Non-invasive diagnostics in fossils - Magnetic Resonance Imaging of pathological belemnites

For more than a decade, Magnetic Resonance Imaging (MRI) has been routinely employed in clinical diagnostics because it allows non-invasive studies of anatomical structures and physiological processes <I>in vivo</I> and to differentiate between healthy and pathological states, particularly of soft tissue. Here, we demonstrate that MRI can likewise be applied to fossilized biological samples and help in elucidating paleopathological and paleoecological questions: Five anomalous guards of Jurassic and Cretaceous belemnites are presented along with putative paleopathological diagnoses directly derived from 3D MR images with microscopic resolution. <I>Syn vivo</I> deformities of both the mineralized internal rostrum and the surrounding former soft tissue can be traced back in part to traumatic events of predator-prey-interactions, and partly to parasitism. Besides, evidence is presented that the frequently observed anomalous apical collar might be indicative of an inflammatory disease. These findings highlight the potential of Magnetic Resonance techniques for further paleontological applications

Three-dimensional Magnetic Resonance Imaging of fossils across taxa

The frequency of life forms in the fossil record is largely determined by the extent to which they were mineralised at the time of their death. In addition to mineral structures, many fossils nonetheless contain detectable amounts of residual water or organic molecules, the analysis of which has become an integral part of current palaeontological research. The methods available for this sort of investigations, though, typically require dissolution or ionisation of the fossil sample or parts thereof, which is an issue with rare taxa and outstanding materials like pathological or type specimens. In such cases, non-destructive techniques could provide a valuable methodological alternative. While Computed Tomography has long been used to study palaeontological specimens, a number of complementary approaches have recently gained ground. These include Magnetic Resonance Imaging (MRI) which had previously been employed to obtain three-dimensional images of pathological belemnites non-invasively on the basis of intrinsic contrast. The present study was undertaken to investigate whether &lt;sup&gt;1&lt;/sup&gt;H MRI can likewise provide anatomical information about non-pathological belemnites and specimens of other fossil taxa. To this end, three-dimensional MR image series were acquired from intact non-pathological invertebrate, vertebrate and plant fossils. At routine voxel resolutions in the range of several dozens to some hundreds of micrometers, these images reveal a host of anatomical details and thus highlight the potential of MR techniques to effectively complement existing methodological approaches for palaeontological investigations in a wide range of taxa. As for the origin of the MR signal, relaxation and diffusion measurements as well as &lt;sup&gt;1&lt;/sup&gt;H and &lt;sup&gt;13&lt;/sup&gt;C MR spectra acquired from a belemnite suggest intracrystalline water or hydroxyl groups, rather than organic residues

Enriched biodiversity data as a resource and service

Background: Recent years have seen a surge in projects that produce large volumes of structured, machine-readable biodiversity data. To make these data amenable to processing by generic, open source “data enrichment” workflows, they are increasingly being represented in a variety of standards-compliant interchange formats. Here, we report on an initiative in which software developers and taxonomists came together to address the challenges and highlight the opportunities in the enrichment of such biodiversity data by engaging in intensive, collaborative software development: The Biodiversity Data Enrichment Hackathon. Results: The hackathon brought together 37 participants (including developers and taxonomists, i.e. scientific professionals that gather, identify, name and classify species) from 10 countries: Belgium, Bulgaria, Canada, Finland, Germany, Italy, the Netherlands, New Zealand, the UK, and the US. The participants brought expertise in processing structured data, text mining, development of ontologies, digital identification keys, geographic information systems, niche modeling, natural language processing, provenance annotation, semantic integration, taxonomic name resolution, web service interfaces, workflow tools and visualisation. Most use cases and exemplar data were provided by taxonomists. One goal of the meeting was to facilitate re-use and enhancement of biodiversity knowledge by a broad range of stakeholders, such as taxonomists, systematists, ecologists, niche modelers, informaticians and ontologists. The suggested use cases resulted in nine breakout groups addressing three main themes: i) mobilising heritage biodiversity knowledge; ii) formalising and linking concepts; and iii) addressing interoperability between service platforms. Another goal was to further foster a community of experts in biodiversity informatics and to build human links between research projects and institutions, in response to recent calls to further such integration in this research domain. Conclusions: Beyond deriving prototype solutions for each use case, areas of inadequacy were discussed and are being pursued further. It was striking how many possible applications for biodiversity data there were and how quickly solutions could be put together when the normal constraints to collaboration were broken down for a week. Conversely, mobilising biodiversity knowledge from their silos in heritage literature and natural history collections will continue to require formalisation of the concepts (and the links between them) that define the research domain, as well as increased interoperability between the software platforms that operate on these concepts

