bluuebunny/crossref_metadata_2025_split huggingface dataset:
Orthodox and Unorthodox Uses of Electronic Cigarettes: A Surveillance of YouTube Video Content
Authors: Guy Mignonne C , Helt Jacob , Palafox Sherilyn , Green Kellie , Soule Eric K , Maloney Sarah F , Eissenberg Thomas , Fagan Pebbles 
Published: June 2018

Abstract

Introduction
Open electronic cigarette (e-cigarette) systems are customizable by consumers and often allow for potential “unorthodox” use of the product; that is, use not as intended by the manufacturer. Little is known about the types and prevalence of unorthodox uses and how these practices are transmitted via popular social media.

Methods
Monthly searches of YouTube were conducted from June through November 2016 using the following search terms: “e-cigarettes,” “vaping,” and “e-juice.” After collecting static and dynamic data on the 150 videos identified, two coders independently coded videos for general information, unorthodox use behaviors, health claims, and production quality and characteristics for orthodox and unorthodox use. Intercoder reliability was high (Cohen’s κ 0.81, p < .001).

Results
One hundred fifty videos were included in the study with a total of 115 551 563 views. We identified nine categories of unorthodox uses of e-cigarettes. Unorthodox use was three times as prevalent as orthodox use. Seventy-seven percent of the unorthodox use videos included recreational e-cigarette use, 57% included modification of mechanical parts and components, and 44.6% included unorthodox substance application (dripping). There were more than twice as many social media links in videos depicting unorthodox compared to orthodox use, but the level of engagement was lower for unorthodox use.

Conclusions
E-cigarette unorthodox use on YouTube is more prevalent than orthodox use, suggesting the need to further investigate the prevalence of unorthodox use among e-cigarette users and the influence of social media on consumer uptake of unorthodox and orthodox uses of e-cigarettes.

Implications
The US Food and Drug Administration has regulatory authority over e-cigarettes, parts and components. Many e-cigarettes currently marketed are open systems. Closed systems may allow less manipulation and may influence the safety of these products. This study provides valuable information on ways that open system e-cigarettes are used and it can inform safety tests that can be conducted by the US Food and Drug Administration to determine whether or not these products should remain on the market. In addition, our definitions of unorthodox use can be incorporated into the Population Assessment of Tobacco on Health Study to better understand the prevalence of these behaviors.
Spin-triplet supercurrents in Josephson junctions containing strong ferromagnetic materials
Authors: Birge Norman O. 
Published: June 2018

The proximity effect between a superconducting material and a non-superconducting normal metal can extend over distances of the order of micrometres at sufficiently low temperatures. If the normal metal is replaced by a ferromagnetic material, the spatial extent of the proximity effect drops precipitously due to the exchange splitting between the majority and minority spin bands in the ferromagnet. In 2001, several theorists predicted that spin-triplet pair correlations could be induced in proximity systems involving multiple ferromagnetic materials (or multiple domains in one material) with non-collinear magnetizations. Such spin-triplet pair correlations should extend deep into the ferromagnet, producing a long-range proximity effect. In this paper, we review our experimental work in this area, which has focused primarily on Josephson junctions containing strong ferromagnetic materials. We show that Josephson junctions containing particular combinations of strong ferromagnetic materials can carry spin-triplet supercurrent over distances of at least several tens of nanometres, whereas spin-singlet supercurrent in similar samples decays over a length scale of about 1 nm. We also mention important work by other groups; however, this article is not intended to be a review of the whole field.
This article is part of the theme issue ‘Andreev bound states’.
Non-equilibrium charge and spin transport in superconducting–ferromagnetic–superconducting point contacts
Authors: Holmqvist C. , Belzig W. , Fogelström M. 
Published: June 2018

