Use of the EM algorithm to detect QTL affecting multiple-traits in an across half-sib family analysis

QTL detection experiments in livestock species commonly use the half-sib design. Each male is mated to a number of females, each female producing a limited number of progeny. Analysis consists of attempting to detect associations between phenotype and genotype measured on the progeny. When family sizes are limiting experimenters may wish to incorporate as much information as possible into a single analysis. However, combining information across sires is problematic because of incomplete linkage disequilibrium between the markers and the QTL in the population. This study describes formulae for obtaining MLEs via the expectation maximization (EM) algorithm for use in a multiple-trait, multiple-family analysis. A model specifying a QTL with only two alleles, and a common within sire error variance is assumed. Compared to single-family analyses, power can be improved up to fourfold with multi-family analyses. The accuracy and precision of QTL location estimates are also substantially improved. With small family sizes, the multi-family, multi-trait analyses reduce substantially, but not totally remove, biases in QTL effect estimates. In situations where multiple QTL alleles are segregating the multi-family analysis will average out the effects of the different QTL alleles.

Repeated occurrence of basal cell carcinoma of the skin and multifailure survival analysis: Follow-up data from the nambour skin cancer prevention trial

The aim of this study was to apply multifailure survival methods to analyze time to multiple occurrences of basal cell carcinoma (BCC). Data from 4.5 years of follow-up in a randomized controlled trial, the Nambour Skin Cancer Prevention Trial (1992-1996), to evaluate skin cancer prevention were used to assess the influence of sunscreen application on the time to first BCC and the time to subsequent BCCs. Three different approaches of time to ordered multiple events were applied and compared: the Andersen-Gill, Wei-Lin-Weissfeld, and Prentice-Williams-Peterson models. Robust variance estimation approaches were used for all multifailure survival models. Sunscreen treatment was not associated with time to first occurrence of a BCC (hazard ratio = 1.04, 95% confidence interval: 0.79, 1.45). Time to subsequent BCC tumors using the Andersen-Gill model resulted in a lower estimated hazard among the daily sunscreen application group, although statistical significance was not reached (hazard ratio = 0.82, 95% confidence interval: 0.59, 1.15). Similarly, both the Wei-Lin-Weissfeld marginal-hazards and the Prentice-Williams-Peterson gap-time models revealed trends toward a lower risk of subsequent BCC tumors among the sunscreen intervention group. These results demonstrate the importance of conducting multiple-event analysis for recurring events, as risk factors for a single event may differ from those where repeated events are considered.

Genetic and environmental influences on extreme personality dispositions in adolescent female twins

Background: The objective was to determine whether the pattern of environmental and genetic influences on deviant personality scores differs from that observed for the normative range of personality, comparing results in adolescent and adult female twins. Methods: A sample of 2,796 female adolescent twins ascertained from birth records provided Junior Eysenck Personality Questionnaire data. The average age of the sample was 17.0 years ( S. D. 2.3). Genetic analyses of continuous and extreme personality scores were conducted. Results were compared for 3,178 adult female twins. Results: Genetic analysis of continuous traits in adolescent female twins were similar to findings in adult female twins, with genetic influences accounting for between 37% and 44% of the variance in Extraversion (Ex), Neuroticism (N), and Social Non-Conformity (SNC), with significant evidence of shared environmental influences (19%) found only for SNC in the adult female twins. Analyses of extreme personality characteristics, defined categorically, in the adolescent data and replicated in the adult female data, yielded estimates for high N and high SNC that deviated substantially (p < .05) from those obtained in the continuous trait analyses, and provided suggestive evidence that shared family environment may play a more important role in determining personality deviance than has been previously found when personality is viewed continuously. However, multiple-threshold models that assumed the same genetic and environmental determinants of both normative range variation and extreme scores gave acceptable fits for each personality dimension. Conclusions: The hypothesis of differences in genetic or environmental factors responsible for N and SNC among female twins with scores in the extreme versus normative ranges was partially supported, but not for Ex.

