Exploratory drilling: how to set up, carry out, and evaluate a seroprevalence study.

Seroprevalence studies represent a very important tool to find out what fraction of population has already met with the new type of coronavirus (e.g. SARS-CoV-2). Without these data, it is almost impossible for the state authorities to manage the epidemic and adopt rational measures. This article brings the results of a medium-sized seroprevalence study which was carried out in the spring of 2020 in South Bohemia. In the Strakonice and Písek regions, the ELISA method was used to test the prevalence of IgA and IgG antibodies in 2011 subjects, volunteers from general public and selected professions working in areas with a higher exposure to the infection. The study showed that already in May 2020, 2.9% of inhabitants of the Strakonice region and 1.9% of inhabitants of the Písek region had antibodies against the coronavirus. These numbers imply that for each PCR positive person, there were at least fifty others who had probably already undergone the infection. The article points out three types of problems that might occur in such a study. First, the study must be planned correctly, and possible outcomes must be pre-assessed. Second, an appropriate test must be selected with known parameters. This enables us to correctly estimate the share of false positive and false negative results. Third, the data must be evaluated in a reasonable way and correct inference must be performed. We offer a set of recommendations how to manage these issues and how to solve problems that inevitably arise in such a large-scale testing.

GA4GH Passport standard for digital identity and access permissions.

The Global Alliance for Genomics and Health (GA4GH) supports international standards that enable a federated data sharing model for the research community while respecting data security, ethical and regulatory frameworks, and data authorization and access processes for sensitive data. The GA4GH Passport standard (Passport) defines a machine-readable digital identity that conveys roles and data access permissions (called "visas") for individual users. Visas are issued by data stewards, including data access committees (DACs) working with public databases, the entities responsible for the quality, integrity, and access arrangements for the datasets in the management of human biomedical data. Passports streamline management of data access rights across data systems by using visas that present a data user's digital identity and permissions across organizations, tools, environments, and services. We describe real-world implementations of the GA4GH Passport standard in use cases from ELIXIR Europe, National Institutes of Health, and the Autism Sharing Initiative. These implementations demonstrate that the Passport standard has provided transparent mechanisms for establishing permissions and authorizing data access across platforms.

Measurement uncertainty evaluation from correlated validation data: Determination of elemental impurities in pharmaceutical products by ICP-MS.

Pharmaceutical products as well as active pharmaceutical ingredients (APIs) are checked for levels of elemental contaminants to guarantee medicines administration will not involve the consumption of level of contaminants greater than their maximum admissible intake. However, the conformity decision is affected by the measurement uncertainty function of analytical steps performance, used standards quality and how measurement performance is assessed during method validation. When an ingredient is considered conform, since the measured concentration is lower than the maximum limit, the risk of a false acceptance depends on how close the measured concentration is from the limit and on the measurement uncertainty. The analytical methods used for pharmaceutical analysis should be validated by ICH and USP recommendations, in order to prove measurements are fit for purpose. The validation must also be economically feasible and have an acceptable duration. This work discusses how to evaluate the uncertainty of elemental analysis in pharmaceutical ingredients from data collected during the validation of the analytical method by following ICH guidelines and USP chapters. A top-down uncertainty evaluation based on results from the analysis of a model API intermediate, with the native analyte after spiking at three concentration levels, where analyses are performed by two analysts in two different days, is presented. The impact of the correlation of some uncertainty components of collected results on the uncertainty evaluation is discussed and considered in the calculations. The developed measurement model was checked by a cross-validation procedure where some validation data was randomly removed and used for an independent model control. The developed uncertainty evaluation methodology was successfully applied to the analysis of Pd in a model API intermediate by ICP-MS after a micro-wave assisted acid digestion, where the risk of a false acceptance of the pharmaceuticals is determined. The measurement performance data and used spreadsheet are made available as Supplementary Material.

Content of distinct metals in periprosthetic tissues and pseudosynovial joint fluid in patients with total joint arthroplasty.

This prospective study examined the content of metals released from total joint arthroplasty into joint fluid, whole blood and periprosthetic tissues. We determined the levels of Ti, V, Nb, Co, Cr, and Mo, using inductively coupled plasma mass spectrometry, in samples from patients who underwent reoperation of total hip or knee arthroplasty. All of the patients (n = 117) included in the study had either metal on polyethylene or ceramic on polyethylene-bearing pairs. First, our results conclusively showed that the majority of released metals were deposited in periprosthetic tissues. In this context, the bloodstream turned out to be an ineffective biomarker of the effects occurring in local tissues. Second, there was a clear time-dependent nature of metallic accumulation. Based on our extensive dataset, we found significantly elevated levels of the released metals in joint fluid and periprosthetic tissues originating from loosened implants compared to stable ones, as well as recognizable differences between the groups with stable implants and aseptic loosening. Finally, it was proved that the concentrations of metals decreased dependent on the distance of the tissue from the implant. © 2018 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 107B: 454-462, 2019.

Common ELIXIR Service for Researcher Authentication and Authorisation.

A common Authentication and Authorisation Infrastructure (AAI) that would allow single sign-on to services has been identified as a key enabler for European bioinformatics. ELIXIR AAI is an ELIXIR service portfolio for authenticating researchers to ELIXIR services and assisting these services on user privileges during research usage. It relieves the scientific service providers from managing the user identities and authorisation themselves, enables the researcher to have a single set of credentials to all ELIXIR services and supports meeting the requirements imposed by the data protection laws. ELIXIR AAI was launched in late 2016 and is part of the ELIXIR Compute platform portfolio. By the end of 2017 the number of users reached 1000, while the number of relying scientific services was 36. This paper presents the requirements and design of the ELIXIR AAI and the policies related to its use, and how it can be used for serving some example services, such as document management, social media, data discovery, human data access, cloud compute and training services.

Grid empowered sharing of medical expertise.

Today, applications for Grids emerge in various scientific fields, each with specific requirements. We present concept and architecture which enables biomedical experts to collaborate and share resources by encapsulating their knowledge and expertise as grid services, with (semi-)formally described semantics. Grid Services allow machine processing of the encapsulated knowledge, while their semantic description provides means for their automated discovery and interaction. This brings new possibilities of building biomedical systems offering machine-driven assistance to the biomedical experts.

Valorisation of glycerol as renewable feedstock: comparison of the exploration of chemical transformation methods aided by high throughput experimentation.

Renewable feedstocks have been in the spotlight of intensive research activities over the past 10 years. Glycerol is one of the feedstock molecules which has been the target of numerous research efforts, for a number of reasons. First of all glycerol is currently readily available due to the fact that it is a couple product of the first generation biodiesel production. Secondly glycerol can be taken as a representative model substrate to explore the options of selective conversion of sugar alcohols to products of value. In our paper we discuss potential routes for the valorisation of glycerol which lead to intermediates already established within the petrochemical value chain and illustrate what impact high throughput experimentation may have as a success factor on research and development for this field. As illustrative examples we have chosen the oxidative transformation of glycerol to acrolein and acrylic acid and the carbonylation of glycerol to C4-acids.