Large-scale duplication events underpin population-level flexibility in tRNA gene copy number in Pseudomonas fluorescens SBW25.

The complement of tRNA genes within a genome is typically considered to be a (relatively) stable characteristic of an organism. Here, we demonstrate that bacterial tRNA gene set composition can be more flexible than previously appreciated, particularly regarding tRNA gene copy number. We report the high-rate occurrence of spontaneous, large-scale, tandem duplication events in laboratory populations of the bacterium Pseudomonas fluorescens SBW25. The identified duplications are up to ∼1 Mb in size (∼15% of the wildtype genome) and are predicted to change the copy number of up to 917 genes, including several tRNA genes. The observed duplications are inherently unstable: they occur, and are subsequently lost, at extremely high rates. We propose that this unusually plastic type of mutation provides a mechanism by which tRNA gene set diversity can be rapidly generated, while simultaneously preserving the underlying tRNA gene set in the absence of continued selection. That is, if a tRNA set variant provides no fitness advantage, then high-rate segregation of the duplication ensures the maintenance of the original tRNA gene set. However, if a tRNA gene set variant is beneficial, the underlying duplication fragment(s) may persist for longer and provide raw material for further, more stable, evolutionary change.

The evaluation of TheraBite and wooden tongue depressor in the treatment of trismus and health-related quality of life.

OBJECTIVE: This study aimed to compare the efficacy of TheraBite system and a wooden tongue depressor in head and neck cancer (HNC) patients and assess their quality of life (QoL) using modified questionnaires. PATIENTS AND METHODS: The effects of exercise using TheraBite and a wooden tongue depressor on trismus were evaluated in 40 HNC and 10 healthy individuals. All patients performed the exercise program for 3 weeks, with a follow-up session. The patients' pre-treatment and post-treatment mouth opening (MO) values were recorded. The HNC patients completed the QoL questionnaire after the treatment. RESULTS: The highest mean value of MO pre-treatment scores was recorded in the control group (p < 0.05). The differences among all the scores for QoL questionnaires were insignificant (p > 0.05). CONCLUSIONS: TheraBite system increased MO compared to a wooden tongue depressor. The questionnaire revealed that radiotherapy had side effects on patients.

Interoperable E-Health System Using Structural and Semantic Interoperability Approaches in CAREPATH.

Technical and semantic interoperability are broadly used components of interoperability technology in healthcare. Technical Interoperability provides interoperability interfaces to enable data exchange within different healthcare systems, despite any underlying heterogeneity. Semantic interoperability make different healthcare systems understand and interpret the meaning of the data that is exchanged, by using and mapping standardized terminologies, coding systems, and data models to describe the concept and structure of data. We propose a solution using Semantic and Structural Mapping techniques within CAREPATH; a research project designed to develop ICT solutions for the care management of elderly multimorbid patients with mild cognitive impairment or mild dementia. Our technical interoperability solution supplies a standard-based data exchange protocol to enable information exchange between local care systems and CAREPATH components. Our semantic interoperability solution supplies programmable interfaces, in order to semantically mediate different clinical data representation formats and incorporating data format and terminology mapping features. The solution offers a more reliable, flexible and resource efficient method across EHRs.

Implementation of HL7 FHIR-Based Interoperability Profiles to Manage Care Plans for Multimorbid Patients with Mild Dementia.

Management of multimorbidity in patients with mild dementia and mild cognitive impairment introduces additional challenges. The CAREPATH project provides an integrated care platform to assist both healthcare professionals and patients and their informal caregivers in the day-to-day management of care plans for this patient population. This paper introduces an HL7 FHIR-based interoperability approach for exchanging care plan action and goals with the patients and collecting feedback and adherence information from patients. In this way, seamless information exchange between healthcare professionals, patients and their informal care givers is achieved to support patients in their self-care management journey and increase their adherence to their care plans despite the burdens of mild dementia.

The birth of a bacterial tRNA gene by large-scale, tandem duplication events.

