Cloning of new Rhodococcus extradiol dioxygenase genes and study of their distribution in different Rhodococcus strains

Four extradiol dioxygenase genes which encode enzymes active against catechol and substituted catechols were cloned from two different Rhodococcus strains, and their nucleotide sequences were determined. A catechol 2,3-dioxygenase gene (edoC) was shown to be identical to the previously described ipbC gene from the isopropylbenzene operon of Rhodococcus erythropolis. Amino acid sequences deduced from the three other genes (edoA, edoB and edoD) were shown to have various degrees of homology to different extradiol dioxygenases, The EdoA and EdoB dioxygenases were classified as belonging to the third family of type I oxygenases and represented two new subfamilies, whereas the EdoD dioxygenase was a type II enzyme. Analysis of six Rhodococcus strains revealed a wide distribution of the above dioxygenase genes. Rhodococcus sp. I1 was shown to harbour all four of the analysed dioxygenase genes. Nucleotide sequences homologous to the edoB gene were present in all of the strains, including R. erythropolis NCIMB 13065, which did not utilize any of the aromatic compounds analysed. The latter finding points to the existence of a silent pathway(s) for degradation of aromatic compounds in this Rhodococcus strain.

Experimental Reconstruction of Work Distribution and Study of Fluctuation Relations in a Closed Quantum System

We report the experimental reconstruction of the nonequilibrium work probability distribution in a closed quantum system, and the study of the corresponding quantum fluctuation relations. The experiment uses a liquid-state nuclear magnetic resonance platform that offers full control on the preparation and dynamics of the system. Our endeavors enable the characterization of the out-of-equilibrium dynamics of a quantum spin from a finite-time thermodynamics viewpoint.

Bounded Rationality and Repeated Network Formation

We define a finite-horizon repeated network formation game with consent and study the differences induced by two levels of individual rationality. Perfectly rational players will remain unconnected at the equilibrium, while nonempty equilibrium networks may form when players are assumed to behave as finite automata of limited complexity. We provide structural properties of the sequences of networks which are likely to form in Nash and subgame perfect Nash equilibria of the repeated game. For instance, players can form totally different connected networks at each period or the sequence of networks can exhibit a total order relationship.

Optimising the use of virtual and conventional simulation: a clinical and economic analysis

Background and purpose: Currently, optimal use of virtual simulation for all treatment sites is not entirely clear. This study presents data to identify specific patient groups for whom conventional simulation may be completely eliminated and replaced by virtual simulation. Sampling and method: Two hundred and sixty patients were recruited from four treatment sites (head and neck, breast, pelvis, and thorax). Patients were randomly assigned to be treated using the usual treatment process involving conventional simulation, or a treatment process differing only in the replacement of conventional plan verification with virtual verification. Data were collected on set-up accuracy at verification, and the number of unsatisfactory verifications requiring a return to the conventional simulator. A micro-economic costing analysis was also undertaken, whereby data for each treatment process episode were also collected: number and grade of staff present, and the time for each treatment episode. Results: The study shows no statistically significant difference in the number of returns to the conventional simulator for each site and study arm. Image registration data show similar quality of verification for each study arm. The micro-costing data show no statistical difference between the virtual and conventional simulation processes. Conclusions: At our institution, virtual simulation including virtual verification for the sites investigated presents no disadvantage compared to conventional simulation.

Is there a role for n-3 long-chain polyunsaturated fatty acids in the regulation of mood and behaviour? A review of the evidence to date from epidemiological studies, clinical studies and intervention trials

Selected biochemical evidence suggests a potential role for n-3 long-chain PUFA (n-3PUFA) in the regulation of mood and behaviour. The present paper reviews the relevant evidence, to date, from epidemiological studies, clinical studies and intervention trials. Most evidence is available investigating a role for n-3PUFA in depression, depressive illness and suicidal behaviour, but work is also available on anxiety and anxiety-related disorders, fatigue and fatigue-related disorders, aggression, hostility and anti-social behaviour, inattention, impulsivity and attention deficit hyperactivity disorder and schizophrenic disorders. For all these aspects of mood and behaviour, the evidence available is currently limited and highly inconsistent, both in terms of study methodology and study findings. There is a clear need for further work in this area.

