Searching for convergence in phylogenetic Markov chain Monte Carlo

Markov chain Monte Carlo (MCMC) is a methodology that is gaining widespread use in the phylogenetics community and is central to phylogenetic software packages such as MrBayes. An important issue for users of MCMC methods is how to select appropriate values for adjustable parameters such as the length of the Markov chain or chains, the sampling density, the proposal mechanism, and, if Metropolis-coupled MCMC is being used, the number of heated chains and their temperatures. Although some parameter settings have been examined in detail in the literature, others are frequently chosen with more regard to computational time or personal experience with other data sets. Such choices may lead to inadequate sampling of tree space or an inefficient use of computational resources. We performed a detailed study of convergence and mixing for 70 randomly selected, putatively orthologous protein sets with different sizes and taxonomic compositions. Replicated runs from multiple random starting points permit a more rigorous assessment of convergence, and we developed two novel statistics, delta and epsilon, for this purpose. Although likelihood values invariably stabilized quickly, adequate sampling of the posterior distribution of tree topologies took considerably longer. Our results suggest that multimodality is common for data sets with 30 or more taxa and that this results in slow convergence and mixing. However, we also found that the pragmatic approach of combining data from several short, replicated runs into a metachain to estimate bipartition posterior probabilities provided good approximations, and that such estimates were no worse in approximating a reference posterior distribution than those obtained using a single long run of the same length as the metachain. Precision appears to be best when heated Markov chains have low temperatures, whereas chains with high temperatures appear to sample trees with high posterior probabilities only rarely. [Bayesian phylogenetic inference; heating parameter; Markov chain Monte Carlo; replicated chains.]

Computer-assisted production scheduling, planning and control in foundries

The present study describes a pragmatic approach to the implementation of production planning and scheduling techniques in foundries of all types and looks at the use of `state-of-the-art' management control and information systems. Following a review of systems for the classification of manufacturing companies, a definitive statement is made which highlights the important differences between foundries (i.e. `component makers') and other manufacturing companies (i.e. `component buyers'). An investigation of the manual procedures which are used to plan and control the manufacture of components reveals the inherent problems facing foundry production management staff, which suggests the unsuitability of many manufacturing techniques which have been applied to general engineering companies. From the literature it was discovered that computer-assisted systems are required which are primarily `information-based' rather than `decision based', whilst the availability of low-cost computers and `packaged-software' has enabled foundries to `get their feet wet' without the financial penalties which characterized many of the early attempts at computer-assistance (i.e. pre-1980). Moreover, no evidence of a single methodology for foundry scheduling emerged from the review. A philosophy for the development of a CAPM system is presented, which details the essential information requirements and puts forward proposals for the subsequent interactions between types of information and the sub-system of CAPM which they support. The work developed was oriented specifically at the functions of production planning and scheduling and introduces the concept of `manual interaction' for effective scheduling. The techniques developed were designed to use the information which is readily available in foundries and were found to be practically successful following the implementation of the techniques into a wide variety of foundries. The limitations of the techniques developed are subsequently discussed within the wider issues which form a CAPM system, prior to a presentation of the conclusions which can be drawn from the study.

Metaphors of identity in dating ads and newspaper articles

This article investigates metaphors of identity in dating ads and in two types of newspaper writing, 'hard' and 'soft' news articles. It focuses on issues of textualization and processing, and particularly on the role of cotext in decoding metaphors. Taking a pragmatic approach founded in the cooperative principle, it argues that the maxims of quality and relation play related but separable roles in the interpretation of identity metaphors; and that this process is guided and constrained by cotextual selections in the environment of the metaphorical term. The particular kinds of cotextual guidance provided by the writer are seen to vary according to genre-driven issues. These include the purpose and stylistic conventions of the genre in which the metaphor occurs and the circumstances under which the text is composed and read. Differing functional motivations are suggested for the use of identity metaphors in each of the genres considered. © Walter de Gruyter 2007.

