bluuebunny/crossref_metadata_2025 huggingface dataset:
Just War Theory in Times of Individual Rights
Authors: Dill Janina
Published: April 2018

Just war theory (JWT) has undergone a radical revision over the last two decades. This chapter discusses the implications of this reformulation for the role of JWT in International Political Theory (IPT) and for JWT’s strategic usefulness. Revisionists’ consistent prioritization of individual rights means JWT now follows the strictures of justified violence according to contemporary IPT. At the same time, the collective nature of war makes it impossible for anyone but the omniscient attacker to properly protect individual rights and thus to directly implement revisionist prescriptions. I argue that revisionism is strategically relevant not in spite of, but because of this lack of practicability on the battlefield. It highlights the impossibility of waging war in accordance with widespread expectations of moral appropriateness, which largely follow the strictures of justified violence according to contemporary IPT. This is a crucial limitation to the political utility of force in twenty-first-century international relations.
Moral Dilemmas of Asymmetric Conflict
Authors: Gross Michael L.
Published: April 2018

Contemporary asymmetric war presents democratic regime with significant challenges. First, the status of non-state actors is ambiguous. Terrorists are not entitled to the protection of international law, but guerrillas should enjoy significant privileges that states do not always acknowledge. Second, lack of uniforms endangers the core obligation to distinguish between combatants and non-combatants. Third, active participation by civilians puts non-combatant immunity at risk if such civilians are liable to defensive harming. Fourth, the increasing use of soft or non-kinetic tactics in the form of media, cyber, legal, and economic warfare is not governed by international law, and may offer non-state actors a significant advantage. Finally, the laws and norms that bind guerrillas are a work in progress. Ideally, they should comply fully with the principles of military ethics, but in practice, some leniency is unavoidable.
The Slow Normalization of Normative Political Theory
Authors: Sutch Peter
Published: April 2018

Reflecting upon the twenty-five years since the cosmopolitan/communitarian distinction provided initial focus to the (re)emergence of International Political Theory (IPT), two things stand out. First, despite the many well-founded criticisms of the way the cosmopolitan/communitarian debate conceived of the theoretical debates in IPT, it has proven remarkably difficult to escape or transcend the core features of cosmopolitanism and communitarianism in IPT. Second, the critical work done in response to the challenges of the early debates has left a more mature and refined IPT. Some of the most interesting and important work is now happening at the interface between IPT and empirical, sociological, and legal studies in IR. It is here, this chapter contends, that the contemporary debates between cosmopolitans engaging with the socio-legal fabric of international society and new-communitarians engaging with the normative implications of evolving transnational and global communities are effecting the normalization of IPT.
Humanitarian Actors and International Political Theory
Authors: Welsh Jennifer M.
Published: April 2018

This chapter examines how contemporary humanitarian institutions interpret and implement their normative responsibilities in international society. It analyses a specific subset of actors—the United Nations and humanitarian NGOs—and the impact of their attempts to privilege a more “individualist,” or cosmopolitan, approach to the mitigation and regulation of armed conflict. The chapter sets out the core values of humanitarian action, including humanity and impartiality, and then illustrates how the process of “individualization”—which challenges the primacy of collective entities such as warring parties or sovereign states —has created both normative and operational dilemmas for humanitarian actors. In the case of the UN, the imperative to protect individual human rights has transformed the practice of peacekeeping, through a robust interpretation of impartiality, while for humanitarian NGOs it has spawned efforts to address not only the immediate suffering produced by armed conflict but also the underlying causes of vulnerability.
The Human Right to Health and the Challenge of Poverty
Authors: Hayden Patrick
Published: April 2018

The human right to health has assumed considerable prominence as one of the most pressing international issues of the twenty-first century. This chapter examines arguments regarding how the mutually reinforcing cycle of poverty, inequality, and poor health affects the disease burden around the world, and considers why the right to health is widely compromised by global health disparities. It first traces the evolution of international concern with health as a basic human right. The following section discusses two competing frameworks—statist and globalist—for conceptualizing the meaning and value of health within current international policy. The final section analyses the right to health in terms of recognition theory’s emphasis on the intersectional injustices of poverty and inequality, which have deleterious effects on health as well as on identity and self-respect.
The Ethical Limits of Global Democracy
Authors: Erman Eva
Published: April 2018

This chapter discusses the ethical limits of global democracy, which are here understood as the conditions under which global democracy should be construed (formulated and justified) and promoted in real politics. The aim is not to develop and defend a substantive account of global democracy, but to bring up some basic concerns that are essential to address when analysing the limits of global democracy as well as to suggest some fruitful ways to approach them. The chapter focuses on two types of moral constraint on construing and promoting global democracy. The first type of constraint is set by empirical concerns, which highlights central methodological discussions of the role of ideal and non-ideal theorizing in International Political Theory (IPT). The second type of constraint is set by normative concerns, which highlights questions about the role of principles of democratic legitimacy and their applicability.
Ethical Foreign Policy in a Multipolar World
Authors: Dunne Tim
Published: April 2018

