Lessons learned from urgent computing in Europe: Tackling the COVID-19 pandemic.

PRACE (Partnership for Advanced Computing in Europe), an international not-for-profit association that brings together the five largest European supercomputing centers and involves 26 European countries, has allocated more than half a billion core hours to computer simulations to fight the COVID-19 pandemic. Alongside experiments, these simulations are a pillar of research to assess the risks of different scenarios and investigate mitigation strategies. While the world deals with the subsequent waves of the pandemic, we present a reflection on the use of urgent supercomputing for global societal challenges and crisis management.

Standardization of electroencephalography for multi-site, multi-platform and multi-investigator studies: insights from the canadian biomarker integration network in depression.

Subsequent to global initiatives in mapping the human brain and investigations of neurobiological markers for brain disorders, the number of multi-site studies involving the collection and sharing of large volumes of brain data, including electroencephalography (EEG), has been increasing. Among the complexities of conducting multi-site studies and increasing the shelf life of biological data beyond the original study are timely standardization and documentation of relevant study parameters. We present the insights gained and guidelines established within the EEG working group of the Canadian Biomarker Integration Network in Depression (CAN-BIND). CAN-BIND is a multi-site, multi-investigator, and multi-project network supported by the Ontario Brain Institute with access to Brain-CODE, an informatics platform that hosts a multitude of biological data across a growing list of brain pathologies. We describe our approaches and insights on documenting and standardizing parameters across the study design, data collection, monitoring, analysis, integration, knowledge-translation, and data archiving phases of CAN-BIND projects. We introduce a custom-built EEG toolbox to track data preprocessing with open-access for the scientific community. We also evaluate the impact of variation in equipment setup on the accuracy of acquired data. Collectively, this work is intended to inspire establishing comprehensive and standardized guidelines for multi-site studies.

[Application of password manager software in health care]. / Jelszómenedzser szoftver alkalmazása az egészségügyben.

When using multiple IT systems, handling of passwords in a secure manner means a potential source of problem. The most frequent issues are choosing the appropriate length and complexity, and then remembering the strong passwords. Password manager software provides a good solution for this problem, while greatly increasing the security of sensitive medical data. This article introduces a password manager software and provides basic information of the application. It also discusses how to select a really secure password manager software and suggests a practical application to efficient, safe and comfortable use for health care. Orv. Hetil., 2016, 157(52), 2066-2073.

Service oriented architecture for clinical decision support: a systematic review and future directions.

The use of a service-oriented architecture (SOA) has been identified as a promising approach for improving health care by facilitating reliable clinical decision support (CDS). A review of the literature through October 2013 identified 44 articles on this topic. The review suggests that SOA related technologies such as Business Process Model and Notation (BPMN) and Service Component Architecture (SCA) have not been generally adopted to impact health IT systems' performance for better care solutions. Additionally, technologies such as Enterprise Service Bus (ESB) and architectural approaches like Service Choreography have not been generally exploited among researchers and developers. Based on the experience of other industries and our observation of the evolution of SOA, we found that the greater use of these approaches have the potential to significantly impact SOA implementations for CDS.

Adverse drug events with hyperkalaemia during inpatient stays: evaluation of an automated method for retrospective detection in hospital databases.

BACKGROUND: Adverse drug reactions and adverse drug events (ADEs) are major public health issues. Many different prospective tools for the automated detection of ADEs in hospital databases have been developed and evaluated. The objective of the present study was to evaluate an automated method for the retrospective detection of ADEs with hyperkalaemia during inpatient stays. METHODS: We used a set of complex detection rules to take account of the patient's clinical and biological context and the chronological relationship between the causes and the expected outcome. The dataset consisted of 3,444 inpatient stays in a French general hospital. An automated review was performed for all data and the results were compared with those of an expert chart review. The complex detection rules' analytical quality was evaluated for ADEs. RESULTS: In terms of recall, 89.5% of ADEs with hyperkalaemia "with or without an abnormal symptom" were automatically identified (including all three serious ADEs). In terms of precision, 63.7% of the automatically identified ADEs with hyperkalaemia were true ADEs. CONCLUSIONS: The use of context-sensitive rules appears to improve the automated detection of ADEs with hyperkalaemia. This type of tool may have an important role in pharmacoepidemiology via the routine analysis of large inter-hospital databases.

