bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantifying the extent to which index event biases influence large genetic association studies
Authors: Yaghootkar Hanieh , Bancks Michael P. , Jones Sam E. , McDaid Aaron , Beaumont Robin , Donnelly Louise , Wood Andrew R. , Campbell Archie , Tyrrell Jessica , Hocking Lynne J. , Tuke Marcus A. , Ruth Katherine S. , Pearson Ewan R. , Murray Anna , Freathy Rachel M. , Munroe Patricia B. , Hayward Caroline , Palmer Colin , Weedon Michael N. , Pankow James S. , Frayling Timothy M. , Kutalik Zoltán 
Published: September 2016

AbstractAs genetic association studies increase in size to 100,000s of individuals, subtle biases may influence conclusions. One possible bias is “index event bias” (IEB), also called “collider bias”, caused by the stratification by, or enrichment for, disease status when testing associations between gene variants and a disease-associated trait. We first provided a statistical framework for quantifying IEB then identified real examples of IEB in a range of study and analytical designs. We observed evidence of biased associations for some disease alleles and genetic risk scores, even in population-based studies. For example, a genetic risk score consisting of type 2 diabetes variants was associated with lower BMI in 113,203 type 2 diabetes controls from the population based UK Biobank study (−0.010 SDs BMI per allele, P=5E-4), entirely driven by IEB. Three of 11 individual type 2 diabetes risk alleles, and 10 of 25 hypertension alleles were associated with lower BMI at p<0.05 in UK Biobank when analyzing disease free individuals only, of which six hypertension alleles remained associated at p<0.05 after correction for IEB. Our analysis suggested that the associations betweenCCND2andTCF7L2diabetes risk alleles and BMI could (at least partially) be explained by IEB. Variants remaining associated after correction may be pleiotropic and include those inCYP17A1(allele associated with hypertension risk and lower BMI). In conclusion, IEB may result in false positive or negative associations in very large studies stratified or strongly enriched for/against disease cases.
Annotation and differential analysis of alternative splicing usingde novoassembly of RNAseq data
Authors: Benoit-Pilven Clara , Marchet Camille , Chautard Emilie , Lima Leandro , Lambert Marie-Pierre , Sacomoto Gustavo , Rey Amandine , Bourgeois Cyril , Auboeuf Didier , Lacroix Vincent 
Published: September 2016

AbstractGenome-wide analyses reveal that more than 90% of multi exonic human genes produce at least two transcripts through alternative splicing (AS). Various bioinformatics methods are available to analyze AS from RNAseq data. Most methods start by mapping the reads to an annotated reference genome, but some start by ade novoassembly of the reads. In this paper, we present a systematic comparison of a mapping-first approach (FaRLine) and an assembly-first approach (KisSplice). These two approaches are event-based, as they focus on the regions of the transcripts that vary in their exon content. We applied these methods to an RNAseq dataset from a neuroblastoma SK-N-SH cell line (ENCODE) differentiated or not using retinoic acid. We found that the predictions of the two pipelines overlapped (70% of exon skipping events were common), but with noticeable differences. The assembly-first approach allowed to find more novel variants, including novel unannotated exons and splice sites. It also predicted AS in families of paralog genes. The mapping-first approach allowed to find more lowly expressed splicing variants, and was better in predicting exons overlapping repeated elements. This work demonstrates that annotating AS with a single approach leads to missing a large number of candidates. We further show that these candidates cannot be neglected, since many of them are differentially regulated across conditions, and can be validated experimentally. We therefore advocate for the combine use of both mapping-first and assembly-first approaches for the annotation and differential analysis of AS from RNAseq data.
HDP-Align: Hierarchical Dirichlet Process Clustering for Multiple Peak Alignment of Liquid Chromatography Mass Spectrometry Data
Authors: Wandy Joe , Daly Rónán , Rogers Simon 
Published: September 2016

