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A new R package to parse plant species occurrence records into unique collection events efficiently reduces data redundancy.

ABSTRACT: Biodiversity data aggregators, such as Global Biodiversity Information Facility (GBIF) suffer from inflation of the number of occurrence records when data from different databases are merged but not fully reconciled. The ParseGBIF workflow is designed to parse duplicate GBIF species occurrence records into unique collection events (gatherings) and to optimise the quality of the spatial data associated with them. ParseGBIF provides tools to verify and standardize species scientific names according to the World Checklist of Vascular Plants taxonomic backbone, and to parse duplicate records into unique 'collection events', in the process compiling the most informative spatial data, where more than one duplicate is available, and providing crude estimates of taxonomic and spatial data quality. When GBIF occurrence records for a medium-sized vascular plant family, the Myrtaceae, were processed by ParseGBIF, the average number of records useful for spatial analysis increased by 180%. ParseGBIF could therefore be valuable in the evaluation of species' occurrences at the national scale in support for national biodiversity plans, identification of plant areas important for biodiversity, sample bias estimation to inform future sampling efforts, and to forecast species range shifts in response to global climate change.

SUBMITTER: de Melo PHA

PROVIDER: S-EPMC10914741 | biostudies-literature | 2024 Mar

REPOSITORIES: biostudies-literature

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A new R package to parse plant species occurrence records into unique collection events efficiently reduces data redundancy.

de Melo Pablo Hendrigo Alves PHA Bystriakova Nadia N Lucas Eve E Monro Alexandre K AK

Scientific reports 20240305 1

Biodiversity data aggregators, such as Global Biodiversity Information Facility (GBIF) suffer from inflation of the number of occurrence records when data from different databases are merged but not fully reconciled. The ParseGBIF workflow is designed to parse duplicate GBIF species occurrence records into unique collection events (gatherings) and to optimise the quality of the spatial data associated with them. ParseGBIF provides tools to verify and standardize species scientific names accordin ...[more]

PMID: 38443673

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Project description:Interleukin-6 has an important role in the pathophysiology of multiple myeloma where it supports the growth and survival of the malignant plasma cells in the bone marrow. It belongs to a family of cytokines which use the glycoprotein 130 chain for signal transduction, such as oncostatin M or leukemia inhibitory factor. Targeting interleukin-6 in plasma cell diseases is currently evaluated in clinical trials with monoclonal antibodies. Here, efforts were made to elucidate the contribution of interleukin-6 and glycoprotein 130 signaling in malignant plasma cell growth in vivo In the xenograft severe combined immune deficiency model employing our interleukin-6-dependent plasma cell line INA-6, the lack of human interleukin-6 induced autocrine interleukin-6 production and a proliferative response to other cytokines of the glycoprotein 130 family. Herein, mice were treated with monoclonal antibodies against human interleukin-6 (elsilimomab/B-E8), the interleukin-6 receptor (B-R6), and with an antibody blocking glycoprotein 130 (B-R3). While treatment of mice with interleukin-6 and interleukin-6 receptor antibodies resulted in a modest delay in tumor growth, the development of plasmacytomas was completely prevented with the anti-glycoprotein 130 antibody. Importantly, complete inhibition was also achieved using F(ab')2-fragments of monoclonal antibody B-R3. Tumors harbor activated signal transducer and activator of transcription 3, and in vitro, the antibody inhibited leukemia inhibitory factor stimulated signal transducer and activator of transcription 3 phosphorylation and cell growth, while being less effective against interleukin-6. In conclusion, the growth of INA-6 plasmacytomas in vivo under interleukin-6 withdrawal remains strictly dependent on glycoprotein 130, and other glycoprotein 130 cytokines may substitute for interleukin-6. Antibodies against glycoprotein 130 are able to overcome this redundancy and should be explored for a possible therapeutic window.

Dataset Information

A new R package to parse plant species occurrence records into unique collection events efficiently reduces data redundancy.

Publications

A new R package to parse plant species occurrence records into unique collection events efficiently reduces data redundancy.

Similar Datasets

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