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.

Innovation in Ireland's 'high-technology' businesses: the roles of interaction and proximity

This thesis explores the drivers of innovation in Irish high-technology businesses and estimates, in particular, the relative importance of interaction with external businesses and other organisations as a source of knowledge for innovation at the business-level. The thesis also examines the extent to which interaction for innovation in these businesses occurs on a local or regional basis. The study uses original survey data of 184 businesses in the Chemical and Pharmaceutical, Information and Communications Technology and Engineering and Electronic Devices sectors. The study considers both product and process innovation at the level of the business and develops new measures of innovation output. For the first time in an Irish study, the incidence and frequency of interaction is measured for each of a range of agents, other group companies, suppliers, customers, competitors, academic-based researchers and innovation-supporting agencies. The geographic proximity between the business and each of the most important of each of each category of agent is measured using average one-way driving distance, which is the first time such a measure has been used in an Irish study of innovation. Utilising econometric estimation techniques, it is found that interaction with customers, suppliers and innovation-supporting agencies is positively associated with innovation in Irish high-technology businesses. Surprisingly, however, interaction with academic-based researchers is found to have a negative effect on innovation output at the business-level. While interaction generally emerges as a positive influence on business innovation, there is little evidence that this occurs at a local or regional level. Furthermore, there is little support for the presence of localisation economies for high-technology sectors, though some tentative evidence of urbanisation economies. This has important implications for Irish regional, enterprise and innovation policy, which has emphasised the development of clusters of internationally competitive businesses. The thesis brings into question the suitability of a cluster-driven network based approach to business development and competitiveness in an Irish context.

Users & use: An exploration of the interaction between the user and the digital archive

This thesis will examine the interaction between the user and the digital archive. The aim of the study is to support an in-depth examination of the interaction process, with a view to making recommendations and tools, for system designers and archival professionals, to promote digital archive domain development. Following a comprehensive literature review process, an urgent requirement for models was identified. The Model of Contextual Interaction presented in this thesis, aims to provide a conceptual model through which the interaction process, between the user and the digital archive, can be examined. Using the five-phased research development framework, the study will present a structured account of its methods, using a multi-method methodology to ensuring robust data collection and analysis. The findings of the study are presented across the Model of Contextual Interaction, and provide a basis on which recommendations and tools for system designers have been made. The thesis concludes with a summary of key findings, and a reflective account of how the findings and the Model of Contextual Interaction have impacted digital provision within the archive domain and how the model could be applied to other domains.

Bridge-vehicle interaction for structural health monitoring: potentials, applications, and limitations

Structural Health Monitoring (SHM) is an integral part of infrastructure maintenance and management systems due to socio-economic, safety and security reasons. The behaviour of a structure under vibration depends on structure characteristics. The change of structure characteristics may suggest the change in system behaviour due to the presence of damage(s) within. Therefore the consistent, output signal guided, and system dependable markers would be convenient tool for the online monitoring, the maintenance, rehabilitation strategies, and optimized decision making policies as required by the engineers, owners, managers, and the users from both safety and serviceability aspects. SHM has a very significant advantage over traditional investigations where tangible and intangible costs of a very high degree are often incurred due to the disruption of service. Additionally, SHM through bridge-vehicle interaction opens up opportunities for continuous tracking of the condition of the structure. Research in this area is still in initial stage and is extremely promising. This PhD focuses on using bridge-vehicle interaction response for SHM of damaged or deteriorating bridges to monitor or assess them under operating conditions. In the present study, a number of damage detection markers have been investigated and proposed in order to identify the existence, location, and the extent of an open crack in the structure. The theoretical and experimental investigation has been conducted on Single Degree of Freedom linear system, simply supported beams. The novel Delay Vector Variance (DVV) methodology has been employed for characterization of structural behaviour by time-domain response analysis. Also, the analysis of responses of actual bridges using DVV method has been for the first time employed for this kind of investigation.

