The BioDICE Taverna plugin for clustering and visualization of biological data: a workflow for molecular compounds exploration

Background: In many experimental pipelines, clustering of multidimensional biological datasets is used to detect hidden structures in unlabelled input data. Taverna is a popular workflow management system that is used to design and execute scientific workflows and aid in silico experimentation. The availability of fast unsupervised methods for clustering and visualization in the Taverna platform is important to support a data-driven scientific discovery in complex and explorative bioinformatics applications. Results: This work presents a Taverna plugin, the Biological Data Interactive Clustering Explorer (BioDICE), that performs clustering of high-dimensional biological data and provides a nonlinear, topology preserving projection for the visualization of the input data and their similarities. The core algorithm in the BioDICE plugin is Fast Learning Self Organizing Map (FLSOM), which is an improved variant of the Self Organizing Map (SOM) algorithm. The plugin generates an interactive 2D map that allows the visual exploration of multidimensional data and the identification of groups of similar objects. The effectiveness of the plugin is demonstrated on a case study related to chemical compounds. Conclusions: The number and variety of available tools and its extensibility have made Taverna a popular choice for the development of scientific data workflows. This work presents a novel plugin, BioDICE, which adds a data-driven knowledge discovery component to Taverna. BioDICE provides an effective and powerful clustering tool, which can be adopted for the explorative analysis of biological datasets.

Design of delay-tolerant space–time codes with limited feedback

In cooperative communication networks, owing to the nodes' arbitrary geographical locations and individual oscillators, the system is fundamentally asynchronous. Such a timing mismatch may cause rank deficiency of the conventional space-time codes and, thus, performance degradation. One efficient way to overcome such an issue is the delay-tolerant space-time codes (DT-STCs). The existing DT-STCs are designed assuming that the transmitter has no knowledge about the channels. In this paper, we show how the performance of DT-STCs can be improved by utilizing some feedback information. A general framework for designing DT-STC with limited feedback is first proposed, allowing for flexible system parameters such as the number of transmit/receive antennas, modulated symbols, and the length of codewords. Then, a new design method is proposed by combining Lloyd's algorithm and the stochastic gradient-descent algorithm to obtain optimal codebook of STCs, particularly for systems with linear minimum-mean-square-error receiver. Finally, simulation results confirm the performance of the newly designed DT-STCs with limited feedback.

Exploration of relational factors: Sino-foreign joint-venture partnering

Purpose – Despite recent threats of economic contraction, China still offers attractive opportunities for foreign companies seeking to expand their business activities through joint venturing (JV) partnering entry strategies. Recent research has indicated a growing recognition of the importance of relational factors in JV partnering. The purpose of this paper is to build on recent research findings that identify critical relation success factors in JVs and explores these in the context of a Hong Kong-based civil aviation services company seeking to expand business activities in Greater China. Design/methodology/approach – While the extant management literature focuses primarily on factors relevant to the inter-partner relationship between partners in the formation stage of a joint venture, this research takes a dynamic stakeholder perspective in respect of the relevant relational factors over the evolution of a partnership. The research described in this paper is based on a case-based study that identifies and examines the relevance and importance of uniquely Chinese factors such as guanxi, renqing and mianzi in the specific context of a strategic partnering relationship. Findings – This phenomenological study provides empirical evidence of critical linkages of these to intrinsically Chinese notions of guanxi, mianzi and renqing – it links these to key strategic partnering success factors identified to be trust, conflict resolution, commitment and cooperation. This study thereby reinforces the importance of the uniquely Chinese relational context in cross-border JVs. Moreover, the research findings suggest that these factors underpin the dynamic bi-directional stakeholder relationship in a Sino-foreign strategic partnership. Originality/value – This study conceptually links the uniquely Chinese relational factors (guanxi, mianzi and renqing) to key success factors supporting the establishment of a strategic partnership in a Sino-foreign context; moreover, it contributes empirical evidence substantiating the proposed conceptual linkage.

