Expected shannon entropy and shannon differentiation between subpopulations for neutral genes under the finite island model

Shannon entropy H and related measures are increasingly used in molecular ecology and population genetics because (1) unlike measures based on heterozygosity or allele number, these measures weigh alleles in proportion to their population fraction, thus capturing a previously-ignored aspect of allele frequency distributions that may be important in many applications; (2) these measures connect directly to the rich predictive mathematics of information theory; (3) Shannon entropy is completely additive and has an explicitly hierarchical nature; and (4) Shannon entropy-based differentiation measures obey strong monotonicity properties that heterozygosity-based measures lack. We derive simple new expressions for the expected values of the Shannon entropy of the equilibrium allele distribution at a neutral locus in a single isolated population under two models of mutation: the infinite allele model and the stepwise mutation model. Surprisingly, this complex stochastic system for each model has an entropy expressable as a simple combination of well-known mathematical functions. Moreover, entropy- and heterozygosity-based measures for each model are linked by simple relationships that are shown by simulations to be approximately valid even far from equilibrium. We also identify a bridge between the two models of mutation. We apply our approach to subdivided populations which follow the finite island model, obtaining the Shannon entropy of the equilibrium allele distributions of the subpopulations and of the total population. We also derive the expected mutual information and normalized mutual information ("Shannon differentiation") between subpopulations at equilibrium, and identify the model parameters that determine them. We apply our measures to data from the common starling (Sturnus vulgaris) in Australia. Our measures provide a test for neutrality that is robust to violations of equilibrium assumptions, as verified on real world data from starlings.

Low allozyme variation in snapper, Pagrus auratus, in Victoria, Australia

The population genetic structure of snapper, Pagrus auratus (Bloch and Schneider), in Victoria was investigated using six polymorphic allozyme loci. Fish were sampled from four sites in Victoria and single locations in South Australia, Western Australia and New Zealand. Although there were distinct genetic differences between the snapper populations from each of the Australian states and New Zealand, only minor and largely insignificant differences were detected among Victorian populations. The results are consistent with previous genetic and tagging studies that indicate no mixing between snapper stocks in Victoria and Spencer Gulf in South Australia. This justifies separate management of the snapper fisheries in these regions. The low levels of polymorphism and heterozygosity in Victorian snapper suggest an isolation by distance model of population structure rather than one of discrete subpopulations.

Young people with an intellectual disability: risk and resilience.

There is a large body of literature about personal risk and resilience among children and adolescents from a variety of subpopulations. However, in intellectual disability research, resilience has almost exclusively been investigated and reported at the level of family stress and coping rather than an individual child's capacity to function adaptively despite severe risk. In this study young people with an intellectual disability, family members and non-family members (carers, teachers and family friends) were interviewed and asked about the young people’s relationships, coping styles, behaviour patterns and resilience. The main features placing these young people at risk included having autism or inflexible patterns of behaviour, displaying some forms of challenging behaviour, difficulty with receptive and expressive communication, living in families with high competing demands for time and living in a relatively unaccommodating community environment. The main factors leading to resilience were an attractive appearance/disposition, ability to get one’s message across, ability to adapt behaviour to changing contexts, low family stress levels and high sense of competence, stable relationships with supportive others and an accommodating/accepting community environment (both school and social).

Blood cells of Murray cod maccullochella peelii peelii (Mitchell)

Analysis of the peripheral blood cells of Murray cod Maccullochella peelii peelii identified seven distinct subpopulations including a novel basophilic cell. Haematological reference ranges were established to facilitate future diagnostic blood sampling of this fish.

Quality of life indexes for national policy: review and agenda for research

A number of governments and public policy institutes have developed ldquoQuality of Life Indexesrdquo – statistics that attempt to measure the quality of life for entire states or regions. We develop 14 criteria for determining the validity and usefulness of such QOL indexes to public policy. We then review 22 of the most-used QOL indexes from around the world. We conclude that many of the indexes are successful in that they are reliable, have established time series measures, and can be disaggregated to study subpopulations. However, many fall short in four areas: (1) indexes vary greatly in their coverage and definitions of domains of QOL, (2) none of the indexes distinguish among the concepts of input, throughput, and output that are used by public policy analysts, (3) they fail to show how QOL outputs are sensitive to public policy inputs, and (4) none have examined convergent validity against each other. We conclude that many of these indexes are potentially very useful for public policy and recommend research to further improve them.

