bluuebunny/crossref_metadata_2025 huggingface dataset:
Using Text Classification for Gene Function Annotation
Authors: Raychaudhuri Soumya
Published: November 2020

Recognizing specific biological concepts described in text is an important task that is receiving increasing attention in bioinformatics. To leverage the literature effectively, sophisticated data analysis algorithms must be able to identify key biological concepts and functions in text. However, biomedical text is complex and diverse in subject matter and lexicon. Very specialized vocabularies have been developed to describe biological complexity. In addition, using computational approaches to understand text in general has been a historically challenging subject (Rosenfeld 2000). In this chapter we will focus on the basics of understanding the content of biological text. We will describe common text classification algorithms. We demonstrate how these algorithms can be applied to the specific biological problem of gene annotation. But text classification is also potentially instrumental to many other areas of bioinformatics; we will see other applications in Chapter 10. There is great interest in assigning functional annotations to genes from the scientific literature. In one recent symposium 33 groups proposed and implemented classification algorithms to identify articles that were specifically relevant for gene function annotation (Hersh, Bhuporaju et al. 2004). In another recent symposium, seven groups competed to assign Gene Ontology function codes to genes from primary text (Valencia, Blaschke et al. 2004). In this chapter we assign biological function codes to genes automatically to investigate the extent to which computational approaches can be applied to identify relevant biological concepts in text about genes directly. Each code represents a specific biological function such as ‘‘signal transduction’’ or ‘‘cell cycle’’. The key concepts in this chapter are presented in the frame box. We introduce three text classification methods that can be used to associate functional codes to a set of literature abstracts. We describe and test maximum entropy modeling, naive Bayes classification, and nearest neighbor classification. Maximum entropy modeling outperforms the other methods, and assigns appropriate functions to articles with an accuracy of 72%. The maximum entropy method provides confidence measures that correlate well with performance.
Finding Gene Names
Authors: Raychaudhuri Soumya
Published: November 2020

Successful use of text mining algorithms to facilitate genomics research hinges on the ability to recognize the names of genes in scientific text. In this chapter we address the critical issue of gene name recognition. Once gene names can be recognized in the scientific text, we can begin to understand what the text says about those genes. This is a much more challenging issue than one might appreciate at first glance. Gene names can be inconsistent and confusing; automated gene name recognition efforts have therfore turned out to be quite challenging to implement with high accuracy. Gene name recognition algorithms have a wide range of useful applications. Until this chapter we have been avoiding this issue and have been using only gene-article indices. In practice these indices are manually assembled. Gene name recognition algorithms offer the possibility of automating and expediting the laborious task of building reference indices. Article indices can be built that associate articles to genes based on whether or not the article mentions the gene by name. In addition, gene name recognition is the first step in doing more detailed sentence-by-sentence text analysis. For example, in Chapter 10 we will talk about identifying relationships between genes from text. Frequently, this requires identifying sentences refering to two gene names, and understanding what sort of relationship the sentence is describing between these genes. Sophisticated natural language processing techniques to parse sentences and understand gene function cannot be done in a meaningful way without recognizing where the gene names are in the first place. The major concepts of this chapter are presented in the frame box. We begin by describing the commonly used strategies that can be used alone or in concert to identify gene names. At the end of the chapter we introduce one successful name finding algorithm that combines many of the different strategies. There are several commonly used approaches that can be exploited to recognize gene names in text (Chang, Shutze, et al. 2004). Often times these approaches can be combined into even more effective multifaceted algorithms.
Conclusion
Authors: Raychaudhuri Soumya
Published: November 2020

The genomics era has presented many new high throughput experimental modalities that are capable of producing large amounts of data on comprehensive sets of genes. In time there will certainly be many more new techniques that explore new avenues in biology. In any case, textual analysis will be an important aspect of the analysis. The body of the peer-reviewed scientific text represents all of our accomplishments in biology, and it plays a critical role in hypothesizing and interpreting any data set. To altogether ignore it is tantamount to reinventing the wheel with each analysis. The volume of relevant literature approaches proportions where it is all but impossible to manually search through all of it. Instead we must often rely on automated text mining methods to access the literature efficiently and effectively. The methods we present in this book provide an introduction to the avenues that one can employ to include text in a meaningful way in the analysis of these functional genomics data sets. They serve as a complement to the statistical methods such as classification and clustering that are commonly employed to analyze data sets. We are hopeful that this book will serve to encourage the reader to utilize and further develop text mining in their own analyses.
Ecology of Marine Sediments
Authors: Gray John S. , Elliott Michael
Published: November 2020

