Many body effects in one-dimensional attractive Bose gases

In this thesis we investigate the properties of ultra-cold quantum gases in reduced dimension and the effects of harmonic confinement on soliton-like properties. We study regimes of agreement between mean-field and many-body theories the generation of entanglement between initially independent finite sized atomic systems. Classical solitons are non-dispersing waves which occur in integrable systems, such as atomic Bose-Einstein condensates in one dimension. Bright and dark solitons are possible, which exist as peaks or dips in density. Quantum solitons are the bound-state solutions to a system satisfying quantum integrability, given via the Bethe Ansatz. Such integrability is broken by the introduction of harmonic confinement. We investigate the equivalence of the classical field and many-body solutions in the limit of large numbers of atoms and derive numerical and variational approaches to examine the ground state energy in harmonic confinement and the fidelity between a Hartree-product solution and a quantum soliton solution. Soliton collisions produce no entanglement between either state and result only in an asymptotic position and phase shift, however external potentials break integrability and thus give the possibility of entangling solitons. We investigate the dynamical entanglement generation between two atomic dimers in harmonic confinement via exact diagonalisation in a basis of Harmonic oscillator functions, making use of the separability of the centre-of-mass component of the Hamiltonian. We show repulsive states show complex dynamics, but with an overall tendency towards states of larger invariant correlation entropy, whereas attractive states resist entanglement unless a phase matching condition is satisfied. This phase matching condition could in theory be used to generate states with highly non-Poissonian number superpositions in atomic systems with controlled number

Supervision of Graduate Students

Graduate education is an essential component of universities; it also contributes substantially to national economies. However, problems in graduate education, especially with respect to completion and quality, have emerged in many countries, including Canada. To address these problems and related issues and practices, a comprehensive three-year research project has been conducted involving questionnaires and interviews in Canada, Australia, Great Britain, and other countries. This paper presents information from questionnaires completed in 1993 by 736 supervisors of graduate students in 37 universities across Canada. Many substantial differences were obtained between the means for items when respondents were classified into eight discipline areas. The responses related to master's and doctoral programs were generally similar.Les études de 2e et 3e cycles constituent une composante essentielle des programmes offerts par les universités. En outre, ces programmes d'études supérieures contribuent de façon subtantielle aux économies nationales. Tout récemment, les problèmes liés à ces programmes d'études ont fait surface dans plusieurs pays dont le Canada. On s'interroge surtout sur la qualité de ces programmes et la durée requise pour les compléter. Pour répondre à ces interrogations d'ordre général et pratique, nous avons mené une importante recherche qui a duré trois ans et qui s'est étendue à plusieurs pays dont le Canada, l'Australie, la Grande Bretagne, et plusieurs autres. La cueillette des données s'est faite à l'aide de questionnaires et d'entrevues. Cet article fait état des résultats obtenus à l'aide de questionnaires administrés en 1993 auprès de 736 directeurs d'études supérieures dans 37 universités canadiennes. Ces résultats ont révélé des différences significatives quant aux moyennes obtenues sur chacun des items lorsque les répondants étaient regroupés en 8 secteurs disciplinaires. En ce qui a trait aux programmes de maîtrise et de doctorat, les réponses aux questions étaient assez semblables.&nbsp

Ancient DNA Provides New Insights into the Evolutionary History of New Zealand's Extinct Giant Eagle

Prior to human settlement 700 years ago New Zealand had no terrestrial mammals—apart from three species of bats—instead, approximately 250 avian species dominated the ecosystem. At the top of the food chain was the extinct Haast's eagle, Harpagornis moorei. H. moorei (10–15 kg; 2–3 m wingspan) was 30%–40% heavier than the largest extant eagle (the harpy eagle, Harpia harpyja), and hunted moa up to 15 times its weight. In a dramatic example of morphological plasticity and rapid size increase, we show that the H. moorei was very closely related to one of the world's smallest extant eagles, which is one-tenth its mass. This spectacular evolutionary change illustrates the potential speed of size alteration within lineages of vertebrates, especially in island ecosystems

Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples

Advances in the sequencing of DNA extracted from media such as soil and water offer huge opportunities for biodiversity monitoring and assessment, particularly where the collection or identification of whole organisms is impractical. However, there are myriad methods for the extraction, storage, amplification and sequencing of DNA from environmental samples. To help overcome potential biases that may impede the effective comparison of biodiversity data collected by different researchers, we propose a standardised set of procedures for use on different taxa and sample media, largely based on recent trends in their use. Our recommendations describe important steps for sample pre-processing and include the use of (a) Qiagen DNeasy PowerSoil® and PowerMax® kits for extraction of DNA from soil, sediment, faeces and leaf litter; (b) DNeasy PowerSoil® for extraction of DNA from plant tissue; (c) DNeasy Blood and Tissue kits for extraction of DNA from animal tissue; (d) DNeasy Blood and Tissue kits for extraction of DNA from macroorganisms in water and ice; and (e) DNeasy PowerWater® kits for extraction of DNA from microorganisms in water and ice. Based on key parameters, including the specificity and inclusivity of the primers for the target sequence, we recommend the use of the following primer pairs to amplify DNA for analysis by Illumina MiSeq DNA sequencing: (a) 515f and 806RB to target bacterial 16S rRNA genes (including regions V3 and V4); (b) #3 and #5RC to target eukaryote 18S rRNA genes (including regions V7 and V8); (c) #3 and #5RC are also recommended for the routine analysis of protist community DNA; (d) ITS6F and ITS7R to target the chromistan ITS1 internal transcribed spacer region; (e) S2F and S3R to target the ITS2 internal transcribed spacer in terrestrial plants; (f) fITS7 or gITS7, and ITS4 to target the fungal ITS2 region; (g) NS31 and AML2 to target glomeromycota 18S rRNA genes; and (h) mICOIintF and jgHCO2198 to target cytochrome c oxidase subunit I (COI) genes in animals. More research is currently required to confirm primers suitable for the selective amplification of DNA from specific vertebrate taxa such as fish. Combined, these recommendations represent a framework for efficient, comprehensive and robust DNA-based investigations of biodiversity, applicable to most taxa and ecosystems. The adoption of standardised protocols for biodiversity assessment and monitoring using DNA extracted from environmental samples will enable more informative comparisons among datasets, generating significant benefits for ecological science and biosecurity applications

'Drowning in here in his bloody sea' : exploring TV cop drama's representations of the impact of stress in modern policing

The Criminal Justice System is a part of society that is both familiar and hidden. It is familiar in that a large part of daily news and television drama is devoted to it (Carrabine, 2008; Jewkes, 2011). It is hidden in the sense that the majority of the population have little, if any, direct contact with the Criminal Justice System, meaning that the media may be a major force in shaping their views on crime and policing (Carrabine, 2008). As Reiner (2000) notes, the debate about the relationship between the media, policing, and crime has been a key feature of wider societal concerns about crime since the establishment of the modern police force. He outlines the recurring themes in post-war debates in this field. For Conservatives there has been an ongoing concern that the media is criminongenic, as it serves to undermine traditional institutions, including the police. From the viewpoint of radical criminology, the impact of the media is two-fold: it exaggerates legitimate concerns about crime and emphasises the bureaucratic and other restrictions under which the police operate (Reiner, 2000). This is seen as undermining due process and legitimatising what can be termed a ‘maverick’ approach to policing. An early example of this can be seen in Clint Eastwood’s Dirty Harry movies (Siegel, 1971) where Harry Callaghan acts as a one-man law enforcement system outside of the formal legal process, a process portrayed as corrupt, inefficient, and concerned with offenders’ rights rather than protecting victims. From a policing perspective, Reiner (2000) argues that film and TV drama creates a simplistic narrative of crime solving that is almost completely divorced from the reality of modern police work, a finding consistent with more recent work by Cummins et al., (2014)