Designing in caves: using immersive visualisations in design practice

This paper describes a study of the use of immersive Virtual reality technologies in the design of a new hospital. It uses Schön’s concept of reflective practice and video-based methods to analyse the ways design teams approach and employ a full scale 3D immersive environment – a CAVE – in collaborative design work. The analysis describes four themes relating to reflective practice occurring in the setting: orienting to the CAVE technology itself, orienting to the representation of the specific design within the CAVE, activities accounting for, or exploring alternatives within the design for the use and users of the space, and more strategic interactions around how to best represent the design and model to the client within the CAVE setting. The analysis also reveals some unique aspects of design work in this environment. Perhaps most significantly, rather than enhancing or adding to an existing understanding of design through paper based or non-immersive digital representations, it is often acting to challenge or surprise the participants as they experience the immersive, full scale version of their own design.

Categories & order systems: Claude Parent and The Serving Library intersections of architecture, art and editorial design

This paper discusses the work of Claude Parent and The Serving Library, considering the critiques generated by their intersecting of architecture, art and editorial design. Through focus on the ways in which hosting environment, architecture and forms of expanded publishing can serve to dissolve disciplinary boundaries and activities of production, spectatorship and reception, it draws on the lineage of 1960s/70s Conceptual Art in considering these practices as a means through which to escape medium specificity and spatial confinement. Relationships between actual and virtual space are then read against this broadening of aesthetic ideas and the theory of critical modernity.

Bone Formation Following Implantation of Titanium Sponge Rods into Humeral Osteotomies in Dogs: A Histological and Histometrical Study

Background: Titanium (Ti) is widely proven to enhance bone contact and growth on its surface. It is expected that bone defects could benefit from Ti to promote healing and to increase strength of the implanted area. Purpose: The present study aimed at comparing the potential of porous Ti sponge rods with synthetic hydroxyapatite (HA) for the healing of bone defects in a canine model. Material and Methods: Six mongrel dogs were submitted to three trephined osteotomies of 6.0 x 4.0 mm in one humerus and after 2 months another three osteotomies were performed in the contralateral humerus. A total of 36 defects were randomly filled either with Ti foam, particulate HA, or coagulum (control). The six animals were killed 4 months after the first surgery for histological and histometrical analysis. Results: The Ti-foam surface was frequently found in intimate contact with new bone especially at the defect walls. Control sites showed higher amounts of newly formed bone at 2 months - Ti (p = 0.000) and HA (p = 0.009) - and 4 months when compared with Ti (p = 0.001). Differently from HA, the Ti foam was densely distributed across the defect area which rendered less space for bone growth in the latter`s sites. The use of Ti foams or HA resulted in similar amounts of bone formation in both time intervals. Nevertheless, the presence of a Ti-foam rod preserved defect`s marginal bone height as compared with control groups. Also, the Ti-foam group showed a more mature bone pattern at 4 months than HA sites. Conclusion: The Ti foam exhibited good biocompatibility, and its application resulted in improved maintenance of bone height compared with control sites. The Ti foam in a rod design exhibited bone ingrowth properties suitable for further exploration in other experimental situations.

Equal Couples in Equal Houses : Cultural perspectives on Swedish solar and bio-pellet heating design

Knowing how to design a heating system that will work mechanically is quite different from knowling how to design a system that users perceive as responsive to their domestic practices and values. In this chapter, social anthropologist Henning argues that the challenge for designers involved in the development or marketing of green buildings with heating systems that are based on renewable sources of energy is to see things from the perspective of those who are supposed to live in these buildings. The chapter focuses on three culture-specific aspects of Swedish households and single-family houses: perceptions of house and home, of private and public space, and of male and female space. Through these three angles, some clues are given as to how design, performance and location of solar and bio-pellet heating systems could be made to resonate with predominant experiences, habits and ways of thinking among both men and women.

