bluuebunny/crossref_metadata_2025 huggingface dataset:
Further Experiments in Language Translation
Authors: Wallace Sinaiko H. , Klare George R.
Published: December 2016

Application of computational linguistics, i.e., language translation by computer, has been proposed as a means of producing readable translations of technical English-to-Vietnamese.

This report is about an experimental study of the readability of translations that could be used for training or equipment maintenance.

The experiments involved assessing the readability of Vietnamese that had been translated from English by three methods: (1) expert human translators, (2) un-edited translation by computer, and (3) edited computer translation. English was a control condition. Readers included two groups of student pilots : 168 in the Vietnamese Air Force (VNAF) and 88 in the USAF. Material that was translated consisted of three 500-word passages sampled from a standard Air Force text, Instrument Flying. Readability was measured by : (1) reading comprehension tests, (2) cloze procedure, and (3) clarity ratings. Time to complete each of these tasks was also measured.

Major conclusions of the study are : (1) expert human translators produce more readable translations of technical English-to-Vietnamese than is done by computer; (2) Vietnamese readers, trained in English, show the highest comprehension when dealing with that language; (3) comprehension loss becomes relatively greater, as more and more difficult material is read, for computer-based translations than for human translations; (4) method of translation does not affect reading speed.
Pasp : Some Views on Automated Syntactical Parsing of Large Language Corpuses
Authors: Boot M.
Published: December 2016

The paper is concerned with some problems of system analysis.

The problems are not mathematically defined. They are concerned with the syntactic parsing of large language corpuses, which are not artificially restricted. (PASP).

After the discussion of some strategies for PASP developed in the past, a more complete strategy is proposed. Major characteristics of this strategy are :

The ad hoc character of some parts of it

The use of a linear string grammar

The definition of probability rules

The translation of the probability rules into a priori rules for the string grammar

The context sensitivity

The flexibility of the system
A Large Scale Program in French Immersion
Authors: Swain Merrill , Barik Henri C.
Published: December 2016

The school performance of pupils in Grades 1-3 of the French immersion program in operation in Ottawa public schools is evaluated in comparison with that of pupils in the regular English program. By the end of Grade I immersion program pupils taught reading in French lag behind their peers in the regular program in English language skills involving English reading, but they show some ability to transfer reading skills from French to English. By the end of Grade 2, following the introduction of English Language Arts into the curriculum for 60 minutes a day, immersion pupils still lag behind their regular program peers in most English language skills considered, although their level of performance is consistent with their grade level. By the end of Grade 3, immersion pupils match regular program pupils in all English language skills tested except spelling. At each grade level pupils in the two programs perform equivalently in mathematical skills and reveal similar IQ measures. Immersion pupils are more proficient in French than pupils of corresponding or higher grade levels receiving daily instruction in French as a second language, and do adequately in comparison with native French-speaking pupils.
Von Der Quantitativen Zur Qualitativen Inhaltsanalyse Literarischer Texte
Authors: Füger W.
Published: December 2016

Some possibilities of interpretative application of a computer-made concordance, reverse dictionary, and frequency-list of Joyce's Dubliners are demonstrated by the example of the suffix -less and the substantives voice and life. General reflections as to how mere quantitative content analysis can be developed into a more exacting qualitative one via the stages of frequency-, valence-, intensity-, and contingency-analysis are currently embarked upon, the inherent limitations of these methods being laid open.

Möglichkeiten interpretatorischer Auswertung einer EDV-er-stellten Konkordanz und Häufigkeitsliste sowie eines rück-laufigen Worterbuchs zu Joyces Dubliners werden vorgeführt am Beispiel der Nachsilbe -less sowie der Substantive voice und life. Grundsatzerwagungen darüber, wie quantitative Inhaltsanalyse sich über die Zwischenstufen von Häufigkeits-, Wertigkeits-, Intensitäts- und Mehrkomponenten- Analyse zu einer anspruchsvolleren qualitativen steigern lässt, werden laufend einbezogen, unter Offenlegung der diesen Verfahren inhärenten Grenzen.
Focal Words and the Recovery of Sentence Meaning
Authors: Darian Dr. Steven
Published: December 2016

In listening and reading, the foreign language learner must be able to process a tremendous amount of information in a short time. In order to do this, he must develop a strategy for choosing those items that help in recovering that information. One way of doing this is to concentrate on focal words: words containing key elements of meaning in the sentence. These words may then be used - in speech and writing - to reconstruct the original message. This paper explores the relationship of focel words to other sentence elements and describes various focal word exercises for listening and reading.
The Historical Memory Law and its role in redesigning semiotic cityscapes in Spain
Authors: Guilat Yael , Espinosa-Ramírez Antonio B.
Published: December 2016

