An ensemble method for predicting subnuclear localizations from primary protein structures

Background Predicting protein subnuclear localization is a challenging problem. Some previous works based on non-sequence information including Gene Ontology annotations and kernel fusion have respective limitations. The aim of this work is twofold: one is to propose a novel individual feature extraction method; another is to develop an ensemble method to improve prediction performance using comprehensive information represented in the form of high dimensional feature vector obtained by 11 feature extraction methods. Methodology/Principal Findings A novel two-stage multiclass support vector machine is proposed to predict protein subnuclear localizations. It only considers those feature extraction methods based on amino acid classifications and physicochemical properties. In order to speed up our system, an automatic search method for the kernel parameter is used. The prediction performance of our method is evaluated on four datasets: Lei dataset, multi-localization dataset, SNL9 dataset and a new independent dataset. The overall accuracy of prediction for 6 localizations on Lei dataset is 75.2% and that for 9 localizations on SNL9 dataset is 72.1% in the leave-one-out cross validation, 71.7% for the multi-localization dataset and 69.8% for the new independent dataset, respectively. Comparisons with those existing methods show that our method performs better for both single-localization and multi-localization proteins and achieves more balanced sensitivities and specificities on large-size and small-size subcellular localizations. The overall accuracy improvements are 4.0% and 4.7% for single-localization proteins and 6.5% for multi-localization proteins. The reliability and stability of our classification model are further confirmed by permutation analysis. Conclusions It can be concluded that our method is effective and valuable for predicting protein subnuclear localizations. A web server has been designed to implement the proposed method. It is freely available at http://bioinformatics.awowshop.com/snlpr​ed_page.php.

A potential role for lamellar insulin-like growth factor-1 receptor in the pathogenesis of hyperinsulinaemic laminitis

The reason why a sustained high concentration of insulin induces laminitis in horses remains unclear. Cell proliferation occurs in the lamellae during insulin-induced laminitis and in other species high concentrations of insulin can activate receptors for the powerful cell mitogen, insulin-like growth factor (IGF)-1. The first aim of this study was to determine if IGF-1 receptors (IGF-1R) are activated in the hoof during insulin-induced laminitis. Gene expression for IGF-1R and the insulin receptor (InsR) was measured using qRT-PCR, in lamellar tissue from control horses and from horses undergoing a prolonged euglycaemic, hyperinsulinaemic clamp (p-EHC), during the mid-developmental (24 h) and acute (46 h) phases of insulin-induced laminitis. Gene expression for both receptors was decreased 13–32-fold (P < 0.05) at both time-points in the insulin-treated horses. A second aim was to determine if the down-regulation of the receptor genes could be accounted for by an increase in circulating IGF-1. Serum IGF-1 was measured at 0, 10, 25 and 46 h post-treatment in horses given a p-EHC for approximately 46 h, and in matched controls administered a balanced, electrolyte solution. There was no increase in serum IGF-1 concentrations during the p-EHC, consistent with down-regulation of both receptors by insulin. Stimulation of the IGF-1R by insulin may lead to inappropriate lamellar epidermal cell proliferation and lamellar weakening, a potential mechanism for hyperinsulinaemic laminitis. Targeting this receptor may provide insights into the pathogenesis or identify a novel therapy for hyperinsulinaemic laminitis.

Insulin and the insulin-like growth factor system : a novel theory for hyperinsulinemic laminitis pathogenesis

Research into hyperinsulinemic laminitis has progressed significantly in recent years with the use of the prolonged-euglycemic, hyperinsulinemic clamp (p-EHC). Previous investigations of laminitis pathophysiology have focused on digital vascular dysfunction, inflammation, altered glucose metabolism within the lamellae, and lamellar basement membrane breakdown by metalloproteinases. The etiopathogenesis of laminitis occurring in association with hyperinsulinemia is yet to be fully characterized, but it may not involve these mechanisms. Insulin stimulates cellular proliferation and can also affect other body systems, such as the insulin-like growth factor (IGF) system. Insulin-like growth factor-1 (IGF-1) is structurally homologous to insulin and, like insulin, binds with strong affinity to a specific tyrosine kinase receptor on the cell surface to produce its effects, which include promoting cell proliferation. Receptors for IGF-1 (IGF-1R) are present in the lamellar epidermis. An alternative theory for the pathogenesis of hyperinsulinemic laminitis is that uncontrolled cell proliferation, mediated through both the insulin receptor (InsR) and IGF-1R, leads to lengthening, weakening, and failure of the lamellae. An analysis of the proliferative activity of lamellar epidermal cells during the developmental and acute phases of hyperinsulinemic laminitis, and lamellar gene expression of the InsR and IGF-1R was undertaken.

