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1.  Task-oriented evaluation of electronic medical records systems: development and validation of a questionnaire for physicians 
Background
Evaluation is a challenging but necessary part of the development cycle of clinical information systems like the electronic medical records (EMR) system. It is believed that such evaluations should include multiple perspectives, be comparative and employ both qualitative and quantitative methods. Self-administered questionnaires are frequently used as a quantitative evaluation method in medical informatics, but very few validated questionnaires address clinical use of EMR systems.
Methods
We have developed a task-oriented questionnaire for evaluating EMR systems from the clinician's perspective. The key feature of the questionnaire is a list of 24 general clinical tasks. It is applicable to physicians of most specialties and covers essential parts of their information-oriented work. The task list appears in two separate sections, about EMR use and task performance using the EMR, respectively. By combining these sections, the evaluator may estimate the potential impact of the EMR system on health care delivery. The results may also be compared across time, site or vendor. This paper describes the development, performance and validation of the questionnaire. Its performance is shown in two demonstration studies (n = 219 and 80). Its content is validated in an interview study (n = 10), and its reliability is investigated in a test-retest study (n = 37) and a scaling study (n = 31).
Results
In the interviews, the physicians found the general clinical tasks in the questionnaire relevant and comprehensible. The tasks were interpreted concordant to their definitions. However, the physicians found questions about tasks not explicitly or only partially supported by the EMR systems difficult to answer. The two demonstration studies provided unambiguous results and low percentages of missing responses. In addition, criterion validity was demonstrated for a majority of task-oriented questions. Their test-retest reliability was generally high, and the non-standard scale was found symmetric and ordinal.
Conclusion
This questionnaire is relevant for clinical work and EMR systems, provides reliable and interpretable results, and may be used as part of any evaluation effort involving the clinician's perspective of an EMR system.
doi:10.1186/1472-6947-4-1
PMCID: PMC356923  PMID: 15018620
2.  Modification of the mean-square error principle to double the convergence speed of a special case of Hopfield neural network used to segment pathological liver color images 
Background
This paper analyzes the effect of the mean-square error principle on the optimization process using a Special Case of Hopfield Neural Network (SCHNN).
Methods
The segmentation of multidimensional medical and colour images can be formulated as an energy function composed of two terms: the sum of squared errors, and a noise term used to avoid the network to be stacked in early local minimum points of the energy landscape.
Results
Here, we show that the sum of weighted error, higher than simple squared error, leads the SCHNN classifier to reach faster a local minimum closer to the global minimum with the assurance of acceptable segmentation results.
Conclusions
The proposed segmentation method is used to segment 20 pathological liver colour images, and is shown to be efficient and very effective to be implemented for use in clinics.
doi:10.1186/1472-6947-4-22
PMCID: PMC539360  PMID: 15588332
3.  GPs' decisions on drug treatment for patients with high cholesterol values: A think-aloud study 
Background
The purpose was to examine how General Practitioners (GPs) use clinical information and rules from guidelines in their decisions on drug treatment for high cholesterol values.
Methods
Twenty GPs were presented with six case vignettes and were instructed to think aloud while successively more information about a case was presented, and finally to decide if a drug should be prescribed or not. The statements were coded for the clinical information to which they referred and for favouring or not favouring prescription.
Results
The evaluation of clinical information was compatible with decision-making as a search for reasons or arguments. Lifestyle-related information like smoking and overweight seemed to be evaluated from different perspectives. A patient's smoking favoured treatment for some GPs and disfavoured treatment for others.
Conclusions
The method promised to be useful for understanding why doctors differ in their decisions on the same patient descriptions and why rules from the guidelines are not followed strictly.
doi:10.1186/1472-6947-4-23
PMCID: PMC539306  PMID: 15596005
4.  Quantitative evaluation of recall and precision of CAT Crawler, a search engine specialized on retrieval of Critically Appraised Topics 
Background
Critically Appraised Topics (CATs) are a useful tool that helps physicians to make clinical decisions as the healthcare moves towards the practice of Evidence-Based Medicine (EBM). The fast growing World Wide Web has provided a place for physicians to share their appraised topics online, but an increasing amount of time is needed to find a particular topic within such a rich repository.