In its Historical Memory Law (October 2007), Spain recognized victims on both sides of its 1936–1939 Civil War and established entitlements for victims and descendants of victims of the war and the Franco regime that followed (1939–1975). The law requires authorities to remove Francoist symbols and signs from public buildings and spaces, rename streets and squares, and cleanse the public space of monuments and artifacts that glorify or commemorate the regime. By allowing exceptions on artistic, architectural, or religious grounds, however, the law triggered persistent public struggles over monuments, memorials, and outdoor sculptures. This article examines the implementation of the law in the city of Granada, via a case study relating to the removal of a sculpture honoring the founder of the Spanish Fascist movement, José Antonio Primo de Rivera. The controversy over the statue sparked a debate in Granada about the implementation of the law in the public space and raised questions about the role of text, material and visual culture in redesigning Linguistic Landscape by articulating contested memories.
Traduire la créolisation
Authors: Bogle Desrine
Published: December 2016

This article proposes the translatological approach called intracultural translation, that is, translation within the same language-culture, coined by Desrine Bogle (2014), with specific reference and application to the Creole language using H. P. Grice’s conversational implicature, Venuti’s application to translation, and Roman Jakobson’s intralinguistic translation as theoretical frameworks. Mirroring the approach of the translator working within Romance languages who employs the Latin roots of these languages to judiciously resolve difficult translation issues, the concept of intracultural translation reinforces the notion of a Creole world view, product of a shared history, as evidenced through a shared linguistic and cultural heritage or “storehouse” from which translators of Creole texts can freely select elements to undertake their activity of intercultural transfer. In seeking to affirm and maintain the cohesiveness of Creole identity against the homogenizing effect of globalization, intracultural translation, currently underexplored and underexploited, is presented as a viable translatological approach to texts in Creole. Intracultural translation is exemplified through a case study of the English translations of three French Creole proverbs in the French Caribbean novel Pluie et vent sur Télumée Miracle by Simone Schwarz-Bart.
Translation of Creole in Caribbean English literature
Authors: Niles Glenda
Published: December 2016

This paper explores the use of Creoles in Caribbean English Literature and how it tends to be translated into Spanish by analyzing the Spanish translations of two novels written by Caribbean author, Oonya Kempadoo. Kempadoo is a relatively new and unknown author. She was born in England to Guyanese parents and grew up in the Caribbean. She lived in several of the islands, including St. Lucia and Trinidad and at present resides in Grenada. Apart from being a novelist, she is a freelance researcher and consultant in the arts, and works with youth and international organizations, where she focuses on social development.

Her first novel,Buxton Spice,was published in 1998. Described as a semi-autobiography byPublisher’s Weekly, it has also been praised for being original and universal in the portrayal of its themes. It is the story of a young girl growing up in Guyana during the Burnham regime. It is written as a series of vignettes, which contributes to the seemingly quick development of Lula from childhood to adolescence, as she learns to explore her sexuality. This novel has been published in the United Kingdom and the United States, and has been translated into Spanish, French, Italian, Dutch, Portuguese and Hebrew. The version used for this investigation was translated by Victor Pozanco and commissioned by Tusquets Publishers.

Kempadoo’s second novel,Tide Running, also forms part of this investigation. As the 2002 winner of the Casa de las Américas Literary prize for Caribbean English and Creole, this novel was translated into Spanish by a Cuban translator as a part of the award. It is the story of an unambitious Tobagonian youth who becomes entangled in a bizarre relationship with an interracial couple. The story highlights several issues, such as poverty, race and social class differences, sex and right and wrong. As a researcher, I felt that it would be enlightening to see how a Caribbean translator, from a country (Cuba) with limited access to mass cultural currents commonplace elsewhere, handles this piece of prose which is so heavily steeped in Trinbagonian culture.
Climate change and the scope for global greenhouse gas reductions.
Authors: Davis J.
Published: December 2016

This article reviews, from a socio-economic perspective, the current state of knowledge and controversies around the causes and consequences of global climate change. It considers the prospects for reducing global emissions of greenhouse gases (GHGs) which, according to the scientific consensus, are the key anthropogenic drivers of climate change. The focus is on two major areas of economic activity, the agriculture, forestry and other land use sector and the energy sector, which together account for around 60% of global GHG emissions. Total global emissions almost doubled in the 40-year period since 1970 and the annual rate of increase rose sharply in the 2000-2010 period. In the medium-to-long term, the emerging and developing economies will have a growing influence on global emissions given their populations and anticipated rates of economic growth. The extent to which the Paris COP21 Agreement can be considered binding on the parties is open to question. It is concluded that there are neither easy nor simple solutions for reducing global emissions. Reductions in emissions intensities should be possible, but it is argued that a stabilization path for total future emissions seems more likely than significant reductions.
Combined immunodeficiency and Epstein-Barr virus–induced B cell malignancy in humans with inherited CD70 deficiency
Authors: Abolhassani Hassan , Edwards Emily S.J. , Ikinciogullari Aydan , Jing Huie , Borte Stephan , Buggert Marcus , Du Likun , Matsuda-Lennikov Mami , Romano Rosa , Caridha Rozina , Bade Sangeeta , Zhang Yu , Frederiksen Juliet , Fang Mingyan , Bal Sevgi Kostel , Haskologlu Sule , Dogu Figen , Tacyildiz Nurdan , Matthews Helen F. , McElwee Joshua J. , Gostick Emma , Price David A. , Palendira Umaimainthan , Aghamohammadi Asghar , Boisson Bertrand , Rezaei Nima , Karlsson Annika C. , Lenardo Michael J. , Casanova Jean-Laurent , Hammarström Lennart , Tangye Stuart G. , Su Helen C. , Pan-Hammarström Qiang
Published: December 2016

