Mapping turnaround times (TAT) to a generic timeline: a systematic review of TAT definitions in clinical domains.

BACKGROUND: Assessing turnaround times can help to analyse workflows in hospital information systems. This paper presents a systematic review of literature concerning different turnaround time definitions. Our objectives were to collect relevant literature with respect to this kind of process times in hospitals and their respective domains. We then analysed the existing definitions and summarised them in an appropriate format. METHODS: Our search strategy was based on Pubmed queries and manual reviews of the bibliographies of retrieved articles. Studies were included if precise definitions of turnaround times were available. A generic timeline was designed through a consensus process to provide an overview of these definitions. RESULTS: More than 1000 articles were analysed and resulted in 122 papers. Of those, 162 turnaround time definitions in different clinical domains were identified. Starting and end points vary between these domains. To illustrate those turnaround time definitions, a generic timeline was constructed using preferred terms derived from the identified definitions. The consensus process resulted in the following 15 terms: admission, order, biopsy/examination, receipt of specimen in laboratory, procedure completion, interpretation, dictation, transcription, verification, report available, delivery, physician views report, treatment, discharge and discharge letter sent. Based on this analysis, several standard terms for turnaround time definitions are proposed. CONCLUSION: Using turnaround times to benchmark clinical workflows is still difficult, because even within the same clinical domain many different definitions exist. Mapping of turnaround time definitions to a generic timeline is feasible.

The single source architecture x4T to connect medical documentation and clinical research.

Clinical trials often require large and redundant documentation efforts, because information systems in patient care and research are separated. In two clinical trials we have assessed the number of study items available in the clinical information system for re-use in clinical research. We have analysed common standards such as HL7, IHE RFD and CDISC ODM, regulatory constraints and the documentation process. Based on this analysis we have designed and implemented an architecture for an integrated clinical trial documentation workflow. Key aspects are the re-use of existing medical routine data and the integration into current documentation workflows.

Multidisciplinary education in medical informatics--a course for medical and informatics students.

Design and implementation of healthcare information systems affect both computer scientists and health care professionals. In this paper we present our approach to integrate the management of information systems in the education of healthcare professionals and computer scientists alike. We designed a multidisciplinary course for medical and informatics students to provide them with practical experience concerning the design and implementation of medical information systems. This course was implemented in the curriculum of the University of Münster in 2009. The key element is a case study that is performed by small teams of medical and informatics students. A practical course on management of information systems can be useful for medical students who want to enhance their knowledge in information systems as well as for informatics students with particular interests in medicine.

Human-Induced Errors in Networked Healthcare Research: Risk Management Under the GDPR.

Modern research projects in healthcare research and medical research are oftentimes multi-centered, multi-disciplinary, and conducted by a consortium of multiple collaborators. Increasingly, the resulting data emanating emerging from different primary and secondary sources is linked on a personal level. The General Data Protection Regulation regulates many fundamental processes in such research projects. Despite the regulatory framework given, it can happen that a collaborator does not handle data properly. We propose a systematic risk management for the handling of data as well as a systematic error management.

Single source information systems to connect patient care and clinical research.

Currently documentation processes for routine patient care and clinical research are kept separate (dual source). Due to overlaps between routine and research documentation, a single source approach provides opportunities to improve efficiency of medical documentation given the large workload of physicians related to documentation. Organisational, technical and regulatory conditions need to be considered for the design of single source systems. We present a single source architecture for clinical studies and provide results from pilot implementations.

A Generic IT Infrastructure for Identity Management and Pseudonymization in Small Research Projects with Heterogeneous and Distributed Data Sources Under Consideration of the GDPR.

Each year, millions of rescue operations occur in Germany. Despite rising numbers, there is a shortfall of systematic quality management (QM). Focusing on finding the required quality parameters, this work aims at linking heterogeneous and distributed data sources on the patient-level. Presented here is necessary IT infrastructure for linking patients' data records properly and efficiently. The focus of the IT infrastructure is to provide a lightweight and easy applicable solution with an utmost generic approach.

