Targeting the Microbiota to Address Diet-Induced Obesity: A Time Dependent Challenge

peer-reviewedLinks between the gut microbiota and host metabolism have provided new perspectives on obesity. We previously showed that the link between the microbiota and fat deposition is age- and time-dependent subject to microbial adaptation to diet over time. We also demonstrated reduced weight gain in diet-induced obese (DIO) mice through manipulation of the gut microbiota with vancomycin or with the bacteriocin-producing probiotic Lactobacillus salivarius UCC118 (Bac+), with metabolic improvement achieved in DIO mice in receipt of vancomycin. However, two phases of weight gain were observed with effects most marked early in the intervention phase. Here, we compare the gut microbial populations at the early relative to the late stages of intervention using a high throughput sequencing-based analysis to understand the temporal relationship between the gut microbiota and obesity. This reveals several differences in microbiota composition over the intervening period. Vancomycin dramatically altered the gut microbiota composition, relative to controls, at the early stages of intervention after which time some recovery was evident. It was also revealed that Bac+ treatment initially resulted in the presence of significantly higher proportions of Peptococcaceae and significantly lower proportions of Rikenellaceae and Porphyromonadaceae relative to the gut microbiota of L. salivarius UCC118 bacteriocin negative (Bac-) administered controls. These differences were no longer evident at the later time. The results highlight the resilience of the gut microbiota and suggest that interventions may need to be monitored and continually adjusted to ensure sustained modification of the gut microbiota.The authors are supported in part by Teagasc, Science Foundation Ireland (in the form of a research centre grant to the Alimentary Pharmabiotic Centre and PI awards to PWOT and PC) and by Alimentary Health Ltd

Evaluating and combining digital video shot boundary detection algorithms

The development of standards for video encoding coupled with the increased power of computing mean that content-based manipulation of digital video information is now feasible. Shots are a basic structural building block of digital video and the boundaries between shots need to be determined automatically to allow for content-based manipulation. A shot can be thought of as continuous images from one camera at a time. In this paper we examine a variety of automatic techniques for shot boundary detection that we have implemented and evaluated on a baseline of 720,000 frames (8 hours) of broadcast television. This extends our previous work on evaluating a single technique based on comparing colour histograms. A description of each of our three methods currently working is given along with how they are evaluated. It is found that although the different methods have about the same order of magnitude in terms of effectiveness, different shot boundaries are detected by the different methods. We then look at combining the three shot boundary detection methods to produce one output result and the benefits in accuracy and performance that this brought to our system. Each of the methods were changed from using a static threshold value for three unconnected methods to one using three dynamic threshold values for one connected method. In a final summing up we look at the future directions for this work

