bluuebunny/crossref_metadata_2025_split huggingface dataset:
propr: An R-package for Identifying Proportionally Abundant Features Using Compositional Data Analysis
Authors: Quinn Thomas , Richardson Mark F. , Lovell David , Crowley Tamsyn 
Published: February 2017

AbstractIn the life sciences, many assays measure only the relative abundances of components for each sample. These data, called compositional data, require special handling in order to avoid misleading conclusions. For example, in the case of correlation, treating relative data like absolute data can lead to the discovery of falsely positive associations. Recently, researchers have proposed proportionality as a valid alternative to correlation for calculating pairwise association in relative data. Although the question of how to best measure proportionality remains open, we present here a computationally efficient R package that implements two proposed measures of proportionality. In an effort to advance the understanding and application of proportionality analysis, we review the mathematics behind proportionality, demonstrate its application to genomic data, and discuss some ongoing challenges in the analysis of relative abundance data.
SvABA: Genome-wide detection of structural variants and indels by local assembly
Authors: Wala Jeremiah , Bandopadhayay Pratiti , Greenwald Noah , O’Rourke Ryan , Sharpe Ted , Stewart Chip , Schumacher Steve , Li Yilong , Weischenfeldt Joachim , Yao Xiaotong , Nusbaum Chad , Campbell Peter , Meyerson Matthew , Zhang Cheng-Zhong , Imielinski Marcin , Beroukhim Rameen 
Published: February 2017

AbstractStructural variants (SVs), including small insertion and deletion variants (indels), are challenging to detect through standard alignment-based variant calling methods. Sequence assembly offers a powerful approach to identifying SVs, but is difficult to apply at-scale genome-wide for SV detection due to its computational complexity and the difficulty of extracting SVs from assembly contigs. We describe SvABA, an efficient and accurate method for detecting SVs from short-read sequencing data using genome-wide local assembly with low memory and computing requirements. We evaluated SvABA’s performance on the NA12878 human genome and in simulated and real cancer genomes. SvABA demonstrates superior sensitivity and specificity across a large spectrum of SVs, and substantially improved detection performance for variants in the 20-300 bp range, compared with existing methods. SvABA also identifies complex somatic rearrangements with chains of short (< 1,000 bp) templated-sequence insertions copied from distant genomic regions. We applied SvABA to 344 cancer genomes from 11 cancer types, and found that templated-sequence insertions occur in ~4% of all somatic rearrangements. Finally, we demonstrate that SvABA can identify sites of viral integration and cancer driver alterations containing medium-sized SVs.
Effects of Historical Coinfection on Host Shift Abilities of Exploitative and Competitive Viruses
Authors: Singhal Sonia , Turner Paul E. 
Published: February 2017

AbstractRapid evolution contributes to frequent emergence of RNA viral pathogens on novel hosts. However, accurately predicting which viral genotypes will emerge has been elusive. Prior work with lytic RNA bacteriophage f6 (family Cystoviridae) suggested that evolution under low multiplicity of infection (MOI; proportion of viruses to susceptible cells) selected for greater host exploitation, while evolution under high MOI selected for better intracellular competition against co-infecting viruses. We predicted that phage genotypes that experienced 300 generations of low MOI ecological history would be relatively advantaged in growth on two novel hosts. We inferred viral growth through changes in host population density, specifically by analyzing five attributes of growth curves of infected bacteria. Despite equivalent growth of evolved viruses on the original host, low MOI evolved clones were generally advantaged relative to high MOI clones in exploiting novel hosts. We also observed genotype-specific differences in clone infectivity: High fitness genotypes on the original host also performed better on novel hosts. Our results indicated that traits allowing greater exploitation of the original host correlated positively with performance on novel hosts. Based on infectivity differences of viruses from high versus low MOI histories, we suggest that prior MOI selection can later affect emergence potential.
Alcatel-Lucent falls, Huawei ascends: new product development makes the difference
Authors: Yan Jie , Wang Le , Xiong Jie 
Published: February 2017