Automated Report Generation for Research Data Repositories: From i2b2 to PDF.

We developed an automated toolchain to generate reports of i2b2 data. It is based on free open source software and runs on a Java Application Server. It is sucessfully used in an ED registry project. The solution is highly configurable and portable to other projects based on i2b2 or compatible factual data sources.

Mapping Equivalence of German Emergency Department Medical Record Concepts with SNOMED CT After Implementation with HL7 CDA.

INTRODUCTION: The German Emergency Department Medical Record (GEDMR) was created by medical domain experts and healthcare providers providing a dataset as well as a form. The trauma module of GEDMR was syntactically standardized using HL7 CDA and semantically standardized using different terminologies including SNOMED CT, LOINC and proprietary coding systems. This study depicts the mapping accuracy with aforementioned syntactical and semantical standards in general and especially the content coverage of SNOMED CT. METHODS: The specification of GEDMR (V2015.1) concepts with eHealth-standards HL7-CDA, LOINC, SNOMED CT was analyzed. A content coverage assessment was made using the ISO TR 12300 rating scheme, following descriptive analysis. RESULTS: The trauma module of GEDMR contains 489 concepts, with 202 concepts expressed via HL7 CDA structure. It is possible to code 89 % of the remaining concepts via SNOMED CT. 79 % provide an advanced level of semantic interoperability, as they represent the source information either lexically or as an approved synonym. DISCUSSION: The terminology binding problem is relevant when combining different standards for syntactic and semantic interoperability with best practice documents and reference specifications providing guidance. A national license and extension for SNOMED CT in Germany as well as an ongoing effort in contributing to the International Version of SNOMED CT would be necessary to gain full coverage for concepts in German Emergency Medicine and to leverage the associated standardization process.

Asynchronous Query Distribution Between Multiple i2b2 Research Data Warehouses: Li2b2-SHRINE.

Clinical Data Ware Houses are established sources for research and quality management. The open source data warehouse software i2b2 enjoys good reputation and wide-spread use in the international medical informatics community. We developed a novel infrastructure to allow queries to be distributed asynchronously between i2b2 data warehouses.

Disseminating a Standard for Medical Records in Emergency Departments Among Different Software Vendors Using HL7 CDA.

A standardized medical record for the emergency department (GEDMR) was released in Germany, but only sparsely and randomly implemented by emergency department (ED) electronic health record (EHR) vendors. A reason for this may be a lacking common language between the medical and the Health Information Technology (HIT) domain. HL7 clinical document architecture (CDA) may leverage this communication gap. This paper reports on the effects of a professional medical association record standard on EHR vendors and the German ED-EHR market. Standard records and data standards are developed and published by different institutions either on governmental, healthcare agency or medical association level. There are some standard records, especially by US cardiology associations, transformed into HL7 C-CDA. GEDMR was modeled as HL7 CDA with the use of interoperable terminologies like LOINC and SNOMED CT. Being part of an emergency department data registry development project, local deployment at 15 project hospitals receiving sufficient funding was performed. Two major ED-EHR vendors adapted GEDMR within their product including CDA export. 106,868 CDAs were produced in six hospitals until now. Four local implementations with four different ED-EHRs were developed, producing 42,256 CDAs. Five additional vendors are adapting or developing an ED-EHR. The GEDMR-CDA implementation guide with funding for implementation in project hospitals had a significant impact on the German ED-EHR market. Within two years after release, a broadening and increasingly self-enforcing support by German ED-EHR vendors is notable.

Heterologous expression and characterization of a novel branching enzyme from the thermoalkaliphilic anaerobic bacterium Anaerobranca gottschalkii.