Vitamin A deficiency in poor, urban, lactating women in Bangladesh: factors influencing vitamin A status

Aims: To investigate the prevalence of vitamin A deficiency among lactating women in a poor urban population of Bangladesh, and to examine the relationship between various factors and vitamin A status. Design: Cross-sectional study. Setting: Maternal and child health clinic in Dhaka City, Bangladesh. Subjects and methods: A total of 120 lactating women aged 17-37 years were randomly selected from women who attended a local maternal and child health clinic in Dhaka City for immunisation of their children. Various socio-economic, personal characteristics, dietary intakes of vitamin A and anthropometric data were collected. Serum retinol (vitamin A) concentration was determined as a measure of vitamin A status. Results: Of the subjects, 37% had low serum vitamin A levels (<30 μg dl(-1)), with 13.3% having sub-clinical vitamin A deficiency (<20 mug dl(-1)). Eighty-seven per cent had vitamin A intakes below the recommended dietary allowance. The lactating women who were either illiterate or received only informal education had significantly (P=0.002) lower serum vitamin A levels compared with those who received formal education. The women whose husbands received formal education had significantly (P=0.05) higher serum vitamin A levels than those whose husbands were either illiterate or received only informal education. The serum vitamin A levels of women in households with poor sanitation/latrine practice were significantly (P=0.03) lower than those of women in households with good sanitation/latrine practice. The women with one child had significantly (P=0.015) lower serum vitamin A levels than those with two or more children. Women with a lactation period of 6 months or more had significantly (P=0.034) lower serum vitamin A levels than women with a lactation period of less than 6 months. The women who consumed less than the median vitamin A intake (274.8 mug day(-1)) had significantly (P=0.01) lower serum vitamin A levels than those who consumed more than the median vitamin A intake. By multiple regression analysis, education level of the women, number of living children, duration of lactation and dietary intake of vitamin A were found to have significant independent relationships with serum vitamin A. The overall F-ratio (6.8) was highly significant (P=0.000), the adjusted R-2 was 0.16 (multiple R=0.44). Conclusion: A significant proportion of poor, urban, lactating women in Bangladesh have vitamin A deficiency. Among the various factors, education level of the women, number of living children, duration of lactation and dietary intake of vitamin A appear to be important in influencing the vitamin A status of these women.

Anaemia and vitamin A deficiency in poor urban pregnant women of Bangladesh

This cross-sectional study investigated the prevalence of anaemia and vitamin A deficiency (VAD) among pregnant women in a poor urban population of Bangladesh. It also examined the association of various socio-economic and dietary factors with anaemia and vitamin A status. A maternal and child health clinic in Dhaka city, Bangladesh was used to obtain the sample. Three hundred and eighty three pregnant women, aged 20-30 years, of 20-30 weeks gestation were randomly selected from women on their first presentation for antenatal care. Socio-economic, pregnancy related information, usual dietary pattern, and anthropometric data were collected. Blood haemoglobin and serum retinol (vitamin A) concentrations were determined. About 40% of the pregnant women were anaemic (haemoglobin <11.0 g/dl) and 45% had low serum vitamin A levels (<30 mug/dl); with 8.6% having sub-clinical VAD (serum retinol <20 μg/dl). The women with low serum vitamin A levels had 1.8 times greater risk of being anaemic than did the women with normal vitamin A status. Food frequency data revealed that a large proportion of these women did not consume egg (49%), milk (25%), meat (31%), liver (83%), large fish (32%), small fish (39%) and sweet pumpkin (52%) at all; while about 25% of the women reported consuming dark green leafy vegetables (DGLV) and 64% reported an intake of fruit at least four servings a week. The pregnant women who were either illiterate or received only informal education (up to grade ten) had significantly lower haemoglobin and serum vitamin A levels compared to those who completed at least a secondary school certificate. The women whose husbands were illiterate or received only informal education had significantly (P=0.01) lower serum vitamin A levels than those whose husbands had received at least a secondary school certificate. The women who came from families with a per-capita income below the poverty line had significantly lower haemoglobin and serum vitamin A levels compared to those who came from families with a per-capita income above the poverty line. The women who consumed three servings or less of DGLV and fruit per week had significantly lower haemoglobin and serum vitamin A levels than those who consumed four or more servings a week. The women who never consumed large fish had significantly lower haemoglobin compared to those who reported at least one serving a week. Furthermore, the women who never consumed sweet pumpkin had significantly lower serum vitamin A than the women who ate at least one serving a week. By multiple regression analysis, intake of meat, DGLV and fruit, and serum vitamin A levels were found to have a significant independent relationship with haemoglobin. The overall F-ratio (9.9) was highly significant (P=0.000), the adjusted R-square was 0.086 (multiple R=0.309). Multiple regression analysis for serum vitamin A also revealed a significant independent relationship with per capita income, haemoglobin levels, intakes of DGLV and sweet pumpkin. The overall F-ratio (10.2) was highly significant (P=0.000), the adjusted R-square was 0.10 (multiple R=0.312). In conclusion, anaemia and vitamin A deficiency were highly prevalent among poor urban pregnant women in Bangladesh. Various socio-economic and dietary factors may influence the anaemia and vitamin A status of these women. The present study emphasizes the need for a comprehensive intervention strategy, which include both nutritional and environmental factors, to improve the nutritional status of this population.

