bluuebunny/crossref_metadata_2025_split huggingface dataset:
14-3-3-Pred: improved methods to predict 14-3-3-binding phosphopeptides
Authors: Madeira Fábio , Tinti Michele , Murugesan Gavuthami , Berrett Emily , Stafford Margaret , Toth Rachel , Cole Christian , MacKintosh Carol , Barton Geoffrey J. 
Published: March 2015

Abstract
Motivation: The 14-3-3 family of phosphoprotein-binding proteins regulates many cellular processes by docking onto pairs of phosphorylated Ser and Thr residues in a constellation of intracellular targets. Therefore, there is a pressing need to develop new prediction methods that use an updated set of 14-3-3-binding motifs for the identification of new 14-3-3 targets and to prioritize the downstream analysis of &gt;2000 potential interactors identified in high-throughput experiments.
Results: Here, a comprehensive set of 14-3-3-binding targets from the literature was used to develop 14-3-3-binding phosphosite predictors. Position-specific scoring matrix, support vector machines (SVM) and artificial neural network (ANN) classification methods were trained to discriminate experimentally determined 14-3-3-binding motifs from non-binding phosphopeptides. ANN, position-specific scoring matrix and SVM methods showed best performance for a motif window spanning from −6 to +4 around the binding phosphosite, achieving Matthews correlation coefficient of up to 0.60. Blind prediction showed that all three methods outperform two popular 14-3-3-binding site predictors, Scansite and ELM. The new methods were used for prediction of 14-3-3-binding phosphosites in the human proteome. Experimental analysis of high-scoring predictions in the FAM122A and FAM122B proteins confirms the predictions and suggests the new 14-3-3-predictors will be generally useful.
Availability and implementation: A standalone prediction web server is available at http://www.compbio.dundee.ac.uk/1433pred. Human candidate 14-3-3-binding phosphosites were integrated in ANIA: ANnotation and Integrated Analysis of the 14-3-3 interactome database.
Contact: cmackintosh@dundee.ac.uk or gjbarton@dundee.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Very high energy emission as a probe of relativistic magnetic reconnection in pulsar winds
Authors: Mochol Iwona , Pétri Jérôme 
Published: March 2015

Abstract
The population of gamma-ray pulsars, including Crab observed in the TeV range, and Vela detected above 50 GeV, challenges existing models of pulsed high-energy emission. Such models should be universally applicable, yet they should account for spectral differences among the pulsars. We show that the gamma-ray emission of Crab and Vela can be explained by synchrotron radiation from the current sheet of a striped wind, expanding with a modest Lorentz factor Γ ≲ 100 in the Crab case, and Γ ≲ 50 in the Vela case. In the Crab spectrum, a new synchrotron self-Compton component is expected to be detected by the upcoming experiment CTA. We suggest that the gamma-ray spectrum directly probes the physics of relativistic magnetic reconnection in the striped wind. In the most energetic pulsars, like Crab, with $\dot{E}_{38}^{3/2}/P_{-2}\gtrsim 0.002$ (where $\dot{E}$ is the spin-down power, P is the pulsar period, and X = Xi × 10i in CGS units), reconnection proceeds in the radiative cooling regime and results in a soft power-law distribution of cooling particles; in less powerful pulsars, like Vela, particle energization is limited by the current sheet size, and a hard particle spectrum reflects the acceleration mechanism. A strict lower limit on the number density of radiating particles corresponds to emission close to the light cylinder, and, in units of the GJ density, it is ≳ 0.5 in the Crab wind, and κ ≳ 0.05 in the Vela wind.
Theatre
Authors: Hutson Lorna 
Published: March 2015

Abstract
In the 1980s, New Historicist critics suggested that Renaissance theater was marked by the Reformation; specifically, that it expressed the vanishing of ritual and sacrament from ordinary people’s lives. More recently, critics like Sarah Beckwith have shown how pre-Reformation theater worked as ritual and sacrament by revealing the extent to which it was implicated in the jurisdiction of confession, penance and absolution for sin. This article revisits the question of how the Reformation abolition of annual mandatory confession affected theater. It qualifies both the New Historicist view of Renaissance theater as evacuated ritual and Beckwith’s view of the Protestant abolition of confession as an exteriorization of penance. Reading the first English Renaissance neoclassical comedy in English, Gammer Gurton’s Needle (c.1553-60), the article shows how profoundly its neoclassical concern with proof and evidence is tied in with a rejection of priestly confession and an invitation to parishioners and neighbors to be more skeptical and less credulous in believing the worst of one another.
Utopian Pleasure
Authors: Greenblatt Stephen 
Published: March 2015

