osteomyelitis or native or prosthetic joint infection. Other less common examples, where careful patient selection is required, include infected diabetic foot ulcers (with or without osteomyelitis), infective endocarditis, empyema, liver, and tubo-ovarian and brain abscesses. Patients are recruited on the basis of clinical syndromes (e.g. lower limb cellulitis) or laboratory referral (e.g. multidrug-resistant UTIs). Active recruitment (e.g. attendance at acute assessment unit board rounds or orthopaedic multidisciplinary teams, MDTs) compared to passive recruitment (waiting for clinical referrals) increases the yield of patients. The suitability of a patient to receive treatment out of hospital or in an ambulatory care setting needs careful assessment and is dependent upon age, comorbidities, and severity of infection. OPAT also requires patients to engage actively and reliably with therapy. Therefore, IV drug users and patients with serious mental health problems are generally not suitable. Commonly used antibiotics are those given once daily as these reduce nursing time, although some nursing teams can administer IV antibiotics up to three times per day. It is imperative to take a drug allergy history and seek an alternative class of antibiotics when a patient complains of severe penicillin allergy.
Obstetrics
Authors: Setna Zeryab
Published: November 2020

This chapter will be of interest and help to all those studying the health-care of women. Obstetrics, like all fields of medicine, continues to evolve at a rapid pace, and keeping up-to-date with the latest literature, guide­lines and protocols can be a daunting task. In the following questions we have tried to encompass all of the important areas of this subject. Pregnancy can be a joyful experience for both the mother and her family. However, it can occasionally be associated with complications, resulting in severe short- and long-term harm to both the mother and her baby. This chapter covers the most important aspects of pregnancy and its commonly associated problems, drawing on important guidelines to highlight the core knowledge and skill practitioners in the field are expected to have.
Eponymous syndromes
Authors: Etheridge Luci , Bonner Alex
Published: November 2020

Eponyms are still widely used in medicine. Most commonly, they describe collections of clinical features (i.e. a syndrome) or particular clinical signs but are also used to name procedures, anatomy, and equipment. As our understanding of pathophysiology and genomics has improved, naming of diseases and clinical signs has tended to reflect that. However, many eponyms still persist from an era when naming patterns of disease or illness presentation enabled clinicians to gather data, recognize problems, and decide on treatments before the pathology or treatment was fully understood. In this chapter, you will be asked questions challenging your ability to recognize clinically relevant eponyms that you may well encounter in your practice as a doctor.
Emergency medicine
Authors: Roberts Catherine
Published: November 2020

Emergency medicine is not all ‘ER’—glamour and fast-moving action; much of it requires caring for relatively minor problems or complex elderly patients. Emergency Departments are busy, high-intensity work environments with a high turnover of patients. In order to make time-critical decisions effectively, it is necessary to have a good breadth and depth of knowledge underpinning a sensible and safe approach to dealing with clinical uncertainty. Patients will present with acute and chronic conditions from all specialties. Gathering information rapidly is important. Gaining clues from the patient and their relative(s) is useful, as is obtaining information on events at the scene from the ambulance paramedics. Hospital notes are often not available and neither is the general practitioner (GP), so decisions are made on the basis of limited information. Rather than making definitive diagnoses confirmed by expensive tests, the role of the emergency physician is to determine the immediate threat to life or limb and to treat that threat, while gathering information to make a ‘most likely’ diagnosis so that treatment can be started. Observing the patient in a Clinical Decision Unit can often help to confirm your suspicions, give you further information on how severe a condition is, or eliminate a possible diagnosis. Ultimately, emergency medicine requires the assessment of risk, evaluation of the added benefit of admission over discharge, and excellent communication. The only way to learn emergency medicine is to practise, to discuss patients, and to develop your analytical and decision-making skills. The following questions are designed to develop some of these skills, by showing you an approach to solving the clinical problems that are commonly encountered in the Emergency Department, how to use tests efficiently and effectively, and some of the options for treatment that are available other than admission under inpatient teams.
Paediatrics
Authors: Whymark Caroline , Junkin Ross , Ramsey Judith
Published: November 2020

