bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single-cell RNA-seq of the Developing Cardiac Outflow Tract Reveals Convergent Development of the Vascular Smooth Muscle Cells at the Base of the Great Arteries
Authors: Liu Xuanyu , Chen Wen , Li Wenke , Priest James R. , Wang Jikui , Zhou Zhou 
Published: November 2018

ABSTRACTRationaleCardiac outflow tract (OFT) is a major hotspot for congenital heart diseases (CHDs). A thorough understanding of the cellular diversity, transitions and regulatory networks of normal OFT development is essential to decipher the etiology of OFT malformations.ObjectiveWe sought to explore the cellular diversity and transitions between cell lineages during OFT development.Methods and ResultsWe performed single-cell transcriptomic sequencing of 55,611 mouse OFT cells from three developmental stages that generally correspond to the early, middle and late stages of OFT remodeling and septation. We identified 17 cell clusters that could be assigned to six cell lineages. Among these lineages, the macrophage and VSMC lineages of the developing OFT have seldom been previously described. Known cellular transitions, such as endothelial to mesenchymal transition, have been recapitulated. In particular, we identified convergent development of the VSMC lineage, where intermediate cell subpopulations were found to be involved in either myocardial to VSMC trans-differentiation or mesenchymal to VSMC transition. Through single-moleculein situhybridization, we observed that cells expressing the myocardial markerMyh7co-expressed the VSMC marker geneCxcl12in OFT walls, thus confirming the existence of myocardial to VSMC trans-differentiation. Moreover, we found that thePenk+cluster c8, a relatively small mesenchymal subpopulation that was undergoing mesenchymal to VSMC transition, was associated with the fusion of OFT cushions. We also uncovered the expression dynamics and critical transcriptional regulators potentially governing cell state transitions. Finally, we developed web-based interactive interfaces to facilitate further data exploration.ConclusionsWe provide a single-cell reference map of cell states for normal OFT development, which will be a valuable resource for the CHD community. Our data support the existence of myocardial to VSMC trans-differentiation and convergent development of the VSMC lineage at the base of the great arteries.
Virus genomes from deep sea sediments expand the ocean megavirome and support independent origins of viral gigantism
Authors: Bäckström Disa , Yutin Natalya , Jørgensen Steffen L. , Dharamshi Jennah , Homa Felix , Zaremba-Niedwiedzka Katarzyna , Spang Anja , Wolf Yuri I. , Koonin Eugene V. , Ettema Thijs J. G. 
Published: November 2018

AbstractThe Nucleocytoplasmic Large DNA Viruses (NCLDV) of eukaryotes (proposed order ”Megavirales”) include the familiesPoxviridae, Asfarviridae, Iridoviridae, Ascoviridae, Phycodnaviridae, Marseilleviridae,andMimiviridae, as well as still unclassified Pithoviruses, Pandoraviruses, Molliviruses and Faustoviruses. Several of these virus groups include giant viruses, with genome and particle sizes exceeding those of many bacterial and archaeal cells. We explored the diversity of the NCLDV in deep-sea sediments from the Loki’s Castle hydrothermal vent area. Using metagenomics, we reconstructed 23 high quality genomic bins of novel NCLDV, 15 of which are closest related to Pithoviruses, 5 to Marseilleviruses, 1 to Iridoviruses, and 2 to Klosneuviruses. Some of the identified Pitho-like and Marseille-like genomes belong to deep branches in the phylogenetic tree of core NCLDV genes, substantially expanding the diversity and phylogenetic depth of the respective groups. The discovered viruses have a broad range of apparent genome sizes including putative giant members of the familyMarseilleviridae, in agreement with multiple, independent origins of gigantism in different branches of the NCLDV. Phylogenomic analysis reaffirms the monophyly of the Pitho-Irido-Marseille branch of NCLDV. Similarly to other giant viruses, the Pitho-like viruses from Loki’s Castle encode translation systems components. Phylogenetic analysis of these genes indicates a greater bacterial contribution than detected previously. Genome comparison suggests extensive gene exchange between members of the Pitho-like viruses andMimiviridae. Further exploration of the genomic diversity of “Megavirales” in additional sediment samples is expected to yield new insights into the evolution of giant viruses and the composition of the ocean megavirome.ImportanceGenomics and evolution of giant viruses is one of the most vigorously developing areas of virus research. Lately, metagenomics has become the main source of new virus genomes. Here we describe a metagenomic analysis of the genomes of large and giant viruses from deep sea sediments. The assembled new virus genomes substantially expand the known diveristy of the Nucleo-Cytoplasmic Large DNA Viruses of eukaryotes. The results support the concept of independent evolution of giant viruses from smaller ancestors in different virus branches.
Deep Unfolded Robust PCA with Application to Clutter Suppression in Ultrasound
Authors: Solomon Oren , Cohen Regev , Zhang Yi , Yang Yi , Qiong He , Luo Jianwen , Sloun Ruud J.G. van , Eldar Yonina C. 
Published: November 2018

