bluuebunny/crossref_metadata_2025_split huggingface dataset:
IBD-Groupon: an efficient method for detecting group-wise identity-by-descent regions simultaneously in multiple individuals based on pairwise IBD relationships
Authors: He Dan 
Published: June 2013

Abstract
Motivation: Detecting IBD tracts is an important problem in genetics. Most of the existing methods focus on detecting pairwise IBD tracts, which have relatively low power to detect short IBD tracts. Methods to detect IBD tracts among multiple individuals simultaneously, or group-wise IBD tracts, have better performance for short IBD tracts detection. Group-wise IBD tracts can be applied to a wide range of applications, such as disease mapping, pedigree reconstruction and so forth. The existing group-wise IBD tract detection method is computationally inefficient and is only able to handle small datasets, such as 20, 30 individuals with hundreds of SNPs. It also requires a previous specification of the number of IBD groups, or partitions of the individuals where all the individuals in the same partition are IBD with each other, which may not be realistic in many cases. The method can only handle a small number of IBD groups, such as two or three, because of scalability issues. What is more, it does not take LD (linkage disequilibrium) into consideration.
Results: In this work, we developed an efficient method IBD-Groupon, which detects group-wise IBD tracts based on pairwise IBD relationships, and it is able to address all the drawbacks aforementioned. To our knowledge, our method is the first practical group-wise IBD tracts detection method that is scalable to very large datasets, for example, hundreds of individuals with thousands of SNPs, and in the meanwhile, it is powerful to detect short IBD tracts. Our method does not need to specify the number of IBD groups, which will be detected automatically. And our method takes LD into consideration, as it is based on pairwise IBD tracts where LD can be easily incorporated.
Contact: dhe@us.ibm.com
Efficient network-guided multi-locus association mapping with graph cuts
Authors: Azencott Chloé-Agathe , Grimm Dominik , Sugiyama Mahito , Kawahara Yoshinobu , Borgwardt Karsten M. 
Published: June 2013

AbstractMotivation: As an increasing number of genome-wide association studies reveal the limitations of the attempt to explain phenotypic heritability by single genetic loci, there is a recent focus on associating complex phenotypes with sets of genetic loci. Although several methods for multi-locus mapping have been proposed, it is often unclear how to relate the detected loci to the growing knowledge about gene pathways and networks. The few methods that take biological pathways or networks into account are either restricted to investigating a limited number of predetermined sets of loci or do not scale to genome-wide settings.Results: We present SConES, a new efficient method to discover sets of genetic loci that are maximally associated with a phenotype while being connected in an underlying network. Our approach is based on a minimum cut reformulation of the problem of selecting features under sparsity and connectivity constraints, which can be solved exactly and rapidly.SConES outperforms state-of-the-art competitors in terms of runtime, scales to hundreds of thousands of genetic loci and exhibits higher power in detecting causal SNPs in simulation studies than other methods. On flowering time phenotypes and genotypes from Arabidopsis thaliana, SConES detects loci that enable accurate phenotype prediction and that are supported by the literature.Availability: Code is available at http://webdav.tuebingen.mpg.de/u/karsten/Forschung/scones/.Contact: chloe-agathe.azencott@tuebingen.mpg.deSupplementary information: Supplementary data are available at Bioinformatics online.
Cake: a bioinformatics pipeline for the integrated analysis of somatic variants in cancer genomes
Authors: Rashid Mamunur , Robles-Espinoza Carla Daniela , Rust Alistair G. , Adams David J. 
Published: June 2013

Abstract
Summary: We have developed Cake, a bioinformatics software pipeline that integrates four publicly available somatic variant-calling algorithms to identify single nucleotide variants with higher sensitivity and accuracy than any one algorithm alone. Cake can be run on a high-performance computer cluster or used as a stand-alone application.
Availabilty: Cake is open-source and is available from http://cakesomatic.sourceforge.net/
Contact: da1@sanger.ac.uk
Supplementary Information: Supplementary data are available at Bioinformatics online.
Known and missing left ventricular ejection fraction and survival in patients with heart failure: a MAGGIC meta‐analysis report
Authors: Poppe Katrina K. , Squire Iain B. , Whalley Gillian A. , Køber Lars , McAlister Finlay A. , McMurray John J.V. , Pocock Stuart , Earle Nikki J. , Berry Colin , Doughty Robert N. ,   on behalf of the Meta‐Analysis Global Group in Chronic Heart Failure (MAGGIC)
Published: June 2013

