bluuebunny/crossref_metadata_2025 huggingface dataset:
International Policy Entrepreneurship
Authors: Mintrom Michael , Luetjens Joannah
Published: February 2019

The concept of the policy entrepreneur lends itself to analysing how actors at the international level draw attention to problems, advance workable proposals, and link outcomes to symbolic values. The international space is a challenging arena for policy advocacy, as it lacks the oversight and well-established systems of policy development commonly found at the national or sub-national level. Policy entrepreneurs acting in the international space face obstacles and opportunities different from their domestic counterparts, particularly in the realms of policy initiation, mediation, and compromise. Here, we distinguish the actions of international policy entrepreneurs from the international engagements of state-based, government actors, the actions of international organizations, and those of civil society advocacy groups. Two examples of international policy entrepreneurship are given. We complete the chapter with an analytical framework to guide future research on international policy entrepreneurship.
International Organizations, Civil Servants, and Whistleblowing
Authors: Bowman James S. , West Jonathan P. , Moloney Kim
Published: February 2019

This chapter examines the principles, problems, and prospects of whistleblowing in the international public service: its significance, relevant laws, and bureaucratic institutions. The discussion begins with whistleblowing based largely on the American experience, because it has some of the most extensive whistleblowing policies in the world. Following a brief summary of the literature, whistleblowing concepts, and the transnational civil service are examined. While not limited to one international agency, the focus is on the United Nations as the world’s largest federation of nation states. The analysis closes with an exploration of whistleblowing guidelines and best practice in the global administrative structure.
Governance and Administration in Global Health Organizations
Authors: Huckel Schneider Carmen
Published: February 2019

The so-called golden era of global health, spanning approximately 1998–2008 was marked not only by an increase in funding and political attention, but arguably by a radical change in the processes of global health policy making. The establishment and consolidation of new global health organizations during this era has been analysed primarily from the perspective of International Relations and questions surrounding legitimate governance beyond the state. Far less attention has been paid to the internal structures and cultures of these new organizations. This includes how they create and reflect new standards of transnational administration, management, and oversight, such as integration of state and non-state actors, formalized input from technical and financial committees, and organizational structures that separate multiple levels of oversight and accountability. This chapter argues for greater attention to be paid to these structural features of global health organizations from a multi-disciplinary perspective incorporating public administration, corporate governance, and organizational sociology.
The Transnationalization of Public Spheres and Global Policy
Authors: Volkmer Ingrid
Published: February 2019

The globalized spheres of digital communication require a substantial revision of conventional conceptions of ‘the public sphere’. This article lays out the core strands of such a new debate by identifying the limitations of traditional public sphere approaches which are caused by the boundedness of the foci on the national ‘container’ model associated with the European nation state. Instead of limiting publicness to national boundaries, new approaches are required to understand the new discursive spheres of connectivity of citizens across all society types, today enabled by digital communication. Such an approach is necessary to map out the new dimension of public discourse. The article concludes with the suggestion of a model of publicness understood as ‘reflective interdependence’ connecting citizens across societies.
Providing Foundations
Authors: Jung Tobias , Harrow Jenny
Published: February 2019

Philanthropy is gaining renewed policy prominence. Focusing on the institutional expressions of philanthropy—philanthropic foundations—this chapter critically explores foundations’ various contributions to, and roles in, global policy. Emphasizing the need to move beyond traditional perspectives, dominant focal points and well-established questions around philanthropy, the chapter argues for a more synthesized, critically reflective, engagement with philanthropy in global policy research. To this end, the importance of examining historic antecedents of contemporary developments in philanthropy and the need for a stronger evidence base are outlined. The chapter concludes by discussing the spectrum of research opportunities philanthropy provides for the global policy and transnational administration field.
Scales and Network Societies
Authors: Coleman William D.
Published: February 2019

The concept of ‘global public policy’ has emerged as scholars widen the depth of their understanding of globalization. What is particularly important is that globalization is an expanding process that leads scholars to focus more broadly on the world through novel lenses. These processes lead scholars to break away from long-standing studies focusing primarily on states as their starting point. Hence, in a globalizing world, the study of public policy needs to be broadened to study its changing nature and roles. Drawing from the thinking of Anna Lowenhaupt Tsing and of Manuel Castells, this chapter provides new ways to begin thinking about public policy beyond states while reaching out to study in more depth the whole world. From this view of the world, the chapter addresses the question: How might public policy making be changing in response to political restructuring in the face of ongoing contemporary globalizing processes?
Meaning in Life and in Work
Authors: Steger Michael F.
Published: February 2019

Work has powerful potential to enrich our lives by providing them with meaning. The idea of meaning in life (MIL) is crucial to almost every measure of human well-being or flourishing, yet there is much less consensus over the idea of meaningful work (MW). Although the two ideas are often used interchangeably, this chapter reviews different conceptualizations of these ideas to see how they are related and takes a “theoretical turn” to consider some shared themes and character strengths, such as “significance,” “coherence,” “transcendence,” “purpose,” and “empathy.” Based on these themes, it proposes two workplace models intended to make it easier for workers to find meaningful pathways in work, and for leaders to create the conditions for the meaningful organization. When these two models work together they can operate to produce social as well as economic value, and personalize work even when faced with dehumanizing effects of robotics.
Self-transcendence and Meaningful Work
Authors: Madden Adrian
Published: February 2019