AbstractContrast enhanced ultrasound is a radiation-free imaging modality which uses encapsulated gas microbubbles for improved visualization of the vascular bed deep within the tissue. It has recently been used to enable imaging with unprecedented subwavelength spatial resolution by relying on super-resolution techniques. A typical preprocessing step in super-resolution ultrasound is to separate the microbubble signal from the cluttering tissue signal. This step has a crucial impact on the final image quality. Here, we propose a new approach to clutter removal based on robust principle component analysis (PCA) and deep learning. We begin by modeling the acquired contrast enhanced ultrasound signal as a combination of a low rank and sparse components. This model is used in robust PCA and was previously suggested in the context of ultrasound Doppler processing and dynamic magnetic resonance imaging. We then illustrate that an iterative algorithm based on this model exhibits improved separation of microbubble signal from the tissue signal over commonly practiced methods. Next, we apply the concept of deep unfolding to suggest a deep network architecture tailored to our clutter filtering problem which exhibits improved convergence speed and accuracy with respect to its iterative counterpart. We compare the performance of the suggested deep network on both simulations and in-vivo rat brain scans, with a commonly practiced deep-network architecture and the fast iterative shrinkage algorithm, and show that our architecture exhibits better image quality and contrast.
Covalent Aurora A regulation by the metabolic integrator coenzyme A
Authors: Tsuchiya Yugo , Byrne Dominic P , Burgess Selena G , Bormann Jenny , Bakovic Jovana , Huang Yueyan , Zhyvoloup Alexander , Peak-Chew Sew , Tran Trang , Bellany Fiona , Tabor Alethea , Chan AW Edith , Guruprasad Lalitha , Garifulin Oleg , Filonenko Valeriy , Ferries Samantha , Eyers Claire E , Carroll John , Skehel Mark , Bayliss Richard , Eyers Patrick A , Gout Ivan 
Published: November 2018

SummaryAurora A is a cell cycle protein kinase implicated in multiple human cancers, and several Aurora A-specific kinase inhibitors have progressed into clinical trials. In this study, we report structural and cellular analysis of a novel biochemical mode of Aurora A inhibition, which occurs through reversible covalent interaction with the universal metabolic integrator coenzyme A (CoA). Mechanistically, the CoA 3’-phospho ADP moiety interacts with Thr 217, an Aurora A selectivity filter, which permits the formation of an unprecedented covalent bond with Cys 290 in the kinase activation segment, lying some 15 Å away. CoA modification (CoAlation) of endogenous Aurora A is rapidly induced by oxidative stresses at Cys 290 in human cells, and microinjection of CoA into mouse embryos perturbs meitoic spindle formation and chromosome alignment. Aurora A regulation by CoA reveals how targeting of Aurora A might be accomplished in the future by development of a ‘double-anchored’ covalent inhibitor.
Dual cryo-radiofrequency ablation enhances lesion depth in beating human left ventricular preparations
Authors: Sulkin Matthew S. , Laughner Jacob I. , Rogge Michael , Philpott Jonathan M. , Efimov Igor R. 
Published: November 2018

