Tissue resolved, gene structure refined equine transcriptome.

BackgroundTranscriptome interpretation relies on a good-quality reference transcriptome for accurate quantification of gene expression as well as functional analysis of genetic variants. The current annotation of the horse genome lacks the specificity and sensitivity necessary to assess gene expression especially at the isoform level, and suffers from insufficient annotation of untranslated regions (UTR) usage. We built an annotation pipeline for horse and used it to integrate 1.9 billion reads from multiple RNA-seq data sets into a new refined transcriptome.ResultsThis equine transcriptome integrates eight different tissues from 59 individuals and improves gene structure and isoform resolution, while providing considerable tissue-specific information. We utilized four levels of transcript filtration in our pipeline, aimed at producing several transcriptome versions that are suitable for different downstream analyses. Our most refined transcriptome includes 36,876 genes and 76,125 isoforms, with 6474 candidate transcriptional loci novel to the equine transcriptome.ConclusionsWe have employed a variety of descriptive statistics and figures that demonstrate the quality and content of the transcriptome. The equine transcriptomes that are provided by this pipeline show the best tissue-specific resolution of any equine transcriptome to date and are flexible for several downstream analyses. We encourage the integration of further equine transcriptomes with our annotation pipeline to continue and improve the equine transcriptome

qPCR Assays for the Detection and Quantification of Multiple Paralytic Shellfish Toxin-Producing Species of Alexandrium

Paralytic shellfish toxin producing dinoflagellates have negatively impacted the shellfish aquaculture industry worldwide, including in Australia and New Zealand. Morphologically identical cryptic species of dinoflagellates that may differ in toxicity, in particular, species of the former Alexandrium tamarense species complex, co-occur in Australia, as they do in multiple regions in Asia and Europe. To understand the dynamics and the ecological drivers of the growth of each species in the field, accurate quantification at the species level is crucial. We have developed the first quantitative polymerase chain reaction (qPCR) primers for A. australiense, and new primers targeting A. ostenfeldii, A. catenella, and A. pacificum. We showed that our new primers for A. pacificum are more specific than previously published primer pairs. These assays can be used to quantify planktonic cells and cysts in the water column and in sediment samples with limits of detection of 2 cells/L for the A. catenella and A. australiense assays, 2 cells/L and 1 cyst/mg sediment for the A. pacificum assay, and 1 cells/L for the A. ostenfeldii assay, and efficiencies of >90%. We utilized these assays to discriminate and quantify co-occurring A. catenella, A. pacificum, and A. australiense in samples from the east coast of Tasmania, Australia

A generic model for the assessment of disease epidemiology: the computational basis of DisMod II

Epidemiology as an empirical science has developed sophisticated methods to measure the causes and patterns of disease in populations. Nevertheless, for many diseases in many countries only partial data are available. When the partial data are insufficient, but data collection is not an option, it is possible to supplement the data by exploiting the causal relations between the various variables that describe a disease process. We present a simple generic disease model with incidence, one prevalent state, and case fatality and remission. We derive a set of equations that describes this disease process and allows calculation of the complete epidemiology of a disease given a minimum of three input variables. We give the example of asthma with age-specific prevalence, remission, and mortality as inputs. Outputs are incidence and case fatality, among others. The set of equations is embedded in a software package called 'DisMod II', which is made available to the public domain by the World Health Organization

Policy mapping for establishing a national emergency health policy for Nigeria

BACKGROUND: The number of potential life years lost due to accidents and injuries though poorly studied has resulted in tremendous economic and social loss to Nigeria. Numerous socio-cultural, economic and political factors including the current epidemic of ethnic and religious conflicts act in concert in predisposing to and enabling the ongoing catastrophe of accident and injuries in Nigeria. METHODS: Using the "policymaker", Microsoft-Windows(®) based software, the information generated on accidents and injuries and emergency health care in Nigeria from literature review, content analysis of relevant documents, expert interviewing and consensus opinion, a model National Emergency Health Policy was designed and analyzed. A major point of analysis for the policy is the current political feasibility of the policy including its opportunities and obstacles in the country. RESULTS: A model National Emergency Health Policy with policy goals, objectives, programs and evaluation benchmarks was generated. Critical analyses of potential policy problems, associated multiple players, diverging interests and implementation guidelines were developed. CONCLUSIONS: "Political health modeling" a term proposed here would be invaluable to policy makers and scholars in developing countries in assessing the political feasibility of policy managing. Political modeling applied to the development of a NEHP in Nigeria would empower policy makers and the policy making process and would ensure a sustainable emergency health policy in Nigeria

Disability weights for comorbidity and their influence on Health-adjusted Life Expectancy

BACKGROUND: Comorbidity complicates estimations of health-adjusted life expectancy (HALE) using disease prevalences and disability weights from Burden of Disease studies. Usually, the exact amount of comorbidity is unknown and no disability weights are defined for comorbidity. METHODS: Using data of the Dutch national burden of disease study, the effects of different methods to adjust for comorbidity on HALE calculations are estimated. The default multiplicative adjustment method to define disability weights for comorbidity is compared to HALE estimates without adjustment for comorbidity and to HALE estimates in which the amount of disability in patients with multiple diseases is solely determined by the disease that leads to most disability (the maximum adjustment method). To estimate the amount of comorbidity, independence between diseases is assumed. RESULTS: Compared to the multiplicative adjustment method, the maximum adjustment method lowers HALE estimates by 1.2 years for males and 1.9 years for females. Compared to no adjustment, a multiplicative adjustment lowers HALE estimates by 1.0 years for males and 1.4 years for females. CONCLUSION: The differences in HALE caused by the different adjustment methods demonstrate that adjusting for comorbidity in HALE calculations is an important topic that needs more attention. More empirical research is needed to develop a more general theory as to how comorbidity influences disability

