bluuebunny/crossref_metadata_2025_split huggingface dataset:
The biochemical standard state
Authors: Sherwood Dennis , Dalby Paul 
Published: August 2018

Abstract
Applying thermodynamics to biological systems requires the use of the biochemical standard state. Many texts do not mention the biochemical standard state, and most of those that do dismiss it in three sentences: ‘The equilibrium constant K refers to pH 0. For biological systems, that’s not convenient, and so the biochemical standard state is defined as pH 7. K then becomes K ′. When K ′ replaces K in all the equations, everything works’. This is most unsatisfactory: it is not obvious why K is linked to pH 0, and replacing K by K ′ seems to be a typographical trick. This chapter therefore explains clearly why K relates to pH 0, why this is important, how K ′ relates to the biologically more relevant pH 7, how the biochemical standard is defined and used, and how equations based on conventional standards can be transformed to the biochemical standard.
The bioenergetics of living cells
Authors: Sherwood Dennis , Dalby Paul 
Published: August 2018

Abstract
Living systems create order, and appear to break the Second Law. This chapter explains, and resolves, this apparent paradox, drawing on the concept of coupled reactions (as introduced in Chapters 13 and 16), as mediated by ‘energy currencies’ such as ATP and NADH. The chapter then examines the key energy-capturing systems in biological systems – glycolysis and the citric acid cycle, and also photosynthesis. Topics covered include how energy is captured in the conversion of glucose to pyruvate, the mitochondrial membrane, respiration, electron transport, ATP synthase, chloroplasts and thylakoids, photosystems I and II, and the light-independent reactions of photosynthesis.
Thermodynamics today – and tomorrow
Authors: Sherwood Dennis , Dalby Paul 
Published: August 2018

Abstract
This last chapter explores the frontiers of how thermodynamics is currently being applied to biology, moving from the scale of the molecule to the scale of the cell. The key theme is ‘self-assembly’ – the process by which macromolecules spontaneously assemble into larger structures such as cell membranes, cell organelles, cells, and ultimately organisms. The starting point is the simplest process of self-assembly, the formation of a liquid from the condensation of a gas, which draws on some results from Chapter 15, and develops the concept of nucleation, this leads to a discussion of protein aggregation, and how virus particles are formed. The chapter, and the book, ends with a key challenge for the future: how can we deliberately design self-assembling systems that can perform valuable functions?
Processes in Microbial Ecology
Authors: Kirchman David L. 
Published: August 2018

Abstract
Processes in Microbial Ecology discusses the major processes carried out by viruses, bacteria, fungi, protozoa, and other protists—the microbes—in freshwater, marine, and terrestrial ecosystems. The book shows how advances in genomic and other molecular approaches have uncovered the incredible diversity of microbes in natural environments and unraveled complex biogeochemical processes carried out by uncultivated bacteria, archaea, and fungi. The microbes and biogeochemical processes are affected by ecological interactions, including competition for limiting nutrients, viral lysis, and predation by protists in soils and aquatic habitats. The book links up processes occurring at the micron scale to events happening at the global scale, including the carbon cycle and its connection to climate change issues. The book ends with a chapter devoted to symbiosis and other relationships between microbes and large organisms, which have large impacts not only on biogeochemical cycles, but also on the ecology and evolution of large organisms, including Homo sapiens.
Genomes and meta-omics for microbes
Authors: Kirchman David L. 
Published: August 2018

