Assessment of the Estonian Research Development Technology and Innovation Funding System

The objectives of the assessment of the RDTI funding system in Estonia as specified by the Terms of Reference are as follows: 1) to conduct a review of the current R&D funding system in Estonia; 2) to review the objectives of the Estonian R&D Strategy 2002-2006; 3) to review best practice in R&D funding elsewhere; and 4) to propose an efficient, transparent and accountable R&D funding system

Evaluating the achievements and impacts of EC framework programme transport projects

Purpose The purpose of this paper is to present what kind of elements and evaluation methods should be included into a framework for evaluating the achievements and impacts of transport projects supported in EC Framework Programmes (FP). Further, the paper discusses the possibilities of such an evaluation framework in producing recommendations regarding future transport research and policy objectives as well as mutual learning for the basis of strategic long term planning. Methods The paper describes the two-dimensional evaluation methodology developed in the course of the FP7 METRONOME project. The dimensions are: (1) achievement of project objectives and targets in different levels and (2) research project impacts according to four impact groups. The methodology uses four complementary approaches in evaluation, namely evaluation matrices, coordinator questionnaires, lead user interviews and workshops. Results Based on the methodology testing, with a sample of FP5 and FP6 projects, the main results relating to the rationale, implementation and achievements of FP projects is presented. In general, achievement of objectives in both FPs was good. Strongest impacts were identified within the impact group of management and co-ordination. Also scientific and end-user impacts of the projects were adequate, but wider societal impacts quite modest. The paper concludes with a discussion both on the theoretical and practical implications of the proposed methodology and by presenting some relevant future research needs

Guidance for studies evaluating the accuracy of rapid tuberculosis drug-susceptibility tests

The development and implementation of rapid molecular diagnostics for tuberculosis (TB) drug-susceptibility testing is critical to inform treatment of patients and to prevent the emergence and spread of resistance. Optimal trial planning for existing tests and those in development will be critical to rapidly gather the evidence necessary to inform World Health Organization review and to support potential policy recommendations. The evidence necessary includes an assessment of the performance for TB and resistance detection as well as an assessment of the operational characteristics of these platforms. The performance assessment should include analytical studies to confirm the limit of detection and assay ability to detect mutations conferring resistance across globally representative strains. The analytical evaluation is typically followed by multisite clinical evaluation studies to confirm diagnostic performance in sites and populations of intended use. This paper summarizes the considerations for the design of these analytical and clinical studies.FIND (Foundation for Innovative New Diagnostics)https://academic.oup.com/jid2020-10-08am2019Medical Microbiolog

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Background The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function. Results Here, we report on the results of the third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experimental assays, resulting in new functional annotations for more than 1000 genes. Specifically, we performed experimental whole-genome mutation screening in Candida albicans and Pseudomonas aureginosa genomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility. We further performed targeted assays on selected genes in Drosophila melanogaster, which we suspected of being involved in long-term memory. Conclusion We conclude that while predictions of the molecular function and biological process annotations have slightly improved over time, those of the cellular component have not. Term-centric prediction of experimental annotations remains equally challenging; although the performance of the top methods is significantly better than the expectations set by baseline methods in C. albicans and D. melanogaster, it leaves considerable room and need for improvement. Finally, we report that the CAFA community now involves a broad range of participants with expertise in bioinformatics, biological experimentation, biocuration, and bio-ontologies, working together to improve functional annotation, computational function prediction, and our ability to manage big data in the era of large experimental screens.Peer reviewe

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

BackgroundThe Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function.ResultsHere, we report on the results of the third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experimental assays, resulting in new functional annotations for more than 1000 genes. Specifically, we performed experimental whole-genome mutation screening in Candida albicans and Pseudomonas aureginosa genomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility. We further performed targeted assays on selected genes in Drosophila melanogaster, which we suspected of being involved in long-term memory.ConclusionWe conclude that while predictions of the molecular function and biological process annotations have slightly improved over time, those of the cellular component have not. Term-centric prediction of experimental annotations remains equally challenging; although the performance of the top methods is significantly better than the expectations set by baseline methods in C. albicans and D. melanogaster, it leaves considerable room and need for improvement. Finally, we report that the CAFA community now involves a broad range of participants with expertise in bioinformatics, biological experimentation, biocuration, and bio-ontologies, working together to improve functional annotation, computational function prediction, and our ability to manage big data in the era of large experimental screens.</p