bluuebunny/crossref_metadata_2025 huggingface dataset:
HDAC3 controls male fertility through enzyme-independent transcriptional regulation at the meiotic exit of spermatogenesis
Authors: Yin Huiqi , Kang Zhenlong , Zhang Yingwen , Gong Yingyun , Liu Mengrou , Xue Yanfeng , He Wenxiu , Wang Yanfeng , Zhang Shuya , Xu Qiushi , Fu Kaiqiang , Zheng Bangjin , Xie Jie , Zhang Jinwen , Wang Yuanyuan , Lin Mingyan , Zhang Yihan , Feng Hua , Xin Changpeng , Guan Yichun , Huang Chaoyang , Guo Xuejiang , Wang P Jeremy , Baur Joseph A , Zheng Ke , Sun Zheng , Ye Lan
Published: April 2021

The transition from meiotic spermatocytes to postmeiotic haploid germ cells constitutes an essential step in spermatogenesis. The epigenomic regulatory mechanisms underlying this transition remain unclear. Here, we find a prominent transcriptomic switch from the late spermatocytes to the early round spermatids during the meiotic-to-postmeiotic transition, which is associated with robust histone acetylation changes across the genome. Among histone deacetylases (HDACs) and acetyltransferases, we find that HDAC3 is selectively expressed in the late meiotic and early haploid stages. Three independent mouse lines with the testis-specific knockout of HDAC3 show infertility and defects in meiotic exit with an arrest at the late stage of meiosis or early stage of round spermatids. Stage-specific RNA-seq and histone acetylation ChIP-seq analyses reveal that HDAC3 represses meiotic/spermatogonial genes and activates postmeiotic haploid gene programs during meiotic exit, with associated histone acetylation alterations. Unexpectedly, abolishing HDAC3 catalytic activity by missense mutations in the nuclear receptor corepressor (NCOR or SMRT) does not cause infertility, despite causing histone hyperacetylation as HDAC3 knockout, demonstrating that HDAC3 enzyme activity is not required for spermatogenesis. Motif analysis of the HDAC3 cistrome in the testes identified SOX30, which has a similar spatiotemporal expression pattern as HDAC3 during spermatogenesis. Depletion of SOX30 in the testes abolishes the genomic recruitment of the HDAC3 to the binding sites. Collectively, these results establish the SOX30/HDAC3 signaling as a key regulator of the transcriptional program in a deacetylase-independent manner during the meiotic-to-postmeiotic transition in spermatogenesis.
The gutSMASH web server: automated identification of primary metabolic gene clusters from the gut microbiota
Authors: Pascal Andreu Victòria , Roel-Touris Jorge , Dodd Dylan , Fischbach Michael A , Medema Marnix H
Published: April 2021

Anaerobic bacteria from the human microbiome produce a wide array of molecules at high concentrations that can directly or indirectly affect the host. The production of these molecules, mostly derived from their primary metabolism, is frequently encoded in metabolic gene clusters (MGCs). However, despite the importance of microbiome-derived primary metabolites, no tool existed to predict the gene clusters responsible for their production. For this reason, we recently introduced gutSMASH. gutSMASH can predict 41 different known pathways, including MGCs involved in bioenergetics, but also putative ones that are candidates for novel pathway discovery. To make the tool more user-friendly and accessible, we here present the gutSMASH web server, hosted at https://gutsmash.bioinformatics.nl/. The user can either input the GenBank assembly accession or upload a genome file in FASTA or GenBank format. Optionally, the user can enable additional analyses to obtain further insights into the predicted MGCs. An interactive HTML output (viewable online or downloadable for offline use) provides a user-friendly way to browse functional gene annotations and sequence comparisons with reference gene clusters as well as gene clusters predicted in other genomes. Thus, this web server provides the community with a streamlined and user-friendly interface to analyze the metabolic potential of gut microbiomes.
On the use of direct-coupling analysis with a reduced alphabet of amino acids combined with super-secondary structure motifs for protein fold prediction
Authors: Anton Bernat , Besalú Mireia , Fornes Oriol , Bonet Jaume , Molina Alexis , Molina-Fernandez Ruben , De las Cuevas Gemma , Fernandez-Fuentes Narcis , Oliva Baldo
Published: April 2021

Direct-coupling analysis (DCA) for studying the coevolution of residues in proteins has been widely used to predict the three-dimensional structure of a protein from its sequence. We present RADI/raDIMod, a variation of the original DCA algorithm that groups chemically equivalent residues combined with super-secondary structure motifs to model protein structures. Interestingly, the simplification produced by grouping amino acids into only two groups (polar and non-polar) is still representative of the physicochemical nature that characterizes the protein structure and it is in line with the role of hydrophobic forces in protein-folding funneling. As a result of a compressed alphabet, the number of sequences required for the multiple sequence alignment is reduced. The number of long-range contacts predicted is limited; therefore, our approach requires the use of neighboring sequence-positions. We use the prediction of secondary structure and motifs of super-secondary structures to predict local contacts. We use RADI and raDIMod, a fragment-based protein structure modelling, achieving near native conformations when the number of super-secondary motifs covers >30–50% of the sequence. Interestingly, although different contacts are predicted with different alphabets, they produce similar structures.
Blockchain-enabled wireless communications: a new paradigm towards 6G
Authors: Wang Jiaheng , Ling Xintong , Le Yuwei , Huang Yongming , You Xiaohu
Published: April 2021

