[Data analysis: challenges and specifics in neuroscience and psychiatry]. / Analýza dat: výzvy a specifika v neurovedách a psychiatrii.

The amount of available data relevant for clinical decision support is rising not only rapidly but at the same time much faster than our ability to analyze and interpret them. Thus, the potential of the data to contribute to determining the diagnosis, therapy and prognosis of an individual patient is not appropriately exploited. The hopes to obtain benefit from the data for an individual patient must be accompanied by a reliable and diligent biostatistical analysis which faces serious challenges not always clear to non-statisticians. The aim of this paper is to discuss principles of statistical analysis of big data in research and routine applications in clinical medicine, focusing on particular aspects of psychiatry. The paper brings arguments in favor of the idea that the biostatistical analysis of data in a specialty field requires different approaches and different experience compared to other clinical fields. This is illustrated by a description of common complications of the analysis of psychiatric data. Challenges of the analysis of big data in both psychiatric research and routine practice are explained, which are far from a routine service activity exploiting standard methods of multivariate statistics and/or machine learning. Important research questions, which are important in the current psychiatric research, are presented and discussed from the biostatistical point of view.

Exponentially weighted moving average chart as a suitable tool for nuchal translucency quality review.

OBJECTIVES: This study aimed to design an exponentially weighted moving average (EWMA) chart for the quality review of nuchal translucency (NT) and to assess its performance compared with the methods currently in use: retrospective distribution-based methods and the cumulative sum (CUSUM) chart. METHODS: The EWMA model was designed for NT quality review using simulation. The NT measurements obtained during routine first-trimester screening in our centre over a two-and-a-half-year period were retrieved from the database. The NT distribution parameters, EWMA and CUSUM chart were established, and the methods were compared. RESULTS: On the basis of the results from the simulation, the optimal EWMA settings were established. A set of 9338 NT measurements obtained from nine sonographers was used to construct the EWMA and CUSUM charts and to calculate the distribution parameters. Distribution-based methods were unable to reveal the temporal periods of poor performance. The EWMA model agreed closely with the CUSUM but had the advantage promptly indicating when the process returned to an in-control state, thus extending its use to long-term prospective and retrospective quality assessments. CONCLUSIONS: The EWMA provides a universal, easy and efficient tool for NT quality review when the prompt and effective detection of suboptimal performance is desired.

System for selecting relevant information for decision support.

We implemented a prototype of a decision support system called SIR which has a form of a web-based classification service for diagnostic decision support. The system has the ability to select the most relevant variables and to learn a classification rule, which is guaranteed to be suitable also for high-dimensional measurements. The classification system can be useful for clinicians in primary care to support their decision-making tasks with relevant information extracted from any available clinical study. The implemented prototype was tested on a sample of patients in a cardiological study and performs an information extraction from a high-dimensional set containing both clinical and gene expression data.

Rare allelic variants determine folate status in an unsupplemented European population.

The role of folates as coenzymes in 1-carbon metabolism and the clinical consequences of disturbed folate metabolism are widely known. Folate status is a complex trait determined by both exogenous and endogenous factors. This study analyzed the association between 12 genetic variants and folate status in a Czech population with no folate fortification program. These 12 genetic variants were selected from 56 variant alleles found by resequencing the coding sequences and adjacent intronic regions of 6 candidate genes involved in folate metabolism or transport (FOLR1, FOLR2, FOLR3, MTHFR, PCFT, and RFC) from 29 individuals with low plasma and erythrocyte folate concentrations. Regression analyses of a cohort of 511 Czech controls not taking folate supplements revealed that only 2 variants in the MTHFR gene were associated with altered folate concentrations in plasma and/or erythrocytes. In our previous study, we observed that the common variant MTHFR c.665C > T (known as c.677C > T; p.A222V) was associated with decreased plasma folate concentrations. In the present study, we show in addition that the rare variant MTHFR c.1958C > T (p.T653M) is associated with significantly increased erythrocyte folate concentrations (P = 0.02). Multivariate regression analysis revealed that this uncommon variant, which is present in 2% of Czech control chromosomes, explains 0.9% of the total variability of erythrocyte folate concentrations; the magnitude of this effect size was comparable with that of the common MTHFR c.665C > T variant. This result indicates that the rare genetic variants may determine folate status to a similar extent as the common allelic variant.

Measuring diversity in medical reports based on categorized attributes and international classification systems.

