Thinking with and outside the box: developing computer support for evidence teaching

B. Schafer, J. Keppens and Q. Shen. Thinking with and outside the Box: Developing Computer Support for Evidence Teaching. P. Robert and M. Redmayne (Eds.), Innovations in Evidence and Proof: Integrating Theory, Research and Teaching, pp. 139-158, 2007.

Synthetic biology: a utilitarian perspective

I examine the positive and negative features of synthetic biology (‘SynBio’) from a utilitarian ethical perspective. The potential beneficial outcomes from SynBio in the context of medicine are substantial; however it is not presently possible to predict precise outcomes due to the nascent state of the field. Potential negative outcomes from SynBio also exist, including iatrogenesis and bioterrorism; however it is not yet possible to quantify these risks. I argue that the application of a ‘precautionary’ approach to SynBio is ethically fraught, as is the notion that SynBio-associated knowledge ought to be restricted. I conclude that utilitarians ought to support a broadly laissez-faire stance in respect of SynBio.

BitBox!: A case study interface for teaching real-time adaptive music composition for video games

Real-time adaptive music is now well-established as a popular medium, largely through its use in video game soundtracks. Commercial packages, such as fmod, make freely available the underlying technical methods for use in educational contexts, making adaptive music technologies accessible to students. Writing adaptive music, however, presents a significant learning challenge, not least because it requires a different mode of thought, and tutor and learner may have few mutual points of connection in discovering and understanding the musical drivers, relationships and structures in these works. This article discusses the creation of ‘BitBox!’, a gestural music interface designed to deconstruct and explain the component elements of adaptive composition through interactive play. The interface was displayed at the Dare Protoplay games exposition in Dundee in August 2014. The initial proof-of- concept study proved successful, suggesting possible refinements in design and a broader range of applications.

Going retro: oxidative stress biomarkers in modern redox biology

The field of redox biology is inherently intertwined with oxidative stress biomarkers. Oxidative stress biomarkers have been utilized for many different objectives. Our analysis indicates that oxidative stress biomarkers have several salient applications: (1) diagnosing oxidative stress, (2) pinpointing likely redox components in a physiological or pathological process, and (3) estimating the severity, progression and/or regression of a disease. On the contrary, oxidative stress biomarkers do not report on redox signaling. Alternative approaches to gain more mechanistic insights are: (1) measuring molecules that are integrated in pathways linking redox biochemistry with physiology, (2) using the exomarker approach and (3) exploiting -omics techniques. More sophisticated approaches and large trials are needed to establish oxidative stress biomarkers in the clinical setting.

Teaching English tense and aspect with the help of cognitive grammar: An empirical study

Form-focused instruction is usually based on traditional practical/pedagogical grammar descriptions of grammatical features. The comparison of such traditional accounts with cognitive grammar (CG) descriptions seems to favor CG as a basis of pedagogical rules. This is due to the insistence of CG on the meaningfulness of grammar and its detailed analyses of the meanings of particular grammatical features. The differences between traditional and CG rules/descriptions are exemplified by juxtaposing the two kinds of principles concerning the use of the present simple and present progressive to refer to situations happening or existing at speech time. The descriptions provided the bases for the instructional treatment in a quasi-experimental study exploring the effectiveness of using CG descriptions of the two tenses, and of their interplay with stative (imperfective) and dynamic (perfective) verbs, and comparing this effectiveness with the value of grammar teaching relying on traditional accounts found in standard pedagogical grammars. The study involved 50 participants divided into three groups, with one of them constituting the control group and the other two being experimental ones. One of the latter received treatment based on CG descriptions and the other on traditional accounts. CG-based instruction was found to be at least moderately effective in terms of fostering mostly explicit grammatical knowledge and its effectiveness turned out be comparable to that of teaching based on traditional descriptions.

Teaching Competences and their Development Via Video-Recording

The article deals with use of case studies for professional preparation of teachers to be. One of the suitable ways to develop professional teaching competences is to apply the method of a case study. A case study means a complex and creative solution for a given teaching situation in simulated teaching conditions. It is based on interactive and situational education and decision taking. A case study improves not only professional and teaching competences for becoming teachers – it also fulfi ls the task to develop at students their auto-evaluating and auto-refl exing skills. To increase professional competences it is mandatory to do a complex analysis of the video-record for the implemented study. A complex analysis is a subject of the research project of a student grant agency at the University of West Bohemia in Pilsen.