Marine sediments provide the largest habitat on planet earth, yet knowledge of the structure and function of their flora and fauna continues to be poorly described in current textbooks. This concise, readable introduction to benthic ecology builds upon the strengths of the previous edition but has been thoroughly revised throughout to incorporate the new technologies and methods that have allowed a rapid and ongoing development of the field. It explores the relationship between community structure and function, and the selection of global examples ensures an international appeal and relevance. The economic value of marine sediments increases daily, reflected in the text with a new emphasis on pollution, climate change, conservation, and management. This accessible textbook is suitable for both advanced undergraduate and graduate students who have had a general ecology course, but no further training in benthic ecology. It will also be of relevance and use to professional researchers and consultants in marine ecology and environmental science who seek a compact but comprehensive introduction to benthic ecology.
The sediment and related environmental factors
Authors: Gray John S. , Elliott Michael
Published: November 2020

Our next major question is, how can we characterize the sediment as a habitat for biota? Marine sediments range from coarse gravels in areas subjected to much wave and current action, to muds typical of low-energy estuarine areas and to fine silts and clays in deep-sea sediments. The settling velocity of those particles and the ability of any particle to be re-suspended, moved, and redeposited depends on the prevailing hydrographic regime (e.g. see Open University 2002). The latter will in turn influence the transport of a species´ dispersal stages, especially larvae which will then be allowed to settle following metamorphosis under the appropriate hydrographic conditions (defined as hydrographic concentration). Hence the presence of fine sediments will indicate the depositing/accreting areas which may also be suitable for passively settling organisms. Clearly the particle size is of major importance in characterizing sediments, although sediments can also be categorized by their origin (fluvial, biogenic, cosmogenic, etc.) and their material (quartz, carbonates, clays, etc.) (Open University 2002). On a typical sandy beach the coarsest particles lie at the top of the beach and grade down to the finest sediments at the waterline. The top of the beach is dry and there is much windblown sand, since coarse sands drain rapidly, whereas at the lower end of the beach the sediments are wet, with frequent standing pools. Coarse sediment is found at the top of the shore because as the waves break on the beach the heaviest particles sediment out first. Finer particles remain in suspension longer and are carried seaward on the wave backwash. Beaches change their slope over the seasons, being steeper in winter and shallower in summer. A greater degree of wave energy will produce steeper beaches, as particles are pushed up the beach and so may be stored there, whereas gentle waves produce shallow, sloping beaches. Waves hitting the shore obliquely will create sediment movement as longshore drift. Subtidally, waves are important in distributing and affecting sediments down to depths of 100 m, but the effect decreases exponentially with depth and so the dominant subtidal influences on sediment transport are currents.
Spatial variations in sediment systems
Authors: Gray John S. , Elliott Michael
Published: November 2020

In this chapter the primary emphasis is on spatial scales of disturbances, and we will follow on from our earlier discussions on the mechanisms of competition and predation and the controversy over their importance in controlling species richness. Huston (1994) realized that the effects of competition, predation, and general physical disturbance were similar in that individuals were removed from the assemblage. We now show that there is a need to link these aspects with the tolerances of individual species, for example to determine in which of these cases the organisms are absent because the conditions now fall outside the optimal tolerance ranges. Thus we discuss disturbance as a general phenomenon which includes the effects of any processes that lead to a reduction in numbers of individuals and/or biomass. Disturbance includes physical disturbance as well as biological processes such as the effects of competition and predation on assemblages. The spatial scales covered range from micrometres to many hundreds of kilometres for the effects of bottom trawling, which is now considered to be one of the most serious and damaging threats to sediment habitats and assemblages. Disturbance effects caused by trawling and by pollution are considered in the following chapters. First, it is necessary to consider scale since many new insights have developed in the past few years of research. In the past couple of decades a new branch of ecology, landscape ecology, has developed, devoted to considering patterns over large areas, and a terminology of spatial scales has been defined. Grain is the first level of spatial resolution; it relates to the individual data unit and can be described as fine-grained to coarse-grained. Extent refers to the overall size of the study area. A map of 100 km2 and one of 100 000 km2 differ in extent by a factor of 1000. Grain and extent are illustrated in Fig. 6.1. A third component is lag, which is the betweensample distance. Figure 6.2 summarizes temporal and spatial scales of disturbances (modified from Zajac et al. 1998). The figure shows the main types of disturbances affecting soft-sediment systems, and separates them into natural and anthropogenic effects (see also Chapter 11, which indicates some of the management responses to these effects).
Qubits and the Framework of Quantum Mechanics
Authors: Kaye Phillip , Laflamme Raymond , Mosca Michele
Published: November 2020

