bluuebunny/crossref_metadata_2025_split huggingface dataset:
Free speech, hate speech, and hate beards
Authors: Leezenberg Michiel 
Published: October 2017

Abstract
This paper explores the discourse and verbal strategies of the Dutch ‘Freedom Party’ (PVV), an islamophobic populist party that emerged in the first decade of the twenty-first century. In particular, it focuses on the linguistic ideologies implicit in PVV discourse, arguing that PVV spokespersons systematically construe their own utterances as mere words, and hence as deserving state protection; and the utterances of others as acts, and more specifically as acts of violence, deserving repression or prosecution. This asymmetric linguistic ideology may help us to explore empirical and normative questions concerning violence in language. In particular, the question of violence and responsibility is discussed on the basis of Norwegian Anders Breivik’s 2011 murderous assault on Norwegian social democrats, which explicitly appealed to PVV leader Wilders and his views on Islam.
Queering violence and narrative
Authors: Lewis Elizabeth Sara , Bastos Liliana Cabral 
Published: October 2017

Abstract
This chapter argues that it is useful to take a queer stance on studying narratives about violence in marginalized communities, considering “queer” a position countering any type of normalization that produces stigmatized margins (Halperin 1995; Louro 2004), not limited to gender and sexuality. Normative, marginalizing discourses, (re)produced by the media, “the talk of crime” (Caldeira 2000) and hate speech (Butler 1997) tend to characterize Brazilian favelas as dangerous places filled with violent criminals, homogenizing and further stigmatizing their residents (Kokoreff 2003; Valladares 2005). We examine how experiences of violence and daily life are constructed in adolescent favela residents’ narratives, focusing on how they destabilize certain aspects of the normative, marginalizing and homogenizing discourses of the media, and how violence and narrative itself are queered in their constructions.
Discursive constructions of deviance in the narratives of a prison inmate
Authors: Biar Liana 
Published: October 2017

Abstract
This chapter aims at identifying a specific type of discourse about violence: the stories of adherence to drug trafficking, their emergence in the research context and the processes of identity construction resulting from said context. The data comes from fieldwork done during 2009 in one of the main prison institutions in Brazil. Interviews were realized with inmate members of Rio de Janeiro criminal gangs who attended the prison school. These interviews were then qualitatively analyzed, from a micro-perspective approach, in light both of studies on oral narratives, based on interactional sociolinguistics, and of identity studies, especially those which consider narrative discourse as a privileged locus for social identity construction and analysis. From the analysis of the narratives’ structure systems of coherence, it was possible to understand the way in which inmates neutralize the force of values and of accepting order so as to give new meaning to deviant actions, as being pleasant or respectable.
Towards an operational category of discourse markers
Authors: Crible Ludivine 
Published: October 2017

Abstract
The field of discourse markers (DMs) studies suffers from lack of consensus on the limits and definition of the category. There seems to be a crucial need for onomasiological studies that account for every kind of DM in cross-linguistic data. This study presents a proposal for an operational, corpus-based definition of DMs that addresses several theoretical and methodological shortcomings in the field. I claim that any categorical definition is only useful insofar as it is endorsed by an empirical model of identification and annotation. Such a model will be described and illustrated by relevant authentic examples from a pilot study on a comparable corpus of French and English interviews.
Discourse markers and discourse relations
Authors: Costăchescu Adriana 
Published: October 2017

Abstract
We investigate if and how Discourse Markers (DMs) can be integrated into a dynamic semantic framework (in the SDRT variant, cf. Asher & Lascarides 2003, 2008, 2009) in order to study the relationships between discursive markers and rhetoric relations in a dialogue. We assume that short answers (Schlangen & Lascarides 2003) and DMs have the same basic characteristics: (i) both are semantically under-specified; (ii) in both cases, the receiver adds, by deduction, significant elements, in order to narrow, or even eliminate the semantic under-specification. We illustrate the possibility of integrating the DMs in the SDRT by examining the behaviour of the French DM quoi ‘what’ in a corpus in expressing rhetorical relations, such as:

Explanation(α, β) (A: – Le curé est arrivé à pied, ou quoi
? B: – Il est venu dans la voiture de Mathurin. ‘A : – The priest arrived on foot, or what? B: – He came in Mathurin’s car’)

Contrast(α, β) (A: – Je vais attendre. B: - Attendre quoi? Ils viennent de sortir. ‘A : I am going to wait. B: – What for? They have just left’);

Phatic(α, β), when the channel is not functioning (A: -Coco! B (who is hard of hearing): –
Quoi
? A: (screaming) – Ils te disent au revoir. ‘A: – Coco! B : -What? A: – They are saying ‘good bye’ to you’).

The study of DMs within SDRT tells us a lot about the deductive processes implied by the good functioning the human communication.
Italian non-canonical negations as modal particles
Authors: Squartini Mario 
Published: October 2017

Abstract
This chapter will focus on the role of information state as a major factor in the development of modal particles derived from negative minimizers. By capitalizing on previous research on Romance non-canonical negations (see especially Schwenter 2003, 2005, 2006), the analysis will describe the special discursive function of the Italian negative operator mica (etym. ‘crumb’) in direct questions, where the textual dynamics ‘given’ vs. ‘new’ interacts with the speaker’s mirative reactions. The occurrence of distinct regional patterns in the use of mica in direct questions indicates different combinations of polarity with the mirative role of the speaker, who, apart from managing information flow, also reacts to unexpected information by matching previous knowledge with new information acquired in discourse.
Vocatives as a source category for pragmatic markers
Authors: Kleinknecht Friederike , Souza Miguel 
Published: October 2017

Abstract
This paper considers familiarizers, a special class of vocatives denoting solidarity and intimacy, as possible sources for pragmatic markers and discourse markers. We argue that affectivity plays a crucial role in the use of vocatives in general and especially in this functional development. More precisely, terms of address have the potential to intensify the affectivity displayed by the speaker. In this quality, they may be employed as linguistic strategies to enhance the expressive and illocutionary force of utterances. These expressive uses may be the source of several more peculiar functions related to turn and information management. While this holds for familiarizers as well as for vocatives in general, not interferring with the deictic force of addressing contained in the vocative form, in several languages there are familiarizers which undergo an inflationary use and end up as mere elements of discourse marking, emphasizing and delimiting sequential units such as turns, utterances, and intonation units. The deictic reference to the collocutor is virtually lost, which is shown by the typical fossilization of the masculine singular form in the newly derived functions. We illustrate this development with vocative-based markers in different languages with special focus on the familiarizers güey in Mexican Spanish and alter in German. Although their sociopragmatic indexicalities are far from identical, this comparative approach reveals some interesting similarities. In our view, a definition as ‘pragmatic markers’ is justified for vocative-based markers at any point of their evolution, while the term ‘discourse marker’ should be restricted to functions that are no longer directly inferable from the vocative’s deictic and expressive qualities.
Paths of development of English DMs
Authors: Mazzon Gabriella 
Published: October 2017

Abstract
Starting from notions of conversational dominance as a locus for face-work, and of the crucial role of specific language items in managing conflict and (dis)agreement in dialogue, the paper will look at some case studies in the development and pragmaticalization stages of various English Discourse Markers (such as now, pray, please, I’m afraid, and well). Beginning with the source forms, the paper will discuss the gradual emergence of subjective and intersubjective meanings, as well as the phenomenon of layering and the tendency toward the development of deontic meanings that some English discourse markers show, possibly indicating a form of cyclical development of functions. The specific case studies presented include both a synchronic and a diachronic perspective.
On the pragmatic expansion of Polish gdzieś tam ‘somewhere (there)/about’
Authors: Adamczyk Magdalena 
Published: October 2017

