bluuebunny/crossref_metadata_2025 huggingface dataset:
Measuring Global Poverty
Authors: Dhongde Shatakshee
Published: November 2018

Economists have long been preoccupied with trying to understand the nature and causes of poverty. From Adam Smith to David Ricardo, Thomas Malthus, Karl Marx, and John Stuart Mill, a common belief among economists is that the benefits of economic growth are rarely experienced by the poorer sections of society. An important issue is how to measure global poverty accurately. International organizations such as the United Nations and the World Bank have endeavored to measure global poverty since the adoption of the Millennium Development Goals (MDG), stated in the UN’s Millennium Declaration which was adopted in 2000 by 189 nations. However, measuring global poverty is far from simple. Estimates of poverty and particularly of global poverty are very sensitive to the underlying assumptions, such as the notion of poverty itself, the choice of welfare indicator, the unit of measurement used, and purchasing power parity rates. One of the significant advances in global poverty studies was the World Bank’s introduction of a poverty line in the 1990 World Development Report (WDR). Despite these efforts, the precise number of poor in the world remains ambiguous. Nevertheless, emerging frontiers in poverty analysis indicate new interest in measuring poverty more broadly. Some ideas that may dominate the future of poverty research include multidimensional poverty, vulnerability to poverty, and chronic poverty.
Mercantilist and Realist Perspectives on the Global Political Economy
Authors: Drezner Daniel W.
Published: November 2018

Mercantilism and realism would appear to go hand in glove with each other. If realism represents both a systemic worldview and explanatory model for world politics, then mercantilism would appear to be the paradigm’s default foreign economic policy doctrine. And, to be sure, there are obvious and strong areas of overlap. Both paradigms stress the autonomous role of the state—and warn against capture by particularistic interests. Both also stress the conditioning effects of the distribution of power in defining national economic interests. Despite these constants, however, over time, the two approaches diverged more and more. Most modern-day writers who sympathize with mercantilism do so from perspectives ranging from left-leaning social democracy to more radical Gramscian critiques. Realists, on the other hand, have tended to gravitate towards the conservative, Burkean side of the political spectrum. While realists and mercantilists might agree on the role that power plays in the global economy, they do not necessarily agree on the normative implications of that insight. Paradoxically, as realism has acquired a more “scientific” cast, it has become less influential in international political economy (IPE) scholarship. For realism to maintain its relevancy in IPE, it must reacquire its deftness in incorporating nonstructural variables into its explanatory framework. The paradigm retains some useful predictive power for how systemic political variables affect global economic outcomes, but it is of little use in discussing the reverse causal effects.
Nuclear Proliferation and Non-Proliferation
Authors: Hymans Jacques E.C.
Published: November 2018

Nuclear proliferation became an increasingly major concern after France and then China joined the nuclear “club” in the 1960s. However, it was not until India’s “peaceful nuclear explosive” test of 1974 that a real sense of potential worldwide crisis emerged, which also spawned a substantial amount of serious writing on the issue. The basic puzzle facing the study of nuclear proliferation is why there is a considerable and persistent disparity between the number of nuclear weapons-capable states and the number of actual nuclear weapons states. Three early works that represented crucial conceptual breakthroughs in the struggle toward a proper descriptive inference of the dynamics of proliferation are William Epstein’s The Last Chance (1976), Stephen M. Meyer’s The Dynamics of Nuclear Proliferation (1984), and Opaque Nuclear Proliferation (1991), edited by Benjamin Frankel. More contemporary political science work features attempts by each of the major international relations paradigms to tackle the proliferation puzzle: realism, psychological constructivism, neoliberal institutionalism, liberalism, and sociological constructivism. While scholars disagree over a host of issues, a consensus on the dynamics of nuclear proliferation may be discerned. In particular, there are five points on which most recent works converge: that proliferation has been historically rare; that we cannot take the demand for nuclear weapons for granted; that domestic politics and identity considerations play a crucial role in shaping proliferation choices; and that theory-guided, in-depth comparative case studies are the most appropriate means of advancing the state of our knowledge at this point in time.
Methods of Foreign Policy Analysis
Authors: Potter Philip B.K.
Published: November 2018

