Three months of COVID‐19: A systematic review and meta‐analysis

The pandemic of 2019 novel coronavirus (SARS‐CoV‐2019), reminiscent of the 2002‐SARS‐CoV outbreak, has completely isolated countries, disrupted health systems and partially paralyzed international trade and travel. In order to be better equipped to anticipate transmission of this virus to new regions, it is imperative to track the progress of the virus over time. This review analyses information on progression of the pandemic in the past 3 months and systematically discusses the characteristics of SARS‐CoV‐2019 virus including its epidemiologic, pathophysiologic, and clinical manifestations. Furthermore, the review also encompasses some recently proposed conceptual models that estimate the spread of this disease based on the basic reproductive number for better prevention and control procedures. Finally, we shed light on how the virus has endangered the global economy, impacting it both from the supply and demand side.     

Implementing security in a distributed web-based EHCR

PURPOSE: In many countries there are initiatives for building an integrated patient-centric electronic health record. There are also initiatives for transnational integrations. These growing demands for integration result from the fact that it can provide improving healthcare treatments and reducing the cost of healthcare services. While in European highly developed countries computerisation in healthcare sector began in the 1970s and reached a high level, some developing countries, and Serbia among them, have started computerisation recently. This is why MEDIS (MEDical Information System) is aimed at integration itself from the very beginning instead of integration of heterogeneous information systems on a middle layer or using HL7 protocol. APPROACH: The implementation of a national healthcare information system requires using standards as integrated and widely accepted solutions. Therefore, we have started building MEDIS to meet the requirements of CEN ENV 13606 and CEN ENV 13729 standards. The prototype version has a distributed component-based architecture with modern security solutions applied. MEDIS has been implemented as a federated system where the central server hosts basic EHCR information about a patient, and clinical servers contain their own part of patients' EHCR. RESULTS: At present, there is an initial version of prototype planned to be deployed at first in a small community. In particular, open source API for X.509 authentication and authorisation has been developed. Our project meets the requirements for education in health informatics, including appropriate knowledge and skills on EHCR. The points included in this article have been presented on several national conferences and widely discussed. CONCLUSION: MEDIS has explored a federated, component-based EHCR architecture and related security aspects. In its initial version it shows acceptable performances and administrative simplicity. It emphasizes the importance of using standards in building EHCR in our country, in order to prepare it for future integrations.     

Natural language generation of surgical procedures

A number of compositional Medical Concept Representation systems are being developed. Although these provide for a detailed conceptual representation of the underlying information, they have to be translated back to natural language for used by end-users and applications. The GALEN programme has been developing one such representation and we report here on a tool developed to generate natural language phrases from the GALEN conceptual representations. This tool can be adapted to different source modelling schemes and to different destination languages or sublanguages of a domain. It is based on a multilingual approach to natural language generation, realised through a clean separation of the domain model from the linguistic model and their link by well defined structures. Specific knowledge structures and operations have been developed for bridging between the modelling 'style' of the conceptual representation and natural language. Using the example of the scheme developed for modelling surgical operative procedures within the GALEN-IN-USE project, we show how the generator is adapted to such a scheme. The basic characteristics of the surgical procedures scheme are presented together with the basic principles of the generation tool. Using worked examples, we discuss the transformation operations which change the initial source representation into a form which can more directly be translated to a given natural language. In particular, the linguistic knowledge which has to be introduced--such as definitions of concepts and relationships is described. We explain the overall generator strategy and how particular transformation operations are triggered by language-dependent and conceptual parameters. Results are shown for generated French phrases corresponding to surgical procedures from the urology domain.     