Construction of an instrument for the measurement of educational philosophy

Thesis (M.Ed.)--Boston Universit

Re-imagining initial teacher identity and learning study: final report

The aim of this research, the Re-imagining Initial Teacher Identity and Learning Study (RIITILS) was to continue writing from and to extend the Learning to Teach Study 1 (LETS1). LETS1, funded by the Department of Education and Skills (DES), was the first study of its kind on the Postgraduate Diploma in Education (PGDE) in Ireland, and involved the development and implementation of a study of initial teacher education in the PGDE in post-primary education, in one School of Education. Its aim was to identify the individual and contextual dynamics of how student teachers develop curricular and cross-curricular competences during initial teacher education (ITE). Within an overall framework that explored how student teachers develop their skills, competences and identity as teachers, it focused on curricular competences in mathematics, science and language teaching, and on the cross-curricular competences of reading and digital literacy and the development of inclusive teaching practices. LETS1 was the first programme level research on the PGDE, familiarly known to generations of student teachers and teachers as ‘the Dip’ or ‘the HDip’. Similarly, RIITILS involved a programme level study of the ‘Dip’, since renamed the Professional Diploma in Education (PDE). We use LETS 2 to denote data collection on undertaken in this second study. LETS 2 utilised and extends three key findings from Learning to Teach Study 1 (LETS 1): post-primary teachers struggled to enact the meaning of ‘real world’ experiences in maths, had limited understanding of how reading literacy impacted their subject and while they felt ready to teach did not feel able to promote inclusion. Using LETS 1 as a unique data set, LETS 2 updated it by collecting data from the 2012/2013 PDE cohort, and extended it by focusing on student teacher development (through interviews, survey and artefacts) to examine how mathematics student teachers engaging with reform oriented Project Maths, in particular, engage with the ‘real world’, reading literacy and inclusion. Drawing on research on teacher education both in Ireland and internationally, the RIITILS report is divided into four main sections: (i) an introduction and overview of the study, (ii) a summary of RIITILS activities including conferences (one in collaboration with US National Science Foundation-funded FIRSTMATH study; and another on the reform and redesign of initial teacher education through deepening engagement with pedagogy, which featured keynote addresses on Japanese Lesson Study in mathematics), as well as participation in local (Institute for Social Sciences in the 21st Century: ISS21) and international (e.g. US National Science Foundation funded TEDS/FIRSTMATH) networks (iii) findings from the four strands of the research: Teacher education policy, mathematics, literacy in subject areas and school university partnerships, and (iv) a list of publications in the form of book chapters, conference proceedings, articles – both published and in progress - from LETS 1 and this IRC-funded study during 2012-13. The IRC-funded RIITILS provided essential support to bring a large number of co-authored publications to conclusion, as well as initiate a number of others. Prior to this IRC-funded study, in addition to the main report and executive summary, two journal articles based on LETS 1 were published: ‘Novice teachers as invisible learners’ (Long et al, 2012, Teachers and Teaching: Theory and Practice), ‘Authoring oneself and being authored as a competent teacher’ (Hall et al, 2012, Irish Educational Studies). Publications based on data from LETS 1 and LETS 2 that have been published from work undertaken during the life-cycle of this 2012-13 IRC funded Advanced Collaborative Research Award focus on: a critical discourse analysis of teacher education policy (Conway, 2013; Conway & Murphy, 2013), teacher education programme design (Conway et al, 2012), literacy in initial teacher education (Murphy et al, 2013, in press), teacher identity (Rutherford, et al, 2013, in press), workplace learning and initial teacher education (Conway, Murphy & Rutherford, 2014, in press; Conway & Munthe, 2014, in press), pilot of FIRSTMATH (Conway, et al, 2014, in press). A number of other articles, involving co-authorship by various configurations of LETS 1 and/or LETS 2 researchers, have been submitted for review and focus on: inclusion and ‘othering’ in teacher education (Kitching et al), current practices and future directions in school-university partnerships in initial teacher education (Connolly et al), the changing construction of literacy from LETS 1 to LETS 2 among student teachers (Conway et al), a Bernsteinian analysis of curricular emotions among student teachers of mathematics (Rutherford et al), a case study, employing a Bakhtinian-framework, of one student teacher’s construction of reform-oriented Project Maths (Rutherford et al), an analysis of changing conceptions of adolescent literacy and their significance for initial teacher education (Curtin et al), student teachers’ construction of modern language teaching (McKeon et al). A number of other manuscripts are well developed and are due for submission shortly and are detailed in the report. Like LETS 1, RIITILS is framed within a socio-cultural perspective on learning, and adopted a mixed methods research design. RIITILS involved four work strands: (i) policy analysis of the rapidly changing teacher education landscape in Ireland, (ii) an analysis of student teachers’ understanding and teaching of mathematics (particularly problem solving in the context of reform-oriented Project Maths), (iii) an analysis of student teachers’ understanding and teaching of literacy in their subject area and (iv) one-to-one and focus group interviews with three schools that have well-developed practices for supporting PDE students. Building directly on LETS 1, LETS 2 data collection on the PDE involved a survey of PDE student teachers, as well as interviews. Nine (n=9) students, who first or second subject was mathematics were interviewed at intervals over the course of the PDE programme, a focus group drawn from the wider group of mathematics pedagogy students was held, and one hundred and two students (n=102) responded to and completed a detailed survey on their learning to teach experience which had been distributed to the entire PDE 2012-2013 cohort. Among the dimensions of learning to teach addressed in the findings are the rapidly changing teacher education policy landscape in Ireland (Strand 1), significantly shaped by both new Teaching Council regulations as well as a policy step change in response to the results from the OECD’s PISA 2009. Strand 2 findings on the teaching of mathematics draw on two theoretical frames to present findings on mathematics teaching in an era of reform: (i) a Bernsteinian analysis of the classification and framing of emotions in mediating student teachers’ construction of mathematics pedagogy, and (ii) a Bakhtinian analysis of the discursive construction of problem solving narrated through a detailed case study of one student teacher who though, he ‘knows maths and likes maths’, as the article title indicates1, grapples with teaching Project Maths given the significant leap it represents from his own experience of learning of mathematics as a student at second and third level. This case conveys the vivid manner in which PDE students are typically experiencing the difference between their own experiences of learning mathematics in second and third level compared to what is now expected of them in teaching Project Maths. Strand 3 provides an analysis of how PDE students constructed literacy in their subject teaching, drawing on data from both the 2008-09 and 2012-13 cohorts and suggests both continuity and some important changes over time. In particular, whereas in LETS 1 student teachers typically associated literacy with support for students for whom English was a second language or had literacy difficulties, there was a notable emphasis on, and sense of responsibility by student teachers for, the wider role of literacy in their subject teaching for all - not just some - students. Strand 4 focuses on school university partnerships, a key aspect of initial teacher education, and as with LETS 1, the role of observation, mentoring and support in schools for PDE students was the focus of analysis. There was a significant increase in observation opportunities for student teachers from LETS 1 to LETS 2, and these opportunities, as was the case in LETS 1, were significantly associated with the presence of school level coordination. From LETS 1 to LETS 2, there was a small decline in the presence of school level coordinators, while assigned and sought after mentoring opportunities were similar, and there was a small increase in the number of student teachers that had no mentor, that is, school level, assigned or sought after, available to them in their school. In addition, LETS 2 identified a range of generative practices in some schools including: (i) discussion between cooperating/mentor teacher and PDE student after university tutor visits, (ii) a school resource book for mentor teachers, passed on year-to-year by the staff person designated to provide overall school coordination for PDE students, and (iii) a planning notebook shared between PDE students and their subject mentor teacher. Many of the findings from the Learning to Teach Studies are not unique to the PDE or to UCC but reflect perennial dilemmas and emerging challenges in the changing landscape of initial teacher education in Ireland and internationally. This fact is important in setting a context for the wider dissemination2 of the findings from Learning to Teach Studies 1 and 2. In conclusion, the purpose of this report was to present the main outcomes of the Re-imagining Initial Teacher Identity and Learning Study in terms of focus, activities and publications. In doing so the report presents work completed as well as on-going analysis and writing given the scale of both studies. Four ideas emerged as important in thinking about the implications of this study: (i) connected maths and reconfiguring experiences past and present, (ii) broadening engagement with literacy within subject teaching, (iii) deepening engagement with pedagogy in schools between PDE student and school mentors, and (iv) bridging between school and university and brokerage within both institutions. These four ‘big ideas’ are, we argue, worthy of attention at two levels, that is, both in terms of the redesign of initial teacher education and in the research on those reformed practices