Self-transcendence is a concept often evoked in different approaches to meaningful work, but which lacks clarity. This chapter considers how the subjective experience of meaningful work, centering on significance and purpose, gives rise to the idea of meaningfulness as the realization of human potential, by connecting the inner and the outer life along spiritual and social dimensions. It points to a conceptualization of self-transcendence that places greater emphasis on the intersubjective nature of meaningfulness. This raises questions such as: if meaningfulness is self-transcendent, where and how is meaning created? If transcendence denotes “beyondness” of the here and now, what does this mean in terms of the nature of work tasks and roles? If self-transcendence is an ineffable, transitory state, what might this mean for research into meaningful work? A shift in the emphasis of future research is necessary if we are to understand the self-transcendent nature of experienced meaningfulness.
To Have Lived Well
Authors: Chalofsky Neal , Cavallero Elizabeth
Published: February 2019

This chapter draws on Aristotelian thinking to differentiate between hedonic and eudaimonic understandings of well-being. A sense of purpose and meaning are fundamental to the more profound experience of eudaimonic well-being, which is associated with authenticity and living in accordance with one’s “true self.” A framework for well-being and meaningfulness is proposed which highlights the interactive effects between the two. Fundamental to both is a sense of self, the work performed by individuals, and the workplace itself. Framing eudaimonic well-being as a fundamental, overarching aim of living, the chapter argues that our work is a significant and influential factor in how we live, and the search for meaningful work is an inherent part of our pursuit of the life well lived.
Ethiopia’s Transition from a Traditional to a Developing Economy, 1890s–1960s
Authors: Shiferaw Bekele
Published: February 2019

At the end of the nineteenth century, Ethiopia had a traditional economy dependent on ox-plough agriculture and crafts. Goods and services were exchanged through the barter system. This changed from the 1890s onwards with modern innovations such as the railway, telephone and telegraph, banking, and a national currency. In the first four decades of the twentieth century, import/export trade expanded, elementary education spread, new towns emerged, and manufacturing enterprises were born. Italian occupation of the country (1936–41) helped push forward the monetization of the economy. In the three decades after liberation (1940s–1960s), advances were made in the development of the services, manufacturing, and financial sectors. Basic education was expanded, and the government adopted a series of development plans to guide the process of economic and social development. The principle of disciplined state planning to transform the economy has continued under the EPRDF although the task remains incomplete.
Infrastructure and Economic Transformation in Ethiopia
Authors: Nuru Seid
Published: February 2019

Investment in infrastructure has a central role in the development agenda and is critical for supporting economic growth and poverty reduction. Infrastructure affects growth through two channels: directly through physical capital accumulation and indirectly through improvement in productivity. Investment in infrastructure enhances private sector activities by lowering the cost of production and opening new markets. Infrastructure investment in power generation, water, sanitation, and housing improves the social well-being of citizens. This chapter examines the pace and scale of infrastructure development in Ethiopia in the post-1991 period. The unparalleled expansion of infrastructure since the EPRDF came to power in 1991 has had a significant influence on the trajectory of Ethiopia’s economic growth. Investment in infrastructure now accounts for more than 15 per cent of GDP annually. Heavy investments in power, roads, rail network, irrigation, aviation, and logistics have helped to unleash the country’s potential both economically and as a major manufacturing hub in Africa.
The Transformation of Smallholder Crop Production in Ethiopia, 1994–2016
Authors: Seyoum Taffesse Alemayehu
Published: February 2019

Smallholder grain production provides a livelihood for the majority of Ethiopians and generates the bulk of the country’s crop output. The sector has been undergoing considerable change in recent years (particularly since 2003). Its total output and productivity have grown at a brisk pace, though starting from a low base. These changes are correlated with greater intensification through the adoption of chemical fertilizers, improved seeds, and other better farm management practices. Public investments in extension, education, health, roads, and telecommunications have promoted this intensification. These changes strongly suggest that smallholder farming is in transition. Nevertheless, it is yet to transform into a modern, highly productive, and commercialized sector. In short, both backward and forward production linkages of the smallholder grain sub-sector are still weak. The sector has significant potential, however. Moreover, rising incomes and accelerating urbanization and industrialization will create huge opportunities. On the other hand, the difficulty of the task is compounded by climate change, water scarcity, environmental degradation, and fast (though decelerating) population growth. Sustainable accommodation of these challenges requires greater specialization and substantial resource reallocation at the farm level and across agro-ecologies, combined with appropriate technological and institutional innovations.
Federalism in Ethiopia’s Transformation
Authors: Mengisteab Kidane
Published: February 2019