The conventional Josephson effect may be modified by introducing spin-active scattering in the interface layer of the junction. Here, we discuss a Josephson junction consisting of two s-wave superconducting leads coupled over a classical spin that precesses with the Larmor frequency due to an external magnetic field. This magnetically active interface results in a time-dependent boundary condition with different tunnelling amplitudes for spin-up and -down quasi-particles and where the precession produces spin-flip scattering processes. As a result, the Andreev states develop sidebands and a non-equilibrium population that depend on the details of the spin precession. The Andreev states carry a steady-state Josephson charge current and a time-dependent spin current, whose current–phase relations could be used to characterize the precessing spin. The spin current is supported by spin-triplet correlations induced by the spin precession and creates a feedback effect on the classical spin in the form of a torque that shifts the precession frequency. By applying a bias voltage, the Josephson frequency adds another complexity to the situation and may create resonances together with the Larmor frequency. These Shapiro resonances manifest as torques and, under suitable conditions, are able to reverse the direction of the classical spin in sub-nanosecond time. Another characteristic feature is the subharmonic gap structure in the DC charge current displaying an even–odd effect attributable to precession-assisted multiple Andreev reflections.
This article is part of the theme issue ‘Andreev bound states’.
Study on Green’s function on topological insulator surface
Authors: Lu Bo , Tanaka Yukio 
Published: June 2018

In the theory of superconducting junctions, Green’s function has an important role for obtaining Andreev bound states, local density of states and Josephson current in a systematic way. In this article, we show how to construct Green’s function on the surface of a topological insulator following McMillan’s formalism where the energy spectrum of electrons obeys a linear dispersion. For a model of a superconductor (S)/ferromagnet (F)/normal metal (N) junction, we show that the generation of a Majorana fermion gives rise to the enhanced local density of states and pair amplitude of odd-frequency pairing. We also derive an extended Furusaki–Tsukada’s formula of DC Josephson current in S/F/S junctions. The obtained Josephson current depends on the direction and magnitude of the magnetization.This article is part of the theme issue ‘Andreev bound states’.
A tradeoff between tolerance and resistance to a major fungal pathogen in elite wheat cultivars
Authors: Mikaberidze Alexey , McDonald Bruce A. 
Published: June 2018

SummaryTolerance and resistance represent two strategies that hosts evolved to protect themselves from pathogens. Tolerance alleviates the reduction in host fitness due to infection without reducing a pathogen’s growth, while resistance reduces pathogen growth. We investigated tolerance of wheat to the major fungal pathogen Zymoseptoria tritici in 335 elite wheat cultivars.We used a novel digital phenotyping approach that included 11,152 infected leaves and counted 2,069,048 pathogen fruiting bodies.We discovered a new component of tolerance that is based on the relationship between the green area remaining on a leaf and the number of pathogen fruiting bodies. We found a negative correlation between tolerance and resistance among intolerant cultivars, presenting the first compelling evidence for a tradeoff between tolerance and resistance to plant pathogens. Surprisingly, the tradeoff arises due to limits in the host resources available to the pathogen and not due to metabolic constraints, contrary to what ecological theory suggests.The mechanism underlying this tradeoff may be relevant for many plant diseases in which the amount of host resources available to the pathogen can limit the pathogen population. Our analysis indicates that European wheat breeders may have selected for tolerance instead of resistance to an important pathogen.
Software update: Moving the R package sommer to multivariate mixed models for genome-assisted prediction
Authors: Covarrubias-Pazaran Giovanny 
Published: June 2018

