The principles of informed consent, confidentiality and privacy are often neglected during patient care in developing countries. We assessed the degree to which doctors in Lahore adhere to these principles during outpatient consultations.The study was conducted at medical out-patient departments (OPDs) of two tertiary care hospitals  of Lahore, selected using multi-stage sampling. 93 patients were selected from each hospital. Doctors' adherence to the principles of informed consent, privacy and confidentiality was observed through client flow analysis performed by trained personnel. Overall patient perception was also assessed regarding these practices and was compared with the assessment made by our data collectors.Some degree of informed consent was obtained from only 9.7% patients in the public hospital and 47.8% in the private hospital. 81.4% of patients in the public hospital and 88.4% in the private hospital were accorded at least some degree of privacy. Complete informational confidentiality was maintained only in 10.8% and 35.5% of cases in public & private hospitals respectively. Informed consent and confidentiality were better practiced in the private compared to the public hospital . There was marked disparity between the patients' perspective of these ethical practices and the assessment of our trained data collectors.Observance of medical ethics is inadequate in hospitals of Lahore. Doctors should be imparted formal training in medical ethics and national legislation on medical ethics is needed. Patients should be made aware of their rights to medical ethics. Medical ethics investigate ethical issues arising in medicine and healthcare provision by applying the principles of moral philosophy. Medical ethics are often defined as 'the disciplined study of morality in medicine'. This moth century [Reports on issues of patient consent can be traced in the US to the early 18 century . These i century ,5. PaterIn one form or the other, respect for privacy and confidentiality has also been a responsibility of the physicians throughout history ,7. RecenWhile most western countries have enshrined these concepts of informed consent, privacy and confidentiality in federal or state laws and codes of ethics, such law-making is almost non-existent in Pakistan although there have been some recent efforts to create ethical guidelines for research and medical practice. Significantly, Pakistan Medical and Dental Council (PMDC), the regulatory body of medical practitioners has formulated a code of ethics for all doctors, although no concrete steps have been taken to ensure their application . HoweverA cross-sectional study was conducted at general medical out-patient departments (OPDs) of two tertiary care hospitals of Lahore during the period March-June 2005. One hospital was from the public sector while the other was from the private sector. The sample was selected using multistage random sampling. In the first stage, 6 major public and 4 major private tertiary care hospitals of Lahore were listed separately. . One hospital was then selected from each list using simple random sampling. Jinnah Hospital was selected from the public sector, while Shalimar Hospital was the private sector hospital included in our study.In the next stage, the outpatient registration record was used to enroll patients for the study. Records showed that a total of 2800 patients attended the medical OPDs in the two hospitals every month. Therefore, assuming the patient perception of good ethical practices to be 55%  and usinEach patient enrolled in the study was issued a tag for identification. Relevant demographic information was obtained from each patient by a trained data collector (of the same gender as the patient). The same data collector then accompanied the patient during his/her flow through the OPD. These trained data collectors were medical doctors undergoing training in an MPH program. Each doctor-patient interaction was observed and evaluated to fill a peer-reviewed 'client flow analysis form' created in the light of existing literature on the subject ,17-19. EThe assessment of these practices was undertaken in a subjective manner by the data collectors who observed each doctor-patient interaction. It was noted whether doctors took informed consent from their patients before beginning history-taking, beginning physical examination, exposing any part of the body for examination, or discussing treatment options at the end. Confidentiality  was assessed by noting whether there were other people who could potentially overhear the doctor-patient discussion or be told information regarding the patient without prior consent. Taking the patient to another room for examination, or at least taking them behind a screen was categorized as being adequate privacy for the patient.At the end of the OPD visit, subjects were asked questions on whether they were satisfied with the way these principles were followed by the doctors interacting with them. The three (yes-or-no) questions asked from the patient were whether he/she was satisfied with the doctor's practice of informed consent, privacy and confidentiality. A yes to all three questions was taken to mean that in the patient's perception, the ethical principles had been well observed. However, if the patient thought that at least one of the principles had been followed to his satisfaction,  the perception was taken to mean that the ethics had been 'somewhat observed'.Prior consent had been obtained from all doctors so as to be allowed to observe and evaluate any doctor-patient interaction during the study period. However, in order to minimize bias, at no point were the doctors informed of the individual patient selection. Hence they remained unaware of which patient interaction was being graded for ethical practices. This had been made clear to them while obtaining consent for their participation. In Pakistan, the nursing departments are often understaffed so that the role of nurses in the outpatient departments is limited and it is almost always the doctors who obtain informed consent from the patients regarding their examination/treatment. Therefore, nurses were not included in the study.Ethical approval for the study was obtained from the review committee of the Center for Health Research, Lahore. The study was conducted in compliance with the 'Ethical Principles for Medical Research involving Human Subjects' of Helsinki Declaration. . PatientData was entered and analyzed using Statistical Package for Social Sciences (SPSS) version 12.0. Results were computed separately for each of the two hospitals included in the study. Two sample t-test was employed to detect any significant difference between the public and private hospitals in the practices of informed consent, privacy and confidentiality. Chi square test was employed to detect an association between the patients' perceptions and the observations of our data collectors.We enrolled and followed 93 patients in each of the two hospitals. Overall, there were 138 females and 48 males (M:F = 1: 2.8). The mean age of the patients in the public hospital was 34.9  while that in the private hospital was 37.6 . Other demographic details are shown in Table Results of adherence to the practice of informed consent, privacy and confidentiality in each hospital are shown in Table Table Tables The present study was designed with a purpose to assess the actual practice of informed consent, privacy and confidentiality by the doctors through direct observation of the entire process of patient care provided in outpatient departments (OPDs) of public and private hospitals, and correlate these ethical practices with patient perception of doctors' ethical practices. Our results show that the doctors took proper informed consent from very few patients coming to these hospitals. One of reasons behind such practice is that the cultural trends in Pakistan still tend to accept the paternalistic model of medical care. This is in line with the Asian culture as a whole, where the decision-making is often left purely to the doctors or other family members. Studies from Kashmir and Japan reflect similar practices wherein patients are willing to accept what doctors choose for them, while doctors are satisfied with their role of a decision-maker. -23. For While the situation in US was not much different till the 1960s , the curImproper consent of some form was taken from a large number of patients at the private hospital but just a few from public hospital. No informed consent was taken from an alarming proportion of patients (90%) at the public hospital. Even in the private hospital more than half the patients were denied their right to informed consent. On the whole, the practice of informed consent was better at the private hospital but still far from the ideal. Several reasons may account for the differences. Firstly, doctors at private hospitals are better paid than their colleagues in the public sector, something that may translate into better performance at work and