Teaching Crossroads: 11th IPB Erasmus Week

In the wake of the latest news regarding IPB’s award for best Polytechnic Institute in Portugal, we would like to congratulate the IPB community who has always striven for the quality of the institution within the national and international academic milieu. We are, undoubtedly, bowled over by the 1st place in the national context (out of the 27 national institutions under evaluation) and the 7th position in the international scope. In fact, it is worth mentioning that the IPB has won this award, three years in a row, being in a leading position in the ranking promoted and sponsored by the European Union. This year’s edition has selected and evaluated over 1300 world higher education institutions. Teaching Crossroads intends thus to give a watershed contribution to the IPB’s successful and most valued pathway. Numbers indicate that Teaching Crossroads has had over 2550 downloads since it first came out. But let’s cut to the chase. Once again, we are delighted to present the 5th number of Teaching Crossroads. This wholly calculated and well-sustained editorial adventure started in 2012 when the first number of Teaching Crossroads first saw the light. This year’s publication includes the areas of Human Geography/anthropology, Information Technology and Forensics and Language and culture, focusing on minority languages. Alongside this, as in the two last previous numbers, we’ve included the specific area for International mobility, Intensive Programmes and Erasmus+ Mobility of Individuals, being the latter financed by the European Union within the Erasmus+ Programme, whereas the former is sponsored uniquely by the foreign partner institution, in this case, Lillebaelt Academy in Denmark. These types of programmes convey very positive and overarching ideas, resonant in cross-cultural and educational benefits, valuable for all the involved partners. We would very kindheartedly like to thank the authors for having contributed with much enlightening and serious articles on a wide array of areas. Pablo M. Orduna Pórtus’s article focuses on border culture and heritage management. The author’s study is placed on two borderlands of the Iberian Peninsula: Roncal Valley (Navarre) and Riverbanks of Douro. Going beyond the linear or physical conception of the border, the author centres his study on the metaphysical and symbolic ideas of the frontier that sustain his anthropological analysis. Michal Popdora manages to find evidence for his proposal of a new conception of teaching Image Processing, based on the student-centered approach. A hands-on experience on a Project-based Learning methodology sustains the teaching project. Grounded on “a forensic-flavored style”, using the author’s own words, he shows how students can become engaged in a highly effective learning process. Cláudia Martins is already a confirmed habitué of this publication, as in every Erasmus Week she delivers a lecture on Portuguese language and culture to visiting teaching and non-teaching staff. This time, the author decided to delve into a Portugal’s official language, Mirandese, spoken in a small designated area in the northeastern part of Portugal, Miranda do Douro and its surrounding area. The author gives account of some thought-provoking facts about the language, from the origin and the survival of the language, however still a minority language, up to the moment when it was acknowledged Portugal’s second official language, together with the challenges that nowadays faces. Luís Frölen Ribeiro, João Eduardo Ribeiro, Carlos Casimiro Costa, António Duarte, Carlos Andrade from the Polytechnic Institute and Arne Svinth, John Madsen, Morten Thomsen, Kent Smidstrup, Carsten John Jacobsen from the Lillebaelt Academy, in Denmark, participate in a joint project which they describe, outlining the main goals and gains of the project. To overcome teaching difficulties regarding the engineering degrees, a 12-ECTS joint course from Lillebaelt Academy and Polytechnic Institute of Bragança was created based on the Danish model. The course Product Development and Industrial Processing was hence created. Rui Pedro Lopes presents an insightful and acute account of the Internationalization programmes in Higher Education in Europe. At one go, the author describes his own experience as a visiting lecturer, within the Erasmus+ programme, to Università Politecnica delle Marche in Ancona, Italy, in a Master’s degree in computer science, bringing to light a personal reflection on the goals and benefits of the mobility for both students and teachers. Finally, the author puts forth some suggestions that would improve the whole mobility process. We sincerely hope to have stimulated you to keep on reading, upholding the belief that these texts can represent valuable sources for both teachers and students in their research work.

A Moslem seeker after God: showing Islam at its best in the life and teaching of al-Ghazali, mystic and theologian of the eleventh century, by Samuel M. Zwemer ...

http://www.archive.org/details/amoslemseeker00zwemuoft

Plasmid biology of natural Lactococcus lactis strains and molecular mechanisms of bacteriophage-host interaction