With the deployment of fifth-generation (5G) wireless networks worldwide, research on sixth-generation (6G) wireless communications has commenced. It is expected that 6G networks can accommodate numerous heterogeneous devices and infrastructures with enhanced efficiency and security over diverse, e.g. spectrum, computing and storage, resources. However, this goal is impeded by a number of trust-related issues that are often neglected in network designs. Blockchain, as an innovative and revolutionary technology that has arisen in the recent decade, provides a promising solution. Building on its nature of decentralization, transparency, anonymity, immutability, traceability and resiliency, blockchain can establish cooperative trust among separate network entities and facilitate, e.g. efficient resource sharing, trusted data interaction, secure access control, privacy protection, and tracing, certification and supervision functionalities for wireless networks, thus presenting a new paradigm towards 6G. This paper is dedicated to blockchain-enabled wireless communication technologies. We first provide a brief introduction to the fundamentals of blockchain, and then we conduct a comprehensive investigation of the most recent efforts in incorporating blockchain into wireless communications from several aspects. Importantly, we further propose a unified framework of the blockchain radio access network (B-RAN) as a trustworthy and secure paradigm for 6G networking by utilizing blockchain technologies with enhanced efficiency and security. The critical elements of B-RAN, such as consensus mechanisms, smart contract, trustworthy access, mathematical modeling, cross-network sharing, data tracking and auditing and intelligent networking, are elaborated. We also provide the prototype design of B-RAN along with the latest experimental results.
The Lost Leg of the Youth Justice and Criminal Evidence Act (1999): Special Measures and Humane Treatment
Authors: Fairclough Samantha
Published: April 2021

This article examines the purpose behind the provision of special measures—adaptations to courtroom formalities—to vulnerable or intimidated people giving evidence in criminal trials. It shows that fostering the principle of humane treatment and improving evidence quality were the initial motivations underpinning the introduction of special measures. The focus in this article is on the principle of humane treatment, and whether the current provision of special measures successfully fosters it. The article conceptualises the principle of humane treatment so that it can be used as the normative measure against which to evaluate the current provision of special measures to vulnerable witnesses and the accused. It concludes that the solely instrumental legal basis on which special measures are currently available risks insufficiently protecting vulnerable or intimidated participants from the harm and distress that the criminal trial often causes, and that this can amount to inhumane treatment.
Mahjong
Authors: Heinz Annelise
Published: April 2021

Mahjong: A Chinese Game and the Making of Modern American Culture illustrates how the spaces between tiles and the moments between games have fostered distinct social cultures in the United States. When this mass-produced game crossed the Pacific it created waves of popularity over the twentieth century. Mahjong narrates the history of this game to show how it has created a variety of meanings, among them American modernity, Chinese American heritage, and Jewish American women’s culture. As it traveled from China to the United States and caught on with Hollywood starlets, high society, middle-class housewives, and immigrants alike, mahjong became a quintessentially American pastime. This book also reveals the ways in which women leveraged a game for a variety of economic and cultural purposes, including entrepreneurship, self-expression, philanthropy, and ethnic community building. One result was the forging of friendships within mahjong groups that lasted decades. This study unfolds in two parts. The first half is focused on mahjong’s history as related to consumerism, with a close examination of its economic and cultural origins. The second half explores how mahjong interwove with the experiences of racial inclusion and exclusion in the evolving definition of what it means to be American. Mahjong players, promoters, entrepreneurs, and critics tell a broad story of American modernity. The apparent contradictions of the game—as both American and foreign, modern and supposedly ancient, domestic and disruptive of domesticity—reveal the tensions that lie at the heart of modern American culture.
The Demands of Liberal Non-Domination
Authors: Schemmel Christian
Published: April 2021

This chapter develops the specific demands of liberal non-domination. It argues that they cover protection against dominatory groups as well as against power relations which are not mediated by authority, or otherwise public; demonstrates how different choices, such as those falling under the basic liberties, connected to intimate personal relationships, or at stake in resource-intensive programs and policies to enhance life options, call for different thresholds of intensity of protection; and how protection must itself be appropriately respectful of people’s moral agency. It goes on to show how the resulting requirements give a wide policy mandate to combat domination not only through formal institutions, but also by fostering a societal ethos and informal social norms, and argues that liberals should not be worried by this wide mandate. It concludes by analysing in which ways demands of protection against domination can, and cannot, be understood as distributive demands.
Conclusion
Authors: Schemmel Christian
Published: April 2021

