bluuebunny/crossref_metadata_2025_split huggingface dataset:
pETM: a penalized Exponential Tilt Model for analysis of correlated high-dimensional DNA methylation data
Authors: Sun Hokeun , Wang Ya , Chen Yong , Li Yun , Wang Shuang 
Published: February 2017

Abstract

Motivation
DNA methylation plays an important role in many biological processes and cancer progression. Recent studies have found that there are also differences in methylation variations in different groups other than differences in methylation means. Several methods have been developed that consider both mean and variance signals in order to improve statistical power of detecting differentially methylated loci. Moreover, as methylation levels of neighboring CpG sites are known to be strongly correlated, methods that incorporate correlations have also been developed. We previously developed a network-based penalized logistic regression for correlated methylation data, but only focusing on mean signals. We have also developed a generalized exponential tilt model that captures both mean and variance signals but only examining one CpG site at a time.

Results
In this article, we proposed a penalized Exponential Tilt Model (pETM) using network-based regularization that captures both mean and variance signals in DNA methylation data and takes into account the correlations among nearby CpG sites. By combining the strength of the two models we previously developed, we demonstrated the superior power and better performance of the pETM method through simulations and the applications to the 450K DNA methylation array data of the four breast invasive carcinoma cancer subtypes from The Cancer Genome Atlas (TCGA) project. The developed pETM method identifies many cancer-related methylation loci that were missed by our previously developed method that considers correlations among nearby methylation loci but not variance signals.

Availability and Implementation
The R package ‘pETM’ is publicly available through CRAN: http://cran.r-project.org.

Supplementary information
Supplementary data are available at Bioinformatics online.
Use of Obstetric Practice Web Sites to Distribute Zika Virus Information to Pregnant Women During a Zika Virus Outbreak
Authors: Lehnert Jonathan D. , Ellingson Mallory K. , Goryoka Grace W. , Kasturi Raghuraj , Maier Emily , Chamberlain Allison T. 
Published: February 2017

Objective:
To describe the current use of obstetric practice Web sites to disseminate Zika virus information to patients.

Design:
Review of 913 randomly selected practice Web sites and associated social media accounts in January and August 2016.

Setting:
Obstetric practice Web sites and associated social media accounts, United States of America.

Participants:
N/A.

Main Outcome Measures:
Proportion of obstetric practice Web sites and linked social media accounts providing Zika virus information.

Results:
Twenty-five percent and 35% of obstetric practice Web sites had information posted about Zika virus in January 2016 and August 2016, respectively. Between the 2 time points, the proportion of practices posting Zika virus content on Facebook and Twitter declined (Facebook: 15% in January, 9% in August; Twitter: 12% in January, 8% in August). In August, the most frequently observed Zika virus–related content themes were the use of insect repellent (14%) and travel advisories (14%). At both time points, practices affiliated with large university hospitals were more likely to have posted information on Zika virus than independent OB/GYN-only practices: January: odds ratio (OR) (95% confidence interval [CI]) = 5.68 (3.50-9.20); August: OR (95% CI) = 8.37 (5.31-13.17). Similarly, practices associated with nonuniversity hospitals were more likely to have posted information than independent OB/GYN-only practices: January: OR (95% CI) = 2.71 (1.88-3.92); August: OR (95% CI) = 6.75 (4.75-9.60).

Conclusion:
Obstetric care practices are not fully utilizing their practice Web sites to relay Zika virus information to their patients. Since practitioner-sponsored Web sites have the capacity to directly reach the populations at greatest risk for Zika virus complications, public health professionals should consider adapting their materials and provider outreach campaigns to more easily accommodate Web site–based information dissemination during this type of public health emergency. There must be greater recognition of the value information gains in the eyes of the patient when it is validated by their own provider, especially when that patient is part of the highest-risk population for a given emergency. Public health organizations should strive to minimize the burden it takes for providers to relay useful resources to patients in order to maximize the impact that those resources can have.
Multiple roles of PIWIL1 in mouse neocorticogenesis
Authors: Viljetic Barbara , Diao Liyang , Liu Jixia , Krsnik Zeljka , Wijeratne Sagara H.R. , Kristopovich Ryan , Dutre-Clarke Marina , Kraushar Matthew L. , Song Jimin , Xing Jinchuan , Chen Kevin C. , Rasin Mladen-Roko 
Published: February 2017