Formative evaluation of ontology learning methods for entity discovery by using existing ontologies as reference standards.

OBJECTIVE: Developing a two-step method for formative evaluation of statistical Ontology Learning (OL) algorithms that leverages existing biomedical ontologies as reference standards. METHODS: In the first step optimum parameters are established. A 'gap list' of entities is generated by finding the set of entities present in a later version of the ontology that are not present in an earlier version of the ontology. A named entity recognition system is used to identify entities in a corpus of biomedical documents that are present in the 'gap list', generating a reference standard. The output of the algorithm (new entity candidates), produced by statistical methods, is subsequently compared against this reference standard. An OL method that performs perfectly will be able to learn all of the terms in this reference standard. Using evaluation metrics and precision-recall curves for different thresholds and parameters, we compute the optimum parameters for each method. In the second step, human judges with expertise in ontology development evaluate each candidate suggested by the algorithm configured with the optimum parameters previously established. These judgments are used to compute two performance metrics developed from our previous work: Entity Suggestion Rate (ESR) and Entity Acceptance Rate (EAR). RESULTS: Using this method, we evaluated two statistical OL methods for OL in two medical domains. For the pathology domain, we obtained 49% ESR, 28% EAR with the Lin method and 52% ESR, 39% EAR with the Church method. For the radiology domain, we obtain 87% ESA, 9% EAR using Lin method and 96% ESR, 16% EAR using Church method. CONCLUSION: This method is sufficiently general and flexible enough to permit comparison of any OL method for a specific corpus and ontology of interest.

[About development of operativeness of medical information data system of central military clinical hospital n. a. N.N.Burdenko].

The authors presented the data about the development of operativeness of medical automated information data system of CMCH n. a. N.N.Burdenko with developing and formation of control center of hospitalization, data processing center, situation room and central archives of diagnostic data. It significantly improved diagnostic and treatment processes in hospital medical and preventive association. Consolidation of dependent prevention and treatment facilities of Moscow Region will provide effective administration of medical supply of attached cohort, administration of hospital association of CMCH n. a. N.N.Burdenko and medical service of the Armed Forces of Russian Federation, in general.

Identifying the medical practice after total hip arthroplasty using an integrated hybrid approach.

A critical option of total hip arthroplasty (THA) is considered only when tried more conservative treatments but continued to have pain, stiffness, or problems with the function of ones hip. THA plays one of major concerns under the waves of the rapid growth of aging populations and the constrained health care resources in Taiwan. Moreover, prior studies indicated that imbalanced class distribution problems do exist in the constructed classification model and cause seriously negative effects on model performances in the health care industry. Therefore, this study proposes an integrated hybrid approach to provide an alternate method for classifying the quality (e.g., the staying length in hospital) of medical practice with an imbalanced class problem after performing a THA procedure for hip replacement patients and their doctors in the health care industry. The proposed approach is constituted by seven components: expert knowledge, global discretization, imbalanced bootstrap technique, reduct and core methods, rough sets, rule induction, and rule filter. The proposed approach is illustrated in practice by examining an experimental dataset from the National Health Insurance Research Database (NHIRD) in Taiwan. The experimental results reveal that the proposed approach has better performance than the listed methods under evaluation criteria. The output created by the rough set LEM2 algorithm is a comprehensible decision rule set that can be applied in knowledge-based health care services as desired. The analytical results provide useful THA information for both academics and practitioners and these results could be applicable to other diseases or to other countries with similar social and cultural practices.

Mobile Medical Education (MoMEd) - how mobile information resources contribute to learning for undergraduate clinical students - a mixed methods study.