Methods
A web-based application, namely the CAT Crawler, was developed by Singapore's Bioinformatics Institute to allow physicians to adequately access available appraised topics on the Internet. A meta-search engine, as the core component of the application, finds relevant topics following keyword input. The primary objective of the work presented here is to evaluate the quantity and quality of search results obtained from the meta-search engine of the CAT Crawler by comparing them with those obtained from two individual CAT search engines. From the CAT libraries at these two sites, all possible keywords were extracted using a keyword extractor. Of those common to both libraries, ten were randomly chosen for evaluation. All ten were submitted to the two search engines individually, and through the meta-search engine of the CAT Crawler. Search results were evaluated for relevance both by medical amateurs and professionals, and the respective recall and precision were calculated.
Results
While achieving an identical recall, the meta-search engine showed a precision of 77.26% (±14.45) compared to the individual search engines' 52.65% (±12.0) (p < 0.001).
Conclusion
The results demonstrate the validity of the CAT Crawler meta-search engine approach. The improved precision due to inherent filters underlines the practical usefulness of this tool for clinicians.
doi:10.1186/1472-6947-4-21
PMCID: PMC539260  PMID: 15588311
5.  Treatment decision-making and the form of risk communication: results of a factorial survey 
Background
Prospective users of preventive therapies often must evaluate complex information about therapeutic risks and benefits. The purpose of this study was to evaluate the effect of relative and absolute risk information on patient decision-making in scenarios typical of health information for patients.
Methods
Factorial experiments within a telephone survey of the Michigan adult, non-institutionalized, English-speaking population. Average interview lasted 23 minutes. Subjects and sample design: 952 randomly selected adults within a random-digit dial sample of Michigan households. Completion rate was 54.3%.
Results
When presented hypothetical information regarding additional risks of breast cancer from a medication to prevent a bone disease, respondents reduced their willingness to recommend a female friend take the medication compared to the baseline rate (66.8% = yes). The decrease was significantly greater with relative risk information. Additional benefit information regarding preventing heart disease from the medication increased willingness to recommend the medication to a female friend relative to the baseline scenario, but did not differ between absolute and relative risk formats. When information about both increased risk of breast cancer and reduced risk of heart disease were provided, typical respondents appeared to make rational decisions consistent with Expected Utility Theory, but the information presentation format affected choices. Those 11% – 33% making decisions contrary to the medical indications were more likely to be Hispanic, older, more educated, smokers, and to have children in the home.
Conclusions
In scenarios typical of health risk information, relative risk information led respondents to make non-normative decisions that were "corrected" when the frame used absolute risk information. This population sample made generally rational decisions when presented with absolute risk information, even in the context of a telephone interview requiring remembering rates given. The lack of effect of gender and race suggests that a standard strategy of presenting absolute risk information may improve patient decision-making.
doi:10.1186/1472-6947-4-20
PMCID: PMC535806  PMID: 15546488
6.  Case-based medical informatics 
Background
The "applied" nature distinguishes applied sciences from theoretical sciences. To emphasize this distinction, we begin with a general, meta-level overview of the scientific endeavor. We introduce the knowledge spectrum and four interconnected modalities of knowledge. In addition to the traditional differentiation between implicit and explicit knowledge we outline the concepts of general and individual knowledge. We connect general knowledge with the "frame problem," a fundamental issue of artificial intelligence, and individual knowledge with another important paradigm of artificial intelligence, case-based reasoning, a method of individual knowledge processing that aims at solving new problems based on the solutions to similar past problems.
We outline the fundamental differences between Medical Informatics and theoretical sciences and propose that Medical Informatics research should advance individual knowledge processing (case-based reasoning) and that natural language processing research is an important step towards this goal that may have ethical implications for patient-centered health medicine.
Discussion
We focus on fundamental aspects of decision-making, which connect human expertise with individual knowledge processing. We continue with a knowledge spectrum perspective on biomedical knowledge and conclude that case-based reasoning is the paradigm that can advance towards personalized healthcare and that can enable the education of patients and providers.
We center the discussion on formal methods of knowledge representation around the frame problem. We propose a context-dependent view on the notion of "meaning" and advocate the need for case-based reasoning research and natural language processing. In the context of memory based knowledge processing, pattern recognition, comparison and analogy-making, we conclude that while humans seem to naturally support the case-based reasoning paradigm (memory of past experiences of problem-solving and powerful case matching mechanisms), technical solutions are challenging.
Finally, we discuss the major challenges for a technical solution: case record comprehensiveness, organization of information on similarity principles, development of pattern recognition and solving ethical issues.
