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| 6. |
- Athan, E., et al.
(author)
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Influence of vancomycin minimum inhibitory concentration on the outcome of methicillin-susceptible Staphylococcus aureus left-sided infective endocarditis treated with antistaphylococcal β-lactam antibiotics: a prospective cohort study by the International Collaboration on Endocarditis
- 2017
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In: Clinical Microbiology and Infection. - : Elsevier BV. - 1198-743X .- 1469-0691. ; 23, s. 544-549
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Journal article (peer-reviewed)abstract
- © 2017 European Society of Clinical Microbiology and Infectious Diseases Objectives Left-sided methicillin-susceptible Staphylococcus aureus (MSSA) endocarditis treated with cloxacillin has a poorer prognosis when the vancomycin minimum inhibitory concentration (MIC) is ≥1.5 mg/L. We aimed to validate this using the International Collaboration on Endocarditis cohort and to analyse whether specific genetic characteristics were associated with a high vancomycin MIC (≥1.5 mg/L) phenotype. Methods All patients with left-sided MSSA infective endocarditis treated with antistaphylococcal β-lactam antibiotics between 2000 and 2006 with available isolates were included. Vancomycin MIC was determined by Etest as either high (≥1.5 mg/L) or low (<1.5 mg/L). Isolates underwent spa typing to infer clonal complexes and multiplex PCR for identifying virulence genes. Univariate analysis was performed to evaluate the association between in-hospital and 1-year mortality, and vancomycin MIC phenotype. Results Sixty-two cases met the inclusion criteria. Vancomycin MIC was low in 28 cases (45%) and high in 34 cases (55%). No significant differences in patient demographic data or characteristics of infection were observed between patients with infective endocarditis due to high and low vancomycin MIC isolates. Isolates with high and low vancomycin MIC had similar distributions of virulence genes and clonal lineages. In-hospital and 1-year mortality did not differ significantly between the two groups (32% (9/28) vs. 27% (9/34), p 0.780; and 43% (12/28) vs. 29% (10/34), p 0.298, for low and high vancomycin MIC respectively). Conclusions In this international cohort of patients with left-sided MSSA endocarditis treated with antistaphylococcal β-lactams, vancomycin MIC phenotype was not associated with patient demographics, clinical outcome or virulence gene repertoire.
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| 9. |
- Porcu, E, et al.
(author)
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Mendelian randomization integrating GWAS and eQTL data reveals genetic determinants of complex and clinical traits
- 2019
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In: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 10:1, s. 3300-
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Journal article (peer-reviewed)abstract
- Genome-wide association studies (GWAS) have identified thousands of variants associated with complex traits, but their biological interpretation often remains unclear. Most of these variants overlap with expression QTLs, indicating their potential involvement in regulation of gene expression. Here, we propose a transcriptome-wide summary statistics-based Mendelian Randomization approach (TWMR) that uses multiple SNPs as instruments and multiple gene expression traits as exposures, simultaneously. Applied to 43 human phenotypes, it uncovers 3,913 putatively causal gene–trait associations, 36% of which have no genome-wide significant SNP nearby in previous GWAS. Using independent association summary statistics, we find that the majority of these loci were missed by GWAS due to power issues. Noteworthy among these links is educational attainment-associated BSCL2, known to carry mutations leading to a Mendelian form of encephalopathy. We also find pleiotropic causal effects suggestive of mechanistic connections. TWMR better accounts for pleiotropy and has the potential to identify biological mechanisms underlying complex traits.
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| 10. |
- Chu, V H, et al.
(author)
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Coagulase-negative staphylococcal prosthetic valve endocarditis--a contemporary update based on the International Collaboration on Endocarditis: prospective cohort study.
