On the utility of alternative amino acid scripts

In this work we propose the hypothesis that replacing the current system of representing the chemical entities known as amino acids using Latin letters with one of several possible alternative symbolic representations will bring significant benefits to the human construction, modification, and analysis of multiple protein sequence alignments. We propose ways in which this might be done without prescribing the choice of actual scripts used. Specifically we propose and explore three ways to encode amino acid texts using novel symbolic alphabets free from precedents. Primary orthographic encoding is the direct substitution of a new alphabet for the standard, Latin-based amino acid code. Secondary encoding imposes static residue groupings onto the orthography of the alphabet by manipulating the shape and/or orientation of amino acid symbols. Tertiary encoding renders each residue as a composite symbol; each such symbol thus representing several alternative amino acid groupings simultaneously. We also propose that the use of a new group-focussed alphabet will free the colouring of amino acid residues often used as a tool to facilitate the representation or construction of multiple alignments for other purposes, possibly to indicate dynamic properties of an alignment such as position-wise residue conservation.

Diversity and the perceived barriers to participation in volunteer activity by older people

The first chapter introduces the subject from a psychological and sociological perspective emphasising the basic human activity of helping those in need. Governmental prominence for policies that assist this activity is briefly discussed with special mention of the programmes that encourage volunteering. Programmes particularly directed at older people, such as the Age Concern ‘Debate of the Age’ are considered briefly. An extensive review of the extant literature is the subject of the second chapter. The pervious research is explored to discover the formulae used to define a volunteer. A definition relative to this research is created. Volunteering issues aggravated by the demographic situation of older people are explored. Empirical volunteer survey research by mutual organisations is explored to ascertain the extent and nature of the already recorded volunteer population. The penultimate section of this chapter investigates the nature of old age and the strategies that older people adopt to enjoy the benefits and contain the problems. The issue of diversity arises from consideration of the literature suggesting that, although it is an essential voluntary sector strength, it is also a further barrier to recruitment. A model diversity is proposed. Chapter three reviews the theoretical processes, procedures and technologies used to collect and analyse the data required to discover the answer to the research problem. Analysis of the questionnaire survey data received is the subject of chapter four. The discovery of the agency uniqueness of volunteer profiles is the principle finding of this part of the research. The fifth chapter is the qualitative analysis of the oral and written statements received. A content analysis of the scripts and texts provided rich data covering motivational factors. Motivational factors were the same for volunteers in the same organisation, but differed between organisations. Finally, the analysed data is collated and discussed progressively toward a theory of diversity. The individuality of each branch of each agency is progressively described culminating in the creation of a model that infers that diversity is a barrier that aggravates all other barriers. The personal realisations of the researcher are described.

Representations of voluntary childlessness in the UK Press, 1990-2008

Representations of voluntary childlessness — the declaration by an individual that he or she does not wish to bear or raise children — were studied in 116 articles published in British national newspapers in the period 1990—2008. Media framing analysis was used to examine broad patterns of framing of the topic, identifying four frames: voluntary childlessness as an individual rights issue, as a form of resistance, as a social trend, and as a personal decision. These frames, it is argued, may act as potential ‘scripts’ for newspaper readers who are debating the decision to start a family.

Toward the atomistic simulation of T cell epitopes automated construction of MHC:peptide structures for free energy calculations

Epitopes mediated by T cells lie at the heart of the adaptive immune response and form the essential nucleus of anti-tumour peptide or epitope-based vaccines. Antigenic T cell epitopes are mediated by major histocompatibility complex (MHC) molecules, which present them to T cell receptors. Calculating the affinity between a given MHC molecule and an antigenic peptide using experimental approaches is both difficult and time consuming, thus various computational methods have been developed for this purpose. A server has been developed to allow a structural approach to the problem by generating specific MHC:peptide complex structures and providing configuration files to run molecular modelling simulations upon them. A system has been produced which allows the automated construction of MHC:peptide structure files and the corresponding configuration files required to execute a molecular dynamics simulation using NAMD. The system has been made available through a web-based front end and stand-alone scripts. Previous attempts at structural prediction of MHC:peptide affinity have been limited due to the paucity of structures and the computational expense in running large scale molecular dynamics simulations. The MHCsim server (http://igrid-ext.cryst.bbk.ac.uk/MHCsim) allows the user to rapidly generate any desired MHC:peptide complex and will facilitate molecular modelling simulation of MHC complexes on an unprecedented scale.

