bluuebunny/crossref_metadata_2025_split huggingface dataset:
High throughput resistance profiling of Plasmodium falciparum infections based on custom dual indexing and Illumina next generation sequencing-technology
Authors: Nag Sidsel , Dalgaard Marlene D. , Kofoed Poul-Erik , Ursing Johan , Crespo Marina , Andersen Lee O’Brien , Aarestrup Frank Møller , Lund Ole , Alifrangis Michael 
Published: May 2017

AbstractGenetic polymorphisms in P. falciparum can be used to indicate the parasite’s susceptibility to antimalarial drugs as well as its geographical origin. Both of these factors are key to monitoring development and spread of antimalarial drug resistance. In this study, we combine multiplex PCR, custom designed dual indexing and Miseq sequencing for high throughput SNP-profiling of 457 malaria infections from Guinea-Bissau, at the cost of 10 USD per sample. By amplifying and sequencing 15 genetic fragments, we cover 20 resistance-conferring SNPs occurring in pfcrt, pfmdr1, pfdhfr, pfdhps, as well as the entire length of pfK13, and the mitochondrial barcode for parasite origin. SNPs of interest were sequenced with an average depth of 2,043 reads, and bases were called for the various SNP-positions with a p-value below 0.05, for 89.8–100% of samples. The SNP data indicates that artemisinin resistance-conferring SNPs in pfK13 are absent from the studied area of Guinea-Bissau, while the pfmdr1 86 N allele is found at a high prevalence. The mitochondrial barcodes are unanimous and accommodate a West African origin of the parasites. With this method, very reliable high throughput surveillance of antimalarial drug resistance becomes more affordable than ever before.
Vestibular Schwannoma with Contralateral Facial Nerve Palsy: A False Localizing Sign
Authors: Bhaskar Mukesh , Kumar Rakesh , Singh Sunil , Meel M. 
Published: May 2017

AbstractVestibular schwannomas are the most common cerebellopontine angle tumors. These tumors commonly present with ipsilateral dysfunction of acoustic, vestibular, trigeminal, and facial nerves. Vestibular schwannoma with involvement of contralateral facial nerve is very unusual, and whenever present, it is considered as a false localizing sign. It seems that displacement and distortion of the brainstem by the large mass lesion may lead to this atypical presentation. We report a case of vestibular schwannoma with contralateral abducens and facial nerve paresis.
Indikatoren für Sprachverständnis bei Kindern mit Migrationshintergrund. Ein Extremgruppenvergleich
Authors: Kiese-Himmel Christiane , Poinstingl Herbert , von Steinbüchel Nicole 
Published: May 2017

Zusammenfassung
Hintergrund Kinder mit Migrationshintergrund und Deutsch als Zweitsprache (DaZ) gelten häufig als sprachauffällig, was jedoch mangels fehlender Untersuchungsinstrumente im jungen Alter schwer zu objektivieren ist. Hierfür sollten empirisch Risikofaktoren bestimmt werden.
Material und Methoden Aus dem Datenpool einer Entwicklungslängsschnittstudie in 7 Kitas in Frankfurt/M. u. Darmstadt wurden Migrantenkinder im Alter von 3–5;11 Jahren durch ihre Testleistung im oralen Sprachverständnis 2 Extremgruppen zugewiesen: „unauffällig“ bei T-Wert ≥46 (N=61) vs. „auffällig“ bei T-Wert ≤32 (N=65). Gruppenunterschiede wurden anhand von Testergebnissen (Intelligenz; Verständnis grammatischer Strukturen; sprachliche Begriffsbildung; Erkennen von semantischen und grammatischen Inkonsistenzen) analysiert.
Ergebnisse Die Intelligenz war in beiden Gruppen durchschnittlich, in der unauffälligen Gruppe über dem Altersmittel gelegen: T-W 54,1; SD 6,7, in der auffälligen darunter: T-W 42,2; SD 8,8 (p<0,001). In allen Sprachleistungen unterschieden sich die Gruppen durchgängig signifikant. Diskriminanzanalytisch wurden 4 Merkmale für die Güte von DaZ identifiziert: Intelligenzhöhe; Erkennen von Sprachinkonsistenzen; Bildungsstand der Mutter; Grammatikbasiertes Sprachverständnis. Bzgl. der vorhergesagten Gruppenzugehörigkeit wurden 88% der Kinder mit auffälligem und 84% der mit unauffälligem Sprachverständnis korrekt zugeordnet.
Schlussfolgerung Die Studie liefert einen akzeptablen Standard, um Migrantenkinder mit gutem Verständnis von DaZ von solchen mit schwachem zu trennen.
The modification of compound nouns by three adjectives
Authors: Berg Thomas 
Published: May 2017