Foreign policy analysis (FPA) is the study of how states, or the individuals that lead them, make foreign policy, execute foreign policy, and react to the foreign policies of other states. This topical breadth results in a subfield that encompasses a variety of questions and levels of analysis, and a correspondingly diverse set of methodological approaches. There are four methods which have become central in foreign policy analysis: archival research, content analysis, interviews, and focus groups. The first major phase of FPA research is termed “comparative foreign policy.” Proponents of comparative foreign policy sought to achieve comprehensive theories of foreign policy behavior through quantitative analysis of “events” data. An important strand of this behavioral work addressed the relationship between trade dependence and foreign policy compliance. On the other hand, second-generation FPA methodology largely abandoned universalized theory-building in favor of historical methods and qualitative analysis. Second-generation FPA researchers place particular emphasis on developing case study methodologies driven by social science principles. Meanwhile, the third-generation of FPA scholarship combines innovative quantitative and qualitative methods. Several methods of foreign policy analysis used by third-generation FPA researchers include computer assisted coding, experiments, simulation, surveys, network analysis, and prediction markets. Ultimately, additional attention should be given to determining the degree to which current methods of foreign policy analysis allow predictive or prescriptive conclusions. FPA scholars should also focus more in reengaging foreign policy analysis with the core of international relations research.
Military Effectiveness
Authors: Biddle Stephen
Published: November 2018

Military effectiveness is defined as the ability to produce favorable military outcomes per se, incluuding the outcomes of minor skirmishes at the tactical level of war and the outcomes of wars or even long-term politico-military competitions at the strategic or grand strategic levels of war. An alternative, narrower definition equates “effectiveness” with skill, the ability to make the most of one’s material resources, or qualities such as “integration” and “responsiveness.” Regardless of definition, military effectiveness is a central issue for international relations and lies at the heart of key policy debates. Until very recently, military effectiveness had generated little sustained interest from scholars. However, a new generation of academics, armed with new methodologies and analytical approaches, has begun to pay more attention to the subject. Contemporary literature on effectiveness describes three classes of candidate determinants: numerical preponderance, technology, and force employment. Despite increasing attention to effectiveness per se and to non-material contributors to effectiveness, especially force employment, many topics deserve further consideration in future research. These include maritime warfare, amphibious warfare, space warfare, and cyber warfare, chemical, biological, or nuclear combat operations; effectiveness in non-combat missions such as peacekeeping, nation building, signaling, or humanitarian assistance; systematic differences in military behavior for non-state actors, or for state actors in the developing world; and the roles of organization, logistics, leadership, morale, ethnic homogeneity, civil–military relations, and social structure, for example, as determinants of military effectiveness.
Peace Operations
Authors: Williams Paul D.
Published: November 2018

Peace operations involve the expeditionary use of uniformed personnel (police and/or military) whose mission is to help secure “international peace and security.” In many ways, peace operations are the most visible activity of the United Nations with a mandate to deter armed conflict through preventive deployment or help to kick-start a peace process through peacemaking initiatives, among other purposes. Peace operations can be grouped into several categories, including preventive diplomacy, peacemaking, peacekeeping, post-conflict peacebuilding, and peace enforcement. There are three clusters of approaches that have tried to think conceptually about the relationship between peace operations and broader processes of global politics: global culture, critical theory, and cosmopolitanism. Questions of success and failure in peace operations have been tackled in the literature, which includes the UN’s own reports as well as books and articles appearing within a range of academic disciplines. Scholars have also analyzed the many challenges facing peace operations ranging from civilian protection and gender issues to public security and policing, privatization, intelligence provision, and state-building. Overcoming these challenges will require, at a minimum, new ways of thinking about the problems concerned, new ways of organizing the relevant institutions, and getting the would-be state-builders to allocate substantial resources. There are also some important questions that deserve greater attention; for example, what types of non-UN peace operations are most effective, under what conditions, and how they compare with UN operations, or how a world order can be constructed in which the peacekeepers have put themselves out of business.
Criminal Tribunals
Authors: Fichtelberg Aaron
Published: November 2018

One the most dramatic development in international law in the 20th century was the formation of international criminal tribunals. Unlike conventional international tribunals, such as the International Court of Justice and the Permanent Court of Arbitration, international criminal tribunals—such as the International Criminal Tribunal for the Former Yugoslavia, the International Criminal Tribunal for Rwanda, and the International Military Tribunal at Nuremberg—are a controversial element of international law and international politics. Precisely because they are aimed at individuals who act under color of law, such as military officials or heads of state, they invoke a number of political challenges. Their combination of international law, human rights, criminal justice, and hotly disputed facts of great moral gravity makes them a subject of intense debate among academics, government officials, and the public at large. Much of the scholarship on international tribunals can be summed up by three periods: pre-Nuremberg, Nuremberg, and post-Cold War developments. Each period reveals shifts in the way that international criminal tribunals were studied and conceptualized in the academic world. In the future, much of the scholarship on international tribunals is expected to be influenced by the impact that the actual tribunals themselves have on international politics.
Domestic Application of International Human Rights Norms and Universal Jurisdiction
Authors: Slye Ronald C.
Published: November 2018