In this section we introduce the framework of quantum mechanics as it pertains to the types of systems we will consider for quantum computing. Here we also introduce the notion of a quantum bit or ‘qubit’, which is a fundamental concept for quantum computing. At the beginning of the twentieth century, it was believed by most that the laws of Newton and Maxwell were the correct laws of physics. By the 1930s, however, it had become apparent that these classical theories faced serious problems in trying to account for the observed results of certain experiments. As a result, a new mathematical framework for physics called quantum mechanics was formulated, and new theories of physics called quantum physics were developed in this framework. Quantum physics includes the physical theories of quantum electrodynamics and quantum field theory, but we do not need to know these physical theories in order to learn about quantum information. Quantum information is the result of reformulating information theory in this quantum framework. We saw in Section 1.6 an example of a two-state quantum system: a photon that is constrained to follow one of two distinguishable paths. We identified the two distinguishable paths with the 2-dimensional basis vectors and then noted that a general ‘path state’ of the photon can be described by a complex vector with |α0|2 +|α1|2 = 1. This simple example captures the essence of the first postulate, which tells us how physical states are represented in quantum mechanics. Depending on the degree of freedom (i.e. the type of state) of the system being considered, H may be infinite-dimensional. For example, if the state refers to the position of a particle that is free to occupy any point in some region of space, the associated Hilbert space is usually taken to be a continuous (and thus infinite-dimensional) space. It is worth noting that in practice, with finite resources, we cannot distinguish a continuous state space from one with a discrete state space having a sufficiently small minimum spacing between adjacent locations. For describing realistic models of quantum computation, we will typically only be interested in degrees of freedom for which the state is described by a vector in a finite-dimensional (complex) Hilbert space.
A Quantum Model of Computation
Authors: Kaye Phillip , Laflamme Raymond , Mosca Michele
Published: November 2020

In Section 1.3, we introduced the circuit model of (classical) computation. We restricted attention to reversible circuits since they can simulate any non-reversible circuit with modest overhead. This model can be generalized to a model of quantum circuits. In the quantum circuit model, we have logical qubits carried along ‘wires’, and quantum gates that act on the qubits. A quantum gate acting on n qubits has the input qubits carried to it by n wires, and n other wires carry the output qubits away from the gate. A quantum circuit is often illustrated schematically by a circuit diagram as shown in Figure 4.1. The wires are shown as horizontal lines, and we imagine the qubits propagating along the wires from left to right in time. The gates are shown as rectangular blocks. For convenience, we will restrict attention to unitary quantum gates (which are also reversible). Recall from Section 3.5.3 that non-unitary (non-reversible) quantum operations can be simulated by unitary (reversible) quantum gates if we allow the possibility of adding an ancilla and of discarding some output qubits. A circuit diagram describing a superoperator being implemented using a unitary operator is illustrated in Figure 4.2. In the example of Figure 4.1, the 4-qubit state |ψi⟩= |0⟩⊗ |0⟩⊗ |0⟩⊗ |0⟩ enters the circuit at the left (recall we often write this state as |ψi⟩ = |0⟩|0⟩|0⟩|0⟩ or |ψi⟩ = |0000⟩.) These qubits are processed by the gates U1, U2, U3, and U4. At the output of the circuit we have the collective (possibly entangled) 4-qubit state |ψf⟩. A measurement is then made of the resulting state. The measurement will often be a simple qubit-by-qubit measurement in the computational basis, but in some cases may be a more general measurement of the joint state. A measurement of a single qubit in the computational basis is denoted on a circuit diagram by a small triangle, as shown in Figure 4.1 (there are other symbols used in the literature, but we adopt this one). The triangle symbol will be modified for cases in which there is a need to indicate different types of measurements.R50
Quantum Error Correction
Authors: Kaye Phillip , Laflamme Raymond , Mosca Michele
Published: November 2020

A mathematical model of computation is an idealized abstraction. We design algorithms and perform analysis on the assumption that the mathematical operations we specify will be carried out exactly, and without error. Physical devices that implement an abstract model of computation are imperfect and of limited precision. For example, when a digital circuit is implemented on a physical circuit board, unwanted electrical noise in the environment may cause components to behave differently than expected, and may cause voltage levels (bit-values) to change. These sources of error must be controlled or compensated for, or else the resulting loss of efficiency may reduce the power of the information-processing device. If individual steps in a computation succeed with probability p, then a computation involving t sequential steps will have a success probability that decreases exponentially as pt. Although it may be impossible to eliminate the sources of errors, we can devise schemes to allow us to recover from errors using a reasonable amount of additional resources. Many classical digital computing devices use error-correcting codes to perform detection of and recovery from errors. The theory of error-correcting codes is itself a mathematical abstraction, but it is one that explicitly accounts for errors introduced by the imperfection and imprecision of realistic devices. This theory has proven extremely effective in allowing engineers to build computing devices that are resilient against errors. Quantum computers are more susceptible to errors than classical digital computers, because quantum mechanical systems are more delicate and more difficult to control. If large-scale quantum computers are to be possible, a theory of quantum error correction is needed. The discovery of quantum error correction has given researchers confidence that realistic large-scale quantum computing devices can be built despite the presence of errors. We begin by considering fundamental concepts for error correction in a classical setting. We will focus on three of these concepts: (a) the characterization of the error model, (b) the introduction of redundancy through encoding, and (c) an error recovery procedure. We will later see that these concepts generalize quite naturally for quantum error correction.
Geomorphology
Authors: Maun M. Anwar
Published: November 2020