What do students want most from written feedback information? Distinguishing necessities from luxuries using a budgeting methodology

Feedback is a key concern for higher education practitioners, yet there is little evidence concerning the aspects of assessment feedback information that higher education students prioritise when their lecturers’ time and resources are stretched. One recent study found that in such circumstances, students actually perceive feedback information itself as a luxury rather than a necessity. We first re-examined that finding by asking undergraduates to ‘purchase’ characteristics to create the ideal lecturer, using budgets of differing sizes to distinguish necessities from luxuries. Contrary to the earlier research, students in fact considered good feedback information the single biggest necessity for lecturers to demonstrate. In a second study we used the same method to examine the characteristics of feedback information that students value most. Here, the most important perceived necessity was guidance on improvement of skills. In both studies, students’ priorities were influenced by their individual approaches to learning. These findings permit a more pragmatic approach to building student satisfaction in spite of growing expectations and demands.

Graded Exercise Therapy Guided Self-Help Trial for Patients with Chronic Fatigue Syndrome (GETSET): Protocol for a Randomized Controlled Trial and Interview Study

Background: Chronic fatigue syndrome, also known as myalgic encephalomyelitis (CFS/ME), is characterized by chronic disabling fatigue and other symptoms, which are not explained by an alternative diagnosis. Previous trials have suggested that graded exercise therapy (GET) is an effective and safe treatment. GET itself is therapist-intensive with limited availability. Objective: While guided self-help based on cognitive behavior therapy appears helpful to patients, Guided graded Exercise Self-help (GES) is yet to be tested. Methods: This pragmatic randomized controlled trial is set within 2 specialist CFS/ME services in the South of England. Adults attending secondary care clinics with National Institute for Health and Clinical Excellence (NICE)-defined CFS/ME (N=218) will be randomly allocated to specialist medical care (SMC) or SMC plus GES while on a waiting list for therapist-delivered rehabilitation. GES will consist of a structured booklet describing a 6-step graded exercise program, supported by up to 4 face-to-face/telephone/Skype™ consultations with a GES-trained physiotherapist (no more than 90 minutes in total) over 8 weeks. The primary outcomes at 12-weeks after randomization will be physical function (SF-36 physical functioning subscale) and fatigue (Chalder Fatigue Questionnaire). Secondary outcomes will include healthcare costs, adverse outcomes, and self-rated global impression change scores. We will follow up all participants until 1 year after randomization. We will also undertake qualitative interviews of a sample of participants who received GES, looking at perceptions and experiences of those who improved and worsened. Results: The project was funded in 2011 and enrolment was completed in December 2014, with follow-up completed in March 2016. Data analysis is currently underway and the first results are expected to be submitted soon. Conclusions: This study will indicate whether adding GES to SMC will benefit patients who often spend many months waiting for rehabilitative therapy with little or no improvement being made during that time. The study will indicate whether this type of guided self-management is cost-effective and safe. If this trial shows GES to be acceptable, safe, and comparatively effective, the GES booklet could be made available on the Internet as a practitioner and therapist resource for clinics to recommend, with the caveat that patients also be supported with guidance from a trained physiotherapist. The pragmatic approach in this trial means that GES findings will be generalizable to usual National Health Service (NHS) practice.

Auditoría integrada de Información + Conocimiento: aplicación en un caso de estudio

Se presentan los resultados de la aplicación de una metodología integradora de auditoría de información y conocimiento, llevada a cabo en un Centro de Investigación del Ministerio de Ciencia, Tecnología y Medio Ambiente de la provincia de Holguín, Cuba, conformada por siete etapas con un enfoque híbrido dirigida a revisar la estrategia y la política de gestión de información y conocimiento, identificar e inventariar y mapear los recursos de I+C y sus flujos, y valorar los procesos asociados a su gestión. La alta dirección de este centro, sus especialistas e investigadores manifestaron la efectividad de la metodología aplicada cuyos resultados propiciaron reajustar la proyección estratégica en relación con la gestión de la I+C, rediseñar los flujos informativos de los procesos claves, disponer de un directorio de sus expertos por áreas y planificar el futuro aprendizaje y desarrollo profesional.