PurposeThis study aims to use the new product development (NPD) perspective to understand why traditional leading telecom equipment companies, such as Alcatel-Lucent (ALu), have stagnated but the newcomer Huawei has achieved steady growth.Design/methodology/approachThis paper takes the form of a comparative case study.FindingsThree significant differences in NPD process between the companies were discovered: first, although both companies claim that they are market-oriented, Huawei’s NPD projects are customer-driven, and ALu projects are joint considerations of customer demand and technology leadership; second, Huawei uses a design-to-value strategy, and ALu applies a design-for-quality-premium strategy; third, resources are allocated and shared at the corporate level in Huawei and at the business division level in ALu.Practical implicationsThis study offers several implications for NPD managers. First, holding a market leader position is more important than being a technology leader. Companies must fundamentally change their mind-sets, restructure NPD models and prioritize and empower marketing and sales departments in the decision-making and management of NPD projects. Second, to maximize customer value, managers must balance cost and quality and avoid overengineering. A quality premium no longer necessarily leads to product competitiveness. Third, to improve the efficiency of NPD performance, companies must build up a mechanism to enable across-boundary resources.Originality/valueThis study highlights a number of key NPD strategy issues. It was conducted in the telecom equipment industry, but NPD managers of other industries will also gain useful insights from the discussion.
Tax havens: conduits for corporate tax malfeasance
Authors: Jalan Akanksha , Vaidyanathan R. 
Published: February 2017

Purpose
This paper is an effort to demystify tax havens – what they mean, what they offer and why they are harmful. It offers a detailed analysis of abusive tax planning by multinational corporations, involving the use of tax havens, shedding light on how corporations use “egregious” tax-sheltering techniques right from their incorporation to avoid payment of income taxes. The paper also discusses global efforts against the phenomenon and policy recommendations.

Design/methodology/approach
The paper brings together definitions from various sources to accurately define and identify tax haven economies. The key contribution of the paper is to diagrammatically explain the use of tax havens by MNCs right from the time they are incorporated. It explains how every big and small corporate decision is motivated by the desire to save taxes and how tax havens come in handy for such corporations.

Findings
This paper finds that base erosion and profit shifting (BEPS) is a pervasive phenomenon, largely due to the suppliers of tax haven operations. Here, corporate decisions are divided into strategic and operational and further subdivided into investing, operating and financing activities, and provide real-life corporate examples of how tax havens fit into almost every corporate decision. This is the key contribution of the paper.

Research limitations/implications
This is a review paper that sums up knowledge about tax havens and their use by MNCs. It does not, however, use empirical data to corroborate its findings. It would be interesting to see empirically whether MNCs with greater tax haven operations actually have lower effective tax rates.

Practical implications
The paper can provide a framework for designing tax policies in a manner that geographical arbitrage can be minimized. It can enable formulation of the necessary incentive structures in the form of penalties, rewards and the like for both the users and providers of tax haven services to curb massive base and profit shifting out of high-tax countries.

Social implications
The paper is one small step in the direction of bringing about equality in tax payments, i.e. to align real tax systems with the canon of equality that Adam Smith once dreamt of. Taxes should be progressive in nature, implying that the amount of taxes paid should increase with one’s income. However, with the advent of offshore financial centres and egregious tax planning techniques, only the smaller corporations and middle-class individuals end up paying taxes, while the rich and bigger corporations get away easily.

Originality/value
The paper explores in detail the manner in which MNCs use, rather exploit, regulatory loopholes in tax systems of different countries to save on tax payments. By shifting their tax base from one country to another, MNCs not only hamper Treasury collections but also breed disrespect for the global tax system. The paper can help in designing tax laws in tune with such corporate motives.
Prospects of an online dispute resolution framework for Islamic Banks in Malaysia
Authors: Oseni Umar A. , Omoola Sodiq O. 
Published: February 2017

