bluuebunny/crossref_metadata_2025_split huggingface dataset:
Homolog detection using global sequence properties suggests an alternate view of structural encoding in protein sequences
Authors: Scheraga Harold A. , Rackovsky S. 
Published: March 2014

Significance
A Fourier-based sequence distance function for proteins is presented, which exhibits high accuracy in structural homology searches. The significance of this work lies in the fact that there has been no independent method available until now with which to compare homologies generated by sequence alignment. The method avoids the limitations of alignment and has the potential to uncover new classes of homologs and to give significant insight into the organization of the protein universe. Because it is very rapid and able to compare arbitrarily large groups of sequences simultaneously and exactly, it also has great promise as a general tool in biomedical research.
Assessing multivariate gene-metabolome associations with rare variants using Bayesian reduced rank regression
Authors: Marttinen Pekka , Pirinen Matti , Sarin Antti-Pekka , Gillberg Jussi , Kettunen Johannes , Surakka Ida , Kangas Antti J. , Soininen Pasi , O’Reilly Paul , Kaakinen Marika , Kähönen Mika , Lehtimäki Terho , Ala-Korpela Mika , Raitakari Olli T. , Salomaa Veikko , Järvelin Marjo-Riitta , Ripatti Samuli , Kaski Samuel 
Published: March 2014

AbstractMotivation: A typical genome-wide association study searches for associations between single nucleotide polymorphisms (SNPs) and a univariate phenotype. However, there is a growing interest to investigate associations between genomics data and multivariate phenotypes, for example, in gene expression or metabolomics studies. A common approach is to perform a univariate test between each genotype–phenotype pair, and then to apply a stringent significance cutoff to account for the large number of tests performed. However, this approach has limited ability to uncover dependencies involving multiple variables. Another trend in the current genetics is the investigation of the impact of rare variants on the phenotype, where the standard methods often fail owing to lack of power when the minor allele is present in only a limited number of individuals.Results: We propose a new statistical approach based on Bayesian reduced rank regression to assess the impact of multiple SNPs on a high-dimensional phenotype. Because of the method’s ability to combine information over multiple SNPs and phenotypes, it is particularly suitable for detecting associations involving rare variants. We demonstrate the potential of our method and compare it with alternatives using the Northern Finland Birth Cohort with 4702 individuals, for whom genome-wide SNP data along with lipoprotein profiles comprising 74 traits are available. We discovered two genes ( XRCC4 and MTHFD2L ) without previously reported associations, which replicated in a combined analysis of two additional cohorts: 2390 individuals from the Cardiovascular Risk in Young Finns study and 3659 individuals from the FINRISK study.Availability and implementation: R-code freely available for download at http://users.ics.aalto.fi/pemartti/gene_metabolome/ .Contact: samuli.ripatti@helsinki.fi ; samuel.kaski@aalto.fiSupplementary information: Supplementary data are available at Bioinformatics online.
Improving MEME via a two-tiered significance analysis
Authors: Tanaka Emi , Bailey Timothy L. , Keich Uri 
Published: March 2014

AbstractMotivation : With over 9000 unique users recorded in the first half of 2013, MEME is one of the most popular motif-finding tools available. Reliable estimates of the statistical significance of motifs can greatly increase the usefulness of any motif finder. By analogy, it is difficult to imagine evaluating a BLAST result without its accompanying E -value. Currently MEME evaluates its EM-generated candidate motifs using an extension of BLAST’s E -value to the motif-finding context. Although we previously indicated the drawbacks of MEME’s current significance evaluation, we did not offer a practical substitute suited for its needs, especially because MEME also relies on the E -value internally to rank competing candidate motifs.Results : Here we offer a two-tiered significance analysis that can replace the E -value in selecting the best candidate motif and in evaluating its overall statistical significance. We show that our new approach could substantially improve MEME’s motif-finding performance and would also provide the user with a reliable significance analysis. In addition, for large input sets, our new approach is in fact faster than the currently implemented E -value analysis.Contact : uri.keich@sydney.edu.au or emi.tanaka@sydney.edu.auSupplementary information : Supplementary data are available at Bioinformatics online.
MRI-based Decision Making of Implant Removal in Deep Wound Infection After Instrumented Lumbar Fusion
Authors: Kanayama Masahiro , Hashimoto Tomoyuki , Shigenobu Keiichi , Oha Fumihiro , Iwata Akira , Tanaka Masaru 
Published: March 2014

Study design:
A retrospective study.

