bluuebunny/crossref_metadata_2025 huggingface dataset:
Mass Spectrometry for Structural Biology: Determining the Composition and Architecture of Protein Complexes
Authors: Pukala Tara L.
Published: September 2017

Knowledge of protein structure and protein–protein interactions is vital for appreciating the elaborate biochemical pathways that underlie cellular function. While many techniques exist to probe the structure and complex interplay between functional proteins, none currently offer a complete picture. Mass spectrometry and associated methods provide complementary information to established structural biology tools, and with rapidly evolving technological advances, can in some cases even exceed other techniques by its diversity in application and information content. This is primarily because of the ability of mass spectrometry to precisely identify protein complex stoichiometry, detect individual species present in a mixture, and concomitantly offer conformational information. This review describes the attributes of mass spectrometry for the structural investigation of multiprotein assemblies in the context of recent developments and highlights in the field.
Structures and Anatomical Distribution of Oxygenated Diterpenes in the Australian Nudibranch Chromodoris reticulata
Authors: Suciati  , Lambert Lynette K. , Garson Mary J.
Published: September 2017

The structures and stereochemistry of six new diterpenes (1–6), two of which contain cyclic imine functionality, have been deduced by 2D NMR spectroscopy. The anatomical distribution of these, and of 17 other diterpenes (7–23) that were also isolated, has been investigated. The known compound aplyroseol-2 (14) was the major compound in the mantle tissue along with some dialdehydes, while the linear furan ambliofuran (7) was the only diterpene found solely in the internal organs. The presence of lactone-acetal-hemiacetal functionality in many of the isolated compounds is a consequence of the reactive dialdehydes present in the mollusc.
Ring-closing Metathesis in Peptides - the Sting is in the Tail!
Authors: van Lierop Bianca J. , Bornschein Christoph , Jackson W. Roy , Robinson Andrea J.
Published: September 2017

Performing ring-closing metathesis on resin-bound peptides provides an expedient route to carbocyclic peptidomimetics of medicinal interest. Some sequences are highly resistant to metathesis and special strategies need to be employed to promote viable ring closure. This paper describes an on-resin, alternating solid-phase peptide synthesis-catalysis method to overcome deleterious aggregation phenomena. It can be used to promote high yielding single-ring closures and regioselective multi-ring construction in peptides.
Diversity patterns of subterranean invertebrate fauna in calcretes of the Yilgarn Region, Western Australia
Authors: Hyde Josephine , Cooper Steven J. B. , Humphreys William F. , Austin Andrew D. , Munguia Pablo
Published: September 2017

Calcrete aquifers are unique groundwater habitats containing stygobiontic species endemic to each calcrete. The evolutionary history of stygofauna suggests the calcretes in Western Australia contain multiple ancient lineages, yet populations experience episodic variation in rainfall patterns, with little-known ecological consequences. The aim of the present study was to document stygofaunal diversity patterns and determine whether they are influenced by rainfall events. The average taxon richness in boreholes peaked shortly after periods of high rainfall, and when dominant taxa were excluded, evenness decreased after periods of both high and low rainfall, indicating that dominant taxa are an important factor in driving the system. Strong abundance–distribution relationships reflected the commonality of taxon groups; common taxon groups had broad distributions and high abundance levels, whereas rare taxon groups had small distributions and low abundance. After periods of intermediate and low rainfall, taxon groups had narrower distributions and the maximum number of individuals per borehole was lower. Finally, the majority of boreholes did not show changes in evenness over the 11-year study period, suggesting a reasonably stable ecosystem with episodic fluctuations that can be attributed to rainfall events. The results of the present study indicate that diversity patterns within boreholes are driven episodically by both external and internal factors, such as rainfall and rapid borehole dominance respectively.
Influence of the water quality on the occurrence of the Neotropical otter (Lontra longicaudis) (Olfers, 1818) in a human-altered river basin
Authors: Resende de Almeida Lana , Ramos Pereira Maria João
Published: September 2017

The seeming tolerance of the Neotropical otter (Lontra longicaudis) to human-altered environments does not prevent it from being under threat in several areas across its distribution range. To improve our knowledge of the tolerance of the species to increasing levels of habitat degradation, and adding ecological information, we evaluated the influence of water quality, vegetation structure, seasonality and stream flow on the occurrence of L. longicaudis. We conducted monthly samplings of non-invasive biological material in 16 points across different classes of water quality in the Sinos River Basin in Rio Grande do Sul, Brazil, between January and August 2015. Water quality and stream flow positively influenced the occurrence of L. longicaudis; still, the species seems to reduce its occurrence only in waters of very low quality, showing tolerance to moderate levels of eutrophication. We conclude that the Neotropical otter is tolerant to human-altered environments, but beyond a certain threshold of water-quality degradation, otter persistence is at risk. Monitoring water quality is key for the preservation of riverine ecosystems, and measures to control water pollution and eutrophication are deemed necessary to guarantee the preservation of viable Neotropical otter populations across its distribution range.
Cold fins, murky waters and the moon: what affects shark catches in the bather-protection program of KwaZulu–Natal, South Africa?
Authors: Wintner Sabine P. , Kerwath Sven E.
Published: September 2017