PurposeThis study aims to examine the prospects of using an online dispute resolution (ODR) platform for resolving relevant Islamic banking disputes in the usual banker–customer relationship in Malaysia. It is argued that through proper regulation, such innovative dispute management mechanism would not only address some legal risks associated with banking disputes but could also prevent reputational risks in the Islamic financial services industry.Design/methodology/approachBased on an internet survey, responses were obtained from about 109 respondents in Malaysia. The data obtained were subjected to multivariate statistical analyses considering factors such as access to justice, attitude of stakeholders, resolving disputes, practical issues and understanding of ODR.FindingsThe results obtained showed that “access to justice”, “attitude of stakeholders” and “resolving disputes” are the most influencing factors affecting the intention to use ODR among stakeholders, particularly customers and bankers in the Islamic financial services industry in Malaysia.Practical implicationsThis study provides a way in which the recently introduced Islamic Financial Services (Financial Ombudsman Scheme) Regulations 2015 can be better enhanced to cater for internet banking disputes which might require an ODR framework.Originality/valueThough there have been numerous studies on the dispute resolution framework in the Islamic banking industry in Malaysia generally, the current study focuses on a less explored framework – ODR– a new framework for handling banking disputes.
Correlation of colour, antioxidant capacity and phytochemical diversity of imported saffron by principal components analysis
Authors: Anuar Nordiyanah , Taha R.M. , Mahmad Noraini , Mohajer Sadegh , Che Musa Siti Aisha Na’illa , Zainal Abidin Zul Hazrin 
Published: February 2017

Purpose
The aim of the present study is to gain correlation between saffron colours, their antioxidant capacity and the constituents of the secondary metabolites of three different saffron samples commonly available in the Malaysian market.

Design/methodology/approach
In this study, saffron samples imported from Iran, Spain and Kashmir were extracted using methanol and the total antioxidant capacity were analysed using 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radical-scavenging assay. Ultra-high performance liquid chromatography (UHPLC) and electrospray ionization coupled with mass spectrometry (ESI-MS/MS) were then used to identify secondary metabolites present in the saffron crude extracts. The colour variation of the saffron extract was expressed by the CIELAB colorimeter in terms of lightness (L*), greenness (a*), yellowness (b*), chroma (C) and hue angle (H°). Principle component analysis (PCA) was carried out to analyse the similarities and correlation between variables.

Findings
This study reveals that antioxidant has a positive correlation with flavanols, especially quercetin and kaempferol. In addition, colour appearance is not necessarily an indicator for the antioxidant level.

Research limitations/implications
The major classes of polyphenolics identified in saffron methanolic crude extract are flavonoids and phenolic acids. Further improvements in the extraction and identification methods may find other compounds that could attribute to the visual factors and antioxidant capacity as a complement for this preliminary study.

Practical implications
This analysis provides comparison basis and valuable information for saffron consumers in Malaysia depending on the consumers’ purpose of whether to have a certain desired colour or health benefits.

Originality/value
A comparative study about saffron product available in Malaysian market is original. To the best of the authors’ knowledge, this is the first attempt of evaluation on a saffron product that has been carried out in Malaysia.
Influence of acid hydrolysis on properties of maize starch adhesive
Authors: Qiao Zhibang , Lv Shanshan , Gu Jiyou , Tan Haiyan , Shi Junyou , Zhang Yanhua 
Published: February 2017

Purpose
The purpose of this paper is to obtain high-solids-content and low-viscosity starch adhesive, and improve bonding strength of the pure starch adhesive.

Design/methodology/approach
Maize starch was treated by hydrochloric acid solution with different concentrations, and acid-thinned starch adhesive was prepared. Polyisocyanate as a crosslinking agent was added to improve water resistance of the pure starch adhesive.

Findings
The physical and chemical properties of the acid-thinned starch adhesive were characterised. Acid hydrolysis did not change structure of starch granules, but increased its crystallinity. After acid modification, starch granules became less smooth and some fragments appeared. Acid treatment had little influence on thermal stability of starch, when acid hydrolysis was not strong. High concentration of HCl solution led to starch granules being destroyed, resulting in decrease in bonding strength. The optimal HCl concentration was 0.5 mol/L. Polyisocyanate addition was beneficial to improve the bonding strength of the acid-thinned starch adhesive.

Research limitations/implications
Acid hydrolysis changed the properties of the starch adhesive.

Practical implications
Acid hydrolysis decreased viscosity of the starch adhesive and improved its solids content, which had a positive effect on the application of the starch adhesive.

Social implications
It was helpful to develop an environment-friendly, natural polymer-based wood adhesive.

