bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of the reduced speed of light approximation on ionization front velocities in cosmological simulations of the epoch of reionization
Authors: Deparis Nicolas , Aubert Dominique , Ocvirk Pierre , Chardin Jonathan , Lewis Joseph 
Published: January 2019

Context. Coupled radiative-hydrodynamics simulations of the epoch of reionization aim to reproduce the propagation of ionization fronts during the transition before the overlap of HII regions. Many of these simulations use moment-based methods to track radiative transfer processes using explicit solvers and are therefore subject to strict stability conditions regarding the speed of light, which implies a great computational cost. The cost can be reduced by assuming a reduced speed of light, and this approximation is now widely used to produce large-scale simulations of reionization.
Aims. We measure how ionization fronts propagate in simulations of the epoch of reionization. In particular, we want to distinguish between the different stages of the fronts’ progression into the intergalactic medium. We also investigate how these stages and their properties are impacted by the choice of a reduced speed of light.
Methods. We introduce a new method for estimating and comparing the ionization front speeds based on maps of the reionization redshifts. We applied it to a set of cosmological simulations of the reionization using a set of reduced speeds of light, and measured the evolution of the ionization front speeds during the reionization process. We only considered models where the reionization is driven by the sources created within the simulations, without potential contributions of an external homogeneous ionizing background.
Results. We find that ionization fronts progress via a two-stage process, the first stage at low velocity as the fronts emerge from high density regions and a second later stage just before the overlap, during which front speeds increase close to the speed of light. For example, using a set of small 8 Mpc h−3 simulations, we find that a minimal velocity of 0.3c is able to model these two stages in this specific context without significant impact. Values as low as 0.05c can model the first low velocity stage, but limit the acceleration at later times. Lower values modify the distribution of front speeds at all times. Using another set of simulations with larger 64 Mpc h−3 volumes that better account for distant sources, we find that reduced speed of light has a greater impact on reionization times and front speeds in underdense regions that are reionized at late times and swept by radiation produced by distant sources. Conversely, the same quantities measured in dense regions with slow fronts are less sensitive to c∼ values. While the discrepancies introduced by reduced speed of light could be reduced by the inclusion of an additional UV background, we expect these conclusions to be robust in the case of simulations with reionizations driven by inner sources.
Wave heating in gravitationally stratified coronal loops in the presence of resistivity and viscosity
Authors: Karampelas K. , Van Doorsselaere T. , Guo M. 
Published: January 2019

Context. In recent years, coronal loops have been the focus of studies related to the damping of different magnetohydrodynamic (MHD) surface waves and their connection with coronal seismology and wave heating. For a better understanding of wave heating, we need to take into account the effects of different dissipation coefficients such as resistivity and viscosity, the importance of the loop physical characteristics, and the ways gravity can factor into the evolution of these phenomena.
Aims. We aim to map the sites of energy dissipation from transverse waves in coronal loops in the presence and absence of gravitational stratification and to compare ideal, resistive, and viscous MHD.
Methods. Using the PLUTO code, we performed 3D MHD simulations of kink waves in single, straight, density-enhanced coronal flux tubes of multiple temperatures.
Results. We see the creation of spatially expanded Kelvin–Helmholtz eddies along the loop, which deform the initial monolithic loop profile. For the case of driven oscillations, the Kelvin–Helmholtz instability develops despite physical dissipation, unless very high values of shear viscosity are used. Energy dissipation gets its highest values near the apex, but is present all along the loop. We observe an increased efficiency of wave heating once the kinetic energy saturates at the later stages of the simulation and a turbulent density profile has developed.
Conclusions. The inclusion of gravity greatly alters the dynamic evolution of our systems and should not be ignored in future studies. Stronger physical dissipation leads to stronger wave heating in our set-ups. Finally, once the kinetic energy of the oscillating loop starts saturating, all the excess input energy turns into internal energy, resulting in more efficient wave heating.
Juggling ideals and constraints
Authors: Dale Liz , Oostdam Ron , Verspoor Marjolijn 
Published: January 2019

