ORCID Profile
0000-0003-1038-3028
Current Organisations
KU Leuven
,
Smithsonian Institution
,
UCSF Medical Center
,
Philadelphia University
,
National Museum of Natural History
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Publications
Perioperative management of obstructive sleep apnea in bariatric surgery: a consensus guideline
Publisher: Elsevier BV
Date: 07-2017
DOI: 10.1016/J.SOARD.2017.03.022
Abstract: The frequency of metabolic and bariatric surgery (MBS) is increasing worldwide, with over 500,000 cases performed every year. Obstructive sleep apnea (OSA) is present in 35%-94% of MBS patients. Nevertheless, consensus regarding the perioperative management of OSA in MBS patients is not established. To provide consensus based guidelines utilizing current literature and, when in the absence of supporting clinical data, expert opinion by organizing a consensus meeting of experts from relevant specialties. The meeting was held in Amsterdam, the Netherlands. A panel of 15 international experts identified 75 questions covering preoperative screening, treatment, postoperative monitoring, anesthetic care and follow-up. Six researchers reviewed the literature systematically. During this meeting, the "Amsterdam Delphi Method" was utilized including controlled acquisition of feedback, aggregation of responses and iteration. Recommendations or statements were provided for 58 questions. In the judgment of the experts, 17 questions provided no additional useful information and it was agreed to exclude them. With the exception of 3 recommendations (64%, 66%, and 66% respectively), consensus (>70%) was reached for 55 statements and recommendations. Several highlights: polysomnography is the gold standard for diagnosing OSA continuous positive airway pressure is recommended for all patients with moderate and severe OSA OSA patients should be continuously monitored with pulse oximetry in the early postoperative period perioperative usage of sedatives and opioids should be minimized. This first international expert meeting provided 58 statements and recommendations for a clinical consensus guideline regarding the perioperative management of OSA patients undergoing MBS.
Taxonomy based on science is necessary for global conservation
Publisher: Public Library of Science (PLoS)
Date: 14-03-2018
Towards a global list of accepted species V. The devil is in the detail
Publisher: Springer Science and Business Media LLC
Date: 22-10-2021
Towards a Quality Assurance and Quality Control Mechanism for Species List Building
Publisher: Pensoft Publishers
Date: 28-08-2023
Abstract: Catalogue of Life (COL) brings together the efforts and contributions of taxonomists from around the world, and addresses the needs of researchers, policy-makers, environmental managers and the wider public for a consistent, up-to-date and authoritative listing of all the world’s known species. The names that science gives to species are fundamental tools that allow us to refer to these units of bio ersity. Knowing the name for a species unlocks everything that has been learned about its biology, distribution and relevance to humans. Every day, taxonomists continue to publish new scientific names and refine our understanding of the world’s species. Over the past 10 years, game-changing progress has been made with the Catalogue of Life and its authoritative taxonomic name indexing services. Major steps were made towards content completion (over 2.1 million species out of all described 2.4 million are now documented and validated through COL (Bánki et al. 2023). The COL data infrastructure and services were rebuilt in collaboration with the Global Bio ersity Information Facility (GBIF). This resulted in the GBIF-COL ChecklistBank, an open global repository for publishing and sharing taxonomic and nomenclatural datasets (& 48,000 datasets, including over 160 Global Species Databases). The data managing/editing process underlying the integration of data into a single checklist (index) could be more transparent with clearly documented protocols and procedures, and is today far too time consuming. In the ChecklistBank infrastructure, there are thousands of data sources at our disposal and we need a powerful, semi-automated, community-expertise based, quality assurance process to warrant the best possible product for users of taxonomic checklists. COL aspires to document, with as much detail as possible, the current quality control and quality assurance processes as they relate to activities that occur at the following levels: 1) data providers, 2) pipeline and data conversions, 3) ChecklistBank infrastructure, and 4) checklist output. Ideally, this should happen throughout the consortium of partners that help the taxonomic community with mobilising and editing authoritative taxonomic data, including initiatives like Atlas of Living Australia, Catalogue of Life China, EDIT Platform for Cybertaxonomy, Integrated Taxonomic Information System, Freshwater Animal Diversity Assessment, TaxonWorks / Species Files, World Flora Online / Rhakhis, World Register of Marine Species / LifeWatch Aphia. In recent years more attention has been given to the principles of creating an authoritative list of the world's species (Garnett et al. 2020). COL has developed and adopted new criteria for the inclusion of taxonomic data sources in the COL Checklist (Hobern et al. 2021). And ChecklistBank, certainly provides more avenues for (automated) quality checks and procedures. But to guarantee the highest confidence in data, we are in need of a transparent and consistent data quality assurance and data quality control mechanism from the creation of taxonomic data, to data publishing, to the delivery into taxonomic data products and the global list of known species. We will present the current status of quality control and quality assurance processes in Catalogue of Life, and discuss what should constitute a quality control and quality assurance mechanism for species list building.
