bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Airway Microbiome at Birth
Authors: Lal Charitharth Vivek , Travers Colm , Aghai Zubair H. , Eipers Peter , Jilling Tamas , Halloran Brian , Carlo Waldemar A. , Keeley Jordan , Rezonzew Gabriel , Kumar Ranjit , Morrow Casey , Bhandari Vineet , Ambalavanan Namasivayam 
Published: August 2016

AbstractAlterations of pulmonary microbiome have been recognized in multiple respiratory disorders. It is critically important to ascertain if an airway microbiome exists at birth and if so, whether it is associated with subsequent lung disease. We found an established diverse and similar airway microbiome at birth in both preterm and term infants, which was more diverse and different from that of older preterm infants with established chronic lung disease (bronchopulmonary dysplasia). Consistent temporal dysbiotic changes in the airway microbiome were seen from birth to the development of bronchopulmonary dysplasia in extremely preterm infants. Genus Lactobacillus was decreased at birth in infants with chorioamnionitis and in preterm infants who subsequently went on to develop lung disease. Our results, taken together with previous literature indicating a placental and amniotic fluid microbiome, suggest fetal acquisition of an airway microbiome. We speculate that the early airway microbiome may prime the developing pulmonary immune system and dysbiosis in its development may set the stage for subsequent lung disease.
Metformin Enhances the Therapy Effects of Anti-IGF-1R mAb Figitumumab to NSCLC
Authors: Cao Hongxin , Dong Wei , Qu Xiao , Shen Hongchang , Xu Jun , Zhu Linhai , Liu Qi , Du Jiajun 
Published: August 2016

AbstractThe insulin-like growth factor (IGF) signaling system plays a critical role in tumorigenesis, highlighting the potential of targeting IGF-1R as an anti-cancer therapy. Although multiple anti-IGF-1R monoclonal antibody (mAb) drugs have been developed, challenges remain in the validation of the therapeutic effects and understanding the molecular mechanism of these mAbs. Herein, we conducted a study to validate the effect of Figitumumab (CP), an anti-IGF-1R mAb, in a panel of non-small cell lung cancer (NSCLC) cell lines. We found all tested cell lines were sensitive to CP, and CP could block IGF-1R and the downstream PI3K/AKT pathway activation. Unexpectedly, we found CP could activate ERK signaling pathway in IGF-1R kinase independent manner, which we further verified was mainly mediated by β-arrestin2. We also investigated the anti-tumor effect of metformin alone as well as its combination with CP to target NSCLC. Metformin could target IGF-1R signaling pathway by attenuating PI3K/AKT and MEK/ERK signaling pathways and down-regulating IGF-1R. Finally, we found that combining metformin with CP could further induce IGF-1R down-regulation and was more effective to target NSCLC cells. Our data suggests the combining of metformin with CP has additive therapeutic value against NSCLC.
Strength Training Prevents Hyperinsulinemia, Insulin Resistance, and Inflammation Independent of Weight Loss in Fructose-Fed Animals
Authors: Botezelli José D. , Coope Andressa , Ghezzi Ana C. , Cambri Lucieli T. , Moura Leandro P. , Scariot Pedro P. M. , Gaspar Rodrigo Stellzer , Mekary Rania A. , Ropelle Eduardo Rochete , Pauli José Rodrigo 
Published: August 2016

