bluuebunny/crossref_metadata_2025_split huggingface dataset:
Imagined spectators
Authors: O’Sullivan Carol 
Published: June 2016

AbstractThis article considers theoretical and methodological questions of language and translation policy in the dissemination of audiovisual products across languages. This is an area where scholarly research is inevitably playing catch-up with rapid change both in the language industries and in film and television production. For example, we have a general sense of ‘dubbing territories’ and ‘subtitling territories’ but in reality the picture is more complex. Norms changed in the course of the home entertainment revolution, with the arrival of the DVD format in the late 1990s ostensibly increasing viewer choice and flexibility of translation provision. The relocation of much audiovisual material to an online environment has also generated fundamental changes in the way that works circulate, with volunteer translators and automated translation processes playing a larger role. Policy developments in access translation have meant that there have also been great changes relatively recently in the availability of SDH subtitling, audio description and other modes of access translation.This is a very broad field which raises many compelling research questions. At the same time, its very breadth does not lend itself to a comprehensive overview. The article will therefore aim to provide an orientation to, rather than a summary of, the theoretical and methodological challenges of research on this topic.
Methods for measuring 1/1 error field in Wendelstein 7-X stellarator
Authors: Bozhenkov S.A. , Lazerson S. , Otte M. , Gates D.A. , Sunn Pedersen T. , Wolf R.C. 
Published: June 2016

Abstract
Wendelstein 7-X is an optimized helical axis stellarator that came into operation at the end of 2015. A m/n  =  5/5 island chain is used in most of its configurations to form a divertor. This island chain at

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=
1

is sensitive to symmetry-breaking error fields, with the resonant 1/1 field being of particular concern because of its influence on the divertor heat flux distribution. Measurement and compensation of the 1/1 mode is therefore necessary. Experimentally, vacuum error fields in W7-X will be studied with a flux surface mapping diagnostic. In this paper numerical simulations for planning and analysing such measurements are presented. Two methods for determining the 1/1 mode are considered: measurement of the island width and measurement of a helical shift of the magnetic axis. Measurement of the resonant island width is a sensitive technique, but the island structure is also affected by other co-resonant components. A complementary method is to measure a helical shift of the magnetic axis in a configuration close to the resonance. This method has a simple interpretation and isolates the 1/1 error field from higher order resonant modes.
The use of plant community attributes to detect habitat quality in coastal environments
Authors: Del Vecchio Silvia , Slaviero Antonio , Fantinato Edy , Buffa Gabriella 
Published: June 2016

AbstractThe monitoring of biodiversity has mainly focused on the species level. However, researchers and land managers are making increasing use of complementary assessment tools that address higher levels of biological organization, i.e. communities, habitats and ecosystems. Recently, a variety of frameworks have been proposed for assessing the conservation status of communities or ecosystems. Among the various criteria proposed, all the protocols suggest considering (i) spatial aspects (range and area), and (ii) qualitative aspects of specific structures and functions. However, changes to ecological function are difficult to quantify and many protocols end up by using qualitative criteria. The aim of this work was to test the efficacy of some plant community attributes for the detection of vegetation quality in sand dune plant communities. We chose plant community attributes that either help to distinguish a habitat from others (diagnostic components) or play a significant role in habitat function and persistence over time. We used a diachronic approach by contrasting up-to-date vegetation data with data from previous studies carried out within the same areas. Changes in species composition were detected through detrended correspondence analyses (detrended correspondence analyses), Multi-Response Permutation Procedures and Indicator Species Analysis, while structural changes were analyzed by comparing species richness, total species cover, ecological groups of species and growth forms through null models. Ecological groups such as native focal species and aliens, and growth forms proved their efficacy in discriminating between habitat types and in describing their changes over time. The approach used in this study may provide an instrument for the assessment of plant community quality that can be applied to other coastal ecosystems.
CART—a chemical annotation retrieval toolkit
Authors: Deghou Samy , Zeller Georg , Iskar Murat , Driessen Marja , Castillo Mercedes , van Noort Vera , Bork Peer 
Published: June 2016

