A two-phase strategy for detecting recombination in nucleotide sequences

Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. Delineating recombination events is important in the study of molecular evolution, as inference of such events provides a clearer picture of the phylogenetic relationships among different gene sequences or genomes. Nevertheless, detecting recombination events can be a daunting task, as the performance of different recombination-detecting approaches can vary, depending on evolutionary events that take place after recombination. We previously evaluated the effects of post-recombination events on the prediction accuracy of recombination-detecting approaches using simulated nucleotide sequence data. The main conclusion, supported by other studies, is that one should not depend on a single method when searching for recombination events. In this paper, we introduce a two-phase strategy, applying three statistical measures to detect the occurrence of recombination events, and a Bayesian phylogenetic approach to delineate breakpoints of such events in nucleotide sequences. We evaluate the performance of these approaches using simulated data, and demonstrate the applicability of this strategy to empirical data. The two-phase strategy proves to be time-efficient when applied to large datasets, and yields high-confidence results.

Self-Similarity of Air-Water Flows in Skimming Flows on Stepped Spillways

Skimming flows on stepped spillways are characterised by a significant rate of turbulent dissipation on the chute. Herein an advanced signal processing of traditional conductivity probe signals is developed to provide further details on the turbulent time and length scales. The technique is applied to a 22° stepped chute operating with flow Reynolds numbers between 3.8 and 7.1 E+5. The new correlation analyses yielded a characterisation of large eddies advecting the bubbles. The turbulent length scales were related to the characteristic depth Y90. Some self-similar relationships were observed systematically at both macroscopic and microscopic levels. These included the distributions of void fraction, bubble count rate, interfacial velocity and turbulence level, and turbulence time and length scales. The self-similarity results were significant because they provided a picture general enough to be used to characterise the air-water flow field in prototype spillways.

Turbulence Characterisation of High-Velocity Free-Surface Flows

In high-velocity free-surface flows, air is continuously being trapped and released through the free-surface. Such high-velocity highly-aerated flows cannot be studied numerically because of the large number of relevant equations and parameters. Herein an advanced signal processing of traditional single- and dual-tip conductivity probes provides some new information on the air-water turbulent time and length scales. The technique is applied to turbulent open channel flows in a large-size facility. The auto- and cross-correlation analyses yield some characterisation of the large eddies advecting the bubbles. The transverse integral turbulent length and time scales are related to the step height: i.e., Lxy/h ~ 0.02 to 0.2, and T.sqrt(g/h) ~ 0.004 to 0.04. The results are irrespective of the Reynolds numbers. The present findings emphasise that turbulent dissipation by large-scale vortices is a significant process in the intermediate zone between the spray and bubbly flow regions (0.3 < C < 0.7). Some self-similar relationships were observed systematically at both macroscopic and microscopic levels. The results are significant because they provide a picture general enough to be used to characterise the air-water flow field in prototype spillways.

Young children, adolescents and alcohol - Part II: Reputation enhancement and self-concept

The research reported builds on our earlier work (Houghton, Carroll, & Odgers, 1998) which explored young children's and adolescents' views pertaining to knowledge and awareness of alcohol and alcohol-related issues. In this second study 640 (286 male and 354 female) school students randomly selected from five primary schools and five high schools in Perth, Western Australia participated. Data were obtained using The Which Group picture booklet questionnaire which comprises five parts and utilises illustrations (drawn by a professional children's artist) to gather information about children's and adolescents' orientations towards alcohol risk social situations, reputation enhancement, self-concept, and other related issues. Of the sample, 73% of males and 70.6% of females had tried alcohol, with beer being consumed most often. Significantly more participants in higher Year levels had tried alcohol. Over 90% said they drank at a party. Multivariate analysis revealed that nine of the 11 dependent variables contributed to the significant main effect of alcohol risk group, of which three were self-concept variables and six were reputation enhancement variables. It appears that individuals with the highest levels of orientation to alcohol risk believe that they are liked by their families, are physically attractive and have greater confidence in themselves. They also have higher levels of Admiration of Alcohol Related Activities and also of prosocial activities. While striving to attain a non-conforming reputation these individuals also wish to be ideally perceived by others as conforming. Gender and Age differences are investigated.

