bluuebunny/crossref_metadata_2025_split huggingface dataset:
Linear Polarization and the Dynamics of Circumstellar Disks of Classical Be Stars
Authors: Halonen Robbie J. , Jones Carol E. 
Published: January 2015

AbstractThe intrinsic linearly polarized light arising from electron scattering of stellar radiation in a non-spherically symmetric distribution of gas is a characterizing feature of classical Be stars. The distinct polarimetric signature provides a mean for directly probing the physical and geometric properties of the gaseous material enveloping these rapidly-rotating massive stars. Using a Monte Carlo radiative transfer computation and a self-consistent radiative equilibrium solution for the circumstellar gas, we explore the role of this observable signature in investigating the dynamical nature of classical Be star disks. In particular, we focus on the potential for using linearly polarized light to develop diagnostics of mass-loss events and to trace the evolution of the gas in a circumstellar disk. An informed context for interpreting the observed linear polarization signature can play an important role in identifying the physical process(es) which govern the formation and dissipation of the gaseous disks surrounding classical Be stars.
Project VeSElkA : Preliminary results for CP stars recently observed with ESPaDOnS
Authors: Khalack Viktor , LeBlanc Francis 
Published: January 2015

AbstractWe present the first results for the estimation of gravity and effective temperature of poorly studied chemically peculiar stars recently observed with the spectropolarimeter ESPaDOnS at CFHT in the frame of the VeSElkA (Vertical Stratification of Elements Abundance) project. A grid of theoretical stellar atmosphere models with the corresponding fluxes has been calculated using the PHOENIX code. We have used these fluxes to fit Balmer line profiles employing the code FITSB2 that produces estimates of the effective temperature, surface gravity and radial velocity for each star.
ξ1CMa: An Extremely Slowly Rotating Magnetic B0.7 IV Star
Authors: Shultz Matt , Wade Gregg , Rivinius Thomas , Marcolino Wagner , Henrichs Huib , Grunhut Jason ,   the MiMeS Collaboration
Published: January 2015

AbstractWe present our analysis of 6 years of ESPaDOnS spectropolarimetry of the magnetic β Cep star ξ1CMa (B1 III). This high-precision magnetometry is consistent with a rotational periodProt> 40 yr. Absorption line profiles can be reproduced with a non-rotating model. We constrainR⋆,L⋆, and the stellar age via a Baade-Wesselink analysis. Spindown due to angular momentum loss via the magnetosphere predicts an extremely long rotational period if the magnetic dipoleBd> 6 kG, a strength also inferred by the best-fit sinusoids to the longitudinal magnetic field measurementsBZwhen phased with a 60-yearProt.
Magnetic fields and internal mixing of main sequence B stars
Authors: Wade G. A. , Folsom C. P. , Grunhut J. , Landstreet J. D. , Petit V. 
Published: January 2015

AbstractWe have obtained high-quality magnetic field measurements of 19 sharp-lined B-type stars with precisely-measured N/C abundance ratios (Nieva & Przybilla 2012). Our primary goal is to test the idea (Meynetet al. 2011) that a magnetic field may explain extra drag (through the wind) on the surface rotation, thus producing more internal shear and mixing, and thus could provide an explanation for the appearance of slowly rotating N-rich main sequence B stars.
The X-ray properties of magnetic massive stars
Authors: Nazé Yaël , Petit Véronique , Rinbrand Melanie , Cohen David , Owocki Stan , ud-Doula Asif , Wade Gregg 
Published: January 2015

AbstractEarly-type stars are well-known to be sources of soft X-rays. However, this high-energy emission can be supplemented by bright and hard X-rays when magnetically confined winds are present. In an attempt to clarify the systematics of the observed X-ray properties of this phenomenon, a large series of Chandra and XMM observations was analyzed, over 100 exposures of 60% of the known magnetic massive stars listed recently by Petit et al. (2013). It is found that the X-ray luminosity is strongly correlated with mass-loss rate, in agreement with predictions of magnetically confined wind models, though the predictions of higher temperature are not always verified. We also investigated the behaviour of other X-ray properties (absorption, variability), yielding additional constraints on models. This work not only advances our knowledge of the X-ray emission of massive stars, but also suggests new observational and theoretical avenues to further explore magnetically confined winds.
Chemotaxis by natural populations of coral reef bacteria
Authors: Tout Jessica , Jeffries Thomas C , Petrou Katherina , Tyson Gene W , Webster Nicole S , Garren Melissa , Stocker Roman , Ralph Peter J , Seymour Justin R 
Published: January 2015

