bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cell shape regulates subcellular organelle location to control early Ca2+signal dynamics in Vascular Smooth Muscle Cells
Authors: Calizo R. C. , Bell M. K. , Ron A. , Hu M. , Bhattacharya S. , Wong N. J. , Janssen W.G.M. , Perumal G. , Pederson P. , Scarlata S. , Hone J. , Azeloglu E. U. , Rangamani P. , Iyengar R. 
Published: July 2017

ABSTRACTThe shape of the cell is connected to its function; however, we do not fully understand underlying mechanisms by which global shape regulates a cell’s functional capabilities. Using theory, experiments and simulation, we investigated how physiologically relevant cell shape changes affect subcellular organization, and consequently intracellular signaling, to control information flow needed for phenotypic function. Vascular smooth muscle cells going from a proliferative and motile circular shape to a contractile fusiform shape show changes in the location of the sarcoplasmic reticulum, inter-organelle distances and differential distribution of receptors in the plasma membrane. These factors together lead to the modulation of signals transduced by the M3muscarinic receptor/Gq/PLCβ pathway at the plasma membrane, amplifying Ca2+dynamics in the cytoplasm and the nucleus resulting in phenotypic changes, as determined by increased activity of myosin light chain kinase in the cytoplasm and enhanced nuclear localization of the transcription factor NFAT. Taken together, our observations show a systems level phenomenon whereby global cell shape affects subcellular organization to modulate signaling that enables phenotypic changes.
Flat-to-curved transition during clathrin-mediated endocytosis correlates with a change in clathrin-adaptor ratio and is regulated by membrane tension
Authors: Bucher Delia , Frey Felix , Sochacki Kem A. , Kummer Susann , Bergeest Jan-Philip , Godinez William J. , Kräusslich Hans-Georg , Rohr Karl , Taraska Justin W. , Schwarz Ulrich S. , Boulant Steeve 
Published: July 2017

AbstractAlthough essential for many cellular processes, the sequence of structural and molecular events during clathrin-mediated endocytosis remains elusive. While it was believed that clathrin-coated pits grow with a constant curvature, it was recently suggested that clathrin first assembles to form a flat structure and then bends while maintaining a constant surface area. Here, we combine correlative electron and light microscopy and mathematical modelling to quantify the sequence of ultrastructural rearrangements of the clathrin coat during endocytosis in mammalian cells. We confirm that clathrin-coated structures can initially grow flat and that lattice curvature does not show a direct correlation with clathrin coat assembly. We demonstrate that curvature begins when 70% of the final clathrin content is acquired. We find that this transition is marked by a change in the clathrin to clathrin-adaptor protein AP2 ratio and that membrane tension suppresses this transition. Our results support the model that mammalian cells dynamically regulate the flat-to-curved transition in clathrin-mediated endocytosis by both biochemical and mechanical factors.
Methyl donor deficient diets cause distinct alterations in lipid metabolism but are poorly representative of human NAFLD
Authors: Lyall Marcus J , Cartier Jessy , Richards James A , Cobice Diego , Thomson John P , Meehan Richard R , Anderton Stephen M , Drake Amanda J 
Published: July 2017

