"Be sustainable": EOSC-Life recommendations for implementation of FAIR principles in life science data handling.

The main goals and challenges for the life science communities in the Open Science framework are to increase reuse and sustainability of data resources, software tools, and workflows, especially in large-scale data-driven research and computational analyses. Here, we present key findings, procedures, effective measures and recommendations for generating and establishing sustainable life science resources based on the collaborative, cross-disciplinary work done within the EOSC-Life (European Open Science Cloud for Life Sciences) consortium. Bringing together 13 European life science research infrastructures, it has laid the foundation for an open, digital space to support biological and medical research. Using lessons learned from 27 selected projects, we describe the organisational, technical, financial and legal/ethical challenges that represent the main barriers to sustainability in the life sciences. We show how EOSC-Life provides a model for sustainable data management according to FAIR (findability, accessibility, interoperability, and reusability) principles, including solutions for sensitive- and industry-related resources, by means of cross-disciplinary training and best practices sharing. Finally, we illustrate how data harmonisation and collaborative work facilitate interoperability of tools, data, solutions and lead to a better understanding of concepts, semantics and functionalities in the life sciences.

Sharing sensitive data in life sciences: an overview of centralized and federated approaches.

Biomedical data are generated and collected from various sources, including medical imaging, laboratory tests and genome sequencing. Sharing these data for research can help address unmet health needs, contribute to scientific breakthroughs, accelerate the development of more effective treatments and inform public health policy. Due to the potential sensitivity of such data, however, privacy concerns have led to policies that restrict data sharing. In addition, sharing sensitive data requires a secure and robust infrastructure with appropriate storage solutions. Here, we examine and compare the centralized and federated data sharing models through the prism of five large-scale and real-world use cases of strategic significance within the European data sharing landscape: the French Health Data Hub, the BBMRI-ERIC Colorectal Cancer Cohort, the federated European Genome-phenome Archive, the Observational Medical Outcomes Partnership/OHDSI network and the EBRAINS Medical Informatics Platform. Our analysis indicates that centralized models facilitate data linkage, harmonization and interoperability, while federated models facilitate scaling up and legal compliance, as the data typically reside on the data generator's premises, allowing for better control of how data are shared. This comparative study thus offers guidance on the selection of the most appropriate sharing strategy for sensitive datasets and provides key insights for informed decision-making in data sharing efforts.

An assessment of the informative value of data sharing statements in clinical trial registries.

BACKGROUND: The provision of data sharing statements (DSS) for clinical trials has been made mandatory by different stakeholders. DSS are a device to clarify whether there is intention to share individual participant data (IPD). What is missing is a detailed assessment of whether DSS are providing clear and understandable information about the conditions for data sharing of IPD for secondary use. METHODS: A random sample of 200 COVID-19 clinical trials with explicit DSS was drawn from the ECRIN clinical research metadata repository. The DSS were assessed and classified, by two experienced experts and one assessor with less experience in data sharing (DS), into different categories (unclear, no sharing, no plans, yes but vague, yes on request, yes with specified storage location, yes but with complex conditions). RESULTS: Between the two experts the agreement was moderate to substantial (kappa=0.62, 95% CI [0.55, 0.70]). Agreement considerably decreased when these experts were compared with a third person who was less experienced and trained in data sharing ("assessor") (kappa=0.33, 95% CI [0.25, 0.41]; 0.35, 95% CI [0.27, 0.43]). Between the two experts and under supervision of an independent moderator, a consensus was achieved for those cases, where both experts had disagreed, and the result was used as "gold standard" for further analysis. At least some degree of willingness of DS (data sharing) was expressed in 63.5% (127/200) cases. Of these cases, around one quarter (31/127) were vague statements of support for data sharing but without useful detail. In around half of the cases (60/127) it was stated that IPD could be obtained by request. Only in in slightly more than 10% of the cases (15/127) it was stated that the IPD would be transferred to a specific data repository. In the remaining cases (21/127), a more complex regime was described or referenced, which could not be allocated to one of the three previous groups. As a result of the consensus meetings, the classification system was updated. CONCLUSION: The study showed that the current DSS that imply possible data sharing are often not easy to interpret, even by relatively experienced staff. Machine based interpretation, which would be necessary for any practical application, is currently not possible. Machine learning and / or natural language processing techniques might improve machine actionability, but would represent a very substantial investment of research effort. The cheaper and easier option would be for data providers, data requestors, funders and platforms to adopt a clearer, more structured and more standardised approach to specifying, providing and collecting DSS. TRIAL REGISTRATION: The protocol for the study was pre-registered on ZENODO ( https://zenodo.org/record/7064624#.Y4DIAHbMJD8 ).