For much of the history of academic International Relations, foreign policy has understated the role of ethics in the theory and practice of statecraft. As discussed in the first part of the chapter, it was not until the critical and normative turn of the 1980s and 1990s that ethics assumed a significant role in the study of foreign policy. Ethics also rose to prominence in the language and commitments of a number of modernizing centre-left governments claiming to be agents of the common good. The second part of the chapter treats humanitarianism as a case study because it illustrates how ethics and foreign policy are configured in practice. While it is true that human rights significantly contributed to the end of the Cold War, it is also the case that erosion of the liberal international order poses stark questions for the resilience of humanitarianism in a deeply divided world.
Feminist International Political Theory
Authors: Sjoberg Laura
Published: April 2018

Through what lenses is International Political Theory (IPT) generated, read, and understood? Feminists in IPT have focused on asking that question and, along with it, substantive questions about the shape and omission of IPT—where are the women in IPT? Where is the gender? How can IPT be seen as gender-neutral when it is almost entirely constituted of the musings of white, Western men? This chapter suggests that there is a long and rich history of feminist IPT which broadens not only the representation of women, gender, and sexuality in IPT but also the scope of IPT itself. Using the example of male prostitutes in the United States military to explore both conceptual range and applicability, this chapter looks to provide both an overview of the contributions of feminist IPT and suggestions for looking forward.
International Law and International Justice
Authors: Charlesworth Hilary
Published: April 2018

This chapter investigates the relationship between the concepts of international justice and international law. It suggests that the idea of an international rule of law is constructed on procedural, rather than substantive, accounts of justice. Against the background of two opposing tendencies in the international legal order that influence ideas of international justice, namely the Westphalian and UN Charter accounts, the chapter considers various attempts to incorporate notions of justice in the international legal order. Examples are drawn from the 1970s campaign for a New International Economic Order at the UN, from international adjudication, from feminist campaigns, and from the work of international legal scholars such as Thomas Franck and Steven Ratner. The chapter argues that the concept of international justice has become associated largely with international criminal law, and indicates the limitations of this linkage.
DBT–PTSD
Authors: Bohus Martin , Priebe Kathlen
Published: April 2018

In addition to the core posttraumatic symptomatology such as s trauma-related intrusions, avoidance, and hyperarousal, patients with complex PTSD related to childhood abuse often also exhibit distortions of emotion regulation, pervasive negative self-concepts, and difficult interpersonal relationships. DBT-PTSD is a comprehensive multicomponent treatment to specifically focus on the sequelae of childhood abuse with and without borderline personality disorder. Based on the principles of DBT, it adds trauma-specific cognitive and skills-assisted exposure-based techniques and interventions to improve acceptance as well as compassion for self and others. It has been developed for and tested in both a three-month residential treatment and a 12-month outpatient programme. The first randomized controlled trial evaluated the treatment under residential conditions, including borderline patients with ongoing self harm. The second large multi-centre trial investigates DBT-PTSD under outpatient conditions, compared to Cognitive Processing Therapy (CPT). This chapter reviews the principles and structure of this new and highly promising DBT-adaptation.
The Future of Security Studies
Authors: Gheciu Alexandra , Wohlforth William C.
Published: April 2018

We situate the chapters that follow in the changing context of the study and practice of international security and show how rigorous thinking about the future informs the volume. Dramatic changes in the international security landscape against the backdrop of the increased salience of the classical security agenda of great power rivalry call for a new state-of-the-field compendium. The state of the field, meanwhile, is not what it was even a few years ago, with the rise of new approaches and the transformation of older ones. By asking leading thinkers to address developments in international security through a future-oriented lens, we are able to present readers with a comprehensive and cutting edge guide to the field.
Methods in Critical Security Studies
Authors: Salter Mark B. , Mutlu Can E.
Published: April 2018

To represent the plurality of methods used within the Critical Studies Security community, this chapter surveys discourse analysis, corporeal analysis, ethnographic research, new materialism, and field analysis. Separating these practical methods from their ontological stakes makes critical analysis mutually intelligible and fosters a collobarative and plural discussion that shies away from doctrinaire orthodoxy. As a guide for analysis, this chapter also sets out some consensus positions about basic methods that are used in this field that critical scholars share and use in different theoretical traditions for their research design: idetifying standards of clarity, fit, and reflexivity by which critical scholarship can be judged, not on its ethical claims or its take on criticality, but rather on grounds of rigor.
Systemic Theory and the Future of Great Power War and Peace
Authors: Copeland Dale
Published: April 2018