BACKGROUND: Mobile technology is increasingly being used by clinicians to access up-to-date information for patient care. These offer learning opportunities in the clinical setting for medical students but the underlying pedagogic theories are not clear. A conceptual framework is needed to understand these further. Our initial questions were how the medical students used the technology, how it enabled them to learn and what theoretical underpinning supported the learning. METHODS: 387 medical students were provided with a personal digital assistant (PDA) loaded with medical resources for the duration of their clinical studies. Outcomes were assessed by a mixed-methods triangulation approach using qualitative and quantitative analysis of surveys, focus groups and usage tracking data. RESULTS: Learning occurred in context with timely access to key facts and through consolidation of knowledge via repetition. The PDA was an important addition to the learning ecology rather than a replacement. Contextual factors impacted on use both positively and negatively. Barriers included concerns of interrupting the clinical interaction and of negative responses from teachers and patients. Students preferred a future involving smartphone platforms. CONCLUSIONS: This is the first study to describe the learning ecology and pedagogic basis behind the use of mobile learning technologies in a large cohort of undergraduate medical students in the clinical environment. We have developed a model for mobile learning in the clinical setting that shows how different theories contribute to its use taking into account positive and negative contextual factors.The lessons from this study are transferable internationally, to other health care professions and to the development of similar initiatives with newer technology such as smartphones or tablet computers.

Creación de un espacio virtual para el apoyo de la docencia en Química Física (Farmacia) / Creation of a virtual environment for supporting the teaching in Physical-Chemistry (Pharmacy)

Un aspecto importante de la práctica docente en el EEES es su interés en el trabajo global del alumno a partir del cual se establece el sistema ECTS de créditos curriculares. Este enfoque requiere una revisión de la metodología docente.Es reconocido que la irrupción de las TIC en todos los sectores sociales, ha tenido una repercusión directa en el sistema educativo. En este contexto, Internet ha demostrado no sólo su importancia como canal de transmisión de contenidos sino su potencial como herramienta docente ya que incorpora interactividad, permite la personalización en la utilización de recursos, se adapta a necesidades particulares en el proceso formativo y permite combinar diferentes tipos de recursos.La aplicación de las TIC en la educación superior es cada día más palpable. Con las limitaciones que imponen los grupos numerosos de alumnos, es clara la tendencia hacia la creación de entornos virtuales como apoyo de la docencia presencial con una integración lo más completa posible en la programación didáctica.La presente comunicación analiza estas cuestiones desde la experiencia acumulada en el desarrollo de diversos recursos docentes y la creación de un entorno específico para algunos grupos de alumnos del curso primero adscritos a las enseñanzas impartidas por el Departamento de Química Física en su sección de Farmacia.El entorno virtual se propone como a) un espacio diseñado no como acumulación de páginas HTML, sino como estructurado de una forma flexible de manera que permita ser actualizado por aportaciones múltiples; b) un espacio interactivo que facilite tanto los intercambios más habituales: profesor-alumnos, como los intercambios transversales entre los alumnos; c) una referencia para alojar recursos que complementen la actividad presencial y d) un lugar de integración de diversas herramientas de aplicación docente(AU)

A important issue regarding the educational practice in the EEES, is the interest in the students’ global work from which curricular ECST system has been established. This particular approach requires a revision of the methodology applied in teaching.It is well known that the Information and Communication Technologies (ICT) have been extended to all social sectors and have produced a special impact on the educational system. In this context, Internet has proved to be not only important as a channel for the transmission of contents but also as a potential educational tool since incorporates interactivity, allows a personalized use of multiple resources, is adaptable to particular needs in the formative process and allows to combine different kinds of resources.The application of ICT in the University studies is more extended every day. In spite of the limitations imposed by the existence of groups formed by a high number of students, a clear trend seems to consolidate nowadays: the creation of virtual environments supporting on-site teaching and which are integrated as much as possible in the study schedules.The present communication focuses on these general aspects in relation with the experience accumulated in the development of several educational resources and the creation of a specific virtual environment for students which enrolled in Physical- Chemistry (Pharmacy section) during the past academic years.The virtual environment developed is a) a designed space not for accumulating static HTML pages but structured for allowing to update it with periodical contributions; b) an interactive space where the usual communicative exchange between students and teacher as well as between students is facilitated; c) a reference in which to incorporate complementary resources in order to support 'on site' teaching; and d) a place to integrate different tools with application in educational matters(AU)