Originality/value
The properties of acid-thinned starch and acid-thinned starch adhesive were studied.
A study on mechanical, thermal and flame retardant properties of epoxy/expandable graphite composites
Authors: Mamani Arezoo , Ebrahimi Morteza , Ataeefard Maryam 
Published: February 2017

Purpose
The purpose of this paper is to investigate the effect of expandable graphite (EG) plates’ incorporation on the mechanical, thermal and fire-retardant properties of an epoxy–aliphatic amine system. In addition, the optimum amount of EG in epoxy/EG composites is determined to achieve the best thermal and mechanical properties at the same time.

Design/methodology/approach
The epoxy/EG composites were prepared by using (1-4) phr of EG. The morphological structure of epoxy/EG composites was studied by using scanning electron microscopy. The thermal, flame-retardant and mechanical properties of epoxy/EG composites were evaluated by using thermogravimetric analysis (TGA), oxygen index test and dynamic mechanical analysis and tensile and impact test, respectively.

Findings
TGA results showed that the incorporation of EG to the epoxy resin increased the initial decomposition temperature and residue weight of the composites. It was found that, with increasing EG concentration up to 4 phr, the oxygen index, glass transition temperature and Young’s modulus of epoxy/EG composites increased up to 60 per cent, 4.1°C and 50 per cent, respectively. On the other hand, the sample with 2 phr EG provided the maximum values of tensile strength, storage modulus, cross-linking density, ultimate tensile strain and impact strength.

Practical implications
Prepared epoxy/EG composites can be used as halogen-free flame-retardant composites. The proposed process for the preparation of the composites is simple and can easily be implicated in the industry.

Originality/value
To the best of the authors’ knowledge, there is no other publication that considers mechanical, thermal and fire-retardant properties of epoxy/EG composites in one paper. In this work, the optimum concentration of EG in epoxy/EG composites was determined, considering all these properties.
Elevated transglutaminase‐2 expression in the epidermis of psoriatic skin and its role in the skin lesion development
Authors: Su Ching‐Chyuan , Su Tzu‐Rong , Lai Ji‐Ching , Tsay Gregory‐J , Lin Hung‐Ke 
Published: February 2017

AbstractPsoriasis, an inflammatory skin disease triggered by the immune system, presents keratinocyte hyperproliferation, differentiation and angiogenesis. The role of transglutaminase‐2 (TG2) in psoriasis has not been fully established yet. In this retrospective, non‐randomized and non‐blinded study, skin biopsies were collected from 37 psoriatic patients and immunohistochemical staining was performed. TG2 staining was positive in all 37 samples, among which 32 were strong and five weak. The localization of TG2 staining was present in the epidermis and spreading from basal layer to stratum granulosum in decreasing staining intensity. However, TG2 was also expressed in the basal layer in the non‐lesional site of psoriasis and the skin of healthy people. The presence of TG2 was not associated with disease duration, stage of disease and subtype of psoriasis. Overexpression of TG2 seems to be an important role in psoriatic development.
Identification of second arginine‐glycine‐aspartic acid motif of ovine vitronectin as the complement C9 binding site and its implication in bacterial infection
Authors: Prasada Rao T. , Lakshmi Prasanth T. , Parvathy R. , Murugavel S. , Karuna Devi , Paritosh Joshi 
Published: February 2017

ABSTRACTVitronectin (Vn), a multifunctional protein of blood and extracellular matrix, interacts with complement C9. This interaction may modulate innate immunity. Details of Vn–C9 interactions are limited. Vn–C9 interactions were assessed by employing a goat homologous system and observing Vn binding to C9 in three different assays. Using recombinant fragments, C9 binding was mapped to the N‐terminus of Vn. Site directed mutagenesis was performed to alter the second arginine glycine aspartic acid (RGD) sequence (RGD‐2) of Vn. Changing R to G or D to A in RGD‐2 caused significant decrease in Vn binding to C9 whereas changing of R to G in the first RGD motif (RGD‐1) had no effect on Vn binding to C9. These results imply that the RGD‐2 of goat Vn is involved in C9 binding. In a competitive binding assay, the presence of soluble RGD peptide inhibited Vn binding to C9 whereas heparin had no effect. Vn binding to C9 was also evaluated in terms of bacterial pathogenesis. Serum dependent inhibition ofEscherichia coligrowth was significantly reverted when Vn or its N‐fragment were included in the assay. The C‐fragment, which did not support C9 binding, also partly nullified serum‐dependent inhibition of bacterial growth, probably through other serum component(s).
Gray‐matter relationships to diagnostic and transdiagnostic features of drug and behavioral addictions
Authors: Yip Sarah W. , Worhunsky Patrick D. , Xu Jiansong , Morie Kristen P. , Constable R. Todd , Malison Robert T. , Carroll Kathleen M. , Potenza Marc N. 
Published: February 2017