Abstract
Corals experience intimate associations with distinct populations of marine microorganisms, but the microbial behaviours underpinning these relationships are poorly understood. There is evidence that chemotaxis is pivotal to the infection process of corals by pathogenic bacteria, but this evidence is limited to experiments using cultured isolates under laboratory conditions. We measured the chemotactic capabilities of natural populations of coral-associated bacteria towards chemicals released by corals and their symbionts, including amino acids, carbohydrates, ammonium and dimethylsulfoniopropionate (DMSP). Laboratory experiments, using a modified capillary assay, and in situ measurements, using a novel microfabricated in situ chemotaxis assay, were employed to quantify the chemotactic responses of natural microbial assemblages on the Great Barrier Reef. Both approaches showed that bacteria associated with the surface of the coral species Pocillopora damicornis and Acropora aspera exhibited significant levels of chemotaxis, particularly towards DMSP and amino acids, and that these levels of chemotaxis were significantly higher than that of bacteria inhabiting nearby, non-coral-associated waters. This pattern was supported by a significantly higher abundance of chemotaxis and motility genes in metagenomes within coral-associated water types. The phylogenetic composition of the coral-associated chemotactic microorganisms, determined using 16S rRNA amplicon pyrosequencing, differed from the community in the seawater surrounding the coral and comprised known coral associates, including potentially pathogenic Vibrio species. These findings indicate that motility and chemotaxis are prevalent phenotypes among coral-associated bacteria, and we propose that chemotaxis has an important role in the establishment and maintenance of specific coral–microbe associations, which may ultimately influence the health and stability of the coral holobiont.
Fumarate induces redox-dependent senescence by modifying glutathione metabolism
Authors: Zheng Liang , Cardaci Simone , Jerby Livnat , MacKenzie Elaine D. , Sciacovelli Marco , Johnson T. Isaac , Gaude Edoardo , King Ayala , Leach Joshua D. G. , Edrada-Ebel RuAngelie , Hedley Ann , Morrice Nicholas A. , Kalna Gabriela , Blyth Karen , Ruppin Eytan , Frezza Christian , Gottlieb Eyal 
Published: January 2015

AbstractMutations in the tricarboxylic acid (TCA) cycle enzyme fumarate hydratase (FH) are associated with a highly malignant form of renal cancer. We combined analytical chemistry and metabolic computational modelling to investigate the metabolic implications of FH loss in immortalized and primary mouse kidney cells. Here, we show that the accumulation of fumarate caused by the inactivation of FH leads to oxidative stress that is mediated by the formation of succinicGSH, a covalent adduct between fumarate and glutathione. Chronic succination of GSH, caused by the loss of FH, or by exogenous fumarate, leads to persistent oxidative stress and cellular senescence in vitro and in vivo. Importantly, the ablation of p21, a key mediator of senescence, in Fh1-deficient mice resulted in the transformation of benign renal cysts into a hyperplastic lesion, suggesting that fumarate-induced senescence needs to be bypassed for the initiation of renal cancers.
Gene therapy restores vision in rd1 mice after removal of a confounding mutation in Gpr179
Authors: Nishiguchi Koji M. , Carvalho Livia S. , Rizzi Matteo , Powell Kate , Holthaus Sophia-Martha kleine , Azam Selina A. , Duran Yanai , Ribeiro Joana , Luhmann Ulrich F. O. , Bainbridge James W. B. , Smith Alexander J. , Ali Robin R. 
Published: January 2015