CDISC standard-based electronic archiving of clinical trials.

OBJECTIVES: Our objectives were to develop, based on the analysis of archived clinical trial documents and data and on the requirements of GCP-compliant electronic archiving, a concept for legally secure and technically feasible archiving of the entire clinical trial, including the essential documents of the trial master file and the study database. METHODS: Based on own experiences with CDISC, existing implementations and future developments, CDISC standards were evaluated concerning requirements for archiving clinical studies. Trial master files of a small, medium and large clinical study were analyzed to collect specifications for electronic archiving of records. RESULTS: Two different ways of long-term storage exist for the clinical trial archive: document-oriented archival and data archiving of the study database. The trial master file has a highly complex structure; its different parts can vary greatly in size, depending of the working style of investigators, number of patients recruited, the number of adverse event reports and the number of queries. The CDISC standard ODM is especially suited for archiving clinical trials, because among other features it contains the entire clinical trial data and full audit trail information. On the other hand SDTM is a content standard suited for data warehouses. Two recent developments in CDISC will affect the archival of studies: the further development of ODM in the area of "eCRF submission" and the use of "Electronic Source Data". CONCLUSIONS: The complexity and size of the trial master file requires new solutions. Though ODM provides effective means to archive the study database, it shows still deficiencies, especially for the joint archiving of data and the complex documentation of the trial master file. A concept was developed in which the ODM standard is part of an integrated archiving of the trial data and documents. ODM archiving of the study database enables long-term storage which is GCP-compliant. Archiving of documents of the trial master file in PDF/A, including links and electronic signatures, as well as the storage of selected study data in a data warehouse at the sponsor site in SDTM are the other components of the concept.

[Surveillance of infectious diseases at the EU level]. / Surveillance von Infektionskrankheiten auf europäischer Ebene.

The basis for EU wide surveillance was Decision 2119/98/EC of the European Parliament and the Council in 1998. Since May 2005 it is the task of the European Centre for Disease Prevention and Control to coordinate and further develop this network. One key function of the ECDC is to standardise European surveillance and especially to harmonise the procedures of the surveillance networks that developed independently of each other. As a first step, the EU case definitions have been revised jointly with the Member States and the Commission. All surveillance networks are evaluated with a standard protocol before a decision is made at the ECDC on the continuation of the individual network activities. Simultaneously, the development of The European Surveillance System (TESSy) progressed. Since the beginning of 2008 data users have been trained and TESSy has been in use since April 2008. In the future the main focus must be the improvement of the quality and comparability of the data as such data are the essential prerequisite for decision making in public health.

The use of the Personal Digital Assistant (PDA) among personnel and students in health care: a review.