The influence of environmental variables on shark catch in the bather-protection program along the eastern coast of South African was investigated for 11 commonly caught species (Carcharhinus limbatus, C. obscurus, C. brachyurus, C. plumbeus, C. brevipinna, C. leucas, Carcharodon carcharias, Carcharias taurus, Sphyrna lewini, S. zygaena, Galeocerdo cuvier). Data for the period 1986–1994 were analysed using generalised additive models and generalised additive mixed models. The influence of temporal and spatial factors was respectively considered and removed within a standardisation procedure to investigate and predict the influence of lunar cycle, sea-surface temperature (SST) and water visibility on daily catch. The catches of C. taurus and C. brevipinna were significantly affected by all three factors. Catches of all other species were affected by at least one of the three factors, e.g. six were affected by lunar phase, six by SST and seven by water visibility. The results suggested that measurable, predictable relationships exist between environmental conditions and presence and, consequently, catch of shark species in this program. Understanding these relationships could be useful to mitigate against unwanted catch and to further reduce risk for bathers.
Soil properties and organic matter quality in relation to climate and vegetation in southern Indian tropical ecosystems
Authors: Mani Shanmugam , Merino Agustín , García-Oliva Felipe , Riotte Jean , Sukumar Raman
Published: September 2017

Soil organic matter (SOM) quantity and quality can be directly altered by climate, and SOM has been proposed as both a significant source and sink of carbon dioxide. To understand the factors that influence SOM, the present study focuses on the relationship between precipitation and soil physical and chemical properties along a rainfall–vegetation gradient in a seasonally dry tropical forest in the Western Ghats, southern India. Soil pH decreased with increasing rainfall, but soil organic carbon (SOC) and nitrogen (N) slightly increased. Rainfall had strong positive correlations with standing litter (Pearson’s r = 0.85), clay content (r = 0.69) and recalcitrant organic matter (r = 0.73) (all P < 0.05), and chemical properties SOC (r = 0.85), N (r = 0.71), magnesium (r = 0.65), iron (r = 0.64) and zinc (r = 0.75) (all P < 0.05). The heavy fraction, which was bound to mineral particles, comprised more than 60% of the SOM in all sites. The heavy fraction was positively correlated with rainfall and showed a higher proportion in the high rainfall forest soils. Thermal recalcitrant organic matter, such as carbohydrates – and other aliphatic compounds, such as lignin and polyphenols – were also higher in high rainfall forest soils, suggesting a greater effect of SOM turnover. The SOM content and quality were lower in the dry forest soils, which were mainly limited by annual precipitation, but clay content also contributed significantly to SOC storage.
Iconic treadmill hypothesis
Authors: Flaksman Maria
Published: September 2017

The paper deals with the process of iconicity loss and touches upon the enigma of iconic words’ continuous and persistent appearance in languages all over the globe. The hypothesis introduced aims at explaining the reasons behind the never-ceasing iconic coinage. The paper also presents a universal four-step model of iconicity loss.
Tracking linguistic primitives
Authors: Johansson Niklas
Published: September 2017

This paper investigates how cross-linguistic phoneme distributions of 56 fundamental oppositional concepts can reveal semantic relationships by looking into the linguistic forms of 75 genetically and areally distributed languages. Based on proposals of semantic primes (Goddard & Wierzbicka 2002), reduced Swadesh lists (Holman et al. 2008), presumed ultraconservative words (Pagel et al. 2013), attested basic antonyms (Paradis, Willners & Jones 2009) and sense perception words, semantic oppositional pairs were selected. Phonemes were divided according to: the frequency of vowels’ second formant and consonants’ energy accumulation, sonority, a combination of the aforementioned two, and general phonetic traits, e.g. voicing. Using a biplot, the phonological relatedness between the investigated concepts was illustrated graphically, and the phoneme distributions’ over- and underrepresentation from the average was calculated for each concept. Salient semantic groupings and relations based solely on phonological contrasts were found for most investigated concepts, including the semantic domains: Small, Intense Vision-Touch, Large, Organic, Horizontal-Vertical Distance, Deictic, Containment, Gender, Parent and Diurnal, and the sole concept old. The most notable relations found were: mother/i vs. father, a three-way deictic distinction and a dimensional tripartite oppositional relationship. Embodiment, oppositional thinking and evidence for more general concepts to precede complex concepts were proposed as explanations for the results.
Continuity and change
Authors: Moreno Cabrera Juan C.
Published: September 2017

