Towards 3D databases and harmonized 3D models at IGME-CSIC

IGME-CSIC has a highly relevant geological and geophysical database that includes a continuous digital geological cartography at 1:50000; 1:200000 and 1:1000000 scales and a fair amount of geophysical data: gravity, magnetic, well-logs in tiff and LAS format, seismic lines in tiff and SEG-Y format, borehole and petrophysical data, together with other geophysical and geological studies. Since the 2004, an important effort has been done to undertake 3D geological and geophysical modelling ranging from local studies (mineral exploration or CO2 storage sites) to regional geology for a better understanding of the subsurface structure and its geodynamic evolution as a base for other studies on natural hazards or mineral resources. These studies were ¿stand alone¿ and now IGME is designing a new strategy. It includes the available data and models harmonization (stratigraphy sequences, structural interpretations, faults distribution, seismic velocity models, spatial distribution of physical properties such as density and magnetic susceptibility, workflows, methodologies, evaluation of uncertainties, visualization, etc.) to comply with the FAIR (Findable, Accessible, Interoperable and Reusable) data standardization. In this way, the new 3D models will be easily integrated and available from the databases. This strategy includes collaboration with the Bureau de Recherches Géologiques et Minières of France (BRGM) and Laboratório Nacional de Energia e Geologia of Portugal (LNEG) in order to harmonize the Spanish geological data and models with their neighbours across national borders. The first step is being done in the framework of GeoERA projects. Plain-language Summary IGME-CSIC owns a large database that includes a highly valuable geological and geophysical data and geophysical studies containing the interpretation of some of the data of Spain (onshore and offshore) Since 2004 the authors of this work have been working in 3D geological and geophysical modelling that includes local (mineral exploration or CO2 storage sites) and regional studies. The goal is to improve our understanding of the subsurface structures and processes as a base for deepening our knowledge in how the natural hazards occur, how to improve the exploration for mineral resources, etc. These studies were made ad hoc within different projects and now IGME-CSIC is designing a workflow to harmonize these models in order to comply with the FAIR (Findable, Accessible, Interoperable and Reusable) data standardization so the models will be available to being used beyond the initial objectives that generated their creation. This strategy includes collaboration with other European institutions like the Bureau de Recherches Géologiques et Minières of France (BRGM) and Laboratório Nacional de Energia e Geologia of Portugal (LNEG) in order to harmonize the models across national borders. The first step is already being done in the framework of the GeoERA projects

Autoantibodies against type I IFNs in patients with life-threatening COVID-19

Interindividual clinical variability in the course of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is vast. We report that at least 101 of 987 patients with life-threatening coronavirus disease 2019 (COVID-19) pneumonia had neutralizing immunoglobulin G (IgG) autoantibodies (auto-Abs) against interferon-w (IFN-w) (13 patients), against the 13 types of IFN-a (36), or against both (52) at the onset of critical disease; a few also had auto-Abs against the other three type I IFNs. The auto-Abs neutralize the ability of the corresponding type I IFNs to block SARS-CoV-2 infection in vitro. These auto-Abs were not found in 663 individuals with asymptomatic or mild SARS-CoV-2 infection and were present in only 4 of 1227 healthy individuals. Patients with auto-Abs were aged 25 to 87 years and 95 of the 101 were men. A B cell autoimmune phenocopy of inborn errors of type I IFN immunity accounts for life-threatening COVID-19 pneumonia in at least 2.6% of women and 12.5% of men

Abdominal and iliac arterial stenoses: comparative double-blinded randomized study of diagnostic accuracy of 3D MR angiography with gadodiamide or gadopentetate dimeglumine.