Progress in promoting data sharing in public health emergencies

In February 2016, the World Health Organization (WHO) declared the Zika virus-related cluster of microcephaly cases and other neurological disorders reported in Brazil, a Public Health Emergency of International Concern (PHEIC).1 Following the declaration, over 30 global health bodies issued a joint statement committing to data sharing to ensure that the global response to the Zika virus and future emergencies, could be informed by the best and most current evidence.2 The statement represented a concerted effort by those involved to address past failures of timely access to relevant data. It also highlighted the lack of a clear path to implementation for data sharing during public health emergencies. In March 2016, the Global Research Collaboration for Infectious Disease Preparedness (GloPID-R) established a data-sharing working group which has been working in coalition with other stakeholders including WHO, scientists, nongovernmental organizations, journals and other agencies. This group is working to identify barriers to data sharing in public health emergencies that should be addressed to better prepare for any future epidemic. We review the progress since the joint statement was made, outline the key challenges related to data sharing and summarize the group’s activities to date

A multi-disciplinary perspective on emergent and future innovations in peer review [version 2; referees: 2 approved]

Peer review of research articles is a core part of our scholarly communication system. In spite of its importance, the status and purpose of peer review is often contested. What is its role in our modern digital research and communications infrastructure? Does it perform to the high standards with which it is generally regarded? Studies of peer review have shown that it is prone to bias and abuse in numerous dimensions, frequently unreliable, and can fail to detect even fraudulent research. With the advent of web technologies, we are now witnessing a phase of innovation and experimentation in our approaches to peer review. These developments prompted us to examine emerging models of peer review from a range of disciplines and venues, and to ask how they might address some of the issues with our current systems of peer review. We examine the functionality of a range of social Web platforms, and compare these with the traits underlying a viable peer review system: quality control, quantified performance metrics as engagement incentives, and certification and reputation. Ideally, any new systems will demonstrate that they out-perform and reduce the biases of existing models as much as possible. We conclude that there is considerable scope for new peer review initiatives to be developed, each with their own potential issues and advantages. We also propose a novel hybrid platform model that could, at least partially, resolve many of the socio-technical issues associated with peer review, and potentially disrupt the entire scholarly communication system. Success for any such development relies on reaching a critical threshold of research community engagement with both the process and the platform, and therefore cannot be achieved without a significant change of incentives in research environments

Using shape expressions (ShEx) to share rdf data models and to guide curation with rigorous validation

International Conference, European Semantic Web Conference, ESWC (16th. 2019. Portorož, Slovenia

Using logical constraints to validate statistical information about disease outbreaks in collaborative knowledge graphs: the case of COVID-19 epidemiology in Wikidata

Ministry of Higher Education and Scientific Research in Tunisia (MoHESR) [PRFCOV19-D1-P1]; Wikimedia Foundation through a rapid grant; WikiCred Grants Initiative of Craig Newmark Philanthropies, Facebook, and Microsoft; Spanish Ministry of Economy and Competitiveness [TIN2017-88877-R]; Alfred P. Sloan Foundation [201911458, G-2021-17106]; Polish National Science Center [2019/35/B/HS6/01056

Representing COVID-19 information in collaborative knowledge graphs: The case of Wikidata

The work done by Houcemeddine Turki, Mohamed Ali Hadj Taieb and Mohamed Ben Aouicha was supported by the Ministry of Higher Education and Scientific Research in Tunisia (MoHESR) in the framework of Federated Research Project PRFCOV19-D1-P1. The work done by Jose Emilio Labra Gayo was partially funded by the Spanish Ministry of Economy and Competitiveness (Society challenges: TIN2017-88877-R). The work done by Daniel Mietchen was supported in part by the Alfred P. Sloan Foundation under grant number G-2019-11458. The work done by Dariusz Jemielniak was funded by Polish National Science Center grant no 2019/35/B/HS6/01056

Getting your DUCs in a row - standardising the representation of Digital Use Conditions

Improving patient care and advancing scientific discovery requires responsible sharing of research data, healthcare records, biosamples, and biomedical resources that must also respect applicable use conditions. Defining a standard to structure and manage these use conditions is a complex and challenging task. This is exemplified by a near unlimited range of asset types, a high variability of applicable conditions, and differing applications at the individual or collective level. Furthermore, the specifics and granularity required are likely to vary depending on the ultimate contexts of use. All these factors confound alignment of institutional missions, funding objectives, regulatory and technical requirements to facilitate effective sharing. The presented work highlights the complexity and diversity of the problem, reviews the current state of the art, and emphasises the need for a flexible and adaptable approach. We propose Digital Use Conditions (DUC) as a framework that addresses these needs by leveraging existing standards, striking a balance between expressiveness versus ambiguity, and considering the breadth of applicable information with their context of use.</p