bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structure of a phleboviral envelope glycoprotein reveals a consolidated model of membrane fusion
Authors: Halldorsson Steinar , Behrens Anna-Janina , Harlos Karl , Huiskonen Juha T. , Elliott Richard M. , Crispin Max , Brennan Benjamin , Bowden Thomas A. 
Published: June 2016

Significance
Severe fever with thrombocytopenia syndrome virus (SFTSV) is a deadly tick-borne viral pathogen. Since first being reported in China in 2009, SFTSV has spread throughout South Korea and Japan, with mortality rates reaching up to 30%. The surface of the SFTSV virion is decorated by two glycoproteins, Gn and Gc. Here, we report the atomic-level structure of the Gc glycoprotein in a conformation formed during uptake of the virion into the host cell. Our analysis reveals the conformational changes that the Gc undergoes during host cell infection and provides structural evidence that these rearrangements are conserved with otherwise unrelated alpha- and flaviviruses.
Economic impact of refugees
Authors: Taylor J. Edward , Filipski Mateusz J. , Alloush Mohamad , Gupta Anubhab , Rojas Valdes Ruben Irvin , Gonzalez-Estrada Ernesto 
Published: June 2016

Significance
The number of refugees displaced by civil conflict or natural disasters is on the rise. Economic impacts of refugees on host countries are controversial and little understood, because data have not been available and the question of refugee impacts does not lend itself to conventional impact evaluation methods. We use a unique Monte Carlo simulation approach with microdata from refugee and host-country surveys to obtain the first estimates of refugee camps’ impacts on surrounding host-country economies and to compare impacts of cash versus in-kind refugee aid. An additional refugee increases total real income within a 10-km radius around two cash camps by significantly more than the aid the refugee receives. Impacts around a camp receiving in-kind (food) aid are smaller.
Human pluripotent stem cells as a model of trophoblast differentiation in both normal development and disease
Authors: Horii Mariko , Li Yingchun , Wakeland Anna K. , Pizzo Donald P. , Nelson Katharine K. , Sabatini Karen , Laurent Louise Chang , Liu Ying , Parast Mana M. 
Published: June 2016

SignificanceHuman pluripotent stem cells (hPSCs) continue to be underappreciated as a model for studying trophoblast differentiation. In this study, we provide a reproducible, two-step protocol by which hPSCs can be differentiated into bipotential cytotrophoblast (CTB) stem-like cells and subsequently into functional, terminally differentiated trophoblasts. In addition, we provide evidence that the response of hPSC-derived CTBs to low oxygen is similar to that of primary CTBs. Finally, using trisomy 21-affected hPSCs, we show, for the first time to our knowledge, that hPSCs can model a trophoblast differentiation defect. We propose that hPSCs are superior to other currently available models for studying human trophoblast differentiation.
Effect of physician disclosure of specialty bias on patient trust and treatment choice
Authors: Sah Sunita , Fagerlin Angela , Ubel Peter 
Published: June 2016

Significance
Disclosure policies, intended to protect consumers, are a popular solution across a range of industries such as health care, financial investments, mortgages, and other services in which professional advisors may suffer from potential bias from misaligned incentives. Using field data (recorded transcripts of surgeon–patient consultations) and a randomized controlled laboratory experiment, we examine and find that disclosures of specialty bias increase patients’ trust and their likelihood of choosing a treatment in accordance with the physicians’ specialty. Professionals and policy makers should be aware of the implications on advisee trust and choice when advocating for the disclosure of advisor bias.
Elementary quantum mechanics of the neutron with an electric dipole moment
Authors: Baym Gordon , Beck D. H. 
Published: June 2016

Significance
A permanent electric dipole moment of the neutron, a manifestation of the violation of time-reversal symmetry in nature, is an important clue to physics beyond the standard model, and is the subject of a number of ongoing large-scale experimental efforts. Although, in the absence of external electric fields, the dipole moment must lie along the neutron spin, the neutron dipole moment and spin are independent; e.g., the external electric field in Compton scattering on the neutron induces a component of the dipole moment parallel to the field. How then should one think generally about the neutron electric dipole moment, including time-reversal violation, within elementary quantum mechanics, and in particular when interpreting experimental searches for a permanent moment?
MiR-137 affects melanin synthesis in mouse melanocyte by repressing the expression ofc-KitandTyrp2inSCF/c-Kitsignaling pathway
Authors: Jiang Shan , Yu Xiuju , Dong Changsheng 
Published: June 2016