Two highly controversial features characterize Ethiopia’s federal system. One is that the federal entities are drawn largely on ethno-linguistic lines. The second is that the arrangement grants the right to self-determination up to secession to nations and nationalities. Critics claim that the arrangement divides the country along ethnic lines and jeopardizes its unity by politicizing ethnicity. Supporters, on the other hand, contend that the arrangement unifies the country by granting ethnic identities protection against marginalization and thereby mitigating ethnically based insurgencies. Despite the controversies, the country has recorded impressive progress in areas of broad socio-economic development. It has also reduced political violence. However, the principal goal of the federal arrangement, which is to bring about a peaceful process of nation building, remains a major challenge. This chapter’s principal objective is to examine why the process of nation building remains fragile.
Agriculture’s Changing Role in Ethiopia’s Economic Transformation
Authors: Dercon Stefan , Gollin Douglas
Published: February 2019

This chapter discusses the role agriculture has played in growth and economic transformation in Ethiopia since the 1990s. Ethiopia’s dominant development strategy narrative since the 1990s has been Agricultural Development-Industrialization (ADLI), which takes its inspiration from dual-economy models of linkages between sectors. We use the theoretical perspectives of these models and of ADLI to discuss progress in growth and poverty in this period. We find that ADLI offered a plausible and seemingly successful strategy for Ethiopia at an earlier stage of its growth and transformation, but it has serious limitations. In more recent years there appears to have been more emphasis on urban and industrial growth and this may also have the potential to boost value added and labour productivity in agriculture—reversing the sectoral dynamics of the ADLI approach. Looking forward, we posit that to make further progress in agriculture, there is a need to acknowledge and facilitate the transmission of urban and international demand, thereby encouraging higher-value crops and higher value addition.
Industrial Policy and Late Industrialization in Ethiopia
Authors: Oqubay Arkebe
Published: February 2019

Ethiopia has emerged as one of the fastest-growing economies in Africa in the early twenty-first century. Despite rapid growth, structural transformation of the economy remains the country’s central challenge. This chapter reviews the origins of Ethiopia’s industrialization and industrial policymaking process in the twentieth century. The Ethiopian government has pursued developmentalism and practised an active industrial policy since the early 2000s. However, a review of industrial policies in priority sectors shows that the outcome has been uneven across sectors, indicating the importance of the interaction between industrial structure, linkage dynamics, and politics/political economy for the evolution and effectiveness of an industrial policy. After examining the fundamental weakness in Ethiopia’s economic structure, this chapter illustrates why and how industrial policy must focus on manufacturing and exports to generate structural transformation and accelerate catch-up. The Ethiopian experience shows that an activist industrial policy goes hand in hand with an activist state.
Rural–Urban Linkages in Ethiopia
Authors: Ferede Tadele , File Belay
Published: February 2019

Rural and urban areas are linked by the reciprocal exchange of unprocessed and processed products and services. The main thrust of this chapter is to quantify the extent of rural–urban linkages by demand and production-based characteristics, using a social accounting matrix (SAM) framework and temporal changes in household consumption. The scale of the links between agriculture and non-agricultural activities, especially manufacturing, appears to be weak despite rapid economic growth over the last couple of decades. The spatial aspects of rural–urban linkages indicates that small towns appear to have strong linkages with rural areas compared to big cities and towns, as small towns have locational advantage. Changes in household demand also affect rural–urban linkages. The future of rural transformation can be shaped by targeted investments in small urban areas and this has the potential to speed up rural transformation.
Uses of high-flow nasal cannula on the community paediatric ward and risk factors for deterioration
Authors: De Santis Diana , Sheriff Falana , Bester Deborah , Shahab Rabia , Hutzal Carolyn
Published: February 2019

Background

High-flow nasal cannula (HFNC) is a form of noninvasive respiratory support used for paediatric acute respiratory illnesses. Past HFNC research has focused on its use in bronchiolitis and in intensive care units, but little is reported on its use in the community hospital setting. We aimed to investigate the paediatric population using HFNC, any adverse events, and risk factors for deterioration.

Methods

A retrospective chart review was performed on patients admitted to a community paediatric ward. Inclusion criteria were patients between 1 day and 17 years of age, admitted between September 2013 and April 2016, and treated with HFNC for at least 4 hours.

Results

A total of 85 children met inclusion criteria. The average age of patients in our study was 3.41 years with 39% of patients >2 years of age. 46% of patients had an admitting diagnosis of bronchiolitis, 33% pneumonia, and 16% with asthma. Transfer rate to tertiary care centre paediatric intensive care unit was 18%. Patients transferred required greater FIO2 (odds ratio [OR] 1.04, P=0.018, confidence interval [CI] 1.007 to 1.082), and were 3.2 times more likely to be positive for respiratory syncytial virus (RSV) (P=0.081, CI 0.868–11.739). There were no adverse events attributed to HFNC in the population.