Drawing from theories that examine security-dilemma spiraling and the dynamics of relative decline, the chapter shows that established theories of major war can be made relevant to the nuclear age—once they have incorporated the importance of Cold War spiraling and inadvertent war.The chapter argues that any theory of international relations that seeks to explain changes in the likelihood of nuclear war must incorporate into its causal logic the willingness of states to take actions that risk an inadvertent slide into war. While it may not be rational to initiate a nuclear war against another great power, it may indeed be rational, under certain circumstances, for leaders to switch to hard-line actions that raise the probability of a war neither side would have actively desired prior to the onset of a crisis.
Security and “Security Studies”
Authors: Krause Keith , Williams Michael
Published: April 2018

The quest for security is one of the most powerful dynamics of modern politics. To ask “what is security and security studies?” is to grapple with an ambiguous, contested, and controversial concept and discipline. This relativity of security—of who or what is being threatened, and from what or whom—has important consequences for understanding security relations between states, within states, and between non-state actors. This chapter traces some of the shifting meanings, practices, and institutions of security, showing how and why they have changed as part of a complex historical process of dealing with the place of violence and order in modern political and social life. New issues and approaches both reflect and challenge these historical lineages, raising key political and analytic questions.
Public–Private Interactions and Practices of Security
Authors: Avant Deborah , Haufler Virginia
Published: April 2018

Though most assume a settled relationship between security and the state, the degree to which different forms of violence are collective endeavors handled by states has varied over time, affecting who or what it secured, how, and what is understood to be public. In the modern era the control and management of violence were core elements of state practice. We examine recent history to show how globalization initiated debates over security and opened avenues for different claims, both about security and about what is public and private. We trace how interactions among intellectuals, governments, transnational activists, and companies shifted who authorizes security, who provides security, and how legitimate and illegitimate force are distinguished—all public concerns. We conclude by discussing current developments that could reinforce or disrupt these trends and claim again that public–private interactions will shape their impact on future global security practices.
The Crime Scene
Authors: Jakobi Anja P.
Published: April 2018

Transnational crime has increasingly become a central topic in international security studies. Yet, crimes differ in their relevance for security, and countermeasures range from early efforts against slavery to current debates on cybersecurity. This chapter starts with an introduction to transnational crime, the difficulties of defining it, and the security risks it embodies. The next section presents the governance of crime, distinguishing between internal and external governance, and how both aspects are needed to consider the threat potential of transnational crime. The subsequent section outlines future scenarios on three major aspects of governing transnational crime: the use of data, the role of formal norms, and the dimensions of security. Taken together, international security benefits from taking into account a complex and differentiated picture of crime. Crime is often a consequence of security weaknesses, not necessarily their cause.
Terrorism
Authors: Cronin Audrey Kurth
Published: April 2018

The chapter discusses driving factors for the future of global terrorism and its academic study. It focuses on the role of old and new media, facilitating terrorist strategies aimed at mobilizing recruits and polarizing societies. Other types of violence kill more people, but terrorism threatens democratic societies by pitting values such as freedom of speech, freedom of the press, and non-discrimination, on the one hand, against protecting the lives of potential victims, on the other. Scholars have responded by seeking predictive “models” of radicalization, sometimes without understanding the local contexts from which operatives emerge. The narrow historical scope of most quantitative databases and the tailoring of inquiries to fit the data available further hobble their efforts. Terrorism is neither a hermetically sealed phenomenon nor the worst type of violence that can occur. Scholars must collaborate more across disciplines if they are to analyze and counter it effectively.
Images and International Security
Authors: Hansen Lene
Published: April 2018

Photographs, cartoons, video—in sum, visual representations—are crucial to how security problems become known and debated. Yet, images have only recently entered security studies as a particular topic in need of research. This chapter shows how technological innovations, major events, and theory development within the larger fields of humanities and the social sciences explain why and how images have entered security studies. Images are important to security politics because they are capable of evoking emotions and they travel across national and linguistic boundaries in ways that words cannot. Striking images have supported the calls for expanding the concept of security to include non-military threats, such as for example HIV/AIDS or famine. But images may also cause conflicts when they are seen as insulting to core values and identities. The study of images is so complex that a pluralistic methodology and multiple epistemologies are warranted.
Realisms
Authors: Quinn Adam
Published: April 2018

Realism is one of the best-known and longest-established approaches to International Security, but the level of diversity that exists within the label often goes underappreciated. This chapter first enumerates and explains the primary divergent strands co-existing within realism: structural, neoclassical, and revived classical realism. It then outlines the ways different types of realist vary in their answers to key social-scientific questions: Should theory be predictive, and if so what kinds of predictions can realism hope to make? Is realism a theory of rational action? Is it purely descriptive and explanatory, or also normative/prescriptive? Do “ideas” matter in a realist framework, and if so in what way? Finally, taking all the preceding into account, can realism still claim to be a distinctive approach, united by some common principle or principles?
The Beautiful Face of Ra
Authors: Magli Giulio
Published: April 2018