- 2009
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In: Heart (British Cardiac Society). - : BMJ. - 1468-201X .- 1355-6037. ; 95:7, s. 570-6
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Journal article (peer-reviewed)abstract
- To describe the contemporary features of coagulase-negative staphylococcal (CoNS) prosthetic valve endocarditis (PVE).Observational study of prospectively collected data from a multinational cohort of patients with infective endocarditis. Patients with CoNS PVE were compared to patients with Staphylococcus aureus and viridans streptococcal (VGS) PVE.The International Collaboration on Endocarditis-Prospective Cohort Study (ICE-PCS) is a contemporary cohort of patients with infective endocarditis from 61 centres in 28 countries.Adult patients in the ICE-PCS with definite PVE and no history of injecting drug use from June 2000 to August 2005 were included.None.Heart failure, intracardiac abscess, death.CoNS caused 16% (n = 86) of 537 cases of definite non-injecting drug use-associated PVE. Nearly one-half (n = 33/69, 48%) of patients with CoNS PVE presented between 60 days and 365 days of valve implantation. The rate of intracardiac abscess was significantly higher in patients with CoNS PVE (38%) than in patients with either S aureus (23%, p = 0.03) or VGS (20%, p = 0.05) PVE. The rate of abscess was particularly high in early (50%) and intermediate (52%) CoNS PVE. In-hospital mortality was 24% for CoNS PVE, 36% for S aureus PVE (p = 0.09) and 9.1% for VGS PVE (p = 0.08). Meticillin resistance was present in 68% of CoNS strains.Nearly one-half of CoNS PVE cases occur between 60 days and 365 days of prosthetic valve implantation. CoNS PVE is associated with a high rate of meticillin resistance and significant valvular complications.
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| 15. |
- Ades, A. E., et al.
(author)
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Zika virus infection in pregnancy : a protocol for the joint analysis of the prospective cohort studies of the ZIKAlliance, ZikaPLAN and ZIKAction consortia
- 2020
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In: BMJ Open. - : BMJ PUBLISHING GROUP. - 2044-6055. ; 10:12
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Journal article (peer-reviewed)abstract
- Introduction: Zika virus (ZIKV) infection in pregnancy has been associated with microcephaly and severe neurological damage to the fetus. Our aim is to document the risks of adverse pregnancy and birth outcomes and the prevalence of laboratory markers of congenital infection in deliveries to women experiencing ZIKV infection during pregnancy, using data from European Commission-funded prospective cohort studies in 20 centres in 11 countries across Latin America and the Caribbean.Methods and analysis: We will carry out a centre-by-centre analysis of the risks of adverse pregnancy and birth outcomes, comparing women with confirmed and suspected ZIKV infection in pregnancy to those with no evidence of infection in pregnancy. We will document the proportion of deliveries in which laboratory markers of congenital infection were present. Finally, we will investigate the associations of trimester of maternal infection in pregnancy, presence or absence of maternal symptoms of acute ZIKV infection and previous flavivirus infections with adverse outcomes and with markers of congenital infection. Centre-specific estimates will be pooled using a two-stage approach.Ethics and dissemination: Ethical approval was obtained at each centre. Findings will be presented at international conferences and published in peer-reviewed open access journals and discussed with local public health officials and representatives of the national Ministries of Health, Pan American Health Organization and WHO involved with ZIKV prevention and control activities.
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| 16. |
- Ambrosioni, J., et al.
(author)
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Epidemiological Changes and Improvement in Outcomes of Infective Endocarditis in Europe in the Twenty-First Century: An International Collaboration on Endocarditis (ICE) Prospective Cohort Study (2000-2012)
- 2023
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In: Infectious Diseases and Therapy. - : Springer Science and Business Media LLC. - 2193-8229 .- 2193-6382. ; 12:4, s. 1083-1101
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Journal article (peer-reviewed)abstract
- Introduction Infective endocarditis (IE) has undergone important changes in its epidemiology worldwide.Methods The study aimed to compare IE epidemiological features and outcomes according to predefined European regions and between two different time periods in the twenty-first century.Results IE cases from 13 European countries were included. Two periods were considered: 2000-2006 and 2008-2012. Two European regions were considered, according to the United Nations geoscheme for Europe: Southern (SE) and Northern-Central Europe (NCE). Comparisons were performed between regions and periods. A total of 4195 episodes of IE were included, 2113 from SE and 2082 from NCE; 2787 cases were included between 2000 and 2006 and 1408 between 2008 and 2012. Median (IQR) age was 63.7 (49-74) years and 69.4% were males. Native valve IE (NVE), prosthetic valve IE (PVE), and device-related IE were diagnosed in 68.3%, 23.9%, and 7.8% of cases, respectively; 52% underwent surgery and 19.3% died during hospitalization. NVE was more prevalent in NCE, whereas device-related IE was more frequent in SE. Higher age, acute presentation, hemodialysis, cancer, and diabetes mellitus all were more prevalent in the second period. NVE decreased and PVE and device-related IE both increased in the second period. Surgical treatment also increased from 48.7% to 58.4% (p < 0.01). In-hospital and 6-month mortality rates were comparable between regions and significantly decreased in the second period.Conclusions Despite an increased complexity of IE cases, prognosis improved in recent years with a significant decrease in 6-month mortality. Outcome did not differ according to the European region (SE versus NCE).