In this study, we describe four patients from two unrelated families of different ethnicities with a primary immunodeficiency, predominantly manifesting as susceptibility to Epstein-Barr virus (EBV)–related diseases. Three patients presented with EBV-associated Hodgkin’s lymphoma and hypogammaglobulinemia; one also had severe varicella infection. The fourth had viral encephalitis during infancy. Homozygous frameshift or in-frame deletions in CD70 in these patients abolished either CD70 surface expression or binding to its cognate receptor CD27. Blood lymphocyte numbers were normal, but the proportions of memory B cells and EBV-specific effector memory CD8+ T cells were reduced. Furthermore, although T cell proliferation was normal, in vitro–generated EBV-specific cytotoxic T cell activity was reduced because of CD70 deficiency. This reflected impaired activation by, rather than effects during killing of, EBV-transformed B cells. Notably, expression of 2B4 and NKG2D, receptors implicated in controlling EBV infection, on memory CD8+ T cells from CD70-deficient individuals was reduced, consistent with their impaired killing of EBV-infected cells. Thus, autosomal recessive CD70 deficiency is a novel cause of combined immunodeficiency and EBV-associated diseases, reminiscent of inherited CD27 deficiency. Overall, human CD70–CD27 interactions therefore play a nonredundant role in T and B cell–mediated immunity, especially for protection against EBV and humoral immunity.
Hilbert scheme of twisted cubics as a simple wall-crossing
Authors: Xia Bingyu
Published: December 2016

We study the Hilbert scheme of twisted cubics in three-dimensional projective space by using Bridgeland stability conditions. We use wall-crossing techniques to describe its geometric structure and singularities, which reproves the classical result of Piene and Schlessinger.
Improved subconvexity bounds for 𝐺𝐿(2)×𝐺𝐿(3) and 𝐺𝐿(3) 𝐿-functions by weighted stationary phase
Authors: McKee Mark , Sun Haiwei , Ye Yangbo
Published: December 2016

Letffbe a fixed self-contragradient Hecke–Maass form forSL(3,Z)SL(3,\mathbb Z), and letuube an even Hecke–Maass form forSL(2,Z)SL(2,\mathbb Z)with Laplace eigenvalue1/4+k21/4+k^2,k≥0k\geq 0. A subconvexity boundO((1+k)4/3+ε)O\big ((1+k)^{4/3+\varepsilon }\big )in the eigenvalue aspect is proved for the central value ats=1/2s=1/2of the Rankin–SelbergLL-functionL(s,f×u)L(s,f\times u). Meanwhile, a subconvexity boundO((1+|t|)2/3+ε)O\big ((1+|t|)^{2/3+\varepsilon }\big )in thettaspect is proved forL(1/2+it,f)L(1/2+it,f). These bounds improved corresponding subconvexity bounds proved by Xiaoqing Li (Annals of Mathematics, 2011). The main techniques in the proofs, other than those used by Li, arennth-order asymptotic expansions of exponential integrals in the cases of the explicit first derivative test, the weighted first derivative test, and the weighted stationary phase integral, for arbitraryn≥1n\geq 1. These asymptotic expansions sharpened the classical results forn=1n=1by Huxley.
Temporality
Authors: Martin Theodore
Published: December 2016

Time is not a strictly literary category, yet literature is unthinkable without time. The events of a story unfold over time. The narration of that story imposes a separate order of time (chronological, discontinuous, in medias res). The reading of that narrative may take its own sweet time. Then there is the fact that literature itself exists in time. Transmitted across generations, literary texts cannot help but remind us of how times have changed. In doing so, they also show us how prior historical moments were indelibly shaped by their own specific philosophies and technologies of timekeeping—from the forms of sacred time that informed medieval writing; to the clash between national time and natural history that preoccupied the Romantics; to the technological standardization of time that shaped 19th-century literature; to the theories of psychological time that emerged in tandem with modernism; to the fragmented and foreshortened digital times that underlie postmodern fiction. Time, in short, shapes literature several times over: from reading experience to narrative form to cultural context. In this way, literature can be read as a peculiarly sensitive timepiece of its own, both reflecting and responding to the complex and varied history of shared time.