Health information systems: failure, success and improvisation

BACKGROUND AND PURPOSE: The generalised assumption of health information systems (HIS) success is questioned by a few commentators in the medical informatics field. They point to widespread HIS failure. The purpose of this paper was therefore to develop a better conceptual foundation for, and practical guidance on, health information systems failure (and success). METHODS: Literature and case analysis plus pilot testing of developed model. RESULTS: Defining HIS failure and success is complex, and the current evidence base on HIS success and failure rates was found to be weak. Nonetheless, the best current estimate is that HIS failure is an important problem. The paper therefore derives and explains the "design-reality gap" conceptual model. This is shown to be robust in explaining multiple cases of HIS success and failure, yet provides a contingency that encompasses the differences which exist in different HIS contexts. The design-reality gap model is piloted to demonstrate its value as a tool for risk assessment and mitigation on HIS projects. It also throws into question traditional, structured development methodologies, highlighting the importance of emergent change and improvisation in HIS. CONCLUSIONS: The design-reality gap model can be used to address the problem of HIS failure, both as a post hoc evaluative tool and as a pre hoc risk assessment and mitigation tool. It also validates a set of methods, techniques, roles and competencies needed to support the dynamic improvisations that are found to underpin cases of HIS success.     

药物基因组学临床决策支持系统综述

近几年来精准医学成为生物医学的一个热门领域,世界各国都致力于率先在这一领域取得突破性的进展。药物基因组学(PGx),通过基因组学和其他“组学”知识来个性化药物选择和药物使用以避免药物不良反应和最大化药物疗效,是精准医学的重要组成部分,也是目前最有希望在临床上实现日常应用的精准医学领域之一。其中药物基因组学临床决策支持(PGx-CDS)系统,是实现PGx临床应用和知识转化必不可少的工具。目前很多临床医疗机构已经开展PGx服务并部署PGx-CDS系统,同时更多的临床医疗和研究机构正在筹备开展这类服务。对目前已出现并被报道的主要PGx-CDS系统和研究进行文献综述,共涉及11个PGx-CDS系统。通过对这些系统的临床应用场景、系统设计、知识表达、干预方式和应用评估等方面的综合回顾,总结目前PGx-CDS系统的研究进展和发展现状,然后对PGx-CDS系统目前面临的主要挑战和未来发展方向进行讨论,为在国内落地PGx服务和PGx-CDS系统提供借鉴。     

Agency in natural and artificial systems

We analyze the conditions for agency in natural and artificial systems. In the case of basic (natural) autonomous systems, self-construction and activity in the environment are two aspects of the same organization, the distinction between which is entirely conceptual: their sensorimotor activities are metabolic, realized according to the same principles and through the same material transformations as those typical of internal processes (such as energy transduction). The two aspects begin to be distinguishable in a particular evolutionary trend, related to the size increase of some groups of organisms whose adaptive abilities depend on motility. Here a specialized system develops, which, in the sensorimotor aspect, is decoupled from the metabolic basis, although it remains dependent on it in the self-constructive aspect. This decoupling reveals a complexification of the organization. In the last section of the article this approach to natural agency is used to analyze artificial systems by posing two problems: whether it is possible to artificially build an organization similar to the natural, and whether this notion of agency can be grounded on different organizing principles.     

Conceptual, Experimental and Compass-beacon Ontologies——The Principles, concepts and methodology of BMKI（Ⅰ）

1 Starting from Inform ation U nit(IU )Radically speaking, any inform ation unit(IU ) needs toansw er these questions: ① W hat object w e are going toknow ? ②W hich aspects of the object w e have chosen tobe observed? ③W hat is the result of the obser…     

New frontiers for health information systems using Epi Info in developing countries: structured application framework for Epi Info (SAFE)

BACKGROUND: For more than two decades, Epi Info software has been used to meet the data management, analysis, and mapping needs of public health professionals in more than 181 countries and 13 languages. Until now, most Epi Info systems have been relatively simple, mainly because of a lack of detailed and structured guidance for developing complex systems. OBJECTIVE AND RESULTS: We created the structured application framework for Epi Info (SAFE), which is a set of guidelines that allows developers to create both simple and complex information systems using accepted good programming practices. This has resulted in application code blocks that are re-useable and easy to maintain, modify, and enhance. The flexibility of SAFE allows various aggregate and case-based application modules to be rapidly created, combined, and updated to create health information systems or sub-systems enabling continuous, incremental enhancement as national and local capacity increases. CONCLUSIONS: SAFE and Epi Info are both cost-free and have low system requirements--characteristics that render this framework and software beneficial for developing countries.     

