qtl.outbred: Interfacing outbred line cross data with the R/qtl mapping software

Background qtl.outbred is an extendible interface in the statistical environment, R, for combining quantitative trait loci (QTL) mapping tools. It is built as an umbrella package that enables outbred genotype probabilities to be calculated and/or imported into the software package R/qtl. Findings Using qtl.outbred, the genotype probabilities from outbred line cross data can be calculated by interfacing with a new and efficient algorithm developed for analyzing arbitrarily large datasets (included in the package) or imported from other sources such as the web-based tool, GridQTL. Conclusion qtl.outbred will improve the speed for calculating probabilities and the ability to analyse large future datasets. This package enables the user to analyse outbred line cross data accurately, but with similar effort than inbred line cross data.

Receiving bankruptcy law into Vietnam

With assistance from foreign donors, countries in developing East Asia are rapidly replacing bureaucratic regulations with statutory norms mainly derived from international trade protocol (eg, WTO and AHA). Using imported legal norms, Vietnam enacted a Law on Business Bankruptcy (LBB) (Luat Pha San Doanh Nghiep) in 1993. By any measure, the [*2] transplanted bankruptcy principles have failed to take root. During the East Asian Economic Crisis (1997-2001) when non-performing business loans dramatically increased, cases heard by the bankruptcy courts in Vietnam declined. This article investigates the ways Vietnamese ideological, cultural and structural conditions have influenced the reception of the LBE. It is concluded that legal transfers are shaped more by political, economic and legal interactions, than by 'chance and prestige'.

Globalisation and manufacturing strategy in the TCF industry

Purpose – The textiles, clothing, and footwear (TCF) industry has struggled in Australia since the government commenced dismantling tariffs. By sourcing from Asia, middlemen undercut established suppliers, and retail chains set benchmark low prices with their imported “house” labels. The policy-makers predicted that local producers would become more efficient, and export to make up for lost sales, but the media paints a picture of rising imports, retrenchments, and factory closures. The research objective was to discover what strategies the survivors (actually) employ in adapting to the pressures of globalisation.

Design/methodology/approach – More than 30 companies were involved in the study, ranging from small family businesses to subsidiaries of big multinationals. Each case study was based on an interview with a senior executive, normally followed by a plant tour. This methodology suits a fresh topic, as it avoids preconceptions and imposes no bounds.

Findings – Results show that the policy change was based on “pie in the sky” forecasts. Increasingly, TCF production is transferred to cheap offshore locations, generally via subcontracting plus the “badging” of foreign designs. To survive, local factories should focus on quality and customer service, preferably in niche markets (like uniforms), or for specific customer groups, and develop technologically advanced products. A move down the supply chain into retailing can also assist. Large multinational corporations that engage in foreign direct investment dominate the management literature.

Originality/value – This paper presents a different perspective, neglected in international operations management, whereby domestically oriented businesses attempt to defend themselves against the adverse consequences of globalisation.

