The Crisis in Scientific Publishing: A Holistic Perspective About Background Issues Associated with Predatory Publishing

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Meridional Survey of the Central Pacific Reveals Iodide Accumulation in Equatorial Surface Waters and Benthic Sources in the Abyssal Plain

The distributions of iodate and iodide were measured along the GEOTRACES GP15 meridional transect at 152°W from the shelf of Alaska to Papeete, Tahiti. The transect included oxygenated waters near the shelf of Alaska, the full water column in the central basin in the North Pacific Basin, the upper water column spanning across seasonally mixed regimes in the north, oligotrophic regimes in the central gyre, and the equatorial upwelling. Iodide concentrations are highest in the permanently stratified tropical mixed layers, which reflect accumulation due to light-dependent biological processes, and decline rapidly below the euphotic zone. Vertical mixing coefficients (Kz), derived from complementary 7Be data, enabled iodide oxidation rates to be estimated at two stations. Iodide half-lives of 3–4 years show the importance of seasonal mixing processes in explaining north-south differences in the transect, and also contribute to the decrease in iodide concentrations with depth below the mixed layer. These estimated half-lives are consistent with a recent global iodine model. No evidence was found for significant inputs of iodine from the Alaskan continental margin, but there is a significant enrichment of iodide in bottom waters overlying deep sea sediments from the interior of the basin

The Bari Manifesto : An interoperability framework for essential biodiversity variables

Essential Biodiversity Variables (EBV) are fundamental variables that can be used for assessing biodiversity change over time, for determining adherence to biodiversity policy, for monitoring progress towards sustainable development goals, and for tracking biodiversity responses to disturbances and management interventions. Data from observations or models that provide measured or estimated EBV values, which we refer to as EBV data products, can help to capture the above processes and trends and can serve as a coherent framework for documenting trends in biodiversity. Using primary biodiversity records and other raw data as sources to produce EBV data products depends on cooperation and interoperability among multiple stakeholders, including those collecting and mobilising data for EBVs and those producing, publishing and preserving EBV data products. Here, we encapsulate ten principles for the current best practice in EBV-focused biodiversity informatics as 'The Bari Manifesto', serving as implementation guidelines for data and research infrastructure providers to support the emerging EBV operational framework based on trans-national and cross-infrastructure scientific workflows. The principles provide guidance on how to contribute towards the production of EBV data products that are globally oriented, while remaining appropriate to the producer's own mission, vision and goals. These ten principles cover: data management planning; data structure; metadata; services; data quality; workflows; provenance; ontologies/vocabularies; data preservation; and accessibility. For each principle, desired outcomes and goals have been formulated. Some specific actions related to fulfilling the Bari Manifesto principles are highlighted in the context of each of four groups of organizations contributing to enabling data interoperability - data standards bodies, research data infrastructures, the pertinent research communities, and funders. The Bari Manifesto provides a roadmap enabling support for routine generation of EBV data products, and increases the likelihood of success for a global EBV framework.Peer reviewe

Building essential biodiversity variables (EBVs) of species distribution and abundance at a global scale

