High quality of SARS-CoV-2 molecular diagnostics in a diverse laboratory landscape through supported benchmark testing and External Quality Assessment

A two-step strategy combining assisted benchmark testing (entry controls) and External Quality Assessments (EQAs) with blinded simulated clinical specimens to enhance and maintain the quality of nucleic acid amplification testing was developed. This strategy was successfully applied to 71 diagnostic laboratories in The Netherlands when upscaling the national diagnostic capacity during the SARS-CoV-2 pandemic. The availability of benchmark testing in combination with advice for improvement substantially enhanced the quality of the laboratory testing procedures for SARS-CoV-2 detection. The three subsequent EQA rounds demonstrated high quality testing with regard to specificity (99.6% correctly identified) and sensitivity (93.3% correctly identified). Even with the implementation of novel assays, changing workflows using diverse equipment and a high degree of assay heterogeneity, the overall high quality was maintained using this two-step strategy. We show that in contrast to the limited value of Cq value for absolute proxies of viral load, these Cq values can, in combination with metadata on strategies and techniques, provide valuable information for laboratories to improve their procedures. In conclusion, our two-step strategy (preparation phase followed by a series of EQAs) is a rapid and flexible system capable of scaling, improving, and maintaining high quality diagnostics even in a rapidly evolving (e.g. pandemic) situation.</p

High quality of SARS-CoV-2 molecular diagnostics in a diverse laboratory landscape through supported benchmark testing and External Quality Assessment

A two-step strategy combining assisted benchmark testing (entry controls) and External Quality Assessments (EQAs) with blinded simulated clinical specimens to enhance and maintain the quality of nucleic acid amplification testing was developed. This strategy was successfully applied to 71 diagnostic laboratories in The Netherlands when upscaling the national diagnostic capacity during the SARS-CoV-2 pandemic. The availability of benchmark testing in combination with advice for improvement substantially enhanced the quality of the laboratory testing procedures for SARS-CoV-2 detection. The three subsequent EQA rounds demonstrated high quality testing with regard to specificity (99.6% correctly identified) and sensitivity (93.3% correctly identified). Even with the implementation of novel assays, changing workflows using diverse equipment and a high degree of assay heterogeneity, the overall high quality was maintained using this two-step strategy. We show that in contrast to the limited value of Cq value for absolute proxies of viral load, these Cq values can, in combination with metadata on strategies and techniques, provide valuable information for laboratories to improve their procedures. In conclusion, our two-step strategy (preparation phase followed by a series of EQAs) is a rapid and flexible system capable of scaling, improving, and maintaining high quality diagnostics even in a rapidly evolving (e.g. pandemic) situation.</p

Early diverging lineages within Cryptomycota and Chytridiomycota dominate the fungal communities in ice-covered lakes of the McMurdo Dry Valleys, Antarctica

Antarctic ice-covered lakes are exceptional sites for studying the ecology of aquatic fungi under conditions of minimal human disturbance. In this study, we explored the diversity and community composition of fungi in five permanently covered lake basins located in the Taylor and Miers Valleys of Antarctica. Based on analysis of the 18S rRNA sequences, we showed that fungal taxa represented between 0.93% and 60.32% of the eukaryotic sequences. Cryptomycota and Chytridiomycota dominated the fungal communities in all lakes; however, members of Ascomycota, Basidiomycota, Zygomycota, and Blastocladiomycota were also present. Of the 1313 fungal OTUs identified, the two most abundant, belonging to LKM11 and Chytridiaceae, comprised 74% of the sequences. Significant differences in the community structure were determined among lakes, water depths, habitat features (i.e., brackish vs. freshwaters), and nucleic acids (DNA vs. RNA), suggesting niche differentiation. Network analysis suggested the existence of strong relationships among specific fungal phylotypes as well as between fungi and other eukaryotes. This study sheds light on the biology and ecology of basal fungi in aquatic systems. To our knowledge, this is the first report showing the predominance of early diverging lineages of fungi in pristine limnetic ecosystems, particularly of the enigmatic phylum Cryptomycota.National Science Foundation/[PLR1439774]/NSF/Estados UnidosNational Science Foundation/[PLR1115245]/NSF/Estados UnidosNational Science Foundation/[PLR 1543537]/NSF/Estados UnidosNational Aeronautics and Space Administration/[NNH14ZDA001N-PSTAR]/NASA/Estados UnidosUCR::Vicerrectoría de Docencia::Ciencias Básicas::Facultad de Ciencias::Escuela de Biologí