AbstractIn bilingual streams in the Netherlands, school subjects are taught in an additional language so that pupils learn both subject content and the target language by using language meaningfully. Teachers of English in bilingual streams (TEBs) are often expected to collaborate with subject teacher colleagues (STs). In addition, they teach separate language lessons. This provides TEBs with specific challenges. This article reports on a focus group (FG) study exploring the extent to which the ideals of stakeholders in bilingual schools in the Netherlands reflect the literature on this topic, using a frame of reference developed for this purpose (Dale, Oostdam, & Verspoor, 2017). Five FGs were held with TEBs and STs from Dutch schools in the network for bilingual education and with members of the network’s quality assurance panels. Each FG consisted of between three and six participants with a similar role in bilingual education; audit panel chairpersons, audit panel secretaries and STs and TEBs from different schools. Participants were asked to discuss what an ideal English teacher would do in English lessons and in cooperation with subject colleagues. Data consists of five transcripts of the FG discussions. On the basis of inductive and deductive analyses (using MaxQDA), the ideals of stakeholders are positioned in the framework to explore to what extent different types of stakeholders have complementary or conflicting views. The findings suggest that stakeholders need to develop more shared understandings and a shared language to allow TEBs to realise their ambitions.
The acquisition of L3 variation among early bilinguals
Authors: Park Mihi , Starr Rebecca Lurie 
Published: January 2019

Abstract
The present study investigates whether prior experience with formal study of an L2 influences L3 Korean learners’ Type 1 variation (i.e., use of obligatory forms) and Type 2 variation (i.e., variation between alternative acceptable variants). The patterns of variation in Korean argument realization of early bilingual learners (English-Chinese/Malay/Indonesian/Tamil) of L3 Korean were assessed in light of the distribution of variants present in classroom input, learners’ prior L2 learning experience and home language background, argument animacy and number, and familiarity of verb structure type.
Our findings demonstrate that prior experience with a typologically-similar L2 facilitates acquisition of grammatical patterns as well as acquisition of native-like patterns of variation between grammatical forms that are constrained by a range of internal linguistic factors. Any L2 experience, regardless of typological proximity, is found to facilitate acquisition of internal linguistic constraints, but not acquisition of grammatical patterns.
Asian slurs and stereotypes in the USA
Authors: Croom Adam M. 
Published: January 2019

AbstractSlurs such aschinkandgookare linguistic expressions that are primarily used to derogate certain group members for their descriptive attributes (such as their ethnicity) and are often considered the most offensive of expressions. Recent work on the semantics and pragmatics of slurs has illuminated several important facts regarding their meaning and use – including that slurs are commonly understood to felicitously apply towards some targets yet not others, that slurs are among the most potentially offensive expressions afforded by natural language, and that slurs are often flexibly employed and of potential use, not only derogatorily to convey offense towards out-group members, but also non-derogatorily to convey affiliation with in-group members or to diminish the derogatory force that the slur is typically understood to carry. Nonetheless, prior scholarship has unfortunately restricted itself primarily to considerations of slurs that typically target members of other groups. Since no account of slurs for Asian-Americans has so far been proposed, the aim of this article is therefore to provide the first systematic and empirically informed analysis of slurs for Asian-Americans that accounts for both their derogatory and appropriative (non-derogatory) use.
MSC: a metagenomic sequence classification algorithm
Authors: Saha Subrata , Johnson Jethro , Pal Soumitra , Weinstock George M , Rajasekaran Sanguthevar 
Published: January 2019

Abstract

Motivation
Metagenomics is the study of genetic materials directly sampled from natural habitats. It has the potential to reveal previously hidden diversity of microscopic life largely due to the existence of highly parallel and low-cost next-generation sequencing technology. Conventional approaches align metagenomic reads onto known reference genomes to identify microbes in the sample. Since such a collection of reference genomes is very large, the approach often needs high-end computing machines with large memory which is not often available to researchers. Alternative approaches follow an alignment-free methodology where the presence of a microbe is predicted using the information about the unique k-mers present in the microbial genomes. However, such approaches suffer from high false positives due to trading off the value of k with the computational resources. In this article, we propose a highly efficient metagenomic sequence classification (MSC) algorithm that is a hybrid of both approaches. Instead of aligning reads to the full genomes, MSC aligns reads onto a set of carefully chosen, shorter and highly discriminating model sequences built from the unique k-mers of each of the reference sequences.