Much biodiversity data is collected worldwide, but it remains challenging to assemble the scattered knowledge for assessing biodiversity status and trends. The concept of Essential Biodiversity Variables (EBVs) was introduced to structure biodiversity monitoring globally, and to harmonize and standardize biodiversity data from disparate sources to capture a minimum set of critical variables required to study, report and manage biodiversity change. Here, we assess the challenges of a 'Big Data' approach to building global EBV data products across taxa and spatiotemporal scales, focusing on species distribution and abundance. The majority of currently available data on species distributions derives from incidentally reported observations or from surveys where presence-only or presence-absence data are sampled repeatedly with standardized protocols. Most abundance data come from opportunistic population counts or from population time series using standardized protocols (e.g. repeated surveys of the same population from single or multiple sites). Enormous complexity exists in integrating these heterogeneous, multi-source data sets across space, time, taxa and different sampling methods. Integration of such data into global EBV data products requires correcting biases introduced by imperfect detection and varying sampling effort, dealing with different spatial resolution and extents, harmonizing measurement units from different data sources or sampling methods, applying statistical tools and models for spatial inter- or extrapolation, and quantifying sources of uncertainty and errors in data and models. To support the development of EBVs by the Group on Earth Observations Biodiversity Observation Network (GEO BON), we identify 11 key workflow steps that will operationalize the process of building EBV data products within and across research infrastructures worldwide. These workflow steps take multiple sequential activities into account, including identification and aggregation of various raw data sources, data quality control, taxonomic name matching and statistical modelling of integrated data. We illustrate these steps with concrete examples from existing citizen science and professional monitoring projects, including eBird, the Tropical Ecology Assessment and Monitoring network, the Living Planet Index and the Baltic Sea zooplankton monitoring. The identified workflow steps are applicable to both terrestrial and aquatic systems and a broad range of spatial, temporal and taxonomic scales. They depend on clear, findable and accessible metadata, and we provide an overview of current data and metadata standards. Several challenges remain to be solved for building global EBV data products: (i) developing tools and models for combining heterogeneous, multi-source data sets and filling data gaps in geographic, temporal and taxonomic coverage, (ii) integrating emerging methods and technologies for data collection such as citizen science, sensor networks, DNA-based techniques and satellite remote sensing, (iii) solving major technical issues related to data product structure, data storage, execution of workflows and the production process/cycle as well as approaching technical interoperability among research infrastructures, (iv) allowing semantic interoperability by developing and adopting standards and tools for capturing consistent data and metadata, and (v) ensuring legal interoperability by endorsing open data or data that are free from restrictions on use, modification and sharing. Addressing these challenges is critical for biodiversity research and for assessing progress towards conservation policy targets and sustainable development goals

An Inhaled Galectin-3 Inhibitor in COVID-19 Pneumonitis (DEFINE):A Phase Ib/IIa Randomised Controlled Trial

RATIONALE: High circulating galectin-3 is associated with poor outcomes in patients with coronavirus disease (COVID-19). We hypothesized that GB0139, a potent inhaled thiodigalactoside galectin-3 inhibitor with antiinflammatory and antifibrotic actions, would be safely and effectively delivered in COVID-19 pneumonitis. OBJECTIVES: Primary outcomes were safety and tolerability of inhaled GB0139 as an add-on therapy for patients hospitalized with COVID-19 pneumonitis. METHODS: We present the findings of two arms of a phase Ib/IIa randomized controlled platform trial in hospitalized patients with confirmed COVID-19 pneumonitis. Patients received standard of care (SoC) or SoC plus 10 mg inhaled GB0139 twice daily for 48 hours, then once daily for up to 14 days or discharge. MEASUREMENTS AND MAIN RESULTS: Data are reported from 41 patients, 20 of which were assigned randomly to receive GB0139. Primary outcomes: the GB0139 group experienced no treatment-related serious adverse events. Incidences of adverse events were similar between treatment arms (40 with GB0139 + SoC vs. 35 with SoC). Secondary outcomes: plasma GB0139 was measurable in all patients after inhaled exposure and demonstrated target engagement with decreased circulating galectin (overall treatment effect post-hoc analysis of covariance [ANCOVA] over days 2–7; P = 0.0099 vs. SoC). Plasma biomarkers associated with inflammation, fibrosis, coagulopathy, and major organ function were evaluated. CONCLUSIONS: In COVID-19 pneumonitis, inhaled GB0139 was well-tolerated and achieved clinically relevant plasma concentrations with target engagement. The data support larger clinical trials to determine clinical efficacy. Clinical trial registered with ClinicalTrials.gov (NCT04473053) and EudraCT (2020–002230–32)

Trace elements at the intersection of marine biological and geochemical evolution