AbstractIn the last decade the use of mixed models has become a pivotal part in the implementation of genome-assisted prediction in plant and animal breeding programs. Exploiting the use genetic correlation among traits through multivariate predictions has been proposed in recent years as a way to boost prediction accuracy and understand pleiotropy and other genetic and ecological phenomena better. Multiple mixed model solvers able to use relationship matrices or deal with marker-based incidence matrices have been released in the last years but multivariate versions are scarse. Such solvers have become quite popular in plant and animal breeding thanks to user-friendly platforms such as R. Among such software one of the most recent and popular is the sommer package. In this short communication we discuss the update of the package that is able to run multivariate mixed models with multiple random effects and different covariance structures at the level of random effects and trait-to-trait covariance along with other functionalities for genetic analysis and field trial analysis to enhance the genome-assisted prediction capabilities of researchers.
Recent mixing of Vibrio parahaemolyticus populations
Authors: Yang Chao , Pei Xiaoyan , Wu Yarong , Yan Lin , Yan Yanfeng , Song Yuqin , Coyle Nicola , Martinez-Urtaza Jaime , Quince Christopher , Hu Qinghua , Jiang Min , Feil Edward , Yang Dajin , Song Yajun , Zhou Dongsheng , Yang Ruifu , Falush Daniel , Cui Yujun 
Published: June 2018

AbstractBackgroundHumans have profoundly affected the ocean environment but little is known about anthropogenic effects on the distribution of microbes. Vibrio parahaemolyticus is found in warm coastal waters and causes gastroenteritis in humans and economically significant disease in shrimps.ResultsBased on data from 1,103 genomes, we show that V. parahaemolyticus is divided into four diverse populations, VppUS1, VppUS2, VppX and VppAsia. The first two are largely restricted to the US and Northern Europe, while the others are found worldwide, with VppAsia making up the great majority of isolates in the seas around Asia. Patterns of diversity within and between the populations are consistent with them having arisen by progressive divergence via genetic drift during geographical isolation. However, we find that there is substantial overlap in their current distribution. These observations can be reconciled without requiring genetic barriers to exchange between populations if dispersal between oceans has increased dramatically in the recent past. We found that VppAsia isolates from the US have an average of 1.01% more shared ancestry with VppUS1 and VppUS2 isolates than VppAsia isolates from Asia itself. Based on time calibrated trees of divergence within epidemic lineages, we estimate that recombination affects about 0.017% of the genome per year, implying that the genetic mixture has taken place within the last few decades.ConclusionsThese results suggest that human activity, such as shipping and aquatic products trade, are responsible for the change of distribution pattern of this marine species.
Mechanics of exploration inDrosophila melanogaster
Authors: Loveless Jane , Lagogiannis Konstantinos , Webb Barbara 
Published: June 2018

AbstractTheDrosophilalarva executes a stereotypical exploratory routine that appears to consist of stochastic alternation between straight peristaltic crawling and reorientation events through lateral bending. We present a model of larval mechanics for axial and transverse motion over a planar substrate, and use it to develop a simple, reflexive neuromuscular model from physical principles. In the absence of damping and driving, the mechanics of the body produces axial travelling waves, lateral oscillations, and unpredictable, chaotic deformations. The neuromuscular system counteracts friction to recover these motion patterns, giving rise to forward and backward peristalsis in addition to turning. The model produces spontaneous exploration, even though the model nervous system has no intrinsic pattern generating or decision making ability, and neither senses nor drives bending motions. Ultimately, our model suggests a novel view of larval exploration as a deterministic superdiffusion process which is mechanistically grounded in the chaotic mechanics of the body.
Reproducible Data Analysis Pipelines for Precision Medicine
Authors: Fjukstad Bjørn , Dumeaux Vanessa , Hallett Michael , Ailo Bongo Lars 
Published: June 2018

AbstractPrecision medicine brings the promise of more precise diagnosis and individualized therapeutic strategies from analyzing a cancer’s genomic signature. Technologies such as high-throughput sequencing enable cheaper data collection at higher speed, but rely on modern data analysis platforms to extract knowledge from these high dimensional datasets. Since this is a rapidly advancing field, new diagnoses and therapies often require tailoring of the analysis. These pipelines are therefore developed iteratively, continuously modifying analysis parameters before arriving at the final results. To enable reproducible results it is important to record all these modifications and decisions made during the analysis process.We built a system, walrus, to support reproducible analyses for iteratively developed analysis pipelines. The approach is based on our experiences developing and using deep analysis pipelines to provide insights and recommendations for treatment in an actual breast cancer case. We designed walrus for the single servers or small compute clusters typically available for novel treatments in the clinical setting. walrus leverages software containers to provide reproducible execution environments, and integrates with modern version control systems to capture provenance of data and pipeline parameters.We have used walrus to analyze a patient’s primary tumor and adjacent normal tissue, including subsequent metastatic lesions. Although we have used walrus for specialized analyses of whole-exome sequencing datasets, it is a general data analysis tool that can be applied in a variety of scientific disciplines. We have open sourced walrus along with example data analysis pipelines at github.com/uit-bdps/walrus.
A repressor-decay timer for robust temporal patterning in embryonic Drosophila neuroblast lineages
Authors: Averbukh Inna , Lai Sen-Lin , Doe Chris Q. , Barkai Naama 
Published: June 2018