To pass the written part of the FRCA, candidates must achieve the pass mark for the SAQs and the MCQ/ SBA papers combined. Therefore, doing particularly well in one paper, or one area, can compensate for another in which you have scored poorly. The 30 SBA questions is an area that candidates commonly find difficult. There is a feeling these questions are unjust and that it is impossible to second guess the examiners and choose the correct option. They feel further punished that four marks are awarded for each correct answer or lost for an incorrect choice. While this reflects the fact that four answers have been eliminated in the course of choosing the best answer, candidates often state it is an unfair ‘all or nothing’ way to mark these questions. They can commonly narrow the choice down to a final two options but report finding it difficult to then choose between them. They receive no credit having successfully eliminated three of the options and cite the SBA element as being the reason they failed the examination. These comments however are not supported by examination success data published by the RCoA. The pass rate for this paper was consistent at around 70% before and after the introduction of the SBA component in September 2011. We believe the concepts behind the SBAs are misunderstood by many. When asked to write a SBA question, candidates inevitably produce a five- part A to E multiple choice question but with only one correct answer. The finer points of SBA questions are lost among quickly written revision aids containing what the authors believe to be examination standard questions, when often they are not. Further, because SBAs are a relatively new element to the FRCA there is a limited bank of questions, and a highly restricted number in the public domain. Both these factors make practice of these questions difficult. Part of exam success is practice of the technique and question type in advance. We believe the practice of SBAs is an area to which candidates do not give enough attention.
Household or Cottage Industries: Modelling Industrial Diversity in New Kingdom Houses and Courtyards
Authors: Hodgkinson Anna   K.
Published: November 2020

Both O45.1 at Amarna and IA1 at Gurob, discussed in Chapter 6, can be said to have been purpose-built and to some extent specialized, with the presence of kilns indicating a somewhat focused set of activities. By contrast, the smaller houses, or groups of the same in New Kingdom settlements have been observed to be generally less industrially focused or specialized on all levels. The present chapter therefore discusses a number of case-studies demonstrating artefact diversity in a range of houses, showcasing their variety both in appearance and in functionality. These case-studies include a range of houses in the Main City at Amarna and a comparison of the artefactual evidence they contained of relevant industrial activities in addition to Site J at Malqata. Excavations at Site J in the 1970s have revealed a series of small ovens, the purpose and locations of which will be discussed together with associated objects. This and the artefactual data from the houses at Amarna will provide an insight into the organization of industrial activities on a household-level. In the course of the spatial analysis undertaken for the Main City North (MCN) at Amarna (see Section 2.4), it has become apparent that thirty-four buildings, dispersed throughout this suburb, contained evidence not only of one industrial activity discussed in this book, but of several. The houses, each of which contains evidence of more than one industry, cover a range of varying sizes. While most of these thirty-four houses had a smaller ground area (less than 900m²), some larger ones also contained evidence of multiple industries. Eight of the thirty-four had an area of less than 100m², while a total of sixteen covered between 100 and 900m², the remaining ten houses being larger than 900m² including their courtyards. While most of the larger houses measured between 900 and 3,000m², three houses are even larger than this, with the largest property, R44.2, which measured over 10,000m², belonging to a ‘Steward of Akhenaten’. Table 7.1 demonstrates the combinations of industries queried with the GIS that were in operation in a number of buildings.
Fortran 90: A simple programming language
Authors: Fehr Hans , Kindermann Fabian
Published: November 2020