The NASCAR phenomenon: Auto racing sponsorships and shareholder wealth

This study presents the first analysis of the impact of NASCAR sponsorship announcements on the stock prices of sponsoring firms. The primary finding of the study-that NASCAR sponsorship announcements were accompanied by the largest increases in shareholder wealth ever recorded in the marketing literature in response to a voluntary marketing program-represents a striking and unambiguous stock market endorsement of the sponsorships. Indeed, the 24 sponsors analyzed in this study experienced mean increases in shareholder wealth of over $300 million dollars, net of all of the costs associated with the sponsorships. A multiple regression analysis of firm-specific stock price changes and select corporate and sponsorship attributes indicates that NASCAR sponsorships with more successful racing teams, corporate (as opposed to product or divisional) sponsorships, and sponsorships with direct ties to the consumer automotive industry are all positively correlated with perceived sponsorship success, while corporate cash flow per share (a well-known proxy for agency conflicts within the firm) is negatively related with shareholder approval.

A way forward for land-use planning to achieve policy goals by using spatial modelling scenarios

This paper investigates how demographic (socioeconomic) and land-use (physical and environmental) data can be integrated within a decision support framework to formulate and evaluate land-use planning scenarios. A case-study approach is undertaken with land-use planning scenarios for a rapidly growing coastal area in Australia, the Shire of Hervey Bay. The town and surrounding area require careful planning of the future urban growth between competing land uses. Three potential urban growth scenarios are put forth to address this issue. Scenario A ('continued growth') is based on existing socioeconomic trends. Scenario B ('maximising rates base') is derived using optimisation modelling of land-valuation data. Scenario C ('sustainable development') is derived using a number of social, economic, and environmental factors and assigning weightings of importance to each factor using a multiple criteria analysis approach. The land-use planning scenarios are presented through the use of maps and tables within a geographical information system, which delineate future possible land-use allocations up until 2021. The planning scenarios are evaluated by using a goal-achievement matrix approach. The matrix is constructed with a number of criteria derived from key policy objectives outlined in the regional growth management framework and town planning schemes. The authors of this paper examine the final efficiency scores calculated for each of the three planning scenarios and discuss the advantages and disadvantages of the three land-use modelling approaches used to formulate the final scenarios.

Cadmium-induced nephropathy in the development of high blood pressure

In recognition of a central role of the kidney in long-term blood pressure control, we undertook an in-depth analysis of the relationship between blood pressure and kidney damage caused by environmental exposure to the common pollutants cadmium and lead. The subjects were 200 healthy Thais, 16 and 60 years of age (100 female non-smokers, 53 male non-smokers, and 47 male smokers). None of these subjects had been exposed to Cd or Pb in the workplace and their urinary Cd concentrations ranged from 0.4 to 37 nM, whereas their urinary Pb concentrations ranged from 0.1 to 30 nM. The prevalence of high blood pressure was 2%, 8% and 19%, respectively in subjects with low, average and high Cd-burden (linear trend chi(2) = 6.4, P = 0.01). Multiple regression analysis revealed a significant positive association between Cd-burden and blood pressure in male nonsmokers (adjusted beta = 0.31, P = 0.02) and an inverse association between blood pressure and urinary Pb excretion rate in male smokers (adjusted beta = -0.38, P = 0.005). Associations between Cd-burden and nephropathies were evidenced by increases in urinary excretion of beta 2-microglobutin (P = 0.02) and N-acetyl-beta-D-glucosaminidase (P = 0.005) in subjects with high Cd-burden, compared with the subjects with average Cd-burden. In addition, an association between Cd-related nephropathy and high blood pressure was evidenced by a 20% increase in the prevalence of high blood pressure in people with NAG-uria (linear trend chi(2) = 4.3, P = 0.04). Our present study provides first evidence for a possible link between renal tubular damage and dysfunction caused by environmental Cd exposure and increased risk of high blood pressure. (c) 2005 Elsevier Ireland Ltd. All rights reserved.