BACKGROUND: Health care personnel need access to updated information anywhere and at any time, and a Personal Digital Assistant (PDA) has the potential to meet these requirements. A PDA is a mobile tool which has been employed widely for various purposes in health care practice, and the level of its use is expected to increase. Loaded with suitable functions and software applications, a PDA might qualify as the tool that personnel and students in health care need. In Sweden today, despite its leadership role in mobile technologies, PDAs are not commonly used, and there is a lack of suitable functions and software applications. OBJECTIVE: The aim of the present review was to obtain an overview of existing research on the use of PDAs among personnel and students in health care. METHODS: The literature search included original peer-reviewed research articles written in English and published from 1996 to 2008. All study designs were considered for inclusion. We excluded reviews and studies focusing on the use of PDAs in classroom situations. From March 2006 to the last update in May 2008, we searched PubMed, CINAHL, Cochrane, IngentaConnect, and a local search engine (ELIN@Kalmar). We conducted a content analysis, using Nielsen's Model of System Acceptability as a theoretical framework in structuring and presenting the results. RESULTS: From the 900 references initially screened, 172 articles were selected and critically assessed until 48 articles remained. The majority originated in North-America (USA: n=24, Canada: n=11). The categories which emerged from our content analysis coincided to a certain extent to Nielsen's Model of System Acceptability (social and practical acceptability), including usefulness (utility and usability) subcategories such as learnability, efficiency, errors, and satisfaction. The studies showed that health care personnel and students used PDAs in patient care with varied frequency. Most of the users were physicians. There is some evidence that the use of a PDA in health care settings might improve decision-making, reduce the numbers of medical errors, and enhance learning for both students and professionals, but the evidence is not strong, with most studies being descriptive, and only 6 randomized controlled trials. Several special software programs have been created and tested for PDAs, and a wide range of situations for their use have been reported for different patient groups. Drug and medical information were commonly accessed by PDA users, and the PDA was often viewed as the preferred tool when compared to paper-based documents. Some users regarded the PDA easy to operate, while others found it difficult in the beginning. CONCLUSIONS: This overview of the use of PDAs revealed a positive attitude towards the PDA, which was regarded as a feasible and convenient tool. The possibility of immediate access to medical information has the potential to improve patient care. The PDA seems to be a valuable tool for personnel and students in health care, but there is a need for further intervention studies, randomized controlled trials, action research, and studies with various health care groups in order to identify its appropriate functions and software applications.

Análisis de terminologías de salud para su utilización como ontologías computacionales en los sistemas de información clínicos / Analysis of health terminologies for use as ontologies in healthcare information systems

Objetivos: Las ontologías son un recurso que permite trabajarinformáticamente con la conceptualización del significadoy evitar la limitación impuesta por los términos normalizados.El objetivo de este estudio es establecer el grado deusabilidad de las terminologías para el diseño de ontologías,que contribuyan a resolver los problemas de interoperabilidadsemántica, y de reutilización de conocimiento en los sistemasde información clínicos.Métodos: Se han analizado 6 de las terminologías más relevantespara el ámbito clínico, epidemiológico, documentaly administrativo-económico. Se valoraron las siguientes cualidades:cobertura conceptual, estructura jerárquica, granularidadconceptual, relaciones conceptuales y grado de formalismoutilizado en la representación conceptual, paraestablecer el grado de usabilidad.Resultados: Se consideran como ontologías ligeras los MeSH,los DeCS y el UMLS, aunque con diferencias entre ellas, alexplicitar los conceptos, el tipo de relación y las restriccionesentre los conceptos asociados. SNOMED y GALEN, con suformalismo declarativo basado en descripciones lógicas, incluyenla explicitación de las cualidades, una mayor restricciónpara relacionar conceptos y las reglas de combinaciónentre ellos, por lo que se consideran como ontologías pesadas.Conclusiones: El análisis de la representación declarada delas terminologías muestra las posibilidades de su reutilizacióncomo ontologías. Su grado de usabilidad dependerá de si sepretende que los sistemas de información clínicos resuelvanlos problemas de interoperabilidad semántica (ontologías ligeras)o además reutilizar su conocimiento para sistemas deayuda a la toma de decisiones (ontologías pesadas) y paratareas de recuperación, extracción y clasificación de informaciónno estructurada(AU)

