bluuebunny/crossref_metadata_2025 huggingface dataset:
Imaging the Networks of Language
Authors: Papanicolaou Andrew C. , Kilintari Marina
Published: February 2017

Among the “higher” functions, language and its cerebral networks is the most intensively explored through behavioral or clinical studies and, more recently, through functional neuroimaging. From the former studies, several models (only partially congruent) have emerged during the past three centuries regarding the organization and topography of the brain mechanisms of the acoustic, phonological, semantic, syntactic, and pragmatic operations in which psycholinguists have divided the language function. The main task of this chapter is to extract from the vast functional neuroimaging literature of language reliable evidence that would be used to disconfirm the various hypotheses comprising the current language models. Most of these hypotheses concern the anatomical structures that could be considered nodes or hubs of the neuronal networks mediating the above-mentioned linguistic operations. Using the same criteria, the authors present neuroimaging evidence relevant to the issue of the neuronal mediation of sign languages, reading, and dyslexia.
Imaging the Networks of Encoding, Consolidation, and Retrieval
Authors: Papanicolaou Andrew C. , Shay Nicole , Holder Christen M.
Published: February 2017

In this chapter, the authors examine the contributions of the functional neuroimaging literature to the specification of the neuronal networks of the mnemonic operations of encoding, consolidation, and retrieval. Although the most basic expectation regarding the involvement of parts of the medial temporal lobes, such as the hippocampus, in these operations was not consistently supported by the results of the neuroimaging studies reviewed, other expectations, such as the material-specific lateralization of activation were adequately supported. The several reasons that account for the limited contributions of neuroimaging to the neurophysiology of memory thus far, ranging from constraints imposed by the nature of the mnemonic operations (e.g., the fact that encoding and retrieval occur in tandem) to practical ones (e.g., difficulties in studying spontaneous retrieval), are outlined.
Planning for Death’s Surprise
Authors: Phelan Peggy
Published: February 2017

The temporal conjunctions of the deaths of Pina Bausch and Merce Cunningham provide an opportunity to think carefully about the afterlife of choreography. While Cunningham died with a formal legacy plan in place and Bausch did not, issues of obligation to art and to living dancers also have bearing on dance legacy. The chapter considers transformations in the proliferation and ease of documentary records, the pressure to make room for the new, gender and sexuality, and postwar consciousness as important factors in the legacy issues of Bausch and Cunningham. Moving between specific details about each choreographer’s death and more abstract structures of death, the surprise of death’s uneven temporal arrival in the living significantly informs the afterlife of Cunningham and Bausch.
Racing in Place
Authors: Gottschild Brenda Dixon
Published: February 2017

This auto-critique examines the intersection of and nexus between dance studies and race/identity studies as viewed through the author’s life in dance and based on her fifty-year career that includes actualizations as professional dancer, professor, scholar-researcher, author, mentor, presenter, and consultant. It is a reflexive turn on the politics of writing, teaching, and speaking race, with dance as the lens. In order to revisit/reassess the backlash that resulted from scrutinizing an iconic “white” dance figure through an Africanist lens, the author dissects an essay that she wrote in 2004 which, in itself, was a deconstruction of the original controversy (dating back to the “culture wars” of the 1990s). Uncovering layer upon layer, the author presents additional complexities by bringing to bear her responses to ongoing issues of systemic and cultural racism as encountered in the dance field and discussed in her recent work.
Dance and Eastern Europe
Authors: Kunst Bojana
Published: February 2017

The chapter focuses on the relation between dance and politics in Eastern European contemporary dance, especially after 1990. Transition, which was the key political and economic term after the fall of the Berlin Wall, also deeply influences the (self-)understanding of Eastern European dance as a delayed practice. The chapter stresses that a decisive difference between these different geopolitical contexts is not an aesthetic one, but is the difference in the ways that performance works are contextualized, institutionalized, and professionalized. Several contemporary dance artists from Eastern Europe have politicized their practices through disclosing the complexity of the position of being in-between. In this sense they do not only critically address the hegemonic aspect of Western contemporary dance (as having a privilege of present), but also critically reaffirm their own history and practice.
Domesticating Dance
Authors: Srinivasan Priya
Published: February 2017

This chapter examines three scenes of “movement”—from the 2004 Tamil film Chandramukhi, the controversial documentary India’s Daughter that aired on BBC in March 2015, and the Star Plus Television serial of the Mahabharata focusing on the “Draupadi Vastra Haran” in 2014—to question how women’s bodies continue to be domesticated to delegitimize the upwardly mobile woman’s desire for remaking herself. The chapter suggests that neoliberalism has specific choreographies of violence perpetrated against women’s bodies. In particular, the author argues that within the choreographies of neoliberalism, neither public nor private space is safe for women in India. The chapter suggests that where women’s erotic dancing has been domesticated by institutionalized patriarchy in the service of capitalist systems, haunting and possession emerge as movement possibilities of the corporeal/incorporeal body that can negotiate the public/private space of a permeating neoliberal order.
Dance and/as Competition in the Privately Owned US Studio
Authors: Foster Susan Leigh
Published: February 2017