Before diving into the art of solving economic problems on a computer, we want to give a short introduction into the syntax and semantics of Fortran 90. As describing all features of the Fortran language would probably fill some hundred pages, we concentrate on the basic features that will be needed to follow the rest of this textbook. Nevertheless, there are various Fortran tutorials on the Internet that can be used as complementary literature. Fortran is pretty old; it is actually considered the first known higher programming language. Going back to a proposal made by John W. Backus, an IBM programmer, in 1953, the term Fortran is derived from The IBM Formula Translation System. Before the release of the first Fortran compiler in April 1957, people used to use assembly languages. The introduction of a higher programming language compiler tremendously reduced the number of code lines needed to write a program. Therefore, the first release of the Fortran programming language grew pretty fast in popularity. From 1957 on, several versions followed the initial Fortran version, namely FORTRAN II and FORTRAN III in 1958, and FORTRAN IV in 1961. In 1966, the American Standards Association (now known as the ANSI) approved a standardized American Standard Fortran. The programming language defined on this standard was called FORTRAN 66. Approving an updated standard in 1977, the ANSI paved the way for a new version of Fortran known as FORTRAN 77. This version became popular in computational economics during the late 80s and early 90s. More than 13 years later, the Fortran 90 standard was released by both the International Organization for Standardization (ISO) and ANSI consecutively. With Fortran 90, the fixed format standard was exchanged by a free format standard and, in addition, many new features like modules, recursive procedures, derived data types, and dynamic memory allocation made the language much more flexible. From Fortran 90 on, there has only been one major revision, in 2003, which introduced object oriented programming features into the Fortran language. However, as object-oriented programming will not be needed and Fortran 90 is by far the more popular language, we will focus on the 1990 version in this book.
The life-cycle model and intertemporal choice
Authors: Fehr Hans , Kindermann Fabian
Published: November 2020

The discussion in the Chapters 3 and 4 centred around static optimization problems.The static general equilibrium model of Chapter 3 features an exogenous capital stock and Chapter 4 discusses investment decisions with risky assets, but in a static context. In this chapter we take a first step towards the analysis of dynamic problems. We introduce the life-cycle model and analyse the intertemporal choice of consumption and individual savings. We start with discussing the most basic version of this model and then introduce labour-income uncertainty to explain different motives for saving. In later sections, we extended the model by considering alternative savings vehicles and explain portfolio choice and annuity demand. Throughout this chapter we follow a partial equilibrium approach, so that factor prices for capital and labour are specified exogenously and not determined endogenously as in Chapter 3. This section assumes that households can only save in one asset. Since we abstract from bequest motives in this chapter, households do save because they need resources to consume in old age or because they want to provide a buffer stock in case of uncertain future outcomes.The first motive is the so-called old-age savings motive while the second is the precautionary savings motive. In order to derive savings decisions it is assumed in the following that a household lives for three periods. In the first two periods the agent works and receives labour income w while in the last period the agent lives from his accumulated previous savings. In order to derive the optimal asset structure a2 and a3 (i.e. the optimal savings), the agent maximizes the utility function . . . U(c1, c2, c3) = u(c1) + βu(c2) + β2u(c3) . . . where β denotes a time discount factor and u(c) = c1−1/γ /1−1/γ describes the preference function with γ ≥ 0 measuring the intertemporal elasticity of substitution.
What Does the SJT Test?
Authors: Metcalfe David , Dev Harveer
Published: November 2020

The SJT was developed to test nine professional attributes identified from a detailed analysis of the FY1 role. These attributes are as follows: However, the SJT recognizes that there is considerable overlap between these attributes and that some cannot be effectively assessed with a written test. As a result, SJT questions focus on the five attributes highlighted in bold. It is worth considering what the SJT requires of candidates according to each key attribute. Candidates must be honest, trustworthy, reliable, and aware of ethical issues (e.g. confidentiality). They should challenge behaviour that is unacceptable or risks patient safety. Candidates should take appropriate responsibility for their own actions and omissions. Candidates must be resilient and remain calm under pressure. Judgement should not be affected by pressure and candidates should develop appropriate coping strategies. Candidates should communicate (verbally and in writing) concisely and clearly. They should be able to vary their communication style appropriately and to negotiate, and be willing to engage others in open dialogue. Candidates should always show respect to patients. They should adopt a collaborative approach to decision- making with patients as well as maintaining courtesy, empathy, and compassion. Candidates should be able to work in partnership while respecting different views. They should share tasks fairly and ask advice from others when necessary. Despite appearances, the SJT is a knowledge- based examination. It is important to remember throughout that questions ask what you should do, rather than what you would do in any given situation. Therefore, it is a test of whether you know the ‘correct’ action and not whether you would act correctly if working as a doctor. For example, a question might introduce you as an FY1 doctor on a busy ward. You are told to examine an elderly patient of the opposite sex and all the nurses are occupied elsewhere. You might have seen doctors examine patients under these circumstances without a chaperone. You might even think that this would be your approach in real life. However, you know on some level that a better solution is to insist on (or at least to offer) the presence of a chaperone.
How to use this Book
Authors: Metcalfe David , Dev Harveer
Published: November 2020