The Conclusion briefly recapitulates the main argument of the book, and discusses different possible avenues for challenging it. It also comments on how relational egalitarianism, and liberal relational egalitarianism in particular, can be fruitfully applied to policy and institutional questions beyond the ones addressed in the book, in collaboration with empirical social science, and identifies the questions and issues which have to be central for an extension of the theory to matters of international, transnational, global, and intergenerational justice.
Handing Down the Faith
Authors: Smith Christian , Adamczyk Amy
Published: April 2021

The most important influence shaping the religious and spiritual lives of children, youth, and teenagers is parents. Yet little research has studied this link in the intergenerational transmission of religion between generations. This book reports the findings of a new, national study of religious parents in the United States. The findings are based on 215 in-depth, personal interviews with religious parents from many traditions and different parts of the country; and on analyses of two nationally representative surveys of American parents. Unlike many studies that focus only on mainstream Christianity, this book reports on parents from a wide range of traditions: mainline Protestant, Catholic, evangelical, black Protestant, Jewish, Muslim, Mormon, Buddhist, and Hindu. It explores the background beliefs informing how and why religious parents seek to pass on religion to their children; examines how parenting styles interact with parent religiousness to shape religious transmission; shows how the approaches of parents now were influenced by their own experiences as children growing up under their parents; reveals how religious parents view their congregations and what they most seek out in a local church, synagogue, temple, or mosque; explores the experiences and outlooks of immigrant parents; and steps back to consider how the field of American religion has transformed over the last 100 years to explain why parents shoulder such a huge responsibility today in transmitting religious faith and practice to children. The book will interest scholars of religion, family, parenting, and socialization; clergy and religious educators and leaders; and religious parents themselves.
A Century of Women’s History from the Papyri
Authors: Bagnall Roger S.
Published: April 2021

This chapter surveys the study of women based on papyrological evidence, a subject to which Sarah Pomeroy has made major contributions. Beginning with the first articles on women in the papyri a century ago, the historiography is presented first chronologically, down to the growth of feminist scholarship in the 1970s and 1980s, and then by subject for the past third of a century. Ancient legal studies, social history, the study of the economy, the development of Late Antiquity as a field, and the emergence of gender studies have all played important roles. The finds of papyri outside Egypt have broadened the subject beyond its Egyptian focus. Although quantitative investigations, based especially on the census returns from Roman Egypt, have played a central role, it is likely that microhistorical studies will be a more fertile direction in the future.
Social Laws and Social Facts
Authors: Milnor Kristina
Published: April 2021

Cassius Dio asserts that the emperor Augustus’ social legislation arose from an imbalance in numbers between men and women among the Roman elite. This chapter considers how this statement has been understood in historical readings of the laws. It also argues that Dio’s assertion should be seen instead as one more instance of the ways that the legislation not only gives us access to knowledge about women’s lives but also attempts to generate more “knowledge” and questions about them. The chapter utilizes feminist epistemology in its discussion of legal and social matters. It is interested in facts as well as the absence of facts in locating women in ancient narratives.
Colonial Terror
Authors: Heath Deana
Published: April 2021

Focusing on India between the early nineteenth century and the First World War, Colonial Terror explores the centrality of the torture of Indian bodies to the law-preserving violence of colonial rule—of some of the ways in which, in other words, extraordinary violence was embedded in the ordinary operation of colonial states. Although enacted largely by Indians on Indian bodies, particularly by subaltern members of the police, the book argues that torture was facilitated, systematized, and ultimately sanctioned by first the East India Company and then the Raj because it benefitted the colonial regime, since rendering the police a source of terror played a key role in the construction and maintenance of state sovereignty. Drawing upon the work of both Giorgio Agamben and Michel Foucault, Colonial Terror contends, furthermore, that it is only possible to understand the terrorizing nature of the colonial police in India by viewing colonial India as a ‘regime of exception’ in which two different forms, or levels, of exceptionality were in operation, one wrought through the exclusion of particular groups or segments of the Indian population from the law and the other by ‘petty sovereigns’ in their enactment of illegal violence in the operation of the law. It was in such fertile ground, in which colonial subjects were both included within the domain of colonial law while also being abandoned by it, that torture was able to flourish.
Temporal Security in IR
Authors: Bachleitner Kathrin
Published: April 2021

The first chapter of this book theoretically conceptualizes collective memory in international relations (IR). The link between the IR discipline and the interdisciplinary collective memory concept is provided through the framework of ontological security. The inquiry begins by extrapolating the nature of ontological security and its most essential component: state identity. It then moves on to theorize collective memory as the underlying carrier of state identity. Collective memory highlights identity’s temporal dimension and manifests it within the collective frameworks of narration. At the end, a new approach, ‘temporal security’, is developed. It combines the ontological security of being with the definition of memory as being-in-time. Security-seeking behaviour for states now implies to be temporally grounded in a consistent narrative that links past, present, and future. The reference point for this as of yet untheorized security need is collective memory. Manifesting itself in the varying forms of political strategy, public identity, state behaviour, and national values, collective memory thus navigates countries through time in IR.
Paul Beatty, the Rhetoric of War, and the Selling Out of Civil Rights
Authors: Anker Elizabeth S.
Published: April 2021

