bluuebunny/crossref_metadata_2025 huggingface dataset:
South Africa’s African National Congress in Exile
Authors: Bundy Colin
Published: May 2018

The African National Congress (ANC) operated in exile for just over three decades, from 1960 to mid-1990. It developed from a flimsy and inexperienced “external mission” to an exiled organization caring for thousands of full-time members and maintaining an army, Umkontho weSizwe (MK), which by the 1980s numbered about 5000 soldiers. Based predominantly in Tanzania, Zambia, and Angola (though with members and offices in many other countries), the exiled movement established schools, hospitals, farms, and factories; it published and broadcast energetically; it lobbied for international support and established a diplomatic presence in dozens of countries. By the late 1980s, it was clear to the apartheid regime that it could not defeat or ignore the ANC but must enter negotiations with the organization. Equally, it was clear to the exiled leadership of the ANC that armed struggle relying on Soviet bloc funding was no longer feasible. Negotiations, and not military victory or seizure of power, was the only available option.

The ANC was pushed to the brink of survival but recovered, cohered, and regrouped, especially after 1976 when its membership and influence increased substantially. By 1990, through a combination of popular support inside South Africa and international solidarity, the ANC was swept to the status of government-in-waiting. Yet the exile experience was by no means an uninterrupted success story. The organization was variously beset by factionalism, rank-and-file disquiet, security failings, and an armed wing that saw little armed action. The ANC’s exile experience has generated controversy: over its relations with the South African Communist Party in exile; its human rights record, especially in the MK camps; and a political culture shaped by secrecy, militarism, and hierarchy. The “reinvention” of the organization in exile was a striking achievement—and it came at a cost.
American Radio and Technological Transformation from Invention to Broadcasting, 1900–1945
Authors: Krysko Michael A.
Published: May 2018

Radio debuted as a wireless alternative to telegraphy in the late 19th century. At its inception, wireless technology could only transmit signals and was incapable of broadcasting actual voices. During the 1920s, however, it transformed into a medium primarily identified as one used for entertainment and informational broadcasting. The commercialization of American broadcasting, which included the establishment of national networks and reliance on advertising to generate revenue, became the so-called American system of broadcasting. This transformation demonstrates how technology is shaped by the dynamic forces of the society in which it is embedded. Broadcasting’s aural attributes also engaged listeners in a way that distinguished it from other forms of mass media. Cognitive processes triggered by the disembodied voices and sounds emanating from radio’s loudspeakers illustrate how listeners, grounded in particular social, cultural, economic, and political contexts, made sense of and understood the content with which they were engaged. Through the 1940s, difficulties in expanding the international radio presence of the United States further highlight the significance of surrounding contexts in shaping the technology and in promoting (or discouraging) listener engagement with programing content.
Juvenile Justice in the United States
Authors: Tanenhaus David S.
Published: May 2018

Juvenile justice is a technical term that refers to the specific area of law and affiliated institutions, most notably the juvenile court, with jurisdiction over the cases of minors who are accused of being miscreants. Although the idea that the law should treat minors differently from adults predates the American Revolution, juvenile justice itself is a Progressive Era invention. Its institutional legitimacy rests on the power and responsibility of the state to act as a parent (parens patriae) on behalf of those who cannot care for themselves. Since the establishment of the world’s first juvenile court in Chicago in 1899, this American idea of creating separate justice systems for juveniles has spread across the nation and much of the world. For more than a century, American states have used their juvenile justice systems to respond to youth crime and delinquency. Since the 1960s, the US Supreme Court has periodically considered whether juvenile courts must provide the same constitutional due process safeguards as adult criminal courts and whether juveniles prosecuted in the criminal justice system can receive the same sentences as adults, such as the death penalty or life without the possibility of parole.
Christian Liturgical Music
Authors: Flynn William T.
Published: May 2018

Music in its widest definition (sound and silence organized in time) is never absent from Christian worship. The diversity of styles and forms employed both chronologically and synchronically, as well as the varied theological, aesthetic, and sociological positions concerning musical norms evident in every ecclesial community, provides a window into the self-representation and theological positioning of each community and often also of the subgroups and individuals within it. Disputes over the norms of Christian liturgical music are commonplace, most often within but also between various ecclesial communities, and may be analyzed for their theological significance. These norms concern (1) the distribution of musical roles, (2) the style of music employed, (3) the relationship between music and words (including whether to use instruments) and (4) the status of traditional repertories. Each of these may be indicative of theological commitments adopted both consciously and unconsciously by members of the community and may reflect differing theological positions, especially concerning ecclesiology. For example, congregants and whole communities may differ in their preferred self-representation of the Church, one preferring the model of the gathered community on earth, another preferring the model of heaven and earth in unity. Some individuals or communities may conceive of their church as part of a larger culture, while others may conceive of their church as a subculture or even a counterculture. New celebrations often arising from a change in spiritual emphases (e.g., the cult of saints) provide an impetus for change even within traditions that conceive of their music as sacral and inviolable. Perceived deficiencies in liturgies, whether due to a need for updating or to return to an earlier, purer form, also provoke musical changes. Careful case studies investigating such interactions between musical and liturgical practice illuminate the theological commitments of both individuals and ecclesial communities, and offer a method for the critical evaluation of the varied musical responses made by Christian communities.
The Reformed Tradition in the Netherlands
Authors: Klaassens Harry
Published: May 2018

