bluuebunny/crossref_metadata_2025_split huggingface dataset:
The speech went on (and on) as Kerry dozed off (*and off)
Authors: Strauss Susan , Chang Heesun , Yoon Jungwan 
Published: November 2018

Abstract
This chapter provides an encapsulated segment of a larger, on-going study centering on a complex set of prepositions and their corresponding phrasal verb particles and adverbs viewed from the methodological and analytic perspective of Conceptual Grammar. Conceptual Grammar is an approach to the analysis and teaching of grammar that combines three paradigms: corpus, discourse analysis, and cognitive linguistics to reveal systematically patterned grammatical meanings. The visual conceptual system is intended to dually represent various gradations of spatial/temporal/metaphorical/abstract meanings in graphic terms, using simple shapes as a mnemonic to aid in the apprehension of conceptual meaning. The system is intended to be generalizable across all uses and meanings of the target lexemes and thus to facilitate productivity of use, serving as a new type of “grammatical rule”.
The role of embodiment in the semantic analysis of phrasal verbs
Authors: Mahpeykar Narges 
Published: November 2018

Abstract
Many of the meanings of prepositions are derived from our bodily experience and conceptualization of the spatial-physical world. This study examines the relationship between frequency and embodied meaning in spatial particles. Tyler and Evans’ Principled Polysemy Model was used to analyze high and low frequency particles. The analysis shows that particles including up, out, off and over appear frequently in phrasal verbs due to a larger set of embodied experiences and a more complex semantic network associated with these particles. In contrast, low frequency particles such as through, under, into and for appear less frequently in phrasal verbs due to the nature of the embodied meanings motivating these uses. Implausible constructions such as hold under and drop up were found to be explainable by examining the basic embodied meanings of the verb and the particle.
Formulaicity and context in second language pragmatics
Authors: Bardovi-Harlig Kathleen 
Published: November 2018

Abstract
Pragmatic routines are realized by a range of expressions at different points on the formulaicity scale, meaning that some expressions are more set than others. This chapter draws on acquisition research to highlight the types of pragmatic knowledge that underpin successful use and emerging use of formulaic language in pragmatics, exploring the alignment of speech act, pragmatic strategy, content, meaning, and form in the acquisition and use of conventional expressions and routines, and the role of context. Examples are drawn primarily from two studies on pragmatics, a large cross-sectional study (N = 179; 5,504 responses to a conversation simulation, Bardovi-Harlig 2009), and an instructional effects study (responses to simulated group work, Bardovi-Harlig, Mossman, and Vellenga, 2015a).
What is happened? Your amazon.com order has shipped
Authors: Ortega Lourdes , Lee Sang-Ki , Miyata Munehiko 
Published: November 2018

Abstract
It is well known that many L2 users overpassivize unaccusatives. The same L2 users may also be reluctant to accept constructions with unaccusative meanings. We examined the responses from 56 L2 users of English on a scaled grammaticality judgment task. We predicted that performance would be negatively affected in the presence of a conceptualizable agent in the discourse scene that biases an external causation construal and with low-frequency verbs and alternating verbs. We found clear effects for frequency and alternation in the hypothesized direction. However, there was no evidence for an independent contribution of the conceptualization bias condition. Our study supports the claim that learners build their L2 grammars by abstracting not only the statistical properties but also the complex, polysemous meanings of the constructions they experience in usage.
Effects of L2 exposure on the use of discourse devices in L2 storytelling
Authors: Nakahama Yuko 
Published: November 2018