Geomorphology is the study of form and structure of sand dunes. Dunes are found in three types of landscapes: sea coasts and lakeshores, river valleys, and arid regions. Coastal dunes are formed along coasts in areas above the high water mark of sandy beaches. They occur in both the northern and southern hemi sphere from the Arctic and Antarctic to the equator, and in arid and semi-arid regions. They are very common in temperate climates but are less frequent in tropical and subtropical coasts. Dunes are also common around river mouths where the sand carried in water is deposited (Carter et al. 1990b). During floods rivers overflow their banks and deposit sand in river valleys that is subsequently dried by wind and shaped into dunes. In dry regions with less than 200 mm of precipitation per year, the weathering of sandstone and other rocks produce sand that is subject to mass movement by wind because of sparsity of vegetation. There are many similarities in processes and patterns of dune form and structure among these three systems, however each location has its own unique features. In this chapter the emphasis will be on the geomorphology of dune systems along the coasts of oceans and lakes. Coastal geomorphologists have been attempting to classify the coastal land forms but they defy a simple classification because of tremendous variability in plant taxa, sand texture, wind velocity, climate, sand supply, coastal wave energy and biotic influences including human impact. According to Carter et al. (1990b) the great variety of coastal land forms around the world is primarily related to sediment availability, climate, wave energy, wind regime and types of vegetation. Classification based on these criteria would be more useful in distinguishing between shoreline dune forms than the use of subjective terms—for example white, grey or yellow dunes—sometimes employed by plant ecologists (Tansley 1953). Cowles (1899) said ´a dune complex is a restless maze´ because the great topographic diversity depends on changes in the dune terrain from day to day, month to month, season to season and year to year.
Influence of supernovae, gamma-ray bursts, solar flares, and cosmic rays on the terrestrial environment
Authors: Dar Arnon
Published: November 2020

Changes in the solar neighbourhood due to the motion of the sun in the Galaxy, solar evolution, and Galactic stellar evolution influence the terrestrial environment and expose life on the Earth to cosmic hazards. Such cosmic hazards include impact of near-Earth objects (NEOs), global climatic changes due to variations in solar activity and exposure of the Earth to very large fluxes of radiations and cosmic rays from Galactic supernova (SN) explosions and gamma-ray bursts (GRBs). Such cosmic hazards are of low probability, but their influence on the terrestrial environment and their catastrophic consequences, as evident from geological records, justify their detailed study, and the development of rational strategies, which may minimize their threat to life and to the survival of the human race on this planet. In this chapter I shall concentrate on threats to life from increased levels of radiation and cosmic ray (CR) flux that reach the atmosphere as a result of (1) changes in solar luminosity, (2) changes in the solar environment owing to the motion of the sun around the Galactic centre and in particular, owing to its passage through the spiral arms of the Galaxy, (3) the oscillatory displacement of the solar system perpendicular to the Galactic plane, (4) solar activity, (5) Galactic SN explosions, (6) GRBs, and (7) cosmic ray bursts (CRBs). The credibility of various cosmic threats will be tested by examining whether such events could have caused some of the major mass extinctions that took place on planet Earth and were documented relatively well in the geological records of the past 500 million years (Myr). A credible claim of a global threat to life from a change in global irradiation must first demonstrate that the anticipated change is larger than the periodical changes in irradiation caused by the motions of the Earth, to which terrestrial life has adjusted itself. Most of the energy of the sun is radiated in the visible range. The atmosphere is highly transparent to this visible light but is very opaque to almost all other bands of the electromagnetic spectrum except radio waves, whose production by the sun is rather small.
Climate change and global risk
Authors: Frame David , Allen Myles R.
Published: November 2020