AbstractThe rd1 mouse with a mutation in the Pde6b gene was the first strain of mice identified with a retinal degeneration. However, AAV-mediated gene supplementation of rd1 mice only results in structural preservation of photoreceptors, and restoration of the photoreceptor-mediated a-wave, but not in restoration of the bipolar cell-mediated b-wave. Here we show that a mutation in Gpr179 prevents the full restoration of vision in rd1 mice. Backcrossing rd1 with C57BL6 mice reveals the complete lack of b-wave in a subset of mice, consistent with an autosomal recessive Mendelian inheritance pattern. We identify a mutation in the Gpr179 gene, which encodes for a G-protein coupled receptor localized to the dendrites of ON-bipolar cells. Gene replacement in rd1 mice that are devoid of the mutation in Gpr179 successfully restores the function of both photoreceptors and bipolar cells, which is maintained for up to 13 months. Our discovery may explain the failure of previous gene therapy attempts in rd1 mice, and we propose that Grp179 mutation status should be taken into account in future studies involving rd1 mice.
A number-form area in the blind
Authors: Abboud Sami , Maidenbaum Shachar , Dehaene Stanislas , Amedi Amir 
Published: January 2015

AbstractDistinct preference for visual number symbols was recently discovered in the human right inferior temporal gyrus (rITG). It remains unclear how this preference emerges, what is the contribution of shape biases to its formation and whether visual processing underlies it. Here we use congenital blindness as a model for brain development without visual experience. During fMRI, we present blind subjects with shapes encoded using a novel visual-to-music sensory-substitution device (The EyeMusic). Greater activation is observed in the rITG when subjects process symbols as numbers compared with control tasks on the same symbols. Using resting-state fMRI in the blind and sighted, we further show that the areas with preference for numerals and letters exhibit distinct patterns of functional connectivity with quantity and language-processing areas, respectively. Our findings suggest that specificity in the ventral ‘visual’ stream can emerge independently of sensory modality and visual experience, under the influence of distinct connectivity patterns.
Quantum Clock Synchronization with a Single Qudit
Authors: Tavakoli Armin , Cabello Adán , Żukowski Marek , Bourennane Mohamed 
Published: January 2015

AbstractClock synchronization for nonfaulty processes in multiprocess networks is indispensable for a variety of technologies. A reliable system must be able to resynchronize the nonfaulty processes upon some components failing causing the distribution of incorrect or conflicting information in the network. The task of synchronizing such networks is related to Byzantine agreement (BA), which can classically be solved using recursive algorithms if and only if less than one-third of the processes are faulty. Here we introduce a nonrecursive quantum algorithm, based on a quantum solution of the detectable BA, which achieves clock synchronization in the presence of arbitrary many faulty processes by using only a single quantum system.
Insolation driven biomagnetic response to the Holocene Warm Period in semi-arid East Asia
Authors: Liu Suzhen , Deng Chenglong , Xiao Jule , Li Jinhua , Paterson Greig A. , Chang Liao , Yi Liang , Qin Huafeng , Pan Yongxin , Zhu Rixiang 
Published: January 2015

AbstractThe Holocene Warm Period (HWP) provides valuable insights into the climate system and biotic responses to environmental variability and thus serves as an excellent analogue for future global climate changes. Here we document, for the first time, that warm and wet HWP conditions were highly favourable for magnetofossil proliferation in the semi-arid Asian interior. The pronounced increase of magnetofossil concentrations at ~9.8 ka and decrease at ~5.9 ka in Dali Lake coincided respectively with the onset and termination of the HWP and are respectively linked to increased nutrient supply due to postglacial warming and poor nutrition due to drying at ~6 ka in the Asian interior. The two-stage transition at ~7.7 ka correlates well with increased organic carbon in middle HWP and suggests that improved climate conditions, leading to high quality nutrient influx, fostered magnetofossil proliferation. Our findings represent an excellent lake record in which magnetofossil abundance is, through nutrient availability, controlled by insolation driven climate changes.
Dynamic Assessment of Morphological Awareness and Third-Grade Literacy Success
Authors: Wolter Julie A. , Pike Katherine 
Published: January 2015

Purpose
The purpose of this study was to examine a dynamic assessment with graduated prompts to assess morphological awareness and determine whether such a task was related to third-grade literacy success.

Method
A dynamic assessment of morphological awareness was adapted and administered to 54 third-grade students in addition to a norm-referenced language and literacy battery.

Results
A dynamic assessment of morphological awareness measured a range of performance including that of emerging morphological awareness abilities and provided rich linguistic insights for how best to scaffold and prompt for such a skill. In addition, the dynamic morphological awareness measure was found to be significantly related to, and to contribute unique variance to, reading comprehension abilities.