Abstract
This paper is the final instalment in a series of studies investigating the modification patterns in complex noun phrases (NPs) in English. It particularly focuses on the modification of two-noun compounds by three attributive adjectives. An analysis of all such NPs from the BNC reveals a strong preference for head modification over modifier modification, similar rates of convergent and divergent modification and the non-occurrence of crossed modification. The single most important factor influencing the modification patterns is functional status. The larger the number of adjectives modifying the head of the compound, the higher the frequency of the modification type (modulo a proximity effect). The absence of crossed modification is expected under the no-crossing constraint, which is understood here not as a formal but as a functional principle ensuring successful communication. The various factors can be tied together under the rubric of accessibility. The probability of selecting a particular modification target is argued to be a function of the accessibility of the nouns in an NP.
Patterns of (inter)subjectivity
Authors: Hofmockel Carolin 
Published: May 2017

AbstractThe prevalent hypothesis in research on pragmatic markers suggests that the left periphery of an utterance attracts predominantly subjective meanings, whereas the right periphery is the locus of intersubjective meanings. The goal of this paper is to test this hypothesis forbutas used in a dataset of spoken Glaswegian English, a variety in whichbutmay occur in both left- and right-peripheral positions. Considering thatbutderives its discursive meaning notper se, but from its embeddedness in particularized contexts, the methodological framework integrates the notion of (inter)subjectivity with the interactional-sociolinguistic concept of contextualization cue to identify (inter)subjective patterned co-occurrences forbut. A fine-grained analysis of the patternsbutforms with subjective and intersubjective cues in its local linguistic context shows that discourse patterns of left-peripheralbuttend to foreground subjective meanings, while discourse patterns of right-peripheralbuttend to foreground more intersubjective meanings, supporting the hypothesis of peripheral asymmetry.
We’re talking about semantics here
Authors: Siebörger Ian , Adendorff Ralph 
Published: May 2017

AbstractThis article describes how procedural knowledge is produced in a meeting of the South African parliament’s Portfolio Committee on Transport, using concepts from Systemic Functional Linguistics (SFL) and Legitimation Code Theory (LCT). Members of this committee argue over whether or not to amend a draft committee report and in the process co-construct procedural norms for future committee meetings. Participants on both sides of the argument useaxiological condensation, in which actions and ideas are associated with each other and charged with a particular moral or affective value (Maton 2014: 130) to portray their version of the procedure to be followed as morally superior to that of their opponents. They also useaxiological rarefaction(Maton 2014: 130) to reinforce their positions by making apparent concessions to those on the other side of the argument. This is revealed through an analysis of thecouplingof ideation and Appraisal (Martin 2000: 161) in the logogenetic unfolding of members’ talk, combined with elements of Interactional Sociolinguistics (Gumperz 1982). The analysis suggests that axiological condensation and rarefaction in this meeting reflect competing visions of what it means to be ‘pro-democracy’ in post-apartheid South Africa.
Management, Spirituality, and Religion (MSR) ways and means: a paper to encourage quality research
Authors: Tackney Charles Thomas , Chappell Stacie , Harris Dan , Pavlovich Kathryn , Egel Eleftheria , Major Richard , Finney Mary , Stoner James 
Published: May 2017

Despite 15 years of functioning as an interest group, our domain of inquiry is relatively young and there are limited theoretical boundaries to support, shape, and assist our efforts. This metaphorical “blank canvas” is both empowering, in that so many inquiries are
open for exploration, and yet also limiting. In this document we highlight three critical elements to emphasize their importance in MSR research: (a) delineating and operationalizing the key terms of religion, spirituality, and workplace spirituality; (b) acknowledging the work to date in
the MSR corpus around definitions of these terms, and (c) being explicit about how ontological and epistemological assumptions inform our methods. The intention is to encourage growth in the quality and rigor of our individual and collective scholarship.
On the apparent power law in CDM halo pseudo-phase space density profiles
Authors: Nadler Ethan O. , Oh S. Peng , Ji Suoqing 
Published: May 2017