Food insecurity, malnutrition and mortality in Maewo and Ambae islands, Vanuatu

Context: This paper reports on findings from the ex-post evaluation of the Maewo Capacity Building project in Maewo Island, Vanuatu, which was funded by World Vision Australia.
Objectives: To examine the extent to which the infrastructure and systems left behind by the project contributed to the improvement of household food security and health and nutritional outcomes in Maewo Island, using Ambae Island as a comparator.
Setting: Two-stage cluster survey conducted from 6 to 20 July 2004, which included anthropometric measures and 4.5-year retrospective mortality data collection.
Participants: A total of 406 households in Maewo comprising 1623 people and 411 households in Ambae comprising 1799 people.
Main outcome measures: Household food insecurity, crude mortality rate (CMR), under-five mortality rate (U5MR) and malnutrition prevalence among children.
Results: The prevalence of food insecurity without hunger was estimated at 15.3%
(95% confidence interval (CI): 12.1, 19.2%) in Maewo versus 38.2% (95% CI: 33.6, 43.0%) in Ambae, while food insecurity with hunger in children did not vary by location. After controlling for the child’s age and gender, children in Maewo had higher weight-for-age and height-for-age Z-scores than children of the same age in Ambae. The CMR was lower in Maewo (CMR ¼ 0.47/10 000 per day, 95% CI: 0.39, 0.55) than in Ambae (CMR ¼ 0.59/10 000 per day, 95% CI: 0.51, 0.67) but no difference existed in U5MR. The major causes of death were similar in both locations, with frequently reported causes being malaria, acute respiratory infection and
diarrhoeal disease.
Conclusions: Project initiatives in Maewo Island have reduced the risks of mortality and malnutrition. Using a cross-sectional ‘external control group’ design, this paper demonstrates that it is possible to draw conclusions about project effectiveness where baseline data are incomplete or absent. Shifting from donor-driven evaluations to impact evaluations has greater learning value for the organisation, and greater value when reporting back to the beneficiaries about project impact and transformational
development in their community. Public health nutritionists working in the field are well versed in the collection and interpretation of anthropometric data for evaluation of nutritional interventions such as emergency feeding programmes. These same skills can be used to conduct impact evaluations, even some time after project completion, and elucidate lessons to be learned and shared. These skills can also be applied more widely to projects which impact on the longer-term nutritional status of
communities and their food security.

Linking future ecosystem services and future human well-being

Ecosystem services are necessary, yet not sufficient for human well-being (however defined). Insufficient access to the ecosystem provisioning service of food is a particularly important factor in the loss of human well-being, but all ecosystem services contribute in some way to well-being. Although perhaps long obvious to ecologists, the links between ecosystems and aspects of human well-being, including health, have been less well understood among the social science community. This situation may now be starting to change, thanks in part to the Millennium Ecosystem Assessment (MA). Causality between ecosystem services and well-being is bidirectional; it is increasingly clear that functioning societies can protect or enhance ecosystem services, and accordingly, that societies with impaired well-being (best documented in the case of chronic diseases such as malaria and HIV/AIDS) can also experience a related decline in ecosystem services.

The future state of human well-being and of ecosystem services is more than the co-evolution of these two fundamental elements. Human well-being also depends, critically, upon the human institutions that govern relationships between human individuals and groups, and also between humans and ecosystem services.

The scenarios working group of the MA found that human well-being is highest in the Global Orchestration scenario, which assumes the fastest evolution of beneficial institutions, and is lowest in the Order from Strength scenario. Human well-being was found to be intermediate in the other two scenarios (Adapting Mosaic and Techno-Garden) even though these scenarios share a much greater recognition of the importance of ecosystem services to human well-being.

Tonic Sol-fa in contemporary choral music practice : a South African case study

The Tonic Sol-fa method of teaching choral singing was propagated throughout Britain during the nineteenth century with the dual objectives of enhancing Christian worship and achieving social reform. It was then imported to South Africa where it was introduced to indigenous people principally through Christian missionary activity and government schools. Although entirely of foreign origin, Tonic Sol-fa was so fully assimilated into African culture that it became effectively 'indigenised'. Due to its widespread use, it became the mainstay of community choral singing and may now be said to represent a significant exogenous aspect of present-day South African musical identity. However, there is little documentation regarding the type and extent of its use in contemporary choral music practice.

This paper will report on the use of Tonic Sol-fa in representative present-day choral music settings. Interview data collected from choir directors, trainers and teachers in Cape Town indicate that there is far from unanimous agreement on several aspects - in particular, the future of Tonic Sol-fa as a pedagogy and notational system. Improving educational opportunities for indigenous South Africans to undertake professional training in music are now threatening the traditional dominance of Tonic Sol-fa in indigenous culture. Nevertheless this research represents a useful case study of the continuing relevance of Tonic Sol-fa to an indigenous population who have 'made it their own' and developed a vibrant choral tradition which continues to both enrich and sustain their lives.

