bluuebunny/crossref_metadata_2025_split huggingface dataset:
Importing food damages domestic environment: Evidence from global soybean trade
Authors: Sun Jing , Mooney Harold , Wu Wenbin , Tang Huajun , Tong Yuxin , Xu Zhenci , Huang Baorong , Cheng Yeqing , Yang Xinjun , Wei Dan , Zhang Fusuo , Liu Jianguo 
Published: May 2018

Significance
Achieving global environmental sustainability and food security is among the world’s biggest challenges. International food trade plays an important role in global food security. It is widely believed that importing countries benefit environmentally from international food trade at the environmental cost of exporting countries. Contrary to the conventional wisdom, our study reveals a major environmental problem in importing countries. The unexpected findings suggest the need to reevaluate environmental consequences of international trade in all importing countries through discussions regarding environmental responsibilities among consumers and producers. There is an urgent need for innovative solutions for reducing environmental pollution and enhancing food security to offset the negative impacts of international trade globally.
Pan-cancer transcriptional signatures predictive of oncogenic mutations reveal that Fbw7 regulates cancer cell oxidative metabolism
Authors: Davis Ryan J. , Gönen Mehmet , Margineantu Daciana H. , Handeli Shlomo , Swanger Jherek , Hoellerbauer Pia , Paddison Patrick J. , Gu Haiwei , Raftery Daniel , Grim Jonathan E. , Hockenbery David M. , Margolin Adam A. , Clurman Bruce E. 
Published: May 2018

SignificanceTumor suppression by the Fbw7 ubiquitin ligase remains poorly understood. Here, we used informatics and engineered cancer cells to show that Fbw7 mutations cause metabolic reprogramming by increasing oxidative phosphorylation and metabolic vulnerabilities that may represent therapeutic targets. Our approach may be applied to study other complex cancer genes.
Osmotic stabilization prevents cochlear synaptopathy after blast trauma
Authors: Kim Jinkyung , Xia Anping , Grillet Nicolas , Applegate Brian E. , Oghalai John S. 
Published: May 2018

SignificanceTrauma due to roadside bombs is an unfortunate consequence of modern warfare and terrorist attacks. Hearing loss often occurs because the cochlea is the body’s most sensitive pressure transducer. Here, we used in vivo imaging of the mouse cochlea using optical coherence tomography to show that increased endolymph volume correlates with damage to the auditory synapse. Reducing endolymph volume by increasing perilymph tonicity treated the synaptic loss. Therefore, this study identifies a treatment for noise-induced hearing loss. Furthermore, it suggests that this treatment may help patients with Meniere’s disease, a disabling syndrome of vertigo and hearing loss due to increased endolymph volume.
Artificial selection reveals sex differences in the genetic basis of sexual attractiveness
Authors: Gosden Thomas P. , Reddiex Adam J. , Chenoweth Stephen F. 
Published: May 2018

Significance
Using artificial selection on fruit fly pheromones, we tested how mate choice by both sexes can cause evolutionary change. Results show that although both sexes choose mates, the evolutionary outcomes are fundamentally different for each sex. Specifically, experimental results show that the evolution of pheromones can only be driven through female choice of males because genetic relationships exist between pheromones, mating success, and fitness. Male choice of females, however, cannot drive evolutionary change by itself because the correlation between pheromones and mating success is generated by environmental rather than genetic variation. Therefore, the traits targeted in females by male choice are likely to evolve through correlated responses to selection on males.
Simulated night shift work induces circadian misalignment of the human peripheral blood mononuclear cell transcriptome
Authors: Kervezee Laura , Cuesta Marc , Cermakian Nicolas , Boivin Diane B. 
Published: May 2018

Significance
Night shift work is associated with adverse health effects, including diabetes, cardiovascular disease, and cancer. Understanding the molecular mechanisms that underlie this association is instrumental in advancing the diagnosis, prevention, and treatment of shift work-related health concerns. We characterized the effect on genome-wide gene expression levels of a 4-day protocol simulating night shifts in healthy human subjects under highly controlled laboratory conditions. We demonstrate that this night shift protocol leads to a dampening of gene expression rhythms and a desynchrony between rhythmic transcripts and the shifted sleep/wake cycle. Moreover, we uncovered key biological processes and regulatory molecules that are altered during this night shift protocol and that may contribute to the development of health problems on the long term.
Interferometric imaging of nonlocal electromechanical power transduction in ferroelectric domains
Authors: Zheng Lu , Dong Hui , Wu Xiaoyu , Huang Yen-Lin , Wang Wenbo , Wu Weida , Wang Zheng , Lai Keji 
Published: May 2018