Abstract
In standard usage gdzieś tam functions as an adverbial adding approximation/indeterminacy to expressions of place, time and number/amount/measure, and as such it is semantically equivalent to English ‘somewhere (there) in some contexts and ‘about’ in others. In conversational speech, however, its use sometimes diverges, more or less markedly, from the standard one, which is manifested both formally and functionally. The present study sets out to examine, locally, the lexico-syntactic cotext of gdzieś tam (to see how it differs depending on whether the expression is used conventionally or otherwise) and, globally, novel, context-sensitive functions that the phrase is capable of performing in a communicative act. A broader issue the paper attempts to address is the extent, if any, to which the canonical meaning of gdzieś tam is reflected in the pragmatically expanded use of the expression.
A pragmatic approach to Joseph Wright’s English Dialect Dictionary
Authors: Giuliani Stephan 
Published: October 2017

Abstract
Joseph Wright’s English Dialect Dictionary (EDD; 1898–1905) represents a landmark publication in Late Modern English dialectology. This article explores the potential of the EDD and its digital version (EDD Online) for historical pragmatic research and discusses essential theoretical and methodological considerations that arise from taking a pragmatic approach towards this complex historical document of non-standard English varieties. Besides traditional lexicographic information, the EDD also contains evidence of a great variety of different dialectal documents that are written to mimic spoken language. Three exemplary discourse markers (DM) – aweel, lor-a-massy and arrah – will be introduced and analysed from a pragmatic perspective.
Just a suggestion
Authors: Beeching Kate 
Published: October 2017

Abstract
This article aims to illustrate what a contrastive perspective, combined with sociolinguistic and corpus approaches, can bring to the investigation of the evolution of pragmatic functions which emerge through language contact (Ingham 2012a) and pragmatic borrowing (Andersen 2014). A recent collection of articles (Lauwers, Vanderbauwhede & Verleyen (eds) 2012) draws attention to the light which cognate forms and ‘false friends’ can shed on pragmaticalisation and semantic change. Sociolinguistic studies drawing on corpora of spoken interaction, which are tagged for demographic features, particularly speakers’ age and gender, coupled with modified matched-guise attitudinal studies, show that the use of new functions of pragmaticalising items reflects the incrementation model, posited by Labov (2001), with concomitant indexical obsolescence (Eckert 2014) of the older functions. The approach is illustrated for juste/just, and the conclusions confirm Dostie’s (2009) thesis that items whose meaning predisposes them to become pragmaticalised may do so to a greater extent in one region/language than in another.
A probabilistic pathway score (PROPS) for classification with applications to inflammatory bowel disease
Authors: Han Lichy , Maciejewski Mateusz , Brockel Christoph , Gordon William , Snapper Scott B , Korzenik Joshua R , Afzelius Lovisa , Altman Russ B 
Published: October 2017

AbstractSummaryGene-based supervised machine learning classification models have been widely used to differentiate disease states, predict disease progression and determine effective treatment options. However, many of these classifiers are sensitive to noise and frequently do not replicate in external validation sets. For complex, heterogeneous diseases, these classifiers are further limited by being unable to capture varying combinations of genes that lead to the same phenotype. Pathway-based classification can overcome these challenges by using robust, aggregate features to represent biological mechanisms. In this work, we developed a novel pathway-based approach, PRObabilistic Pathway Score, which uses genes to calculate individualized pathway scores for classification. Unlike previous individualized pathway-based classification methods that use gene sets, we incorporate gene interactions using probabilistic graphical models to more accurately represent the underlying biology and achieve better performance. We apply our method to differentiate two similar complex diseases, ulcerative colitis (UC) and Crohn’s disease (CD), which are the two main types of inflammatory bowel disease (IBD). Using five IBD datasets, we compare our method against four gene-based and four alternative pathway-based classifiers in distinguishing CD from UC. We demonstrate superior classification performance and provide biological insight into the top pathways separating CD from UC.Availability and ImplementationPROPS is available as a R package, which can be downloaded at http://simtk.org/home/props or on Bioconductor.Supplementary informationSupplementary data are available at Bioinformatics online.
PyBEL: a computational framework for Biological Expression Language
Authors: Hoyt Charles Tapley , Konotopez Andrej , Ebeling Christian 
Published: October 2017

Abstract

Summary
Biological Expression Language (BEL) assembles knowledge networks from biological relations across multiple modes and scales. Here, we present PyBEL; a software package for parsing, validating, converting, storing, querying, and visualizing networks encoded in BEL.