Ablaut Reduplication (AR), as in see-saw, knick-knack, is frequently used in different languages to mimic movement. In this paper, I will discuss its possible iconic interpretations. Following and developing an idea originally suggested by Thun (1963: 75–87), I will show that AR is associated with a physical (visual or acoustic) alternating movement in the following way: reduplication in AR mimics continuity, including repetition, plurality, distribution and habitualness (Fischer 2011: 67), and vowel alternation mimics change including variation, change of direction, instability, uncertainty, vacillation, reciprocity and interruption. I will show that all these meanings can be derived from the combination of the two abstract notions of continuity and change as applied to different aspects of reality and from the results of various semantic shifts associated with reduplicative constructions in general (Fischer 2011: 65–67). I will discuss examples from different languages (including English, French, Spanish, Basque, Estonian, Khakas and Chinese) in order to check the general character of the proposed iconic analysis of AR expressions.
Iconicity in English literary neologisms
Authors: Shamina Elena A.
Published: September 2017

The article deals with literary neologisms that, being a part of a literary character’s artificial language, have to be made understandable for the reader. The study shows that R. Dahl in his book The BFG attains this purpose (consciously or unconsciously) by supplying motivation for the words in the BFG’s vocabulary and other features of his speech. The BFG’s syntax, morphology and phonetics are governed by the English language usage (sometimes non-standard and colloquial), which means they are motivated secondarily. Some of the lexical items, too, are coined with the help of secondary motivation. Most of them, though, are shown to be motivated primarily, with their sound form and meaning in close unconventional interrelation. This kind of relationship between the form and the meaning is typical for iconic language signs that are demonstrated to convey in the BFG’s speech concepts of size, iteration, positive or negative attitudes and various types of sounds. The results of the perception experiments with English and Russian participants reported in the article, on the one hand, prove the iconic character of (at least some) neologisms from the book and, on the other hand, supply examples of universal iconicity being restricted or modified by language specific factors.
The ocean of surging emotion
Authors: Kostetskaya Anastasia
Published: September 2017

This article explores how Symbolist cognitive poetics governs links between the form of the poem and the visual and non-visual imagery pertaining to spiritual transcendence. It investigates how this experience is iconically represented via the blending of human and water ontologies in the poem “Feather Grass” (1895) by the Russian Symbolist poet Konstantin Bal'mont. The emergent structure of this blend, observed throughout Bal'mont’s poetry, points to flux and permeability of the human emotional terrain, including emotional memory. The blend consistently maps the transition from the earthly to the spiritual as a continuous fluid transmutation or liquescence (Kostetskaya 2015: 413). It facilitates the dissolution of various boundaries and the removal of the central Symbolist duality of realia (concrete reality) versus realiora (the true reality of the innermost and supra-material spheres). The liquescence of emotional fabric manifests itself across various features of the poem, such as prosody, rhyme, sound pattern and repetition. The structure of the poem blends various liquescent topologies in order to render non-representational sensations associated with the evocation of emotional memory: it is circular, reminiscent of rings formed on a water surface when a stone is thrown in; simultaneously, it is vertical representing the dynamics of sinking and rising; it also evokes the idea of water as a prototypical mirror.
Ekphrasis, cognition, and iconicity
Authors: Panagiotidou Maria-Eirini
Published: September 2017

The paper examines the relationship between iconicity and ekphrasis from the viewpoint of cognitive poetics and literary stylistics. Cognitive poetics draws on cognitive linguistics, literary linguistics, psychology, and neuroscience to explore the relationship between the creation and interpretation of literary texts and the workings of the human mind. The following analysis focuses on W. D. Snodgrass’s ekphrastic poem “Van Gogh: ‘The Starry Night’” and explores how readers are invited to mentally reconstruct van Gogh’s painting. A close reading of the text demonstrates how the poem mirrors the explosive imagery of the night sky and contrasts it with the serene atmosphere of the village. Moreover, the analysis considers how Snodgrass attempts to reconcile the visual and the verbal media so as to present them as working in unison and enable readers to experience the painting.
Bridging the gap between image and metaphor through cross-modal iconicity
Authors: Elleström Lars
Published: September 2017

Our minds are capable of perceiving similarities not only within the same but also across different sensory areas and different cognitive domains. Iconicity is representation based on similarity, and cross-modal iconicity, which is an extremely widespread phenomenon, should be understood as iconicity that crosses the borders of different kinds of material, spatiotemporal, and sensorial modes, and, furthermore, the border between sensory structures and cognitive configurations. For instance, a visual entity may resemble and thus iconically represent something that is auditory or abstractly cognitive. The aim of this semiotic study, substantially based on empirical findings in psychological, cognitive, and neurological research, is to suggest a general theoretical framework for conceptualizing cross-modal iconicity and relating different kinds of mono-modal and cross-modal iconicity to each other. Its chief argument is that perception and conception of images and metaphors should be understood as the two extremes in a continuum of iconic representation where cross-modal iconicity bridges the apparent gap between mono-modal, sensory-based iconicity and cognitive iconicity. It offers an outline of material, spatiotemporal, and sensorial modes and their interrelations; a thorough account of cross-modal iconicity; a conceptual structure for charting degrees of similarity and iconicity with the aid of cross-modality; an array of examples illustrating the continuum of iconicity from image to metaphor; and a brief discussion of the notion of image schema as an explanatory factor for cross-modal iconicity.
Iconicity, ‘intersemiotic translation’ and the sonnet in the visual poetry of Avelino De Araújo
Authors: Vila-Cabanes Isabel
Published: September 2017

