Rewilding and restoring nature in a changing world

Overview of the PLoS ONE collection 'Rewilding and Restoration'

Three-Photon Absorption Spectra and Bandgap Scaling In Direct-Gap Semiconductors

This paper presents three-photon absorption (3PA) measurement results for nine direct-gap semiconductors, including full 3PA spectra for ZnSe, ZnS, and GaAs. These results, along with our theory of 3PA using an eight-band Kane model (four bands with double spin degeneracy), help to explain the significant disagreements between experiments and theory in the literature to date. 3PA in the eight-band model exhibits quantum interference between the various possible pathways that is not observed in previous two-band theories. We present measurements of degenerate 3PA coefficients in InSb, GaAs, CdTe, CdSe, ZnTe, CdS, ZnSe, ZnO, and ZnS. We examine bandgap, Eg, scaling using -band tunneling and perturbation theories that show agreement with the predicted Eg−7 dependence; however, for those semiconductors for which we measured full 3PA spectra, we observe significant discrepancies with both two-band theories. On the other hand, our eight-band model shows excellent agreement with the spectral data. We then use our eight-band theory to predict the 3PA spectra for 15 different semiconductors in their zinc-blende form. These results allow prediction and interpretation of the 3PA coefficients for various narrow to wide bandgap semiconductors

Surveyed common data access policies preferences amongst European Reference Networks

Background: Data sharing amongst existing Rare Disease (RD) registries, even though being a process that presents multiple barriers, would enrich and ease research, as well as facilitate interoperability between the registries themselves. Methods: To understand their preferences on sharing data, we surveyed 24 European Reference Networks (ERNs) from the RD Domain. Results: The answers show that most ERNs are willing to share a set of Common Data Elements for free with authenticated users at an aggregated or pseudonymized level the moment the data is collected. The one exception is the industry sector, to which ERNs prefer to ask for a fee. Objective: Our aim is to create a reference for how most RD registries are willing to share their data, improving the ability of other stakeholders to make informed decisions to make their data interoperable.</p

Towards FAIRification of sensitive and fragmented rare disease patient data:challenges and solutions in European reference network registries

INTRODUCTION: Rare disease patient data are typically sensitive, present in multiple registries controlled by different custodians, and non-interoperable. Making these data Findable, Accessible, Interoperable, and Reusable (FAIR) for humans and machines at source enables federated discovery and analysis across data custodians. This facilitates accurate diagnosis, optimal clinical management, and personalised treatments. In Europe, twenty-four European Reference Networks (ERNs) work on rare disease registries in different clinical domains. The process and the implementation choices for making data FAIR (‘FAIRification’) differ among ERN registries. For example, registries use different software systems and are subject to different legal regulations. To support the ERNs in making informed decisions and to harmonise FAIRification, the FAIRification steward team was established to work as liaisons between ERNs and researchers from the European Joint Programme on Rare Diseases. RESULTS: The FAIRification steward team inventoried the FAIRification challenges of the ERN registries and proposed solutions collectively with involved stakeholders to address them. Ninety-eight FAIRification challenges from 24 ERNs’ registries were collected and categorised into “training” (31), “community” (9), “modelling” (12), “implementation” (26), and “legal” (20). After curating and aggregating highly similar challenges, 41 unique FAIRification challenges remained. The two categories with the most challenges were “training” (15) and “implementation” (9), followed by “community” (7), and then “modelling” (5) and “legal” (5). To address all challenges, eleven types of solutions were proposed. Among them, the provision of guidelines and the organisation of training activities resolved the “training” challenges, which ranged from less-technical “coffee-rounds” to technical workshops, from informal FAIR Games to formal hackathons. Obtaining implementation support from technical experts was the solution type for tackling the “implementation” challenges. CONCLUSION: This work shows that a dedicated team of FAIR data stewards is an asset for harmonising the various processes of making data FAIR in a large organisation with multiple stakeholders. Additionally, multi-levelled training activities are required to accommodate the diverse needs of the ERNs. Finally, the lessons learned from the experience of the FAIRification steward team described in this paper may help to increase FAIR awareness and provide insights into FAIRification challenges and solutions of rare disease registries. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13023-022-02558-5