AbstractAlterations in neural structure have been reported in both cocaine‐use disorder and gambling disorder, separately, suggesting similarities across addiction diagnoses. Individual variation in neural structure has also been associated with impulsivity, a dimensional construct implicated in addictions. This study combines categorical (diagnosis‐based) and dimensional (transdiagnostic) approaches to identify neural structural alterations linked to addiction subtypes and trait impulsivity, respectively, across individuals with gambling disorder (n = 35), individuals with cocaine‐use disorder (n = 37) and healthy comparison individuals (n = 37). High‐resolution T1‐weighted data were analyzed using modulated voxel‐based morphometry (VBM). Statistical analyses were conducted using whole‐brain general‐linear models, corrected for family‐wise error (pFWE < .05). Categorical analyses indicated a main effect of diagnostic group on prefrontal (dorsal anterior cingulate and ventromedial prefrontal cortex) gray matter volumes (GMVs), involving decreased GMVs among cocaine‐use disorder participants only. Dimensional analyses indicated a negative association between trait impulsivity and cortical (insula) and subcortical (amygdala and hippocampus) GMVs across all participants. Conjunction analysis indicated little anatomical overlap between regions identified as differentiating diagnostic groups and regions covarying with impulsivity. These data provide first evidence of neural structural differences between gambling disorder and an illicit substance‐use disorder. They further indicate dissociable effects of diagnostic groupings and trait impulsivity on neural structure among individuals with behavioral and drug addictions. Study findings highlight the importance of considering both categorical and dimensional (e.g. Research Domain Criteria; RDoC) analysis approaches within the context of addictions research.
Electronic cigarettes and mental illness: Reviewing the evidence for help and harm among those with psychiatric and substance use disorders
Authors: Hefner Kathryn , Valentine Gerald , Sofuoglu Mehmet 
Published: February 2017

Background and ObjectivesAdults with mental illness (MI) use combustible tobacco at increased rates and have greater difficulty quitting smoking. Given the increasing popularity of electronic cigarettes (e‐cigarettes), their use by those with MI has important health implications. While preliminary evidence suggests potential benefits of e‐cigarette use for those with MI, well‐controlled, systematic research examining appeal, correlates, and consequences of e‐cigarette use in this vulnerable population is lacking. This review evaluated current knowledge of e‐cigarette use and potential for help and/or harm among adults with MI.MethodsThe search strategy resulted in k = 88 reports, of which k = 9 were deemed relevant.ResultsE‐cigarette use is prevalent among those with MI, as is concurrent use of e‐cigarettes and combustibles. E‐cigarettes appeal to those with MI as a viable alternative to combustible tobacco, and their use does not appear to exacerbate nicotine addiction or psychiatric symptoms. However, the long‐term impact of e‐cigarette use on combustible tobacco use and other health indices is largely unknown.Discussion and ConclusionsRigorous research and improved knowledge regarding risks and benefits of e‐cigarette use within this vulnerable population are needed to inform whether special consideration is warranted towards those with MI in developing tobacco control policies and health communications. Recommendations for future e‐cigarette research include improved assessment of the following: 1) psychodiagnostic variability, 2) flavor preferences, 3) the longitudinal impact on combustible tobacco use, and 4) impact of tobacco product communications.Scientific SignificanceAs with combustible cigarettes, individuals with MI may display unique e‐cigarette use patterns from that of the general population. (Am J Addict 2017;26:306–315)