Application of activated persulfate for the inactivation of fecal bacterial indicators in water.

Activated persulfate, as a member of the broad group of Advanced Oxidation Processes (AOPs), has emerged as a promising method for the elimination of microorganisms in aqueous matrices. This study evaluates the disinfection efficiency of this technique with respect to the inactivation of Escherichia coli and Enterococcus faecalis in water samples, as representative Gram negative and Gram positive bacterial indicators, respectively. In this perspective, various activators were employed, namely, ferric ion, heating, ultrasound application and UVA irradiation, which exhibited different bactericidal effect, depending on the operating conditions and the structural properties of each species. The highest disinfection rates were achieved with 200 mg/L of persulfate and ferric ion or heating as activators. For instance, 6 Log reductions were recorded within only 10-15 min when 30 mg/L of iron were applied, whereas the same bacterial removal was noted upon heat-activation at 50 °C, but in longer periods (i.e. 45-60 min). Nevertheless, in all cases E. faecalis was more resistant than E. coli, which was readily inactivated in shorter treatment periods. The overall process activity was deteriorated above the limit of 200 mg/L of persulfate. Ultrasound application exhibited lower performance, as even more prolonged treatment was required (120-150 min) for the same bacterial decay with the persulfate concentration not affecting substantially the process. In an attempt to improve the ultrasound activity, it was combined together with iron but with no synergistic results, as no actual enhancement of the method was observed. Finally, UVA did not seem to serve as an activator under the applied conditions, taking into account that it resulted in negligible loss of bacterial viability. Based on the current results, activated persulfate may be used successfully for disinfection purposes; however, the appropriate establishment of process variables is mostly required, considering the various resistance levels of aquatic microorganisms under stressed conditions.

Molecularly Imprinted Polymer Coated Quantum Dots for Multiplexed Cell Targeting and Imaging.

Advanced tools for cell imaging are of great interest for the detection, localization, and quantification of molecular biomarkers of cancer or infection. We describe a novel photopolymerization method to coat quantum dots (QDs) with polymer shells, in particular, molecularly imprinted polymers (MIPs), by using the visible light emitted from QDs excited by UV light. Fluorescent core-shell particles specifically recognizing glucuronic acid (GlcA) or N-acetylneuraminic acid (NANA) were prepared. Simultaneous multiplexed labeling of human keratinocytes with green QDs conjugated with MIP-GlcA and red QDs conjugated with MIP-NANA was demonstrated by fluorescence imaging. The specificity of binding was verified with a non-imprinted control polymer and by enzymatic cleavage of the terminal GlcA and NANA moieties. The coating strategy is potentially a generic method for the functionalization of QDs to address a much wider range of biocompatibility and biorecognition issues.

ECRIN - CESSDA strategies for cross metadata mappings in selected areas between life sciences and social sciences and humanities.