AbstractPIWI-interacting RNAs (piRNAs) and their associated PIWI proteins play an important role in repressing transposable elements in animal germlines. However, little is known about the function of PIWI proteins and piRNAs in the developing brain. Here, we investigated the role of an important PIWI family member, Piwi-like protein 1 (Piwil1; also known as Miwi in mouse) in the developing mouse neocortex. Using aPiwil1knock-out (Piwil1KO) mouse strain, we found that Piwil1 is essential for several steps of neocorticogenesis, including neocortical cell cycle, neuron migration and dendritogenesis. Piwil1 deletion resulted in increased cell cycle re-entry at embryonic day 17 (E17) when predominantly intracortically projecting neurons are being produced. Prenatal Piwil1 deletion increased the number of Pax6+ radial glia at postnatal day 0 (P0). Furthermore, Piwil1 deletion disrupted migration of Satb2+ neurons within deep layers at E17, P0 and P7. Satb2+ neurons showed increased co-localization with Bcl11b (also known as Ctip2), marker of subcortically projecting neurons. Piwil1 knockouts had disrupted neocortical circuitry represented by thinning of the corpus callosum and altered dendritogenesis. We further investigated if Piwil1 deletion disrupted expression levels of neocortical piRNAs by small RNA-sequencing in neocortex. We did not find differential expression of piRNAs in the neocortices ofPiwil1KO, while differences were observed in otherPiwil1KO tissues. This result suggests that Piwil1 may act independently of piRNAs and have novel roles in higher cognitive centers, such as neocortex. In addition, we report a screen of piRNAs derived from tRNA fragments in developing neocortices. Our result is the first report of selective subsets of piRNAs and tRNA fragments in developing prenatal neocortices and helps clarify some outstanding questions about the role of the piRNA pathway in the brain.
Environmentally-Friendly Workflow Based on Supercritical Fluid Chromatography and Tandem Mass Spectrometry Molecular Networking For the Discovery of Potent Anti-Viral Leads From Plants
Authors: Nothias Louis-Félix , Boutet-Mercey Stéphanie , Cachet Xavier , Torre Erick De La , Laboureur Laurent , Gallard Jean-François , Retailleau Pascal , Brunelle Alain , Dorrestein Pieter C. , Costa Jean , Bedoya Luis M. , Roussi Fanny , Leyssen Pieter , Alcami José , Paolini Julien , Litaudon Marc , Touboul David 
Published: February 2017

ABSTRACTA supercritical fluid chromatography-based targeted purification workflow using tandem mass spectrometry and molecular networking was developed to analyze, annotate and isolate secondary metabolites from complex mixture. This approach was applied for targeted isolation of new antiviral diterpene esters fromEuphorbia semiperfoliatawhole plant extract. The analysis of bioactive fractions revealed that unknown diterpene esters, including jatrophane esters and phorboids esters, were present in the samples. The purification procedure using semi-preparative-supercritical fluid chromatography led to the isolation and identification of two jatrophane esters (13and14) and four 4-deoxyphorbol esters (15-18). Compound16was found to display antiviral activity against chikungunya virus (EC50= 0.45µM), while compound15was found to be a potent and selective inhibitor of HIV-1 replication in a recombinant virus assay (EC50= 13 nM). This study showed that supercritical fluid chromatography-based workflow and molecular networking can facilitate and accelerate the discovery of bioactive small molecules by targeted molecules of interest, while minimizing the use of toxic solvents.
Understanding microblog continuance usage intention: an integrated model
Authors: Zhang Keliang , Min Qingfei , Liu Zhenhua , Liu Zilong 
Published: February 2017

Purpose
The purpose of this paper is to explore the factors affecting users’ continuous microblog usage intention. In recent years, the number of microblog users has gradually declined. This research can reveal microblog users’ needs and provide the improvement direction of microblog services.

Design/methodology/approach
By integrating Wixom and Todd’s theoretical framework, the Uses and Gratifications Theory and the DeLone and McLean Information System Success Model, a conceptual model is proposed. In this model, gratification is defined as a kind of behavioral attitude, and satisfaction is viewed as an object-based attitude. The survey data were collected online and analyzed using the partial least squares method.