Linguas en contacto na escrita electrónica galega

La escritura electrónica es en la actualidad una modalidad gráfica de gran éxito que en los últimos años comenzó a ser albo de diversas investigaciones lingüísticas. Sin embargo, un análisis exclusivamente gramatical, desvinculado del medio social en el que se utiliza, parece insuficiente para entender un fenómeno de tal complejidad. Consecuentemente, analizamos sus características en base a los condicionamientos sociolingüísticos presentes en el caso gallego. Así, examinamos las implicaciones de la situación de contacto y conflicto lingüístico entre el gallego y el español, señalamos las motivaciones de la alternancia de código y de las interferencias lingüísticas –que no siempre coinciden con las que operan en la lengua común- y observamos que estas prácticas son consecuencia de la confluencia de factores sociolingüísticos con otros de naturaleza pragmática.

Expanding Agri-Food Production and Employment in the Presence of Climate Policy Constraints: Quantifying the Trade-Off in Ireland

This chapter explores the trade-off between competing objectives of employment creation and climate policy commitments in Irish agriculture. A social accounting matrix (SAM) multiplier model is linked with a partial equilibrium agricultural sector model to simulate the impact of a number of GHG emission reduction scenarios, assuming these are achieved through a constraint on beef production. Limiting the size of the beef sector helps to reduce GHG emissions with a very limited impact on the value of agricultural income at the farm level. However, the SAM multiplier analysis shows that there would be significant employment losses in the wider economy. From a policy perspective, a pragmatic approach to GHG emissions reductions in the agriculture sector, which balances opportunities for economic growth in the sector with opportunities to reduce associated GHG emissions, may be required.

Growing Well-beings: the Positive Experience of Care Farms

Objectives: Care farms enable people who are in some way vulnerable to engage with agricultural places and farming activities. This study investigates how this impacts on the health and well-being of service users and explores associated processes and outcomes. Design: A mixed methods design was adopted that allowed for the integration of quantitative measurements of change with qualitative descriptions of this change. A pragmatic approach provided sufficient flexibility to support the investigation of complex contexts. Methods: A total of 216 service users completed an initial questionnaire, and 137 (63%) of this number provided comparative data in a follow-up questionnaire. Questionnaires contained multiple choice and open-ended questions alongside standardized health and well-being measures requiring Likert-format responses. Semi-structured interviews with 33 service users allowed personal experiences to be detailed. Results: Statistical analysis of well-being measure scores identified significant positive relationships with the length of time people had been attending the care farm. Questionnaire and interview data presented health benefits as being enabled by the farm environment, the positive experience as supporting personal development, and associated social interactions as becoming increasingly influential as time progressed. Conclusions: The health and well-being outcomes that result from participating at a care farm influence multiple elements of the human condition and apply amongst vulnerable people with a wide range of personal needs. Care farms have access to a potentially unique range of resources that can support many service users in becoming happier and healthier individuals.

Entrepreneurial Orientation: do we actually know as much as we think we do?

International audience

Le processus d’élaboration des politiques publiques comme espace d’autodétermination : les cas de l’Accord de Kelowna et de la Loi sur le contrôle par les Premières Nations de leur système d’éducation