A qualitative study of patients’ feedback about Outpatient Parenteral Antimicrobial Therapy (OPAT) services in Northern England: implications for service improvement

Objective Outpatient parenteral antimicrobial therapy (OPAT) provides opportunities for improved cost savings, but in the UK, implementation is patchy and a variety of service models are in use. The slow uptake in the UK and Europe is due to a number of clinical, financial and logistical issues, including concern about patient safety. The measurement of patient experience data is commonly used to inform commissioning decisions, but these focus on functional aspects of services and fail to examine the relational aspects of care. This qualitative study examines patients’ experiences of OPAT. Design In-depth, semistructured interviews. Setting Purposive sample of OPAT patients recruited from four acute National Health Service (NHS) Trusts in Northern England. These NHS Trusts between them represented both well-established and recently set-up services running nurse at home, hospital outpatient and/or selfadministration models. Participants We undertook 28 semistructured interviews and one focus group (n=4). Results Despite good patient outcomes, experiences were coloured by patients' personal situation and material circumstances. Many found looking after themselves at home more difficult than they expected, while others continued to work despite their infection. Expensive car parking, late running services and the inconvenience of waiting in for the nurse to arrive frustrated patients, while efficient services, staffed by nurses with the specialist skills needed to manage intravenous treatment had the opposite effect. Many patients felt a local, general practitioner or community health centre based service would resolve many of the practical difficulties that made OPAT inconvenient. Patients could find OPAT anxiety provoking but this could be ameliorated by staff taking the time to reassure patients and provide tailored information. Conclusion Services configurations must accommodate the diversity of the local population. Poor communication can leave patients lacking the confidence needed to be a competent collaborator in their own care and affect their perceptions of the service

Calculation of health expectancies with administrative data for North Rhine-Westphalia, a Federal State of Germany, 1999–2005

Pinheiro JP, Krämer A. Calculation of health expectancies with administrative data for North Rhine-Westphalia, a Federal State of Germany, 1999-2005. Population Health Metrics. 2009;7(1):4.OBJECTIVES: The main objectives of this study were to prove the feasibility of health expectancy analyses with regional administrative health statistics and to explore the utility of the calculated health expectancies in describing the health state of the population living in North Rhine-Westphalia, a Federal State of Germany. MATERIALS AND METHODS: Administrative population and mortality data as well as health data on disability and long-term care provided by public services were used to calculate: a) the life expectancy and b) the health expectancies Severe-Disability-Free Life Expectancy (SDFLE) and Long-Term-Care-Free Life Expectancy (LTCFLE) from 1999 to 2005. Calculations were done using the Sullivan method. RESULTS: SDFLE at birth was 69.9 years (males 66.2 and females 73.2 years) in 1999 and it increased to 71.7 years (males 68.6 and females 74.7 years) in 2005. The proportion of the SDFLE on the total life expectancy at birth was 89.8% (males 88.6 and females 90.8%) in 1999 and 90.7% (males 89.8 and females 91.4%) in 2005.LTCFLE at birth was 75.3 years (males 73.1 and females 77.5 years) in 1999 and it increased to 76.6 years (males 74.7 and females 78.6 years) in 2005. The proportion of the LTCFLE on the total life expectancy at birth was 96.8% (males 97.8 and females 96.1%) in 1999 and 96.8% (males 97.8 and females 96.2%) in 2005. DISCUSSION AND CONCLUSION: Both health expectancies indicate an improvement in the quantity as well as in the quality of healthy life for the population living in North Rhine Westphalia and therefore suggest a compression of morbidity from 1999 to 2005. The findings however have several limitations in their sensitivity, since we applied dichotomous valuations to the health states. In addition, the results are restricted to comparisons over time because the morbidity concepts do not allow for comparisons with populations other than the German one. Refined calculations with other summary measures of population health and with health data on other morbidity concepts are therefore reasonable

Improving the Quantitative Basis of the Surgical Burden in Low-Income Countries

Theo Vos discusses how surgery is beginning to be considered an essential component of primary health care in low-income countries, and how we need to improve our understanding of the burden of surgical conditions in these settings

Cross-national agreement on disability weights: the European Disability Weights Project

BACKGROUND: Disability weights represent the relative severity of disease stages to be incorporated in summary measures of population health. The level of agreement on disability weights in Western European countries was investigated with different valuation methods. METHODS: Disability weights for fifteen disease stages were elicited empirically in panels of health care professionals or non-health care professionals with an academic background following a strictly standardised procedure. Three valuation methods were used: a visual analogue scale (VAS); the time trade-off technique (TTO); and the person trade-off technique (PTO). Agreement among England, France, the Netherlands, Spain, and Sweden on the three disability weight sets was analysed by means of an intraclass correlation coefficient (ICC) in the framework of generalisability theory. Agreement among the two types of panels was similarly assessed. RESULTS: A total of 232 participants were included. Similar rankings of disease stages across countries were found with all valuation methods. The ICC of country agreement on disability weights ranged from 0.56 [95% CI, 0.52–0.62] with PTO to 0.72 [0.70–0.74] with VAS and 0.72 [0.69–0.75] with TTO. The ICC of agreement between health care professionals and non-health care professionals ranged from 0.64 [0.58–0.68] with PTO to 0.73 [0.71–0.75] with VAS and 0.74 [0.72–0.77] with TTO. CONCLUSIONS: Overall, the study supports a reasonably high level of agreement on disability weights in Western European countries with VAS and TTO methods, which focus on individual preferences, but a lower level of agreement with the PTO method, which focuses more on societal values in resource allocation