Abstract
Lucretius’s didactic masterpiece De rerum natura advances propositions, drawn from Epicurus, which the Renaissance book-hunter Poggio Bracciolini and his contemporaries found difficult to absorb. Epicurus’s convictions included an insistence on the superiority of reason over faith, a steadfast refusal of pious fear, a concomitant refusal to believe in afterlife, a belief in the mortality of the soul, a rejection of religion, and an advocacy of the pursuit of pleasure. To many orthodox Christians such arguments were the very definition of atheism. This article examines three responses to De rerum natura: “The Renunciation of Youthful Indiscretion” by Marsilio Ficino, “The Divorce Settlement” by Poggio Bracciolini, and “Dialogical Disavowal” by Lorenzo Valla. It also considers how the link between humanism, wealth, and the exercise of power in England conditioned the most remarkable Renaissance English response to Lucretius and to everything he brought back into circulation. Finally, it analyzes Thomas More’s Utopia, its theory of the nature of pleasure, and its treatment of Epicureanism and the afterlife.
Poetic Fame
Authors: Cooper Helen 
Published: March 2015

Abstract
Poetry is intertwined with fame: it needs to be known, and to be associated with a named poet. In their dramatization of Geoffrey Chaucer’s Knight’s Tale, William Shakespeare and John Fletcher declare that Chaucer is more famous than Petrarch or any contemporary English poets. Shakespeare’s attitude to Chaucer thus highlights the contrast between the high admiration with which he was received in the sixteenth century and the widespread refusal in modern times to recognize him as England’s laureate poet. Numerous other poets, including Edmund Spenser and Ben Jonson, paid tribute to Chaucer throughout the sixteenth and early seventeenth centuries. This article examines Chaucer’s fame as a poet, his own attitude to fame, and its relation to humanism, Catholicism and Protestantism.
Style
Authors: Nolan Maura 
Published: March 2015

AbstractPoetic style may be analyzed by starting with the smallest measurable units of poetry. Style has two aspects that are often contradictory: the particular and the general. The notion of style underwent numerous changes over the years between Geoffrey Chaucer and Thomas Wyatt. This article examines the question of style by juxtaposing three poets, three centuries, and two literary-historical periods. It considers the relationship between the Middle Ages and the Renaissance as well as embeddedness of Chaucer, Wyatt, and John Lydgate in those periods in stylistic terms and describes an alternative way of thinking about literary style that reveals the secretive manner that history works in art. It discusses the troublesome poetic terrain of stresses, absences of stress, feet, and meter as a way of scrutinizing the “styles” of Chaucer, Lydgate, and Wyatt in “Truth,” “The World is Variable,” and “What Vaileth Trouth,” respectively.
Idleness
Authors: Kearney James 
Published: March 2015

AbstractThis essay examines the role that the specter of idleness played in the ongoing transformation of labor in England during the late medieval and early modern periods. It begins by tracing an historical shift in Christian conceptions of labor through a knotty genealogy of ideas about labor and idleness that extends from the fourteenth to the seventeenth centuries. The essay then turns to an early sixteenth-century text that is not often considered in either medieval or early modern histories of Christian thought about labor: Thomas More’s Utopia (1516). The essay contends that Utopia is fundamentally shaped by More’s meditation on labor and idleness and that that meditation opens the utopian text out toward a vexed history of ideas concerning human work that extends forward from the fourteenth century. With its idiosyncratic but historically resonant meditation on human labor, More’s Utopia represents a particularly useful vantage point from which to address the ongoing transformation of Christian conceptions of work in late medieval and early modern England.
Autobiography and the History of Reading
Authors: Cummings Brian 
Published: March 2015

