bluuebunny/crossref_metadata_2025_split huggingface dataset:
Freshwater ecosystems
Authors: Taberlet Pierre , Bonin Aurélie , Zinger Lucie , Coissac Eric 
Published: March 2018

Abstract
Chapter 12 “Freshwater ecosystems” focuses on the study of freshwater organisms via eDNA analysis. It addresses the particularities of the production, persistence, transport, and detectability of eDNA in surface waters. Biomonitoring freshwater ecosystems is imposed by law in more and more countries (e.g., European Council 2000) and the potential of eDNA for this purpose has been identified relatively early. This chapter revisits several studies dealing with eDNA-based analysis of macroinvertebrates (e.g., to track seasonal variation in the ecosystem scale), diatoms (for water quality assessment purposes), aquatic plants (e.g., for invasive species detection), fish, amphibians, and other vertebrates (for species inventories and biomass estimation). Finally, Chapter 12 discusses whether rivers can be good conveyor belts of the biodiversity at the scale of an entire catchment.
Marine environments
Authors: Taberlet Pierre , Bonin Aurélie , Zinger Lucie , Coissac Eric 
Published: March 2018

Abstract
Chapter 13 “Marine environments” focuses on different applications of eDNA to study marine biodiversity. After a brief description of the current knowledge on DNA cycle in pelagic and benthic environments, this chapter revisits how DNA metabarcoding, and more generally environmental genomics have revolutionized the field of marine microbiology through the discovery of novel taxa and by unveiling large-scale patterns of diversity for marine bacteria, protists, and viruses. This chapter then presents recent applications of DNA metabarcoding for both basic research or biomonitoring purposes to study marine invertebrates and fish populations and diversity, as well as the detection of invasive species. Current gaps and methodological challenges are also discussed.
Terrestrial ecosystems
Authors: Taberlet Pierre , Bonin Aurélie , Zinger Lucie , Coissac Eric 
Published: March 2018

Abstract
Chapter 14 “Terrestrial ecosystems” focuses on the use of eDNA analysis for the study of terrestrial organisms, especially those found in or associated with soil. While eDNA-based analyses have rapidly gained momentum in the freshwater ecology community, first for single-species detection and more recently for diversity surveys, their success has been less immediate among terrestrial ecologists. Soil microbiologists are a notable exception, as they quickly realized that targeting DNA directly in the environment could free them from cultivating microorganisms prior to any community census. This chapter first addresses the particularities of detectability, persistence, and mobility of eDNA in soil. Then, it revisits several remarkable studies dealing with the characterization of plant, earthworm, or soil microbial communities, as well as soil functional diversity. Finally, Chapter 14 reviews one of the most fascinating opportunities offered by eDNA metabarcoding (i.e., the possibility to carry out multitaxa diversity surveys).
Paleoenvironments
Authors: Taberlet Pierre , Bonin Aurélie , Zinger Lucie , Coissac Eric 
Published: March 2018

Abstract
One of the most fascinating facets of eDNA lies in the possibility of exploiting it to reconstruct past environments in paleoecology and in archaeology. Chapter 15, entitled “Paleoenvironments,” reviews different pioneer studies that scrutinized ancient eDNA extracted from different substrates (e.g., lake sediments, permafrost, or archaeological midden material), to address a wide range of questions. These include, for example, the taxonomic identification of archaeological fish bones in Madagascar from bulk samples, the reconstruction of past plant communities based on the large-scale analysis of permafrost samples, or the assessment of past human diet in Greenland based on midden material. Midden material from archaeological sites represents a valuable source of information for tracking food habits of ancient human communities. It also provides information about the surrounding biodiversity, using humans as biodiversity samplers, which is also explored here.
Host-associated microbiota
Authors: Taberlet Pierre , Bonin Aurélie , Zinger Lucie , Coissac Eric 
Published: March 2018