Conclusion

HFNC is being utilized in the community hospital setting for children of varied age and types of respiratory illnesses. Children requiring higher FIO2 are at risk of respiratory deterioration which may identify them earlier for transfer to tertiary care. Further research into the safety and efficacy of HFNC for different paediatric illnesses in the community is needed.
Inquiline social parasites as tools to unlock the secrets of insect sociality
Authors: Cini Alessandro , Sumner Seirian , Cervo Rita
Published: February 2019

Insect societies play a crucial role in the functioning of most ecosystems and have fascinated both scientists and the lay public for centuries. Despite the long history of study, we are still far from understanding how insect societies have evolved and how social cohesion in their colonies is maintained. Here we suggest inquiline social parasites of insect societies as an under-exploited experimental tool for understanding sociality. We draw on examples from obligate inquiline (permanent) social parasites in wasps, ants and bees to illustrate how these parasites may allow us to better understand societies and learn more about the evolution and functioning of insect societies. We highlight three main features of these social parasite–host systems—namely, close phylogenetic relationships, strong selective pressures arising from coevolution and multiple independent origins—that make inquiline social parasites particularly suited for this aim; we propose a conceptual comparative framework that considers trait losses, gains and modifications in social parasite–host systems. We give examples of how this framework can reveal the more elusive secrets of sociality by focusing on two cornerstones of sociality: communication and reproductive division of labour. Together with social parasites in other taxonomic groups, such as cuckoos in birds, social parasitism has a great potential to reveal the mechanisms and evolution of complex social groups.

This article is part of the theme issue ‘The coevolutionary biology of brood parasitism: from mechanism to pattern’.
Convergent evolution of reduced eggshell conductance in avian brood parasites
Authors: McClelland Stephanie C. , Jamie Gabriel A. , Waters Katy , Caldas Lara , Spottiswoode Claire N. , Portugal Steven J.
Published: February 2019

Brood parasitism has evolved independently in several bird lineages, giving rise to strikingly similar behavioural adaptations that suggest convergent evolution. By comparison, convergence of physiological traits that optimize this breeding strategy has received much less attention, yet these species share many similar physiological traits that optimize this breeding strategy. Eggshell structure is important for embryonic development as it controls the flux of metabolic gases, such as O2, CO2and H2O, into and out of the egg; in particular, water vapour conductance (GH2O) is an essential process for optimal development of the embryo. Previous work has shown that common cuckoos (Cuculus canorus) have a lower than expected eggshellGH2Ocompared with their hosts. Here, we sought to test whether this is a trait found in other independently evolved avian brood parasites, and therefore reflects a general adaptation to a parasitic lifestyle. We analysedGH2Ofor seven species of brood parasites from four unique lineages as well as for their hosts, and combined this with species from the literature. We found lower than expectedGH2Oamong all our observed brood parasites both compared with hosts (except for brown-headed cowbirds (Molothrus ater)) and compared with the expected rates given their phylogenetic positions. These findings suggest that a loweredGH2Omay be a general adaptation for brood parasitism, perhaps helping the parasite nestling to develop greater aerobic fitness.

This article is part of the theme issue ‘The coevolutionary biology of brood parasitism: from mechanism to pattern’.
Patterns of host use by brood parasiticMaculineabutterflies across Europe
Authors: Tartally András , Thomas Jeremy A. , Anton Christian , Balletto Emilio , Barbero Francesca , Bonelli Simona , Bräu Markus , Casacci Luca Pietro , Csősz Sándor , Czekes Zsolt , Dolek Matthias , Dziekańska Izabela , Elmes Graham , Fürst Matthias A. , Glinka Uta , Hochberg Michael E. , Höttinger Helmut , Hula Vladimir , Maes Dirk , Munguira Miguel L. , Musche Martin , Nielsen Per Stadel , Nowicki Piotr , Oliveira Paula S. , Peregovits László , Ritter Sylvia , Schlick-Steiner Birgit C. , Settele Josef , Sielezniew Marcin , Simcox David J. , Stankiewicz Anna M. , Steiner Florian M. , Švitra Giedrius , Ugelvig Line V. , Van Dyck Hans , Varga Zoltán , Witek Magdalena , Woyciechowski Michal , Wynhoff Irma , Nash David R.
Published: February 2019

The range of hosts exploited by a parasite is determined by several factors, including host availability, infectivity and exploitability. Each of these can be the target of natural selection on both host and parasite, which will determine the local outcome of interactions, and potentially lead to coevolution. However, geographical variation in host use and specificity has rarely been investigated.Maculinea(=Phengaris) butterflies are brood parasites ofMyrmicaants that are patchily distributed across the Palæarctic and have been studied extensively in Europe. Here, we review the published records of ant host use by the EuropeanMaculineaspecies, as well as providing new host ant records for more than 100 sites across Europe. This comprehensive survey demonstrates that while all but one of theMyrmicaspecies found onMaculineasites have been recorded as hosts, the most common is often disproportionately highly exploited. Host sharing and host switching are both relatively common, but there is evidence of specialization at many sites, which varies amongMaculineaspecies. We show that mostMaculineadisplay the features expected for coevolution to occur in a geographic mosaic, which has probably allowed these rare butterflies to persist in Europe.