Lacticin 3147, enterocin AS-48, lacticin 481, variacin, and sakacin P are bacteriocins offering promising perspectives in terms of preservation and shelf-life extension of food products and should find commercial application in the near future. The studies detailing their characterization and bio-preservative applications are reviewed. Transcriptomic analyses showed a cell wall-targeted response of Lactococcus lactis IL1403 during the early stages of infection with the lytic bacteriophage c2, which is probably orchestrated by a number of membrane stress proteins and involves D-alanylation of membrane lipoteichoic acids, restoration of the physiological proton motive force disrupted following bacteriophage infection, and energy conservation. Sequencing of the eight plasmids of L. lactis subsp. cremoris DPC3758 from raw milk cheese revealed three anti-phage restriction/modification (R/M) systems, immunity/resistance to nisin, lacticin 481, cadmium and copper, and six conjugative/mobilization regions. A food-grade derivative strain with enhanced bacteriophage resistance was generated via stacking of R/M plasmids. Sequencing and functional analysis of the four plasmids of L. lactis subsp. lactis biovar. diacetylactis DPC3901 from raw milk cheese revealed genes novel to Lactococcus and typical of bacteria associated with plants, in addition to genes associated with plant-derived lactococcal strains. The functionality of a novel high-affinity regulated system for cobalt uptake was demonstrated. The bacteriophage resistant and bacteriocin-producing plasmid pMRC01 places a metabolic burden on lactococcal hosts resulting in lowered growth rates and increased cell permeability and autolysis. The magnitude of these effects is strain dependent but not related to bacteriocin production. Starters’ acidification capacity is not significantly affected. Transcriptomic analyses showed that pMRC01 abortive infection (Abi) system is probably subjected to a complex regulatory control by Rgg-like ORF51 and CopG-like ORF58 proteins. These regulators are suggested to modulate the activity of the putative Abi effectors ORF50 and ORF49 exhibiting topology and functional similarities to the Rex system aborting bacteriophage λ lytic growth.

Team-teaching for inclusive learning: Purposes, practices and perceptions of a team-teaching initiative in Irish post-primary schools

Background. Schools unequivocally privilege solo-teaching. This research seeks to enhance our understanding of team-teaching by examining how two teachers, working in the same classroom at the same time, might or might not contribute to the promotion of inclusive learning. There are well-established policy statements that encourage change and moves towards the use of team-teaching to promote greater inclusion of students with special educational needs in mainstream schools and mainstream classrooms. What is not so well established is the practice of team-teaching in post-primary settings, with little research conducted to date on how it can be initiated and sustained, and a dearth of knowledge on how it impacts upon the students and teachers involved. Research questions and aims. In light of the paucity and inconclusive nature of the research on team-teaching to date (Hattie, 2009), the orientating question in this study asks ‘To what extent, can the introduction of a formal team-teaching initiative enhance the quality of inclusive student learning and teachers’ learning at post-primary level?’ The framing of this question emerges from ongoing political, legal and educational efforts to promote inclusive education. The study has three main aims. The first aim of this study is to gather and represent the voices and experiences of those most closely involved in the introduction of team-teaching; students, teachers, principals and administrators. The second aim is to generate a theory-informed understanding of such collaborative practices and how they may best be implemented in the future. The third aim is to advance our understandings regarding the day-to-day, and moment-to-moment interactions, between teachers and students which enable or inhibit inclusive learning. Sample. In total, 20 team-teaching dyads were formed across seven project schools. The study participants were from two of the seven project schools, Ash and Oak. It involved eight teachers and 53 students, whose age ranged from 12-16 years old, with 4 teachers forming two dyads per school. In Oak there was a class of first years (n=11) with one dyad and a class of transition year students (n=24) with the other dyad. In Ash one class group (n=18) had two dyads. The subjects in which the dyads engaged were English and Mathematics. Method. This research adopted an interpretive paradigm. The duration of the fieldwork was from April 2007 to June 2008. Research methodologies included semi-structured interviews (n=44), classroom observation (n=20), attendance at monthly teacher meetings (n=6), questionnaires and other data gathering practices which included school documentation, assessment findings and joint examination of student work samples (n=4). Results. Team-teaching involves changing normative practices, and involves placing both demands and opportunities before those who occupy classrooms (teachers and students) and before those who determine who should occupy these classrooms (principals and district administrators). This research shows how team-teaching has the potential to promote inclusive learning, and when implemented appropriately, can impact positively upon the learning experiences of both teachers and students. The results are outlined in two chapters. In chapter four, Social Capital Theory is used in framing the data, the change process of bonding, bridging and linking, and in capturing what the collaborative action of team-teaching means, asks and offers teachers; within classes, between classes, between schools and within the wider educational community. In chapter five, Positioning Theory deductively assists in revealing the moment-to-moment, dynamic and inclusive learning opportunities, that are made available to students through team-teaching. In this chapter a number of vignettes are chosen to illustrate such learning opportunities. These two theories help to reveal the counter-narrative that team-teaching offers, regarding how both teachers and students teach and learn. This counter-narrative can extend beyond the field of special education and include alternatives to the manner in which professional development is understood, implemented, and sustained in schools and classrooms. Team-teaching repositions teachers and students to engage with one another in an atmosphere that capitalises upon and builds relational trust and shared cognition. However, as this research study has found, it is wise that the purposes, processes and perceptions of team-teaching are clear to all so that team-teaching can be undertaken by those who are increasingly consciously competent and not merely accidentally adequate. Conclusions. The findings are discussed in the context of the promotion of effective inclusive practices in mainstream settings. I believe that such promotion requires more nuanced understandings of what is being asked of, and offered to, teachers and students. Team-teaching has, and I argue will increasingly have, its place in the repertoire of responses that support effective inclusive learning. To capture and extend such practice requires theoretical frameworks that facilitate iterative journeys between research, policy and practice. Research to date on team-teaching has been too focused on outcomes over short timeframes and not focused enough on the process that is team-teaching. As a consequence team-teaching has been under-used, under-valued, under-theorised and generally not very well understood. Moving from classroom to staff room and district board room, theoretical frameworks used in this research help to travel with, and understand, the initiation, engagement and early consequences of team-teaching within and across the educational landscape. Therefore, conclusions from this study have implications for the triad of research, practice and policy development where efforts to change normative practices can be matched by understandings associated with what it means to try something new/anew, and what it means to say it made a positive difference.