International audiencePURPOSE: To prospectively evaluate accuracy of gadolinium-enhanced three-dimensional (3D) magnetic resonance (MR) angiography with gadodiamide and gadopentetate dimeglumine (0.1 mmol/kg), with intraarterial DSA as reference standard, for imaging abdominal and iliac arterial stenoses. MATERIALS AND METHODS: The study was approved by all institutional review boards; informed consent was obtained from each subject before procedures. Two hundred forty-seven subjects were included; 240 received either contrast agent and were available for safety analysis; 222 were available for accuracy analysis. Enhanced 3D MR angiography and DSA were performed; image data were evaluated in a double-blinded randomized study. Stenoses were classified as not relevant ( or =50%). For detection of main stenosis, accuracy with enhanced 3D MR angiography compared with that with DSA was determined. RESULTS: The difference in accuracy for imaging with gadodiamide and gadopentetate was 3.6%. Noninferiority was inferred because the lower bound of the exact two-sided 95% confidence interval was -10.1 and was above the noninferiority margin (-15%). Accuracy for detection of the main stenosis was low, 56.4% for gadodiamide and 52.8% for gadopentetate group. Subgroup analysis with exclusion of inferior mesenteric artery and internal iliac arteries and the most false-positive stenosis classifications yielded better results: 76.6% and 71.6%, respectively. Sensitivity, specificity, and negative and positive predictive values did not differ substantially between study groups. In the main analysis, values were 44%, 96%, 35%, and 97% for gadodiamide and 44%, 83%, 30%, and 90% for gadopentetate, respectively. In the subgroup analysis, values were 66%, 95%, 61%, and 96% for gadodiamide and 63%, 86%, 58%, and 88% for gadopentetate, respectively. CONCLUSION: Noninferiority of gadodiamide versus gadopentetate was verified based on the primary end point, which was accuracy for detection of the main stenosis with enhanced 3D MR angiography compared with DSA

Assessment of plasma chitotriosidase activity, CCL18/PARC concentration and NP-C suspicion index in the diagnosis of Niemann-Pick disease type C : A prospective observational study

Niemann-Pick disease type C (NP-C) is a rare, autosomal recessive neurodegenerative disease caused by mutations in either the NPC1 or NPC2 genes. The diagnosis of NP-C remains challenging due to the non-specific, heterogeneous nature of signs/symptoms. This study assessed the utility of plasma chitotriosidase (ChT) and Chemokine (C-C motif) ligand 18 (CCL18)/pulmonary and activation-regulated chemokine (PARC) in conjunction with the NP-C suspicion index (NP-C SI) for guiding confirmatory laboratory testing in patients with suspected NP-C. In a prospective observational cohort study, incorporating a retrospective determination of NP-C SI scores, two different diagnostic approaches were applied in two separate groups of unrelated patients from 51 Spanish medical centers (n = 118 in both groups). From Jan 2010 to Apr 2012 (Period 1), patients with ≥2 clinical signs/symptoms of NP-C were considered 'suspected NP-C' cases, and NPC1/NPC2 sequencing, plasma chitotriosidase (ChT), CCL18/PARC and sphingomyelinase levels were assessed. Based on findings in Period 1, plasma ChT and CCL18/PARC, and NP-C SI prediction scores were determined in a second group of patients between May 2012 and Apr 2014 (Period 2), and NPC1 and NPC2 were sequenced only in those with elevated ChT and/or elevated CCL18/PARC and/or NP-C SI ≥70. Filipin staining and 7-ketocholesterol (7-KC) measurements were performed in all patients with NP-C gene mutations, where possible. In total across Periods 1 and 2, 10/236 (4%) patients had a confirmed diagnosis o NP-C based on gene sequencing (5/118 [4.2%] in each Period): all of these patients had two causal NPC1 mutations. Single mutant NPC1 alleles were detected in 8/236 (3%) patients, overall. Positive filipin staining results comprised three classical and five variant biochemical phenotypes. No NPC2 mutations were detected. All patients with NPC1 mutations had high ChT activity, high CCL18/PARC concentrations and/or NP-C SI scores ≥70. Plasma 7-KC was higher than control cut-off values in all patients with two NPC1 mutations, and in the majority of patients with single mutations. Family studies identified three further NP-C patients. This approach may be very useful for laboratories that do not have mass spectrometry facilities and therefore, they cannot use other NP-C biomarkers for diagnosis

Autoantibodies against type I IFNs in patients with life-threatening COVID-19

International audienceInterindividual clinical variability in the course of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is vast. We report that at least 101 of 987 patients with life-threatening coronavirus disease 2019 (COVID-19) pneumonia had neutralizing immunoglobulin G (IgG) autoantibodies (auto-Abs) against interferon-ω (IFN-ω) (13 patients), against the 13 types of IFN-α (36), or against both (52) at the onset of critical disease; a few also had auto-Abs against the other three type I IFNs. The auto-Abs neutralize the ability of the corresponding type I IFNs to block SARS-CoV-2 infection in vitro. These auto-Abs were not found in 663 individuals with asymptomatic or mild SARS-CoV-2 infection and were present in only 4 of 1227 healthy individuals. Patients with auto-Abs were aged 25 to 87 years and 95 of the 101 were men. A B cell autoimmune phenocopy of inborn errors of type I IFN immunity accounts for life-threatening COVID-19 pneumonia in at least 2.6% of women and 12.5% of men