Globalisation, food and health in Pacific Island countries

Pacific Island countries (PICs) are experiencing an epidemic of obesity and consequent chronic diseases. Despite investment in the development of National Plans of Action for Nutrition (NPANs) and interventions to promote healthy eating and physical activity, nutritional status appears to show little improvement. This paper presents a synthesis of the findings from two research papers that were prepared for a 2003 food safety and quality meeting in Nadi, Fiji. The findings indicate that although lifestyle behaviours might be the immediate cause of dietary imbalances, greater attention should focus on omnipresent influences of globalisation as a critical element of the nutrition transition in the Pacific. In particular, those aspects of globalisation mediated through the World Trade Organization (WTO) Agreements that are placing pressures on food security and fostering increased dependence on imported food of poor nutritional quality. Rapid, significant and sustainable improvements in public health in PICs require interventions that can tackle these underlying contributors to ill health. There are opportunities to explore the use of food regulatory approaches to influence the composition, availability and accessibility of food products. Within the context of the WTO Agreements the legitimacy of food regulatory approaches will depend upon the case to demonstrate the relationship between the intervention and the protection of food security and public health nutrition. The challenges in realising these opportunities are: 1) to have the capacity to construct a case, 2) meet the technical and financial demands to administer and enforce regulatory approaches, and 3) to take advantage of opportunities available and to be able to fully participate in the international policy-making process.

Mortality rates, prevalence of malnutrition, and prevalence of lost pregnancies among the drought-ravaged population of Tete province Mozambique

Background: Tete Province, Mozambique has experienced chronic food insecurity and a dramatic fall in livestock numbers due to the cyclic problems characterized by the floods in 2000 and severe droughts in 2002 and 2003. The Province has been a beneficiary of emergency relief programs, which have assisted >22% of the population. However, these programs were not based on sound epidemiological data, and they have not established baseline data against which to assess the impact of the programs. Objective: The objective of this study was to document mortality rates, causes of death, the prevalence of malnutrition, and the prevalence of lost pregnancies after 2.5 years of humanitarian response to the crisis. Methods: A two-stage, 30-cluster household survey was conducted in the Cahora Bassa and Changara districts from 22 October to 08 November 2004. A total of 838 households were surveyed, with a population size of 4,688 people. Results: Anthropometric data were collected among children 6-59 months of age. In addition, crude mortality rates (CMRs), under five mortality rates (U5MRs), causes of deaths, and prevalence of lost pregnancies were determined among the sample population. The prevalence of malnutrition was 8.0% (95% confidence interval (CI)=6.2-9.8%) for acute malnutrition, 26.9% (95% CI=24.0-29.9%) for being underweight, and 37.0% (95% CI=33.8-40.2%) for chronic malnutrition. Boys were more likely to be underweight than were girls (odds ratio (OR)=1.34; 95% CI=1.00, 1.82; p<0.05) after controlling for age, household size, and food aid beneficiary status. Similarly, children 30-59 months of age were significantly less likely to suffer from acute malnutrition (OR=0.45; 95% CI=0.26, 0.79; p<0.01) and less likely to be underweight (OR=0.37; 95% CI=0.27, 0.51; p<0.01) than children 6-29 months of age, after adjusting for the other, aforementioned factors. The proportion of lost pregnancies was estimated at 7.7% (95% CI=4.5-11.0%). A total of 215 deaths were reported during the year preceding the survey. Thirty-nine (18.1%) children <5 years of age died. The CMR was 1.23/10 000/day (95% CI=1.08-1.38), and an U5MR was 1.03/10 000/day (95% CI=0.71-1.35). Diarrheal diseases, malaria, tuberculosis, and human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS) accounted for more than two-thirds of all deaths. Conclusions: The observed CMR in Tete Province, Mozambique is three times higher than the baseline rate for sub-Saharan Africa and 1.4 times higher than the CMR cut-off point used to define excess mortality in emergencies. The current humanitarian response in Tete Province would benefit from an improved alignment of food aid programming in conjunction with diarrheal disease control, HIV/AIDS, and malaria prevention and treatment programs. The impact of the food programs would be improved if mutually acceptable food aid programme objectives, verifiable indicators relevant to each objective, and beneficiary targets and selection criteria are developed. Periodic re-assessments and evaluations of the impact of the program and evidenced-based decision-making urgently are needed to avert a chronic dependency on food aid.

