bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative assembly hubs: Web-accessible browsers for comparative genomics
Authors: Nguyen Ngan , Hickey Glenn , Raney Brian J. , Armstrong Joel , Clawson Hiram , Zweig Ann , Karolchik Donna , Kent William James , Haussler David , Paten Benedict 
Published: August 2014

Abstract
Motivation: Researchers now have access to large volumes of genome sequences for comparative analysis, some generated by the plethora of public sequencing projects and, increasingly, from individual efforts. It is not possible, or necessarily desirable, that the public genome browsers attempt to curate all these data. Instead, a wealth of powerful tools is emerging to empower users to create their own visualizations and browsers.
Results: We introduce a pipeline to easily generate collections of Web-accessible UCSC Genome Browsers interrelated by an alignment. It is intended to democratize our comparative genomic browser resources, serving the broad and growing community of evolutionary genomicists and facilitating easy public sharing via the Internet. Using the alignment, all annotations and the alignment itself can be efficiently viewed with reference to any genome in the collection, symmetrically. A new, intelligently scaled alignment display makes it simple to view all changes between the genomes at all levels of resolution, from substitutions to complex structural rearrangements, including duplications. To demonstrate this work, we create a comparative assembly hub containing 57 Escherichia coli and 9 Shigella genomes and show examples that highlight their unique biology.
Availability and implementation: The source code is available as open source at: https://github.com/glennhickey/progressiveCactus The E.coli and Shigella genome hub is now a public hub listed on the UCSC browser public hubs Web page.
Contact: benedict@soe.ucsc.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Optimal fine-scale structures in compliance minimization for a uniaxial load
Authors: Kohn Robert V. , Wirth Benedikt 
Published: August 2014

We consider the optimization of the topology and geometry of an elastic structureO⊂R2subjected to a fixed boundary load, i.e. we aim to minimize a weighted sum of material volumeVol(O), structure perimeterPer(O)and structure complianceComp(O)(which is the work done by the load). As a first simple and instructive case, this paper treats the situation of an imposed uniform uniaxial tension load in two dimensions. If the weightεof the perimeter is small, optimal geometries exhibit very fine-scale structure which cannot be resolved by numerical optimization. Instead, we prove how the minimum energy scales inε, which involves the construction of a family of near-optimal geometries and thus provides qualitative insights. The construction is based on a classical branching procedure with some features unique to compliance minimization. The proof of the energy scaling also requires an ansatz-independent lower bound, which we derive once via a classical convex duality argument (which is restricted to two dimensions and the uniaxial load) and once via a Fourier-based refinement of the Hashin–Shtrikman bounds for the effective elastic moduli of composite materials. We also highlight the close relation to and the differences from shape optimization with a scalar PDE-constraint and a link to the pattern formation observed in intermediate states of type-I superconductors.
The genomic landscape of polymorphic human nuclear mitochondrial insertions
Authors: Dayama Gargi , Emery Sarah B. , Kidd Jeffrey M. , Mills Ryan E. 
Published: August 2014

ABSTRACTThe transfer of mitochondrial genetic material into the nuclear genomes of eukaryotes is a well-established phenomenon. Many studies over the past decade have utilized reference genome sequences of numerous species to characterize the prevalence and contribution of nuclear mitochondrial insertions to human diseases. The recent advancement of high throughput sequencing technologies has enabled the interrogation of genomic variation at a much finer scale, and now allows for an exploration into the diversity of polymorphic nuclear mitochondrial insertions (NumtS) in human populations. We have developed an approach to discover and genotype previously undiscovered Numt insertions using whole genome, paired-end sequencing data. We have applied this method to almost a thousand individuals in twenty populations from the 1000 Genomes Project and other data sets and identified 138 novel sites of Numt insertions, extending our current knowledge of existing Numt locations in the human genome by almost 20%. Most of the newly identified NumtS were found in less than 1% of the samples we examined, suggesting that they occur infrequently in nature or have been rapidly removed by purifying selection. We find that recent Numt insertions are derived from throughout the mitochondrial genome, including the D-loop, and have integration biases consistent with previous studies on older, fixed NumtS in the reference genome. We have further determined the complete inserted sequence for a subset of these events to define their age and origin of insertion as well as their potential impact on studies of mitochondrial heteroplasmy.
Linkages between investment flows and financial development
Authors: A. Asongu Simplice 
Published: August 2014