AbstractThermally-mediated ablation has utilized various energy sources, including cryothermal, radiofrequency (RF), microwave, laser, and high-frequency ultrasound with the goal of creating lesions to terminate focal sources or block reentrant wavefronts. RF- and cryo-ablation (CR) cause cell death through different mechanisms, and leave behind tissue with altered thermal-electric properties. We aimed to assess the effect of sequential RF and CR combinations on lesion size. Left ventricular (LV) wedge preparations (n=17) were dissected from ten donated human hearts and four epicardial ablation protocols were compared: 1) RF-RF (n=7); 2) CR-CR (n=7); 3) RF-CR (n=7); and 4) CR-RF (n=7). Preparations were continuously paced and perfused with oxygenated Tyrode solution. Ablated tissue was perfused for 3 hours, sectioned, and stained with 2,3,5-triphenyltetrazolium chloride to delineate necrosis. The effect of initial thermal-electric tissue properties on lesion depth during RF application was determined using a finite element method (FEM). CR-RF generated the deepest lesion (p<0.05) compared to protocols 1-3, while lesion width and area were similar among protocols. No energy combination produced a transmural lesion (n=0 of 28) in LV preparations. FEM showed that electrical conductivity plays a more significant role in lesion creation compared to thermal conductivity. A 33% increase in the initial thermal and electrical tissue conductivity generated a 21% deeper lesion. We conclude that sequential application of CR followed by RF created the deepest lesion in beating human LV preparations. This increase in lesion depth may translate into improved therapeutic outcomes for arrhythmias with intramural origins.
Proliferation Saturation Index in an adaptive Bayesian approach to predict patient-specific radiotherapy responses
Authors: Sunassee Enakshi D. , Tan Dean , Ji Tianlin , Brady Renee , Moros Eduardo G. , Caudell Jimmy J. , Yartsev Slav , Enderling Heiko 
Published: November 2018

AbstractPurposeRadiotherapy prescription dose and dose fractionation protocols vary little between individual patients having the same tumor grade and stage. To personalize radiotherapy a predictive model is needed to simulate radiation response. Previous modeling attempts with multiple variables and parameters have been shown to yield excellent data fits at the cost of nonidentifiability and clinically unrealistic results.Materials and MethodsWe develop a mathematical model based on a proliferation saturation index (PSI) that is a measurement of pre-treatment tumor volume-to-carrying capacity ratio that modulates intrinsic tumor growth and radiation response rates. In an adaptive Bayesian approach, we utilize an increasing number of data points for individual patients for predicting response to subsequent radiation doses.ResultsModel analysis shows that using PSI as the only patient-specific parameter, model simulations can fit longitudinal clinical data with high accuracy (R2=0.84). By analyzing tumor response to radiation using daily CT scans early in the treatment, response to the remaining treatment fractions can be predicted after two weeks with high accuracy (c-index=0.89).ConclusionThe PSI model may be suited to forecast treatment response for individual patients and offer actionable decision points for mid-treatment protocol adaptation. The presented work provides an actionable image-derived biomarker prior to and during therapy to personalize and adapt radiotherapy.
IL-11 neutralising therapies target hepatic stellate cell-induced liver inflammation and fibrosis in NASH
Authors: Widjaja Anissa A. , Singh Brijesh K. , Adami Eleonora , Viswanathan Sivakumar , D’Agostino Giuseppe A. , Dong Jinrui , Ng Benjamin , Tan Jessie , Paleja Bhairav S. , Tripathi Madhulika , Lim Sze Yun , Chothani Sonia P. , Lim Wei Wen , Rabes Anne , Sombetzki Martina , Bruinstroop Eveline , Sinha Rohit A. , Albani Salvatore , Yen Paul M. , Schafer Sebastian , Cook Stuart A. 
Published: November 2018

