| 1. |
- Schoch, C. L., et al.
(author)
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A class-wide phylogenetic assessment of Dothideomycetes
- 2009
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In: Studies in mycology. - : Westerdijk Fungal Biodiversity Institute. - 0166-0616 .- 1872-9797. ; 64, s. 1-15
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Research review (peer-reviewed)abstract
- We present a comprehensive phylogeny derived from 5 genes, nucSSU, nucLSU rDNA, TEF1, RPB1 and RPB2, for 356 isolates and 41 families (six newly described in this volume) in Dothideomycetes. All currently accepted orders in the class are represented for the first time in addition to numerous previously unplaced lineages. Subclass Pleosporomycetidae is expanded to include the aquatic order Jahnulales. An ancestral reconstruction of basic nutritional modes supports numerous transitions from saprobic life histories to plant associated and lichenised modes and a transition from terrestrial to aquatic habitats are confirmed. Finally, a genomic comparison of 6 dothideomycete genomes with other fungi finds a high level of unique protein associated with the class, supporting its delineation as a separate taxon.
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| 2. |
- Schoch, CL, et al.
(author)
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Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi
- 2012
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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. - 1091-6490. ; 109:16, s. 6241-6246
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Journal article (peer-reviewed)abstract
- Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative protein-coding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.
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| 3. |
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| 4. |
- Nikogosian, I.K., et al.
(author)
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Multiple subduction imprints in the mantle below Italy detected in a single lava flow.
- 2016
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In: Earth and Planetary Science Letters. - : Elsevier BV. - 0012-821X .- 1385-013X. ; 449, s. 12-19
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Journal article (peer-reviewed)abstract
- Post-collisional magmatism reflects the regional subduction history prior to collision but the link between the two is complex and often poorly understood. The collision of continents along a convergent plate boundary commonly marks the onset of a variety of transitional geodynamic processes. Typical responses include delamination of subducting lithosphere, crustal thickening in the overriding plate, slab detachment and asthenospheric upwelling, or the complete termination of convergence. A prominent example is the Western–Central Mediterranean, where the ongoing slow convergence of Africa and Europe (Eurasia) has been accommodated by a variety of spreading and subduction systems that dispersed remnants of subducted lithosphere into the mantle, creating a compositionally wide spectrum of magmatism. Using lead isotope compositions of a set of melt inclusions in magmatic olivine crystals we detect exceptional heterogeneity in the mantle domain below Central Italy, which we attribute to the presence of continental material, introduced initially by Alpine and subsequently by Apennine subduction. We show that superimposed subduction imprints of a mantle source can be tapped during a melting episode millions of years later, and are recorded in a single lava flow.
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| 5. |
- Vergouwen, Daphne P. C., et al.
(author)
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The enigma of sclera-specific autoimmunity in scleritis
- 2024
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In: Journal of Autoimmunity. - : Elsevier. - 0896-8411 .- 1095-9157. ; 144
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Journal article (peer-reviewed)abstract
- Scleritis is a severe and painful ophthalmic disorder, in which a pathogenic role for collagen-directed autoimmunity was repeatedly suggested. We evaluated the presence of sclera-specific antibodies in a large cohort of patients with non-infectious scleritis. Therefore, we prospectively collected serum samples from 121 patients with non-infectious scleritis in a multicenter cohort study in the Netherlands. In addition, healthy (n = 39) and uveitis controls (n = 48) were included. Serum samples were tested for anti-native human type II collagen antibodies using a validated enzyme-linked immunosorbent assay (ELISA). Further, sclera-specific antibodies were determined using indirect immunofluorescence (IIF) on primate retinal/scleral cryosections. Lastly, human leukocyte antigen (HLA) typing was performed in 111 patients with scleritis. Anti-type II collagen antibodies were found in 13% of scleritis patients, in 10% of healthy controls and in 11% of uveitis controls (p = 0.91). A specific reaction to scleral nerve tissue on IIF was observed in 33% of patients with scleritis, which was higher than in healthy controls (11%; p = 0.01), but similar to uveitis controls (25%; p = 0.36). Reactivity to the scleral nerve tissue was significantly associated with earlier onset of scleritis (48 versus 56 years; p < 0.001), bilateral involvement (65% versus 42%; p = 0.01), and less frequent development of scleral necrosis (5% versus 22%; p = 0.02). HLA-B27 was found to be twice as prevalent in patients with scleritis (15.3%) compared to a healthy population (7.2%). In conclusion, scleral nerve autoantibody reactivity was more common in scleritis and uveitis patients in contrast to healthy controls. Further research is needed to characterize these scleral-nerve directed antibodies and assess their clinical value.