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| 17. |
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| 18. |
- Cabell, Cristopher H, et al.
(author)
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Use of surgery in patients with native valve infective endocarditis: results from the International Collaboration on Endocarditis Merged Database.
- 2005
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In: American heart journal. - : Elsevier BV. - 1097-6744 .- 0002-8703. ; 150:5, s. 1092-8
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Journal article (peer-reviewed)abstract
- BACKGROUND: Early surgery has been shown to be beneficial for patients with infective endocarditis (IE), yet surgery is not used in most patients. Evidence of the uncertainty around the use of surgery can be found in the wide variations in the use of cardiac surgery in IE with few precise indications for cardiac surgery yet defined. The aim of the study was to characterize patients with native valve IE relative to surgery and to determine if patients who benefit from an early surgical intervention can be identified. METHODS: The International Collaboration on Endocarditis Merged Database was used to quantify the differences between patients with IE receiving medical and surgical intervention in 1516 patients with definite native valve IE. Propensity models were built to identify a group of patients that benefit from early surgery. RESULTS: Patients in the early surgical group were more likely to be male, younger, and with less comorbidities compared with the early medical group (P < .001 for all) and were less likely to have infection with Staphylococcus aureus or viridans group streptococci (P < .05 for all). Intracardiac abscess and heart failure were much more common in the surgical group (P < .001 for all). In an unadjusted comparison, there was no statistically significant survival advantage in the surgical group. However, in the propensity analysis, in the subgroup of patients with the most indications for surgery, there was a significant decrease in mortality associated with early surgery (11.2% vs 38.0%, P < .001). CONCLUSIONS: The benefits of surgery are not seen uniformly in all patients with native valve IE, but are most realized in a targeted population. This observation requires confirmation in other populations of patients with definite IE.
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| 19. |
- Chirouze, C., et al.
(author)
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Enterococcal endocarditis in the beginning of the 21st century: analysis from the International Collaboration on Endocarditis-Prospective Cohort Study
- 2013
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In: Clinical Microbiology and Infection. - : Elsevier BV. - 1198-743X. ; 19:12, s. 1140-1147
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Journal article (peer-reviewed)abstract
- Enterococci are reportedly the third most common group of endocarditis-causing pathogens but data on enterococcal infective endocarditis (IE) are limited. The aim of this study was to analyse the characteristics and prognostic factors of enterococcal IE within the International Collaboration on Endocarditis. In this multicentre, prospective observational cohort study of 4974 adults with definite IE recorded from June 2000 to September 2006, 500 patients had enterococcal IE. Their characteristics were described and compared with those of oral and group D streptococcal IE. Prognostic factors for enterococcal IE were analysed using multivariable Cox regression models. The patients' mean age was 65years and 361/500 were male. Twenty-three per cent (117/500) of cases were healthcare related. Enterococcal IE were more frequent than oral and group D streptococcal IE in North America. The 1-year mortality rate was 28.9% (144/500). E.faecalis accounted for 90% (453/500) of enterococcal IE. Resistance to vancomycin was observed in 12 strains, eight of which were observed in North America, where they accounted for 10% (8/79) of enterococcal strains, and was more frequent in E.faecium than in E.faecalis (3/16 vs. 7/364 , p0.01). Variables significantly associated with 1-year mortality were heart failure (HR 2.4, 95% CI 1.73.5, p<0.0001), stroke (HR 1.9, 95% CI 1.32.8, p0.001) and age (HR 1.02 per 1-year increment, 95% CI 1.011.04, p0.002). Surgery was not associated with better outcome. Enterococci are an important cause of IE, with a high mortality rate. Healthcare association and vancomycin resistance are common in particular in North America.
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| 20. |
- Chirouze, C, et al.
(author)
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Prognostic factors in 61 cases of Staphylococcus aureus prosthetic valve infective endocarditis from the International Collaboration on Endocarditis merged database.
