bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chinese writers of English RAs as creators of a research space in a national context
Authors: Chen Xinren 
Published: November 2018

Abstract
Based on Swales’ (1990, 2004) CARS
model, this study examines 95 research articles (RAs) published by Chinese English-language writers doing Applied
Linguistics across three periods of time to find out whether and to what extent they move over time towards the
conventional construction of the identity as creators of a research space in the introductory part of their RAs
published in a national context. The findings confirm the occurrence of the diachronic change, which is ascribed to
the accrued influence of international academic conventions on Chinese English-language writers. Hopefully, this study
can help improve the teaching and writing of RA Introductions for the purposes of English-language international
publication and enrich existing research on identity construction in academic discourse.
Conference abstracts in English
Authors: Povolná Renata 
Published: November 2018

Abstract
With the growing internationalisation of all scholarship the use of English as an international lingua franca has
become an important prerequisite for scholars who intend to submit their abstracts and present their research to an
academic audience at international conferences. Consequently, scholars from non-Anglophone backgrounds have to master
the writing of this research-process genre (Swales, 1990) in English, since
otherwise they may risk being refused participation at conferences and publication in conference proceedings. This
chapter analyses the textual organisation of conference abstracts (CAs) written in English with the aim of finding out
whether there is intercultural variation in rhetorical moves and their linguistic realisations applied by Anglophone
scholars and those from some countries where Slavonic languages are spoken.
Not the same, but how different?
Authors: Murillo Silvia 
Published: November 2018

Abstract
Reformulation markers can be considered indicators of rhetorical conventions (Cuenca, 2003). In this paper I contrast these markers in the SciELF corpus of unedited research papers
(building on previous work [Murillo, submitted]) and in a comparable ENL
(English as a Native Language) corpus (SERAC), focusing on the overall frequency, the relative frequency of each
marker and the discourse processes they introduce (Murillo, 2012). The
results reveal statistically significant differences between the two corpora regarding the specific choice of
reformulation markers and the processes introduced by them. Further, the “similects” of the SciELF corpus (Mauranen, 2012) present very different trends. ELF does not seem to constitute
a homogeneous use of the English language, at least at the lexico-grammatical level.
Elements of denial in Capeverdean
Authors: Pratas Fernanda 
Published: November 2018

Abstract
This paper aims at showing that Capeverdean, a Portuguese-based Creole, is a strict Negative Concord language. In fact, n-words (Laka 1990) like ningen ‘no.one’ and nada ‘nothing’ always co-occur with sentential negation, be they in preverbal or postverbal position. This means that they are prohibited in all non-negative clauses, including modal contexts. Syntactically, they show a behavior typical of weak Negative Polarity Items (NPIs) as described in Martins (2000). Following Giannakidou (2002), I propose that, semantically, these n-words are universal quantifiers with no intrinsic negative meaning. Finally, I briefly address the adverbs tioxi and nunka, which roughly mean ‘never’: the former is also a weak NPI but not a quantifier, the latter may be ambiguous between a strong and a weak NPI, and seems a quantifier.
Bayesian generalized biclustering analysis via adaptive structured shrinkage
Authors: Li Ziyi , Chang Changgee , Kundu Suprateek , Long Qi 
Published: November 2018

Summary
Biclustering techniques can identify local patterns of a data matrix by clustering feature space and sample space at the same time. Various biclustering methods have been proposed and successfully applied to analysis of gene expression data. While existing biclustering methods have many desirable features, most of them are developed for continuous data and few of them can efficiently handle -omics data of various types, for example, binomial data as in single nucleotide polymorphism data or negative binomial data as in RNA-seq data. In addition, none of existing methods can utilize biological information such as those from functional genomics or proteomics. Recent work has shown that incorporating biological information can improve variable selection and prediction performance in analyses such as linear regression and multivariate analysis. In this article, we propose a novel Bayesian biclustering method that can handle multiple data types including Gaussian, Binomial, and Negative Binomial. In addition, our method uses a Bayesian adaptive structured shrinkage prior that enables feature selection guided by existing biological information. Our simulation studies and application to multi-omics datasets demonstrate robust and superior performance of the proposed method, compared to other existing biclustering methods.
The Superficial White Matter in Autism and Its Role in Connectivity Anomalies and Symptom Severity
Authors: Hong Seok-Jun , Hyung Brian , Paquola Casey , Bernhardt Boris C 
Published: November 2018