Dyslipidaemia in rural Australia : the evidence treatment gaps

Aims & rationale/Objectives : Hypercholesterolaemia accounts for 11.6% of total deaths and 6.2% of the disability burden for the Australian population.1 This paper reports population lipid profiles for three rural Australian populations, and assesses evidence-treatment gaps against the most recent (2005-2007) Australian guidelines.

Methods : Three population surveys were undertaken in the Greater Green Triangle. 3,320 adults aged 25-74 yrs were randomly selected using age/gender stratified electoral roll samples and of these 1563 subjects participated in the survey. Anthropometric, clinical and self-administered questionnaire data relating to chronic disease risk were collected in accordance with the WHO MONICA protocol.2 A detailed investigation of dyslipidaemia was included.

Principal findings : All required data was available for 1255 participants. Age-standardised mean total cholesterol (TC), triglycerides, LDL cholesterol and HDL cholesterol concentrations were 5.36 mmol/l, 1.42 mmol/l, 3.23 mmol/l and 1.48 mmol/l, respectively. Amongst those taking lipid-lowering medication, just 11% categorised as secondary prevention/diabetes, and 39% as primary prevention, achieved all lipid targets. In the 20% of untreated participants at high risk of a primary cardiovascular event, 26% were aware of their hypercholesterolaemia and just 2% achieved all lipid targets (2.8% achieved TC?5.5 mmol, 8.5% achieved LDL<3.5 mmol/l). 11.2% of the overall population used lipid-lowering medication (95% was statin monotherapy).

Implications : Most adults do not achieve their target lipid profile. This paper identifies the subpopulations and lipid components which need to be targeted for future interventions. It also identifies substantial evidence-treatment gaps which should be addressed to help improve lipid profiles at a population level.

Patterns of use and exchange of genetic resources of the striped catfish Pangasianodon hypophthalmus (Sauvage 1878)

The present paper reviews the use and exchange of genetic resources of the migratory freshwater fish Pangasianodon hypophthalmus (Sauvage 1878) (the striped or sutchi catfish). This species is naturally distributed in the Mekong River and Chao Phraya River basins, and is cultured in several countries, but current production occurs predominantly in the Mekong Delta, Vietnam. Catfish aquaculture in Vietnam has evolved from extensive systems using wild-caught seed to an intensified farming system that is entirely dependent on hatchery-produced seed. Genetic improvement programmes on catfish have started in Vietnam, but are still in their infancy. Genetic studies have revealed several subpopulations of the species. Apart from selective breeding and the production of hybrids with closely related species, no other technologies have been applied to improve the performance of catfish. The use and exchange of P. hypophthalmus genetic resources have brought benefits to rural communities. Aquaculture development of catfish has evolved from being seen as an exploitation of natural resources to an activity that can reduce pressure on wild fish populations. Management of aquaculture stocks need to be rationalised to minimise the potential impacts it might cause to wild populations.

Is adiposity an under-recognized risk factor for tendinopathy? A systematic review

Objective : Tendon injuries have been reported to occur more frequently in individuals with increased adiposity. Treatment also appears to have poorer outcomes among these individuals. Our objective was to examine the extent and consistency of associations between adiposity and tendinopathy.

Methods : A systematic review of observational studies was conducted. Eight electronic databases were searched (Allied and Complementary Medicine, Biological Abstracts, CINAHL, Current Contents, EMBase, Medline, SPORTDiscus, and Web of Science) and citation tracking was performed on included reports. Studies were included if they compared adiposity between subjects with and without tendon injury or examined adiposity as a predictor of conservative treatment success.

Results : Four longitudinal cohorts, 14 cross-sectional studies, 8 case-control studies, and 2 interventional studies (28 in total) met the inclusion criteria, providing a total of 19,949 individuals. Forty-two subpopulations were identified, 18 of which showed elevated adiposity to be associated with tendon injury (43%). Sensitivity analyses indicated a clustering of positive findings among studies that included clinical patients (81% positive) and among case-control studies (77% positive).

Conclusion : Elevated adiposity is frequently associated with tendon injury. Published reports suggest that elevated adiposity is a risk factor for tendon injury, although this association appears to vary depending on aspects of study design and measurement. Adiposity is of particular interest in tendon research because, unlike a number of other reported risk factors for tendon injury, it is somewhat preventable and modifiable. Further research is required to determine if reducing adiposity will reduce the risk of tendon injury or improve the results of treatment.

Utility-based quality of life of overweight and obese adolescents

Objective : To explore the relationship between overweight/obesity and utility in adolescents.