In the famous projects of ancient Egyptian architecture, sunlight had always a special role. An expert use of light and shadows helped in creating halls filled with sacredness in many temples; but most of all the Sun was the visible face of Ra, the Sun God. As a consequence, religious and funerary architectural projects were connected with the sun rays on special days of the year through astronomical alignments. The chapter focuses on a few key examples—the Akhet hierophanies at Giza and Amarna, and the winter solstice alignment at Karnak—showing the potentialities of modern archaeoastronomy in understanding key aspects of ancient Egyptian monuments and religion.
Business
Authors: Börzel Tanja A. , Deitelhoff Nicole
Published: April 2018

Business has become an important governor in areas of limited statehood (ALS). While the shadow of hierarchy is not necessary to incentivize companies, their contributions to governance still seem to require a minimum of statehood to be effective and legitimate. These findings point to a dilemma for (business) governance in ALS: companies are most likely to provide collective goods and services beyond their purview where those are needed the least to compensate for the lack of state governance. Yet, the literature has mostly focused on multinational companies that have their headquarters in democracies with consolidated statehood. Future research should focus on business in the non-OECD world to explore whether and to what degree consolidated statehood is necessary for governance by business to be effective and legitimate.
Coercion and Trusteeship
Authors: Lake David A.
Published: April 2018

The governance problem arises when society lacks an ‘ultimate’ authority able to regulate competition and limit conflict between social actors. A variant of the cycling problem in social choice theory, the governance problem can be potentially solved by one of several modes. This chapter focuses on two related modes, coercion and trusteeship, in which a dominant group within society or an external power, respectively, imposes a policy and set of institutions on society. The first section examines the governance problem in areas of limited statehood. The second section outlines the role for the state in solving the governance problem, and how states emerged as successful actors in the now consolidated states of Europe. The third section explores coercion and trusteeship as solutions to the governance problem. It concludes with the somewhat pessimistic argument that trusteeship, though perhaps preferred on normative grounds, is unlikely to succeed in building strong, consolidated states.
Migration
Authors: Lavenex Sandra
Published: April 2018

Starting from the observation that statehood and migration are co-constitutive, the chapter first recapitulates the evolution of migration governance in ‘areas of consolidated statehood’. It then turns to areas of limited statehood and shows that limited statehood indeed reflects in limited state involvement in migration governance, in particular regarding migrants’ rights, and that differences in countries’ formal commitments (e.g. between Asian and African states) have little repercussions on political practice. In addition, many governance functions linked to the provision of collective goods are assumed by international and private actors. Finally, consolidated states have engaged in intensive external governance promotion towards countries of origin and transit of migrants in an attempt to regain control over undesired migration flows. While symbolically upholding the notion of sovereignty, these practices of externalization may be interpreted as deliberate limitation of statehood.
Histories of Governance
Authors: Esders Stefan , Hölck Lasse , Rinke Stefan
Published: April 2018

This contribution reviews historical modes of governance from ancient, medieval, and early modern times to discuss the mutual benefit of the governance concept for political and historical sciences. Focused on the transitional periods of the European Middle Ages and colonial history, the inclusion of culturally heterogeneous populations into one and the same political entity by the spread of basic values is singled out as common topic between the disciplines. Indiscriminate classifications of modern governance phenomena as ‘new medievalism’ are thus criticized by pointing to the fact that self-governance, the spread of common binding rules or rituals of self-commitment, has been the rule throughout human social evolution. Historical examples are given to show that areas of limited statehood are not ungoverned, but rather spaces of contested governance provided by a variety of actors ranging from official state agents and churchmen to local communities.
Geographies of Limited Statehood
Authors: Korf Benedikt , Raeymaekers Timothy , Schetter Conrad , Watts Michael J.
Published: April 2018

Starting from the presupposition that areas of limited statehood (ALS) are not ungoverned, but ‘differently’ governed, this chapter proposes a spatial grammar that analyses authority and governance as a socio-spatial relationship. This spatial grammar distinguishes four types of dynamic socio-spatial relations—territory, place, scale, and network—and enables us to spatially analyse (a) how political authority is contested, claimed, upheld, and disrupted; (b) how political life is negotiated, regulated, and practised; and (c) how these practices and their effects are spatially situated. We apply this spatial grammar to four case studies, each providing insight into one type of socio-spatial relations. These cases from Nigeria, Sri Lanka, Afghanistan, and Democratic Republic of the Congo (DRC), explain how the negotiation, contestation, and disruption of political authority is spatially situated and embedded in ALS. A spatial grammar focuses on the shifting, overlapping, and contradictory practices of claiming political and regulatory power.
External State Actors
Authors: Lederer Markus
Published: April 2018

This chapter focuses on external state governance, asking which state governors do what, why, how, and with what ambition? What kind of governance do external state governors provide, under which conditions are their governance contributions effective and legitimate, and what consequences do they have? When answering these questions, the main argument is that attempts to strengthen statehood and sometimes even the idea of state-building should not be dismissed too early, as such efforts can, under certain conditions, be considered effective and legitimate. Successful governance in areas of limited statehood (ALS), however, requires taking into account the politics in the respective area as well as a realization on the side of external state governors that governance in ALS often has to start ‘at home’—in the world of consolidated statehood.
Franco Basaglia
Authors: Foot John
Published: April 2018