Abstract
Autobiography as a concept asks deep questions about the periodization of history. It is also a scene of persistent rivalry in the construction of medieval and Renaissance models of history. Since Jakob Burckhardt’s Die Kultur der Renaissance in Italien of 1860, there has been a war of ownership over the rise of human subjectivity. This article examines the debate over the history of autobiography by focusing on St. Augustine and his Confessions. It considers the exposure of the Confessions to different kinds of reading during the late medieval period, including that by Petrarch. It argues that the Confessions has been read more extensively in the twentieth century than ever before and that the Augustine of the “invention of subjectivity” is a writer of a specifically twentieth-century imagination. In this way it also assesses the impact of the Reformation on the Confessions.
Formative Mappings, Political Trappings
Authors: Fong Edmund , Hattam Victoria 
Published: March 2015

Abstract
Contemporary scholarship on racial and ethnic politics in the United States has broadly followed three main approaches in assessing the history of race and ethnicity in the United States. We therefore map three different ways of seeing the relationship between race and ethnicity contained within Whiteness Studies, scholarship on cultural pluralism and multiculturalism, and scholarship on intersections and Intersectionality. Each locates the history of racial and ethnic difference within a larger political problematic, each attaches a different significance and valence between racial and ethnic categories, and each bears with it the particular political investments constituting its origins. By highlighting the divergent ways racial and ethnic categories are mobilized we underscore the irreducibly political nature of race and ethnicity and their ongoing generative role in American politics.
Corpus Linguistics and Information Structure Research
Authors: Lüdeling Anke , Ritz Julia , Stede Manfred , Zeldes Amir 
Published: March 2015

AbstractThis chapter describes the contributions that Corpus Linguistics (the study of linguistic phenomena by means of systematically exploiting collections of naturally-occurring linguistic data) can make to IS research. It discusses issues of designing a corpus that can serve as a basis for qualitative or quantitative studies, and then turns to the central issue of data annotation: what corpora are available that have been annotated with IS-related annotations, and how can such annotations be evaluated? In case a corpus does not have direct IS annotation, can other types of annotations, especially in the form of multi-layer annotation, be used as indirect evidence for the presence of IS phenomena? Next, the present state of the art in automatic IS annotation (by means of techniques from computational linguistics) is sketched, and finally, several sample studies that exploit IS annotations are introduced briefly.
Constraint Conflict and Information Structure
Authors: Samek-Lodovici Vieri 
Published: March 2015

AbstractThis article examines the insights brought about by a conflict-based approach to the study of information structure. It does so mainly, but not exclusively, through a chronological survey of particularly significant analyses that modelled the syntactic displacements induced by focalization as the effect of prosodic constraints governing the position of prosodic prominence. The historic and conceptual relations between these analyses are highlighted, together with the main theoretical issues they raise and address. While most analyses are based on optimality theory, the article does not assume any prior knowledge of this framework and is accessible to all scholars.
Verum Focus
Authors: Lohnstein Horst 
Published: March 2015

AbstractThis chapter aims to shed light on a phenomenon first described as verum focus by Höhle. He characterizes its semantic effect as emphasizing the expression of truth of a proposition. In German, the phenomenon typically appears in the left periphery of main and embedded clauses. Höhle relates it to a linguistic object VERUM occuring in the syntactic/semantic structure of clauses. After presenting several approaches which make crucial use of VERUM, the concept of truth and its linguistic realization in clausal structures is discussed. This leads to a perspective that connects verum focus to the part of the sentence that spells out the intention of the sentence meaning: the sentence mood. This line of reasoning intends to promote the view that verum focus can be derived from the systematic interaction of sentence mood with the regular properties of focus assignment.
Game versus Substance in Political News
Authors: Patterson Thomas E. 
Published: March 2015