Purpose– The purpose of this paper is to introduce previously missing financial components (efficiency, activity and size) in the assessment of the finance-investment nexus.Design/methodology/approach– Vector autoregressive models in the perspectives of Vector Error Correction Model and short-run Granger causality are employed. There is usage of optimally specified econometric methods as opposed to purely discretionary model specifications in mainstream literature.Findings– Three main findings are established: first, while finance led investment elasticities are positive, investment elasticities of finance are negative; second, but for Guinea Bissau, Mozambique and Togo, finance does not seem to engender portfolio investment; and finally, contrary to mainstream literature, financial efficiency appears to impact investment more than financial depth.Practical implications– Four policy implications result: first, extreme caution is needed in the use of single equation analysis for economic forecasts; second, financial development leads more to investment flows than the other way round; third, financial allocation efficiency is more relevant as means to attracting investment flows than financial depth; and finally, the somewhat heterogeneous character of the findings also point to shortcomings in blanket policies that are not contingent on country-specific trends in the finance-investment nexus.Originality/value– First, contrary to the mainstream approach we use four measures of financial intermediary development (depth, efficiency, activity and size) as well as four types of investment flows (domestic, foreign, portfolio and total). Second, the chosen investment and financial indicators are derived upon preliminary robust correlation analyses from the broadest macroeconomic data set available on investment and financial intermediary flows.
Importance of satisfaction with food for older adults’ quality of life
Authors: Jeong Jihye , Seo Sunhee 
Published: August 2014

Purpose– The purpose of this paper is to examine the relationships among satisfaction with food-related life (SWFL), perceived foodservice quality, and quality of life for older adults.Design/methodology/approach– A survey done using face-to-face interviews of older adults residing in long-term care facilities. A total of 238 older adults participated in this study.Findings– The results showed that perceived foodservice quality had a strong association with SWFL; SWFL had a significant positive association with quality of life; perceived foodservice quality positively related to quality of life. Increased SWFL would improve quality of older adults.Research limitations/implications– This study has limitations related to convenience sample. Different sampling could help with generalization of results.Practical implications– Foodservice managers in long-term care facilitates should try to maximize food and service qualities for residents because improving food and service quality improves their quality of life. For example, offering a variety of menus to allow older adults to enjoy food and improve their SWFL.Originality/value– This study emphasized that food was important to older adults and helped determine quality of life for them. SWFL was rarely empirically examined in the previous research.
Can increased organic consumption mitigate climate changes?
Authors: Ravn Heerwagen Lennart , Mørch Andersen Laura , Christensen Tove , Sandøe Peter 
Published: August 2014

Purpose
– The purpose of this paper is to investigate the evidence for a positive correlation between increased consumption of organic products and potential climate change mitigation via decreased consumption of meat and it is discussed to what extent organic consumption is motivated by climate change concerns.

Design/methodology/approach
– A fixed effects model together with a factor analysis and ordinary least square are used to analyse household purchase data for 2,000 households in 2006-2010 combined with survey questionnaire data from 2008.

Findings
– A small but statistically significant correlation between increasing organic budget shares and decreasing meat budget shares is found. People include food-related behaviour such as the purchase of organic food and reduced meat consumption as ways to mitigate climate change. However, other behavioural modifications such as reduction of car usage and household heating are perceived as more important strategies.

Research limitations/implications
– Other food-related mitigation strategies could be investigated. The climate effect of different diets – and how to motivate consumers to pursue them – could be investigated. Individual as opposed to household data would supplement the analyses.

Practical implications
– Demand-side policies aiming at climate-friendly consumption could be a central factor in combating climate change. Already, food-related mitigation strategies such as lowered meat consumption are established practices among a group of organic consumers. As some consumers believe that climate change can be mitigated by consuming organic food, the authors propose that this is taken into account in the development of organic farming.

Originality/value
– The authors propose a shift from analysing the climate-friendliness of production to addressing the climate-friendliness of consumption using consumption of organic food as a case. The authors link stated concerns for climate changes with actual food-related behaviour.
Effect of low glycaemic index diets on satiety
Authors: Maria de Medeiros Batista Sonia , Addison Machado Moreira Emilia , Medeiros Rataichesck Fiates Giovanna , Alice Altemburg de Assis Maria , Teixeira Evanilda 
Published: August 2014

Purpose
– The purpose of the paper is to determine the effects of a hypocaloric diet with a low-glycaemic index (GI) on weight loss and postprandial blood glucose and assess both the satiety and palatability of the diet.

Design/methodology/approach
– A clinical trial was conducted with ten women (mean age: 38.8±11.3 years; body mass index: 27.2±3.5 kg/m2) submitted to a hypocaloric diet, assessments were performed at baseline and after seven days of treatment.

