Ultrasonographic renal volume measurements in early autosomal dominant polycystic disease: Comparison with CT-scan renal volume calculations

AbstractPurposeTo investigate the correlation and concordance between the ellipsoid volume calculated by ultrasonography measurements (Vol3DUS) and the reference kidney volume measured by CT (VolTDM) in early autosomal dominant polycystic kidney disease (ADPKD).Materials and methodsProspective study of the correlation and concordance of renal volumes in 24 patients with early ADPKD (48 kidneys analysed separately), with calculation of Vol3DUS using the formula for an ellipsoid in three different manners and VolTDM measurement by manual contouring. Calculations of correlation coefficients (r) and coefficients of intra-class correlation (ICC) with confidence intervals at 95%.ResultsThe US volume was strongly correlated with the CT volume by using the maximum width in a transverse section (r=0.83) with a mean Vol3DUS=692±348ml [180; 2069]. The most reproducible ultrasonography measurement was the height. When the kidney volume exceeded 800ml, US underestimated the volume. However, the median error was −57.5ml [−1090; 183] and 85% of the Vol3DUS calculated differed by more than 5% from the reference measurement.ConclusionThe correlation between the US calculated volumes and the CT volumes was strong. However, the median error with ellipsoid US volume was too high to detect a small renal variation in early ADPKD

Analysis of Friedreich's ataxia patient clinical data reveals importance of accurate GAA repeat determination in disease prognosis and gender differences in cardiac measures

Friedreich's ataxia (FRDA) is a rare autosomal recessive inherited neurodegenerative disease which is the result of a triplet repeat expansion in the intronic region of the frataxin FXN gene resulting in depleted frataxin protein expression. Disease onset is usually in childhood and causes progressive damage to the nervous system resulting in progressive disability. This work uses computer aided classification techniques to identify which measures of the disease progression, including accurate determination of the shortest allele repeat length, are the most informative when trying to predict likely disease progression and prognosis. Further we investigate the possibility of a gender difference in the progression of the disease. Our results highlight the importance of accurate determination GAA repeat length in any clinical predictions showing that the number of repeats is the best prognostic tool in FRDA and is strongly linked to the age at onset disease. Further that there are possible gender dependent differences in cardiac measurements recorded from patients of similar age of onset and GAA repeat length.EFACT

Removal of Hepatitis B virus surface HBsAg and core HBcAg antigens using microbial fuel cells producing electricity from human urine

© 2019, The Author(s). Microbial electrochemical technology is emerging as an alternative way of treating waste and converting this directly to electricity. Intensive research on these systems is ongoing but it currently lacks the evaluation of possible environmental transmission of enteric viruses originating from the waste stream. In this study, for the first time we investigated this aspect by assessing the removal efficiency of hepatitis B core and surface antigens in cascades of continuous flow microbial fuel cells. The log-reduction (LR) of surface antigen (HBsAg) reached a maximum value of 1.86 ± 0.20 (98.6% reduction), which was similar to the open circuit control and degraded regardless of the recorded current. Core antigen (HBcAg) was much more resistant to treatment and the maximal LR was equal to 0.229 ± 0.028 (41.0% reduction). The highest LR rate observed for HBsAg was 4.66 ± 0.19 h−1 and for HBcAg 0.10 ± 0.01 h−1. Regression analysis revealed correlation between hydraulic retention time, power and redox potential on inactivation efficiency, also indicating electroactive behaviour of biofilm in open circuit control through the snorkel-effect. The results indicate that microbial electrochemical technologies may be successfully applied to reduce the risk of environmental transmission of hepatitis B virus but also open up the possibility of testing other viruses for wider implementation

A post-mortem survey on end-of-life decisions using a representative sample of death certificates in Flanders, Belgium: research protocol

Background: Reliable studies of the incidence and characteristics of medical end-of-life decisions with a certain or possible life shortening effect (ELDs) are indispensable for an evidence-based medical and societal debate on this issue. This article presents the protocol drafted for the 2007 ELD Study in Flanders, Belgium, and outlines how the main aims and challenges of the study (i.e. making reliable incidence estimates of end-of-life decisions, even rare ones, and describing their characteristics; allowing comparability with past ELD studies; guaranteeing strict anonymity given the sensitive nature of the research topic; and attaining a sufficient response rate) are addressed in a post-mortem survey using a representative sample of death certificates. Study design: Reliable incidence estimates are achievable by using large at random samples of death certificates of deceased persons in Flanders (aged one year or older). This entails the cooperation of the appropriate administrative authorities. To further ensure the reliability of the estimates and descriptions, especially of less prevalent end-of-life decisions (e.g. euthanasia), a stratified sample is drawn. A questionnaire is sent out to the certifying physician of each death sampled. The questionnaire, tested thoroughly and avoiding emotionally charged terms is based largely on questions that have been validated in previous national and European ELD studies. Anonymity of both patient and physician is guaranteed through a rigorous procedure, involving a lawyer as intermediary between responding physicians and researchers. To increase response we follow the Total Design Method (TDM) with a maximum of three follow-up mailings. Also, a non-response survey is conducted to gain insight into the reasons for lack of response. Discussion: The protocol of the 2007 ELD Study in Flanders, Belgium, is appropriate for achieving the objectives of the study; as past studies in Belgium, the Netherlands, and other European countries have shown, strictly anonymous and thorough surveys among physicians using a large, stratified, and representative death certificate sample are most suitable in nationwide studies of incidence and characteristics of end-of-life decisions. There are however also some limitations to the study design