Numerical simulation of the charge balance and temperature evolution in an electron beam ion trap

A computer code has been developed to simulate and study the evolution of ion charge states inside the trap region of an electron beam ion trap. In addition to atomic physics phenomena previously included in similar codes such as electron impact ionization, radiative recombination, and charge exchange, several aspects of the relevant physics such as dielectronic recombination, ionization heating, and ion cloud expansion have been included for the first time in the model. The code was developed using object oriented concepts with database support, making it readable, accurate, and well organized. The simulation results show a good agreement with various experiments, and give useful information for selection of operating conditions and experiment design.

Resolving genetic functions within microbial populations: In situ analyses using rRNA and mRNA stable isotope probing coupled with single-cell raman-fluorescence in situ hybridization

Prokaryotes represent one-half of the living biomass on Earth, with the vast majority remaining elusive to culture and study within the laboratory. As a result, we lack a basic understanding of the functions that many species perform in the natural world. To address this issue, we developed complementary population and single-cell stable isotope (C-13)-linked analyses to determine microbial identity and function in situ. We demonstrated that the use of rRNA/mRNA stable isotope probing (SIP) recovered the key phylogenetic and functional RNAs. This was followed by single-cell physiological analyses of these populations to determine and quantify in situ functions within an aerobic naphthalene-degrading groundwater microbial community. Using these culture-independent approaches, we identified three prokaryote species capable of naphthalene biodegradation within the groundwater system: two taxa were isolated in the laboratory (Pseudomonas fluorescens and Pseudomonas putida), whereas the third eluded culture (an Acidovorax sp.). Using parallel population and single-cell stable isotope technologies, we were able to identify an unculturable Acidovorax sp. which played the key role in naphthalene biodegradation in situ, rather than the culturable naphthalene-biodegrading Pseudomonas sp. isolated from the same groundwater. The Pseudomonas isolates actively degraded naphthalene only at naphthalene concentrations higher than 30 mu M. This study demonstrated that unculturable microorganisms could play important roles in biodegradation in the ecosystem. It also showed that the combined RNA SIP-Raman-fluorescence in situ hybridization approach may be a significant tool in resolving ecology, functionality, and niche specialization within the unculturable fraction of organisms residing in the natural environment.

Nonlinear Dynamics of Rotating Multi-Component Pair Plasmas and e-p-i Plasmas

The propagation of small amplitude stationary profile nonlinear electrostatic excitations in a pair plasma is investigated, mainly drawing inspiration from experiments on fullerene pair-ion plasmas. Two distinct pair ion species are considered of opposite polarity and same mass, in addition to a massive charged background species, which is assumed to be stationary, given the frequency scale of interest. In the pair-ion context, the third species is thought of as a background defect (e.g. charged dust) component. On the other hand, the model also applies formally to electron-positron-ion (e-p-i) plasmas, if one neglects electron-positron annihilation. A two-fluid plasma model is employed, incorporating both Lorentz and Coriolis forces, thus taking into account the interplay between the gyroscopic (Larmor) frequency ?c and the (intrinsic) plasma rotation frequency O0. By employing a multi-dimensional reductive perturbation technique, a Zakharov-Kuznetsov (ZK) type equation is derived for the evolution of the electric potential perturbation. Assuming an arbitrary direction of propagation, with respect to the magnetic field, we derive the exact form of nonlinear solutions, and study their characteristics. A parametric analysis is carried out, as regards the effect of the dusty plasma composition (background number density), species temperature(s) and the relative strength of rotation to Larmor frequencies. It is shown that the Larmor and mechanical rotation affect the pulse dynamics via a parallel-to-transverse mode coupling diffusion term, which in fact diverges at ?c ? ±2O0. Pulses collapse at this limit, as nonlinearity fails to balance dispersion. The analysis is complemented by investigating critical plasma compositions, in fact near-symmetric (T- ˜ T+) “pure” (n- ˜ n+) pair plasmas, i.e. when the concentration of the 3rd background species is negligible, case in which the (quadratic) nonlinearity vanishes, so one needs to resort to higher order nonlinear theory. A modified ZK equation is derived and analyzed. Our results are of relevance in pair-ion (fullerene) experiments and also potentially in astrophysical environments, e.g. in pulsars.

Recruitment bias and clinical characterstics of participants with severe cerebral palsy in a cross-sectional survey

Aim.  This article is a report of recruitment bias in a sample of 5–25-year-old patients with severe cerebral palsy.

Background.  The way in which study participants are recruited into research can be a source of bias.