Spectrum sensing optimisation for dynamic primary user signal

We propose a multi-layer spectrum sensing optimisation algorithm to maximise sensing efficiency by computing the optimal sensing and transmission durations for a fast changing, dynamic primary user. Dynamic primary user traffic is modelled as a random process, where the primary user changes states during both the sensing period and transmission period to reflect a more realistic scenario. Furthermore, we formulate joint constraints to correctly reflect interference to the primary user and lost opportunity of the secondary user during the transmission period. Finally, we implement a novel duty cycle based detector that is optimised with respect to PU traffic to accurately detect primary user activity during the sensing period. Simulation results show that unlike currently used detection models, the proposed algorithm can jointly optimise the sensing and transmission durations to simultaneously satisfy the optimisation constraints for the considered primary user traffic.

The results of acetabular impaction grafting in 129 primary cemented total hip arthroplasties

Between 1995 and 2003, 129 cemented primary THRs were performed using full acetabular impaction grafting to reconstruct acetabular deficiencies. These were classified as cavitary in 74 and segmental in 55 hips. Eighty-one patients were reviewed at mean 9.1 (6.2-14.3) years post-operatively. There were seven acetabular component revisions due to aseptic loosening, and a further 11 cases that had migrated >5mm or tilted >5° on radiological review - ten of which reported no symptoms. Kaplan-Meier analysis of revisions for aseptic loosening demonstrates 100% survival at nine years for cavitary defects compared to 82.6% for segmental defects. Our results suggest that the medium-term survival of this technique is excellent when used for purely cavitary defects but less predictable when used with large rim meshes in segmental defects.

Layered silicates in Chondritic Porous Aggregate W7029*A : a case of primary growth

An important subset of extraterrestrial particles that reach the Earth's stratosphere include the so-called Chondritic Porous Aggregates (CPA's) [1-3]. In general, CPA's have a fluffy morphology and consist of numerous (>104)subparticles that are often <100A in size [4]. Mineral species in CPA's include Mg-rich pyroxene and olivine, Fe- and (Fe,Ni)-sulphides, taenite, Fe,Ni-carbides, magnetite, Ti-metal, a Bi-phase (metal or oxide), and variable amounts of carbonaceous material [1, 5-7]. Hydrated silicates are rare in CPA's and are limited to aggregates that have not been severely altered (thermo-metamorphosed) during atmospheric entry [8]. The presence of hydrated silicates in one cosmic dust particle was established by X-ray diffraction [2] and has been inferred in others by infra-red spectroscopy [8]. If CPA's are cometary, their mineralogy and morphology suggest that at least two episodes of aggregation occurred and that variations in porosity may be related to local differences in ice-to-dust ratio [3].

Education for sustainability : a case study of pre-service primary teachers' knowledge and efficacy

This study investigated the relationships between knowledge and efficacy for teaching sustainability in a sample of 266 pre-service primary teachers at a large, metropolitan university in Australia. A survey gathered information about the participant’s attitudes and self-efficacy for education for sustainability, along with their perceived and actual knowledge of environmental sustainability issues. The participants typically believed they were confident in their abilities to engage with education for sustainability with self-efficacy increasing with increased levels of perceived knowledge. However no relationship was found between perceived knowledge and actual knowledge which suggests that the participants either do not feel constrained by their lack of knowledge, or are perhaps unaware of their actual knowledge of sustainability issues. This lack of relationship may have implications for the development of pedagogical content knowledge with pre-service teachers potentially developing shallow, tokenistic approaches to Education for Sustainability.

Numerical techniques for simulating a fractional mathematical model of epidermal wound healing

A number of mathematical models investigating certain aspects of the complicated process of wound healing are reported in the literature in recent years. However, effective numerical methods and supporting error analysis for the fractional equations which describe the process of wound healing are still limited. In this paper, we consider the numerical simulation of a fractional mathematical model of epidermal wound healing (FMM-EWH), which is based on the coupled advection-diffusion equations for cell and chemical concentration in a polar coordinate system. The space fractional derivatives are defined in the Left and Right Riemann-Liouville sense. Fractional orders in the advection and diffusion terms belong to the intervals (0, 1) or (1, 2], respectively. Some numerical techniques will be used. Firstly, the coupled advection-diffusion equations are decoupled to a single space fractional advection-diffusion equation in a polar coordinate system. Secondly, we propose a new implicit difference method for simulating this equation by using the equivalent of Riemann-Liouville and Grünwald-Letnikov fractional derivative definitions. Thirdly, its stability and convergence are discussed, respectively. Finally, some numerical results are given to demonstrate the theoretical analysis.

