bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inclusive ethnographies
Authors: Szabó Tamás Péter , Troyer Robert A. 
Published: January 2018

Abstract
In ethnographically oriented linguistic landscape studies, social spaces are
studied in co-operation with research participants, many times through mobile
encounters such as walking. Talking, walking, photographing and video recording
as well as writing the fieldwork diary are activities that result in the
accumulation of heterogeneous, multimodal corpora. We analyze data from a
Hungarian school ethnography project to reconstruct fieldwork encounters and
analyze embodiment, the handling of devices (e.g. the photo camera) and verbal
interaction in exploratory, participant-led walking tours. Our analysis shows
that situated practices of embodied conduct and verbal interaction blur the
boundaries between observation and observers, and thus LL research is not only
about space- and place-making and sense-making routines, but the fieldwork
encounters are also transformative and contribute to space- and place-making
themselves. Our findings provide insight for ethnographic researchers and enrich
the already robust qualitative and quantitative strategies employed in the
field.
Genre and metacultural displays
Authors: Järlehed Johan 
Published: January 2018

AbstractThis paper argues that studies of the LL could merit from a more detailed social semiotic examination of particular sign-genres. It describes genre as normative system open to change, on the one hand, and as complex historical and cultural configurations of semiotic resources and affordances, on the other. Based on illustrative analysis of how the discursive interaction of ‘pride’ and ‘profit’ is affecting Galician and Basque street-name signing, the paper makes the following points: (1) genre depends on discourse, and discourse depends on genre; (2) particular materializations of a genre actualize distinct resources and highlight different affordances; (3) detailed and contextualized analysis of determined sign genres can reveal ideological layering in the LL; (4) when a genre is taken ‘out of place’ or is recontextualized, its typical repertoire of resources is rearranged and new affordances emerge.
“When you speak to a police officer and (call them)du”
Authors: Blood Rosalind 
Published: January 2018

AbstractThis study examines the development of pragmatic awareness of the German second person pronoun system by Australian study-abroad participants during a six-week language course in Germany. Data includes oral pre- and post- Language Awareness Interviews, semi-structured interviews and participant observation. Students displayed a greater awareness of the German address system and showed a growing confidence and sophistication in justifying their choices of address forms as well as an increased reliance on information acquired from native and expert speakers throughout their stay in Germany. Interview data and field notes indicate that students were socialised into second language (L2) practices of address term use by way of explicit correction from L2 speech community members on incorrect use of address forms. Such correction appears to have influenced their pragmatic development. The study supports previous research stating that even short stays abroad can encourage improvement in language features that are difficult to acquire in the classroom (Hassall, 2013) and shows why this is particularly beneficial in the context of German Studies due to the preference for direct and explicit speech in the German speech community.
“Hold the phone!”
Authors: Marks Annie 
Published: January 2018

AbstractThe initial paradigm of Video Relay Service (VRS) in the United States viewed interpreters as merely conduits for telephone communication; however, this paradigm has begun to shift. Recent research suggests that VRS interpreters are actively involved in coordinating interpreted interaction (Marks 2015;Warnicke and Plejert 2012,2016). This study aims add to the body of VRS research by analyzing features of turn management in ASL-English video relay interpreted calls. These features of turn management are grouped into two categories: techniques and strategies. Techniques denote acts that are performed in addition to the rendition, and strategies refer to instances of turn management that are embedded within renditions. Results show that VRS interpreters employ a variety of turn management techniques and strategies, especially in cases of overlapping talk between Deaf and hearing callers. The findings presented are relevant to the shifting paradigm of VRS interpreter work and training.
Why is that creature grunting?
Authors: Costal Tomás 
Published: January 2018