Abstract
Motivation: Data on bioactivities of drug-like chemicals are rapidly accumulating in public repositories, creating new opportunities for research in computational systems pharmacology. However, integrative analysis of these data sets is difficult due to prevailing ambiguity between chemical names and identifiers and a lack of cross-references between databases.
Results: To address this challenge, we have developed CART, a Chemical Annotation Retrieval Toolkit. As a key functionality, it matches an input list of chemical names into a comprehensive reference space to assign unambiguous chemical identifiers. In this unified space, bioactivity annotations can be easily retrieved from databases covering a wide variety of chemical effects on biological systems. Subsequently, CART can determine annotations enriched in the input set of chemicals and display these in tabular format and interactive network visualizations, thereby facilitating integrative analysis of chemical bioactivity data.
Availability and Implementation: CART is available as a Galaxy web service (cart.embl.de). Source code and an easy-to-install command line tool can also be obtained from the web site.
Contact: bork@embl.de
Supplementary information: Supplementary data are available at Bioinformatics online.
SETH detects and normalizes genetic variants in text
Authors: Thomas Philippe , Rocktäschel Tim , Hakenberg Jörg , Lichtblau Yvonne , Leser Ulf 
Published: June 2016

Abstract
Summary: Descriptions of genetic variations and their effect are widely spread across the biomedical literature. However, finding all mentions of a specific variation, or all mentions of variations in a specific gene, is difficult to achieve due to the many ways such variations are described. Here, we describe SETH, a tool for the recognition of variations from text and their subsequent normalization to dbSNP or UniProt. SETH achieves high precision and recall on several evaluation corpora of PubMed abstracts. It is freely available and encompasses stand-alone scripts for isolated application and evaluation as well as a thorough documentation for integration into other applications.
Availability and Implementation: SETH is released under the Apache 2.0 license and can be downloaded from http://rockt.github.io/SETH/.
Contact: thomas@informatik.hu-berlin.de or leser@informatik.hu-berlin.de
RANKS: a flexible tool for node label ranking and classification in biological networks
Authors: Valentini Giorgio , Armano Giuliano , Frasca Marco , Lin Jianyi , Mesiti Marco , Re Matteo 
Published: June 2016

Abstract
Summary: RANKS is a flexible software package that can be easily applied to any bioinformatics task formalizable as ranking of nodes with respect to a property given as a label, such as automated protein function prediction, gene disease prioritization and drug repositioning. To this end RANKS provides an efficient and easy-to-use implementation of kernelized score functions, a semi-supervised algorithmic scheme embedding both local and global learning strategies for the analysis of biomolecular networks. To facilitate comparative assessment, baseline network-based methods, e.g. label propagation and random walk algorithms, have also been implemented.
Availability and Implementation: The package is available from CRAN: https://cran.r-project.org/. The package is written in R, except for the most computationally intensive functionalities which are implemented in C.
Contact: valentini@di.unimi.it
Supplementary information: Supplementary data are available at Bioinformatics online.
COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment and paired-end read LinkAge
Authors: Lu Yang Young , Chen Ting , Fuhrman Jed A , Sun Fengzhu 
Published: June 2016

