Propagation of low power low divergence Gaussian fields in unbiased self-defocusing photorefractive media and their interactions

Many optical networks are limited in speed and processing capability due to the necessity for the optical signal to be converted to an electrical signal and back again. In addition, electronically manipulated interconnects in an otherwise optical network lead to overly complicated systems. Optical spatial solitons are optical beams that propagate without spatial divergence. They are capable of phase dependent interactions, and have therefore been extensively researched as suitable all optical interconnects for over 20 years. However, they require additional external components, initially high voltage power sources were required, several years later, high power background illumination had replaced the high voltage. However, these additional components have always remained as the greatest hurdle in realising the applications of the interactions of spatial optical solitons as all optical interconnects. Recently however, self-focusing was observed in an otherwise self-defocusing photorefractive crystal. This observation raises the possibility of the formation of soliton-like fields in unbiased self-defocusing media, without the need for an applied electrical field or background illumination. This thesis will present an examination of the possibility of the formation of soliton-like low divergence fields in unbiased self-defocusing photorefractive media. The optimal incident beam and photorefractive media parameters for the formation of these fields will be presented, together with an analytical and numerical study of the effect of these parameters. In addition, preliminary examination of the interactions of two of these fields will be presented. In order to complete an analytical examination of the field propagating through the photorefractive medium, the spatial profile of the beam after propagation through the medium was determined. For a low power solution, it was found that an incident Gaussian field maintains its Gaussian profile as it propagates. This allowed the beam at all times to be described by an individual complex beam parameter, while also allowing simple analytical solutions to the appropriate wave equation. An analytical model was developed to describe the effect of the photorefractive medium on the Gaussian beam. Using this model, expressions for the required intensity dependent change in both the real and imaginary components of the refractive index were found. Numerical investigation showed that under certain conditions, a low powered Gaussian field could propagate in self-defocusing photorefractive media with divergence of approximately 0.1 % per metre. An investigation into the parameters of a Ce:BaTiO3 crystal showed that the intensity dependent absorption is wavelength dependent, and can in fact transition to intensity dependent transparency. Thus, with careful wavelength selection, the required intensity dependent change in both the real and imaginary components of the refractive index for the formation of a low divergence Gaussian field are physically realisable. A theoretical model incorporating the dependence of the change in real and imaginary components of the refractive index on propagation distance was developed. Analytical and numerical results from this model are congruent with the results from the previous model, showing low divergence fields with divergence less than 0.003 % over the propagation length of the photorefractive medium. In addition, this approach also confirmed the previously mentioned self-focusing effect of the self-defocusing media, and provided an analogy to a negative index GRIN lens with an intensity dependent focal length. Experimental results supported the findings of the numerical analysis. Two low divergence fields were found to possess the ability to interact in a Ce:BaTiO3 crystal in a soliton-like fashion. The strength of these interactions was found to be dependent on the degree of divergence of the individual beams. This research found that low-divergence fields are possible in unbiased self-defocusing photorefractive media, and that soliton-like interactions between two of these fields are possible. However, in order for these types of fields to be used in future all optical interconnects, the manipulation of these interactions, together with the ability for these fields to guide a second beam at a different wavelength, must be investigated.

The Drinking Expectancy Questionnaire for Men who have Sex with Men (DEQ-MSM): A measure of substance-related beliefs

Introduction and Aims. Alcohol expectancies are associated with drinking behaviour and post-drinking use thoughts, feelings and behaviours. The expectancies held by specific cultural or sub-cultural groups have rarely been investigated. This research maps expectancies specific to gay and other men who have sex with men (MSM) and their relationship with substance use. This study describes the specific development of a measure of such beliefs for alcohol, the Drinking Expectancy Questionnaire for Men who have Sex with Men (DEQ-MSM). Design and Methods. Items selected through a focus group and interviews were piloted on 220 self-identified gay or other MSM via an online questionnaire. Results. Factor analysis revealed three distinct substance reinforcement domains ('Cognitive impairment', 'Sexual activity' and 'Social and emotional facilitation'). These factors were associated with consumption patterns of alcohol, and in a crucial test of discriminant validity were not associated with the consumption of cannabis or stimulants. Similarities and differences with existing measures will also be discussed. Discussion and Conclusions. The DEQ-MSM represents a reliable and valid measure of outcome expectancies, related to alcohol use among MSM, and represents an important advance as no known existing alcohol expectancy measure, to date, has been developed and/or normed for use among this group. Future applications of the DEQ-MSM in health promotion, clinical settings and research may contribute to reducing harm associated with alcohol use among MSM, including the development of alcohol use among young gay men.