Although the poetic work of the Brazilian artist Avelino de Araújo has recently attracted the attention of literary criticism, there are only few scholarly studies about the paramount role of iconicity in his non-verbal poetry. It is the main purpose of this paper to examine how iconicity and intersemiotic translation unfold in his visual sonnets. Araújo transforms the canonical poetic form into a postmodern visual experiment, playing with the sonnet’s structural, metrical, and communicative conventions. I open with a brief discussion of the still ambiguous term ‘visual poetry’ in contemporary art and a contextualization of Araújo’s poetry. Then, I explore the role of iconicity and intersemiotic relations between words – the titles – and images in the collection Livro de sonetos (1994). While some poems tackle political, social, and aesthetic topics such as hunger, censorship, segregation and the construction of meaning, other pieces are playful experiments on the sonnet form. Finally, I will look at Araújo’s innovative reinterpretation of the classical sonnet as a successful ‘variation’ of the genre and I briefly refer to the poet’s recent animated sonnets, since, as Greber (2002: 568) notes, “The generic invariance of the sonnet is its variance.”
Reading across the gutter
Authors: Riquet Johannes
Published: September 2017

This paper offers a metapoetic analysis of the train journeys in Hergé’s Tintin series as a comment on the reading experience, discussing the process of reading comics in terms of a phenomenology of interruption. Comics are structurally dependent on interruptions: divided into strips and panels that are separated by “gutters”, they disrupt the flow of reading. Implying movement and division, mirroring the direction of reading and referring beyond the individual panels in which they appear only partially, Hergé’s trains and railways lines can be usefully understood as diagrams of the reader’s progression from panel to panel. The many accidents and interruptions that mark the railway journeys in Tintin resonate with the anxieties around speed and transportation that accompanied the railroad from its inception; it is argued that these interruptions are transferred to the reader’s experience of the fragmented space of the comic book itself. This paper thus contends that the series’ unified and controlled vision of a global network is disrupted by the spatial structure of the comic book as experienced in the reading process. This disruption is epitomised by the railroad, and Tintin’s trains are diagrammatically related to the process of reading comics as a process marked by interruptions.
Iconicity in Buddhist language and literature
Authors: Herlofsky William J.
Published: September 2017

This chapter will examine iconicity in Buddhist language and literature by analyzing the multidimensional iconicity in the gyate mantra that appears at the end of the Heart Sutra (Herlofsky 2013, 2014). It will be shown how the method of analysis for the four dimensions of poetry suggested by Abrams (2012) is also applicable to the analysis of multidimensional iconicity in this Buddhist mantra. After a brief discussion of mantra and an explanation of the method to be used, the mantra to be analyzed will be introduced, and the visual appearance of two pictographic (form miming form) versions of the mantra will be discussed. The sounds of the words of the mantra will then be identified, and how the sounds are elicited from the pronunciation of the words for the items represented in the pictographs (form miming form) will be illustrated. The discussion will then proceed to a brief explanation of the meaning of the sutra, describing how the five ‘lines’ of the mantra are related to five stages of enlightenment (form miming meaning). And finally, there will be an illustration of how the articulation of the sounds of the mantra can be seen as an orchestrated performance of iconically motivated vocal gestures (form miming meaning).
Performative iconicity
Authors: Zirker Angelika
Published: September 2017

From the beginning of Shakespeare’s dramatic long poem The Rape of Lucrece, Tarquin and Lucrece are presented as antagonists: lust-breathed Tarquin (3) vs. chaste Lucrece (7). This opposition also connects them with one another, and the key to their relationship lies in a statement that is uttered late in the poem, when Lucrece is looking at the Troy painting and says: “These contraries such unity do hold” (1558). The characterisation of both Tarquin and Lucrece on the level of content is mirrored on the level of language. For example, when Tarquin in the second line of the epyllion is described to be “borne by the trustless wings of false desire”, the apparent parallelism (adjective followed by a noun) in fact contains an antagonistic structure. Throughout the poem, the inner debate that characterises him before the rape of Lucrece is presented in terms of self-division on the level of content; linguistically, this is rendered by means of chiasmus. In the following, I will show that the relations of synonymy and parallelism as well as of chiasmus and oxymoron can be found throughout the poem, and that they are part of the larger setup of the text in that they imitate the content iconically, i.e. form and meaning correspond to each other. They also become performative as the language enacts the content. Parallelism and chiasmus are part of the semiotic setup and of the dramatic structure of the poem, and they go beyond mere poetic form and content (in the sense of action) as they are also part of the complex technique of character representation.
Why notational iconicity is a form of operational iconicity
Authors: Krämer Sybille
Published: September 2017