AbstractThe aim of this study was to compare the effects of aerobic, strength, and combined training on metabolic disorders induced by a fructose-rich diet. Wistar rats (120 days old) were randomized into five groups (n = 8–14): C (control diet and sedentary), F (fed the fructose-rich diet and sedentary), FA (fed the fructose-rich diet and subject to aerobic exercise), FS (fed the fructose-rich diet and subject to strength exercise), and FAS (fed the fructose-rich diet and subject to combined aerobic and strength exercises). After the 8-week experiment, glucose homeostasis, blood biochemistry, tissue triglycerides, and inflammation were evaluated and analyzed. The strength protocol exerted greater effects on glucose homeostasis, insulin sensitivity, and liver lipid contents than other protocols (all P < 0.05). All three exercise protocols induced a remarkable reduction in inflammation, tissue triglyceride content, and inflammatory pathways, which was achieved through c-Jun NH2-terminal kinase (JNK) phosphorylation and factor nuclear kappa B (NFkB) activation in both the liver and the muscle. Our data suggest that strength training reduced the severity of most of the metabolic disorders induced by a fructose-rich diet and could be the most effective strategy to prevent or treat fructose-induced metabolic diseases.
Resting state brain dynamics and its transients: a combined TMS-EEG study
Authors: Bonnard Mireille , Chen Sophie , Gaychet Jérôme , Carrere Marcel , Woodman Marmaduke , Giusiano Bernard , Jirsa Viktor 
Published: August 2016

AbstractThe brain at rest exhibits a spatio-temporally rich dynamics which adheres to systematic behaviours that persist in task paradigms but appear altered in disease. Despite this hypothesis, many rest state paradigms do not act directly upon the rest state and therefore cannot confirm hypotheses about its mechanisms. To address this challenge, we combined transcranial magnetic stimulation (TMS) and electroencephalography (EEG) to study brain’s relaxation toward rest following a transient perturbation. Specifically, TMS targeted either the medial prefrontal cortex (MPFC), i.e. part of the Default Mode Network (DMN) or the superior parietal lobule (SPL), involved in the Dorsal Attention Network. TMS was triggered by a given brain state, namely an increase in occipital alpha rhythm power. Following the initial TMS-Evoked Potential, TMS at MPFC enhances the induced occipital alpha rhythm, called Event Related Synchronisation, with a longer transient lifetime than TMS at SPL and a higher amplitude. Our findings show a strong coupling between MPFC and the occipital alpha power. Although the rest state is organized around a core of resting state networks, the DMN functionally takes a special role among these resting state networks.
Observing the ocean interior in support of integrated management
Authors: Trenkel Verena M. , Handegard Nils Olav , Weber Thomas C. 
Published: July 2016

Abstract
Active- and passive-acoustic methods are widely used tools for observing, monitoring, and understanding marine ecosystems. From 25 to 28 May 2015, 214 scientists from 31 nations gathered for an ICES symposium on Marine Ecosystem Acoustics (SoME Acoustics) to discuss three major themes related to acoustic observations of marine ecosystems: (i) recent developments in acoustic and platform technologies; (ii) acoustic characterisation of aquatic organisms, ecosystem structure, and ecosystem processes; and (iii) contribution of acoustics to integrated ecosystem assessments and management. The development of, and access to new instruments, such as broad bandwidth systems, enables insightful ecological studies and innovative management approaches. Unresolved ecological questions and the increasing move towards ecosystem based management pose further challenges to scientists and instrument developers. Considering the SoME Acoustics presentations in the context of three previous ICES symposia on fisheries acoustics, topics increasingly emphasize ecosystem studies and management. The continued expansion of work and progress in marine ecosystem acoustics is due to the cross-disciplinary work of fisheries acousticians, engineers, ecologists, modellers, and others. An analysis of the symposium co-authorship network reveals a highly connected acoustic science community collaborating around the globe.
Conceptualizing Consciousness in Consumer Research
Authors: Williams Lawrence E , Poehlman T Andrew 
Published: August 2016

AbstractAn outsized focus on the explanatory value of conscious thought can constrain opportunities to more rigorously examine the influence of less obvious drivers of consumer behavior. This article proposes a more precise, disaggregated, and minimized perspective on consciousness, distinguishing it from other higher-order mental processes (i.e., deliberation, intentionality, control, and effort). A more circumscribed perspective on consciousness, we argue, facilitates attempts to examine the causal impact of low-level, biological, or otherwise unconscious influences, bringing these into the frame of inquiry. Accordingly, we outline how a reduced reliance on consciousness as an explanatory construct deepens inquiry into the processes guiding choice, self-control, and persuasion. Lastly, in a set of recommendations centering on theory, methods, and training, we suggest ways for consumer researchers to evaluate more critically whether the contents of consciousness play a meaningful role in driving behavior.
Long-term complications of definitive chemoradiotherapy for esophageal cancer using the classical method
Authors: Ito Hitoshi , Itasaka Satoshi , Sakanaka Katsuyuki , Araki Norio , Mizowaki Takashi , Hiraoka Masahiro 
Published: July 2016