Abstract
The sequencing of entire genomes of microbes grown in pure cultures is now routine. The sequence data from cultivated microbes have provided insights into these microbes and their uncultivated relatives. Sequencing studies have found that bacterial genomes range from 0.18 Mb (intracellular symbiont) to 13 Mb (a soil bacterium), whereas genomes of eukaryotes are much bigger. Genomes from eukaryotes and prokaryotes are organized quite differently. While bacteria and their small genomes often grow faster than eukaryotes, there is no correlation between genome size and growth rates among the bacteria examined so far. Genomic studies have also highlighted the importance of genes exchanged (“horizontal gene transfer”) between organisms, seemingly unrelated, as defined by rRNA gene sequences. Microbial ecologists use metagenomics to sequence all microbes in a community. This approach has revealed unsuspected physiological processes in microbes, such as the occurrence of a light-driven proton pump, rhodopsin, in bacteria (dubbed proteorhodopsin). Genomes from single cells isolated by flow cytometry have also provided insights about the ecophysiology of both bacteria and protists. Oligotrophic bacteria have streamlined genomes, which are usually small but with a high fraction of genomic material devoted to protein-encoding genes, and few transcriptional control mechanisms. The study of all transcripts from a natural community, metatranscriptomics, has been informative about the response of eukaryotes as well as bacteria to changing environmental conditions.
The ecology of viruses
Authors: Kirchman David L. 
Published: August 2018

Abstract
In addition to grazing, another form of top-down control of microbes is lysis by viruses. Every organism in the biosphere is probably infected by at least one virus, but the most common viruses are thought to be those that infect bacteria. Viruses come in many varieties, but the simplest is a form of nucleic acid wrapped in a protein coat. The form of nucleic acid can be virtually any type of RNA or DNA, single or double stranded. Few viruses in nature can be identified by traditional methods because their hosts cannot be grown in the laboratory. Direct count methods have found that viruses are very abundant, being about ten-fold more abundant than bacteria, but the ratio of viruses to bacteria varies greatly. Viruses are thought to account for about 50% of bacterial mortality but the percentage varies from zero to 100%, depending on the environment and time. In addition to viruses of bacteria and cyanobacteria, microbial ecologists have examined viruses of algae and the possibility that viral lysis ends phytoplankton blooms. Viruses infecting fungi do not appear to lyse their host and are transmitted from one fungus to another without being released into the external environment. While viral lysis and grazing are both top-down controls on microbial growth, they differ in several crucial respects. Unlike grazers, which often completely oxidize prey organic material to carbon dioxide and inorganic nutrients, viral lysis releases the organic material from hosts more or less without modification. Perhaps even more important, viruses may facilitate the exchange of genetic material from one host to another. Metagenomic approaches have been used to explore viral diversity and the dynamics of virus communities in natural environments.
Processes in anoxic environments
Authors: Kirchman David L. 
Published: August 2018

Abstract
During organic material degradation in oxic environments, electrons from organic material, the electron donor, are transferred to oxygen, the electron acceptor, during aerobic respiration. Other compounds, such as nitrate, iron, sulfate, and carbon dioxide, take the place of oxygen during anaerobic respiration in anoxic environments. The order in which these compounds are used by bacteria and archaea (only a few eukaryotes are capable of anaerobic respiration) is set by thermodynamics. However, concentrations and chemical state also determine the relative importance of electron acceptors in organic carbon oxidation. Oxygen is most important in the biosphere, while sulfate dominates in marine systems, and carbon dioxide in environments with low sulfate concentrations. Nitrate respiration is important in the nitrogen cycle but not in organic material degradation because of low nitrate concentrations. Organic material is degraded and oxidized by a complex consortium of organisms, the anaerobic food chain, in which the by-products from physiological types of organisms becomes the starting material of another. The consortium consists of biopolymer hydrolysis, fermentation, hydrogen gas production, and the reduction of either sulfate or carbon dioxide. The by-product of sulfate reduction, sulfide and other reduced sulfur compounds, is oxidized back eventually to sulfate by either non-phototrophic, chemolithotrophic organisms or by phototrophic microbes. The by-product of another main form of anaerobic respiration, carbon dioxide reduction, is methane, which is produced only by specific archaea. Methane is degraded aerobically by bacteria and anaerobically by some archaea, sometimes in a consortium with sulfate-reducing bacteria. Cultivation-independent approaches focusing on 16S rRNA genes and a methane-related gene (mcrA) have been instrumental in understanding these consortia because the microbes remain uncultivated to date. The chapter ends with some discussion about the few eukaryotes able to reproduce without oxygen. In addition to their ecological roles, anaerobic protists provide clues about the evolution of primitive eukaryotes.
Introduction to geomicrobiology
Authors: Kirchman David L. 
Published: August 2018