AimsTreatment of patients with heart failure (HF) relies on measurement of LVEF. However, the extent to which EF is recorded varies markedly. We sought to characterize the patient group that is missing a measure of EF, and to explore the association between missing EF and outcome.Methods and resultsIndividual data on 30 445 patients from 28 observational studies in the Meta‐Analysis Global Group in Chronic Heart Failure (MAGGIC) project were used to compare the prevalence of co‐morbidities and outcome across three groups of HF patients: those with missing EF (HF‐mEF), reduced EF (HF‐REF), and preserved EF (HF‐PEF). A total of 29% had HF‐mEF, 52% HF‐REF, and 19% HF‐PEF. Compared with patients in whom EF was known, patients with HF‐mEF were older, had a greater prevalence of COPD and previous stroke, and were smokers. Patients with HF‐mEF were less likely to receive evidence‐based treatment than those with HF‐REF. Adjusted mortality in HF‐mEF was similar to that in HF‐REF and greater than that in HF‐PEF at 3 years [HF‐REF, hazard ratio (HR) 1.03, 95% confidence interval (CI) 0.95–1.12); HF‐PEF, HR 0.78, 95% CI 0.71–0.86].ConclusionMissing EF is common. The short‐ and long‐term outcome of patients with HF‐mEF is poor and they exhibit different co‐morbidity profiles and treatment patterns compared with patients with known EF. HF patients with missing EF represent a high risk group.
Alternative Gene Form Discovery and Candidate Gene Selection from Gene Indexing Projects
Authors: Burke John , Wang Hui , Hide Winston , Davison Daniel B. 
Published: June 2013

Several efforts are under way to partition single-read expressed sequence tag (EST), as well as full-length transcript data, into large-scale gene indices, where transcripts are in common index classes if and only if they share a common progenitor gene. Accurate gene indexing facilitates gene expression studies, as well as inexpensive and early gene sequence discovery through assembly of ESTs that are derived from genes that have not been sequenced by classical methods. We extend, correct, and enhance the information obtained from index groups by splitting index classes into subclasses based on sequence dissimilarity (diversity). Two applications of this are highlighted in this report. First it is shown that our method can ameliorate the damage that artifacts, such as chimerism, inflict on index integrity. Additionally, we demonstrate how the organization imposed by an effective subpartition can greatly increase the sensitivity of gene expression studies by accounting for the existence and tissue- or pathology-specific regulation of novel gene isoforms and polymorphisms. We apply our subpartitioning treatment to the UniGene gene indexing project to measure a marked increase in information quality and abundance (in terms of assembly length and insertion/deletion error) after treatment and demonstrate cases where new levels of information concerning differential expression of alternate gene forms, such as regulated alternative splicing, are discovered.[Tables 2and 3 can be viewed in their entirety as Online Supplements athttp://www.genome.org.]
A portable application for supporting ABA intervention
Authors: Artoni Silvia , Claudia Buzzi Maria , Buzzi Marina , Fenili Claudia , Leporini Barbara , Mencarini Simona , Senette Caterina 
Published: June 2013

PurposeApplied Behavior Analysis (ABA) is a scientific method for modelling human behavior, successfully applied in the context of Autism. Recording and sharing measurable data (on subjects’ performance) between caregivers guarantees consistency of learning programs and allows monitoring the learning enhancements. Data are usually recorded on paper, which requires considerable effort and is subject to error. The purpose of this paper is to describe a portable application developed to support ABA tutors in their work with autistic subjects. It allows gathering data from ABA sessions, giving tutors rapid access to information, also in graphical formats.Design/methodology/approachThe tool was designed via participatory design. Various ABA team members were involved, in order to make the application respond perfectly to their needs. The approach aims to ensure maximum usability, while minimizing errors and ambient interference.FindingsThe use of mobile devices (i.e. tablets or smartphones) allows mobility and ease of interaction, enabling efficient data collection and processing. Data plotting allows one to easily interpret gathered data.Social implicationsThe proposed application, free open source software, can be a valuable aid for supporting the ABA intervention and favor the inclusion of children with autism.Originality/valueAvailable software to assist tutors during therapy sessions is often proprietary, and research prototypes are not freely available, so paper forms are still widespread. Besides, without attention to usability requirements, assisting tools would be comparable in efficiency with data insertion on paper. Our software was specifically designed following ABA principles and favors efficient data entry allowing natural interaction with touch screen interfaces: drag and drop, taps and gestures. Furthermore, it is shared in the public domain.
Visual noun navigation framework for the blind
Authors: Molina Edgardo , Diallo Alpha , Zhu Zhigang 
Published: June 2013

