bluuebunny/crossref_metadata_2025 huggingface dataset:
Costs and Cost-Effectiveness in Eating Disorders
Authors: Crow Scott
Published: February 2017

Costs and cost-effectiveness are now well recognized as important aspects of the burdens of and treatment for eating disorders. Ample evidence indicates that, leading up to and following diagnosis, the cost burdens associated with eating disorders are high; this is true whether viewed from the perspective of a healthcare payer or from a societal perspective. On the other hand, it is important to note that studies involving cost modeling and direct cost collection in treatment have shown that treatment of eating disorders is quite cost-effective. Cost is now increasingly examined as an outcome in eating disorder treatment trials. This remains an area of great need for further research.
Unintended Water Allocation
Authors: Hooper Virginia , Lankford Bruce
Published: February 2017

This chapter argues that two types of process affect the allocation of water between users. The first of these are a set of intentional strategies, which dominate the literature on water allocation. These include institutional allocating mechanisms and the purposeful appropriation of water. The second type of process is unintended and occurs through indirect action or inaction. Through this second type of process, people, sectors, and places nevertheless gain water share. Unintended allocation arises from within the ungoverned spaces and “wicked problems” of land and water transformations in two interrelated ways: (1) via external changes in non-water sectors and (2) via internal changes within the water management sector. This unintended or hidden type of water allocation process is largely overlooked. Yet, it is potentially important because volumes of water moved through unintentional allocation can be large, and it can undermine well-intentioned policy interventions in the water and land management sectors.
Learnability
Authors: Fodor Janet , Sakas William
Published: February 2017

The study of natural language learnability is necessarily multidisciplinary. Its aim is to devise and evaluate possible psychological mechanisms by which a system bounded by the cognitive capabilities and linguistic exposure of a young child might be able to arrive at rich knowledge of an adult human language. The abstract formal models that launched this discipline have over the years become increasingly responsive to theoretical linguistic discoveries about the properties of natural language grammars, many embracing parameter theory in particular as a systemization of the ways in which grammars may differ. The concept of grammar acquisition as the setting of parameters has inspired a number of recent learning models, whose details are compared and contrasted here. But it has not swept away all learnability problems, as it has become clear that the input cues needed to trigger the correct parameter settings are often ambiguous or opaque.
The Role of Universal Grammar in Nonnative Language Acquisition
Authors: Schwartz Bonnie , Sprouse Rex
Published: February 2017

Children, at least children acquiring their native language (L1), develop grammars vastly underdetermined by the primary linguistic data available to them, converging on both obvious and subtle properties of the target language (TL), rapidly, (essentially) uniformly, and reflexively (i.e., without effort or intentional instruction). In contrast, (adult) nonnative language (L2) acquisition, even under optimal conditions of TL exposure, displays more varied outcomes, frequently with readily observable divergence from the TL, often despite concerted effort and instruction. The standard assumption in mainstream generative grammar is that (L1) children display target convergence because early language acquisition is guided and constrained by the set of innate domain-specific cognitive structures generally referred to as Universal Grammar (UG). This chapter considers conceptual issues surrounding as well as empirical evidence for and against the claim that (despite initial appearances) some or all of the principles and primes of UG likewise guide and constrain (adult) L2 acquisition.
Principles and Parameters of Universal Grammar
Authors: Huang C.-T. James , Roberts Ian
Published: February 2017

The Principles-and-Parameters Theory marked an important milestone in formal linguistic theoryby offering a plausible solution to the logical problem of language acquisition, leading to a productive field of inquiry that uncovered important universal properties and macro-patterns of parametric variation among an unprecedented number of languages. Recent advances in parametric theory have capitalized on microparametric variation, raising certain questions about the status of macro-parameters. In this chapter, developing recent work and using the facts of Chinese as a paradigm case, we show that (a) both macro- and microparameters are needed in linguistic theory, (b) macroparameters are simply aggregates of microparameters acting in concert with a conservative learning strategy, and (c) the (micro)parameters themselves are hierarchically organized. Assuming a ‘three factors’ model, we take parameters to be emergent properties that result from the interaction of a radically unspecified UG, experience, and third-factor principles like Feature Economy and Input Generalization.
Linguistic Typology
Authors: Holmberg Anders
Published: February 2017

Linguistic typology is a research program that aims to describe and understand linguistic variation, distinguishing between properties which are shared across languages for historical reasons and properties shared for other reasons to do with ‘the nature of language.’ The preferred method is comparison of very large numbers of languages, sampled so as to control for genealogical and areal biases. The preferred mode of explanation is in terms of functional rather than formal notions. This chapter discusses the history of the research program, from Greenbergian universals to the present-day greater focus on probabilistic correlations between linguistic properties, with particular attention given to areal features. Some problems and shortcomings of this generally very successful research program are discussed, including problems of methodology and use of data, with special focus on its flagship WALS database. The relation between typology and generative linguistics and their relation to universal grammar is discussed.
Language Pathology
Authors: Tsimpli Ianthi , Kambanaros Maria , Grohmann Kleanthes
Published: February 2017