AbstractThe transformation of hepatic stellate cells (HSCs) into myofibroblasts is the defining pathobiology in non-alcoholic steatohepatitis (NASH). Here we show that key NASH factors induce IL-11, which drives an autocrine and ERK-dependent activation loop to initiate and maintain HSC-to-myofibroblast transformation, causing liver fibrosis. IL-11 is upregulated in NASH andIl11ra1-deleted mice are strongly protected from liver fibrosis, inflammation and steatosis in murine NASH. Therapeutic inhibition of IL11RA or IL-11 with novel neutralizing antibodies robustly inhibits NASH pathology in preclinical models and reverses established liver fibrosis by promoting HSC senescence and favourable matrix remodelling. When given early in NASH, IL-11 inhibition prevents liver inflammation and steatosis, reverses severe hepatocyte damage and reduces hepatic immune cells and TGFβ1 levels. Our findings show an unappreciated and central role for IL-11 in HSCs and prioritise IL-11 signalling as a new therapeutic target in NASH while revealing an unexpected pro-inflammatory function for IL-11 in stromal immunity.
The Toll pathway inhibits tissue growth and regulates cell fitness in an infection-dependent manner
Authors: Germani Federico , Hain Daniel , Sternlicht Denise , Moreno Eduardo , Basler Konrad 
Published: November 2018

AbstractThe Toll pathway regulates the cellular response to infection via the transcriptional upregulation of antimicrobial peptides. Apart from its role in innate immunity, this pathway has also been reported to be important for the elimination of loser cells in a process referred to as cell competition, which can be locally triggered by secreted factors released from winner cells. In this work we provide evidence that the inhibition of Toll signaling not only increases the fitness of loser cells, but also bestows a clonal growth advantage on wild-type cells. We further demonstrate that this growth advantage depends on basal infection levels since it is no longer present under axenic conditions but exacerbated upon intense pathogen exposure. Thus, the Toll pathway functions as a fine-tuned pro-apoptotic and anti-proliferative regulator, underlining the existence of a trade-off between innate immunity and growth during development.
Comparative transcriptome and proteome profiling of the chlorophyll metabolism pathway in four cultivars ofMagnolia officinalis
Authors: Wu Qinahua , Wei Dan , Liu Yuping , Ren Chaoxiang , Liu Qianqian , Chen Cuiping , chen Jiang , Pei Jin 
Published: November 2018

AbstractMagnolia officinalisis an important herb in Chinese medicine that has good therapeutic effects on gastrointestinal motility and helps regulate the spleen and stomach.Magnolia officinalisRehd.et Wils. (abbreviated as CH)、Magnolia officinalisRehd.et Wils. var. biloba’ DaAoye’ (abbreviated as DA)、Magnolia officinalisRehd.et Wils. var. biloba‘XiaoAoye’ (abbreviated as XA)、Magnolia officinalisRehd.et Wils. var. biloba‘Liuye’ (abbreviated as LY) are the four main cultivars in Dujiangyan city, Sichuan province in China, and DA has better medicinal effects and higher levels of green pigment than the other three cultivars. Proteomics research not only provides new insights into protein expression patterns but also enables the identification of many attractive candidates for further research on the effects of pesticides on chlorophyll metabolism inMagnolia officinalis. Transcriptome and proteome analysis of the four mainMagnolia officinaliscultivars in Sichuan province in China identified 125,100 unigenes and 6,012 proteins. Proteomic data and parallel reaction monitoring (PRM) revealed that porphobilinogen deaminase, uroporphyrinogen decarboxylase, oxygen-dependent coproporphyrinogen-III oxidase, protoporphyrinogen oxidase 1, magnesium protoporphyrin IX methyltransferase, magnesium-protoporphyrin IX monomethyl ester oxidative cyclase, and protochlorophyllide reductase-like protein, all of which are involved in chlorophyll synthesis, have higher expression levels in DA than in the other three cultivars. This finding is consistent with the observation that DA has the highest concentration of chlorophyll (37.56 mg/g Fw) of the four cultivars. This research is beneficial to the understanding of the differences in the growth of the four cultivars on the molecular level.
From an “idea generator” to a “solution facilitator”
Authors: Lee Pui Yuen , Lau Kung Wong 
Published: November 2018