The gene encoding the branching enzyme (BE) from the thermoalkaliphilic, anaerobic bacterium Anaerobranca gottschalkii was fused with a twin arginine translocation protein secretory-pathway-dependent signal sequence from Escherichia coli and expressed in Staphylococcus carnosus. The secreted BE was purified using hydrophobic interaction and gel filtration chromatography. The monomeric enzyme (72 kDa) shows maximal activity at 50 degrees C and pH 7.0. With amylose the BE displays high transglycosylation and extremely low hydrolytic activity. The conversion of amylose and linear dextrins was analysed by applying high-performance anion exchange chromatography and quantitative size-exclusion chromatography. Amylose (10(4)-4 x 10(7) g/mol) was converted to a major extent to products displaying molecular masses of 10(4)-4 x 10(5) g/mol, indicating that the enzyme could be applicable for the production of starch or dextrins with narrow molecular mass distributions. The majority of the transferred oligosaccharides, determined after enzymatic hydrolysis of the newly synthesized alpha-1,6 linkages, ranged between 10(3) and 10(4) g/mol, which corresponds to a degree of polymerisation (DP) of 6-60. The minimal donor chain length is DP 16. Furthermore, the obtained results support the hypotheses of a random endocleavage mechanism of BE and the occurrence of interchain branching.

Desulfotignum phosphitoxidans sp. nov., a new marine sulfate reducer that oxidizes phosphite to phosphate.

A new sulfate-reducing bacterium was isolated from marine sediment with phosphite as sole electron donor and CO(2) as the only carbon source. Strain FiPS-3 grew slowly, with doubling times of 3-4 days, and oxidized phosphite, hydrogen, formate, acetate, fumarate, pyruvate, glycine, glutamate, and other substrates nearly completely, with concomitant reduction of sulfate to sulfide. Acetate was formed as a side product to a small extent. Glucose, arabinose, and proline were partly oxidized and partly fermented to acetate plus propionate. Growth with phosphite, hydrogen, or formate was autotrophic. Also, in the presence of sulfate, CO dehydrogenase was present, and added acetate did not increase growth rates or growth yields. In the absence of sulfate, phosphite oxidation was coupled to homoacetogenic acetate formation, with growth yields similar to those in the presence of sulfate. Cells were small rods, 0.6 - 0.8 x 2-4 microm in size, and gram-negative, with a G+C content of 53.9 mol%. They contained desulforubidin, but no desulfoviridin. Based on sequence analysis of the 16S rRNA gene and the sulfite reductase genes dsrAB, strain FiPS-3 was found to be closely related to Desulfotignum balticum. However, physiological properties differed in many points from those of D. balticum. These findings justify the establishment of a new species, Desulfotignum phosphitoxidans.

Characterisation of a thermoalkali-stable cyclodextrin glycosyltransferase from the anaerobic thermoalkaliphilic bacterium Anaerobranca gottschalkii.

The thermoalkaliphilic anaerobic bacterium Anaerobranca gottschalkii produces an extracellular CGTase when grown on starch at 55 degrees C and pH 9.0. The gene encoding this CGTase was cloned and successfully expressed in Escherichia coli. It encodes a protein consisting of 721 amino acids with a signal sequence of 34 amino acids. On SDS-polyacrylamide gels, the purified CGTase from A. gottschalkii displayed the expected molecular mass of 78 kDa. The recombinant enzyme was purified with a yield of 13.5% and displayed a specific activity of 210 units/mg. This CGTase, which represents the first report of a CGTase from an anaerobic thermoalkaliphile, was active at a broad range of temperature and pH, namely 55-70 degrees C and pH 5-10. It completely converted amylose, amylopectin and native starch to cyclodextrins, preferentially alpha-cyclodextrin. With a longer incubation period, the alpha-cyclodextrin to beta-cyclodextrin ratio declined. Variations in substrate type and concentration influenced the product pattern. Increasing the substrate concentration (0.5-20.0%) and glucans containing branching points (alpha-1,6 glycosidic linkages) shifted the product pattern to: beta-cyclodextin > alpha-cyclodextrin > gamma-cyclodextrin. In addition to these cyclodextrins, larger cyclodextrins (>8 glucose units) were formed in the initial reaction period. The CGTase was stabilised against thermal inactivation by calcium ions and high substrate concentrations; and 5 mM of CaCl(2) shifted the apparent melting point of the enzyme from 60 degrees C to 69 degrees C.