AbstractNon-alcoholic fatty liver disease (NAFLD) is a global health issue. Dietary methyl donor restriction is used to induce a NAFLD/non-alcoholic steatohepatitis (NASH) phenotype in rodents, however the extent to which this model reflects human NAFLD remains incompletely understood. To address this, we undertook hepatic transcriptional profiling of methyl donor restricted rodents and compared these to published human NAFLD datasets.Adult C57BL/6J mice were maintained on control, choline deficient (CDD) or methionine/choline deficient (MCDD) diets for four weeks; the effects on methyl donor and lipid biology were investigated by bioinformatic analysis of hepatic gene expression profiles followed by a cross-species comparison with human expression data of all stages of NAFLD.Compared to controls, expression of the very low density lipoprotein (VLDL) packaging carboxylesterases (Ces1d,Ces1f,Ces3b) and the NAFLD risk allelePnpla3were suppressed in MCDD; withPnpla3and the liver predominantCesisoform,Ces3b, also suppressed in CDD. With respect to 1-carbon metabolism, down-regulation ofChka,Chkb,Pcty1a,GnmtandAhcywith concurrent upregulation ofMat2asuggests a drive to maintain S-adenosylmethionine levels. There was minimal similarity between global gene expression patterns in either dietary intervention and any stage of human NAFLD, however some common transcriptomic changes in inflammatory, fibrotic and proliferative mediators were identified in MCDD, NASH and HCC.In conclusion, this study suggests suppression of VLDL assembly machinery may contribute to hepatic lipid accumulation in these models, but that CDD and MCDD rodent diets are minimally representative of human NAFLD at the transcriptional level.Summary statementWe used transcriptional profiling of methyl donor restricted rodents to examine effects on methyl donor and lipid biology. We report novel mechanisms for lipid accumulation in this model and describe significant disparity between both dietary interventions and human disease.
The effect of depth variation on disparity tasks in natural scenes
Authors: Iyer Arvind V. , Burge Johannes 
Published: July 2017

ABSTRACTLocal depth variation is a distinctive property of natural scenes and its effects on perception have only recently begun to be investigated. Here, we demonstrate how natural depth variation impacts performance in two fundamental tasks related to stereopsis: half-occlusion detection and disparity detection. We report the results of a computational study that uses a large database of calibrated natural stereo-images with precisely co-registered laser-based distance measurements. First, we develop a procedure for precisely sampling stereo-image patches from the stereo-images, based on the distance measurements. The local depth variation in each stereo-image patch is quantified by disparity contrast. Next, we show that increased disparity contrast degrades performance in half-occlusion detection and disparity detection tasks, and changes the size and shape of the optimal spatial integration areas (“receptive fields”) for computing the task-relevant decision variables. Then, we show that a simple binocular image statistic predicts disparity contrast in natural scenes. Finally, we report results on the most likely patterns of disparity variation in natural scenes. Our findings motivate computational and psychophysical investigations of the mechanisms that underlie disparity estimation in local regions of natural scenes.
Strategies for positioning animal welfare as personally relevant
Authors: van Riemsdijk Lenka , Ingenbleek Paul T.M. , Houthuijs Marleen , van Trijp Hans C.M. 
Published: July 2017

PurposeNext to organic food products, an assortment of ethical products is emerging in the supermarket that targets the large market segment of consumers that are open for ethical product choices but do not restrict themselves to them. The purpose of this paper is to examine the positioning strategies that marketers use to persuade consumers in this segment to buy animal-friendly products (AFPs).Design/methodology/approachThe authors approach product positioning from a consumption values perspective from which they examine strategies that make animal welfare (AW) personally relevant to the buyer because they reinforce AW with suitable consumption value (functional, emotional, social, sensory, epistemic and/or ethical). Using data from 129 AFPs from a Dutch supermarket, the authors explore the positioning strategies of these products.FindingsThe results identified four different strategies used to position AFPs in a Dutch supermarket. They respectively call upon consumers’ emotions, functional or sensory perceptions, curiosity and sense of public welfare. The findings also show substantial category differences, with fresh products relying predominantly on emotional value and processed food on functional value.Originality/valueThis study is the first to empirically explore positioning strategies of AFPs on the basis of their consumption values. The study offers a novel perspective to understand how companies try to extend the market for AFPs, thus providing a basis for a new research agenda.
Consumer preferences towards healthier reformulation of a range of processed meat products
Authors: Shan Liran Christine , Regan Áine , Monahan Frank J. , Li Chenguang , Lalor Fiona , Murrin Celine , Wall Patrick G. , McConnon Áine 
Published: July 2017

Purpose
In response to increasing public health concerns about processed meat consumption, many innovations in meat technology focus on health-oriented product reformulations. Processed meat is not a homogeneous food category. The purpose of this paper is to explore consumer perception of the “healthier” reformulation of different processed meat products using two approaches: salt and fat reduction; and enrichment with healthy ingredients.