Universal Grammar (UG) denotes the species-specific faculty of language, presumed to be invariant across individuals. Over the years, it has shrunk from a full-blown set of principles and parameters to a much smaller set of properties, possibly as small as just containing the linguistic structure-building operation Merge, which in turn derives the uniquely human language property of recursion (Hauser et al., 2002). UG qua human faculty of language is further assumed to constitute the ‘optimal solution to minimal design specifications’ (Chomsky 2001:1), a perfect system for language. Unfortunately, the human system or physiology does not always run perfectly smooth in an optimal fashion. There are malfunctions, misformations, and other aberrations throughout. The language system is no exception. This chapter will present language pathology from the perspective of the underlying system: What can non-intact language tell us about UG?
Universal Grammar and Philosophy of Language
Authors: Ludlow Peter
Published: February 2017

Universal Grammar (UG) is a parametric system that establishes individual norms for language users. This is the sense in which UG is part of a competence theory instead of a performance theory. By establishing individual norms it does not control our linguistic behavior but acts as a kind of regulator that warns us when we diverge from an optimal set-point value. These warnings take the form of linguistic judgments. These linguistic judgments are surfacey—they don’t tell us what rules have been violated; they merely tell us when something is amiss, or which of two forms is more optimal. They are merely judgments of acceptability. While this approach leads us into the rule-following arguments of Wittgenstein and Kripke, those arguments can be defused if handled with care.
On the History of Universal Grammar
Authors: McGilvray James
Published: February 2017

As with other technical natural science terms, ‘Universal Grammar’ or ‘UG’ is defined not by ordinary usage, but within a science. While the methodological foundations (where to look, and how) of the natural science of language were laid in the 17th century, it is only with the advent of formal tools due to Church, Turing, and others in the 1930s and the efforts of Chomsky from the 1950s on that that science came to fruition. In this chapter, I outline the brief history of the technical term UG and assess the progress of the natural science of language. And as Chomsky does in his ‘Cartesian Linguistics,’ while acknowledging Descartes’s many errors, I sketch his lasting contributions to natural science method and to the nativist and internalist scientific study of the mind.
Phonology in Universal Grammar
Authors: Miller Brett , Myler Neil , Vaux Bert
Published: February 2017

This chapter draws a distinction between Universal Grammar (the initial state of the computational system that underwrites the human capacity for language) and the Language Acquisition Device (the complex of components of the mind/brain involved in constructing grammar+lexicon pairs upon exposure to primary linguistic data). It then considers whether there are any substantive phonological components of Universal Grammar strictu sensu. Two of the strongest empirical arguments for the existence of such phonological content in UG have been (i) apparent constraints on the space of variation induced from the typological record, and (ii) apparently universal dispreferences against certain phonological configurations (known as markedness). The chapter examines these arguments in the light of recent literature, concluding that the phenomena submit at least as well to historical, phonetic, or other non-UG explanations. We suggest that language acquisition experiments, involving natural and artificial languages, may be a more fruitful domain for future research into these questions.
Paul and Politics
Authors: Lopez Davina C. , Penner Todd
Published: February 2017

abstract: ‘Paul and Politics’ is a highly contested site of examination in contemporary Pauline Studies. Debates about whether, how, and to what ends Pauline literature can be read politically reach back to the beginnings of historical-critical engagement with New Testament texts in Germany, and have gained traction in the last several decades, particularly, in the United States at least, in the aftermath of the political and military engagements of the past decade and more. This essay maps several broad perspectives and approaches that New Testament scholars adopt in deliberating ‘Paul and Politics’, highlighting methodological questions and trends in the field, as well as some of the main points of contention.
The Pauline Letters in Contemporary Research
Authors: Das A. Andrew
Published: February 2017

Paul’s letters address the particular situations of first-century audiences. Mirror-reading, as exemplified in Galatians scholarship, is fraught with potential difficulties and must be executed cautiously. The Thessalonians received Paul’s apocalyptic message in a social situation of conflict and alienation. The First Letter to the Corinthians admonished unity in the gospel for a fragmented congregation. Interpreters of Paul’s Second Letter to the Corinthians grapple with whether this is a single letter or multiple letters and the proper ordering of the chapters. Reconstructions of the Roman situation often assume erroneously that Paul is writing to a mixed community of Jews and Gentiles after a mass expulsion and return of the Jewish communities. Philippians, a single letter, primarily addresses a conflict between two women. Philemon is not an attempted reconciliation of a runaway slave to his master but an explanation of the need for further assistance from a changed man.
Probability and Randomness
Authors: Eagle Antony
Published: February 2017

Early work on the frequency theory of probability made extensive use of the notion of randomness, conceived of as a property possessed by disorderly collections of outcomes. Growing out of this work, a rich mathematical literature on algorithmic randomness and Kolmogorov complexity developed through the twentieth century, but largely lost contact with the philosophical literature on physical probability. The present chapter begins with a clarification of the notions of randomness and probability, conceiving of the former as a property of a sequence of outcomes, and the latter as a property of the process generating those outcomes. A discussion follows of the nature and limits of the relationship between the two notions, with largely negative verdicts on the prospects for any reduction of one to the other, although the existence of an apparently random sequence of outcomes is good evidence for the involvement of a genuinely chancy process.
Human Understandings of Probability
Authors: Smithson Michael
Published: February 2017