Exercise and the microbiota

The authors are supported in part by research grants from Science Foundation Ireland including a centre grant (Alimentary Pharmabiotic Centre; Grant Numbers SFI/12/RC/2273 and 12/RC/2273). Dr. Orla O’Sullivan is funded by a Starting Investigator Research Grant from Science Foundation Ireland (Grant number 13/SIRG/2160). Dr. Paul Cotter is funded by a Principal Investigator Award from Science Foundation Ireland P.D.C are supported by a SFI PI award (Grant number 11/PI/1137).peer-reviewedSedentary lifestyle is linked with poor health, most commonly obesity and associated disorders, the corollary being that exercise offers a preventive strategy. However, the scope of exercise biology extends well beyond energy expenditure and has emerged as a great ‘polypill’, which is safe, reliable and cost-effective not only in disease prevention but also treatment. Biological mechanisms by which exercise influences homeostasis are becoming clearer and involve multi-organ systemic adaptations. Most of the elements of a modern lifestyle influence the indigenous microbiota but few studies have explored the effect of increased physical activity. While dietary responses to exercise obscure the influence of exercise alone on gut microbiota, professional athletes operating at the extremes of performance provide informative data. We assessed the relationship between extreme levels of exercise, associated dietary habits and gut microbiota composition, and discuss potential mechanisms by which exercise may exert a direct or indirect influence on gut microbiota.The authors are supported in part by research grants from Science Foundation Ireland including a centre grant (Alimentary Pharmabiotic Centre; Grant Numbers SFI/12/RC/2273 and 12/RC/2273). Dr. Orla O’Sullivan is funded by a Starting Investigator Research Grant from Science Foundation Ireland (Grant number 13/SIRG/2160). Dr. Paul Cotter is funded by a Principal Investigator Award from Science Foundation Ireland P.D.C are supported by a SFI PI award (Grant number 11/PI/1137)