A radical psychiatrist, Franco Basaglia was born in Venice in 1924. He came into contact with phenomenological texts while studying psychiatry at the University of Padua in the 1940s and 1950s. When he became Director of the Psychiatric Hospital in the north-eastern city of Gorizia in 1961 he began to apply these ideas to the reform of the hospital. Wards were opened, walls knocked down (by the patients), and meetings held. Gorizia became a beacon for change in 1968 with the publication of Basaglia’s edited volume L’istituzione negata (The Negated Institution) (Einaudi 1968). A movement developed which culminated in the 1978 “Basaglia Law,” which closed down the entire Italian asylum system.
Bourdieu and the Body
Authors: Connell Catherine , Mears Ashley
Published: April 2018

Chapter abstract The work of Pierre Bourdieu provides a framework to see how class position is written on the body and expressed through classed styles of walking, talking, gesturing, eating, drinking, and so forth. This chapter considers how Bourdieu’s work on the body has informed and advanced empirical research on the body. From Bourdieu’s perspective, each body is the visible product of the composition and volumes of class-specific capitals accrued over the course of a lifetime, and it can be a powerful resource, or liability, depending upon the fit between one’s bodily capital and the field in which one is positioned. In particular, the chapter considers how women’s bodies have signified status for men’s class projects far more than the reverse, one of the many gendered implications of bodily capital and class reproduction.
The Development of Doctrine
Authors: Kaplan Grant , Coolman Holly Taylor
Published: April 2018

This chapter considers two fundamental points of reference in modern accounts of how Christian doctrine may be said to develop. First, the chapter considers the arguments of the members of the Tübingen school, with a particular focus on Johann Sebastian Drey (1777–1853) and Johann Adam Möhler (1796–1838). The second half of the chapter focuses on the work of St John Henry Cardinal Newman (1801–90). Although the degree to which Newman knew his Tübingen predecessors is hotly debated, there was a deep affinity between their approaches. The chapter considers the achievement of Newman’s An Essay on the Development of Christian Doctrine against the background of his corpus as a whole.
Thomism From 1962–2012
Authors: Bonino Serge-Thomas
Published: April 2018

There are good reasons for thinking that Thomism (inspired by Thomas Aquinas), or at least a certain kind of Thomism, was undercut by the Second Vatican Council. Thomist categories are used sparingly and Thomist metaphysics hardly features. And yet a number of factors have enabled Thomism to renew itself in the post-conciliar Church. The persistence of institutions within which Thomism is taught, the vitality of recent historical studies on Thomas Aquinas, the renewal of a specifically theological interest in Thomas, and the persistent utility of Thomas in the exploration of the relationship between faith and reason have enabled Thomism to flourish.
Computational Treatment of Multiword Expressions
Authors: Ramisch Carlos , Villavicencio Aline
Published: April 2018

In natural-language processing, multiword expressions (MWEs) have been the focus of much attention in their many forms, including idioms, nominal compounds, verbal expressions, and collocations. In addition to their relevance for lexicographic and terminographic work, their ubiquity in language affects the performance of tasks like parsing, word sense disambiguation, and natural-language generation. They lend a mark of naturalness and fluency to applications that can deal with them, ranging from machine translation to information retrieval. This chapter presents an overview of their linguistic characteristics and discusses a variety of proposals for incorporating them into language technology, covering type-based discovery, token-based identification, and MWE-aware language technology applications.
Justification
Authors: Lane Anthony N. S.
Published: April 2018

The last seventy years have seen many dialogues between Roman Catholics and Protestants (mainly, but not exclusively, Lutherans) on the doctrine of justification. This article surveys eight of these dialogues, their culmination in the 1999 Joint Declaration on the Doctrine of Justification, and the impact of this last document. Also considered are nine doctrinal issues raised by the dialogues: justification as the chief article of faith; human incapacity; the definition of justification; why we are accounted righteous; remaining sin in the Christian; faith alone; lapse and restoration; merit and reward; and assurance of salvation. The conclusion is that considerable progress has been made in clearing up misunderstandings and that the two sides have drawn together. It remains to be seen how solid and lasting is this achievement.
Method in Ecumenism
Authors: Abraham William J.
Published: April 2018

Method can mean either the steps taken to achieve church unity or the principles appropriate to the study of ecumenism. Most ecumenists have sought organic unity; they have hoped that agreement on the issue of authority would further this end. This turned out to be impossible, and recently there has been a shift from epistemology to pneumatology. This shift allows for a third option beyond the claims of Catholicism and Orthodoxy, on the one hand, and Magisterial Protestantism, on the other, as regards ecclesial continuity. We can think of the creation of the church as the reinstantiation of primitive Christianity in the wake of Pentecost. Messianic Judaism provides telling warrant for pursuing this option. This shift also provides fresh hope for ecumenism by moving beyond conciliar conversations about doctrine, and calling instead for gift-sharing—that is, the realistic sharing of what we actually think are gifts for the common good.
Orthodox
Authors: Grdzelidze Tamara
Published: April 2018

