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

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

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

Candidate single nucleotide polymorphisms and thromboembolism in acute lymphoblastic leukemia - A NOPHO ALL2008 study

Introduction: Thromboembolism is a serious toxicity of acute lymphoblastic leukemia treatment, and contributes to substantial morbidity and mortality. Several single nucleotide polymorphisms have been associated with thromboembolism in the general population; however, their impact in patients with acute lymphoblastic leukemia, particularly in children, remains uncertain. Materials and methods: We collected constitutional DNA and prospectively registered thromboembolic events in 1252 patients, 1-45 years, with acute lymphoblastic leukemia included in the Nordic Society of Pediatric Hematology and Oncology ALL2008 protocol in the Nordic and Baltic countries (7/2008-7/2016). Based on previously published data and a priori power calculations, we selected four single nucleotide polymorphisms: F5 rs6025, F11 rs2036914, FGG rs2066865, and ABO rs8176719. Results: The 2.5 year cumulative incidence of thromboembolism was 7.1% (95% confidence interval (CI) 5.6-8.5). F11 rs2036914 was associated with thromboembolism (hazard ratio (HR) 1.52, 95%CI 1.11-2.07) and there was a borderline significant association for FGG rs2066865 (HR 1.37, 95%CI 0.99-1.91), but no association for ABO rs8176719 or F5 rs6025 in multiple cox regression. A genetic risk score based on F11 rs2036914 and FGG rs2066865 was associated with thromboembolism (HR 1.45 per risk allele, 95%CI 1.15-1.81), the association was strongest in adolescents 10.0-17.9 years (HR 1.64). Conclusion: If validated, a F11 rs2036914/FGG rs2066865 risk prediction model should be tested as a stratification tool for prevention of thromboembolism in patients with acute lymphoblastic leukemia.Peer reviewe

Antibiotic treatment of rat dams affects bacterial colonization and causes decreased weight gain in pups

Monica Tulstrup et al. show that antibiotic treatment of female rats during pregnancy leads to altered intestinal colonization in early life and lower body weight in adulthood. They find that this effect correlates with lower feed intake and increased expression of satiety hormone at weaning