Abstract
We investigate the apparent power-law scaling of the pseudo-phase space density (PPSD) in cold dark matter (CDM) haloes. We study fluid collapse, using the close analogy between the gas entropy and the PPSD in the fluid approximation. Our hydrodynamic calculations allow for a precise evaluation of logarithmic derivatives. For scale-free initial conditions, entropy is a power law in Lagrangian (mass) coordinates, but not in Eulerian (radial) coordinates. The deviation from a radial power law arises from incomplete hydrostatic equilibrium (HSE), linked to bulk inflow and mass accretion, and the convergence to the asymptotic central power-law slope is very slow. For more realistic collapse, entropy is not a power law with either radius or mass due to deviations from HSE and scale-dependent initial conditions. Instead, it is a slowly rolling power law that appears approximately linear on a log–log plot. Our fluid calculations recover PPSD power-law slopes and residual amplitudes similar to N-body simulations, indicating that deviations from a power law are not numerical artefacts. In addition, we find that realistic collapse is not self-similar; scalelengths such as the shock radius and the turnaround radius are not power-law functions of time. We therefore argue that the apparent power-law PPSD cannot be used to make detailed dynamical inferences or extrapolate halo profiles inwards, and that it does not indicate any hidden integrals of motion. We also suggest that the apparent agreement between the PPSD and the asymptotic Bertschinger slope is purely coincidental.
Cardiac Abnormalities in Type 1 Facioscapulohumeral Muscular Dystrophy
Authors: Labombarda Fabien , Maurice Maxime , Simon Jean-Philippe , Legallois Damien , Guyant-Maréchal Lucie , Bedat-Millet Anne-Laure , Merle Philippe , Saloux Eric , Chapon Françoise , Milliez Paul 
Published: May 2017

Abstract

Objectives:
We conducted a retrospective study to characterize the cardiac complications in patients with genetically confirmed type 1 facioscapulohumeral dystrophy.

Methods:
We reviewed baseline cardiac investigations, including electrocardiogram, Holter electrocardiogram and echocardiogram, as well as cardiac complications that occurred during follow-up in 56 adult patients (37 men, mean duration of disease: 20 years).

Results:
Baseline evaluation revealed minor cardiac anomalies in 23 patients including incomplete right bundle branch block (iRBBB) in 13 patients (23%). Over a mean follow-up period of 7.2 years, there was no cardiac death, no patient developed cardiomyopathy, and 28 patients (50%) experienced cardiac anomalies. Among these patients, 3 had one or more major events (heart failure and/or atrial fibrillation). The remaining 25 patients presented minor cardiac anomalies of which iRBBB was the most frequent (25%).

Conclusions:
Cardiac anomalies identified during the follow-up of patients with type 1 facioscapulohumeral dystrophy are mainly minor anomalies, dominated by the iRBBB.
Immune Myopathy With Perimysial Pathology Associated With Interstitial Lung Disease and Anti-EJ Antibodies
Authors: Kwon Patrick M. , Zhou Lan , Motiwala Rajeev , Kerr Leslie D. , Shin Susan C. 
Published: May 2017

Abstract

Objectives:
We report a case of immune myopathy with perimysial pathology associated with anti-glycyl-transfer RNA synthetase (anti-EJ) antibody and an excellent treatment response.

Methods:
Chart review.

Results:
A 36-year-old woman presented with 3 months of fatigue, weight loss, progressive weakness in a scapuloperoneal distribution, and dysphagia. Nerve conduction studies, electromyography, and ultrasound suggested an irritable myopathy. She had marked elevations of creatine kinase and positive anti-glycyl-transfer RNA synthetase (anti-EJ) antibodies. A left biceps muscle biopsy revealed inflammation of the perimysium and surrounding perimysial blood vessels with focal fragmentation of the perimysium. Further evaluation revealed interstitial lung disease. Treatment with prednisone and mycophenolate mofetil led to marked clinical improvement of her symptoms.

