bluuebunny/crossref_metadata_2025_split huggingface dataset:
Baseline mutation profiling of 1134 samples of circulating cell-free DNA and blood cells from healthy individuals
Authors: Xia Ligang , Li Zhoufang , Zhou Bo , Tian Geng , Zeng Lidong , Dai Hongyu , Deng Fang , Xie Yuancai , Lu Shixin , Li Xiaohua , Liu Chaoyu , Huang Weiren , He Jiankui 
Published: November 2016

AbstractThe molecular alteration in circulating cell-free DNA (cfDNA) in plasma can reflect the status of the human body in a timely manner. Hence, cfDNA has emerged as important biomarkers in clinical diagnostics, particularly in cancer. However, somatic mutations are also commonly found in healthy individuals, which extensively interfere with the diagnostic results in cancer. This study was designed to examine the background somatic mutations in white blood cells (WBC) and cfDNA for healthy controls based on the sequencing data from 1134 samples, to understand the patterns and origin of mutations detected in cfDNA. We determined the mutation frequencies in both the WBC and cfDNA groups of the samples by a panel of 50 cancer-associated genes which covered 20K nucleotide regions using ultra-deep sequencing with average depth >40000 folds. Our results showed that most of mutations in cfDNA originated from WBC. We also observed that NPM1 gene was the most frequently mutant gene in both WBC and cfDNA. Our study highlighted the importance of sequencing both cfDNA and WBC, to improve the sensitivity and accuracy for calling cancer-related mutations from circulating tumor DNA, and shielded light on developing the early cancer diagnosis by cfDNA sequencing.
An interaction map of circulating metabolites, immune gene networks and their genetic regulation
Authors: Nath Artika P. , Ritchie Scott C. , Byars Sean G. , Fearnley Liam G. , Havulinna Aki S. , Joensuu Anni , Kangas Antti J. , Soininen Pasi , Wennerström Annika , Milani Lili , Metspalu Andres , Männistö Satu , Würtz Peter , Kettunen Johannes , Raitoharju Emma , Kähönen Mika , Juonala Markus , Palotie Aarno , Ala-Korpela Mika , Ripatti Samuli , Lehtimäki Terho , Abraham Gad , Raitakari Olli , Salomaa Veikko , Perola Markus , Inouye Michael 
Published: November 2016

AbstractThe interaction between metabolism and the immune system plays a central role in many cardiometabolic diseases. We integrated blood transcriptomic, metabolomic, and genomic profiles from two population-based cohorts, including a subset with 7-year follow-up sampling. We identified topologically robust gene networks enriched for diverse immune functions including cytotoxicity, viral response, B cell, platelet, neutrophil, and mast cell/basophil activity. These immune gene modules showed complex patterns of association with 158 circulating metabolites, including lipoprotein subclasses, lipids, fatty acids, amino acids, and CRP. Genome-wide scans for module expression quantitative trait loci (mQTLs) revealed five modules with mQTLs of bothcisandtranseffects. The strongest mQTL was inARHGEF3(rs1354034) and affected a module enriched for platelet function. Mast cell/basophil and neutrophil function modules maintained their metabolite associations during 7-year follow-up, while our strongest mQTL inARHGEF3also displayed clear temporal stability. This study provides a detailed map of natural variation at the blood immuno-metabolic interface and its genetic basis, and facilitates subsequent studies to explain inter-individual variation in cardiometabolic disease.
Metabolome Identification by Systematic Stable Isotope Labeling Experiments and False Discovery Analysis with a Target-Decoy Strategy
Authors: Jones Drew R. , Wang Xusheng , Shaw Tim , Cho Ji-Hoon , Chen Ping-Chung , Dey Kaushik Kumar , Zhou Suiping , Li Yuxin , Kim Nam Chul , Taylor J. Paul , Kolli Udhghatri , Li Jiaxu , Peng Junmin 
Published: November 2016

