bluuebunny/crossref_metadata_2025_split huggingface dataset:
The ordering alignment of gold nanorods in liquid crystals and its applications to polarization-sensitive SERS
Authors: Wang Y L , Chen L Y , Liu Q K , Cai F H , Qian J 
Published: February 2016

Abstract
Gold nanorods (GNRs) were synthesized, coated with poly(ethylene glycol) (PEG) chains, and uniformly dispersed into the lyotropic nematic liquid crystal (LC) matrix by our proposed method. The GNRs-LC composites were found to exhibit good stability over days and have high density of GNRs. The extinction spectra of the composites were found to be polarization sensitive when the shearing force were applied, due to the alignment of GNRs driven by the LC molecules, which was also in accordance to the simulation results. A type of Raman reporter, 3,3'-diethylthiatricarbocyanine iodide (DTTC), was co-conjugated onto the GNRs with PEG molecules, and then incorporated into the LC matrix. Thus, its Raman signals could be enhanced by the localized surface plasmon resonance (LSPR) of the GNRs. These surface-enhanced Raman scattering (SERS) signals were found to be polarization sensitive when the shearing force was applied, due to the polarization sensitive enhancement of the local field of GNRs. The nanocomposites with tunable SPR peaks and SERS signals have potential applications in optoelectronic devices.
Study of humidity on the structure and optical properties of cesium iodide thin film
Authors: Liang Bo , Liu Shuang , Guo Lina , Chen Dejun , Liu Yong , Zhong Zhiyong , Xiong Liufeng 
Published: February 2016

Abstract
We report the influence of 70% 5% humid exposed air at room temperature on the structure of 500nm thick CsI film. By means of scanning electron microscopy (SEM) and X- ray diffusion (XRD) analysis, the surface morphology and polycrystalline structure were investigated. After 24 hour exposure to humid air, the grain size of CsI film has a drastic change, and so as to the preferential growth orientation. Infrared spectra showed a hydroxyl absorption peak after 3h exposure. And in long term exposure (24h), the absorption peak broadened with the band center shifting toward lower wavenumbers.
Direct phase extraction of self-mixing displacement measurement using Hilbert transform
Authors: Tao Yufeng , Wang Ming , Guo Dongmei , Zhang Jiahuan 
Published: February 2016

Abstract
Signals of a self-mixing interferometer established on a semiconductor laser diode are analyzed. Phase is extracted out for decoding measurement which contained in self-mixing fringes. The semiconductor laser diode works as light source and receiver without modulation. By combining Hilbert transform with phase condition of self-mixing interference, micron- displacement is reconstructed by phase information at week or even moderate feedback level. Theoretical analysis and simulation results are presented before verification of experimental measurement. Practical feedback level is estimated by a data fitting technique with a programmable high-resolution PZT. Consistence of the results promises that direct phase extraction on self-mixing interferometer is available for micron-displacement measurement with a nanometer accuracy.
An efficient model to predict guided wave radiation by finite-sized sources in multilayered anisotropic plates with account of caustics
Authors: Stévenin M , Lhémery A , Grondel S 
Published: February 2016

Abstract
Elastic guided waves (GW) are used in various non-destructive testing (NDT) methods to inspect plate-like structures, generated by finite-sized transducers. Thanks to GW long range propagation, using a few transducers at permanent positions can provide a full coverage of the plate. Transducer diffraction effects take place, leading to complex radiated fields. Optimizing transducers positioning makes it necessary to accurately predict the GW field radiated by a transducer. Fraunhofer-like approximations applied to GW in isotropic homogeneous plates lead to fast and accurate field computation but can fail when applied to multi-layered anisotropic composite plates, as shown by some examples given.
Here, a model is proposed for composite plates, based on the computation of the approximate Green's tensor describing modal propagation from a source point, with account of caustics typically seen when strong anisotropy is concerned. Modal solutions are otherwise obtained by the Semi-Analytic Finite Element method. Transducer diffraction effects are accounted for by means of an angular integration over the transducer surface as seen from the calculation point, that is, over energy paths involved, which are mode-dependent. The model is validated by comparing its predictions with those computed by means of a full convolution integration of the Green's tensor with the source over transducer surface. Examples given concern disk and rectangular shaped transducers commonly used in NDT.
Large proper motion of the Thorne–Żytkow object candidate HV 2112 reveals its likely nature as foreground Galactic S-star
Authors: Maccarone Thomas J. , de Mink Selma E. 
Published: February 2016