Something like a phonographic dogma dominates the theory of writing: writing is considered to be a fixed version of spoken language. This essay intends to overcome the speech-oriented concept of writing by conceptualizing the idea of ‘notational iconicity’. Being hybrids, written texts embody both, linguistic and iconic attributes. The decisive argument in favour of ‘notational iconicity’ is not only its visuality, but the two-dimensional spatiality and operativity of writing. This kind of operational iconicity is inherent to almost all written texts and is based on the fact that written texts materially and perceptively present themselves synoptically and simultaneously. Inscribed surfaces open up a neatly arranged and controllable space of aisthetic presentation and tactile manipulations: Every written configuration can be reconfigured; thus writing is a paper-tool, a laboratory for cognitive and aesthetic activities. At this point the connection between writing and other forms of graphical media like graphs and diagrams matters: The cultural technique of ‘flattening out’ constitutes an important strand in our media evolution, for communication as cognition, for composition as computation.
The iconicity of literary analysis
Authors: Bauer Matthias , Brockmann Saskia
Published: September 2017

In this paper, we propose that the iconicity of Logical Form can help us evaluate the adequateness of an interpretation. We consider the relationship between iconicity, literary texts, formal semantic analysis and interpretation. With the help of an example taken from the poem “This was a Poet –” (Fr446, J448) by Emily Dickinson, we explain in which way a formal semantic analysis is iconic of the meaning of a text. We then compare this iconic analysis to other interpretative utterances about literary texts, in particular to statements that can be considered allegories of the text meaning. With this comparison we come to the conclusion that a formal semantic analysis does not restrict interpretation, but serves as guidance towards finding out about all relevant and complex structures that should also be followed in an interpretation. A linguistic analysis is thus to be seen as a measure to test the adequacy of interpretations.
Robert Brandom’s Normative Inferentialism
Authors: Turbanti Giacomo
Published: September 2017

The philosophy of language of Robert Brandom is based on a theoretical structure composed of three main elements: the normative analysis of linguistic practices, the inferential characterization of conceptual contents and the expressive articulation of the relations between the former two. Normative pragmatics aims to explain how linguistic practices are sufficient to confer contentful states in those who engage in them. Inferential semantics provides a theory of such pragmatic significances in terms of the inferential relations that articulate conceptual contents. Rational expressivism is the thesis that concept application is essentially a process of turning something that can only be done into something that can also be said. Such a threefold structure is the core of normative inferentialism. This book is a concise, self-contained and comprehensive presentation of this philosophical enterprise. It guides the reader through the analysis of Brandom's imposing theoretical apparatus, the discovery of the roots of his approach in American pragmatism and German idealism, till the exploration of some of its most interesting and recent outcomes in pragmatics and semantics. It is a valuable resource for both those who approach Brandom's work for the first time and those who are interested in the potential of normative inferentialism.
Discourse-pragmatic Variation in Context
Authors: D’Arcy Alexandra
Published: September 2017

Like is a ubiquitous feature of English with a deep history in the language, exhibiting regular and constrained variable grammars over time. This volume explores the various contexts of like, each of which contributes to the reality of contemporary vernaculars: its historical context, its developmental context, its social context, and its ideological context. The final chapter examines the ways in which these contexts overlap and inform current understanding of acquisition, structure, change, and embedding. The volume also features an extensive appendix, containing numerous examples of like in its pragmatic functions from a range of English corpora, both diachronic and synchronic. The volume will be of interest to students and scholars of English historical linguistics, grammaticalization, language variation and change, discourse-pragmatics and the interface of these fields with formal linguistic theory.
Key compounds contributing to the fruity aroma characterization in Japanese raw soy sauce
Authors: Meng Qi , Imamura Miho , Katayama Hiroshi , Obata Akio , Sugawara Etsuko
Published: September 2017

In order to clarify the aroma characteristics of raw soy sauce (RS), the application of gas chromatography−olfactometry analysis to the aroma concentrate from a RS revealed 76 aroma peaks, of which 25 peaks showed fruit-like aromas. Furthermore, the head space aromatic compounds of RS were analyzed with 32 peaks detected. Ethyl 2-methylpropanoate, ethyl butanoate, ethyl 2-methylbutanoate, ethyl 3-methylbutanoate, and ethyl 4-methylpentanoate were detected with higher flavor dilution factor (FD factor) than other aroma compounds by aroma extract dilution analysis. Quantitative analysis suggested that these compounds were common in all RS samples tested in this study, and were present at higher concentrations than their perception thresholds. The concentrations and the FD factors of these compounds were significantly decreased during the heating of the RS. Fruitiness is one of the key aroma characteristics of RS and the ethyl esters identified in this study are the key components contributing to this distinct aroma.
A Study of Thermal Stability And Crystallization Kinetics of SbSeGe Glassy Alloys
Authors: Sharda S , Sharma P , Sharma V
Published: September 2017

