Identification of "pathologs" (disease-related genes) from the RIKEN mouse cDNA dataset using human curation plus FACTS, a new biological information extraction system

Background: A major goal in the post-genomic era is to identify and characterise disease susceptibility genes and to apply this knowledge to disease prevention and treatment. Rodents and humans have remarkably similar genomes and share closely related biochemical, physiological and pathological pathways. In this work we utilised the latest information on the mouse transcriptome as revealed by the RIKEN FANTOM2 project to identify novel human disease-related candidate genes. We define a new term patholog to mean a homolog of a human disease-related gene encoding a product ( transcript, anti-sense or protein) potentially relevant to disease. Rather than just focus on Mendelian inheritance, we applied the analysis to all potential pathologs regardless of their inheritance pattern. Results: Bioinformatic analysis and human curation of 60,770 RIKEN full-length mouse cDNA clones produced 2,578 sequences that showed similarity ( 70 - 85% identity) to known human-disease genes. Using a newly developed biological information extraction and annotation tool ( FACTS) in parallel with human expert analysis of 17,051 MEDLINE scientific abstracts we identified 182 novel potential pathologs. Of these, 36 were identified by computational tools only, 49 by human expert analysis only and 97 by both methods. These pathologs were related to neoplastic ( 53%), hereditary ( 24%), immunological ( 5%), cardio-vascular (4%), or other (14%), disorders. Conclusions: Large scale genome projects continue to produce a vast amount of data with potential application to the study of human disease. For this potential to be realised we need intelligent strategies for data categorisation and the ability to link sequence data with relevant literature. This paper demonstrates the power of combining human expert annotation with FACTS, a newly developed bioinformatics tool, to identify novel pathologs from within large-scale mouse transcript datasets.

The evidence for better health from health assessments: A large clustered randomised controlled trial

Aim: To test the efficacy of a comprehensive health assessment using the CHAP tool in adults with an intellectual disability (ID). Method: A cluster randomised control design was used. The intervention group received the CHAP, while the control group received usual care. This tool directed carers to gather a health history, which was reviewed by the person’s general practitioner (GP) who completed a medical examination and a healthcare plan. The tool acted as an advocacy tool, a ticket-of-entry to the GPs surgery and educated the GP and the caregiver about the deficits in the healthcare of adults with ID. The healthcare of the participants was followed for one-year after intervention by the collection of data from GP and service providers’ notes. Also interviews were performed with all those involved. Results: We obtained a representative sample of  adults with ID (RR%). We found the intervention group received a significant increase in many health promotion/disease prevention activities e.g. hearing screening was  times and a Pap smear was  times more likely to have occurred in the intervention groups.We also found a trend towards earlier detection of disease. Conclusions: The CHAP process improves the provision of health screening/promotion activities and should be implemented.

Estimates of global and regional potential health gains from reducing multiple major risk factors

Background Estimates of the disease burden due to multiple risk factors can show the potential gain from combined preventive measures. But few such investigations have been attempted, and none on a global scale. Our aim was to estimate the potential health benefits from removal of multiple major risk factors. Methods We assessed the burden of disease and injury attributable to the joint effects of 20 selected leading risk factors in 14 epidemiological subregions of the world. We estimated population attributable fractions, defined as the proportional reduction in disease or mortality that would occur if exposure to a risk factor were reduced to an alternative level, from data for risk factor prevalence and hazard size. For every disease, we estimated joint population attributable fractions, for multiple risk factors, by age and sex, from the direct contributions of individual risk factors. To obtain the direct hazards, we reviewed publications and re-analysed cohort data to account for that part of hazard that is mediated through other risks. Results Globally, an estimated 47% of premature deaths and 39% of total disease burden in 2000 resulted from the joint effects of the risk factors considered. These risks caused a substantial proportion of important diseases, including diarrhoea (92%-94%), lower respiratory infections (55-62%), lung cancer (72%), chronic obstructive pulmonary disease (60%), ischaemic heart disease (83-89%), and stroke (70-76%). Removal of these risks would have increased global healthy life expectancy by 9.3 years (17%) ranging from 4.4 years (6%) in the developed countries of the western Pacific to 16.1 years (43%) in parts of sub-Saharan Africa. Interpretation Removal of major risk factors would not only increase healthy life expectancy in every region, but also reduce some of the differences between regions, The potential for disease prevention and health gain from tackling major known risks simultaneously would be substantial.