‘Working with the team’ : an exploratory study of improved type 2 diabetes management in a new model of integrated primary/secondary care

This study aimed to explore how a new model of integrated primary/secondary care for type 2 diabetes management, the Brisbane South Complex Diabetes Service (BSCDS), related to improved diabetes management in a selected group of patients. We used a qualitative research design to obtain detailed accounts from the BSCDS via semi-structured interviews with 10 patients. The interviews were fully transcribed and systematically coded using a form of thematic analysis. Participants’ responses were grouped in relation to: (1) Patient-centred care; (2) Effective multiprofessional teamwork; and (3) Empowering patients. The key features of this integrated primary/secondary care model were accessibility and its delivery within a positive health care environment, clear and supportive interpersonal communication between patients and health care providers, and patients seeing themselves as being part of the team-based care. The BSCDS delivered patient-centred care and achieved patient engagement in ways that may have contributed to improved type 2 diabetes management in these participants.

Feminist ethics and menopause : autonomy and decision-making in primary medical care

The construction of menopause as a long-term risk to health and the adoption of discourses of prevention has made necessary a decision by women about medical treatment; specifically regarding the use of hormone replacement therapy. In a study of general practitioners’ accounts of menopause and treatment in Australia, women's ‘choice’, ‘informed decision-making’ and ‘empowerment’ were key themes through which primary medical care for women at menopause was presented. These accounts create a position for women defined by the concept of individual choice and an ethic of autonomy. These data are a basis for theorising more generally in this paper. We critically examine the construct of ‘informed decision-making’ in relation to several approaches to ethics including bioethics and a range of feminist ethics. We identify the intensification of power relations produced by an ethic of autonomy and discuss the ways these considerations inform a feminist ethics of decision-making by women. We argue that an ‘ethic of autonomy’ and an ‘offer of choice’ in relation to health care for women at menopause, far from being emancipatory, serves to intensify power relations. The dichotomy of choice, to take or not to take hormone replacement therapy, is required to be a choice and is embedded in relations of power and bioethical discourse that construct meanings about what constitutes decision-making at menopause. The deployment of the principle of autonomy in medical practice limits decision-making by women precisely because it is detached from the construction of meaning and the self and makes invisible the relations of power of which it is a part.

Activities for Pearl Barley and Charlie Parsley by Aaron Blabey Puffin Books 2007 Target group: Upper Primary

An upper primary multiliteracies project based on the children’s book “Pearl Barley and Charlie Parsley” by Aaron Blabey. The main theme explored is same and different.

Primary classroom teachers' use of social and emotional wellbeing programs and the factors influencing program use

There has been a rapid escalation in the development and evaluation of social and emotional well-being (SEW) programs in primary schools over the last few decades. Despite the plethora of programs available, primary teachers’ use of SEW programs is not well documented in Australian schools, with even less consideration of the factors influencing program use. A cross-sectional survey was undertaken with primary classroom teachers across twelve schools in the Brisbane and Sunshine Coast Education Districts in Queensland, Australia, during 2005. A checklist of SEW programs and an audit of SEW practices in schools were employed to investigate the number, range and types of SEW programs used by primary classroom teachers and the contextual factors influencing program use. Whilst the majority of implementation studies have been conducted under intervention conditions, this study was designed to capture primary classroom teachers’ day-to-day use of SEW programs and the factors influencing program use under real-world conditions. The findings of this research indicate that almost three quarters of the primary classroom teachers involved in the study reported using at least one SEW program during 2005. Wide variation in the number and range of programs used was evident, suggesting that teachers are autonomous in their use of SEW programs. Evidence-based SEW programs were used by a similar proportion of teachers to non-evidence-based programs. However, irrespective of the type of program used, primary teachers overwhelmingly reported using part of a SEW program rather than the whole program. This raises some issues about the quality of teachers’ program implementation in real-world practice, especially with respect to programs that are evidence-based. A content analysis revealed that a wide range of factors have been examined as potential influences on teachers’ implementation of health promotion programs in schools, including SEW programs, despite the limited number of studies undertaken to date. However, variation in the factors examined and study designs employed both within and across health promotion fields limited the extent to which studies could be compared. A methodological and statistical review also revealed substantial variation in the quality of reporting of studies. A variety of factors were examined as potential influences on primary classroom teachers’ use of SEW programs across multiple social-ecological levels of influence (ranging from community to school and individual levels). In this study, parent or caregiver involvement in class activities and the availability of wellbeing-related policies in primary schools were found to be influential in primary classroom teachers’ use of SEW programs. Teachers who often or always involve parents or caregivers in class activities were at a higher odds of program use relative to teachers who never or rarely involved parents or caregivers in class activities. However, teachers employed in schools with the highest number of wellbeing-related policies available were at a lower odds of program use relative to teachers employed in schools with fewer wellbeing-related policies available. Future research should investigate primary classroom teachers’ autonomy and motivations for using SEW programs and the reasons behind the selection and use of particular types of programs. A larger emphasis should also be placed upon teachers not using SEW programs to identify valid reasons for non-use. This would provide another step towards bridging the gap between the expectations of program developers and the needs of teachers who implement programs in practice. Additionally, the availability of wellbeing-related school policies and the types of activities that parents and caregivers are involved with in the classroom warrant more in-depth investigation. This will help to ascertain how and why these factors influence primary classroom teachers’ use of SEW programs on a day-to-day basis in schools.