Abstract
DNA-based approaches have enabled the multifaceted role of microbes for the fitness and performance of their host to be revealed. The increasing recognition of the crucial role of microorganisms for the fitness and performance of plants and animals has led to the concepts of holobiont (i.e., a host and its microbiota), and hologenome (i.e., the collective genomes of a holobiont). Here a brief review is provided of the advances that have been made in this field by using DNA-based approaches. Chapter 16 “Host-associated microbiota” summarizes this area of research by presenting past and recent major findings, as well as new research avenues for unraveling host-microbiota interactions in non-model animals and plants.
Analysis of bulk samples
Authors: Taberlet Pierre , Bonin Aurélie , Zinger Lucie , Coissac Eric 
Published: March 2018

Abstract
Chapter 18 “Analysis of bulk samples” deals with the particular case of biodiversity surveys based on bulk samples. A bulk sample is an environmental sample containing mainly organisms from the taxonomic group under study, such as insect samples obtained from a Malaise trap, or eukaryote-enriched samples obtained from filtered or size-fractionated water samples. One important characteristic of bulk samples is that they usually provide good-quality DNA in high amounts. Chapter 18 presents several seminal studies based on bulk samples that aimed at monitoring arthropod, nematode, or marine metazoan diversity. The advantages and limitations of the classical barcoding COI marker versus metabarcoding markers for bulk sample analysis are also discussed. Finally, Chapter 18 reviews two alternative strategies to limit the taxonomic biases associated with the use of the COI marker (i.e., mitochondrial enrichment via differential centrifugation or capture, followed by extraction and shotgun sequencing).
Of Fragments and Feelings
Authors: Beck Hans 
Published: March 2018

AbstractDrawing on the tenets of the emotional or affective turn in the Humanities and Social Sciences, the article revisits the topic of Roman funeral orations (laudationes funebres). Several funeral speeches from the Republican period survive in fragments. These have become the object of in-depth philological and historical scholarship. Beyond the typical approach to fragments and corresponding orations, which is characterized as content-based, Beck zooms in on the moment when the speeches were delivered. In doing so, he captures the full breadth of the sensory experience of funeral orations in the Forum: their visual display, their soundscape and issues of audibility, as well as the scents that magnified the emotional experience. The article concludes that it was through emotional economies rather than authentic contents that funeral oratory wielded a lasting impact over Roman society.
Fragments of Epideictic Oratory
Authors: Pepe Cristina 
Published: March 2018

AbstractFuneral eulogies are among the older examples of Roman oratory. The practice of honouring the dead with a laudatio funebris (funeral oration) was in the earliest stage reserved to males, but from the late Republic it became customary for women as well. This chapter examines the fragments and testimonia of female funeral eulogies. Although these remains are not abundant, they open some significant unusual perspectives on Roman oratory. First, they show how a speaker managed the task of eulogizing a woman in a society where the rules of rhetoric were laid out by men and intended for the encomium of men. Secondly, they raise other issues which go beyond the boundaries of ‘gender’ differences: laudationes funebres were performed in different venues and before different audiences, according to the social standing of the speaker and the deceased. These aspects strongly affected the aim of the speech, its content, and its style.
What Black Death was to Western Europe, Communism was to Central and Eastern Europe
Authors: Piatkowski Marcin 
Published: March 2018

Abstract
I argue in this chapter that despite its ultimate social, economic, and moral bankruptcy, communism imposed on Poland after 1945 sowed the seeds of the country’s economic success after 1989. The old, feudal social structures were bulldozed to snap Poland out of growth-inhibiting extractive society equilibrium, creating a classless society, boosting social mobility, and securing good quality of education for all. Forced industrialization and unprecedented labour movements supported solid GDP growth rates in Poland until the 1960s, but low returns on investment, lack of technological progress, and external shocks caused declining growth rates in the 1970s, and economic stagnation in the 1980s. I conclude that the assumption that if Poland had returned to capitalism after 1945, it would have developed as quickly as the West, is simplistic. I show that a capitalist Poland would have faced significant challenges to growth, and convergence with the West would not have been guaranteed.
Poland’s Transition Success Story
Authors: Piatkowski Marcin 
Published: March 2018