Objectives: Ontologies are a resource that allow the conceptof meaning to be represented informatically, thus avoiding thelimitations imposed by standardized terms. The objective of thisstudy was to establish the extent to which terminologies couldbe used for the design of ontologies, which could be serve asan aid to resolve problems such as semantic interoperability andknowledge reusability in healthcare information systems.Methods: To determine the extent to which terminologies couldbe used as ontologies, six of the most important terminologiesin clinical, epidemiologic, documentation and administrative-economiccontexts were analyzed. The following characteristics wereverified: conceptual coverage, hierarchical structure, conceptualgranularity of the categories, conceptual relations, and thelanguage used for conceptual representation.Results: MeSH, DeCS and UMLS ontologies were consideredlightweight. The main differences among these ontologies concernconceptual specification, the types of relation and the restrictionsamong the associated concepts. SNOMED andGALEN ontologies have declaratory formalism, based on logicaldescriptions. These ontologies include explicit qualitiesand show greater restrictions among associated concepts andrule combinations and were consequently considered as heavyweight.Conclusions: Analysis of the declared representation of theterminologies shows the extent to which they could be reusedas ontologies. Their degree of usability depends on whetherthe aim is for healthcare information systems to solve problemsof semantic interoperability (lightweight ontologies) orto reuse the systems’ knowledge as an aid to decision making(heavyweight ontologies) and for non-structured informationretrieval, extraction, and classification(AU)

Data privacy considerations in Intensive Care Grids.

Novel eHealth systems are being designed to provide a citizen-centered health system, however the even demanding need for computing and data resources has required the adoption of Grid technologies. In most of the cases, this novel Health Grid requires not only conveying patient's personal data through public networks, but also storing it into shared resources out of the hospital premises. These features introduce new security concerns, in particular related with privacy. In this paper we survey current legal and technological approaches that have been taken to protect a patient's personal data into eHealth systems, with a particular focus in Intensive Care Grids. However, thanks to a security analysis applied over the Intensive Care Grid system (ICGrid) we show that these security mechanisms are not enough to provide a comprehensive solution, mainly because the data-at-rest is still vulnerable to attacks coming from untrusted Storage Elements where an attacker may directly access them. To cope with these issues, we propose a new privacy-oriented protocol which uses a combination of encryption and fragmentation to improve data's assurance while keeping compatibility with current legislations and Health Grid security mechanisms.

Security, safety, and related technology - the triangle of eHealth service provision.

The developing of innovative solutions in the emerging eHealth market requires strong economic efforts which may be justified only in presence of particularly suitable boundary conditions. Among the factors retained of primary importance for the development of eHealth, a correct approach to id-management is unanimously considered fundamental. Three keywords in the id-management context appear particularly important: standardization, security and safety. Standardization may contribute to increase the size and duration of the eHealth market, while security and safety may encourage all the stakeholders to trust in a appropriate and safe management of all the very sensitive personal data involved in the eHealth applications. The aim of the present paper is analyzing some security and safety issues in eHealth from the particular prospective of the identity management and standardization. The paper highlights the mission of the EU funded "BioHealth" project whose mission is to increase the stakeholders' knowledge about existing and emerging standards in eHealth with particular reference to identity management.

A framework for semantic interoperability in healthcare: a service oriented architecture based on health informatics standards.

Healthcare information is composed of many types of varying and heterogeneous data. Semantic interoperability in healthcare is especially important when all these different types of data need to interact. Presented in this paper is a solution to interoperability in healthcare based on a standards-based middleware software architecture used in enterprise solutions. This architecture has been translated into the healthcare domain using a messaging and modeling standard which upholds the ideals of the Semantic Web (HL7 V3) combined with a well-known standard terminology of clinical terms (SNOMED CT).

The adoption of IT security standards in a healthcare environment.

Security is a vital part of daily life to Hospitals that need to ensure that the information is adequately secured. In Portugal, more CIOs are seeking that their hospital IS departments are properly protecting information assets from security threats. It is imperative to take necessary measures to ensure risk management and business continuity. Security management certification provides just such a guarantee, increasing patient and partner confidence. This paper introduces one best practice for implementing four security controls in a hospital datacenter infrastructure (ISO27002), and describes the security assessment for implementing such controls.