Alloys of Sb10Se90-xGex
(x = 0, 19, 21, 23, 25, 27) have been prepared using melt quenching technique. Differential thermal analysis has been used to determine the three characteristic temperatures, glass transition (Tg
), glass crystallization (Tc
) and melting temperature (Tm
), at four heating rates 5, 10, 15 and 20 K/min. The thermal stability and ease of glass formation have been evaluated in terms of Hruby parameter and reduced glass transition temperature respectively. The activation energy for glass crystallization (Ec
) has been calculated using Kissinger's method and Marseglia theory. The composition dependence of Tg
and Ec
has also been discussed.
The Effects of Audiovisual Inputs on Solving the Cocktail Party Problem in the Human Brain: An fMRI Study
Authors: Li Yuanqing , Wang Fangyi , Chen Yongbin , Cichocki Andrzej , Sejnowski Terrence
Published: September 2017

At cocktail parties, our brains often simultaneously receive visual and auditory information. Although the cocktail party problem has been widely investigated under auditory-only settings, the effects of audiovisual inputs have not. This study explored the effects of audiovisual inputs in a simulated cocktail party. In our fMRI experiment, each congruent audiovisual stimulus was a synthesis of 2 facial movie clips, each of which could be classified into 1 of 2 emotion categories (crying and laughing). Visual-only (faces) and auditory-only stimuli (voices) were created by extracting the visual and auditory contents from the synthesized audiovisual stimuli. Subjects were instructed to selectively attend to 1 of the 2 objects contained in each stimulus and to judge its emotion category in the visual-only, auditory-only, and audiovisual conditions. The neural representations of the emotion features were assessed by calculating decoding accuracy and brain pattern-related reproducibility index based on the fMRI data. We compared the audiovisual condition with the visual-only and auditory-only conditions and found that audiovisual inputs enhanced the neural representations of emotion features of the attended objects instead of the unattended objects. This enhancement might partially explain the benefits of audiovisual inputs for the brain to solve the cocktail party problem.
Challenges to quantifying glass eel abundance from large and dynamic estuaries
Authors: Walmsley Sarah , Bremner Julie , Walker Alan , Barry Jon , Maxwell David
Published: September 2017

European eel Anguilla anguilla recruitment into the rivers of the northeastern Atlantic has declined substantially since the 1980s. Monitoring of recruiting juveniles, or glass eels, is usually undertaken in small estuaries and rivers. Sampling of large-scale estuaries is rare, due to the size of the sampling area and the resources needed to provide adequate sampling levels. Here we describe surveys for glass eels in the UK’s largest estuarine system, the Severn Estuary/Bristol Channel. We sampled across a 20 km-wide stretch of the estuary in 2012 and 2013, using a small-meshed net deployed from a commercial fishing trawler, and the surveys yielded over 2500 glass eels. Eels were more abundant in the surface layer (0–1.4 m depth) than at depth (down to 8.4 m depth), were more abundant close to the south shore than along the north shore or middle of the estuary, and were more abundant in lower salinity water. Numbers were higher in the second year than in the first and eels were more abundant in February than April. The difficulties and logistics of sampling in such a large estuary are discussed, along with the level of resources required to provide robust estimates of glass eel abundance.
Inversions of the Ledoux discriminant: a closer look at the tachocline
Authors: Buldgen Gaël , Salmon S. J. A. J. , Godart M. , Noels A. , Scuflaire R. , Dupret M. A. , Reese D. R. , Colgan J. , Fontes C. J. , Eggenberger P. , Hakel P. , Kilcrease D. P. , Richard O.
Published: September 2017

Modelling the base of the solar convective envelope is a tedious problem. Since the first rotation inversions, solar modellers are confronted with the fact that a region of very limited extent has an enormous physical impact on the Sun. Indeed, it is the transition region from differential to solid body rotation, the tachocline, which furthermore is influenced by turbulence and is also supposed to be the seat of the solar magnetic dynamo. Moreover, solar models show significant disagreement with the sound-speed profile in this region. In this Letter, we show how helioseismology can provide further constraints on this region by carrying out an inversion of the Ledoux discriminant. We compare these inversions for standard solar sodels built using various opacity tables and chemical abundances and discuss the origins of the discrepancies between solar models and the Sun.
The cosmic microwave background Cold Spot anomaly: the impact of sky masking and the expected contribution from the integrated Sachs–Wolfe effect
Authors: Naidoo Krishna , Benoit-Lévy Aurélien , Lahav Ofer
Published: September 2017

We re-analyse the cosmic microwave background (CMB) Cold Spot (CS) anomaly with particular focus on understanding the bias a mask (contaminated by Galactic and point sources) may introduce. We measure the coldest spot, found by applying the Spherical Mexican Hat Wavelet transform on 100 000 cut-sky (masked) and full-sky CMB simulated maps. The CS itself is barely affected by the mask; we estimate a 94 per cent probability that the CS is the full-sky temperature minimum. However, ∼48 per cent (masked fraction of the mask) of full-sky minima are obscured by the mask. Since the observed minima are slightly hotter than the full-sky ensemble of minima, a cut-sky analysis would have found the CS to be significant at ∼2.2σ with a wavelet angular scale of R = 5°. None the less, comparisons to full-sky minima show the CS significance to be only ∼1.9σ and <2σ for all R. The CS on the last scattering surface may be hotter due to the integrated Sachs–Wolfe effect in the line of sight. However, our simulations show that this is on average only ∼10 per cent (about 10 μK but consistent with zero) of the CS temperature profile. This is consistent with Lambda and cold dark matter reconstructions of this effect based on observed line-of-sight voids.
Human interactome of the influenza B virus NS1 protein
Authors: Patzina Corinna , Botting Catherine H. , García-Sastre Adolfo , Randall Richard E. , Hale Benjamin G.
Published: September 2017

