Dataset Information

Every fifth published metagenome is not available to science.

ABSTRACT: Have you ever sought to use metagenomic DNA sequences reported in scientific publications? Were you successful? Here, we reveal that metagenomes from no fewer than 20% of the papers found in our literature search, published between 2016 and 2019, were not deposited in a repository or were simply inaccessible. The proportion of inaccessible data within the literature has been increasing year-on-year. Noncompliance with Open Data is best predicted by the scientific discipline of the journal. The number of citations, journal type (e.g., Open Access or subscription journals), and publisher are not good predictors of data accessibility. However, many publications in high-impact factor journals do display a higher likelihood of accessible metagenomic data sets. Twenty-first century science demands compliance with the ethical standard of data sharing of metagenomes and DNA sequence data more broadly. Data accessibility must become one of the routine and mandatory components of manuscript submissions-a requirement that should be applicable across the increasing number of disciplines using metagenomics. Compliance must be ensured and reinforced by funders, publishers, editors, reviewers, and, ultimately, the authors.

SUBMITTER: Eckert EM

PROVIDER: S-EPMC7159239 | biostudies-literature | 2020 Apr

REPOSITORIES: biostudies-literature

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Publications

Every fifth published metagenome is not available to science.

Eckert Ester M EM Di Cesare Andrea A Fontaneto Diego D Berendonk Thomas U TU Bürgmann Helmut H Cytryn Eddie E Fatta-Kassinos Despo D Franzetti Andrea A Larsson D G Joakim DGJ Manaia Célia M CM Pruden Amy A Singer Andrew C AC Udikovic-Kolic Nikolina N Corno Gianluca G

PLoS biology 20200403 4

Have you ever sought to use metagenomic DNA sequences reported in scientific publications? Were you successful? Here, we reveal that metagenomes from no fewer than 20% of the papers found in our literature search, published between 2016 and 2019, were not deposited in a repository or were simply inaccessible. The proportion of inaccessible data within the literature has been increasing year-on-year. Noncompliance with Open Data is best predicted by the scientific discipline of the journal. The n ...[more]

PMID: 32243442

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Project description:ObjectivesWith low-dose computed tomography(CT) lung cancer screening, many studies with an increasing number of patients with ground-glass opacity (GGO) are published. Hence, the present study aimed to analyze the published studies on GGO using bibliometric analysis. The findings could provide a basis for future research in GGO and for understanding past advances and trends in the field.MethodsPublished studies on GGO were obtained from the Web of Science Core Collection. A bibliometric analysis was conducted using the R package and VOSviewer for countries, institutions, journals, authors, keywords, and articles relevant to GGO. In addition, a bibliometric map was created to visualize the relationship.ResultsThe number of publications on GGO has been increasing since 2011. China is ranked as the most prolific country; however, Japan has the highest number of citations for its published articles. Seoul National University and Professor Jin Mo Goo from Korea had the highest publications. Most top 10 journals specialized in the field of lung diseases. Radiology is a comprehensive journal with the greatest number of citations and highest H-index than other journals. Using bibliometric analysis, research topics on "prognosis and diagnosis," "artificial intelligence," "treatment," "preoperative positioning and minimally invasive surgery," and "pathology of GGO" were identified. Artificial intelligence diagnosis and minimally invasive treatment may be the future of GGO. In addition, most top 10 literatures in this field were guidelines for lung cancer and pulmonary nodules.ConclusionsThe publication volume of GGO has increased rapidly. The top three countries with the highest number of published articles were China, Japan, and the United States. Japan had the most significant number of citations for published articles. Most key journals specialized in the field of lung diseases. Artificial intelligence diagnosis and minimally invasive treatment may be the future of GGO.

Project description:Habitat quality regulates fitness and population density, making it a key driver of population size. Hence, increasing habitat quality is often a primary goal of species conservation. Yet, assessments of fitness and density are difficult and costly to obtain. Therefore, species conservation often uses "best available science," extending inferences across taxa, space, or time, and inferring habitat quality from studies of habitat selection. However, there are scenarios where habitat selection is not reflective of habitat quality, and this can lead to maladaptive management strategies. The New England cottontail (Sylvilagus transitionalis) is an imperiled shrubland obligate lagomorph whose successful recovery hinges on creation of suitable habitat. Recovery of this species is also negatively impacted by the non-native eastern cottontail (Sylvilagus floridanus), which can competitively exclude New England cottontails from preferred habitat. Herein, we evaluate habitat quality for adult and juvenile New England and eastern cottontails using survival and density as indicators. Our findings did not support selection following an ideal free distribution by New England cottontails. Instead, selected resources, which are a target of habitat management, were associated with low survival and density and pointed to a complex trade-off between density, survival, habitat, and the presence of eastern cottontails. Further, movement distance was inversely correlated with survival in both species, suggesting that habitat fragmentation limits the ability of cottontails to freely distribute based on habitat quality. While habitat did not directly regulate survival of juvenile cottontails, tick burden had a strong negative impact on juvenile cottontails in poor body condition. Given the complex interactions among New England cottontails, eastern cottontails, and habitat, directly assessing and accounting for factors that limit New England cottontail habitat quality in management plans is vital to their recovery. Our study demonstrates an example of management for possible ecological trap conditions via the application of incomplete knowledge.

Dataset Information

Every fifth published metagenome is not available to science.

Publications

Every fifth published metagenome is not available to science.

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