bluuebunny/crossref_metadata_2025_split huggingface dataset:
GEMSiRV: a software platform for GEnome-scale metabolic model simulation, reconstruction and visualization
Authors: Liao Yu-Chieh , Tsai Ming-Hsin , Chen Feng-Chi , Hsiung Chao A. 
Published: May 2012

Abstract
Motivation: Genome-scale metabolic network models have become an indispensable part of the increasingly important field of systems biology. Metabolic systems biology studies usually include three major components—network model construction, objective- and experiment-guided model editing and visualization, and simulation studies based mainly on flux balance analyses. Bioinformatics tools are required to facilitate these complicated analyses. Although some of the required functions have been served separately by existing tools, a free software resource that simultaneously serves the needs of the three major components is not yet available.
Results: Here we present a software platform, GEMSiRV (GEnome-scale Metabolic model Simulation, Reconstruction and Visualization), to provide functionalities of easy metabolic network drafting and editing, amenable network visualization for experimental data integration and flux balance analysis tools for simulation studies. GEMSiRV comes with downloadable, ready-to-use public-domain metabolic models, reference metabolite/reaction databases and metabolic network maps, all of which can be input into GEMSiRV as the starting materials for network construction or simulation analyses. Furthermore, all of the GEMSiRV-generated metabolic models and analysis results, including projects in progress, can be easily exchanged in the research community. GEMSiRV is a powerful integrative resource that may facilitate the development of systems biology studies.
Availability: The software is freely available on the web at http://sb.nhri.org.tw/GEMSiRV.
Contact: jade@nhri.org.tw
A holistic in silico approach to predict functional sites in protein structures
Authors: Segura Joan , Jones Pamela F. , Fernandez-Fuentes Narcis 
Published: May 2012

Abstract
Motivation: Proteins execute and coordinate cellular functions by interacting with other biomolecules. Among these interactions, protein–protein (including peptide-mediated), protein–DNA and protein–RNA interactions cover a wide range of critical processes and cellular functions. The functional characterization of proteins requires the description and mapping of functional biomolecular interactions and the identification and characterization of functional sites is an important step towards this end.
Results: We have developed a novel computational method, Multi-VORFFIP (MV), a tool to predicts protein-, peptide-, DNA- and RNA-binding sites in proteins. MV utilizes a wide range of structural, evolutionary, experimental and energy-based information that is integrated into a common probabilistic framework by means of a Random Forest ensemble classifier. While remaining competitive when compared with current methods, MV is a centralized resource for the prediction of functional sites and is interfaced by a powerful web application tailored to facilitate the use of the method and analysis of predictions to non-expert end-users.
Availability: http://www.bioinsilico.org/MVORFFIP
Supplementary information: Supplementary data are available at Bioinformatics online.
Contact: naf4@aber.ac.uk; narcis.fernandez@gmail.com
BreakFusion: targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data
Authors: Chen Ken , Wallis John W. , Kandoth Cyriac , Kalicki−Veizer Joelle M. , Mungall Karen L. , Mungall Andrew J. , Jones Steven J. , Marra Marco A. , Ley Timothy J. , Mardis Elaine R. , Wilson Richard K. , Weinstein John N. , Ding Li 
Published: May 2012

Abstract
Summary: Despite recent progress, computational tools that identify gene fusions from next-generation whole transcriptome sequencing data are often limited in accuracy and scalability. Here, we present a software package, BreakFusion that combines the strength of reference alignment followed by read-pair analysis and de novo assembly to achieve a good balance in sensitivity, specificity and computational efficiency.
Availability: http://bioinformatics.mdanderson.org/main/BreakFusion
Contact: kchen3@mdanderson.org; lding@genome.wustl.edu
Supplementary information: Supplementary data are available at Bioinformatics online
Prevalence of preclinical and clinical heart failure in the elderly. A population‐based study in Central Italy
Authors: Mureddu Gian Francesco , Agabiti Nera , Rizzello Vittoria , Forastiere Francesco , Latini Roberto , Cesaroni Giulia , Masson Serge , Cacciatore Giuseppe , Colivicchi Furio , Uguccioni Massimo , Perucci Carlo Alberto , Boccanelli Alessandro ,   on behalf of the PREDICTOR Study Group
Published: May 2012