‘Being in a womb’ or ‘playing musical chairs’ : the impact of place and space on infant feeding in NICUs

Background: Becoming a parent of a preterm baby requiring neonatal care constitutes an extraordinary life situation in which parenting begins and evolves in a medical and unfamiliar setting. Although there is increasing emphasis within maternity and neonatal care on the influence of place and space upon the experiences of staff and service users, there is a lack of research on how space and place influence relationships and care in the neonatal environment. The aim of this study was to explore, in-depth, the impact of place and space on parents’ experiences and practices related to feeding their preterm babies in Neonatal Intensive Care Units (NICUs) in Sweden and England. Methods: An ethnographic approach was utilised in two NICUs in Sweden and two comparable units in England, UK. Over an eleven month period, a total of 52 mothers, 19 fathers and 102 staff were observed and interviewed. A grounded theory approach was utilised throughout data collection and analysis. Results: The core category of ‘the room as a conveyance for an attuned feeding’ was underpinned by four categories: the level of ‘ownership’ of space and place; the feeling of ‘at-homeness’; the experience of ‘the door or a shield’ against people entering, for privacy, for enabling a focus within, and for regulating socialising and the; ‘window of opportunity’. Findings showed that the construction and design of space and place was strongly influential on the developing parent-infant relationship and for experiencing a sense of connectedness and a shared awareness with the baby during feeding, an attuned feeding. Conclusions: If our proposed model is valid, it is vital that these findings are considered when developing or reconfiguring NICUs so that account is taken of the influences of spatiality upon parent’s experiences. Even without redesign there are measures that may be taken to make a positive difference for parents and their preterm babies.

Parent’s experiences of feeding their preterm infant in Neonatal Units in Sweden. : Ethnographic design

Introduction: Studies have shown that having a preterm infant may cause stress and powerlessness for parents. It is important to support parents around the feeding situation, and that the Neonatal Intensive Care Unit (NICU) has appropriate space and place to help the family to bond to each other. For the healthcare professionals it is important to promote skin-to-skin contact and breastfeeding; particularly for preterm infants. There are many studies on parent’s experiences of NICUs and a few studies on parent’s experiences of feeding their infant in the NICU. Objective: The objective of this study was to explore parents experiences of feeding their infant in the NICU. Design: The study was conducted using an ethnographic design. Results: A global theme of ‘The journey in feeding’ was developed from four organising themes: ‘Ways of infant feeding’; ‘Environmental influences’; ‘Relationships’ and ‘Emotional factors’. These themes illustrate the challenges mothers reported with different methods of feeding. The environment had a big impact on parent’s experiences of infant feeding. Some mothers felt that breastfeeding seemed unnatural because their infant was so tiny but breastfeeding and skin-to-skin contact helped them to bond to their infant. The mothers thought it was difficult to keep up with the milk production by only pumping. Routines were not inviting parents to find their own rhythm. They also felt stressed about the weighing. Healthcare professionals had positive and negative influences on the parents. Conclusions: This study demonstrates that while all parents expressed the wish to breastfeed, their ‘journey in feeding’ was highly influenced by method of feeding, environmental, relational and emotional factors. The general focus upon routines and assessing milk intake generated anxiety and reduced relationality. Midwives and neonatal nurses need to ensure that they emphasise and support the relational aspects of parenting and avoid over-emphasising milk intake and associated progress of the infant

Universal Design in Higher Education

While colleges and universities increasingly draw upon the concept of Universal Design to create an ideal learning environment, it can be challenging to apply the concept practically in the classroom. This project explores innovative ways to incorporate Universal Design into campus architecture, classroom technology and curriculum development. Further, this brief describes different approaches used by universities to garner faculty interest and offer effective training in Universal Design.

Organizações culturais e (re)configuração do espaço: o caso do Istituto Europeo di Design, na cidade do Rio de Janeiro