Going Molecular: Sequence-based spatiotemporal biodiversity evidence in GBIF
Publisher: Pensoft Publishers
Date: 13-06-2019
DOI: 10.3897/BISS.3.37036
Abstract: The Global Bio ersity Information Facility (GBIF) was established by governments in 2001, largely through the initiative and leadership of the natural history collections community, following the 1999 recommendation by a working group under the Megascience Forum (predecessor of the Global Science Forum) of the Organization for Economic Cooperation and Development (OECD). Over 20 years, GBIF has helped develop standards and convened a global community of data-publishing institutions, aggregrating over one billion specimen occurrence records freely and openly available for use in research and policy making. These GBIF mediated data range from vouchered museum specimens to observation records generated by humans and machines. New data are being generated from integrated remote sensing, ecological s ling, and molecular sequencing that have strong geospatial components but lack traditional vouchers. GBIF is working with partners to develop best practices of bringing this data into the GBIF architecture. Following discussions during the second Global Bio ersity Information Conference in 2018, GBIF and the European Bioinformatics Institute (EMBL-EBI), supported by ELIXIR, have extended collaboration to share species occurrence records known only from their genetic material. When these data providers contribute data coordinates along with the sequences to the European Nucleotide Archive (ENA), the records will appear on GBIF maps and in spatial searches. This collaboration enables significant new molecular data streams to become discoverable through GBIF.org: by mid-March 2019, over 7.8m in idual occurrence records via the ENA, and over 13.2m records as standardized Darwin Core s ling-event datasets via MGnify, a resource that provides taxonomic and functional annotations on sequences derived from environmental sequencing projects. Sequence-based occurrence records published by ENA and MGnify boost representation of microbial ersity which was underrepresented at GBIF. The ELIXIR-ENA-MGnify-GBIF partnership is working on further refinement of the dynamic data linkages, frequency of updates and other improvements. The API-based tool that connects GBIF data infrastructures is open to new data contributors and for indexes of molecular occurrences. Indexing of these data streams is dependent on the presence of a name (any rank) with the sequence. Under the current Codes of nomenclature, animals, fungi, plants, and algae cannot be described based on exclusively sequence data. Yet, a significant volume of bio ersity data has only been represented by DNA sequences. Barcoding and sequence clustering procedures vary among taxa and research communities, but clusters can be related to a taxon with a Latin name. Many DNA similarity clusters do not contain a sequence from a formally described taxon however these sequence clusters provide provisional molecular names for nomenclatural communication. In the best cases, curated libraries of reference sequences, their metadata, clusters, alignments, and links to in iduals and physical material become de facto naming conventions for certain taxonomic groups, and co-exist with Latin names. Integration of molecular names into the taxonomic backbone of GBIF started with Fungi and UNITE, a data management and identification environment for fungal ITS barcodes with 87,000+ fungal species hypotheses demarcating 800,000+ sequence specimens as of March 2019. Checklist publication of all names in UNITE through GBIF.org including Linnaean names and stable, DOI-trackable molecular sequence based ‘species hypotheses’, enables indexing of fungal metabarcoding data worldwide, such as BIOWIDE. As names are currently essential to indexing the world’s occurrence data, GBIF will develop similar linkages with names in the Barcode of Life data system (BOLD) and in SILVA - a resource for high-quality ribosomal RNA sequence data and taxonomy, and welcomes other reference systems to this development. Expanding the molecular data streams (Fig. 1) allows GBIF to address spatial, temporal and taxonomic gaps and biases, and to support large-scale data-intensive research openly and worldwide.
Towards a global list of accepted species VI: The Catalogue of Life checklist
Publisher: Springer Science and Business Media LLC
Date: 11-10-2021
Widespread support for a global species list with a formal governance system
Publisher: Proceedings of the National Academy of Sciences
Date: 30-10-2023
Related Organisations
Virginia Institute Of Marine Science
Location: United States of America
National Museum Of Natural History
Location: United States of America
Related Funding Activities
No related grants have been discovered for Thomas Orrell.