Heterogeneity of Microglial Activation in the Innate Immune Response in the Brain

The immune response in the brain has been widely investigated and while many studies have focused on the proinflammatory cytotoxic response, the brain’s innate immune system demonstrates significant heterogeneity. Microglia, like other tissue macrophages, participate in repair and resolution processes after infection or injury to restore normal tissue homeostasis. This review examines the mechanisms that lead to reduction of self-toxicity and to repair and restructuring of the damaged extracellular matrix in the brain. Part of the resolution process involves switching macrophage functional activation to include reduction of proinflammatory mediators, increased production and release of anti-inflammatory cytokines, and production of cytoactive factors involved in repair and reconstruction of the damaged brain. Two partially overlapping and complimentary functional macrophage states have been identified and are called alternative activation and acquired deactivation. The immunosuppressive and repair processes of each of these states and how alternative activation and acquired deactivation participate in chronic neuroinflammation in the brain are discussed

Evidence of a causal and modifiable relationship between kidney function and circulating trimethylamine N-oxide

The host-microbiota co-metabolite trimethylamine N-oxide (TMAO) is linked to increased cardiovascular risk but how its circulating levels are regulated remains unclear. We applied "explainable" machine learning, univariate, multivariate and mediation analyses of fasting plasma TMAO concentration and a multitude of phenotypes in 1,741 adult Europeans of the MetaCardis study. Here we show that next to age, kidney function is the primary variable predicting circulating TMAO, with microbiota composition and diet playing minor, albeit significant, roles. Mediation analysis suggests a causal relationship between TMAO and kidney function that we corroborate in preclinical models where TMAO exposure increases kidney scarring. Consistent with our findings, patients receiving glucose-lowering drugs with reno-protective properties have significantly lower circulating TMAO when compared to propensity-score matched control individuals. Our analyses uncover a bidirectional relationship between kidney function and TMAO that can potentially be modified by reno-protective anti-diabetic drugs and suggest a clinically actionable intervention for decreasing TMAO-associated excess cardiovascular risk

Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology

Microbiota-host-diet interactions contribute to the development of metabolic diseases. Imidazole propionate is a novel microbially produced metabolite from histidine, which impairs glucose metabolism. Here, we show that subjects with prediabetes and diabetes in the MetaCardis cohort from three European countries have elevated serum imidazole propionate levels. Furthermore, imidazole propionate levels were increased in subjects with low bacterial gene richness and Bacteroides 2 enterotype, which have previously been associated with obesity. The Bacteroides 2 enterotype was also associated with increased abundance of the genes involved in imidazole propionate biosynthesis from dietary histidine. Since patients and controls did not differ in their histidine dietary intake, the elevated levels of imidazole propionate in type 2 diabetes likely reflects altered microbial metabolism of histidine, rather than histidine intake per se. Thus the microbiota may contribute to type 2 diabetes by generating imidazole propionate that can modulate host inflammation and metabolism