AbstractMotivationThe advent of next-generation sequencing technologies enables researchers to sequence complex microbial communities directly from the environment. Because assembly typically produces only genome fragments, also known as contigs, instead of an entire genome, it is crucial to group them into operational taxonomic units (OTUs) for further taxonomic profiling and down-streaming functional analysis. OTU clustering is also referred to as binning. We present COCACOLA, a general framework automatically bin contigs into OTUs based on sequence composition and coverage across multiple samples.ResultsThe effectiveness of COCACOLA is demonstrated in both simulated and real datasets in comparison with state-of-art binning approaches such as CONCOCT, GroopM, MaxBin and MetaBAT. The superior performance of COCACOLA relies on two aspects. One is using L1 distance instead of Euclidean distance for better taxonomic identification during initialization. More importantly, COCACOLA takes advantage of both hard clustering and soft clustering by sparsity regularization. In addition, the COCACOLA framework seamlessly embraces customized knowledge to facilitate binning accuracy. In our study, we have investigated two types of additional knowledge, the co-alignment to reference genomes and linkage of contigs provided by paired-end reads, as well as the ensemble of both. We find that both co-alignment and linkage information further improve binning in the majority of cases. COCACOLA is scalable and faster than CONCOCT, GroopM, MaxBin and MetaBAT.Availability and implementationThe software is available at https://github.com/younglululu/COCACOLA.Supplementary informationSupplementary data are available at Bioinformatics online.
Perceived Physical Appearance: Assessing Measurement Equivalence in Black, Latino, and White Adolescents
Authors: Epperson Anna E. , Depaoli Sarah , Song Anna V. , Wallander Jan L. , Elliott Marc N. , Cuccaro Paula , Tortolero Emery Susan , Schuster Mark 
Published: June 2016

Objective This aim of this study was to examine whether the construct of physical appearance perception differed among the three largest racial/ethnic groups in the United States using an adolescent sample. Methods Black (46%), Latino (31%), and White (23%) adolescents in Grade 10 from the Healthy Passages study (N = 4,005) completed the Harter’s Self-Perception Profile for Adolescents–Physical Appearance Scale (SPPA–PA) as a measure of physical appearance perception. Results Overall, Black adolescents had a more positive self-perception of their physical appearance than Latino and White adolescents. However, further analysis using measurement invariance testing revealed that the construct of physical appearance perception, as measured by SPPA–PA, was not comparable across the three racial/ethnic groups in both males and females. Conclusions These results suggest that observed differences may not reflect true differences in perceptions of physical appearance. Measures that are equivalent across racial/ethnic groups should be developed to ensure more precise measurement and understanding.
Active Trigger Points in the Cervical Musculature Determine the Altered Activation of Superficial Neck and Extensor Muscles in Women With Migraine
Authors: Florencio Lidiane L. , Ferracini Gabriela N. , Chaves Thais C. , Palacios-Ceña María , Ordás-Bandera Carlos , Speciali José G. , Falla Deborah , Grossi Débora B. , Fernández-de-las-Peñas César 
Published: June 2016

Objective:
Previous studies have demonstrated the presence of active trigger points (TrPs) in women with migraine reproducing their headache attacks. No study has investigated whether these TrPs can alter cervical muscle function in migraine. Our objective was to analyze differences in the activation of superficial neck flexor and extensor muscles in women with migraine considering the presence of active TrPs in the splenius capitis (SC), the upper trapezius (UT), and the sternocleidomastoid (SCM) muscles.

Methods:
Surface electromyography (EMG) was recorded from the superficial flexors (SCM and anterior scalene) and the extensor (SC, UT) muscles bilaterally as participants performed a staged task of cranio-cervical flexion (CCF; 5 contractions representing a progressive increase in CCF range of motion) in 70 women with migraine. They were stratified according to the presence or the absence of active TrPs in the SCM, the SC, or the UT musculature. A comparison of EMG normalized root mean square (RMS) values was conducted with a 2×5 analysis of covariance with the task level as the within-subject variable, group stratified by active TrPs as the between-subjects variable and the presence of neck pain as a covariable.

Results:
All patients exhibited active TrPs in their cervical muscles, which reproduced their migraine. Women with migraine exhibiting active TrPs in the SCM (P<0.01), the UT (P<0.05), or the SC (P<0.05) muscles had lower normalized RMS values of their superficial neck flexors than those without active TrPs in the same muscles. In addition, individuals exhibiting active TrPs in the SC and the UT (both, P<0.05) muscles had higher normalized RMS values in the SC muscle than those without active TrPs in the same muscles.

