Towards 3D structure prediction of large RNA molecules: an integer programming framework to insert local 3D motifs in RNA secondary structure

Motivation: The prediction of RNA 3D structures from its sequence only is a milestone to RNA function analysis and prediction. In recent years, many methods addressed this challenge, ranging from cycle decomposition and fragment assembly to molecular dynamics simulations. However, their predictions remain fragile and limited to small RNAs. To expand the range and accuracy of these techniques, we need to develop algorithms that will enable to use all the structural information available. In particular, the energetic contribution of secondary structure interactions is now well documented, but the quantification of non-canonical interactions—those shaping the tertiary structure—is poorly understood. Nonetheless, even if a complete RNA tertiary structure energy model is currently unavailable, we now have catalogues of local 3D structural motifs including non-canonical base pairings. A practical objective is thus to develop techniques enabling us to use this knowledge for robust RNA tertiary structure predictors

Combinatorial RNA Design: Designability and Structure-Approximating Algorithm

In this work, we consider the Combinatorial RNA Design problem, a minimal instance of the RNA design problem which aims at finding a sequence that admits a given target as its unique base pair maximizing structure. We provide complete characterizations for the structures that can be designed using restricted alphabets. Under a classic four-letter alphabet, we provide a complete characterization of designable structures without unpaired bases. When unpaired bases are allowed, we provide partial characterizations for classes of designable/undesignable structures, and show that the class of designable structures is closed under the stutter operation. Membership of a given structure to any of the classes can be tested in linear time and, for positive instances, a solution can be found in linear time. Finally, we consider a structure-approximating version of the problem that allows to extend bands (helices) and, assuming that the input structure avoids two motifs, we provide a linear-time algorithm that produces a designable structure with at most twice more base pairs than the input structure.Comment: CPM - 26th Annual Symposium on Combinatorial Pattern Matching, Jun 2015, Ischia Island, Italy. LNCS, 201

Using reflexivity to enhance in-depth interviewing skills for the clinician researcher

<p>Abstract</p> <p>Background</p> <p>Primary health care clinicians are being encouraged to undertake qualitative research, however the in-depth interviewing skills required are not as straightforward as might be first supposed. While there are benefits and certain skills that clinicians can bring to interview-based research, there are important new skills to develop. To date there has been neither discussion about these new skills, nor any preparatory guidelines for clinicians entering into interview-based research in the qualitative research literature. In the absence of formal guidelines, we suggest the use of reflexivity throughout the interview process as a means to become more accomplished in this area. We present our own experiences as a novice general practitioner (GP) researcher undertaking a PhD study and her experienced supervisors. The PhD study used critical phenomenology through in-depth interviews to understand the experience of the patient-doctor relationship between same-sex attracted women and their usual GP in Australia.</p> <p>Results</p> <p>We used reflexivity to improve the rigour of the data collection. This enabled improved probing, fewer assumptions, avoidance of premature interpretation, and an accentuated sense of curiosity during interviews. We also enlisted reciprocity between interviewer and interviewee as a tool to improve engagement and trust, share interview control, and ultimately improve the depth of the interview content.</p> <p>Conclusion</p> <p>Preparatory recommendations for novice clinician research interviewers include the importance of recognising the multiple identities that they bring to the interview. In this setting in particular this involves acknowledging the clinician interviewer as a potential insider in relation to interviewees and negotiating shared understanding to avoid insider assumptions. Other essential requirements are having an experienced research supervisor, arranging pilot interviews that include active feedback on interviewing style from interviewees, and being reflexive during interviews. More formal guidelines for in-depth interviewing skills development are needed.</p

Tied to the worldly work of writing: parent as ethnographer

Parent narratives have contributed to ethnographic accounts of the lives of autistic children (Kelly, 2005) but there are fewer examples of parents producing their own autoethnographies. This paper explores the affordances of an online blog for enabling a parent of an autistic child to produce a written record of practice which may be considered 'autoethnographic'. Richardson’s (2005) framework for ethnography as Creative Analytic Process is applied to extracts from a blog post in order to consider its contribution; reflexivity; aesthetic merit; and impact. The paper addresses the methodological and ethical implications of reconceptualising parents as researchers and the potential contribution of new writing platforms to the development of auto/ethnography. Key words: Autism, Auto/ethnography, Blog, Disability, Mothe