Findings
– Significant reductions were found in body weight (1.1±0.7 kg; p=0.001), triccipital skinfold (2.87±3.24 mm; p=0.021) and waist circumference (3.6±4.8 cm; p=0.041). Mean fasting and postprandial blood glucose values were 88.7±6.1 mg/dL and 91.6±9.6 mg/dL, respectively. Responses regarding satiety and palatability of the low-GI diet were predominantly “extremely satisfied” and “I liked it very much,” respectively, for all meals and throughout all seven days of the study.

Originality/value
– The present study demonstrated the benefits of a low-GI diet with regard to weight loss, blood glucose control and satiety. The diet proved to be palatable, which could favor compliance with long-term treatment.
Attitudes towards genetically modified animals in food production
Authors: J. Frewer Lynn , Coles David , Houdebine Louis-Marie , A. Kleter Gijs 
Published: August 2014

Purpose
– Food products developed using genetically modified (GM) animals may soon be introduced in Europe and beyond. Their successful commercialisation depends on consumer acceptance, and so it is timely to review the existing literature in this respect. The paper aims to discuss these issues.

Design/methodology/approach
– A systematic review identified 42 English language peer reviewed papers assessing public opinion of GM animals associated with food production. Thematic analysis was applied to the results to identify and explain consumer attitudes.

Findings
– Publication peaked in 2004, and declined thereafter. European consumers were less accepting of GM animal technology than the US and Asian consumers, although the latter reported more ethical concern. Risk and benefit perceptions, ethical concerns (e.g. related to animal welfare) may explain negative consumer attitudes towards animals in food production.

Research limitations/implications
– There is a lack of data on consumer attitudes to GM animals applied to food production, in particular in relation to consumers in emerging economies and developing countries. This is problematic as applications of GM animal products are about to enter the market.

Practical implications
– There is a need to track changes in public opinion as GM food production animals are further developed. The introduction and commercialisation of applications with specific characteristics may further shape consumer attitudes.

Social implications
– Methods need to be developed to involve consumers and other stakeholders in shaping future applications of agri-food applications of GM animals.

Originality/value
– The review collates existing quantitative and qualitative knowledge regarding the drivers of consumer attitudes towards GM animals used in food production using systematic review methodology.
The role of formal industry clusters in the internationalization of new ventures
Authors: Colovic Ana , Lamotte Olivier 
Published: August 2014

Purpose– The purpose of this study is to investigate the internationalization of international new ventures (INVs). Specifically, this research explores the ways in which a formal cluster can facilitate the internationalization process of these firms.Design/methodology/approach– The authors studied how four INVs benefitted from the actions of two clusters in France – Systematic and Mov’eo – as they internationalized. They conducted semi-structured interviews with the CEOs and other representatives of the INVs and with the members of the cluster management teams.Findings– The findings indicate that clusters can facilitate the internationalization of INVs by providing resources, networking opportunities and legitimacy to help them reach global markets and by increasing the speed of internationalization.Originality/value– By analyzing the specific role that a formal cluster plays in the internationalization of INVs, this research contributes to the literature examining the link between location and INV internationalization. The authors argue that the cluster’s role can be considered as that of an intermediary organization helping INVs to expand globally.
International new ventures: rapid internationalization across different industry contexts
Authors: Andersson Svante , Evers Natasha , Kuivalainen Olli 
Published: August 2014

Purpose– The purpose of this article is to, first, offer insights into the relationship between industry idiosyncrasies and international new ventures (INVs), and then present a research conceptual framework that identifies the role of industry factors in new venture internationalization processes and strategies. Second, the authors introduce the content of this special issue.Design/methodology/approach– This conceptual article builds on extant studies on INVs operating in different industrial contexts. Particular attention is given to the role of industry influences in the processes of new venture internationalization, in terms of speed, geographical scope and entry strategy. Such factors are discussed to formulate a conceptual framework as a basis for further research.Findings– The conceptual framework identifies key industry factors as well as emergent factors that influence the new venture internationalization process, in terms of speed, geographical scope and entry strategy. Such key influencing factors are competition and structure, industry life cycle, industry concentration, knowledge intensity, local cluster internationalization and global industry integration. Emergent factors are identified as new business models, technology and industry network dynamics.Research limitations/implications– This article is conceptual in nature, and thus empirical research is recommended in diverse contexts.Practical implications– Further analysis of industry factors is a valid research avenue for understanding INVs.Originality/value– This special issue offers new insights into how industry factors influence INVs’ internationalization processes in terms of speed, scope and entry strategy.
The internationalization strategies of rapidly internationalizing high-tech UK SMEs
Authors: Crick Dave , Crick James 
Published: August 2014