Abstract
Geomicrobiology, the marriage of geology and microbiology, is about the impact of microbes on Earth materials in terrestrial systems and sediments. Many geomicrobiological processes occur over long timescales. Even the slow growth and low activity of microbes, however, have big effects when added up over millennia. After reviewing the basics of bacteria–surface interactions, the chapter moves on to discussing biomineralization, which is the microbially mediated formation of solid minerals from soluble ions. The role of microbes can vary from merely providing passive surfaces for mineral formation, to active control of the entire precipitation process. The formation of carbonate-containing minerals by coccolithophorids and other marine organisms is especially important because of the role of these minerals in the carbon cycle. Iron minerals can be formed by chemolithoautotrophic bacteria, which gain a small amount of energy from iron oxidation. Similarly, manganese-rich minerals are formed during manganese oxidation, although how this reaction benefits microbes is unclear. These minerals and others give geologists and geomicrobiologists clues about early life on Earth. In addition to forming minerals, microbes help to dissolve them, a process called weathering. Microbes contribute to weathering and mineral dissolution through several mechanisms: production of protons (acidity) or hydroxides that dissolve minerals; production of ligands that chelate metals in minerals thereby breaking up the solid phase; and direct reduction of mineral-bound metals to more soluble forms. The chapter ends with some comments about the role of microbes in degrading oil and other fossil fuels.
Symbioses and microbes
Authors: Kirchman David L. 
Published: August 2018

Abstract
The book ends with a chapter devoted to discussing interactions between microbes and higher plants and animals. Symbiosis is sometimes used to describe all interactions, even negative ones, between organisms in persistent, close contact. This chapter focuses on interactions that benefit both partners (mutualism), or one partner while being neutral to the other (commensalism). Microbes are essential to the health and ecology of vertebrates, including Homo sapiens. Microbial cells outnumber human cells on our bodies, aiding in digestion and warding off pathogens. In consortia similar to the anaerobic food chain of anoxic sediments, microbes are essential in the digestion of plant material by deer, cattle, and sheep. Different types of microbes form symbiotic relationships with insects and help to explain their huge success in the biosphere. Protozoa are crucial for wood-boring insects, symbiotic bacteria in the genus Buchnera provide sugars to host aphids while obtaining essential amino acids in exchange, and fungi thrive in subterranean gardens before being harvested for food by ants. Symbiotic dinoflagellates directly provide organic material to support coral growth in exchange for ammonium and other nutrients. Corals are now threatened worldwide by rising oceanic temperatures, decreasing pH, and other human-caused environmental changes. At hydrothermal vents in some deep oceans, sulfur-oxidizing bacteria fuel an entire ecosystem and endosymbiotic bacteria support the growth of giant tube worms. Higher plants also have many symbiotic relationships with bacteria and fungi. Symbiotic nitrogen-fixing bacteria in legumes and other plants fix more nitrogen than free-living bacteria. Fungi associated with plant roots (“mycorrhizal”) are even more common and potentially provide plants with phosphorus as well as nitrogen. Symbiotic microbes can provide other services to their hosts, such as producing bioluminescence, needed for camouflage against predators. In the case of the bobtail squid, bioluminescence is only turned on when populations of the symbiotic bacteria reach critical levels, determined by a quorum sensing mechanism.
Harmony as licensing
Authors: van der Hulst Harry 
Published: August 2018

AbstractThis chapter develops an explicit theory of vowel harmony based on unary elements and lateral and positional licensing which is embedded in a general dependency-based theory of phonological structure (called ‘Radical CV Phonology’). Harmony is analyzed in terms of a licensing requirement, which results in ‘agreement’, both intra-morphemically and inter-morphemically, that is, within the domain of the word In essence, the view put forward is that lexical vowel harmony involves the selection of lexically listed allomorphs. Licensing will be the selection mechanism for the proper allomorph. The chapter discusses the treatment of morpheme-internal harmony, trigger and targets in harmony, and the notion of cyclicity.
Labial harmony
Authors: van der Hulst Harry 
Published: August 2018