In this chapter developments in theories and research on human understandings and judgements of probability are examined. The concept of probability as a degree of belief and the systematic study of human probability judgements have emerged only recently, but have stimulated numerous fruitful debates about the nature of rationality, belief formation, decision-making, and uncertainty itself. The chapter begins with a review of how the connection between probability and degrees of belief was developed and elaborated to form a prescriptive framework, followed by a brief summary of debates concerning rationality and uncertainty. It then surveys models of human probability judgements based on probability weighting functions, ways in which these judgements depend on how relevant information is presented, mental shortcuts (or “heuristics”) underpinning such judgements, the extent to which probability judgements are miscalibrated, fallacies in judgements of probabilities of compound and conditional events, and debates concerning the effective communication of probabilistic information.
Probability Elicitation
Authors: Hora Stephen
Published: February 2017

Probability Elicitation refers to the practice and methods of encoding the judgments of experts into probabilities or probability distributions. Such probabilistic judgments are often used to provide information that cannot be obtained directly from data, observation, or first principles. Best practices have been developed for probability elicitation by statisticians, psychologists, and decision analysts, among others, and have been found useful in the evaluation of risks and prediction of future events. These best principles include methods for qualifying experts and selecting the number of experts to employ, the organization of these experts, and techniques for encoding the judgments as probabilities. Studies have been conducted to evaluate the reliability of these elicited probabilities, to develop a set of desirable properties for these judgments and the measurement of these properties, and to compare various methods and protocols used to obtain the judgments.
The Bayesian Network Story
Authors: Neapolitan Richard , Jiang Xia
Published: February 2017

Bayesian networks are now among the leading architectures for reasoning with uncertainty in artificial intelligence. This chapter concerns their story, namely what they are, how and why they came into being, how we obtain them, and what they actually represent. First, it is shown that a standard application of Bayes’ Theorem constitutes inference in a two-node Bayesian network. Then more complex Bayesian networks are presented. Next the genesis of Bayesian networks and their relationship to causality is presented. A technique for learning Bayesian networks from data follows. Finally, a discussion of the philosophy of the probability distribution represented by a Bayesian network is provided.
The Origins of Probabilistic Epistemology
Authors: Galavotti Maria Carla
Published: February 2017

The notion of probability received great attention from 20th-century mathematicians and philosophers alike. This chapter focusses on a number of thinkers who not only devoted great efforts to the notion of probability and its foundations, but also developed a thoroughly probabilistic epistemological perspective. Special attention will be paid to Hans Reichenbach, Harold Jeffreys, and Bruno de Finetti. Although these authors embraced diverging interpretations of probability, namely frequentism in the case of Reichenbach, logicism in the case of Jeffreys, and subjectivism in the case of de Finetti, they shared the conviction that probability is an essential ingredient not just of science, but of human knowledge at large, and laid the foundations of a probabilistic approach to epistemology that is today mainstream.
Reception
Authors: Haubold Johannes
Published: February 2017

This chapter considers the reception, projection, and invention of Babylonian literature in the Roman Empire, taking into account the perspectives of classical authors as well as the experiences and aspirations of ancient readers. It first reviews the development of cuneiform literature in the Hellenistic period and how it influenced Greek and Roman ideas about the wisdom of the Chaldeans. It then discusses Babylonian fictions before turning to the ancient reception and definition of Babylonian literature, with particular emphasis on how maps of reading interacted with literary production in the Roman Empire. It also describes how the development of individual literatures in the empire was informed by shared notions about place, language, and literature and how, under different circumstances, the very idea of what constituted a literature (Syrian, Egyptian, Greek, etc.) could change over time.
The Politics of Speaking about the Body
Authors: Burt Ramsay
Published: February 2017

This chapter argues that some of the more radical developments in theatre dance initiated by Steve Paxton, Yvonne Rainer, Deborah Hay, and others in the 1960s and 1970s were supported by problematically dualistic ways of speaking and writing about “the body.” By valuing the rational “mind” over the supposedly irrational “body,” the normative hierarchy was inverted. The chapter discusses the way in which this concern with “the body” in minimalist performances by Yvonne Rainer became political in the context of protests against the Vietnam War. The new sensitivity to corporeality that emerged from minimalism then formed the basis for Hay’s Circle Dances and Paxton’s Magnesium. Drawing on Boltanski and Chiapello’s discussion of the political critique of the 1960s and 1970s counterculture, and Jean-Luc Nancy and Giorgio Agamben’s discussion of community, the chapter analyses the politics underlying the way that these dance practices involved talking and writing about “the body.”
Dancing in the Here and Now
Authors: Murphy Jacqueline Shea
Published: February 2017