This chapter examines the role of dance competitions in contemporary private dance studio training, arguing that the focus on judging and winning has substantially altered the ways that dance is experienced by both performers and viewers. Comparing contemporary studio practices with those from the early twentieth century, the author considers how the business of teaching dance has opened up new demands for teacher training and for dances that can be taught and performed, and hence new markets for the circulation and distribution of dances. The chapter situates the contemporary focus on competition within the neoliberal globalized economy and speculates about how dancers as workers are commodifying feeling itself.
The Politics of Perception
Authors: Albright Ann Cooper
Published: February 2017

Perception is the place where vision and sensation merge to produce embodied meaning, the crossroads where individuals meet or miss one another—either connecting in good faith with a shared experience, or stumbling through missteps that can result in a defensive posture or a sense of distrust of others. It is through individuals’ bodies that perception meets up with politics. This chapter was precipitated by the author’s reflections on the actions, demonstrations, and events instigated by the shootings of Michael Brown in Ferguson, and of Tamir Rice in Cleveland, especially with respect to how those events rippled through a politically active Midwestern campus. The chapter argues that dance practices focused on perception can be mobilized to train for a politically responsive body, one that is both capable of strategic resistance and resilient enough to survive the exhaustion of public advocacy and action.
Switch
Authors: DeFrantz Thomas F.
Published: February 2017

Moving from the political margins toward a black mainstream, many African American social dances often emerge in queer communities of color. This chapter explores politically embodied consequences and affects of queer social dances that enjoy concentrated attention outside their originary communities. J-setting, voguing, and hand-dancing—a form of queer dance popular in the 1970s–1980s—offer sites to consider the materialization of queer black aesthetic gesture, in dances that redefine gender identities and confirm fluid political economies of social dance and motion. These queer dances simultaneously resist and reinscribe gender conformity in their aesthetic devices; they also suggest alternative histories of black social dance economies in which queer creativity might be valued as its own end. Ultimately, the chapter suggests a haunting presence of queers-of-color aesthetic imperatives within political mobilizations of black social dance, continually—and ironically—conceived as part and parcel of rhetorics of liberation and freedom of movement.
Identity Politics and Political Will
Authors: George-Graves Nadine
Published: February 2017

The career of acclaimed tap dancer Jeni LeGon is remarkable not only for her style but also for the ways in which she navigated the racial politics of the 1930s Hollywood film industry. This chapter examines how identity politics affected LeGon’s movements on and off both stage and screen. Hollywood lacked the political will to commit to LeGon, but she countered with a black will to maintain control and subjectivity. As a light-complexioned African American woman cast in a variety of ethnic roles she demonstrates the fungibility of black and brown bodies. When she presented as both cutesy and powerhouse, and when she performed male lines of business in pants, she troubled conceptions of gender. That the same body read subservient in white films and leading lady in black films tells us about not only the practices of an industry but also the audience’s phenomenological experiences of race.
Toward a Choreo-Political Theory of Articulation
Authors: Franko Mark
Published: February 2017

This chapter discusses the political interpretation of dance from the perspective of the critical and theoretical category of articulation in the political theory of Lefort, Althusser, Laclau, and Mouffe. It proposes the tropes of sovereignty, the individual, and the impersonal to work through the significance of articulation to a theory of the political in dance. As such it is an extension of Franko’s earlier arguments on the co-embededness of the politics and aesthetics of dance toward a theory of the conjunctural. This is not to render political content contingent and hence removed from form but it is to affirm temporalities at work in the way form is perceived to carry political content and ultimately to articulate that content effectively and persuasively. The apparent segregation of dance the political is paradoxically the condition upon which this articulation is reliant.
Performing Collectively
Authors: van Eikels Kai
Published: February 2017

One person alone can create and fashion a thing, but it will need many people to realize something by way of praxis. Because actions consist in volatile movements, they become political only through reactions to their being performed. Performing arts and political action thus both explore the possibilities of making a difference through doing that which—while intervening into complex symbolic and imaginary systems—strips down to the concrete, bodily effect of affecting others. Performing, therefore, has an essentially collective reality. Offering an alternative to the rhetoric of bond and rupture that grounds many theories of collectivity, this chapter accesses collectivity from the organizational potential of a relative distance between performers, both in space and in time. Certain forms of collectivity emerge for the very reason that performing bodies are energetically independent and only loosely coupled in their ways of communicating.
Rehearsing In-Difference
Authors: Siegmund Gerald
Published: February 2017