AbstractPreviously, we created miR-137 overexpressing transgenic mice that produced lighten color phenotypes including gray mice phenotype. However, the miR-137 functional role in coat color regulation is still not well understood. In this study, the quantity of melanin granule and the relative expression of TYRP2 in gray miR-137 overexpression transgenic mouse skin were significantly lower than that in C57BL/6J black mouse skin. The mRNA and protein expression level of c-Kit and c-Kit downstream gene Tyrp2 in miR-137 expression plasmid-transfected melanocytes were significantly down-regulated comparing with that of the control melanocytes. In melanocytes, miR-137 overexpression could decrease the enhanced expression of c-Kit and Tyrp2 and the increased melanin production caused by UV treatment. The target relationship of miR-137 and c-Kit was identified by luciferase assay. The results suggest that miR-137 could inhibit melanogenesis in mouse skin melanocytes by repressing the expression of c-Kit and Tyrp2 in SCF/c-Kit signaling pathway.
Conceptual study of an ICRH traveling-wave antenna system for low-coupling conditions as expected in DEMO
Authors: Ragona R. , Messiaen A. 
Published: June 2016

Abstract
For the central heating of a fusion reactor ion cyclotron radio frequency heating (ICRH) is the first choice method as it is able to couple RF power to the ions without density limit. The drawback of this heating method is the problem of excitation of the magneto-sonic wave through the plasma boundary layer from the antenna located along the wall, without exceeding its voltage standoff. The amount of coupling depends on the antenna excitation and the surface admittance at the antenna output due to the plasma profile. The paper deals with the optimization of the antenna excitation by the use of sections of traveling-wave antennas (TWAs) distributed all along the reactor wall between the blanket modules. They are mounted and fed in resonant ring system(s). First, the physics of the coupling of a strap array is studied by simple models and the coupling code ANTITER II. Then, after the study of the basic properties of a TWA section, its feeding problem is solved by hybrids driving them in resonant ring circuit(s). The complete modeling is obtained from the matrices of the TWA sections connected to one of the feeding hybrid(s). The solution is iterated with the coupling code to determine the loading for a reference low-coupling ITER plasma profile. The resulting wave pattern up to the plasma bulk is derived. The proposed system is totally load resilient and allows us to obtain a very selective exciting wave spectrum. A discussion of some practical implementation problems is added.
Free-boundary ideal MHD stability of W7-X divertor equilibria
Authors: Nührenberg C. 
Published: June 2016

Abstract
Plasma configurations describing the stellarator experiment Wendelstein 7-X (W7-X) are computationally established taking into account the geometry of the test-divertor unit and the high-heat-flux divertor which will be installed in the vacuum chamber of the device (Gasparotto et al 2014 Fusion Eng. Des. 89 2121). These plasma equilibria are computationally studied for their global ideal magnetohydrodynamic (MHD) stability properties. Results from the ideal MHD stability code cas3d (Nührenberg 1996 Phys. Plasmas
3 2401), stability limits, spatial structures and growth rates are presented for free-boundary perturbations. The work focusses on the exploration of MHD unstable regions of the W7-X configuration space, thereby providing information for future experiments in W7-X aiming at an assessment of the role of ideal MHD in stellarator confinement.
Rotational shear effects on edge harmonic oscillations in DIII-D quiescent H-mode discharges
Authors: Chen Xi , Burrell K.H. , Ferraro N.M. , Osborne T.H. , Austin M.E. , Garofalo A.M. , Groebner R.J. , Kramer G.J. , Luhmann N.C. , McKee G.R. , Muscatello C.M. , Nazikian R. , Ren X. , Snyder P.B. , Solomon W.M. , Tobias B.J. , Yan Z. 
Published: June 2016