This article is part of the theme issue ‘The coevolutionary biology of brood parasitism: from mechanism to pattern’.
Transfer of Meiothermus chliarophilus (Tenreiro et al.1995) Nobre et al. 1996, Meiothermus roseus Ming et al. 2016, Meiothermus terrae Yu et al. 2014 and Meiothermus timidus Pires et al. 2005, to Calidithermus gen. nov., as Calidithermus chliarophilus comb. nov., Calidithermus roseus comb. nov., Calidithermus terrae comb. nov. and Calidithermus timidus comb. nov., respectively, and emended description of the genus Meiothermus
Authors: Raposo Pedro , Viver Tomeu , Albuquerque Luciana , Froufe Hugo , Barroso Cristina , Egas Conceição , Rosselló-Móra Ramon , da Costa Milton S.
Published: February 2019

Chemotaxonomic parameters, phylogenetic analysis of the 16S rRNA gene, phylogenetic analysis of 90 housekeeping genes and 855 core genes, amino acid identity (AAI), average nucleotide identity (ANI) and genomic characteristics were used to examine the 13 species of the genusMeiothermuswith validly published names to reclassify this genus. The results indicate that the species of the genusMeiothermuscan be divided into three lineages on the basis of the results of the phylogenetic analysis, AAI, the guanine+cytosine (G+C) mole ratio, the ability to synthesize the red-pigmented carotenoid canthaxanthin and the colony colour, as well as other genomic characteristics. The results presented in this study circumscribe the genusMeiothermusto the speciesMeithermus ruber,Meiothermuscateniformans,Meiothermustaiwanensis,Meiothermuscerbereus,Meiothermus hypogaeus,Meiothermusluteus,MeiothermusrufusandMeiothermusgranaticius, for which it is necessary to emend the genusMeiothermus. The speciesMeiothermussilvanus, which clearly represents a separate genus level lineage was not reclassified in this study for lack of any distinctive phenotypic or genotypic characteristics. The results of this study led us to reclassify the speciesMeiothermuschliarophilus,Meiothermustimidus,MeiothermusroseusandMeiothermusterraeas species of a novel genus for which we propose the epithetCalidithermusgen. nov.
Bacterial Phage Tail-like Structure Kills Eukaryotic Cells by Injecting a Nuclease Effector
Authors: Rocchi Iara , Ericson Charles , Malter Kyle E. , Zargar Sahar , Eisenstein Fabian , Pilhofer Martin , Beyhan Sinem , Shikuma Nicholas J.
Published: February 2019

Many bacteria interact with target organisms using syringe-like structures called Contractile Injection Systems (CIS). CIS structurally resemble headless bacteriophages and share evolutionarily related proteins such as the tail tube, sheath, and baseplate complex. Recent evidence shows that CIS are specialized to puncture membranes and often deliver effectors to target cells. In many cases, CIS mediate trans-kingdom interactions between bacteria and eukaryotes, however the effectors delivered to target cells and their mode of action are often unknown. In this work, we establish an in vitro model to study a CIS called Metamorphosis Associated Contractile structures (MACs) that target eukaryotic cells. We show that MACs kill two eukaryotic cell lines, Fall Armyworm Sf9 cells and J774A.1 murine macrophage cells through the action of a newly identified MAC effector, termed Pne1. To our knowledge, Pne1 is the first CIS effector exhibiting nuclease activity against eukaryotic cells. Our results define a new mechanism of CIS-mediated bacteria-eukaryote interaction and are a first step toward understanding structures with the potential to be developed as novel delivery systems for eukaryotic hosts.
Climatic Factors in Relation to Diarrhea for Informed Public Health Decision-Making: A Novel Methodological Approach
Authors: Ikeda Takayoshi , Kapwata Thandi , Behera Swadhin K. , Minakawa Noboru , Hashizume Masahiro , Sweijd Neville , Mathee Angela , Wright Caradee Yael
Published: February 2019

Background

Diarrheal disease is one of the leading causes of morbidity and mortality globally, particularly in children under 5 years of age. Factors related to diarrheal disease incidence include infection, malnutrition, and exposure to contaminated water and food. Climate factors also contribute to diarrheal disease.

Objectives

We aimed to explore the relationship between temperature, precipitation and diarrhea case counts of hospital admissions among vulnerable communities living in a rural setting in South Africa.

Methods

We applied a novel approach of ‘contour analysis’ to visually examine simultaneous observations in frequencies of anomalously high and low diarrhea case counts occurring in a season and assigning colors to differences that were statistically significant based on chi-squared test results.

Results

There was a significantly positive difference between high and low ‘groups’ when there was a lack of rain (0 mm of cumulative rain) for 1 to 2 weeks in winter for children under 5.

Diarrhea prevalence was greater among children under 5 years when conditions were hotter than usual during winter and spring.