Investigations into selective metabolic aspects of bifidobacteria: carbohydrate metabolism, fatty acid biosynthesis and plasmid biology

The gastrointestinal tract (GIT) is a diverse ecosystem, and is colonised by a diverse array of bacteria, of which bifidobacteria are a significant component. Bifidobacteria are Gram-positive, saccharolytic, non-motile, non-sporulating, anaerobic, Y-shaped bacteria, which possess a high GC genome content. Certain bifidobacteria possess the ability to produce conjugated linoleic acid (CLA) from linoleic acid (LA) by a biochemical pathway that is hypothesised to be achieved via a linoleic isomerase. In Chapter two of this thesis it was found that the MCRA-specifying gene is not involved in CLA production in B. breve NCFB 2258, and that this gene specifies an oleate hydratase involved in the conversion of oleic acid into 10-hydroxystearic acid. Prebiotics are defined as non-digestible food ingredients that beneficially affect the host by selectively stimulating growth and/or activity of one or a limited number of bacteria in the colon. Key to the development of such novel prebiotics is to understand which carbohydrates support growth of bifidobacteria and how such carbohydrates are metabolised. In Chapter 3 of this thesis we describe the identification and characterisation of two neighbouring gene clusters involved in the metabolism of raffinose-containing carbohydrates (plus related carbohydrate melibiose) and melezitose by Bifidobacterium breve UCC2003. The fourth chapter of this thesis describes the analysis of transcriptional regulation of the raf and mel clusters. In the final experimental chapter two putative rep genes, designated repA7017 and repB7017, are identified on the megaplasmid pBb7017 of B. breve JCM 7017, the first bifidobacterial megaplasmid to be reported. One of these, repA7017, was subjected to an in-depth characterisation. The work described in this thesis has resulted in an improved understanding of bifidobacterial fatty acid and carbohydrate metabolism, Furthermore, attempts were made to develop novel genetic tools.

Aspects of the biology of Mya arenaria and Ensis spp. (Mollusca; Bivalvia) in the Irish Sea and adjacent areas