Design/methodology/approach
Seven focus group interviews were carried out with 40 Irish regular meat consumers (30 female, ten male) who were solely or jointly responsible for food shopping. Two rounds of card sorting procedures were employed to reveal perceptions on reformulation of 20 different processed meat products. Thematic analysis was used for analysing transcripts.

Findings
Health and flavour concerns and product popularity were the main factors influencing participants’ perceptions. Some participants were unsure or had misconceptions about the healthiness of certain meat products. Participants suggested reducing salt and fat content in processed meat products they perceived as the least healthy ones (theme 1) and improving the healthiness of products which were favoured by children (theme 2) and those meat products which people consumed regularly as a source of protein (theme 3). Participants were not in favour of any reformulation of speciality-type products (theme 4).

Originality/value
Consumer insights identified in this study can inform future approaches to making processed meats healthier.
The global competitiveness of European wine producers
Authors: Balogh Jeremiás Máté , Jámbor Attila 
Published: July 2017

Purpose
Comparative advantage is an important indicator in the analysis of international trade flow; however, in empirical studies on agriculture it is often neglected. The purpose of this paper is to analyse global comparative advantage in the European Union (EU) wine industry and to test the duration and stability of trade indices.

Design/methodology/approach
The paper applies the theory of comparative advantages by using the Balassa indices to European wine trade (based on the 16 biggest producers) data from the period 2000-2013. Moreover, it applies stability and duration analysis on comparative advantages calculated.

Findings
Results suggest that Bulgaria, Cyprus, France, Greece, Italy, Portugal, and Spain are the highest ranked European wine producers in the world market and have the largest comparative advantages. However, duration and stability tests indicate that trade advantages have weakened for the majority of these countries. The paper discusses a number of reasons for this downturn, including changes to Common Agricultural Policy wine regulation, economic crisis, and the rise of New World wine producers.

Originality/value
The originality of the paper is that it applies the theory of comparative advantage to top wine exporters in the EU. The paper also makes valuable contributions to the wine literature by analysing the duration and stability of comparative advantage in the global wine trade. Moreover, the identification of industry-specific causes for changing patterns in comparative advantage in the EU might be important to the wine industry.
Clients and cases: ambiguity and the division of labour in professional service firms
Authors: Alvehus Johan 
Published: July 2017

PurposeBy drawing on a detailed case study of the work of tax consultants, the purpose of this paper is to develop a more detailed understanding of the role of ambiguity in professional work, and its relationship to the division of labour in professional service firms (PSFs).Design/methodology/approachThe paper is based on a three-year, longitudinal interpretive case study comprising 42 interviews, supplemented by observations and document data.FindingsThe research determines that processes of “obfuscation” and “privatisation” separate client work from case work. This maintains a division of labour between junior and senior professionals, which in turn facilitates financial leverage. The findings indicate that a more nuanced view on the role and origins of ambiguity is needed; particularly the role ambiguity plays in the division of labour. While inherent in professional work, ambiguity is also an effect of the way work processes are organised in order to obtain leverage.Research limitations/implicationsThe research is based on a case study. Therefore, the paper explores its topic in empirical detail, but at the same time calls for exploring the topic in different contexts. The paper encourages further research on the role ambiguity plays being constituted by structural arrangements, and on the way the core of professionalism is inverted by the division of labour. The paper highlights the value of detailed empirical approaches for understanding professional work.Practical implicationsThe paper draws attention to the way ambiguity becomes a part in sustaining a division of labour among professional workers, and to the importance of this in maintaining financial leverage as well as in creating a precarious work situation for junior professionals.Social implicationsThe paper raises concerns about the way professional work is legitimated in society as opposed to how it is constructed in PSFs.Originality/valueThe paper challenges prevalent notions of professional work as ambiguous, offering instead a way of engaging with professional work processes in detail, theoretically and methodologically. Traditional assumptions about the division of labour and the “core” of professional work are problematized, and traditional assumptions about ambiguity as a cause of specific structural arrangements are questioned.
Learning domain taxonomies: the TaxoLine approach
Authors: El Idrissi Esserhrouchni Omar , Frikh Bouchra , Ouhbi Brahim , Ibrahim Ismail Khalil 
Published: July 2017

Purpose
The aim of this paper is to present an online framework for building a domain taxonomy, called TaxoLine, from Web documents automatically.