Discussion

Dry conditions may lead to increased water storage raising the risks of water contamination. Reduced use of water for personal hygiene and cleaning of outdoor pit latrines affect sanitation quality. Rural communities require adequate and uninterrupted water provision and healthcare providers should raise awareness about potential diarrheal risks especially during the dry season.
Minimal effects of proto-Y chromosomes on house fly gene expression in spite of evidence that selection maintains stable polygenic sex determination
Authors: Son Jae Hak , Kohlbrenner Tea , Heinze Svenia , Beukeboom Leo , Bopp Daniel , Meisel Richard P.
Published: February 2019

Sex determination is the developmental process by which organismal sex is established. Sex determination evolves fast, often due to changes in the master regulators at the top of the pathway. In addition, some species are polymorphic for multiple different master regulators within natural populations. Understanding the forces that maintain this polygenic sex determination can be informative of the factors that drive the evolution of sex determination. The house fly,Musca domestica, is a well-suited model to those ends because natural populations harbor male-determining loci on each of the six chromosomes and a bi-allelic female-determiner. Multiple lines of evidence suggest that natural selection maintains polygenic sex determination in house fly. However, previous work found that there are very few sequence differences between proto-Y chromosomes and their homologous X chromosomes. This suggests that there is not much genetic variation upon which natural selection could act to maintain polygenic sex determination in house fly. To address this paradox, we performed RNA-seq experiments that examine the effects of the two most common proto-Y chromosomes on gene expression. We find that the proto-Y chromosomes do indeed have a relatively minor effect on gene expression, as expected based on the minimal X-Y sequence differences. Despite these minimal gene expression differences, we identify some patterns that are consistent with sex-specific selection acting on phenotypic effects of proto-Y chromosomes. Our results suggest that, if natural selection maintains polygenic sex determination in house fly, the phenotypic differences under selection are minor and possibly depend on ecological contexts that were not tested in our experimental design.
Joint inference and alignment of genome structures enables characterization of compartment-independent reorganization across cell types
Authors: Rieber Lila , Mahony Shaun
Published: February 2019

Cell-type-specific chromosome conformation is correlated with differential gene regulation. Broad compartmentalization into two compartments (A & B) is proposed to be the main driver of cell-specific chromosome organization. However it is unclear what fraction of chromosome conformation changes between cell types and conditions is independent of changes in compartmentalization and whether any such compartment-independent reorganization is functionally important. We developed MultiMDS to jointly infer and align 3D chromosomal structures, thereby enabling a quantitative comparison of locus-specific changes across Hi-C datasets. We compared Hi-C datasets from yeast, which lack compartmentalization, grown with and without galactose. These comparisons confirmed known relocalizations as well as identifying additional examples. We also compared mammalian datasets across a variety of cell lines. We found a consistent enrichment for changes along the A/B compartment (nuclear interior/nuclear periphery) axis, even when comparing the same cell type from different individuals. Despite the prevalence of compartment changes, we consistently find compartment-independent relocalizations of loci that are within the A compartment in both compared cell types. Some such intra-compartment relocalizations involve loci that display enhancer-associated histone marks in one cell type and polycomb-associated histone marks in the other. MultiMDS thus enables a new way to compare chromosome conformations across two Hi-C datasets.

Availability

https://github.com/seqcode/multimds
Volatile organic chemical analyser (eNose) diagnosis of dogs naturally infected with visceral leishmaniasis in Brazil
Authors: Staniek ME , Sedda L , Gibson TD , de Souza CF , Costa EM , Dillon RJ , Hamilton JGC
Published: February 2019

Visceral leishmaniasis (VL) in Brazil is a neglected vector-borne tropical parasitic disease that is responsible for several thousand human deaths every year. The numbers of cases more than doubled between 1990 and 2016. Transmission occurs when sand flies become infected after feeding on infected dogs (the reservoir host) and then subsequently on humans. A major component of the VL control effort is the identification and euthanasia of infected dogs to remove them as a source of infection. Rapid, accurate identification of infected dogs would be key to this strategy.

Here we demonstrate the potential of a volatile organic chemical analyser (eNose) to rapidly and accurately identify dogs infected with Leishmania infantum parasites. The eNose could discriminate between the odours present in the hair of infected and uninfected dogs with greater than 95% sensitivity and 95% specificity. The device was sufficiently sensitive to be able to identify infected dogs even when parasite loads in the circulating blood were very low.