Method.  A cross-sectional survey of 5–25-year-old patients with severe cerebral palsy using standardized questionnaires with parents/carers was undertaken in 2007/2008. A case register was used as the sampling frame, and 260 families were approached: 178/260 (68%) responded and 82/260 families never replied (non-respondents). Among responders: 127/178 (71%) opted in to the study, but only 123/127 were assessed, and 82/178 were opted out (or refused). Multivariable logistic regression giving odds ratios was used to study the association between participant characteristics and study outcomes (responders vs. non-responders; opting in vs. opting out; assessed vs. eligible, but not assessed).

Results.  Responders (compared with non-responders) were significantly more likely to have a family member with cerebral palsy who was male and resident in more affluent areas. Families who opted in (compared with those opting out and refusing) were more likely to have a family member with cerebral palsy and intellectual impairment and to reside in certain geographical areas. Families who were actually assessed (compared with all eligible, but not assessed) were more likely to have a family member with cerebral palsy and intellectual impairment.

Conclusion.  Several sources of bias were identified during recruitment for this study. This has implications for the interpretation and conclusions of surveys of people with disabilities and complex needs.

John P. Mackintosh, Devolution and the Union

This article provides a discussion of the political thinking of John P. Mackintosh (1929–1978) around the debate over Scottish devolution, and the constitutional reform of the UK, during the 1960s and 1970s. The article explores Mackintosh's ‘Union State’ vision of the UK and connects this to his interest in, and study of, the Northern Ireland experience of devolution from 1921 to 1972. It also considers the significance of Mackintosh's confrontations with Scottish nationalism and suggests that his unionism was representative of a more authentic and rooted tradition than is usually acknowledged. The article offers an evaluation of Mackintosh's legacy and considers the extent to which the questions he posed, and the lines of argument he advanced, have retained their relevance and interest in the new context of partial devolution in the UK, and in the current period of renewed constitutional speculation and debate over the future of the Union and the UK.

Remote Sensing and GIScience in Geomorphological Mapping

The rapid proliferation of remote sensing and geographic information systems (GIS) into geomorphologic mapping has increased the objectivity and efficiency of landform segmentation, measurement, and classification. The near ubiquitous presence of Earth-observing satellites provides an array of perspectives to visualize the biophysical characteristics of landscapes, access inhospitable terrain on a predictable schedule, and study landscape processes when conditions are hazardous. GIS technology has altered the analysis, visualization, and dissemination of landform data due to the shared theoretical concepts that are fundamental to geomorphology and GIScience. The authors review geospatial technology applications in landform mapping (including emerging issues) within glacial, volcanic, landslide, and fluvial research.

Encouraging and equipping students to engage critically with science in the news: what can we learn from the literature?

Many educational reforms have as one of their key goals the promotion of scientific literacy and they encourage engagement with science in the news as one aspect of this. The research indicates teachers using the news do so for a variety of reasons, sometimes with tangential links to the promotion of scientific literacy. Demonstrating the relevance of science to the world beyond the classroom or making links to socio-scientific issues and promoting discussion on ethical dilemmas are all seen as potential reasons for engaging with science–related news. However, media related issues are often not addressed. Increasingly the need for a more comprehensive approach, including, for example, teaching about media awareness in the context of science reporting, is highlighted. The steady growth of literature describing the use of science-related news along with research studies charting students’ responses to science news media has stimulated discussion and study of pedagogical issues and prompted this review. Key literature relevant to students’ engagement with science-related news reports has been contextualised and reviewed to identify core issues for teachers, teacher educators and curriculum planners. These are listed under the headings of curriculum, pedagogy and assessment, the implications are considered and directions for further research suggested.

A defeasible reasoning model of inductive concept learning from examples and communication

This paper introduces a logical model of inductive generalization, and specifically of the machine learning task of inductive concept learning (ICL). We argue that some inductive processes, like ICL, can be seen as a form of defeasible reasoning. We define a consequence relation characterizing which hypotheses can be induced from given sets of examples, and study its properties, showing they correspond to a rather well-behaved non-monotonic logic. We will also show that with the addition of a preference relation on inductive theories we can characterize the inductive bias of ICL algorithms. The second part of the paper shows how this logical characterization of inductive generalization can be integrated with another form of non-monotonic reasoning (argumentation), to define a model of multiagent ICL. This integration allows two or more agents to learn, in a consistent way, both from induction and from arguments used in the communication between them. We show that the inductive theories achieved by multiagent induction plus argumentation are sound, i.e. they are precisely the same as the inductive theories built by a single agent with all data. © 2012 Elsevier B.V.