Conclusions:
Our case adds to the growing spectrum of inflammatory myopathies and highlights the importance of performing a comprehensive, multisystem workup.
What's in the Literature?
Authors: Bromberg Mark , Silvestri Nicholas J. , Lacomis David 
Published: May 2017

Abstract
In this edition, we provide a detailed summary of an informative book, “GBS100: Celebrating a Century of Progress in Guillain–Barré Syndrome” developed by the Peripheral Nerve Society to honor the centenary of the original paper on Guillain–Barré Syndrome. We also review various studies in myasthenia gravis including: management with rituximab; the efficacy of early fast-acting treatment with corticosteroids; and various dosing strategies for tacrolimus. Finally, we review new studies including: the potential pathogenesis, risk factors, and functional decline of patients with inclusion body myositis; MxA immunoreactivity in dermatomyositis; diagnostic approaches for evaluating patients with myalgia, fatigue, and exercise intolerance; MRI patterns in genetic muscle disease; and MRI as an outcome measure in facioscapulohumeral muscular dystrophy.
LAMELLAR HOLE-ASSOCIATED EPIRETINAL PROLIFERATION IN LAMELLAR MACULAR HOLE AND FULL-THICKNESS MACULAR HOLE IN HIGH MYOPIA
Authors: Lai Tso-Ting , Yang Chung-May 
Published: May 2017

Purpose:
To report findings and surgical outcomes of lamellar macular hole (LMH) or full-thickness macular hole (FTMH) accompanied by lamellar hole-associated epiretinal proliferation (LHEP) in eyes with high myopia (HM).

Methods:
Consecutive cases of HM with LMH or FTMH containing LHEP were retrospectively reviewed (study group, 43 cases). Cases of HM without LHEP (22) and those of non-HM with LHEP (30) served as Control A and B.

Results:
The study group showed larger (928.7 ± 381.9 μm) and deeper (remained base thickness: 79.7 ± 23.7 μm) LMH retinal defect than that in Control A (466.2 ± 179.1 and 99.9 ± 24.9) and B (647.1 ± 346.7 and 99.1 ± 38.1). Lamellar hole-associated epiretinal proliferation in the study group had a higher rate of wide extension (42.3%) and growing along the posterior hyaloid (PH, 53.8%). Patients with LMH who underwent surgery in the study group and Control A showed limited best corrected visual acuity (BCVA) improvement (0–1 and 1–2 ETDRS lines, respectively), while Control B had significant improvement (4–5 lines). For full-thickness macular holes, the study group was the youngest (50.0 ± 11.4) and LHEP was more likely to grow on the posterior hyaloid (23.5%); the postoperative best corrected visual acuity, however, was similar to that in Control A (20/63–20/80).

Conclusion:
Lamellar hole-associated epiretinal proliferation in HM tended to be more widespread and adherent to the posterior hyaloid than in eyes without HM. Visual outcomes after LMH repair in eyes with LHEP and HM are less favorable than eyes with LHEP and without HM, but similar to eyes with HM and without LHEP.
Oxidative lipidomics: applications in critical care
Authors: Anthonymuthu Tamil S. , Kim-Campbell Nahmah , Bayır Hülya 
Published: May 2017

Purpose of review
Lipid peroxidation has long been established as a key player in the pathophysiology of critical illness. Recent developments in oxidative lipidomics have aided in deciphering the molecular mechanisms of lipid oxidation in health and disease. This review discusses recent achievements and recent developments in oxidative lipidomics and its contribution to the understanding of critical illness.

Recent findings
Most studies involving acute injury focus on identifying the end products of lipid peroxidation. This misses the early events and targets of peroxidation mechanisms. Recent developments in liquid chromatography tandem mass spectrometry-based oxidative lipidomics have enabled the identification of a wide variety of enzymatically generated lipid oxidation products. Such lipid mediators have been found to play an important role in injury, inflammation, and recovery in disease states such as sepsis or head trauma.

Summary
Multiple lipid oxidation products are formed either through enzymatic pathways or through random chemical reactions. These products are often biologically active and can contribute to the regulation of cellular signaling. Oxidative lipidomics has contributed to the identification and quantification of lipid peroxidation products, the mechanism and time course of their production after injury, and synergistic functioning with other regulatory processes in the body. These advances in knowledge will help guide the future development of interventions in critical illness.
Measuring compensation in neurodegeneration using MRI
Authors: Gregory Sarah , Long Jeffrey D. , Tabrizi Sarah J. , Rees Geraint 
Published: May 2017

Purpose of review
Despite signs of cortical and subcortical loss, patients with prodromal and early-stage neurodegenerative disease are able to perform at a level comparable to the normal population. It is presumed that the onset of compensatory processes, that is changes in brain activation within a function-specific network or in the recruitment of a region outside of the task-network, underlies this maintenance of normal performance. However, in most studies to date, increased brain activity is not correlated with indices of both disease and performance and what appears to be compensation could simply be a symptom of neurodegeneration.