Estimates of global and regional potential health gains from reducing multiple major risk factors

Background Estimates of the disease burden due to multiple risk factors can show the potential gain from combined preventive measures. But few such investigations have been attempted, and none on a global scale. Our aim was to estimate the potential health benefits from removal of multiple major risk factors. Methods We assessed the burden of disease and injury attributable to the joint effects of 20 selected leading risk factors in 14 epidemiological subregions of the world. We estimated population attributable fractions, defined as the proportional reduction in disease or mortality that would occur if exposure to a risk factor were reduced to an alternative level, from data for risk factor prevalence and hazard size. For every disease, we estimated joint population attributable fractions, for multiple risk factors, by age and sex, from the direct contributions of individual risk factors. To obtain the direct hazards, we reviewed publications and re-analysed cohort data to account for that part of hazard that is mediated through other risks. Results Globally, an estimated 47% of premature deaths and 39% of total disease burden in 2000 resulted from the joint effects of the risk factors considered. These risks caused a substantial proportion of important diseases, including diarrhoea (92%-94%), lower respiratory infections (55-62%), lung cancer (72%), chronic obstructive pulmonary disease (60%), ischaemic heart disease (83-89%), and stroke (70-76%). Removal of these risks would have increased global healthy life expectancy by 9.3 years (17%) ranging from 4.4 years (6%) in the developed countries of the western Pacific to 16.1 years (43%) in parts of sub-Saharan Africa. Interpretation Removal of major risk factors would not only increase healthy life expectancy in every region, but also reduce some of the differences between regions, The potential for disease prevention and health gain from tackling major known risks simultaneously would be substantial.

Micronesian banana, taro, and other foods: newly recognized sources of provitamin A and other carotenoids

Vitamin A deficiency (VAD) and chronic diseases are serious problems in the Federated States of Micronesia and other Pacific island countries. Nutrition education programs to address these in Micronesia have had limited success, partly due to lack of information on nutrient content in local foods. The study objective was to identify local plant foods rich in provitamin A and other carotenoids that have high levels of cultural acceptability. Food cultivars likely to be carotenoid-rich (suggested by coloration) were identified using an ethnographic approach including key informant interviews. Raw and cooked samples (mostly cultivars previously not analyzed) of 12 banana, 13 giant swamp taro, 10 breadfruit cultivars and four other local foods were analyzed by high-performance liquid chromatography. Many banana and taro cultivars were found with significant levels of beta- and alpha-carotene; the beta-carotene levels ranged from 30 to 2780 mug/100 g (banana) and. 50 to 2040 mug/100 g (taro). The results highlight the potential significance of cultivar differences in human nutrition, important for evaluation of the diet, establishment of locally relevant dietary guidelines, and research on the relationship between diet, health, and disease. These highly acceptable food cultivars could play an important role in VAD and chronic disease prevention programs in the Pacific. (C) 2003 Elsevier Science Ltd. All rights reserved.

Co-existing conditions for deaths from infectious and parasitic diseases in Australia

Objective: To examine the frequency distribution of co-existing conditions for deaths where the underlying cause was infectious and parasitic diseases. Materials and methods: Besides the underlying cause of death, the distributions of co-existing conditions for deaths from infectious and parasitic diseases were examined in total and by various age and sex groups, at individual and chapter levels, using 1998 Australian mortality data. Results: In addition to the underlying cause of death, the average number of reported co-existing conditions for a single infectious and parasitic death was 1.62. The most common co-existing conditions were respiratory failure, acute renal failure non-specific causes, ischaemic heart disease, pneumonia and diabetes. When studying the distribution of co-existing conditions at the ICD-9 chapter level, it was found that the circulatory system diseases were the most important. There was an increasing trend in the number of reported co-existing conditions from 60 years of age upwards. Gender differences existed in the frequency of some reported co-existing conditions. The most common organism types of co-existing conditions were other bacterial infection and other viruses. Conclusions: The study indicated that the quality of death certificates is less than satisfactory for the 1998 Australian mortality data. The findings may be helpful in clarifying the ICD coding rules and the development of disease prevention strategies. (C) 2003 International Society for Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Developments in National Physical Activity Policy: An international review and recommendations towards better practice

Physical activity (PA) is increasingly considered an important public health issue and as such requires the development of good public health policy. This paper provides a summary of the literature on policy development and defines what a policy on PA may usefully comprise. The results of an international review of national level PA policies, using a defined set of criteria, are reported. Considerable similarities were found in the methods and approaches to policy development on PA across countries, with most adopting an intersectoral approach, with consultation and partnership between sectors occurring at a high level of government. The need for action across the lifespan is recognised, as is the need for multiple strategies across a variety of settings. A review of Australian PA policy found that, after promising strategic developments through Active Australia in the late 1990s, PA policy and the role of the federal health sector has become less clear, with PA policy existing now only as a component part integrated into other chronic disease prevention policy initiatives. Recommendations towards better practice in policy making are made with particular reference to developing a clearly defined integrated national PA policy in the Australian context.