Climate change is among the most talked about and investigated global risks. No other environmental issue receives quite as much attention in the popular press, even though the impacts of pandemics and asteroid strikes, for instance, may be much more severe. Since the first Intergovernmental Panel on Climate Change (IPCC) report in 1990, significant progress has been made in terms of (1) establishing the reality of anthropogenic climate change and (2) understanding enough about the scale of the problem to establish that it warrants a public policy response. However, considerable scientific uncertainty remains. In particular scientists have been unable to narrow the range of the uncertainty in the global mean temperature response to a doubling of carbon dioxide from pre-industrial levels, although we do have a better understanding of why this is the case. Advances in science have, in some ways, made us more uncertain, or at least aware of the uncertainties generated by previously unexamined processes. To a considerable extent these new processes, as well as familiar processes that will be stressed in new ways by the speed of twentyfirst century climate change, underpin recent heightened concerns about the possibility of catastrophic climate change. Discussion of ‘tipping points’ in the Earth system (for instance Kemp, 2005; Lenton, 2007) has raised awareness of the possibility that climate change might be considerably worse than we have previously thought, and that some of the worst impacts might be triggered well before they come to pass, essentially suggesting the alarming image of the current generation having lit the very long, slow-burning fuse on a climate bomb that will cause great devastation to future generations. Possible mechanisms through which such catastrophes could play out have been developed by scientists in the last 15 years, as a natural output of increased scientific interest in Earth system science and, in particular, further investigation of the deep history of climate. Although scientific discussion of such possibilities has usually been characteristically guarded and responsible, the same probably cannot be said for the public debate around such notions.
References and Remarks on Rotating Fluids
Authors: Chemin Jean-Yves , Desjardins Benoit , Gallagher Isabelle , Grenier Emmanuel
Published: November 2020

The problem investigated in this part can be seen as a particular case of the study of the asymptotic behavior (when ε tends to 0) of solutions of systems of the type where Δε is a non-negative operator of order 2 possibly depending on ε, and A is a skew-symmetric operator. This framework contains of course a lot of problems including hyperbolic cases when Δε = 0. Let us notice that, formally, any element of the weak closure of the family (uε)ε>0 belongs to the kernel of A. We can distinguish from the beginning two types of problems depending on the nature of the initial data. The first case, known as the well-prepared case, is the case when the initial data belong to the kernel of A. The second case, known as the ill-prepared case, is the general case. In the well-prepared case, let us mention the pioneer paper by S. Klainerman and A. Majda about the incompressible limit for inviscid fluids. A lot of work has been done in this case. In the more specific case of rotating fluids, let us mention the work by T. Beale and A. Bourgeois and T. Colin and P. Fabrie. In the case of ill-prepared data, the nature of the domain plays a crucial role. The first result in this case was established in 1994 in the pioneering work by S. Schochet for periodic boundary conditions. In the context of general hyperbolic problems, he introduced the key concept of limiting system (see the definition on page 125). In the more specific case of viscous rotating fluids, E. Grenier proved in 1997 in Theorem 6.3, page 125, of this book. At this point, it is impossible not to mention the role of the inspiration played by the papers by J.-L. Joly, G. Métivier and J. Rauch (see for instance and). In spite of the fact that the corresponding theorems have been proved afterwards, the case of the whole space, the purpose of Chapter 5 of this book, appears to be simpler because of the dispersion phenomena.
The Jaw Displaced
Authors: Weiner J. S. , Stringer Chris
Published: November 2020

On the basis of our preliminary arguments and our anatomical re-examination of the fragments, Mr. W. N. Edwards, the Keeper of Geology of the Natural History Museum, felt justified in allowing the specimens of mandible, cranium, and teeth to be drilled for much larger samples than could ever have been sanctioned hitherto. These larger samples and the use of improved chemical methods guaranteed a high degree of analytical reliability. The drilling itself gave us an encouraging start. As the drilling proceeded, Dr. Oakley and his assistant perceived a distinct smell of ‘burning horn’ when the jaw was sampled, but they noticed nothing of the sort with any of the cranial borings. This subjective indication of some distinct difference between the constitution of jaw and cranium soon gained objective confirmation. The drilled sample from the jaw proved to be utterly unlike those from the cranium. In keeping with the belief in its fossil or semi-fossilized character, the latter produced a fine particulate granular powder, whereas the jaw yielded little shavings of bone, just as did a fresh bone sampled as a control. Here was the beginning of the series of findings which progressively widened the gulf between jaw and cranium. Very soon Dr. Oakley obtained clear chemical evidence to justify fully the strong suspicion of the modernity of the jaw and of the totally distinct origin of the cranium. An improved technique for estimating small quantities of fluorine produced this decisive result. The cranial fragments of site I were found to contain fluorine in a concentration of 0.1 per cent., a value somewhat similar to that of specimens of known Late Ice Age. The jaw and the three teeth on the contrary gave much lower figures, at levels below 0.03 per cent., values well within the range of known modern and fresh specimens. Indeed, these values are on the borderline of the sensitivity of the method. The fluorine test gave its verdict twice over. For the two cranial fragments from the second Piltdown site contained a fluorine concentration of 0.1 per cent, and the isolated molar which went with these fragments contained less than 0.01 per cent.
The Principals and Their Part
Authors: Weiner J. S. , Stringer Chris
Published: November 2020

