The use of general and specific combining abilities in a context of gene expression relevant to plant breeding

Many common traits are believed to be a composite reflection of multiple genetic and environmental factors. Recent advances suggest that subtle variations in the regulation of gene expression may contribute to quantitative traits. The nature of sequence variation affecting the regulation of gene expression either in cis (that is, affecting the expression of only one of the two alleles in a heterozygous diploid) or in trans (that is, affecting the expression of both alleles in a heterozygous diploid) is a key and usually unknown feature for the breeders. If the change in expression acts entirely in cis, then the structural gene can be treated as a candidate gene and a potential target for marker-assisted selection. Therefore, gene surveys for cis-regulatory variation are a first step in identifying potential targets for marker-assisted breeding. Here, we discuss in detail the ¿genome-wide analysis of allele-specific expression differences¿ (GASED) approach. The GASED approach was developed to screen for cis-regulatory variation on a genome-wide scale. In GASED, mRNA abundance is treated as if it were a quantitative phenotypic response variable, whose genetic between-F1 hybrid variance is partitioned into additive and non-additive components. In plant breeding, this partitioning of the genetic variance is well known in the context of estimation of general and specific combining abilities for diallel crossing schemes. We demonstrate the GASED method using Arabidopsis thaliana data. The method can be used to screen for cis-regulatory variation in any crop species for which diallel crossing schemes are appropriate and genomic tools are available

Cost-effectiveness of management strategies for acute urethritis in the developing world.

OBJECTIVE: To recommend a cost-effective approach for the management of acute male urethritis in the developing world, based on the findings of a theoretical study. METHODS: A model was developed to assess the cost-effectiveness of three urethritis management strategies in a theoretical cohort of 1000 men with urethral syndrome. (1) All patients were treated with cefixime and doxycycline for gonococcal urethritis (GU) and nongonococcal urethritis (NGU), respectively, as recommended by WHO. (2) All patients were treated with doxycycline for NGU; treatment with cefixime was based on the result of direct microscopy of a urethral smear. (3) All patients were treated with cotrimoxazole or kanamycin for GU and doxycycline for NGU. Cefixime was kept for patients not responding to the first GU treatment. Strategy costs included consultations, laboratory diagnosis (where applicable) and drugs. The outcome was the rate of patients cured of urethritis. Cost-effectiveness was measured in terms of cost per cured urethritis. RESULTS: Strategy costs in our model depended largely on drug costs. The first strategy was confirmed as the most effective but also the most expensive approach. Cefixime should cost no more than US$1.5 for the strategy to be the most cost-effective. The second strategy saved money and drugs but proved a valuable alternative only when laboratory performance was optimal. The third strategy with cotrimoxazole was the least expensive but a low follow-up visit rate, poor treatment compliance or lower drug efficacy limited effectiveness. Maximizing compliance by replacing cotrimoxazole with single-dose kanamycin had the single greatest impact on the effectiveness of the third strategy. CONCLUSION: Our model suggested that a cost-effective approach would be to treat gonorrhoea with a single-dose antibiotic selected from locally available products that cost no more than US$ 1.5

'You can't just hit a button’: an ethnographic study of strategies to repurpose data from advanced clinical information systems for clinical process improvement

Background Current policies encourage healthcare institutions to acquire clinical information systems (CIS) so that captured data can be used for secondary purposes, including clinical process improvement. Such policies do not account for the extra work required to repurpose data for uses other than direct clinical care, making their implementation problematic. This paper aims to analyze the strategies employed by clinical units to use data effectively for both direct clinical care and clinical process improvement. Methods Ethnographic methods were employed. A total of 54 contextual interviews with health professionals spanning various disciplines and 18 hours of observation were carried out in 5 intensive care units in England using an advanced CIS. Case studies of how the extra work was achieved in each unit were derived from the data and then compared. Results We found that extra work is required to repurpose CIS data for clinical process improvement. Health professionals must enter data not required for clinical care and manipulation of this data into a machine-readable form is often necessary. Ambiguity over who should be responsible for this extra work hindered CIS data usage for clinical process improvement. We describe 11 strategies employed by units to accommodate this extra work, distributing it across roles. Seven of these motivated data entry by health professionals and four addressed the machine readability of data. Many of the strategies relied heavily on the skill and leadership of local clinical customizers. Conclusions To realize the expected clinical process improvements by the use of CIS data, clinical leaders and policy makers need to recognize and support the redistribution of the extra work that is involved in data repurposing. Adequate time, funding, and appropriate motivation are needed to enable units to acquire and deliver the necessary skills in CIS customization