Abstract
Chemoradiation therapy is widely used to treat both inoperable and operable patients, and is less invasive than surgery. Although the number of long-term survivors who have received chemoradiation therapy is increasing, the long-term toxicity pattern and cumulative incidence of toxicity regarding this modality are poorly understood. Classically, chemoradiation therapy for esophageal cancer consists of an anterior–posterior field and a subsequent oblique boost field. We retrospectively analyzed patients who were treated with definitive chemoradiation therapy for esophageal cancer using this classical method from 1999 to 2008. For the assessment of toxicity, the National Cancer Institute Common Toxicity Criteria Version 3.0 was adopted. A total of 101 patients were analyzed. The median follow-up time was 16 months for all patients and 62 months for the surviving patients. Eleven patients experienced late toxicities of ≥Grade 3. Two patients died of late toxicities. The 3- and 5-year cumulative incidences for the first late cardiopulmonary toxicities of ≥Grade 3 were 17.4% and 20.8%, respectively. Cardiopulmonary effusions were observed within the first 3 years of completion of the initial treatment in seven out of eight patients. Sudden death and cardiac ischemia were observed over a 10-year period. Older age was found to be a risk factor for late toxicity after definitive chemoradiation therapy for esophageal cancer. Substantial toxicities were observed in patients who had received chemoradiation therapy for esophageal cancer using the classical method. To minimize the incidence of late toxicity, more sophisticated radiation techniques may be useful.
Identification and characterization of wheat drought-responsive MYB transcription factors involved in the regulation of cuticle biosynthesis
Authors: Bi Huihui , Luang Sukanya , Li Yuan , Bazanova Natalia , Morran Sarah , Song Zhihong , Perera M. Ann , Hrmova Maria , Borisjuk Nikolai , Lopato Sergiy 
Published: August 2016

AbstractA plant cuticle forms a hydrophobic layer covering plant organs, and plays an important role in plant development and protection from environmental stresses. We examined epicuticular structure, composition, and a MYB-based regulatory network in two Australian wheat cultivars, RAC875 and Kukri, with contrasting cuticle appearance (glaucousness) and drought tolerance. Metabolomics and microscopic analyses of epicuticular waxes revealed that the content of β-diketones was the major compositional and structural difference between RAC875 and Kukri. The content of β-diketones remained the same while those of alkanes and primary alcohols were increased by drought in both cultivars, suggesting that the interplay of all components rather than a single one defines the difference in drought tolerance between cultivars. Six wheat genes encoding MYB transcription factors (TFs) were cloned; four of them were regulated in flag leaves of both cultivars by rapid dehydration and/or slowly developing cyclic drought. The involvement of selected MYB TFs in the regulation of cuticle biosynthesis was confirmed by a transient expression assay in wheat cell culture, using the promoters of wheat genes encoding cuticle biosynthesis-related enzymes and the SHINE1 (SHN1) TF. Two functional MYB-responsive elements, specifically recognized by TaMYB74 but not by other MYB TFs, were localized in the TdSHN1 promoter. Protein structural determinants underlying the binding specificity of TaMYB74 for functional DNA cis -elements were defined, using 3D protein molecular modelling. A scheme, linking drought-induced expression of the investigated TFs with downstream genes that participate in the synthesis of cuticle components, is proposed.
Optical and radio astrometry of the galaxy associated with FRB 150418
Authors: Bassa C. G. , Beswick R. , Tingay S. J. , Keane E. F. , Bhandari S. , Johnston S. , Totani T. , Tominaga N. , Yasuda N. , Stappers B. W. , Barr E. D. , Kramer M. , Possenti A. 
Published: July 2016