Interaction of additive and quantization noises in digital PLLs

Phase-locked loops (PLLs) are a crucial component in modern communications systems. Comprising of a phase-detector, linear filter, and controllable oscillator, they are widely used in radio receivers to retrieve the information content from remote signals. As such, they are capable of signal demodulation, phase and carrier recovery, frequency synthesis, and clock synchronization. Continuous-time PLLs are a mature area of study, and have been covered in the literature since the early classical work by Viterbi [1] in the 1950s. With the rise of computing in recent decades, discrete-time digital PLLs (DPLLs) are a more recent discipline; most of the literature published dates from the 1990s onwards. Gardner [2] is a pioneer in this area. It is our aim in this work to address the difficulties encountered by Gardner [3] in his investigation of the DPLL output phase-jitter where additive noise to the input signal is combined with frequency quantization in the local oscillator. The model we use in our novel analysis of the system is also applicable to another of the cases looked at by Gardner, that is the DPLL with a delay element integrated in the loop. This gives us the opportunity to look at this system in more detail, our analysis providing some unique insights into the variance `dip' seen by Gardner in [3]. We initially provide background on the probability theory and stochastic processes. These branches of mathematics are the basis for the study of noisy analogue and digital PLLs. We give an overview of the classical analogue PLL theory as well as the background on both the digital PLL and circle map, referencing the model proposed by Teplinsky et al. [4, 5]. For our novel work, the case of the combined frequency quantization and noisy input from [3] is investigated first numerically, and then analytically as a Markov chain via its Chapman-Kolmogorov equation. The resulting delay equation for the steady-state jitter distribution is treated using two separate asymptotic analyses to obtain approximate solutions. It is shown how the variance obtained in each case matches well to the numerical results. Other properties of the output jitter, such as the mean, are also investigated. In this way, we arrive at a more complete understanding of the interaction between quantization and input noise in the first order DPLL than is possible using simulation alone. We also do an asymptotic analysis of a particular case of the noisy first-order DPLL with delay, previously investigated by Gardner [3]. We show a unique feature of the simulation results, namely the variance `dip' seen for certain levels of input noise, is explained by this analysis. Finally, we look at the second-order DPLL with additive noise, using numerical simulations to see the effects of low levels of noise on the limit cycles. We show how these effects are similar to those seen in the noise-free loop with non-zero initial conditions.

Interaction strengths and net effects in food web models

Understanding how dynamic ecological communities respond to anthropogenic drivers of change such as habitat loss and fragmentation, climate change and the introduction of alien species requires that there is a theoretical framework able to predict community dynamics. At present there is a lack of empirical data that can be used to inform and test predictive models, which means that much of our knowledge regarding the response of ecological communities to perturbations is obtained from theoretical analyses and simulations. This thesis is composed of two strands of research: an empirical experiment conducted to inform the scaling of intraspecific and interspecific interaction strengths in a three species food chain and a series of theoretical analyses on the changes to equilibrium biomass abundances following press perturbations. The empirical experiment is a consequence of the difficulties faced when parameterising the intraspecific interaction strengths in a Lotka-Volterra model. A modification of the dynamic index is used alongside the original dynamic index to estimate intraspecific interactions and interspecific interaction strengths in a three species food. The theoretical analyses focused on the effect of press perturbations to focal species on the equilibrium biomass densities of all species in the community; these perturbations allow for the quantification of a species total net effect. It was found that there is a strong and consistent positive relationship between a species body size and its total net effect for a set of 97 synthetic food webs and also for the Ythan Estuary and Tuesday Lake food webs (empirically described food webs). It is shown that ecological constraints (due to allometric scaling) on the magnitude of entries in the community matrix cause the patterns observed in the inverse community matrix and thus explain the relationship between a species body mass and its total net effect in a community.

Identifying novel molecular mechanisms of ghrelin receptor signalling underlying neural control of food intake: interaction with stress and impulsivity

The gut-hormone, ghrelin, activates the centrally expressed growth hormone secretagogue 1a (GHS-R1a) receptor, or ghrelin receptor. The ghrelin receptor is a G-protein coupled receptor (GPCR) expressed in several brain regions, including the arcuate nucleus (Arc), lateral hypothalamus (LH), ventral tegmental area (VTA), nucleus accumbens (NAcc) and amygdala. Activation of the GHS-R1a mediates a multitude of biological activities, including release of growth hormone and food intake. The ghrelin signalling system also plays a key role in the hedonic aspects of food intake and activates the dopaminergic mesolimbic circuit involved in reward signalling. Recently, ghrelin has been shown to be involved in mediating a stress response and to mediate stress-induced food reward behaviour via its interaction with the HPA-axis at the level of the anterior pituitary. Here, we focus on the role of the GHS-R1a receptor in reward behaviour, including the motivation to eat, its anxiogenic effects, and its role in impulsive behaviour. We investigate the functional selectivity and pharmacology of GHS-R1a receptor ligands as well as crosstalk of the GHS-R1a receptor with the serotonin 2C (5-HT2C) receptor, which represent another major target in the regulation of eating behaviour, stress-sensitivity and impulse control disorders. We demonstrate, to our knowledge for the first time, the direct impact of GHS-R1a signalling on impulsive responding in a 2-choice serial reaction time task (2CSRTT) and show a role for the 5-HT2C receptor in modulating amphetamine-associated impulsive action. Finally, we investigate differential gene expression patterns in the mesocorticolimbic pathway, specifically in the NAcc and PFC, between innate low- and high-impulsive rats. Together, these findings are poised to have important implications in the development of novel treatment strategies to combat eating disorders, including obesity and binge eating disorders as well as impulse control disorders, including, substance abuse and addiction, attention deficit hyperactivity disorder (ADHD) and mood disorders.