Over the course of the 20th century, literary time has become an increasingly prominent issue for literary critics. Time was first installed at the heart of literary criticism by way of narrative theory and narratology, which sought to explain narrative’s irreducibly temporal structure. Soon, though, formalist and phenomenological approaches to time would give way to more historically and politically attuned methods, which have emphasized modern time’s enmeshment in imperialism, industrial capitalism, and globalization. In today’s critical landscape, time is a crucial and contested topic in a wide range of subfields, offering us indispensable insights into the history and ideology of modernity; the temporal politics of nationalism, colonialism, and racial oppression; the alternate timescales of environmental crisis and geological change; and the transformations of life and work that structure postmodern and postindustrial society.
Sequence Organization
Authors: Raymond Chase Wesley
Published: December 2016

The adjacency pair is the most basic and normatively accountable sequential structure in interaction. This structure can be expanded through pre-sequences, insert-sequences, and post-expansions, which can be seen to be relevantly oriented to by interactants themselves. Various forces drive this normative organization, including issues related to epistemics, intersubjectivity, progressivity, and affiliation. Larger structures—for example, sequences of sequences, overall structural organization, and storytelling—also exist in interaction but are nonetheless composed of smaller units of talk. While potentially open to a certain amount of cultural variation, sequence organization exists cross-linguistically and cross-culturally as a general structural feature of human social interaction.
Public Culture
Authors: Hariman Robert
Published: December 2016

The concept of public culture refers most broadly to the dynamic negotiation of beliefs, values, and attitudes regarding collective association through media and other social practices that are defined by norms of open access and voluntary response. The concept is a recent innovation and applies primarily to modern societies, where public culture is the envelope of communication practices within which public opinion is formed; those practices can include news, entertainment, the arts, advertising, social media, and many other means for representing and judging any individual, institution, or custom having collective significance. The term “public” emphasizes relatively unrestricted communication across civil society regarding governance and other matters affecting the general welfare. The term “culture” emphasizes that public opinion depends on contextual factors that emerge through multiple media and embodied responsiveness. These considerations provide a basis for analysis of distinctively modern relationships across civil society, media technologies, and political action in a global context.
Elite News Coverage of Climate Change
Authors: Boykoff Maxwell , Luedecke Gesa
Published: December 2016

During the past three decades, elite news media have become influential translators of climate change linking science, policy, and the citizenry. Historical trends in public discourse—shaped in significant part by elite media—demonstrate news media’s critical role in shaping public perception and the level of concern towards climate change. Media representations of climate change and global warming are embedded in social, cultural, political, and economic dimensions that influence individual-level processes such as everyday journalistic practices. Media have a strong influence on policy decision-making, attitudes, perspectives, intentions, and behavioral change, but those connections can be challenging to pinpoint; consequently, examinations of elite news coverage of climate change, particularly in recent decades, have sought to gain a stronger understanding of these complex and dynamic webs of interactions. In so doing, research has more effectively traced how media have taken on varied roles in the climate change debate, from watch dogs to lap dogs to guard dogs in the public sphere. Within these areas of research, psychological aspects of media influence have been relatively underemphasized. However, interdisciplinary and problem-focused research investigations of elite media coverage stand to advance considerations of public awareness, discourse, and engagement. Elite news media critically contribute to public discourse and policy priorities through their “mediating” and interpretative influences. Therefore, a review of examinations of these dynamics illuminate the bridging role of elite news coverage of climate change between formal science and policy, and everyday citizens in the public sphere.
Climate Change Communication in Austria
Authors: Rhomberg Markus
Published: December 2016

Research on climate change communication is a neglected field in Austria. Only slowly, scientists as well as policy makers are entering the domain of communicating climate change, especially in subprojects of larger funding initiatives by the Austrian Environment Ministry and the Ministry for Transport, Innovation and Technology. In the field of communication research, only sporadic studies can be found: Some of them are investigating science-policy-interfaces and communication among stakeholders; others are focusing on awareness of climate change, especially in climate sensitive areas like (winter) tourism, agriculture, and forestry, which are significant economic fields in Austria and in which major efforts have to be taken to enhance adaptive capacities. Only a few studies are dealing with media representations of climate. Therefore, this article outlines a future research program, based on the assessment of existing scholarship. More scientific efforts should be given to the following fields of research: public communication of stakeholders, studies on media representation of climate change and framing and its effects as well as comparative studies with countries sharing comparable climate scenarios, and the strong need for adapting to climate change (e.g., from Alpine regions) as well as similar political structures.
Climate Change Communication in Hong Kong and Taiwan
Authors: Shih Tsung-Jen
Published: December 2016

