Environmental data and the Internet: openness and digital data management

In recent years the Geological Survey of Denmark and Greenland (GEUS) has, for a variety of reasons, worked intensively on implementing Internet technologies. The most important aim has been to provide public and private companies with access to many of the geological databases and maps at the Survey, thus substantially increasing the value of the geological data. In this way GEUS is implementing the intentions of the United Nations Aarhus-convention in respect of access to information, public participation in decision-making and access to justice in environmental matters (UNEC 1998). Another important objective has been to improve the procedures that deal with data input, registration and quality control of the large amounts of data that GEUS receives from regional authorities, private drilling companies and advisers, as well as that acquired by the activities of its own geological staff. This complies with the Danish Government’s initiatives for making the public sector more efficient through digital data management

The human gastrointestinal microbiota and prostate cancer development and treatment

The human gastrointestinal microbiome contains commensal bacteria and other microbiota that have been gaining increasing attention in the context of cancer development and response to treatment. Microbiota play a role in the maintenance of host barrier surfaces that contribute to both local inflammation and other systemic metabolic functions. In the context of prostate cancer, the gastrointestinal microbiome may play a role through metabolism of estrogen, an increase of which has been linked to the induction of prostatic neoplasia. Specific microbiota such as Bacteroides, Streptococcus, Bacteroides massiliensis, Faecalibacterium prausnitzii, Eubacterium rectalie, and Mycoplasma genitalium have been associated with differing risks of prostate cancer development or extensiveness of prostate cancer disease. In this Review, we discuss gastrointestinal microbiota’s effects on prostate cancer development, the ability of the microbiome to regulate chemotherapy for prostate cancer treatment, and the importance of using Next Generation Sequencing to further discern the microbiome’s systemic influence on prostate cancer

An in vitro chicken gut model demonstrates transfer of a multidrug resistance plasmid from Salmonella to commensal Escherichia coli

The chicken gastrointestinal tract is richly populated by commensal bacteria that fulfill various beneficial roles for the host, including helping to resist colonization by pathogens. It can also facilitate the conjugative transfer of multidrug resistance (MDR) plasmids between commensal and pathogenic bacteria which is a significant public and animal health concern as it may affect our ability to treat bacterial infections. We used an in vitro chemostat system to approximate the chicken cecal microbiota, simulate colonization by an MDR Salmonella pathogen, and examine the dynamics of transfer of its MDR plasmid harboring several genes, including the extended-spectrum beta-lactamase blaCTX-M1 We also evaluated the impact of cefotaxime administration on plasmid transfer and microbial diversity. Bacterial community profiles obtained by culture-independent methods showed that Salmonella inoculation resulted in no significant changes to bacterial community alpha diversity and beta diversity, whereas administration of cefotaxime caused significant alterations to both measures of diversity, which largely recovered. MDR plasmid transfer from Salmonella to commensal Escherichia coli was demonstrated by PCR and whole-genome sequencing of isolates purified from agar plates containing cefotaxime. Transfer occurred to seven E. coli sequence types at high rates, even in the absence of cefotaxime, with resistant strains isolated within 3 days. Our chemostat system provides a good representation of bacterial interactions, including antibiotic resistance transfer in vivo It can be used as an ethical and relatively inexpensive approach to model dissemination of antibiotic resistance within the gut of any animal or human and refine interventions that mitigate its spread before employing in vivo studies.IMPORTANCE The spread of antimicrobial resistance presents a grave threat to public health and animal health and is affecting our ability to respond to bacterial infections. Transfer of antimicrobial resistance via plasmid exchange is of particular concern as it enables unrelated bacteria to acquire resistance. The gastrointestinal tract is replete with bacteria and provides an environment for plasmid transfer between commensals and pathogens. Here we use the chicken gut microbiota as an exemplar to model the effects of bacterial infection, antibiotic administration, and plasmid transfer. We show that transfer of a multidrug-resistant plasmid from the zoonotic pathogen Salmonella to commensal Escherichia coli occurs at a high rate, even in the absence of antibiotic administration. Our work demonstrates that the in vitro gut model provides a powerful screening tool that can be used to assess and refine interventions that mitigate the spread of antibiotic resistance in the gut before undertaking animal studies

