bluuebunny/crossref_metadata_2025_split huggingface dataset:
YAMO: Yet Another Methodology for large-scale faceted Ontology construction
Authors: Dutta Biswanath , CHATTERJEE USASHI , Madalli Devika P. 
Published: February 2015

Purpose
– This paper aims to propose a brand new ontology development methodology, called Yet Another Methodology for Ontology (YAMO) and demonstrate, step by step, the building of a formally defined large-scale faceted ontology for food.

Design/methodology/approach
– YAMO is motivated by facet analysis and an analytico-synthetic classification approach. The approach ensures quality of the system precisely; it makes the system flexible, hospitable, extensible, sturdy, dense and complete. YAMO consists of two-way approaches: top-down and bottom-up. Based on YAMO, domain food, formally defined as large-scale ontology, is designed. To design the ontology and to define the scope and boundary of the domain, a group of people were interviewed to get a practical overview, which provided more insight to the theoretical understanding of the domain.

Findings
– The result obtained from evaluating the ontology is a very impressive one. Based on the study, it was found that 94 per cent of the user’s queries were successfully met. This shows the efficiency and effectiveness of the YAMO methodology. An evaluator opined that the ontology is very deep and exhaustive.

Practical implications
– The authors envision that the current work will have great implications on ontology developers and practitioners. YAMO will allow ontologists to construct a very deep, high-quality and large-scale ontology.

Originality/value
– This paper illustrates a brand new ontology development methodology and demonstrates how the methodology can be applied to build a large-scale high-quality domain ontology.
Semantic network edges: a human-machine approach to represent typed relations in social networks
Authors: Pattuelli M. Cristina , Miller Matthew 
Published: February 2015

Purpose
– The purpose of this paper is to describe a novel approach to the development and semantic enhancement of a social network to support the analysis and interpretation of digital oral history data from jazz archives and special collections.

Design/methodology/approach
– A multi-method approach was applied including automated named entity recognition and extraction to create a social network, and crowdsourcing techniques to semantically enhance the data through the classification of relations and the integration of contextual information. Linked open data standards provided the knowledge representation technique for the data set underlying the network.

Findings
– The study described here identifies the challenges and opportunities of a combination of a machine and a human-driven approach to the development of social networks from textual documents. The creation, visualization and enrichment of a social network are presented within a real-world scenario. The data set from which the network is based is accessible via an application programming interface and, thus, shareable with the knowledge management community for reuse and mash-ups.

Originality/value
– This paper presents original methods to address the issue of detecting and representing semantic relationships from text. Another element of novelty is in that it applies semantic web technologies to the construction and enhancement of the network and underlying data set, making the data readable across platforms and linkable with external data sets. This approach has the potential to make social networks dynamic and open to integration with external data sources.
Operations strategy processes and performance
Authors: Jagoda Kalinga , Kiridena Senevi 
Published: February 2015

Purpose– The purpose of this paper is to explore the significance and dynamics of alternative operations strategy (OS) processes towards developing a more complete picture of the strategy process-context-performance nexus. The findings are based on the statistical analysis of empirical evidence drawn from the contract apparel manufacturing industry in a developing country.Design/methodology/approach– Using a structured questionnaire and the key-informant approach data were collected from 109 contract apparel manufacturing firms in Sri Lanka. Cluster analysis was used to identify alternative configurations of strategy process modes.Findings– The analyses confirmed that the existence of alternative forms of OS development is statistically significant and that the alternative configurations of strategy process modes tested can all lead to superior performance, under certain circumstances.Research limitations/implications– The generalizability of these findings to other industry sectors within developing countries should be treated with caution, mainly due to the fact that the vast majority organizations selected for this study were subsidiaries of large international companies or comparable local counterparts. In order to better understand the linkages between OS and performance, data should be collected from multiple countries preferably using mixed-methods approaches.Originality/value– The findings are expected to contribute to operations management theory as they corroborate, with statistical evidence, the findings of recent qualitative studies. The results also confirm the existence of OS processes in developing countries that are consistent with the conceptual understanding developed in the context of developed countries.
Unified assembly- and disassembly-line model formulae
Authors: McGovern Seamus M. , Gupta Surendra M. 
Published: February 2015