Abstract
Video games today are highly complex audiovisual products. Their nature is not
only multisemiotic but also interactive. Their potential audience has certain
expectations and, especially in the case of digital blockbusters, final users
need the advantage of knowledge and the force of numbers. A faux
pas in design, continuity or playability will most likely be
conducive to social media outrage, and will see official apologies be released
presently. Conversely, accessibility shortcomings rarely or never have the same
impact.
The present study puts forward the advantages of including Subtitles for the Deaf and Hard of Hearing (SDH) in
popular video games and offers an in-depth analysis of a selection of recent
multimedia titles. Drawing on the work of Bernal Merino (2015), O’Hagan
and Mangiron (2013) and Trabattoni (2014) on the special characteristics of video games, the
main elements around which they are structured and the aspects that determine
their success or failure, the author will endeavour to advance a convincing
argument in favour of the introduction of SDH subtitling conventions.
Development and validation of a high-resolution mapping platform to
aid in the public awareness of radiological hazards
Authors: Martin Peter G , Connor Dean , Payton Oliver D , Leal-Olloqui Macarena , Keatley Anya C , Scott Thomas B 
Published: January 2018

Abstract
The distribution, quantification and exposure-related effects of radiation in the
environment, arising from both natural and anthropogenic sources, is of great
(and growing) concern for global populations. Recent events at the Fukushima
Daiichi Nuclear Plant (FDNPP) have further highlighted the importance of
developing radiation mapping technologies that not only contribute to the
continued assessment of contamination, but can serve as an educational tool for
members of the public regarding both its behaviour and extent. With an even
greater number of people possessing smart-phone technology, a lightweight and
portable ‘connected system’ has been developed to demonstrate to
users the calibrated radioactive dose rate in an area, viewable in real-time
through a dedicated phone application. As well as allowing for system users to
be alerted where variations in dose rate are experienced, the combined results
from multiple systems are viewable through a custom-built desktop
application—permitting the output obtained via any number of units to be
similarly displayed in real-time. A successful initial trialling of the system
is described at a former tin mine in Cornwall (south-west England)—known
to exhibit low, but identifiable radiation anomalies in discrete areas.
Additional applications outside of its educational usage are also discussed.
Computational drug repositioning using low-rank matrix approximation and randomized algorithms
Authors: Luo Huimin , Li Min , Wang Shaokai , Liu Quan , Li Yaohang , Wang Jianxin 
Published: January 2018

Abstract

Motivation
Computational drug repositioning is an important and efficient approach towards identifying novel treatments for diseases in drug discovery. The emergence of large-scale, heterogeneous biological and biomedical datasets has provided an unprecedented opportunity for developing computational drug repositioning methods. The drug repositioning problem can be modeled as a recommendation system that recommends novel treatments based on known drug–disease associations. The formulation under this recommendation system is matrix completion, assuming that the hidden factors contributing to drug–disease associations are highly correlated and thus the corresponding data matrix is low-rank. Under this assumption, the matrix completion algorithm fills out the unknown entries in the drug–disease matrix by constructing a low-rank matrix approximation, where new drug–disease associations having not been validated can be screened.

Results
In this work, we propose a drug repositioning recommendation system (DRRS) to predict novel drug indications by integrating related data sources and validated information of drugs and diseases. Firstly, we construct a heterogeneous drug–disease interaction network by integrating drug–drug, disease–disease and drug–disease networks. The heterogeneous network is represented by a large drug–disease adjacency matrix, whose entries include drug pairs, disease pairs, known drug–disease interaction pairs and unknown drug–disease pairs. Then, we adopt a fast Singular Value Thresholding (SVT) algorithm to complete the drug–disease adjacency matrix with predicted scores for unknown drug–disease pairs. The comprehensive experimental results show that DRRS improves the prediction accuracy compared with the other state-of-the-art approaches. In addition, case studies for several selected drugs further demonstrate the practical usefulness of the proposed method.

Availability and implementation
http://bioinformatics.csu.edu.cn/resources/softs/DrugRepositioning/DRRS/index.html

Supplementary information
Supplementary data are available at Bioinformatics online.
pepKalc: scalable and comprehensive calculation of electrostatic interactions in random coil polypeptides
Authors: Tamiola Kamil , Scheek Ruud M , van der Meulen Pieter , Mulder Frans A A 
Published: January 2018

Abstract

Motivation
Polypeptide sequence length is the single dominant factor hampering the effectiveness of currently available software tools for de novo calculation of amino acid-specific protonation constants in disordered polypeptides.