Abstract
This study builds on Nakahama, Tyler and van Lier (2001), which showed that conversation provides a plethora of learning opportunities as opposed to decontextualized, mechanical types of activities. The study investigates second language (L2) storytelling by Japanese learners of English as a second language (ESL) and English as a foreign language (EFL) while talking with native speaker interlocutors. Major differences were found between the two groups. ESL learners produced more words and discourse markers (DMs) than their EFL counterparts. Furthermore, while the EFL learners’ narratives were monologic, the ESL learners’ narratives were dialogic and involved NS collaborations. Negotiation of meaning was found in both groups when non-understanding occurred during the storytelling. However, while the EFL learners’ errors received recasts from the NS, the ESL learners’ errors went uncorrected by their interlocutor.
Cochlear implantation in patients afflicted with inner ear malformations – the Pécs experience
Authors: Bako Peter , Nemeth Adrienn , Molnar Krisztian , Toth Tamas , Harmat Kinga , Rath Gabor , Gerlinger Imre 
Published: November 2018

Purpose:
To successfully analyze the surgical and audiological results of cochlear implantation in patients afflicted with inner ear malformations. This study briefly presents our surgical strategies, the selected implants and the audiological results.

Method:
Objective hearing threshold was measured using an auditory brainstem response and middle latency response audiometry. Structural imaging of high resolution temporal bone computer tomography and inner ear MR scan was performed in support of all patients. Images revealed bilateral cochlear malformation in seven patients. Three ears with common cavity deformity, two ears with incomplete partition type I and three ears suffering from cochlear hypoplasia were all rehabilitated using cochlear implantation. The type of the electrode and the surgical technique were individually determined reflective of the type of malformation. The success of the surgery and potential postoperative complications were duly noted and fully registered. Postoperative audiological measurements were performed and the results were analyzed.

Results:
The average audiological follow-up was 40.3 months. The average free field, pure-tone threshold of speech frequencies (0.5–3 kHz) gained postoperatively were within the range of 32.5–41.6 dB. In two of the procedures, a cerebrospinal fluid gusher did occur and was successfully managed intraoperatively, all without any postoperative complications.

Conclusion:
Temporal bone high resolution CT and inner ear MRI imaging are mandatory to detect and characterize the inner ear malformation. Early implantation of malformed cochlea is crucial towards achieving ideal postoperative audiological results. Notably, an intraoperative gusher is not regarded as a contraindication of the cochlear implantation.
Citizenship as a Communicative Effect
Authors: Jonnalagadda Indivar 
Published: November 2018

AbstractUsing ethnographic field notes on the media circulation and uptake of two specific government orders in Hyderabad, India, I propose a semiotic approach to looking at how emblems of citizenship are not simply products of state ideologies, but rather products of a dialogic relationship (sometimes contentious, often ordinary) between “state” and “citizens,” and always with reference to a history of communicative events between the two. I argue that citizenship should be understood as a communicative effect that is mediated not solely by sovereign power and strident collective movements, but more often through everyday processes by which emblems of citizenship are entextualized and the discursive interactions through which substantive claims are mobilized, negotiated, and contested. Such an approach can add both epistemological and methodological specificity to political anthropology and push it beyond the limitations of an anthropology of the state.
Modeling the functional link between movement, feeding activity, and condition in a marine predator
Authors: Pirotta Enrico , Schwarz Lisa K , Costa Daniel P , Robinson Patrick W , New Leslie 
Published: November 2018

AbstractThe ability to quantify animals’ feeding activity and the resulting changes in their body condition as they move in the environment is fundamental to our understanding of a population’s ecology. We use satellite tracking data from northern elephant seals (Mirounga angustirostris), paired with simultaneous diving information, to develop a Bayesian state-space model that concurrently estimates an individual’s location, feeding activity, and changes in condition. The model identifies important foraging areas and times, the relative amount of feeding occurring therein, and thus the different behavioral strategies in which the seals engage. The fitness implications of these strategies can be assessed by looking at the resulting variation in individuals’ condition, which in turn affects the condition and survival of their offspring. Therefore, our results shed light on the processes affecting an individual’s decision-making as it moves and feeds in the environment. In addition, we demonstrate how the model can be used to simulate realistic patterns of disturbance at different stages of the trip, and how the predicted accumulation of lipid reserves varies as a consequence. Particularly, disturbing an animal in periods of high feeding activity or shortly after leaving the colony was predicted to have the potential to lead to starvation. In contrast, an individual could compensate even for very severe disturbance if such disturbance occurred outside the main foraging grounds. Our modeling approach is applicable to marine mammal species that perform drift dives and can be extended to other species where an individual’s buoyancy can be inferred from its diving behavior.
Genome-wide search of nucleosome patterns using visual analytics
Authors: Santamaría Rodrigo , Therón Roberto , Durán Laura , García Alicia , González Sara , Sánchez Mar , Antequera Francisco 
Published: November 2018