European choreographers Pina Bausch and Jérôme Bel share a critical line of inquiry into the established dance practices of their time, putting both the identity of their subjects and the identity of the genre of dance at risk. By addressing and including their own rehearsal processes in the performance, Bausch and Bel play with their own aesthetic strategies and their coming into being as social practices. As the author argues, the political, here, lies in the blurring of definite and defining categories, thus creating ambivalent and polyvalent scenes that defy explanation. Yet, Bausch and Bel’s work on repetition also produces an excess of energy that blurs distinctions and differences. As an emotional response to a rhythm that is created out of the in-difference to difference, this force undoes what subjects have learned socially. It is here that their freedom lies.
Dance and Politics in China
Authors: Kolb Alexandra
Published: February 2017

This chapter contextualizes stage dance developments in China in the twentieth and twenty-first centuries (through Republican, Maoist, and reformist periods) against the backdrop of the country’s changing sociopolitical conditions and relationships with the Western world. It explores, in historical terms, the interface between Chinese dance and politics to suggest that Westernizing impulses lay behind many of China’s attempts at modernization, leading to hybrid performance practices that are quite unique. The chapter then focuses on the intercultural ArtsCross initiative (2009–2013), a series of projects between the Beijing Dance Academy, Middlesex University London, and Taipei National University of the Arts, which exemplifies the quest for a more equitable form of East-West exchange in the context of globalization and China’s reformist ideological agenda. This section includes a comparative reading of Chinese and Western training and devising processes, as witnessed in these projects, and analysis of Guo Lei’s hybrid choreography Mask.
The Legacy of Newton for the Pre-Critical Kant
Authors: Massimi Michela
Published: February 2017

This chapter assesses Newton’s legacy for Kant by concentrating on the evolution of Kant’s view of space in the pre-Critical period (1748–1768), with two main goals in mind. The first goal is to draw attention to the role that Newton’s matter theory and chemistry played for the young Kant. The second is to argue against the received view that has portrayed the young Kant as embracing Newton’s absolute space in 1768 via the argument from incongruent counterparts (short-lived as this conversion to Newton’s absolute space proved to be). By contrast to the received view, this chapter shows that in the period 1748–1768, Kant was working with a thoroughgoing relationalism, consonant with Kant’s matter theory, which was, in turn, inspired by speculative Newtonian experimentalism itself. Hence, the case is made for a slightly different interpretive stance on Newton’s legacy for the young Kant.
Newton and the Cartesians
Authors: Schmaltz Tad M.
Published: February 2017

This chapter explores the relation during the early modern period of the views of Isaac Newton and the Newtonians to those of Réne Descartes and the Cartesians. The focus is on the early eighteenth-century conflict within the French Académie des sciences between Newtonian gravitational theory and Cartesian vortical physics. Against a revisionary view in the literature, it is argued that Nicolas Malebranche and Bernard le Bovier de Fontenelle are properly characterized as the main defenders of Cartesianism within the Académie. This is despite the fact that Malebranche and Fontenelle disagreed with each other on fundamental issues, and despite the fact that both deviated substantially from Descartes. There also is a consideration of the distinctive contributions to the development of French Newtonianism in the technical work, within the Académie, of Pierre-Louis Maupertuis, and in the more popular work, outside of that institution, of Voltaire.
Newton and Leibniz on the Relativity of Motion
Authors: Arthur Richard T. W.
Published: February 2017

In some respects, there is more agreement between Newton and Leibniz on the relativity of motion than is generally recognized. Both were convinced Copernicans, and both accepted that motion could not be a merely extrinsic denomination—there would have to be true motions, and not just apparent ones. And both sought to discriminate true from apparent motions by reference to the causes of motion and to force. Where they differed was in their radically divergent understandings of how causes are related to forces, of how forces are to be determined in relation to quantity of motion, and of the ontological status of absolute or mathematical space. This chapter aims to throw light on the two philosophers’ respective views on the relativity of motion by considering them in their historical genesis.
Neuroethics
Authors: Morse Stephen J.
Published: February 2017

This chapter discusses whether the findings of the new neuroscience based largely on functional brain imaging raise new normative questions and entail normative conclusions for ethical and legal theory and practice. After reviewing the source of optimism about neuroscientific contributions and the current scientific status of neuroscience, it addresses a radical challenge neuroscience allegedly presents: whether neuroscience proves persons do not have agency. It then considers a series of discrete topics in neuroethics and neurolaw, including the “problem” of responsibility, enhancement of normal functioning, threats to civil liberty, competence, informed consent, end-of-life issues, neuroevidence in criminal cases, and the ethics of caution. It suggests that the ethical and legal resources to respond to the findings of neuroscience already exist and will do so for the foreseeable future.
“Beyond the Lines of Poetry”
Authors: Stubbs Tara
Published: February 2017

This article aims to provide a brief recent history of Irish-American literary studies, then focuses on how Irish-American poetics might be employed as an evaluative critical lens through which to regard Irish, American, and transnational exchange. It discusses whether Irish-American poetics can be used as a critical framework for reading poetry that might not traditionally be labeled “Irish-American,” at least in terms of more obvious ethnic claims or cultural affiliations. This in turn might allow asking larger questions about how, when, and why transnational cultural encounters are assessed and described, and what this might reveal about the ways in which critics, readers, and writers respond to imaginative resources.
Drugs and Prisons
Authors: Wheatley Michael , Weekes John R. , Moser Andrea E. , Thibault Kathleen
Published: February 2017