Summary
Medical Informatics is an applied science that should be committed to advancing patient-centered medicine through individual knowledge processing. Case-based reasoning is the technical solution that enables a continuous individual knowledge processing and could be applied providing that challenges and ethical issues arising are addressed appropriately.
doi:10.1186/1472-6947-4-19
PMCID: PMC544898  PMID: 15533257
7.  Use of and attitudes to a hospital information system by medical secretaries, nurses and physicians deprived of the paper-based medical record: a case report 
Background
Most hospitals keep and update their paper-based medical records after introducing an electronic medical record or a hospital information system (HIS). This case report describes a HIS in a hospital where the paper-based medical records are scanned and eliminated. To evaluate the HIS comprehensively, the perspectives of medical secretaries and nurses are described as well as that of physicians.
Methods
We have used questionnaires and interviews to assess and compare frequency of use of the HIS for essential tasks, task performance and user satisfaction among medical secretaries, nurses and physicians.
Results
The medical secretaries use the HIS much more than the nurses and the physicians, and they consider that the electronic HIS greatly has simplified their work. The work of nurses and physicians has also become simplified, but they find less satisfaction with the system, particularly with the use of scanned document images.
Conclusions
Although the basis for reference is limited, the results support the assertion that replacing the paper-based medical record primarily benefits the medical secretaries, and to a lesser degree the nurses and the physicians. The varying results in the different employee groups emphasize the need for a multidisciplinary approach when evaluating a HIS.
doi:10.1186/1472-6947-4-18
PMCID: PMC526259  PMID: 15488150
8.  Prospective study of clinician-entered research data in the Emergency Department using an Internet-based system after the HIPAA Privacy Rule 
Background
Design and test the reliability of a web-based system for multicenter, real-time collection of data in the emergency department (ED), under waiver of authorization, in compliance with HIPAA.
Methods
This was a phase I, two-hospital study of patients undergoing evaluation for possible pulmonary embolism. Data were collected by on-duty clinicians on an HTML data collection form (prospective e-form), populated using either a personal digital assistant (PDA) or personal computer (PC). Data forms were uploaded to a central, offsite server using secure socket protocol transfer. Each form was assigned a unique identifier, and all PHI data were encrypted, but were password-accessible by authorized research personnel to complete a follow-up e-form.
Results
From April 15, 2003-April 15 2004, 1022 prospective e-forms and 605 follow-up e-forms were uploaded. Complexities of PDA use compelled clinicians to use PCs in the ED for data entry for most forms. No data were lost and server log query revealed no unauthorized entry. Prospectively obtained PHI data, encrypted upon server upload, were successfully decrypted using password-protected access to allow follow-up without difficulty in 605 cases. Non-PHI data from prospective and follow-up forms were available to the study investigators via standard file transfer protocol.
Conclusions
Data can be accurately collected from on-duty clinicians in the ED using real-time, PC-Internet data entry in compliance with the Privacy Rule. Deidentification-reidentification of PHI was successfully accomplished by a password-protected encryption-deencryption mechanism to permit follow-up by approved research personnel.
doi:10.1186/1472-6947-4-17
PMCID: PMC526297  PMID: 15479471
9.  Doublet method for very fast autocoding 
Background
Autocoding (or automatic concept indexing) occurs when a software program extracts terms contained within text and maps them to a standard list of concepts contained in a nomenclature. The purpose of autocoding is to provide a way of organizing large documents by the concepts represented in the text. Because textual data accumulates rapidly in biomedical institutions, the computational methods used to autocode text must be very fast. The purpose of this paper is to describe the doublet method, a new algorithm for very fast autocoding.
Methods
An autocoder was written that transforms plain-text into intercalated word doublets (e.g. "The ciliary body produces aqueous humor" becomes "The ciliary, ciliary body, body produces, produces aqueous, aqueous humor"). Each doublet is checked against an index of doublets extracted from a standard nomenclature. Matching doublets are assigned a numeric code specific for each doublet found in the nomenclature. Text doublets that do not match the index of doublets extracted from the nomenclature are not part of valid nomenclature terms. Runs of matching doublets from text are concatenated and matched against nomenclature terms (also represented as runs of doublets).