Children's understanding of pictorial and mental representations

Two studies demonstrate dissociation between children's understanding of pictorial representations (photos and drawings) and mental representations (beliefs). In Study 1, 37 preschoolers were tested on false belief, appearance-reality, false photo, and false drawing tasks. The false picture tasks were significantly easier, and no correlation was found between children's performances on false belief and false picture tasks. Ln Study 2, 30 children who failed a false belief pretest were randomly assigned to 3 training groups: Belief (trained on false belief tasks), Picture (trained on false picture tasks), or Control (trained on number conservation tasks). Training was conducted in 2 sessions over the course of 2 weeks, tasks were presented and feedback was provided. All children were posttested on theory of mind tasks, false picture tasks, and a number conservation task. The posttest results showed differential patterns of performance, with the Belief group scoring highest on the theory of mind posttests, the Picture group scoring highest on the false picture posttests, and the Control group scoring highest on the number conservation posttest. Results are discussed with respect to competing models of theory of mind development.

Coupling of a Jahn-Teller pseudorotation with a hindered internal rotation in an isolated molecule: 9-hydroxytriptycene

The irregular vibronic structure in the S-1<--S-0 resonant two-photon ionization (R2PI) spectrum of supersonically cooled triptycene is a result of a classic Exe Jahn-Teller effect [A. Furlan et al., J. Chem. Phys. 96, 7306 (1992)]. This is well characterized and can be used as an effective probe of intramolecular perturbations. Here we examine the S-1<--S-0 R2PI spectrum of 9-hydroxytriptycene and the fluorescence from various excited state vibronic levels. In this system the pseudorotation of the Jahn-Teller vibration is strongly coupled to the torsional motion of the bridgehead hydroxy group. This torsional motion results in a tunneling splitting in both the ground and excited states. The population of the upper level in the ground electronic state results in additional vibronic transitions becoming symmetry allowed in the R2PI spectrum that are forbidden in the bare triptycene molecule. The assignment of the R2PI and fluorescence spectra allows the potential energy surfaces of these vibrational modes to be accurately quantified. The full C-3v vibronic point group must be used to interpret the spectra. The time scale of the internal rotation of the-OH group and the butterfly flapping of the Jahn-Teller pseudorotation are of similar magnitude. The tunneling between the nine minima on the three dimensional potential energy surface is such that the Jahn-Teller pseudorotation occurs in concert with the-OH internal rotation. The Berry phase that is acquired during this motion is discussed. The simple physical picture emerges of the angle between two of the three benzene moieties opening in three equivalent ways in the S-1 electronic state. This geometry follows the position of the hydroxy group, which preferentially orients itself to point between these two rings. (C) 1998 American Institute of Physics. [S0021-9606(98)02348-4].

Women's health Australia: On the progress of the main cohort studies

More than 41,000 women aged 18-23, 45-50, and 70-75 years in 1996 are participating in the Australian Longitudinal Study on Women's Health (Women's Health Australia). Baseline surveys were conducted for all three cohorts in 1996, and the first follow-up survey of the mid-age group in 1998 has achieved a response rate exceeding 90%. The main findings so far reflect the large differences in the life experiences of the three cohorts. The young women report high levels of stress. The physical and mental health of those with young children is worse than for those without children, but confounding by sociodemographic characteristics may account for the differences. Two thirds of young women in the healthy weight or underweight range would like to weigh less, and early onset of dieting is associated with poorer physical and mental health. Most of the women in the mid-age group have multiple roles-in paid work, home duties, and caring for children and other dependents. The potential of the study to investigate the long-term impact of such busy lives on health outcomes is considerable. At this stage, the main health issues for these women relate to tiredness, weight gain, and menopause. The older cohort presents a picture of positive aging. These women are heavier users of health services than the mid-age and younger women, and they are also more satisfied with these services. Although their physical health is poorer, their mental health is better, and they report less stress than women in the other two cohorts. The follow-up survey of this group, planned for 1999, will focus on the coping strategies used by these women. An overall goal of the project is to understand the interactions among social roles, life events, and women's health in order to provide a basis for improved health policies and services. Analysis of these interactions, which relies on both quantitative and qualitative data, poses many challenges that will be addressed as the longitudinal data become available.