This chapter discusses the work of two Native American dance makers, Emily Johnson/Catalyst and DANCING EARTH Indigenous Contemporary Dance Creations, directed by Rulan Tangen. It argues that these choreographers access, strengthen, and enact Indigenous intellectual discourse and knowledge as artistically and politically generative: one, by making contemporary dance that is not always foregrounded as “Indigenous”; and the other that insistently is. Each, in different but related ways, creates work that reflects contemporary conditions, challenges ongoing settler colonization and the federal legal requirements for “recognition” that seek to sustain it, and asserts the import of its own creative intelligence—on its own terms. This dance work, the chapter suggests, draws from specific genealogies of Indigenous peoples and practices to produce a vibrant, contemporary, Indigenous present and future. The piece addresses ways this is both simple, and a radical act.
Politics of Fake It!
Authors: Janza Janes
Published: February 2017

The interview of Janez Janša by Janez Janša elaborates on the economy of culture based on the performance Fake it! from 2007, which is described as a translation of seminal choreographies, in contrast to re-enactments or reconstructions. The re-enactment does not render an inherently ephemeral work present, but it underlines its absence. Thus a re-enactment performs the impossibility of being in another place/time; and that is its basic political impact. The choreographies chosen to be performed in Fake it! function as performatives in the Austian sense: by performing them, the economy of their absence and the cultural policy, which supports their absence, are performed. The choreographies in Fake it! are socialized; they became a public good and strengthen the embedding of dance in culture.
Of Corporeal Rewritings, Translations, and the Politics of Difference in Dancing
Authors: Chatterjea Ananya
Published: February 2017

This chapter begins with the premise that embodied practices and works move across different contexts, and proposes that such migrations provide crucial insight into registers of power. While dance and embodied practices generally invite in audiences and/or participants, these journeys almost always are about access, which resonates differently in different contexts. It analyzes choreographic strategies and the “micropolitics of technique” in specific works by Rennie Harris, Nora Chipaumire, Rosy Simas, and Rulan Tangen in order to explore the different ways in which choreographers reimagine classical “masterpieces” and meta-narratives of “otherness,” thus upsetting traditional relations of power. It also tracks the contrasting journeys in the broad spread of the movement forms of ballet and yoga, where difference comes to be snuffed out through acts of “translation,” consolidating existing hierarchies.
Dancing Disabled
Authors: Kuppers Petra
Published: February 2017

This chapter provides ways of linking phenomenology, feminist analysis, embodiment in dance, and corporeal representational politics. It engages Iris Marion Young’s argument about “Throwing Like a Girl,” addressing the pervasive structure at the heart of the meaning of femininity: the “disabling” object/subject bind that throws woman out of agency, and into the image. Using Young, Simone de Beauvoir, and Maurice Merleau Ponty as historical touchstones, the chapter shows how this agency/object bracket is at work in disability representation, and how examples of contemporary dance practice can fruitfully destabilize this scene. Dancers discussed include Gerda Koenig, a German dance artist and choreographer of DIN A 13, and Bill Shannon, a US dance artist.
Black Swan, White Nose
Authors: Schwadron Hannah
Published: February 2017

This chapter analyzes Darren Aronofsky’s Black Swan (2010) as a Jewish horror film with fake lesbian monsters. The Swan Lake remake offers a site of racial and sexual containment for Jewish actresses in ballet roles. Against damaging pressures of professional dance on the female psyche, the film recasts White and Black Swan roles as monstrous representations of the Ethnic Other, the Woman, and the Sexual Deviant. Analysis of select plot and performance components challenge fatal disfigurements of the film’s female characters: In what ways does Black Swan use ballet to appropriate social and political identities with tenuous relationships to the mainstream? How might these appropriations amount to an ultimate domestication of the very identities the film puts forward for thrilling appeal? This linkage of dance and politics intersects critical race theory, queer theory, and horror film theory as revealing dimensions of classical dance in narrative cinema.
Brown in Black and White
Authors: Moreno James
Published: February 2017

In 1956, the Mexican American modern dance choreographer José Limón presented The Emperor Jones, an all-male dance based on the 1920 Eugene O’Neill play. Limón’s Emperor loosely follows the plot of O’Neill’s play, which famously tells the story of an African American Pullman porter who makes himself emperor of a “West Indies” island. To portray O’Neill’s characters, Limón put himself and his all-male cast in black body paint. Limón’s painted body is examined as three bodies: a brown Mexican body; a white “American” body (with the privilege to represent the Other); and the black body of the Brutus Jones character. Focusing on Limón’s homosocial casting, performance techniques, and engagement with minstrelsy, this article shows how Limón’s freedom to dance as a brown, black, and white body did not reveal the decline of raced and gendered borders, but rather their resilient presence as part of the field on which his dances were produced.
Is It OK to Dance on Graves?
Authors: Giersdorf Jens
Published: February 2017

Catalyzed by Boris Charmatz’s restaging of his 2012–2013 choreography 20 Dancers for the XX Century in June 2014 at the Soviet War Memorial in Berlin, this chapter investigates the complex relationship between modernism and socialist realism in choreography. Concepts like socialism, capitalism, and modernity are not static entities. As discursive models, they rely on other historically determined discourses that accompany them. Modernity and its related concept of modernism require a counterpart against which to be defined. For decades, socialism and socialist realist artistic productions that emphasized political engagement with the social served as antagonists to capitalist modernity and modernism’s autonomous formalism. This text highlights the enduring politics of influential artistic periodizations and their choreographic restagings.
Social Class Oppression as Social Exclusion: A Relational Perspective
Authors: Walker Amelia Dean , Smith Laura
Published: February 2017