Significance
The conversion between electrical and acoustic signals in piezoelectric materials is of fundamental importance for their applications. Because of the much slower speed of sound than speed of light in solids, mesoscopic imaging is imperative for the study of electroacoustic behaviors at microwave frequencies. In this paper, the electromechanical power transduction in lithium niobate domains is spatially resolved by microwave impedance microscopy. Because of the sign reversal of piezoelectric tensor in opposite domains, the interaction between electric fields and elastic waves leads to fringe patterns that are fundamentally different from the acoustic displacement fields. This approach uncovers hidden information in the piezoelectric transduction process and opens a frontier to explore various elastic phenomena in materials and devices.
Robustness and universality of surface states in Dirac materials
Authors: Shtanko Oles , Levitov Leonid 
Published: May 2018

Significance
We predict that generic Dirac materials host ballistically propagating surface states. Despite being nontopological, these states are robust and insensitive to surface disorder, occurring in a universal manner at generic boundaries, both atomically smooth and disordered. These properties originate from the multicomponent character of the Dirac–Bloch wavefunction, which results in strong coupling to generic boundaries. Dispersion of the surface states can be tuned by external gates to exhibit a variety of different regimes, including flat bands and linear crossings within the bulk bandgap. These surface states provide a natural explanation for anomalous long-range edge transport observed recently in a variety of Dirac materials in both topological and nontopological phases.
IonStar enables high-precision, low-missing-data proteomics quantification in large biological cohorts
Authors: Shen Xiaomeng , Shen Shichen , Li Jun , Hu Qiang , Nie Lei , Tu Chengjian , Wang Xue , Poulsen David J. , Orsburn Benjamin C. , Wang Jianmin , Qu Jun 
Published: May 2018

Significance
Reliable proteome-wide quantification in large biological cohorts is highly valuable for clinical and pharmaceutical research yet remains extremely challenging despite recent technical advancements. Specifically, elevated missing data levels and compromised quantitative quality are common issues for prevalent methods. Here, we describe an IonStar technique taking advantage of sensitive and selective MS1 ion current-base quantification via innovations in effective and reproducible quantitative feature generation. Compared with several label-free strategies, IonStar showed superior performance in large-cohort analysis, manifested by excellent accuracy/precision, extremely low missing data, and confident discovery of subtle protein changes. In a proof-of-concept study, we demonstrated that IonStar quantified >7,000 unique proteins in 100 brain samples with no missing data and excellent quantitative quality, which has not been achievable by existing methods.
Polypentagonal ice-like water networks emerge solely in an activity-improved variant of ice-binding protein
Authors: Mahatabuddin Sheikh , Fukami Daichi , Arai Tatsuya , Nishimiya Yoshiyuki , Shimizu Rumi , Shibazaki Chie , Kondo Hidemasa , Adachi Motoyasu , Tsuda Sakae 
Published: May 2018

Significance
This study expands our knowledge of protein hydration, which is highly related to the macromolecular antifreeze property of proteins. We examined a polypentagonal network formation of waters for a series of artificial variants of a 65-residue ice-binding protein. The polypentagonal waters were created solely on the surface of an activity-improved variant, which appeared to contain two sets of water clusters exhibiting a perfect position match to the waters constructing the first prism and pyramidal ice planes. These data suggest that a minute structural change in a protein organizes the surface waters into a polypentagonal arrangement, which merges with the intrinsically disordered ice surface and freezes to specific ice crystal planes.
Recurrent bridgehead effects accelerate global alien ant spread
Authors: Bertelsmeier Cleo , Ollier Sébastien , Liebhold Andrew M. , Brockerhoff Eckehard G. , Ward Darren , Keller Laurent 
Published: May 2018