Abstract
In this chapter I assess the optimal way to measure countries’ economic performance and assert that changes in median income are a better measure than GDP. I also argue in favour of increased focus on measurement of well-being, quality of life, and happiness. I document Poland’s historically unprecedented success, increasing its income from around $10,300 in 1990 to almost $27,000 PPP in 2017, becoming the most successful economy in Europe and among its peers in the world. I claim that Poland’s economic success is unique because it was achieved despite the country’s lack of natural resources, low debt leverage, and a vibrant democracy. It is unique also because Poland’s growth was inclusive; it was the only democratic country in the post-Soviet camp in which 100 per cent of society increased their incomes faster than in the West. Higher incomes translated into the highest levels of well-being and happiness on record.
Fundamental Sources of Poland’s Growth
Authors: Piatkowski Marcin 
Published: March 2018

Abstract
In this chapter I focus on the fundamental causes of the Polish growth miracle, namely the adoption of Western institutions. I start by documenting how the prospect of the EU accession drove the institution building. I show what institutions Poland adopted and how they were key to the country’s economic performance. I argue that Poland was among the fastest adopters of Western institutions, which helped it grow more rapidly than other transition economies. I then focus on the fundamental question of why Poland wanted to adopt good institutions from the West. I argue that Poland built good institutions because of the positive legacy of communism, a historically unprecedented social consensus to ‘return to Europe’, Westernized and growth-oriented elites, and emergence of a strong middle class. Western European readiness to embrace Eastern Europe was also critical. I conclude by offering insights and policy recommendations for other countries.
Conclusions and the Way Forward
Authors: Piatkowski Marcin 
Published: March 2018

Abstract
In this chapter I summarize the main conclusions of the book and describe scenarios for the future. I provide twelve lessons from Poland’s economic success, including the difficulty of moving from an extractive to an inclusive society, the importance of a strong and efficient state, and the need for a more interdisciplinary study of economics. I argue that Poland has never been more prosperous, humane, safe, civilized, and happy than today, and that progress will continue. Poland might reach the level of income of Spain, but is not likely to reach the levels of the core of Europe, Germany, France, or the Netherlands. This would require that Poland becomes a creator rather than an absorber of ideas. It would necessitate further changes in the country’s developmental DNA, in its institutions, and culture. Poland has made a great start. But it has only reached the end of the beginning.
Knowledge and the Cathartic Value of Repentance
Authors: Rabinowitz Dani 
Published: March 2018

Abstract
An austere form of legalism lies at the heart of Judaism. Apart from a limited set of exceptions, every adult Jew is required to observe the full gamut of relevant biblical and rabbinic laws. Success in this endeavor is handsomely rewarded and failure severely punished. Despite the apparent bleakness of this legalism, the system licenses a divine pardon in cases where the offending individual repents. This chapter opens with a discussion of this clemency, as understood by Moses Maimonides, before moving on to a reading of a Talmudic debate that introduces an epistemic puzzle regarding repentance. With the epistemic contours of repentance thus exposed, the remainder of the chapter deals with the manner in which Timothy Williamson’s work on knowledge can undermine the cathartic value of repentance. The chapter concludes with a short note marking the implications for Christianity and Islam.
Constructing Thermal Equilibrium (1866–1871)
Authors: Darrigol Olivier 
Published: March 2018

Abstract
This chapter is the first subset of a set of critical summaries Boltzmann’s writings on kinetic-molecular theory. It covers a first period in which he tried to construct the laws of thermal equilibrium, including the existence of the entropy function and the Maxwell–Boltzmann law, by various means including the principle of least action, Maxwell’s collision formula, the ergodic hypothesis, and a procedure of adiabatic variation. This is an immensely fertile period in which Boltzmann introduced several of the basic concepts, problems, and difficulties of modern statistical mechanics.
The Boltzmann Equation and the H Theorem (1872–1875)
Authors: Darrigol Olivier 
Published: March 2018