This essay explores how illegal drugs are linked to imprisonment, especially in the United States. First, the chapter considers statistics that demonstrate how the high U.S. imprisonment rate is driven by the criminalization of substance misuse, despite the high incidence of drug use in the general population. Prison populations that include a mixture of drug users and drug dealers are virtually guaranteed to find ways of bringing drugs into prison, and the demand is increased by the desire to ease the pains of imprisonment. The illicit drug economy in prisons and the associated violence is a threat to the safety of both staff and prisoners. Discussed are ways drugs enter correctional institutions and the methods used to disrupt supply routes. Types of treatment to reduce demand are considered. The complex mix of issues affecting drug use in prisons means that a careful, balanced approach to care and control is needed.
Implementing Prison-based Treatment Programs
Authors: McGuire James
Published: February 2017

The “success” of a prison program can be defined, in part, as the ability to effectively reintegrate released offenders back into the community and secure reductions in criminal recidivism. This essay considers the challenges and issues involved in transferring the “what works” literature on potentially successful prison programs from research into practice. Implementation guidelines for prison programs are considered as well as the importance of evaluating and accrediting prison-based treatment programs. To this end, I review the obstacles to translating theoretically sound programs into practice and whether these obstacles can be surmounted given the design and nature of imprisonment. Assuming effective programs can be established in a prison setting, proper monitoring and evaluation of these programs are discussed as linchpins of sustaining the success of these programs.
Ergot Alkaloids of the Family Clavicipitaceae
Authors: Florea Simona , Panaccione Daniel G. , Schardl Christopher L.
Published: February 2017

Ergot alkaloids are highly diverse in structure, exhibit diverse effects on animals, and are produced by diverse fungi in the phylum Ascomycota, including pathogens and mutualistic symbionts of plants. These mycotoxins are best known from the fungal family Clavicipitaceae and are named for the ergot fungi that, through millennia, have contaminated grains and caused mass poisonings, with effects ranging from dry gangrene to convulsions and death. However, they are also useful sources of pharmaceuticals for a variety of medical purposes. More than a half-century of research has brought us extensive knowledge of ergot-alkaloid biosynthetic pathways from common early steps to several taxon-specific branches. Furthermore, a recent flurry of genome sequencing has revealed the genomic processes underlying ergot-alkaloid diversification. In this review, we discuss the evolution of ergot-alkaloid biosynthesis genes and gene clusters, including roles of gene recruitment, duplication and neofunctionalization, as well as gene loss, in diversifying structures of clavines, lysergic acid amides, and complex ergopeptines. Also reviewed are prospects for manipulating ergot-alkaloid profiles to enhance suitability of endophytes for forage grasses.
Reynolds number trend of hierarchies and scale interactions in turbulent boundary layers
Authors: Baars W. J. , Hutchins N. , Marusic I.
Published: February 2017

Small-scale velocity fluctuations in turbulent boundary layers are often coupled with the larger-scale motions. Studying the nature and extent of this scale interaction allows for a statistically representative description of the small scales over a time scale of the larger, coherent scales. In this study, we consider temporal data from hot-wire anemometry at Reynolds numbers ranging from
Re

τ

≈2800 to 22 800, in order to reveal how the scale interaction varies with Reynolds number. Large-scale conditional views of the representative amplitude and frequency of the small-scale turbulence, relative to the large-scale features, complement the existing consensus on large-scale modulation of the small-scale dynamics in the near-wall region. Modulation is a type of scale interaction, where the amplitude of the small-scale fluctuations is continuously proportional to the near-wall footprint of the large-scale velocity fluctuations. Aside from this amplitude modulation phenomenon, we reveal the influence of the large-scale motions on the characteristic frequency of the small scales, known as frequency modulation. From the wall-normal trends in the conditional averages of the small-scale properties, it is revealed how the near-wall modulation transitions to an intermittent-type scale arrangement in the log-region. On average, the amplitude of the small-scale velocity fluctuations only deviates from its mean value in a confined temporal domain, the duration of which is fixed in terms of the local Taylor time scale. These concentrated temporal regions are centred on the internal shear layers of the large-scale uniform momentum zones, which exhibit regions of positive and negative streamwise velocity fluctuations. With an increasing scale separation at high Reynolds numbers, this interaction pattern encompasses the features found in studies on internal shear layers and concentrated vorticity fluctuations in high-Reynolds-number wall turbulence.