greater care for the patients. Secondly, doctors in the private sector are often employed on contracts that need regular renewal. Doctors' work is regularly monitored and assessed, and this renewal is often linked to patient satisfaction with care. Hence doctors in the private sector are more likely to respect the patients' fundamental rights related to their medical management. On the other hand, jobs in the public sector are secure and more or less permanent in nature. At the same time, there is little or no accountability of the doctors since there is usually no effort to elicit patients' opinion about the care provided to them. The results of our study are in line with those from a study conducted in a public sector hospital in Karachi that concluded that the current practice of informed consent was below the internationally acceptable standards . Even thSimilarly, the principle of confidentiality  was also inadequately practised in our study. This is not surprising since even a study in a country like Canada, has shown that quite a few of the family physicians do not fully understand their obligations towards patient confidentiality . FurhterProvision of privacy during physical examinations was also inadequate in both hospitals. However, privacy-related practices were still somewhat better than the practices of informed consent and informational privacy. The private hospital again showed better ethical practices than the public hospital although in this case the difference was not statistically significant. This may be because in both settings, doctors have no choice but to carry out these examinations behind a screen, especially examinations requiring significant exposure. A study conducted at a private hospital in Karachi also shows that patients felt some lack of privacy on a significant number of occasions (47%) . Our figOur study shows that compared to the public hospital, more patients in the private hospital believed that ethical practices were well observed by doctors interacting with them. This is fairly in line with the assessment of our data collectors where principles of informed consent, informational privacy and physical privacy were more often applied in the private hospitals as discussed earlier. We compared whether the patients' perception of these ethical practices matched correctly with the assessment of our data collectors. In 38/93 instances in the public hospital and 24/93 in the private hospital, patients' perception differed with the assessment of our trained data collector. This is a significant number, and again shows that many patients are unaware of, or misunderstand their ethical rights [It is noteworthy, that there are also some other reasons for inadequate ethical practices in Pakistan. For example, although innovative ethical curricula have been shown to improve the confidence and practice of doctors with regards to medical ethics , PMDC doHowever, regardless of the excuses provided for the lack of medical ethics, it should be kept in mind that the principles of informed consent, confidentiality and physical privacy must always be applied in medical practice ,4,6,38.Adherence to principles of ethics in medical practice is inadequate in Pakistan. Formal training in bioethics should be incorporated in undergraduate and postgraduate medical training so that the healthcare providers understand the concept, process and application of medical ethics. Local languages should be utilized in written and verbal consent. Forms for written consent should be easy to understand for even the less educated patients. Every patient should be interviewed and examined in a separate room to ensure informational and physical privacy and the number of medical staff should compliment the patient load at any hospital. Sincere attempts need to be made at legalizing the value and processes of medical ethics and public health programs should aim at making the patients aware of their legal rights to informed consent, confidentiality and privacy.The authors declare that they have no competing interests.AH did the overall supervision, participated in the conception of the idea, preparation of the questionnaire and writing of the manuscript. NF was involved in designing the study, and performing data analysis. SN helped in the preparation of the questionnaire and writing the manuscript. SH helped in writing the protocol, data collection, its entry and analysis. AR participated in the conception of the idea, protocol writing, data collection and analysis. HI participated in the conception of the idea, preparation of questionnaire, data collection and entry. SZI was involved in the overall supervision, data analysis and manuscript writing.The pre-publication history for this paper can be accessed here:


Stress urinary incontinence (SUI) is a common problem. In the Netherlands, yearly 64.000 new patients, of whom 96% are women, consult their general practitioner because of urinary incontinence. Approximately 7500 urodynamic evaluations and approximately 5000 operations for SUI are performed every year. In all major national and international guidelines from both gynaecological and urological scientific societies, it is advised to perform urodynamics prior to invasive treatment for SUI, but neither its effectiveness nor its cost-effectiveness has been assessed in a randomized setting.The Value of Urodynamics prior to Stress Incontinence Surgery (VUSIS) study evaluates the positive and negative effects with regard to outcome, as well as the costs of urodynamics, in women with symptoms of SUI in whom surgical treatment is considered.A multicentre diagnostic cohort study will be performed with an embedded randomized controlled trial among women presenting with symptoms of (predominant) SUI.Urinary incontinence has to be demonstrated on clinical examination and/or voiding diary. Physiotherapy must have failed and surgical treatment needs to be under consideration.Patients will be excluded in case of previous incontinence surgery, in case of pelvic organ prolapse more than 1 centimeter beyond the hymen and/or in case of residual bladder volume of more than 150 milliliter on ultrasound or catheterisation.Patients with discordant findings between the diagnosis based on urodynamic investigation and the diagnosis based on their history, clinical examination and/or micturition diary will be randomized to operative therapy or individually tailored therapy based on all available information.Patients will be followed for two years after treatment by their attending urologist or gynaecologist, in combination with the completion of questionnaires.Six hundred female patients will be recruited for registration from approximately twenty-seven hospitals in the Netherlands. We aspect that one hundred and two women with discordant findings will be randomized.The primary outcome of this study is clinical improvement of incontinence as measured with the validated Dutch version of the Urinary Distress Inventory (UDI). Secondary outcomes of this study include costs, cure of incontinence as measured by voiding diary parameters, complications related to the intervention, re-interventions, and generic quality of life changes.Clinical Trials NCT00814749. Stress urinary incontinence (SUI) is a frequently occurring problem. The Health Council of the Netherlands estimated that yearly 64.000 new patients, of whom 96% are women, consult their general practitioner because of urinary incontinence .In all major national and international guidelines of professional organizations and authorities, it is advised to perform urodynamics prior to invasive treatment for SUI, e.g. the guidelines of the Dutch Urological Association, the Dutch Society of Obstetrics and Gynaecology, International Continence Society and European Association of Urology,3.Usual care in the Netherlands for urinary incontinence in the general practitioners setting is an investigation by history, clinical examination and voiding diary. When there is no clear indication for urge incontinence or neurological disease, the patient will be referred for physiotherapy. In case there is no improvement the patient will subsequently be referred to the gynaecologist or urologist . PatientUrodynamics do not generate major morbidity but are generally considered as unpleasant by the patients, and inhere a risk of urinary tract infections as high as 20% . UrodynaThe assumption is that the urodynamic setting is capable of making a distinction between several pathophysiological mechanisms causing the same micturition symptoms. If this holds true, the outcome of the available treatment options derived from the urodynamic based diagnosis would be better than treatment based on diagnosis made without urodynamics. However, the urodynamic investigations that differentiate between several types of SUI and specify for the type of operation, lack validation and predictive value in individual cases .Moreover, since the introduction of easy to administer midurethral polypropylene slings, a simplified reasoning