The Effect of RNA Secondary Structure on&nbsp;the&nbsp;Self-Assembly of Viral Capsids

Previous work has shown that purified capsid protein (CP) of cowpea chlorotic mottle virus (CCMV) is capable of packaging both purified single-stranded RNA molecules of normal composition (comparable numbers of A, U, G, and C nucleobases) and of varying length and sequence, and anionic synthetic polymers such as polystyrene sulfonate. We find that CCMV CP is also capable of packaging polyU RNAs, which-unlike normal-composition RNAs-do not form secondary structures and which act as essentially structureless linear polymers. Following our canonical two-step assembly protocol, polyU RNAs ranging in length from 1000 to 9000 nucleotides (nt) are completely packaged. Surprisingly, negative-stain electron microscopy shows that all lengths of polyU are packaged into 22-nm-diameter particles despite the fact that CCMV CP prefers to form 28-nm-diameter (T&nbsp;= 3) particles when packaging normal-composition RNAs. PolyU RNAs &gt;5000 nt in length are packaged into multiplet capsids, in which a single RNA molecule is shared between two or more 22-nm-diameter capsids, in analogy with the multiplets of 28-nm-diameter particles formed with normal-composition RNAs &gt;5000 nt long. Experiments in which viral RNA competes for viral CP with polyUs of equal length show that polyU, despite its lack of secondary structure, is packaged more efficiently than viral RNA. These findings illustrate that the secondary structure of the RNA molecule-and its absence-plays an essential role in determining capsid structure during the self-assembly of CCMV-like particles

Targeting mechanisms of tailed bacteriophages

Phages differ substantially in the bacterial hosts that they infect. Their host range is determined by the specific structures that they use to target bacterial cells. Tailed phages use a broad range of receptor-binding proteins, such as tail fibres, tail spikes and the central tail spike, to target their cognate bacterial cell surface receptors. Recent technical advances and new structure-function insights have begun to unravel the molecular mechanisms and temporal dynamics that govern these interactions. Here, we review the current understanding of the targeting machinery and mechanisms of tailed phages. These new insights and approaches pave the way for the application of phages in medicine and biotechnology and enable deeper understanding of their ecology and evolution.status: publishe

Rapport richtlijnanalyse diepe veneuze trombose en longembolie.

Dit rapport beschrijft de analyse van zeven richtlijnen voor DVT en/of longembolie (geselecteerd door het Zorginstituut Nederland) en geeft duiding aan de gevonden verschillen in het licht van onder andere de wetenschappelijke onderbouwing en methodologie. Het Zorginstituut Nederland zal de resultaten van deze richtlijnanalyse opnemen in een rapport over de stand van wetenschap en praktijk

Guidelines' risk assessment recommendations for venous thromboembolism prophylaxis: A comparison and implementability appraisal

Introduction: Venous thromboembolism (VTE) prophylaxis guidelines for non-surgical patients recommend VTE- and bleeding risk assessment to guide prophylactic strategies. These recommendations differ between guidelines and implementation is suboptimal. Assessing a guideline's implementability characteristics helps predicting the ease of implementation and reveals barriers. Objectives: We aimed to compare guidelines' risk assessment recommendations and critically appraise the implementability characteristics. Material and methods: Two guidelines, one from the American College of Chest Physicians and one from the National Institute for Health and Care Excellence were selected for comparison. Risk assessment methods and subsequent prophylactic recommendations were compared. Eight experts then appraised the guideline recommendations on intrinsic implementability characteristics using the GuideLine Implementability Appraisal (GLIA) instrument. GLIA identifies barriers and facilitators for guideline implementation in nine dimensions. Results: Eleven out of 20 individual VTE-risk factors and 2 out of 19 individual bleeding-risk factors used, were present in both guidelines. Additionally, a high VTE- or bleeding risk was defined differently between the two guidelines. The GLIA appraisal identified implementation barriers within all recommendations analyzed. On content level, barriers were identified in recommendations addressing bleeding risk assessment, mechanical prophylaxis and critical care patients. On implementability level, barriers were identified in decidability, flexibility, effect on process of care and computability dimensions. Conclusion: Depending on the guideline used, VTE-prophylaxis will most likely be provided to different non-surgical patient populations, primarily due to discordance in bleeding risk assessment. Revising the recommendations, taking into account the most apparent implementation barriers, should be considered. However, insufficient evidence to support the recommendations currently complicates this