Methods : Data were collected from 2890 adolescents attending 13 secondary schools in the state of Victoria, Australia. The Assessment of Quality of Life 6-Dimension (AQoL-6D) questionnaire was used to measure individual utility. Adolescent's height and weight were measured and weight status categories assigned according to the World Health Organization adolescent growth standards. Multivariate linear regression analyses were undertaken for the whole population and subpopulations of boys and girls to estimate the mean differences in utility scores between 1) overweight and healthy weight and 2) obese and healthy weight adolescents, while controlling for demographic and socioeconomic status variables.

Results : The mean age of adolescents was 14.6 years, 56.2% were boys, 22.2% were overweight, and 9.4% were obese. The mean utility of healthy weight adolescents was 0.860. After adjustments, the overweight and obese groups reported significantly lower mean utility scores (differences: −0.018 and −0.059, respectively, relative to the healthy weight group). This can be interpreted as equivalent to a stated willingness to sacrifice 1.8% and 5.9% of a life in perfect health or 2.3% and 6.8% of a life at healthy weight. A significant utility difference associated with overweight was only experienced by girls (−0.039, P = 0.003). Both sexes experienced significant utility differences associated with obesity, but the magnitude was double for girls (−0.084, P < 0.001) relative to boys (−0.041, P = 0.022).

Conclusion : Utility is lower among overweight and more so among obese adolescents.

The global obesity pandemic : shaped by global drivers and local environments

The simultaneous increases in obesity in almost all countries seem to be driven mainly by changes in the global food system, which is producing more processed, affordable, and effectively marketed food than ever before. This passive overconsumption of energy leading to obesity is a predictable outcome of market economies predicated on consumption-based growth. The global food system drivers interact with local environmental factors to create a wide variation in obesity prevalence between populations. Within populations, the interactions between environmental and individual factors, including genetic makeup, explain variability in body size between individuals. However, even with this individual variation, the epidemic has predictable patterns in subpopulations. In low-income countries, obesity mostly affects middle-aged adults (especially women) from wealthy, urban environments; whereas in high-income countries it affects both sexes and all ages, but is disproportionately greater in disadvantaged groups. Unlike other major causes of preventable death and disability, such as tobacco use, injuries, and infectious diseases, there are no exemplar populations in which the obesity epidemic has been reversed by public health measures. This absence increases the urgency for evidence-creating policy action, with a priority on reduction of the supply-side drivers.

Stressor categorization : acute physical and psychological stressors elicit distinctive recruitment patterns in the amygdala and in medullary noradrenergic cell groups

It has been hypothesized that the brain categorizes stressors and utilizes neural response pathways that vary in accordance with the assigned category. If this is true, stressors should elicit patterns of neuronal activation within the brain that are category-specific. Data from previous immediate–early gene expression mapping studies have hinted that this is the case, but interstudy differences in methodology render conclusions tenuous. In the present study, immunolabelling for the expression of c-fos was used as a marker of neuronal activity elicited in the rat brain by haemorrhage, immune challenge, noise, restraint and forced swim. All stressors elicited c-fos expression in 25–30% of hypothalamic paraventricular nucleus corticotrophin-releasing-factor cells, suggesting that these stimuli were of comparable strength, at least with regard to their ability to activate the hypothalamic–pituitary–adrenal axis. In the amygdala, haemorrhage and immune challenge both elicited c-fos expression in a large number of neurons in the central nucleus of the amygdala, whereas noise, restraint and forced swim primarily elicited recruitment of cells within the medial nucleus of the amygdala. In the medulla, all stressors recruited similar numbers of noradrenergic (A1 and A2) and adrenergic (C1 and C2) cells. However, haemorrhage and immune challenge elicited c-fos expression in subpopulations of A1 and A2 noradrenergic cells that were significantly more rostral than those recruited by noise, restraint or forced swim. The present data support the suggestion that the brain recognizes at least two major categories of stressor, which we have referred to as ‘physical’ and ‘psychological’. Moreover, the present data suggest that the neural activation footprint that is left in the brain by stressors can be used to determine the category to which they have been assigned by the brain.

A coarse-grained parallel genetic algorithm employing cluster analysis for multi-modal numerical optimisation

This paper describes a technique for improving the performance of parallel genetic algorithms on multi-modal numerical optimisation problems. It employs a cluster analysis algorithm to identify regions of the search space in which more than one sub-population is sampling. Overlapping clusters are merged in one sub-population whilst a simple derating function is applied to samples in all other sub-populations to discourage them from further sampling in that region. This approach leads to a better distribution of the search effort across multiple subpopulations and helps to prevent premature convergence. On the test problems used, significant performance improvements over the traditional island model implementation are realised.