ABSTRACTWe introduce a formula-based strategy and algorithm (JUMPm) for global metabolite identification and false discovery analysis in untargeted mass spectrometry-based metabolomics. JUMPm determines the chemical formulas of metabolites from unlabeled and stable-isotope labeled metabolome data, and derives the most likely metabolite identity by searching structure databases. JUMPm also estimates the false discovery rate (FDR) with a target-decoy strategy based on the octet rule of chemistry. With systematic stable isotope labeling of yeast, we identified 2,085 chemical formulas (10% FDR), 892 of which were assigned with metabolite structures. We evaluated JUMPm with a library of synthetic standards, and found that 96% of the formulas were correctly identified. We extended the method to mammalian cells with direct isotope labeling and by heavy yeast spike-in. This strategy and algorithm provide a powerful a practical solution for global identification of metabolites with a critical measure of confidence.
Structural and Functional Characterization of the Alanine Racemase fromStreptomyces coelicolorA3(2)
Authors: Tassoni Raffaella , van der Aart L.T. , Ubbink M. , Van Wezel G. P. , Pannu N. S. 
Published: November 2016

AbstractThe conversion of L-alanine (L-Ala) into D-alanine (D-Ala) in bacteria is performed by pyridoxal phosphate-dependent enzymes called alanine racemases. D-Ala is an essential component of the bacterial peptidoglycan and hence required for survival. The Gram-positive bacteriumStreptomyces coelicolorhas at least one alanine racemase encoded byalr. Here, we describe analrdeletion mutant of S.coelicolorwhich depends on D-Ala for growth and shows increased sensitivity to the antibiotic D-cycloserine (DCS). The crystal structure of the alanine racemase (Alr) was solved with and without the inhibitors DCS or propionate, at 1.64 Å and 1.51 Å resolution, respectively. The crystal structures revealed that Alr is a homodimer with residues from both monomers contributing to the active site. The dimeric state of the enzyme in solution was confirmed by gel filtration chromatography, with and without L-Ala or D-cycloserine. Specificity of the enzyme was 66 +/− 3 U mg−1for the racemization of L-to D-Ala, and 104 +/− 7 U mg−1for the opposite direction. Comparison of Alr from S.coelicolorwith orthologous enzymes from other bacteria, including the closely related D-cycloserine-resistant Alr from S.lavendulae, strongly suggests that structural features such as the hinge angle or the surface area between the monomers do not contribute to D-cycloserine resistance, and the molecular basis for resistance therefore remains elusive.
Evaluation of quantum dot conjugated antibodies for immunofluorescent labelling of cellular targets
Authors: Francis Jennifer E. , Mason David , Lévy Raphaël 
Published: November 2016

AbstractSemiconductor quantum dots (Qdots) have been utilised as probes in fluorescent microscopy and provide an alternative to fluorescent dyes and fluorescent proteins, due to their brightness, photostability, and the possibility to excite different Qdots with a single wavelength. In spite of these attractive properties, their take up by biologists has been somewhat limited and only a few Qdot conjugates are commercially available for the labelling of cellular targets. Although, many protocols have been reported for the specific labelling of proteins with Qdots, the majority of these relied on Qdot-conjugated antibodies synthesised specifically by the authors and therefore not broadly available, which limits the scope of applications and complicates replication. Here, the specificity of a commercially available Qdot conjugated secondary antibody (Qdot-Ab), for different antigens, was tested. Antigens were labelled simultaneously with a fluorescent dye coupled to a secondary antibody (Dye-Ab) and the Qdot-Ab. Although, the Dye-Ab labelled all of the intended target proteins, the Qdot-Ab only bound to some of the protein targets in the cytosol and could not reach the nucleus even after extensive cell permeabilisation.
The impact of advertising on children’s psychological wellbeing and life satisfaction
Authors: Opree Suzanna J. , Buijzen Moniek , van Reijmersdal Eva A. 
Published: November 2016

Purpose
It is generally believed that children’s advertising exposure decreases life satisfaction. This paper aims to investigate whether and how it does by examining the relation between advertising exposure and life satisfaction (Aim 1), as well as the mediating roles of psychological wellbeing (Aim 2) and its underlying dimensions (Aim 3).