Taiwan and Hong Kong are similar in their determination to combat climate change. Not only have they set up objectives about carbon emission reduction, but they also have actively enacted laws and policies to achieve these goals. However, the public is not considered to play an important role in policymaking in either Taiwan or Hong Kong. On the other hand, these two regions differ in several aspects about how and why they are addressing this issue. First, Taiwan’s efforts to reduce carbon emission are voluntary, with the goal of gaining international recognition, whereas Hong Kong is obliged to engage in carbon reduction due to its subordinate status to the People’s Republic of China (PRC). Second, while Taiwan is trying to reduce its reliance on nuclear power as an energy source, Hong Kong sees it as a useful way to cut down carbon emissions. Third, Taiwan has established new, specialized governmental institutions to integrate resources, whereas efforts taken by Hong Kong mainly revolve around existing government agencies. In terms of public opinion about climate change, the Taiwanese are much more concerned about the issue and know more about it than their counterparts in Hong Kong. Finally, the media in Taiwan pay more attention to climate change than the media in Hong Kong. This article suggests potential directions for future research in this area.
Conflict Management of Territorial Disputes
Authors: Wiegand Krista E.
Published: December 2016

Despite the decline in interstate wars, there remain dozens of interstate disputes that could erupt into diplomatic crises and evolve into military escalation. By far the most difficult interstate dispute that exists are territorial disputes, followed by maritime and river boundary disputes. These disputes are not only costly for the states involved, but also potentially dangerous for states in the region and allies of disputant states who could become entrapped in armed conflicts. Fortunately, though many disputes remain unresolved and some disputes endure for decades or more than a century, many other disputes are peacefully resolved through conflict management tools.

Understanding the factors that influence conflict management—the means by which governments decide their foreign policy strategies relating to interstate disputes and civil conflicts—is critical to policy makers and scholars interested in the peaceful resolution of such disputes. Though conflict management of territorial and maritime disputes can include a spectrum of management tools, including use of force, most conflict management tools are peaceful, involving direct bilateral negotiations between the disputant states, non-binding third party mediation, or binding legal dispute resolution. Governments most often attempt the most direct dispute resolution method, which is bilateral negotiations, but often, such negotiations break down due to uncompromising positions of the disputing states, leading governments to turn to other resolution methods. There are pros and cons of each of the dispute resolution methods and certain factors will influence the decisions that governments make about the management of their territorial and maritime disputes. Overall, the peaceful resolution of territorial and maritime disputes is an important but complicated issue for states both directly involved and indirectly affected by the persistence of such disputes.
Visuality and Criminology
Authors: Schept Judah
Published: December 2016

There can be no doubt that criminology has taken something of a visual turn, as evidenced by increasing numbers of articles, conference panels, edited volumes, monographs, and seminar series that support visual research within criminology and related fields (Brown, 2014; Carrabine, 2012; Brown & Carrabine, 2016; Lippens et al., 2013). This development has come with important calls for both direct, empirical engagement with images, as well as new methodological approaches that mobilize images for a “politically charged analysis” (Hayward, 2010, p. 3). While visual criminology, as it has come to be known, has taken up the importance of the image, the issue of representation, and the photograph, it has been slower to engage on the terrain of visuality, a concept that can sometimes slip into shorthand for the realm of the visual, but which means something more closely resembling an authorized view of society and history (Mirzoeff, 2011a). Visuality is the production, representation, and naturalization of state power that at once fabricates order and, in doing so, organizes the available vocabularies for describing and challenging it. Visuality is a mechanism by which the quotidian violence underwriting authority is made illegible and unseeable. a process that relies on knowledge production for legitimacy and consent.

It is here, at the intersections of visuality’s naturalization of the everyday violence of law and its naturalization of an authorized constellation of ideas and terms from which to draw meaning about the world, that the role of criminology must be considered. As a science of crime and punishment, criminology is both subordinate to the terms and ideologies of the state and continually reproduces and reifies those terms by providing the gloss of scientific objectivity. Criminology is largely managerial and reformist, a discipline dependent on the state as much for grant monies and evaluation projects as for the very normative terms of study—crime, law, punishment—that underwrite its very existence and relevance.

Yet, the relationship between criminology and visuality is not one of wholehearted subservience and hegemony. Even as the discipline should be understood as an important intellectual prosthetic in the state’s fabrication of social order through technologies of illumination, capture, and mapping, visuality is never complete and criminology is not uniform. Indeed, criminology has an established if uneven lineage of radical interventions into the common sense of state violence. The question remains open as to the role criminology might play in enacting counter-visuality, an intellectual and political project aimed at inscribing in the social body the capacities to render such violence legible.
Deep homology in the age of next-generation sequencing
Authors: Tschopp Patrick , Tabin Clifford J.
Published: December 2016

The principle of homology is central to conceptualizing the comparative aspects of morphological evolution. The distinctions between homologous or non-homologous structures have become blurred, however, as modern evolutionary developmental biology (evo-devo) has shown that novel features often result from modification of pre-existing developmental modules, rather than arising completely de novo. With this realization in mind, the term ‘deep homology’ was coined, in recognition of the remarkably conserved gene expression during the development of certain animal structures that would not be considered homologous by previous strict definitions. At its core, it can help to formulate an understanding of deeper layers of ontogenetic conservation for anatomical features that lack any clear phylogenetic continuity. Here, we review deep homology and related concepts in the context of a gene expression-based homology discussion. We then focus on how these conceptual frameworks have profited from the recent rise of high-throughput next-generation sequencing. These techniques have greatly expanded the range of organisms amenable to such studies. Moreover, they helped to elevate the traditional gene-by-gene comparison to a transcriptome-wide level. We will end with an outlook on the next challenges in the field and how technological advances might provide exciting new strategies to tackle these questions.