This chapter aims to clarify the role of the Orthodox Church in the ecumenical movement. Historically present in the movement from the beginning, and theologically challenging the understanding of unity in the movement right up to the present day, the Orthodox tradition has shown ambivalence in relation to other Christians and especially with regard to their claims to ecclesiality. An ecclesiological challenge has become the most remarkable characteristic of the Orthodox in the inter-Christian context. Nevertheless, the Orthodox tradition has demonstrated the capacity to reach agreements through dialogue in spite of difficulties associated with other Christian traditions such as the relativization of the inherited tradition. Among achievements on the way to Christian unity is rapprochement between the two Orthodox families, Eastern and Oriental. Many questions remain to be answered within the Orthodox Church in order to bring new breath into inter-Christian dialogue.
Genomewide characterisation of the genetic diversity of carotenogenesis in bacteria of the order Sphingomonadales
Authors: Siddaramappa Shivakumara , Viswanathan Vandana , Thiyagarajan Saravanamuthu , Narjala Anushree
Published: April 2018

The order Sphingomonadales is a taxon of bacteria with a variety of physiological features and carotenoid pigments. Some of the coloured strains within this order are known to be aerobic anoxygenic phototrophs that contain characteristic photosynthesis gene clusters (PGCs). Previous work has shown that majority of the ORFs putatively involved in the biosynthesis of C40 carotenoids are located outside the PGCs in these strains. The main purpose of this study was to understand the genetic basis for the various colour/carotenoid phenotypes of the strains of Sphingomonadales. Comparative analyses of the genomes of 41 strains of this order revealed that there were different patterns of clustering of carotenoid biosynthesis (crt) ORFs, with four ORF clusters being the most common. The analyses also revealed that co-occurrence of crtY and crtI is an evolutionarily conserved feature in Sphingomonadales and other carotenogenic bacteria. The comparisons facilitated the categorisation of bacteria of this order into four groups based on the presence of different crt ORFs. Yellow coloured strains most likely accumulate nostoxanthin, and contain six ORFs (group I: crtE, crtB, crtI, crtY, crtZ, crtG). Orange coloured strains may produce adonixanthin, astaxanthin, canthaxanthin and erythroxanthin, and contain seven ORFs (group II: crtE, crtB, crtI, crtY, crtZ, crtG, crtW). Red coloured strains may accumulate astaxanthin, and contain six ORFs (group III: crtE, crtB, crtI, crtY, crtZ, crtW). Non-pigmented strains may contain a smaller subset of crt ORFs, and thus fail to produce any carotenoids (group IV). The functions of many of these ORFs remain to be characterised.
Targeted Reactivation of FMR1 Transcription in Fragile X Syndrome Embryonic Stem Cells
Authors: Haenfler Jill M. , Skariah Geena , Rodriguez Caitlin M. , Rocha Andre Monteiro da , Parent Jack M. , Smith Gary D. , Todd Peter K.
Published: April 2018

Fragile X Syndrome (FXS) is the most common inherited cause of intellectual disability and autism. It results from expansion of a CGG nucleotide repeat in the 5’ untranslated region of FMR1. Large expansions elicit repeat and promoter hyper-methylation, heterochromatin formation, FMR1 transcriptional silencing, and loss of the Fragile X protein, FMRP. Efforts aimed at correcting the sequelae resultant from FMRP loss have thus far proven insufficient, perhaps because of FMRP’s pleiotropic functions. As the repeats do not disrupt the FMRP coding sequence, reactivation of endogenous FMR1 gene expression could correct the proximal event in FXS pathogenesis. Here we utilize the CRISPR/dCAS9 system to selectively re-activate transcription from the silenced FMR1 locus. Fusion of the transcriptional activator VP192 to dCAS9 robustly enhances FMR1 transcription and increases FMRP levels when targeted directly to the CGG repeat in human cells. Using a previously uncharacterized FXS human embryonic stem cell (hESC) line which acquires transcriptional silencing with serial passaging, we achieved locus-specific transcriptional re-activation of FMR1 mRNA expression despite promoter and repeat methylation. These studies demonstrate that FMR1 mRNA expression can be selectively reactivated in human patient cells, creating a pathway forward for therapeutic development in Fragile X Syndrome.
A Novel Household Water Insecurity Scale: Procedures and Psychometric Analysis among Postpartum Women in Western Kenya
Authors: Boateng Godfred O. , Collins Shalean M. , Mbullo Patrick , Wekesa Pauline , Onono Maricianah , Neilands Torsten B. , Young Sera L.
Published: April 2018