Abstract
This chapter examines the game schema in news coverage. It argues that substance is often subordinated to the competitive game, particularly during election campaigns but also in governing situations. Moreover, because journalists tend to see politics as a political game, their reporting of policy leadership and problems is often framed in game-like terms The chapter discusses the game schema in theoretical perspective and looks at research on the game schema in US presidential and congressional elections and other contexts. The research on the media effects of game schema is reviewed. The chapter closes by offering future directions for research on the game schema.
Syntaxin1A-mediated Resistance and Hypersensitivity to Isoflurane in Drosophila melanogaster
Authors: Zalucki Oressia H. , Menon Hareesh , Kottler Benjamin , Faville Richard , Day Rebecca , Bademosi Adekunle T. , Lavidis Nickolas , Karunanithi Shanker , van Swinderen Bruno 
Published: March 2015

AbstractAbstract
Isoflurane targets synaptic release mechanisms in addition to sleep pathways in flies. Different mutations in syntaxin1A confer resistance and hypersensitivity across multiple behavioral and electrophysiological endpoints in flies.
Supplemental Digital Content is available in the text.

Background:
Recent evidence suggests that general anesthetics activate endogenous sleep pathways, yet this mechanism cannot explain the entirety of general anesthesia. General anesthetics could disrupt synaptic release processes, as previous work in Caenorhabditis elegans and in vitro cell preparations suggested a role for the soluble NSF attachment protein receptor protein, syntaxin1A, in mediating resistance to several general anesthetics. The authors questioned whether the syntaxin1A-mediated effects found in these reductionist systems reflected a common anesthetic mechanism distinct from sleep-related processes.

Methods:
Using the fruit fly model, Drosophila melanogaster, the authors investigated the relevance of syntaxin1A manipulations to general anesthesia. The authors used different behavioral and electrophysiological endpoints to test the effect of syntaxin1A mutations on sensitivity to isoflurane.

Results:
The authors found two syntaxin1A mutations that confer opposite general anesthesia phenotypes: syxH3-C, a 14-amino acid deletion mutant, is resistant to isoflurane (n = 40 flies), and syxKARRAA, a strain with two amino acid substitutions, is hypersensitive to the drug (n = 40 flies). Crucially, these opposing effects are maintained across different behavioral endpoints and life stages. The authors determined the isoflurane sensitivity of syxH3-C at the larval neuromuscular junction to assess effects on synaptic release. The authors find that although isoflurane slightly attenuates synaptic release in wild-type animals (n = 8), syxH3-C preserves synaptic release in the presence of isoflurane (n = 8).

Conclusion:
The study results are evidence that volatile general anesthetics target synaptic release mechanisms; in addition to first activating sleep pathways, a major consequence of these drugs may be to decrease the efficacy of neurotransmission.
The interplay between DNA methylation and sequence divergence in recent human evolution
Authors: Hernando-Herraez Irene , Heyn Holger , Fernandez-Callejo Marcos , Vidal Enrique , Fernandez-Bellon Hugo , Prado-Martinez Javier , Sharp Andrew J , Esteller Manel , Marques-Bonet Tomas 
Published: March 2015

AbstractDNA methylation is a key regulatory mechanism in mammalian genomes. Despite the increasing knowledge about this epigenetic modification, the understanding of human epigenome evolution is in its infancy. We used whole genome bisulfite sequencing to study DNA methylation and nucleotide divergence between human and great apes. We identified 360 and 210 differentially hypo- and hypermethylated regions (DMRs) in humans compared to non-human primates and estimated that 20% and 36% of these regions, respectively, were detectable throughout several human tissues. Human DMRs were enriched for specific histone modifications and contrary to expectations, the majority were located distal to transcription start sites, highlighting the importance of regions outside the direct regulatory context. We also found a significant excess of endogenous retrovirus elements in human-specific hypomethylated regions suggesting their association with local epigenetic changes.We also reported for the first time a close interplay between inter-species genetic and epigenetic variation in regions of incomplete lineage sorting, transcription factor binding sites and human differentially hypermethylated regions. Specifically, we observed an excess of human-specific substitutions in transcription factor binding sites located within human DMRs, suggesting that alteration of regulatory motifs underlies some human-specific methylation patterns. We also found that the acquisition of DNA hypermethylation in the human lineage is frequently coupled with a rapid evolution at nucleotide level in the neighborhood of these CpG sites. Taken together, our results reveal new insights into the mechanistic basis of human-specific DNA methylation patterns and the interpretation of inter-species non-coding variation.Author summaryHuman and great apes, their closest living relatives, differ in numerous morphological and cognitive aspects, however their protein sequences are highly similar. It has long been hypothesized that human specific traits may be explained by changes in regulatory elements rather than by changes in primary sequence. In this context, evolutionary biologists have identified regulatory regions based on nucleotide sequence acceleration or conservation. However, epigenetics adds an extra layer of information that cannot be detected when comparing DNA sequences. The current study provides one of the first genome-wide comparison of genetic and epigenetic variation among humans and our closest living relatives. We identify and describe hundreds of regions presenting a human-specific DNA methylation pattern compared to great apes. We also report a local interplay between DNA methylation changes and the underlying nucleotide sequence in regions of incomplete lineage sorting and in regions of transcription factor binding, suggesting that both phenomena are closely associated.
Phosphatidylinositol 4-Phosphate Negatively Regulates Chloroplast Division in Arabidopsis
Authors: Okazaki Kumiko , Miyagishima Shin-ya , Wada Hajime 
Published: March 2015