L’objectif du présent mémoire est double. D’une part, il cherche à identifier les facteurs qui permettent au gouvernement canadien et aux peuples autochtones de s’entendre sur des politiques publiques, malgré la persistance d’une logique coloniale. Nous verrons que l’atteinte d’une entente est conditionnelle à la légitimité du processus d’élaboration de la politique publique d’un point de vue autochtone. D’autre part, ce travail invite à penser le processus d’élaboration des politiques publiques comme espace potentiel d’autodétermination. Étant donné la malléabilité des règles qui encadrent l’élaboration des politiques publiques en contexte canadien, le gouvernement – s’il en a la volonté - peut modeler le processus d’élaboration de façon à le rendre plus égalitaire et donc plus légitime d’un point de vue autochtone. Il sera démontré que, dans une optique de changements progressifs, un tel processus d’élaboration peut permettre aux peuples autochtones de regagner une certaine autonomie décisionnelle et ainsi atténuer les rapports de pouvoir inégalitaires. Notre cadre théorique a été construit à l’aide de différents courants analytiques, issus notamment des littératures sur le colonialisme, sur les politiques publiques et sur la légitimité. La comparaison de deux études de cas, soit les processus d’élaboration de l’Accord de Kelowna et du projet de loi C-33, Loi sur le contrôle par les Premières Nations de leur système d’éducation, permettra d’illustrer nos arguments et d’en démontrer l’applicabilité pratique. En somme, nous verrons comment la première étude de cas permet de concevoir l’élaboration des politiques publiques comme espace potentiel d’autodétermination, et comment la deuxième, au contraire, démontre que cette sphère peut encore en être une d’oppression.

Le processus d’élaboration des politiques publiques comme espace d’autodétermination : les cas de l’Accord de Kelowna et de la Loi sur le contrôle par les Premières Nations de leur système d’éducation

L’objectif du présent mémoire est double. D’une part, il cherche à identifier les facteurs qui permettent au gouvernement canadien et aux peuples autochtones de s’entendre sur des politiques publiques, malgré la persistance d’une logique coloniale. Nous verrons que l’atteinte d’une entente est conditionnelle à la légitimité du processus d’élaboration de la politique publique d’un point de vue autochtone. D’autre part, ce travail invite à penser le processus d’élaboration des politiques publiques comme espace potentiel d’autodétermination. Étant donné la malléabilité des règles qui encadrent l’élaboration des politiques publiques en contexte canadien, le gouvernement – s’il en a la volonté - peut modeler le processus d’élaboration de façon à le rendre plus égalitaire et donc plus légitime d’un point de vue autochtone. Il sera démontré que, dans une optique de changements progressifs, un tel processus d’élaboration peut permettre aux peuples autochtones de regagner une certaine autonomie décisionnelle et ainsi atténuer les rapports de pouvoir inégalitaires. Notre cadre théorique a été construit à l’aide de différents courants analytiques, issus notamment des littératures sur le colonialisme, sur les politiques publiques et sur la légitimité. La comparaison de deux études de cas, soit les processus d’élaboration de l’Accord de Kelowna et du projet de loi C-33, Loi sur le contrôle par les Premières Nations de leur système d’éducation, permettra d’illustrer nos arguments et d’en démontrer l’applicabilité pratique. En somme, nous verrons comment la première étude de cas permet de concevoir l’élaboration des politiques publiques comme espace potentiel d’autodétermination, et comment la deuxième, au contraire, démontre que cette sphère peut encore en être une d’oppression.

Comparative Functional Analysis of Boundary Infrastructures, Library Classification, and Folksonomies

This paper outlines three information organization frameworks: library classification, social tagging, and boundary infrastructures. It then outlines functionality of these frameworks. The paper takes a neo-pragmatic approach. The paper finds that these frameworks are complementary, and by understanding the differences and similarities that obtain between them, researchers and developers can begin to craft a vocabulary of evaluation.