Organisms differ in the types and numbers of tRNA genes that they carry. While the evolutionary mechanisms behind tRNA gene set evolution have been investigated theoretically and computationally, direct observations of tRNA gene set evolution remain rare. Here, we report the evolution of a tRNA gene set in laboratory populations of the bacterium Pseudomonas fluorescens SBW25. The growth defect caused by deleting the single-copy tRNA gene, serCGA, is rapidly compensated by large-scale (45-290 kb) duplications in the chromosome. Each duplication encompasses a second, compensatory tRNA gene (serTGA) and is associated with a rise in tRNA-Ser(UGA) in the mature tRNA pool. We postulate that tRNA-Ser(CGA) elimination increases the translational demand for tRNA-Ser(UGA), a pressure relieved by increasing serTGA copy number. This work demonstrates that tRNA gene sets can evolve through duplication of existing tRNA genes, a phenomenon that may contribute to the presence of multiple, identical tRNA gene copies within genomes.

Increasing the Size-Selectivity in Laser-Based g/h Liquid Flow Synthesis of Pt and PtPd Nanoparticles for CO and NO Oxidation in Industrial Automotive Exhaust Gas Treatment Benchmarking.

PtPd catalysts are state-of-the-art for automotive diesel exhaust gas treatment. Although wet-chemical preparation of PtPd nanoparticles below 3 nm and kg-scale synthesis of supported PtPd/Al2O3 are already established, the partial segregation of the bimetallic nanoparticles remains an issue that adversely affects catalytic performance. As a promising alternative, laser-based catalyst preparation allows the continuous synthesis of surfactant-free, solid-solution alloy nanoparticles at the g/h-scale. However, the required productivity of the catalytically relevant size fraction <10 nm has yet to be met. In this work, by optimization of ablation and fragmentation conditions, the continuous flow synthesis of nanoparticles with a productivity of the catalytically relevant size fraction <10 nm of >1 g/h is presented via an in-process size tuning strategy. After the laser-based preparation of hectoliters of colloid and more than 2 kg of PtPd/Al2O3 wash coat, the laser-generated catalysts were benchmarked against an industry-relevant reference catalyst. The conversion of CO by laser-generated catalysts was found to be equivalent to the reference, while improved activity during NO oxidation was achieved. Finally, the present study validates that laser-generated catalysts meet the size and productivity requirements for industrial standard operating procedures. Hence, laser-based catalyst synthesis appears to be a promising alternative to chemical-based preparation of alloy nanoparticles for developing industrial catalysts, such as those needed in the treatment of exhaust gases.

From Raw Data to FAIR Data: The FAIRification Workflow for Health Research.

BACKGROUND: FAIR (findability, accessibility, interoperability, and reusability) guiding principles seek the reuse of data and other digital research input, output, and objects (algorithms, tools, and workflows that led to that data) making them findable, accessible, interoperable, and reusable. GO FAIR - a bottom-up, stakeholder driven and self-governed initiative - defined a seven-step FAIRification process focusing on data, but also indicating the required work for metadata. This FAIRification process aims at addressing the translation of raw datasets into FAIR datasets in a general way, without considering specific requirements and challenges that may arise when dealing with some particular types of data. OBJECTIVES: This scientific contribution addresses the architecture design of an open technological solution built upon the FAIRification process proposed by "GO FAIR" which addresses the identified gaps that such process has when dealing with health datasets. METHODS: A common FAIRification workflow was developed by applying restrictions on existing steps and introducing new steps for specific requirements of health data. These requirements have been elicited after analyzing the FAIRification workflow from different perspectives: technical barriers, ethical implications, and legal framework. This analysis identified gaps when applying the FAIRification process proposed by GO FAIR to health research data management in terms of data curation, validation, deidentification, versioning, and indexing. RESULTS: A technological architecture based on the use of Health Level Seven International (HL7) FHIR (fast health care interoperability resources) resources is proposed to support the revised FAIRification workflow. DISCUSSION: Research funding agencies all over the world increasingly demand the application of the FAIR guiding principles to health research output. Existing tools do not fully address the identified needs for health data management. Therefore, researchers may benefit in the coming years from a common framework that supports the proposed FAIRification workflow applied to health datasets. CONCLUSION: Routine health care datasets or data resulting from health research can be FAIRified, shared and reused within the health research community following the proposed FAIRification workflow and implementing technical architecture.

Localisation, Personalisation and Delivery of Best Practice Guidelines on an Integrated Care and Cure Cloud Architecture: The C3-Cloud Approach to Managing Multimorbidity.