AbstractMatching peak features across multiple LC-MS runs (alignment) is an integral part of all LC-MS data processing pipelines. Alignment is challenging due to variations in the retention time of peak features across runs and the large number of peak features produced by a single compound in the analyte. In this paper, we propose a Bayesian non-parametric model that aligns peaks via a hierarchical cluster model using both peak mass and retention time. Crucially, this method provides confidence values in the form of posterior probabilities allowing the user to distinguish between aligned peaksets of high and low confidence. The results from our experiments on a diverse set of proteomic, glycomic and metabolomic data show that the proposed model is able to produce alignment results competitive to other widely-used benchmark methods, while at the same time, provide a probabilistic measure of confidence in the alignment results, thus allowing the possibility to trade precision and recall.AvailabilityOur method has been implemented as a stand-alone application in Java, available for download athttp://github.com/joewandy/HDP-Align.
“Quality does not sell itself”
Authors: Giacalone Davide , Fosgaard Toke Reinholt , Steen Ida , Münchow Morten 
Published: September 2016

Purpose
Food quality is a multi-dimensional concept comprising both objective and subjective components. Quality as defined from an industry perspective usually relies on different instrumental assessment and on ratings of “experts” which may not necessarily align with consumers’ perception of quality. The purpose of this paper is to deal with consumers perceptions of intrinsic quality in coffee from a sensory scientific and behavioral economic perspective.

Design/methodology/approach
In a blind taste test (n=205), naïve consumers tasted two cups of coffee and decided which they preferred. The two coffees varied greatly in their “objective” quality (based on expert grading) and retail value. Consumers were then revealed that one of the cups contained a coffee that was much more expensive than the other, and that they could get a free cup of their preferred coffee if they could correctly identify the most expensive one.

Findings
The results showed that preferences were equally distributed among the high- and low-quality samples, and that consumers did not perform better than chance level in the identification task. These results suggest that current grading systems used in the industry may be poorly correlated with the way consumers actually experience coffee, and thus that quality inference in the marketplace is more likely influenced by external cues (e.g. brand, label and price) than to intrinsic product quality. Nevertheless, the results also show that consumers who correctly answered the identification task were also significantly more likely to prefer the high-quality sample. This tentatively suggests that better sensory expertise is correlated with a preference for higher quality, though future studies are needed to confirm the correctedness of this interpretation.

Originality/value
This work highlights the difficulty of objectively defining food quality, and the limited usefulness of experts’ ratings widely used in the industry. Managerial implications of these findings, as well as implications for consumer policy, are discussed.
Prioritization guidelines for green food packaging development
Authors: Molina-Besch Katrin 
Published: September 2016

Purpose
Current literature emphasises using a holistic perspective on green packaging development (GPD) as an important strategy for reducing the environmental impact of products’ supply chain (SC). In practice, however, it can be difficult for packaging developers to strike a balance between all the different environmental requirements on packaging, and trade-offs are common. Life cycle assessment (LCA) can provide this type of information, but many food companies lack the time and resources to conduct detailed assessments. The purpose of this paper is to provide prioritization guidelines for food GPD based on a systematic review of food LCAs.

Design/methodology/approach
As basis for the suggested guidelines, 48 food LCAs covering eight types of food were reviewed following a standardized format. The review consisted of a quantitative analysis of the global warming potential results and a qualitative analysis of the LCAs’ conclusions.

Findings
The prioritization guidelines propose three priority areas for food GPD that companies can select from based on product characteristics. They also provide suggestions for improving packaging in the three priority areas.

Originality/value
The proposed guidelines can help food companies develop packaging solutions that contribute to minimising the environmental impact along food SCs. The review focuses on the role of packaging in food SCs, which has not been previously analysed in published LCA reviews.
The influence of experience and deliberate learning on SME export performance
Authors: Evangelista Felicitas , Mac Lancy 
Published: September 2016