Background: The recent COVID-19 (Corona Virus Disease 2019) pandemic dramatically underlined the multi-faceted nature of health research, requiring input from basic biological sciences, pharmaceutical technologies, clinical research), social sciences and public health and social engineering. Systems that could work across different disciplines would therefore seem to be a useful idea to explore. In this study we investigated whether metadata schemas and vocabularies used for discovering scientific studies and resources in the social sciences and in clinical research are similar enough to allow information from different source disciplines to be easily retrieved and presented together. Methods: As a first step a literature search was performed, exemplarily identifying studies and resources, in which data from social sciences have been usefully employed or integrated with that from clinical research and clinical trials. In a second step a comparison of metadata schemas and related resource catalogues in ECRIN (European Clinical Research Infrastructure Network) and CESSDA (Consortium of European Social Science Data Archives) was performed. The focus was on discovery metadata, here defined as the metadata elements used to identify and locate scientific resources. Results: A close view at the metadata schemas of CESSDA and ECRIN and the basic discovery metadata as well as a crosswalk between ECRIN and CESSDA metadata schemas have shown that there is considerable resemblance between them. Conclusions: The resemblance could serve as a promising starting point to implement a common search mechanism for ECRIN and CESSDA metadata. In the paper four different options for how to proceed with implementation issues are presented.

An iterative and interdisciplinary categorisation process towards FAIRer digital resources for sensitive life-sciences data.

For life science infrastructures, sensitive data generate an additional layer of complexity. Cross-domain categorisation and discovery of digital resources related to sensitive data presents major interoperability challenges. To support this FAIRification process, a toolbox demonstrator aiming at support for discovery of digital objects related to sensitive data (e.g., regulations, guidelines, best practice, tools) has been developed. The toolbox is based upon a categorisation system developed and harmonised across a cluster of 6 life science research infrastructures. Three different versions were built, tested by subsequent pilot studies, finally leading to a system with 7 main categories (sensitive data type, resource type, research field, data type, stage in data sharing life cycle, geographical scope, specific topics). 109 resources attached with the tags in pilot study 3 were used as the initial content for the toolbox demonstrator, a software tool allowing searching of digital objects linked to sensitive data with filtering based upon the categorisation system. Important next steps are a broad evaluation of the usability and user-friendliness of the toolbox, extension to more resources, broader adoption by different life-science communities, and a long-term vision for maintenance and sustainability.

In Vivo Estimation of the Biological Effects of Endocrine Disruptors in Rabbits after Combined and Long-Term Exposure: Study Protocol.

Recently, an increasing number of chemical compounds are being characterized as endocrine disruptors since they have been proven to interact with the endocrine system, which plays a crucial role in the maintenance of homeostasis. Glyphosate is the active substance of the herbicide Roundup®, bisphenol A (BPA) and di (2-ethylhexyl) phthalate (DEHP) are used as plasticizers, while triclosan (TCS), methyl (MePB), propyl (PrPB), and butyl (BuPB) parabens are used as antimicrobial agents and preservatives mainly in personal care products. Studies indicate that exposure to these substances can affect humans causing developmental problems and problems in the endocrine, reproductive, nervous, immune, and respiratory systems. Although there are copious studies related to these substances, there are few in vivo studies related to combined exposure to these endocrine disruptors. The aim of the present pilot study is the investigation and assessment of the above substances' toxicity in rabbits after twelve months of exposure to glyphosate (both pure and commercial form) and to a mixture of all the above substances at subtoxic levels. The lack of data from the literature concerning rabbits' exposure to these substances and the restrictions of the 3Rs Principle will result in a limited number of animals available for use (four animals per group, twenty animals in total).

Accessibility and Web Quality Information for People with Disabilities in Healthcare Structures.

People with disabilities are a major part of the society. The fact of being able to service themselves without any additional help in their everyday life is an important right, as well as the right to have equal opportunities in utilizing all health- related services in their community. Our research was carried out on a group of people with disabilities through a semi structured interview to clarify their needs regarding the accessibility of health services and the accessibility of the existing related information. In addition to the analysis of the accessible techniques of digital information, the accessibility, reliability and relevance of the information existing on health websites in Greece are evaluated. The assessment of the accessibility of information provided online is carried out based on the WCAG2.0 standard of the World Wide Web Consortium (W3C). Through these surveys and procedures, we reach conclusions on the deficiencies of accessibility and solutions for improvement are proposed. The results present the need for improvement in the information related to the healthcare sector, as we realize that a very low percentage covers the three key factors as mentioned above. With recommendations we target towards a more inclusive health care sector for all individuals.