Abstract
In the quiescent H-mode (QH-mode) regime, edge harmonic oscillations (EHOs) play an important role in avoiding transient edge localized mode (ELM) power fluxes by providing benign and continuous edge particle transport. A detailed theoretical, experimental and modeling comparison has been made of low-n (n  ⩽  5) EHO in DIII-D QH-mode plasmas. The calculated linear eigenmode structure from the extended magentoohydrodynamics (MHD) code M3D-C1 matches closely the coherent EHO properties from external magnetics data and internal measurements using the ECE, BES, ECE-Imaging and microwave imaging reflectometer (MIR) diagnostics, as well as the kink/peeling mode properties found by the ideal MHD code ELITE. Numerical investigations indicate that the low-n EHO-like solutions from M3D-C1 are destabilized by rotation and/or rotational shear while high-n modes are stabilized. This effect is independent of the rotation direction, suggesting that EHOs can be destabilized in principle with rotation in either direction. The modeling results are consistent with observations of EHO, support the proposed theory of the EHO as a low-n kink/peeling mode destabilized by edge E  ×  B rotational shear, and improve our understanding and confidence in creating and sustaining QH-mode in present and future devices.
Integrated gene set analysis for microRNA studies
Authors: Garcia-Garcia Francisco , Panadero Joaquin , Dopazo Joaquin , Montaner David 
Published: June 2016

AbstractMotivation: Functional interpretation of miRNA expression data is currently done in a three step procedure: select differentially expressed miRNAs, find their target genes, and carry out gene set overrepresentation analysis. Nevertheless, major limitations of this approach have already been described at the gene level, while some newer arise in the miRNA scenario.Here, we propose an enhanced methodology that builds on the well-established gene set analysis paradigm. Evidence for differential expression at the miRNA level is transferred to a gene differential inhibition score which is easily interpretable in terms of gene sets or pathways. Such transferred indexes account for the additive effect of several miRNAs targeting the same gene, and also incorporate cancellation effects between cases and controls. Together, these two desirable characteristics allow for more accurate modeling of regulatory processes.Results: We analyze high-throughput sequencing data from 20 different cancer types and provide exhaustive reports of gene and Gene Ontology-term deregulation by miRNA action.Availability and Implementation: The proposed methodology was implemented in the Bioconductor library mdgsa. http://bioconductor.org/packages/mdgsa. For the purpose of reproducibility all of the scripts are available at https://github.com/dmontaner-papers/gsa4mirnaContact: david.montaner@gmail.comSupplementary information: Supplementary data are available at Bioinformatics online.
RTCR: a pipeline for complete and accurate recovery of T cell repertoires from high throughput sequencing data
Authors: Gerritsen Bram , Pandit Aridaman , Andeweg Arno C. , de Boer Rob J. 
Published: June 2016

Abstract
Motivation: High Throughput Sequencing (HTS) has enabled researchers to probe the human T cell receptor (TCR) repertoire, which consists of many rare sequences. Distinguishing between true but rare TCR sequences and variants generated by polymerase chain reaction (PCR) and sequencing errors remains a formidable challenge. The conventional approach to handle errors is to remove low quality reads, and/or rare TCR sequences. Such filtering discards a large number of true and often rare TCR sequences. However, accurate identification and quantification of rare TCR sequences is essential for repertoire diversity estimation.
Results: We devised a pipeline, called Recover TCR (RTCR), that accurately recovers TCR sequences, including rare TCR sequences, from HTS data (including barcoded data) even at low coverage. RTCR employs a data-driven statistical model to rectify PCR and sequencing errors in an adaptive manner. Using simulations, we demonstrate that RTCR can easily adapt to the error profiles of different types of sequencers and exhibits consistently high recall and high precision even at low coverages where other pipelines perform poorly. Using published real data, we show that RTCR accurately resolves sequencing errors and outperforms all other pipelines.
Availability and Implementation: The RTCR pipeline is implemented in Python (v2.7) and C and is freely available at http://uubram.github.io/RTCR/along with documentation and examples of typical usage.
Contact: b.gerritsen@uu.nl
A simple model predicts UGT-mediated metabolism
Authors: Dang Na Le , Hughes Tyler B. , Krishnamurthy Varun , Swamidass S. Joshua 
Published: June 2016