The ways we think about systemic inequalities can open up new forms of resistance and reform. This chapter explores and extends understandings of social class oppression with an aim to re-imagine psychologists’ role in contesting economic inequalities. It argues that social class injustice is produced through and constituted by forms of social exclusion. In emphasizing the ways that poor people are excluded from everyday sources of power, security, and democratic rights, the chapter highlights the relational dimension of social class, demonstrating that class is something that happens in human relationships. From a relational view, class is embodied through the everyday processes in which we all participate, and patterns of systemic injustice are enacted among individuals occupying different social class locations. A relational approach opens up new possibilities for counteracting the social exclusion of poor people, both for psychologists and for citizens committed to social change.
Systematic Development ofPhytophthoraSpecies-Specific Mitochondrial Diagnostic Markers for Economically Important Members of the Genus
Authors: Miles Timothy D. , Martin Frank N. , Robideau Gregg P. , Bilodeau Guillaume J. , Coffey Michael D.
Published: February 2017

The genus Phytophthora contains many invasive species to the U.S.A. that have the potential to cause significant damage to agriculture and native ecosystems. A genus and species-specific diagnostic assay was previously reported based on mitochondrial gene order differences that allowed for the systematic development of 14 species-specific TaqMan probes for pathogen detection ( Bilodeau et al. 2014 ). In this study, an additional 32 species-specific TaqMan probes for detection of primarily invasive species have been validated against 145 Phytophthora taxa as well as a range of Pythium and plant DNA samples. All validated probes were found to be species-specific and could be multiplexed with a genus-specific probe. The lower limit of linear detection using purified genomic DNA ranged from 1 to 100 fg in all assays. In addition, 124 unique TaqMan probes for Phytophthora spp. developed in silico are presented, which, if testing confirms they are species-specific, will provide diagnostic capabilities for approximately 89% of the genus. To enhance sensitivity of detection for several species that contained a single nucleotide polymorphism (SNP) in the reverse primer, a second primer was developed that is added in a small amount to the master mix. Furthermore, a PCR-RFLP system was developed that could be used to identify individual species when multiple species are present in a sample, without requiring cloning or sequencing. Several experiments were also conducted to compare various qPCR thermal cyclers and independent validation experiments with another research laboratory to identify possible limitations when the assays are used on a range of equipment in different labs. This system represents a comprehensive, hierarchal approach to increase the detection capability and provide tools to help prevent the introduction of invasive Phytophthora species.
Preventative Disease Management and Grower Decision Making: A Case Study of California Wine-Grape Growers
Authors: Hillis Vicken , Lubell Mark , Kaplan Jonathan , Baumgartner Kendra
Published: February 2017

Preventative disease management is challenging to farmers because it requires paying immediate costs in the hopes of returning uncertain future benefits. Understanding farmer decision making about prevention has the potential to reduce disease incidence and minimize the need for more costly postinfection practices. For example, the grapevine trunk-disease complex (esca, Botryosphaeria dieback, Eutypa dieback, and Phomopsis dieback) significantly affects vineyard productivity and longevity. Given the chronic nature of the infections and inability to eradicate the fungal pathogens, the preventative practices of delayed pruning, applications of pruning-wound protectants, and double pruning (also known as prepruning) are the most effective means of management. We surveyed wine-grape growers in six regions of California on their use of these three practices. In spite of acknowledging the yield impacts of trunk diseases, a substantial number of respondents either choose not to use preventative practices or incorrectly adopted them in mature vineyards, too late in the disease cycle to be effective. Growers with more negative perceptions of cost efficacy were less likely to adopt preventative practices or were more likely to time adoption incorrectly in mature vineyards. In general, preventative management may require strong intervention in the form of policy or extension to motivate behavioral change.
Avirulence (AVR) Gene-Based Diagnosis Complements Existing Pathogen Surveillance Tools for Effective Deployment of Resistance (R) Genes Against Rice Blast Disease
Authors: Selisana S. M. , Yanoria M. J. , Quime B. , Chaipanya C. , Lu G. , Opulencia R. , Wang G.-L. , Mitchell T. , Correll J. , Talbot N. J. , Leung H. , Zhou B.
Published: February 2017