Solid-phase synthesis of molecularly imprinted polymer nanolabels: Affinity tools for cellular bioimaging of glycans.

Hyaluronic acid (HA) is a glycosaminoglycan that plays many roles in health and disease and is a key biomarker of certain cancers. Therefore, its detection at an early stage, by histochemical methods, is of importance. However, intracellular HA can be masked by other HA-binding macromolecules, rendering its visualization somehow problematic. We show that fluorescent molecularly imprinted polymer nanogels (MIP-NPs), can localize and detect intracellular HA. MIP-NPs were synthesized by solid-phase synthesis on glass beads (GBs). GBs were functionalized with terminal alkyne groups on which an azide derivative of the template molecule glucuronic acid was immobilized via click chemistry. Immobilization via the anomeric carbon left the template's carboxyl moiety free to enable strong stoichiometric electrostatic interactions with a benzamidine-based functional monomer, to confer selective recognition to the MIP-NPs. Due to the two-point orientation of the template, the resulting MIP-NPs were endowed with improved binding site homogeneity and specificity, reminiscent of monoclonal antibodies. These synthetic antibodies were then applied for probing and staining HA, of which glucuronic acid is a substructure (epitope), on human epidermal cells. Their excellent sensitivity, small size and water compatibility, enabled the MIP-NPs to visualize HA, as evidenced by confocal fluorescence micrographs.

Tracking Hyaluronan: Molecularly Imprinted Polymer Coated Carbon Dots for Cancer Cell Targeting and Imaging.

War against cancer constantly requires new affinity tools to selectively detect, localize, and quantify biomarkers for diagnosis or prognosis. Herein, carbon nanodots (CDs), an emerging class of fluorescent nanomaterials, coupled with molecularly imprinted polymers (MIPs), are employed as a biocompatible optical imaging tool for probing cancer biomarkers. First, N-doped CDs were prepared by hydrothermal synthesis using starch as carbon source and l-tryptophan as nitrogen atom provider to achieve a high quantum yield of 25.1 ± 2%. The CDs have a typical size of ∼3.2 nm and produce an intense fluorescence at 450 nm upon excitation with UV light. A MIP shell for specific recognition of glucuronic acid (GlcA) was then synthesized around the CDs, using the emission of the CDs as an internal light source for photopolymerization. GlcA is a substructure (epitope) of hyaluronan, a biomarker for certain cancers. The biotargeting and bioimaging of hyaluronan on fixated human cervical cancer cells using CD core-MIP shell nanocomposites is demonstrated. Human keratinocytes were used as noncancerous reference cells and indeed, less staining was observed by the CD-MIP.

Cell and Tissue Imaging with Molecularly Imprinted Polymers.

Advanced tools for cell imaging are of particular interest as they can detect, localize and quantify molecular targets like abnormal glycosylation sites that are biomarkers of cancer and infection. Targeting these biomarkers is often challenging due to a lack of receptor materials. Molecularly imprinted polymers (MIPs) are promising artificial receptors; they can be tailored to bind targets specifically, be labeled easily, and are physically and chemically stable. Herein, we demonstrate the application of MIPs as artificial antibodies for selective labeling and imaging of cellular targets, on the example of hyaluronan and sialylation moieties on fixated human skin cells and tissues. Thus, fluorescently labeled MIP nanoparticles templated with glucuronic acid (MIPGlcA) and N-acetylneuraminic acid (MIPNANA) are respectively applied. Two different fluorescent probes are used: (1) MIPGlcA particles, ~400 nm in size are labeled with the dye rhodamine that target the extracellular hyaluronan on cells and tissue specimens and (2) MIP-coated InP/ZnS quantum dots (QDs) of two different colors, ~125 nm in size that target the extracellular and intracellular hyaluronan and sialylation sites. Green and red emitting QDs are functionalized with MIPGlcA and MIPNANA respectively, enabling multiplexed cell imaging. This is a general approach that can also be adapted to other target molecules on and in cells.