has found ground that states that every type of SUI is treated in the same way and therefore no urodynamic investigation would be needed.The value of urodynamics has never been the specific subject of a randomized controlled trial . SeveralA retrospective cohort study on TVT has concluded that urodynamics do not have a predictive value on outcome after midurethral sling surgery . In a raThe subjective and objective outcome of surgical intervention with or without preoperative urodynamic investigation has not been compared, with the exception of one retrospective study on colposuspension and one cohort study on TVT ,12. In tThe strong conclusion from the Cochrane Review on the value of urodynamics was that a randomized trial is needed .Thus, the role of urodynamics in the objectivation of SUI in women is nowadays questionable and very much under debate. In 25–30% of the women the symptom of SUI is not demonstrable probably due to the artificial situation during the investigation [If urodynamics are not needed to diagnose types of SUI, this could be to prevent complications of surgery such as an overactive bladder. However in almost half of the patients with overactive bladder symptoms, there are no abnormal detrusor contractions visible on urodynamics . On the The introduction of minimally invasive techniques for SUI therapy, such as the midurethral tension free tape procedure, has led to an enormous increase in the number of operations in the Netherlands. In 1999, 1,600 operations were performed. This number has increased to over 4,000 in 2003 and is expected to be 5,000 by today .We estimate that two thirds of all women with symptoms of SUI who had urodynamics will proceed to surgery and one third will be given another non-surgical intervention which is usually medication. From this calculation it appears that for this indication urodynamics are performed approximately 7500 times per year in the Netherlands.At expected costs of about 300 euro per test, urodynamics stand for 2.25 million euro health insurance charges.In case urodynamics would be omitted, costs of possible extra complications are foreseen. We estimate a maximum of 10% additional urgency complaints ,18. AntiIn conclusion, it is likely that urodynamics do not have a role in the quality of care for women with SUI and that urodynamic testing in women with SUI is not cost-effective.For this study our hypothesis was that there is no difference between outcome of surgery and individually tailored therapy in women with a discrepancy between urodynamic findings and findings from other investigations, such as history and clinical examination. In case of confirmation of this hypothesis, urodynamic investigation in women with predominant SUI could be safely omitted.The primary aim of the VUSIS study is to evaluate whether urodynamic testing is effective in patients with symptoms of SUI in whom surgical treatment is consideredThe VUSIS is a multidisciplinary, multicentre diagnostic cohort study with a randomized controlled trial (RCT) embedded. All women with symptoms of predominantly SUI in whom surgical treatment is considered will undergo urodynamic investigation. Only women with a discordant finding compared to history and physical examination will be randomized. Patients with concordant urodynamics will be registered [see figure The study has been approved by the institutional review board of the Radboud University Nijmegen Medical Centre, in Nijmegen. Ethical approval for this study has been obtained on 02-10-2008, number 2006/197.Eligible patients will be identified by gynaecologists and urologists from participating hospitals in the Netherlands [see Additional file In all patients the following items will be recorded at inclusion:1. History and clinical examination2. 48 h-Bladder (voiding and incontinence) diary3. Validated Quality of Life questionnaires 4. Urinalysis for the detection of urinary tract infection5. Residual urine measured by ultrasoundAll women will undergo urodynamic investigation. Urodynamics will be performed according to International Continence Society standards and consists of free flow and measurement of residual, provocative filling cystometry with abdominal leak point pressure measurement, pressure flow study and a urethral pressure profilometry in rest and during stress. The outWhen the result of the urodynamics does not confirm the history of SUI, or shows relative contra-indications for operation, the investigation is called discordant. Whether a test result is discordant is decided by the attending urologist or gynaecologist. Figure Women with discordant findings on urodynamics will be approached to participate in the randomized controlled part of the study.After they have given informed consent, the patients with discordant test results at urodynamics are randomly assigned to the study or control group. In the study group, the decision for intervention will be based on history and clinical examination only, which will be surgical treatment; a midurethral sling. The choice for the kind of procedure is left to the discretion of the attending doctor. In the control group the decision for therapy will be based on history and clinical examination in combination with the result of the discordant findings on urodynamics. This includes medical treatment, prolonged physiotherapy, pessary treatment, but also surgical treatment can be one of the chosen therapies.All women with SUI, who present at one of the participating hospitals, will be referred to a gynaecologist, urologist or a specifically appointed research nurse for counselling. Eligible women will receive an information sheet. Once women with discordant test results have given consent for the trial, they are randomized through a website, according to a computer-generated randomization sequence. Stratification will be applied for centre. Randomization will be 1:1 for operative treatment and individual treatment.Patients in the RCT will be followed up from trial entry until the end of the study (anticipated average: two years). Follow-up is composed of the same items as recorded at inclusion.After six weeks, six, twelve and twenty-four months patients will visit their attending gynaecologist or urologist. Physical examination will be performed and consists of detection of erosions, stress test for urinary leakage, and measurement of the residual volume. The patients will complete the questionnaires at all moments of follow-up.After the intervention additional therapy is possible in both arms and will be recorded in the Case Record Form.The cohort group will receive the same questionnaires once, at one year after the intervention.The primary outcome of this study is clinical improvement of incontinence as measured with the validated Dutch version of the UDI.Secondary outcomes of this study include costs, cure of incontinence as measured with voiding diaries, complications such as re-operation or overactive bladder symptoms, and quality of life.The trial results will be incorporated in a diagnostic model to compare the current strategy  with the alternative strategy .The study design will enable us to compare the costs and effects of the following strategies:I. Immediate midurethral sling without preceding urodynamic evaluation.II. Urodynamic evaluation in all patients and midurethral sling depending on urodynamic evaluation results.III. Sequential or probabilistic combinations, based on the prior probability of the fact that the urodynamic evaluation will change management.The primary outcome of this study is the improvement of UDI at 12 months after baseline. The power calculation is performed using the non-inferiority assumption. The calculation is based on registration of 600 patients in the cohort study, of whom 200 will have discordant findings. When approximately 50% of the women give informed consent for randomization, 102 women with discordant findings will be randomized (51 to each group). As based on the non-inferiority assumption, the mean improvement in UDI in both groups is expected to be 35 with standard deviation of 10. A difference in mean improvement of 5 or less is considered as non-inferior (power 80% using one-sided testing at 0.05).For each patient, utilization of health care services will be recorded prospectively, using Case Record Forms, including urodynamic testing, surgery for SUI, re-operations, medical treatment for detrusor instability, care for urinary incontinence, and care for urinary retention. By multiplying these volumes of care with unit cost prices, direct medical costs incurred by SUI during the follow up period will be calculated for each patient. For unit cost prices, national guidelines will be used . For costs of care for urinary incontinence and urinary retention, data from the literature will be used, converted to 2006 prices. We incorporated the health related quality of life questionnaire euroqol 5D in our study to be able to calculate QALYs , which is a measure of health outcome. A QALY is the change in quality of life induced by the