Dutch Reformed liturgy started with Dutch refugees in London, where they used a Dutch translation of Martin Bucers’s liturgy at Strasbourg as well as the liturgy that John à Lasco brought back from Emden, Germany. When these refugees fled again, this time to Frankenthal, Germany, they formed their liturgy and theology at Heidelberg University. So Dutch Reformed liturgy was born outside its own boundaries—in Europe!

In The Netherlands itself, Dutch Reformed liturgy was grounded at the National Council of the Dutch Reformed Church at Dordrecht, in 1674 and 1678. Here the national synod made several decisions on liturgical practices as well of the use of the psalms. They also took initiative to begin a Dutch Bible translation: the famous Statenvertaling.

The 17th and 18th centuries of the Dutch Reformed liturgy are characterized by a long sermon as the heart of the liturgy, extended with the reading of the Ten Commandments, the Creed, and a prayer of confession of sins. Only psalms were sung in a 1773 translation, and without an organ, because it was seen as a pagan instrument.

Another national synod in 1817 dealt with the liturgy; now the he singing of a hymn became obligatory, a decision that led to many quarrels and the first schism in the Protestant Church of The Netherlands. Also the synod decided that the ministers should wear black gowns. But instead of set rules and forms, liturgical freedom was absolute.

At the beginning of the 20th century, new attention was directed at liturgical practices—many parishes started to experiment. A Dutch version of the ecumenical ordinarium came up, based on the Missale Romanum and the Book of Common Prayer. New hymn books saw the light in 1973 and in 2013, when several Protestant churches took part. However, there are still two mainstream liturgies. The first one, Liturgy A, is the orthodox liturgy with set forms, use of psalms only, reading of the Ten Commandments, and the Heidelberger Catechism with emphasis on the sermon and the Scripture reading. The second mainstream liturgy, Liturgy B, is the ordinary ecumenical with liturgical acclamations, the use of hymns, and the participation of a scholar or choir.

The Lord’s Supper has both an A and B form: didactic form or worship prayer based on the classical form of the mass.

A Service Book was published in 1998 (part 1) and 2004 (part 2), consisting of all liturgical texts and forms for both liturgies A and B. There is still liturgical freedom, as the Dutch are not amused by obligatory items of any kind!
Japanese Buddhisms in Diaspora
Authors: Porcu Elisabetta
Published: May 2018

Buddhism has been a missionary religion from its beginning. Japan was among the countries where this “foreign” religion arrived and was assimilated, adapted, and reshaped into new forms specifically connected to the new geographical and cultural environment. Buddhism traveled long distances from India through China and Korea, bringing with it flows of people, ideas, technologies, material cultures, and economies. More than ten centuries after its arrival in Japan, the first phase of propagation of Japanese Buddhism started and was linked to the history of Japanese migrants to Hawaii, North America, and Brazil since the 19th century. This was a history of diaspora, a term that implies not only the physical—and often traumatic—dispersion of people who left their homes for unknown places, but also a reconfiguration of their identities through the adaptation to these new places and their cultures.

The main role of Buddhist priests sent from Japan was to assist and provide comfort to the newly formed communities of migrant laborers, who very often experienced racial discrimination and lived under harsh conditions. Temples became important loci of Japanese community life, as well as centers for the preservation of Japanese culture. Diasporic communities felt the urge to keep a bond with the homeland and a reconnection with some past traditions, while, at the same time, striving toward integration in the new society.

Japanese Buddhist denominations in diasporic communities had therefore to accommodate different needs and adjust their teachings and practices to better suit their host cultures. Some of them underwent substantial changes, while others placed more emphasis on some practices instead of others. Moreover, Japanese Buddhist schools had to find a way to balance between their traditional role in Japan, which was—and still is—closely related to funerary rituals and memorials, and the new stimuli and requests coming from the new generations of Japanese migrants (nisei and sansei) and the non-Japanese spiritual seekers, the latter mostly interested in meditative practices and not in funeral Buddhism. In short, what needed to be done was to overcome a status of “ethnic” religion without, however, losing its own identity.
The Incas of the Andes
Authors: Ramirez Susan Elizabeth
Published: May 2018