A predictive model for bone marrow disease in cytopenia based on noninvasive procedures

Bone marrow specimens are the core of the diagnostic workup of patients with cytopenia. To explore whether next-generation sequencing (NGS) could be used to rule out malignancy without bone marrow specimens, we incorporated NGS in a model to predict presence of disease in the bone marrow of patients with unexplained cytopenia. We analyzed the occurrence of mutations in 508 patients with cytopenia, referred for primary workup of a suspected hematologic malignancy from 2015 to 2020. We divided patients into a discovery (n = 340) and validation (n = 168) cohort. Targeted sequencing, bone marrow biopsy, and complete blood count were performed in all patients. Mutations were identified in 267 (53%) and abnormal bone marrow morphology in 188 (37%) patients. Patients with isolated neutropenia had the lowest frequency of both mutations (21%) and abnormal bone marrow morphology (5%). The median number of mutations per patient was 2 in patients with abnormal bone marrow morphology compared with 0 in patients with a nondiagnostic bone marrow morphology (P < .001). In a multivariable logistic regression, mutations in TET2, SF3B1, U2AF1, TP53, and RUNX1 were significantly associated with abnormal bone marrow morphology. In the validation cohort, a model combining mutational status and clinical data identified 34 patients (20%) without abnormal bone marrow morphology with a sensitivity of 100% (95% confidence interval: 93%-100%). Overall, we show that NGS combined with clinical data can predict the presence of abnormal bone marrow morphology in patients with unexplained cytopenia and thus can be used to assess the need of a bone marrow biopsy

European mineral intelligence – collecting, harmonizing and sharing data on European raw materials

The major share of raw materials needed to sustain our present lifestyle and even more importantly, required for the crucial green transition, are sourced outside Europe. The European Commission aims to enhance Europe's resilience and strengthen domestic sourcing. Although Europe has a long tradition of mining and extractive activities, it is acknowledged that there are several challenges to achieve European sourcing of certain raw materials such as the critical raw materials. A basic prerequisite to enable access to domestic raw materials is information on raw material occurrences, current and past mining activities, resources and reserves. The Geological Survey organizations (GSOs) of Europe play a key role in generating, compiling, gathering and storing the most up-to-date information as well as long-term data series on raw materials at national and regional levels. Over the last decade, the GSOs have joined forces and taken essential steps to harmonize and share data on raw materials. The results of this co-operation are illustrated as interactive maps on the European Geological Data Infrastructure (EGDI). This paper describes the data compiled in co-operation between the GSOs, and analyses the strengths and weaknesses of, as well as opportunities for and threats towards, the data

Towards a Digital Information Platform for Locating and Assessing Environmental Impacts of Submarine Groundwater Discharge: Examples from the Baltic Sea

The number of studies on submarine groundwater discharge (SGD) and the evidence of its significance in biogeochemical cycling and potential impacts on the chemical and ecological status of coastal waters is increasing globally. Here, we briefly present SGD studies from the Baltic Sea identified along the coastlines of Denmark, Finland, Germany, Poland, Sweden and Russia in the southwestern, southern and north–northeastern parts of the Baltic Sea. We introduce a digital SGD map viewer and information platform enabling easy overview and access to information on identified SGD sites in the coastal areas of the Baltic Sea. SGDs potentially transport critical pollutants from urban and agricultural areas on land to the marine environment. The pollutants include nutrients, dissolved organic and inorganic carbon, metals, pharmaceuticals, and other emerging contaminants, potentially harming marine ecosystems and biodiversity and possibly contributing to the poor chemical or ecological status of coastal waters, affecting human and environmental health. We focus on case studies from Finland, Germany, Poland and Denmark that include the results and interpretations from the applied geochemical, geophysical and geological methods, as well as bionic autonomous underwater vehicles (AUVs) for locating, investigating, modelling and visualizing SGD sites in 2D and 3D. The potential Pan-European or even global SGD information platform established within the European Geological Data Infrastructure (EGDI) enables the easy combination and comparison of map layers such as seabed sediment types and coastal habitats. The EGDI map viewer provides easy access to information from SGD studies and may serve as an entry point to relevant information on SGDs, including contents of pollutants, [...