- 2004
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In: Clinical infectious diseases : an official publication of the Infectious Diseases Society of America. - : Oxford University Press (OUP). - 1537-6591. ; 38:9, s. 1323-7
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Research review (peer-reviewed)abstract
- Staphylococcus aureus prosthetic valve infective endocarditis (SA-PVIE) is associated with a high mortality rate, but prognostic factors have not been clearly elucidated. The International Collaboration on Endocarditis merged database (ICE-MD) contained 2212 cases of definite infective endocarditis (as defined using the Duke criteria), 61 of which were SA-PVIE. Overall mortality rate was 47.5%, stroke was associated with an increased risk of death, and early valve replacement was not associated with a significant survival benefit in the whole population; however, patients who developed cardiac complications and underwent early valve replacement had the lowest mortality rate (28.6%).
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| 21. |
- Gustavsson, Leif, et al.
(author)
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The role of wood material for greenhouse gas mitigation
- 2006
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In: Mitigation and Adaptation Strategies for Global Change. - : Springer Science and Business Media LLC. - 1381-2386 .- 1573-1596. ; 11:5-6, s. 1097-1127
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Journal article (peer-reviewed)abstract
- Based on an interdisciplinary perspective the role of wood as a carbon sink, as a multipurpose material, and as a renewable energy source for the net reduction of greenhouse gases is discussed. We synthesize aspects from engineering, natural and social sciences to better understand the role of wood substitution in CO2 mitigation.We also formulate some recommendations on filling knowledge gaps that could be useful for policy making regarding how wood substitution could be further expanded. There are sufficient wood resources to substantially increase the use of wood for material and energy purposes. However, a number of factors hinder a wider use of wood for energy and material purposes. Furthermore, an analysis of wood substitution is a very complex issue, since the substitution influencing factors are to be found along the entire wood supply chain and involve several industries, socio-economic and cultural aspects, traditions, price dynamics, and structural and technical change. To improve the knowledge about wood as a substitute for other resources and the implications, it would be helpful to better integrate research from different disciplines on the subject and to cover different scales from a project to an economy-wide level.
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| 22. |
- Hoen, B, et al.
(author)
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Emergence of endocarditis due to group D streptococci: findings derived from the merged database of the International Collaboration on Endocarditis.
- 2005
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In: European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology. - : Springer Science and Business Media LLC. - 0934-9723. ; 24:1, s. 12-6
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Journal article (peer-reviewed)abstract
- The aim of the present study was to compare the epidemiological and clinical characteristics of Streptococcus bovis endocarditis with those of endocarditis caused by oral streptococci, using data obtained from a large international database of uniformly defined cases of infective endocarditis. S. bovis, a well-known cause of infective endocarditis, remains the common name used to designate group D nonenterococcal streptococci. In some countries, the frequency of S. bovis endocarditis has increased significantly in recent years. Data from the International Collaboration on Endocarditis merged database was used to identify the main characteristics of S. bovis endocarditis and compared them with those of infective endocarditis (IE) due to oral streptococci. The database contained 136 cases of S. bovis IE and 511 cases of IE due to oral streptococci. Patients with S. bovis IE were significantly older those with IE due to oral streptococci (63+/-16 vs. 55+/-18 years, P<0.00001). The proportion of streptococcal IE due to S. bovis increased from 10.9% before 1989 to 23.3% after 1989 (P=0.0007) and was 56.7% in France as compared with 9.4% in the rest of Europe and 6.0% in the USA (P<0.00001). Patients with S. bovis IE had more comorbidity and never used intravenous drugs. Complication rates, rates of valve replacement, and mortality rates were similar in the two groups. In conclusion, this study confirmed that S. bovis IE has unique characteristics when compared to endocarditis due to oral streptococci and that it emerged in the 1990s, mainly in France, a finding that is yet unexplained.
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| 23. |
- Hop, Paul J., et al.