Infections, antibiotic treatment and mortality in patients admitted to ICUs in countries considered to have high levels of antibiotic resistance compared to those with low levels

Background: Antimicrobial resistance is an increasing concern in ICUs worldwide. Infection with an antibiotic resistant (ABR) strain of an organism is associated with greater mortality than infection with the non-resistant strain, but there are few data assessing whether being admitted to an intensive care unit (ICU) with high levels of antimicrobial resistance is associated with a worse outcome than being admitted to an ICU with low rates of resistance. The aim of this study was, therefore, to compare the characteristics of infections and antibiotic treatments and patient outcomes in patients admitted to ICUs in countries considered as having high levels of antibiotic resistance and those admitted to ICUs in countries considered as having low levels of antibiotic resistance.Methods: Data from the large, international EPIC II one-day point prevalence study on infections in patients hospitalized in ICUs were used. For the current study, we compared the data obtained from patients from two groups of countries: countries with reported MRSA rates of ≥ 25% (highABR: Greece, Israel, Italy, Malta, Portugal, Spain, and Turkey) and countries with MRSA rates of < 5% (lowABR: Denmark, Finland, Netherlands, Norway, and Sweden).Results: On the study day, 1187/2204 (53.9%) patients in the HighABR ICUs were infected and 255/558 (45.7%) in the LowABR ICUs (P < 0.01). Patients in the HighABR ICUs were more severely ill than those in the LowABR ICUs, as reflected by a higher SAPS II score (35.6 vs 32.7, P < 0.05) and had longer median ICU (12 days vs 5 days) and hospital (24 days vs 16 days) lengths of stay. They also had higher crude ICU (20.0% vs 15.4%) and hospital (27.0% vs 21.5%) mortality rates (both P < 0.05). However, after multivariable adjustment and matched pair analysis there were no differences in ICU or hospital mortality rates between High or LowABR ICU patients overall or among those with infections.Conclusions: Being hospitalized in an ICU in a region with high levels of antimicrobial resistance is not associated per se with a worse outcome. © 2014 Hanberger et al.; licensee BioMed Central Ltd

Infections, antibiotic treatment and mortality in patients admitted to ICUs in countries considered to have high levels of antibiotic resistance compared to those with low levels

Background: Antimicrobial resistance is an increasing concern in ICUs worldwide. Infection with an antibiotic resistant (ABR) strain of an organism is associated with greater mortality than infection with the non-resistant strain, but there are few data assessing whether being admitted to an intensive care unit (ICU) with high levels of antimicrobial resistance is associated with a worse outcome than being admitted to an ICU with low rates of resistance. The aim of this study was, therefore, to compare the characteristics of infections and antibiotic treatments and patient outcomes in patients admitted to ICUs in countries considered as having high levels of antibiotic resistance and those admitted to ICUs in countries considered as having low levels of antibiotic resistance. Methods: Data from the large, international EPIC II one-day point prevalence study on infections in patients hospitalized in ICUs were used. For the current study, we compared the data obtained from patients from two groups of countries: countries with reported MRSA rates of greater than= 25% (highABR: Greece, Israel, Italy, Malta, Portugal, Spain, and Turkey) and countries with MRSA rates of less than 5% (lowABR: Denmark, Finland, Netherlands, Norway, and Sweden). Results: On the study day, 1187/2204 (53.9%) patients in the HighABR ICUs were infected and 255/558 (45.7%) in the LowABR ICUs (P less than 0.01). Patients in the HighABR ICUs were more severely ill than those in the LowABR ICUs, as reflected by a higher SAPS II score (35.6 vs 32.7, P less than 0.05) and had longer median ICU (12 days vs 5 days) and hospital (24 days vs 16 days) lengths of stay. They also had higher crude ICU (20.0% vs 15.4%) and hospital (27.0% vs 21.5%) mortality rates (both P less than 0.05). However, after multivariable adjustment and matched pair analysis there were no differences in ICU or hospital mortality rates between High or LowABR ICU patients overall or among those with infections. Conclusions: Being hospitalized in an ICU in a region with high levels of antimicrobial resistance is not associated per se with a worse outcome

Infections, antibiotic treatment and mortality in patients admitted to ICUs in countries considered to have high levels of antibiotic resistance compared to those with low levels

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