Abstract
Motivation: Uridine diphosphate glucunosyltransferases (UGTs) metabolize 15% of FDA approved drugs. Lead optimization efforts benefit from knowing how candidate drugs are metabolized by UGTs. This paper describes a computational method for predicting sites of UGT-mediated metabolism on drug-like molecules.
Results: XenoSite correctly predicts test molecule’s sites of glucoronidation in the Top-1 or Top-2 predictions at a rate of 86 and 97%, respectively. In addition to predicting common sites of UGT conjugation, like hydroxyl groups, it can also accurately predict the glucoronidation of atypical sites, such as carbons. We also describe a simple heuristic model for predicting UGT-mediated sites of metabolism that performs nearly as well (with, respectively, 80 and 91% Top-1 and Top-2 accuracy), and can identify the most challenging molecules to predict on which to assess more complex models. Compared with prior studies, this model is more generally applicable, more accurate and simpler (not requiring expensive quantum modeling).
Availability and implementation: The UGT metabolism predictor developed in this study is available at http://swami.wustl.edu/xenosite/p/ugt.
Contact: swamidass@wustl.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
The Space of Freedom in a Context of War, Exile and Endless Instability: A Sociolinguistic Approach to Autobiographical Narratives on Catalan Exile
Authors: Iglésias-Franch Narcís 
Published: June 2016

Abstract
In the recent numerous publications on the autobiographies of Catalan writers who went into exile in 1939, themes such as memory, identity crisis or travel have been studied in depth. In this article, I propose a sociolinguistic interpretation of a series of autobiographical works by exiled authors such as Xavier Benguerel, Lluís Ferran de Pol and Antoni Rovira i Virgili. According to the theoretical framework of sociolinguistic studies, autobiographical narratives can be analysed using three different approaches: first, the way authors narrate how ‘things’ are or were; second, how ‘things’ or events were experienced; and, finally, the ways in which ‘things’ or events are narrated. Language is not only historical data or an individual experience which authors narrate in their autobiographical narratives. This sociolinguistic approach to the autobiographical narratives of Catalan exiles shows the close link between language and identity, and between language and morality.
Pervasive microRNA Duplication in Chelicerates: Insights from the Embryonic microRNA Repertoire of the Spider
Parasteatoda tepidariorum
Authors: Leite Daniel J. , Ninova Maria , Hilbrant Maarten , Arif Saad , Griffiths-Jones Sam , Ronshaugen Matthew , McGregor Alistair P. 
Published: June 2016

Abstract
MicroRNAs are small (∼22 nt) noncoding RNAs that repress translation and therefore regulate the production of proteins from specific target mRNAs. microRNAs have been found to function in diverse aspects of gene regulation within animal development and many other processes. Among invertebrates, both conserved and novel, lineage specific, microRNAs have been extensively studied predominantly in holometabolous insects such as Drosophila melanogaster . However little is known about microRNA repertoires in other arthropod lineages such as the chelicerates. To understand the evolution of microRNAs in this poorly sampled subphylum, we characterized the microRNA repertoire expressed during embryogenesis of the common house spider Parasteatoda tepidariorum . We identified a total of 148 microRNAs in P. tepidariorum representing 66 families. Approximately half of these microRNA families are conserved in other metazoans, while the remainder are specific to this spider. Of the 35 conserved microRNAs families 15 had at least two copies in the P. tepidariorum genome. A BLAST-based approach revealed a similar pattern of duplication in other spiders and a scorpion, but not among other chelicerates and arthropods, with the exception of a horseshoe crab. Among the duplicated microRNAs we found examples of lineage-specific tandem duplications, and the duplication of entire microRNA clusters in three spiders, a scorpion, and in a horseshoe crab. Furthermore, we found that paralogs of many P. tepidariorum microRNA families exhibit arm switching, which suggests that duplication was often followed by sub- or neofunctionalization. Our work shows that understanding the evolution of microRNAs in the chelicerates has great potential to provide insights into the process of microRNA duplication and divergence and the evolution of animal development.
Effects of combined radiofrequency field exposure on amyloid-beta–induced cytotoxicity in HT22 mouse hippocampal neurones
Authors: Lee Jong-Sun , Kim Jeong-Yub , Kim Hee-Jin , Kim Jeong Cheol , Lee Jae-Seon , Kim Nam , Park Myung-Jin 
Published: June 2016