Purpose
– There is a rich body of literature on sequencing assembly and on sequencing disassembly, but little that either fuses or contrasts the two, which may be valuable for long-range planning in the closed-loop supply chain and simply convenient in terms of consistency in nomenclature and mathematical formulations. The purpose of this paper is to concisely unify and summarize assembly and disassembly formulae – as well as to add new formulations for completeness – and then demonstrate the similarities and differences between assembly and disassembly.

Design/methodology/approach
– Along with several familiar assembly-line formulae which are adapted here for disassembly, five (two specific and three general) metrics and a comparative performance formula from disassembly-line balancing are proposed for use in assembly- and disassembly-line sequencing and balancing either directly, through generalization, or with some extension. The size of assembly and disassembly search spaces are also quantified and formulated. Three new metrics are then developed from each of the general metrics to demonstrate the process of using these general formulae as prototypes.

Findings
– The three new metrics along with several of the original metrics are selectively applied to a simple, notional case study product to be sequenced on an assembly line and then on a disassembly line. Using these analytical results, the inherent differences between assembly and disassembly, even for a seemingly trivial product, are illustrated.

Originality/value
– The research adds several new assembly/disassembly metrics, a case study, unifies the evaluation formulae that assembly and disassembly hold in common as well as structuring prototype formulae for flexibility in generating new evaluation criteria for both, and quantifies (using the case study) how assembly and disassembly – while certainly possessing similarities – also demonstrate measurable differences that can be expected to affect product design, planning, production, and end-of-life processing.
Integrating marine biodiversity through Philippine local development plans
Authors: Raquino Mark  Edison , Pajaro Marivic , Watts Paul 
Published: February 2015

Purpose
– The purpose of this paper is to highlight how data from marine protected area (MPA) surveys can be used to facilitate the development of systematic approaches to monitoring biodiversity within local government development plans and across marine bioregions.

Design/methodology/approach
– The study focussed on coastal Barangays of the Municipality of San Luis, Aurora Philippines. A Participatory Coastal Resource Assessment (PCRA) was conducted to gather information on corals and reef fishery resources. Resultant Simpson’s biodiversity indices were calculated and compared to other MPA sites. Linkages to enhanced marine curriculum in a San Luis high school were evaluated by utilizing cultural consensus theory (CCT) on previously reported local student perception surveys as a further effort on defining pathways for localized transformation.

Findings
– San Luis MPA biodiversity indices ranged from 0.56-0.8 on a scale of 0-1. This initial analysis demonstrates how local monitoring can be connected to resource assessment through biodiversity considerations and in developing local plans for site improvement linked to local economies. Results are used to demonstrate the potential for further development of an integrated approach to biodiversity monitoring across and between bioregions as a step forward in strengthening science for MPAs and biodiversity conservation for the Philippines.

Practical implications
– The study could be used to pilot study strengthening of coastal resource management (CRM) at Municipal and Barangay levels and as well through application of CCT to the topics. The results will be used to reinforce the formulation of San Luis local development plans to better consider marine resource assessment.

