bluuebunny/crossref_metadata_2025_split huggingface dataset:
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.
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.”
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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 &lt;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.
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

ABSTRACTInitially 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

AbstractShort AbstractTraveling 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 AbstractEpidemics, 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

AbstractWe 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

ABSTRACTTemporal 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.
Temporally feathered intensity modulated radiation therapy: a planning technique to reduce normal tissue toxicity
Authors: López Alfonso Juan Carlos , Parsai Shireen , Joshi Nikhil , Godley Andrew , Shah Chirag , Koyfman Shlomo A. , Caudell Jimmy J. , Fuller Clifton D. , Enderling Heiko , Scott Jacob G. 
Published: September 2017

AbstractPurposeIntensity modulated radiation therapy (IMRT) has allowed optimization of three-dimensional spatial radiation dose distributions permitting target coverage while reducing normal tissue toxicity. However, radiation-induced normal tissue toxicity is a major contributor to patients’ quality of life and often a dose-limiting factor in the definitive treatment of cancer with radiation therapy. We propose the next logical step in the evolution of IMRT using canonical radiobiological principles, optimizing the temporal dimension through which radiation therapy is delivered to further reduce radiation-induced toxicity by increased time for normal tissue recovery. We term this novel treatment planning strategy “temporally feathered radiotherapy” (TFRT).MethodsTFRT plans were generated as a composite of five simulated treatment plans each with altered constraints on particular hypothetical organs at risk (OARs) to be delivered sequentially. For each of these TFRT plans, OARs chosen for feathering receive higher doses while the remaining OARs receive lower doses than the standard fractional dose delivered in a conventional fractionated IMRT plan. Each TFRT plan is delivered a specific weekday, which in effect leads to a higher dose once weekly followed by four lower fractional doses to each temporally feathered OAR. We compared normal tissue toxicity between TFRT and conventional fractionated IMRT plans by using a dynamical mathematical model to describe radiation-induced tissue damage and repair over time.ResultsModel-based simulations of TFRT demonstrated potential for reduced normal tissue toxicity compared to conventionally planned IMRT. The sequencing of high and low fractional doses delivered to OARs by TFRT plans suggested increased normal tissue recovery, and hence less overall radiation-induced toxicity, despite higher total doses delivered to OARs compared to conventional fractionated IMRT plans. The magnitude of toxicity reduction by TFRT planning was found to depend on the corresponding standard fractional dose of IMRT and organ-specific recovery rate of sublethal radiation-induced damage.ConclusionsTFRT is a novel technique for treatment planning and optimization of therapeutic radiotherapy that considers the non-linear aspects of tissue repair to optimize toxicity profiles. Model-based simulations of TFRT to carefully conceptualized clinical cases have demonstrated potential for normal tissue toxicity reduction in a previously described dynamical model of normal tissue complication probability (NTCP).
Comparison of two ancient DNA extraction protocols for skeletal remains from tropical environments
Authors: Nieves-Colón Maria A. , Ozga Andrew T. , Pestle William J. , Cucina Andrea , Tiesler Vera , Stanton Travis W. , Stone Anne C. 
Published: September 2017

ABSTRACTObjectivesThe tropics harbor a large part of the world’s biodiversity and have a long history of human habitation. However, paleogenomics research in these climates has been constrained so far by poor ancient DNA yields. Here we compare the performance of two DNA extraction methods on ancient samples of teeth and petrous portions excavated from tropical and semitropical sites in Tanzania, Mexico, and Puerto Rico (N=12).Materials and MethodsAll samples were extracted twice, built into double-stranded sequencing libraries, and shotgun sequenced on the Illumina HiSeq 2500. The first extraction protocol, Method D, was previously designed for recovery of ultrashort DNA fragments from skeletal remains. The second, Method H, modifies the first by adding an initial EDTA wash and an extended digestion and decalcification step.ResultsNo significant difference was found in overall ancient DNA yields or post-mortem damage patterns recovered from samples extracted with either method, irrespective of tissue type. However, Method H samples had higher endogenous content and more mapped reads after quality-filtering, but also higher clonality. In contrast, samples extracted with Method D had shorter average DNA fragments.DiscussionBoth methods successfully recovered endogenous ancient DNA. But, since surviving DNA in ancient or historic remains from tropical contexts is extremely fragmented, our results suggest that Method D is the optimal choice for working with samples from warm and humid environments. Additional optimization of extraction conditions and further testing of Method H with different types of samples may allow for improvement of this protocol in the future.