O presente estudo tem como objetivo investigar de que maneira a possibilidade de instalação do Istituto Europeo di Design (IED) no bairro da Urca, na cidade do Rio de Janeiro, interfere na (re)configuração do espaço. Para o estudo desse processo adotou-se o conceito de espaço definido por Milton Santos, que o caracteriza como um conjunto indissociável de sistemas de objetos e ações, considerando necessária sua análise numa perspectiva histórica. Para ampliação das considerações sobre poder, identificação e caracterização dos atores sociais e das relações entre eles estabelecidas foram utilizados conceitos propostos por Carlos Matus para a análise da realidade social. A pesquisa de campo, de natureza qualitativa, coletou dados secundários a partir de notícias sobre o processo de revitalização do antigo Cassino da Urca e instalação do Istituto Europeo di Design no local, publicadas em jornais e revistas impressos, jornais on line e blogs, assim como dados primários, a partir de observação não estruturada das instalações ao redor do prédio do antigo Cassino da Urca, participação em reuniões da associação de bairro e entrevistas semi-estruturadas com representantes de organizações envolvidas no processo. Para o tratamento dos dados coletados, realizou-se análise argumentativa e interpretativa a partir da teoria utilizada. Com base nas notícias e documentos consultados, foi definido o período de análise, desde a cessão do prédio do antigo Cassino da Urca ao IED, em agosto de 2006, até o anúncio de parceria com outra organização, pelo instituto, em maio de 2012. O estudo permitiu identificar que a instalação do IED na Urca interferiu na configuração do espaço, principalmente no que se refere à formação e à atuação da associação de moradores do bairro, à instalação de novos empreendimentos comerciais no entorno do prédio já restaurado e, por consequência, na paisagem do bairro. Destaca-se também que a instalação do IED gerou mudanças que extrapolam os limites territoriais do bairro. Com base nos dados analisados, destaca-se que a relação de cooperação entre a Prefeitura Municipal do Rio de Janeiro e o IED foi estabelecida em torno da valorização por parte da Prefeitura do domínio de uma capacidade técnica pelo IED, nas áreas de atuação da organização, que são o ensino, pesquisa e consultoria nas áreas de arquitetura, design, moda e comunicação, o que reforça o argumento da valorização atual de organizações culturais no processo de (re)configuração do espaço urbano, quanto aos aspectos econômicos, simbólicos e sociais.

The gay subject in business and its discursive formation: an exploration on power, knowledge and sexuality

Issues related to the reality of lesbian, gay, bisexual and transgender (LGBT) individuals are being incorporated into institutional and social discourses, and show the challenges that must be overcome towards citizenship. The inclusion of gay rights in the domain of institutions like the United Nations and the Brazilian Secretariat of Human Rights are a response to broader movements that places the gay subject as an important topic of debate in the social-political sphere. In this scenario, some institutions deserve close attention from researchers related to gay issues, the business environment being a good example. In this domain, diversity has become an important topic of debate between scholars, where the question of sexual identity in most cases does not appear. The literature that actually focuses on the theme is explored through approaches that are not able to break with universalisms and a normatized vocabulary. Therefore, this research explores discursive structures related to sexuality and examines the meanings construed throughout these structures as described by gay individuals working in business. Furthermore, it investigates patterns of discursive normative structures and consequential challenges faced by gay people in the working environment, and also complements the current debate both in the socio-political sphere and in academic reality on LGBT challenges. The Foucauldian notions of discourse, knowledge and power, and the main concepts of queer theory are incorporated to the analysis, as well as concepts related to the politics of post-colonial sexuality, subordination, and hegemonic forces, together with role of reflexivity in modernity and its impacts on secularized mental structures. The research design takes a phenomenological approach and bases its knowledge claim on a participatory perspective, where the sample chosen for data collection consisted of gay individuals working in the business environment, aiming at generate categories of meanings through the description of their experiences.

The transformation between exploration and exploitation applied to inventors of packaging innovations

While the inventor is often the driver of an invention in the early stages, he/she needs to move between different social networks for knowledge in order to create and capture value. The main objective of this research is to propose a literature-based framework based on innovation network theory and complemented with C-K theory, in order to analyze the invention/innovation process of inventors and the product concepts in a packaging industry context. Empirical input from three case studies of packaging inventions and their inventors is used to elaborate the suggested framework.The article identifies important gaps in the literature of innovation networks. This is addressed through a theoretical framework based on network theories, complemented with C-K theory for the product design level. The strength-of-ties dimension of the theoretical framework suggests, in agreement with the mainstream literature and the cases presented, that weak ties are required to access the knowledge related to exploration networks and strong ties are required to utilize the knowledge in the exploitation network. The transformation network is an intermediate step acting as a bridge where entrepreneurs can find required knowledge. The transformation network is also an intermediate step where entrepreneurs find financing and companies interested in commercializing inventions. (C) 2010 Elsevier Ltd. All rights reserved.