Conclusions
These results suggest that morphological awareness is an important factor to consider when addressing students' literacy performance in early elementary school and that dynamic assessment appears to be a clinically valuable tool when examining early morphological awareness abilities.
Free class AB–AB Miller opamp with high current enhancement
Authors: Roman‐Loera Alejandro , Ramirez‐Angulo Jaime , Lopez‐Martin Antonio , Carvajal Ramon G. 
Published: January 2015

A two‐stage (Miller) operational amplifier (opamp) with both class AB input and output stages is introduced. It has a well‐controlled quiescent current and generates dynamic output currents of up to a factor 45 times larger than the quiescent current. It uses very compact circuitry with small static power consumption in order to achieve class AB–AB operation and can operate with a low supply voltage. Experimental results of a test chip fabricated using 0.18 μm CMOS technology and simulations in 130, 90, 65 and 45 nm verify the proposed circuit.
Gaussian process test for high-throughput sequencing time series: application to experimental evolution
Authors: Topa Hande , Jónás Ágnes , Kofler Robert , Kosiol Carolin , Honkela Antti 
Published: January 2015

Abstract
Motivation: Recent advances in high-throughput sequencing (HTS) have made it possible to monitor genomes in great detail. New experiments not only use HTS to measure genomic features at one time point but also monitor them changing over time with the aim of identifying significant changes in their abundance. In population genetics, for example, allele frequencies are monitored over time to detect significant frequency changes that indicate selection pressures. Previous attempts at analyzing data from HTS experiments have been limited as they could not simultaneously include data at intermediate time points, replicate experiments and sources of uncertainty specific to HTS such as sequencing depth.
Results: We present the beta-binomial Gaussian process model for ranking features with significant non-random variation in abundance over time. The features are assumed to represent proportions, such as proportion of an alternative allele in a population. We use the beta-binomial model to capture the uncertainty arising from finite sequencing depth and combine it with a Gaussian process model over the time series. In simulations that mimic the features of experimental evolution data, the proposed method clearly outperforms classical testing in average precision of finding selected alleles. We also present simulations exploring different experimental design choices and results on real data from Drosophila experimental evolution experiment in temperature adaptation.
Availability and implementation: R software implementing the test is available at https://github.com/handetopa/BBGP .
Contact: hande.topa@aalto.fi , agnes.jonas@vetmeduni.ac.at , carolin.kosiol@vetmeduni.ac.at , antti.honkela@hiit.fi
Supplementary information: Supplementary data are available at Bioinformatics online.
Detection of Dirofilaria immitis (Nematoda: Filarioidea) by Polymerase Chain Reaction in Aedes albopictus, Anopheles punctipennis, and Anopheles crucians (Diptera: Culicidae) From Georgia, USA
Authors: Licitra Beth , Chambers Eric W. , Kelly Rosmarie , Burkot Thomas R. 
Published: January 2015

Abstract
Potential mosquito vectors of Dirofilaria immitis (Leidy) (Nematoda: Filarioidea), the causative agent of dog heartworm in the southeastern region of the United States, were collected with CDC light traps and gravid traps in seven counties in the state of Georgia, USA. The presence of D. immitis in these mosquitoes was detected by polymerase chain reaction using species-specific primers for the D. immitis surface or cuticular antigen. Overall, 1,574 mosquitoes of 13 species in seven genera were collected; 92% of the specimens were Aedes albopictus (Skuse), Aedes vexans (Meigen), or Anopheles punctipennis (Say). Ae. albopictus, An. punctipennis, and Anopheles crucians Wiedemann were positive for D. immitis DNA. Ae. albopictus had the highest maximum likelihood rate of infection (2.30%; 95% confidence interval [CI] = 1.15–4.00%) followed by An. crucians (1.38%: 95% CI = 0.04–6.93%), and An. punctipennis (0.85%: 95% CI 0.03–4.29%). The detection of D. immitis DNA in the heads and thoraxes of Ae. albopictus (0.40%; 95% CI = 0.12–2.02%) indicates that these mosquitoes can support the development of D. immitis to the infective stage 3 larvae.
Breeding of Ornidia obesa (Diptera: Syrphidae: Eristalinae) on Pig Carcasses in Brazil
Authors: Martins E. , Neves J. A. , Moretti T. C. , Godoy W.A.C. , Thyssen P. J. 
Published: January 2015