"We're worth what we are paid": Unravelling the 'paradox of the contented female worker'

Pay satisfaction research has suggested that women are more satisfied with their pay than men, even though, in general, women earn less. This paper argues that this body of research has misconceptualised this phenomenon as an issue of women only. It also argues that previous explanations for this gender pay paradox have not adequately explained these patterns of satisfaction. A social constructionist approach to pay satisfaction is proposed which situates satisfaction within the context of structural inequality. This draws upon the scholarly work of feminist scholars and the conceptual ideas of Pierre Bourdieu. This theoretical approach is explored with data from qualitative interviews with support staff at universities in the United Kingdom. This evidence suggests that their pay satisfaction is influenced by beliefs about the ‘value’ of different occupations

"Aye, but it were wasted on thee": Cricket, British Asians, ethnic identities, and the 'magical recovery of community'

People in sport tend to possess rather jaded perceptions of its colour-blindness and thus, they are reluctant to confront the fact that, quite often racism is endemic. Yorkshire cricket in particular, has faced frequent accusations from minority ethnic communities of inveterate and institutionalised racism and territorial defensiveness. Drawing upon semi-structured interviews conducted with amateur white and British Asian cricketers, this paper examines the construction of regional identities in Yorkshire at a time when traditional myths and invented traditions of Yorkshire and 'Yorkshireness' are being deconstructed. This is conceptualised through a reading of John Clarke's 'magical recovery of community'. Although cricket has been multiracial for decades, I argue that some people's position as insiders is more straightforward than others. I present evidence to suggest that, regardless of being committed to Yorkshire and their 'Yorkshireness', white Yorkshire people may never fully accept British Asians as 'one of us'. Ideologically and practically, white Yorkshire people are engaged in constructing British Asians as anathema to Yorkshire culture. The paper concludes by advocating that, for sports cultures to be truly egalitarian, the ideology of sport itself has to change. True equality will only ever be achieved within a deracialised discourse that not only accepts difference, but embraces it

An Alternative Ethics? Justice and Care as Guiding Principles for Qualitative Research

The dominant conception of social research ethics is centred on deontological and consequentialist principles. In place of this, some qualitative researchers have proposed a very different approach. This appeals to a range of commitments that transform the goal of research as well as framing how it is pursued. This new ethics demands a participatory form of inquiry, one in which the relationship between researchers and researched is equalized. In this paper we examine this alternative approach, focusing in particular on two of the principles that are central to it: justice and care. We argue that there are some significant defects and dangers associated with this new conception of research ethics

Critical pathways for the management of preeclampsia and severe preeclampsia in institutionalised health care settings

BACKGROUND: Preeclampsia is a complex disease in which several providers should interact continuously and in a coordinated manner to provide proper health care. However, standardizing criteria to treat patients with preeclampsia is problematical and severe flaws have been observed in the management of the disease. This paper describes a set of critical pathways (CPs) designed to provide uniform criteria for clinical decision-making at different levels of care of pregnant patients with preeclampsia or severe preeclampsia. METHODS: Clinicians and researchers from different countries participated in the construction of the CPs. The CPs were developed using the following steps: a) Definition of the conceptual framework; b) Identification of potential users: primary care physicians and maternal and child health nurses in ambulatory settings; ob/gyn and intensive care physicians in secondary and tertiary care levels. c) Structural development. RESULTS: The CPs address the following care processes: 1. Screening for preeclampsia, risk assessment and classification according to the level of risk. 2. Management of preeclampsia at primary care clinics. 3. Evaluation and management of preeclampsia at secondary and tertiary care hospitals: 4. Criteria for clinical decision-making between conservative management and expedited delivery of patients with severe preeclampsia. CONCLUSION: Since preeclampsia continues to be one of the primary causes of maternal deaths and morbidity worldwide, the expected impact of these CPs is the contribution to improving health care quality in both developed and developing countries. The CPs are designed to be applied in a complex health care system, where different physicians and health providers at different levels of care should interact continuously and in a coordinated manner to provide care to all preeclamptic women. Although the CPs were developed using evidence-based criteria, they could require careful evaluation and remodelling according to each system's demands. Additionally, the CPs need to be tested in large-scale, multi-level studies in order to thoroughly examine and evaluate their efficacy and effectiveness