treatment multiplied by the duration of the treatment effect and it provides the number of QALYs gained. QALYs can then be related to medical costs to arrive at a final common denominator of cost/QALY. This parameter can be used to compare the cost-effectiveness of the treatment.Multivariate analysis of covariance with group, centre and the baseline covariate as independent variables will be used to estimate differences in improvement of the UDI after 12 months between the groups with 95% confidence intervals. As the UDI data are likely to be skewed, data will be log transformed prior to analysis. Other variables (i.e. IIQ) will be analyzed similarly.Patient recruitment began in January 2009 and is planned to continue until January 2010. The follow-up has a duration of 24 months, so will continue until January 2012. The study is conducted in cooperation with several centers ensembled in the urogynaecology consortium. Most of the clinics have disposition over a research nurse, who attributes in administration and completion of the case record forms. All data are collected web based.The outcome of the study will be important for the debate on the value of urodynamics. In the current international operative practice for SUI there is a huge increase in the number of operations. Hence the value of time consuming and costly urodynamic investigations should be very clear. The study is planned to be a starting point for a doctor's thesis. The results of our study will be submitted to different national and international scientific societies such as the International Continence Society and the International Urogynecologic Association, and is planned to be published in international scientific journals.The authors declare that they have no competing interests.KK and MV were responsible for the identification of the research question, and contributed to drafting of the study protocol. JH and BW have contributed to the development of the protocol and study design. All authors discussed the study design and commented on the protocol. SL was responsible for the drafting of this paper. All authors provided comments on the drafts and have read and approved the final version.The pre-publication history for this paper can be accessed here:Participating hospitals in the Netherlands. This list gives an overview of the participating hospitals in the VUSIS study, all hospitals are located in the Netherlands.Click here for file


Expressed sequence tag (EST) collections are composed of a high number of single-pass, redundant, partial sequences, which need to be processed, clustered, and annotated to remove low-quality and vector regions, eliminate redundancy and sequencing errors, and provide biologically relevant information. In order to provide a suitable way of performing the different steps in the analysis of the ESTs, flexible computation pipelines adapted to the local needs of specific EST projects have to be developed. Furthermore, EST collections must be stored in highly structured relational databases available to researchers through user-friendly interfaces which allow efficient and complex data mining, thus offering maximum capabilities for their full exploitation.We have created EST2uni, an integrated, highly-configurable EST analysis pipeline and data mining software package that automates the pre-processing, clustering, annotation, database creation, and data mining of EST collections. The pipeline uses standard EST analysis tools and the software has a modular design to facilitate the addition of new analytical methods and their configuration. Currently implemented analyses include functional and structural annotation, SNP and microsatellite discovery, integration of previously known genetic marker data and gene expression results, and assistance in cDNA microarray design. It can be run in parallel in a PC cluster in order to reduce the time necessary for the analysis. It also creates a web site linked to the database, showing collection statistics, with complex query capabilities and tools for data mining and retrieval.. This site also provides detailed instructions for installation and configuration of the software package. The code is under active development to incorporate new analyses, methods, and algorithms as they are released by the bioinformatics community.The software package presented here provides an efficient and complete bioinformatics tool for the management of EST collections which is very easy to adapt to the local needs of different EST projects. The code is freely available under the GPL license and can be obtained at  Recent advances in high-throughput sequencing technology have provided a mechanism to gain genomics insight on species without a complete genome sequence by generating expressed sequence tags collections . ESTs aDue to the high number of sequences in most ESTs datasets, different computer-based methods are required to process, annotate, record, display, and retrieve the data. These methods are applied sequentially from the input raw sequence data to the final searchable, fully annotated EST database, and knowledge of computing science is needed to arrange them in an efficient and reliable analysis pipeline. The usual approach to this problem is to build an in-house prepared set of script programs that semi-automates the analysis. This solution requires highly skilled bioinformatics staff capable of programming and using the scripts, and is inefficient because a different pipeline should be prepared for each project, and because the resulting semi-automated process is difficult to maintain and lacks reproducibility. It would therefore be more convenient to use a well tested, freely available automatic tool. In our opinion, this application should ideally have the following features: 1) to be fully automated in a pipeline covering all the steps from the input chromatogram files to a clean, annotated web-searchable EST database, 2) to be highly modular and adaptable, 3) to be able to run in parallel in a personal computer (PC) cluster, thus benefiting from the multiprocessing capabilities of these systems, 4) to use third-party freely-available programs, in order to ease the incorporation of the improvements made by others programmers, 5) to include a highly-configurable and extensible user-friendly interface to perform data mining by combining any search criteria, fitting the final user needs, and 6) to be based on an open source license to allow a continuous development by a community of users and programmers, as well as its customization for the particular needs of different projects.Some applications, including PipeOnLine , ESTAP , PartiGeIn an attempt to fulfill the need for an analysis software which accomplishes all the mentioned requirements, we have developed a software package, namely EST2uni . This pipeline has been tested through three genomics projects which we are involved in: Citrus Functional Genomics Project , ChillPeThe EST2uni package consists of: 1) a set of Perl modules that perform both the EST analysis and the database creation, 2) a set of PHP scripts to generate the browseable database-interacting web pages, and 3) a set of PHP modules with the functions called by the PHP scripts. The EST analyses are performed by the main Perl script, which manages the execution of several third-party, freely-available, standard tools commonly used for EST analysis, as well as a number of home-made analyses. The running parameters used by the pipeline and the external tools are stored in a well-documented, plain text configuration file which can be modified with a text editor. This configuration file contains all the required information to run the pipeline, like file paths, analyses to be performed, and paths and parameters for the programs installed to run the analyses. The software package is distributed with a single minimal-analysis example configuration file where default parameters used by EST2uni and external tools can be inspected and modified if desired. Running parameters considered as default ones by developers of the external tools used have been selected as a starting point in this example configuration file. Each annotation analysis is controlled by a different Perl module, and the results from different analyses are stored at independent tables in the database to facilitate the future addition of new methods and analyses. As a consequence, all analyses can be run independently at different times, and the annotation modules could be re-run at any time with updated external databases. Parallelization is also managed by an independent Perl module which splits the analysis in small tasks, manages their execution in different nodes, and join the results, using the load distribution tool Condor, as explained above. It should however be easy to hack the code in order to use a different load distribution tool.The package is distributed with a complete working web site built by EST2uni using PHP. The visual design is controlled by using CSS, and special attention has been paid