Evidence for a common role for the serine-type Plasmodium falciparum serine repeat antigen proteases : implications for vaccine and drug design

Serine repeat antigens (SERAs) are a family of secreted “cysteine-like” proteases of Plasmodium parasites. Several SERAs possess an atypical active-site serine residue in place of the canonical cysteine. The human malaria parasite Plasmodium falciparum possesses six “serine-type” (SERA1 to SERA5 and SERA9) and three “cysteine-type” (SERA6 to SERA8) SERAs. Here, we investigate the importance of the serine-type SERAs to blood-stage parasite development and examine the extent of functional redundancy among this group. We attempted to knock out the four P. falciparum serine-type SERA genes that have not been disrupted previously. SERA1, SERA4, and SERA9 knockout lines were generated, while only SERA5, the most strongly expressed member of the SERA family, remained refractory to genetic deletion. Interestingly, we discovered that while SERA4-null parasites completed the blood-stage cycle normally, they exhibited a twofold increase in the level of SERA5 mRNA. The inability to disrupt SERA5 and the apparent compensatory increase in SERA5 expression in response to the deletion of SERA4 provides evidence for an important blood-stage function for the serine-type SERAs and supports the notion of functional redundancy among this group. Such redundancy is consistent with our phylogenetic analysis, which reveals a monophyletic grouping of the serine-type SERAs across the genus Plasmodium and a predominance of postspeciation expansion. While SERA5 is to some extent further validated as a target for vaccine and drug development, our data suggest that the expression level of other serine-type SERAs is the only barrier to escape from anti-SERA5-specific interventions.

Unhealthy landscapes: policy recommendations on land use change and infectious disease emergence

Anthropogenic land use changes drive a range of infectious disease outbreaks and emergence events and modify the transmission of endemic infections. These drivers include agricultural encroachment, deforestation, road construction, dam building, irrigation, wetland modification, mining, the concentration or expansion of urban environments, coastal zone degradation, and other activities. These changes in turn cause a cascade of factors that exacerbate infectious disease emergence, such as forest fragmentation, disease introduction, pollution, poverty, and human migration. The Working Group on Land Use Change and Disease Emergence grew out of a special colloquium that convened international experts in infectious diseases, ecology, and environmental health to assess the current state of knowledge and to develop recommendations for addressing these environmental health challenges. The group established a systems model approach and priority lists of infectious diseases affected by ecologic degradation. Policy-relevant levels of the model include specific health risk factors, landscape or habitat change, and institutional (economic and behavioral) levels. The group recommended creating Centers of Excellence in Ecology and Health Research and Training, based at regional universities and/or research institutes with close links to the surrounding communities. The centers' objectives would be 3-fold: a) to provide information to local communities about the links between environmental change and public health ; b) to facilitate fully interdisciplinary research from a variety of natural, social, and health sciences and train professionals who can conduct interdisciplinary research ; and c) to engage in science-based communication and assessment for policy making toward sustainable health and ecosystems.

Ecosystems and human well-being : health synthesis

This report synthesizes the findings from the Millennium Ecosystem Assessment's (MA) global and sub-global assessments of how ecosystem changes do, or could, affect human health and well-being. Main topics covered are: Food, fresh water, timber, fibre, and fuel, nutrient and waste management, pollution, processing and detoxification, cultural, spiritual and recreational services, climate regulation, and extreme weather events.

Purchase commitments : Big business bias or solution to the 'neglected diseases' dilemma?