This article is part of the themed issue ‘Toward the development of high-fidelity models of wall turbulence at large Reynolds number’.
Phase relations in a forced turbulent boundary layer: implications for modelling of high Reynolds number wall turbulence
Authors: Duvvuri Subrahmanyam , McKeon Beverley
Published: February 2017

Phase relations between specific scales in a turbulent boundary layer are studied here by highlighting the associated nonlinear scale interactions in the flow. This is achieved through an experimental technique that allows for targeted forcing of the flow through the use of a dynamic wall perturbation. Two distinct large-scale modes with well-defined spatial and temporal wavenumbers were simultaneously forced in the boundary layer, and the resulting nonlinear response from their direct interactions was isolated from the turbulence signal for the study. This approach advances the traditional studies of large- and small-scale interactions in wall turbulence by focusing on the direct interactions between scales with triadic wavenumber consistency. The results are discussed in the context of modelling high Reynolds number wall turbulence.

This article is part of the themed issue ‘Toward the development of high-fidelity models of wall turbulence at large Reynolds number’.
A statistical state dynamics approach to wall turbulence
Authors: Farrell B. F. , Gayme D. F. , Ioannou P. J.
Published: February 2017

This paper reviews results obtained using statistical state dynamics (SSD) that demonstrate the benefits of adopting this perspective for understanding turbulence in wall-bounded shear flows. The SSD approach used in this work employs a second-order closure that retains only the interaction between the streamwise mean flow and the streamwise mean perturbation covariance. This closure restricts nonlinearity in the SSD to that explicitly retained in the streamwise constant mean flow together with nonlinear interactions between the mean flow and the perturbation covariance. This dynamical restriction, in which explicit perturbation–perturbation nonlinearity is removed from the perturbation equation, results in a simplified dynamics referred to as the restricted nonlinear (RNL) dynamics. RNL systems, in which a finite ensemble of realizations of the perturbation equation share the same mean flow, provide tractable approximations to the SSD, which is equivalent to an infinite ensemble RNL system. This infinite ensemble system, referred to as the stochastic structural stability theory system, introduces new analysis tools for studying turbulence. RNL systems provide computationally efficient means to approximate the SSD and produce self-sustaining turbulence exhibiting qualitative features similar to those observed in direct numerical simulations despite greatly simplified dynamics. The results presented show that RNL turbulence can be supported by as few as a single streamwise varying component interacting with the streamwise constant mean flow and that judicious selection of this truncated support or ‘band-limiting’ can be used to improve quantitative accuracy of RNL turbulence. These results suggest that the SSD approach provides new analytical and computational tools that allow new insights into wall turbulence.

This article is part of the themed issue ‘Toward the development of high-fidelity models of wall turbulence at large Reynolds number’.
Statistical evidence of anasymptotic geometric structure to the momentum transporting motions in turbulent boundary layers
Authors: Morrill-Winter Caleb , Philip Jimmy , Klewicki Joseph
Published: February 2017

The turbulence contribution to the mean flow is reflected by the motions producing the Reynolds shear stress (〈−
uv
〉) and its gradient. Recent analyses of the mean dynamical equation, along with data, evidence that these motions asymptotically exhibit self-similar geometric properties. This study discerns additional properties associated with the
uv
signal, with an emphasis on the magnitudes and length scales of its negative contributions. The signals analysed derive from high-resolution multi-wire hot-wire sensor data acquired in flat-plate turbulent boundary layers. Space-filling properties of the present signals are shown to reinforce previous observations, while the skewness of
uv
suggests a connection between the size and magnitude of the negative excursions on the inertial domain. Here, the size and length scales of the negative
uv
motions are shown to increase with distance from the wall, whereas their occurrences decrease. A joint analysis of the signal magnitudes and their corresponding lengths reveals that the length scales that contribute most to 〈−
uv
〉 are distinctly larger than the average geometric size of the negative
uv
motions. Co-spectra of the streamwise and wall-normal velocities, however, are shown to exhibit invariance across the inertial region when their wavelengths are normalized by the width distribution,
W
(
y
), of the scaling layer hierarchy, which renders the mean momentum equation invariant on the inertial domain.

This article is part of the themed issue ‘Toward the development of high-fidelity models of wall turbulence at large Reynolds number’.
Modelling high Reynolds number wall–turbulence interactions in laboratory experiments using large-scale free-stream turbulence
Authors: Dogan Eda , Hearst R. Jason , Ganapathisubramani Bharathram
Published: February 2017

A turbulent boundary layer subjected to free-stream turbulence is investigated in order to ascertain the scale interactions that dominate the near-wall region. The results are discussed in relation to a canonical high Reynolds number turbulent boundary layer because previous studies have reported considerable similarities between these two flows. Measurements were acquired simultaneously from four hot wires mounted to a rake which was traversed through the boundary layer. Particular focus is given to two main features of both canonical high Reynolds number boundary layers and boundary layers subjected to free-stream turbulence: (i) the footprint of the large scales in the logarithmic region on the near-wall small scales, specifically the modulating interaction between these scales, and (ii) the phase difference in amplitude modulation. The potential for a turbulent boundary layer subjected to free-stream turbulence to ‘simulate’ high Reynolds number wall–turbulence interactions is discussed. The results of this study have encouraging implications for future investigations of the fundamental scale interactions that take place in high Reynolds number flows as it demonstrates that these can be achieved at typical laboratory scales.