Future improvements to VOC analyser technology, portability and ease of use suggest that this methodology could significantly improve the diagnosis of VL infected dogs in Brazil and elsewhere and with other parasitic diseases such as Malaria, Chaga’s Disease and Leishmania in humans.
Interacting fruit flies synchronize behavior
Authors: Klibaite Ugne , Shaevitz Joshua W.
Published: February 2019

Social behaviors are ubiquitous and crucial to an animal’s survival and success. The behaviors an animal performs in a social setting are affected by internal factors, inputs from the environment, and interaction with others. To quantify social behaviors, we need to measure both the stochastic nature of behavior of isolated individuals and how these behaviors change as a function of the environment and features of social interaction. We probed the behavior of male and female fruit flies in a circular arena as individuals and within all possible pairings. By combining measurements of the animals’ position in the arena with an unsupervised analysis of their behaviors, we fully define the effects of position in the environment and the presence of a partner on locomotion, grooming, singing, and other behaviors that make up an animal’s repertoire. We find that geometric context tunes behavioral preference, pairs of animals synchronize their behavioral preferences across trials, and paired individuals display signatures of behavioral mimicry.
hilldiv: an R package for the integral analysis of diversity based on Hill numbers
Authors: Alberdi Antton , Gilbert M Thomas P
Published: February 2019

Hill numbers provide a powerful framework for measuring, comparing and partitioning the diversity of biological systems as characterised using high throughput DNA sequencing approaches. In order to facilitate the implementation of Hill numbers into such analyses, whether focusing on diet reconstruction, microbial community profiling or more general ecosystem characterisation analyses, we present a new R package. ‘Hilldiv’ provides a set of functions to assist analysis of diversity based on Hill numbers, using count tables (e.g. OTU, ASV) and associated phylogenetic trees as inputs. Multiple functionalities of the library are introduced, including diversity measurement, diversity profile plotting, diversity comparison between samples and groups, multi-level diversity partitioning and (dis)similarity measurement. All of these are grounded in abundance-based and incidence-based Hill numbers, and can accommodate phylogenetic or functional correlation among OTUs or ASVs. The package can be installed from CRAN or Github, and tutorials and example scripts can be found in the package’s page (https://github.com/anttonalberdi/hilldiv).
The architect of virus assembly: the portal protein complex nucleates procapsid assembly in bacteriophage P22
Authors: Motwani Tina , Teschke Carolyn M.
Published: February 2019

The genetic material of tailed dsDNA bacteriophages, herpesviruses and adenoviruses is packaged into a precursor capsid through a 12-mer ring-shaped protein complex called the portal protein, located at a unique 5-fold vertex. In several phages and viruses, including T4, Φ29, and HSV-1, the dodecameric portal protein forms a nucleation complex with scaffolding proteins to initiate procapsid assembly, thereby ensuring incorporation of only one portal complex per capsid. However, for bacteriophage P22, the role of its portal protein in initiation of procapsid assembly is unclear. We recently developed anin vitroP22 assembly assay where portal protein is co-assembled into procapsid-like particles. We also showed that scaffolding protein catalyzes oligomerization of monomeric portal protein into 12-mer rings, and possibly forming a scaffolding-protein nucleation complex that results in one portal complex per P22 procapsid. Here, we present evidence substantiating that P22 portal protein, similar to the other dsDNA viruses, can act as an assembly nucleator. We find that the presence of P22 portal protein is able to increase the rate of particle assembly. Additionally, we show that P22 portal protein proper contributes to proper morphology of the assembled particles. Our results highlight a key function of portal protein as an assembly initiator, a feature likely conserved among these classes of dsDNA viruses.
Systematic Analysis of Metabolic Pathway Distributions of Bacterial Energy Reserves
Authors: Wang Liang , Yang Jianye , Huang Yue , Liu Qinghua , Xu Yaping , Piao Xue , Wise Michael J.
Published: February 2019

Metabolism of energy reserves are essential for bacterial functions such as pathogenicity, metabolic adaptation, and environmental persistence, etc. Previous bioinformatics studies have linked gain or loss of energy reserves such as glycogen and polyphosphate (polyP) with host-pathogen interactions and bacterial virulence based on a comparatively small number of bacterial genomes or proteomes. Thus, understanding the distribution patterns of energy reserves metabolism across bacterial species provides a shortcut route to look into bacterial lifestyle and physiology theoretically. So far, five major energy reserves have been identified in bacteria due to their effective capacity to support bacterial persistence under nutrient deprivation conditions, which include wax ester (WE), triacylglycerol (TAG), polyhydroxyalkanoates (PHA), polyphosphate, and glycogen. Although unknown pathways directly involved in energy reserves keep being discovered with the continuous endeavour of molecular microbiologists and it is currently rather clear about the enzymes related with the metabolism of energy reserves, there is a lack of systematic study of the pathway or key enzyme distributions of the five energy reserves in bacteria from an evolutionary point of view. With the fast development of sequencing technology, abundant bacterial proteomes are available in public database now. In this study, we sourced 8214 manually reviewed bacterial reference proteomes from UniProt database and used statistical models to search homologous sequences of key enzymes related with energy reserves. The distribution patterns of the pathways for energy reserves metabolism are visualized in taxonomy-based phylogenetic trees. According to the study, it was revealed that specific pathways and enzymes are associated with certain types of bacterial groups, which provides evolutionary insights into the understanding of their origins and functions. In addition, the study also confirmed that loss of energy reserves is correlated with bacterial genome reduction. Through this analysis, a much clearer picture about energy reserves metabolism in bacteria is present, which could serve a guide for further theoretical and experimental analyses of energy reserves metabolism in bacteria.
Enhanced TF binding site maps improve regulatory networks learned from accessible chromatin data
Authors: Kulkarni Shubhada R. , Jones D. Marc , Vandepoele Klaas
Published: February 2019