BACKGROUND: C3-Cloud is an integrated care ICT infrastructure offering seamless patient-centered approach to managing multimorbidity, deployed in three European pilot sites. Challenge: The digital delivery of best practice guidelines unified for multimorbidity, customized to local practice, offering the capability to improve patient personalization and benefit. METHOD: C3-Cloud has adopted a co-production approach to developing unified multimorbidity guidelines, by collating and reconciling best practice guidelines for each condition. Clinical and technical teams at pilot sites and the C3-Cloud consortium worked in tandem to create the specification and technical implementation. RESULTS: C3-Cloud offers CDSS for diabetes, renal failure, depression and congenital heart failure, with over 300 rules and checks that deliver four best practice guidelines in parallel, customized for each pilot site. CONCLUSIONS: The process provided a traceable, maintainable and audited digitally delivered collated and reconciled guidelines.

A Collaborative Platform for Management of Chronic Diseases via Guideline-Driven Individualized Care Plans.

Older age is associated with an increased accumulation of multiple chronic conditions. The clinical management of patients suffering from multiple chronic conditions is very complex, disconnected and time-consuming with the traditional care settings. Integrated care is a means to address the growing demand for improved patient experience and health outcomes of multimorbid and long-term care patients. Care planning is a prevalent approach of integrated care, where the aim is to deliver more personalized and targeted care creating shared care plans by clearly articulating the role of each provider and patient in the care process. In this paper, we present a method and corresponding implementation of a semi-automatic care plan management tool, integrated with clinical decision support services which can seamlessly access and assess the electronic health records (EHRs) of the patient in comparison with evidence based clinical guidelines to suggest personalized recommendations for goals and interventions to be added to the individualized care plans. We also report the results of usability studies carried out in four pilot sites by patients and clinicians.

A Privacy Management Analysis (PMA) of Exchanging International Patient Summary.

This paper provides a summary of the Privacy Management Analysis method followed for the analysis of the International Patient Summary exchange use cases of Trillium II Project. The objective is to recommend the required security and privacy measures by providing traceability from Regulations/Principles/Preferences to the recommended Security & Privacy Measures that needs to be implemented in pilots.

A Semantic Transformation Methodology for the Secondary Use of Observational Healthcare Data in Postmarketing Safety Studies.

Background: Utilization of the available observational healthcare datasets is key to complement and strengthen the postmarketing safety studies. Use of common data models (CDM) is the predominant approach in order to enable large scale systematic analyses on disparate data models and vocabularies. Current CDM transformation practices depend on proprietarily developed Extract-Transform-Load (ETL) procedures, which require knowledge both on the semantics and technical characteristics of the source datasets and target CDM. Purpose: In this study, our aim is to develop a modular but coordinated transformation approach in order to separate semantic and technical steps of transformation processes, which do not have a strict separation in traditional ETL approaches. Such an approach would discretize the operations to extract data from source electronic health record systems, alignment of the source, and target models on the semantic level and the operations to populate target common data repositories. Approach: In order to separate the activities that are required to transform heterogeneous data sources to a target CDM, we introduce a semantic transformation approach composed of three steps: (1) transformation of source datasets to Resource Description Framework (RDF) format, (2) application of semantic conversion rules to get the data as instances of ontological model of the target CDM, and (3) population of repositories, which comply with the specifications of the CDM, by processing the RDF instances from step 2. The proposed approach has been implemented on real healthcare settings where Observational Medical Outcomes Partnership (OMOP) CDM has been chosen as the common data model and a comprehensive comparative analysis between the native and transformed data has been conducted. Results: Health records of ~1 million patients have been successfully transformed to an OMOP CDM based database from the source database. Descriptive statistics obtained from the source and target databases present analogous and consistent results. Discussion and Conclusion: Our method goes beyond the traditional ETL approaches by being more declarative and rigorous. Declarative because the use of RDF based mapping rules makes each mapping more transparent and understandable to humans while retaining logic-based computability. Rigorous because the mappings would be based on computer readable semantics which are amenable to validation through logic-based inference methods.

Postmarketing Safety Study Tool: A Web Based, Dynamic, and Interoperable System for Postmarketing Drug Surveillance Studies.