NS1 proteins of influenza A and B viruses share limited sequence homology, yet both are potent manipulators of host cell processes, particularly interferon (IFN) induction. Although many cellular partners are reported for A/NS1, only a few (e.g. PKR and ISG15) have been identified for B/NS1. Here, affinity-purification and mass spectrometry were used to expand the known host interactome of B/NS1. We identified 22 human proteins as new putative targets for B/NS1, validating several, including DHX9, ILF3, YBX1 and HNRNPC. Consistent with two RNA-binding domains in B/NS1, many of the identified factors bind RNA and some interact with B/NS1 in an RNA-dependent manner. Functional characterization of several B/NS1 interactors identified SNRNP200 as a potential positive regulator of host IFN responses, while ILF3 exhibited dual roles in both IFN induction and influenza B virus replication. These data provide a resource for future investigations into the mechanisms underpinning host cell modulation by influenza B virus NS1.
Characterization of feedback-resistant mevalonate kinases from the methanogenic archaeons Methanosaeta concilii and Methanocella paludicola
Authors: Kazieva Ekaterina , Yamamoto Yoko , Tajima Yoshinori , Yokoyama Keiichi , Katashkina Joanna , Nishio Yousuke
Published: September 2017

The inhibition of mevalonate kinase (MVK) by downstream metabolites is an important mechanism in the regulation of isoprenoid production in a broad range of organisms. The first feedback-resistant MVK was previously discovered in the methanogenic archaeon Methanosarcinamazei. Here, we report the cloning, expression, purification, kinetic characterization and inhibition analysis of MVKs from two other methanogens, Methanosaetaconcilii and Methanocellapaludicola. Similar to the M. mazei MVK, these enzymes were not inhibited by diphosphomevalonate (DPM), dimethylallyl diphosphate (DMAPP), isopentenyldiphosphate (IPP), geranylpyrophosphate (GPP) or farnesylpyrophosphate (FPP). However, they exhibited significantly higher affinity to mevalonate and higher catalytic efficiency than the previously characterized enzyme.
GIGYF2 mediates post-transcriptional mRNA repression through recruitment of the CCR4/NOT complex
Authors: Ramirez Cinthia Claudia Amaya , Hubbe Petra , Mandel Nicolas , Béthune Julien
Published: September 2017

Initially identified as a factor involved in tyrosine kinase receptor signalling, GRB10-interacting GYF protein 2 (GIGYF2) has later been shown to interact with the 5’ cap-binding protein m4EHP as part of a translation repression complex, and to mediate post-transcriptional repression of tethered reporter mRNAs. We recently observed that GIGYF2 also interacts with the miRNA-induced silencing complex and modulates its translation repression activity. Here we have further investigated how GIGYF2 represses mRNA function. In RNA tethering reporter assays we show that GIGYF2 exerts its action through a combination of translational repression and stimulated mRNA decay. Using truncation variants we identify two distinct effector domains within GIGYF2. In this assay GIGYF2-mediated repression is independent of m4EHP but dependent on the deadenylation activity of the CCR4/NOT complex. We further show that GIGYF2 interacts with multiple subunits of the CCR4/NOT complex and interestingly depletion of the CNOT1 scaffold subunit does not affect GIGYF2-mediated repression. Finally, we identify endogenous mRNA targets of GIGYF2 that recapitulate m4EHP - independent repression. Altogether, we propose that GIGYF2 has two distinct mechanisms of repression: one depends on m4EHP binding and affects translation, the other is m4EHP-independent and relies on the deadenylation activity of the CCR4/NOT complex.
Neither pulled nor pushed: Genetic drift and front wandering uncover a new class of reaction-diffusion waves
Authors: Birzu Gabriel , Hallatschek Oskar , Korolev Kirill S.
Published: September 2017

Short Abstract

Traveling waves describe diverse natural phenomena from crystal growth in physics to range expansions in biology. Two classes of waves exist with very different properties: pulled and pushed. Pulled waves are driven by high growth rates at the expansion edge, where the number of organisms is small and fluctuations are large. In contrast, fluctuations are suppressed in pushed waves because the region of maximal growth is shifted towards the population bulk. Although it is commonly believed that expansions are either pulled or pushed, we found an intermediate class of waves with bulk-driven growth, but exceedingly large fluctuations. These waves are unusual because their properties are controlled by both the leading edge and the bulk of the front.