Active ageing : developing a quantitative multi-dimensional measure

With estimates that two billion of the world’s population will be 65 years or older by 2050, ensuring that older people ‘age well’ is an international priority. To date, however, there is significant disagreement and debate about how to define and measure ‘ageing well’, with no consensus on either terminology or measurement. Thus, this chapter describes the research rationale, methodology and findings of the Australian Active Ageing Study (Triple A Study), which surveyed 2620 older Australians to identify significant contributions to quality of life for older people: work, learning, social participation, spirituality, emotional wellbeing, health, and life events. Exploratory factor analyses identified eight distinct elements (grouped into four key concepts) which appear to define ‘active ageing’ and explained 55% of the variance: social and life participation (25%), emotional health (22%), physical health and functioning (4%) and security (4%). These findings highlight the importance of understanding and supporting the social and emotional dimensions of ageing, as issues of social relationships, life engagement and emotional health dominated the factor structure. Our intension is that this paper will prompt informed debate and discussion on defining and measuring active ageing, facilitating exploration and understanding of the complexity of issues that intertwine, converge and enhance the ageing experience.

Points of convergence and divergence : normative, institutional and operational relationships between R2P and POC

As an international norm, the Responsibility to Protect (R2P) has gained substantial influence and institutional presence—and created no small controversy—in the ten years since its first conceptualisation. Conversely, the Protection of Civilians in Armed Conflict (PoC) has a longer pedigree and enjoys a less contested reputation. Yet UN Security Council action in Libya in 2011 has thrown into sharp relief the relationship between the two. UN Security Council Resolutions 1970 and 1973 follow exactly the process envisaged by R2P in response to imminent atrocity crimes, yet the operative paragraphs of the resolutions themselves invoke only PoC. This article argues that, while the agendas of PoC and R2P converge with respect to Security Council action in cases like Libya, outside this narrow context it is important to keep the two norms distinct. Peacekeepers, humanitarian actors, international lawyers, individual states and regional organisations are required to act differently with respect to the separate agendas and contexts covered by R2P and PoC. While overlap between the two does occur in highly visible cases like Libya, neither R2P nor PoC collapses normatively, institutionally or operationally into the other.

Synthesizing and databasing fossil calibrations: divergence dating and beyond

Divergence dating studies, which combine temporal data from the fossil record with branch length data from molecular phylogenetic trees, represent a rapidly expanding approach to understanding the history of life. National Evolutionary Synthesis Center hosted the first Fossil Calibrations Working Group (3–6 March, 2011, Durham, NC, USA), bringing together palaeontologists, molecular evolutionists and bioinformatics experts to present perspectives from disciplines that generate, model and use fossil calibration data. Presentations and discussions focused on channels for interdisciplinary collaboration, best practices for justifying, reporting and using fossil calibrations and roadblocks to synthesis of palaeontological and molecular data. Bioinformatics solutions were proposed, with the primary objective being a new database for vetted fossil calibrations with linkages to existing resources, targeted for a 2012 launch.

Time dependency of molecular rate estimates and systematic overestimation of recent divergence times

Studies of molecular evolutionary rates have yielded a wide range of rate estimates for various genes and taxa. Recent studies based on population-level and pedigree data have produced remarkably high estimates of mutation rate, which strongly contrast with substitution rates inferred in phylogenetic (species-level) studies. Using Bayesian analysis with a relaxed-clock model, we estimated rates for three groups of mitochondrial data: avian protein-coding genes, primate protein-coding genes, and primate d-loop sequences. In all three cases, we found a measurable transition between the high, short-term (<1–2 Myr) mutation rate and the low, long-term substitution rate. The relationship between the age of the calibration and the rate of change can be described by a vertically translated exponential decay curve, which may be used for correcting molecular date estimates. The phylogenetic substitution rates in mitochondria are approximately 0.5% per million years for avian protein-coding sequences and 1.5% per million years for primate protein-coding and d-loop sequences. Further analyses showed that purifying selection offers the most convincing explanation for the observed relationship between the estimated rate and the depth of the calibration. We rule out the possibility that it is a spurious result arising from sequence errors, and find it unlikely that the apparent decline in rates over time is caused by mutational saturation. Using a rate curve estimated from the d-loop data, several dates for last common ancestors were calculated: modern humans and Neandertals (354 ka; 222–705 ka), Neandertals (108 ka; 70–156 ka), and modern humans (76 ka; 47–110 ka). If the rate curve for a particular taxonomic group can be accurately estimated, it can be a useful tool for correcting divergence date estimates by taking the rate decay into account. Our results show that it is invalid to extrapolate molecular rates of change across different evolutionary timescales, which has important consequences for studies of populations, domestication, conservation genetics, and human evolution.