Elizabeth Anker situates Paul Beatty’s The Sellout in a literary tradition that enlists satire as an instrument of critique. Anker demonstrates that Beatty violates race-related taboos in order to confront readers with the avoidances that those taboos impose. Beatty’s biting humor, with its slippage between metaphor and reality, serves to disrupt the self-satisfaction and complacency that mark conventional narratives about the legacy of the Civil War and the civil rights movement in American constitutional politics. The Sellout shows us, in Anker’s view, that the tradition of written constitutionalism and its celebratory symbolism of “quill and ink” has often served instead to enable and legitimize the criminalization and disenfranchisement of African Americans. Moreover, courts have assimilated a racialized language of urban combat—including the so-called wars on poverty, drugs, and crime—that has perpetuated structural racism, reinforcing standards of decorum and good citizenship that have operated as barriers to inclusion in the liberal democratic public sphere.
Ethnomusicology and the Meeting of Knowledges in Music
Authors: Carvalho José Jorge de
Published: April 2021

Universities in Latin America (and, to a certain extent, in the entire non-Western world) were created in the colonial and republican periods as replicas of modern European universities, which had stabilized criteria for the classification, organization, and hierarchy of knowledge and for the legitimation of truth following closely the Napoleonic and Humboldtian reforms in the 1800s. Traditional Latin American traditions of knowledge, both scientific and artistic, were discriminated against and totally excluded from the university curricula in the name of an exclusively eurocentric epistemic paradigm. As a consequence of this epistemicide, all the music schools today, both basic and superior, teach primarily the erudite European musical genres, whereas the popular, Indigenous and African-derived musical traditions, which are extremely rich in the entire continent, do not form part of the curriculum available for music students. In order to offer a positive alternative to this monothematic and historically limited musical environment, we have devised the methodology of the Meeting of Knowledges, through which masters of traditional music, most of them people with little or no formal literacy, are hired to teach regular courses in music, dance, theater, and correlated arts, in courses given equal relevance and prestige to those of the Western erudite musical tradition. Started in the University of Brasília in 2010, the Meeting of Knowledges has already expanded substantially. This chapter sums up the theoretical and methodological foundations of the Meeting of Knowledges and explore connections with other epistemic and political interventions in ethnomusicology and music education.
Programming Precision? Requiring Robust Transparency for AWS
Authors: Barela Steven J. , Plaw Avery
Published: April 2021

The possibility of allowing a machine agency over killing human beings is a justifiably concerning development, particularly when we consider the challenge of accountability in the case of illegal or unethical employment of lethal force. We have already seen how key information can be hidden or contested by deploying authorities, in the case of lethal drone strikes, for example. Therefore, this chapter argues that any effective response to autonomous weapons systems (AWS) must be underpinned by a comprehensive transparency regime that is fed by robust and reliable reporting mechanisms. This chapter offers a three-part argument in favor of a robust transparency regime. Firstly, there is a preexisting transparency gap in the deployment of core weapon systems that would be automated (such as currently remote-operated UCAVs). Second, while the Pentagon has made initial plans for addressing moral, ethical, and legal issues raised against AWS, there remains a need for effective transparency measures. Third, transparency is vital to ensure that AWS are only used with traceable lines of accountability and within established parameters. Overall this chapter argues that there is an overwhelming interest and duty for actors to ensure robust, comprehensive transparency, and accountability mechanisms. The more aggressively AWS are used, the more rigorous these mechanisms should be.
The Better Instincts of Humanity: Humanitarian Arguments in Defense of International Arms Control
Authors: Jevglevskaja Natalia , Liivoja Rain
Published: April 2021

Disagreements about the humanitarian risk-benefit balance of weapons technology are not new. The history of arms control negotiations offers many examples of weaponry that was regarded ‘inhumane’ by some, while hailed by others as a means to reduce injury or suffering in conflict. The debate about autonomous weapons systems reflects this dynamic, yet also stands out in some respects, notably largely hypothetical nature of concerns raised in regard to these systems as well as ostensible disparities in States’ approaches to conceptualizing autonomy. This chapter considers how misconceptions surrounding autonomous weapons technology impede the progress of the deliberations of the Group of Governmental Experts on Lethal Autonomous Weapons Systems. An obvious tendency to focus on the perceived risks posed by these systems, much more so than potential operational and humanitarian advantages they offer, is likely to jeopardize the prospect of finding a meaningful resolution to the debate.
Autonomous Weapons and the Future of Armed Conflict
Authors: Leveringhaus Alex
Published: April 2021