Developing and evaluating interventions that are applicable and relevant to inpatients and those who care for them; a multiphase, pragmatic action research approach

Background Randomised controlled trials may be of limited use to evaluate the multidisciplinary and multimodal interventions required to effectively treat complex patients in routine clinical practice; pragmatic action research approaches may provide a suitable alternative. Methods A multiphase, pragmatic, action research based approach was developed to identify and overcome barriers to nutritional care in patients admitted to a metropolitan hospital hip-fracture unit. Results Four sequential action research cycles built upon baseline data including 614 acute hip-fracture inpatients and 30 purposefully sampled clinicians. Reports from Phase I identified barriers to nutrition screening and assessment. Phase II reported post-fracture protein-energy intakes and intake barriers. Phase III built on earlier results; an explanatory mixed-methods study expanded and explored additional barriers and facilitators to nutritional care. Subsequent changes to routine clinical practice were developed and implemented by the treating team between Phase III and IV. These were implemented as a new multidisciplinary, multimodal nutritional model of care. A quasi-experimental controlled, ‘before-and-after’ study was then used to compare the new model of care with an individualised nutritional care model. Engagement of the multidisciplinary team in a multiphase, pragmatic action research intervention doubled energy and protein intakes, tripled return home discharge rates, and effected a 75% reduction in nutritional deterioration during admission in a reflective cohort of hip-fracture inpatients. Conclusions This approach allowed research to be conducted as part of routine clinical practice, captured a more representative patient cohort than previously reported studies, and facilitated exploration of barriers and engagement of the multidisciplinary healthcare workers to identify and implement practical solutions. This study demonstrates substantially different findings to those previously reported, and is the first to demonstrate that multidisciplinary, multimodal nutrition care reduces intake barriers, delivers a higher proportional increase in protein and energy intake compared with baseline than other published intervention studies, and improves patient outcomes when compared with individualised nutrition care. The findings are considered highly relevant to clinical practice and have high translation validity. The authors strongly encourage the development of similar study designs to investigate complex health problems in elderly, multi-morbid patient populations as a way to evaluate and change clinical practice.

A pragmatic Bayesian approach to wind field retrieval

The ERS-1 Satellite was launched in July 1991 by the European Space Agency into a polar orbit at about 800 km, carrying a C-band scatterometer. A scatterometer measures the amount of backscatter microwave radiation reflected by small ripples on the ocean surface induced by sea-surface winds, and so provides instantaneous snap-shots of wind flow over large areas of the ocean surface, known as wind fields. Inherent in the physics of the observation process is an ambiguity in wind direction; the scatterometer cannot distinguish if the wind is blowing toward or away from the sensor device. This ambiguity implies that there is a one-to-many mapping between scatterometer data and wind direction. Current operational methods for wind field retrieval are based on the retrieval of wind vectors from satellite scatterometer data, followed by a disambiguation and filtering process that is reliant on numerical weather prediction models. The wind vectors are retrieved by the local inversion of a forward model, mapping scatterometer observations to wind vectors, and minimising a cost function in scatterometer measurement space. This thesis applies a pragmatic Bayesian solution to the problem. The likelihood is a combination of conditional probability distributions for the local wind vectors given the scatterometer data. The prior distribution is a vector Gaussian process that provides the geophysical consistency for the wind field. The wind vectors are retrieved directly from the scatterometer data by using mixture density networks, a principled method to model multi-modal conditional probability density functions. The complexity of the mapping and the structure of the conditional probability density function are investigated. A hybrid mixture density network, that incorporates the knowledge that the conditional probability distribution of the observation process is predominantly bi-modal, is developed. The optimal model, which generalises across a swathe of scatterometer readings, is better on key performance measures than the current operational model. Wind field retrieval is approached from three perspectives. The first is a non-autonomous method that confirms the validity of the model by retrieving the correct wind field 99% of the time from a test set of 575 wind fields. The second technique takes the maximum a posteriori probability wind field retrieved from the posterior distribution as the prediction. For the third technique, Markov Chain Monte Carlo (MCMC) techniques were employed to estimate the mass associated with significant modes of the posterior distribution, and make predictions based on the mode with the greatest mass associated with it. General methods for sampling from multi-modal distributions were benchmarked against a specific MCMC transition kernel designed for this problem. It was shown that the general methods were unsuitable for this application due to computational expense. On a test set of 100 wind fields the MAP estimate correctly retrieved 72 wind fields, whilst the sampling method correctly retrieved 73 wind fields.