AimsWe conducted a population‐based cross‐sectional study to assess the prevalence of both preclinical and clinical heart failure (HF) in the elderly.Methods and resultsA sample of 2001 subjects, 65‐ to 84‐year‐old residents in the Lazio Region (Italy), underwent physical examination, biochemistry/N‐terminal pro brain natriuretic peptide (NT‐proBNP) assessment, electrocardiography, and echocardiography. Systolic left ventricular dysfunction (LVD) was defined as left ventricular ejection fraction (LVEF) <50%. Diastolic LVD was defined by a Doppler‐derived multiparametric algorithm. The overall prevalence of HF was 6.7% [95% confidence interval (CI) 5.6–7.9], mainly due to HF with preserved LVEF (HFpEF) (4.9%; 95% CI 4.0–5.9), and did not differ by gender. A systolic asymptomatic LVD (ALVD) was detected more frequently in men (1.8%; 95% CI 1.0–2.7) than in women (0.5%; 95% CI 0.1–1.0; P = 0.005), whereas the prevalence of diastolic ALVD was comparable between genders (men: 35.8%; 95% CI = 32.7–38.9; women: 35.0%; 95% CI = 31.9–38.2). The NT‐proBNP levels and severity of LVD increased with age. Overall, 1623 subjects (81.1% of the entire studied population) had preclinical HF (Stage A: 22.2% and stage B: 59.1% respectively). A large number of subjects in stage B of HF showed risk factor levels not at target.ConclusionsIn a population‐based study, the prevalence of preclinical HF in the elderly is high. The prevalence of clinical HF is mainly due to HFpEF and is similar between genders.
Microeconomic impacts of a state‐funded farmer loan program
Authors: Pederson Glenn , Chung Wonho , Nel Roelof 
Published: May 2012

PurposeThe purpose of this paper is to determine if there are positive microeconomic effects from a state‐funded loan participation program on farm productivity and investment behavior.Design/methodology/approachThe authors take the approach that access to credit solves a liquidity problem. If a credit constraint exists it results in a suboptimal allocation of resources and a reduction in farm output and profitability. A two‐stage regression model approach is used to analyze farmer survey and loan application data. In the first stage, a probit regression model is used to identify the farmers who are likely to be credit rationed. In the second stage, switching regression models are used to observe the effect of credit rationing on farm productivity and on farm investment behavior.FindingsIt is found that there are liquidity effects of credit constraints for a significant share of the beginning and low‐resource farmers who participated in the state‐funded farm loan program. After controlling for various farm and farmer characteristics, the estimated productivity and investment demand equations imply that a 1 percent increase in credit received by credit constrained farmers under the state program increased their gross income by about 0.49 percent, and their investments in depreciable assets by about 0.33 percent.Originality/valueThis paper is the first to apply the switching regression model to a state‐funded farm loan program for the purpose of evaluating the financial impacts on farmer participants.
Land registration, credit and agricultural investment in Africa
Authors: Domeher Daniel , Abdulai Raymond 
Published: May 2012

PurposeThe purpose of this paper is to critically examine the argument linking land registration to agricultural investment and to provide theoretical reasons as to why this linkage may not materialise in Africa within the short to medium term.Design/methodology/approachThe paper takes the form of a critical review of the relevant literature on land registration, access to credit and agricultural investment; arguments are built on empirical studies found in the literature and theoretical concepts.FindingsIt has been established in this paper that the links between landed property registration and agricultural investments are made defective in Africa by factors such as poverty, lack of appropriate agro‐based infrastructure and the fact that land registrationper sedoes not improve the profitability of agriculture, neither does it improve access to credit.Research limitations/implicationsThe fact that this paper is based on literature review may be seen as a weakness to some extent.Originality/valueEven though previous researchers have looked at the relationship between landed property registration and agricultural investment in the developing world, they fall short of critically explaining why land registration has been found not to enhance agricultural investment. This paper fills the gap through a combination of various theoretical and practical arguments which could call for a rethinking on the policies for promoting agricultural growth. The rigorous theoretical argument may also provide the basis for further empirical research.
Implications of within county yield heterogeneity for modeling crop insurance premiums
Authors: Cooper Joseph , Zulauf Carl , Langemeier Michael , Schnitkey Gary 
Published: May 2012

PurposeFarm level data are essential to accurate setting of crop insurance premium rates, but their time series tends to be too short to allow them to be the sole data source. County level data are available in longer time series, however. The purpose of this paper is to present a methodology to make full use of the information inherent in each of these data sets.Design/methodology/approachThe paper uses a novel application of statistical tools for using farm and county level yield data to generate farm level yield densities that explicitly incorporate within county yield heterogeneity while accounting for systemic risk and other spatial or intertemporal correlations among farms within the county.FindingsThe empirical analysis shows that current approaches used by the Risk Management Agency to individualize premiums for a farm result in substantial mispricing of crop insurance premiums because they do not adequately capture farm yield variability and yield correlations between farms. The new premium setting method is empirically shown to substantially reduce government subsidies for crop insurance premiums.Originality/valueThe paper demonstrates how to extract more information from available data when setting crop insurance premiums, which allows the government to more closely tailor premiums to the farm than do current approaches.
Development process of organic and local food breakfasts
Authors: Tikkanen Irma , Kasurinen Antero 
Published: May 2012