AbstractIn autism spectrum disorders (ASDs), the majority of neuroimaging studies have focused on the analysis of cortical morphology. White matter changes remain less understood, particularly their association to cortical structure and function. Here, we focused on region that has gained only little attention in ASD neuroimaging: the superficial white matter (SWM) immediately beneath the cortical interface, a compartment playing a prominent role in corticogenesis that incorporates long- and short-range fibers implicated in corticocortical connectivity. Studying a multicentric dataset of ASD and neurotypical controls, we harnessed surface-based techniques to aggregate microstructural SWM diffusion features. Multivariate analysis revealed SWM anomalies in ASD compared with controls in medial parietal and temporoparietal regions. Effects were similar in children and adolescents/adults and consistent across sites. Although SWM anomalies were more confined when correcting for cortical thickness and surface area, findings were overall robust. Diffusion anomalies modulated functional connectivity reductions in ASD and related to symptom severity. Furthermore, mediation models indicated a link between SWM changes, functional connectivity, and symptom load. Analyses targeting the SWM offer a novel perspective on the interplay between structural and functional network perturbations in ASD, highlighting a potentially important neurobiological substrate contributing to its diverse behavioral phenotype.
Ontological Security, Civilian Power, and German Foreign Policy Toward Russia1
Authors: Eberle Jakub , Handl Vladimír 
Published: November 2018

AbstractThe article analyzes Germany's policies toward Russia from an ontological security perspective. We argue that foreign policy should be seen as a tool that allows states to maintain a sense of a reasonably stable self, which enables them to cope in the changing world. We develop a three-layered model conceptualizing ontological security through narratives about the self, a significant other, and the international system and show its particular relevance for explicating policy change. When threatened by a crisis, states respond by narrative adjustment that highlights continuity on some levels, while enabling change on other levels. Developing the argument that Germany's ontological security is based in the “civilian power” narrative, we use our model to reconstruct Germany's response to Russia's wars in Georgia and Ukraine. In both cases, the discourse highlighted the ongoing validity of civilian power on the level of the international order, while challenges were accommodated by adjustments on the level of the self and the significant other. Ontological security was restored vis-à-vis the changing world by reinforcing the civilian power as a norm, while shifting blame to either both Germany and Russia (2008), or Russia exclusively (2014), for not adhering to it at a given time.
Incorporating a location-based socioeconomic index into a de-identified i2b2 clinical data warehouse
Authors: Gardner Bret J , Pedersen Jay G , Campbell Mary E , McClay James C 
Published: November 2018

Abstract

Objective
Clinical research data warehouses are largely populated from information extracted from electronic health records (EHRs). While these data provide information about a patient’s medications, laboratory results, diagnoses, and history, her social, economic, and environmental determinants of health are also major contributing factors in readmission, morbidity, and mortality and are often absent or unstructured in the EHR. Details about a patient’s socioeconomic status may be found in the U.S. census. To facilitate researching the impacts of socioeconomic status on health outcomes, clinical and socioeconomic data must be linked in a repository in a fashion that supports seamless interrogation of these diverse data elements. This study demonstrates a method for linking clinical and location-based data and querying these data in a de-identified data warehouse using Informatics for Integrating Biology and the Bedside.

Materials and Methods
Patient data were extracted from the EHR at Nebraska Medicine. Socioeconomic variables originated from the 2011-2015 five-year block group estimates from the American Community Survey. Data querying was performed using Informatics for Integrating Biology and the Bedside. All location-based data were truncated to prevent identification of a location with a population &lt;20 000 individuals.

Results
We successfully linked location-based and clinical data in a de-identified data warehouse and demonstrated its utility with a sample use case.

Discussion
With location-based data available for querying, research investigating the impact of socioeconomic context on health outcomes is possible. Efforts to improve geocoding can readily be incorporated into this model.

Conclusion
This study demonstrates a means for incorporating and querying census data in a de-identified clinical data warehouse.
Natural language processing of symptoms documented in free-text narratives of electronic health records: a systematic review
Authors: Koleck Theresa A , Dreisbach Caitlin , Bourne Philip E , Bakken Suzanne 
Published: November 2018

Abstract

Objective
Natural language processing (NLP) of symptoms from electronic health records (EHRs) could contribute to the advancement of symptom science. We aim to synthesize the literature on the use of NLP to process or analyze symptom information documented in EHR free-text narratives.

Materials and Methods
Our search of 1964 records from PubMed and EMBASE was narrowed to 27 eligible articles. Data related to the purpose, free-text corpus, patients, symptoms, NLP methodology, evaluation metrics, and quality indicators were extracted for each study.