Qualitative analysis of the interdisciplinary interaction between data analysis specialists and novice clinical researchers.

BACKGROUND: The inherent complexity of statistical methods and clinical phenomena compel researchers with diverse domains of expertise to work in interdisciplinary teams, where none of them have a complete knowledge in their counterpart's field. As a result, knowledge exchange may often be characterized by miscommunication leading to misinterpretation, ultimately resulting in errors in research and even clinical practice. Though communication has a central role in interdisciplinary collaboration and since miscommunication can have a negative impact on research processes, to the best of our knowledge, no study has yet explored how data analysis specialists and clinical researchers communicate over time. METHODS/PRINCIPAL FINDINGS: We conducted qualitative analysis of encounters between clinical researchers and data analysis specialists (epidemiologist, clinical epidemiologist, and data mining specialist). These encounters were recorded and systematically analyzed using a grounded theory methodology for extraction of emerging themes, followed by data triangulation and analysis of negative cases for validation. A policy analysis was then performed using a system dynamics methodology looking for potential interventions to improve this process. Four major emerging themes were found. Definitions using lay language were frequently employed as a way to bridge the language gap between the specialties. Thought experiments presented a series of "what if" situations that helped clarify how the method or information from the other field would behave, if exposed to alternative situations, ultimately aiding in explaining their main objective. Metaphors and analogies were used to translate concepts across fields, from the unfamiliar to the familiar. Prolepsis was used to anticipate study outcomes, thus helping specialists understand the current context based on an understanding of their final goal. CONCLUSION/SIGNIFICANCE: The communication between clinical researchers and data analysis specialists presents multiple challenges that can lead to errors.

Peer assisted learning in health education.

There are many forms of Peer Assisted Learning (PAL). There are well-established theoretical models as to why PAL is proven to be effective across educational sectors. To maximise gains from PAL careful consideration needs to be given to the roles of peers. Evidence suggests that PAL projects with clearly defined roles for interaction result in strongest outcomes. Effect Sizes (ES) from meta-analyses of peer assisted learning indicate ES of between 0.25-0.50. Outcomes can be social and emotional as well as academic. PAL generally requires adaptation of existing resources and can be cost-effective to implement compared to other educational developments.

Effects of peer network interactions on adolescent cannabis use

Purpose
This study capitalises on three waves of longitudinal data from a cohort of 4351 secondary school pupils to examine the effects on individuals’ cannabis use uptake of both peer cannabis use and position within a peer network.

Design/methodology/approach
Both cross-sectional and individual fixed effects models are used to estimate the effect on cannabis use of nominated friends’ cannabis use, of reciprocity and transitivity of nominations across the friendship cluster, and of interactions between these nominated friends. Post hoc analyses parsed the behaviour of reciprocating and non-reciprocating friends.

Findings
Cannabis use varied depending on the stability of friendship network and the degree of reciprocity and interconnectedness within the group. Behavioural influence was strong, but interaction effects were observed between the prevalence of cannabis use among friends, the structure of the friendship group and ego’s proximity to group members. These interactions demonstrate that behavioural influence is more salient in more cohesive groups. When reciprocating and non-reciprocating friends’ mean cannabis use were separated, influence from reciprocating friends was estimated at twice the magnitude of other friends.

Originality/value
While preventing any one individual from using cannabis is likely to have a multiplier effect on classmates, the bonds and interactions between classmates will determine which classmates are affected by this multiplier and the salience of that effect.

Peer tutoring in a medical school: perceptions of tutors and tutees

Background: Peer tutoring has been described as “people from similar social groupings who are not professional teachers helping each other to learn and learning themselves by teaching”. Peer tutoring is well accepted as a source of support in many medical curricula, where participation and learning involve a process of socialisation.
Peer tutoring can ease the transition of the junior students from the university class environment to the hospital workplace. In this paper, we apply the Experienced Based Learning (ExBL) model to explore medical students’ perceptions of their experience of taking part in a newly established peer tutoring program at a hospital based
clinical school.
Methods: In 2014, all students at Sydney Medical School – Central, located at Royal Prince Alfred Hospital were invited to voluntarily participate in the peer tutoring program. Year 3 students (n = 46) were invited to act as tutors for Year 1 students (n = 50), and Year 4 students (n = 60) were invited to act as tutors for Year 2 students (n = 51). Similarly, the ‘tutees’ were invited to take part on a voluntary basis. Students were invited to attend focus groups, which were held at the end of the program. Framework analysis was used to code and categorise data into themes.
Results: In total, 108/207 (52 %) students participated in the program. A total of 42/106 (40 %) of Year 3 and 4 students took part as tutors; and of 66/101 (65 %) of Year 1 and 2 students took part as tutees. Five focus groups were held, with 50/108 (46 %) of students voluntarily participating. Senior students (tutors) valued the opportunity to practice and improve their medical knowledge and teaching skills. Junior students (tutees) valued the opportunity for additional practice and patient interaction, within a relaxed, small group learning environment.
Conclusion: Students perceived the peer tutoring program as affording opportunities not otherwise available within the curriculum. The peer teaching program provided a framework within the medical curriculum for senior students to practice and improve their medical knowledge and teaching skills. Concurrently, junior students were provided with a valuable learning experience that they reported as being qualitatively different to traditional teaching by faculty.