Results
We have developed pepKalc, a robust simulation software for the comprehensive evaluation of protein electrostatics in unfolded states. Our software completely removes the limitations of the previously reported Monte-Carlo approaches in the computation of protein electrostatics by using a hybrid approach that effectively combines exact and mean-field calculations to rapidly obtain accurate results. Paired with a modern architecture GPU, pepKalc is capable of evaluating protonation behavior for an arbitrary-size polypeptide in a sub-second time regime.

Availability and implementation
http://protein-nmr.org and https://github.com/PeptoneInc/pepkalc
Spatial patterns of large jellyfish Chrysaora plocamia blooms in the Northern Humboldt Upwelling System in relation to biological drivers and climate
Authors: Quiñones Javier , Chiaverano Luciano M , Ayón Patricia , Adams Grant D , Mianzan Hermes W , Acha E Marcelo 
Published: January 2018

Abstract
In the Northern Humboldt Upwelling System (NHUS), one of the most productive ecosystems in the world, the large jellyfish Chrysaora plocamia exhibits high inter-annual variability in population size, often resulting in massive blooms. In this study, we examined the geographic patterns C. plocamia in the NHUS and their spatial overlap with ichthyoplankton, zooplankton, and chlorophyll a concentration (Chl a) during two El Niño (EN) years (1982–1983 and 1986–1987), and a neutral year (2014). During EN years, the spatial extent of C. plocamia medusae was larger than in the neutral year. In 1982–1983, medusae were concentrated mainly in the central-southern and southern regions of Peru, where they were associated with zooplankton, sardine larvae, and Chl a. In 1986–1987, medusae occurred in the northern and southern regions and spatially overlapped with sardine larvae and Chl a, and with zooplankton and anchoveta larvae, respectively. In 2014, medusae occurred mainly in the northern region, where they were associated with zooplankton, Chl a, and anchoveta eggs and larvae. Our results indicate strong EN effects on the distribution and abundance of C. plocamia, which can have consequences for zooplankton and ichthyoplankton abundance, as well as fisheries, in the NHUS.
Prospective Tractography-Based Targeting for Improved Safety of Focused Ultrasound Thalamotomy
Authors: Krishna Vibhor , Sammartino Francesco , Agrawal Punit , Changizi Barbara K , Bourekas Eric , Knopp Michael V , Rezai Ali 
Published: January 2018

Abstract

BACKGROUND
Focused ultrasound thalamotomy (FUS-T) was recently approved for the treatment of refractory essential tremor (ET). Despite its noninvasive approach, FUS-T reinitiated concerns about the adverse effects and long-term efficacy after lesioning.

OBJECTIVE
To prospectively assess the outcomes of FUS-T in 10 ET patients using tractography-based targeting of the ventral intermediate nucleus (VIM).

METHODS
VIM was identified at the intercommissural plane based on its neighboring tracts: the pyramidal tract and medial lemniscus. FUS-T was performed at the center of tractography-defined VIM. Tremor outcomes, at baseline and 3 mo, were assessed independently by the Tremor Research Group. We analyzed targeting coordinates, clinical outcomes, and adverse events. The FUS-T lesion location was analyzed in relation to unbiased thalamic parcellation using probabilisitic tractography. Quantitative diffusion-weighted imaging changes were also studied in fiber tracts of interest.

RESULTS
The tractography coordinates were more anterior than the standard. Intraoperatively, therapeutic sonications at the tractography target improved tremor (>50% improvement) without motor or sensory side effects. Sustained improvement in tremor was observed at 3 mo (tremor score: 18.3 ± 6.9 vs 8.1 ± 4.4, P = .001). No motor weakness and sensory deficits after FUS-T were observed during 6-mo follow-up. Ataxia was observed in 3 patients. FUS-T lesions overlapped with the VIM parcellated with probablisitic tractography. Significant microstructural changes were observed in the white matter connecting VIM with cerebellum and motor cortex.