Recent findings
MRI studies have explored compensation in neurodegenerative disease, claiming that compensation is evident across a number of disorders, including Alzheimer's and Parkinson's disease, but generally always in early stages; after this point, compensation is generally no longer able to operate under the severe burden of disease. However, none of these studies explicitly adopted a particular model of compensation. Thus, we also discuss our recent attempts to operationalize compensation for empirical testing.

Summary
There is clear evidence of compensatory processes in the early stages of neurodegenerative disease. However, for a more complete understanding, this requires more explicit empirical modelling.
Structure-Function Analysis of Nonarteritic Anterior Ischemic Optic Neuropathy and Age-Related Differences in Outcome
Authors: Sun Ming-Hui , Liao Yaping Joyce 
Published: May 2017

Background:
The optic nerve head is vulnerable to ischemia leading to anterior ischemic optic neuropathy (AION), the most common acute optic neuropathy in those older than 50 years of age.

Methods:
We performed a cross-sectional study of 55 nonarteritic anterior ischemic optic neuropathy (NAION) eyes in 34 patients to assess clinical outcome and perform structure-function correlations.

Results:
The peak age of NAION onset was between 50 and 55 years. Sixty-seven percent of patients presented with their first event between the ages of 40 and 60 years, and 32% presented at ≤50 years. Those with NAION onset at age ≤50 years did not have significantly better visual outcome per logMAR visual acuity, automated perimetric mean deviation (PMD) or optical coherence tomography (OCT) measurements. Kaplan–Meier survival curve and multivariate Cox proportional regression analysis showed that age >50 years at NAION onset was associated with greater risk of second eye involvement, with hazard ratio of 20. Older age at onset was significantly correlated with greater thinning of the ganglion cell complex (GCC) (P = 0.022) but not with logMAR visual acuity, PMD, or thinning of retinal nerve fiber layer (RNFL). Using area under receiver operating characteristic curve analyses, we found that thinning of RNFL and GCC was best able to predict visual outcome, and that mean RNFL thickness >65 μm or macular GCC thickness >55 μm significantly correlated with good visual field outcome.

Conclusions:
We showed that NAION onset at age >50 years had a greater risk of second eye involvement. Patients with OCT mean RNFL thickness >65 μm and mean macular ganglion cell complex thickness >55 μm had better visual outcomes.
Unsupervised multiple kernel learning for heterogeneous data integration
Authors: Mariette Jérôme , Villa-Vialaneix Nathalie 
Published: May 2017

AbstractRecent high-throughput sequencing advances have expanded the breadth of available omics datasets and the integrated analysis of multiple datasets obtained on the same samples has allowed to gain important insights in a wide range of applications. However, the integration of various sources of information remains a challenge for systems biology since produced datasets are often of heterogeneous types, with the need of developing generic methods to take their different specificities into account.We propose a multiple kernel framework that allows to integrate multiple datasets of various types into a single exploratory analysis. Several solutions are provided to learn either a consensus meta-kernel or a meta-kernel that preserves the original topology of the datasets. We applied our framework to analyse two public multi-omics datasets. First, the multiple metagenomic datasets, collected during theTARAOceans expedition, was explored to demonstrate that our method is able to retrieve previous findings in a single KPCA as well as to provide a new image of the sample structures when a larger number of datasets are included in the analysis. To perform this analysis, a generic procedure is also proposed to improve the interpretability of the kernel PCA in regards with the original data. Second, the multi-omics breast cancer datasets, provided by The Cancer Genome Atlas, is analysed using a kernel Self-Organizing Maps with both single and multi-omics strategies. The comparison of this two approaches demonstrates the benefit of our integration method to improve the representation of the studied biological system.Proposed methods are available in the R packagemixKernel, released on CRAN. It is fully compatible with themixOmicspackage and a tutorial describing the approach can be found onmixOmicsweb sitehttp://mixomics.org/mixkernel/.