The Inca (also Inka) Empire, called by the Andeans themselves “Tawantinsuyu,” referred to its four parts: the Chinchaysuyu, the Antisuyu, the Collasuyu, and the Cuntisuyu. Inter-disciplinary research pictures an assemblage of ethnic groups under a dynasty of rulers, believed to have supernatural origins. This multi-cultural state, overseen by a decimally-defined administrative system, was united by kinship ties; the worship of the sun, the moon and ethnic ancestors; negotiation; reciprocity; and force. At its height, it spread from Northwestern Argentina, through Bolivia, Peru, and Ecuador, and included about half of Chile and the southern frontier of Colombia. Troubles began in the 1520s as a strange disease decimated the native population, claiming the emperor himself. Yet, the Inca’s jurisdiction continued to expand until circa 1532, the date when Francisco Pizarro and his followers and allies marched across the Andes and confronted the Andean emperor Atahualpa in the plaza of the highland ceremonial center of Cajamarca.
Atrocity, Race, and Region in the Early Haitian Revolution: The Fond d’Icaque Rising
Authors: Geggus David
Published: May 2018

Set within a larger analysis of class relations in the Haitian Revolution, this is a microhistory that intersects with several important themes in the revolution: rumor, atrocity, the arming of slaves, race relations, and the origins and wealth of the free colored population. It is an empirical investigation of an obscure rebellion by free men of color in the Grande Anse region in 1791. Although the rebellion is obscure, it is associated with an atrocity story that has long resonated in discussion of the revolution. Formerly the least-known segment of Caribbean society, research has shed much new light on free people of color in recent decades, but much remains to be clarified. In certain ways, they are the key to understanding the Haitian Revolution, because of their anomalous position in Saint Domingue society and the way their activism precipitated its unraveling. The Grande Anse region had a unique experience of the revolution in that white supremacy and slavery were maintained there longer than in any other part of the colony. Based primarily on unexploited or little-known sources the article demonstrates the range and depth of research that remains possible and suggests that a regional focus is best way to advance current scholarship on the Haitian Revolution.
Constitutionalism in the Hispanic World
Authors: Rodríguez O. Jaime E.
Published: May 2018

The concept of a constitution, a political entity that determines how a people are governed, emerged in ancient times. The government of the Roman Republic (509–27 BC) influenced the Western world. Later, Romanized Visigoths adopted a charter, the Fuero Juzgo (654), in the Iberian Peninsula that integrated Roman and Visigothic legal systems. The document influenced regional political entities throughout the Middle Ages. In the 13th century, each of the realms of the Iberian Peninsula adopted individual rather than shared fundamental codes. In 1265, King Alfonso X established Castilla’s and Leon’s first constitution, the Siete Partidas. The New World obtained its own legal system, known as the Derecho Indiano (Laws of the Indies). Like the kingdoms of the Iberian Peninsula, those of America created a compact between the monarch and the citizens of each realm rather than Hispanic America as a whole. These systems of uncodified legislation evolved to meet changing circumstances and societal norms. They provided corporations and individuals expanding opportunities for indirect and direct experience in self-government.

In 1808, an unexpected upheaval transformed the Hispanic world. The French invaded Spain. Emperor Napoleon Bonaparte lured the royal family into France, compelled them to abdicate in his favor, and then granted the Spanish monarchy to his brother, José. The Spanish people did not accept the usurper king, José I. They formed the Junta Central to oppose the invaders. As the French continued to conquer the nation, they convened a Cortes, which met on September 24, 1810, in the port of Cádiz. Approximately 220 deputies, including sixty-five Americans and two Filipinos, eventually participated in the extraordinary Cortes of Cádiz. Deputies representing overseas dominions played a central role in developing the most progressive constitution of the 19th century. Despite the political chaos that surrounded the constituent congress, the delegates debated and eventually reached consensus on a modern, flexible charter that reconciled the competing interests of the multiplicity of areas and ideological positions represented at the assembly. They produced a constitution for the entire Hispanic world that made the executive and the judiciary subordinate to the legislature. It also increased the scope of political activity by establishing representative government at three levels: the city or town with a thousand or more inhabitants (constitutional ayuntamiento), the province (provincial deputation), and the monarchy (Cortes). The charter transferred political power from the center to the localities, and incorporated large numbers of people into the political process for the first time by redefining the concept of active citizenship (i.e., those eligible to vote). This fundamental document formed the basis for constitutional development throughout the Hispanic monarchy and for most charters promulgated in the nations that emerged after the breakup of that political entity.
Football (Soccer) in Brazil
Authors: Buarque de Hollanda Bernardo
Published: May 2018