Conclusions:
The presence of active TrPs in the cervical musculature determines an altered activation of superficial neck and extensor muscles during low-load, isometric CCF contractions in women with migraine.
All Fatigue is Not Created Equal
Authors: Boggero Ian A. , Rojas-Ramirez Marcia V. , Carlson Charles R. 
Published: June 2016

Objectives:
Fatigue is known to be a pathway through which depression, psychological distress, pain intensity, and sleep disturbance influence pain interference, but the independent effects of fatigue on pain interference after controlling for these variables remains unknown. In addition, no study to date has tested whether fatigue subtypes of general fatigue, mental fatigue, emotional fatigue, physical fatigue, or vigor differentially predict pain interference.

Methods:
The current study tested these associations using archival medical data of 2133 chronic orofacial pain patients, who completed a battery of psychological questionnaires at the time of their first appointment at an orofacial pain clinic.

Results:
Hierarchical linear regression analysis revealed that after controlling for depression, psychological distress, sleep disturbance, pain intensity, and demographic variables, fatigue predicted higher pain interference (B=0.70, SE=0.17, P<0.001, η2=0.01). Physical fatigue (B=1.70, SE=0.48, P<0.001, η2=0.01) and vigor (B=−3.24, SE=0.47, P<0.001, η2=0.03) were independently associated with pain interference after controlling for the aforementioned variables.

Discussion:
The findings suggest that fatigue is an important independent predictor of pain interference and not merely a mediator. These findings also suggest that not all fatigue is created equal. Interventions aimed at reducing pain interference should target specific fatigue symptoms of physical fatigue and vigor. Future research investigating the independent associations of fatigue subtypes on pain outcomes may help clarify the nature of the interrelationships between pain and fatigue.
The Association Between Corticomotor Excitability and Motor Skill Learning in People With Painful Hand Arthritis
Authors: Parker Rosalind S. , Lewis Gwyn N. , Rice David A. , McNair Peter J. 
Published: June 2016

Objectives:
Previous studies have shown a tendency for reduced motor cortex inhibition in chronic pain populations. People with chronic pain also routinely demonstrate motor deficiencies, including skill learning. The goals of the current study were to (1) provide a thorough analysis of corticomotor and intracortical excitability in people with chronic arthritic hand pain, and (2) examine the relationship between these measures and performance on a motor skill learning task.

Methods:
Twenty-three people with arthritic hand pain and 20 pain-free controls participated in a cross-sectional study. Transcranial magnetic stimulation was used to assess corticomotor and intracortical excitability of the first dorsal interosseus muscle. Participants then completed a 30-minute motor skill training task involving the index finger of the same hand.

Results:
Hand arthritis participants showed evidence of reduced intracortical inhibition and enhanced facilitation, which correlated with duration of hand pain. Arthritis participants were initially poorer at the motor skill task but over the total training time performance was equivalent between groups. There were no associations found between measures of intracortical excitability and motor skill learning.

Discussion:
Our findings are the first to provide evidence of cortical disinhibition in people with painful arthritis, as previously demonstrated in other chronic pain populations. Cortical excitability changes may progress the longer pain persists, with increased pain duration being associated with greater cortical disinhibition. There was no evidence that these changes in cortical excitability are related to impaired motor function or skill learning.
Early MRI Detection and Closed Bone Graft Epiphysiodesis May Alter the Course of Avascular Necrosis Following Unstable Slipped Capital Femoral Epiphysis
Authors: Napora Joshua K. , Gilmore Allison , Son-Hing Jochen P. , Grimberg Dominic C. , Thompson George H. , Liu Raymond W. 
Published: June 2016

Background:
Unstable slipped capital femoral epiphysis (SCFE) has an increased incidence of avascular necrosis (AVN). Early identification and surgical intervention for AVN may help preserve the femoral head.

Methods:
We retrospectively reviewed 48 patients (50 hips) with unstable SCFE managed between 2000 and 2014. AVN was diagnosed based on 2 different postoperative protocols. Seventeen patients (17 hips) had a scheduled magnetic resonance imaging (MRI) between 1 and 6 months from initial surgery, and the remaining 31 patients (33 hips) were evaluated by plain radiographs alone. If AVN was diagnosed, we offered core decompression and closed bone graft epiphysiodesis (CBGE) to mitigate its affects. At final follow-up, we assessed progression of AVN using the Steinberg classification.