AbstractThis chapter analyzes labial harmony systems such as Turkish, other Turkic languages, and several other languages. Labial harmony rarely occurs by itself, often co-occurring with palatal harmony in Turkic languages. After a detailed analysis of vowel harmony in Standard Turkish—which pays extensive attention to disharmonic roots—the chapter offers a typology of labial harmony systems in Turkic languages in general, based on several typological studies. Other topics that receive special attention are epenthetic vowels, labial attraction, defective patterns, dependencies among different harmonies, diphthongs, stand-alone labial harmony, and the decline of labial harmony in a wide variety of Turkic languages.
Typology of African tongue root systems
Authors: van der Hulst Harry 
Published: August 2018

AbstractThe focus of this chapter is African languages and the various manifestations of tongue root harmony. While there is general agreement on the fact that a typical manifestation of vowel harmony involves the position of the tongue root, there is much controversy both on the phonetic detail of the tongue root distinction and on the nature of the phonological primes that are needed to account for tongue root harmony. Specific topics addressed include: the markedness paradox, patterns of merger, and opacity and transparency. There is also a discussion of vowel harmony in Bantu-C.
Other cases of vowel harmony
Authors: van der Hulst Harry 
Published: August 2018

AbstractThis Chapter discusses a number of cases of vowel harmony ‘on various continents’ and in various language families which have been reported as being either ‘unique’ (sometimes just because of their language family affiliation) or controversial in terms of their properties. Although the data on these languages is too limited to allow very specific analysis, the chapter will discuss them on the basis of the available data, and suggest ways of fitting them into the model that has been tested in the preceding six chapters. Among others, the following languages will be discussed: Middle Korean, Chukchi, Nez Perce, Karajá, Djingili, Kimaragang, Maltese, Assamese, Telugu, Pasiego Spanish, and Chamorro.
Frankfurt
Authors: Schamp Eike W. 
Published: August 2018

Abstract
The European banking crisis and the subsequent euro crisis triggered considerable shocks in Germany’s financial world which fully revealed the weaknesses of the German banking sector. Changing regulation and the low-interest-rate policy from the European Central Bank put the bank’s business models into question. Furthermore, delays became apparent in the improvement of Frankfurt’s sector-specific infrastructure. Frankfurt’s resilience in the crises results from the entangled agency by various actors at local, national, and European levels. Employment in the financial sector at large remained rather stable. Frankfurt increased its role as a European centre in bank and insurance supervision and considerably improved its infrastructure in higher education and research as well as in the digital economy. Although still fragile in various aspects, Frankfurt may become a potential winner on the European continent from the forthcoming Brexit.
Singapore
Authors: Lai Karen P.Y. 
Published: August 2018

Abstract
This chapter examines the spatial and temporal dynamics shaping the development of financial markets and activities to account for the rise of Singapore as an international financial centre (IFC). The analysis draws upon the preceding 1997 Asian financial crisis as industry changes and policy response back then set the stage for subsequent industry shifts, which have shaped the responses and impacts of firms, regulators, and consumers following the 2008 Global Financial Crisis. Key industry shifts include banking liberalization and changing forms of financial consumption in Singapore. The growing prominence of financial markets and emerging sectors, such as Islamic banking and finance (IBF) and offshore renminbi (RMB), and fintech are also examined in terms of their importance for Singapore’s future role as an IFC.
Brutus and His Mirrors (Brutus10.4–6, 13.7–10, 29.2–3, 40.7–8)
Authors: Hutchinson G. O. 
Published: August 2018

AbstractThis chapter and the next look at the Life of Brutus. This chapter looks at all the passages in the Life which display rhythmic density by the criteria given in ch. 3. Notably, they do not appear at the peaks of action—such as Caesar’s assassination or Brutus’ suicide; rather they involve moments of comparison and reflection. Three of them confront Brutus with Cassius, a central comparative concern internal to the Life: an explicit and sustained comparison of character, and two scenes of interaction, including a point where Brutus looks back on his own life. The other moment confronts Brutus with his brave wife, Porcia. Two of the passages also involve comparison with another vital figure of the Life, the Younger Cato. One of the passages is closely similar to the later Appian, and shows us Plutarch reshaping a source
The Fall of the Crassi (Crassus23.7–24.3, 25.12–14, 26.6–9, 30.2–5)
Authors: Hutchinson G. O. 
Published: August 2018