PurposeThis paper aims to describe the development process of two organic and local food breakfasts to be served in a small and independent coffee shop in Finland.Design/methodology/approachA conceptual framework is established concerning corporate social responsibility (CSR) and new product development process. Previous research related to organic food, local food, and breakfasts is introduced. Action research is applied.FindingsTwo organic and local food breakfasts were developed as a process and sold during eight months in the case coffee shop. The process comprised nine stages. The components for the two breakfasts were received from nine suppliers.Practical implicationsThe practical implications on the case coffee shop are that the customers' requests on organic and local food breakfasts were met; the coffee shop improved its sales and profits; and the service concept was moved into a more sustainable direction. The implications on the local society are that the sales of organic and local food producers increased and their employment improved.Originality/valueTwo organic and local food breakfasts were developed based on the product development process. The developed breakfasts can be used as a reference model in coffee shops, in restaurants, and in teaching.
Value net – a new business model for the food industry?
Authors: Kähkönen Anni‐Kaisa 
Published: May 2012

PurposeThe study aims to discuss the new value creation logic of value nets and analyze the characteristics of value nets in the context of the food industry. Previous research has shown that along with the growing importance of networking, the value creation logic is also changing from traditional chains to dynamic networks. The objective of this study is to define the characteristics of value nets and to analyze the suitability of the value net as a value creation and business model in the food industry.Design/methodology/approachThe study utilizes a case research as a method and analyzes a value net from the Finnish food industry. The empirical data comprises 29 individual semi‐structured interviews conducted with the personnel of four case companies.FindingsThe findings of the study suggest that the value net as a business model and value creation model is also suitable for food sector companies. The value net has several characteristics that were found to be significant and useful for food companies. Moreover, food companies can obtain remarkable benefits by utilizing value nets.Practical implicationsThe results of the study carry implications for managers and practitioners in terms of shedding light on the value net as a value creation model and business model in the food industry. Managers need to be aware of the developments in value creation logic and recognize that value can no longer be added in a sequential chain, but the perspective should move towards networks in which value is co‐created by the network actors.Originality/valueThus far, studies on value nets have concentrated mainly on the ICT sector and there is a limited amount of research on the food industry. The food sector, therefore, offers a new empirical context in which to conduct research on value nets. Food companies are focusing more and more on value creation and networking, and the research of value nets is therefore highly relevant to the business development of the food industry.
The effects of social‐economic status of consumers on purchasing, behaving and attitude to food products
Authors: Koç Beşir , Ceylan Melike 
Published: May 2012

PurposeThe aim of the study is to group consumers according to their own perception of socio‐economic status and to determine consumption habits, behaviors, approach and tendency towards food products.Design/methodology/approachIn this study, consumers in urban areas of Van, in Turkey, were grouped according to their self‐perceived social‐economic status and their behaviors and attitudes on purchase of food products are examined according to that social‐economic status. The study was conducted in Van province, Turkey, during 2007‐2008. Face to face interviews with 300 consumers work through the survey data was collected. Participants were asked to indicate their socio‐economic status from a choice of top, middle and bottom level groups.FindingsWithin the top and middle level of this grouping, the percentage of high school graduates is high; at the bottom level of this status, the proportion of university graduates is high. A large percentage of the consumers are public servants and business owners. It was observed that as the socio‐economic status increased, the proportion of business owners increased as well. Consumers in lower status groups spend the biggest portion of their income on food products. As the wages increase, the level of spending on food product decreases proportionally and the ability to make savings increases. The highest status consumers always check the price labels of the food products with a high percentage (66.67 percent). More than half of consumers do not believe that producers write all information and ingredients of the products on the packaging. A total of 77 percent of study participants stated that they were open to trying new food products. Consumers within the top socio‐economic groups are most careful about food ingredients.Originality/valueIn this study, the consumers themselves are classified according to their socio‐economic status. These are the top, middle and bottom status as determined. Consumers are clustered according to the general characteristics of the correspondence analysis.
Increasing the competitive positions of countries through employee training
Authors: Yan Cheung Hoi , Chan Alex W.H. 
Published: May 2012

PurposeThe purpose of this paper is to look at the competitiveness motive and mastery motive across 33 countries. The competitiveness motive is found to be a significant but negative predictor of employee training.Design/methodology/approachThe dataset was collected from two sources. Competitiveness motive and mastery motive scores of countries were collected from Lynn's study (1991); and work relation variables, such as employee training, worker motivation, and the world competitiveness score, were collected from the IMD World Competitiveness Yearbook 2008. Correlations, regression models and Sobel test were applied for analysis.FindingsAlthough people with a strong competitiveness motive are eager to beat others, the results indicate that they may not see training as an effective method of beating others in terms of the competitiveness positions of their country. Employee training is found to be related to the work motivation of employees, and thus to the competitiveness positions of countries. Some suggestions are made for such outcomes.Practical implicationsThe paper highlights the importance of employee training in organizations.Originality/valueThe paper demonstrates the importance of training with regard to global competitiveness positions.
Write‐in comments in employee surveys
Authors: Borg Ingwer , Zuell Cornelia 
Published: May 2012