Design/methodology/approach
TaxoLine proposes an innovative methodology that combines frequency and conditional mutual information to improve the quality of the domain taxonomy. The system also includes a set of mechanisms that improve the execution time needed to build the ontology.

Findings
The performance of the TaxoLine framework was applied to nine different financial corpora. The generated taxonomies are evaluated against a gold-standard ontology and are compared to state-of-the-art ontology learning methods.

Originality/value
The experimental results show that TaxoLine produces high precision and recall for both concept and relation extraction than well-known ontology learning algorithms. Furthermore, it also shows promising results in terms of execution time needed to build the domain taxonomy.
MATVIZ: a semantic query and visualization approach for metallic materials data
Authors: Zhang Xiaoming , Chen Huilin , Ruan Yanqin , Pan Dongyu , Zhao Chongchong 
Published: July 2017

Purpose
With the rapid development of materials informatics and the Semantic Web, the semantic-driven solution has emerged to improve traditional query technology, which is hard to discover implicit knowledge from materials data. However, it is a nontrivial thing for materials scientists to construct a semantic query, and the query results are usually presented in RDF/XML format which is not convenient for users to understand. This paper aims to propose an approach to construct semantic query and visualize the query results for metallic materials domain.

Design/methodology/approach
The authors design a query builder to generate SPARQL query statements automatically based on domain ontology and query conditions inputted by users. Moreover, a semantic visualization model is defined based on the materials science tetrahedron to support the visualization of query results in an intuitive, dynamic and interactive way.

Findings
Based on the Semantic Web technology, the authors design an automatic semantic query builder to help domain experts write the normative semantic query statements quickly and simply, as well as a prototype (named MatViz) is developed to visually show query results, which could help experts discover implicit knowledge from materials data. Moreover, the experiments demonstrate that the proposed system in this paper can rapidly and effectively return visualized query results over the metallic materials data set.

Originality/value
This paper mainly discusses an approach to support semantic query and visualization of metallic materials data. The implementation of MatViz will be a meaningful work for the research of metal materials data integration.
A nonlinear method for multiparameter inversion of pre‐stack seismic data based on anisotropic Markov random field
Authors: Zhang Hongbing , Guo Qiang , Liang Lifeng , Cao Chenghao , Shang Zuoping 
Published: July 2017

ABSTRACTMultiparameter inversion for pre‐stack seismic data plays a significant role in quantitative estimation of subsurface petrophysical properties. However, it remains a complicated problem due to the non‐unique results and unstable nature of the processing; the pre‐stack seismic inversion problem is ill‐posed and band‐limited. Combining the full Zoeppritz equation and additional assumptions with edge‐preserving regularisation can help to alleviate these problems. To achieve this, we developed an inversion method by constructing a new objective function that includes edge‐preserving regularisation and soft constraints based on anisotropic Markov random fields and is intended especially for layered formations. We applied a fast simulated annealing algorithm to solve the nonlinear optimisation problem. The method directly obtains reflectivity RPP values using the full Zoeppritz equation instead of its approximations and effectively controls the stability of the multiparameter inversion by assuming a sectionally constant S‐ and P‐wave velocity ratio and using the generalised Gardner equation. We substituted the inverted parameters, i.e., the P‐wave velocity, the fitting deviation of S‐wave velocity, and the density were inverted instead of the P‐wave velocity, the S‐wave velocity, and the density, and the generalised Gardner equation was applied as a constraint. Test results on two‐dimensional synthetic data indicated that our substitution obtained improved results for multiparameter inversion. The inverted results could be improved by utilising high‐order anisotropic Markov random field neighbourhoods at early stages and low‐order anisotropic Markov random field neighbourhoods in the later stages. Moreover, for layered formations, using a large horizontal weighting coefficient can preserve the lateral continuity of layers, and using a small vertical weighting coefficient allows for large longitudinal gradients of the interlayers. The inverted results of the field data revealed more detailed information about the layers and matched the logging curves at the wells acceptably over most parts of the curves.
Benzoate and Sorbate Salts: A Systematic Review of the Potential Hazards of These Invaluable Preservatives and the Expanding Spectrum of Clinical Uses for Sodium Benzoate
Authors: Piper Joseph D. , Piper Peter W. 
Published: July 2017