PurposeThe purpose of this paper is to determine the relative importance of deliberate learning, learning from experience and relevant learning co-variates in pursuing market learning, and to assess the impact of market learning on export performance in smaller firms.Design/methodology/approachA theoretical model was initially developed and subsequently tested using survey data. The standard two step approach of first testing the measurement model and then estimating the structural model was adopted.FindingsThe results provide concrete evidence that among SMEs, deliberate learning has a greater impact on export market learning as compared to experience accumulation, and that market learning has a significant effect on export performance. The results also show that absorptive capacity and commitment to learning are significant co-variates of market learning.Originality/valueThis paper focuses on the role of deliberate learningvis-a-vislearning by experience in achieving foreign market learning and export performance in smaller firms. It addresses a major limitation of organisational learning studies which tend to focus mainly on experiential learning and organisational learning in large organisations.
Double layer water-borne heat insulation coatings containing hollow glass microspheres (HGMs)
Authors: Zhang Dawei , Li Haiyang , Qian Hongchang , Wang Luntao , Li Xiaogang 
Published: September 2016

PurposeThis study aims to construct a double layer heat insulation coating based on hollow glass microspheres (HGMs) and to investigate the effect of particle size on barrier property and heat insulation performance.Design/methodology/approachThe waterborne double layer coating was composed of an anticorrosive epoxy ester primer and an HGM-containing silicone acrylic topcoat. With varied HGM sizes (20 μm, 40 μm, 60 μm and a 1:3 w/w mixture of 20 and 60 μm particles), the coating was immersed in 3.5 wt% NaCl solution for 28 days and was then subjected to a salt spray test for 450 h. The barrier properties of the coating were evaluated through electrochemical impedance spectroscopy. Heat insulation performance was examined using a self-made device.FindingsThe addition of HGMs decreased the barrier properties of the coating by creating particle/resin interfaces for water penetration. In the HGMs-containing coatings, the use of larger HGMs showed relatively good barrier properties because of the lower particle density. The coating with smaller particles yielded a higher heat insulating capacity as indicated by lower equilibrium temperatures.Research limitations/implicationsFuture work will be focused on improving the barrier properties of the coating. Field exposure tests should also be performed to assess the long-term performance of the coating.Practical implicationsThe mechanical properties of the coatings in this study also implied that HGMs can be used to develop scratch-resistant and impact-resistant coatings. Other potential applications for further studies include the uses of HGMs for coatings with improved fire retardancy and electromagnetic interference shielding.Originality/valueA double layer coating was developed to provide balanced performance on both anticorrosion and heat insulation. The effects of HGM size were particularly highlighted.
Coloration of aluminum pigment using SiO2 and γ-glycidoxypropyltrimethoxysilane with dichlorotriazine reactive dye
Authors: Tawiah Benjamin , Zhang Liping , Tian Anli , Fu Shai Shao 
Published: September 2016

Purpose
The purpose of this paper is to colour aluminium pigment to the highest chroma using SiO2 and organic silane with dichlorotriazine reactive dye and investigate its reaction mechanism, chemical stability and thermal properties to improve its applicability in surface coatings.

Design/methodology/approach
Aluminium pigment was encapsulated by the catalysed sol-gel method using SiO2, followed by modification with γ-glycidoxypropyltrimethoxysilane (GPTMS). Purified reactive dye (1-Amino-4-[3-(4,6-dichlorotriazin-2-ylamino)-4-sulfophenylamino]anthraquinone-2-sulfonic acid (X-BR)) was covalently immobilized onto modified SiO2 to obtain coloured aluminium pigment. The reaction mechanism, chemical stability and thermophysical properties were investigated by Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy, X-ray diffraction, scanning electron microscope, transmission electron microscope and thermogravimetric analyses (TGA).

Findings
The results showed that X-BR was covalently attached to modified Al/SiO2 with maximum colour grafting of 95 per cent when the dosage of GPTMS and X-BR per weight of modified Al/SiO2 was 25 and 15 per cent, respectively, at pH 8.5 and a temperature of 40°C. The coloured aluminium pigment had good chemical stability with excellent anti-migration properties in many solvents.

Research limitations/implications
The organic silane used required a careful control of pH to ensure maximum colour grafting efficiency meanwhile other silanes with amine groups could also be used effectively with different kinds of colorants besides reactive dyes.

Practical implications
The method used is less cumbersome and provides a simple route to preparing coloured aluminium pigment.