Abstract
Using the Southern Proper Motion (SPM) catalogue, we show that the candidate Thorne–Żytkow object HV 2112 has a proper motion implying a space velocity of about 3000$\,\rm {km}\,\rm {s}^{-1}$if the object is located at the distance of the Small Magellanic Cloud (SMC). The proper motion is statistically different from that of the SMC at approximately 4σ in SPM, although the result can drop to about 3σ significance by including the UCAC4 data and considering systematic uncertainties in addition to the statistical ones. Assuming the measurement is robust, this proper motion is sufficient to exclude its proposed membership of the SMC and to argue instead that it is likely to be a foreground star in the Milky Way halo. The smaller distance and therefore lower brightness argue against its proposed nature as a Thorne–Żytkow object (the hypothesized star-like object formed when a normal star and a neutron star merge) or a Asymptotic Giant Branch (AGB) star. Instead we propose a binary scenario where this star is the companion of a former massive AGB star, which polluted the object with via its stellar wind, i.e. a special case of an extrinsic S star. Our new scenario solves two additional problems with the two existing scenarios for its nature as Thorne–Żytkow object or present-day super AGB star. The puzzling high ratio of the strength of calcium to iron absorption lines is unexpected for SMC supergiants, but is fully consistent with the expectations for halo abundances. Secondly, its strong variability can now be explained naturally as a manifestation of the Mira phenomenon. We discuss further observational tests that could distinguish between the foreground and SMC scenarios in advance of the improved proper motion measurements likely to come from Gaia.
The Lyman-continuum photon production efficiency in the high-redshift Universe
Authors: Wilkins Stephen M. , Feng Yu , Di-Matteo Tiziana , Croft Rupert , Stanway Elizabeth R. , Bouwens Rychard J. , Thomas Peter 
Published: February 2016

Abstract
The Lyman-continuum photon production efficiency (ξion) is a critical ingredient for inferring the number of photons available to reionize the intergalactic medium. To estimate the theoretical production efficiency in the high-redshift Universe we couple the BlueTides cosmological hydrodynamical simulation with a range of stellar population synthesis models. We find Lyman-continuum photon production efficiencies of log10(ξion/erg−1 Hz) ≈ 25.1–25.5 depending on the choice of stellar population synthesis model. These results are broadly consistent with recent observational constraints at high-redshift though favour a model incorporating the effects of binary evolution.
Understanding inherited genetic risk of adult glioma – a
review
Authors: Rice Terri , Lachance Daniel H. , Molinaro Annette M. , Eckel-Passow Jeanette E. , Walsh Kyle M. , Barnholtz-Sloan Jill , Ostrom Quinn T. , Francis Stephen S. , Wiemels Joseph , Jenkins Robert B. , Wiencke John K. , Wrensch Margaret R. 
Published: February 2016

Abstract
During the past six years, researchers have made major progress identifying common inherited genetic variation that increases risk for primary adult glioma. This paper summarizes knowledge about rare familial cancer syndromes that include adult glioma and reviews the available literature on the more recently discovered common inherited variation. Ten independent inherited variants in eight chromosomal regions have been convincingly associated with increased risk for adult glioma. Most of these variants increase relative risk of primary adult glioma by 20% to 40%, but the TP53 variant rs78378222 confers a two-fold relative risk (ie, 200%), and rs557505857 on chromosome 8 confers a six-fold relative risk of IDH-mutated astrocytomas and oligodendroglial tumors (ie, 600%). Even with a six-fold relative risk, the overall risk of developing adult glioma is too low for screening for the high-risk variant on chromosome 8. Future studies will help clarify which inherited adult glioma risk variants are associated with subtypes defined by histology and/or acquired tumor mutations. This review also provides an information sheet for primary adult glioma patients and their families.
chromstaR: Tracking combinatorial chromatin state dynamics in space and time
Authors: Taudt Aaron , Nguyen Minh Anh , Heinig Matthias , Johannes Frank , Colomé-Tatché Maria 
Published: February 2016