This article is part of the themed issue ‘Toward the development of high-fidelity models of wall turbulence at large Reynolds number’.
Daisyfield gene drive systems harness repeated genomic elements as a generational clock to limit spread
Authors: Min John , Noble Charleston , Najjar Devora , Esvelt Kevin M.
Published: February 2017

Methods of altering wild populations are most useful when inherently limited to local geographic areas. Here we describe a novel form of gene drive based on the introduction of multiple copies of an engineered ‘daisy’ sequence into repeated elements of the genome. Each introduced copy encodes guide RNAs that target one or more engineered loci carrying the CRISPR nuclease gene and the desired traits. When organisms encoding a drive system are released into the environment, each generation of mating with wild-type organisms will reduce the average number of the guide RNA elements per ‘daisyfield’ organism by half, serving as a generational clock. The loci encoding the nuclease and payload will exhibit drive only as long as a single copy remains, placing an inherent limit on the extent of spread.
The Arabidopsis Framework Model version 2 predicts the organism-level effects of circadian clock gene mis-regulation
Authors: Chew Yin Hoon , Seaton Daniel D. , Mengin Virginie , Flis Anna , Mugford Sam T. , George Gavin M. , Moulin Michael , Hume Alastair , Zeeman Samuel C. , Fitzpatrick Teresa B. , Smith Alison M. , Stitt Mark , Millar Andrew J.
Published: February 2017

Predicting a multicellular organism’s phenotype quantitatively from its genotype is challenging, as genetic effects must propagate across scales. Circadian clocks are intracellular regulators that control temporal gene expression patterns and hence metabolism, physiology and behaviour. Here we explain and predict canonical phenotypes of circadian timing in a multicellular, model organism. We used diverse metabolic and physiological data to combine and extend mathematical models of rhythmic gene expression, photoperiod-dependent flowering, elongation growth and starch metabolism within a Framework Model for the vegetative growth ofArabidopsis thaliana, sharing the model and data files in a structured, public resource. The calibrated model predicted the effect of altered circadian timing upon each particular phenotype in clock-mutant plants under standard laboratory conditions. Altered night-time metabolism of stored starch accounted for most of the decrease in whole-plant biomass, as previously proposed. Mobilisation of a secondary store of malate and fumarate was also mis-regulated, accounting for any remaining biomass defect. We test three candidate mechanisms for the accumulation of these organic acids. Our results link genotype through specific processes to higher-level phenotypes, formalising our understanding of a subtle, pleiotropic syndrome at the whole-organism level, and validating the systems approach to understand complex traits starting from intracellular circuits.

This work updates the first biorXiv version, February 2017,https://doi.org/10.1101/105437, with an expanded description and additional analysis of the same core data sets and the same FMv2 model, summary tables and supporting, follow-on data from three further studies with further collaborators. This biorXiv revision constitutes the second version of this report.
Evaluating Bayesian spatial methods for modelling species distributions with clumped and restricted occurrence data
Authors: Redding David W. , Lucas Tim C. D. , Blackburn Tim , Jones Kate E.
Published: February 2017

1. Statistical approaches for inferring the spatial distribution of taxa (Species Distribution Models, SDMs) commonly rely on available occurrence data, which is often non-randomly distributed and geographically restricted. Although available SDM methods address some of these problems, the errors could be more directly and accurately modelled using a spatially-explicit approach. Software to implement spatial autocorrelation terms into SDMs are now widely available, but whether such approaches for inferring SDMs are an improvement over existing methodologies is unknown.

2. Here, within a simulated environment using 1000 generated species’ ranges, we compared the performance of two commonly used non-spatial SDM methods (Maximum Entropy Modelling, MAXENT and Boosted Regression Trees, BRT) to a spatially-explicit Bayesian SDM method (Integrated Laplace Approximation, INLA), when the underlying data exhibit varying combinations of clumping and geographic restriction. Finally, we tested whether any recommended methodological settings for all methods were further impacted by spatially non-random patterns in these data.

3. Spatially-explicit INLA was the most consistently accurate method, being most or equal most accurate in 5 out of 8 data sampling scenarios. Within high-coverage sample datasets, all methods performed fairly similarly, but when sampling points were randomly spread BRT had a 1-3% greater accuracy over the other methods and when samples were clumped, spatial-INLA had a 4%-8% better in AUC score. Alternatively, when sampling points were restricted to a small section of the true range, all methods were on average 10-12% less accurate, with higher variation among the methods. None of the recommended settings for the different methods were found to be sensitive to clumping or restriction of data, except the complexity of the INLA spatial term.