Findings
The results suggest that users’ continuance intention (behavioral intention) is jointly determined by users’ gratification (behavioral-based attitude) and their habitual microblog usage behavior. Likewise, gratification is positively affected by satisfaction (object-based attitude) which is a joint function of system quality and information quality (object-based beliefs).

Originality/value
In this research, Wixom and Todd’s principle is applied as the basic theoretical framework; gratification is viewed as a behavior attitude and user satisfaction is identified as an object-based attitude. This research model is a new lens for continuance usage research.
Born global firms’ growth and collaborative entry mode: the role of transnational entrepreneurs
Authors: Liu Yipeng 
Published: February 2017

PurposeThe purpose of this paper is to investigate the role of transnational entrepreneurs in growing born global firms, with a focus on the growth process facilitated by collaborative entry mode.Design/methodology/approachThe author chose the solar photovoltaic industry as the empirical setting. This industry is a particularly good context for the study because many firms in this industry sell knowledge-intensive products internationally from their inception. The primary data consist of 32 in-depth interviews with entrepreneurs, industry association representatives, research institute scholars, and professional service firms.FindingsThe study highlights the importance of transnational entrepreneurs who develop born global firms to maturity by using their technological knowledge, international connections, and bicultural advantages to navigate and leverage institutional complexity. Collaborative entry mode with distributors enables born global firms’ high growth rapidly, whereas transnational entrepreneurs play a central role in building and expanding international network. Initial public offering in overseas stock exchange accelerates the high growth trajectory of born global firm by signalling its maturity.Research limitations/implicationsThe author took a process perspective by examining the growth and maturity of born global firms by collaborative partnership; the author’s focus on the role of transnational entrepreneurs highlighted entrepreneurs’ sensitivity to institutional complexity along the growth trajectory.Practical implicationsThe author recommends both incumbent and entrepreneurial firms in developed economies collaborate with transnational entrepreneurs in various business areas. Industry firms may be able to cooperate on product and marketing development, and professional service firms can offer services to expand born global firms further, because transnational entrepreneurs follow the global “rules of the game”.Originality/valueThe author shed important light on the role of transnational entrepreneurs throughout the growth of born global firms via collaborative entry mode. Furthermore, the author develops a multilevel framework for analysing the combined influence of transnational entrepreneur and institutional complexity on the growth of born global firm.
International diversification for portfolios of European fixed-income mutual funds
Authors: Zagaglia Paolo 
Published: February 2017

Purpose
The purpose of this paper is to study the scope for country diversification in international portfolios of mutual funds for the “core” EMU countries. The author uses a sample of daily returns for country indices of French, German and Italian funds to investigate the quest for international diversification. The author focuses on fixed-income mutual funds during the period of the financial market turmoil since 2007.

Design/methodology/approach
The author compute optimal portfolio allocations from both unconstrained and constrained mean-variance frameworks that take as input the out-of-sample forecasts for the conditional mean, volatility and correlation of country-level indices for funds returns. The author also applies a portfolio allocation model based on utility maximization with learning about the time-varying conditional moments. The author compares the out-of-sample forecasting performance of 12 multivariate volatility models.

Findings
The author finds that there is a “core” EMU country also for the mutual fund industry: optimal portfolios allocate the largest portfolio weight to German funds, with Italian funds assigned a lower weight in comparison to French funds. This result is remarkably robust across competing forecasting models and optimal allocation strategies. It is also consistent with the findings from a utility-maximization model that incorporates learning about time-varying conditional moments.

Originality/value
This is the first study on optimal country-level diversification for a mutual fund investor focused on European countries in the fixed-income space for the turmoil period. The author uses a large array of econometric models that captures the salient features of a period characterized by large changes in volatility and correlation, and compare the performance of different optimal asset allocation models.
‘Doing good by proxy’: human‐animal kinship and the ‘donation’ of canine blood
Authors: Ashall Vanessa , Hobson‐West Pru 
Published: February 2017