Results
The doublet autocoder was compared for speed and performance against a previously published phrase autocoder. Both autocoders are Perl scripts, and both autocoders used an identical text (a 170+ Megabyte collection of abstracts collected through a PubMed search) and the same nomenclature (neocl.xml, containing over 102,271 unique names of neoplasms). In side-by-side comparison on the same computer, the doublet method autocoder was 8.4 times faster than the phrase autocoder (211 seconds versus 1,776 seconds). The doublet method codes 0.8 Megabytes of text per second on a desktop computer with a 1.6 GHz processor. In addition, the doublet autocoder successfully matched terms that were missed by the phrase autocoder, while the phrase autocoder found no terms that were missed by the doublet autocoder.
Conclusions
The doublet method of autocoding is a novel algorithm for rapid text autocoding. The method will work with any nomenclature and will parse any ascii plain-text. An implementation of the algorithm in Perl is provided with this article. The algorithm, the Perl implementation, the neoplasm nomenclature, and Perl itself, are all open source materials.
doi:10.1186/1472-6947-4-16
PMCID: PMC521082  PMID: 15369595
10.  Seal of transparency heritage in the CISMeF quality-controlled health gateway 
Background
It is an absolute necessity to continually assess the quality of health information on the Internet. Quality-controlled subject gateways are Internet services which apply a selected set of targeted measures to support systematic resource discovery.
Methods
The CISMeF health gateway became a contributor to the MedCIRCLE project to evaluate 270 health information providers. The transparency heritage consists of using the evaluation performed on providers that are referenced in the CISMeF catalogue for evaluating the documents they publish, thus passing on the transparency label from the publishers to their documents.
Results
Each site rated in CISMeF has a record in the CISMeF database that generates an RDF into HTML file. The search tool Doc'CISMeF displays information originating from every publisher evaluated with a specific MedCIRCLE button, which is linked to the MedCIRCLE central repository. Starting with 270 websites, this trust heritage has led to 6,480 evaluated resources in CISMeF (49.8% of the 13,012 resources included in CISMeF).
Conclusion
With the MedCIRCLE project and transparency heritage, CISMeF became an explicit third party.
doi:10.1186/1472-6947-4-15
PMCID: PMC521492  PMID: 15367332
11.  Screening for Parkinson's disease with response time batteries: A pilot study 
Background
Although significant response time deficits (both reaction time and movement time) have been identified in numerous studies of patients with Parkinson's disease (PD), few attempts have been made to evaluate the use of these measures in screening for PD.
Methods
Receiver operator characteristic curves were used to identify cutoff scores for a unit-weighted composite of two choice response tasks in a sample of 40 patients and 40 healthy participants. These scores were then cross-validated in an independent sample of 20 patients and 20 healthy participants.
Results
The unit-weighted movement time composite demonstrated high sensitivity (90%) and specificity (90%) in the identification of PD. Movement time was also significantly correlated (r = 0.59, p < 0.025) with the motor score of the Unified Parkinson's Disease Rating Scale (UPDRS).
Conclusions
Measures of chronometric speed, assessed without the use of biomechanically complex movements, have a potential role in screening for PD. Furthermore, the significant correlation between movement time and UPDRS motor score suggests that movement time may be useful in the quantification of PD severity.
doi:10.1186/1472-6947-4-14
PMCID: PMC518971  PMID: 15361256
12.  Feasibility of a patient decision aid regarding disclosure of personal health information: qualitative evaluation of the Health Care Information Directive 
Background
Concerns regarding the privacy of health information are escalating owing both to the growing use of information technology to store and exchange data and to the increasing demand on the part of patients to control the use of their medical records. The objective of this study was to evaluate the Health Care Information Directive (HCID), a recently-developed patient decision aid that aims to delineate the level of health information an individual is willing to share.
Methods
We convened a series of four focus group meetings with several communities in a large Canadian city. A total of 28 men and women participated, representing health care consumer advocates, urban professionals, senior citizens, and immigrants who speak English as a second language. Data were analysed using qualitative methods.
Results
Participants lacked substantial knowledge regarding the fate and uses of personal health information. They expressed mistrust concerning how their information will be used and protected. Several suggestions were made towards customizing the use of data according to specific needs rather than broad and full access to their charts. Furthermore, despite concern regarding the implementation of a tool like the HCID, participants were hopeful that a refined instrument could contribute to the improved regulation of health information.