Abstract
A fading radio source, coincident in time and position with the fast radio burst FRB 150418, has been associated with the galaxy WISE J071634.59−190039.2. Subsequent observations of this galaxy have revealed that it contains a persistent, but variable, radio source. We present e-Multi-Element Radio Linked Interferometer Network, Very Long Baseline Array, and Australia Telescope Compact Array radio observations and Subaru optical observations of WISE J071634.59−190039.2 and find that the persistent radio source is unresolved and must be compact (&lt;0.01 kpc), and that its location is consistent with the optical centre of the galaxy. We conclude that it is likely that WISE J071634.59−190039.2 contains a weak radio active galactic nucleus.
When and where did GW150914 form?
Authors: Lamberts A. , Garrison-Kimmel S. , Clausen D. R. , Hopkins P. F. 
Published: July 2016

Abstract
The recent LIGO detection of gravitational waves (GW150914), likely originating from the merger of two ∼ 30M⊙ black holes suggests progenitor stars of low metallicity ([Z/Z⊙] ≲ 0.3), constraining when and where the progenitor of GW150914 may have formed. We combine estimates of galaxy properties (star-forming gas metallicity, star formation rate and merger rate) across cosmic time to predict the low redshift black hole – black hole merger rate as a function of present day host galaxy mass, Mgal, the formation redshift of the progenitor system zf and different progenitor metallicities Zp. For $Z_\mathrm{p}\geqslant 0.1 \rm Z_{{\odot }}$, the signal is dominated by binaries in massive galaxies with zf ≃ 2 while below $Z_\mathrm{p}\leqslant 0.1\rm Z_{{\odot }}$ most mergers come from binaries formed around zf ≃ 0.5 in dwarf galaxies. Additional gravitational wave detections from merging massive black holes will provide constraints on the mass–metallicity relation and massive star formation at high redshifts.
Definitive test of the Rh = ct universe using redshift drift
Authors: Melia Fulvio 
Published: August 2016

Abstract
The redshift drift of objects moving in the Hubble flow has been proposed as a powerful model-independent probe of the underlying cosmology. A measurement of the first- and second-order redshift derivatives appears to be well within the reach of upcoming surveys using as the Extremely Large Telescope high resolution spectrometer (ELT-HIRES) and the Square Kilometer Phase 2 Array (SKA). Here we show that an unambiguous prediction of the Rh = ct cosmology is zero drift at all redshifts, contrasting sharply with all other models in which the expansion rate is variable. For example, multiyear monitoring of sources at redshift z = 5 with the ELT-HIRES is expected to show a velocity shift Δv = −15 cm s−1 yr−1 due to the redshift drift in Planck ΛCDM, while Δv = 0 cm s−1 yr−1 in Rh = ct. With an anticipated ELT-HIRES measurement error of ±5 cm s−1 yr−1 after 5 yr, these upcoming redshift drift measurements might therefore be able to differentiate between Rh = ct and Planck ΛCDM at ∼3σ, assuming that any possible source evolution is well understood. Such a result would provide the strongest evidence yet in favour of the Rh = ct cosmology. With a 20-yr baseline, these observations could favour one of these models over the other at better than 5σ.
rehh 2.0: a reimplementation of the R package rehh to detect positive selection from haplotype structure
Authors: Gautier Mathieu , Klassmann Alexander , Vitalis Renaud 
Published: August 2016

AbstractIdentifying genomic regions with unusually high local haplotype homozygosity represents a powerful strategy to characterize candidate genes responding to natural or artificial positive selection. To that end, statistics measuring the extent of haplotype homozygosity within (e.g., EHH, iHS) and between (Rsb or XP-EHH) populations have been proposed in the literature. Therehhpackage for R was previously developed to facilitate genome-wide scans of selection, based on the analysis of long-range haplotypes. However, its performance wasn’t sufficient to cope with the growing size of available data sets. Here we propose a major upgrade of therehhpackage, which includes an improved processing of the input files, a faster algorithm to enumerate haplotypes, as well as multi-threading. As illustrated with the analysis of large human haplotype data sets, these improvements decrease the computation time by more than an order of magnitude. This new version ofrehhwill thus allow performing iHS-, Rsb- or XP-EHH-based scans on large data sets. The packagerehh2.0 is available from the CRAN repository (http://cran.r-project.org/web/packages/rehh/index.html) together with help files and a detailed manual.
Rapid resistome mapping using nanopore sequencing
Authors: van der Helm Eric , Imamovic Lejla , Hashim Ellabaan Mostafa M , van Schaik Willem , Koza Anna , Sommer Morten O. A. 
Published: August 2016