4. INLA-based modelling approaches can be successfully used to account for spatial autocorrelation in an SDM context and, by taking account of random effects, produce outputs that can better elucidate the role of covariates in predicting species occurrence. Given that it is often unclear what the drivers are behind data clumping in an empirical occurrence dataset, or indeed how geographically restricted these data are, spatially-explicit INLA-based SDMs may be the better choice when modelling the spatial distribution of target species.
Education and coronary heart disease: a Mendelian randomization study
Authors: Tillmann Taavi , Vaucher Julien , Okbay Aysu , Pikhart Hynek , Peasey Anne , Kubinova Ruzena , Pajak Andrzej , Tamosiunas Abdonas , Malyutina Sofia , Fischer Krista , Veronesi Giovanni , Palmer Tom , Bowden Jack , Davey Smith George , Bobak Martin , Holmes Michael V
Published: February 2017

Objectives

To determine whether educational attainment is a causal risk factor in the development of coronary heart disease.

Design

Mendelian randomization study, where genetic data are used as proxies for education, in order to minimize confounding. A two-sample design was applied, where summary level genetic data was analysed from two publically available consortia.

Setting

In the main analysis, we analysed genetic data from two large consortia (CARDIoGRAM and SSGAC), comprising of 112 cohorts from predominantly high-income countries. In addition, we also analysed genetic data from 7 additional large consortia, in order to identify putative causal mediators.

Participants

The main analysis was of 589 377 men and women, predominantly of European origin.

Exposure

A one standard deviation increase in the genetic predisposition towards higher education (i.e. 3.6 years of additional schooling). This was measured by 162 genetic variants that have been previously associated with education.

Main outcome

Combined fatal and nonfatal coronary heart disease (63 746 events).

Results

3.6 years of additional education lowered the risk of coronary heart disease by a third (odds ratio = 0.67, 95% confidence interval [CI], 0.59 to 0.77, p=0.01). Equivalent increases in education were also causally associated with reductions in smoking, BMI and improvements in blood lipid profiles.

Conclusions

More time spent in education is causally associated with a large reduction in the risk of coronary heart disease. This may be partly explained by changes to smoking, BMI and a blood lipids. These findings offer support for policy interventions that increase education, in order to also reduce the burden of cardiovascular disease.
Recent origin of Neotropical orchids in the world’s richest plant biodiversity hotspot
Authors: Alejandro Pérez-Escobar Oscar , Chomicki Guillaume , Condamine Fabien L. , Karremans Adam P. , Bogarín Diego , Matzke Nicholas J. , Silvestro Daniele , Antonelli Alexandre
Published: February 2017

• The Andean mountains of South America are the most species-rich biodiversity hotspot worldwide with about 15% of the world’s plant species, in only 1% of the world’s land surface. Orchids are a key element of the Andean flora, and one of the most prominent components of the Neotropical epiphyte diversity, yet very little is known about their origin and diversification.

• We address this knowledge gap by inferring the biogeographical history and evolutionary dynamics of the two largest Neotropical orchid groups (Cymbidieae and Pleurothallidinae), using two unparalleled, densely-sampled orchid phylogenies (including 400+ newly generated DNA sequences), comparative phylogenetic methods, geological and biological datasets.

• We find that the majority of Andean orchid lineages only originated in the last 15 million years. Most Andean lineages are derived from lowland Amazonian ancestors, with additional contributions from Central America and the Antilles. Species diversification is correlated with Andean orogeny, and multiple migrations and re-colonizations across the Andes indicate that mountains do not constrain orchid dispersal over long timescales.

• Our study sheds new light on the timing and geography of a major Neotropical radiation, and suggests that mountain uplift promotes species diversification across all elevational zones.
Visibility graphs for fMRI data: multiplex temporal graphs and their modulations across resting state networks
Authors: Sannino Speranza , Stramaglia Sebastiano , Lacasa Lucas , Marinazzo Daniele
Published: February 2017

Visibility algorithms are a family of methods that map time series into graphs, such that the tools of graph theory and network science can be used for the characterization of time series. This approach has proved a convenient tool and visibility graphs have found applications across several disciplines. Recently, an approach has been proposed to extend this framework to multivariate time series, allowing a novel way to describe collective dynamics. Here we test their application to fMRI time series, following two main motivations, namely that (i) this approach allows to simultaneously capture and process relevant aspects of both local and global dynamics in an easy and intuitive way, and (ii) this provides a suggestive bridge between time series and network theory which nicely fits the consolidating field of network neuroscience. Our application to a large open dataset reveals differences in the similarities of temporal networks (and thus in correlated dynamics) across resting state networks, and gives indications that some differences in brain activity connected to psychiatric disorders could be picked up by this approach.
Volatility risk and stock return predictability on global financial crises
Authors: Kongsilp Worawuth , Mateus Cesario
Published: February 2017

Purpose

The purpose of this paper is to investigate the role of volatility risk on stock return predictability specified on two global financial crises: the dot-com bubble and recent financial crisis.