Abstract

Motivation
The Burrows-Wheeler transform (BWT) is widely used for the fast alignment of high-throughput sequence data. This method also has potential applications in other areas of bioinformatics, and it can be specially useful for the fast searching of patterns on coverage data from different sources.

Results
We present a nucleosome pattern search method that converts levels of nucleosomal occupancy to a sequence-like format to which BWT searches can be applied. The method is embedded in a nucleosome map browser, ‘Nucleosee‘, an interactive visual tool specifically designed to enhance BWT searches, giving them context and making them suitable for visual discourse analysis of the results. The proposed method is fast, flexible and sufficiently generic for the exploration of data in a broad and interactive way.

Availability and implementation
The proposed algorithm and visual browser are available for testing at http://cpg3.der.usal.es/nucleosee. The source code and installation packages are also available at https://github.com/rodrigoSantamaria/nucleosee.

Supplementary information
Supplementary data are available at Bioinformatics online.
Detection of rare disease variants in extended pedigrees using RVS
Authors: Sherman Thomas , Fu Jack , Scharpf Robert B , Bureau Alexandre , Ruczinski Ingo 
Published: November 2018

Abstract

Summary
Family-based sequencing studies enable researchers to identify highly penetrant genetic variants too rare to be tested in conventional case-control studies, by studying co-segregation of variant and disease phenotypes. When multiple affected subjects in a family are sequenced, the probability that a variant or a set of variants is shared identical-by-descent by some or all affected relatives provides evidence against the null hypothesis of complete absence of linkage and association. The Rare Variant Sharing software package RVS implements a suite of tools to assess association and linkage between rare genetic variants and a dichotomous disease indicator in family pedigrees.

Availability and Implementation
RVS is available as open source software from the Bioconductor webpage at https://bioconductor.org/packages/release/bioc/html/RVS.html.

Supplementary information
Supplementary data are available at Bioinformatics online.
Differential Representations of Perceived and Retrieved Visual Information in Hippocampus and Cortex
Authors: Lee Sue-Hyun , Kravitz Dwight J , Baker Chris I 
Published: November 2018

AbstractMemory retrieval is thought to depend on interactions between hippocampus and cortex, but the nature of representation in these regions and their relationship remains unclear. Here, we performed an ultra-high field fMRI (7T) experiment, comprising perception, learning and retrieval sessions. We observed a fundamental difference between representations in hippocampus and high-level visual cortex during perception and retrieval. First, while object-selective posterior fusiform cortex showed consistent responses that allowed us to decode object identity across both perception and retrieval one day after learning, object decoding in hippocampus was much stronger during retrieval than perception. Second, in visual cortex but not hippocampus, there was consistency in response patterns between perception and retrieval, suggesting that substantial neural populations are shared for both perception and retrieval. Finally, the decoding in hippocampus during retrieval was not observed when retrieval was tested on the same day as learning suggesting that the retrieval process itself is not sufficient to elicit decodable object representations. Collectively, these findings suggest that while cortical representations are stable between perception and retrieval, hippocampal representations are much stronger during retrieval, implying some form of reorganization of the representations between perception and retrieval.
Acquisition of Spatial Search Strategies and Reversal Learning in the Morris Water Maze Depend on Disparate Brain Functional Connectivity in Mice
Authors: Shah Disha , Verhoye Marleen , Van der Linden Annemie , D’Hooge Rudi 
Published: November 2018