Combinatorial, additive and dose-dependent drug–microbiome associations

Data availability: The source data for the figures are provided at Zenodo (https://doi.org/10.5281/zenodo.4728981). Raw shotgun sequencing data that support the findings of this study have been deposited at the ENA under accession codes PRJEB41311, PRJEB38742 and PRJEB37249 with public access. Raw spectra for metabolomics have been deposited in the MassIVE database under the accession codes MSV000088043 (UPLC–MS/MS) and MSV000088042 (GC–MS). The metadata on disease groups and drug intake are provided in Supplementary Tables 1–3. The demographic, clinical and phenotype metadata, and processed microbiome and metabolome data for French, German and Danish participants are available at Zenodo (https://doi.org/10.5281/zenodo.4674360).Code availability: The new drug-aware univariate biomarker testing pipeline is available as an R package (metadeconfoundR; Birkner et al., manuscript in preparation) at Github (https://github.com/TillBirkner/metadeconfoundR) and at Zenodo (https://doi.org/10.5281/zenodo.4721078). The latest version (0.1.8) of this package was used to generate the data shown in this publication. The code used for multivariate analysis based on the VpThemAll package is available at Zenodo (https://doi.org/10.5281/zenodo.4719526). The phenotype and drug intake metadata, processed microbiome, and metabolome data and code resources are available for download at Zenodo (https://doi.org/10.5281/zenodo.4674360). The code for reproducing the figures is provided at Zenodo (https://doi.org/10.5281/zenodo.4728981).During the transition from a healthy state to cardiometabolic disease, patients become heavily medicated, which leads to an increasingly aberrant gut microbiome and serum metabolome, and complicates biomarker discovery1,2,3,4,5. Here, through integrated multi-omics analyses of 2,173 European residents from the MetaCardis cohort, we show that the explanatory power of drugs for the variability in both host and gut microbiome features exceeds that of disease. We quantify inferred effects of single medications, their combinations as well as additive effects, and show that the latter shift the metabolome and microbiome towards a healthier state, exemplified in synergistic reduction in serum atherogenic lipoproteins by statins combined with aspirin, or enrichment of intestinal Roseburia by diuretic agents combined with beta-blockers. Several antibiotics exhibit a quantitative relationship between the number of courses prescribed and progression towards a microbiome state that is associated with the severity of cardiometabolic disease. We also report a relationship between cardiometabolic drug dosage, improvement in clinical markers and microbiome composition, supporting direct drug effects. Taken together, our computational framework and resulting resources enable the disentanglement of the effects of drugs and disease on host and microbiome features in multimedicated individuals. Furthermore, the robust signatures identified using our framework provide new hypotheses for drug–host–microbiome interactions in cardiometabolic disease.This work was supported by the European Union’s Seventh Framework Program for research, technological development and demonstration under grant agreement HEALTH-F4-2012-305312 (METACARDIS). Part of this work was also supported by the EMBL, by the Metagenopolis grant ANR-11-DPBS-0001, by the H2020 European Research Council (ERC-AdG-669830) (to P.B.), and by grants from the Deutsche Forschungsgemeinschaft (SFB1365 to S.K.F. and L.M.; and SFB1052/3 A1 MS to M.S. (209933838)). Assistance Publique-Hôpitaux de Paris is the promoter of the clinical investigation (MetaCardis). M.-E.D. is supported by the NIHR Imperial Biomedical Research Centre and by grants from the French National Research Agency (ANR-10-LABX-46 (European Genomics Institute for Diabetes)), from the National Center for Precision Diabetic Medicine – PreciDIAB, which is jointly supported by the French National Agency for Research (ANR-18-IBHU-0001), by the European Union (FEDER), by the Hauts-de-France Regional Council (Agreement 20001891/NP0025517) and by the European Metropolis of Lille (MEL, Agreement 2019_ESR_11) and by Isite ULNE (R-002-20-TALENT-DUMAS), also jointly funded by ANR (ANR-16-IDEX-0004-ULNE), the Hauts-de-France Regional Council (20002845) and by the European Metropolis of Lille (MEL). R.J.A. is a member of the Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Bioscience. The Novo Nordisk Foundation Center for Basic Metabolic Research is an independent research institution at the University of Copenhagen partially funded by an unrestricted donation from the Novo Nordisk Foundation

Combinatorial, additive and dose-dependent drug–microbiome associations

During the transition from a healthy state to cardiometabolic disease, patients become heavily medicated, which leads to an increasingly aberrant gut microbiome and serum metabolome, and complicates biomarker discovery. Here, through integrated multi-omics analyses of 2,173 European residents from the MetaCardis cohort, we show that the explanatory power of drugs for the variability in both host and gut microbiome features exceeds that of disease. We quantify inferred effects of single medications, their combinations as well as additive effects, and show that the latter shift the metabolome and microbiome towards a healthier state, exemplified in synergistic reduction in serum atherogenic lipoproteins by statins combined with aspirin, or enrichment of intestinal Roseburia by diuretic agents combined with beta-blockers. Several antibiotics exhibit a quantitative relationship between the number of courses prescribed and progression towards a microbiome state that is associated with the severity of cardiometabolic disease. We also report a relationship between cardiometabolic drug dosage, improvement in clinical markers and microbiome composition, supporting direct drug effects. Taken together, our computational framework and resulting resources enable the disentanglement of the effects of drugs and disease on host and microbiome features in multimedicated individuals. Furthermore, the robust signatures identified using our framework provide new hypotheses for drug–host–microbiome interactions in cardiometabolic disease