Originality/value
– This paper provides a new perspective on the use of quantitative measures of biodiversity to assist with local development plans. Projecting integrated biodiversity monitoring across and between bioregions is considered as a potential tool for facilitating climate change mitigation.
The problematic differentiation between property bonds and leases in healthcare provision
Authors: Ellison Andrew , Squires Graham , Dempsey Patrick 
Published: February 2015

Purpose– There are some 487,000 places in long-stay residential care and nursing homes in the UK representing an industry worth some £15.2 billion per annum. Creating leases with guaranteed rental uplifts, a property bond in all but name, now attracts significant investment into healthcare. This is argued to be unsustainable, as evidenced by the collapse of Southern Cross Healthcare. The purpose of this paper is to provide insight into institutional investment for sustainable healthcare provision.Design/methodology/approach– It is carried out via a range of unstructured and semi-structured interviews with a purposive sample of a small elite of professionals involved at the summit of this investment market and analysis of secondary literature concerning the wider international property market regarding the way in which advisers and investors view the security and value of these new instruments.Findings– It is found that the differentiation between rental growth and indexed rental uplifts reveal a misunderstanding of the nature of the investment vehicles currently being marketed.Practical implications– The implication of the research, is that much modern private healthcare provision is financially unsustainable, as has begun to be recognised in recent government regulation and guidance.Originality/value– This research provides new and original insight into institutional investment for sustainable healthcare provision
Detection of genes expressed in Bordetella bronchiseptica colonizing rat trachea by in vivo expressed‐tag immunoprecipitation method
Authors: Abe Hiroyuki , Kamitani Shigeki , Fukui‐Miyazaki Aya , Shinzawa Naoaki , Nakamura Keiji , Horiguchi Yasuhiko 
Published: February 2015

ABSTRACTAnalyses of bacterial genes expressed in response to the host environment provide clues to understanding the host‐pathogen interactions that lead to the establishment of infection. In this study, a novel method named In Vivo Expressed‐Tag ImmunoPrecipitation (IVET‐PI) was developed for detecting genes expressed in bacteria that are recovered in a small numbers from host tissues. IVET‐IP was designed to overcome some drawbacks of previous similar methods. We applied IVET‐IP to Bordetella bronchiseptica colonizing rat trachea and identified 173 genes that were expressed in the bacteria over the entire course of an infection. These gene products included two transcriptional factors that are involved in the expression of filamentous hemagglutinin, adenylate cyclase toxin, and major virulence factors for the bordetellae. We consider that this method might provide novel insight into the course of Bordetella infection.
A basin‐scale application of environmental DNA assessment for rare endemic species and closely related exotic species in rivers: a case study of giant salamanders in Japan
Authors: Fukumoto Sou , Ushimaru Atushi , Minamoto Toshifumi 
Published: February 2015

Summary

To prevent the invasion of exotic species causing a decline in an endangered endemic species, it is important to determine the distribution of both species at an early stage, when the density of the exotic species is still low, and to manage the invasion immediately. However, distinguishing between closely related species is difficult because they share similar characteristics.

The identification of DNA fragments sampled from a body of water (environmental DNA) has become a popular technique for rapidly determining the distribution of a target species. In this study, we analysed environmental DNA in water samples from 37 sites across the Katsura River basin in Japan. We used TaqMan real‐time PCR to distinguish the Japanese giant salamander Andrias japonicus from the closely related Chinese giant salamander Andrias davidianus, which is known to invade Japanese rivers and hybridize with the Japanese species.

In environmental samples, we detected mtDNA of the endemic species at 25 sites and mtDNA of the exotic species at nine sites. The DNA detection sites were concentrated in the upstream region. The exotic species DNA was found beyond the limits of an earlier capturing survey.

Synthesis and applications. Using environmental DNA to monitor the two salamander species requires less time and effort than traditional surveys, so a wide‐ranging survey can be conducted rapidly. Our results showed that performing three environmental DNA surveys for each site between autumn and winter is desirable for giant salamanders. Further collection of environmental DNA, in combination with conventional population surveys, will provide valuable information that can help protect rare endemic species in a variety of aquatic ecosystems and can help monitor the invasion of exotic species.
Temperature affects c‐di‐GMP signalling and biofilm formation in Vibrio cholerae
Authors: Townsley Loni , Yildiz Fitnat H. 
Published: February 2015