Conclusion
This study indicated poor knowledge concerning the uses of personal health information, distrust concerning security provisions, and cautious support for a patient decision aid such as the HCID to improve control over health data.
doi:10.1186/1472-6947-4-13
PMCID: PMC518970  PMID: 15361257
13.  Wireless local area network in a prehospital environment 
Background
Wireless local area networks (WLANs) are considered the next generation of clinical data network. They open the possibility for capturing clinical data in a prehospital setting (e.g., a patient's home) using various devices, such as personal digital assistants, laptops, digital electrocardiogram (EKG) machines, and even cellular phones, and transmitting the captured data to a physician or hospital. The transmission rate is crucial to the applicability of the technology in the prehospital setting.
Methods
We created two separate WLANs to simulate a virtual local are network environment such as in a patient's home or an emergency room (ER). The effects of different methods of data transmission, number of clients, and roaming among different access points on the file transfer rate were determined.
Results
The present results suggest that it is feasible to transfer small files such as patient demographics and EKG data from the patient's home to the ER at a reasonable speed. Encryption, user control, and access control were implemented and results discussed.
Conclusions
Implementing a WLAN in a centrally managed and multiple-layer-controlled access control server is the key to ensuring its security and accessibility. Future studies should focus on product capacity, speed, compatibility, interoperability, and security management.
doi:10.1186/1472-6947-4-12
PMCID: PMC517505  PMID: 15339336
14.  A quantitative analysis of qualitative studies in clinical journals for the 2000 publishing year 
Background
Quantitative studies are becoming more recognized as important to understanding health care with all of its richness and complexities. The purpose of this descriptive survey was to provide a quantitative evaluation of the qualitative studies published in 170 core clinical journals for 2000.
Methods
All identified studies that used qualitative methods were reviewed to ascertain which clinical journals publish qualitative studies and to extract research methods, content (persons and health care issues studied), and whether mixed methods (quantitative and qualitative methods) were used.
Results
60 330 articles were reviewed. 355 reports of original qualitative studies and 12 systematic review articles were identified in 48 journals. Most of the journals were in the discipline of nursing. Only 4 of the most highly cited health care journals, based on ISI Science Citation Index (SCI) Impact Factors, published qualitative studies. 37 of the 355 original reports used both qualitative and quantitative (mixed) methods. Patients and non-health care settings were the most common groups of people studied. Diseases and conditions were cancer, mental health, pregnancy and childbirth, and cerebrovascular disease with many other diseases and conditions represented. Phenomenology and grounded theory were commonly used; substantial ethnography was also present. No substantial differences were noted for content or methods when articles published in all disciplines were compared with articles published in nursing titles or when studies with mixed methods were compared with studies that included only qualitative methods.
Conclusions
The clinical literature includes many qualitative studies although they are often published in nursing journals or journals with low SCI Impact Factor journals. Many qualitative studies incorporate both qualitative and quantitative methods.
doi:10.1186/1472-6947-4-11
PMCID: PMC503397  PMID: 15271221
15.  Algorithms for optimizing drug therapy 
Background
Drug therapy has become increasingly efficient, with more drugs available for treatment of an ever-growing number of conditions. Yet, drug use is reported to be sub optimal in several aspects, such as dosage, patient's adherence and outcome of therapy. The aim of the current study was to investigate the possibility to optimize drug therapy using computer programs, available on the Internet.
Methods
One hundred and ten officially endorsed text documents, published between 1996 and 2004, containing guidelines for drug therapy in 246 disorders, were analyzed with regard to information about patient-, disease- and drug-related factors and relationships between these factors. This information was used to construct algorithms for identifying optimum treatment in each of the studied disorders. These algorithms were categorized in order to define as few models as possible that still could accommodate the identified factors and the relationships between them. The resulting program prototypes were implemented in HTML (user interface) and JavaScript (program logic).
Results
Three types of algorithms were sufficient for the intended purpose. The simplest type is a list of factors, each of which implies that the particular patient should or should not receive treatment. This is adequate in situations where only one treatment exists. The second type, a more elaborate model, is required when treatment can by provided using drugs from different pharmacological classes and the selection of drug class is dependent on patient characteristics. An easily implemented set of if-then statements was able to manage the identified information in such instances. The third type was needed in the few situations where the selection and dosage of drugs were depending on the degree to which one or more patient-specific factors were present. In these cases the implementation of an established decision model based on fuzzy sets was required. Computer programs based on one of these three models could be constructed regarding all but one of the studied disorders. The single exception was depression, where reliable relationships between patient characteristics, drug classes and outcome of therapy remain to be defined.