Objective:
The aim of the study was to review the treatment of deep wound infection after posterior instrumented lumbar fusion, and thereby to optimize the decision-making process of implant removal or retention on the basis of magnetic resonance imaging (MRI) assessment.

Summary of Background Data:
Biofilm formed on the surface of the spinal implant prevents infiltration of antibiotics and makes the infection treatment more complicated. The decision of implant removal, if necessary, should be made appropriately, but the problem is a lack of consensus for implant removal or retention.

Methods:
A total of 1445 consecutive patients who underwent posterior instrumented lumbar fusion were reviewed retrospectively. There were 23 deep wound infections (1.6%) requiring surgical treatment. MR images were used to evaluate the presence or absence of osteomyelitis of the instrumented vertebra and intervertebral abscess.

Results:
Six patients in the negative MRI group (n=7) were successfully treated by a single salvage surgery without implant removal; fusion occurred in 86% of the patients. However, in the positive MRI group (n=13), 4 patients required implant removal at the initial surgery and 5 patients eventually warranted implant removal after an average of 2.4 additional operations. Notably, 3 of the 4 patients who kept the implants ended up with a loss of fixation stability attributed to screw loosening with a progressive destruction of the instrumented vertebra. Therefore, the fusion rate was only 23% for the MRI-positive patients. Furthermore, making a wrong decision regarding implant removal increased the number of salvage surgeries and frequently resulted in progressive bone destruction and pseudarthrosis.

Conclusions:
Once vertebral osteomyelitis and/or intervertebral abscess were evident in MR images, all the hardware should be removed. Failure to adhere to this recommendation resulted in multiple additional failed operations, and ultimately pseudarthrosis with further bony destruction.
Efficacy and Toxicity of Every 2 Weeks Docetaxel Regimen in Comparison With Weekly or Every 3 Weeks in Metastatic Prostate Cancer
Authors: Malhotra Akshiv , Welch Donna , Rosenbaum Paula , Poiesz Bernard J. 
Published: March 2014

Objectives:
The aim of this study was to compare weekly (q1w), 2 weekly (q2w), and 3 weekly (q3w) regimens of docetaxel in metastatic castration-resistant prostate cancer (CRPC).

Materials and Methods:
We retrospectively studied patients treated with q1w, q2w, or q3w docetaxel regimens at 30, 60, and 75 mg/m2, respectively. The choice and duration of treatment was decided by their oncologist. Patients were assessed for response, progression-free survival (PFS), and overall survival (OS), and toxicity.

Results:
Twelve, 14, and 15 patients were in the q1w, q2w, and q3w arms, respectively. Patients’ age, metastases, and mean prostate-specific antigen at start and nadir were similar among groups. Mean total dose (MTD) was higher (not significantly) in the q2w group. Response rates, mean, and median PFS and OS ranked q2w>q3w>q1w (not significantly). However, hazard ratios for PFS for the q2w and q3w arms were statistically superior to the q1w arm when adjusted for age and total dose. The same was true for OS when q3w was compared with q1w. There were no significant differences between the q2w and q3w arms. Toxicities were not different between any of the arms, save for grade 1/2 neuropathy (lower in q1w compared with q2w).