Significance
Because of the globalization of trade and travel, worldwide invasion rates are high. A potential driver of the global acceleration of new invasions is the so-called bridgehead effect, in which initial invasive populations serve as the source of additional invasions via secondary introductions. However, the frequency and overall importance of secondary introductions remain largely unknown. Using a remarkable dataset, spanning nearly 100 years (1914–2013), of ant interceptions at air and maritime ports in the United States and New Zealand, we found that most ant introductions arise via secondary transport via intermediate regions. Our analyses also reveal positive feedback between the introduction and establishment stages of the invasion process via secondary introductions acting as a critical driver of increasing global invasion rates.
Phase-transition temperature suppression to achieve cubic GeTe and high thermoelectric performance by Bi and Mn codoping
Authors: Liu Zihang , Sun Jifeng , Mao Jun , Zhu Hangtian , Ren Wuyang , Zhou Jingchao , Wang Zhiming , Singh David J. , Sui Jiehe , Chu Ching-Wu , Ren Zhifeng 
Published: May 2018

Significance
Phase-transition behavior in thermoelectric materials is detrimental for their application in thermoelectric devices. Here we designed, and experimentally realized the high thermoelectric performance of cubic GeTe-based material by suppressing the phase transition from a cubic to a rhombohedral structure to below room temperature through a simple Bi and Mn codoping on the Ge site. Bi doping reduced the hole concentration while Mn alloying largely suppressed the phase-transition temperature and also induced modification of the valence bands. Our work provides the basis for studying phase transitions in other thermoelectric materials to optimize these materials for applications.
Exhaustive Classification of the Invariant Solutions for a Specific Nonlinear Model Describing Near Planar and Marginally Long-Wave Unstable Interfaces for Phase Transition
Authors: Ahangari Fatemeh 
Published: May 2018

Abstract

Problems of thermodynamic phase transition originate inherently in solidification, combustion and various other significant fields. If the transition region among two locally stable phases is adequately narrow, the dynamics can be modeled by an interface motion. This paper is devoted to exhaustive analysis of the invariant solutions for a modified Kuramoto-Sivashinsky equation in two spatial and one temporal dimensions is presented. This nonlinear partial differential equation asymptotically characterizes near planar interfaces, which are marginally long-wave unstable. For this purpose, by applying the classical symmetry method for this model the classical symmetry operators are attained. Moreover, the structure of the Lie algebra of symmetries is discussed and the optimal system of subalgebras, which yields the preliminary classification of group invariant solutions is constructed. Mainly, the Lie invariants corresponding to the infinitesimal symmetry generators as well as associated similarity reduced equations are also pointed out. Furthermore, the nonclassical symmetries of this nonlinear PDE are also comprehensively investigated.
Impact of the Cotton–Mouton effect on Faraday polarimetry measurements using circular polarization
Authors: Chen J , Ding W X , Brower D L 
Published: May 2018

Abstract
A comprehensive understanding of the impact of the Cotton–Mouton effect on Faraday polarimetry measurements using counter-rotating circular polarization (CP) probe beams has been developed. By using the Jones theory, an analytic study shows that the Cotton–Mouton effect cancels to first order with coupling into the Faraday measurement only at higher orders. A Jones-based numerical study shows the coupling effect strongly depends on the Cotton–Mouton effect, Faraday effect, and wavelength chosen for the measurement. For realistic DIII-D plasma conditions and far-infrared wavelength, numerical calculation suggests the measurement is dominated by the Faraday effect while the coupling effect leads to a small but finite correction. By statistical comparison between the experimental measurement and the Jones-based numerical calculation under various plasma parameters, the impact of the Cotton–Mouton effect has been verified. Proper treatment of the coupling effect is essential in the data analysis under certain conditions for polarimetric measurement using CP in present devices and beyond.
Evidence of evolutionary history and selective sweeps in the genome of Meishan pig reveals its genetic and phenotypic characterization
Authors: Zhao Pengju , Yu Ying , Feng Wen , Du Heng , Yu Jian , Kang Huimin , Zheng Xianrui , Wang Zhiquan , Liu George E , Ernst Catherine W , Ran Xueqin , Wang Jiafu , Liu Jian-Feng 
Published: May 2018

Abstract

Background
Meishan is a pig breed indigenous to China and famous for its high fecundity. The traits of Meishan are strongly associated with its distinct evolutionary history and domestication. However, the genomic evidence linking the domestication of Meishan pigs with its unique features is still poorly understood. The goal of this study is to investigate the genomic signatures and evolutionary evidence related to the phenotypic traits of Meishan via large-scale sequencing.