Football appeared in Brazil in the end of the 19th century, among a favorable environment for the practice of English sports. These sports were initially practiced not professionally by English migrants and young students of Law, Engineering, and Medicine. Fluminense was the first club from Rio de Janeiro, at that time the capital of the country, to be dedicated exclusively to practice football. In the beginning, football represented nobility for the local elite. The social profile of people who attended matches at Fluminense’s field was very near to that of the players, be it for family reasons, friendship, or other motivations. Young women who went there desired to see their distinguished idols, and from this practice many relationships started. While this idyllic image of the past was produced, a historical point of view can notice a decisive enhancement in social segments interested in football. In the decade of 1910, a collective enthusiasm arose for football, mainly due to the fact that it was easy to practice and watch football in any kind of open space. This allowed it to spread out of clubs and the National Team. Far from the spatial and economic restriction of performance arts, football could be practiced and watched freely, in most diverse situations.
The clubs’ lack of structure to allocate players and fans contributed in making football a popular game, since they needed to seek public spaces to practice. At this point, the club that opposed to Fluminense has been Flamengo, which until then was not more than a regatta club. When it opened a football department, it practiced in open fields near the beaches. Many passersby started to look out their training and matches, and some of them adopted Flamengo as their club even if not participating of its internal sphere. The players became idols, first in the neighborhood and then in the whole city. This encouraged the talk about football in bars and cafés, with reflections on the increasing number of people to attend matches. Historian Leonardo Pereira says that in a few years football has become a mania. The making of the first national team to dispute friendly matches against England and Argentina has also stimulated football’s repercussion. Noticing public interest over matches with teams from different cities or countries, sports press left its poor attitude about football and began to carefully pay attention to this kind of rivalry and the consequent emotions each fan is able to express for his team, especially the National Team.
Toward a Sociolinguistics of Modern Sub-Saharan African South–South Migrations
Authors: Vigouroux Cécile B.
Published: May 2018

Despite their large demographic size, intra-continental African migrations have hardly been taken into account in the theorizing on migration in transnational studies and related fields. Research questions have been framed predominantly from a South-to-North perspective on population movements. This may be a consequence of the fact that the extent and complexity of modern population movements and contacts within Africa are hard to assess, owing mainly to lack of reliable data. For sociolinguists the challenge is even greater, partly because of the spotty knowledge of linguistic diversity in the continent and the scarcity of adequate sociolinguistic descriptions of the ways in which Africans manage their language repertoires. Despite these limitations, a sociolinguistics of intra-continental African migrations will contribute significantly to a better understanding of the conditions, nature, and periodicity of population contacts and interactional dynamics. It will help explain why geographic mobility entails reshaping sociocultural practices, including the language repertoires of both the migrants and the people they come in contact with. Moreover, the peculiarity of African economies, which rely heavily on informal non-institutionalized practices, prompts a rethinking of assumptions regarding the acquisition of the host country’s language(s) as the primary facilitator of the migrants’ socioeconomic inclusion. A sociolinguistic understanding of migrations within Africa can help to formulate new questions and enrich the complex pictures that the study of other parts of the world has already shaped.
Dialectology
Authors: Childs Becky
Published: May 2018

The field of dialectology, the study of the language of an area or group of people, has a long tradition within linguistics. From the earliest dialect studies, a focus on rigorous methodological practices has been an ever-present component of this discipline. Traditional methodologies can be seen in the work of the early dialect atlases, which relied heavily on mail questionnaires or fieldworkers that would chronicle the pronunciation, grammatical features, and lexicon of residents of particular regions. More recent technological innovations, such as GIS and online survey methods and applications, have brought multidisciplinary approaches to the study of dialects, as well as allowing for broader and more robust studies of geographic areas and social groups.

The influence and interface of dialectology on various linguistic disciplines is noteworthy. Dialectological methods have most commonly been utilized in historical linguistics, sociolinguistics/language variation and change, and language endangerment/documentation. Within each of these disciplines, the adoption of methods from dialectology has allowed for the systematic study of language across geographic and social space, as well as across time.
Organic Farming
Authors: Radovich Theodore J. K.
Published: May 2018

Organic farming occupies a unique position among the world’s agricultural systems. While not the only available model for sustainable food production, organic farmers and their supporters have been the most vocal advocates for a fully integrated agriculture that recognizes a link between the health of the land, the food it produces, and those that consume it. Advocacy for the biological basis of agriculture and the deliberate restriction or prohibition of many agricultural inputs arose in response to potential and observed negative environmental impacts of new agricultural technologies introduced in the 20th century. A primary focus of organic farming is to enhance soil ecological function by building soil organic matter that in turn enhances the biota that soil health and the health of the agroecosystem depends on.