Abstract
Alzheimer's disease (AD) is the most common progressive and irreversible neurodegenerative disease and it is caused by neuronal death in the brain. Recent studies have shown that non-ionizing radiofrequency (RF) radiation has some beneficial cognitive effects in animal models of AD. In this study, we examined the effect of combined RF radiation on amyloid-beta (Aβ)–induced cytotoxicity in HT22 rat hippocampal neurons. Treatment with Aβ suppressed HT22 cell proliferation in a concentration-dependent manner. RF exposure did not affect cell proliferation, and also had a marginal effect on Aβ-induced suppression of growth in HT22 cells. Cell cycle analysis showed that Aβ decreased the G1 fraction and increased the subG1 fraction, indicating increased apoptosis. Accordingly, Aβ increased the annexin V/propidium iodide (PI)–positive cell fraction and the degradation of poly (ADP ribose) polymerase and caspase-3 in HT22 cells. However, RF alone and the combination of Aβ and RF did not affect these events significantly. Aβ increased reactive oxygen species (ROS) generation, thereby suppressing cell proliferation. This was abrogated by N-acetylcysteine (NAC) treatment, indicating that Aβ-induced ROS generation is the main cause of suppression of proliferation. NAC also restored Aβ-induced annexin V/PI–positive cell populations. However, RF did not have a significant impact on these events. Finally, Aβ stimulated the ataxia telangiectasia and Rad3-related protein/checkpoint kinase 1 DNA single-strand breakage pathway, and enhanced beta-site amyloid precursor protein expression; RF had no effect on them. Taken together, our results demonstrate that RF exposure did not significantly affect the Aβ-induced decrease of cell proliferation, increase of ROS production, or induction of cell death in these cells.
Human Immunodeficiency Virus and Allergic Bronchopulmonary Aspergillosis: Case Report and Review of Literature
Authors: Galiatsatos Panagis , Melia Michael T. , Silhan Leann L. 
Published: June 2016

Abstract
Allergic bronchopulmonary aspergillosis (ABPA) results from a hypersensitivity response to airways colonization with Aspergillus fumigatus, and it occurs most often in individuals with asthma or cystic fibrosis. Allergic bronchopulmonary aspergillosis is an indolent, but potentially progressive, disease in patients. In patients infected with human immunodeficiency virus (HIV), ABPA is rare, and its description in the literature is limited to case reports. We describe the occurrence of ABPA in a 37-year-old woman with well controlled HIV infection. This represents the first documented case of ABPA in an HIV-infected patient whose only pulmonary comorbidity included the ramifications of prior acute respiratory distress syndrome due to Pneumocystis jirovecii pneumonia. We also review prior case reports of ABPA in HIV-infected patients and consider risk factors for its development.
Therapeutic Trial of Rifabutin After Rifampicin-Associated DRESS Syndrome in Tuberculosis-Human Immunodeficiency Virus Coinfected Patients
Authors: Lehloenya Rannakoe J. , Dlamini Sipho , Muloiwa Rudzani , Kakande Betty , Ngwanya Mzudumile R. , Todd Gail , Dheda Keertan 
Published: June 2016

AbstractElimination of a rifamycin from the treatment regimen for tuberculosis negatively impacts outcomes. Cross-reactivity between the rifamycins after drug eruptions is unclear. We report 6 consecutive human immunodeficiency virus-infected patients with rifampicin-associated drug rash with eosinophilia and systemic symptoms (DRESS) syndrome confirmed on diagnostic rechallenge. The patients subsequently tolerated rifabutin. These data inform clinical management of tuberculosis-associated drug reactions.