Abstract
Learning has been proposed to coincide with changes in connections between brain regions. In the present study, we used resting-state fMRI (rsfMRI) to map brain-wide functional connectivity (FC) in mice that were trained in the hidden-platform version of the Morris water maze. C57BL6 mice were investigated in a small animal MRI scanner following 2, 10, or 15 days of acquisition learning, or 5 days of reversal learning. Spatial learning coincided with progressive and changing FC between telencephalic regions that have been implemented in spatial learning (such as hippocampus, cingulate, visual, and motor cortex). Search strategy assessment demonstrated that the use of cognitively advanced spatial strategies correlated positively with extensive telencephalic connectivity, whereas non-spatial strategies correlated negatively with connectivity. FC patterns were different and more extensive after reversal learning compared with after extended acquisition learning, which could explain why reversal learning has been shown to be more sensitive to subtle functional defects.
Targeting cervical cancer campaigns on teenage high schoolers in resource-limited economies: lessons from an intervention study of Nigerian senior secondary school girls
Authors: Ifediora Chris O , Azuike Emmanuel C 
Published: November 2018

Abstract

Background
Given the dearth of government-sponsored programmes, preventive lifestyles and practices are the realistic hopes for millions of women in developing countries against cervical cancer. Early interventions for teenage high school girls have been advocated recently, but evidence-base for sustainable activities at this demographic is lacking. This article reduces this gap by determining the impact of two cervical cancer education techniques.

Method
This is a 6-month interventional cohort study of 432 female high school students in South-eastern Nigeria.

Results
A total of 317 (73.4%) and 301 (69.7%) valid responses were received from the pre-intervention (16.8 ± 1.5 years) and post-intervention (17.2 ± 1.6 years) surveys, respectively. About 213 (70.8%) were fully engaged with the interventions. Logistic regression revealed that participants who were ‘engaged’ with the interventions, either through symposium attendance or by reading of the printed handouts, showed significant improvements across multiple cervical cancer parameters regarding knowledge on ‘pap smears’ (analysed with four items), ‘HPV vaccine’ (two items) and ‘risk factors’ (two items). Improvements in Knowledge of ‘early symptoms’ were not improved, with ‘post-coital bleeding’ [odds ratio (OR) = 0.95; P = 0.87] and ‘being asymptomatic’ (OR = 0.69; P = 0.32) remaining statistically similar between the engaged and the unengaged. If ‘engagement’ with either intervention was disregarded, a chi-square analysis identified no significant improvement in knowledge on any parameter.

Conclusion
Ensuring ‘engagement’ with intervention campaigns is vital to achieving effective and sustainable cervical cancer knowledge. Engagement may be achieved by repeating the education activities across all the years/classes that make up high school in each developing country, along with formal examinations at each level.
Strong approximation of monotone stochastic partial differential equations driven by white noise
Authors: Liu Zhihui , Qiao Zhonghua 
Published: November 2018

Abstract
We establish an optimal strong convergence rate of a fully discrete numerical scheme for second-order parabolic stochastic partial differential equations with monotone drifts, including the stochastic Allen–Cahn equation, driven by an additive space-time white noise. Our first step is to transform the original stochastic equation into an equivalent random equation whose solution possesses more regularity than the original one. Then we use the backward Euler in time and spectral Galerkin in space to fully discretise this random equation. By the monotonicity assumption, in combination with the factorisation method and stochastic calculus in martingale-type 2 Banach spaces, we derive a uniform maximum norm estimation and a Hölder-type regularity for both stochastic and random equations. Finally, the strong convergence rate of the proposed fully discrete scheme is obtained. Several numerical experiments are carried out to verify the theoretical result.
Standard work-up of the low-risk kidney transplant candidate: a European expert survey of the ERA-EDTA Developing Education Science and Care for Renal Transplantation in European States Working Group
Authors: Maggiore Umberto , Abramowicz Daniel , Budde Klemens , Crespo Marta , Mariat Christophe , Oberbauer Rainer , Pascual Julio , Peruzzi Licia , Schwartz Sorensen Soren , Viklicky Ondrej , Watschinger Bruno , Oniscu Gabriel C , Heemann Uwe , Hilbrands Luuk B ,   ERA-EDTA DESCARTES Working Group
Published: November 2018