Originality/value
The use of organic-inorganic SiO2/γ- GPTMS with purified reactive dye to covalently colour aluminium pigment to the highest chroma is novel and will help advance the frontiers of knowledge on coloration of aluminium pigments.
Mathematical modeling of delamination factor on end milling of hybrid GFRP composites through RSM
Authors: Jenarthanan M.P. , Lakshman Prakash A. , Jeyapaul R. 
Published: September 2016

Purpose
This paper aims to develop a mathematical model for delamination during end milling by using response surface methodology (RSM) and to determine how the input parameters (cutting speed, depth of cut and feed rate) influence the output response (delamination) in machining of hybrid glass fibre reinforced plastic (GFRP; abaca and glass) composite using solid carbide end mill cutter.

Design/methodology/approach
Three factors, three levels Box–Behnken design in RSM is used to carry out the experimental investigation. Shop microscope Mitutoyo TM-500 is used to measure the width of maximum damage of the machined hybrid GFRP composites. The “Design Expert 8.0” is used to analyse the data collected graphically. Analysis of variance is carried out to validate the model and for determining the most significant parameter.

Findings
The RSM is used to predict the input factors influencing the delamination on the machined surfaces of hybrid GFRP composite at different cutting conditions with the chosen range of 95 per cent confidence intervals. Analysis on the influences of the entire individual input machining parameters on the delamination has been carried out using RSM.

Originality/value
Effect of milling of hybrid GFRP composite on delamination with solid carbide end mill has not been analysed yet using RSM.
The Mass Production of Redundant, Misleading, and Conflicted Systematic Reviews and Meta‐analyses
Authors: IOANNIDIS JOHN P.A. 
Published: September 2016

Policy Points:
Currently, there is massive production of unnecessary, misleading, and conflicted systematic reviews and meta‐analyses. Instead of promoting evidence‐based medicine and health care, these instruments often serve mostly as easily produced publishable units or marketing tools.
Suboptimal systematic reviews and meta‐analyses can be harmful given the major prestige and influence these types of studies have acquired.
The publication of systematic reviews and meta‐analyses should be realigned to remove biases and vested interests and to integrate them better with the primary production of evidence.
ContextCurrently, most systematic reviews and meta‐analyses are done retrospectively with fragmented published information. This article aims to explore the growth of published systematic reviews and meta‐analyses and to estimate how often they are redundant, misleading, or serving conflicted interests.MethodsData included information from PubMed surveys and from empirical evaluations of meta‐analyses.FindingsPublication of systematic reviews and meta‐analyses has increased rapidly. In the period January 1, 1986, to December 4, 2015, PubMed tags 266,782 items as “systematic reviews” and 58,611 as “meta‐analyses.” Annual publications between 1991 and 2014 increased 2,728% for systematic reviews and 2,635% for meta‐analyses versus only 153% for all PubMed‐indexed items. Currently, probably more systematic reviews of trials than new randomized trials are published annually. Most topics addressed by meta‐analyses of randomized trials have overlapping, redundant meta‐analyses; same‐topic meta‐analyses may exceed 20 sometimes. Some fields produce massive numbers of meta‐analyses; for example, 185 meta‐analyses of antidepressants for depression were published between 2007 and 2014. These meta‐analyses are often produced either by industry employees or by authors with industry ties and results are aligned with sponsor interests. China has rapidly become the most prolific producer of English‐language, PubMed‐indexed meta‐analyses. The most massive presence of Chinese meta‐analyses is on genetic associations (63% of global production in 2014), where almost all results are misleading since they combine fragmented information from mostly abandoned era of candidate genes. Furthermore, many contracting companies working on evidence synthesis receive industry contracts to produce meta‐analyses, many of which probably remain unpublished. Many other meta‐analyses have serious flaws. Of the remaining, most have weak or insufficient evidence to inform decision making. Few systematic reviews and meta‐analyses are both non‐misleading and useful.ConclusionsThe production of systematic reviews and meta‐analyses has reached epidemic proportions. Possibly, the large majority of produced systematic reviews and meta‐analyses are unnecessary, misleading, and/or conflicted.
The Exnovation of Chronic Care Management Processes by Physician Organizations
Authors: RODRIGUEZ HECTOR P. , HENKE RACHEL MOSHER , BIBI SALMA , RAMSAY PATRICIA P. , SHORTELL STEPHEN M. 
Published: September 2016

