bluuebunny/crossref_metadata_2025_split huggingface dataset:
Are all global alignment algorithms and implementations correct?
Authors: Flouri Tomáš , Kobert Kassian , Rognes Torbjørn , Stamatakis Alexandros 
Published: November 2015

Abstract.Pairwise sequence alignment is perhaps the most fundamental bioinformatics operation. An optimal global alignment algorithm was described in 1970 by Needleman and Wunsch. In 1982 Gotoh presented an improved algorithm with lower time complexity. Gotoh’s algorithm is frequently cited (1447 citations, Google Scholar, May 2015), taught and, most importantly, used as well as implemented. While implementing the algorithm, we discovered two mathematical mistakes in Gotoh’s paper that induce sub-optimal sequence alignments. First, there are minor indexing mistakes in the dynamic programming algorithm which become apparent immediately when implementing the procedure. Hence, we report on these for the sake of completeness. Second, there is a more profound problem with the dynamic programming matrix initialization. This initialization issue can easily be missed and find its way into actual implementations. This error is also present in standard text books. Namely, the widely used books by Gusfield and Waterman. To obtain an initial estimate of the extent to which this error has been propagated, we scrutinized freely available undergraduate lecture slides. We found that 8 out of 31 lecture slides contained the mistake, while 16 out of 31 simply omit parts of the initialization, thus giving an incomplete description of the algorithm. Finally, by inspecting ten source codes and running respective tests, we found that five implementations were incorrect. Note that, not all bugs we identified are due to the mistake in Gotoh’s paper. Three implementations rely on additional constraints that limit generality. Thus, only two out of ten yield correct results. We show that the error introduced by Gotoh is straightforward to resolve and provide a correct open-source reference implementation. We do believe though, that raising the awareness about these errors is critical, since the impact of incorrect pairwise sequence alignments that typically represent one of the very first stages in any bioinformatics data analysis pipeline can have a detrimental impact on downstream analyses such as multiple sequence alignment, orthology assignment, phylogenetic analyses, divergence time estimates, etc.
Overview: Modeling Heterogeneous Tumor Tissue as a Multiphase Material
Authors: Frieboes Hermann B. 
Published: November 2015

AbstractTumors are typically heterogeneous tissues comprised of multiple cell species in addition to extra-cellular matrix (ECM) and water fluid. It is difficult to model these components at the tissue (10−3–10−2m) scale, where individual cells cannot be represented without prohibitive computational burden. Assuming that same-kind components tend to cluster together, a multiphase approach can be applied to represent heterogeneous tumor tissue at this larger physical scale. This method enables simulating mixture of elements within tissues, e.g., geno-/phenotypic heterogeneity underlying mutation- or microenvironment-driven tumor progression. Further, by not explicitly tracking interfaces, this methodology facilitates realistic modeling of tissue in 3-D.
Connecting Boolean Integrase Logic gates to a novel alkane control signal via engineered level matching
Authors: Folliard Thomas , Bonnet Jerome , Ward John , Baganz Frank , Grant Chris , Endy Drew 
Published: November 2015

ABSTRACTBoolean Integrase Logic gates use phage integrases that respond to transcriptional signals to implement logical functions within living cells via DNA recombination. Control of biological systems using these logic gates has many applications, including biomanufacturing, healthcare, or environmental remediation. Gates are highly sensitive to background transcriptional noise producing unwanted integrase expression and uncontrolled, permanent gate switching. Consequently, connecting gates to novel control signals requires time-consuming directed evolution of regions regulating integrase expression. Here we present an approach in which the activity of an alkane biosensor is tuned to match levels of existing integrase control signals. By adjusting AlkS expression, we tuned the transcriptional output ofPalkbto match the output of existing integrase controllers. We successfully connectedPalkbto two integrases with different transcriptional control requirements and demonstrated the original logic function was conserved. Our method complements directed evolution approaches to connect Boolean integrate logic gates to novel transcriptional sources and will ultimately facilitate the systematicin silicodesign of gates responding to various control signals.
Do recovery experiences moderate the relationship between workload and work-family conflict?
Authors: Molino Monica , Cortese Claudio G. , Bakker Arnold B. , Ghislieri Chiara 
Published: November 2015