Domestic courts play an important role in the adjudication of international law, including international human rights law. The relationship between international and domestic law has often been characterized as a continuum between monism and dualism. In a monist system, international law is automatically a part of domestic law, and a conflict between the two is resolved in favor of international law. In a dualist system, domestic law is superior to international law within the domestic legal system, while international law is superior to domestic law within the international legal system. A conflict between domestic law and international law is thus not always resolved in the same way in both systems. In addition, one of the areas with the most active use of international law in a domestic legal system is under a theory of universal jurisdiction. Universal jurisdiction most often involves both the incorporation of international law into a domestic legal system and the assertion outward (extraterritorially) of domestic judicial system. Universal jurisdiction arose initially in the context of criminal prosecutions, but is also found to some extent in civil litigation, particularly in the United States. Under the principle of universal jurisdiction, a state may assert jurisdiction over an offender regardless of the nationality of the offender or victim, the place of commission of the wrongful act, or any other link to the state asserting jurisdiction.
Feminist Contributions and Challenges to Peace Studies
Authors: Confortini Catia Cecilia
Published: November 2018

Many women across the world have addressed issues of peace and war since antiquity, from Christine de Pizan and Jane Addams to Betty Reardon and Elise Boulding. Although a few feminist scholars in the social sciences consider themselves “peace studies” (PS) scholars, other feminists contribute to PS by tackling peace and violence issues. PS comprises peace research, peace education, and peace activism. Feminists improve on and challenge these fields by insisting on expanded definitions of peace that suggest continuity between different forms of violence; highlighting the diverse roles played by women and other marginalized groups in violent conflicts and in peace processes; complicating our understanding of peace and violence while foregrounding gender as a social and symbolic construct involving relations of power; and proposing transformative ways of conceptualizing peace, war, and postconflict transitions. By seeing all forms of violence along a continuum, feminists transform PS’ understandings of peace. Furthermore, feminism brings women to the center of PS by making them visible as actors in both peace and conflict. Finally, feminism envisions a peaceful future that take into consideration women, other marginalized people, and gender. A number of themes continue to emerge from feminist engagement with PS, such as forgiveness, reconciliation, and transitional justice—themes situated at the intersection of peace/violence and religion.
Feminist Perspectives on Human Rights
Authors: Parisi Laura
Published: November 2018

Feminism has provided some new perspectives to the discourse on human rights over the years. Contemporary feminist scholarship has sought to critique the liberalism on which the conception of formal “equality” in the international human rights laws has been derived on a number of grounds. Two of the most pertinent critiques for this discussion are: the androcentric construction of human rights; and the perpetuation of the false dichotomy between the public and private spheres. This exploration of the relationship between liberalism and women’s human rights constitutes a significant shift in which many feminists had realized that the emphasis on “sameness” with men was limited in its utility. This shift rejected the “sameness” principle of the liberal feminists and brought gender-specific abuses into the mainstream of human rights theory and practice. By gender mainstreaming international institutions and future human rights treaties, specific women’s rights could be defined as human rights more generally. Feminists have since extended their critique of androcentrism and the public–private dichotomy to the study of gender inequalities and economic globalization, which is an important systemic component of structural indivisibility. In particular, the broader women’s human rights movement has come to realize that civil-political liberties and socioeconomic rights are inextricable, though there is disagreement over the exact nature of this relationship.
Feminist Perspectives on the Environment
Authors: Sapra Sonalini 
Published: November 2018

The field of gender and environmental studies deals with the ways that gender roles shape the access to and management of resources. From being dominated by old debates on whether the earth is our mother goddess or whether women are inherently closer to nature than men, gender and environmental studies has evolved into a largely activist-informed and materially-focused discipline. Feminist perspectives are now being articulated in a variety of wide-ranging themes and issues such as environmental justice, global climate change, population debates, disasters, water, and militarization. The main feminist perspectives for studying women and the environment can be divided into two “umbrella” groups: the “ecofeminist” camp and the “materialist” camp. The ecofeminist group argues that there is an “innate” connection between domination of nature and the oppression of women and that there exists a system of patriarchy in human society that leads to the domination of the “Other.” The materialist camp rejects this claim. It makes use of two approaches, feminist environmentalism and Feminist Political Ecology (FPE), to contend that women’s oppression is rooted in structural and material inequalities. Some of these feminist perspectives, including ecofeminism and feminist environmentalism, are applied by the field of Gender, Environment, and Development (GED) to the environmental policy domain. Three transnational environmental organizations doing GED work are GenderCC—Women for Climate Justice, Women’s Environment and Development Organization (WEDO), and Development Alternatives for Women in a New Era (DAWN).
Human Rights and the State
Authors: Cardenas Sonia
Published: November 2018