Acceptability and feasibility of a community-based screening programme for melanoma in Australia

The evaluation of a community-based screening programme for melanoma (SkinWatch) in 18 regional communities (total adult population >30 years 63 035) in Queensland, Australia is described. The aim of the SkinWatch programme was to promote whole-body skin screening for melanoma by primary care physicians. The programme included community education, education and support for local medical practitioners and open-access skin screening clinics. Programme delivery was achieved through assistance of local volunteers. All programme activities and resources were recorded for process evaluation. A baseline telephone survey (n = 3110) and a telephone survey four months after programme launch (n = 680) assessed community awareness of the SkinWatch programme and, 37 face-to-face interviews with community members, doctors and community leaders were conducted to assess satisfaction with the programme. A sample of 1043 of 16 383 residents who attended the skin screening clinics provided as part of the programme were interviewed to assess reasons for attending, and positive and negative aspects of SkinWatch programme. Community awareness of the SkinWatch programme increased by over 30% (p < 0.001) within four months of the start of the programme. Interview participants described the SkinWatch programme as a useful service for the communities and 90% stated they would revisit the clinics. A total of 43% of all attendees were over 50 years old, and nearly 50% were men. These findings demonstrate the acceptability and feasibility of a community-based screening programme for melanoma in rural areas. Volunteers were instrumental in increasing community ownership of and involvement in the SkinWatch programme.

A cost-effectiveness analysis of fluvastatin in patients with diabetes after successful percutaneous coronary intervention

Background: The Lescol Intervention Prevention Study (LIPS) was a multinational randomized controlled trial that showed a 47% reduction in the relative risk of cardiac death and a 22% reduction in major adverse cardiac events (MACEs) from the routine use of fluvastatin, compared with controls, in patients undergoing percutaneous coronary intervention (PCI, defined as angioplasty with or without stents). In this study, MACEs included cardiac death, nonfatal myocardial infarction, and subsequent PCI and coronary artery bypass graft. Diabetes was the greatest risk factor for MACEs. Objective: This study estimated the cost-effectiveness of fluvastatin when used for secondary prevention of MACEs after PCI in people with diabetes. Methods: A post hoc subgroup analysis of patients with diabetes from the LIPS was used to estimate the effectiveness of fluvastatin in reducing myocardial infarction, revascularization, and cardiac death. A probabilistic Markov model was developed using United Kingdom resource and cost data to estimate the additional costs and quality-adjusted life-years (QALYs) gained over 10 years from the perspective of the British National Health Service. The model contained 6 health states, and the transition probabilities were derived from the LIPS data. Crossover from fluvastatin to other lipid-lowering drugs, withdrawal from fluvastatin, and the use of lipid-lowering drugs in the control group were included. Results: In the subgroup of 202 patients with diabetes in the LIPS trial, 18 (15.0%) of 120 fluvastatin patients and 21 (25.6%) of 82 control participants were insulin dependent (P = NS). Compared with the control group, patients treated with fluvastatin can expect to gain an additional mean (SD) of 0.196 (0.139) QALY per patient over 10 years (P < 0.001) and will cost the health service an additional mean (SD) of 10 (E448) (P = NS) (mean [SD] US $16 [$689]). The additional cost per QALY gained was;(51 (US $78). The key determinants of cost-effectiveness included the probabilities of repeat interventions, cardiac death, the cost of fluvastatin, and the time horizon used for the evaluation. Conclusion: Fluvastatin was an economically efficient treatment to prevent MACEs in these patients with diabetes undergoing PCI.

Development of a DNA-based method for detection and identification of Phytophthora species

Phytophthora diseases cause major losses to agricultural and horticultural production in Australia and worldwide. Most Phytophthora diseases are soilborne and difficult to control, making disease prevention an important component of many disease management strategies. Detection and identification of the causal agent, therefore, is an essential part of effective disease management. This paper describes the development and validation of a DNA-based diagnostic assay that can detect and identify 27 different Phytophthora species. We have designed PCR primers that are specific to the genus Phytophthora. The resulting amplicon after PCR is subjected to digestion by restriction enzymes to yield a specific restriction pattern or fingerprint unique to each species. The restriction patterns are compared with a key comprising restriction patterns of type specimens or representative isolates of 27 different Phytophthora species. A number of fundamental issues, such as genetic diversity within and among species which underpin the development and validation of DNA-based diagnostic assays, are addressed in this paper.