Postmarketing drug surveillance is a crucial aspect of the clinical research activities in pharmacovigilance and pharmacoepidemiology. Successful utilization of available Electronic Health Record (EHR) data can complement and strengthen postmarketing safety studies. In terms of the secondary use of EHRs, access and analysis of patient data across different domains are a critical factor; we address this data interoperability problem between EHR systems and clinical research systems in this paper. We demonstrate that this problem can be solved in an upper level with the use of common data elements in a standardized fashion so that clinical researchers can work with different EHR systems independently of the underlying information model. Postmarketing Safety Study Tool lets the clinical researchers extract data from different EHR systems by designing data collection set schemas through common data elements. The tool interacts with a semantic metadata registry through IHE data element exchange profile. Postmarketing Safety Study Tool and its supporting components have been implemented and deployed on the central data warehouse of the Lombardy region, Italy, which contains anonymized records of about 16 million patients with over 10-year longitudinal data on average. Clinical researchers in Roche validate the tool with real life use cases.

Environmental fluctuations restrict eco-evolutionary dynamics in predator-prey system.

Environmental fluctuations, species interactions and rapid evolution are all predicted to affect community structure and their temporal dynamics. Although the effects of the abiotic environment and prey evolution on ecological community dynamics have been studied separately, these factors can also have interactive effects. Here we used bacteria-ciliate microcosm experiments to test for eco-evolutionary dynamics in fluctuating environments. Specifically, we followed population dynamics and a prey defence trait over time when populations were exposed to regular changes of bottom-up or top-down stressors, or combinations of these. We found that the rate of evolution of a defence trait was significantly lower in fluctuating compared with stable environments, and that the defence trait evolved to lower levels when two environmental stressors changed recurrently. The latter suggests that top-down and bottom-up changes can have additive effects constraining evolutionary response within populations. The differences in evolutionary trajectories are explained by fluctuations in population sizes of the prey and the predator, which continuously alter the supply of mutations in the prey and strength of selection through predation. Thus, it may be necessary to adopt an eco-evolutionary perspective on studies concerning the evolution of traits mediating species interactions.

Adverse drug event notification on a semantic interoperability framework.

Adverse drug events (ADEs) are common, costly and one of the most important issues in contemporary pharmacotherapy. Current drug safety surveillance methods are largely based on spontaneous reports. However, this is known to be rather ineffective. There is a lack of automated systems checking potential ADEs on routine data captured in electronic health records (EHRs); present systems are usually built directly on top of specific clinical information systems through proprietary interfaces. In the context of the European project "SALUS", we aim to provide an infrastructure as well as a tool-set for accessing and analyzing clinical patient data of heterogeneous clinical information systems utilizing standard methods. This paper focuses on two components of the SALUS architecture: The "Semantic Interoperability Layer" (SIL) enables an access to disparate EHR sources in order to provide the patient data in a common data model for ADE detection within the "ADE Detection and Notification Tool" (ANT). The SIL in combination with the ANT can be used in different clinical environments to increase ADE detection and reporting rates. Thus, our approach promises a profound impact in the domain of pharmacovigilance.

Standard-based EHR-enabled applications for clinical research and patient safety: CDISC - IHE QRPH - EHR4CR & SALUS collaboration.

Integration profiles collaboratively developed by CDISC and IHE for integrating data from Electronic Health Records (EHRs) with clinical research and pharmacovigilance are limited to resolving lexical/syntactic data integration issues and do not address semantic barriers. This paper describes the collaboration between two European projects - EHR4CR and SALUS - in implementing ISO/IEC 11179-based metadata registries (MDRs) and semantically integrated cross-platform data access. A common "semantic MDR" provides a framework for bidirectional/cross-MDR mapping and federated queries are enabled using the newly-defined IHE Data Exchange (DEX) profile. In the pilot implementation, mappings for 178 EHR4CR and 199 SALUS metadata elements were persisted in the semantic MDR. The DEX profile was then used to access semantically equivalent data elements in SALUS or EHR4CR participating EHR systems. ISO/IEC 11179-based MDRs and DEX integration profile address the goal of developing pan-EU computable semantic integration of data from clinical care, clinical research, and patient safety platforms.

A federated semantic metadata registry framework for enabling interoperability across clinical research and care domains.