The modern state’s role vis-à-vis human rights has always been ambiguous. States are the basic guarantors of human rights protections, just as they can be brutal violators of human rights. This basic tension is rooted in the very notion of statehood, and it pervades much of the literature on human rights. As the central organizing principle in international relations, state sovereignty would seem to be antithetical to human rights. Sovereignty, after all, is ultimately about having the last word; it is virtually synonymous with the principle of territorial non-interference. Meanwhile, humanitarian intervention would at first glance seem to be a contravention of state sovereignty. Yet not all observers interpret human rights pressures as a challenge to state sovereignty. Modern states can be highly adaptive, no less so when confronted with human rights demands. One of the principal, if overlooked, ways in which states have adapted to rising global human rights pressures is by creating new institutions. This is reflected in the formation of national human rights institutions (NHRIs): permanent state bodies created to promote and protect human rights domestically. These state institutions are remarkable due to their rapid and widespread proliferation around the world, the extent to which they sometimes represent a strategy of appeasement but nonetheless can be consequential, and their potential for domesticating international human rights standards.
The Conduct and Consequences of War
Authors: Prorok Alyssa K. , Huth Paul K.
Published: November 2018

The academic study of warfare has expanded considerably over the past 15 years. Whereas research used to focus almost exclusively on the onset of interstate war, more recent scholarship has shifted the focus from wars between states to civil conflict, and from war onset to questions of how combatants wage and terminate war. Questioned as well are the longer-term consequences of warfare for countries and their populations. Scholarship has also shifted away from country-conflict-year units of analysis to micro-level studies that are attentive to individual-level motives and explanations of spatial variation in wartime behavior by civilians and combatants within a country or armed conflict. Today, research focuses on variations in how states and rebel groups wage war, particularly regarding when and how wars expand, whether combatants comply with the laws of war, when and why conflicts terminate, and whether conflicts end with a clear military victory or with a political settlement through negotiations. Recent research also recognizes that strategic behavior continues into the post-conflict period, with important implications for the stability of the post-conflict peace. Finally, the consequences of warfare are wide-ranging and complex, affecting everything from political stability to public health, often long after the fighting stops.
Leadership and Organizational Development
Authors: Newberry Derek , Gruebel Eric
Published: November 2018

Since at least the 1930s, anthropologists have been conducting research on the dynamics and features of leadership and organizational development. After a period of dormancy lasting from the middle of the century to the end of the 1970s, work in the field has taken off. Drawing on two of anthropology’s defining features—the ethnographic method and the culture concept—scholars working within the field have provided an alternative and productive approach to a subject studied across a range of disciplines.

As is the case throughout anthropology, no one definition of culture serves as the universal touchstone for the anthropological study of organizations. Still, anthropologists working within the field commonly reject any notion of culture as static, uniform, or fully bounded within an organization. Unlike in the traditional management scholarship, there are few explanatory frameworks on effective leadership or organizational functioning in the anthropological literature. This different emphasis is a byproduct of the larger trend toward reflexivity over the last two decades, in which anthropologists have increasingly challenged both the concept of “culture” itself and attempts to develop broad theoretical frameworks.

For anthropologists of organizations, this shift has created a division between more academically oriented scholars who produce small-scale ethnographies that resist generalization and applied anthropologists who have created more practical, method-focused guides to the field. At the same time, academics and practitioners in fields like design-thinking and industrial-organizational psychology have developed their own, anthropologically informed approaches and theories for understanding leadership and cultural change in organizations. Entering the third decade of the 20th century, it remains to be seen whether the field will continue down this divided path or instead reconnect with its roots in broad cultural theory, leading to greater efforts to synthesize practical, academic, and interdisciplinary approaches to develop new theoretical frameworks.
Chan Literature
Authors: Broughton Jeffrey L.
Published: November 2018

An extensive printed Chan literature came into wide circulation during the Song dynasty (960–1279). This Song corpus included more-or-less intact texts from the Tang (618–907) and Five Dynasties (907–960), Tang and Five-Dynasties texts heavily reworked by Song editors, and a vast newly created set of Song Chan texts. This printed Chan literature spread among the educated elite during the Song period. In total, several hundred woodblock-printed texts from the Song and Yuan (1271–1368) periods, the classic age of Chan textual production, still exist, but many editions from the Ming (1368–1644) and later have also been preserved. In addition, Chan texts can be found within the Dunhuang-manuscript corpus. There are eight major Chan genres (omitting “rules of purity” or qinggui as too technical): yulu (collections of sayings of individual masters); flame-of-the-lamp records (biographical material and sayings of masters arranged as a series of inheritors of the flame of the lamp); poetry (both prosaic religious verse and highly allusive classical shi poetry); “standards” with attached poetry/prose comments (often called by Western scholars “gong’an/kōan collections”); compendia; collections of letters by Chan masters to scholar-officials, students, and peers; pretend dialogues; and glossary material. The language of the Chan records is a hybrid, a mixture of the written elegant language (wenyan) and a type of written Chinese based on spoken language. In time, the language of the Chan records became a sacerdotal language for Chan insiders, not only in China but in Korea and Japan as well. The language patterns of Chan literature—for instance, its proclivity for using everyday words and phrases as stand-ins for more imposing Buddhist-sounding equivalents—account for a great deal of its power and beauty. However, those language patterns also constitute serious obstacles for the modern reader. In short, the texts are very difficult to read because they are not simply “classical Chinese” nor are they modern vernacular. A stylistic convergence of the Chan records and classical Chinese poetry can be seen, particularly in the context of jueju quatrains of seven or five syllables. The sayings of the records often embody aesthetic ideals of Chinese poetry: lexical economy, emphasis on the imagistic, and minimal use of nonimagistic or abstract words.
Commerce, Consumerism, and Christianity in America
Authors: Logan Dana
Published: November 2018