ProposeThe purpose of this paper is to propose a local orientation and navigation framework based on visual features that provide location recognition, context augmentation, and viewer localization information to a blind or low‐vision user.Design/methodology/approachThe authors consider three types of “visual noun” features: signage, visual‐text, and visual‐icons that are proposed as a low‐cost method for augmenting environments. These are used in combination with an RGB‐D sensor and a simplified SLAM algorithm to develop a framework for navigation assistance suitable for the blind and low‐vision users.FindingsIt was found that signage detection cannot only help a blind user to find a location, but can also be used to give accurate orientation and location information to guide the user navigating a complex environment. The combination of visual nouns for orientation and RGB‐D sensing for traversable path finding can be one of the cost‐effective solutions for navigation assistance for blind and low‐vision users.Research limitations/implicationsThis is the first step for a new approach in self‐localization and local navigation of a blind user using both signs and 3D data. The approach is meant to be cost‐effective but it only works in man‐made scenes where a lot of signs exist or can be placed and are relatively permanent in their appearances and locations.Social implicationsBased on 2012 World Health Organization, 285 million people are visually impaired, of which 39 million are blind. This project will have a direct impact on this community.Originality/valueSignage detection has been widely studied for assisting visually impaired people in finding locations, but this paper provides the first attempt to use visual nouns as visual features to accurately locate and orient a blind user. The combination of visual nouns with 3D data from an RGB‐D sensor is also new.
Realizing the dream of owning a home
Authors: Opoku Robert A. , Abdul‐Muhmin Alhassan G. 
Published: June 2013

PurposeThis study aims to investigate the house purchase behavior of low‐income Saudis regarding the sources of financing they wish to have access to, their preferences for alternative financing options, and the monthly payment amounts they could afford to make in case of mortgage financing across demographic groups.Design/methodology/approachA survey with a sample of 815 low‐income respondents with a monthly income of SR7,000 was conducted using a structured questionnaire.FindingsThe main findings of the study are that the loan from the government Real Estate Development Fund (REDF) is found to be the most preferred financing alternative, the second being cash payment; whilst the most frequently indicated option for monthly mortgage payments is between SR1,000 and SR1,500 (US$267 and US$400) among low‐income Saudis.Research limitations/implicationsThis study provides a snapshot of low‐income Saudi consumers' knowledge of financing options and their choice among alternative financing options.Practical implicationsThis also offers opportunities for real estate developers to seek competitive advantage by coming up with innovative financing options to target low‐income earners.Originality/valueThere is limited published work exploring consumer knowledge of house purchase finance options that captures this phenomenon from the perspectives of low‐income Saudi consumers. This study contributes in filling this gap.
Information support technologies of integrated production planning and control for OEM driven networked manufacturing
Authors: Chen Zhixiang , Li Li 
Published: June 2013

PurposeThe purpose of this paper is to study the information support technologies of integrated production planning control for OEM (original equipment manufacturer) driven networked manufacturing systems, and offer implications to firms for implementing networked manufacturing.Design/methodology/approachOEM driven networked manufacturing and its operations modes and support technologies are first discussed. Then, integration framework of production planning and control is proposed and relative technologies are discussed. Finally, a case of the application of information support technologies in networked manufacturing is illustrated.FindingsBoth theory analysis and case experience show that information integration and sharing are critical for effective operations of OEM driven networked manufacturing and an integrated production planning and control system can benefit firms for successfully operating a networked manufacturing system.Practical implicationsIt is valuable to develop and apply integrated production planning and control systems in OEM driven networked manufacturing, Firms should pay more attention to information sharing and communication with partners and utilize advanced information technologies to synchronize the operations of partners.Originality/valueIntegration framework of production planning and control proposed in this paper has originality and the technology strategies are also practical. Managerial ideas, technology framework and application strategies of integrated production planning and control are helpful for firms to implement OEM driven networked manufacturing.
The shopping experience of older supermarket consumers
Authors: Yin Yuanyuan , Pei Eujin , Ranchhod Ashok 
Published: June 2013