Design/methodology/approach
Three-wave panel data were collected among 1,133 8-12-year-olds. Psychological wellbeing was measured overall and per dimension (i.e. environmental mastery, personal growth, purpose in life, self-acceptance, autonomy and positive relationships with others).

Findings
The authors found a nonsignificant total effect of advertising exposure at Wave 1 on life satisfaction at Wave 3: The negative direct effect was annulled by the positive indirect effect via overall psychological wellbeing at Wave 2. Detailed analysis revealed that personal growth and autonomy functioned as positive mediators, and purpose in life as a negative mediator in the relation between advertising exposure and life satisfaction.

Social implications
This research informs the ethical debate surrounding child-directed advertising, showing it might stimulate children’s sense of control over their environment, openness to new experiences, direction in life and sense of self-agency.

Originality/value
This study is the first to examine advertising’s effect on life satisfaction and psychological wellbeing simultaneously. The study used a large sample and a longitudinal panel design, allowing conclusions about the specific effects of advertising exposure.
Brickbats and bouquets for marketing
Authors: Kitchen Philip J. , Sheth Jagdish N. 
Published: November 2016

Purpose
The purpose of this paper is to consider the development and application of marketing theory and practice over time and its current status. The terms “brickbats” and “bouquets” are used as metaphors to extend praise or criticism for marketing. In doing so, the authors draw upon the views of leading theorists over time and apply these in the current environmental context.

Design/methodology/approach
The approach adopted is discursive, critical and conceptual.

Findings
Following literature review, and drawing upon current examples, marketing as a discipline is subject to both kudos and criticisms. Nonetheless, it is concluded optimistically in that marketing can be an even greater source for societal good. That “goodness” is partly based upon the added impetus of social media adoption and use by consumers, the need for growth and accelerative innovation in the digital age coupled with the democratisation of consumption. Nonetheless, the authors offer the caveat that free competitive markets lead to market failures, and the need for market regulation by governments is becoming more evident.

Research limitations/implications
The implications of the paper are profound. Academics should be concerned in and involved with marketing theory. Questions need to be raised concerning non-robust definitions of marketing and its application. The authors wait for a consumer-led approach to marketing to add depth to the marketing theory.

Practical implications
Marketers need to be made more accountable for their actions. Consumers need to become part of the marketing process. Marketing claims need to be verified by delivered benefits. Companies need to take steps to ensure that the marketing process does not end at purchase. Satisfaction needs to be made manifest. Likewise, dissatisfactions need to be managed well as part of the marketing process.

Social implications
Too much marketing currently is relatively unregulated in the sense that there are so few opportunities to evade its myriad reach and – despite social media – little chance of changing marketing practice for the good of societies. Many criticisms of marketing practice are not being addressed in the literature.

Originality/value
Marketing is a vibrant force in all nations and markets. It is deeply rooted in business practice. It is contemporaneous and relevant. It is global and national. But, it is not entirely all good news. There are caveats and criticisms as well as kudos and praise. While both are addressed here, the topic needs to be considered for marketing and its accompanying theory and practice to change.
Supply chain quality management: an empirical study
Authors: Zhong Jianlan , Ma Yizhong , Tu Yiliu , Li Xia 
Published: November 2016