Life requires a wide variety of bioessential trace elements to act as structural components and reactive centers in metalloenzymes. These requirements differ between organisms and have evolved over geological time, likely guided in some part by environmental conditions. Until recently, most of what was understood regarding trace element concentrations in the Precambrian oceans was inferred by extrapolation, geochemical modeling, and/or genomic studies. However, in the past decade, the increasing availability of trace element and isotopic data for sedimentary rocks of all ages has yielded new, and potentially more direct, insights into secular changes in seawater composition – and ultimately the evolution of the marine biosphere. Compiled records of many bioessential trace elements (including Ni, Mo, P, Zn, Co, Cr, Se, and I) provide new insight into how trace element abundance in Earth's ancient oceans may have been linked to biological evolution. Several of these trace elements display redox-sensitive behavior, while others are redox-sensitive but not bioessential (e.g., Cr, U). Their temporal trends in sedimentary archives provide useful constraints on changes in atmosphere-ocean redox conditions that are linked to biological evolution, for example, the activity of oxygen-producing, photosynthetic cyanobacteria. In this review, we summarize available Precambrian trace element proxy data, and discuss how temporal trends in the seawater concentrations of specific trace elements may be linked to the evolution of both simple and complex life. We also examine several biologically relevant and/or redox-sensitive trace elements that have yet to be fully examined in the sedimentary rock record (e.g., Cu, Cd, W) and suggest several directions for future studies

An evaluation of sedimentary molybdenum and iron as proxies for pore fluid paleoredox conditions

Author Posting. © The Author(s), 2018. This is the author's version of the work. It is posted here under a nonexclusive, irrevocable, paid-up, worldwide license granted to WHOI. It is made available for personal use, not for redistribution. The definitive version was published in American Journal of Science 318 (2018): 527-556, doi:10.2475/05.2018.04.Iron speciation and trace metal proxies are commonly applied together in efforts to identify anoxic settings marked by the presence of free sulfide (euxinia) or dissolved iron (ferruginous) in the water column. Here, we use a literature compilation from modern localities to provide a new empirical evaluation of coupled Fe speciation and Mo concentrations as a proxy for pore water sulfide accumulation at non-euxinic localities. We also present new Fe speciation, Mo concentration, and S isotope data from the Friends of Anoxic Mud (FOAM) site in Long Island Sound, which is marked by pore water sulfide accumulation of up to 3 mM beneath oxygen-containing bottom waters. For the operationally defined Fe speciation scheme, ‘highly reactive’ Fe (FeHR) is the sum of pyritized Fe (Fepy) and Fe dominantly present in oxide phases that is available to react with pore water sulfide to form pyrite. Observations from FOAM and elsewhere confirm that Fepy/FeHR from non-euxinic sites is a generally reliable indicator of pore fluid redox, particularly the presence of pore water sulfide. Molybdenum (Mo) concentration data for anoxic continental margin sediments underlying oxic waters but with sulfidic pore fluids typically show authigenic Mo enrichments (2-25 ppm) that are elevated relative to the upper crust (1-2 ppm). However, compilations of Mo concentrations comparing sediments with and without sulfidic pore fluids underlying oxic and low oxygen (non-euxinic) water columns expose non-unique ranges for each, exposing false positives and false negatives. False positives are most frequently found in sediments from low oxygen water columns (for example, Peru Margin), where Mo concentration ranges can also overlap with values commonly found in modern euxinic settings. FOAM represents an example of a false negative, where, despite elevated pore water sulfide concentrations and evidence for active Fe and Mn redox cycling in FOAM sediments, sedimentary Mo concentrations show a homogenous vertical profile across 50 cm depth at 1-2 ppm. A diagenetic model for Mo provides evidence that muted authigenic enrichments are derived from elevated sedimentation rates. Consideration of a range of additional parameters, most prominently pore water Mo concentration, can replicate the ranges of most sedimentary Mo concentrations observed in modern non-euxinic settings. Together, the modern Mo and Fe data compilations and diagenetic model provide a framework for identifying paleo-pore water sulfide accumulation in ancient settings and linked processes regulating seawater Mo and sulfate concentrations and delivery to sediments. Among other utilities, identifying ancient accumulation of sulfide in pore waters, particularly beneath oxic bottom waters, constrains the likelihood that those settings could have hosted organisms and ecosystems with thiotrophy at their foundations.DSH, TWL, NJP, and CRT acknowledge support from the NASA Astrobiology Institute under Cooperative Agreement No. NNA15BB03A issued through the Science Mission Directorate. Financial support was provided to NR and TWL by NSF-OCE and an appointment to the NASA Postdoctoral Program, as well as to BCG via a postdoctoral fellowship from the Agouron Institute. DSH was supported by a WHOI postdoctoral fellowship