AbstractChloroplast division is performed by the constriction of envelope membranes at the division site. Although constriction of a ring-like protein complex has been shown to be involved in chloroplast division, it remains unknown how membrane lipids participate in the process. Here, we show that phosphoinositides with unknown function in envelope membranes are involved in the regulation of chloroplast division in Arabidopsis thaliana. PLASTID DIVISION1 (PDV1) and PDV2 proteins interacted specifically with phosphatidylinositol 4-phosphate (PI4P). Inhibition of phosphatidylinositol 4-kinase (PI4K) decreased the level of PI4P in chloroplasts and accelerated chloroplast division. Knockout of PI4Kβ2 expression or downregulation of PI4Kα1 expression resulted in decreased levels of PI4P in chloroplasts and increased chloroplast numbers. PI4Kα1 is the main contributor to PI4P synthesis in chloroplasts, and the effect of PI4K inhibition was largely abolished in the pdv1 mutant. Overexpression of DYNAMIN-RELATED PROTEIN5B (DRP5B), another component of the chloroplast division machinery, which is recruited to chloroplasts by PDV1 and PDV2, enhanced the effect of PI4K inhibition, whereas overexpression of PDV1 and PDV2 had additive effects. The amount of DRP5B that associated with chloroplasts increased upon PI4K inhibition. These findings suggest that PI4P is a regulator of chloroplast division in a PDV1- and DRP5B-dependent manner.
The Calcium-Dependent Protein Kinase CPK28 Regulates Development by Inducing Growth Phase-Specific, Spatially Restricted Alterations in Jasmonic Acid Levels Independent of Defense Responses in Arabidopsis
Authors: Matschi Susanne , Hake Katharina , Herde Marco , Hause Bettina , Romeis Tina 
Published: March 2015

AbstractPhytohormones play an important role in development and stress adaptations in plants, and several interacting hormonal pathways have been suggested to accomplish fine-tuning of stress responses at the expense of growth. This work describes the role played by the CALCIUM-DEPENDENT PROTEIN KINASE CPK28 in balancing phytohormone-mediated development in Arabidopsis thaliana, specifically during generative growth. cpk28 mutants exhibit growth reduction solely as adult plants, coinciding with altered balance of the phytohormones jasmonic acid (JA) and gibberellic acid (GA). JA-dependent gene expression and the levels of several JA metabolites were elevated in a growth phase-dependent manner in cpk28, and accumulation of JA metabolites was confined locally to the central rosette tissue. No elevated resistance toward herbivores or necrotrophic pathogens was detected for cpk28 plants, either on the whole-plant level or specifically within the tissue displaying elevated JA levels. Abolishment of JA biosynthesis or JA signaling led to a full reversion of the cpk28 growth phenotype, while modification of GA signaling did not. Our data identify CPK28 as a growth phase-dependent key negative regulator of distinct processes: While in seedlings, CPK28 regulates reactive oxygen species-mediated defense signaling; in adult plants, CPK28 confers developmental processes by the tissue-specific balance of JA and GA without affecting JA-mediated defense responses.