Results
We found that the unique domestication of Meishan pigs occurred in the Taihu Basin area between the Majiabang and Liangzhu Cultures, during which 300 protein-coding genes have underwent positive selection. Notably, enrichment of the FoxO signaling pathway with significant enrichment signal and the harbored gene IGF1R were likely associated with the high fertility of Meishan pigs. Moreover, NFKB1 exhibited strong selective sweep signals and positively participated in hyaluronan biosynthesis as the key gene of NF-kB signaling, which may have resulted in the wrinkled skin and face of Meishan pigs. Particularly, three population-specific synonymous single-nucleotide variants occurred in PYROXD1, MC1R, and FAM83G genes; the T305C substitution in the MCIR gene explained the black coat of the Meishan pigs well. In addition, the shared haplotypes between Meishan and Duroc breeds confirmed the previous Asian-derived introgression and demonstrated the specific contribution of Meishan pigs.

Conclusions
These findings will help us explain the unique genetic and phenotypic characteristics of Meishan pigs and offer a plausible method for their utilization of Meishan pigs as valuable genetic resources in pig breeding and as an animal model for human wrinkled skin disease research.
The research data management platform (RDMP): A novel, process driven, open-source tool for the management of longitudinal cohorts of clinical data
Authors: Nind Thomas , Galloway James , McAllister Gordon , Scobbie Donald , Bonney Wilfred , Hall Christopher , Tramma Leandro , Reel Parminder , Groves Martin , Appleby Philip , Doney Alex , Guthrie Bruce , Jefferson Emily 
Published: May 2018

Abstract

Background
The Health Informatics Centre at the University of Dundee provides a service to securely host clinical datasets and extract relevant data for anonymized cohorts to researchers to enable them to answer key research questions. As is common in research using routine healthcare data, the service was historically delivered using ad-hoc processes resulting in the slow provision of data whose provenance was often hidden to the researchers using it. This paper describes the development and evaluation of the Research Data Management Platform (RDMP): an open source tool to load, manage, clean, and curate longitudinal healthcare data for research and provide reproducible and updateable datasets for defined cohorts to researchers.

Results
Between 2013 and 2017, RDMP tool implementation tripled the productivity of data analysts producing data releases for researchers from 7.1 to 25.3 per month and reduced the error rate from 12.7% to 3.1%. The effort on data management reduced from a mean of 24.6 to 3.0 hours per data release. The waiting time for researchers to receive data after agreeing a specification reduced from approximately 6 months to less than 1 week. The software is scalable and currently manages 163 datasets. A total 1,321 data extracts for research have been produced, with the largest extract linking data from 70 different datasets.

Conclusions
The tools and processes that encompass the RDMP not only fulfil the research data management requirements of researchers but also support the seamless collaboration of data cleaning, data transformation, data summarization and data quality assessment activities by different research groups.
On Integrable Field Theories as Dihedral Affine Gaudin Models
Authors: Vicedo Benoît 
Published: May 2018

Abstract
We introduce the notion of a classical dihedral affine Gaudin model, associated with an untwisted affine Kac–Moody algebra $\widetilde{\mathfrak{g}}$ equipped with an action of the dihedral group $D_{2T}$, $T \geq 1$ through (anti-)linear automorphisms. We show that a very broad family of classical integrable field theories can be recast as examples of such classical dihedral affine Gaudin models. Among these are the principal chiral model on an arbitrary real Lie group $G_0$ and the $\mathbb{Z}_T$-graded coset $\sigma $-model on any coset of $G_0$ defined in terms of an order $T$ automorphism of its complexification. Most of the multi-parameter integrable deformations of these $\sigma $-models recently constructed in the literature provide further examples. The common feature shared by all these integrable field theories, which makes it possible to reformulate them as classical dihedral affine Gaudin models, is the fact that they are non-ultralocal. In particular, we also obtain affine Toda field theory in its lesser-known non-ultralocal formulation as another example of this construction. We propose that the interpretation of a given classical non-ultralocal integrable field theory as a classical dihedral affine Gaudin model provides a natural setting within which to address its quantisation. At the same time, it may also furnish a general framework for understanding the massive ordinary differential equations (ODE)/integrals of motion (IM) correspondence since the known examples of integrable field theories for which such a correspondence has been formulated can all be viewed as dihedral affine Gaudin models.
Identifying surgical site infections in electronic health data using predictive models
Authors: Grundmeier Robert W , Xiao Rui , Ross Rachael K , Ramos Mark J , Karavite Dean J , Michel Jeremy J , Gerber Jeffrey S , Coffin Susan E 
Published: May 2018