AbstractBiological timers synchronize patterning processes during embryonic development. In theDrosophilaembryo, neural progenitors (neuroblasts; NBs) produce a sequence of unique neurons whose identities depend on the sequential expression of temporal transcription factors (TTFs). The stereotypy and precision of the NB lineages indicate reproducible temporal progression of the TTF timer. To examine the basis of this robustness, we combine theory and experiments. The TTF timer is commonly described as a relay of activators, but its regulatory circuit is also consistent with a repressor-decay timer, in which expression of each TTF begins once its repressor is sufficiently reduced. We find that repressor-decay timers are more robust to parameter variations compared to activator-relay timers. This suggests that thein-vivoTTF sequence progresses primarily by repressor-decay, a prediction that we support experimentally. Our results emphasize the role of robustness in the evolutionary design of patterning circuits.
HPAanalyze: An R Package that Facilitates the Retrieval and Analysis of The Human Protein Atlas Data
Authors: Tran Anh Nhat , Dussaq Alex M. , Kennell Timothy , Willey Christopher D. , Hjelmeland Anita B. 
Published: June 2018

ABSTRACTBackgroundThe Human Protein Atlas (HPA) aims to map human proteins via multiple technologies including imaging, proteomics and transcriptomics. Access of the HPA data is mainly via web-based interface allowing views of individual proteins, which may not be optimal for data analysis of a gene set, or automatic retrieval of original images.ResultsHPAanalyze is an R package for retrieving and performing exploratory analysis of data from HPA. HPAanalyze provides functionality for importing data tables and xml files from HPA, exporting and visualizing data, as well as downloading all staining images of interest. The package is free, open source, and available via Bioconductor and Github.ConclusionsHPAanalyze integrates into the R workflow via the tidyverse philosophy and data structures, and it can be used in combination with Bioconductor packages for easy analysis of HPA data.
Neural representations of social valence bias economic interpersonal choices
Authors: Díaz-Gutiérrez Paloma , Arco Juan E. , Alguacil Sonia , González-García Carlos , Ruz María 
Published: June 2018

AbstractPrior personal information is highly relevant during social interactions. Such knowledge aids in the prediction of others, and it affects choices even when it is unrelated to actual behaviour. In this investigation, we aimed to study the neural representation of positive and negative personal expectations, how these impact subsequent choices, and the effect of mismatches between expectations and encountered behaviour. We employed functional Magnetic Resonance Imaging in combination with a version of the Ultimatum Game (UG) where participants were provided with information about their partners’ moral traits previous to their fair or unfair offers. Univariate and multivariate analyses revealed the implication of the supplementary motor area (SMA) and inferior frontal gyrus (IFG) in the representation of expectations about the partners in the game. Further, these regions also represented the valence of expectations, together with the ventromedial prefrontal cortex (vmPFC). Importantly, the performance of multivariate classifiers in these clusters correlated with a behavioural choice bias to accept more offers following positive descriptions, highlighting the impact of the valence on the expectations on participants’ economic decisions. Altogether, our results suggest that expectations based on social information guide future interpersonal decisions and that the neural representation of such expectations in the vmPFC is related to their influence on behaviour.
Effects of pathogenic CNVs on physical traits in participants of the UK Biobank
Authors: Owen David , Bracher-Smith Mathew , Kendall Kimberley , Rees Elliott , Einon Mark , Escott-Price Valentina , Owen Michael J , O’Donovan Michael C , Kirov George 
Published: June 2018