Results
Symptom-related information was presented as a primary outcome in 14 studies. EHR narratives represented various inpatient and outpatient clinical specialties, with general, cardiology, and mental health occurring most frequently. Studies encompassed a wide variety of symptoms, including shortness of breath, pain, nausea, dizziness, disturbed sleep, constipation, and depressed mood. NLP approaches included previously developed NLP tools, classification methods, and manually curated rule-based processing. Only one-third (n = 9) of studies reported patient demographic characteristics.

Discussion
NLP is used to extract information from EHR free-text narratives written by a variety of healthcare providers on an expansive range of symptoms across diverse clinical specialties. The current focus of this field is on the development of methods to extract symptom information and the use of symptom information for disease classification tasks rather than the examination of symptoms themselves.

Conclusion
Future NLP studies should concentrate on the investigation of symptoms and symptom documentation in EHR free-text narratives. Efforts should be undertaken to examine patient characteristics and make symptom-related NLP algorithms or pipelines and vocabularies openly available.
How scientists can take the lead in establishing ethical practices for social media research
Authors: Pagoto Sherry , Nebeker Camille 
Published: November 2018

Abstract
Social media use has become ubiquitous in the United States, providing unprecedented opportunities for research. However, the rapidly evolving research landscape has far outpaced federal regulations for the protection of human subjects. Recent highly publicized scandals have raised legitimate concerns in the media about how social media data are being used. These circumstances combined with the absence of ethical standards puts even the best intentioned scientists at risk of possible research misconduct. The scientific community may need to lead the charge in insuring the ethical use of social media data in scientific research. We propose 6 steps the scientific community can take to lead this charge. We underscore the important role of funding agencies and universities to create the necessary ethics infrastructure to allow social media research to flourish in a way that is pro-technology, pro-science, and most importantly, pro-humanity.
The Geographic Variation of Surveillance and Zoonotic Spillover Potential of Influenza Viruses in Domestic Poultry and Swine
Authors: Berger Kathryn A , Pigott David M , Tomlinson Francesca , Godding David , Maurer-Stroh Sebastian , Taye Biruhalem , Sirota Fernanda L , Han Alvin , Lee Raphael T C , Gunalan Vithiagaran , Eisenhaber Frank , Hay Simon I , Russell Colin A 
Published: November 2018

Abstract

Background
Avian and swine influenza viruses circulate worldwide and pose threats to both animal and human health. The design of global surveillance strategies is hindered by information gaps on the geospatial variation in virus emergence potential and existing surveillance efforts.

Methods
We developed a spatial framework to quantify the geographic variation in outbreak emergence potential based on indices of potential for animal-to-human and secondary human-to-human transmission. We then compared our resultant raster model of variation in emergence potential with the global distribution of recent surveillance efforts from 359105 reports of surveillance activities.

Results
Our framework identified regions of Southeast Asia, Eastern Europe, Central America, and sub-Saharan Africa with high potential for influenza virus spillover. In the last 15 years, however, we found that 78.43% and 49.01% of high-risk areas lacked evidence of influenza virus surveillance in swine and domestic poultry, respectively.

Conclusions
Our work highlights priority areas where improved surveillance and outbreak mitigation could enhance pandemic preparedness strategies.
Chronic aspects of leprosy—neglected but important
Authors: Lockwood Diana N J 
Published: November 2018

AbstractThe chronic aspects of leprosy are discussed here. They are a consequence of the peripheral nerve damage that affects many patients during their lifetime with leprosy. The peripheral nerve damage leaves people unable to feel and with weakness in their hands and feet. They are at risk of damaging their hands and feet, causing the disabilities and deformities that characterise late leprosy.More than 200 000 new leprosy patients are diagnosed globally each year. Better data are needed from cohort studies to estimate the number of patients developing nerve damage and modelling studies are needed to estimate the number of patients who develop disabilities. For some of them, this will be a lifelong disability.Nerve damage is caused by inflammation in leprosy-affected nerves. Patients with nerve damage of &lt;6-mo duration need treatment with steroids. About 66% of multibacillary patients will develop nerve damage. Plastic graded monofilaments can be used to detect nerve damage in leprosy and diabetic clinics. Assessing nerve damage and treating patients with steroids in leprosy programmes needs to be strengthened. The World Health Organization has a successful programme for supplying antibiotics for treating leprosy infection to national leprosy programmes. They should take responsibility for providing steroids to national programmes since this is a core part of the treatment for &gt;66% of multibacillary patients. Patients need to be asked about neuropathic pain symptoms and treated if necessary.Treated leprosy patients are at risk of developing ulcers in their feet. Treatment and prevention needs to be improved through health education, providing protective footwear and patient empowerment.
Host-pathogen coevolution increases genetic variation in susceptibility to infection
Authors: Duxbury Elizabeth ML , Day Jonathan P , Vespasiani Davide Maria , Thüringer Yannik , Tolosana Ignacio , Smith Sophia CL , Tagliaferri Lucia , Kamacioglu Altug , Lindsley Imogen , Love Luca , Unckless Robert L , Jiggins Francis M , Longdon Ben 
Published: November 2018