Conclusion
Algorithms for optimizing drug therapy can, with presumably rare exceptions, be developed for any disorder, using standard Internet programming methods.
doi:10.1186/1472-6947-4-10
PMCID: PMC493275  PMID: 15265240
16.  Some methods for blindfolded record linkage 
Background
The linkage of records which refer to the same entity in separate data collections is a common requirement in public health and biomedical research. Traditionally, record linkage techniques have required that all the identifying data in which links are sought be revealed to at least one party, often a third party. This necessarily invades personal privacy and requires complete trust in the intentions of that party and their ability to maintain security and confidentiality. Dusserre, Quantin, Bouzelat and colleagues have demonstrated that it is possible to use secure one-way hash transformations to carry out follow-up epidemiological studies without any party having to reveal identifying information about any of the subjects – a technique which we refer to as "blindfolded record linkage". A limitation of their method is that only exact comparisons of values are possible, although phonetic encoding of names and other strings can be used to allow for some types of typographical variation and data errors.
Methods
A method is described which permits the calculation of a general similarity measure, the n-gram score, without having to reveal the data being compared, albeit at some cost in computation and data communication. This method can be combined with public key cryptography and automatic estimation of linkage model parameters to create an overall system for blindfolded record linkage.
Results
The system described offers good protection against misdeeds or security failures by any one party, but remains vulnerable to collusion between or simultaneous compromise of two or more parties involved in the linkage operation. In order to reduce the likelihood of this, the use of last-minute allocation of tasks to substitutable servers is proposed. Proof-of-concept computer programmes written in the Python programming language are provided to illustrate the similarity comparison protocol.
Conclusion
Although the protocols described in this paper are not unconditionally secure, they do suggest the feasibility, with the aid of modern cryptographic techniques and high speed communication networks, of a general purpose probabilistic record linkage system which permits record linkage studies to be carried out with negligible risk of invasion of personal privacy.
doi:10.1186/1472-6947-4-9
PMCID: PMC471556  PMID: 15222890
17.  A Wireless Health Outcomes Monitoring System (WHOMS): development and field testing with cancer patients using mobile phones 
Background
Health-Related Quality of Life assessment is widely used in clinical research, but rarely in clinical practice. Barriers including practical difficulties administering printed questionnaires have limited their use. Telehealth technology could reduce these barriers and encourage better doctor-patient interaction regarding patient symptoms and quality-of-life monitoring. The aim of this study was to develop a new system for transmitting patients' self-reported outcomes using mobile phones or the internet, and to test whether patients can and will use the system via a mobile phone.
Methods
We have developed a prototype of a Wireless Health Outcomes Monitoring System, which allows structured questionnaires to be sent to the patient by their medical management team. The patients' answers are directly sent to an authorised website immediately accessible by the medical team, and are displayed in a graphic format that highlights the patient's state of health. In the present study, 97 cancer inpatients were asked to complete a ten-item questionnaire. The questionnaire was delivered by display on a mobile phone, and was answered by the patients using the mobile phone keypad.
Results
Of the 97 patients, 56 (58%) attempted the questionnaire, and all of these 56 completed it. Only 6% of the total number of questions were left unanswered by patients. Forty-one (42%) patients refused to participate, mostly due to their lack of familiarity with mobile phone use. Compared with those who completed the questionnaire, patients who refused to participate were older, had fewer years of education and were less familiar with new communications technology (mobile phone calls, mobile phone SMS, internet, email).
Conclusion
More than half of the patients self-completed the questionnaire using the mobile phone. This proportion may increase with the use of multichannel communications which can be incorporated into the system. The proportion may also increase if the patient's partner and/or family were able to assist the patient with using the technology. These preliminary results encourage further studies to identify specific diseases or circumstances where this system could be useful in patients' distance monitoring. Such a system is likely to detect patient suffering earlier, and to activate a well-timed intervention.
doi:10.1186/1472-6947-4-7
PMCID: PMC441394  PMID: 15196308
18.  Resources for comparing the speed and performance of medical autocoders 
Background
Concept indexing is a popular method for characterizing medical text, and is one of the most important early steps in many data mining efforts. Concept indexing differs from simple word or phrase indexing because concepts are typically represented by a nomenclature code that binds a medical concept to all equivalent representations. A concept search on the term renal cell carcinoma would be expected to find occurrences of hypernephroma, and renal carcinoma (concept equivalents). The purpose of this study is to provide freely available resources to compare speed and performance among different autocoders. These tools consist of: 1) a public domain autocoder written in Perl (a free and open source programming language that installs on any operating system); 2) a nomenclature database derived from the unencumbered subset of the publicly available Unified Medical Language System; 3) a large corpus of autocoded output derived from a publicly available medical text.