American Christianity and commerce are bound together by their mutual history. In colonial America, Puritans excelled at the skills of capitalism, and in the 19th, 20th, and 21st centuries, Christian corporations have tied together religious and corporate culture. Even when corporations and churches have maintained a distinct boundary between faith and the market, American religion and capitalism seem to be uniquely compatible. Ministers and gurus use mass media to disseminate their message (via TV, radio, bookstores). Religious folk in the United States tend to act like consumers, choosing their theologies and churches based on their individual needs and desires, rather than relying on tradition to dictate their religious practices. Selling and buying in the American marketplace share many similarities with Christian categories of piety and evangelization. Further, corporations and religious communities have since the early 20th century collaborated in politics and social movements. In much of the scholarship on Christianity and commerce in the United States, this relationship is discussed as a strategic partnership between two distinct spheres of life: religion and the market. Recent scholarship, however, has questioned this neat division, arguing that the fluid relationship among commerce, consumption, and Christianity in the United States emerges from the historical co-development of capitalism and religion. If Christianity and the market in the United States look very similar, or are particularly friendly, it is because they were never separate to begin with.
War and Religion in American History
Authors: Ebel Jonathan H.
Published: November 2018

As a subfield of the study of religion, the study of religion and war has access to but has not yet applied the methodological and theoretical tools of a diverse and vibrant discipline. For sound evidentiary reasons as well as out of force of habit, scholars writing about religion and war in American history have drawn heavily on explicitly theologically engaged textual sources, for example, sermons, diaries, and letters. Less common are studies that examine the stuff of popular culture and the military-industrial complex, for example, material culture, film, novels, weapons programs, and military training manuals, for their religious and moral investments. If the study of religion and war in American history is to remain vital and in touch with the changing relationship between the nation, its faiths, and its wars, scholars must assimilate broader definitions of religion and build their studies using a more diverse archive. The words of chaplains and soldiers remain important, to be sure, but consideration of the tools of war, how they are used, and what Americans believe about soldiers, leads to a fuller and more textured understanding of the many influences that religion and war have exerted and continue to exert on each other.
Autism and Suicide
Authors: Shtayermman Oren
Published: November 2018

This article reviews the changes in the autism spectrum disorder (ASD) diagnosis in the Diagnostic Statistical Manual (DSM)-5. It reviews the risk factors associated with suicide in the general population and the link between these risk factors and individuals on the autism spectrum. When discussing autism and suicide (as a spectrum), the complexities that the two present influence parents, researchers, and practitioners. As an added dimension of convolution, there are only a small number of published studies in the area of autism and suicide, and many have marked the importance of awareness and connection between autism and suicide. The article presents the most recent and available research on ASDs and suicide. Methodological challenges related to these studies will be discussed as well as the implications for research, practice, and education.
Health Disparities and Inequities
Authors: Wexler Sandra , Copeland Valire Carr
Published: November 2018

Despite technological advances and changes in healthcare delivery, some groups in the United States continue to have better health-related outcomes than others. This article discusses health disparities and inequities—differences in health status and healthcare utilization that are influenced by complex social, structural, economic, and cultural factors. It begins by exploring the “problem” with health disparities—what makes them problematic and for whom they are problematic. Factors contributing to health inequities, commonly referred to as social determinants, are then reviewed. Finally, the article considers early 21st-century policy and programmatic responses as well as future directions, including social workers’ role as macro practitioners.
Mixed Methods Research
Authors: Watkins Daphne C.
Published: November 2018

Mixed methods research integrates both qualitative and quantitative methods into a single study to produce a more inclusive and expansive understanding of a topic. This article defines mixed methods in social work research, and discusses design notation, language, popular mixed methods designs, and data integration. Using mixed methods provides an opportunity for social workers to take advantage of the strengths of both qualitative and quantitative approaches and to offset their weaknesses. It is important that social workers engaged in mixed methods research maximize the interpretation of their findings and articulate the advantages of using mixed methods over qualitative or quantitative methods alone. Given the unique features of the profession, it is imperative that social workers carve out a distinctive mixed methods niche for social work researchers and practitioners.
Cancer-specific expression quantitative loci are affected by expression dysregulation
Authors: Sheng Quanhu , Samuels David C , Yu Hui , Ness Scott , Zhao Ying-yong , Guo Yan
Published: November 2018