AbstractThe Battle of Carrhae gives Plutarch his real opportunity to rival Thucydides on Sicily: a striking example of the second Life outdoing the first. The Life of Crassus is marked by dense passages which are particularly prolonged and amassed. They involve a moment of greatness for Crassus which outdoes a similar moment for Nicias (see ch. 13); it presents direct speech, after the death of Crassus’ son. These especially heightened passages in the Life form an arc, from initial terror at the Parthians, to noble death and acceptance of death; but the detail complicates this structure. The comparison of father and son is also important to the design; so too ethnography and Plutarch’s treatment of the Parthians. Cassius Dio’s later non-rhythmic account provides a foil.
Antigonus and the Athenians Change Their Tunes (Demetrius28, 29.4, 30.2–31.1)
Authors: Hutchinson G. O. 
Published: August 2018

AbstractThis passage shows a different handling of a major battle, the Battle of Ipsus, in which Antigonus Monophthalmus dies and his son Demetrius Poliorcetes is defeated. Plutarch does not greatly use rhythmic density to enhance the brief treatment of the battle. Instead he exploits rhythmic density to portray changes, under the pressure of the event, in Antigonus’ mindset and in the relationship of father and son, and to advance an ethical story on political power and insight. Demetrius is brought to understand the psychological reality behind the Athenians’ glorification of him; Plutarch expands the thought politically and philosophically. The effect of the battle, before and after, is what matters, not the battle; comparison, change, and philosophy are involved in the rhythmic heightening.
The Deaths of King and Kindred (Agis16.6–17.5, 17.9–18.3; 19.5–21.1)
Authors: Hutchinson G. O. 
Published: August 2018

AbstractA catastrophe in Hellenistic Sparta is portrayed in rhythmic passages that contrast with each other. The comparisons involved in and between both are intricate, within a particularly complex comparative structure, where two Spartan kings, Agis and Cleomenes, are compared with two Roman nobiles, Ti. and C. Gracchus. The king Cleombrotus is compared with Agis and with his own wife; Agis’ death is made part of a structure in which the most important figure is his mother. The accounts gain more force from rhetoric, multiple characterization, and perversion of legality and the constitution. Rhythm creates a powerful narrative; if the source is Phylarchus, the source is unrhythmic. The passages have been underestimated through scorn for Pylarchus and under-appreciation of Plutarch’s rhythmic writing.
Conclusion
Authors: Hutchinson G. O. 
Published: August 2018

AbstractForm, on the most detailed level, turns out to be inextricably connected with expression, meaning, and larger structure. Perhaps modern scholars underestimate form, as is apparent from the greater importance of metre in ancient conceptions of poetic genre. Rhythm plays an important part in building up the worlds of the rhythmic narrative writing that has been considered. At climactic moments of Chariton, rhythm intensifies the supremacy of love in the erotic scheme of values; in the moments of Plutarch, it helps the presentation of a broader scheme of values, where politics is not simply set aside, but where the individual can transcend powerlessness and death. Philosophy, comparison, the evolution and unpredictability of people are presented the more forcefully through passages heightened by rhythm; rhythm as elsewhere marks meaning and expresses thought. The greatness of Plutarch’s writing emerges much more strongly when we start to read him rhythmically.
The Harmonic Oscillator
Authors: Mann Peter 
Published: August 2018

Abstract
This chapter discusses the harmonic oscillator, which is a model ubiquitous to all branches of physics. The harmonic oscillator is a system with well-known solutions and has been fully investigated since it was first developed by Robert Hooke in the seventeenth century. These factors ensure that the harmonic oscillator is as relevant to a swinging pendulum as it is to a quantum field. Due to the importance of this model, the chapter investigates its dynamical properties, including the superposition principle in solutions, and construct a probability density function in a single dimension. The chapter also discusses Hooke’s law, modes and the Morse potential. In addition, in an exercise, the chapter introduces series solutions to ordinary differential equations.