Section 2 of this book is organized into five chapters, each representing a professional attribute to which SJT questions are mapped: commitment to professionalism (Chapter 9), coping with pressure (Chapter 10), effective communication (Chapter 11), patient focus (Chapter 12), and working effectively as part of a team (Chapter 13). Each section contains 40 questions, split equally between multiple choice and ranking items. The book ends with Section 3, which contains abbreviated practice tests (Chapter 14) that use a mix of different questions. You will notice throughout the book that most questions cover multiple domains. This is true for those in the SJT as well. It is easy to imagine scenarios that test all five domains with very little effort; for example, a senior nurse pressures you to do something to the detriment of a patient. Do not become distracted by trying to guess which domain(s) are being tested. Although the SJT requires knowledge, the answers to questions cannot be learnt by rote. This is what the test creators mean when they say candidates cannot be ‘coached’ to score highly. The benefit in working through these examples is thinking about the issues they raise. For this reason, the ‘wrong’ answers are at least as valuable as those that are ‘correct’. When practising questions in other subjects (e.g. anatomy), most students read the question, choose an answer, and then check that they picked correctly. The best approach to this book is to read a scenario and then consciously think about which details make (C) a better choice than (D), or vice versa. Only when you have done this should you check our answer and explanation. SJT questions go through a commendably thorough process of assessment and evaluation. The answers are determined by a consensus panel of ‘experts’, most of whom are senior doctors. Our own questions have been through an abbreviated review process using the contributors listed on. This group of contributors broadly reflects the type of people used by the SJT team to validate their items, i.e. members include Clinical Supervisors, doctors with recent experience of the Foundation Programme, and others working closely with FY1 doctors (e.g. senior nurses).
Renal Medicine
Authors: White William
Published: November 2020

The kidney causes problems for medical students and junior doctors alike— the convoluted journey from plasma to urine, the conundrum of what is reabsorbed and excreted where, and the tangled web of the glomerulonephritides are traditionally learnt, rather than actually understood. As in all clinical medicine, a good place to start is with the fundamen­tals of the organ in question. Passage from plasma to urine follows the pathway: ● Blood ● Glomerulus ● Tubules ● Collecting duct ● Ureter ● Bladder ● Urethra. The primary functions of the kidney are: ● Removal of toxins ● Electrolyte homeostasis ● Maintenance of acid– base balance ● Activation of vitamin D ● Stimulation of erythropoiesis ● Maintenance of blood volume. The challenge then is to implement these basics by being sensitive to deviations from normal physiology: recognizing the accumulation of any potential toxins (hyperkalaemia, uraemia, and acidosis) or the lack of any synthetic products (hypocalcaemia and anaemia), suggesting triggers for such deviations, and pinpointing the specific parts of the anatomy that may be malfunctioning in some way so as to cause impairment. Despite its bad reputation, the kidney reveals more about itself than any other organ and, in theory, should be the easiest to monitor. It achieves this through its raison d’être: urine. Its presence, absence, con­tents, smell, and colour offer a running commentary on the activity of the renal tract at any given point in time— it is the internal, intangible work­ings of specialized cells made physical, measurable, and dippable. So, far from being those much- feared Objective Structured Clinical Examination (OSCE) stations, the dipstick and the catheter are our friends. Or they should be, for it is our ability to harness the information that they pro­vide, allied to the series of numbers on the oft- requested ‘U&Es’ (urea and electrolytes), against a background of wide- ranging symptoms that will make us sensitive to the running of the kidney. This— not just our ability to regurgitate the three types of renal tubular acidosis— is what is at stake in this chapter.
Haematology
Authors: Furmedge Dan , Sinharay Ricky
Published: November 2020