Long Abstract

Epidemics, flame propagation, and cardiac rhythms are classic examples of reaction-diffusion waves that describe a switch from one alternative state to another. Only two types of waves are known: pulled, driven by the leading edge, and pushed, driven by the bulk of the wave. Here, we report a distinct class of semi-pushed waves for which both the bulk and the leading edge contribute to the dynamics. These hybrid waves have the kinetics of pushed waves, but exhibit giant fluctuations similar to pulled waves. The transitions between pulled, semi-pushed, and fully-pushed waves occur at universal ratios of the wave velocity to the Fisher velocity. We derive these results in the context of a species invading a new habitat by examining front diffusion, rate of diversity loss, and fluctuation-induced corrections to the expansion velocity. All three quantities decrease as a power law of the population density with the same exponent. We analytically calculate this exponent taking into account the fluctuations in the shape of the wave front. For fully-pushed waves, the exponent is −1 consistent with the central limit theorem. In semi-pushed waves, however, the fluctuations average out much more slowly, and the exponent approaches 0 towards the transition to pulled waves. As a result, a rapid loss of genetic diversity and large fluctuations in the position of the front occur even for populations with cooperative growth and other forms of an Allee effect. The evolutionary outcome of spatial spreading in such populations could therefore be less predictable than previously thought.
Genomic basis for RNA alterations revealed by whole-genome analyses of 27 cancer types
Authors:   PCAWG Transcriptome Core Group, Calabrese Claudia , Davidson Natalie R. , Fonseca Nuno A. , He Yao , Kahles André , Lehmann Kjong-Van , Liu Fenglin , Shiraishi Yuichi , Soulette Cameron M. , Urban Lara , Demircioğlu Deniz , Greger Liliana , Li Siliang , Liu Dongbing , Perry Marc D. , Xiang Linda , Zhang Fan , Zhang Junjun , Bailey Peter , Erkek Serap , Hoadley Katherine A. , Hou Yong , Kilpinen Helena , Korbel Jan O. , Marin Maximillian G. , Markowski Julia , Nandi Tannistha , Pan-Hammarström Qiang , Pedamallu Chandra Sekhar , Siebert Reiner , Stark Stefan G. , Su Hong , Tan Patrick , Waszak Sebastian M. , Yung Christina , Zhu Shida ,   PCAWG Transcriptome Working Group, Awadalla Philip , Creighton Chad J. , Meyerson Matthew , Ouellette B.F. Francis , Wu Kui , Yang Huangming ,   ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Network, Brazma Alvis , Brooks Angela N. , Göke Jonathan , Rätsch Gunnar , Schwarz Roland F. , Stegle Oliver , Zhang Zemin
Published: September 2017

We present the most comprehensive catalogue of cancer-associated gene alterations through characterization of tumor transcriptomes from 1,188 donors of the Pan-Cancer Analysis of Whole Genomes project. Using matched whole-genome sequencing data, we attributed RNA alterations to germline and somatic DNA alterations, revealing likely genetic mechanisms. We identified 444 associations of gene expression with somatic non-coding single-nucleotide variants. We found 1,872 splicing alterations associated with somatic mutation in intronic regions, including novel exonization events associated with Alu elements. Somatic copy number alterations were the major driver of total gene and allele-specific expression (ASE) variation. Additionally, 82% of gene fusions had structural variant support, including 75 of a novel class called “bridged” fusions, in which a third genomic location bridged two different genes. Globally, we observe transcriptomic alteration signatures that differ between cancer types and have associations with DNA mutational signatures. Given this unique dataset of RNA alterations, we also identified 1,012 genes significantly altered through both DNAandRNA mechanisms. Our study represents an extensive catalog of RNA alterations and reveals new insights into the heterogeneous molecular mechanisms of cancer gene alterations.
Temporal epigenomic profiling identifies AHR and GLIS1 as super-enhancer controlled regulators of mesenchymal multipotency
Authors: Gérard Deborah , Schmidt Florian , Ginolhac Aurélien , Schmitz Martine , Halder Rashi , Ebert Peter , Schulz Marcel H. , Sauter Thomas , Sinkkonen Lasse
Published: September 2017

Temporal data on gene expression and context-specific open chromatin states can improve identification of key transcription factors (TFs) and the gene regulatory networks (GRNs) controlling cellular differentiation. However, their integration remains challenging. Here, we delineate a general approach for data-driven and unbiased identification of key TFs and dynamic GRNs, called EPIC-DREM. We generated time-series transcriptomic and epigenomic profiles during differentiation of mouse multipotent bone marrow stromal cells (MSCs) towards adipocytes and osteoblasts. Using our novel approach we constructed time-resolved GRNs for both lineages. To prioritize the identified shared regulators, we mapped dynamic super-enhancers in both lineages and associated them to target genes with correlated expression profiles. We identified aryl hydrocarbon receptor (AHR) and Glis family zinc finger 1 (GLIS1) as mesenchymal key TFs controlled by dynamic MSC-specific super-enhancers that become repressed in both lineages. AHR and GLIS1 control differentiation-induced genes and we propose they function as guardians of mesenchymal multipotency.