AbstractIt is common to find considerable genetic variation in susceptibility to infection in natural populations. We have investigated whether natural selection increases this variation by testing whether host populations show more genetic variation in susceptibility to pathogens that they naturally encounter than novel pathogens. In a large cross-infection experiment involving four species ofDrosophilaand four host-specific viruses, we always found greater genetic variation in susceptibility to viruses that had coevolved with their host. We went on to examine the genetic architecture of resistance in one host species, finding that there are more major-effect genetic variants in coevolved host-parasite interactions. We conclude that selection by pathogens increases genetic variation in host susceptibility, and much of this effect is caused by the occurrence of major-effect resistance polymorphisms within populations.
Cell assemblies in the cortico-hippocampal-reuniens network during slow oscillations
Authors: Angulo-Garcia David , Ferraris Maëva , Ghestem Antoine , Nallet-Khosrofian Lauriane , Bernard Christophe , Quilichini Pascale P 
Published: November 2018

AbstractThe nucleus reuniens (NR) is an important anatomical and functional relay between the medial prefrontal cortex (mPFC) and the hippocampus (HPC). Whether the NR controls neuronal assemblies, a hallmark of information exchange between the HPC and mPFC for memory transfer/consolidation, is not known. Using simultaneous LFP and unit recordings in NR, HPC and mPFC in rats during slow oscillations under anesthesia, we identified a reliable sequential activation of NR neurons at the beginning of UP states, which preceded mPFC ones. NR sequences were spatially organized, from dorsal to ventral NR. Chemical inactivation of the NR disrupted mPFC sequences at the onset of UP states as well as HPC sequences present during sharp-wave ripples. We conclude that the NR contributes to the coordination and stabilization of mPFC and HPC neuronal sequences during slow oscillations, possibly via the early activation of its own sequences.Significance StatementNeuronal assemblies are believed to be instrumental to code/encode/store information. They can be recorded in different brain regions, suggesting that widely distributed networks of networks are involved in such information processing. The prefrontal cortex, the hippocampus and the thalamic nucleus reuniens constitute a typical example of a complex network involved in memory consolidation. In this study, we show that spatially organized cells assemblies are recruited in the nucleus reuniens at the UP state onset during slow oscillations. Nucleus reuniens activity appears to be necessary to the stability of prefrontal cortex and hippocampal cell assembly formation during slow oscillations. This result further highlights the role of the Nucleus Reuniens as a functional hub for exchanging and processing memories.
T cells instruct dendritic cells to produce inflammasome independent IL-1β causing systemic inflammation
Authors: Jain Aakanksha , Irizarry-Caro Ricardo A. , Chawla Amanpreet S. , Philip Naomi H. , Carroll Kaitlin R. , Katz Jonathan D. , Oberst Andrew , Chervonsky Alexander V. , Pasare Chandrashekhar 
Published: November 2018

AbstractWhile IL-1β is critical for anti-microbial host defense, it is also a key mediator of autoimmune inflammation. Inflammasome activation following pathogenic insults is known to result in IL-1β production. However, the molecular events that produce IL-1β during T cell driven autoimmune diseases remain unclear. Here, we have discovered an inflammasome-independent pathway of IL-1β production that is triggered upon cognate interactions between dendritic cells and effector CD4 T cells. Analogous to inflammasome activation, this “T cell-instructed IL-1β also relies on two independent signaling events. TNFα produced by activated CD4 T cells engages TNFR signaling on DCs leading to pro-IL-1β synthesis. Subsequently, FasL, also expressed by effector CD4 T cells, engages Fas on DCs leading to caspase-8 dependent pro-IL-1β cleavage. Remarkably, this two-step mechanism is completely independent of pattern recognition receptor activation. IL-1β produced upon cognate DC-effector CD4 T cell interaction causes wide spread leukocyte infiltration, a hallmark of systemic inflammation as well as autoimmune pathology. This study has uncovered a novel feature of DC-T cell cross-talk that allows for active IL-1β secretion independent of innate sensing pathways and provides a mechanistic explanation for IL-1β production and its downstream consequences in CD4 T cell driven autoimmune pathology.