Abstract
Ornidia obesa F. (Diptera: Syrphidae) is usually neglected in forensic entomology, although adults are rather frequent on vertebrate carrion. In this study, conducted in southeastern Brazil in 2008, we used two pig carcasses, one killed by cocaine overdose and the other by shooting, to evaluate mainly the possible influences of the type of death on the larval development of O. obesa in the pig remains. We recorded the breeding of 218 adult specimens of this syrphid fly from the carcass killed by shooting, and none from the carcass killed by cocaine. These observations may open a new perspective for the use of O. obesa in forensic studies, considering its breeding preferences and its complete development on vertebrate carrion.
Investigation of force-freeness of a solar emerging magnetic field via application of the virial theorem to magnetohydrodynamic simulations
Authors: Kang Jihye , Magara Tetsuya 
Published: January 2015

Abstract
Force-freeness of a solar magnetic field is a key to reconstructing the invisible coronal magnetic structure of an emerging flux region on the Sun where active phenomena such as flares and coronal mass ejections frequently occur. We have performed magnetohydrodynamic simulations which are adjusted to investigate force-freeness of an emerging magnetic field by using the virial theorem. Our focus is on how the force-free range of an emerging flux region develops and how it depends on the twist of a pre-emerged magnetic field. As an emerging flux region evolves, the upper limit of the force-free range continuously increases while the lower limit is asymptotically reduced to the order of a photospheric pressure scale height above the solar surface. As the twist becomes small the lower limit increases and then seems to be saturated. We also discuss the applicability of the virial theorem to an evolving magnetic structure on the Sun.
Ancestry-specific association mapping in admixed populations
Authors: Skotte Line , Jørsboe Emil , Korneliussen Thorfinn Sand , Moltke Ida , Albrechtsen Anders 
Published: January 2015

AbstractDuring the last decade genome–wide association studies have proven to be a powerful approach to identifying disease-causing variants. However, for admixed populations, most current methods for association testing are based on the assumption that the effect of a genetic variant is the same regardless of its ancestry. This is a reasonable assumption for a causal variant, but may not hold for the genetic variants that are tested in genome–wide association studies, which are usually not causal. The effects of non-causal genetic variants depend on how strongly their presence correlate with the presence of the causal variant, which may vary between ancestral populations because of different linkage disequilibrium patterns and allele frequencies.Motivated by this, we here introduce a new statistical method for association testing in recently admixed populations, where the effect size is allowed to depend on the ancestry of a given allele. Our method does not rely on accurate inference of local ancestry, yet using simulations we show that in some scenarios it gives a dramatic increase in statistical power to detect associations. In addition, the method allows for testing for difference in effect size between ancestral populations, which can be used to help determine if a SNP is causal. We demonstrate the usefulness of the method on data from the Greenlandic population.
Integrating crop growth models with whole genome prediction through approximate Bayesian computation
Authors: Technow Frank , Messina Carlos D. , Totir L. Radu , Cooper Mark 
Published: January 2015

AbstractGenomic selection, enabled by whole genome prediction (WGP) methods, is revolutionizing plant breeding. Existing WGP methods have been shown to deliver accurate predictions in the most common settings, such as prediction of across environment performance for traits with additive gene effects. However, prediction of traits with non-additive gene effects and prediction of genotype by environment interaction (G×E), continues to be challenging. Previous attempts to increase prediction accuracy for these particularly difficult tasks employed prediction methods that are purely statistical in nature. Augmenting the statistical methods with biological knowledge has been largely overlooked thus far. Crop growth models (CGMs) attempt to represent the impact of functional relationships between plant physiology and the environment in the formation of yield and similar output traits of interest. Thus, they can explain the impact of G×E and certain types of non-additive gene effects on the expressed phenotype.Approximate Bayesian computation(ABC), a novel and powerful computational procedure, allows the incorporation of CGMs directly into the estimation of whole genome marker effects in WGP. Here we provide a proof of concept study for this novel approach and demonstrate its use with synthetic data sets. We show that this novel approach can be considerably more accurate than the benchmark WGP method GBLUP in predicting performance in environments represented in the estimation set as well as in previously unobserved environments for traits determined by non-additive gene effects. We conclude that this proof of concept demonstrates that using ABC for incorporating biological knowledge in the form of CGMs into WGP is a very promising and novel approach to improving prediction accuracy for some of the most challenging scenarios in plant breeding and applied genetics.