Miniscule research resources are allocated to researching the diseases of developing countries such as malaria, tuberculosis (TB), dengue fever, river blindness, Chagas disease and leishmaniasis, and the strains of HIV prevalent in Africa. Plainly, the patent system and the commercial model of drug research fail to respond to the needs of the poor for the simple reason that the poor exercise little purchasing power. But pressures are mounting on governments and corporations to tackle the ‘neglected diseases’ calamity. An important argument in an intense global debate is that corporations would respond to the needs of developing countries if the diseases of the poor could be made profitable. This is the idea developed by Kremer and Glennerster in a crisply written book, Strong Medicine: Creating Incentives for Pharmaceutical Research on Neglected Diseases.

Sociocultural factors relating to Tongans' and Indigenous Fijians' patterns of eating, physical activity and body size

This paper reviews literature between 1974 and 2007 that addresses the impact of sociocultural factors on reported patterns of eating, physical activity (activity) and body size of Tongans and indigenous Fijians (Fijians) in their countries of origin. There have been changes in diet (more imported and fewer traditional foods), activity (reduced, especially in urban settings), residence (rural-urban shift) and body size (increased obesity and at a younger age). The prevalence of overweight/obesity in Tongans and Fijians has increased rapidly over the last two decades and remains among the highest in the world (>80% in Tonga; >40% in Fiji), with more females reported to be obese than males. The few studies that investigated sociocultural influences on patterns of eating, activity and/or body size in this population have examined the impact of hierarchical organisation, rank and status (sex, seniority), values (respect, care, co-operation) and/or role expectations. It is important to examine how sociocultural factors influence eating, activity and body size in order to i) establish factors that promote or protect against obesity, ii) inform culturally-appropriate interventions to promote healthy lifestyles and body size, and iii) halt the obesity epidemic, especially in cultural groups with a high prevalence of obesity. There is an urgent need for more systematic investigations of key sociocultural factors, whilst taking into account the complex interplay between sociocultural factors, behaviours and other influences (historical; socioeconomic; policy; external global influences; physical environment).

Blood-stage Plasmodium infection induces CD8+ T lymphocytes to parasite-expressed antigens, largely regulated by CD8α+ dendritic cells

Although CD8+ T cells do not contribute to protection against the blood stage of Plasmodium infection, there is mounting evidence that they are principal mediators of murine experimental cerebral malaria (ECM). At present, there is no direct evidence that the CD8+ T cells mediating ECM are parasite-specific or, for that matter, whether parasite-specific CD8+ T cells are generated in response to blood-stage infection. To resolve this and to define the cellular requirements for such priming, we generated transgenic P. berghei parasites expressing model T cell epitopes. This approach was necessary as MHC class I-restricted antigens to blood-stage infection have not been defined. Here, we show that blood-stage infection leads to parasite-specific CD8+ and CD4+ T cell responses. Furthermore, we show that P. berghei-expressed antigens are cross-presented by the CD8α+ subset of dendritic cells (DC), and that this induces pathogen-specific cytotoxic T lymphocytes (CTL) capable of lysing cells presenting antigens expressed by blood-stage parasites. Finally, using three different experimental approaches, we provide evidence that CTL specific for parasite-expressed antigens contribute to ECM.

Truncation of Plasmodium berghei merozoite surface protein 8 does not affect in vivo blood-stage development

Merozoite surface protein 8 (MSP8) has shown promise as a vaccine candidate in the Plasmodium yoelii rodent malaria model and has a proposed role in merozoite invasion of erythrocytes. However, the temporal expression and localisation of MSP8 are unusual for a merozoite antigen. Moreover, in Plasmodium falciparum the MSP8 gene could be disrupted with no apparent effect on in vitro growth. To address the in vivo function of full-length MSP8, we truncated MSP8 in the rodent parasite Plasmodium berghei. PbΔMSP8 disruptant parasites displayed a normal blood-stage growth rate but no increase in reticulocyte preference, a phenomenon observed in P. yoelii MSP8 vaccinated mice. Expression levels of erythrocyte surface antigens were similar in P. berghei wild-type and PbΔMSP8-infected erythrocytes, suggesting that a parasitophorous vacuole function for MSP8 does not involve global trafficking of such antigens. These data demonstrate that a full-length membrane-associated form of PbMSP8 is not essential for blood-stage growth.