Avirulence (AVR) genes in Magnaporthe oryzae, the fungal pathogen that causes the devastating rice blast disease, have been documented to be major targets subject to mutations to avoid recognition by resistance (R) genes. In this study, an AVR-gene-based diagnosis tool for determining the virulence spectrum of a rice blast pathogen population was developed and validated. A set of 77 single-spore field isolates was subjected to pathotype analysis using differential lines, each containing a single R gene, and classified into 20 virulent pathotypes, except for 4 isolates that lost pathogenicity. In all, 10 differential lines showed low frequency (<24%) of resistance whereas 8 lines showed a high frequency (>95%), inferring the effectiveness of R genes present in the respective differential lines. In addition, the haplotypes of seven AVR genes were determined by polymerase chain reaction amplification and sequencing, if applicable. The calculated frequency of different AVR genes displayed significant variations in the population. AVRPiz-t and AVR-Pii were detected in 100 and 84.9% of the isolates, respectively. Five AVR genes such as AVR-Pik-D (20.5%) and AVR-Pik-E (1.4%), AVRPiz-t (2.7%), AVR-Pita (0%), AVR-Pia (0%), and AVR1-CO39 (0%) displayed low or even zero frequency. The frequency of AVR genes correlated almost perfectly with the resistance frequency of the cognate R genes in differential lines, except for International Rice Research Institute-bred blast-resistant lines IRBLzt-T, IRBLta-K1, and IRBLkp-K60. Both genetic analysis and molecular marker validation revealed an additional R gene, most likely Pi19 or its allele, in these three differential lines. This can explain the spuriously higher resistance frequency of each target R gene based on conventional pathotyping. This study demonstrates that AVR-gene-based diagnosis provides a precise, R-gene-specific, and differential line-free assessment method that can be used for determining the virulence spectrum of a rice blast pathogen population and for predicting the effectiveness of target R genes in rice varieties.
A self-sustaining process model of inertial layer dynamics in high Reynolds number turbulent wall flows
Authors: Chini G. P. , Montemuro B. , White C. M. , Klewicki J.
Published: February 2017

Field observations and laboratory experiments suggest that at high Reynolds numbers
Re
the outer region of turbulent boundary layers self-organizes into quasi-uniform momentum zones (UMZs) separated by internal shear layers termed ‘vortical fissures’ (VFs). Motivated by this emergent structure, a conceptual model is proposed with dynamical components that collectively have the potential to generate a self-sustaining interaction between a single VF and adjacent UMZs. A large-
Re
asymptotic analysis of the governing incompressible Navier–Stokes equation is performed to derive reduced equation sets for the streamwise-averaged and streamwise-fluctuating flow within the VF and UMZs. The simplified equations reveal the dominant physics within—and isolate possible coupling mechanisms among—these different regions of the flow.

This article is part of the themed issue ‘Toward the development of high-fidelity models of wall turbulence at large Reynolds number’.
Prospectus: towards the development of high-fidelity models of wall turbulence at large Reynolds number
Authors: Klewicki J. C. , Chini G. P. , Gibson J. F.
Published: February 2017

Recent and on-going advances in mathematical methods and analysis techniques, coupled with the experimental and computational capacity to capture detailed flow structure at increasingly large Reynolds numbers, afford an unprecedented opportunity to develop realistic models of high Reynolds number turbulent wall-flow dynamics. A distinctive attribute of this new generation of models is their grounding in the Navier–Stokes equations. By adhering to this challenging constraint, high-fidelity models ultimately can be developed that not only predict flow properties at high Reynolds numbers, but that possess a mathematical structure that faithfully captures the underlying flow physics. These first-principles models are needed, for example, to reliably manipulate flow behaviours at extreme Reynolds numbers. This theme issue of
Philosophical Transactions of the Royal Society A
provides a selection of contributions from the community of researchers who are working towards the development of such models. Broadly speaking, the research topics represented herein report on dynamical structure, mechanisms and transport; scale interactions and self-similarity; model reductions that restrict nonlinear interactions; and modern asymptotic theories. In this prospectus, the challenges associated with modelling turbulent wall-flows at large Reynolds numbers are briefly outlined, and the connections between the contributing papers are highlighted.

This article is part of the themed issue ‘Toward the development of high-fidelity models of wall turbulence at large Reynolds number’.
Reynolds stress scaling in pipe flow turbulence—first results from CICLoPE
Authors: Örlü R. , Fiorini T. , Segalini A. , Bellani G. , Talamelli A. , Alfredsson P. H.
Published: February 2017

This paper reports the first turbulence measurements performed in the Long Pipe Facility at the Center for International Cooperation in Long Pipe Experiments (CICLoPE). In particular, the Reynolds stress components obtained from a number of straight and boundary-layer-type single-wire and X-wire probes up to a friction Reynolds number of 3.8×10
4
are reported. In agreement with turbulent boundary-layer experiments as well as with results from the Superpipe, the present measurements show a clear logarithmic region in the streamwise variance profile, with a Townsend–Perry constant of
A
2
≈1.26. The wall-normal variance profile exhibits a Reynolds-number-independent plateau, while the spanwise component was found to obey a logarithmic scaling over a much wider wall-normal distance than the other two components, with a slope that is nearly half of that of the Townsend–Perry constant, i.e.
A

2,
w

≈
A
2
/2. The present results therefore provide strong support for the scaling of the Reynolds stress tensor based on the attached-eddy hypothesis. Intriguingly, the wall-normal and spanwise components exhibit higher amplitudes than in previous studies, and therefore call for follow-up studies in CICLoPE, as well as other large-scale facilities.