Policy Points
The rate of adoption of chronic care management processes (CMPs) by physician organizations has been fairly slow in spite of demonstrated effectiveness of CMPs in improving outcomes of chronic care.
Exnovation (ie, removal of innovations) by physician organizations largely explains the slow population‐level increases in practice use of CMPs over time.
Expanded health information technology functions may aid practices in retaining CMPs. Low provider reimbursement by Medicaid programs, however, may contribute to disinvestment in CMPs by physician organizations.
ContextExnovation is the process of removal of innovations that are not effective in improving organizational performance, are too disruptive to routine operations, or do not fit well with the existing organizational strategy, incentives, structure, and/or culture. Exnovation may contribute to the low overall adoption of care management processes (CMPs) by US physician organizations over time.MethodsThree national surveys of US physician organizations, which included common questions about organizational characteristics, use of CMPs, and health information technology (HIT) capabilities for practices of all sizes, and Truven Health Insurance Coverage Estimates were integrated to assess organizational and market influences on the exnovation of CMPs in a longitudinal cohort of 1,048 physician organizations. CMPs included 5 strategies for each of 4 chronic conditions (diabetes, asthma, congestive heart failure, and depression): registry use, nurse care management, patient reminders for preventive and care management services to prevent exacerbations of chronic illness, use of nonphysician clinicians to provide patient education, and quality of care feedback to physicians.FindingsOver one‐third (34.1%) of physician organizations exnovated CMPs on net. Quality of care data feedback to physicians and patient reminders for recommended preventive and chronic care were discontinued by over one‐third of exnovators, while nurse care management and registries were largely retained. Greater proportions of baseline Medicaid practice revenue (incidence rate ratio [IRR] = 1.44, p < 0.001) and increasing proportions of revenue from Medicaid (IRR = 1.02, p < 0.05) were associated with greater CMP exnovation by physician organizations on net. Practices with greater expansion of HIT functionality exnovated fewer CMPs (IRR = 0.91, p < 0.001) compared to practices with less expansion of HIT functionality.ConclusionsExnovation of CMPs is an important reason why the population‐level adoption of CMPs by physician organizations has remained low. Expanded HIT functions and changes to Medicaid reimbursement and incentives may aid the retention of CMPs by physician organizations.
Effect of Scavenging Circulating Reactive Carbonyls by Oral Pyridoxamine in Uremic Rats on Peritoneal Dialysis
Authors: Mori Yoshitaka , Kakuta Takatoshi , Miyakogawa Takayo , Takekoshi Susumu , Yuzawa Hiroko , Kobayashi Hiroyuki , Kawakami Atsushi , Miyata Toshio , Fukagawa Masafumi 
Published: September 2016

AbstractPyridoxamine, a reactive carbonyl (RCO) scavenger, can ameliorate peritoneal deterioration in uremic peritoneal dialysis (PD) rats when given via dialysate. We examined the effects of scavenging circulating RCOs by oral pyridoxamine. Rats underwent nephrectomy and 3 weeks of twice daily PD either alone or with once daily oral pyridoxamine. PD solution was supplemented with methylglyoxal, a major glucose‐derived RCO, to quench intraperitoneal pyridoxamine. Oral pyridoxamine achieved comparable blood and dialysate pyridoxamine concentrations, suppressed pentosidine accumulation in the blood but not in the mesenterium or dialysate, and reduced the increases in small solute transport and mesenteric vessel densities, with no effects on submesothelial matrix layer thickening or serum creatinine. Thus, reducing circulating RCOs by giving oral pyridoxamine with PD provides limited peritoneal protection. However, orally given pyridoxamine efficiently reaches the peritoneal cavity and would eliminate intraperitoneal RCOs. Oral pyridoxamine is more clinically favorable and may be as protective as intraperitoneal administration.