The rapid growth in demand for organic products in the late 20th and early 21st centuries is based on consumer perception that organically grown food is better for the environment and human health. Although there have been some documented trends in chemical quality differences between organic and non-organic products, the meaningful impact of the magnitude of these differences is unclear. There is stronger evidence to suggest that organic systems pose less risk to the environment, particularly with regard to water quality; however, as intensity of management in organic farming increases, the potential risk to the environment is expected to also increase. In the early 21st century there has been much discussion centered on the apparent bifurcation of organic farming into two approaches: “input substitution” and “system redesign.” The former approach is a more recent phenomenon associated with pragmatic considerations of scaling up the size of operations and long distance shipping to take advantage of distant markets. Critics argue that this approach represents a “conventionalization” of organic agriculture that will erode potential benefits of organic farming to the environment, human health, and social welfare. A current challenge of organic farming systems is to reconcile the different views among organic producers regarding issues arising from the rapid growth of organic farming.
International Environmental Conventions on Biodiversity
Authors: Nummelin Matti , Urho Niko
Published: May 2018

Conservation and sustainable use of biodiversity have been in the center of policy creation for half a century. The main international biodiversity conventions and processes include the Convention on Biological Diversity (CBD) and its protocols, the Convention on Trade in Endangered Species of Wild Fauna and Flora (CITES), the Convention on Wetlands of International Importance (Ramsar Convention), the World Heritage Convention (WHC), the Convention on Conservation of Migratory Species of Wild Animals (CMS), the International Treaty on Plant Genetic Resources for Food and Agriculture (ITPGRFA), the International Plant Protection Convention (IPPC), the Commission on Genetic Resources for Food and Agriculture (CGRFA), and the International Convention on the Regulation of Whaling (ICRW). The governance of marine biodiversity in areas beyond national jurisdiction (BBNJ) is also discussed, as political focus has shifted to the protection of the oceans and is expected to culminate in the adoption of a new international convention under the United Nations Convention on Law of Seas (UNCLOS). Other conventions and processes with links to biodiversity include the United Nations Convention to Combat Desertification (UNCCD), the United Nations Framework Convention on Climate Change (UNFCCC), and the United Nations Forum on Forests (UNFF).

Despite the multitude of instruments, governments are faced with the fact that biodiversity loss is spiraling and international targets are not being met. The Earth’s sixth mass extinction event has led to various initiatives to fortify the relevance of biodiversity in the UN system and beyond to accelerate action on the ground. In face of an ever more complex international policy landscape on biodiversity, country delegates are seeking to enhance efficiency and reduce fragmentation by enhancing synergies among multilateral environmental agreements and strengthening their science−policy interface. Furthermore, biodiversity has been reflected throughout the 2030 Agenda on Sustainable Development and is gradually gaining more ground in the human rights context. The Global Pact for the Environment, a new international initiative that is aiming to reinforce soft law commitments and increase coherence among environmental treaties, holds the potential to influence and strengthen the way biodiversity conventions function, but extensive discussions are still needed before concrete action is agreed upon.
Payments versus Direct Controls for Environmental Externalities in Agriculture
Authors: Weersink Alfons , Pannell David
Published: May 2018

The production of food, fiber, and fuel often results in negative externalities due to impacts on soil, water, air, or habitat. There are two broad ways to incentivize farmers to alter their land use or management practices on that land to benefit the environment: (1) provide payments to farmers who adopt environmentally beneficial actions and (2) introduce direct controls or regulations that require farmers to undertake certain actions, backed up with penalties for noncompliance. Both the provision of payments for environmentally beneficial management practices (BMPs) and a regulatory requirement for use of a BMP alter the incentives faced by farmers, but they do so in different ways, with different implications and consequences for farmers, for the policy, for politics, and consequently for the environment. These two incentive-based mechanisms are recommended where the private incentives conflict with the public interest, and only where the private incentives are not so strong as to outweigh the public benefits. The biggest differences between them probably relate to equity/distributional outcomes and politics rather than efficiency. Governments often seem to prefer to employ beneficiary-pays mechanisms in cases where they seek to alter farmers’ existing practices, and polluter-pays mechanisms when they seek to prevent farmers from changing from their current practices to something worse for the environment. The digital revolution has the potential to help farmers produce more food on less land and with fewer inputs. In addition to reducing input levels and identifying unprofitable management zones to set aside, the technology could also alter the transaction costs of the policy options.
Payments for Ecosystem Services: Program Design and Participation
Authors: James Natasha , Sills Erin
Published: May 2018

Payments for ecosystem or environmental services (PES) are broadly defined as payments (in kind or in cash) to participants (often landowners) who volunteer to provide the services either to a specific user or to society at large. Payments are typically conditional on agreed rules of natural resource management rather than on delivery of the services. The rules range from protection of native ecosystems to installation of conservation practices. The earliest proponents of PES were economists who argued that they are a cost-effective way to conserve forests, manage watersheds, and protect biodiversity. Political support for PES rests on the claim that these programs can alleviate poverty among participants as well as protect the environment. More recent literature and experience with PES reveals barriers to achieving cost-effectiveness and poverty alleviation, including many related to the distribution of participation. The Costa Rican experience illustrates the choices that must be made and the potential for innovation in the design of PES programs.
Effects of temperature and food availability on the survival and growth of larval Arctic cod (Boreogadus saida) and walleye pollock (Gadus chalcogrammus)
Authors: Koenker Brittany L , Laurel Benjamin J , Copeman Louise A , Ciannelli Lorenzo
Published: May 2018