Surveyed common data access policies preferences amongst European Reference Networks

Background: Data sharing amongst existing Rare Disease (RD) registries, even though being a process that presents multiple barriers, would enrich and ease research, as well as facilitate interoperability between the registries themselves. Methods: To understand their preferences on sharing data, we surveyed 24 European Reference Networks (ERNs) from the RD Domain. Results: The answers show that most ERNs are willing to share a set of Common Data Elements for free with authenticated users at an aggregated or pseudonymized level the moment the data is collected. The one exception is the industry sector, to which ERNs prefer to ask for a fee. Objective: Our aim is to create a reference for how most RD registries are willing to share their data, improving the ability of other stakeholders to make informed decisions to make their data interoperable.</p

Semantic modelling of common data elements for rare disease registries, and a prototype workflow for their deployment over registry data

BACKGROUND: The European Platform on Rare Disease Registration (EU RD Platform) aims to address the fragmentation of European rare disease (RD) patient data, scattered among hundreds of independent and non-coordinating registries, by establishing standards for integration and interoperability. The first practical output of this effort was a set of 16 Common Data Elements (CDEs) that should be implemented by all RD registries. Interoperability, however, requires decisions beyond data elements - including data models, formats, and semantics. Within the European Joint Programme on Rare Diseases (EJP RD), we aim to further the goals of the EU RD Platform by generating reusable RD semantic model templates that follow the FAIR Data Principles. RESULTS: Through a team-based iterative approach, we created semantically grounded models to represent each of the CDEs, using the SemanticScience Integrated Ontology as the core framework for representing the entities and their relationships. Within that framework, we mapped the concepts represented in the CDEs, and their possible values, into domain ontologies such as the Orphanet Rare Disease Ontology, Human Phenotype Ontology and National Cancer Institute Thesaurus. Finally, we created an exemplar, reusable ETL pipeline that we will be deploying over these non-coordinating data repositories to assist them in creating model-compliant FAIR data without requiring site-specific coding nor expertise in Linked Data or FAIR. CONCLUSIONS: Within the EJP RD project, we determined that creating reusable, expert-designed templates reduced or eliminated the requirement for our participating biomedical domain experts and rare disease data hosts to understand OWL semantics. This enabled them to publish highly expressive FAIR data using tools and approaches that were already familiar to them

High-level integration of murine intestinal transcriptomics data highlights the importance of the complement system in mucosal homeostasis.

BACKGROUND: The mammalian intestine is a complex biological system that exhibits functional plasticity in its response to diverse stimuli to maintain homeostasis. To improve our understanding of this plasticity, we performed a high-level data integration of 14 whole-genome transcriptomics datasets from samples of intestinal mouse mucosa. We used the tool Centrality based Pathway Analysis (CePa), along with information from the Reactome database. RESULTS: The results show an integrated response of the mouse intestinal mucosa to challenges with agents introduced orally that were expected to perturb homeostasis. We observed that a common set of pathways respond to different stimuli, of which the most reactive was the Regulation of Complement Cascade pathway. Altered expression of the Regulation of Complement Cascade pathway was verified in mouse organoids challenged with different stimuli in vitro. CONCLUSIONS: Results of the integrated transcriptomics analysis and data driven experiment suggest an important role of epithelial production of complement and host complement defence factors in the maintenance of homeostasis

Aquaponics in the Built Environment

Aquaponics’ potential to transform urban food production has been documented in a rapid increase of academic research and public interest in the field. To translate this publicity into real-world impact, the creation of commercial farms and their relationship to the urban environment have to be further examined. This research has to bridge the gap between existing literature on growing system performance and urban metabolic flows by considering the built form of aquaponic farms. To assess the potential for urban integration of aquaponics, existing case studies are classified by the typology of their building enclosure, with the two main categories being greenhouses and indoor environments. This classification allows for some assumptions about the farms’ performance in their context, but a more in-depth life cycle assessment (LCA) is necessary to evaluate different configurations. The LCA approach is presented as a way to inventory design criteria and respective strategies which can influence the environmental impact of aquaponic systems in the context of urban built environments