to the modularity of the PHP code, so that it is very easy to add new functionalities to the web pages and to customize their appearance. This adaptation should be easily performed by any project administrator because the PHP code appearing on the browseable web pages is minimal . MySQL authentication can be used to maintain the privacy of the data of the different projects.A standard EST analysis pipeline includes the following steps: 1) EST pre-processing, 2) EST assembly, and 3) functional and structural annotation of the resulting unigenes. Below we describe the analysis and methods currently implemented in EST2uni  and/or preferences . When no clone in an unigene satisfies all the above mentioned restrictions, these can be progressively relaxed until a representative is selected. Since clones from different unigenes in a superunigene are very similar, they are expected to have the same mRNA targets under standard hybridization conditions when used as probes in cDNA microarrays , and supUnigenes can be annotated using different modules, following user specifications in the configuration file. SSR microsatellites can be detected with sputnik . PutativFor functional annotation, different similarity search tools can be used. Unigene comparisons against a set of user-defined nucleotide and/or protein databases are carried out by BLAST  using thEST2uni is ready to incorporate microarray expression data for each unigene. Normalized expression data coming from different arrays and experiments can be easily added to the database and referred to the corresponding unigenes. Database can also store details about biological samples, tissues and conditions used for each experiment, while referencial integrity is required to reproduce the standard work flux in microarray experiments. There are several ways of retrieving this expression data from the web site depending on the number of unigenes involved. A graphical representation of expression data in all the microarray experiments done is created for each unigene, which is accesible from the individual unigene web pages. Bulk data retrieval is also posible, so that expression data for all unigenes or for any set of unigenes obtained in a query can be easily obtained. Furthermore, this data can be directly sent to the GEPAS analysis suite  or downlExecution times in standard EST analysis pipelines are usually very long because of the high number of sequences to be processed and the big computational costs of some analyses performed. EST2uni can achieve a reduction in these execution times by parallelization, because it can be run either in sequential mode or in a parallel environment using a load distribution tool. When run in parallel mode, EST2uni divides the analysis in several tasks that are asigned to different processing nodes and manages the execution of these tasks with the aim of keeping the different nodes busy, thus taking maximum advantages of the processing resources available in the system. These tasks are created by splitting the set of sequences to analyze in several chunks, and running independent subanalysis in parallel. EST2uni sends these jobs to the load distribution tool cue and checks that they run as expected. The pipeline is distributed with the code necessary to use CONDOR  as the lAlthough some of the work load is done by third-party tools with its own parallel implementations , we decided to use this EST2uni-driven unique model of parallelization for the whole because this approach enables to run in parallel even those analysis tools which are not designed to be run in that way. Moreover, because the different parallel tools have different parallelization infrastructures and requirements, the parallel code implemented in EST2uni is directly applied to their sequential implementations, so avoiding use of the parallel versions. Anyway, if a load distribution tool cannot be installed, the pipeline is also able to take advantage of parallelization by using the parallel versions of the third-party capable software like mpiBLAST  or HMMERRegarding the ability of EST2uni to properly manage parallelization in the analysis of big EST collections, Figure EST2uni creates and populates a structured MySQL relational database where the results of the different analyses are stored automatically by the pipeline. This database is key element for the pipeline, since the different analysis modules used in the pipeline get their input data from the database and write their output to it. The database contains information about all the data obtained, from cDNA libraries, isolated clones, and raw sequences to analysis results, as well as additional information about genetic maps and markers or expression data provided by users, or the representative clone selected for each unigene. It can also include information about the researchers and research centers involved, as well as journal publications or public accession numbers of sequences derived from the project. Access to the database can be password-protected in order to keep the data private.EST2uni includes a web site interface to the database through a powerful data mining tool with an advanced querying interface and high integration among all kinds of data Figure . It is nThe unigenes obtained as query results can be inspected individually, but also bulk downloads of the sequences, names or orthologues are allowed. In order to globally analyze the Gene Ontology terms of the result set, it is possible to automatically submit the orthologues in some model species to Babelomics . In a siThe web site also provides some statistics of the full EST collection, like contigs/singletons distribution, unigene length distribution, number of ESTs per unigene distribution, or number of unigenes annotated with the different functional and structural criteria. It also provides statistics for each single library, like number of ESTs, singletons, contigs, unigenes, novelty, and redundancy. Tables for global and library-specific Gene Ontology annotations are also provided where unigenes annotated in each functional category can be directly retrieved, and libraries can be compared for the Gene Ontology annotation of their unigenes.Although other tools which perform EST analysis and database creation have been developed, none of them accomplishes all the characteristics we consider essential for the research community Table . First, We have developed an EST analysis tool capable of converting, in a fully automatic and time-effective way, a set of trace files or plain sequences in a highly structured and annotated EST database with a user-oriented web interface for efficient data mining. The EST analysis pipeline includes standard pre-processing, clustering and annotation programs, and can incorporate gene expression data to the database. The software is highly modular, which facilitates the incorporation of new methods and analyses, meeting the needs of different EST projects. Running options are also easily adapted to local needs by simply modifying an extensively documented single configuration text file which provides the parameters to be used by the different analyses. Once configured, the pipeline runs without user assistance, from the input files to the final annotated EST database. The EST analysis can be run either in a single standard computer, or in a PC-cluster, thus taking advantage of the multiprocessing capabilities of these systems, which allows reduction of the time required to complete the EST analysis. The web site deployed is a powerful data mining tool with a complex, yet easy to use, query interface, that also provides functionalities for bulk data retrieval and download. It also eases the use of several tools, like primer design and BLAST searches against the database. Access to the data can be restricted by passwords to keep the data private. The development team of EST2uni is continuously improving the end-user interface, the quality of the analyses, and the integration with other tools. We have set up a public subversion server , and a mTo sum up, we conceive this bioinformatics tool as an open and evolving project, and all the bioinformatics community is invited to participate, using and improving the tool that we have created for our specific EST projects  declares that there are no competing interests.JMB and JF conceived and designed the pipeline structure, the database schema, and the web site, wrote the code, tested EST2uni as end-users, and drafted the manuscript. FG wrote the code for parallelization, tested its efficiency, and drafted the parallelization section of the manuscript. AR managed the parallelization project, and critically revised the manuscript. VC and FN critically revised the manuscript, and coordinated the Citrus Functional Genomics Project and the Spanish Melon Genomics Project, respectively, which provided the EST data which were utilized in the development and testing of EST2uni. JMB guided and coordinated the development of EST2uni. All authors read and approved the final manuscript.