Methods
A simple lexical autocoder was written that parses plain-text into a listing of all 1,2,3, and 4-word strings contained in text, assigning a nomenclature code for text strings that match terms in the nomenclature. The nomenclature used is the unencumbered subset of the 2003 Unified Medical Language System (UMLS). The unencumbered subset of UMLS was reduced to exclude homonymous one-word terms and proper names, resulting in a term/code data dictionary containing about a half million medical terms. The Online Mendelian Inheritance in Man (OMIM), a 92+ Megabyte publicly available medical opus, was used as sample medical text for the autocoder.
Results
The autocoding Perl script is remarkably short, consisting of just 38 command lines. The 92+ Megabyte OMIM file was completely autocoded in 869 seconds on a 2.4 GHz processor (less than 10 seconds per Megabyte of text). The autocoded output file (9,540,442 bytes) contains 367,963 coded terms from OMIM and is distributed with this manuscript.
Conclusions
A public domain Perl script is provided that can parse through plain-text files of any length, matching concepts against an external nomenclature. The script and associated files can be used freely to compare the speed and performance of autocoding software.
doi:10.1186/1472-6947-4-8
PMCID: PMC441395  PMID: 15198804
19.  Description and validation of a Markov model of survival for individuals free of cardiovascular disease that uses Framingham risk factors 
Background
Estimation of cardiovascular disease risk is increasingly used to inform decisions on interventions, such as the use of antihypertensives and statins, or to communicate the risks of smoking. Crude 10-year cardiovascular disease risk risks may not give a realistic view of the likely impact of an intervention over a lifetime and will underestimate of the risks of smoking. A validated model of survival to act as a decision aid in the consultation may help to address these problems. This study aims to describe the development of such a model for use with people free of cardiovascular disease and evaluates its accuracy against data from a United Kingdom cohort.
Methods
A Markov cycle tree evaluated using cohort simulation was developed utilizing Framingham estimates of cardiovascular risk, 1998 United Kingdom mortality data, the relative risk for smoking related non-cardiovascular disease risk and changes in systolic blood pressure and serum total cholesterol total cholesterol with age. The model's estimates of survival at 20 years for 1391 members of the Whickham survey cohort between the ages of 35 and 65 were compared with the observed survival at 20-year follow-up.
Results
The model estimate for survival was 75% and the observed survival was 75.4%. The correlation between estimated and observed survival was 0.933 over 39 subgroups of the cohort stratified by estimated survival, 0.992 for the seven 5-year age bands from 35 to 64, 0.936 for the ten 10 mmHg systolic blood pressure bands between 100 mmHg and 200 mmHg, and 0.693 for the fifteen 0.5 mmol/l total cholesterol bands between 3.0 and 10.0 mmol/l. The model significantly underestimated mortality in those people with a systolic blood pressure greater than or equal to 180 mmHg (p = 0.006).
The average gain in life expectancy from the elimination of cardiovascular disease risk as a cause of death was 4.0 years for all the 35 year-old men in the sample (n = 24), and 1.8 years for all the 35 year-old women in the sample (n = 32).
Conclusions
This model accurately estimates 20-year survival in subjects from the Whickham cohort with a systolic blood pressure below 180 mmHg.
doi:10.1186/1472-6947-4-6
PMCID: PMC434521  PMID: 15157279
20.  Estimation of hospital emergency room data using otc pharmaceutical sales and least mean square filters 
Background
Surveillance of Over-the-Counter pharmaceutical (OTC) sales as a potential early indicator of developing public health conditions, in particular in cases of interest to Bioterrorism, has been suggested in the literature. The data streams of interest are quite non-stationary and we address this problem from the viewpoint of linear adaptive filter theory: the clinical data is the primary channel which is to be estimated from the OTC data that form the reference channels.