AbstractBackgroundPost-translational modifications of histone residue tails are an important component of genome regulation. It is becoming increasingly clear that the combinatorial presence and absence of various modifications define discrete chromatin states which determine the functional properties of a locus. An emerging experimental goal is to track changes in chromatin state maps across different conditions, such as experimental treatments, cell-types or developmental time points.ResultsHere we present chromstaR, an algorithm for the computational inference of combinatorial chromatin state dynamics across an arbitrary number of conditions. ChromstaR uses a multivariate Hidden Markov Model to determine the number of discrete combinatorial chromatin states using multiple ChIP-seq experiments as input and assigns every genomic region to a state based on the presence/absence of each modification in every condition. We demonstrate the advantages of chromstaR in the context of three common experimental data scenarios. First, we study how different histone modifications combine to form combinatorial chromatin states in a single tissue. Second, we infer genome-wide patterns of combinatorial state differences between two cell types or conditions. Finally, we study the dynamics of combinatorial chromatin states during tissue differentiation involving up to six differentiation points. Our findings reveal a striking sparcity in the combinatorial organization and temporal dynamics of chromatin state maps.ConclusionschromstaR is a versatile computational tool that facilitates a deeper biological understanding of chromatin organization and dynamics. The algorithm is implemented as an R-package and freely available fromhttp://bioconductor.org/packages/chromstaR/.
Translational plasticity facilitates the accumulation of nonsense genetic variants in the human population
Authors: Jagannathan Sujatha , Bradley Robert K. 
Published: February 2016

ABSTRACTGenetic variants that disrupt protein-coding DNA are ubiquitous in the human population, with ~100 such loss-of-function variants per individual. While most loss-of-function variants are rare, a subset have risen to high frequency and occur in a homozygous state in healthy individuals. It is unknown why these common variants are well-tolerated, even though some affect essential genes implicated in Mendelian disease. Here, we combine genomic, proteomic, and biochemical data to demonstrate that many common nonsense variants do not ablate protein production from their host genes. We provide computational and experimental evidence for diverse mechanisms of gene rescue, including alternative splicing, stop codon readthrough, alternative translation initiation, and C-terminal truncation. Our results suggest a molecular explanation for the mild fitness costs of many common nonsense variants, and indicate that translational plasticity plays a prominent role in shaping human genetic diversity.
A Comparison of the Costs and Benefits of Bacterial Gene Expression
Authors: Price Morgan N. , Wetmore Kelly M. , Deutschbauer Adam M. , Arkin Adam P. 
Published: February 2016

AbstractTo study how a bacterium allocates its resources, we compared the costs and benefits of most of the proteins inEscherichia coliK-12 during growth in minimal glucose medium. Proteins that are important for fitness are usually highly expressed, and 95% of these proteins are expressed at above 13 parts per million (ppm). Conversely, proteins that do not measurably benefit the host tend to be weakly expressed, with a median expression of 13 ppm. In aggregate, genes with no detectable benefit account for 31% of protein production, or about 22% if we correct for genetic redundancy. Although some of the apparently unnecessary expression could have subtle benefits in minimal glucose medium, the majority of the burden is due to genes that are important in other conditions. We propose that over 10% of the cell’s protein is “on standby” in case conditions change.
Viral coinfection is shaped by host ecology and virus-virus interactions across diverse microbial taxa and environments
Authors: Díaz Muñoz Samuel L. 
Published: February 2016