Arctic cod (Boreogadus saida) is an ecologically significant species that is uniquely adapted to occupy ice edges, but warming and loss of sea ice are hypothesized to favour more facultative gadids, such as walleye pollock (Gadus chalcogrammus). To test this hypothesis, we experimentally measured the growth and survival of Arctic cod and walleye pollock at two larval stages across a range of temperature and food conditions in the laboratory. Results indicated early and late-stage Arctic cod larvae have a competitive growth and survival advantage over walleye pollock at low temperatures. However, these advantages are lost under warmer, food-productive conditions where walleye pollock larvae survived and experienced accelerated growth rates. Growth models developed from this study emphasize the need to account for both species- and stage-specific differences in the thermal response of closely related marine fish larvae. More broadly, these new vital rate data provide a mechanistic framework to forecast spatial-temporal shifts of gadids at the Arctic-boreal interface resulting from climatic warming and altered productivity regimes.
A Sweet Romance: Divergent Effects of Romantic Stimuli on the Consumption of Sweets
Authors: Yang Xiaojing , Mao Huifang , Jia Lei , Bublitz Melissa G
Published: May 2018

Drawing from research on food consumption, conceptual metaphors, and assimilation and contrast, we examine how exposure to romantic stimuli (e.g., watching a romantic ad, reading a romantic note) affects consumers’ subsequent consumption of sweets. Across five studies, we find that romantic stimuli exposure increases sweet food consumption among abstract thinkers but reduces sweet food intake among concrete thinkers. We also identify the moderating role of metaphor content on this finding such that the effects of romantic exposure on the consumption of sweets occur only when the metaphoric association between love and sweetness is highlighted but dissipate when a competing metaphor is accentuated.
Draft Genome Resources for the Phytopathogenic Fungi Monilinia fructicola, M. fructigena, M. polystroma, and M. laxa, the Causal Agents of Brown Rot
Authors: Rivera Yazmín , Zeller Kurt , Srivastava Subodh , Sutherland Jeremy , Galvez Marco , Nakhla Mark , Poniatowska Anna , Schnabel Guido , Sundin George , Abad Z. Gloria
Published: May 2018

Fungi in the genus Monilinia cause brown rot disease of stone and pome fruits. Here, we report the draft genome assemblies of four important phytopathogenic species: M. fructicola, M. fructigena, M. polystroma, and M. laxa. The draft genome assemblies were 39 Mb (M. fructigena), 42 Mb (M. laxa), 43 Mb (M. fructicola), and 45 Mb (M. polystroma) with as few as 550 contigs (M. laxa). These are the first draft genome resources publicly available for M. laxa, M. fructigena, and M. polystroma.
Generalized and Lateralized Rhythmic Patterns
Authors: Schmitt Sarah E.
Published: May 2018

The relationship between generalized and lateralized rhythmic delta activity (RDA) and seizures is more ambiguous than the relationship between periodic discharges and seizures. Although frontally predominant generalized RDA is not associated with seizures, occipitally predominant RDA may be associated with the absence of seizures. Lateralized RDA seems to be more strongly associated with the presence of seizure activity. Appropriate recognition of generalized RDA and lateralized rhythmic delta activity may be confounded by benign etiologies of RDA, such as phi rhythm, slow alpha variant, subclinical rhythmic electrographic discharges of adults, or hyperventilation-induced high-amplitude rhythmic slowing. Angelman syndrome and NMDA-receptor antibody encephalitis can also produce morphologically distinct patterns of RDA.
Generalized Periodic Discharges: A Topical Review
Authors: Sully Krystal E. , Husain Aatif M.
Published: May 2018

Generalized periodic discharges (GPDs) are generalized discharges that recur with a relatively uniform morphology and duration. They have a quantifiable interdischarge interval. Over the past decade, our understanding of these waveforms has improved considerably. The nomenclature has changed, and etiologic references have been removed. Many disease states can cause GPDs, such as anoxia, toxic/metabolic encephalopathy, infections, nonconvulsive status epilepticus, and hypothermia. Generally, GPDs are morphologically similar regardless of etiology. Generalized periodic discharges that are associated with nonconvulsive status epilepticus are treated with antiseizure drugs, while others are not necessarily aggressively treated. Prognosis for most patients with GPDs is guarded, although this is also dependent on the underlying etiology. As our understanding of GPDs increases, it is also clear that there is much more to be learned about these waveforms.
Definition and Classification of Periodic and Rhythmic Patterns
Authors: Maciel Carolina B. , Hirsch Lawrence J.
Published: May 2018