Challenges and Stimulating Factors for the Incorporation of Economic Considerations in Clinical Practice Guidelines:A Scoping Review

RATIONALE, AIMS AND OBJECTIVES: The incorporation of economic considerations in clinical practice guidelines (CPGs) could help promote cost-conscious decision-making in healthcare. Though healthcare expenditures increase, and resources are becoming scarcer, the extent to which economic considerations are incorporated into CPGs remains limited. This scoping review aims to identify the challenges and potential stimulating factors to incorporate economic considerations in CPGs. METHOD: This scoping review was conducted following the Joanna Briggs Institute Methodology and findings were reported according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR) guidelines. A systematic search was conducted in eight databases considering literature published from July 2017 and onwards. Data extraction was conducted via an iterative and inductive approach to identify challenges and potential stimulating factors from the included reports. Included documents focused on the (para)medical field and reported on CPG development and economic considerations. RESULTS: The search identified 2445 documents from which 33 documents were included for analysis. The analysis identified five challenges: discourse surrounding economic considerations in CPGs, methodological ambiguities, scarcity of (high-quality) economic evidence, transferability of evidence, and resource constraints. Additionally, three potential stimulating factors were identified: acceptance, economic evidence knowledge, and guidance on incorporating economic considerations. CONCLUSION: These findings reflect the complexity of incorporating economic considerations in CPGs. The identified challenges highlight the need for clearer guidance (i.e. by training) and standardised methodologies for incorporating economic considerations in CPGs. The potential stimulating factors provide a roadmap for future efforts to enhance the integration of economic evidence in CPGs. Collaborative initiatives between health economists, CPG developers, and other stakeholders are essential to drive progress in this area and promote cost-conscious decision-making in healthcare

Unravelling Education Needs for Clinical Practice Guideline Development:A Survey Performed in the Netherlands

ObjectiveThe development of clinical practice guidelines (CPG) has evolved into a rigorous and complex process. There is a need for training of CPG developers including methodologists, panel members and patient representatives. This study explored the educational needs and experiences of CPG developers, with specific attention to the patient perspective and economic considerations.Study Design and SettingAn anonymised mixed-method survey was distributed among CPG developers and panel members in the Netherlands. The survey, developed in collaboration with Dutch CPG development organisations and patient organisations, aimed to capture insights into the developers' roles, training needs, and the incorporation of economic considerations and patient perspectives in CPG development. Data analysis involved qualitative content analysis and descriptive quantitative analysis.ResultsA total of 271 responses were analysed. Respondents described role-specific tasks and tasks overlapping between roles. Experience, guidance, and training influenced the respondents' feeling of preparedness for their tasks. Respondents expressed the need for content-related training, including CPG development methodology. They also raised the importance of process-related topics in training, such as the inclusion of different perspectives and responsibilities during CPG development. About half of the respondents (46%) indicated that economic considerations were included in their CPGs, however, there was no uniformity in approach. The patient perspective was included by 89% of the respondents, also in varying manners. Overall, respondents underscored the importance of both topics in CPG development (training) to ensure a future-proof healthcare system.ConclusionThis study underscores the importance of tailored CPG development training programmes addressing the specific competencies required for the different roles in CPG development. Thereby, recognising a holistic approach encompassing both content- and process-related aspects. Addressing economic considerations and the patient perspective in training will contribute to CPGs that support a patient-centred and sustainable healthcare system

The societal construction of ‘boys’ underachievement’ in educational policies: a cross‐national comparison

Objective: Patient-directed knowledge tools are designed to engage patients in dialogue or deliberation, to support patient decision-making or self-care of chronic conditions. However, an abundance of these exists. The tools themselves and their purposes are not always clearly defined; creating challenges for developers and users (professionals, patients). The study's aim was to develop a conceptual framework of patient-directed knowledge tool types.Methods: A face-to-face evidence-informed consensus meeting with 15 international experts. After the meeting, the framework went through two rounds of feedback before informal consensus was reached.Results: A conceptual framework containing five patient-directed knowledge tool types was developed. The first part of the framework describes the tools' purposes and the second focuses on the tools' core elements.Conclusion: The framework provides clarity on which types of patient-directed tools exist, the purposes they serve, and which core elements they prototypically include. It is a working framework and will require further refinement as the area develops, alongside validation with a broader group of stakeholders.Practice implications: The framework assists developers and users to know which type a tool belongs, its purpose and core elements, helping them to develop and use the right tool for the right job. (C) 2019 Elsevier B.V. All rights reserved.Analysis and support of clinical decision makin