Association between adolescent leisure, peer social capital and academic performance among Canadian youth

Previous research shows discrepant findings between youth leisure programming (before and after school programs, structured summer program, day camp, overnight camp), academic performance and other youth developmental outcomes. Studies underscores the importance of family, community and school social capital in educational success of youth, investigation of peer social capital in the leisure context and academic performance outcomes is limited. This study uses a sample of 10 and 11 year olds (N=1764) from the Canadian National Longitudinal Survey of Children and Youth (NLSCY) Cycle 6, to study the association between youth leisure programming, peer social capital and academic performance. Ordinal logistic regression models consistently showed a positive association between overnight camp and academic performance even after controlling for determinants of health, and measures of family, school and community social capital. Similarly, the measure of peer social capital was positively associated with academic performance. Most importantly, the interaction between overnight camp participation and peer social capital was significantly associated with academic performance. Study findings, highlight overnight camp opportunities and peer social

Parent and Peer Factors Relating to Adolescent Antisocial Behaviour: Investigating the Moderating Role of Temperament

The purpose of this study was to examine whether certain temperament characteristics (fearfulness, surgency, frustration, and effortful control) moderate the association between authoritative parenting dimensions (psychological autonomy granting, acceptance-involvement, and monitoring knowledge) or friends' antisocial behaviour, and self-reported antisocial behaviour among adolescents. Questionnaires on adolescent temperament and authoritative parenting were completed by 484 mothers and their adolescent children (54.8% female). In addition, the adolescents responded to measures regarding friends' antisocial behavior and their own antisocial behaviour. Adolescent participants ranged between 13 and 17 years of age (M = 14.96 years, SD = 1.39) and lived in a region of southern Ontario. As predicted, the results indicated that effortful control moderated the association between parental monitoring knowledge and adolescent antisocial behaviour. Also, as predicted, effortful control moderated the relation between friends' antisocial behaviour and adolescents' self-reports of antisocial behaviour although the relation was sex-specific to girls. Unexpected results included a significant monitoring knowledge by frustration by sex interaction, and a significant friends' antisocial behaviour by age interaction. In general, the findings were consistent with the expectation that the relation of parenting and peer factors to antisocial behaviour would depend on adolescents' temperamental predispositions. However, effortful control, which contributes to individual differences in self-regulation abilities, served this moderating role to a greater extent than the measures of temperamental reactivity, including fearfulness, surgency and frustration-proneness. Implications of these results are discussed with reference to parenting or classroom-based interventions that may be especially helpful for adolescents with poor self-regulation abilities.

Peer Tutors in the School of Medicine

Since 2003 the School of Medicine at the Universidad del Rosario in Bogotá, Colombia, offers to the students a program named Peer Tutors. The program’s objectives are: to generate a social interaction mechanism that favors knowledge construction side by side with advanced peers; to promote the development of ethical, moral and coexistence oriented values through an academic experience, and to generate a space to explore specific academic interests and teacher´s potential. This article presents the theoretic frame that supports the importance of social interaction in knowledge construction, as well as some indicators that allow a first appraisal of the program. Several achievements that account for the synergic value of an experience that not only fulfills the function of initiating a process of teaching formation and academic support, but that also builds a proactive attitude before learning, are highlighted.

Living with ASD: how do children and their parents assess their difficulties with social interaction and understanding?

Social interaction and understanding in autistic spectrum disorder (ASD) are key areas of concern to practitioners and researchers alike. However, there is a relative lack of information about the skills and competencies of children and young people with ASD who access ordinary community facilities including mainstream education. In particular, contributions by parents and their children have been under-utilized. Using two structured questionnaires, 19 children with ASD reported difficulties with social skills including social engagement and temper management and also reported difficulties with social competence, affecting both friendships and peer relationships. Parents rated the children's social skill and competence as significantly worse than did the children themselves, but there was considerable agreement about the areas that were problematic. Using an informal measure to highlight their children's difficulties, parents raised issues relating to conversation skills, social emotional reciprocity and peer relationships. The implications for assessment and intervention are discussed.