Results
Microbiome researchers are generally interested in two objectives of a taxonomic classifier: (i) to detect prevalence, i.e. the taxa present in a sample, and (ii) to estimate their relative abundances. MSC is primarily designed to detect prevalence and experimental results show that MSC is indeed a more effective and efficient algorithm compared to the other state-of-the-art algorithms in terms of accuracy, memory and runtime. Moreover, MSC outputs an approximate estimate of the abundances.

Availability and implementation
The implementations are freely available for non-commercial purposes. They can be downloaded from https://drive.google.com/open?id=1XirkAamkQ3ltWvI1W1igYQFusp9DHtVl.
SMuRF: portable and accurate ensemble prediction of somatic mutations
Authors: Huang Weitai , Guo Yu Amanda , Muthukumar Karthik , Baruah Probhonjon , Chang Mei Mei , Jacobsen Skanderup Anders 
Published: January 2019

Abstract

Summary
Somatic Mutation calling method using a Random Forest (SMuRF) integrates predictions and auxiliary features from multiple somatic mutation callers using a supervised machine learning approach. SMuRF is trained on community-curated matched tumor and normal whole genome sequencing data. SMuRF predicts both SNVs and indels with high accuracy in genome or exome-level sequencing data. Furthermore, the method is robust across multiple tested cancer types and predicts low allele frequency variants with high accuracy. In contrast to existing ensemble-based somatic mutation calling approaches, SMuRF works out-of-the-box and is orders of magnitudes faster.

Availability and implementation
The method is implemented in R and available at https://github.com/skandlab/SMuRF. SMuRF operates as an add-on to the community-developed bcbio-nextgen somatic variant calling pipeline.

Supplementary information
Supplementary data are available at Bioinformatics online.
Crisflash: open-source software to generate CRISPR guide RNAs against genomes annotated with individual variation
Authors: Jacquin Adrien L S , Odom Duncan T , Lukk Margus 
Published: January 2019

Abstract

Summary
CRISPR/Cas9 system requires short guide RNAs (sgRNAs) to direct genome modification. Most currently available tools for sgRNA design operate only with standard reference genomes, and are best suited for small-scale projects. To address these limitations, we developed Crisflash, a software tool for fast sgRNA design and potential off-target discovery, built for performance and flexibility. Crisflash can rapidly design CRISPR guides against any sequenced genome or genome sequences, and can optimize guide accuracy by incorporating user-supplied variant data. Crisflash is over an order of magnitude faster than comparable tools, even using a single CPU core, and efficiently and robustly scores the potential off-targeting of all possible candidate CRISPR guide oligonucleotides.

Availability and implementation
https://github.com/crisflash

Supplementary information
Supplementary data are available at Bioinformatics online.
Of Saints, Shrines, and Tractors: Untangling the Meaning of Islam in Soviet Central Asia
Authors: Sartori Paolo 
Published: January 2019