The Composition of Human Milk and Infant Faecal Microbiota Over the First Three Months of Life: A Pilot Study

peer-reviewedHuman milk contains a diverse array of bioactives and is also a source of bacteria for the developing infant gut. The aim of this study was to characterize the bacterial communities in human milk and infant faeces over the first 3 months of life, in 10 mother-infant pairs. The presence of viable Bifidobacterium and Lactobacillus in human milk was also evaluated. MiSeq sequencing revealed a large diversity of the human milk microbiota, identifying over 207 bacterial genera in milk samples. The phyla Proteobacteria and Firmicutes and the genera Pseudomonas, Staphylococcus and Streptococcus were the predominant bacterial groups. A core of 12 genera represented 81% of the microbiota relative abundance in milk samples at week 1, 3 and 6, decreasing to 73% at week 12. Genera shared between infant faeces and human milk samples accounted for 70–88% of the total relative abundance in infant faecal samples, supporting the hypothesis of vertical transfer of bacteria from milk to the infant gut. In addition, identical strains of Bifidobacterium breve and Lactobacillus plantarum were isolated from the milk and faeces of one mother-infant pair. Vertical transfer of bacteria via breastfeeding may contribute to the initial establishment of the microbiota in the developing infant intestine

The Role of TLR2 and Bacterial Lipoprotein in Enhancing Airway Inflammation and Immunity

Non-typeable Haemophilus influenzae (NTHI) colonizes the lower respiratory tract of patients with chronic obstructive pulmonary disease and also causes exacerbations of the disease. The 16-kDa lipoprotein P6 has been widely studied as a potential vaccine antigen due to its highly conserved expression amongst NTHI strains. Although P6 is known to induce potent inflammatory responses, its role in the pathogenesis of NTHI infection in vivo has not been examined. Additionally, the presence of an amino-terminal lipid motif on P6 serves to activate host Toll-like receptor 2 (TLR2) signaling. The role of host TLR2 and NTHI expression of the lipoprotein P6 on the induction of airway inflammation and generation of adaptive immune responses following chronic NTHI stimulation was evaluated with TLR2-deficient mice and a P6-deficient NTHI strain. Absence of either host TLR2 or bacterial P6 resulted in diminished levels of immune cell infiltration within lungs of mice exposed to NTHI. Pro-inflammatory cytokine secretion was also reduced in lungs that did not express TLR2 or were exposed to NTHI devoid of P6. Induction of specific antibodies to P6 was severely limited in TLR2-deficient mice. Although mice exposed to the P6-deficient NTHI strain were capable of generating antibodies to other surface antigens of NTHI, these levels were lower compared to those observed in mice exposed to P6-expressing NTHI. Therefore, cognate interaction between host TLR2 and bacterial P6 serves to enhance lung inflammation and elicit robust adaptive immune responses during NTHI exposure. Strategies to limit NTHI inflammation while simultaneously promoting robust immune responses may benefit from targeting the TLR2:P6 signaling axis

Dublin City University video track experiments for TREC 2002

Dublin City University participated in the Feature Extraction task and the Search task of the TREC-2002 Video Track. In the Feature Extraction task, we submitted 3 features: Face, Speech, and Music. In the Search task, we developed an interactive video retrieval system, which incorporated the 40 hours of the video search test collection and supported user searching using our own feature extraction data along with the donated feature data and ASR transcript from other Video Track groups. This video retrieval system allows a user to specify a query based on the 10 features and ASR transcript, and the query result is a ranked list of videos that can be further browsed at the shot level. To evaluate the usefulness of the feature-based query, we have developed a second system interface that provides only ASR transcript-based querying, and we conducted an experiment with 12 test users to compare these 2 systems. Results were submitted to NIST and we are currently conducting further analysis of user performance with these 2 systems