ABSTRACTBackgroundCopy number variants (CNVs) have been shown to increase risk for physical anomalies, developmental, psychiatric and medical disorders. Some of them have been associated with changes in weight, height, and other physical traits. As most studies have been performed on children and young people, these effects of CNVs in adulthood are not well established.MethodsThe UK Biobank recruited half a million adults who provided a variety of physical measurements. We called all CNVs from the Affymetrix microarrays and selected a set of 54 CNVs implicated as pathogenic (including their reciprocal deletions/duplications) and that were present in five or more persons. Linear regression analysis was used to establish their association with 16 physical traits, relevant to human health.Results396,725 participants of white British or Irish descent (excluding first-degree relatives) passed our quality control filters. There were 214 CNV/trait associations significant at a false discovery rate of 0.1, most of them novel. These traits are associated with adverse health outcomes: e.g. increased weight, waist-to-hip ratio, pulse rate and body fat composition. Deletions at 16p11.2, 16p12.1,NRXN1and duplications at 16p13.11 and 22q11.2 produced the highest numbers of significant associations. CNVs at 1q21.1, 2q13, 16p11.2, 16p11.2 distal, 16p12.1, 17p12 and 17q12 demonstrated one or more mirror image effects of deletions versus duplications.ConclusionsCarriers of many CNVs should be monitored for physical traits that increase morbidity and mortality. Genes within these CNVs can give insights into biological processes and therapeutic interventions.
Differential profiles of soluble and cellular toll like receptor 2 and 4 in chronic periodontitis
Authors: AlQallaf H. , Hamada Y. , Blanchard S. , Shin D. , Gregory R.L. , Srinivasan M. 
Published: June 2018

AbstractChronic periodontitis is a common inflammatory disease initiated by a complex microbial biofilm and mediated by the host response causing destruction of the supporting tissues of the teeth. Host recognition of pathogens is mediated by toll-like receptors (TLRs) that bind conserved molecular patterns shared by groups of microorganisms. The oral epithelial cells respond to most periodontopathic bacteria via TLR-2 and TLR-4. Many studies have previously reported the presence of elevated numbers of viable exfoliated epithelial cells (SEC) in the saliva of patients with chronic periodontitis. In addition to the membrane-associated receptors, soluble forms of TLR-2 (sTLR-2) and TLR-4 (sTLR-4) have been identified and are thought to play a regulatory role by binding microbial ligands. sTLR-2 has been shown to arise from ectodomain shedding of the extracellular domain of the membrane receptor and sTLR-4 is thought to be an alternate spliced form. The objective of this study was to investigate the potential value of salivary sTLR-2/4 and the paired epithelial cell-associated TLR-2/4 mRNA as diagnostic markers for chronic periodontitis. Unstimulated whole saliva was collected after obtaining informed consent from 40 individuals in either periodontitis or gingivitis cohorts. The levels of sTLR-2/4 were measured by enzyme-linked immunosorbent assay (ELISA). SEC TLR-2/4 transcripts were quantitated by real time polymerase chain reaction. While levels of sTLR-2 exhibited an inverse correlation, sTLR-4 positively correlated with clinical parameters in the gingivitis cohort. Interestingly, both correlations were lost in the periodontitis cohort indicating a dysregulated host response. On the other hand, while sTLR-2 and the paired SEC associated TLR-2 mRNA exhibited a direct correlation (r2=0.62), that of sTLR4 and SEC TLR-4 mRNA exhibited an inverse correlation (r2=0.53) in the periodontitis cohort. Collectively, assessments of salivary sTLR2 and sTLR4 together with the respective transcripts in SECs could provide clinically relevant markers of disease progression from gingivitis to periodontitis.