Mental playmates: Siblings, executive functioning and theory of mind

This study assessed the theory of mind (ToM) and executive functioning (EF) abilities of 124 typically developing preschool children aged 3 to 5 years in relation to whether or not they had a child-aged sibling (i.e. a child aged 1 to 12 years) at home with whom to play and converse. On a ToM battery that included tests of false belief, appearance-reality (AR) and pretend representation, children who had at least 1 child-aged sibling scored significantly higher than both only children and those whose only siblings were infants or adults. The numbers of child-aged siblings in preschoolers' families positively predicted their scores on both a ToM battery (4 tasks) and an EF battery (2 tasks), and these associations remained significant with language ability partialled out. Results of a hierarchical multiple regression analysis revealed that independent contributions to individual differences in ToM were made by language ability, EF skill and having a child-aged sibling. However, even though some conditions for mediation were met, there was no statistically reliable evidence that EF skills mediated the advantage of presence of child-aged siblings for ToM performance. While consistent with the theory that distinctively childish interaction among siblings accelerates the growth of both TOM and EF capacities, alternative evidence and alternative theoretical interpretations for the findings were also considered.

Comparability of perceptual analysis of speech characteristics in Australian and Swedish speakers with multiple sclerosis

The aims of the present study were to compare the perceptual assessments of deviant speech signs (dysarthria) exhibited by Australian and Swedish speakers with multiple sclerosis (MS) and to explore whether judgements of dysarthria differed depending on whether the speakers and the judges spoke the same or different languages. Ten Australian and 10 Swedish individuals with MS (matched as closely as possible for age, gender, progression type and severity of dysarthria) were assessed by 2 Australian and 2 Swedish clinically experienced judges using a protocol including 33 speech parameters. Results show that the following perceptual dimensions were identified by both pairs of judges in both groups of speakers to a just noticeable or moderate degree: imprecise consonants, inappropriate pitch level, reduced general rate, and glottal fry. The reliability (Spearman rank-order correlation) of the consensus ratings from the Australian and the Swedish judges was high, with a mean rho of 85.7 for the Australian speakers and mean rho of 84.3 for the Swedish speakers. The most difficult perceptual parameters to assess (i.e. to agree on) included harshness, level of pitch and loudness, precision of consonants and general stress pattern. The study indicated that perceptual assessments of speech characteristics in individuals with MS are informative and can be achieved with high inter-judge reliability irrespective of the judge's knowledge of the speaker's language. Copyright (C) 2003 S. Karger AG, Basel.

Multiple origins of parasitism in lice: phylogenetic analysis of SSU rDNA indicates that the Phthiraptera and Psocoptera are not monophyletic

The Paraneoptera (Hemipteroid Assemblage) comprises the orders Thysanoptera (thrips), Hemiptera (bugs), Phthiraptera (lice) and Psocoptera (booklice and barklice). The phylogenetic relationships among the Psocodea (Phthiraptera and Psocoptera), Thysanoptera and Hemiptera are unresolved, as are some relationships within the Psocodea. Here, we present phylogenetic hypotheses inferred from SSU rDNA sequences; the most controversial of which is the apparent paraphyly of the Phthiraptera, which are parasites of birds and mammals, with respect to one family of Psocoptera, the Liposcelididae. The order Psocoptera and the suborder that contains the Liposcelididae, the Troctomorpha, are also paraphyletic. The two remaining psocopteran suborders, the Psocomorpha and the Trogiomorpha, are apparently monophyletic. The Liposcelididae is most closely related to lice from the suborder Amblycera. These results suggest that the taxonomy of the Psocodea needs revision. In addition, there are implications for the evolution of parasitism in insects; parasitism may have evolved twice in lice or have evolved once and been subsequently lost in the Liposcelididae.

Low frequency of CHEK2 1100delC allele in Australian multiple-case breast cancer families: functional analysis in heterozygous individuals

A protein-truncating variant of CHEK2, 1100delC, is associated with a moderate increase in breast cancer risk. We have determined the prevalence of this allele in index cases from 300 Australian multiple-case breast cancer families, 95% of which had been found to be negative for mutations in BRCA1 and BRCA2. Only two (0.6%) index cases heterozygous for the CHEK2 mutation were identified. All available relatives in these two families were genotyped, but there was no evidence of co-segregation between the CHEK2 variant and breast cancer. Lymphoblastoid cell lines established from a heterozygous carrier contained approximately 20% of the CHEK2 1100delC mRNA relative to wild-type CHEK2 transcript. However, no truncated CHK2 protein was detectable. Analyses of expression and phosphorylation of wild-type CHK2 suggest that the variant is likely to act by haploinsufficiency. Analysis of CDC25A degradation, a downstream target of CHK2, suggests that some compensation occurs to allow normal degradation of CDC25A. Such compensation of the 1100delC defect in CHEK2 might explain the rather low breast cancer risk associated with the CHEK2 variant, compared to that associated with truncating mutations in BRCA1 or BRCA2.