(author)
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Genome-wide study of DNA methylation shows alterations in metabolic, inflammatory, and cholesterol pathways in ALS
- 2022
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In: Science Translational Medicine. - : American Association for the Advancement of Science. - 1946-6234 .- 1946-6242. ; 14:633
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Journal article (peer-reviewed)abstract
- Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with an estimated heritability between 40 and 50%. DNA methylation patterns can serve as proxies of (past) exposures and disease progression, as well as providing a potential mechanism that mediates genetic or environmental risk. Here, we present a blood-based epigenome-wide association study meta-analysis in 9706 samples passing stringent quality control (6763 patients, 2943 controls). We identified a total of 45 differentially methylated positions (DMPs) annotated to 42 genes, which are enriched for pathways and traits related to metabolism, cholesterol biosynthesis, and immunity. We then tested 39 DNA methylation-based proxies of putative ALS risk factors and found that high-density lipoprotein cholesterol, body mass index, white blood cell proportions, and alcohol intake were independently associated with ALS. Integration of these results with our latest genome-wide association study showed that cholesterol biosynthesis was potentially causally related to ALS. Last, DNA methylation at several DMPs and blood cell proportion estimates derived from DNA methylation data were associated with survival rate in patients, suggesting that they might represent indicators of underlying disease processes potentially amenable to therapeutic interventions.
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| 24. |
- Kuijt, Suzanne J. H., et al.
(author)
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Interaction between the GROWTH-REGULATING FACTOR and KNOTTED1-LIKE HOMEOBOX Families of Transcription Factors1[W]
- 2014
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In: Plant Physiology. - : Oxford University Press (OUP). - 0032-0889 .- 1532-2548. ; 164:4, s. 1952-1966
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Journal article (peer-reviewed)abstract
- KNOTTED1-LIKE HOMEOBOX (KNOX) genes are important regulators of meristem function, and a complex network of transcription factors ensures tight control of their expression. Here, we show that members of the GROWTH-REGULATING FACTOR (GRF) family act as players in this network. A yeast (Saccharomyces cerevisiae) one-hybrid screen with the upstream sequence of the KNOX gene Oskn2 from rice (Oryza sativa) resulted in isolation of OsGRF3 and OsGRF10. Specific binding to a region in the untranslated leader sequence of Oskn2 was confirmed by yeast and in vitro binding assays. ProOskn2: beta-glucuronidase reporter expression was down-regulated by OsGRF3 and OsGRF10 in vivo, suggesting that these proteins function as transcriptional repressors. Likewise, we found that the GRF protein BGRF1 from barley (Hordeum vulgare) could act as a repressor on an intron sequence in the KNOX gene Hooded/Barley Knotted3 (Bkn3) and that AtGRF4, AtGRF5, and AtGRF6 from Arabidopsis (Arabidopsis thaliana) could repress KNOTTED-LIKE FROM ARABIDOPSIS THALIANA2 (KNAT2) promoter activity. OsGRF overexpression phenotypes in rice were consistent with aberrant meristematic activity, showing reduced formation of tillers and internodes and extensive adventitious root/shoot formation on nodes. These effects were associated with down-regulation of endogenous Oskn2 expression by OsGRF3. Conversely, RNA interference silencing of OsGRF3, OsGRF4, and OsGRF5 resulted in dwarfism, delayed growth and inflorescence formation, and up-regulation of Oskn2. These data demonstrate conserved interactions between the GRF and KNOX families of transcription factors in both monocot and dicot plants.
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| 25. |
- Lappalainen, Tuuli, et al.
(author)
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Transcriptome and genome sequencing uncovers functional variation in humans
- 2013
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 501:7468, s. 506-511
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Journal article (peer-reviewed)abstract
- Genome sequencing projects are discovering millions of genetic variants in humans, and interpretation of their functional effects is essential for understanding the genetic basis of variation in human traits. Here we report sequencing and deep analysis of messenger RNA and microRNA from lymphoblastoid cell lines of 462 individuals from the 1000 Genomes Project-the first uniformly processed high-throughput RNA-sequencing data from multiple human populations with high-quality genome sequences. We discover extremely widespread genetic variation affecting the regulation of most genes, with transcript structure and expression level variation being equally common but genetically largely independent. Our characterization of causal regulatory variation sheds light on the cellular mechanisms of regulatory and loss-of-function variation, and allows us to infer putative causal variants for dozens of disease-associated loci. Altogether, this study provides a deep understanding of the cellular mechanisms of transcriptome variation and of the landscape of functional variants in the human genome.
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| 26. |
- Laurie, Steven, et al.