Purpose– The purpose of this paper is to investigate the role of four recovery experiences (psychological detachment from work, relaxation, mastery, and control) in preventing work-family conflict (WFC). Specifically, on the basis of WFC and recovery theories the authors hypothesized that workload would be positively related to WFC, and that recovery experiences would moderate this relationship.Design/methodology/approach– The research involved 597 Italian employees (on pay-role or self-employed) from different occupational sectors. Participants filled-in an on-line questionnaire. Moderated structural equation modelling were used to test the hypotheses.Findings– Results showed a positive relationship of workload with WFC. Regarding the hypothesized interaction effects, the relationship between workload and WFC was particularly strong under condition of low (vs high) psychological detachment, low relaxation, and low control.Originality/value– This study highlights the beneficial role of recovery experiences in preventing the spillover of workload to the family domain, showing their moderating effects for the first time. These findings have several implications for both future research and practitioners.
The impact on the psychological contract of differentiating employees into talent pools
Authors: Seopa Noko , Wöcke Albert , Leeds Camilla 
Published: November 2015

Purpose
– This research stems from the need by organisations to retain their key talent in the context of the change in the psychological contract manifested from the emergence of boundaryless careers. Many organisations have segmented their workforce to develop talent pools of high potential employees to meet the organisation’s current and future critical skills needs. The purpose of this paper is to investigate the impact of inclusion or exclusion in the talent pool on the psychological contract.

Design/methodology/approach
– The study presents findings from 195 employees from three different organisations, about 50 per cent of whom were in talent pools. Various instruments in the literature were used to measure the psychological contract and the other constructs of organisational citizenship behaviour, trust and turnover intention of employees in the talent pools in comparison to those not in talent pools.

Findings
– The study shows that being part of the talent pool has a positive impact on the relational psychological contract and organisational commitment but does not necessarily translate into trust and the intention to stay with organisations.

Research limitations/implications
– The study was conducted in three large firms with well-developed and entrenched talent management strategies. The results may be different in firms with less formal talent management strategies or those firms that do not use talent pools. Despite these limitations, the study is valuable in showing the differences in relationships between employees recognised as more important and those not recognised in the same way.

Practical implications
– Talent strategy should not ignore employees not in talent pools as they have shown that they display an aspiration to build long-term relationships with their employers and could represent a future source of potential. It is recommended that organisations should continue to segment their workforce to determine who should form part of the talent pool.

Social implications
– The results indicate the high complexity in understanding contemporary employment relationships and could be closely related to the previous findings on trust. Despite being identified as potential employees for development into linchpin and pivotal positions in their organisation, these employees were no different to employees not in talent pools when it came to trust and the intention to leave their organisation.

Originality/value
– Employees in talent pools and those not in talent pools were similar in their intention to leave their organisations in circumstances where their expectations were not met. This finding is contrary to the expectation and indicates that relational psychological contracts do not have a moderating impact on the intention to leave where expectations are not met.
Brand experimental value versus brand functional value: which matters more for the brand?
Authors: Delgado-Ballester Elena , Fernandez Sabiote Estela 
Published: November 2015

Purpose
– The purpose of this study is to analyze the relative higher impact of brand experiential value over brand functional value in generating brand equity, consumer–brand identification and positive word-of-mouth (WOM). It also analyzes whether the impact of these brand values in building brand outcomes depends on consumers’ age.

Design/methodology/approach
– Information was collected from a sample of 332 consumers by personal interviews. Respondents provide information about their consumption experiences with a specific brand from a stated list of 14 experiential and non-experiential brands.

Findings
– Results suggest that the effect of brand experiential value on brand equity and consumer-brand identification was higher than that of brand functional value. By contrast, positive WOM was more influenced by brand functional value. Furthermore, the results also confirm that as consumers age, brand experiential value exhibits a significant higher effect than brand functional value on brand outcomes.

Research limitations/implications
– A potential shortcoming is the common method bias. As far as one questionnaire was used to measure all study constructs, the strength of the causal relationships among constructs may have been inflated.

Practical implications
– For brand managers, the key implications concern on how to effectively allocate brand investment to build stronger brand equity and consumer-brand identification and stimulated positive WOM.