In order to enable secondary use of Electronic Health Records (EHRs) by bridging the interoperability gap between clinical care and research domains, in this paper, a unified methodology and the supporting framework is introduced which brings together the power of metadata registries (MDR) and semantic web technologies. We introduce a federated semantic metadata registry framework by extending the ISO/IEC 11179 standard, and enable integration of data element registries through Linked Open Data (LOD) principles where each Common Data Element (CDE) can be uniquely referenced, queried and processed to enable the syntactic and semantic interoperability. Each CDE and their components are maintained as LOD resources enabling semantic links with other CDEs, terminology systems and with implementation dependent content models; hence facilitating semantic search, much effective reuse and semantic interoperability across different application domains. There are several important efforts addressing the semantic interoperability in healthcare domain such as IHE DEX profile proposal, CDISC SHARE and CDISC2RDF. Our architecture complements these by providing a framework to interlink existing data element registries and repositories for multiplying their potential for semantic interoperability to a greater extent. Open source implementation of the federated semantic MDR framework presented in this paper is the core of the semantic interoperability layer of the SALUS project which enables the execution of the post marketing safety analysis studies on top of existing EHR systems.

A semantically enriched clinical guideline model enabling deployment in heterogeneous healthcare environments.

Clinical guidelines are developed to assist healthcare practitioners to make decisions on patient's medical problems, and as such they communicate with external applications to retrieve patient data to initiate medical actions through clinical workflows, and transmit information to alert/reminder systems. The interoperability problems in the healthcare information technology domain prevent wider deployment of clinical guidelines because each deployment requires a tedious custom adaptation phase. In this paper, we provide machine-processable mechanisms that express the semantics of clinical guideline interfaces so that automated processes can be used to access the clinical resources for guideline deployment and execution. To be able to deploy the semantically extended guidelines to healthcare settings semiautomatically, the underlying application's semantics must also be available. We describe how this can be achieved based on two prominent implementation technologies in use in the eHealth domain: integrating healthcare enterprise cross-enterprise document sharing integration profile for discovering and exchanging electronic healthcare records and Web service technology for interacting with the clinical workflows and wireless medical sensor devices. The system described in this paper is realized within the scope of the SAPHIRE Project.

Bond strengths of all-ceramics: acid vs laser etching.

Various applications of dental lasers on dental materials have been proposed for surface modifications. This study evaluated whether laser etching could be an alternative to hydrofluoric acid (HF) etching. One hundred and ten lithia-based all-ceramic specimens (Empress 2) (R: 4 mm, h: 4 mm) were prepared and divided into five groups (n = 22/group). The untreated specimens served as the control, while one of the experimental groups was treated with 9.5% HF for 30 seconds. Three remaining test groups were treated with different laser (Er:YAG laser wavelength:2940 nm, OpusDent) power settings: 300 mJ, 600 mJ and 900 mJ. Ten specimens in each group were luted to the other 10 specimens by a dual-curing cement (Variolink II), and shear-bond strength (SBS) tests were performed (Autograph, crosshead speed: 0.5 mm/minute). The results were statistically analyzed (Kruskal Wallis and Mann Whitney-U, alpha = .05). Mean SBS (MPa) were 31.9 +/- 4.0, 41.4 +/- 4.3, 42.8 +/- 6.2, 29.2 +/- 4.5 and 27.4 +/- 3.8 for the control and HF, 300, 600 and 900 mJ groups, respectively. SEM evaluations revealed different surface morphologies depending on the laser parameters. The differences between HF acid and 300 mJ, when compared with the control, 600 and 900 mJ groups, were significant (p < .05). The 300 mJ laser group exhibited the highest shear-bond strength values, indicating that laser etching could also be used for surface treatments.

Enhancing IHE XDS for federated clinical affinity domain support.

One of the key problems in healthcare informatics is the inability to share patient records across enterprises. To address this problem, an important industry initiative called "integrating the healthcare enterprise (IHE)" specified the "cross enterprise document sharing (XDS)" profile. In the IHE XDS, healthcare enterprises that agree to work together form a "clinical affinity domain" and store healthcare documents in an ebXML registry/repository architecture to facilitate their sharing. The affinity domains also agree on a common set of policies such as coding lists to be used to annotate clinical documents in the registry/repository and the common schemes for patient identification. However, since patients expect their records to follow them as they move from one clinical affinity domain to another, there is a need for affinity domains to be federated to enable information exchange. In this paper, we describe how IHE XDS can be enhanced to support federated clinical affinity domains. We demonstrate that federation of affinity domains are facilitated when ontologies, rather than coding term lists, are used to annotate clinical documents. Furthermore, we describe a patient identification protocol that eliminates the need to keep a master patient index file for the federation.