Electronic syndromic surveillance for early outbreak detection may be a simple, effective tool to rapidly bring reliable and actionable outbreak data to the attention of public health authorities in the developing world.Twenty-nine signs and symptoms from patients with conditions compatible with infectious diseases are collected from selected Provincial hospitals and analyzed daily. Data is e-mailed on a daily basis to a central data management and analysis center. Automated data analysis may be viewed at the hospital or the Early Warning Outbreak Response System (EWORS) hub at the central level .The Indonesian Ministry of Health (MoH) has adopted EWORS since 2006 and will use it as a complementary surveillance tool in wider catchment areas throughout the country. Socialization to more users is still being conducted under collaboration of three Directorate Generals (DGs) of the MoH; DG of NIHRD, DG of Medical Services and DG of Communicable Disease Control and Prevention. Currently, EWORS is being adapted to facilitate detecting a potential outbreak of pandemic influenza in the region, and automated procedures for outbreak detection have been added. Indonesia is the largest archipelago with approximately 17,700 islands  in Indonesia is a hospital-based network of computerized linkages that provides syndromic surveillance for early detection of infectious disease outbreaks. It establishes trend information that helps to distinguish epidemic from endemic disease activity. The objective of the EWORS program is to get information about infectious disease activity more quickly, and thus allow more timely public health interventions .LitBangKes) of the Indonesian Ministry of Health (MoH). The EWORS program complements the existing reportable disease surveillance conducted by the Surveillance Directorate of the Indonesian CDC, which uses a manual, paper-based system to collect data from Provincial and District Health Offices.The EWORS program was developed in 1998 by the U.S. Naval Medical Research Unit #2 (NAMRU-2) and the National Institute of Health Research and Development (NIHRD)  has trained 35 sites in five countries  to use the EWORS program. Worldwide, EWORS is now available in six different languages .The symptom- and syndrome-oriented approach makes EWORS capable of detecting outbreaks of new diseases, including man-made biological threats. Currently, EWORS is being adapted to facilitate the detection of potential initial outbreaks of pandemic influenza in the region. Automated procedures for outbreak detection have also been added.Vibrio cholera infection or hemorrhagic manifestation suggestive of dengue virus infection (dengue hemorrhagic fever). Additionally, the EWORS's symptom-oriented approach makes it capable of detecting outbreaks of new diseases, including man-made biological threats. Intensive on-site training and subsequent upgrading and re-training of each hospital's staff are conducted to ensure standardization of data collection and analysis within and between sites.We selected a number of major public hospitals in some provinces as EWORS sentinel surveillance sites, mostly located in areas with substantial epidemic potential. Twenty-nine signs and symptoms, as well as demographic data, e.g., age, sex, address, are collected on a daily basis from patients visiting a pediatric clinic, internal medicine or emergency room with conditions compatible with a suspected infectious disease and recorded on a standardized form. At the end of each day, the forms are submitted to the EWORS operator for data entry into the system. Data is transmitted on a daily basis via e-mail to the central data management and analysis center (hub) at the National Institute of Health Research and Development, Ministry of Health and stored securely both in the hospital computer's hard drive as well as in the SQL server at the data center. Data may be analyzed at the hospital or the hub for case count trends over time, as well as demographic trends in abnormal increases of cases with clinical signs and symptoms consistent with a syndrome, such as watery diarrhea, that could reflect a In 1999, EWORS was implemented in 11 hospitals in 8 provinces. In 2008, only 9 hospitals in 7 provinces continued to participate in the program  in the west, spread to Jakarta (Java Island) and then to Bali Island. It also spread to Makassar, Sulawesi Province, in the north. What we observed was an excess of fever hemorrhagic cases starting in Medan in November 2003  must be well trained and have delegation of authority to continue this program. The data entry clerk should have suitable work space, ideally a room dedicated to EWORS.The program manager must be able to analyze the data in a manner that is clear, standardized, and useful for public health control measures. The analysis should be more frequent during an outbreak. This program needs team work among all the people who make the system work, from the hospital to the provincial or district health officer. The delivery system of the data can be day by day.Discussions are currently underway about expanding the EWORS system to all provincial hospitals in Indonesia in 2008. We are also considering including private hospitals in the EWORS program. We would like to give a Quality Award to hospitals who properly maintain the EWORS program. We have improved guidance on data analysis in 2007. In 2008, we plan to study EWORS data using a sensitivity test in nine hospitals, so we can compare EWORS data with routine surveillance data collected at the district health office.The EWORS program was developed to complement the existing disease surveillance and provide a simple, flexible surveillance system that detects disease outbreaks early after their onset. The program complements the existing reportable disease surveillance conducted by the Surveillance Directorate of the Indonesian CDC, which uses a manual, paper-based system to collect data from Provincial and District Health Offices. The program's success is dependent on many factors such as human resources, hospital commitment, computer networking, and technical expertise. Because of limited clinical laboratory data in many developing countries, widely implementing the EWORS syndromic surveillance system may allow for more rapid mapping of infectious disease outbreaks and aid control efforts.Currently, EWORS is being adapted to facilitate detection of a potential outbreak of pandemic influenza in the region, and automated procedures for outbreak detection have been added.The authors declare that they have no competing interests.The corresponding author is the chief coordinator of EWORS activities in Indonesia.