Barriers to the secondary use of data in critical care

Purpose: We explore the challenges of the secondary use of data in clinical information systems (CIS) which critical care units in the National Health Service (England) are facing. Methods: We conducted an online survey of Critical Care Units in England regarding their practices in collecting and using clinical information systems and data. Results: Critical care units use CIS’s typically independently of hospital information systems and focus mainly on using data for auditing, management reporting and research. Respondents reported that extracting data from their CIS was difficult and that they would use stored data more if it were easier to access. Data extraction takes time and who extracts data, the training they receive and the tools they use affect the extraction and use of data. Conclusion: A number of key challenges affects the secondary use of data in critical care: a lack of integration of information systems within critical care and across departments; barriers to accessing data; mismatched data tools and user requests. Data are predominantly used for reporting and research with less emphasis on using data to inform clinical practice

Crop growth models for the -omics era: the EU-SPICY project

The prediction of phenotypic responses from genetic and environmental information is an area of active research in genetics, physiology and statistics. Rapidly increasing amounts of phenotypic information become available as a consequence of high throughput phenotyping techniques, while more and cheaper genotypic data follow from the development of new genotyping platforms. , A wide array of -omics data can be generated linking genotype and phenotype. Continuous monitoring of environmental conditions has become an accessible option. This wealth of data requires a drastic rethinking of the traditional quantitative genetic approach to modeling phenotypic variation in terms of genetic and environmental differences. Where in the past a single phenotypic trait was partitioned in a genetic and environmental component by analysis of variance techniques, nowadays we desire to model multiple, interrelated and often time dependent, phenotypic traits as a function of genes (QTLs) and environmental inputs, while we would like to include transcription information as well. The EU project 'Smart tools for Prediction and Improvement of Crop Yield' (KBBE-2008-211347), or SPICY, aims at the development of genotype-to-phenotype models that fully integrate genetic, genomic, physiological and environmental information to achieve accurate phenotypic predictions across a wide variety of genetic and environmental configurations. Pepper (Capsicum annuum) is chosen as the model crop, because of the availability of genetically characterized populations and of generic models for continuous crop growth and greenhouse production. In the presentation the objectives and structure of SPICY as well as its philosophy will be discussed

Utilisation of sexual health services by female sex workers in Nepal

Background The Nepal Demographic Health Survey (NDHS) in 2006 showed that more than half (56%) of the women with sexually transmitted infections (STIs), including HIV, in Nepal sought sexual health services. There is no such data for female sex workers (FSWs) and the limited studies on this group suggest they do not even use routine health services. This study explores FSWs use of sexual health services and the factors associated with their use and non-use of services. Methods This study aimed to explore the factors associated with utilisation of sexual health services by FSWs in the Kathmandu Valley of Nepal, and it used a mixed-method approach consisting of an interviewer administered questionnaire-based survey and in-depth interviews. Results The questionnaire survey, completed with 425 FSWs, showed that 90% FSWs self-reported sickness, and (30.8%) reported symptoms of STIs. A quarter (25%) of those reporting STIs had never visited any health facilities especially for sexual health services preferring to use non-governmental clinics (72%), private clinics (50%), hospital (27%) and health centres (13%). Multiple regression analysis showed that separated, married and street- based FSWs were more likely to seek health services from the clinics or hospitals. In- depth interviews with 15 FSWs revealed that FSWs perceived that personal, structural and socio-cultural barriers, such as inappropriate clinic opening hours, discrimination, the judgemental attitude of the service providers, lack of confidentiality, fear of public exposure, and higher fees for the services as barriers to their access and utilisation of sexual health services. Conclusion FSWs have limited access to information and to health services, and operate under personal, structural and socio-cultural constraints. The ‘education’ to change individual behaviour, health worker and community perceptions, as well as the training of the health workers, is necessary