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| 6. |
- De Cock, Roosmarijn F W, et al.
(author)
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A Neonatal Amikacin Covariate Model Can Be Used to Predict Ontogeny of Other Drugs Eliminated Through Glomerular Filtration in Neonates
- 2014
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In: Pharmaceutical research. - : Springer Science and Business Media LLC. - 0724-8741 .- 1573-904X. ; 31:3, s. 754-767
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Journal article (peer-reviewed)abstract
- PURPOSERecently, a covariate model characterizing developmental changes in clearance of amikacin in neonates has been developed using birth bodyweight and postnatal age. The aim of this study was to evaluate whether this covariate model can be used to predict maturation in clearance of other renally excreted drugs.METHODSFive different neonatal datasets were available on netilmicin, vancomycin, tobramycin and gentamicin. The extensively validated covariate model for amikacin clearance was used to predict clearance of these drugs. In addition, independent reference models were developed based on a systematic covariate analysis.RESULTSThe descriptive and predictive properties of the models developed using the amikacin covariate model were good, and fairly similar to the independent reference models (goodness-of-fit plots, NPDE). Moreover, similar clearance values were obtained for both approaches. Finally, the same covariates as in the covariate model of amikacin, i.e. birth bodyweight and postnatal age, were identified on clearance in the independent reference models.CONCLUSIONSThis study shows that pediatric covariate models may contain physiological information since information derived from one drug can be used to describe other drugs. This semi-physiological approach may be used to optimize sparse data analysis and to derive individualized dosing algorithms for drugs in children.
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| 7. |
- Getahun, H, et al.
(author)
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Management of latent Mycobacterium tuberculosis infection: WHO guidelines for low tuberculosis burden countries
- 2015
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In: The European respiratory journal. - : European Respiratory Society (ERS). - 1399-3003 .- 0903-1936. ; 46:6, s. 1563-1576
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Journal article (peer-reviewed)abstract
- Latent tuberculosis infection (LTBI) is characterised by the presence of immune responses to previously acquired Mycobacterium tuberculosis infection without clinical evidence of active tuberculosis (TB). Here we report evidence-based guidelines from the World Health Organization for a public health approach to the management of LTBI in high risk individuals in countries with high or middle upper income and TB incidence of <100 per 100 000 per year. The guidelines strongly recommend systematic testing and treatment of LTBI in people living with HIV, adult and child contacts of pulmonary TB cases, patients initiating anti-tumour necrosis factor treatment, patients receiving dialysis, patients preparing for organ or haematological transplantation, and patients with silicosis. In prisoners, healthcare workers, immigrants from high TB burden countries, homeless persons and illicit drug users, systematic testing and treatment of LTBI is conditionally recommended, according to TB epidemiology and resource availability. Either commercial interferon-gamma release assays or Mantoux tuberculin skin testing could be used to test for LTBI. Chest radiography should be performed before LTBI treatment to rule out active TB disease. Recommended treatment regimens for LTBI include: 6 or 9 month isoniazid; 12 week rifapentine plus isoniazid; 3–4 month isoniazid plus rifampicin; or 3–4 month rifampicin alone.
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| 8. |
- Heuberger, Peter S. C., et al.