Internal systems for quality and safety were assessed in 89 hospitals in six European states, by external teams using standardised criteria and procedures, as part of the Methods of Assessing Response to Quality Improvement Strategies (MARQuIS) project. The assessments were made primarily to identify the current use of quality management systems in the sample hospitals, and also to demonstrate a potential tool for comparable assessment of hospitals in general. The large majority of the hospitals had a formal, documented infrastructure to manage quality and safety, but a significant minority had no designated mission, programme or coordination. In two-thirds of hospitals, the governing body was active in defining policy and programmes for improvement, and received reports on quality, safety and patient satisfaction at least once a year. The brief on-site assessments identified systematic variations, within and between countries, in structures and processes of governance and to document the uptake of best practice. Unacceptable variations in practice could be reduced, to the benefit of consumers and providers, by developing and publishing basic organisational standards relevant to all European states. The simple assessment criteria designed for this project could be developed into a practical tool for self-assessment, peer review or benchmarking of hospitals across national borders. This assessment, combined with explicit, relevant and achievable standards, could provide a vehicle to promote the voluntary uptake of best practice and consistency in quality and safety among hospitals in Europe. Leadership and organisational culture are widely claimed to be essential ingredients of an effective programme to improve quality and safety. Their prevalence in healthcare organisations is hard to estimate directly, but may be inferred from proxy measures of organisational structure and activity.In North America, the responsibilities of hospital trustees and managers for performance, quality and safety—and the required basic structures and systems—have long been defined. In Canada, for example, a panel on accountability in the voluntary sector specifically identified the role of the governing body to include “responsibility for outcomes, including problems created or not corrected by an organisation or its officials and staff”.The report of a study of four Organisation for Economic Co-operation and Development (OECD) countries has commented“It was formerly taken for granted that the institutions of professional self-regulation would ensure adequate quality of care. However, as scandals and evidence of medical errors and quality shortfalls have emerged in various OECD countries, doubt has been cast on the ability of those institutions to live up to their responsibilities.”In eastern Europe, the devolution of hospital responsibilities from central to local government has led, in the absence of effective control mechanisms, to “an accountability vacuum” in the region.In the UK, the public inquiry into management failures in a provincial teaching hospital identified a chain of root causes from local management up to the Department of Health.Hospital governance was not the principal focus of the Methods of Assessing Response to Quality Improvement Strategies (MARQuIS) project,The primary aim of the study was to assess the relationship between quality improvement strategies and the (self-reported) compliance to quality requirements for cross-border patient care and to get additional information to validate the findings of a preliminary questionnaire.to compare results from questionnaires with information obtained from different methods and to validate it by “triangulation”;to obtain detailed evidence of the institutionalisation of quality and safety, and the use of different strategies, including descriptive variables of hospital structure, process and performance.The secondary aim was to develop and test a simple tool and procedures that could be used for self-assessment or peer review. There are few published precedents to multinational on-site hospital assessment and comparative reporting. Quantitative data-based studies, such as the Performance Assessment Tool for Quality Improvement in Hospitals (PATH) project,It was thus necessary to build on a variety of models in order to design an innovative assessment tool to meet the objectives and constraints of the MARQuIS project.The aim was not to promote change in the quality improvement of the hospitals but to describe them according to criteria which had been defined as important for this research project. For that purpose, the methodology was different from that used for organisational development, such as accreditation. Ideally, the hospitals would have been totally “blind” to the assessments and the criteria to avoid distorting the results, but, in reality, the hospitals had to have advance warning in order to consent to participate, to schedule visits and to share the burden of data collection. The assessment criteria and procedures would have to be relevant, understandable and measurable not only in a range of hospitals  but also in a variety of political, management and funding systems.To fit within the available time and funding, and to minimise complexity and observer variation, several principles were adopted:Organisation: coordinators for each participating country would arrange the recruitment and cascade training of a cadre of visitors , based on training given to all the country coordinators at one joint workshop.Assessment teams: visits to selected hospitals would be organised by country coordinators; each team would comprise two members, without interchange of assessors between countries.Visit schedule: each would be scheduled over 1.5 days; the primary data collection would take 12 man-hours.Hospital preparation: to minimise preparation time for the hospital, there would be no self-assessment.Assessment tool: to focus on documentary evidence and observation rather than interview with staff; minimal analysis, interpretation or free text would be required from visitors.Assessment procedures: would rely on hospitals to collect documentary evidence before the visit, but avoid direct access to patients, or their personal records; would limit the number of locations visited within the hospital and rely on representative tracers and small sample sizes.The criteria were designed to relate to values and policies identified in previous work packages; to be verifiable from documentation, interview or direct observation; and to be based as far as possible on existing, tested external assessment criteria for internal systems.The contents of the preliminary survey questionnaire were designed around the quality dimensions that were adopted for the WHO PATH indicators project: clinical effectiveness, production efficiency, staff orientation, responsive governance, and, especially, safety and patient-centredness. The survey questions were then mapped against the classification of quality strategies and tools published by WHOIterative analysis and discussion with country coordinators produced a prototype version for testing in two sites  in October 2006. This included a list, provided in advance to the hospitals, of 88 documents that the visitors needed to access on site to evidence some 90% of the criteria. The documents included minutes, reports, policies and procedures at hospital and department level.A five-point scoring system was adopted to differentiate between various stages in the development, use and impact of quality systems. In general, the scale reflected: A: exceptional compliance >90%;B: extensive compliance 66–90%;C: broad compliance 41–65%;D: minor compliance 15–40%;E: negligible compliance <15%. The percentages were more as a guide rather than as a statistical value, but helped to describe a non-parametric distribution of variation between hospitals. In some instances, intermediate values were not permitted, such as where a “yes” or “no” answer was required.Lessons from the test sites  were combined with feedback from the research partners and the country coordinators to produce a final version. This comprised 233 criteria under nine headings .The MARQuIS field test had two phases: the first phase consisted of the assessment of the quality improvement system in a sample of European hospitals using a self-administered questionnaire. The second phase was the on-site external assessment of a sample of 105 of the 389 hospitals that answered the questionnaire.level of maturity of their quality improvement as determined by a selection of questions from the MARQuIS questionnaire ;number of hospitals per country that had answered the questionnaire ;type of hospital—teaching, university, non-teaching;representativeness of the hospitals from the group categorised as “known to deliver cross-border care”.Country coordinators confirmed consent of hospitals to on-site assessments and coordinated schedules and logistics. The visiting team received, 1 week in advance, a basic descriptive profile of the hospital extracted from the questionnaire response, but were completely blind to the detailed responses. Hospitals received a list of required documents in advance, but no other detail of the assessment tool.The Hospital Programme for Europe  was responsible for overall coordination of the site visits and for monitoring the achievement of agreed schedules. HOPE also set up a register of frequently asked questions from teams in the field and a hotline for technical problems on-site.Data were collected from January to April 2007. Most external assessments took 2 days, even when the schedule was adapted to the size and the number of departments to be assessed in each hospital. About 90% of the criteria were directly assessed based on hospital documentation, 5% on information directly asked of hospital staff and the remaining 5% were directly observed by the surveyors. Surveyors sent a completed report format for each of the hospitals to the country coordinator for checking completeness and consistency before submission to the project coordinator (FAD) for validation and compilation into one general database prior to statistical analysis with SPSS V.15.Although all the hospitals participating in the MARQuIS field test had originally agreed to participate in the external assessment, some of them later declined. The most common reasons for not participating as reported to the country coordinators were being too busy to handle a 2-day visit , and changes in the management team (current managers were not the ones who had agreed participation and were not interested in the project). Despite assurances