(author)
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The RD-Connect Genome-Phenome Analysis Platform : Accelerating diagnosis, research, and gene discovery for rare diseases
- 2022
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In: Human Mutation. - : John Wiley & Sons. - 1059-7794 .- 1098-1004. ; 43:6, s. 717-733
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Journal article (peer-reviewed)abstract
- Rare disease patients are more likely to receive a rapid molecular diagnosis nowadays thanks to the wide adoption of next-generation sequencing. However, many cases remain undiagnosed even after exome or genome analysis, because the methods used missed the molecular cause in a known gene, or a novel causative gene could not be identified and/or confirmed. To address these challenges, the RD-Connect Genome-Phenome Analysis Platform (GPAP) facilitates the collation, discovery, sharing, and analysis of standardized genome-phenome data within a collaborative environment. Authorized clinicians and researchers submit pseudonymised phenotypic profiles encoded using the Human Phenotype Ontology, and raw genomic data which is processed through a standardized pipeline. After an optional embargo period, the data are shared with other platform users, with the objective that similar cases in the system and queries from peers may help diagnose the case. Additionally, the platform enables bidirectional discovery of similar cases in other databases from the Matchmaker Exchange network. To facilitate genome-phenome analysis and interpretation by clinical researchers, the RD-Connect GPAP provides a powerful user-friendly interface and leverages tens of information sources. As a result, the resource has already helped diagnose hundreds of rare disease patients and discover new disease causing genes.
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| 27. |
- McDonald, J R, et al.
(author)
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Enterococcal endocarditis: 107 cases from the international collaboration on endocarditis merged database.
- 2005
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In: The American journal of medicine. - : Elsevier BV. - 0002-9343. ; 118:7, s. 759-66
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Journal article (peer-reviewed)abstract
- PURPOSE: To describe clinical features and outcomes of enterococcal left-sided native valve endocarditis and to compare it to endocarditis caused by other pathogens. SUBJECTS AND METHODS: Patients in the International Collaboration on Endocarditis-Merged Database were included if they had left-sided native valve endocarditis. Demographic characteristics, clinical features, and outcomes were analyzed. Multivariable analysis evaluated enterococcus as a predictor of mortality. RESULTS: Of 1285 patients with left-sided native valve endocarditis, 107 had enterococcal endocarditis. Enterococcal endocarditis was most frequently seen in elderly men, frequently involved the aortic valve, tended to produce heart failure rather than embolic events, and had relatively low short-term mortality. Compared to patients with non-enterococcal endocarditis, patients with enterococcal endocarditis had similar rates of nosocomial acquisition, heart failure, embolization, surgery, and mortality. Compared to patients with streptococcal endocarditis, patients with enterococcal endocarditis were more likely to be nosocomially acquired (9 of 59 [15%] vs 2 of 400 [1%]; P <.0001) and have heart failure (49 of 107 [46%] vs 234 of 666 [35%]; P = 0.03). Compared to patients with S. aureus endocarditis, patients with enterococcal endocarditis were less likely to embolize (28 of 107 [26%] vs 155 of 314 [49%]; P <.0001) and less likely to die (12 of 107 [11%] vs 83 of 313 [27%]; P = 0.001). Multivariable analysis of all patients with left-sided native valve endocarditis showed that enterococcal endocarditis was associated with lower mortality (odds ratio [OR] 0.49; 95% confidence interval [CI] 0.24 to 0.97). CONCLUSIONS: Enterococcal native valve endocarditis has a distinctive clinical picture with a good prognosis.
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| 28. |
- Miro, J M, et al.
(author)
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Staphylococcus aureus native valve infective endocarditis: report of 566 episodes from the International Collaboration on Endocarditis Merged Database.