Relaxed phylogenetics and dating with confidence

In phylogenetics, the unrooted model of phylogeny and the strict molecular clock model are two extremes of a continuum. Despite their dominance in phylogenetic inference, it is evident that both are biologically unrealistic and that the real evolutionary process lies between these two extremes. Fortunately, intermediate models employing relaxed molecular clocks have been described. These models open the gate to a new field of “relaxed phylogenetics.” Here we introduce a new approach to performing relaxed phylogenetic analysis. We describe how it can be used to estimate phylogenies and divergence times in the face of uncertainty in evolutionary rates and calibration times. Our approach also provides a means for measuring the clocklikeness of datasets and comparing this measure between different genes and phylogenies. We find no significant rate autocorrelation among branches in three large datasets, suggesting that autocorrelated models are not necessarily suitable for these data. In addition, we place these datasets on the continuum of clocklikeness between a strict molecular clock and the alternative unrooted extreme. Finally, we present analyses of 102 bacterial, 106 yeast, 61 plant, 99 metazoan, and 500 primate alignments. From these we conclude that our method is phylogenetically more accurate and precise than the traditional unrooted model while adding the ability to infer a timescale to evolution.

Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times

The estimation of phylogenetic divergence times from sequence data is an important component of many molecular evolutionary studies. There is now a general appreciation that the procedure of divergence dating is considerably more complex than that initially described in the 1960s by Zuckerkandl and Pauling (1962, 1965). In particular, there has been much critical attention toward the assumption of a global molecular clock, resulting in the development of increasingly sophisticated techniques for inferring divergence times from sequence data. In response to the documentation of widespread departures from clocklike behavior, a variety of local- and relaxed-clock methods have been proposed and implemented. Local-clock methods permit different molecular clocks in different parts of the phylogenetic tree, thereby retaining the advantages of the classical molecular clock while casting off the restrictive assumption of a single, global rate of substitution (Rambaut and Bromham 1998; Yoder and Yang 2000).

Evolutionary relationships and divergence times among the native rats of Australia

Background The genus Rattus is highly speciose and has a complex taxonomy that is not fully resolved. As shown previously there are two major groups within the genus, an Asian and an Australo-Papuan group. This study focuses on the Australo-Papuan group and particularly on the Australian rats. There are uncertainties regarding the number of species within the group and the relationships among them. We analysed 16 mitochondrial genomes, including seven novel genomes from six species, to help elucidate the evolutionary history of the Australian rats. We also demonstrate, from a larger dataset, the usefulness of short regions of the mitochondrial genome in identifying these rats at the species level. Results Analyses of 16 mitochondrial genomes representing species sampled from Australo-Papuan and Asian clades of Rattus indicate divergence of these two groups ~2.7 million years ago (Mya). Subsequent diversification of at least 4 lineages within the Australo-Papuan clade was rapid and occurred over the period from ~ 0.9-1.7 Mya, a finding that explains the difficulty in resolving some relationships within this clade. Phylogenetic analyses of our 126 taxon, but shorter sequence (1952 nucleotides long), Rattus database generally give well supported species clades. Conclusions Our whole mitochondrial genome analyses are concordant with a taxonomic division that places the native Australian rats into the Rattus fuscipes species group. We suggest the following order of divergence of the Australian species. R. fuscipes is the oldest lineage among the Australian rats and is not part of a New Guinean radiation. R. lutreolus is also within this Australian clade and shallower than R. tunneyi while the R. sordidus group is the shallowest lineage in the clade. The divergences within the R. sordidus and R. leucopus lineages occurring about half a million years ago support the hypotheses of more recent interchanges of rats between Australia and New Guinea. While problematic for inference of deeper divergences, we report that the analysis of shorter mitochondrial sequences is very useful for species identification in rats.

Validity and reliability of instruments designed to measure factors influencing the overuse of antibiotics

Background: Antibiotic overuse is a global public health issue that is influenced by several factors. The degree and prevalence of antibiotic overuse is difficult to measure directly. A more practical approach, such as the use of a psycho-social measurement instrument, might allow for the observation and assessment of patterns of antibiotic use. Study objective: The aim of this paper is to review the nature, validity, and reliability of measurement scales designed to measure factors associated with antibiotic misuse/overuse. Design: This study is descriptive and includes a systematic integration of the measurement scales used in the literature to measure factors associated with antibiotic misuse/overuse. The review included 70 international scientific publications from 1992 to 2010. Main results: Studies have presented scales to measure antibiotic misuse. However, the workup of these instruments is often not mentioned, or the scales are used with only early-phase validation, such as content or face validity. Other studies have discussed the reliability of these scales. However, the full validation process has not been discussed in any of the reviewed measurement scales. Conclusion: A reliable, fully validated measurement scale must be developed to assess the factors associated with the overuse of antibiotics. Identifying these factors will help to minimize the misuse of antibiotics.