The objective evidence for the deception at Piltdown was overwhelming. The frauds extended to every aspect of the discovery—geological, archaeological, anatomical, and chemical—so that proof could be adduced three or four times over. Moreover, every time a new line of investigation was applied, it confirmed, as we have seen, what all previous evidence had established. The two Piltdown ‘men’ were forgeries, the tools were falsifications, the animal remains had been planted. The skill of the deception should not be underestimated, and it is not at all difficult to understand why forty years should have elapsed before the exposure; for it needed all the new discoveries of palaeontology to arouse suspicion, and completely new chemical and X-ray techniques to prove the suspicion justified. Professor Le Gros Clark, Dr. Oakley, and I wrote in our report that ‘Those who took part in the excavation at Piltdown had been the victims of an elaborate and inexplicable deception’. Inexplicable, indeed, for the principals were known to us as men of acknowledged distinction and highly experienced in palaeontological investigation. Woodward, in 1912, was a man of established reputation. Dawson enjoyed a solid esteem. Teilhard de Chardin was, of course, only at the beginning of his palaeontological career. Knowing their place in the world of science, we felt sure that these investigators, whose integrity there was not the slightest reason to question, had been victims—like the scientific world at large—of the deception. Arthur Smith Woodward (who was of an age with Dawson) at the time of the discovery had been Keeper of the Department of Geology at the British Museum since 1901, the year of his election to the Royal Society, and had scores of papers of very great merit to his credit. His work on fossil reptiles and fishes was on a monumental scale, and he had also made discoveries in mammalian palaeontology. He was without doubt the leading authority in his own field. His position was abundantly recognized by many awards and by appointment to many high offices—for example, Secretary, and in the Piltdown years successively Vice-President and President, of the Geological Society.
Lineaments of the Forger
Authors: Weiner J. S. , Stringer Chris
Published: November 2020

If we hope to identify the perpetrator of the Piltdown fraud, or to get near doing so, we may begin with some quite obvious questions. This may help us to sketch out what manner of man we are dealing with and perhaps give us a few clues. How could the faked jaw have been obtained? We can at once dispose of the notion that any difficulty would have been experienced in procuring an ape’s mandible, or in all probability several, for the forger may have used up a number before he was satisfied. Then, as now, they could be bought from, or through, a local taxidermist, or, if not, then easily enough from one of the famous London firms. One would almost certainly go to Gerrard’s in Camden Town, who have been established in this business (in their Camden Town address) since 1860. Anyone who has ever worked in a museum would know of the firm. Mr. Gerrard tells me that unmatched jaws and other odd bones were probably easier to come by in the years before World War I than now. Before the blitz of the last war blotted out their premises, once a month one could attend a ‘taxidermists’ ’ auction in the rooms of Stevens in King Street, and a collector could hope to pick up an enormous variety of specimens and bones. Odd bits of the skeleton, such as teeth and mandibles, were cheap enough in those days. Ape and human jaws could be easily come by and many geologists had them. Lewis Abbott, for example, when he wrote of the Piltdown jaw in 1913, had access to skeletal material for his comparative study; he mentions some of the simian features of the fossil jaw as ‘obtaining in a chimpanzee jaw now before me’. The field of inquiry is therefore not particularly narrowed down by a consideration of this sort. Flints like the ‘worked’, so-called, pre-Chellean flint implements at Piltdown could also have been obtained or even made without particular difficulty; but at once we are aware that we are dealing with a reasonably informed archaeologist.
North America II: The Central and Northern Plains
Authors: Mitchell Peter
Published: November 2020

The Central and Northern Plains are home to many of the peoples popularly considered quintessential Native Americans. First brought to the widespread attention of Europeans and Euro-Americans as the ‘noble savages’ of nineteenth-century romantic paintings and travel accounts, they were later stereotyped in dime novels and Hollywood movies as an inconvenient—and ultimately removed—barrier to white expansion and settlement. Only relatively recently has that image given way to the more rounded, if still over-romanticized, one seen in films like Dances with Wolves. However, the extrapolation of Plains equestrian groups as a generalization for all Native Americans is not the reason to focus on them here. rather, it is because of the great wealth of evidence—ethnographic, historical, and archaeological—that relates to the impacts on them of the horse. Those impacts affected village-based farming communities along the Missouri river and its tributaries as well as the mobile societies of the open grasslands. Using evidence from both, I look at how having horses affected the ways in which people hunted bison, moved themselves and their goods, and structured their use of the landscape, as well as at how changing patterns of warfare and trade influenced the broader organization of society. These topics also relate to several broader issues. One is the relationship between the horse and two other agents of change: the spread of firearms and the involvement of Native peoples in trading furs and bison robes to Europeans. Another concerns the different responses to the horse by those who used it to enhance a mobile hunting way of life and those who sought to integrate it within an economy and social system in which horticulture and permanent settlements were paramount. A third relates to the ecological constraints on people’s ability to keep horses on the Plains: what were they? What was done to mitigate them? And how did they affect the region’s history between the initial acquisition of horses in the early 1700s and the loss of independence that followed the Battle of the Little Big Horn in 1876 and culminated with the Wounded Knee Massacre of 1890?
The Grand Bargain
Authors: Susskind Richard , Susskind Daniel
Published: November 2020