PurposeThis paper aims to focus on supply chain quality (SCQ) in the hospitality industry in China, and to stress the importance of the synergy of quality management (QM) and supply chain management (SCM). The authors have investigated the relationship among QM practices, SCM practices, SCQ and hotel performance, and examined the effect of contextual variables.Design/methodology/approachThis study mainly uses a questionnaire survey to collect data relating to the research hypotheses. Structural equation model technique is suited for our research purposes, and the LISREL software is implemented to test the conceptual model.FindingsThe results show that QM practices and SCM practices are significantly correlated. QM practices/SCM practices are positively related to SCQ, and consequently influence hotel performance. SCQ has the mediating effect between QM/SCM practices and hotel performance. Contextual variables truly play a moderator between QM/SCM practices and SCQ.Research limitations/implicationsHotel managers should look beyond their own hotels into supply chain to manage quality, highlight the importance of interdepartmental or external (i.e. customers or suppliers) connectedness, such as building close and long-term relationships with well-chosen suppliers, encouraging customer involvement and establishing an effective interface for accumulating information regarding customers’ needs and feedback. Hotel managers are also able to realize the influence of contextual variables (e.g. the new normal state of the Chinese economy), and further to gain chance of hotel’s survival.Originality/valueThis study focuses on SCQ and tries to fill a gap in the exiting literature on SCQ management in hospitality industry.
The best match-up of airline advertising endorsement and flight safety message
Authors: Kim Seongseop (Sam) , Wang Kuo-Ching , Jhu Wan-Ting , Gao Yang (Young) 
Published: November 2016

PurposeThis paper aims to explore the effectiveness of children as advertisement endorsers in the airline context, including images of safety and reliability.Design/methodology/approachThis paper is intended to examine the advertising effect of endorsers (celebrities, CEOs, experts, consumers and children) in the context of the airline industry. A factorial experiment was conducted to test the communication effect (CE) of ten groups of advertisement combinations (five endorser types – with/without safety attribute).FindingsThe results indicate that a child endorser yielded a better CE than celebrity, CEO or typical consumer endorsers. Second, advertisements that emphasized safety had better CE than those without this emphasis. The group combining children and safety generated a better CE than most of the other groups comprising different combinations.Practical implicationsA child endorser and a safety message are recommended to be used in advertisements for airlines because flight passengers place importance on safety. Fragile image of child reinforces safety of an airline.Originality/valueThe integration of advertising endorsement and message into a conceptual model allows the current results to provide meaningful theoretical and practical implications.
Psychological diversity climate: justice, racioethnic minority status and job satisfaction
Authors: Madera Juan M. , Dawson Mary , Guchait Priyanko 
Published: November 2016

Purpose
The purpose of this paper was to develop and test a model examining how hotel managers’ psychological diversity climate affects job satisfaction, the moderating effect of racioethnic minority status and the mediating role of organizational justice.

Design/methodology/approach
A sample of frontline managers from 164 individual hotel properties was used. Hierarchical linear regression analysis was used to examine the underlying mechanism through which psychological diversity climate impacts job satisfaction.

Findings
The results found support for the mediating effect of organizational justice between managers’ psychological diversity climate and job satisfaction. Racioethnic identity moderated the relationship between psychological diversity climate and organizational justice, thereby supporting the mediated-moderated model proposed in the current research.

Practical implications
The findings show the importance of improving employee perceptions of diversity climate and organizational justice, particularly through recruitment practices, incorporating diversity into the corporate values, adopting formal diversity management practices and educating managers about the importance of diversity through formal training methods.

Originality/value
Little research has examined the underlying mechanisms that explain why psychological diversity climate affects organizational attitudes. Even less research has examined whether the link between a perceived positive diversity climate and job satisfaction is stronger for racioethnic minorities. These results provide meaningful insights for researchers because the hospitality industry is one of the largest employers of racioethnic minorities and immigrant employees.
See no evil, hear no evil, speak no evil? Underreporting of abuse in care homes
Authors: Moore Steve 
Published: November 2016

PurposeThe purpose of this paper is to present some of the findings from an empirical, mixed methods research project that reveal underreporting and active concealment of abuse in private sector care homes.Design/methodology/approachSemi-structured interviews were undertaken with 36 care home personnel. An anonymously completed questionnaire was also used concurrently among newly appointed staff in newly opened care homes, to elicit additional quantitative and qualitative data.FindingsA significant number of respondents reported awareness of acts of abuse that had not been reported within the care home or externally to the authorities. Some respondents were aware that where occurrences of abuse had been reported, no subsequent action was taken, and external authorities were not always involved in responses to abuse. A significant number of respondents were aware of deliberate strategies used to deter reports of abuse to external agencies.Research limitations/implicationsThough the research draws upon the experiences of only 36 care home personnel through interviews, and 94 questionnaire respondents who had witnessed occurrences of abuse, data suggest that a significant proportion of abuse in care homes remains unreported.Originality/valueThe research has revealed staffs’ experiences of underreporting of abuse in private sector care homes. Findings indicate that changes are required to current methods of scrutiny of occurrences of abuse in care homes and the strengthening of incentives to report it.
Innovative financial intermediation and long term capital pools for infrastructure
Authors: Annamalai Thillai Rajan , Hari Smitha 
Published: November 2016