This chapter considers how autonomous weapons systems (AWS) impact the armed conflicts of the future. Conceptually, the chapter argues that AWS should not be seen as on a par with precision weaponry, which makes them normatively problematic. Against this background, the chapter considers the relationship between AWS and two narratives, The Humane Warfare Narrative and the Excessive Risk Narrative, which have been used to theorize contemporary armed conflict. AWS, the chapter contends, are unlikely to usher in an era of humane warfare. Rather, they are likely to reinforce existing trends with regard to the imposition of excessive risk on noncombatants in armed conflict. Future conflicts in which AWS are deployed are thus likely to share many characteristics of the risk-transfer wars of the late twentieth and early twenty-first centuries. The chapter concludes by putting these abstract considerations to the test in the practical context of military intervention.
Blind Brains and Moral Machines: Neuroscience and Autonomous Weapon Systems
Authors: Evans Nicholas G.
Published: April 2021

While the majority of neuroscience research promises novel therapies for treating dementia and post-traumatic stress disorder, among others, a lesser-known branch of neuroscientific research informs the construction of artificial intelligence inspired by human neurophysiology. For those concerned with the normative implications of autonomous weapons systems (AWS), however, a tension arises between the primary attraction of AWS, their theoretic capacity to make better decisions in armed conflict, and the relatively low-hanging fruit of modeling machine intelligence on the very thing that causes humans to make (relatively) bad decisions—the human brain. This chapter examines human cognition as a model for machine intelligence, and some of its implications for AWS development. It first outlines recent neuroscience developments as drivers for advances in artificial intelligence. This chapter then expands on a key distinction for the ethics of AWS: poor normative decisions that are a function of poor judgments given a certain set of inputs, and poor normative decisions that are a function of poor sets of inputs. It argues that given that there are cases in the second category of decisions in which we judge humans to have acted wrongly, we should likewise judge AWS platforms. Further, while an AWS may in principle outperform humans in the former, it is an open question of design whether they can outperform humans in the latter. Finally, this chapter then discusses what this means for the design and control of, and ultimately liability for AWS behavior, and sources of inspiration for the alternate design of AWS platforms.
Normative Epistemology for Lethal Autonomous Weapons Systems
Authors: Devitt S. Kate
Published: April 2021

The rise of human-information systems, cybernetic systems, and increasingly autonomous systems requires the application of epistemic frameworks to machines and human-machine teams. This chapter discusses higher-order design principles to guide the design, evaluation, deployment, and iteration of Lethal Autonomous Weapons Systems (LAWS) based on epistemic models. Epistemology is the study of knowledge. Epistemic models consider the role of accuracy, likelihoods, beliefs, competencies, capabilities, context, and luck in the justification of actions and the attribution of knowledge. The aim is not to provide ethical justification for or against LAWS, but to illustrate how epistemological frameworks can be used in conjunction with moral apparatus to guide the design and deployment of future systems. The models discussed in this chapter aim to make Article 36 reviews of LAWS systematic, expedient, and evaluable. A Bayesian virtue epistemology is proposed to enable justified actions under uncertainty that meet the requirements of the Laws of Armed Conflict and International Humanitarian Law. Epistemic concepts can provide some of the apparatus to meet explainability and transparency requirements in the development, evaluation, deployment, and review of ethical AI.
Wetlands
Authors: Husain Faisal H.
Published: April 2021

This chapter focuses on Ottoman policies to manage the exploitation of wetlands in the Tigris-Euphrates alluvial plain. In the early modern period, ever-more powerful empires engaged in ambitious wetland drainage projects in the name of improvement. This chapter offers a counterexample of an empire that used its bureaucratic and financial capabilities to benefit from the exploitation of wetland resources. The Ottoman administration paid particular attention to the cultivation of rice and the husbandry of water buffalo. Both productive activities became major sources of revenue for the state, and their sustenance depended on the ecological integrity of the Tigris-Euphrates marshes.
Making a harpsichord sound like a piano
Authors: Adelson Robert
Published: April 2021

Following an apprenticeship with the Strasbourg-based Silbermann brothers, the young Sébastien Erard moved to Paris to begin building keyboard instruments. There he benefited from the patronage of the duchesse de Villeroy, who offered him a workshop, where he was soon joined by his brother Jean-Baptiste. The Erards’ success with pianos motivated them to find a way of giving harpsichords the same expressive possibilities. Their innovations were considered a threat by musical instrument makers and dealers in Paris, who specialised in the import and resale of English pianos. In 1785, Louis XVI granted the Erards a royal privilege exempting them from membership in the guild which governed the activities of Paris instrument builders.
Liszt and the introduction of the new piano
Authors: Adelson Robert
Published: April 2021