SummaryBiofilm formation is crucial to the environmental survival and transmission of Vibrio cholerae, the facultative human pathogen responsible for the disease cholera. During its infectious cycle, V. cholerae experiences fluctuations in temperature within the aquatic environment and during the transition between human host and aquatic reservoirs. In this study, we report that biofilm formation is induced at low temperatures through increased levels of the signalling molecule, cyclic diguanylate (c‐di‐GMP). Strains harbouring in frame deletions of all V. cholerae genes that are predicted to encode diguanylate cyclases (DGCs) or phosphodiesterases (PDEs) were screened for their involvement in low‐temperature‐induced biofilm formation and Vibrio polysaccharide gene expression. Of the 52 mutants tested, deletions of six DGCs and three PDEs were found to affect these phenotypes at low temperatures. Unlike wild type, a strain lacking all six DGCs did not exhibit a low‐temperature‐dependent increase in c‐di‐GMP, indicating that these DGCs are required for temperature modulation of c‐di‐GMP levels. We also show that temperature modulates c‐di‐GMP levels in a similar fashion in the Gram‐negative pathogen Pseudomonas aeruginosa but not in the Gram‐positive pathogen Listeria monocytogenes. This study uncovers the role of temperature in environmental regulation of biofilm formation and c‐di‐GMP signalling.
Virulence determinants of the human pathogenic fungus Aspergillus fumigatus protect against soil amoeba predation
Authors: Hillmann Falk , Novohradská Silvia , Mattern Derek J. , Forberger Tilmann , Heinekamp Thorsten , Westermann Martin , Winckler Thomas , Brakhage Axel A. 
Published: February 2015

SummaryFilamentous fungi represent classical examples for environmentally acquired human pathogens whose major virulence mechanisms are likely to have emerged long before the appearance of innate immune systems. In natural habitats, amoeba predation could impose a major selection pressure towards the acquisition of virulence attributes. To test this hypothesis, we exploited the amoeba Dictyostelium discoideum to study its interaction with Aspergillus fumigatus, two abundant soil inhabitants for which we found co‐occurrence in various sites. Fungal conidia were efficiently taken up by D. discoideum, but ingestion was higher when conidia were devoid of the green fungal spore pigment dihydroxynaphtalene melanin, in line with earlier results obtained for immune cells. Conidia were able to survive phagocytic processing, and intracellular germination was initiated only after several hours of co‐incubation which eventually led to a lethal disruption of the host cell. Besides phagocytic interactions, both amoeba and fungus secreted cross inhibitory factors which suppressed fungal growth or induced amoeba aggregation with subsequent cell lysis, respectively. On the fungal side, we identified gliotoxin as the major fungal factor killing Dictyostelium, supporting the idea that major virulence attributes, such as escape from phagocytosis and the secretion of mycotoxins are beneficial to escape from environmental predators.
The composition of arbuscular mycorrhizal fungal communities differs among the roots, spores and extraradical mycelia associated with five Mediterranean plant species
Authors: Varela‐Cervero Sara , Vasar Martti , Davison John , Barea José Miguel , Öpik Maarja , Azcón‐Aguilar Concepción 
Published: February 2015

SummaryArbuscular mycorrhizal fungi (AMF) are essential constituents of most terrestrial ecosystems. AMF species differ in terms of propagation strategies and the major propagules they form. This study compared the AMF community composition of different propagule fractions – colonized roots, spores and extraradical mycelium (ERM) – associated with five Mediterranean plant species in Sierra de Baza Natural Park (Granada, Spain). AMF were identified using 454 pyrosequencing of the SSU rRNA gene. A total of 96 AMF phylogroups [virtual taxa (VT)] were detected in the study site, including 31 novel VT. After per‐sample sequencing depth standardization, 71 VT were recorded from plant roots, and 47 from each of the spore and ERM fractions. AMF communities differed significantly among the propagule fractions, and the root‐colonizing fraction differed among host plant species. Indicator VT were detected for the root (13 Glomus VT), spore (Paraglomus VT281, VT336, Pacispora VT284) and ERM (Diversispora VT62) fractions. This study provides detailed evidence from a natural system that AMF taxa are differentially allocated among soil mycelium, soil spores and colonized root propagules. This has important implications for interpreting AMF diversity surveys and designing applications of AMF in vegetation restoration.
Fitting proposals to their sequential environment: a comparison of turn designs for proposing treatment in ongoing outpatient psychiatric consultations in Japan
Authors: Kushida Shuya , Yamakawa Yuriko 
Published: February 2015