Abstract
This chapter covers Boltzmann’s writings about the Boltzmann equation and the H theorem in the period 1872–1875, through which he succeeded in deriving the irreversible evolution of the distribution of molecular velocities in a dilute gas toward Maxwell’s distribution. Boltzmann also used his equation to improve on Maxwell’s theory of transport phenomena (viscosity, diffusion, and heat conduction). The bulky memoir of 1872 and the eponymous equation probably are Boltzmann’s most famous achievements. Despite the now often obsolete ways of demonstration, despite the lengthiness of the arguments, and despite hidden difficulties in the foundations, Boltzmann there displayed his constructive skills at their best.
The Probabilistic Turn (1876–1884)
Authors: Darrigol Olivier 
Published: March 2018

Abstract
This chapter deals with writings in which Boltzmann expressed the statistical nature of the entropy law and temporarily made the relation between entropy and combinatorial probability a basic constructive tool of his theory. In 1881, he discovered that this relation derived from what we now call the microcanonical distribution, and he approved Maxwell’s recent foundation of the equilibrium problem on the microcanonical ensemble. Boltzmann also kept working on problems he had tackled in earlier years. He proposed a new solution to the problem of specific heats, and he performed enormous calculations for the viscosity and diffusion coefficients in the hard-ball model. In a lighter genre, he conceived a new way of determining molecular sizes, and he speculated on a gas model in which the molecular forces would be entirely attractive.
Consolidation (1887–1895)
Authors: Darrigol Olivier 
Published: March 2018

Abstract
This chapter covers a period in which Boltzmann returned to the collision-based approach and consolidated it in answer to criticism and suggestions by William Thomson, Hendrik Lorentz, George Bryan, Gustav Kirchhoff, and Max Planck. He corrected errors in alleged counterexamples of equipartition by William Burnside and William Thomson; and in 1887, when the Dutch theorist Hendrik Lorentz detected an error in his earlier derivation of the H theorem for polyatomic gases, he devised a highly ingenious alternative. In 1894, he offered a new, simplified derivation of the Maxwell–Boltzmann distribution based on an idea by the British mathematician George Bryan. Together with Bryan, he also provided a kinetic-molecular model for the equalization of the temperatures of two contiguous gases. He denounced what he believed to be an error in Gustav Kirchhoff’s derivation of Maxwell’s distribution, and he strengthened Max Planck’s alternative derivation based on time reversal.
The Critical Turn (1895–1899)
Authors: Darrigol Olivier 
Published: March 2018

Abstract
In the writings of this period, we see Boltzmann responding to criticism by British kinetic theorists and by the German mathematician Ernst Zermelo regarding the equipartition of energy and the H theorem. Boltzmann also acted as a critic of other authors. He ridiculed Joseph Bertrand’s attack on Maxwell’s kinetic-molecular reasoning and, after much pounding on Max Planck’s early radiation theory, he managed to convince Planck to alter his approach to irreversibility. Boltzmann also gave a last critical review of the problem of specific heats. During the same period, he was working on his Gastheorie and this prompted him to discuss Johannes Diderik van der Waals’s theory in the light of the Maxwell–Boltzmann theory, with similar reasoning adapted to the problem of chemical dissociation.
Optical Imaging of Metabolic Dynamics in Animals
Authors: Shi Lingyan , Zheng Chaogu , Shen Yihui , Chen Zhixing , Silveira Edilson S. , Zhang Luyuan , Wei Mian , Liu Chang , de Sena-Tomas Carmen , Targoff Kimara , Min Wei 
Published: March 2018