Conclusions:
The MTD, response rates, PFS, and OS in the q1w and q3w arms were similar to published reports. Although we had a small number of patients, our findings suggest that both dose concentration and total docetaxel dose may be important in the treatment of CRPC and q2w dosing is an option in patients intolerant of a higher dose concentration.
Do Parents and Children Agree? Quality‐of‐Life Assessment of Children With Inflammatory Bowel Disease and Their Parents
Authors: Gallo Julieta , Grant Amy , Otley Anthony R. , Orsi Marina , MacIntyre Brad , Gauvry Silvia , Lifschitz Carlos 
Published: March 2014

ABSTRACTBackground and Objectives:Multi‐item measures of inflammatory bowel disease (IBD) activity based on clinical, laboratory, and/or endoscopic variables do not take into consideration the impact on the patients' emotional aspects and adaptation to the disease. The aim of the present study was to evaluate concordance between parent and child ratings of health‐related quality of life on the IMPACT‐III questionnaire in children with IBD.Methods:The IMPACT‐III questionnaire was used to measure quality of life in 27 patients (mean age 14.2 ± 3 years, 40% girls) and one of their parents (82% mothers). Most of the patients had inactive disease at the time of the study. Differences between parent‐proxy ratings and child ratings on the IMPACT‐III were compared via paired‐samples t tests, intraclass correlation coefficients, and standardized difference scores.Results:Parent‐proxy and patient ratings were similar on total IMPACT‐III and its related domains (bowel symptoms, systemic symptoms, social functioning, body image, treatment/interventions), except that significant differences on emotional functioning ratings were found (P = 0.003). Intraclass correlation coefficients showed medium‐to‐large effect sizes (range 0.52–0.88) and standardized difference scores showed varying degrees of bias depending on the domain measured (range −0.64 to 0.32).Conclusions:Parents served as a good proxy for quality‐of‐life ratings in this population of pediatric patients with IBD. The degree of concordance between parent and child scores, however, varied, as observed in the present study in which parents underreported their child's health‐related quality of life on the IMPACT‐III emotional functioning domain.
Composites and MIL-STD-1530C
Authors: Warren Aaron , Heslehurst Rikard , Wilson Eric 
Published: March 2014

Purpose
– The purpose of this paper is to discuss changes to MIL-STD-1530C “Aircraft Structural Integrity Program” to account for the increased usage of composites in aircraft structures.

Design/methodology/approach
– The evolution of the Aircraft Structural Integrity Program is presented and the five tasks that comprise the program are assessed for compatibility with composite aircraft structures.

Findings
– This paper identifies a number of recommended changes to MIL-STD-1530C to ensure that the unique behaviour of composites is considered within the Aircraft Structural Integrity Program.

Originality/value
– This paper recommends changes to MIL-STD-1530C to account for composite aircraft structures, thus providing assurance compatibility of the Aircraft Structural Integrity Program with composite materials.
Improvement of fatigue limit by shot peening for high-strength steel containing a crack-like surface defect
Authors: Yasuda Jun , Takahashi Koji , Okada Hideki 
Published: March 2014

Purpose
– The purpose of this study is to clarify the influence of stress ratio (R) on the effects of shot peening (SP) on the fatigue limit of high-strength steel containing an artificial small defect.

Design/methodology/approach
– SP was subjected on the specimens with a semi-circular slit with a depth of a=0.1, 0.2 and 0.3 mm. Then, bending fatigue tests were carried out under R=0.4.

Findings
– The fatigue limits of specimens with a semi-circular slit were improved by SP under R=0.4. The fatigue limits of the SP specimens with a semi-circular slit under a=0.2 mm fractured outside the slit, and they had considerably high fatigue limits equal to specimens without a slit. Therefore, a semi-circular slit with a depth of under a=0.2 mm could be rendered harmless by SP under R=0.4. Compared to the results of R=0, the increasing ratios of fatigue limits under R=0.4 were lower than those under R=0. However, the size of semi-circular slit that could be rendered harmless by SP was same. In addition, it was found that whether the semi-circular slit is rendered harmless or not is decided by the relationship between the stress intensity factor range of semi-circular cracks and the threshold stress intensity factor regardless of stress ratio.

Practical implications
– The proposed method can be applied to mechanical parts used in vehicles, aircraft and trains.