Our ability to measure household-level food insecurity has revealed its critical role in a range of physical, psychosocial, and health outcomes. Currently, there is no analogous, standardized instrument for quantifying household-level water insecurity, which prevents us from understanding both its prevalence and consequences. Therefore, our objectives were to develop and validate a household water insecurity scale appropriate for use in our cohort in western Kenya. We used a range of qualitative techniques to develop a preliminary set of 29 household water insecurity questions, and administered those questions at 15 and 18 months postpartum, concurrent with a suite of other survey modules. These data were complemented by data on quantity of water used and stored, and microbiological quality. Inter-item and item-total correlations were performed to reduce scale items to 20. Exploratory factor and parallel analyses were used to determine the latent factor structure; a unidimensional scale was hypothesized and tested using confirmatory factor and bifactor analyses, along with multiple statistical fit indices. Reliability was assessed using Cronbach’s alpha and the coefficient of stability, which produced a coefficient alpha of 0.97 at 15 and 18 months postpartum and a coefficient of stability of 0.62. Predictive, convergent and discriminant validity of the final household water insecurity scale were supported, based on relationships with food insecurity, perceived stress, per capita household water use, and time and money spent acquiring water. The resultant scale is a valid and reliable instrument. It can be used in this setting to test a range of hypotheses about the role of household water insecurity in numerous physical and psychosocial health outcomes, to identify the households most vulnerable to water insecurity, and to evaluate the effects of water-related interventions. To extend its applicability, we encourage efforts to develop a cross-culturally valid scale using robust qualitative and quantitative techniques.
A multiplexed homology-directed DNA repair assay reveals the impact of ~1,700 BRCA1 variants on protein function
Authors: Starita Lea M. , Islam Muhtadi M. , Banerjee Tapahsama , Adamovich Aleksandra I. , Gullingsrud Justin , Fields Stanley , Shendure Jay , Parvin Jeffrey D.
Published: April 2018

Loss-of-function mutations in BRCA1 confer a predisposition to breast and ovarian cancer. Genetic testing for mutations in the BRCA1 gene frequently reveals a missense variant for which the impact on the molecular function of the BRCA1 protein is unknown. Functional BRCA1 is required for homology directed repair (HDR) of double-strand DNA breaks, a key activity for maintaining genome integrity and tumor suppression. Here we describe a multiplex HDR reporter assay to simultaneously measure the effect of hundreds of variants of BRCA1 on its role in DNA repair. Using this assay, we measured the effects of ~1,700 amino acid substitutions in the first 302 residues of BRCA1. Benchmarking these results against variants with known effects, we demonstrate accurate discrimination of loss-of-function versus benign variants. We anticipate that this assay can be used to functionally characterize BRCA1 missense variants at scale, even before the variants are observed in results from genetic testing.
Robustness of bristle number to temperature and genetic background varies with bristle type and is regulated by miR-9a
Authors: Matamoro-Vidal A. , Tully T. , Courtier-Orgogozo V.
Published: April 2018

Robustness is the invariance of a given phenotype when faced with a given incoming genetic or environmental variation. Such essential property is being studied in a wide diversity of traits in many organisms but it is difficult to compare the results obtained on the robustness of different traits with each other given the differences that exist between traits in the way they are measured, in their genetic architecture and development. In this study, we assessed robustness of bristle number to incoming genetic and environmental variation for eight bristle types in the fruit fly Drosophila melanogaster, allowing for a straightforward comparison of the robustness observed between bristle types. We measured the response of bristle number mean and variance to changes in temperature and in the number of copies of two genes (scute and miR-9a) known to be involved in bristle development. Many combinations between the three factors were tested, thus allowing to test for the effect of each factor in different contexts for the two other factors – to which we refer herein as different backgrounds. We have found different responses between bristle types, suggesting that they present different levels of robustness to the factors tested. In addition, we have found that temperature and miR-9a affect more generally the variance of the traits rather than their means, thus fulfilling a criteria usually admitted to identify robustness factors.
The Fair Proportion is a Shapley Value on phylogenetic networks too
Authors: Coronado Tomás M. , Riera Gabriel , Rosselló Francesc
Published: April 2018

The Fair Proportion of a species in a phylogenetic tree is a very simple measure that has been used to assess its value relative to the overall phylogenetic diversity represented by the tree. It has recently been proved by Fuchs and Jin to be equal to the Shapley Value of the coallitional game that sends each subset of species to its rooted Phylogenetic Diversity in the tree. We prove in this paper that this result extends to the natural translations of the Fair Proportion and the rooted Phylogenetic Diversity to rooted phylogenetic networks. We also generalize to rooted phylogenetic networks the expression for the Shapley Value of the unrooted Phylogenetic Diversity game on a phylogenetic tree established by Haake, Kashiwada and Su.
Loss of YAP/TAZ impaired the proliferation and differentiation ability of neural progenitor cells
Authors: Kong Shanshan
Published: April 2018