The Erards realised that as brilliant as the double-escapement action was, it required an equally brilliant pianist to introduce it to the public. The Erards first thought to ask the Austrian pianist and composer Johann Nepomuk Hummel (1778–1837), but soon found another pianist to promote their invention: a musician whose talents eclipsed not only those of Morel, but also those of all other living pianists. Franz Liszt (1811–86), then only twelve years old and largely unknown outside of Vienna, arrived in Paris and became the leading advocate for Erard’s new invention. Liszt’s relationship with the Erard family quickly became advantageous to both parties. For the Erards, Liszt’s arrival was a godsend, as his superhuman technique demonstrated the advantages of their invention. Similarly, Erard’s new piano became an essential part of Liszt’s early success, as its magnificently responsive action and powerful tone allowed the pianist to push his virtuosity to new heights.
Metaphysical Exile
Authors: Pippin Robert
Published: April 2021

This is the first detailed interpretation of J. M. Coetzee’s “Jesus” trilogy as a whole. Robert Pippin treats the three “fictions” as a philosophical fable, in the tradition of Plato’s Republic, More’s Utopia, Rousseau’s Emile, or Nietzsche’s Thus Spoke Zarathustra. Everyone in the mythical land explored by Coetzee is an exile, removed from their homeland and transported to a strange new place, and they have all had most of the memories of their homeland “erased.” While also discussing the social and psychological dimensions of the fable, Pippin treats the literary aspects of the fictions as philosophical explorations of the implications of a deeper kind of spiritual homelessness, a version that characterizes late modern life itself, and he treats the theme of forgetting as a figure for modern historical amnesia and indifference to reflection and self-knowledge. So, the state of exile is interpreted as “metaphysical” as well as geographical. In the course of an interpretation of the central narrative about a young boy’s education, Pippin shows how a number of issues arise, are discussed and lived out by the characters, all in ways that also suggest the limitations of traditional philosophical treatments of themes like eros, beauty, social order, art, family, non-discursive forms of intelligibility, self-deception, and death. Pippin also offers an interpretation of the references to Jesus in the titles, and he traces and interprets the extensive inter-textuality of the fictions, the many references to the Christian Bible, Plato, Cervantes, Goethe, Kleist, Wittgenstein, and others. Throughout, the attempt is to show how the literary form of Coetzee’s fictions ought to be considered, just as literary—a form of philosophical reflection.
Reforming the French National Church
Authors: Bruening Michael W.
Published: April 2021

Marguerite of Navarre’s evangelical network never abandoned its strategy of pushing for reform within the existing French church. The Meaux group of the early 1520s, led by Bishop Guillaume Briçonnet and Jacques Lefèvre d’Étaples, sought to “bring the Gospel to the people.” Lefèvre and Gérard Roussel made a crucial decision in 1526 to return to France from exile, instead of joining the international Reformed community. This move paved the way for them to continue down the path of internal reform, an effort that hit its peak in 1533, when Roussel preached to huge crowds in Paris. Hopes were dashed the next year with the royal reaction to the Affair of the Placards, but Roussel continued to encourage evangelical reform during his last years as Bishop of Oloron.
Introduction to Scanning Tunneling Microscopy
Authors: Chen C. Julian
Published: April 2021

The scanning tunnelling microscope (STM) was invented by Binnig and Rohrer and received a Nobel Prize of Physics in 1986. Together with the atomic force microscope (AFM), it enables non-destructive observing and mapping atoms and molecules on solid surfaces down to a picometer resolution. A recent development is the non-destructive observation of wavefunctions in individual atoms and molecules, including nodal structures inside the wavefunctions. STM and AFM have become indespensible instruments for scientists of various disciplines, including physicists, chemists, engineers, and biologists to visualize and utilize the microscopic world around us. Since the publication of the first edition in 1993, this book has been recognized as a standard introduction for everyone that starts working with scanning probe microscopes, and a useful reference book for those more advanced in the field. After an Overview chapter accessible for newcomers at an entry level presenting the basic design, scientific background, and illustrative applications, the book has three Parts. Part I, Principles, provides the most systematic and detailed theory of its scientific bases from basic quantum mechancis and condensed-metter physics in all available literature. Quantitative analysis of its imaging mechanism for atoms, molecules, and wavefunctions is detailed. Part II, Instrumentation, provides down to earth descriptions of its building components, including piezoelectric scanners, vibration isolation, electronics, software, probe tip preparation, etc. Part III, Related methods, presenting two of its most important siblings, scanning tunnelling specgroscopy and atomic force miscsoscopy. The book has five appendices for background topics, and 405 references for further readings.
Electronics and Control
Authors: Chen C. Julian
Published: April 2021

This chapter discusses electronics and computer interfaces for STM and AFM. For STM, the detection of the minute tunneling current is of paramount importance. Thus, the basic concepts and analysis of the current amplifier, or more accurately speaking, the transimpedence amplifier, is discussed. It includes the typical circuits and an analysis of the gain, noise, frequency response, microphone effect due to the coaxial cable, and the logarithmic amplifier to make the distance dependence of the output signal linear. the feedback system is then discussed, including a typical circuit, as well as the analyses of the steady-state response and the transient response. Finally, the architecture of the computer interface system with the algorithm of automatic approaching is discussed.
Earthing Philosophy of Technology
Authors: Roos Andreas
Published: April 2021