This article is part of the themed issue ‘Evo-devo in the genomics era, and the origins of morphological diversity’.
New genes from old: asymmetric divergence of gene duplicates and the evolution of development
Authors: Holland Peter W. H. , Marlétaz Ferdinand , Maeso Ignacio , Dunwell Thomas L. , Paps Jordi
Published: December 2016

Gene duplications and gene losses have been frequent events in the evolution of animal genomes, with the balance between these two dynamic processes contributing to major differences in gene number between species. After gene duplication, it is common for both daughter genes to accumulate sequence change at approximately equal rates. In some cases, however, the accumulation of sequence change is highly uneven with one copy radically diverging from its paralogue. Such ‘asymmetric evolution’ seems commoner after tandem gene duplication than after whole-genome duplication, and can generate substantially novel genes. We describe examples of asymmetric evolution in duplicated homeobox genes of moths, molluscs and mammals, in each case generating new homeobox genes that were recruited to novel developmental roles. The prevalence of asymmetric divergence of gene duplicates has been underappreciated, in part, because the origin of highly divergent genes can be difficult to resolve using standard phylogenetic methods.

This article is part of the themed issue ‘Evo-devo in the genomics era, and the origins of morphological diversity’.
Cavefish and the basis for eye loss
Authors: Krishnan Jaya , Rohner Nicolas
Published: December 2016

Animals have colonized the entire world from rather moderate to the harshest environments, some of these so extreme that only few animals are able to survive. Cave environments present such a challenge and obligate cave animals have adapted to perpetual darkness by evolving a multitude of traits. The most common and most studied cave characteristics are the regression of eyes and the overall reduction in pigmentation. Studying these traits can provide important insights into how evolutionary forces drive convergent and regressive adaptation. The blind Mexican cavefish (Astyanax mexicanus) has emerged as a useful model to study cave evolution owing to the availability of genetic and genomic resources, and the amenability of embryonic development as the different populations remain fertile with each other. In this review, we give an overview of our current knowledge underlying the process of regressive and convergent evolution using eye degeneration in cavefish as an example.

This article is part of the themed issue ‘Evo-devo in the genomics era, and the origins of morphological diversity’.
Development and genetics in the evolution of land plant body plans
Authors: Jill Harrison C.
Published: December 2016

The colonization of land by plants shaped the terrestrial biosphere, the geosphere and global climates. The nature of morphological and molecular innovation driving land plant evolution has been an enigma for over 200 years. Recent phylogenetic and palaeobotanical advances jointly demonstrate that land plants evolved from freshwater algae and pinpoint key morphological innovations in plant evolution. In the haploid gametophyte phase of the plant life cycle, these include the innovation of mulitcellular forms with apical growth and multiple growth axes. In the diploid phase of the life cycle, multicellular axial sporophytes were an early innovation priming subsequent diversification of indeterminate branched forms with leaves and roots. Reverse and forward genetic approaches in newly emerging model systems are starting to identify the genetic basis of such innovations. The data place plant evo-devo research at the cusp of discovering the developmental and genetic changes driving the radiation of land plant body plans.

This article is part of the themed issue ‘Evo-devo in the genomics era, and the origins of morphological diversity’.
The E3 ubiquitin ligase UBR5 regulates centriolar satellite stability and primary cilia formation via ubiquitylation of CSPP-L
Authors: Shearer Robert F. , Frikstad Kari-Anne Myrum , McKenna Jessie , McCloy Rachael A. , Deng Niantao , Burgess Andrew , Stokke Trond , Patzke Sebastian , Saunders Darren N.
Published: December 2016

Primary cilia are crucial for signal transduction in a variety of pathways, including Hedgehog and Wnt. Disruption of primary cilia formation (ciliogenesis) is linked to numerous developmental disorders (known as ciliopathies) and diseases, including cancer. The Ubiquitin-Proteasome System (UPS) component UBR5 was previously identified as a putative modulator of ciliogenesis in a functional genomics screen. UBR5 is an E3 Ubiquitin ligase that is frequently deregulated in tumours, but its biological role in cancer is largely uncharacterised, partly due to a lack of understanding of interacting proteins and pathways. We validated the effect of UBR5 depletion on primary cilia formation using a robust model of ciliogenesis, and identified CSPP1, a centrosomal and ciliary protein required for cilia formation, as a UBR5-interacting protein. We show that UBR5 ubiquitylates CSPP1, and that UBR5 is required for cytoplasmic organization of CSPP1-comprising centriolar satellites in centrosomal periphery. Hence, we have established a key role for UBR5 in ciliogenesis that may have important implications in understanding cancer pathophysiology.
Inter-Subject Alignment of MEG Datasets in a Common Representational Space
Authors: Zhang Qiong , Borst Jelmer P. , Kass Robert E. , Anderson John R.
Published: December 2016