A comparison of the ability of PLFA and 16s rRNA gene metabarcoding to resolve soil community change and predict ecosystem functions

Soil bacterial community structure has traditionally been measured using phospholipid fatty acid (PLFA) profiling. However, with the development of high-throughput sequencing technologies and metabarcoding techniques, more studies are now using 16S rRNA gene metabarcoding to measure bacterial community structure. Metabarcoding provides a much greater level of detail than PLFA profiling does, but it remains unclear whether or not the two techniques have a similar ability to answer many of the common questions asked by ecologists. We test the relative ability of the two techniques to quantify differences in bacterial community structure among five land uses (natural and planted forest, unimproved and improved grasslands, and vineyards), and to predict ecosystem functions. We also test whether PLFA- and metabarcoding-based metrics indicative of microbial growth strategies are correlated to each other. We show that both techniques showed broadly similar patterns of bacterial community composition change with land use and a remarkably similar ability to predict a wide range of ecosystem functions (carbon and nutrient cycling, and responses to drought). However, they were also complementary, as each showed different strengths in discriminating land uses and predicting ecosystem functions. PLFA metrics (i.e. the gram-positive:gram-negative ratio and fungal:bacterial ratio) were strongly correlated with the equivalent 16S rRNA gene metabarcoding metrics (i.e. the gram-positive:gram-negative and oligotrophic:copiotrophic ratios), although PLFA metrics were less well correlated with the Proteobacteria:Acidobacteria ratio. For many ecological questions the two techniques thus give broadly comparable results, providing confidence in the ability of both techniques to quantify meaningful changes in bacterial communities

Biases in the metabarcoding of plant pathogens using rust fungi as a model system

International audiencePlant pathogens such as rust fungi (Pucciniales) are of global economic and ecological importance. This means there is a critical need to reliably and cost-effectively detect, identify, and monitor these fungi at large scales. We investigated and analyzed the causes of differences between next-generation sequencing (NGS) metabarcoding approaches and traditional DNA cloning in the detection and quantification of recognized species of rust fungi from environmental samples. We found significant differences between observed and expected numbers of shared rust fungal operational taxonomic units (OTUs) among different methods. However, there was no significant difference in relative abundance of OTUs that all methods were capable of detecting. Differences among the methods were mainly driven by the method's ability to detect specific OTUs, likely caused by mismatches with the NGS metabarcoding primers to some Puccinia species. Furthermore, detection ability did not seem to be influenced by differences in sequence lengths among methods, the most appropriate bioinformatic pipeline used for each method, or the ability to detect rare species. Our findings are important to future metabarcoding studies, because they highlight the main sources of difference among methods, and rule out several mechanisms that could drive these differences. Furthermore, strong congruity among three fundamentally different and independent methods demonstrates the promising potential of NGS metabarcoding for tracking important taxa such as rust fungi from within larger NGS metabarcoding communities. Our results support the use of NGS metabarcoding for the large-scale detection and quantification of rust fungi, but not for confirming the absence of species

Individual-Based Allometric Equations Accurately Measure Carbon Storage and Sequestration in Shrublands

Many studies have quantified uncertainty in forest carbon (C) storage estimation, but there is little work examining the degree of uncertainty in shrubland C storage estimates. We used field data to simulate uncertainty in carbon storage estimates from three error sources: (1) allometric biomass equations; (2) measurement errors of shrubs harvested for the allometry; and (3) measurement errors of shrubs in survey plots. We also assessed uncertainty for all possible combinations of these error sources. Allometric uncertainty had the greatest independent effect on C storage estimates for individual plots. The largest error arose when all three error sources were included in simulations (where the 95% confidence interval spanned a range equivalent to 40% of mean C storage). Mean C sequestration (1.73 Mg C ha–1 year–1) exceeded the margin of error produced by the simulated sources of uncertainty. This demonstrates that, even when the major sources of uncertainty were accounted for, we were able to detect relatively modest gains in shrubland C storage