AbstractThis article demonstrates the relevance of animals to medical sociology by arguing that pet owners’ accounts of veterinary decision‐making can highlight key sociological themes which are important to both human and animal health. Based on semi‐structured interviews, the article argues that interspecies ‘kinship’ allows for the extension of sociological claims regarding altruism, self‐interest and mutuality from human blood donation to companion animal blood ‘donation’. Furthermore, this study extends sociological understanding of the human‐animal bond by showing how the dog's status as kin meant they were expected to donate blood, and that the act of donation itself represents an important opportunity for family ‘display’. However, owners who do not or cannot donate blood themselves describe pet blood donation as an opportunity to lessen associated feelings of guilt or obligation through ‘doing good by proxy’. These findings raise critical sociological and ethical questions concerning the risks and benefits of donation, and for how we understand third‐party decision making. Finally, the article argues for the close entanglement of human and animal health, and concludes that sociologists of health and medicine should explore the radical possibility that decision‐making in healthcare more generally might be influenced by experiences at the veterinary clinic, and vice versa. (A Virtual Abstract of this paper can be viewed at: https://www.youtube.com/channel/UC_979cmCmR9rLrKuD7z0ycA)
Offspring birthweight by gestational age and parental cardiovascular mortality: a population‐based cohort study
Authors: Morken N‐H , Halland F , DeRoo LA , Wilcox AJ , Skjærven R 
Published: February 2017

ObjectiveTo estimate risk of parental cardiovascular disease mortality by offspring birthweight.DesignPopulation‐based cohort study.Setting and populationNorwegian mothers and fathers with singleton births during 1967–2002 were followed until 2009 by linkage to the Norwegian cause of death registry.MethodsHazard ratios by offspring absolute birthweight in grams and birthweight adjusted for gestational age (z‐score) were calculated using Cox regression and adjusted for parental age at delivery and year of first birth. Stratified analyses on preterm and term births were performed.Main outcome measuresMaternal and paternal cardiovascular mortality.ResultsWe followed 711 726 mothers and 700 212 fathers and found a strong link between maternal cardiovascular mortality and offspring birthweight but only slight evidence of associations in fathers. Adjusting birthweight for gestational age (by z‐score) uncovered an unexpected strong association of large birthweight (z‐score > 2.5) with mothers’ cardiovascular mortality (hazard ratio 3.0, 95% CI 2.0–4.6). This risk was apparently restricted to preterm births. In stratified analyses (preterm and term births) hazard ratios for maternal cardiovascular mortality were 1.5 (1.03–2.2) for large preterm babies and 0.9 (0.7–1.2) for large term babies (P‐value for interaction = 0.02), using normal weight preterm and term, respectively, as references.ConclusionWomen having large preterm babies are at increased risk of both diabetes and cardiovascular mortality. The birth of a large preterm baby should increase clinical vigilance for onset of diabetes and other cardiovascular disease risk factors.Tweetable abstractBirth of a large preterm baby should increase vigilance for cardiovascular‐disease risk factors.
Polysaccharides L900/2 and L900/3 isolated from Lactobacillus rhamnosus LOCK 0900 modulate allergic sensitization to ovalbumin in a mouse model
Authors: Górska Sabina , Schwarzer Martin , Srutkova Dagmar , Hermanova Petra , Brzozowska Ewa , Kozakova Hana , Gamian Andrzej 
Published: February 2017

SummaryHere, we compared the abilities of polysaccharides L900/2 and L900/3, which were previously isolated from Lactobacillus rhamnosus LOCK 0900, to modulate the immune response to bystander antigens in a mouse model of ovalbumin (OVA) sensitization. In vivo, both polysaccharides reduced the levels of OVA‐specific IgE, IgE‐dependent basophil degranulation and IgG2a antibodies, but had no effect on the levels of OVA‐specific IgA or IgG1. Interestingly, both polysaccharides triggered recall cellular responses with distinct properties. L900/3 significantly suppressed the OVA‐induced upregulations of IL‐4, IL‐5, IL‐10 and IL‐13 in re‐stimulated spleen cells and mesenteric lymph nodes. Our findings support and expand on our previous in vitro studies by demonstrating that polymer L900/3 might modulate the Th1/Th2 balance and could be a promising candidate molecule for preventing allergic sensitization.
Anaesthetic hypersensitivity reactions in France between 2011 and 2012: the 10th GERAP epidemiologic survey
Authors: Tacquard C. , Collange O. , Gomis P. , Malinovsky J.‐M. , Petitpain N. , Demoly P. , Nicoll S. , Mertes P. M. 
Published: February 2017