- 2005
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In: Clinical infectious diseases : an official publication of the Infectious Diseases Society of America. - : Oxford University Press (OUP). - 1537-6591. ; 41:4, s. 507-14
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Journal article (peer-reviewed)abstract
- BACKGROUND: Staphylococcus aureus native valve infective endocarditis (SA-NVIE) is not completely understood. The objective of this investigation was to describe the characteristics of a large, international cohort of patients with SA-NVIE. METHODS: The International Collaboration on Endocarditis Merged Database (ICE-MD) is a combination of 7 existing electronic databases from 5 countries that contains data on 2212 cases of definite infective endocarditis (IE). RESULTS: Of patients with native valve IE, 566 patients [corrected] had IE due to S. aureus, and 1074 patients had IE due to pathogens other than S. aureus (non-SA-NVIE). Patients with S. aureus IE were more likely to die (20% vs. 12%; P < .001), to experience an embolic event (61% [corrected] vs. 31%; P < .001), or to have a central nervous system event (21% [corrected] vs. 13%; P < .001) and were less likely to undergo surgery (26% vs. 39%; P < .001) than were patients with non-SA-NVIE. Multivariate analysis of prognostic factors of mortality identified age (odds ratio [OR], 1.4; 95% confidence interval [CI], 1.1-1.7), periannular abscess (OR, 2.4; 95% CI, 1.0 [corrected] -5.6), heart failure (OR, 3.9; 95% CI, 2.3-6.7), and absence of surgical therapy (OR, 2.3; 95% CI, 1.3-4.2) as variables that were independently associated with mortality in patients with SA-NVIE. After adjusting for patient-, pathogen-, and treatment-specific characteristics by multivariate analysis, geographical region was also found to be associated with mortality in patients with SA-NVIE (P < .001). CONCLUSIONS: S. aureus is an important and common cause of IE. The outcome of SA-NVIE is worse than that of non-SA-NVIE. Several clinical parameters are independently associated with mortality for patients with SA-NVIE. The clinical characteristics and outcome of SA-NVIE vary significantly by geographic region, although the reasons for such regional variations in outcomes of SA-NVIE are unknown and are probably multifactorial. A large, prospective, multinational cohort study of patients with IE is now under way to further investigate these observations.
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| 29. |
- Mooij, Wolf M., et al.
(author)
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Serving many at once : How a database approach can create unity in dynamical ecosystem modelling
- 2014
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In: Environmental Modelling & Software. - : Elsevier BV. - 1364-8152 .- 1873-6726. ; 61, s. 266-273
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Journal article (peer-reviewed)abstract
- Simulation modelling in ecology is a field that is becoming increasingly compartmentalized. Here we propose a Database Approach To Modelling (DATM) to create unity in dynamical ecosystem modelling with differential equations. In this approach the storage of ecological knowledge is independent of the language and platform in which the model will be run. To create an instance of the model, the information in the database is translated and augmented with the language and platform specifics. This process is automated so that a new instance can be created each time the database is updated. We describe the approach using the simple Lotka-Volterra model and the complex ecosystem model for shallow lakes PCLake, which we automatically implement in the frameworks OSIRIS, GRIND for MATLAB, ACSL, R, DUFLOW and DELWAQ. A clear advantage of working in a database is the overview it provides. The simplicity of the approach only adds to its elegance.
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| 30. |
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| 31. |
- 't Hoen, Peter A C, et al.
(author)
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Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories
- 2013
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In: Nature Biotechnology. - : Springer Science and Business Media LLC. - 1087-0156 .- 1546-1696. ; 31:11, s. 1015-1022
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Journal article (peer-reviewed)abstract
- RNA sequencing is an increasingly popular technology for genome-wide analysis of transcript sequence and abundance. However, understanding of the sources of technical and interlaboratory variation is still limited. To address this, the GEUVADIS consortium sequenced mRNAs and small RNAs of lymphoblastoid cell lines of 465 individuals in seven sequencing centers, with a large number of replicates. The variation between laboratories appeared to be considerably smaller than the already limited biological variation. Laboratory effects were mainly seen in differences in insert size and GC content and could be adequately corrected for. In small-RNA sequencing, the microRNA (miRNA) content differed widely between samples owing to competitive sequencing of rRNA fragments. This did not affect relative quantification of miRNAs. We conclude that distributing RNA sequencing among different laboratories is feasible, given proper standardization and randomization procedures. We provide a set of quality measures and guidelines for assessing technical biases in RNA-seq data.
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| 32. |
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| 33. |
- van Gerven, Luuk P. A., et al.