Design/methodology/approach

Using a broad sample of stock options traded on the American Stock Exchange and the Chicago Board Options Exchange from January 2001 to December 2010, the effect of different idiosyncratic volatility forecasting measures are examined on future stock returns in four different periods (Bear and Bull markets).

Findings

First, the authors find clear and robust empirical evidence that the implied idiosyncratic volatility is the best stock return predictor for every sub-period both in Bear and Bull markets. Second, the cross-section firm-specific characteristics are important when it comes to stock returns forecasts, as the latter have mixed positive and negative effects on Bear and Bull markets. Third, the authors provide evidence that short selling constraints impact negatively on stock returns for only a Bull market and that liquidity is meaningless for both Bear and Bull markets after the recent financial crisis.

Practical implications

These results would be helpful to disclose more information on the best idiosyncratic volatility measure to be implemented in global financial crises.

Originality/value

This study empirically analyses the effect of different idiosyncratic volatility measures for a period that involves both the dotcom bubble and the recent financial crisis in four different periods (Bear and Bull markets) and contributes the existing literature on volatility measures, volatility risk and stock return predictability in global financial crises.
Variable-fidelity CFD models and co-Kriging for expedited multi-objective aerodynamic design optimization
Authors: Koziel Slawomir , Tesfahunegn Yonatan , Leifsson Leifur
Published: February 2017

Purpose

Strategies for accelerated multi-objective optimization of aerodynamic surfaces are investigated, including the possibility of exploiting surrogate modeling techniques for computational fluid dynamic (CFD)-driven design speedup of such surfaces. The purpose of this paper is to reduce the overall optimization time.

Design/methodology/approach

An algorithmic framework is described that is composed of: a search space reduction, fast surrogate models constructed using variable-fidelity CFD models and co-Kriging, and Pareto front refinement. Numerical case studies are provided demonstrating the feasibility of solving real-world problems involving multi-objective optimization of transonic airfoil shapes and accurate CFD simulation models of such surfaces.

Findings

It is possible, through appropriate combination of surrogate modeling techniques and variable-fidelity models, to identify a set of alternative designs representing the best possible trade-offs between conflicting design objectives in a realistic time frame corresponding to a few dozen of high-fidelity CFD simulations of the respective surfaces.

Originality/value

The proposed aerodynamic design optimization algorithmic framework is novel and holistic. It proved useful for fast design of aerodynamic surfaces using high-fidelity simulation data in moderately sized search space, which is extremely challenging when using conventional methods due to the excessive computational cost.
Worker outcomes of LGBT-supportive policies: a cross-level model
Authors: Pichler Shaun , Ruggs Enrica , Trau Raymond
Published: February 2017

Purpose

The purpose of this paper is to develop a cross-level conceptual model of organizational- and individual-level outcomes of lesbian, gay, bisexual, and transgender (LGBT)-supportive policies for all workers regardless of their sexual orientation.

Design/methodology/approach

This is a conceptual paper based on an integration of propositions from perceived organizational support and organizational justice theories.

Findings

The model suggests that LGBT-supportive policies should be related to perceptions of organizational support directly and indirectly through diversity climate and perceptions of distributive, procedural, and interactional justice.

Practical implications

The model implies that employees should feel more supported and more fairly treated among firms with LGBT-supportive policies and practices, and that these feelings will be reciprocated.

Originality/value

This is the first paper to develop propositions about the outcomes of LGBT-supportive policies for all workers, and advances the literature by developing a multi-level model of outcomes of these policies.
The OWA distance operator and its application in business failure
Authors: Scherger Valeria , Terceño Antonio , Vigier Hernán
Published: February 2017

Purpose

The purpose of this paper is to develop a goodness index based on Hamming distance and ordered weighted averaging distance (OWAD), which is useful to make decisions. These alternative measures enrich the results of diagnostic fuzzy models and facilitate the experts’ task in decision-making. An application to a set of firms to verify the results is also presented.

Design/methodology/approach

The paper follows the basis of OWA operators to design a methodology to reduce the map of causes of business failure into monitoring key areas.

Findings

The present paper introduces two alternative measures to test the proposal of grouping. In the empirical application, the superiority of the minimum T-norm over other decision rules is verified. The ordered weighted averaging distance (OWAD) goodness index predicts a better adjustment over the index built using OWA and Hamming distance measures.

Practical implications

A useful mechanism to reduce the map of causes or diseases detected in key areas is added through this analysis. At the same time, these key areas can be disaggregated once some alert indicator is identified; this allows knowing the causes that require special attention. This application of OWA can encourage the development of suitable computer systems for monitoring the firm’s problems, alerting regarding failures and easing decision-making.

Originality/value

A comparison of grouping causes into key areas through a goodness index based on Hamming distance and OWAD is proposed. These contributions enrich the Vigier and Terceño (2008) model and could be applied to any model of fuzzy diagnosis to test the results.