BACKGROUND: Narrative medical reports do not use standardized terminology and often bring insufficient information for statistical processing and medical decision making. Objectives of the paper are to propose a method for measuring diversity in medical reports written in any language, to compare diversities in narrative and structured medical reports and to map attributes and terms to selected classification systems. METHODS: A new method based on a general concept of f-diversity is proposed for measuring diversity of medical reports in any language. The method is based on categorized attributes recorded in narrative or structured medical reports and on international classification systems. Values of categories are expressed by terms. Using SNOMED CT and ICD 10 we are mapping attributes and terms to predefined codes. We use f-diversities of Gini-Simpson and Number of Categories types to compare diversities of narrative and structured medical reports. The comparison is based on attributes selected from the Minimal Data Model for Cardiology (MDMC). RESULTS: We compared diversities of 110 Czech narrative medical reports and 1119 Czech structured medical reports. Selected categorized attributes of MDMC had mostly different numbers of categories and used different terms in narrative and structured reports. We found more than 60% of MDMC attributes in SNOMED CT. We showed that attributes in narrative medical reports had greater diversity than the same attributes in structured medical reports. Further, we replaced each value of category (term) used for attributes in narrative medical reports by the closest term and the category used in MDMC for structured medical reports. We found that relative Gini-Simpson diversities in structured medical reports were significantly smaller than those in narrative medical reports except the "Allergy" attribute. CONCLUSIONS: Terminology in narrative medical reports is not standardized. Therefore it is nearly impossible to map values of attributes (terms) to codes of known classification systems. A high diversity in narrative medical reports terminology leads to more difficult computer processing than in structured medical reports and some information may be lost during this process. Setting a standardized terminology would help healthcare providers to have complete and easily accessible information about patients that would result in better healthcare.

Health data collecting and sharing: case studies of Czech e-health applications.

The paper shows the importance of e-health applications for electronic healthcare development. It describes several e-health applications for health data collecting and sharing that are running in the Czech Republic. These are IZIP system, electronic health record MUDR and K4CARE project applications. The e3-health concept is considered as a tool for judging e-health applications in different healthcare settings.

Multiple disciplines synergy tools for Ph.D. Students of biomedical informatics at Charles University in Prague.

The poster describes doctoral degree studies in biomedical informatics at Charles University in Prague. Particularly important in educational programmes and knowledge dissemination is the role of Internet. Therefore we also describe special activities concerned with the specific research at the First Faculty of Medicine of Charles University in Prague. These are selected tools for blended learning tools, ExaMe system and the role of the European Journal for Biomedical Informatics (EJBI), an official multilingual journal of EFMI, for Ph.D. student's cooperation and understanding the multidisciplinary field of biomedical informatics [1].

EuroMISE Center: research and education in biomedical and healthcare informatics.

EuroMISE Center was established in the year 1994bas the joint workplace of Charles University in Prague and Academy of Sciences of the Czech Republic with the support of the European project focused on higher education in methodology field of healthcare. Nowadays, the EuroMISE Center is working as the joint workplace of five organizations. We describe in more details history and nowadays activities of the EuroMISE Center in the field of research, higher education and e3 Health applications.

TVT-S in the U position--anatomical study.

INTRODUCTION AND HYPOTHESIS: The objective is to describe the anatomical position of tension-free vaginal tape Secur (TVT-S) in the U position regarding possible injury and fixation site. METHODS: We placed TVT-S inserters bilaterally in 13 embalmed and five fresh frozen female bodies. After dissection, we measured distances from the obturator bundle. RESULTS: In embalmed bodies, the mean distance of TVT-S from the obturator bundle was 2.83 cm (standard deviation (SD) 0.87 cm) on the left, 2.92 cm (SD 1.24 cm) on the right. Perforation of the fascia of obturator internus muscle occurred in 38.5%. In fresh frozen bodies, results were fundamentally similar (p > 0.05). CONCLUSIONS: There is a risk of injury to the obturator bundle and urinary bladder during TVT-S; however, there is a significant risk of inserting the TVT-S inserter outside the obturator internus muscle (into the lesser pelvis). The position of TVT-S does not change significantly after legs mal-positioning.

Anatomical study of position of the TVT-O to the obturator nerve influenced by the position of the legs during the procedure: based upon findings at formalin-embalmed and fresh-frozen bodies.