Web-based infectious disease reporting using XML forms

OBJECTIVE: Exploring solutions for infectious disease information sharing among hospital and public health information systems is imperative to the improvement of disease surveillance and emergent response. This paper aimed at developing a method to directly transmit real-time data of notifiable infectious diseases from hospital information systems to public health information systems on the Internet by using a standard eXtensible Markup Language (XML) format. METHODS: The mechanism and work flow by which notifiable infectious disease data are created, reported and used at health agencies in China was evaluated. The capacity of all participating providers to use electronic data interchange to submit transactions of data required for the notifiable infectious disease reporting was assessed. The minimum data set at national level that is required for reporting for national notifiable infectious disease surveillance was determined. The standards and techniques available worldwide for electronic health data interchange, such as XML, HL7 messaging, CDA and ATSM CCR, etc. were reviewed and compared, and an XML implementation format needed for this purpose was defined for hospitals that are able to access the Internet to provide a complete infectious disease reporting. RESULTS: There are 18,703 county or city hospitals in China. All of them have access to basic information infrastructures including computers, e-mail and the Internet. Nearly 10,000 hospitals possess hospital information systems used for electronically recording, retrieving and manipulating patients' information. These systems collect 23 data items required in the minimum data set for national notifiable infectious disease reporting. In order to transmit these data items to the disease surveillance system and local health information systems instantly and without duplication of data input, an XML schema and a set of standard data elements were developed to define the content, structure and semantics of the data set. These standards make it possible to view and analyse the data accurately outside the hospital information systems in many different document formats. The paper also identified other issues involved in notifiable disease reporting in the future, such as the adoption of approved vocabulary standards and implementation problems such as the route, secure transfer, parsing, and objective identifying of the XML message. CONCLUSIONS: XML is an increasingly important standard for exchange and transmission of data between disparate applications and systems. As in its early stages of developing an interoperable health information system in China, the XML document structures could be a way to exchange the notifiable case information among interest parties on the web at present.     

Considering complexity in healthcare systems

A recent trend in the literature has been to characterize healthcare activities in terms of complex systems theory. Complexity has often been loosely and variously defined, with meanings ranging from “not simple” to “complicated” to “intractable.” In this paper, we consider various aspects of complexity and how they relate to modern healthcare practice, with the aim of developing research approaches for studying complex healthcare environments. We propose a theoretical lens for understanding and studying complexity in healthcare systems based on degrees of interrelatedness of system components. We also describe, with relevant caveats, how complex healthcare systems are generally decomposable, rendering them more tractable for further study. The ideas of interrelatedness among the components of a system as a measure of complexity and functional decomposition as a mechanism for studying meaningful subcomponents of a complex system can be used as a framework for understanding complex healthcare systems. Using examples drawn from current literature and our own research, we explain the feasibility of this approach for understanding, studying, and managing complex healthcare systems.     

SANDS: a service-oriented architecture for clinical decision support in a National Health Information Network

In this paper, we describe and evaluate a new distributed architecture for clinical decision support called SANDS (Service-oriented Architecture for NHIN Decision Support), which leverages current health information exchange efforts and is based on the principles of a service-oriented architecture. The architecture allows disparate clinical information systems and clinical decision support systems to be seamlessly integrated over a network according to a set of interfaces and protocols described in this paper. The architecture described is fully defined and developed, and six use cases have been developed and tested using a prototype electronic health record which links to one of the existing prototype National Health Information Networks (NHIN): drug interaction checking, syndromic surveillance, diagnostic decision support, inappropriate prescribing in older adults, information at the point of care and a simple personal health record. Some of these use cases utilize existing decision support systems, which are either commercially or freely available at present, and developed outside of the SANDS project, while other use cases are based on decision support systems developed specifically for the project. Open source code for many of these components is available, and an open source reference parser is also available for comparison and testing of other clinical information systems and clinical decision support systems that wish to implement the SANDS architecture.The SANDS architecture for decision support has several significant advantages over other architectures for clinical decision support. The most salient of these are:

1. Greater modularity than other architectures, allowing for work to be distributed.

2. The potential for creating and sustaining a commercial market for clinical decision support.

3. Reduced cost and risk of trying new decision support systems because of its ability to easily integrate a variety of decision support services, and to easily remove them, if desired, as well.

4. Significant freedom for developers of clinical decision support systems to choose the way they represent knowledge and internally implement their system, in comparison to other approaches which constrain such developers to a particular knowledge representation formalism.

5. Unification of the direction and agenda of decision support research and development with promising near-term efforts to improve interoperability of clinical systems.

Comparison of different methods of bacterial detection in blood components

Background Over the last two decades, the residual risk of acquiring a transfusion-transmitted viral infection has been reduced to less than 1 : 1 000 000 via improvements in different techniques (e.g. donor selection, leuco-depletion, introduction of 3rd or 4th generation enzyme-linked immunosorbent assays and mini-pool nucleic acid testing (MP-NAT). In contrast, the risk for transfusion-associated bacterial infections has remained fairly stable, and is estimated to be in a range between 1 : 2000 and 1 : 3000. Platelets are at an especially higher risk for bacterial contamination, because they are stored at room temperature, which provides good culture conditions for a broad range of bacterial strains. To improve bacterial safety of blood products, different detection systems have been developed that can be divided into culture systems like BacT/ALERT or Pall eBDS, rapid detection systems like NAT systems, immunoassays and systems based on the FACS technique. Culture systems are used for routine bacterial screening of platelets in many countries, whereas rapid detection systems so far are mainly used in experimental spiking studies. Nevertheless, pathogen-reduction systems are currently available for platelet concentrates and plasma, and are under investigation for erythrocytes. Methods In this review, the functional principles of the different assays are described and discussed with regard to their analytical sensitivity, analytical specificity, diagnostic sensitivity, diagnostic specificity and clinical efficiency. The detection methods were clustered into three groups: (i) detection systems currently used for routine screening of blood products, (ii) experimental detection systems ready to use for routine screening of blood products, and (iii) new experimental detection systems that need to be investigated in additional spiking studies and clinical trials. Results A recent International Society of Blood Transfusion international forum reported on bacterial detection methods in 12 countries. Eight countries have implemented BacT/ALERT into blood donor screening, whereas in three countries only quality controls were done by culture methods. In one country, shelf-life was reduced to 3 days, so no bacterial screening was implemented. Screening data with culture methods can be used to investigate the prevalence of bacterial contamination in platelets. Differing results between the countries could be explained by different test definitions and different test strategies. Nevertheless, false-negative results causing severe transfusion-related septic reactions have been reported all over the world due to a residual risk of sample errors. Rapid screening systems NAT and FACS assays have improved over the last few years and are now ready to be implemented in routine screening. Non-specific amplification in NAT can be prevented by pre-treatment with Sau3AI, filtration of NAT reagents, or reduction of the number of polymerase chain reaction cycles. FACS systems offer easy fully automated handling and a handling time of only 5 min, which could be an option for re-testing day-5 platelets. New screening approaches like immunoassays, detection of bacterial adenosine triphosphate, or detection of esterase activity need to be investigated in additional studies. Conclusion Bacterial screening of blood products, especially platelets, can be done with a broad range of technologies. The ideal system should be able to detect one colony-forming unit per blood bag without a delay in the release process. Currently, we are far away from such an ideal screening system. Nevertheless, pathogen-inactivation systems are available, but a system for all blood components will not be expected in the next few years. Therefore, existing culture systems should be complemented by rapid systems like NAT or FACS especially for day-5 platelets.     