Abstract
In this article I suggest that in the Soviet period Central Asians cultivated and conceptualized Islam as an episteme. They did this by reaching beyond alienating (and often ephemeral) categories offered to them by the state. I argue that the constitution of an Islamic culture was made possible, among other things, by Central Asians’ encounters with the past, most notably with what they perceived as an Islamic past. We observe the curious phenomenon of Central Asians’ continuous interaction with the Islamic historical sites that escaped the bulldozers of the Soviet campaigns of religious repression. For some, encounters with the past might be accidental. For many others, the exploration of the past represented a purposive, self-conscious, and reiterated emotional act. I show that Central Asians in the Soviet period—even if at school they were taught little about, and were usually offered a distorted vision of, the Islamic history of their region—were still able to access their past through the surviving architectural presence of Islam. Monumental sites, however, were not enough for Muslims to understand the past and use it to construct their own identity. Such artifacts acquired meaning through an interpretive framework provided by Sufi narratives about saints and their miracles. Therefore, shrines represented for Central Asia a collective memory space, i.e., a place in which the past was preserved for mobilization in the present through narrative.
Sedentary Behaviors, TV Viewing Time, and Risk of Young-Onset Colorectal Cancer
Authors: Nguyen Long H , Liu Po-Hong , Zheng Xiaobin , Keum NaNa , Zong Xiaoyu , Li Xiao , Wu Kana , Fuchs Charles S , Ogino Shuji , Ng Kimmie , Willett Walter C , Chan Andrew T , Giovannucci Edward L , Cao Yin 
Published: January 2019

Abstract

Background
Colorectal cancer (CRC) diagnosed before age 50 years, or young-onset CRC, is increasing globally with undefined etiology. A sedentary lifestyle is an emerging risk factor for CRC after age 50 years, but its role in young-onset CRC is unknown.

Methods
We prospectively evaluated sedentary behaviors, primarily time watching television (TV), and risk of young-onset CRC among 89 278 women in the Nurses’ Health Study II ages 25–42 years at recruitment (1991–2011). We used Cox proportional hazards modelling to estimate relative risks (RR) and 95% confidence intervals (CIs). Statistical tests were two-sided.

Results
We documented 118 young-onset CRCs over 1 262 540 person-years. Sedentary TV viewing time was statistically significantly associated with increased risk of young-onset CRC, after adjusting for putative risk factors, including obesity and physical activity. Compared to no more than 7 hours per week, women with 7.1–14 hours per week of TV time had a multivariable relative risk (RR) of 1.12 (95% confidence interval [CI] = 0.72 to 1.75), further increased for greater than 14 hours per week (RR = 1.69, 95% CI = 1.07 to 2.67, Ptrend = .03). This association was observed among participants without a CRC family history and was more pronounced for rectal cancer (RR for >14 vs ≤7 hours per week 2.44, 95% CI = 1.03 to 5.78, Ptrend = .04). Overweight or obese participants may be more susceptible.

Conclusion
Independent of exercise and obesity, prolonged sedentary TV viewing time, a surrogate for a more inactive lifestyle, was associated with increased risk of young-onset CRC, particularly of the rectum. These findings provide further evidence on the importance of maintaining an active lifestyle.
Regulating Child Sex Robots: Restriction or Experimentation?
Authors: Danaher John 
Published: January 2019

Abstract
In July 2014, the roboticist Ronald Arkin suggested that child sex robots could be used to treat those with paedophilic predilections in the same way that methadone is used to treat heroin addicts. Taking this onboard, it would seem that there is reason to experiment with the regulation of this technology. But most people seem to disagree with this idea, with legal authorities in both the UK and US taking steps to outlaw such devices. In this article, I subject these different regulatory attitudes to critical scrutiny. In doing so, I make three main contributions to the debate. First, I present a framework for thinking about the regulatory options that we confront when dealing with child sex robots. Secondly, I argue that there is a prima facie case for restrictive regulation, but that this is contingent on whether Arkin’s hypothesis has a reasonable prospect of being successfully tested. Thirdly, I argue that Arkin’s hypothesis probably does not have a reasonable prospect of being successfully tested. Consequently, we should proceed with utmost caution when it comes to this technology.
LFMM 2: Fast and Accurate Inference of Gene-Environment Associations in Genome-Wide Studies
Authors: Caye Kevin , Jumentier Basile , Lepeule Johanna , François Olivier 
Published: January 2019