CONCLUSION
This is the first report of prospective VIM targeting with tractography for FUS-T. These results suggest that tractography-guided targeting is safe and has satisfactory short-term clinical outcomes.
A set of experimentally validated, mutually orthogonal primers for combinatorially specifying genetic components
Authors: Subramanian Subu K , Russ William P , Ranganathan Rama 
Published: January 2018

Abstract
The design and synthesis of novel genes and deoxyribonucleic acid (DNA) sequences is a central technique in synthetic biology. Current methods of high throughput gene synthesis use pooled oligonucleotides obtained from custom-designed DNA microarray chips, and rely on orthogonal (non-interacting) polymerase chain reaction primers to specifically de-multiplex, by amplification, the precise subset of oligonucleotides necessary to assemble a full length gene. The availability of a large validated set of mutually orthogonal primers is therefore a crucial reagent for high-throughput gene synthesis. Here, we present a set of 166 20-nucleotide primers that are experimentally verified to be non-interacting, capable of specifying 13 695 unique genes. These primers represent a valuable resource to the synthetic biology community for specifying genetic components that can be assembled through a scalable and modular architecture.
An Exploration of Emergency Physicians’ Attitudes Toward Patients With Substance Use Disorder
Authors: Mendiola Cecelia Kathleen , Galetto Giorgio , Fingerhood Michael 
Published: January 2018

Objectives:
Much is known about some healthcare professionals’ attitudes toward patients with substance use disorders, but few studies have specifically looked at emergency department (ED) physicians. Individuals with substance use disorders are more likely to be people who chronically, frequently use the ED, and thus ED physicians are in a unique position to provide early identification and intervention for people struggling with addiction. The purpose of this study was to understand ED physicians’ attitudes toward patients with substance use disorder with the aim of decreasing stigma and improving the care of ED patients with substance use disorder.

Methods:
An anonymous Qualtrics survey was emailed to 115 emergency physicians in the Johns Hopkins Health System. The survey contained (1) demographics and (2) the medical condition regard scale, http://links.lww.com/JAM/A67. Participants were offered a $10 Amazon gift card to complete the survey.

Results:
The response rate was 50% (n = 58) and the completion rate was 43% (n = 50). Physicians had lower regard for patients with substance use disorders than other medical conditions with behavioral components. Of note, 54% of respondents indicated that they at least “somewhat agree” that they “prefer not to work with patients with substance use who have pain.”

Conclusions:
A significant portion of our study population had low regard for patients with substance use. Future research is needed to determine significant contributing factors and develop interventions to mitigate negative attitudes among ED physicians toward patients with substance use disorder.
Effect of Epidural Infusion Bolus Delivery Rate on the Duration of Labor Analgesia
Authors: Lange Elizabeth M. S. , Wong Cynthia A. , Fitzgerald Paul C. , Davila Wilmer F. , Rao Suman , McCarthy Robert J. , Toledo Paloma 
Published: January 2018

Abstract

Background
Programmed intermittent boluses of local anesthetic have been shown to be superior to continuous infusions for maintenance of labor analgesia. High-rate epidural boluses increase delivery pressure at the catheter orifice and may improve drug distribution in the epidural space. We hypothesized that high-rate drug delivery would improve labor analgesia and reduce the requirement for provider-administered supplemental boluses for breakthrough pain.

Methods
Nulliparous women with a singleton pregnancy at a cervical dilation of less than or equal to 5 cm at request for neuraxial analgesia were eligible for this superiority-design, double-blind, randomized controlled trial. Neuraxial analgesia was initiated with intrathecal fentanyl 25 μg. The maintenance epidural solution was bupivacaine 0.625 mg/ml with fentanyl 1.95 μg/ml. Programmed (every 60 min) intermittent boluses (10 ml) and patient controlled bolus (5 ml bolus, lockout interval: 10 min) were administered at a rate of 100 ml/h (low-rate) or 300 ml/h (high-rate). The primary outcome was percentage of patients requiring provider-administered supplemental bolus analgesia.

Results
One hundred eight women were randomized to the low- and 102 to the high-rate group. Provider-administered supplemental bolus doses were requested by 44 of 108 (40.7%) in the low- and 37 of 102 (36.3%) in the high-rate group (difference –4.4%; 95% CI of the difference, –18.5 to 9.1%; P = 0.67). Patient requested/delivered epidural bolus ratio and the hourly bupivacaine consumption were not different between groups. No subject had an adverse event.