Integrated Personal Health and Care Services deployment: Experiences in eight European countries

ObjectivesThe deployment and adoption of Integrated Personal Health and Care Services in Europe has been slow and fragmented. There have been many initiatives and projects of this kind in different European regions, many of which have not gone beyond the pilot stage. We investigated the necessary conditions for mainstreaming these services into care provision.MethodsWe conducted a qualitative analysis of 27 Telehealth, Telecare and Integrated Personal Health System projects, implemented across 20 regions in eight European countries. The analysis was based on Suter's ten key principles for successful health systems integration.ResultsOut of the 27 cases, we focussed on 11 which continued beyond the pilot stage. The key facilitators that are necessary for successful deployment and adoption in the European regions of our study are reorganisation of services, patient focus, governance mechanisms, interoperable information systems, policy commitment, engaged professionals, national investments and funding programmes, and incentives and financing.ConclusionIn those cases which provided evidence of success beyond the pilot stage, we observed a promising trend: awareness and introduction of Integrated Personal Health and Care Services in European regions has increased. Further research will reveal the weight of each facilitator and which combinations of facilitators lead to rapid adoption.     

The outcomes of regional healthcare information systems in health care: A review of the research literature

The resulting regional healthcare information systems were expected to have effects and impacts on health care procedures, work practices and treatment outcomes. The aim is to find out how health information systems have been investigated, what has been investigated and what are the outcomes. A systematic review was carried out of the research on the regional health information systems or organizations. The literature search was conducted on four electronic Cinahl Medline, Medline/PubMed and Cochrane. The common type of study design was the survey research and case study, and the data collection was carried out via different methodologies. They found out different types of regional health information systems (RHIS). The systems were heterogeneous and were in different phases of these developments. The RHIS outcomes focused on the five main areas: flow of information, collaboration, process redesign, system usability and organization culture. The RHIS improved the clinical data access, timely information, and clinical data exchange and improvement in communication and coordination within a region between professionals but also there was inadequate access to patient relevant clinical data. There were differences in organization culture, vision and expectations of leadership and consistency of strategic plan. Nevertheless, there were widespread participation by both healthcare providers and patients.     

Catalogue of knowledge and skills for sleep medicine

Sleep medicine is evolving globally into a medical subspeciality in its own right, and in parallel, behavioural sleep medicine and sleep technology are expanding rapidly. Educational programmes are being implemented at different levels in many European countries. However, these programmes would benefit from a common, interdisciplinary curriculum. This ‘catalogue of knowledge and skills’ for sleep medicine is proposed, therefore, as a template for developing more standardized curricula across Europe. The Board and The Sleep Medicine Committee of the European Sleep Research Society (ESRS) have compiled the catalogue based on textbooks, standard of practice publications, systematic reviews and professional experience, validated subsequently by an online survey completed by 110 delegates specialized in sleep medicine from different European countries. The catalogue comprises 10 chapters covering physiology, pathology, diagnostic and treatment procedures to societal and organizational aspects of sleep medicine. Required levels of knowledge and skills are defined, as is a proposed workload of 60 points according to the European Credit Transfer System (ECTS). The catalogue is intended to be a basis for sleep medicine education, for sleep medicine courses and for sleep medicine examinations, serving not only physicians with a medical speciality degree, but also PhD and MSc health professionals such as clinical psychologists and scientists, technologists and nurses, all of whom may be involved professionally in sleep medicine. In the future, the catalogue will be revised in accordance with advances in the field of sleep medicine.     