Tackling haematology is never easy. Revision can be a struggle, as it may not always be obvious which topic areas will be directly relevant to clin­ical practice. We still, however, benefit from an understanding of these areas and an appreciation of how to do and interpret the basics and when more expertise is required. Sometimes the answers require a trip right back to the stem cell. A junior doctor’s most frequent contact with haematology is in interpreting a full blood count. In this task, the core skills of the chapter come to the fore— in response to an anaemia, we should be able to explore the possibilities of iron deficiency, vitamin deficiency, and haem­olysis. On seeing a thrombocytopenia or an abnormal clotting profile, we should be able to make a clinical assessment and perform further appropriate tests, with a view to suggesting differential diagnoses. The questions in this chapter aim to build confidence in these tasks. There is a lot more to haematology, however, than a blood count. As a junior doctor, there will be regular practical challenges such as pre­scribing and altering anticoagulation therapy, overseeing the safe delivery of a blood transfusion, and managing acute situations such as sickle- cell crises. The way forward is to be able to master these basics and start to see the bigger picture. This means developing a feel for the more subtle symptoms and signs of haematological disease and becoming proactive in the face of abnormal blood results. As with all of the chapters in this book, it is a way of thinking that is crucial— one that allows confident management of common situations and recognition of potentially catastrophic conditions, but also one that encourages creativity and initiative. When faced with a clinical conun­drum, we should have the knowledge and confidence to ask appropri­ately: ‘Is the answer in the blood?’
Neurology
Authors: Paterson Ross , Sztriha Laszlo
Published: November 2020

The face of neurology in clinical practice is changing. Neurology is no longer primarily a diagnostic specialty. As more therapeutic treatments become available in all fields from epilepsy to multiple sclerosis, early and accurate diagnosis is increasingly required so that patients can benefit from early treatment aiming to reduce the lifelong burden of neuro­logical disease. Diagnosis of neurological disorders is often considered by junior doc­tors to be highly complex and, as such, is responsible for a great deal of anxiety. One of the most difficult challenges can be determining the loca­tion of the lesion. A helpful approach to this is by analysis of the patterns that each lesion produces. Table 8.1 describes some of the common patterns seen in clinical practice, and the questions in this chapter will attempt to highlight some of the other specific presentations needed in assessing the neurology patient.
Surgery
Authors: Griffiths Shelly
Published: November 2020

Starting a surgical job can feel like learning a completely new language. It may be the first time seeing patients in acute severe pain with a variety of lumps and bumps and a past history of previously unheard of complex operations. It can be easy to get hung up on whether the distended large bowel loop on the X- ray is a caecal or sigmoid volvulus or whether the strangulated hernia is femoral or inguinal. Ultimately, however, the most important point is that, as a junior doctor, it is being able to recognize that the patient is acutely unwell and may require an operation that will save lives. Ironically, a surgical rotation involves little time in the operating theatre— mostly, it will be spent dealing with problems during the peri-­operative period. This may start a week or two before the patient is even admitted, in the shape of a pre- assessment clinic, though these are increasingly nurse- led clinics with minimal input from junior doctors. Such clinics are, however, a good opportunity to see stable patients with interesting pathology and good clinical signs and to establish how well they look before the majority of their large bowel or their stomach is removed. The preoperative preparation of the patient goes beyond bloods and a cursory chat, and will require one to be on the lookout for previously undiagnosed cardiorespiratory or rheumatological conditions, among others, that might affect the patient getting to sleep or staying safely asleep under anaesthesia. Liaising with the anaesthetist about possible sources of difficulty well in advance of the planned procedure will ensure that operations do not get cancelled. The acute abdomen will take centre stage during general surgical takes. A thorough history and sound anatomical knowledge will help create a list of differential diagnoses. Accurate and careful palpation of the abdomen will reveal peritonism and the presence of any masses, and simple bedside observations and tests can greatly aid the diagnosis. Surgical specialties have a heavy reliance on imaging— erect chest X- ray, ultrasound, computed tomography (CT)/ magnetic resonance imaging (MRI) scan— each providing different information for the symp­toms displayed.