Acute susceptibility of aged mice to infection with Candida albicans

The effect of aging on host resistance to systemic candidosis was assessed by monitoring the course of infection in 16-month-old CBA/CaH mice (aged non-immune) and in a comparable group that had been infected with a sublethal dose of Candida albicans at 6 weeks of age (aged immune). Aged non-immune mice showed rapid progression of the disease, with a marked increase in the number of mycelia in the brain and kidney, and early morbidity, Foci of myocardial necrosis were evident, but inflammatory cells were sparse. The histological picture in the aged immune mice was similar to that in the aged non-immune group, although fewer mycelial aggregates were seen. Both groups of aged mice showed a significantly lower fungal burden in the brain on day 1 of infection, but on day 4, colony counts increased significantly in the aged non-immune mice, Comparison of cytokine gene expression in the infected brains showed that the relative amount of interferon-gamma and tumour necrosis factor-alpha cDNA were similar in all three groups. Interleukin-6 was elevated in both infected non-immune and uninfected aged mice. Aged immune mice showed no morbidity after challenge, and both colonisation and tissue damage were reduced in comparison with the aged non-immune animals.

The last glacial cycle from the humid tropics of northeastern Australia: comparison of a terrestrial and a marine record

A detailed pollen record from the Ocean Drilling Program Site 820 core, located on the upper part of the continental slope off the coast of northeast Queensland, was constructed to compare with the existing pollen record from Lynch's Crater on the adjacent Atherton Tableland and allow the production of a regional picture of vegetation and environmental change through the last glacial cycle. Some broad similarities in patterns of vegetation change are revealed, despite the differences between sites and their pollen catchments, which can be related largely to global climate and sea-level changes. The original estimated time scale of the Lynch's Crater record is largely confirmed from comparison with the more thoroughly dated ODP record. Conversely, the Lynch's Crater pollen record has assisted in dating problematic parts of the ODP record. In contrast to Lynch's Crater, which reveals a sharp and sustained reduction in drier araucarian forest around 38,000 yrs BP, considered to have been the result of burning by Aboriginal people, the ODP record indicates, most likely, a stepwise reduction, dating from 140,000 yrs BP or beyond. The earliest reduction shows lack of a clear connection between Araucaria decline and increased burning and suggests that people may not have been involved at this stage. However, a further decline in araucarian forest, possibly around 45,000 yrs BP, which has a more substantial environmental impact and is not related to a time of major climate change, is likely, at least partially, the result of human burning. The suggestion, from the ODP core oxygen isotope record, of a regional sea-surface temperature increase of around 4 degrees C between about 400,000 and 250,000 yrs BP, may have had some influence on the overall decline in Araucaria and its replacement by sclerophyll vegetation. (C) 2000 Elsevier Science B.V. All rights reserved.

Lessons from a comprehensive clinical audit of users of psychiatric services who committed suicide

Objective: Characteristics of patients who committed suicide were examined to provide a picture of the treatment they received before death and to determine whether and how the suicides could have been pre vented by the service system. Methods: The unnatural-deaths register was matched to the psychiatric case register in the state of Victoria in Australia to identify suicides by people with a history of public-sector psychiatric service use who committed suicide between July 1, 1989, and June 30, 1994. Data on patient and treatment characteristics were examined by three experienced clinicians, who made judgments about whether the suicide could have been prevented had the service system responded differently. Quantitative and qualitative data were descriptively analyzed. Results: A total of 629 psychiatric patients who had committed suicide were identified. Seventy-two percent of the patients were male, 62 percent were under 40 years old, and 51 percent were unmarried. They had a range of disorders, with the most common being schizophrenia or schizoaffective disorder (36 percent). Sixty-seven percent had previously attempted suicide. A total of 311 patients (49 percent) received care within four weeks of death. Twenty percent of the suicides were considered preventable. Key factors associated with preventability were poor staff-patient relationships, incomplete assessments, poor assessment and treatment of depression and psychological problems, and poor continuity of care. Conclusions: Opportunities exist for the psychiatric service system to alter practices at several levels and thereby reduce patient suicides.

Virus or not? Phylogenetics of polydnaviruses and their wasp carriers

Our current, still limited, understanding of the comparative biology and evolution of polydnaviruses (PDVs) is reviewed, especially in the context of the possible origins of these parasitoid viruses and of their coevolution with carrier wasps. A hypothetical scenario of evolution of PDVs from ascovirus (or ascovirus-like) ancestors is presented, with examples of apparent extant transitional forms. PDVs appear, in the case of bracoviruses, to show phylogenetic relationships that mirror those of their wasp carriers: with ichno-viruses, the picture is less clear. Ongoing sequencing studies of entire PDV genomes from diverse wasp species are likely to greatly contribute to our understanding of PDV evolution. (C) 2003 Elsevier Science Ltd. All rights reserved.