Chewing lice from wild birds in northern Greece.

Greece represents an important area for wild birds due to its geographical position and habitat diversity. Although the bird species in Greece are well recorded, the information about the chewing lice that infest them is practically non-existent. Thus, the aim of the present study was to record the species of lice infesting wild birds in northern Greece and furthermore, to associate the infestation prevalence with factors such as the age, sex, migration and social behaviour of the host as well as the time of the year. In total 729 birds, (belonging to 9 orders, 32 families and 68 species) were examined in 7 localities of northern Greece, during 9 ringing sessions from June 2013 until October 2015. Eighty (11%) of the birds were found to be infested with lice. In 31 different bird species, 560 specimens of lice, belonging to 33 species were recorded. Mixed infestations were recorded in 11 cases where birds were infested with 2-3 different lice species. Four new host-parasite associations were recorded i.e. Menacanthus curuccae from Acrocephalus melanopogon, Menacanthus agilis from Cettia cetti, Myrsidea sp. from Acrocephalus schoenobaenus, and Philopretus citrinellae from Spinus spinus. Moreover, Menacanthus sinuatus was detected on Poecile lugubris, rendering this report the first record of louse infestation in this bird species. The statistical analysis of the data collected showed no association between parasitological parameters (prevalence, mean and median intensity and mean abundance) in two different periods of the year (breeding vs post-breeding season). However, there was a statistically significant difference in the prevalence of infestation between a) migrating and sedentary passerine birds (7.4% vs 13.2%), b) colonial and territorial birds (54.5% vs 9.6%), and c) female and male birds in breeding period (2.6% vs 15.6%).

Fluorescent molecularly imprinted polymers as plastic antibodies for selective labeling and imaging of hyaluronan and sialic acid on fixed and living cells.

Altered glycosylation levels or distribution of sialic acids (SA) or hyaluronan in animal cells are indicators of pathological conditions like infection or malignancy. We applied fluorescently-labeled molecularly imprinted polymer (MIP) particles for bioimaging of fixed and living human keratinocytes, to localize hyaluronan and sialylation sites. MIPs were prepared with the templates D-glucuronic acid (GlcA), a substructure of hyaluronan, and N-acetylneuraminic acid (NANA), the most common member of SA. Both MIPs were found to be highly selective towards their target monosaccharides, as no cross-reactivity was observed with other sugars like N-acetyl-D-glucosamine, N-acetyl-D-galactosamine, D-glucose and D-galactose, present on the cell surface. The dye rhodamine and two InP/ZnS quantum dots (QDs) emitting in the green and in the red regions were used as fluorescent probes. Rhodamine-MIPGlcA and rhodamine-MIPNANA were synthesized as monodispersed 400nm sized particles and were found to bind selectively their targets located in the extracellular region, as imaged by epifluorescence and confocal microscopy. In contrast, when MIP-GlcA and MIP-NANA particles with a smaller size (125nm) were used, the MIPs being synthesized as thin shells around green and red emitting QDs respectively, it was possible to stain the intracellular and pericellular regions as well. In addition, simultaneous dual-color imaging with the two different colored QDs-MIPs was demonstrated. Importantly, the MIPs were not cytotoxic and did not affect cell viability; neither was the cells morphology affected as demonstrated by live cell imaging. These synthetic receptors could offer a new and promising imaging tool to monitor disease progression.

Cell and Tissue Imaging with Molecularly Imprinted Polymers as Plastic Antibody Mimics.

Molecularly imprinted polymers can be used as "plastic antibodies" for cell and tissue imaging, as demonstrated using hyaluronan on cell surfaces as a model target. Fluorescent nanoparticles binding a hyaluronan substructure, glucuronic acid, are used to image fixated and living cells and tissues. Plastic antibodies can be tailored to specific targets and easily labeled, and are physically and chemically stable.