AbstractSodium benzoate and potassium sorbate are extremely useful agents for food and beverage preservation, yet concerns remain over their complete safety. Benzoate can react with the ascorbic acid in drinks to produce the carcinogen benzene. A few children develop allergy to this additive while, as a competitive inhibitor of D‐amino acid oxidase, benzoate can also influence neurotransmission and cognitive functioning. Model organism and cell culture studies have raised some issues. Benzoate has been found to exert teratogenic and neurotoxic effects on zebrafish embryos. In addition, benzoate and sorbate are reported to cause chromosome aberrations in cultured human lymphocytes; also to be potently mutagenic toward the mitochondrial DNA in aerobic yeast cells. Whether the substantial human consumption of these compounds could significantly increase levels of such damages in man is still unclear. There is no firm evidence that it is a risk factor in type 2 diabetes. The clinical administration of sodium benzoate is of proven benefit for many patients with urea cycle disorders, while recent studies indicate it may also be advantageous in the treatment of multiple sclerosis, schizophrenia, early‐stage Alzheimer's disease and Parkinson's disease. Nevertheless, exposure to high amounts of this agent should be approached with caution, especially since it has the potential to generate a shortage of glycine which, in turn, can negatively influence brain neurochemistry. We discuss here how a small fraction of the population might be rendered—either through their genes or a chronic medical condition—particularly susceptible to any adverse effects of sodium benzoate.
Perineural invasion present exclusively in central tissue blocks of Mohs surgical excisions of basal cell carcinoma
Authors: Young Lauren , Coates Dougal , Pagliaro John , Francis David , Williamson Richard , Gaspar Zoran 
Published: July 2017

AbstractPerineural invasion (PNI) may be present in basal cell carcinomas (BCC) treated with Mohs micrographic surgery. This single‐centre, non‐randomised, prospective study demonstrates the potential for PNI to exist exclusively within the central tissue blocks of Mohs specimens.
Roles of APOL1 G1 and G2 variants in sickle cell disease patients: kidney is the main target
Authors: Kormann Raphaël , Jannot Anne‐Sophie , Narjoz Céline , Ribeil Jean‐Antoine , Manceau Sandra , Delville Marianne , Joste Valentin , Prié Dominique , Pouchot Jacques , Thervet Eric , Courbebaisse Marie , Arlet Jean‐Benoît 
Published: July 2017

SummaryIn African‐American patients with sickle cell disease (SCD), APOL1 G1 and G2 variants are associated with increased risk of sickle cell nephropathy (SCN). To determine the role of APOL1 variants in SCD patients living in Europe, we genotyped 152 SCD patients [aged 30·4 (24·3–36·4) years], mainly of Sub‐Saharan African ancestry, for APOL1 G1 and G2 and for variants of four genes with kidney tropism (GSTM1, GSTT1, GSTP1, and HMOX1). Homozygous or double‐heterozygous APOL G1 and G2 genotypes were strongly associated with end stage renal disease (P = 0·003) and worse Kidney Disease: Improving Global Outcomes stages (P = 0·001). Further, these genotypes were associated in an age‐dependent manner with lower estimated glomerular filtration rate (eGFR, P = 0·008), proteinuria (P = 0·009) and albuminuria (P < 0·001) but not with other SCD complications. Compared to APOL1 G1/wild type (WT), the APOL1 G2/WT genotype was associated with a lower eGFR (P = 0·04) in an age‐dependent manner, suggesting that the G2/WT patients are likely to have worse kidney prognosis. Other genes variants analysed were not associated with SCN or other SCD complications. Our data indicate that APOL1 screening should be considered for the management of SCD patients, including those of non‐African‐American origin, as those with homozygous or double heterozygous variants are clearly at higher risk of SCN.