Results:
Overall 13 hips (26%) with unstable SCFEs developed AVN. MRI revealed AVN in 7 of 17 hips (41%) at a mean of 2.5 months postoperatively (range, 1.0 to 5.2 mo). Six hips diagnosed by MRI received surgical intervention (4 CBGE, 1 free vascularized fibula graft, and 1 repinning due to screw cutout) at a mean of 4.1 months (range, 1.3 to 7.2 mo) postoperatively. None of the 4 patients treated with CBGE within 2 months postoperatively progressed to stage IVC AVN. The 2 patients treated after 4 months postoperatively both progressed to stage VC AVN.
Plain radiographs demonstrated AVN in 6 of 33 hips (18%) at a mean of 6.8 months postoperatively (range, 2.1 to 21.1 mo). One patient diagnosed with stage IVB AVN at 2.4 months had screw cutout and received CBGE at 2.5 months from initial pinning. The remaining 5 were not offered surgical intervention. Five of the 6 radiographically diagnosed AVN, including the 1 treated with CBGE, progressed to stage IVC AVN or greater.

Conclusions:
Although all patients with positive MRI scans developed radiographic AVN, none of the 4 patients treated with CBGE within 2 months after pinning developed grade IVC or greater AVN. Early MRI detection and CBGE may mitigate the effects of AVN after SCFE.

Level of Evidence:
Level III—retrospective comparative study.
The “Double Medial Malleolus”: A New Physical Finding in Talocalcaneal Coalition
Authors: Rocchi Vanna , Huang Ming-Tung , Bomar James D. , Mubarak Scott 
Published: June 2016

Purpose:
It has been the observation of the senior author that there is a bony fullness or “double medial malleolus” over the middle facet as a consistent finding with most talocalcaneal coalitions (TCC). To document this observation, we reviewed records and radiographs in 3 patient groups.

Methods:
Part 1: retrospective chart review was completed for 111 feet to determine the clinical presence of a palpable “double medial malleolus.” Part 2: computed tomography (CT) scans for evaluation of tarsal coalition or symptomatic flatfoot between January 2006 and December 2014 were retrospectively reviewed for the same cohort. Soft tissue thickness was measured as the shortest distance between bone and skin surface at both the medial malleolus and the middle facet/coalition. The volume of the middle facet or coalition was measured at their midpoint. These findings were compared among feet with TCC (n=53), calcaneonavicular coalition (CNC) (n=20), and flatfoot (n=38).

Results:
Part 1—clinical: from medical records, 38 feet (34%) had documented record of a palpable medial prominence. Of the feet reviewed with a “double medial malleolus,” all had TCC (no false positives or false negatives). Clinical and CT prominence demonstrated significant correlation (r
s=0.519, P=0.001). Part 2—radiographic: CT observation of “double medial malleolus” is significantly associated with TCC (P<0.001). CT observation of double medial malleolus is 81% sensitive and 79% specific as a predictive test for TCC. The middle facet-to-skin distance was significantly closer in those with TCC versus controls (P<0.001). The ratio was larger in patients with TCC versus CNC (P=0.006) or flatfeet (P<0.001). Volume was nearly twice the size in patients with TCC versus the controls (P<0.001).

Conclusions:
TCCs have a bony prominence below the medial malleolus on clinical exam and CT scan not present in flatfeet or CNCs. This abnormal middle facet is almost twice the size of the normal middle facet. Obesity or severe valgus may mask this finding. If a palpable bony prominence is noted just below the medial malleolus during examination of a painful foot with a decrease in subtalar motion, the likely diagnosis is TCC. With this added clinical finding, appropriate images can be ordered to confirm the diagnosis of the latter. We advise CT scans with 3D images for surgical planning. The primary finding for tarsal coalitions in textbooks is decreased subtalar motion. This new finding of a palpable enlarged medial prominence just below the medial malleolus is highly associated with TCCs.

Level of Evidence:
Level III.