AbstractInfection of more than one virus in a host, coinfection, is common across taxa and environments. Viral coinfection can enable genetic exchange, alter the dynamics of infections, and change the course of viral evolution. Yet, a systematic test of the factors explaining variation in viral coinfection across different taxa and environments awaits completion. Here I employ three microbial data sets of virus-host interactions covering cross-infectivity, culture coinfection, and single-cell coinfection (total: 6,564 microbial hosts, 13,103 viruses) to provide a broad, comprehensive picture of the ecological and biological factors shaping viral coinfection. I found evidence that ecology and virus-virus interactions are recurrent factors shaping coinfection patterns. Host ecology was a consistent and strong predictor of coinfection across all three datasets: cross-infectivity, culture coinfection, and single-cell coinfection. Host phylogeny or taxonomy was a less consistent predictor, being weak or absent in the cross-infectivity and single-cell coinfection models, yet it was the strongest predictor in the culture coinfection model. Virus-virus interactions strongly affected coinfection. In the largest test of superinfection exclusion to date, prophage sequences reduced culture coinfection by other prophages, with a weaker effect on extrachromosomal virus coinfection. At the single-cell level, prophage sequences eliminated coinfection. Virus-virus interactions alsoincreasedculture coinfection with ssDNA-dsDNA coinfections >2x more likely than ssDNA-only coinfections. The presence of CRISPR spacers was associated with a ~50% reduction in single-cell coinfection in a marine bacteria, despite the absence of exact spacer matches in any active infection. Collectively, these results suggest the environment bacteria inhabit and the interactions among surrounding viruses are two factors consistently shaping viral coinfection patterns. These findings highlight the role of virus-virus interactions in coinfection with implications for phage therapy, microbiome dynamics, and viral infection treatments.
Partial derivatives meta-analysis: pooled analyses when individual participant data cannot be shared
Authors: Adams Hieab HH , Adams Hadie , Launer Lenore J , Seshadri Sudha , Schmidt Reinhold , Bis Joshua C , Debette Stephanie , Nyquist Paul A , Van der Grond Jeroen , Mosley Thomas H , Yang Jingyun , Teumer Alexander , Hilal Saima , Roshchupkin Gennady V , Wardlaw Joanna M , Satizabal Claudia L , Hofer Edith , Chauhan Ganesh , Smith Albert , Yanek Lisa R , Van der Lee Sven J , Trompet Stella , Chouraki Vincent , Arfanakis Konstantinos A , Becker James T , Niessen Wiro J , de Craen Anton JM , Crivello Fabrice F , Lin Li An , Fleischman Debra A , Wong Tien Yin , Franco Oscar H , Wittfeld Katharina , Jukema J Wouter , De Jager Philip L , Hofman Albert , DeCarli Charles , Rizopoulos Dimitris , Longstreth WT , Mazoyer Bernard M , Gudnason Vilmundar , Bennett David A , Deary Ian J , Ikram M Kamran , Grabe Hans J , Fornage Myriam , Van Duijn Cornelia M , Vernooij Meike W , Ikram M Arfan ,   on behalf of the HD-READY Consortium
Published: February 2016

AbstractJoint analysis of data from multiple studies in collaborative efforts strengthens scientific evidence, with the gold standard approach being the pooling of individual participant data (IPD). However, sharing IPD often has legal, ethical, and logistic constraints for sensitive or high-dimensional data, such as in clinical trials, observational studies, and large-scale omics studies. Therefore, meta-analysis of study-level effect estimates is routinely done, but this compromises on statistical power, accuracy, and flexibility. Here we propose a novel meta-analytical approach, named partial derivatives meta-analysis, that is mathematically equivalent to using IPD, yet only requires the sharing of aggregate data. It not only yields identical results as pooled IPD analyses, but also allows post-hoc adjustments for covariates and stratification without the need for site-specific re-analysis. Thus, in case that IPD cannot be shared, partial derivatives meta-analysis still produces gold standard results, which can be used to better inform guidelines and policies on clinical practice.
Genomic prediction and estimation of marker interaction effects
Authors: Rönnegård Lars , Shen Xia 
Published: February 2016

AbstractThe standard models for genomic prediction assume additive polygenic marker effects. For epistatic models including marker interaction effects, the number of effects to be fitted becomes large, which require computational tools tailored specifically for such models. Here, we extend the methods implemented in the R package bigRR so that marker interaction effects can be computed. Simulation results based on marker data fromArabidopsis thalianashow that the inclusion of interaction effects between markers can give a small but significant improvement in genomic predictions. The methods were implemented in the R package EPISbi-gRR available in the bigRR project on R-Forge. The package includes an introductory vignette to the functions available in EPISbigRR.R package URL:https://r-forge.r-project.org/R/?group_id=1301
Bioanalyzer chips can be used interchangeably for many analyses of DNA or RNA
Authors: Davies Jessica , Denyer Tom , Hadfield James 
Published: February 2016