This study was undertaken to investigate the general biology, including the reproductive cycle and health status, of two clam taxa in Irish waters, with particular reference to the Irish Sea area. Monthly samples of the soft shell clam, Mya arenaria, were collected from Bannow Bay, Co. Wexford, Ireland, for sixteen months, and of the razor clam, Ensis spp. from the Skerries region (Irish Sea) between June 2010 and September 2011. In 2010, M. arenaria in Bannow Bay matured over the summer months, with both sexes either ripe or spawning by August. The gonads of both sexes of E. siliqua developed over autumn and winter 2010, with the first spawning individuals being recorded in January 2011. Two unusually cold winters, followed by a warmer than average spring, appear to have affected M. arenaria and E. siliqua gametogenesis at these sites. It was noted that wet weight of E. siliqua dropped significantly in the summer of both 2010 and 2011, after spawning, which may impact on the economic viability of fishing during this period. Additional samples of M. arenaria were collected at Flaxfort (Ireland), and Ensis spp. at Oxwich (Wales), and the pathology of all clams was examined using both histological and molecular methods. No pathogenic conditions were observed in M. arenaria while Prokaryote inclusions, trematode parasites, Nematopsis spp. and inflammatory pathologies were observed at low incidences in razor clams from Ireland but not from Wales; the first time these conditions have been reported in Ensis spp. in northern European waters. Mya arenaria from sites in Europe and eastern and western North America were investigated for genetic variation using both mitochondrial (cytochrome oxidase I (COI) and 16S ribosomal RNA genes) and nuclear markers (10 microsatellite loci). Both mitochondrial CO1 and all nuclear markers showed reduced levels of variation in certain European samples, with significant differences in haplotype and allelic composition between most samples, particularly those from the two different continents, but with the same common haplotypes or alleles throughout the range. The appearance of certain unique rare haplotypes and microsatellite alleles in the European samples suggest a complicated origin involving North American colonization but also possible southern European Pleistocene refugia. Specimens of Ensis spp. were obtained from five coastal areas around Ireland and Wales and species-specific PCR primers were used to amplify the internal transcribed spacer region 1 (ITS1) and the mitochondrial DNA CO1 gene and all but 15 razor clams were identified as Ensis siliqua. Future investigations should focus on continued monitoring of reproductive biology and pathology of the two clam taxa (in particular, to assess the influence of environmental change), and on genetics of southern European M. arenaria and sequencing the CO1 gene in Ensis individuals to clarify species identity

Aspects of the biology of the parasite Bonamia ostreae with a view to gaining a greater understanding of how to alleviate its impact on the European flat oyster, Ostrea edulis.

The parasite Bonamia ostreae has decimated Ostrea edulis stocks throughout Europe. The complete life cycle and means of transmission of the parasite remains unknown. The methods used to diagnose B. ostreae were examined to determine sensitivity and reproducibility. Two methods, with fixed protocols, should be used for the accurate detection of infection within a sample. A 13-month study of two stocks of O. edulis with varying periods of exposure to B. ostreae, was undertaken to determine if varying lengths of exposure would translate into observations of differing susceptibility. Oyster stocks can maintain themselves over extended periods of time in B. ostreae endemic areas. To identify a well performing spat stock, which could be used to repopulate beds within the region, hatchery bred spat from three stocks found in the North sea were placed on a B. ostreae infected bed and screened for growth, mortality and prevalence of infection. Local environmental factors may influence oyster performance, with local stocks better adapted to these conditions. Sediment and macroinvertebrate species were screened to investigate mechanisms by which B. ostreae may be maintaining itself on oyster beds. Mytilus edulis was positive, indicating that B. ostreae may use incidental carriers as a method of maintaining itself. The ability of oyster larvae to pick up infection from the surrounding environment was investigated by collecting larvae from brooding oysters from different areas. Larvae may acquire the pathogen from the water column during the process of filter feeding by the brooding adult, even when the parents themselves are uninfected. A study was undertaken to elucidate the activity of the parasite during the initial stage of infection, when it cannot be detected within the host. A naïve stock screened negative for infection throughout the trial, using heart imprints and PCR yet B. ostreae was detected by in-situ hybridisation.

The reproductive biology of the exploited razor clam, Ensis siliqua, in the Irish Sea

Knowledge of the reproductive cycle of a species is a prerequisite for sustainable management of a fishery. The infaunal marine bivalve, Ensis siliqua, is a commercially important species in Europe, and is exploited in many countries, including Ireland, where it is sold by wet weight. Seasonal variations in the reproductive cycle of subtidal razor clams from the Skerries region of the Irish Sea, an important fisheries area, were examined between June 2010 and September 2011 while monitoring weight. Histological examination revealed that the E. siliqua sex-ratio was not different from parity, and no hermaphrodites were observed in the samples collected. In the summer months of 2010 all female clams were either spent or in early development, with just a small percentage of males still spawning. The gonads of both sexes developed over the autumn and winter months of 2010, with the first spawning individuals recorded in January 2011. Spawning peaked in March 2011, but unlike in 2010, spawning continued through June and July with all animals spent in August 2011. The earlier and longer spawning period found in this species in 2011 compared to 2010 may have been due to the colder than normal temperature observed during the winter of 2010 plus the relatively warmer temperatures of Spring 2011, which could have affected the gametogenic development of E. siliqua in the Irish Sea. It was noted that wet weight dropped in the summer months of both years, immediately after the spawning period which may impact on the practicality of fishing for this species during this period. Timing of development and spawning is compared with other sites in the Irish Sea and elsewhere in Europe, including the Iberian Peninsula.