AbstractThis study is an attempt to describe an interactional strategy that psychiatrists use in making decisions for treatment in ongoing outpatient psychiatric consultations in Japan. Using conversation analysis (CA), we compare sequential environments where psychiatrists use two turn designs for proposing a treatment: the inclusive ‘we’ form (for example ‘let's’ and ‘how about’) and the declarative evaluation (for example, ‘it might be better’). The inclusive ‘we’ form is used to create the moment for decision when the sequential environment is ready for decision‐making. The declarative evaluation is used to propose a treatment cautiously when the sequential environment is not yet ready for decision‐making. Taken together, psychiatrists fit the turn design of a proposal to its sequential environment in such a way as to display their attention to the patients’ perspectives. In conclusion, we argue that our finding provides further evidence for the claim made by a growing body of CA research that, unlike the traditional sociological understanding of doctor–patient interaction, doctors do not simply impose their perspectives upon the patients but steer medical encounters to their preferred direction by orienting to the patients’ perspectives.
The meaning of a label for teenagers negotiating identity: experiences with autism spectrum disorder
Authors: Mogensen Lise , Mason Jan 
Published: February 2015

AbstractThere is a lack of consideration for the effects that labels such as autism, and the associated diagnostic processes, have on the children to whom they are applied. In this article we present research conducted with five teenagers diagnosed with autism. Through a collaborative, participatory research approach, these teenagers shared their experiences of their diagnosis using communication methods of their choice. The young people's accounts illustrate the understandings they had of autism. Important findings from the research illustrate how the participants integrated this knowledge with their sense of self, how they negotiated issues of identity and the meanings that feeling ‘different’ had for them. Whether the diagnosis was experienced as advantage or disadvantage by the young people depended on the extent to which it facilitated knowledge and control. The article concludes with a discussion of the significance a diagnosis may have for the ways in which children and young people construct their personal identity and their social relations, and in terms of negotiating control in their lives. We suggest that ways of minimising stigma and marginalisation associated with a diagnosis of autism need to be considered at a policy level.
Pastoral power and gynaecological examinations: a Foucauldian critique of clinician accounts of patient‐centred consent
Authors: Cook Catherine , Brunton Margaret 
Published: February 2015

AbstractInvasive non‐sedated clinical procedures such as gynaecological examinations are normalised; however, there is limited research highlighting the relational and technical skills required for clinicians to ensure patients’ continued consent. A considerable body of research emphasises that women dislike examinations, leading to their non‐compliance or a delayed follow up for gynaecological and sexual health problems. However, medical research focuses on ‘problem’ women; the role of clinicians receives limited appraisal. This article draws on interviews with sexual health clinicians in New Zealand, from metropolitan and provincial locations. The gynaecological care of women in New Zealand attained international notoriety with the 1988 publication of Judge Cartwright's inquiry into ethical shortcomings in cervical cancer research at the National Women's Hospital. Judge Cartwright's recommendations included patient‐centred care in order to ensure informed consent had been received for clinical procedures and research participation. This article's critical analysis is that, although clinicians’ language draws on humanistic notions of patient‐centredness, Foucault's notion of secularised pastoral power enables a more nuanced appreciation of the ethical work undertaken by clinicians when carrying out speculum examinations. The analysis highlights both the web of power relations present during examination practices and the strategies clinicians use to negotiate women's continued consent; which is significant because consent is usually conceptualised as an event, rather than an unfolding, unstable process.