Pooling neural imaging data across subjects requires aligning recordings from different subjects. In magnetoencephalography (MEG) recordings, sensors across subjects are poorly correlated both because of differences in the exact location of the sensors, and structural and functional differences in the brains. It is possible to achieve alignment by assuming that the same regions of different brains correspond across subjects. However, this relies on both the assumption that brain anatomy and function are well correlated, and the strong assumptions that go into solving the underdetermined inverse problem given the high dimensional source space. In this paper, we investigated an alternative method that bypasses source-localization. Instead, it analyzes the sensor recordings themselves and aligns their temporal signatures across subjects. We used a multivariate approach, multi-set canonical correlation analysis (M-CCA), to transform individual subject data to a low dimensional common representational space. We evaluated the robustness of this approach over a synthetic dataset, by examining the effect of different factors that add to the noise and individual differences in the data. On a MEG dataset, we demonstrated that M-CCA performs better than a method that assumes perfect sensor correspondence and a method that applies source localization. Lastly, we described how the standard M-CCA algorithm could be further improved with a regularization term that incorporates spatial sensor information.
Rampant Reverse Evolution towards Specialization in Commensal Bacteria Colonizing the Gut
Authors: Sousa A. , Ramiro R. S. , Barroso-Batista J. , Güleresi D. , Lourenço M. , Gordo I.
Published: December 2016

The maintenance of diversity in the gut microbiota is a signature of host health. Yet how strain variation emerges and changes over time in this ecosystem is poorly understood. Here we use a natural yet controlled system to track the effects of natural selection by the genetic signatures it leaves in evolving populations. By following the emergence of intra-species diversity in anEscherichia colistrain, we unravel a recurrent case of violation of Dollo’s law, which proposes that evolution is unidirectional and irreversible. We demonstratede novoacquisition of a primordial lost phenotype via compensatory mutation and also genetic reversion, the latter leaving no trace of the past. We show that this reverse evolution generates two coexisting phenotypes, resource generalist and specialist, whose abundance can be controlled by diet supplementation. While specialists’ abundance is low, they avoid competition with the gut microbiota, whereas generalist abundance is dependent on microbiota composition. Our results highlight how a single genetic change can have large ecological consequences.
Closed-loop estimation of retinal network sensitivity reveals signature of efficient coding
Authors: Ferrari Ulisse , Gardella Christophe , Marre Olivier , Mora Thierry
Published: December 2016

According to the theory of efficient coding, sensory systems are adapted to represent natural scenes with high fidelity and at minimal metabolic cost. Testing this hypothesis for sensory structures performing non-linear computations on high dimensional stimuli is still an open challenge. Here we develop a method to characterize the sensitivity of the retinal network to perturbations of a stimulus. Using closed-loop experiments, we explore selectively the space of possible perturbations around a given stimulus. We then show that the response of the retinal population to these small perturbations can be described by a local linear model. Using this model, we computed the sensitivity of the neural response to arbitrary temporal perturbations of the stimulus, and found a peak in the sensitivity as a function of the frequency of the perturbations. Based on a minimal theory of sensory processing, we argue that this peak is set to maximize information transmission. Our approach is relevant to testing the efficient coding hypothesis locally in any context where no reliable encoding model is known.
Inferring hidden causal relations between pathway members using reduced Google matrix of directed biological networks
Authors: Lages José , Shepelyansky Dima L. , Zinovyev Andrei
Published: December 2016

Signaling pathways represent parts of the global biological network which connects them into a seamless whole through complex direct and indirect (hidden) crosstalk whose structure can change during development or in pathological conditions. We suggest a novel methodology, called Googlomics, for the structural analysis of directed biological networks using spectral analysis of their Google matrices, using parallels with quantum scattering theory, developed for nuclear and mesoscopic physics and quantum chaos. We introduce the reduced Google matrix method for the regulatory biological networks and demonstrate how its computation allows inferring hidden causal relations between the members of a signaling pathway or a functionally related group of genes. We investigate how the structure of hidden causal relations can be reprogrammed as the result of changes in the transcriptional network layer during cancerogenesis. The suggested Googlomics approach rigorously characterizes complex systemic changes in the wiring of large causal biological networks.
Unicycler: resolving bacterial genome assemblies from short and long sequencing reads
Authors: Wick Ryan R. , Judd Louise M. , Gorrie Claire L. , Holt Kathryn E.
Published: December 2016

1.