AbstractThe Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA) enables small-scale gel electrophoretic separation of nucleic acids on a microfluidic chip. Shortage of chips and excess reagents is a common issue. This report explored the compatibility of two commonly used Bioanalyzer reagents with three Bioanalyzer chip types. Microfluidic electrophoretic separation of DNA and RNA using DNA High Sensitivity and RNA 6000 Nano reagents, respectively, was successfully performed on multiple chip types, following the assay-specific protocol. For RNA quality and next-generation sequencing library size estimation, the Bioanalyzer chips tested can be used interchangeably. These findings will be valuable for any laboratory using the Agilent Bioanalyzer in a shared facility.
Cutting the Gordian knot [?]: a response to Lukka and Vinnari (2014)
Authors: Lowe Alan D. , De Loo Ivo , Nama Yesh 
Published: February 2016

Purpose– The purpose of this paper is to constructively discuss the meaning and nature of (theoretical) contribution in accounting research, as represented by Lukka and Vinnari (2014) (hereafter referred to as LV). The authors aim is to further encourage debate on what constitutes management accounting theory (or theories) and how to modestly clarify contributions to the extant literature.Design/methodology/approach– The approach the authors take can be seen as (a)n interdisciplinary literature sourced analysis and critique of the movement’s positioning and trajectory” (Parker and Guthrie, 2014, p. 1218). The paper also draws upon and synthesizes the present authors and other’s contributions to accounting research using actor network theory.Findings– While a distinction between domain and methods theories … may appear analytically viable, it may be virtually impossible to separate them in practice. In line with Armstrong (2008), the authors cast a measure of doubt on the quest to significantly extend theoretical contributions from accounting research.Research limitations/implications– Rather than making (apparently) grandiose claims about (theoretical) contributions from individual studies, the authors suggest making more modest claims from the research. The authors try to provide a more appropriate and realistic approach to the appreciation of research contributions.Originality/value– The authors contribute to the debate on how theoretical contributions can be made in the accounting literature by constructively debating some views that have recently been outlined by LV. The aim is to provide some perspective on the usefulness of the criteria suggested by these authors. The authors also suggest and highlight (alternative) ways in which contributions might be discerned and clarified.
Shared perceptions of supervisor conflict management style
Authors: Way Kirsten A. , Jimmieson Nerina L , Bordia Prashant 
Published: February 2016

Purpose– This study aims to investigate the extent to which employee outcomes (anxiety/depression, bullying and workers’ compensation claims thoughts) are affected by shared perceptions of supervisor conflict management style (CMS). Further, this study aims to assess cross-level moderating effects of supervisor CMS climate on the positive association between relationship conflict and these outcomes.Design/methodology/approach– Multilevel modeling was conducted using a sample of 401 employees nested in 69 workgroups.Findings– High collaborating, low yielding and low forcing climates (positive supervisor climates) were associated with lower anxiety/depression, bullying and claim thoughts. Unexpectedly, the direction of moderation showed that the positive association between relationship conflict and anxiety/depression and bullying was stronger for positive supervisor CMS climates than for negative supervisor CMS climates (low collaborating, high yielding and high forcing). Nevertheless, these interactions revealed that positive supervisor climates were the most effective at reducing anxiety/depression and bullying when relationship conflict was low. For claim thoughts, positive supervisor CMS climates had the predicted stress-buffering effects.Research limitations/implications– Employees benefit from supervisors creating positive CMS climates when dealing with conflict as a third party, and intervening when conflict is low, when their intervention is more likely to minimize anxiety/depression and bullying.Originality/value– By considering the unique perspective of employees’ shared perceptions of supervisor CMS, important implications for the span of influence of supervisor behavior on employee well-being have been indicated.