AbstractBackgroundExisting guidelines on the evaluation and preparation of recipients for kidney transplantation target the entire spectrum of patients with end-stage renal disease. Within the ERA-EDTA Developing Education Science and Care for Renal Transplantation in European States (DESCARTES) Working Group, it was proposed that in a subset of relatively young patients (&lt;40 years) without significant comorbidities (such as diabetes or cardiovascular disease), the work-up for transplantation could be restricted to a small set of tests.MethodsAiming for agreement between transplant centres across Europe, we surveyed the opinion of 80 transplant professionals from 11 European states on the composition of a minimal work-up.ResultsWe show that there is a wide agreement among European experts that the work-up for kidney transplantation of the low-risk candidate, as opposed to the standard risk candidate, could include a limited number of investigations. However, there is some disagreement regarding the small number of diagnostic procedures, which is related to geographical location within Europe and the professional background of respondents.ConclusionsBased on the results of the survey, published guidelines and expert meetings by the DESCARTES Working Group, we have formulated a proposal for the work-up of low-risk kidney transplant candidates.
Recent advances in structural studies of the CRISPR-Cas-mediated genome editing tools
Authors: Zhu Yuwei , Huang Zhiwei 
Published: November 2018

Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and accompanying CRISPR-associated (Cas) proteins provide RNA-guided adaptive immunity for prokaryotes to defend themselves against viruses. The CRISPR-Cas systems have attracted much attention in recent years for their power in aiding the development of genome editing tools. Based on the composition of the CRISPR RNA-effector complex, the CRISPR-Cas systems can be divided into two classes and six types. In this review, we summarize recent advances in the structural biology of the CRISPR-Cas-mediated genome editing tools, which helps us to understand the mechanism of how the guide RNAs assemble with diverse Cas proteins to cleave target nucleic acids.
Star formation and polycyclic aromatic hydrocarbons in ELAIS N1 galaxies as seen by AKARI
Authors: Kovács Tímea O , Burgarella Denis , Kaneda Hidehiro , Molnár Dániel Cs , Oyabu Shinki , Pinter Sandor , Toth L Viktor 
Published: November 2018

Abstract
We have examined the relationship between star formation and polycyclic aromatic hydrocarbons (PAHs) in a variety of galaxies. PAHs are excited by the ultraviolet photons of young stars, but they are disassociated by strong UV radiation in starbursts. Therefore their emission (which is in the wavelength range covered by AKARI) can be used as a star formation tracer in main sequence galaxies. We selected our targets in the ELAIS N1 field with AKARI detections, matched them with the Herschel Point Source Catalog, and collected other publicly available photometric data. Their spectral energy distributions (SEDs) were fitted, and several parameters of the galaxies were estimated, e.g., star formation rate (SFR), stellar mass, and the fraction of PAHs compared to dust mass (qPAH), and we examined the relationships between these parameters. The final sample consisted of 48 galaxies, with redshifts from 0.04 to 2.36. The estimated qPAH values were lower on average than typical values in the literature. This could be due to various reasons, such as low metallicity, or ongoing active galactic nucleus or starburst activity. Of our sample, 83% of the objects fell in the star-forming main sequence of galaxies, while only 8% could be considered as starbursts. We found a decreasing qPAH trend with increasing AV and consequently LIR, suggesting the possible presence of compact star-forming regions. We compared the qPAH values with the known relations of the PAH luminosities, but they did not always follow the same trends (SFR, LIR), and showed only slight correlation with the PAH luminosities.