Metal ion levels post unilateral primary Exeter total hip replacement

There has been much discussion and controversy in the media recently regarding metal toxicity following large head metal on metal (MoM) total hip replacement (THR). Patients have been reported as having hugely elevated levels of metal ions with, at times, devastating systemic, neurolgical and/or orthopaedic sequelae. However, no direct correlation between metal ion level and severity of metallosis has yet been defined. Normative levels of metal ions in well functioning, non Cobalt-Chrome hips have also not been defined to date. The Exeter total hip replacement contains no Cobalt-Chrome (Co-Cr) as it is made entirely from stainless steel. However, small levels of these metals may be present in the modular head of the prosthesis, and their effect on metal ion levels in the well functioning patient has not been investigated. We proposed to define the “normal” levels of metal ions detected by blood test in 20 well functioning patients at a minimum 1 year post primary Exeter total hip replacement, where the patient had had only one joint replaced. Presently, accepted normal levels of blood Chromium are 10–100 nmol/L and plasma Cobalt are 0–20 nmol/L. The UK Modern Humanities Research Association (MHRA) has suggested that levels of either Cobalt or Chromium above 7 ppb (equivalent to 135 nmol/L for Chromium and 120 nmol/L for Cobalt) may be significant. Below this level it is indicated that significant soft tissue reaction and tissue damage is less likely and the risk of implant failure is reduced. Hips were a mixture of cemented and hybrid procedures performed by two experienced orthopaedic consultants. Seventy percent were female, with a mixture of head sizes used. In our cohort, there were no cases where the blood Chromium levels were above the normal range, and in more than 70% of cases, levels were below recordable levels. There were also no cases of elevated plasma Cobalt levels, and in 35% of cases, levels were negligible. We conclude that the implantation with an Exeter total hip replacement does not lead to elevation of blood metal ion levels.

Developing media production skills for literacy in a primary school classroom : digital materials, embodied knowledge and material contexts

This chapter investigates the relationship between technical and operational skills and the development of conceptual knowledge and literacy in Media Arts learning. It argues that there is a relationship between the stories, expressions and ideas that students aim to produce with communications media, and their ability to realise these in material form through technical processes in specific material contexts. Our claim is that there is a relationship between the technical and the operational, along with material relations and the development of conceptual knowledge and literacy in media arts learning. We place more emphasis on the material aspects of literacy than is usually the case in socio-cultural accounts of media literacy. We provide examples from a current project to demonstrate that it is just as important to address the material as it is the discursive and conceptual when considering how students develop media literacy in classroom spaces.

Promoting handwashing with soap behaviour in Kenyan schools : learning from puppetry trials among primary school children in Kenya

While previous research clearly shows that handwashing with soap can prevent many serious illnesses and deaths among children in developing countries, handwashing rates remain low in countries like Kenya. This PhD study explored conditions needed for a successful handwashing with soap initiatives in primary schools in Kenya. It explored the use of puppetry as an approach in communicating hygiene messages as a form of interactive, community-driven method. The research considered a range of conditions that affect such interventions including infrastructure; hardware and software; policy that influence health programs; different actors who have a role to play; and factors affecting sustainability.