Virtual Machine Performance Benchmarking

The attractions of virtual computing are many: reduced costs, reduced resources and simplified maintenance. Any one of these would be compelling for a medical imaging professional attempting to support a complex practice on limited resources in an era of ever tightened reimbursement. In particular, the ability to run multiple operating systems optimized for different tasks (computational image processing on Linux versus office tasks on Microsoft operating systems) on a single physical machine is compelling. However, there are also potential drawbacks. High performance requirements need to be carefully considered if they are to be executed in an environment where the running software has to execute through multiple layers of device drivers before reaching the real disk or network interface. Our lab has attempted to gain insight into the impact of virtualization on performance by benchmarking the following metrics on both physical and virtual platforms: local memory and disk bandwidth, network bandwidth, and integer and floating point performance. The virtual performance metrics are compared to baseline performance on “bare metal.” The results are complex, and indeed somewhat surprising.     

Distinctions between orthographic long-term memory and working memory

Research in the cognitive and neural sciences has long posited a distinction between the long-term memory (LTM) storage of information and the short-term buffering of information that is being actively manipulated in working memory (WM). This basic type of distinction has been posited in a variety of domains, including written language production—spelling. In the domain of spelling, the primary source of empirical evidence regarding this distinction has been cognitive neuropsychological studies reporting deficits selectively affecting what the cognitive neuropsychological literature has referred to as the orthographic lexicon (LTM) or the graphemic buffer (WM). Recent papers have reexamined several of the hallmark characteristics of impairment affecting the graphemic buffer, with implications for our understanding of the nature of the orthographic LTM and WM systems. In this paper, we present a detailed case series study of 4 individuals with acquired spelling deficits and report evidence from both error types and factors influencing error rates that support the traditional distinction between these cognitive systems involved in spelling. In addition, we report evidence indicating possible interaction between these systems, which is consistent with a variety of recent findings in research on spelling.     

Temporal abstraction and temporal Bayesian networks in clinical domains: A survey

ObjectivesTemporal abstraction (TA) of clinical data aims to abstract and interpret clinical data into meaningful higher-level interval concepts. Abstracted concepts are used for diagnostic, prediction and therapy planning purposes. On the other hand, temporal Bayesian networks (TBNs) are temporal extensions of the known probabilistic graphical models, Bayesian networks. TBNs can represent temporal relationships between events and their state changes, or the evolution of a process, through time. This paper offers a survey on techniques/methods from these two areas that were used independently in many clinical domains (e.g. diabetes, hepatitis, cancer) for various clinical tasks (e.g. diagnosis, prognosis). A main objective of this survey, in addition to presenting the key aspects of TA and TBNs, is to point out important benefits from a potential integration of TA and TBNs in medical domains and tasks. The motivation for integrating these two areas is their complementary function: TA provides clinicians with high level views of data while TBNs serve as a knowledge representation and reasoning tool under uncertainty, which is inherent in all clinical tasks.MethodsKey publications from these two areas of relevance to clinical systems, mainly circumscribed to the latest two decades, are reviewed and classified. TA techniques are compared on the basis of: (a) knowledge acquisition and representation for deriving TA concepts and (b) methodology for deriving basic and complex temporal abstractions. TBNs are compared on the basis of: (a) representation of time, (b) knowledge representation and acquisition, (c) inference methods and the computational demands of the network, and (d) their applications in medicine.ResultsThe survey performs an extensive comparative analysis to illustrate the separate merits and limitations of various TA and TBN techniques used in clinical systems with the purpose of anticipating potential gains through an integration of the two techniques, thus leading to a unified methodology for clinical systems. The surveyed contributions are evaluated using frameworks of respective key features. In addition, for the evaluation of TBN methods, a unifying clinical domain (diabetes) is used.ConclusionThe main conclusion transpiring from this review is that techniques/methods from these two areas, that so far are being largely used independently of each other in clinical domains, could be effectively integrated in the context of medical decision-support systems. The anticipated key benefits of the perceived integration are: (a) during problem solving, the reasoning can be directed at different levels of temporal and/or conceptual abstractions since the nodes of the TBNs can be complex entities, temporally and structurally and (b) during model building, knowledge generated in the form of basic and/or complex abstractions, can be deployed in a TBN.