This article is part of the themed issue ‘Toward the development of high-fidelity models of wall turbulence at large Reynolds number’.
WheatNet: A genome-scale functional network for hexaploid bread wheat,Triticum aestivum
Authors: Lee Tak , Hwang Sohyun , Yeong Kim Chan , Shim Hongseok , Kim Hyojin , Ronald Pamela C. , Marcotte Edward M. , Lee Insuk
Published: February 2017

Gene networks provide a system-level overview of genetic organizations and enable the dissection of functional modules underlying complex traits. Here we report the generation of WheatNet, the first genome-scale functional network for T. aestivum and a companion web server (www.inetbio.org/wheatnet). WheatNet was constructed by integrating 20 distinct genomics datasets, including 156,000 wheat-specific co-expression links mined from 1,929 microarray data. A unique feature of WheatNet is that each network node represents either a single gene or a group of genes. We computationally partitioned gene groups mimicking homeologous genes by clustering 99,386 wheat genes, resulting in 20,248 gene groups comprising 63,401 genes and 35,985 individual genes. Thus, WheatNet was constructed using 56,233 nodes, and the final integrated network has 20,230 nodes and 567,000 edges. The edge information of the integrated WheatNet and all 20 component networks are available for download.
The GridCAT: A toolbox for automated analysis of human grid cell codes in fMRI
Authors: Stangl Matthias , Shine Jonathan , Wolbers Thomas
Published: February 2017

Human fMRI studies examining the putative firing of grid cells (i.e., the grid code) suggest that this cellular mechanism supports not only spatial navigation, but also more abstract cognitive processes. This research area, however, remains relatively unexplored, perhaps us to the complexities of data analysis. To overcome this, we have developed the Matlab-based Grid Code Analysis Toolbox (GridCAT), providing a graphical user interface, and open-source code, for the analysis of fMRI data. The GridCAT performs all analyses, from estimation and fitting of the grid code in the general linear model, to the generation of grid code metrics and plots. Moreover, it is flexible in allowing the specification of bespoke analysis pipelines; example data are provided to demonstrate the GridCAT’s main functionality. We believe the GridCAT is essential to opening this research area to the imaging community, and helping to elucidate the role of human grid codes in higher-order cognitive processes.

Highlights

The putative firing of grid cells (i.e., the grid code) can be examined using fMRI

Necessary steps for grid code analysis are reviewed

The Matlab-based grid code analysis toolbox (GridCAT) is introduced

Automated grid code analysis can be conducted either via a graphical user interface or open-source code

A detailed manual and an example dataset are provided
Advanced Protection Against Marine Biofouling Using Solar Light
Authors: Scandura Gabriele , Ciriminna Rosaria , Ozer Lütfiye Yıldız , Meneguzzo Francesco , Palmisano Giovanni , Pagliaro Mario
Published: February 2017

We undertook prolonged testing of a new xerogel coating (AquaSun) to protect from marine biofouling a surface probe immersed in the seawater of Abu Dhabi. Electron microscopy, Raman mapping, and photoluminescence experiments coupled to extensive analyses of marine water before and after 122 days of testing showed excellent action against biofouling when irradiating the probe with visible light. Considering the high chemical and mechanical stability and the low cost of the sol-gel coating, the technology has significant potentialen routeto replacing conventional antifouling and foul release coatings with a single product of broad applicability.
Reward and punishment enhance motor adaptation in stroke
Authors: Quattrocchi Graziella , Greenwood Richard , Rothwell John C , Galea Joseph M , Bestmann Sven
Published: February 2017

The effects of motor learning, such as motor adaptation, in stroke rehabilitation are often transient, thus mandating approaches that enhance the amount of learning and retention. Previously, we showed in young individuals that reward-and punishment-feedback have dissociable effects on motor adaptation, with punishment improving adaptation and reward enhancing retention. If these findings were able to generalise to stroke patients, they would provide a way to optimize motor learning in these patients. Therefore, we tested this in 45 chronic stroke patients allocated in three groups. Patients performed reaching movements with their paretic arm with a robotic manipulandum. After training (day 1), day 2 involved adapting to a novel force-field. During this adaptation phase, patients received performance-based feedback according to the group they were allocated: reward, punishment or no feedback (neutral). On day 3, patients readapted to the force-field but all groups now received neutral feedback. All patients adapted, with reward and punishment groups displaying greater adaptation and readaptation than the neutral group, irrespective of demographic, cognitive or functional differences. Remarkably, the reward and punishment groups adapted to similar degree as healthy controls. Finally, the reward group showed greater retention. This study provides, for the first time, evidence that reward and punishment can enhance motor adaptation in stroke patients. Further research on reinforcement-based motor learning regimes is warranted to translate these promising results into clinical practice and improve motor rehabilitation outcomes in stroke patients.
Ubiquitylation activates a peptidase that promotes cleavage and destabilization of its activating E3 ligases and diverse growth regulatory proteins to limit cell proliferation in Arabidopsis
Authors: Dong Hui , Dumenil Jack , Lu Fu-Hao , Na Li , Vanhaeren Hannes , Naumann Christin , Klecker Maria , Prior Rachel , Smith Caroline , McKenzie Neil , Saalbach Gerhard , Chen Liangliang , Xia Tian , Gonzalez Nathalie , Seguela Mathilde , Inzé Dirk , Dissmeyer Nico , Li Yunhai , Bevan Michael W.
Published: February 2017