AbstractObjectiveThe objective was to prospectively derive and validate a prediction rule for detecting cases warranting investigation for surgical site infections (SSI) after ambulatory surgery.MethodsWe analysed electronic health record (EHR) data for children who underwent ambulatory surgery at one of 4 ambulatory surgical facilities. Using regularized logistic regression and random forests, we derived SSI prediction rules using 30 months of data (derivation set) and evaluated performance with data from the subsequent 10 months (validation set). Models were developed both with and without data extracted from free text. We also evaluated the presence of an antibiotic prescription within 60 days after surgery as an independent indicator of SSI evidence. Our goal was to exceed 80% sensitivity and 10% positive predictive value (PPV).ResultsWe identified 234 surgeries with evidence of SSI among the 7910 surgeries available for analysis. We derived and validated an optimal prediction rule that included free text data using a random forest model (sensitivity = 0.9, PPV = 0.28). Presence of an antibiotic prescription had poor sensitivity (0.65) when applied to the derivation data but performed better when applied to the validation data (sensitivity = 0.84, PPV = 0.28).ConclusionsEHR data can facilitate SSI surveillance with adequate sensitivity and PPV.
Calcium signaling during salt stress and in the regulation of ion homeostasis
Authors: Manishankar Prabha , Wang Nili , Köster Philipp , Alatar Abdulrahman A , Kudla Jörg 
Published: May 2018

Abstract
Soil composition largely defines the living conditions of plants and represents one of their most relevant, dynamic, and complex environmental cues. The effective concentrations of many either tolerated or essential ions and compounds in the soil usually differ from the optimum that would be most suitable for plants. In this regard, salinity—caused by excess NaCl—represents a widespread adverse growth condition, but shortage of ions such as K+, NO3−, and Fe2+ also restrains plant growth. During the past years, many components and mechanisms that function in the sensing and establishment of ion homeostasis have been identified and characterized. Here, we reflect on recent insights that extended our understanding of components and mechanisms which govern and fine-tune plant salt stress tolerance and ion homeostasis. We put special emphasis on mechanisms that allow for interconnection of the salt overly sensitive pathway with plant development and discuss newly emerging functions of Ca2+ signaling in salinity tolerance. Moreover, we review and discuss accumulating evidence for a central and unifying role for Ca2+ signaling and Ca2+-dependent protein phosphorylation in regulating sensing, uptake, transport, and storage processes of various ions. Finally, based on this cross-field inventory, we deduce emerging concepts and questions arising for future research.
Revealing the velocity structure of the filamentary nebula in NGC 1275 in its entirety
Authors: Gendron-Marsolais M , Hlavacek-Larrondo J , Martin T B , Drissen L , McDonald M , Fabian A C , Edge A C , Hamer S L , McNamara B , Morrison G 
Published: May 2018

ABSTRACT
We have produced for the first time a detailed velocity map of the giant filamentary nebula surrounding NGC 1275, the Perseus cluster’s brightest galaxy, and revealed a previously unknown rich velocity structure across the entire nebula. These new observations were obtained with the optical imaging Fourier transform spectrometer SITELLE at CFHT. With its wide field of view ( ∼11 arcmin × 11 arcmin), SITELLE is the only integral field unit spectroscopy instrument able to cover the 80 kpc  ×  55 kpc ( 3.8 arcmin × 2.6 arcmin) large nebula in NGC 1275. Our analysis of these observations shows a smooth radial gradient of the [N ii]λ6583/H α line ratio, suggesting a change in the ionization mechanism and source across the nebula. The velocity map shows no visible general trend or rotation, indicating that filaments are not falling uniformly onto the galaxy, nor being uniformly pulled out from it. Comparison between the physical properties of the filaments and Hitomi measurements of the X-ray gas dynamics in Perseus is also explored.