Molecular evolution and phylogeny of elapid snake venom three-finger toxins

Animal venom components are of considerable interest to researchers across a wide variety of disciplines, including molecular biology, biochemistry, medicine, and evolutionary genetics. The three-finger family of snake venom peptides is a particularly interesting and biochemically complex group of venom peptides, because they are encoded by a large multigene family and display a diverse array of functional activities. In addition, understanding how this complex and highly varied multigene family evolved is an interesting question to researchers investigating the biochemical diversity of these peptides and their impact on human health. Therefore, the purpose of our study was to investigate the long-term evolutionary patterns exhibited by these snake venom toxins to understand the mechanisms by which they diversified into a large, biochemically diverse, multigene family. Our results show a much greater diversity of family members than was previously known, including a number of subfamilies that did not fall within any previously identified groups with characterized activities. In addition, we found that the long-term evolutionary processes that gave rise to the diversity of three-finger toxins are consistent with the birth-and-death model of multigene family evolution. It is anticipated that this three-finger toxin toolkit will prove to be useful in providing a clearer picture of the diversity of investigational ligands or potential therapeutics available within this important family.

Late Quaternary Milankovitch-scale climatic change and variability and its impact on monsoonal Australasia

Four pollen and charcoal records derived from marine cores around the northern perimeter of Australia are examined to provide a regional picture of patterns, causes and impacts of climate change over the last 100-300 ka. The availability of radiocarbon dates and oxygen isotope records for the cores provides primary chronological control. Spectral analysis of components of these records demonstrates an overall importance of Milankovitch frequencies with clear glacial-interglacial cyclicity dominated by variation in precipitation. In addition, a number of pollen taxa, as well as charcoal particles, exhibit a 30 ka frequency that is considered, from its relationship with biomass burning and with results of past modelling, to reflect changes in the intensity of El Nino-Southern Oscillation (ENSO) variability. Pollen components of all records show a decline, frequently stepwise, in more fire-sensitive vegetation and its replacement with more fire-tolerant vegetation. There is some evidence that this trend is linked to an onset or general increase in ENSO activity and perhaps also to variation in monsoon activity dating from about 300 ka BP that was caused by changes to oceanic circulation within the Indonesian region. The trend may have accelerated within the last 45 ka due to burning by indigenous people. (C) 2003 Elsevier B.V. All rights reserved.

Visiting-economists through Hirschman`s eyes

Since the nineteenth century, Latin America and other poor areas of the world received periodical visits from missions of economic experts. This paper analyzes the picture that Hirschman draws of these money doctors, whose main task was to advise on the economic and financial reforms that were deemed necessary for economic development. Hirschman coins the expression `visiting-economist syndrome` to criticize the work done by these money doctors. I discuss whether Hirschman, as a money doctor himself, was able to acquire immunity from the disease he feared.

Regional Effects of Port Infrastructure: A Spatial CGE Application to Brazil

This article attempts to elucidate one of the mechanisms that link trade barriers, in the form of port costs, and subsequent growth and regional inequality. Prior attention has focused on inland or link costs, but port costs can be considered as a further barrier to enhancing trade liberalization and growth. In contrast to a highway link, congestion at a port may have severe impacts that are spread over space and time whereas highway link congestion may be resolved within several hours. Since a port is part of the transportation network, any congestion/disruption is likely to ripple throughout the hinterland. In this sense, it is important to model properly the role nodal components play in the context of spatial models and international trade. In this article, a spatial computable general equilibrium (CGE) model that is integrated to a transport network system is presented to simulate the impacts of increases in port efficiency in Brazil. The role of ports of entry and ports of exit are explicitly considered to grasp the holistic picture in an integrated interregional system. Measures of efficiency for different port locations are incorporated in the calibration of the model and used as the benchmark in our simulations. Three scenarios are evaluated: (1) an overall increase in port efficiency in Brazil to achieve international standards; (2) efficiency gains associated with decentralization in port management in Brazil; and (3) regionally differentiated increases in port efficiency to reach the boundary of the national efficiency frontier.