Originality/value
– Despite the greater importance that the experiential perspective is gaining in the brand literature and the voices proclaiming that experiential value will matter most, this is the first empirical research paper that analyzes that the relative superiority of experiential value over functional value depends on the brand outcomes pursued and consumers’ age.
Deconstructing consumer discipline
Authors: Cronin James Martin , McCarthy Mary , Delaney Mary 
Published: November 2015

Purpose– The purpose of this paper is to build an understanding of what we term “consumer discipline” by unpacking the practices and strategies by which people manage and exert control over what they consume. This is facilitated by looking at the context of food, an everyday necessity imbued with sizeable importance in terms of its impact on personal well-being, and how it is experienced by individuals who must manage the constraints of a chronic illness.Design/methodology/approach– Drawing on the Foucauldian concept of governmentality and theories surrounding the social facilitation of self-management, this paper analyses interviews with 17 consumers diagnosed with diabetes or coronary heart disease.Findings– By exploring how the chronically ill generate different strategies in managing what they eat and how they think about it, this paper outlines four analytical areas to continue the discussion of how consumption is disciplined and its conceptualisation in marketing and health-related research: “the Individual”, “the Other”, “the Market” and “the Object”.Practical implications– The results signal to policymakers the aspects of health promotion that can be enhanced to improve self-management amongst consumers in the pursuit of well-being.Originality/value– This paper makes two contributions: it conceptualises consumer discipline as a practice that involves self-control but also comprises the capabilities to self-manage one’s identity and relationships through leveraging personal and social strategies across various contexts; and it identifies macro influences such as the market as negotiable powers that can be contested or resisted to help assist in one’s self-management.
When does metric use matter less?
Authors: Mintz Ofer , Currim Imran S. 
Published: November 2015

Purpose– This paper aims to develop a conceptual framework, in an effort toward building a contingent theory of drivers and consequences of managerial metric use in marketing mix decisions, this paper develops a conceptual framework to test whether the relationship between metric use and marketing mix performance is moderated by firm and managerial characteristics.Design/methodology/approach– Based on reviews of the marketing, finance, management and accounting literatures, and homophily, firm resource- and decision-maker-based theories and 22 managerial interviews, a conceptual model is proposed. It is tested via generalized least squares – seemingly unrelated regression estimation of 1,287 managerial decisions.Findings– Results suggest that the impact of metric use on marketing mix performance is lower in firms which are more market oriented, larger and with worse recent business performance and for marketing and higher-level managers, while organizational involvement has a lesser nuanced effect.Research limitations/implications– While much is written on the importance of metric use to improve performance, this work is a first step toward understanding which settings are more difficult than others to accomplish this.Practical implications– Results allow identification of several conditional managerial strategies to improve marketing mix performance based on metric use.Originality/value– This paper contributes to the metric literature, as prior research has generally focused on the development of metrics or the linking of marketing efforts with performance metrics, but paid little attention to understanding the relationship between managerial metric use and performance of the marketing mix decision and has not considered how the relationship is moderated by firm and managerial characteristics.
Legislators’ perceptions of unaccompanied children seeking asylum
Authors: Hedlund Daniel , Cederborg Ann-Christin 
Published: November 2015

Purpose
– The purpose of this paper is to explore how individual legislators perceive unaccompanied minors seeking asylum, their life situation, needs and best interests.

Design/methodology/approach
– The total number of participants were 15. Thematic analysis (Braun and Clarke, 2006) was used in order to identify and analyze patterns in the interview data. The authors focused on their responses to the questions about the best interest of the child in migration policy and practice, and how this principle was related to unaccompanied children seeking asylum.

Findings
– The main finding is that chronological age becomes a key sign for how legislators understand the life situation, needs and best interests of unaccompanied children. Also, the findings from this study suggest that the moralizing welfare ideology of the past is still present in political discourse and social planning, construing unaccompanied minors as an ambivalent category between civilization and savagery. The findings from this study indicate that legislators enact reforms of importance for unaccompanied children without considering them as agents of their own future, with their own motives and reasons to seek asylum.

Practical implications
– The findings from this study indicate a need to adapt the understanding of the existing Aliens Act (SFS 2005:716) to the knowledge that unaccompanied minors need to be assessed on their own terms.

Originality/value
– This study contributes to increasing the understanding about how the subjective values of legislators may have influenced migration reform in Sweden that can be valuable to both legal and social research, as well as policy planners.
Best-value supply chains and firms’ competitive performance: empirical studies of their linkage
Authors: Li Xun , Wu Qun , Holsapple Clyde W. 
Published: November 2015

Purpose– Best-value supply chains characterized by agility, adaptability, and alignment, have become a crucial strategic means for firms to create and sustain competitive advantage in today’s turbulent environment. The purpose of this paper is to investigate linkage between best-value supply chains and firms’ competitive performance.Design/methodology/approach– In Study 1, survey data from 76 firms is used to test the impact of the three qualities of best-value supply chains on firms’ competitive performance. In Study 2, to test if a firm’s competitive advantage can be sustained through building best-value supply chains, a long-run performance analysis is conducted, which is based on a stock portfolio of firms identified from the American Marketing Association’s annual list of “Supply Chain Top 25.”Findings– The results of Study 1 indicate that the three qualities of best-value supply chains are positively related to firms’ competitive performance. The results of Study 2 show that firms having best-value supply chains generate significant and positive abnormal returns for shareholders over time.Originality/value– This is a multiple-method research, providing two-level empirical evidence to the investigation of theoretical linkage between best-value supply chains and firms’ competitive performance.
The assurance of food safety in supply chains via relational networking
Authors: Schoenherr Tobias , Narasimhan Ram , Bandyopadhyay Piyas (P) 
Published: November 2015