Originality/value
– This is the first paper to investigate the fatigue limits after SP in materials containing a surface defect under positive stress ratio. In this study, the authors investigated the influence of stress ratio on the effects of SP on the fatigue limit containing a surface defects.
Developing superior value propositions: a strategic marketing imperative
Authors: Payne Adrian , Frow Pennie 
Published: March 2014

Purpose
– Scholars identify the value proposition as representing the essence of strategy and the firm's single most important organizing principle. However, research suggests less than 10 per cent of companies formally develop value propositions. The purpose of this paper is to undertake case study research investigating the process by which leading companies develop their value propositions.

Design/methodology/approach
– The research identifies that the financial services and telecommunications vertical markets are viewed as the highly sophisticated industry sectors in terms of customer management. These industry sectors are selected for investigation. The paper develops case studies of two companies’ approaches to developing value propositions in the business-to-business (B2B) and business-to-consumer (B2C) sectors within these vertical markets.

Findings
– This paper contributes to the marketing literature by examining how two large and complex service enterprises have adopted structured processes for developing innovative value proposition within the B2B and B2C sectors. The authors argue that innovation in value proposition development represents a substantive opportunity for marketing to reassert its influence in the boardroom.

Practical implications
– This case study research provides guidelines of the processes by which enterprises can successfully develop innovative value propositions.

Originality/value
– This research is considered to be the first case-based academic exploration of the formal processes by which large organizations develop value propositions.
The road back to relevance
Authors: Klaus Philipp , Edvardsson Bo 
Published: March 2014

Purpose
– Based upon primary research, the purpose of this paper is to highlight the three main sources of frustration about the marketing scholars’ community current status quo. It delivers feasible solutions and describes, using the example of the Special Issue, how to overcome these challenges and provide the research environment all desire.

Design/methodology/approach
– Editorial paper summarizing the Special Issue's contributions and observations from the marketing scholar community.

Findings
– The three main sources of frustration for marketing scholars about the current system are, first, review and publishing processes, second, the dominant epistemological and methodological approach in academe, encouraging an increasing specialization and reliance on generating more and more quantitatively driven knowledge and finally, the lack of acceptance (and outright disdain) for research with a managerial, applied emphasis.

Practical implications
– But it surely is not mission impossible to build the research environment that is wanted. To build the research environment the community desires and to be “back where we belong,” to be relevant means the need to do more than just engaging in lip service. Rather than complying with the system causing frustration, the paper asks all to take an active part in the change process. The paper strongly encourages all, as editors, reviewers, colleagues, mentors and supervisors to do so and take some chances. Engage in and support brave research.

Social implications
– The authors hope that the paper will stimulate research widely accessible to both managers, and a broader audience. This will eventually lead to a better reputation and public opinion toward marketing scholars and research.

Originality/value
– Rather than simply stating the main frustrations of the marketing scholar community, and calling for changes, the authors demonstrate how these challenges can be overcome, and deliver platforms to communicate and lead both the conversation and the actions to achieve the research community most desire.
Branding paradigms and the shift of methodological approaches to branding
Authors: Mazurek Marica 
Published: March 2014

Purpose– The aim of this paper is to discuss and conceptually support the statement that a critical and holistic approach to branding requires interplay of the methods and methodologies of different disciplines and the so-called decompositional approach.Design/methodology/approach– The study is based on the thorough secondary research based on content analysis of the studied literature dealing with the methodological approach to brand management and branding, especially the comparison of brand management categorization and development of approaches from the customer centrality and strategic priority to the adaptive and relational paradigms.Findings– The major outcome of this research is the confirmation of the fact that changes of paradigmatic approaches to research are rooted in economic and social changes. The predominance of relational, community, cultural approaches stem from the growth of customers' value and a new role of customers in the economic and social sphere.Research limitations/implications– The topic of branding in management in tourism destinations is still emerging, especially understanding of transition of paradigms and approaches to the research of branding in tourism.Practical implications– Important is the explanation of differences between the approaches to branding and especially the fact that some of the approaches (relational, community and cultural approach) are based on systems-thinking and contribute to the competitive advantage creation.Originality/value– The paper aims to highlight the fact how global social and economic forces and changing cycles (Kondratiev) have influenced the empirical research and the implementation of ideas on economic interventions and social problems topics. This fact embraced major themes in a society and has influenced research on innovation and branding. It might be compelling to discuss the changes in paradigms and explain why social responsibility and other core themes resonate and influence the managerial practices in tourism and the paradigms in research of tourism dealing with brand management.
Towards viral systems thinking: a cross-cultural study of sustainable tourism ads
Authors: Batat Wided , Prentovic Sonja 
Published: March 2014