Expression quantitative trait loci (eQTLs) have been touted as the missing piece that can bridge the gap between genetic variants and phenotypes. Over the past decade, we have witnessed a sharp rise of effort in the identification and application of eQTLs. The successful application of eQTLs relies heavily on their reproducibility. The current eQTL databases such as Genotype-Tissue Expression (GTEx) were populated primarily with eQTLs deriving from germline single nucleotide polymorphisms and normal tissue gene expression. The novel scenarios that employ eQTL models for prediction purposes often involve disease phenotypes characterized by altered gene expressions. To evaluate eQTL reproducibility across diverse data sources and the effect of disease-specific gene expression alteration on eQTL identification, we conducted an eQTL study using 5178 samples from The Cancer Genome Atlas (TCGA). We found that the reproducibility of eQTLs between normal and tumor tissues was low in terms of the number of shared eQTLs. However, among the shared eQTLs, the effect directions were generally concordant. This suggests that the source of the gene expression (normal or tumor tissue) has a strong effect on the detectable eQTLs and the effect direction of the eQTLs. Additional analyses demonstrated good directional concordance of eQTLs between GTEx and TCGA. Furthermore, we found that multi-tissue eQTLs may exert opposite effects across multiple tissue types. In summary, our results suggest that eQTL prediction models need to carefully address tissue and disease dependency of eQTLs. Tissue–disease-specific eQTL databases can afford more accurate prediction models for future studies.
CAARS: comparative assembly and annotation of RNA-Seq data
Authors: Rey Carine , Veber Philippe , Boussau Bastien , Sémon Marie
Published: November 2018

Motivation

RNA sequencing (RNA-Seq) is a widely used approach to obtain transcript sequences in non-model organisms, notably for performing comparative analyses. However, current bioinformatic pipelines do not take full advantage of pre-existing reference data in related species for improving RNA-Seq assembly, annotation and gene family reconstruction.

Results

We built an automated pipeline named CAARS to combine novel data from RNA-Seq experiments with existing multi-species gene family alignments. RNA-Seq reads are assembled into transcripts by both de novo and assisted assemblies. Then, CAARS incorporates transcripts into gene families, builds gene alignments and trees and uses phylogenetic information to classify the genes as orthologs and paralogs of existing genes. We used CAARS to assemble and annotate RNA-Seq data in rodents and fishes using distantly related genomes as reference, a difficult case for this kind of analysis. We showed CAARS assemblies are more complete and accurate than those assembled by a standard pipeline consisting of de novo assembly coupled with annotation by sequence similarity on a guide species. In addition to annotated transcripts, CAARS provides gene family alignments and trees, annotated with orthology relationships, directly usable for downstream comparative analyses.

Availability and implementation

CAARS is implemented in Python and Ocaml and is freely available at https://github.com/carinerey/caars.

Supplementary information

Supplementary data are available at Bioinformatics online.
World Pneumonia Day 2011–2016: Twitter contents and retweets
Authors: Adnan Md Mohiuddin , Yin Jingjing , Jackson Ashley M , Tse Zion Tsz Ho , Liang Hai , Fu King-Wa , Saroha Nitin , Althouse Benjamin M , Fung Isaac Chun-Hai
Published: November 2018

Background

Twitter is used for World Pneumonia Day (WPD; November 12) communication. We evaluate if themes of #pneumonia tweets were associated with retweet frequency.

Methods

A total of 28 181 original #pneumonia tweets were retrieved (21 November 2016), from which six subcorpora, 1 mo before and 1 mo after WPD 2011–2016, were extracted (n=6721). Underlying topics were identified via latent Dirichlet allocation and were manually coded into themes. The association of themes with retweet count was assessed via multivariable hurdle regression.

Results

Compared with personal experience tweets, tweets that both raised awareness and promoted intervention were 2.62 times as likely to be retweeted (adjusted odds ratio [aOR] 2.62 [95% 1.79 to 3.85]) and if retweeted had 37% more retweets (adjusted prevalence ratio [aPR] 1.37 [95% CI 1.06 to 1.78]). Tweets that raised concerns about vaccine price were twice as likely to be retweeted (aOR 2.29 [95% CI 1.36 to 3.84]) and if retweeted, had double the retweet count (aPR 2.05 [95% CI 1.27 to 3.29]) of tweets sharing personal experience.