to hospitals that the resulting data would remain confidential to the research project, several hospitals were discouraged by anxieties of possible repercussions from participation. Of the initially planned 105 hospitals, 89 were finally included in the external assessments. The distribution of these hospitals by country is shown in The results relating to ward level, in particular to patient safety and cross-border care, are described in separate papers.Hospital mission statements were reviewed to check if they explicitly stated that the hospital was committed to quality and safety. Fifteen hospitals did not have an official published mission, so they could not be included in this analysis. Of the 74 hospitals that had a mission statement, 89% explicitly committed the organisation to quality improvement, whereas 50% committed the organisation to improving safety.Governing body responsibilities and involvement with the hospitals’ quality improvement system were specifically assessed by checking if they had directly participated in some quality improvement activities during 2006. The degree of extensive or full participation is given in Governing bodies without a mission statement received less information on quality and safety than those with such a statement. Those with a statement which specified commitment to quality and safety  received more information than those which did not. Almost two-thirds of them approved an annual programme for improvement, half received regular reports on quality and safety, and received reports on surveys of patient experience .In 73 of the hospitals assessed (82%), there was a committee assigned to quality improvement; two-thirds of these held three or more meetings in the previous year, whereas the remainder met more rarely  or had not kept any written records . A documMost hospitals (78%) had a designated leader of quality improvement directly accountable to the chief executive officer (CEO) ; a few mPersonnel records were reviewed for medical and nursing staff. The content of medical staff files  was rated as appropriate (extensively or fully compliant) in 75% of hospitals . For nurFormal review of individual medical staff once every 3 years to determine their continued competence to provide patient care services was rated extensive or full in a minority (27%) of hospitals. Qualified nurses had an appraisal and development plan documented annually in almost half the hospitals assessed.There is wide variation within and between six European countries in the management of quality and safety in hospitals. In some hospitals, basic systems are lacking; in others they exist but do not function. This should be of concern to patients, providers, funding agencies and governmentsValuable experience could be shared between hospitals through a voluntary code of European practice, based on the findings of this MARQuIS study, the recommendations of other European research projects, and other authoritative guidance and directivesCompliance with this common code could be promoted by voluntary self-assessment and peer review, using a measurement tool similar to the one designed for the external assessment of hospitals in this studyThe uneven representation of the countries involved in this study inhibits direct correlations with national systems, policy, legislation or culture but represents a spectrum of reality. The number of hospitals visited and the depth of investigation were limited by practicalities of time and money but were sufficient to show wide variations. Whenever possible, if one given hospital declined to participate, another hospital with similar characteristics was selected as a “replacement” in order to mitigate the effect of self-selection.Few queries were received from the survey teams while in the field, but interpretation of terms such as “teaching accreditation” and “governing body” needed clarification. Discrimination between quality and safety  may have been artificial. Omission of “safety” might result either from local interpretation  or from the relatively low level of awareness about the significance of patient safety as a distinct quality dimension. Although the assessment tool was progressively abbreviated and simplified before it was applied, several teams felt pressed for time to collect the required data. Nevertheless, time constraints led to compromises both in the design and application of the tool, including:bias towards the observable: reliance on retrieval and completeness of management records;simplicity rather than sophisticated and comprehensive analysis and explanation;minimal dialogue with clinical staff and none with patients;reliance on representative tracers ;small sample sizes .Interobserver variation within and between countries may have been reduced by initial joint training and written guidelines but may have been enabled by translation of the tool into local language, in cascading of training at national level, and by differing cultural assumptions and local health systems.The large majority of hospitals in this study met common expectations of internal quality systems—planning, leadership, committees, guidelines and activities—but few could demonstrate improved procedures, let alone outcomes. In many hospitals, mission statements, plans, committees and systems were evident only on paper.Top-level commitment and leadership are frequently stated requirements to develop an organisational culture for effective improvement in quality and safety. Most governing bodies in this study demonstrated this commitment by setting and monitoring policies and procedures. A small proportion either did not document or were not involved in leading the agenda for quality, safety or patient satisfaction. In four out of 10 hospitals, the governing body had not approved an annual programme or received formal reports on quality, safety or patient satisfaction during the past year.In several countries, litigation, legislation or public inquiries have made clear that governing bodies may be held liable for failures of systems and individuals within the hospitals which they govern. Even if this legal principle has not yet been established in every European country, governing bodies may be well advised to take an active role in defining, measuring and improving standards in healthcare.Although most hospitals have a formal infrastructure to manage quality and safety, a significant minority have no designated coordinator, documented programme or committees. “Quality” committees were documented in all but 20% of hospitals in this study, but one in 10 had not met in the past year.Professional clinical staff accepted corporate responsibility for the quality of care in most hospitals, but were accountable to the governing body for this in only a minority of hospitals . The principle, long adopted in North America, of at least 3-yearly review of medical staff  has clearly not reached European hospitals; 75% have no such system.The organisation and management of clinical staff are key determinants of hospital quality systems, particularly relating to doctors, and in the private sector. The structured systems of North America, such as medical staff bylaws, credentialling and peer review, deserve attention in Europe to fill the evident gap in professional accountability, self-regulation and clinical governance.Apparently, in a minority of hospitals, there is no leadership of quality and safety by the professions, the management or the governing body. The raw figures gathered in this study give no insight into why some hospitals appear to show so little interest in issues such as safety, performance or patients’ experiences. Lack of litigation, competition, comparative information or financial incentives may sustain a tradition of perceived security in hospitals.Corporate responsibility lies primarily with governing bodies of individual hospitals but public sector ministries and private sector regulators must also share the burden of stewardship. Accountability and structures should be embedded in guidance routinely issued by regional and national authorities.The project overall focused on the quality requirements for cross-border patients within the European Union, including different quality strategies at a national level and how these have been applied by hospitals in a sample of states. This paper focuses on how the on-site external assessments were carried out and discusses a subset of the resulting findings which relate to hospital governance, and the implications of both for organisational development and harmonisation of hospitals in general.Despite its limitations this study has generated some cogent questions for professions, managers, governing bodies and regional and national health authorities about the nature of governance and accountability. The familiar trappings of quality systems found in most of the hospitals—mission statement, committees and coordinators—are not consistently effective in assuring professions, managers, governing bodies or patients of quality and safety in their hospitals. And the small proportion of hospitals which have no such systems should be a concern both to their responsible authorities and to the populations they serve. Many of these issues cross national borders but remain the responsibility of individual states. Yet the European vision, including cross-border patient care, medical tourism, market competition and reciprocal recognition of clinical training, demands more clear and consistent definition of the organisation of hospital services and accountability for the duty of care.Some European Union member states, such as France, Ireland and the UK, have already defined and published organisational standards for hospitals, and established a national body to monitor compliance. Some, such as Spain and Italy, have devolved a national intention for standards-based assessment to regional governments. Some states, such as Netherlands and Poland, have third party, voluntary accreditation, with varying incentives for participation.This study has shown many opportunities for improving healthcare services by sharing experience of effective quality management, both within and between countries. Even without statutory or governmental enforcement, best practice and guidance from many sources could usefully be developed into a voluntary code of conduct for all hospitals in Europe. The measurement tool, piloted in this project, could be developed into a practical mechanism for voluntary self-assessment or peer review for organisational development of individual hospitals and to promote consistency of quality and safety for patients across European borders.