There are two possible futures for the professions. The first is reassuringly familiar. It is a more efficient version of what we already have today. On this model, professionals continue working much as they have done since the middle of the nineteenth century, but they heavily standardize and systematize their routine activities. They streamline their old ways of working. The second future is a very different proposition. It involves a transformation in the way that the expertise of professionals is made available in society. The introduction of a wide range of increasingly capable systems will, in various ways, displace much of the work of traditional professionals. In the short and medium terms, these two futures will be realized in parallel. In the long run, the second future will dominate, we will find new and better ways to share expertise in society, and our professions will steadily be dismantled. That is the conclusion to which this book leads. The first step in our argument involves taking stock of the professions we currently have. We do this, in this opening chapter, to provide a foundation of solid thinking about the professions—about their purpose and common features, their strengths and weaknesses—upon which we build later. We start by sketching an informal portrait of today’s professions. We follow this with a more systematic attempt to explain which occupational groups belong to the professions and why. We then discuss the history of the professions and look at the ‘grand bargain’, the traditional arrangement that grants professionals both their special status and their monopolies over numerous areas of human activity. Next, we reflect on various theoretical accounts of the professions, which leads us to identify a series of fundamental problems with our professions as currently organized. We close with a call for a new mindset, and point to a series of biases that are likely to inhibit professionals from thinking freely about their future. To set off at an easy pace, we begin with a set of non-theoretical, everyday views about the professions. On reflection, most people would say that the professions are at the heart of our social and working lives.
From the Vanguard
Authors: Susskind Richard , Susskind Daniel
Published: November 2020

In this chapter we change pace. We run through a group of different professions and offer a glimpse of the many ways in which they are changing, largely because of technology. The picture we present, although wide-ranging and varied, is not held out as comprehensive. It reflects activity only in particular parts of the world, predominantly the Anglo-American region, and at just one point in time—the middle of the second decade of the twenty- first century. In years to come, when we look back on the pages that follow, we will no doubt see, with the acuity of hindsight, that we missed some great case studies, that we included some which might better have been omitted, and that some of our exemplars no longer exist. This is to be expected. It would require many more volumes to carry out an exhaustive survey of technological change across the professions, and it would demand supernatural prescience to isolate the eventual winners. But to dwell on any particular case—success, failure, or omission—would be to misunderstand what we are trying to achieve in this chapter and through much of the book. To paraphrase the literary critic Harold Bloom, we are seeking to look beyond any particular ripple on the surface and, with a broad sweep through our chosen professions, to capture the deeper current of change that we sense is flowing below. In The Patient Will See You Now, Eric Topol, cardiologist and professor of genomics, anticipates that ‘[w]e are embarking on a time when each individual will have all their own medical data and the computing power to process it . . . from womb to tomb . . . even to prevent an illness before it happens’. There are many other commentators who are making predictions in this spirit. And the contrast with the current and long-established practice of medicine by doctors could not be starker. Traditionally, when people suspect something might be amiss with their health they book an appointment, they show up in person, they sit in one or more face-to-face interactions with individual experts, who in turn prescribe courses of action, often to be implemented by the patients once they leave.
Left iliac fossa pain
Authors: Farne Hugo , Norris-Cervetto Edward , Warbrick-Smith James
Published: November 2020

In Figure 17.1 the differential diagnosis is arranged in order of likelihood in a woman of this age, with more likely diagnoses in larger font and less likely diagnoses in smaller font. Pathologies that should be excluded at the earliest possible opportunity are shown in bold. There are a number of gynaecological pathologies that can cause acute LIF pain. Some, such as ectopic pregnancy, mittelschmerz (mid-cycle pain), or haemorrhage into a functional ovarian cyst, can only occur in menstruating women. Others, such as pelvic inflammatory disease or torsion/rupture of an ovarian cyst, are far more likely to be seen in women younger than Mrs Hamilton, but can be kept in mind as rare differentials for someone of her age. Testicular torsion can cause referred pain to either the left or right iliac fossa and tends to occur in boys and young men. Haemorrhage into a testicular tumour can also cause left or right iliac fossa pain. Thus, don’t forget to examine the testes. You should ask the standard array of questions about the pain—remember the mnemonic SOCRATES: Site: Where is the pain, and has it always been there? Pain that is initially poorly localized, midline, and colicky but which then migrates to the LIF and becomes constant is highly suggestive of acute diverticulitis (akin to left-sided appendicitis). Pain that migrates down the left flank and iliac fossa is more consistent with the migration of a ureteric stone. Onset: Gradual or sudden? Sudden onset of pain is suggestive of perforation of a viscus, or of acute haemorrhage (e.g. into an ovarian cyst or from a ruptured AAA) or torsion (of an ovary or testis). Character: Is the pain colicky or constant? Is it sharp or dull? Acute diverticulitis is often preceded by colicky midline pain. Ureteric calculi may result in colicky pain. Established diverticulitis, and the other differential diagnoses from our list would all produce constant abdominal pain. Sharp pain is most suggestive of haemorrhage, perforation, or torsion. Radiation: Does the pain radiate to the groin (typical of ureteric pain)? Alleviating factors: Does anything make the pain better? Discomfort due to irritable bowel syndrome (IBS) may be relieved by defecation.
Limb weakness
Authors: Farne Hugo , Norris-Cervetto Edward , Warbrick-Smith James
Published: November 2020