Conclusions

The #pneumonia tweets that both raised awareness and promoted interventions and those discussing vaccine price were more likely to engage users than tweets about personal experience. These results help health professionals craft WPD messages that will engage the audience.
Hassall’s corpuscles with cellular-senescence features maintain IFNα production through neutrophils and pDC activation in the thymus
Authors: Wang Jianwei , Sekai Miho , Matsui Takeshi , Fujii Yosuke , Matsumoto Mitsuru , Takeuchi Osamu , Minato Nagahiro , Hamazaki Yoko
Published: November 2018

Hassall’s corpuscles (HCs) are composed of cornifying, terminally differentiated medullary thymic epithelial cells (mTECs) that are developed under the control of Aire. Here, we demonstrated that HC-mTECs show features of cellular senescence and produce inflammatory cytokines and chemokines including CXCL5, thereby recruiting and activating neutrophils to produce IL-23 in the thymic medulla. We further indicated that thymic plasmacytoid dendritic cells (pDCs) expressing IL-23 receptors constitutively produced Ifna, which plays a role in single positive (SP) cell maturation, in an Il23a-dependent manner. Neutrophil depletion with anti-Ly6G antibody injection resulted in a significant decrease of Ifna expression in the thymic pDCs, suggesting that thymic neutrophil activation underlies the Ifna expression in thymic pDCs in steady state conditions. A New Zealand White mouse strain showing HC hyperplasia exhibited greater numbers and activation of thymic neutrophils and pDCs than B6 mice, whereas Aire-deficient B6 mice with defective HC development and SP thymocyte maturation showed significantly compromised numbers and activation of these cells. These results collectively suggested that HC-mTECs with cell-senescence features initiate a unique cell activation cascade including neutrophils and pDCs leading to the constitutive IFNα expression required for SP T-cell maturation in the thymic medulla.
Natural language processing and machine learning to identify alcohol misuse from the electronic health record in trauma patients: development and internal validation
Authors: Afshar Majid , Phillips Andrew , Karnik Niranjan , Mueller Jeanne , To Daniel , Gonzalez Richard , Price Ron , Cooper Richard , Joyce Cara , Dligach Dmitriy
Published: November 2018

Objective

Alcohol misuse is present in over a quarter of trauma patients. Information in the clinical notes of the electronic health record of trauma patients may be used for phenotyping tasks with natural language processing (NLP) and supervised machine learning. The objective of this study is to train and validate an NLP classifier for identifying patients with alcohol misuse.

Materials and Methods

An observational cohort of 1422 adult patients admitted to a trauma center between April 2013 and November 2016. Linguistic processing of clinical notes was performed using the clinical Text Analysis and Knowledge Extraction System. The primary analysis was the binary classification of alcohol misuse. The Alcohol Use Disorders Identification Test served as the reference standard.

Results

The data corpus comprised 91 045 electronic health record notes and 16 091 features. In the final machine learning classifier, 16 features were selected from the first 24 hours of notes for identifying alcohol misuse. The classifier’s performance in the validation cohort had an area under the receiver-operating characteristic curve of 0.78 (95% confidence interval [CI], 0.72 to 0.85). Sensitivity and specificity were at 56.0% (95% CI, 44.1% to 68.0%) and 88.9% (95% CI, 84.4% to 92.8%). The Hosmer-Lemeshow goodness-of-fit test demonstrates the classifier fits the data well (P = .17). A simpler rule-based keyword approach had a decrease in sensitivity when compared with the NLP classifier from 56.0% to 18.2%.

Conclusions

The NLP classifier has adequate predictive validity for identifying alcohol misuse in trauma centers. External validation is needed before its application to augment screening.
The reception of Greek figurative terracottas in the Age of Enlightenment1
Authors: Uhlenbrock Jaimee P
Published: November 2018

While figurative terracottas from Greco-Roman antiquity were brought to light in considerable numbers from sites on the Italian mainland and in Sicily in the seventeenth century, they were consistently overlooked as important and representative examples of classical art. It was only in the later eighteenth century in Sicily that important collections of Greek figurative terracottas were assembled that began to attract the attention of northern Europeans. A demand for these accessible examples of miniature Greek sculpture arose that ultimately contributed to the formation of some of the most important antiquities collections in Europe.
Detection Rate of Colorectal Cancer or Precancer Adenoma by Colonoscopy After 1, 2, or 3 Positive Results via Fecal Immunochemical Testing
Authors: Hancock Jill A , Palmer Glen A
Published: November 2018

Background

Single-vial fecal immunochemical testing (FIT) is an accepted method of colorectal cancer (CRC) screening. The available 3-vial FIT data set allows for comparison of colonoscopy results using various screening methods.

Objective

To determine the optimal number of vials for a strong FIT-screening program by examining whether using only a single vial impacts the use of colonoscopy for CRC screening.

Methods

Patients were given 3-vial FIT collection kits that were processed with a positive hemoglobin cut-off detection level of 100 ng per mL. If FIT results were positive, colonoscopy testing was performed using standard practices.