The growing use of continuous video-EEG recording in the inpatient setting, in particular in patients with varying degrees of encephalopathy, has yielded a window to the brain with an excellent temporal resolution. This increasingly available tool has become more than an instrument to detect nonconvulsive seizures (its primary use), and clinical indications span from ischemia detection in acute brain injuries, neuroprognostication of comatose patients, to monitoring the degree of encephalopathy. In this context, abnormal findings such as periodic discharges and rhythmic delta activity were increasingly recognized; however, significant subjectivity remained in the interpretation of these findings pertaining to key features regarding their spatial involvement, prevalence of occurrence, duration, associated morphologic features, and behavior. In 2005, the American Clinical Neurophysiology Society proposed standardized definitions and classification of electroencephalographic rhythmic and periodic patterns. This was subsequently revised in 2011 and in 2012 and is now being used by centers worldwide, with the final version published in early 2013 as an official guideline of the ACNS. The resulting uniform terminology has allowed for significant advances in the understanding of the pathophysiology, epileptogenic potential, and overall clinical implication of these patterns. Investigators across multiple institutions are now able to collaborate while exploring diagnostic and therapeutic algorithms to these patterns, an effort that may soon provide definitive evidence guiding treating clinicians on the management of these patients.
Enzyme promiscuity shapes evolutionary innovation and optimization
Authors: Guzmán Gabriela I. , Sandberg Troy E. , LaCroix Ryan A. , Nyerges Akos , Papp Henrietta , Raad Markus de , King Zachary A. , Northen Trent R. , Notebaart Richard A. , Pál Csaba , Palsson Bernhard O. , Papp Balázs , Feist Adam M.
Published: May 2018

Evidence suggests that novel enzyme functions evolved from low-level promiscuous activities in ancestral enzymes. Yet, the evolutionary dynamics and physiological mechanisms of how such side activities contribute to systems-level adaptations are poorly understood. Furthermore, it remains untested whether knowledge of an organism’s promiscuous reaction set (‘underground metabolism’) can aid in forecasting the genetic basis of metabolic adaptations. Here, we employ a computational model of underground metabolism and laboratory evolution experiments to examine the role of enzyme promiscuity in the acquisition and optimization of growth on predicted non-native substrates inE. coliK-12 MG1655. After as few as 20 generations, the evolving populations repeatedly acquired the capacity to grow on five predicted novel substrates–D-lyxose, D-2-deoxyribose, D-arabinose, m-tartrate, and monomethyl succinate–none of which could support growth in wild-type cells. Promiscuous enzyme activities played key roles in multiple phases of adaptation. Altered promiscuous activities not only established novel high-efficiency pathways, but also suppressed undesirable metabolic routes. Further, structural mutations shifted enzyme substrate turnover rates towards the new substrate while retaining a preference for the primary substrate. Finally, genes underlying the phenotypic innovations were accurately predicted by genome-scale model simulations of metabolism with enzyme promiscuity. Computational approaches will be essential to synthesize the complex role of promiscuous activities in applied biotechnology and in models of evolutionary adaptation.
Whale watching with BulkVis: A graphical viewer for Oxford Nanopore bulk fast5 files
Authors: Payne Alexander , Holmes Nadine , Rakyan Vardhman , Loose Matthew
Published: May 2018

Motivation

The Oxford Nanopore Technologies (ONT) MinION is used for sequencing a wide variety of sample types with diverse methods of sample extraction. Nanopore sequencers output fast5 files containing signal data subsequently base called to fastq format. Optionally, ONT devices can collect data from all sequencing channels simultaneously in a bulk fast5 file enabling inspection of signal in any channel at any point. We sought to visualise this signal to inspect challenging or difficult to sequence samples, or where flow cell performance is modified by an external agent, such as ‘Read Until’.

Results

The BulkVis tool can load a bulk fast5 file and overlays MinKNOW classifications on the signal trace. Users can navigate to a channel and time or, given a fastq header from a read, jump to its specific position. BulkVis can export regions as Nanopore base caller compatible reads. Using BulkVis, we find long reads can be incorrectly divided by MinKNOW resulting in single DNA molecules being split into two or more reads. The longest seen to date is 2,272,580 bases in length and reported in eleven consecutive reads. We provide helper scripts that identify and reconstruct split reads given a sequencing summary file and alignment to a reference. We note that incorrect read splitting appears to vary according to input sample type and is more common in ‘ultra long’ read preparations.