The characteristic shapes and sizes of organs are established by cell proliferation patterns and final cell sizes, but the underlying molecular mechanisms coordinating these are poorly understood. Here we characterize a ubiquitin-activated peptidase called DA1 that limits the duration of cell proliferation during organ growth in Arabidopsis thaliana. The peptidase is activated by two RING E3 ligases, Big Brother (BB) and DA2, which are subsequently cleaved by the activated peptidase and destabilized. In the case of BB, cleavage leads to destabilization by the RING E3 ligase PROTEOLYSIS 1 (PRT1) of the N-end rule pathway. DA1 peptidase activity also cleaves the deubiquitylase UBP15, which promotes cell proliferation, and the transcription factors TEOSINTE BRANCED 1/CYCLOIDEA/PCF 15 (TCP15) and TCP22, which promote cell proliferation and repress endoreduplication. We propose that DA1 peptidase activity regulates the duration of cell proliferation and the transition to endoreduplication and differentiation during organ formation in plants by coordinating the destabilization of regulatory proteins.
Structural study of the novel deuterated calix[4]pyrrole complex d
12-meso-tetrakis(4-methoxyphenyl)-meso-tetramethylcalix[4]pyrrole–pyridine N-oxide–acetonitrile (1/1/1)
Authors: He Ying-Chun , Pan Ji-Gang , Liu Dian-Sheng
Published: February 2017

Calix[4]pyrroles act as powerful receptors for electron-rich neutral guests and anionic guests in organic solvents. For the electron-rich neutral guest pyridine N-oxide, calix[4]pyrrole, with a deep cavity, provides an appropriate environment. The ability of calix[4]pyrrole to host binding guest molecules is the result of hydrogen bonding, π–π, C—H...π and hydrophobic interactions of the cavity. The novel title complex, C52H40D12N4O4·C5H5NO·C2H3N, based on d
12-meso-tetrakis(4-methoxyphenyl)-meso-tetramethylcalix[4]pyrrole, has been assembled using an excess of pyridine N-oxide and is the first deuterated complex of calix[4]pyrrole. A single-crystal X-ray study shows that the receptor adopts a cone conformation with the N-oxide fragment encapsulated deep within the cavity. 1H NMR spectroscopy was used to probe the molecular binding formation in CD3CN. The results are consistent with the single-crystal X-ray study in identifying that the pyridine N-oxide molecule occupies the cavity of the calix[4]pyrrole molecule. UV–vis spectroscopy revealed that the calix[4]pyrrole receptor molecules are able to form 1:1 inclusion complexes in CH3CN.
Syntheses and structures of two new coordination polymers generated from a 4-aminotriazole-bridged organic ligand and CoII salts
Authors: Wang Xue-Ru , Ma Jian-Ping , Dong Yu-Bin
Published: February 2017

Organic ligands and counter-anions influence the coordination spheres of metal cations and hence the construction of coordination polymers (CPs). The specific bent geometries of five-membered heterocyclic triazole bridging organic ligands are capable of generating CPs with novel patterns not easily obtained using rigid linear ligands. A multidentate 4-aminotriazole-bridged organic ligand, namely 4-amino-3,5-bis(4,3′-bipyridyl-5′-yl)-4H-1,2,4-triazole (L) has been prepared and used to synthesize two CoII coordination polymers, namely poly[[[μ2-4-amino-3,5-bis(4,3′-bipyridyl-5′-yl)-4H-1,2,4-triazole-κ2
N:N′]bis(methanol-κO)cobalt(II)] bis(perchlorate)], {[Co(C22H16N8)2(CH3OH)2](ClO4)2}
n
, (I), and poly[[μ3-4-amino-3,5-bis(4,3′-bipyridyl-5′-yl)-4H-1,2,4-triazole-κ3
N:N′:N′′]dichloridocobalt(II)], [CoCl2(C22H16N8)]
n
, (II), using CoX
2 salts [X = ClO4 for (I) and Cl for (II)] under solvothermal conditions. Single-crystal X-ray structure analysis revealed that they both feature two-dimensional networks. Cobalt is located on an inversion centre in (I) and in a general position in (II). In (I), L functions as a bidentate cis-conformation ligand linking CoII ions, while it functions as a tridentate trans-conformation linker binding CoII ions in (II). In addition, O—H...N and N—H...O hydrogen bonds and C—H...π interactions exist in (I), while N—H...Cl and π–π interactions exist in (II), and these weak interactions play an important role in aligning the two-dimensional nets of (I) and (II) in the solid state. As the compounds were synthesized under the same conditions, the significant structural variations between (I) and (II) are believed to be determined by the different sizes and coordination abilities of the counter-anions. IR spectroscopy and diffuse reflectance UV–Vis spectra were also used to investigate the title compounds.