(author)
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Orthonormal basis functions in time and frequency domain : Hambo transform theory
- 2004
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In: SIAM Journal of Control and Optimization. - 0363-0129 .- 1095-7138. ; 42:4, s. 1347-1373
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Journal article (peer-reviewed)abstract
- The class of finite impulse response (FIR), Laguerre, and Kautz functions can be generalized to a family of rational orthonormal basis functions for the Hardy space H2 of stable linear dynamical systems. These basis functions are useful for constructing efficient parameterizations and coding of linear systems and signals, as required in, e.g., system identification, system approximation, and adaptive filtering. In this paper, the basis functions are derived from a transfer function perspective as well as in a state space setting. It is shown how this approach leads to alternative series expansions of systems and signals in time and frequency domain. The generalized basis functions induce signal and system transforms (Hambo transforms), which have proved to be useful analysis tools in various modelling problems. These transforms are analyzed in detail in this paper, and a large number of their properties are derived. Principally, it is shown how minimal state space realizations of the system transform can be obtained from minimal state space realizations of the original system and vice versa.
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| 9. |
- Jochum, K. P., et al.
(author)
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MPI-DING reference glasses for in situ microanalysis: New reference values for element concentrations and isotope ratios
- 2006
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In: Geochemistry Geophysics Geosystems. - 1525-2027. ; 7:15 Febr
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Journal article (peer-reviewed)abstract
- [1] We present new analytical data of major and trace elements for the geological MPI-DING glasses KL2-G, ML3B-G, StHs6/80-G, GOR128-G, GOR132-G, BM90/21-G, T1-G, and ATHO-G. Different analytical methods were used to obtain a large spectrum of major and trace element data, in particular, EPMA, SIMS, LA-ICPMS, and isotope dilution by TIMS and ICPMS. Altogether, more than 60 qualified geochemical laboratories worldwide contributed to the analyses, allowing us to present new reference and information values and their uncertainties ( at 95% confidence level) for up to 74 elements. We complied with the recommendations for the certification of geological reference materials by the International Association of Geoanalysts (IAG). The reference values were derived from the results of 16 independent techniques, including definitive ( isotope dilution) and comparative bulk ( e. g., INAA, ICPMS, SSMS) and microanalytical ( e. g., LA-ICPMS, SIMS, EPMA) methods. Agreement between two or more independent methods and the use of definitive methods provided traceability to the fullest extent possible. We also present new and recently published data for the isotopic compositions of H, B, Li, O, Ca, Sr, Nd, Hf, and Pb. The results were mainly obtained by high-precision bulk techniques, such as TIMS and MC-ICPMS. In addition, LA-ICPMS and SIMS isotope data of B, Li, and Pb are presented.
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| 10. |
- Mason, P.R.D., et al.
(author)
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In situ determination of sulfur isotopes in sulfur-rich materials by laser ablation multiple-collector inductively coupled plasma mass spectrometry (LA-MC-ICP-MS)
- 2006
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In: JOURNAL OF ANALYTICAL ATOMIC SPECTROMETRY. - : Royal Society of Chemistry (RSC). - 0267-9477. ; 21:2, s. 177-186
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Journal article (peer-reviewed)abstract
- A new method has been developed for the accurate and precise measurement of sulfur isotopes (S-32, S-33, S-34) in solids on a scale down to 80-100 pin by laser ablation multiple collector inductively coupled plasma mass spectrometry (LA-MC-ICP-MS). The method was developed independently on two different sets of instrumentation, both of which give equivalent results with comparable accuracy and precision. The first instrumental set-up utilizes Xe gas in a hexapole collision and reaction cell for interference attenuation coupled with a mass discrimination correction by external normalization using a nebulised vapour of Cl-37/Cl-35 standard solution. The second employs high mass resolution by sector field mass spectrometry to avoid the interfering O2+ isobars with a Si-30/Si-29 standard aerosol for external normalization. The external isotope mass discrimination correction was applied using the exponential law and was further calibrated for both sets of instrumentation by linear interpolation in a sample-standard bracketing method. Mean delta(34)S(V-CDT) and delta(33)S(V-CDT) show excellent agreement (within analytical error, typically 0.6 and 1.5%, respectively) with compiled data for IAEA-S series AgS standard reference materials. Results for NIST SRM 127 (sulfate) were less accurate when calibrated against the IAEA-S series sulfides, whilst significant and consistent deviations in accuracy of up to 3%. were observed in both sets of instrumentation for Soufre de Lacq SRM sulfur. Such generic matrix effects may be widespread in LA-ICP-MS due to differential ablation rates, particle formation, particle transport efficiency and ionization efficiency in an argon plasma.
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