Purpose
– Taking a social network perspective, the purpose of this paper is to develop a framework for the assurance of food safety via relational networking.

Design/methodology/approach
– The authors consider both informal and formal relational networking, and explore a firm’s learning orientation, risk aversion and consumer pressure as potential precursors to such relational networking. It is further hypothesized that relational networking generates both industry and supply chain knowledge, which is suggested to be beneficial for contamination detection. The model is tested with survey data collected among food-producing firms in India, the world’s second largest food producer.

Findings
– The authors find a positive influence of consumer pressure on both a firm’s learning orientation and risk aversion, which in turn affect both informal and formal relational networking. Informal networking further generated industry knowledge and was beneficial for contamination detection. Formal relational networking influenced supply chain knowledge, which in turn enabled contamination detection.

Originality/value
– Recent food product-related safety breaches, which have, in the worst case, led to fatalities, illustrate the importance of food safety in supply chains. This study represents the first systematic investigation of relational networking in the context of food safety from the perspective of social network theory.
Linking network targets and site capabilities
Authors: Thomas Simone , Scherrer-Rathje Maike , Fischl Maria , Friedli Thomas 
Published: November 2015

Purpose– To cope with the increasing challenges of globalisation, various manufacturing companies have established intra-company manufacturing networks. The purpose of this paper is to link the strategic network targets (i.e. accessibility, thriftiness represented by economies of scale and economies of scope, mobility, and learning) with the capabilities and characteristics of the constituting sites of the manufacturing network and thus facilitate the identification of mismatches and the discussion of possible development paths for the network.Design/methodology/approach– The authors derive a conceptual framework from the literature which is tested with a single case; a manufacturing network consisting of eight manufacturing sites. Case data were collected based on 24 interviews with operations managers at network level and a standardised online survey among the sites’ management teams.Findings– Results indicate that manufacturing network and site levels need to be related when striving for a fit between manufacturing strategy, network strategy, and site capabilities and characteristics.Research limitations/implications– Single case studies have only limited generalisability. Nevertheless, the case demonstrates the usefulness of several dimensions when analysing manufacturing networks on site and network level.Originality/value– This paper represents the first attempt to link strategic targets of intra-company manufacturing networks with site capabilities and characteristics. Thereby, it provides a theoretical basis for future research on the relationship between strategic targets of manufacturing networks and their fulfilment. The developed manufacturing site portfolio, moreover, extends the site role typology discussion by a multi-dimensional perspective and represents a starting point for a multi-faceted discussion of site roles.
Decision-making towards achieving world-class total productive maintenance
Authors: Piechnicki Ademir Stefano , Sola Antonio Vanderley Herrero , Trojan Flávio 
Published: November 2015

Purpose
– World-class total productive maintenance (TPM) status depends on critical success factors (CSF) to be properly implemented. The relevant literature has identified several CSF; however, researchers have not investigated the degree of importance of each phase of the process. The purpose of this paper is to prioritize the CSFs that influence TPM implementation during each phase of the process in order to aid decision making in companies.

Design/methodology/approach
– The main CSF are identified from a literature review. This paper focusses on the judgments of managers who are experts in TPM implementation in companies which have received TPM awards for excellence. The judgments are processed using the analytic hierarchy process (AHP) method. Three aggregation methods (geometric mean, Copeland and fuzzy) are employed for comparative analysis.

Findings
– Although the literature highlights some important CSF, the relevance of these factors is not the same in each phase of TPM implementation. Analysis shows that ranking using the Copeland method is most coherent.

Research limitations/implications
– This research was carried out in some Brazilian companies.

Practical implications
– If managers are aware of the CSF to be prioritized in each phase, this facilitates decision making, resulting in a more effective implementation of TPM.

Social implications
– If TPM implementation is effective, this stimulates the personnel involved and avoids the possibility of the program being abandoned.

Originality/value
– The originality of this paper consists in the proposed model to prioritize CSF during each phase of the implementation of TPM.