Availability

The software is available freely under an MIT license athttps://github.com/LooseLab/bulkVis. The software requires python3 to run.
Quantification of EnterohemorrhagicEscherichia coliO157:H7 proteome using TMT-Based Analysis
Authors: Silva Wanderson M. , Bei Jinlong , Amigo Natalia , Valacco Pía , Amadio Ariel , Zhang Qi , Wu Xiuju , yu Ting , Larzabal Mariano , Chen Zhuang , Cataldi Angel
Published: May 2018

EnterohemorrhagicEscherichia coli(EHEC) O157:H7 is a human pathogen responsible for diarrhea, hemorrhagic colitis and hemolytic uremic syndrome (HUS). EHEC infection is distributed worldwide and numerous outbreaks of diseases caused by enterohemorrhagic have been reported. To promote a comprehensive insight into the molecular basis of EHEC O157:H7 physiology and pathogenesis, the combined proteome of EHEC O157:H7 strains, Clade 8 and Clade 6 isolated from cattle in Argentina, and the standard EDL933 (clade 3) strain has been analyzed. TMT (Tandem Mass Tags)-based quantitative proteomic and emPAI analyses were performed to estimate the protein abundance in EHEC proteome. 2,234 non-redundant proteins of EHEC O157:H7 were identified. A comparison of this result within silicodata of EHEC O157:H7 genome showed that approximately 40% of the predicted proteome of this pathogen were covered. According to the emPAI analysis, 85 proteins were among the most abundant (e.g. GAPDH, FliC H-antigen, Enolase, and GroEL). Tellurite resistance proteins were also highly abundant. COG analysis showed that although most of the identified proteins are related to cellular metabolism, the majority of the most abundant proteins are associated with translation processes. A KEGG enrichment analysis revealed that Glycolysis / Gluconeogenesis was the most significant pathway. On the other hand, the less abundant detected proteins are those related to DNA processes, cell respiration and prophage. Among the proteins that composed the Type III Secretion System, the most abundant protein was EspA. Altogether, the results show a subset of important proteins that contribute to physiology and pathogenicity of EHEC O157:H7.

IMPORTANCE

The study of the abundance of proteins present within a complex mixture of proteins in a cell, under different conditions, can provide important information about the activities of individual protein components and protein networks that are cornerstones for the comprehension of physiological adaptations in response to biological demands promoted by environmental changes. We generated a comprehensive and accurate quantitative list of EHEC O157:H7 proteome, which provides a description of the most abundant proteins produced by this pathogen that were related to physiology and pathogenesis of EHEC. This study provides information and extends the understanding on functional genomics and the biology of this pathogen.
The mechanics of predator-prey interactions: first principles of physics predict predator-prey size ratios
Authors: Portalier Sébastien M. J. , Fussmann Gregor F. , Loreau Michel , Cherif Mehdi
Published: May 2018

Robust predictions of predator-prey interactions are fundamental for the understanding of food webs, their structure, dynamics, resistance to species loss and invasions and role in ecosystem functioning. Most current food web models are empirically based. Thus, they are sensitive to the quality of the data, and ineffective in predicting non-described and disturbed food webs. There is a need for mechanistic models that predict the occurrence of a predator-prey interaction based on the traits of organisms and the properties of their environment.

Here, we present such a model that focuses on the predation act itself. We built a Newtonian, mechanical model for the processes of searching, capture and handling of a prey item by a predator. Associated with general metabolic laws, we predict the net energy gain from predation for pairs of predator and prey species depending on their body sizes.

Predicted interactions match well with data from the most extensive predator-prey database, and overall model accuracy is greater than the niche model.

Our model shows that it is possible to accurately predict the structure of food webs using only a few ecomechanical traits. It underlines the importance of physical constraints in structuring food webs.
Scalable continuous evolution of genes at mutation rates above genomic error thresholds
Authors: Ravikumar Arjun , Arzumanyan Garri A. , Obadi Muaeen K.A. , Javanpour Alex A. , Liu Chang C.
Published: May 2018

Directed evolution is a powerful approach for engineering biomolecules and understanding adaptation1-3. However, experimental strategies for directed evolution are notoriously low-throughput, limiting access to demanding functions, multiple functions in parallel, and the study of molecular evolution in replicate. Here, we report OrthoRep, a yeast orthogonal DNA polymerase-plasmid pair that stably mutates ~100,000-fold faster than the host genome in vivo, exceeding error thresholds of genomic replication that lead to single-generation extinction4. User-defined genes in OrthoRep continuously and rapidly evolve through serial passaging, a highly scalable process. Using OrthoRep, we evolved drug resistant malarial DHFRs 90 times and uncovered a more complex fitness landscape than previously realized5-9. We find rare fitness peaks that resist the maximum soluble concentration of the antimalarial pyrimethamine – these resistant variants support growth at pyrimethamine concentrations >40,000-fold higher than the wild-type enzyme can tolerate – and also find that epistatic interactions direct adaptive trajectories to convergent outcomes. OrthoRep enables a new paradigm of routine, high-throughput evolution of biomolecular and cellular function.