An aspect-oriented and model-driven approach for managing dynamic variability

Constructing and executing distributed systems that can adapt to their operating context in order to sustain provided services and the service qualities are complex tasks. Managing adaptation of multiple, interacting services is particularly difficult since these services tend to be distributed across the system, interdependent and sometimes tangled with other services. Furthermore, the exponential growth of the number of potential system configurations derived from the variabilities of each service need to be handled. Current practices of writing low-level reconfiguration scripts as part of the system code to handle run time adaptation are both error prone and time consuming and make adaptive systems difficult to validate and evolve. In this paper, we propose to combine model driven and aspect oriented techniques to better cope with the complexities of adaptive systems construction and execution, and to handle the problem of exponential growth of the number of possible configurations. Combining these techniques allows us to use high level domain abstractions, simplify the representation of variants and limit the problem pertaining to the combinatorial explosion of possible configurations. In our approach we also use models at runtime to generate the adaptation logic by comparing the current configuration of the system to a composed model representing the configuration we want to reach. © 2008 Springer-Verlag Berlin Heidelberg.

Empowering, degrading or a 'mutually exploitative' exchange For women?: Characterising the power relations of the strip club

This paper seeks to characterise the gendered and sexualised power relations of both female and male strip clubs, and to signal what this means for establishing positive definitions of female desire. It is argued that while it is not useful to present female strippers, or female patrons of male strip clubs as purely passive victims of male heterosexism within these venues, it is equally damaging to assume that these venues represent a whole-scale challenge to conventional oppressive gender and sexual relations for women. Some research has even suggested that both strippers and their patrons are engaged in a 'mutually exploitative' power relationship. Moreover, further empirical research documents key points where female dancers have perhaps wielded 'more' power over patrons at certain moments, and female dancers have highlighted feelings of empowerment and highlighted potential for gender and sexual relations which position women as passive to be subverted within stripping. However, such feelings are often temporally specific and are not applicable to all women in the strip industry. It may be particularly hard for these to manifest in women concentrated in the least economically-rewarding areas of the industry who have less 'power' to resist compromising their bodily boundaries. Furthermore, it is argued that women watching male strippers does little to reverse the 'male gaze', and nor does this male occupation carry as much negative social stigma with it as female stripping suffers. It is thus argued that the overwhelming picture, stemming largely from accounts of former dancers and from empirical studies of individual clubs, suggests these venues in fact do very little to challenge normative hetero-oppressive sexual scripts.

Sexuality and Christianity:understanding the attitudes and negotiations of young adults in the UK

Christianity has historically incorporated numerous strands of thinking on sexuality; in some cases, problematizing sexuality through the endorsement of celibacy and asceticism while at other historical and contextual moments, marriage and procreation become ideals (Price 2006). Contemporary Christians negotiate many sexual scripts (including ‘secular’ ones), but ‘appropriate’ Christian sexuality is still usually defined in terms of monogamy, the containment of sex within marriage, and heterosexuality. This chapter will explore the attitudes, beliefs and practices toward sexuality of young Christian women and men aged between 18 and 25 and living in the UK, based on a qualitative and quantitative research project entitled Religion, Youth and Sexuality: A Multi-faith Exploration, which utilized questionnaires, in-depth interviews and video diaries. The chapter will consider the variations in attitude between young people from different Christian denominations in relation to three themes: sex outside of marriage, celibacy and monogamy.

Renegotiating sexual intimacy in the context of altered embodiment:the experiences of women with breast cancer and their male partners following mastectomy and reconstruction

OBJECTIVE: Breast cancer diagnosis and treatments can have a profound impact upon women's well-being, body image, and sexual functioning, but less is known about the relational context of their coping and the impact upon their intimate partners. Our study focuses upon couples' experiences of breast cancer surgery, and its impact on body image and sexual intimacy. METHOD: Utilizing a dyadic design, we conducted 8 semistructured individual interviews, with 4 long-term heterosexual couples, after the women had undergone mastectomy with reconstruction. Interviews explored both partners' experiences of diagnosis, decision-making, and experiences of body image and sexual intimacy. Interpretative phenomenological analysis (IPA) was adopted; this is a qualitative research approach characterized by in-depth analysis of the personal meaning of experiences. RESULTS: Findings illustrate the positive acceptance that partners may express toward their wives' postsurgical bodies. They illuminate ways in which gendered coping styles and normative sexual scripts may shape couples' negotiations of intimacy around "altered embodiment." Reciprocal communication styles were important for couples' coping. The management of expectations regarding breast reconstruction may also be helpful. CONCLUSIONS: The insights from the dyadic, multiple perspective design suggest that psychologists must situate the meaning of supportive relationships and other protective factors in the context of complex life events and histories, in order to understand and support people's developing responses to distress. (PsycINFO Database Record