This chapter reviews four major strands of twentieth-century philosophy of technology and shows how all of them have predominantly thought of technology as immaterial. This suggests that modern people have widely embraced the popular image of ‘lightbulbs as bright ideas’ in relation to technology. While research on the biosphere emerged from an understanding of the world as a complex interplay of geological forces and biogeochemical cycles of matter-energy, technology was interpreted as ontologically immaterial, springing forth from human cognition, consciousness, design, or semiotic networks. It follows that the interpretation of nature that is today employed to understand the dire state of the planet is broadly absent in the conception of the most favoured (technological) solutions. To remedy this discrepancy, this chapter argues that we should understand technology as ontologically material in order to see how it is essentially a means for ecologically unequal exchange.
Aristotle’s Viewpoint
Authors: Charles David
Published: April 2021

Aristotle’s view, as understood in Chapters 1–6, is summarized and then distinguished from several more recent theories of psychological phenomena, such as various versions of functionalism and non-reductionist materialism. His hylomorphic theory of natural objects is also differentiated from various forms of neo-Aristotelian hylomorphism. Aristotle, it is argued, is attempting to account for the causal role of form, its being definitionally prior to matter, and its role in grounding the unity of natural objects in a way different from that suggested in these contemporary theories. The ontological nature of Aristotle’s forms is further discussed. The aim of this chapter is to emphasize the distinctness of Aristotle’s account from several recent theories, not to argue for its superiority.
Conclusion
Authors: Dean Andrew
Published: April 2021

This chapter briefly examines the endurance of debates about ‘irony’ today. It argues that contemporary claims about the politics of irony in fact reflect unresolved debates from the reception of ‘postmodern metafiction’ more generally. This is especially the case following the emergence of a ‘new sincerity’. The chapter suggests that the contemporary public reception of ‘postmodernism’—its aesthetics and politics—generally misrecognizes the object of critique. This reception does not recognize what career metafictionists such as J. M. Coetzee, Janet Frame, and Philip Roth were actually doing. The chapter concludes by suggesting the history of postwar fiction, freed from the encumbrances of various critical enterprises, should now proceed by paying closer attention to the careers and archives of the writers we are examining.
Determinants of phytoplankton size structure in warm, shallow lakes
Authors: Erdoğan Şeyda , Beklİoğlu Meryem , Litchman Elena , Miller Elizabeth T , Levі Etі E , Bucak Tuba , Tavşanoğlu Ülkü Nіhan
Published: April 2021

Body size is an important trait of any organism, including phytoplankton, because it affects physiological and morphological performance, reproduction, population growth rate and competitive interactions. Understanding how interacting top-down and bottom-up factors influence phytoplankton cell size in different aquatic environments is still a challenge. Structural equation modeling (SEM) is a comprehensive multivariate statistical tool for detecting cause–effect relationship among different variables and their hierarchical structure in complex networks (e.g. trophic interactions in ecosystems). Here, several SEM models were employed to investigate the direct and indirect interaction pathways affecting the phytoplankton size structure in 44 mostly eutrophic and hypereutrophic permanent lakes in western Turkey. Among the 15 environmental variables tested, only rotifers and Carlson’s Trophic Index (TSI) had significant direct positive effect on the mean phytoplankton size and size variance, respectively. The results indicate that both bottom-up and top-down factors significantly affect phytoplankton community size structure in eutrophic and hypereutrophic lakes in warm climates. Rotifer grazing increased the abundance of large-sized phytoplankton species, such as filamentous and colonial cyanobacteria and TSI affected phytoplankton size variance, with a higher size variance in hypereutrophic lakes.
The effect of COVID-19 public health restrictions on the health of people with musculoskeletal conditions and symptoms: the CONTAIN study
Authors: Macfarlane Gary J , Hollick Rosemary J , Morton LaKrista , Heddle Maureen , Bachmair Eva-Maria , Anderson R Stuart , Whibley Daniel , Keenan Karen Forrest , Murchie Peter , Stelfox Kevin , Beasley Marcus J , Jones Gareth T
Published: April 2021

Objective

To quantify the change in quality of life, disease-specific indicators, health and lifestyle before and during the COVID-19 pandemic among people with musculoskeletal diagnoses and symptoms.

Methods

We undertook an additional follow-up of two existing UK registers involving people with axial spondyloarthritis (axSpA) or psoriatic arthritis (PsA) and participants in a trial in the UK who had regional pain and were identified at high risk of developing chronic widespread pain. Participants completed the study questionnaire between July and December 2020, throughout which time there were public health restrictions in place.

Results

The number of people taking part in the study was 1054 (596 axSpA, 162 PsA, 296 regional pain). In comparison with their previous (pre-pandemic) assessment, there was an age-adjusted significant, small decrease in quality of life measured by EQ-5D [−0.020 (95% CI −0.030, −0.009)] overall and across all population groups examined. This was primarily related to poorer mental health and pain. There was a small increase in fibromyalgia symptoms, but a small decrease in sleep problems. There was a small deterioration in axSpA disease activity, and disease-specific quality of life and anxiety in PsA participants. Predictors of poor quality of life were similar pre- and during the pandemic. The effect of lockdown on activity differed according to age, gender and deprivation.