Method
The OTC data are grouped into a few categories and we estimate the clinical data using each individual category, as well as using a multichannel filter that encompasses all the OTC categories. The estimation (in the least mean square sense) is performed using an FIR (Finite Impulse Response) filter and the normalized LMS algorithm.
Results
We show all estimation results and present a table of effectiveness of each OTC category, as well as the effectiveness of the combined filtering operation. Individual group results clearly show the effectiveness of each particular group in estimating the clinical hospital data and serve as a guide as to which groups have sustained correlations with the clinical data.
Conclusion
Our results indicate that Multichannle adaptive FIR least squares filtering is a viable means of estimating public health conditions from OTC sales, and provide quantitative measures of time dependent correlations between the clinical data and the OTC data channels.
doi:10.1186/1472-6947-4-5
PMCID: PMC419503  PMID: 15113417
21.  Characterization of digital medical images utilizing support vector machines 
Background
In this paper we discuss an efficient methodology for the image analysis and characterization of digital images containing skin lesions using Support Vector Machines and present the results of a preliminary study.
Methods
The methodology is based on the support vector machines algorithm for data classification and it has been applied to the problem of the recognition of malignant melanoma versus dysplastic naevus. Border and colour based features were extracted from digital images of skin lesions acquired under reproducible conditions, using basic image processing techniques. Two alternative classification methods, the statistical discriminant analysis and the application of neural networks were also applied to the same problem and the results are compared.
Results
The SVM (Support Vector Machines) algorithm performed quite well achieving 94.1% correct classification, which is better than the performance of the other two classification methodologies. The method of discriminant analysis classified correctly 88% of cases (71% of Malignant Melanoma and 100% of Dysplastic Naevi), while the neural networks performed approximately the same.
Conclusion
The use of a computer-based system, like the one described in this paper, is intended to avoid human subjectivity and to perform specific tasks according to a number of criteria. However the presence of an expert dermatologist is considered necessary for the overall visual assessment of the skin lesion and the final diagnosis.
doi:10.1186/1472-6947-4-4
PMCID: PMC394338  PMID: 15113418
22.  Monitoring of IVF birth outcomes in Finland: a data quality study 
Background
The collection of information on infertility treatments is important for the surveillance of potential health consequences and to monitor service provision.
Study design
We compared the coverage and outcomes of IVF children reported in aggregated IVF statistics, the Medical Birth Register (subsequently: MBR) and research data based on reimbursements for IVF treatments in Finland in 1996–1998.
Results
The number of newborns were nearly equal in the three data sources (N = 4331–4384), but the linkage between the MBR and the research data revealed that almost 40% of the reported IVF children were not the same individuals. The perinatal outcomes in the three data sources were similar, excluding the much lower incidence of major congenital anomalies in the IVF statistics (157/10 000 newborns) compared to other sources (409–422/10 000 newborns).
Conclusion
The differences in perinatal outcomes in the three data sets were in general minor, which suggests that the observed non-recording in the MBR is most likely unbiased.
doi:10.1186/1472-6947-4-3
PMCID: PMC385243  PMID: 15070411
23.  Coupling computer-interpretable guidelines with a drug-database through a web-based system – The PRESGUID project 
Background
Clinical Practice Guidelines (CPGs) available today are not extensively used due to lack of proper integration into clinical settings, knowledge-related information resources, and lack of decision support at the point of care in a particular clinical context.
Objective
The PRESGUID project (PREScription and GUIDelines) aims to improve the assistance provided by guidelines. The project proposes an online service enabling physicians to consult computerized CPGs linked to drug databases for easier integration into the healthcare process.
Methods
Computable CPGs are structured as decision trees and coded in XML format. Recommendations related to drug classes are tagged with ATC codes. We use a mapping module to enhance computerized guidelines coupling with a drug database, which contains detailed information about each usable specific medication. In this way, therapeutic recommendations are backed up with current and up-to-date information from the database.
Results
Two authoritative CPGs, originally diffused as static textual documents, have been implemented to validate the computerization process and to illustrate the usefulness of the resulting automated CPGs and their coupling with a drug database. We discuss the advantages of this approach for practitioners and the implications for both guideline developers and drug database providers. Other CPGs will be implemented and evaluated in real conditions by clinicians working in different health institutions.
doi:10.1186/1472-6947-4-2
PMCID: PMC375539  PMID: 15053828

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