Purpose
– In the postmodern consumer society, factors such as sustainability, responsible behaviour and digital environment have direct consequences on rethinking sustainable tourism promotion through 2.0 communication policy embedded within a specific cultural context. The aim of this research is to analyse and discuss the application of 2.0 systems thinking (ST) in three countries (France, UK and Serbia) to promote sustainable tourism thinking.

Design/methodology/approach
– Online tourism ads available on YouTube, Vimeo, and Dailymotion, related to the cultural contexts of the UK, France and Serbia, have been analysed through a qualitative approach based on the use of visual methods. Furthermore, sustainable tourism dimensions and discourses have been identified in each context by applying intra- and intertextual analysis.

Findings
– The results show that the use of 2.0 ST to promote sustainable tourism should take into account environmental and socio-cultural issues in each cultural context. These findings show that both the UK and France promote sustainable tourism logic through applying a 2.0 ST. This is not the case with Serbia where online sustainable tourism videos are underrepresented and the online content is different from the one in the UK and France.

Research limitations/implications
– This research might help tourism researchers and professionals to understand cultural differences when promoting sustainable tourism through a 2.0 communication and online videos. The results show that tourism system has to be considered as a complex and a dynamic framework where intense interlinking of social media with political, cultural, promotional, and organizational aspects of tourism systems in different countries is present.

Practical implications
– The proposed framework in this study represents a tool that will enable tourism professionals to improve their sustainable tourism communication, especially the environmental and socio-cultural dimensions when considering a 2.0 communication approach.

Originality/value
– The original aspect of this research is related to the analysis of interactive videos in tourism studies and to the introduction of a new framework based on 2.0 ST, used to promote sustainable tourism in a cross-cultural context.
Building a model of researching the sustainable entrepreneurship in the tourism sector
Authors: Crnogaj Katja , Rebernik Miroslav , Bradac Hojnik Barbara , Omerzel Gomezelj Doris 
Published: March 2014

Purpose– The tourism sector is heavily dependent on entrepreneurship and cannot survive in the long run if it is not both sustainable and entrepreneurial at the same time; these three areas – entrepreneurship, sustainability, and tourism – are rarely linked in research and are not reflected in appropriate policy-making measures. Thus, the purpose of this paper is to develop a conceptual multilevel model that will provide a requisitely holistic means for studying sustainable entrepreneurship in the tourism sector.Design/methodology/approach– In the process of developing a model, the authors took into account the principle of requisite variety and considered various dimensions related to sustainable entrepreneurship implicated at three levels of analysis – namely, individual (entrepreneur), organizational (SME), and national/regional (tourism destination).Findings– The proposed model provides systemic and systematic views on sustainable entrepreneurship in the tourism sector and contains various levels of analysis. The holistic framework for studying sustainable entrepreneurship in the tourism helps highlight influential elements from an economics point of view as well as their measurable and internationally comparable outcomes.Originality/value– The suggested model represents an initial step toward the measurement of sustainable entrepreneurship in tourism at various levels, thereby making a valuable contribution to future research designs seeking to evaluate the benefits of sustainable entrepreneurship. The paper provides an important foundation for evidence-based policy making with the aim of fostering requisitely holistic behavior and innovative, responsible, and sustainable entrepreneurship practices in the tourism sector.