PurposeThe rise of social media marketing has brought significant implications for advertising industry and its organizations. The traditional role of advertising professionals had been changing from a clear identity to an unclear one. However, previous research has studied relatively little about advertising professionals’ roles and identities or how they may be changing in the social media marketing era. The paper aims to discuss these issues.Design/methodology/approachA qualitative, interpretive approach was taken in this study. It involved 32 in-depth interviews with advertising professionals in advertising organizations differing in size, digital focus and ownership in different multinational full-service advertising organizations and digital organizations.FindingsThe findings indicated that the role of advertising professionals is innovating from a traditional “idea generator” to a “solution facilitator” in response to the social media marketing.Originality/valueThis study identified the key experiences of advertising professionals that they were found to have divergent role identities linked to their identification with traditional and digital organizations.
Market moods: an investor sentiment event study
Authors: French Jordan 
Published: November 2018

Purpose
The purpose of this paper is to provide insight to practitioners who wish to forecast market returns based on event occurrences.

Design/methodology/approach
Using 64 distinct events that reoccurred from 2007 to 2016 in six different nations of both developing and developed economies, this study used an event study methodology to test whether or not sentiment impacted market returns.

Findings
This study found that investor sentiment did impact market returns. Furthermore, events that were in developed economies or were negative impacted the market returns more than events that are in developing economies or positive. The study also provides important information on the speed of price adjustment to new information. The events selected include festive holidays, bombings, natural disasters and sports matches, among other events which had been found to alter mood. This paper also found no empirical difference between using the statistical mean and economic capital asset pricing models. However, the Wilcoxon rank test did provide more significant events than the more conservative Corrado rank test.

Originality/value
Most comprehensive investor sentiment impact on market returns paper using an event study methodology. The results have implications for those who wish to forecast market returns based on event occurrences.
A scientometric analysis of e-participation research
Authors: Qi Tuotuo , Wang Tianmei , Ma Yanlin , Zhang Wei , Zhu Yanchun 
Published: November 2018

Purpose
Due to the increasing demand for public services, as a new form of public governance, e-participation has emerged. Scholars from various disciplines have published plenty of research results on e-participation. This paper aims to reveal the research status frontiers directly by mapping knowledge domains.

Design/methodology/approach
The authors take 1,322 articles on e-participation published in Web of Science from 2001 to 2017 as research object. They then run the information visualization software CiteSpace to drill deeper into the literature data.

Findings
The study found that e-participation research has the obvious interdisciplinary feature; the author and institution cooperation networks with less internal cooperation are relatively sparse; the USA ranks first in the field of e-participation research, followed by the UK, with the other countries lagged behind; and e-participation through social media is gradually becoming the new research focus.

Originality/value
Based on the objective data and information visualization technology, the research intuitively reveals the research status and development trend of e-participation.
Practical relevance of theory-driven supply chain management research
Authors: Liu Xiaohong , McKinnon Alan C. 
Published: November 2018

PurposeThe purpose of this paper is to examine the extent to which theory-driven supply chain management (SCM) research is of practical relevance. It does this on the basis of empirical research in China.Design/methodology/approachA two-pronged approach was adopted. First, 57 theory-driven SCM studies based in China published in ten leading journals between 2006 and 2015 were surveyed. Second, a questionnaire survey of Chinese managers identified their practical concerns and assessed their alignment with the content of the academic papers.FindingsSome academic research on SCM does probe industry-relevant problems. From an academic perspective, this confirms that theory-driven SCM research can be of practical value. Overall, however, the survey found that much of the SCM research works do not translate into actionable knowledge for practitioners. Academic research in this field could pursue a more pragmatic path and enhance its practical utility. Two critical components of this path, “practical observation” and “practical verification,” are highlighted.Research limitations/implicationsAs the literature review was confined to ten leading journals, relevant papers in other journals were possibly excluded. The research was confined to China and so the results are not necessarily generalizable to other countries.Practical implicationsChinese academics and practitioners could collaborate in defining research agendas and directions. This would help researchers direct their theory building to issues of relevance to business.Originality/valueTo the best of the authors’ knowledge, this is the first study to investigate the relevance of theory-driven SCM research from academic and practitioner perspectives in China. It shows how this research might have greater impact on business practice.