The Illumina DNA sequencing platform generates accurate but short reads, which can be used to produce accurate but fragmented genome assemblies. Pacific Biosciences and Oxford Nanopore Technologies DNA sequencing platforms generate long reads that can produce more complete genome assemblies, but the sequencing is more expensive and error prone. There is significant interest in combining data from these complementary sequencing technologies to generate more accurate “hybrid” assemblies. However, few tools exist that truly leverage the benefits of both types of data, namely the accuracy of short reads and the structural resolving power of long reads. Here we present Unicycler, a new tool for assembling bacterial genomes from a combination of short and long reads, which produces assemblies that are accurate, complete and cost-effective. Unicycler builds an initial assembly graph from short reads using thede novoassembler SPAdes and then simplifies the graph using information from short and long reads. Unicycler utilises a novel semi-global aligner, which is used to align long reads to the assembly graph. Tests on both synthetic and real reads show Unicycler can assemble larger contigs with fewer misassemblies than other hybrid assemblers, even when long read depth and accuracy are low. Unicycler is open source (GPLv3) and available atgithub.com/rrwick/Unicycler.
Structure of a fungal form of aspartate-semialdehyde dehydrogenase fromAspergillus fumigatus
Authors: Dahal Gopal P. , Viola Ronald E.
Published: December 2016

Aspartate-semialdehyde dehydrogenase (ASADH) functions at a critical junction in the aspartate biosynthetic pathway and represents a validated target for antimicrobial drug design. This enzyme catalyzes the NADPH-dependent reductive dephosphorylation of β-aspartyl phosphate to produce the key intermediate aspartate semialdehyde. The absence of this entire pathway in humans and other mammals will allow the selective targeting of pathogenic microorganisms for antimicrobial development. Here, the X-ray structure of a new form of ASADH from the pathogenic fungal speciesAspergillus fumigatushas been determined. The overall structure of this enzyme is similar to those of its bacterial orthologs, but there are some critical differences both in biological assembly and in secondary-structural features that can potentially be exploited for the development of species-selective drugs with selective toxicity against infectious fungal organisms.
Analysing animal social network dynamics: the potential of stochastic actor‐oriented models
Authors: Fisher David N. , Ilany Amiyaal , Silk Matthew J. , Tregenza Tom
Published: December 2016

Animals are embedded in dynamically changing networks of relationships with conspecifics. These dynamic networks are fundamental aspects of their environment, creating selection on behaviours and other traits. However, most social network‐based approaches in ecology are constrained to considering networks as static, despite several calls for such analyses to become more dynamic.

There are a number of statistical analyses developed in the social sciences that are increasingly being applied to animal networks, of which stochastic actor‐oriented models (SAOMs) are a principal example. SAOMs are a class of individual‐based models designed to model transitions in networks between discrete time points, as influenced by network structure and covariates. It is not clear, however, how useful such techniques are to ecologists, and whether they are suited to animal social networks.

We review the recent applications of SAOMs to animal networks, outlining findings and assessing the strengths and weaknesses of SAOMs when applied to animal rather than human networks. We go on to highlight the types of ecological and evolutionary processes that SAOMs can be used to study.

SAOMs can include effects and covariates for individuals, dyads and populations, which can be constant or variable. This allows for the examination of a wide range of questions of interest to ecologists. However, high‐resolution data are required, meaning SAOMs will not be useable in all study systems. It remains unclear how robust SAOMs are to missing data and uncertainty around social relationships.

Ultimately, we encourage the careful application of SAOMs in appropriate systems, with dynamic network analyses likely to prove highly informative. Researchers can then extend the basic method to tackle a range of existing questions in ecology and explore novel lines of questioning.
Novel thermostable antibiotic resistance enzymes from the Atlantis II Deep Red Sea brine pool
Authors: Elbehery Ali H. A. , Leak David J. , Siam Rania
Published: December 2016

The advent of metagenomics has greatly facilitated the discovery of enzymes with useful biochemical characteristics for industrial and biomedical applications, from environmental niches. In this study, we used sequence‐based metagenomics to identify two antibiotic resistance enzymes from the secluded, lower convective layer of Atlantis II Deep Red Sea brine pool (68°C, ~2200 m depth and 250‰ salinity). We assembled > 4 000 000 metagenomic reads, producing 43 555 contigs. Open reading frames (ORFs) called from these contigs were aligned to polypeptides from the Comprehensive Antibiotic Resistance Database using BLASTX. Two ORFs were selected for further analysis. The ORFs putatively coded for 3′‐aminoglycoside phosphotransferase [APH(3′)] and a class A beta‐lactamase (ABL). Both genes were cloned, expressed and characterized for activity and thermal stability. Both enzymes were active in vitro, while only APH(3′) was active in vivo. Interestingly, APH(3′) proved to be thermostable (Tm = 61.7°C and ~40% residual activity after 30 min of incubation at 65°C). On the other hand, ABL was not as thermostable, with a Tm = 43.3°C. In conclusion, we have discovered two novel AR enzymes with potential application as thermophilic selection markers.