Conclusions
Labor analgesia quality, assessed by need for provider- and patient-administered supplemental analgesia and hourly bupivacaine consumption was not improved by high-rate epidural bolus administration.
Postoperative Inflammation After Endoscopic Cyclophotocoagulation: Racial Distribution and Effect on Outcomes
Authors: Edmiston Anna M. , SooHoo Jeffrey R. , Seibold Leonard K. , Kahook Malik Y. , Palestine Alan G. , Pantcheva Mina B. 
Published: January 2018

Purpose:
To assess the prevalence of postoperative anterior chamber reaction or persistent anterior uveitis (PAU) by race and its effect on intraocular pressure (IOP) and visual acuity (VA) after combined phacoemulsification and endoscopic cyclophotocoagulation (ECP) in primary open-angle glaucoma.

Patients and Methods:
A retrospective analysis of all patients with primary open-angle glaucoma who underwent combined phacoemulsification cataract extraction with ECP from January 1, 2007 to October 31, 2015. VA, IOP, presence of anterior chamber cells, steroid treatment, and number of IOP lowering drops were analyzed preoperatively and up to 3 months postoperatively. Patients were categorized according to self-reported race. PAU was treated according to severity and presence of symptoms.

Results:
Two hundred twenty-three eyes met the inclusion criteria. PAU was present in 22.4% of eyes. PAU was significantly correlated with race, particularly African American race. PAU was also associated with a lack of improvement in inflammation at week 1 compared with day 1 postoperatively. However, there was no significant difference in VA, IOP, or reduction of IOP lowering drops in those with or without PAU. When comparing African Americans to whites, PAU and its treatment were not associated with a difference in IOP reduction at 3 months.

Conclusions:
PAU is common after combined phacoemulsification and ECP and is significantly correlated with race. Although PAU may require prolonged postoperative treatment, our data does not support poorer VA or IOP outcomes.
Systematic review and meta-analysis of genetic risk factors for neuropathic pain
Authors: Veluchamy Abirami , Hébert Harry L. , Meng Weihua , Palmer Colin N.A. , Smith Blair H. 
Published: January 2018

Abstract
Neuropathic pain (NP) is an increasingly common chronic pain state and a major health burden, affecting approximately 7% to 10% of the general population. Emerging evidence suggests that genetic factors could partially explain individual susceptibility to NP and the estimated heritability in twins is 37%. The aim of this study was to systematically review and summarize the studies in humans that have investigated the influence of genetic factors associated with NP. We conducted a comprehensive literature search and performed meta-analyses of all the potential genetic variants associated with NP. We reviewed 29 full-text articles and identified 28 genes that were significantly associated with NP, mainly involved in neurotransmission, immune response, and metabolism. Genetic variants in HLA genes, COMT, OPRM1, TNFA, IL6, and GCH1, were found to have an association with NP in more than one study. In the meta-analysis, polymorphisms in HLA-DRB1*13 (odds ratio [OR], 2.96; confidence interval [CI], 1.93-4.56), HLA-DRB1*04 (OR, 1.40; CI, 1.02-1.93), HLA-DQB1*03 (OR, 2.86; CI, 1.57-5.21), HLA-A*33 (OR, 2.32; CI, 1.42-3.80), and HLA-B*44 (OR, 3.17; CI, 2.22-4.55) were associated with significantly increased risk of developing NP, whereas HLA-A*02 (OR, 0.64; CI, 0.47-0.87) conferred reduced risk and neither rs1799971 in OPRM1 (OR, 0.55; CI, 0.27-1.11) nor rs4680 in COMT (OR, 0.95; CI, 0.81-1.13) were significantly associated with NP. These findings demonstrate an important and specific contribution of genetic factors to the risk of developing NP. However, large-scale replication studies are required to validate these candidate genes. Our review also highlights the need for genome-wide association studies with consistent case definition to elucidate the genetic architecture underpinning NP.