Results

Detection of CRC and precursor adenoma was examined in 932 patients, with a positive colonoscopy sensitivity of 56.2% and 3.0% CRC detection after 3-vial FIT; after single-vial screening, those values were 60.9% and 4.7%, respectively.

Conclusions

Prescreening patients with FIT testing before colonoscopy allows colonoscopy testing to be targeted to higher-risk patients. Implementing use of only a single vial from the 3-vial FIT screening kit would reduce the colonoscopy reflex rate, colonoscopy complication numbers, facility costs, and patient distress by more than 40%, compared with 3-vial screening.
A clinical approach to respiratory disease in patients with hematological malignancy, with a focus on respiratory infection
Authors: Periselneris J , Brown J S
Published: November 2018

Respiratory complications, in particular infections, are common in the setting of hematological malignancy and after hematopoetic stem cell transplant. The symptoms can be nonspecific; therefore, it can be difficult to identify and treat the cause. However, an understanding of the specific immune defect, clinical parameters such as speed of onset, and radiological findings, allows the logical diagnostic and treatment plan to be made. Radiological findings can include consolidation, nodules, and diffuse changes such as ground glass and tree-in-bud changes. Common infections that induce these symptoms include bacterial pneumonia, invasive fungal disease, Pneumocystis jirovecii and respiratory viruses. These infections must be differentiated from inflammatory complications that often require immune suppressive treatment. The diagnosis can be refined with the aid of investigations such as bronchoscopy, computed tomography (CT) guided lung biopsy, culture, and serological tests. This article gives a schema to approach patients with respiratory symptoms in this patient group; however, in the common scenario of a rapidly deteriorating patient, treatment often has to begin empirically, with the aim to de-escalate treatment subsequently after targeted investigations.
External Validation of the Subarachnoid Hemorrhage International Trialists (SAHIT) Predictive Model Using the Barrow Ruptured Aneurysm Trial (BRAT) Cohort
Authors: Mascitelli Justin R , Cole Tyler , Yoon Seungwon , Nakaji Peter , Albuquerque Felipe C , McDougall Cameron G , Zabramski Joseph M , Lawton Michael T , Spetzler Robert F
Published: November 2018

BACKGROUND

The Subarachnoid Hemorrhage International Trialists (SAHIT) repository is a collection of randomized clinical trials, prospective observational studies, and hospital registries that was used to create a predictive model of unfavorable outcome/mortality following aneurysmal SAH.

OBJECTIVE

To externally validate the SAHIT model using Barrow Ruptured Aneurysm Trial (BRAT) data, which was not included in the SAHIT repository.

METHODS

This is a post hoc analysis of the prospective, randomized BRAT. Three models were created: (1) Core (age, hypertension, World Federation of Neurosurgical Societies grade), (2) neuroimaging (aneurysm size/location, Fisher score), and (3) full model (model 1 and 2 plus treatment type). The performance of the models was evaluated by measures of model discrimination (area under the curve [AUC]) and model calibration (goodness of fit test, calibration in-the-large, calibration slope).

RESULTS

A total of 338 patients (average age 54 years; 67.7% good clinical grade; average aneurysm size 6.7 mm; 84.1% anterior circulation) were included. Due to a large number of crossovers, more aneurysms were clipped than coiled (67.5% vs 32.5%, respectively). A total of 10.1% of the patients died and 29.6% experienced an unfavorable outcome. For unfavorable outcome, the AUCs for the three models were: 0.728, 0.732, and 0.734, respectively. For mortality, the AUCs for the three models were: 0.721, 0.739, and 0.744, respectively. Overall, all models showed good calibration, and the measures of calibration fell within 95% CI of those produced in the SAHIT study.

CONCLUSION

Using the BRAT data, we have externally validated the SAHIT model for predicting unfavorable outcome and mortality after SAH. The model may be used to counsel patients and families on prognosis following aneurysmal SAH.
Three Z Camelopardalis-type dwarf novae exhibiting IW Andromedae-type phenomenon
Authors: Kato Taichi
Published: November 2018

I found that V507 Cyg, IM Eri, and FY Vul are Z Cam-type dwarf novae and they showed sequences of standstill terminated by brightening, in contrast to fading as ordinary Z Cam stars do, followed by damping oscillation. These sequences are characteristic to IW And-type objects (also known as anomalous Z Cam stars). New additions to the IW And-type objects suggest that the IW And-type phenomenon is more prevalent among Z Cam stars. I suspect that the regularity of the pattern of the IW And-type phenomenon suggests a previously unknown type of limit-cycle oscillation, and I suggest that the standstill in these objects is somehow maintained in the inner part of the disk and that the thermal instability starting from the outer part of the disk terminates the standstill to complete the cycle.