BackgroundImmediate hypersensitivity reactions during anaesthesia are rare but potentially life‐threatening. The epidemiology changes with time and evolving professional practice, and hence needs to be monitored. Our objective was to follow this epidemiology.MethodsThis was a retrospective, observational study in French hospital clinics, conducted by GERAP members (Groupe d’Étude des Réactions Anaphylactoïdes Périopératoires). Consecutive patients seen in allergo‐anaesthesia outpatient clinics, who had experienced a hypersensitivity reaction during anaesthesia between 1 January 2011 and 31 December 2012, were included. Demographic data, allergy history, drugs received before the reaction, symptoms of the reaction, results of blood samples (histamine, tryptase, IgE‐specific assays), and results of the allergy assessment were recorded.ResultsThe most common causes of allergic reactions were (Neuromuscular Blocking Agents) NMBAs (N = 302; 60.6%), antibiotics (N = 91, 18.2%, Cephalosporin N = 49, 10%) and dyes (N = 27; 5.4%). Latex as an allergic agent was involved in 26 cases (5.2%), hypnotics in 11 cases (2.2%) and opioids in seven cases (1.4%). Of the NMBAs, Rocuronium had the highest proportion of reactions (13.8 reactions/100,000 vials sold) followed by Suxamethonium (13.3/100,000 vials sold). Cisatracurium had the lowest proportion of reactions (0.4/100,000 vials sold). Patients were sensitized to two or more NMBAs in 48.9% of cases and without testing, cross‐sensitivity cannot be predicted.ConclusionsWhen compared with the previous GERAP studies, NMBAs are still the most frequently triggering allergens, with marked differences between individual NMBAs, but they are now followed by antibiotics (of which greater than 50% were cephalosporins) and dyes. Anaesthetists must be aware of the differences between drugs and of the pattern of emerging allergens. For the future of safe anaesthesia, allergy assessment is essential.
Myeloid‐MyD88 Contributes to Ethanol‐Induced Liver Injury in Mice Linking Hepatocellular Death to Inflammation
Authors: Zhou Hao , Yu Minja , Roychowdhury Sanjoy , Sanz‐Garcia Carlos , Pollard Katherine A. , McMullen Megan R. , Liu Xiuli , Li Xiaoxia , Nagy Laura E. 
Published: February 2017

BackgroundToll‐like receptor 4 (TLR4) is critical for ethanol (EtOH)‐induced liver injury. TLR4 signaling is mediated by 2 proximal adaptor molecules: myeloid differentiation primary response protein (MyD88) and TLR‐domain‐containing adaptor‐inducing interferon‐β (TRIF). Studies utilizing global knockouts of MyD88 and TRIF identified a predominant role for TRIF signaling in the progression of EtOH‐induced liver injury. In contrast, IL‐1 receptor, which signals solely via the MyD88 pathway, is also known to mediate EtOH‐induced liver injury. We postulated that a cell‐specific role for MyD88 in myeloid cells might explain these apparently discrepant roles of MyD88. Here we made use of myeloid‐specific MyD88‐deficient (MyD88LysM‐KO) mice generated by crossing LysM‐CRE mice with MyD88fl/fl mice to test this hypothesis.MethodsMyD88LysM‐KO and littermate controls were fed a Lieber–DeCarli EtOH‐containing diet or pair‐fed control diets for 25 days.ResultsLittermate control, but not MyD88LysM‐KO, mice developed early stages of EtOH‐induced liver injury including elevated plasma alanine aminotransferase and increased hepatic triglycerides. Lobular inflammation and expression of pro‐inflammatory cytokines/chemokines was increased in control but not MyD88LysM‐KO. Further, EtOH‐induced inflammasome activation, indicated by the presence of cleaved caspase‐1 and mature IL‐1β protein, was also ameliorated in livers of MyD88LysM‐KO mice. In contrast, chronic EtOH‐induced apoptosis, assessed via TUNEL staining, was independent of myeloid‐MyD88 expression.ConclusionsCollectively, these data demonstrate a cell‐specific role for MyD88 in the development of chronic EtOH‐induced liver injury. While MyD88LysM‐KO still exhibited hepatocellular apoptosis in response to chronic EtOH, the absence of MyD88 on myeloid cells prevented the development of hepatic steatosis and inflammation.