Determining where transcription factors (TF) bind in genomes provides insights into which transcriptional programs are active across organs, tissue types, and environmental conditions. Recent advances in high-throughput profiling of regulatory DNA have yielded large amounts of information about chromatin accessibility. Interpreting the functional significance of these datasets requires knowledge of which regulators are likely to bind these regions. This can be achieved by using information about TF binding preferences, or motifs, to identify TF binding events that are likely to be functional. Although different approaches exist to map motifs to DNA sequences, a systematic evaluation of these tools in plants is missing. Here we compare four motif mapping tools widely used in the Arabidopsis research community and evaluate their performance using chromatin immunoprecipitation datasets for 40 TFs. Downstream gene regulatory network (GRN) reconstruction was found to be sensitive to the motif mapper used. We further show that the low recall of FIMO, one of the most frequently used motif mapping tools, can be overcome by using an Ensemble approach, which combines results from different mapping tools. Several examples are provided demonstrating how the Ensemble approach extends our view on transcriptional control for TFs active in different biological processes. Finally, a new protocol is presented to efficiently derive more complete cell type-specific GRNs through the integrative analysis of open chromatin regions, known binding site information, and expression datasets.
Classifying drugs by their arrhythmogenic risk using machine learning
Authors: Costabal Francisco Sahli , Seo Kinya , Ashley Euan , Kuhl Ellen
Published: February 2019

An undesirable side effect of drugs are cardiac arrhythmias, in particular a condition called torsades de pointes. Current paradigms for drug safety evaluation are costly, lengthy, and conservative, and impede efficient drug development. Here we combine multiscale experiment and simulation, high-performance computing, and machine learning to create an easy-to-use risk assessment diagram to quickly and reliable stratify the pro-arrhythmic potential of new and existing drugs. We capitalize on recent developments in machine learning and integrate information across ten orders of magnitude in space and time to provide a holistic picture of the effects of drugs, either individually or in combination with other drugs. We show, both experimentally and computationally, that drug-induced arrhythmias are dominated by the interplay of two currents with opposing effects: the rapid delayed rectifier potassium current and the L-type calcium current. Using Gaussian process classification, we create a classifier that stratifies safe and arrhythmic domains for any combinations of these two currents. We demonstrate that our classifier correctly identifies the risk categories of 23 common drugs, exclusively on the basis of their concentrations at 50% current block. Our new risk assessment diagram explains under which conditions blocking the L-type calcium current can delay or even entirely suppress arrhythmogenic events. Using machine learning in drug safety evaluation can provide a more accurate and comprehensive mechanistic assessment of the pro-arrhythmic potential of new drugs. Our study shapes the way towards establishing science-based criteria to accelerate drug development, design safer drugs, and reduce heart rhythm disorders.
Switching on the light: using metagenomic shotgun sequencing to characterize the intestinal microbiome of Atlantic cod
Authors: Riiser Even Sannes , Haverkamp Thomas H.A. , Varadharajan Srinidhi , Borgan Ørnulf , Jakobsen Kjetill S. , Jentoft Sissel , Star Bastiaan
Published: February 2019

The biological roles of the intestinal microbiome and how it is impacted by environmental factors are yet to be determined in wild marine fish species. Atlantic cod (Gadus morhua) is an ecologically important species with a wide-spread distribution in the North Atlantic Ocean. 16S rRNA-based amplicon analyses found no geographical differentiation between the intestinal microbiome of Atlantic cod from different locations. Nevertheless, it is unclear if this lack of differentiation results from an insufficient resolution of this method to resolve fine-scaled biological complexity. Here, we take advantage of the increased resolution provided by metagenomic shotgun sequencing to investigate the intestinal microbiome of 19 adult Atlantic cod individuals from two coastal populations in Norway – located 470 km apart. Our results show that the intestinal microbiome is dominated by theVibrionalesorder, consisting of varying abundances ofPhotobacterium, AliivibrioandVibriospecies. Moreover, resolving the species community to unprecedented resolution, we identify two abundant species,P. iliopiscariumandP. kishitanii,which comprise over 50% of the classified reads. Interestingly, genomic data shows that the intestinalP. kishitaniistrains have functionally intactluxgenes, and its high abundance suggests that fish intestines form an important part of its ecological niche. These observations support a hypothesis that bioluminescence plays an ecological role in the marine food web. Despite our improved taxonomical resolution, we identify no geographical differences in bacterial community structure, indicating that the intestinal microbiome of these coastal cod is colonized by a limited number of closely related bacterial species with a broad geographical distribution that are well suited to thrive in this host-associated environment.