PurposeThe purpose of this research is to investigate the difficulties and challenges faced by the older supermarket consumers in order to form insights into potential ways of applying IT support and design solutions within the supermarket service for older consumers. The rationale for this research stemmed from observations and discussions with supermarkets with regards to the use of IT and better process design for a growing segment of their consumer base.Design/methodology/approachA mixed research methodology was used for this research. Firstly, an ethnographic approach based on direct observations was felt appropriate as this would offer a visual unbiased view of the processes involved in the shopping experience. Secondly, it was felt that it would be appropriate to support these findings with semi‐structured interviews. The data was clustered to provide contextual awareness of the problems involved within the shopping experience.FindingsThe findings indicated a range of areas where senior consumers faced difficulties. One major problem was around understanding where certain products were placed on shelves and why. The other areas of concern were access to products (shelf height), poor signage, labelling and inappropriate portion sizes.Research limitations/implicationsThe main research limitation is the small sample size that was studied. Obviously with a much larger sample a wider range of problems would be uncovered. The other area of concern is the fact that studying particular customers invades the privacy of customers that are inadvertently caught up on videos. In future, it may make sense to get participants to film themselves and talk into smart mobiles, recording real‐time data.Practical implicationsThe research indicates that it is important for supermarkets to improve signage and customer support, and use IT more freely in most areas. The use of electronic ink signage is a new and important area that they could invest in. This would allow real‐time updates.Social implicationsAs many countries are faced with growing numbers of senior citizens, it is important that their lives are made easier and the shopping experience improved.Originality/valueThere are limited attempts at the use of an ethnographic approach to explore elderly consumers’ shopping experiences in the UK. The existing studies do not look at the practicalities of everyday shopping problems faced by this segment of the population. It also adds value to the retailers’ understanding of the behaviour patterns of this important customer segment, at the same time offering solutions to certain problems such as signage and directions through the utilisation of IT.
The NYSE and NASDAQ issue proposed rules to implement the SEC compensation committee independence and advisor rules
Authors: Lilienfeld Doreen , Cannon John , Gitlitz Bennett Amy , Spera George 
Published: June 2013

PurposeThe purpose of this paper is to explain the amendments to the listing standards of the New York Stock Exchange (NYSE) and the NASDAQ Stock Market (Nasdaq), which were approved by the Securities and Exchange Commission (the SEC) on January 11, 2013 to implement the SEC's final rules on the independence of compensation committees and their selection of advisors pursuant to Rule 952 of the Dodd‐Frank Wall Street Reform and Consumer Protection Act of 2010 (Dodd Frank).Design/methodology/approachAfter a summary of notable provisions, the paper explains effective dates and respective Nasdaq and NYSE listing standards pertaining to compensation committee compensation; director independence standards, advisors, and charters; certain exemptions for foreign issuers; exemptions for certain types of companies and partnerships; and recommended next steps for companies that are subject to the amended listing standards.FindingsOver the past few years, the independence of compensation committees and their advisors has been a hot button corporate governance issue. Dodd‐Frank prohibits national securities exchanges from listing any equity security of an issuer that is not in compliance with the exchanges' compensation committee independence and advisor requirements.Practical implicationsThe listing standards generally become effective on July 1, 2013; however, listed companies have until the earlier of: their first annual meeting after January 15, 2014; or October 31, 2014, to comply with certain requirements including the independence structure of their compensation committees.Originality/valueThe paper provides practical advice from experienced financial services lawyers.
Building brand value in major Spanish cities: an analysis through municipal websites
Authors: Sáez Lucía , Periáñez Iñaki , Mediano Lucía 
Published: June 2013

PurposeUrban managers increasingly focus on establishing the city as a brand to ensure a competitive force that enables the city to position itself at home and abroad. The purpose of this paper is to analyze the development of city branding from the market orientation of the capital cities of Spain's regional Autonomous Communities.Design/methodology/approachThe analysis uses a set of variables representing the different aspects that shape market orientation, and variables related to the development and implementation of city branding strategies. The methodology for collecting information on the cities under study is based on content analysis, and its specific application to the analysis of websites.FindingsThe research carried out reveals the existence of four distinct groups of Spain's cities that can be differentiated in terms of the importance that they give to the different areas of market orientation and the development of city branding strategies.Research limitations/implicationsThe cities considered give an insight into the strategies of brand creation and development at major Spanish cities but tell nothing about secondary cities. The scope of the study is purely domestic. The authors intend to expand it to include cities elsewhere in Europe, to enable comparisons to be drawn of the processes of creation and development of city branding in different countries. The municipal web sites used as a source of information show some volatility, and as a result need to be reviewed from time to time.Originality/valueAlthough web sites as marketing tools offer significant advantages, such as accessibility of information, provision of relevant information, handling of complaints, low cost, and customer service, there has been very little research into their role in urban management. Using the content provided by each municipality's official web site as a source, this paper offers a different perspective which complements research performed through other methods.
Embedding healthy eating: nudging or toolbox?
Authors: Schröder Monika , Lyon Phil 
Published: June 2013

PurposeThe purpose of this paper is to examine the rationale and limitations of public nudging approaches currently to be found in the UK food choice environment.Design/methodology/approachThe paper uses a critical review of the literature with case studies.FindingsNudging has potential value to assist healthier food choices, although the current focus of proponents tends to be the individual micro‐environment for selection rather than the wider food choice context. Ethical questions are raised by nudging as a policy and limited evidence of success to date would suggest that a combination of personalised tools and public nudges – individual empowerment and attention to the choice environment – might be more effective for embedded healthier eating.Originality/valueThis paper contrasts the underlying assumptions of the nudge approach by reference to the behavioural toolbox.