The definition of weakness is important, because many patients who self-describe a ‘weak limb’ will actually have a clumsy limb (ataxia), a numb limb (reduced sensation), or a limb that is too painful to move. The time course of the onset of the symptoms in general reflects the time course of the underlying pathology: • Sudden onset (seconds to minutes) usually implies either trauma (e.g. displaced vertebral fractures due to major trauma) or certain vascular insults (e.g. stroke, transient ischaemic attack (TIA)). • Subacute onset (hours to days) suggests a progressive demyelination (e.g. Guillain–Barre syndrome, multiple sclerosis) or a slowly expanding haematoma (e.g. subdural haematoma). • Chronic onset (weeks to months), is consistent with pathologies such as a slow-growing tumour or motor neuron disease (progressive degeneration of motor neurons). As only acute and subacute limb weakness will present acutely to generalists in hospital (chronic onset cases will most likely be referred to neurology from primary care), we have limited the chapter to these cases. Limb movement requires an intact pathway from the cerebral cortex, down the corona radiata, internal capsule, and pons, along the corticospinal tract of the spinal cord, out along a nerve root, and down a peripheral nerve to the neuromuscular junction and muscle itself. If a patient has limb weakness, there must be a lesion somewhere in this pathway. Figure 26.2 gives the differential diagnosis for limb weakness. Mr Walker has presented with rapid onset of left-sided arm weakness. Key clues in the history to elicit include: • Exact time of onset? This is critical in suspected strokes because the window of time in which to confirm the diagnosis and administer thrombolysis (if appropriate) is only 4.5 hours from onset of symptoms (after that, you risk doing more harm than good to the patient). If you suspect a stroke in a patient within that time frame, call the thrombolysis team immediately. In this case, all we can say is that the onset was at some point in the 7 hours between 11 p.m. (when he went to sleep) and 6 a.m. (when he woke up), so we cannot confidently say the onset was within 4.5 hours.
The decoration of early shrines and temples
Authors: Potts Charlotte R.
Published: November 2020

An integral part of the transition from ‘huts’ to ‘houses’ in the seventh and early sixth century BC was the adoption of a new roofing system using wooden beams and terracotta tiles instead of traditional thatch. The two elements of the new system formed an integrated unit, with special tiles designed and positioned to protect the perishable wooden beams from rain, wind, and fire; many also carried painted and moulded decorations that have encouraged study of their iconography as well as function. The disappearance of wooden trusses and supporting mud-brick walls from the archaeological record means that thousands of these durable tiles and architectural terracottas now comprise the primary evidence for the size, form, and decoration of many early Etruscan and Latial superstructures. Excavations in the last seventy years have yielded new information about the distribution of the decorative elements of these roofs in Etruria and Latium, and in particular about the different types of buildings on which they appeared. It is clear that architectural terracottas were initially placed on a wide variety of buildings, unlike their Greek counterparts, but gradually became the preserve of religious architecture. This chapter will examine the nature and location of these roofs, their imagery, and explanations for their increasingly limited use. As such it will offer a detailed analysis of the process by which terracottas became a means of differentiating religious buildings from vernacular architecture during the sixth century BC. Tile production appears to have begun in central Italy by the middle of the seventh century BC and can be associated with significant changes in society and economy. With an approximate weight of 60 kilograms per square metre for tiles and up to 85 kilograms per square metre for the supporting roof beams, the downward and outward pressure of tiled roofs had to be countered with strong, preferably stonebased, walls following rectangular or square plans, the careful selection of timbers to span greater distances, and specialized craftsmen to make, fit, and repair the roofs. All of these factors imply more sedentary communities than hut architecture, growing technical infrastructure, and an ability and readiness to invest in the greater capital expense of a tiled roof.