Abstract
Gene-environment association (GEA) studies are essential to understand the past and ongoing adaptations of organisms to their environment, but those studies are complicated by confounding due to unobserved demographic factors. Although the confounding problem has recently received considerable attention, the proposed approaches do not scale with the high-dimensionality of genomic data. Here, we present a new estimation method for latent factor mixed models (LFMMs) implemented in an upgraded version of the corresponding computer program. We developed a least-squares estimation approach for confounder estimation that provides a unique framework for several categories of genomic data, not restricted to genotypes. The speed of the new algorithm is several order faster than existing GEA approaches and then our previous version of the LFMM program. In addition, the new method outperforms other fast approaches based on principal component or surrogate variable analysis. We illustrate the program use with analyses of the 1000 Genomes Project data set, leading to new findings on adaptation of humans to their environment, and with analyses of DNA methylation profiles providing insights on how tobacco consumption could affect DNA methylation in patients with rheumatoid arthritis.
Software availability: Software is available in the R package lfmm at https://bcm-uga.github.io/lfmm/.
ellipsis in inquisitive semantics
Authors: AnderBois Scott 
Published: January 2019

AbstractWork in inquisitive semantics has developed an alternative-rich notion of semantic content which is uniform across questions and assertions. This chapter explores the ramifications of this view for the theory of ellipsis. It examines these issues primarily by focusing on the analysis of a particular ellipsis process in English: sluicing. Empirically, it reviews a number of arguments in favor of an account of sluicing incorporating inquisitive semantics, most notably cases where truth-conditionally equivalent sentences have differential behavior for sluicing. Theoretically, the chapter demonstrates how a theory of ellipsis building on Merchant (2001) but based on an inquisitive semantics helps address this data. Beyond this, it briefly discusses motivations for extending this sort of approach to other ellipsis processes and compares the proposed account with other potential ways of incorporating inquisitive semantics into a theory of ellipsis.
Ellipsis and Acquisition
Authors: Roeper Tom 
Published: January 2019

AbstractEllipsis provides a quintessential acquisition challenge—deleted material is an obvious instance of poverty of the stimulus. This chapter reviews the naturalistic and experimental evidence to evaluate how far UG allows immediate correct projection of VP and NP ellipsis, based on Merchant’s (2014) E-features. It develops an acquisition theory whereby a child moves, step by step, from Open Interfaces to isomorphic Strict Interfaces between LF and syntax which entails full reconstruction. The approach both utilizes pro as an initial default and explains why it remains in the final grammar for particularly complex constructions. It follows an economy principle: minimize recovery by contextual inference. The analysis is extended to sluicing, ACD, fragments, and the projection of QUD, and engages English, Portuguese, German, Dutch, Italian, and African-American English.
Ellipsis and Computational Linguistics
Authors: Hardt Daniel 
Published: January 2019

AbstractThis chapter considers approaches to ellipsis within computational linguistics. It begins with the structure of the ellipsis site—a topic that has received little attention in computational linguistics. There are two prominent accounts of the recovery of ellipsis: that of Lappin and McCord (1990) and Dalrymple et al. (1991). The topic of licensing follows. This topic has not been directly addressed in the computational literature, but the chapter covers two related issues of direct computational interest: the identification and generation of ellipsis occurrences. This is followed by three additional topics: identifying the antecedent, dialogue, and text mining.
Ellipsis in Categorial Grammar
Authors: Jacobson Pauline 
Published: January 2019

AbstractOne of the fundamental tenets of (most versions of) Categorial Grammar is that the syntax and semantics work ‘in tandem’: the syntax proves expressions well-formed while the semantics assigns them a meaning. Under this view (termed Direct Compositionality), it is difficult at best to state a rule deleting or silencing material under identity with some other overt linguistic material in the discourse context, which suggests that the common wisdom that there is ‘silent linguistic material’ is incorrect. This chapter explores an alternative way to view VP-ellipsis without silent linguistic material. Using conventions developed in earlier work within variable-free semantics and Direct Compositionality, it is shown that such an approach extends immediately to Antecedent Contained Deletion (which is just a special case of ‘transitive verb phrase ellipsis’) as well as to pseudogapping. The chapter also briefly explores the analysis of fragment answers to questions without invoking silent linguistic material, and shows that some of the apparent challenges to this view are in fact not real challenges.