A multiple account framework for cost-benefit analysis

The paper presents a spreadsheet-based multiple account framework for cost-benefit analysis which incorporates all the usual concerns of cost-benefit analysts such as shadow-pricing to account for market failure. distribution of net benefits. sensitivity and risk analysis, cost of public funds, and environmental effects. The approach is generalizable to a wide range of projects and situations and offers a number of advantages to both analysts and decision-makers, including transparency, a check on internal consistency, and a detailed summary of project net benefits disaggregated by stakeholder group. Of particular importance is the ease with which this framework allows for a project to be evaluated from alternative decision-making perspectives and under alternative policy scenarios where the trade-offs among the project's stakeholders can readily be identified and quantified. (C) 2004 Elsevier Ltd. All rights reserved.

Variance components analyses of multiple asthma traits in a large sample of Australian families ascertained through a twin proband

Background: Intermediate phenotypes are often measured as a proxy for asthma. It is largely unclear to what extent the same set of environmental or genetic factors regulate these traits. Objective: Estimate the environmental and genetic correlations between self-reported and clinical asthma traits. Methods: A total of 3073 subjects from 802 families were ascertained through a twin proband. Traits measured included self-reported asthma, airway histamine responsiveness (AHR), skin prick response to common allergens including house dust mite (Dermatophagoides pteronyssinus [D. pter]), baseline lung function, total serum immunoglobulin E (IgE) and eosinophilia. Bivariate and multivariate analyses of eight traits were performed with adjustment for ascertainment and significant covariates. Results: Overall 2716 participants completed an asthma questionnaire and 2087 were clinically tested, including 1289 self-reported asthmatics (92% previously diagnosed by a doctor). Asthma, AHR, markers of allergic sensitization and eosinophilia had significant environmental correlations with each other (range: 0.23-0.89). Baseline forced expiratory volume in 1 s (FEV1) showed low environmental correlations with most traits. Fewer genetic correlations were significantly different from zero. Phenotypes with greatest genetic similarity were asthma and atopy (0.46), IgE and eosinophilia (0.44), AHR and D. pter (0.43) and AHR and airway obstruction (-0.43). Traits with greatest genetic dissimilarity were FEV1 and atopy (0.05), airway obstruction and IgE (0.07) and FEV1 and D. pter (0.11). Conclusion: These results suggest that the same set of environmental factors regulates the variation of many asthma traits. In addition, although most traits are regulated to great extent by specific genetic factors, there is still some degree of genetic overlap that could be exploited by multivariate linkage approaches.

An integrated analysis of five double-blind, randomized controlled trials evaluating the safety and efficacy of a hyaluronan product for intra-articular injection in osteoarthritis of the kneel

Objective: Five double-blind, randomized, saline-controlled trials (RCTs) were included in the United States marketing application for an intra-articular hyaluronan (IA-HA) product for the treatment of osteoarthritis (OA) of the knee. We report an integrated analysis of the primary Case Report Form (CRF) data from these trials. Method. Trials were similar in design, patient population and outcome measures - all included the Lequesne Algofunctional Index (LI), a validated composite index of pain and function, evaluating treatment over 3 months. Individual patient data were pooled; a repeated measures analysis of covariance was performed in the intent-to-treat (ITT) population. Analyses utilized both fixed and random effects models. Safety data from the five RCTs were summarized. Results: A total of 1155 patients with radiologically confirmed knee OA were enrolled: 619 received three or five IA-HA injections; 536 received. placebo saline injections. In the active and control groups, mean ages were 61.8 and 61.4 years; 62.4% and 58.8% were women; baseline total Lequesne scores 11.03 and 11.30, respectively. Integrated analysis of the pooled data set found a statistically significant reduction (P < 0.001) in total Lequesne score with hyaluronan (HA) (-2.68) vs placebo (-2.00); estimated difference -0.68 (95% CI: -0.56 to -0.79), effect size 0.20. Additional modeling approaches confirmed robustness of the analyses. Conclusions: This integrated analysis demonstrates that multiple design factors influence the results of RCTs assessing efficacy of intra-articular (IA) therapies, and that integrated analyses based on primary data differ from meta-analyses using transformed data. (C) 2006 OsteoArthritis Research Society International. Published by Elsevier Ltd. All rights reserved.