(author)
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Advantages of concurrent use of multiple software frameworks in water quality modelling using a database approach
- 2015
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In: Fundamental and Applied Limnology. - : Schweizerbart. - 1863-9135. ; 186:1-2, s. 5-20
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Journal article (peer-reviewed)abstract
- Water quality modelling deals with multidisciplinary questions ranging from fundamental to applied. Addressing this broad range of questions requires multiple analysis techniques and therefore multiple frameworks. Through the recently developed database approach to modelling (DATM), it has become possible to run a model in multiple software frameworks without much overhead. Here we apply DATM to the ecosystem model for ditches PCDitch and its twin model for shallow lakes PCLake. Using DATM, we run these models in six frameworks (ACSL, DELWAQ, DUFLOW, GRIND for MATLAB, OSIRIS and R), and report on the possible model analyses with tools provided by each framework. We conclude that the dynamic link between frameworks and models resulting from DATM has the following main advantages: it allows one to use the framework one is familiar with for most model analyses and eases switching between frameworks for complementary model analyses, including the switch between a 0-D and 1-D to 3-D setting. Moreover, the strength of each framework - including runtime performance - can now be easily exploited. We envision that a community-based further development of the concept can contribute to the future development of water quality modelling, not only by addressing multidisciplinary questions but also by facilitating the exchange of models and process formulations within the community of water quality modellers.
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| 34. |
- Vanherberghen, B, et al.
(author)
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Human and murine inhibitory natural killer cell receptors transfer from natural killer cells to target cells
- 2004
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In: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424. ; 101:48, s. 16873-16878
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Journal article (peer-reviewed)abstract
- Intercellular transfer of proteins across the immunological synapse is emerging as a common outcome of immune surveillance. We previously reported that target-cell MHC class I protein transfers onto natural killer (NK) cells expressing cognate killer Ig-like receptors (KIRs). We now show that, for both murine and human cells, target cells expressing inhibitory MHC class I ligands acquire cognate inhibitory NK receptors. Other cell-surface proteins, but not a cytoplasmic dye, also transferred from human NK cells to target cells across an inhibitory immunological synapse. The number of KIRs acquired from NK cells correlated with the level of expression of cognate MHC class I protein on target cells. Treatment with cytoskeletal inhibitors demonstrated that the target-cell cytoskeleton influences intercellular transfer of proteins in both directions. In contrast to constitutively expressed KIRs, a fraction of acquired KIRs could be removed by mild acid wash, demonstrating a difference between some of the acquired KIRs and constitutively expressed KIRs. An accumulation of phosphotyrosine at the location of the transferred KIRs implies a signaling capacity for NK cell proteins transferred to target cells. Thus, intercellular protein transfer between immune cells is bidirectional and could facilitate new aspects of immune cell communication.
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| 35. |
- Wang, Andrew, et al.
(author)
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The use and effect of surgical therapy for prosthetic valve infective endocarditis: a propensity analysis of a multicenter, international cohort.
- 2005
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In: American heart journal. - : Elsevier BV. - 1097-6744 .- 0002-8703. ; 150:5, s. 1086-91
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Journal article (peer-reviewed)abstract
- BACKGROUND: Although surgical intervention is often used in the treatment of prosthetic valve infective endocarditis (PVIE), an understanding of its effect on survival has been limited by the biases of observational studies and lack of controlled trials. METHODS: The International Collaboration on Endocarditis Merged Database is a large, multicenter, international registry of patients with definite endocarditis by Duke criteria, including 367 patients with PVIE. Clinical, microbiologic, and echocardiographic variables were analyzed to determine those factors associated with the use of surgery for PVIE. Logistic regression analysis was performed to create a propensity model of predictors of surgery use. Patients who underwent surgery during initial hospitalization were matched by propensity score with patients treated with medical therapy alone. Logistic regression analysis was performed to determine variables independently associated with inhospital mortality in this matched subset. RESULTS: Surgical therapy for PVIE was performed in 148 (42%) of 367 patients. Inhospital mortality was similar for patients treated with surgery compared with those treated with medical therapy alone (25.0% vs 23.4%, P = .729). Surgical therapy was independently associated with patient age, microorganism, intracardiac abscess, and congestive heart failure. After adjustment for these determinants, inhospital mortality was predicted by brain embolization (OR 11.12, 95% CI 4.16-29.73) and Staphylococcus aureus infection (OR 3.67, 95% CI 1.29-9.74), with a trend toward benefit for surgery (OR 0.56, 95% CI 0.23-1.36). CONCLUSIONS: Despite the frequent use of surgery for the treatment of PVIE, this condition continues to be associated with a high inhospital mortality rate in the contemporary era. After adjustment for factors related to surgical intervention, brain embolism and S aureus infection were independently associated with inhospital mortality and a trend toward a survival benefit of surgery was evident.
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