Minimal similarity in songs suggests limited exchange between humpback whales (Megaptera novaeangliae) in the southern Indian ocean

Comparing humpback whale song from different breeding assemblages can reveal similarities in song due to acoustically interacting males, and therefore indirectly test whether males from different breeding sites are mixing. Northern Hemisphere song comparisons illustrated that whales within ocean basins share similar songs and are subpopulations within a larger population, whereas whales in different ocean basins are isolated populations and therefore do not share songs. During the 2006 breeding season, recordings were collected in Madagascar and Western Australia, and were compared visually plus aurally. Both regions shared one theme, whereas each region had four and six private themes, respectively. This study had a substantially low number of shared themes. The co-occurrence of one theme was interpreted as an indication of limited exchange between these breeding assemblages, and we speculate that limited song similarity is due to inter-oceanic interactions. Male(s) from an Indian Ocean breeding group could be exposed to novel song when they geographically overlap, and acoustically interact, with males from a different ocean basin. Novel song could induce rapid temporal changes as new song content is incorporated, thereby minimizing song similarities between that breeding group and other Indian Ocean breeding groups that were not exposed to the novel song.

X4 and R5 HIV-1 have distinct post-entry requirements for uracil DNA glycosylase during infection of primary cells

It has been assumed that R5 and X4 HIV utilize similar strategies to support viral cDNA synthesis post viral entry. In this study, we provide evidence to show that R5 and X4 HIV have distinct requirements for host cell uracil DNA glycosylase (UNG2) during the early stage of infection. UNG2 has been previously implicated in HIV infection, but its precise role remains controversial. In this study we show that, although UNG2 is highly expressed in different cell lines, UNG2 levels are low in the natural host cells of HIV. Short interfering RNA knockdown of endogenous UNG2 in primary cells showed that UNG2 is required for R5 but not X4 HIV infection and that this requirement is bypassed when HIV enters the target cell via vesicular stomatitis virus envelope-glycoprotein-mediated endocytosis. We also show that short interfering RNA knockdown of UNG2 in virus-producing primary cells leads to defective R5 HIV virions that are unable to complete viral cDNA synthesis. Quantitative PCR analysis revealed that endogenous UNG2 levels are transiently up-regulated post HIV infection, and this increase in UNG2 mRNA is ∼10–20 times higher in R5 versus X4 HIV-infected cells. Our data show that both virion-associated UNG2 and HIV infection-induced UNG2 expression are critical for reverse transcription during R5 but not X4 HIV infection. More importantly, we have made the novel observation that R5 and X4 HIV have distinct host cell factor requirements and differential capacities to induce gene expression during the early stages of infection. These differences may result from activation of distinct signaling cascades and/or infection of divergent T-lymphocyte subpopulations.

Diabetes and risk of physical disability in adults: a systematic review and meta-analysis

Background
According to previous reports, the risk of disability as a result of diabetes varies from none to double. Disability is an important measure of health and an estimate of the risk of disability as a result of diabetes is crucial in view of the global diabetes epidemic. We did a systematic review and meta-analysis to estimate this risk.

Methods
We searched Ovid, Medline, Embase, Cochrane Library, and Cumulative Index to Nursing and Allied Health Literature up to Aug 8, 2012. We included studies of adults that compared the risk of disability—as measured by activities of daily living (ADL), instrumental activities of daily living (IADL), or mobility—in people with and without any type of diabetes. We excluded studies of subpopulations with specific illnesses or of people in nursing homes. From the studies, we recorded population characteristics, how diabetes was diagnosed (by doctor or self-reported), domain and definition of disability, and risk estimates for disability. We calculated pooled estimates by disability type and type of risk estimate (odds ratio [OR] or risk ratio [RR]).

Results
Our systematic review returned 3224 results, from which 26 studies were included in our meta-analyses. Diabetes increased the risk of mobility disability (15 studies; OR 1·71, 95% CI 1·53—1·91; RR 1·51, 95% CI 1·38—1·64), of IADL disability (ten studies; OR 1·65, 95% CI 1·55—1·74), and of ADL disability (16 studies; OR 1·82, 95% CI 1·63—2·04; RR 1·82, 95% CI 1·40—2·36).

Interpretation
Diabetes is associated with a strong increase in the risk of physical disability. Efforts to promote healthy ageing should account for this risk through prevention and management of diabetes.

Funding
Monash University, Baker IDI Bright Sparks Foundation, Australian Postgraduate Award, VicHealth, National Health and Medical Research Council, Australian Research Council, Victorian Government.