Purpose
Developing countries are increasingly looking to private sector investment for infrastructure development. Successful development of private infrastructure projects, however, depends on adequate availability of long-term debt to complement private sector equity. As domestic bond markets in many emerging countries are not very deep, availability of long-term debt funding for infrastructure has been limited. Recently, a new form of financial intermediation has emerged in India with the creation of infrastructure debt funds (IDFs) to create capital pools for long-term debt funding. This paper aims to analyse the effectiveness of IDFs for financing infrastructure projects.

Design/methodology/approach
This paper uses a case study approach. The case studies were written using both secondary and primary information. Secondary information was obtained from various sources such as policy papers, websites and other published sources. Primary information was obtained from interviews with the top management of three IDFs. Information obtained from multiple sources was triangulated for consistency and correctness.

Findings
IDFs have emerged as an effective intermediation mechanism for attracting long-term capital by offering a new investment product with appropriate risk-adjusted returns. For the fund seekers, IDFs are able to provide long-term capital at lower rates and higher flexibility. Unlike commercial banks, IDFs are able to add value to the projects apart from funding by periodic monitoring of the projects.

Practical implications
Creating new forms of financial intermediation can help in reducing the financing gap for infrastructure projects, especially in emerging countries.

Originality/value
IDFs have been analysed from a perspective of financial intermediation. The effectiveness of IDFs in bridging the funding shortfall has been evaluated from multiple perspectives.
SEC targets broker-dealer implications of transaction-based deal fees
Authors: Daniel Jason 
Published: November 2016

Purpose
To explain a US Securities and Exchange Commission (SEC) enforcement action against a registered investment adviser to private equity funds for allegedly providing brokerage services in connection with the acquisition and disposition of the securities of portfolio companies while not being registered as a broker dealer, making undisclosed use of fund assets, and failing to adopt policies and procedures designed to prevent the alleged violations.

Design/methodology/approach
Describes the services provided by the investment adviser, the compensation paid, and the SEC’s other bases for enforcement, and draws conclusions for private equity fund advisers.

Findings
The SEC has begun pursuing transaction-based compensation paid to private equity fund advisers relating to portfolio company transactions as illegal brokerage commissions. The Commission also continues to target the adviser’s undisclosed use of client fund capital, especially in private equity funds.

Originality/value
Practical explanation by experienced investment management lawyer.
Who is the “reasonable investor”?
Authors: Tuttle Jonathan R. , Kaplan Matthew E. , Pedersen Benjamin R. 
Published: November 2016

Purpose
To discuss how two recent court decisions applied the materiality standard concerning information disclosed to investors and the definition of a “reasonable investor”.

Design/methodology/approach
Explains the origins and evolution of the materiality standard and the “reasonable investor” paradigm, discusses the difficulty in applying the materiality standard in the absence of a clear definition of the “reasonable investor”, and addresses potential implications of two 2016 cases, Flannery v. SEC and United States v. Litvak, on whether materiality should be applied on a subjective, rather than objective, basis and evidentiary burdens in proving materiality.

Findings
Flannery and Litvak suggest that, in assessing what information is material to a “reasonable investor”, courts may place increasing weight on the relative sophistication of investors, the types of securities and the nature of the markets in which they are investing, and types of information investors in those securities and markets typically consider to be material.

Originality/value
Informed analysis by experienced practitioners in capital markets, financial services and securities litigation.