Conclusion

Important lessons include focusing on addressing anxiety and providing enhanced support for self-management in the absence of normal health care being available, and awareness that all population groups are likely to be affected.
Do Country-Level Creditor Protections Affect Firm-Level Debt Structure Concentration?
Authors: John Kose , Kaviani Mahsa S , Kryzanowski Lawrence , Maleki Hosein
Published: April 2021

We study the effects of country-level creditor protections on the firm-level choice of debt structure concentration. Using data from forty-six countries, we show that firms form more concentrated debt structures in countries with stronger creditor protection. We propose a trade-off framework of optimal debt structure and show that in strong creditor rights regimes, the benefit of forming concentrated structures outweighs its cost. Because strong creditor protections increase liquidation bias, firms choose concentrated debt structures to improve the probability of successful distressed debt renegotiations. Firms with ex ante higher bankruptcy costs, including those with higher intangibility, cash flow volatility, R&D expenses, and leverage, exhibit stronger effects. Firms with restricted access to capital are also affected more. A difference-in-differences analysis of firms’ debt structure responses to creditor rights reforms confirms the cross-country results. Our findings are robust to alternative settings and a battery of robustness checks.
LncRNA MEG3 Involved in NiO NPs-Induced Pulmonary Fibrosis via Regulating TGF-β1-Mediated PI3K/AKT Pathway
Authors: Zhan Haibing , Sun Xingchang , Wang Xiaoxia , Gao Qing , Yang Mengmeng , Liu Han , Zheng Jinfa , Gong Xuefeng , Feng Sanwei , Chang Xuhong , Sun Yingbiao
Published: April 2021

Long noncoding RNA maternally expressed gene 3 (MEG3) involves in fibrotic diseases, but its role in nickel oxide nanoparticles (NiO NPs)-induced pulmonary fibrosis remains unclear. The present study aimed to explore the relationships among MEG3, transforming growth factor-β1 (TGF-β1) and phosphoinositide 3-kinase (PI3K)/AKT pathway in NiO NPs-induced pulmonary fibrosis. Wistar rats were intratracheally instilled with NiO NPs twice a week for 9 weeks, and human lung adenocarcinoma epithelial cells (A549 cells) were exposed to NiO NPs for 24 h. The pathological alterations and increased hydroxyproline indicated that NiO NPs caused pulmonary fibrosis in rats. The up-regulated type I collagen (Col-I) suggested that NiO NPs-induced collagen deposition in A549 cells. Meanwhile, NiO NPs could significantly down-regulate MEG3, up-regulate TGF-β1 and activate PI3K/AKT signaling pathway both in vivo and in vitro. However, we found that the PI3K/AKT pathway activated by NiO NPs could be suppressed by 10 μM TGF-β1 inhibitor (SB431542) in A549 cells. The protein markers (Col-I, Fibronectin, and alpha-smooth muscle actin) of collagen deposition up-regulated by NiO NPs were reduced by 10 μM PI3K inhibitor (LY294002). Furthermore, we further found that overexpressed MEG3 inhibited the expression of TGF-β1, resulting in the inactivation of PI3K/AKT pathway and the reduction of collagen formation. In summary, our results validated that MEG3 could arrest NiO NPs-induced pulmonary fibrosis via inhibiting TGF-β1-mediated PI3K/AKT pathway.
LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data
Authors: Al Qaffas Ahmed , Nichols Jenna , Davison Andrew J , Ourahmane Amine , Hertel Laura , McVoy Michael A , Camiolo Salvatore
Published: April 2021

Long-read, single-molecule DNA sequencing technologies have triggered a revolution in genomics by enabling the determination of large, reference-quality genomes in ways that overcome some of the limitations of short-read sequencing. However, the greater length and higher error rate of the reads generated on long-read platforms make the tools used for assembling short reads unsuitable for use in data assembly and motivate the development of new approaches. We present LoReTTA (Long Read Template-Targeted Assembler), a tool designed for performing de novo assembly of long reads generated from viral genomes on the PacBio platform. LoReTTA exploits a reference genome to guide the assembly process, an approach that has been successful with short reads. The tool was designed to deal with reads originating from viral genomes, which feature high genetic variability, possible multiple isoforms, and the dominant presence of additional organisms in clinical or environmental samples. LoReTTA was tested on a range of simulated and experimental datasets and outperformed established long-read assemblers in terms of assembly contiguity and accuracy. The software runs under the Linux operating system, is designed for easy adaptation to alternative systems, and features an automatic installation pipeline that takes care of the required dependencies. A command-line version and a user-friendly graphical interface version are available under a GPLv3 license at https://bioinformatics.cvr.ac.uk/software/ with the manual and a test dataset.