Purpose– The purpose of this paper is to investigate aspects of causation and effectuation decision-making in respect of the planned and unplanned nature of the internationalization strategies of a small sample of rapidly internationalizing, high-tech UK small and medium enterprises (SMEs). These exhibit four different rates of scale of international intensity (percentage of overseas sales to total sales) and market scope (geographical coverage and commitment).Design/methodology/approach– Interviews with managers of 16 independently owned high-technology-oriented manufacturing SMEs were undertaken in this investigation to reduce the potential effect of bias from parental decision-making and firm size, also trade sectoral conditions. These were drawn from an existing database.Findings– Aspects of both causation and effectuation logic were evident in planned and unplanned aspects of decision-making. Moreover, industry factors were seen to affect internationalization strategies in various ways and not least in respect of the need to exploit windows of opportunity in international niche markets and the usefulness of utilizing managers’ experience and networks in the sector in which firms operated.Originality/value– The contribution of this study is to build on earlier work where authors have used different terminology to describe firms that have internationalized soon after their foundation. Specifically, with respect to the planned versus unplanned nature of respective internationalization strategies and the causation as opposed to effectuation logic in decision-making.
Does openness enhance financial sector development? The experience of the Arab world
Authors: Al-Fayoumi Nedal , Abuzayed Bana 
Published: August 2014

Purpose– The purpose of this paper is to examine if the simultaneous openness to trade and capital account can promote financial sector development.Design/methodology/approach– Based on a sample of 12 Arab countries over the period from 1985 to 2011, the data were analyzed using the dynamic and static panel data analysis. In particular, the authors apply three estimate techniques: the generalized method of moments, fixed effects and random effects.Findings– The empirical results do not support the simultaneous openness hypothesis. Even trade and financial openness have an important separate role in enhancing financial sector development; their interaction effect is harmful. This empirical evidence indicates that opening Arab countries to both trade and capital account will not necessarily promote financial sector development.Research limitations/implications– Some Arab countries are not included in the study sample because of the lack of data.Practical implications– The main implication of this study is: opening Arab countries for trade and capital account at the same time will not improve the development of financial sector.Social implications– The paper examines one of the most important issues in developing countries; where, the people want to know if the country openness to trade and finance will generate a social and economic welfare for them.Originality/value– This study can be considered as one of the rare studies that examine the simultaneous openness issue in the developing countries. It recommends regulators and policy makers to take gradual steps toward adopting trade and financial openness in the Arab countries.
Children's socialization in consumption: the role of marketing
Authors: Carlos Estrela Rui , Costa Pereira Francisco , Bruno Ventura Jorge 
Published: August 2014

Purpose– The purpose of this paper is to intend to understand how children organize their representational heritage of brands and what influences they may have had to build it.Design/methodology/approach– The authors carried out a research divided into two parts, one with a questionnaire in which the authors characterized children and identify their behaviours when they are watching TV and surfing the net with an open question which asked them to list which brands they knew. Another qualitative research in which two focus groups were followed with the parents on the consumption habits of their children. The sample includes 602 children between eight and 11 years old. Regarding the parents, 19 participated in the two focus groups, a first in a middle-class area and a second in a lower-class area.Findings– Children spend many hours during the week and the weekend watching TV and on the internet. As for the representation of consumption, the data were processed by gathering the brands per product categories with specific software that showed the authors, through a lexicographical analysis, a mental representation that anchors on two cores. One regards food and gathers in a star a wide range of product categories and other regarding clothing, more cognitively complex, forming stars and circles.Research limitations/implications– It was not possible to isolate two samples of children in middle class and lower class as was done with the parents, which did not allow checking this symbolic dimension of brands between these two groups. Parents’ occupations did not allow the authors to clearly identify social classes and in the attempts the authors made that were not reliable by combining the occupation of the father and of the mother.Practical implications– Children are an important group to be studied, since their attitudes towards products and brands are still in a formative stage and their current experiences will affect their preferences for brands and their behaviours on the market as suggest the authors. This study may contribute to the development of marketing strategies for children by identifying the meanings of food and clothing brands that they own.Social implications– This research offers the authors clues so that in the future it can be confirmed that lower-classes children are more attentive to the symbolic dimension of brands as a way of self-expression.Originality/value– A new research method using mental maps which allows for a sharper, more specific analysis, where the distinction between genders and age groups can be detected very clearly.