Availability and implementation
PyBEL is implemented in platform-independent, universal Python code. Its source is distributed under the Apache 2.0 License at https://github.com/pybel.

Supplementary information
Supplementary data are available at Bioinformatics online.
Cancer progression models and fitness landscapes: a many-to-many relationship
Authors: Diaz-Uriarte Ramon 
Published: October 2017

Abstract

Motivation
The identification of constraints, due to gene interactions, in the order of accumulation of mutations during cancer progression can allow us to single out therapeutic targets. Cancer progression models (CPMs) use genotype frequency data from cross-sectional samples to identify these constraints, and return Directed Acyclic Graphs (DAGs) of restrictions where arrows indicate dependencies or constraints. On the other hand, fitness landscapes, which map genotypes to fitness, contain all possible paths of tumor progression. Thus, we expect a correspondence between DAGs from CPMs and the fitness landscapes where evolution happened. But many fitness landscapes—e.g. those with reciprocal sign epistasis—cannot be represented by CPMs.

Results
Using simulated data under 500 fitness landscapes, I show that CPMs’ performance (prediction of genotypes that can exist) degrades with reciprocal sign epistasis. There is large variability in the DAGs inferred from each landscape, which is also affected by mutation rate, detection regime and fitness landscape features, in ways that depend on CPM method. Using three cancer datasets, I show that these problems strongly affect the analysis of empirical data: fitness landscapes that are widely different from each other produce data similar to the empirically observed ones and lead to DAGs that infer very different restrictions. Because reciprocal sign epistasis can be common in cancer, these results question the use and interpretation of CPMs.

Availability and implementation
Code available from Supplementary Material.

Supplementary information
Supplementary data are available at Bioinformatics online.
Lifeways and territorial innovation: values and practices for promoting collective appropriation of territory
Authors: Herrera Obeimar B , Parra Manuel , Livscovsky Iris , Ramos Pedro , Gallardo Daniela 
Published: October 2017

Abstract
In recent decades, most multilateral organizations and other agents of change have used the theoretical approach of sustainable livelihoods to guide their work. This approach has been criticized in recent years for promoting a short-term materialist focus in development projects, thus limiting its practical usefulness and feasibility. Due to the necessity for renewed proposals, a group of community cargos and researchers have developed a long-term comparative retrospective study that goes beyond the conventional approach. It provides a framework with a broader theoretical scope and applied utility grounded on local self-management: lifeways and territorial innovation. Our constructivist approach, based on Bourdieu´s Social Reproduction theory, is aimed at promoting and triggering a sense of territoriality within the communities and further onto the more extensive territory. Since the work was developed along with people from rural communities, we utilized the concept of Social Learning as to enrich the former theoretical principle.
Hierarchical attention networks for information extraction from cancer pathology reports
Authors: Gao Shang , Young Michael T , Qiu John X , Yoon Hong-Jun , Christian James B , Fearn Paul A , Tourassi Georgia D , Ramanthan Arvind 
Published: October 2017