PURPOSE: Groin pain is one of the complications after TVT-O procedure. The aim was to examine the position and safety of the tape after TVT-O procedure. METHODS: We inserted TVT-O in 14 formalin-embalmed bodies with legs malpositioned (group 1) and in 5 fresh-frozen bodies with legs malpositioned (group 2) and in 5 fresh-frozen bodies with legs correctly positioned (group 3). After dissection distances from the branches of obturator nerve were measured. RESULTS: In group 1, the mean distance from the anterior branch of the obturator nerve was 8.6 mm on the left, 7.1 mm on the right. Mean distance from the posterior branch of the obturator nerve was 8.4 mm on the left, 8.9 mm on the right. In group 2, the mean distance from the anterior branch of the obturator nerve was 8.0 mm on the left, 8.0 mm on the right. Mean distance from the posterior branch of the obturator nerve was 5.0 mm on the left, 8.00 mm on the right. In group 3, the mean distance from the anterior branch of the obturator nerve was 24 mm on the left, 23 mm on the right. Mean distance from the posterior branch of the obturator nerve was 23 mm on the left, 23 mm on the right. Statistical analysis was performed with confirmation of significant difference between group of bodies with legs positioned correctly and other groups with malpositioned legs. CONCLUSIONS: The position of the legs is crucial for correct placement of TVT-O.

Evaluation of possibilities in demographic data exchange support in Czech healthcare.

This paper summarizes the evaluation of two standardized approaches to implementation of messages for demographic data exchange between the preventive cardiology outpatient department located at the Institute of Computer Science AS CR, v.v.i. in Prague and the Outpatients Department of Cardiology of Municipal Hospital in Caslav. Our setting consists of four independent systems maintaining different clinical data (scheduling system, hospital information system, EHR system and a digital ECG). The aim is to avoid repetitive patient demographic data entry. We evaluate the suitability of IHE Patient Administration Management Profile (including HL7 v.2.5) and Czech national standard DASTA using Standard Evaluation Framework proposed and published in 2008 by J. Mykkänen et al. Besides the evaluation of standards, we also discuss some aspects of the framework.

Real-time quality control of nuchal translucency measurements using the exponentially weighted moving average chart.

OBJECTIVE: The establishment of ongoing audits for first-trimester nuchal translucency (NT) measurements is of paramount importance. The exponentially weighted moving average (EWMA) chart has been published as an efficient tool for NT quality control with the advantages of being suitable for real-time long-term monitoring. This study aimed to assess the efficacy of real-time NT quality control using EWMA charts. MATERIALS AND METHODS: This was an ongoing prospective study conducted from January 2011 to December 2017 at the Centre for Fetal Medicine Gennet in Prague. The quality of NT measurements was assessed using the NT retrospective distribution parameters and EWMA charts, and the results were presented to the sonographers during collective meetings. RESULTS: Overall, 28,928 NT measurements obtained from six sonographers were eligible for the study. Looking at individual EWMA charts, we observed four main outcomes. First, there was a clear improvement in the performance of sonographers with initially poor performances. Second, the performance of sonographers with an initially satisfactory quality was maintained. Third, there was an observed deterioration of the performance without the audits. Last, the sonographers appreciated an unequivocal and straightforward graphical presentation of EWMA curves. CONCLUSION: EWMA proved to be an efficient and suitable tool for real-time monitoring of NT quality and led to an overall improvement of the sonographers' performance.

Challenges of interoperability using HL7 v3 in Czech healthcare.

The paper describes several classification systems that could improve patient safety through semantic interoperability among contemporary electronic health record systems (EHR-Ss) with support of the HL7 v3 standard. We describe a proposal and a pilot implementation of a semantic interoperability platform (SIP) interconnecting current EHR-Ss by using HL7 v3 messages and concepts mappings on most widely used classification systems. The increasing number of classification systems and nomenclatures requires designing of various conversion tools for transfer between main classification systems. We present the so-called LIM filler module and the HL7 broker, which are parts of the SIP, playing the role of such conversion tools. The analysis of suitability and usability of individual terminological thesauri has been started by mapping of clinical contents of the Minimal Data Model for Cardiology (MDMC) to various terminological classification systems. A national-wide implementation of the SIP would include adopting and translating international coding systems and nomenclatures, and developing implementation guidelines facilitating the migration from national standards to international ones. Our research showed that creation of such a platform is feasible; however, it will require a huge effort to adapt fully the Czech healthcare system to the European environment.

Empowering clinicians by eHealth technologies in decision-making tasks.

We present three types of eHealth applications that can enhance quality of clinical decision-making. Formalized electronic medical guidelines are bringing medical knowledge close to clinicians. eHealth tools for evaluation knowledge and competency in a given clinical decision-making problem are demonstrated by systems ExaMe and TECOM. The TECOM system supports training of clinical competence in a given decision-making problems using real clinical cases. The TECOM system estimates the decision-maker abilities using a coefficient of prediction or a classical error rate. Transfer of data and knowledge important for clinical decision-making without language barriers is demonstrated on features of the European Journal for Biomedical Informatics.

Task force of the EFMI journals: background, rationale and purpose.