PurposeItems that ask the respondent for a comment in his/her own words are becoming increasingly popular in online employee surveys, but research on such comments is scarce. The purpose of this paper is to analyze, theoretically and empirically, what kind of comments are generated in employee surveys by respondents who differ in terms of job satisfaction and commitment.Design/methodology/approachThe data studied here are from an online employee survey conducted in 2004 in a multinational IT organization with a German headquarter. Some 24,000 employees generated about 75,000 comments focusing on 15 topic fields. The comments were additionally coded on their tone, using a computerized dictionary approach especially developed for this purpose. Frequencies, wordiness, and the tone of different types of comments are measured. The statistical relationship of comments to job satisfaction and to organizational commitment is analyzed.FindingsSome 40 per cent of the respondents provide comments. Most comments have a negative tone. Negative comments are wordier than positive ones. The likelihood of writing comments is inversely related to the respondents’ job satisfaction and to their organizational commitment. Dissatisfied employees and employees with low commitment also write more negative and wordier comments.Practical implicationsThe study sets benchmarks on what to expect when using open‐ended comment fields in employee surveys. A methodology for analyzing huge text files with respect to their tone is presented.Originality/valueThis is the first paper that investigates a realistically large data set of comments. It also shows how to use computer methods to relate frequencies, wordiness, and tone of comments to standard variables such as job satisfaction or commitment.
The impact of internal and external market orientation on performance in local public organisations
Authors: Rodrigues Ana Paula , Carlos Pinho José 
Published: May 2012

PurposeThis study aims to build on and extend the literature of market orientation by examining the impact of sub‐dimensions of both internal and external market orientation on financial and non‐financial performance in the local public sector context.Design/methodology/approachIn line with previous studies on market orientation, a quantitative research design was adopted. The data collection was performed through a mail survey of a sample of local Portuguese public organisations (municipality executive board members). Structural equation modelling was used as a means to analyse the hypothesised relationships.FindingsSix out of 12 hypotheses are supported. Concerning the sub‐components of external market orientation, the study finds that the dissemination and responsiveness of external information impacts strongly on non‐financial performance. In turn, external information generation and responsiveness impacts positively on financial performance. With respect to internal market orientation, results revealed a lower impact of different sub‐dimensions on performance. Specifically, the only dimension that impacts positively on organisational performance (financial and non‐financial) is internal information generation. This reinforces the view that there is a need to strengthen internal information dissemination and responsiveness to enhance organisational performance.Originality/valueThis paper offers original and unique findings and to the best of the authors' knowledge this research is one of the few studies addressing the role of internal and external sub‐dimensions of market orientation on performance in the local public sector. The findings of this study add weight to the recent emphasis on disaggregate approaches to (internal and external) market orientation‐performance link.
Can after sale service generate brand equity?
Authors: Ahmad Sajjad , Mohsin Butt Muhammad 
Published: May 2012

PurposeThis research attempts to empirically expand the Aaker's consumer based brand equity model in hybrid business firms by incorporating after sales service as a new dimension. Exploring and understanding the drivers of consumer based brand equity in a hybrid business context will help in building industry specific competitive barriers and generating brand wealth.Design/methodology/approachThe data were collected from Pakistani adults using a structured questionnaire based on established scales. Convenience sampling was used to gather data from 205 respondents across the major cities of Pakistan. To test the proposed research model the data were analyzed using confirmatory factor analysis.FindingsThe results support the proposed five‐factor model of consumer based brand equity for the automotive industry. The results support the notion that after sales service is related but is a separate dimension of consumer based brand equity in the automotive sector.Research limitations/implicationsThis proposed CBBE model was tested in the automotive sector of Pakistan. However, the automotive industry is special in the sense that it builds brands at dual level. This study only investigates consumer based brand equity at marque level. Future studies can expand on this work by investigating consumer based brand equity both at marque and model levels.Practical implicationsThe establishment of after sale services as a separate but independent dimension of consumer based brand equity for the hybrid business organizations provides a fresh reminder regarding the possibilities of new sources for building brand equity. Managers can focus on delivering excellent after sale services to build and enhance the equity of their brands in hybrid business organizations.Originality/valueThis study expands Aaker's brand equity model by empirically establishing after sales service as a fifth dimension for the firms operating on hybrid business model.