YAP (Yes-associated protein) and TAZ (transcriptional coactivator with PDZ-binding motif) are downstream effectors of the Hippo pathway, they activate the expression of transcriptional targets that promote cell growth, cell proliferation, and prevent apoptosis. Here I examined the function of YAP/TAZ in mouse neocortex development through conditional deletion of Yap and Taz by Emx1-Cre. Loss of YAP/TAZ cause the hydrocephalus after birth, leads to aberrant development and dilated ventricle in adult stage, this phenotype can be detected as early as P0. YAP/TAZ are expressed in Sox2+ neural progenitor cells, when YAP/TAZ are deleted, the neuroepithelial cell junctions are disrupted; the numbers of Sox2+ cell and Tbr2+ cell are reduced and the ratio of tbr2/Sox2 is also reduced at E15.5. Results of cell cycle analyzing experiments display YAP/TAZ deletion increased the cell cycle exit. The improperly increased expression of Tuj1+ in progenitor cells in the YAP/TAZ deleted cortex indicates the premature of Sox2+ progenitor cells. Together, our results reveal that YAP/TAZ deletion changed the polarity of neuroepithelial cells, and increased the cell cycle exit, reduced the differentiation of Sox2+ cells into Tbr2+ cells through promoting the premature of Tuj1+ cells. These results define the functions of YAP/TAZ in keeping the cell polarity neural progenitors and ensuring their proliferation and differentiation, and also reveal the roles of YAP/TAZ in developing cortex.
Network-based assessment of the vulnerability of Italian regions to bovine brucellosis
Authors: Darbon Alexandre , Valdano Eugenio , Poletto Chiara , Giovannini Armando , Savini Lara , Candeloro Luca , Colizza Vittoria
Published: April 2018

The endemic circulation of bovine brucellosis in cattle herds has a markedly negative impact on economy, due to decreased fertility, increased abortion rates, reduced milk and meat production. It also poses a direct threat to human health. In Italy, despite the long lasting efforts and the considerable economic investment, complete eradication of this disease still eludes the southern regions, as opposed to the northern regions that are disease-free. Here we introduced a novel quantitative network-based approach able to fully exploit the highly resolved databases of cattle trade movements and outbreak reports to yield estimates of the vulnerability of a cattle market to brucellosis. Tested on the affected regions, the introduced vulnerability indicator was shown to be accurate in predicting the number of bovine brucellosis outbreaks, thus confirming the suitability of our tool for epidemic risk assessment. We evaluated the dependence of regional vulnerability to brucellosis on a set of factors including premises spatial distribution, trading patterns, farming practices, herd market value, compliance to outbreak regulations, and exploring different epidemiological conditions. Animal trade movements were identified as a major route for brucellosis spread between farms, with an additional potential risk attributed to the use of shared pastures. By comparing the vulnerability of disease-free regions in the north to affected regions in the south, we found that more intense trade and higher market value of the cattle sector in the north, likely inducing more efficient biosafety measures, together with poor compliance to trade restrictions following outbreaks in the south were key factors explaining the diverse success in eradicating brucellosis. Our modeling scheme is both synthetic and effective in gauging regional vulnerability to brucellosis persistence. Its general formulation makes it adaptable to other diseases and host species, providing a useful tool for veterinary epidemiology and policy assessment.
SPORTS1.0: A Tool for Annotating and Profiling Non-coding RNAs Optimized for rRNA- and tRNA-derived Small RNAs
Authors: Shi Junchao , Ko Eun-A , Sanders Kenton M. , Chen Qi , Zhou Tong
Published: April 2018

High-throughput RNA-seq has revolutionized the process of small RNA (sRNA) discovery, leading to a rapid expansion of sRNA categories. In addition to the previously well-characterized sRNAs such as microRNAs (miRNAs), Piwi-interacting RNA (piRNAs), and small nucleolar RNA (snoRNAs), recent emerging studies have spotlighted on tRNA-derived sRNAs (tsRNAs) and rRNA-derived sRNAs (rsRNAs) as new categories of sRNAs that bear versatile functions. Since existing software and pipelines for sRNA annotation are mostly focused on analyzing miRNAs or piRNAs, here we developed the sRNA annotation pipeline optimized for rRNA- and tRNA- derived sRNAs (SPORTS1.0). SPORTS1.0 is optimized for analyzing tsRNAs and rsRNAs from sRNA-seq data, in addition to its capacity to annotate canonical sRNAs such as miRNAs and piRNAs. Moreover, SPORTS1.0 can predict potential RNA modification sites based on nucleotide mismatches within sRNAs. SPORTS1.0 is precompiled to annotate sRNAs for a wide range of 68 species across bacteria, yeast, plant, and animal kingdoms, while additional species for analyses could be readily expanded upon end users’ input. For demonstration, by analyzing sRNA datasets using SPORTS1.0, we reveal that distinct signatures are present in tsRNAs and rsRNAs from different mouse cell types. We also find that compared to other sRNA species, tsRNAs bear the highest mismatch rate which is consistent with their highly modified nature. SPORTS1.0 is an open-source software and can be publically accessed at https://github.com/junchaoshi/sports1.0.