AbstractObjectiveWe explored how a deep learning (DL) approach based on hierarchical attention networks (HANs) can improve model performance for multiple information extraction tasks from unstructured cancer pathology reports compared to conventional methods that do not sufﬁciently capture syntactic and semantic contexts from free-text documents.Materials and MethodsData for our analyses were obtained from 942 deidentiﬁed pathology reports collected by the National Cancer Institute Surveillance, Epidemiology, and End Results program. The HAN was implemented for 2 information extraction tasks: (1) primary site, matched to 12 International Classification of Diseases for Oncology topography codes (7 breast, 5 lung primary sites), and (2) histological grade classiﬁcation, matched to G1–G4. Model performance metrics were compared to conventional machine learning (ML) approaches including naive Bayes, logistic regression, support vector machine, random forest, and extreme gradient boosting, and other DL models, including a recurrent neural network (RNN), a recurrent neural network with attention (RNN w/A), and a convolutional neural network.ResultsOur results demonstrate that for both information tasks, HAN performed signiﬁcantly better compared to the conventional ML and DL techniques. In particular, across the 2 tasks, the mean micro and macroF-scores for the HAN with pretraining were (0.852,0.708), compared to naive Bayes (0.518, 0.213), logistic regression (0.682, 0.453), support vector machine (0.634, 0.434), random forest (0.698, 0.508), extreme gradient boosting (0.696, 0.522), RNN (0.505, 0.301), RNN w/A (0.637, 0.471), and convolutional neural network (0.714, 0.460).ConclusionsHAN-based DL models show promise in information abstraction tasks within unstructured clinical pathology reports.
A bequest to Christine of Lorraine from Catherine de’ Medici
Authors: Michahelles Kerrie-rue 
Published: October 2017

Abstract
The French royal family was living in exile at Blois when the Queen Mother of France, Catherine de’ Medici (b. 1519), dictated her will on the morning of her death, on 5 January 1589. She bequeathed to her granddaughter, Christine of Lorraine (1565–1637), one half of her movable possessions. This paper explores the nature and meanings embedded in the testamentary bequest and the corresponding inventory of the movable goods acquired by Christine through this gift and eventually brought to Florence on the occasion of her marriage in 1589 to Ferdinando de’ Medici, Grand Duke of Tuscany (1549–1609). A translation of the inventory is provided in an online appendix.
Ventriculoscopic Surgery for Cystic Retrochiasmatic Craniopharyngiomas: Indications, Surgical Technique, and Short-Term Patient Outcomes
Authors: Hollon Todd C , Savastano Luis E , Altshuler David , Barkan Ariel L , Sullivan Stephen E 
Published: October 2017

Abstract

BACKGROUND
Attempted gross-total resection for the management of cystic retrochiasmatic craniopharyngiomas can cause severe hypothalamic dysfunction and decrease overall survival. Ventriculoscopic surgery is a minimally invasive alternative; however, potential indications and technique have not been well defined.

OBJECTIVE
To present our indications and technique for the ventriculoscopic treatment of cystic retrochiasmatic craniopharyngiomas.

METHODS
We evaluated all patients with retrochiasmatic craniopharyngiomas for ventriculoscopic surgery. Indications and operative technique were developed to minimize operative morbidity, relieve mass effect, and optimize functional outcome. Cyst size and functional outcomes were statistically evaluated to determine radiographic and short-term clinical outcome.

RESULTS
Indications for ventriculoscopic surgery included (1) radiographic evidence of hypothalamic involvement and (2) major cystic component. Ten patients met indications, and mean follow-up was 2.5 ± 1.6 yr. The surgical technique included wide cyst fenestration at the foramen of Monro, and fenestration of inferior cyst wall/third ventriculostomy (“through-and-through” technique). Preoperative Karnofsky performance status was 70 ± 15 and was inversely correlated with preoperative cyst size (13 ± 13 cm3). A statistically significant reduction in cyst size was found on early postoperative imaging (2.1 ± 4.3 cm3). Seven patients received postoperative radiotherapy. Postoperative performance scores (81 ± 8.3) had improved; no patient suffered functional decline. Pre- and postoperative body mass indices were similar. No patient had short-term hypothalamic obesity.

CONCLUSION
Ventriculoscopic surgery, with or without adjuvant treatments, can reduce early postoperative tumor volume and improve short-term functional status in cystic retrochiasmatic craniopharyngiomas with hypothalamic involvement; it should be considered a minimally invasive option in the multimodal treatment of craniopharyngiomas. Further studies are needed to determine long-term efficacy.