The paper presents an analysis of how EFMI disseminates new knowledge and the active medical informatics journals in EFMI member countries was carried out as an outcome of the EFMI Council meeting in London in 2008. The analysis identifies eight active major informatics journals and a several other publications. Most are subscription-based and are published at least quarterly. There is a possibility for the editors to meet regularly and form a community of practice with the aim of further improving their effectiveness in disseminating new knowledge and best practice in medical informatics. It is feasible to share expertise and it may be possible to harmonise several aspects of preparation and submission of manuscripts so that some identified barriers in publishing are reduced.

Education in biomedical informatics and eHealth.

The long-term effect of education in the field of biomedical informatics and eHealth on efficiency and quality of healthcare is discussed. Selected educational methods and tools are presented and their applications are shown.

Medical knowledge representation system.

The aim of this article is to present a design of a Medical Knowledge Representation System (MEKRES). The system automatically offers relevant formalized knowledge by extended GLIF (Guidelines Interchange Format) models to participants (patient, physician, operator, ..) on the basis of acquired data. This selection algorithm is based on key attributes and cooperation with knowledge ontologies.

Formalization of clinical practice guidelines.

Clinical practice guidelines are textual recommendations based on the consensus of medical experts with the aim to solve diagnostic and therapeutic problems. For more advanced use in real medical applications it is necessary to find out mathematical models of physicians' decision-making processes. The acquisition of a formal model from text-based guidelines is a crucial point for development of decision support systems. We introduce a system for formalization and presentation of medical knowledge contained in clinical practice guidelines where knowledge formalization is based on the GLIF model.

Voice-controlled data entry in dental electronic health record.

The EuroMISE Center focuses on new approaches in the field of electronic health record (EHR). Among others, the structured health documentation in dentistry in the form of an EHR is being systematically studied. This paper describes the evolution of the EHR developed at the EuroMISE Center named MUDRLite and its graphical component for dentists called DentCross. The summary of features of the DentCross component is followed by a brief description of automatic speech recognition and an ASR module. The problems with data insertion into EHR during examination of a dental patient lead to further research in the area of the automatic speech recognition in medical practice. Cooperation of engineers, informaticians and dental physicians resulted in an application called DentVoice which is a successful application of the ASR module and the DentCross component of the MUDRLite EHR. The junction of voice control and graphical representation of dental arch makes hand-busy activities in dental praxis easier, quicker and more comfortable. This will result in a better quality of the data stored in a structured form in dental EHR, thus enabling better decision making and use of decision support systems.

Tool-supported Interactive Correction and Semantic Annotation of Narrative Clinical Reports.

OBJECTIVES: Our main objective is to design a method of, and supporting software for, interactive correction and semantic annotation of narrative clinical reports, which would allow for their easier and less erroneous processing outside their original context: first, by physicians unfamiliar with the original language (and possibly also the source specialty), and second, by tools requiring structured information, such as decision-support systems. Our additional goal is to gain insights into the process of narrative report creation, including the errors and ambiguities arising therein, and also into the process of report annotation by clinical terms. Finally, we also aim to provide a dataset of ground-truth transformations (specific for Czech as the source language), set up by expert physicians, which can be reused in the future for subsequent analytical studies and for training automated transformation procedures. METHODS: A three-phase preprocessing method has been developed to support secondary use of narrative clinical reports in electronic health record. Narrative clinical reports are narrative texts of healthcare documentation often stored in electronic health records. In the first phase a narrative clinical report is tokenized. In the second phase the tokenized clinical report is normalized. The normalized clinical report is easily readable for health professionals with the knowledge of the language used in the narrative clinical report. In the third phase the normalized clinical report is enriched with extracted structured information. The final result of the third phase is a semi-structured normalized clinical report where the extracted clinical terms are matched to codebook terms. Software tools for interactive correction, expansion and semantic annotation of narrative clinical reports has been developed and the three-phase preprocessing method validated in the cardiology area. RESULTS: The three-phase preprocessing method was validated on 49 anonymous Czech narrative clinical reports in the field of cardiology. Descriptive statistics from the database of accomplished transformations has been calculated. Two cardiologists participated in the annotation phase. The first cardiologist annotated 1500 clinical terms found in 49 narrative clinical reports to codebook terms using the classification systems ICD 10, SNOMED CT, LOINC and LEKY. The second cardiologist validated annotations of the first cardiologist. The correct clinical terms and the codebook terms have been stored in a database. CONCLUSIONS: We extracted structured information from Czech narrative clinical reports by the proposed three-phase preprocessing method and linked it to electronic health records. The software tool, although generic, is tailored for Czech as the specific language of electronic health record pool under study. This will provide a potential etalon for porting this approach to dozens of other less-spoken languages. Structured information can support medical decision making, quality assurance tasks and further medical research.