AbstractThe emergence of antibiotic resistance in human pathogens has become a major threat to modern medicine and in particular hospitalized patients. The outcome of antibiotic treatment can be affected by the composition of the gut resistome either by enabling resistance gene acquisition of infecting pathogens or by modulating the collateral effects of antibiotic treatment on the commensal microbiome. Accordingly, knowledge of the gut resistome composition could enable more effective and individualized treatment of bacterial infections. Yet, rapid workflows for resistome characterization are lacking. To address this challenge we developed the poreFUME workflow that deploys functional metagenomic selections and nanopore sequencing to resistome mapping. We demonstrate the approach by functionally characterizing the gut resistome of an ICU patient. The accuracy of the poreFUME pipeline is >97 % sufficient for the reliable annotation of antibiotic resistance genes. The poreFUME pipeline provides a promising approach for efficient resistome profiling that could inform antibiotic treatment decisions in the future.
Modeling volatility on the Karachi Stock Exchange, Pakistan
Authors: Akhtar Shahan , Khan Naimat U. 
Published: August 2016

Purpose
The current paper aims to fill a gap in the literature by analyzing the nature of volatility on the Karachi Stock Exchange (KSE) 100 index of the KSE, and develop an understanding as to which model is most suitable for measuring volatility among those used. The study contributes significantly to the literature as, compared with the limited previous studies of Pakistan undertaken in the past, it covers three types of data (i.e. daily, weekly and monthly) for the whole period from the introduction of the KSE 100 index on November 2, 1991 to December 31, 2013. In addition, to analyze the impact of global financial crises upon volatility, the data have been divided into pre-crisis (1991-2007) and post-crisis (2008-2013) periods.

Design/methodology/approach
This study has used an advanced set of volatility models such as autoregressive conditional heteroskedasticity [ARCH (1)], generalized autoregressive conditional heteroskedasticity [GARCH (1, 1)], GARCH in mean [GARCH-M (1, 1)], exponential GARCH [E-GARCH (1, 1)], threshold GARCH [T-GARCH (1, 1)], power GARCH [P-GARCH (1, 1)] and also a simple exponentially weighted moving average (EWMA) model.

Findings
The results reveal that daily, weekly and monthly return series show non-normal distribution, stationarity and volatility clustering. However, the heteroskedasticity is absent only in the monthly returns making only the EWMA model usable to measure the volatility level in the monthly series. The P-GARCH (1, 1) model proved to be a better model for modeling volatility in the case of daily returns, while the GARCH (1, 1) model proved to be the most appropriate for weekly data based on the Schwarz information criterion (SIC) and log likelihood (LL) functionality. The study shows high persistence of volatility, a mean reverting process and an absence of a risk premium in the KSE market with an insignificant leverage effect only in the case of weekly returns. However, a significant leverage effect is reported regarding the daily series of the KSE 100 index. In addition, to analyze the impact of global financial crises upon volatility, the findings show that the subperiods demonstrated a slightly low volatility and the global economic crisis did not cause a rise in volatility levels.

Originality/value
Previously, the literature about volatility modeling in Pakistan’s markets has been limited to a few models of relatively small sample size. The current thesis has attempted to overcome these limitations and used diverse models for three types of data series (daily, weekly and monthly). In addition, the Pakistani economy has been beset by turmoil throughout its history, experiencing a range of shocks from the mild to the extreme. This paper has measured the impact of those shocks upon the volatility levels of the KSE.