AbstractDirect visualization of metabolic dynamics in living tissues with high spatial and temporal resolution is essential to understanding many biological processes. Here we introduce a platform that combinesdeuteriumoxide (D2O) probing withstimulatedRamanscattering microscopy (DO-SRS) to imagein situmetabolic activities. Enzymatic incorporation of D2O-derived deuterium into macromolecules generates carbon-deuterium (C-D) bonds, which track biosynthesis in tissues and can be imaged by SRSin situ. Within the broad vibrational spectra of C-D bonds, we discovered lipid-, protein-, and DNA-specific Raman shifts and developed spectral unmixing methods to obtain C-D signals with macromolecular selectivity. DO-SRS enabled us to probede novolipogenesis in animals, image protein biosynthesis without tissue bias, and simultaneously visualize lipid and protein metabolism and reveal their different dynamics. DO-SRS, being noninvasive, universally applicable, and cost-effective, can be adapted to a broad range of biological systems to study development, tissue homeostasis, aging, and tumor heterogeneity.
Complex Interplay between Serum and Fibroblasts in 3D Hepatocyte Co-culture
Authors: Mittal Nikhil , Li Huan , Ananthanarayanan Abhishek , Yu Hanry 
Published: March 2018

AbstractPrevious studies have suggested that primary hepatocytes cultured in vitro undergo a rapid loss of function. On the other hand, in the clinic, drug induced liver injury typically manifests 5 days to 3 months after starting a medication. Thus, novel approaches that can maintain the function of primary human hepatocytes for longer durations of time may enable the development of improved in vitro assays for detecting hepatotoxicity. Previous studies have demonstrated that two-dimensional micro-patterning of hepatocytes with fibroblasts leads to improved maintenance of the hepatocyte phenotype relative to hepatocyte monocultures, in serum containing medium. Additionally, we, and others, have shown that three-dimensional culture of hepatocytes leads to enhanced function (in serum-free medium). In this study we wanted to (i) examine the effect of combining the above two approaches on hepatocyte function, and (ii) to further delineate the effect of serum on hepatocyte function. We developed a user-friendly and inexpensive approach for constructing layered spheroids. Similar to previous results in two-dimensional (2d) culture, we observed that 3d culture of hepatocytes alone (i.e. monoculture) in serum-containing medium led to an increase in the urea production rate, but near-complete loss of cytochrome activity in both lots of primary human hepatocytes (PHH) tested. In serum-free sandwich culture, cytochrome activity was maintained at the level observed in freshly thawed PHH for one lot, but almost completely lost in another lot. Spheroid culture of both lots of PHH in serum-free medium led to maintenance of CYP3A4 and CYP1A2 activity at the fresh thaw level, though CYP2B6 activity was reduced. In contrast to PHH monoculture, co-cultures of PHH with NIH 3T3 fibroblast cells benefitted from the presence of serum, and led to 3-5-fold increases in CYP activity relative to even serum-free spheroid monocultures. Layering of the fibroblasts did not result in improvements over mixed co-cultures. These results indicate the importance of appropriate serum-free monoculture control experiments in the evaluation of novel biomaterials and techniques for hepatocyte co-culture. Further, urea production and cytochrome production are decoupled; therefore, urea production is an insufficient readout when developing models for pharmaceutical applications.
Evolutionary stability of plant-pollinator networks: efficient communities, hysteresis, and a pollination dilemma
Authors: Metelmann Soeren , Sakai Shoko , Kondoh Michio , Telschow Arndt 
Published: March 2018

AbstractMutualistic interactions between species such as pollination and plant–mycorrhiza interactions are ubiquitous in nature and essential for ecosystem functioning. Often dozens or even hundreds of species with different degree of specialization form complex networks of interdependence. How the complexity evolved and is maintained are fundamental questions in ecology. Here, we present a new game theoretical approach to model complex mutualistic interactions, which we apply to pollination networks. The theoretical analysis revealed multiple evolutionary stable network structures that form a gradient from generalism toward specialism with increasing availability of pollination service. In particular, we found that efficient communities evolve only under pollination oversupply, but that pollination shortage selects for inefficient network structures due to a pollination dilemma. These results suggest that availability of pollination services is a key factor structuring pollination networks and offer a new explanation for the geographical differences in pollination faunas that have long been recognized by ecologists. The study bridges the gap between network studies, game theory, and the natural history of pollination, which have hitherto been studied largely independently.