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- Sachdev, P. S., et al.
(författare)
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STROKOG (stroke and cognition consortium): An international consortium to examine the epidemiology, diagnosis, and treatment of neurocognitive disorders in relation to cerebrovascular disease
- 2017
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Ingår i: Alzheimer's & Dementia. - : Wiley. - 1552-5260 .- 1552-5279. ; 7, s. 11-23
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Tidskriftsartikel (refereegranskat)abstract
- Introduction The Stroke and Cognition consortium (STROKOG) aims to facilitate a better understanding of the determinants of vascular contributions to cognitive disorders and help improve the diagnosis and treatment of vascular cognitive disorders (VCD). Methods Longitudinal studies with ≥75 participants who had suffered or were at risk of stroke or TIA and which evaluated cognitive function were invited to join STROKOG. The consortium will facilitate projects investigating rates and patterns of cognitive decline, risk factors for VCD, and biomarkers of vascular dementia. Results Currently, STROKOG includes 25 (21 published) studies, with 12,092 participants from five continents. The duration of follow-up ranges from 3months to 21years. Discussion Although data harmonization will be a key challenge, STROKOG is in a unique position to reuse and combine international cohort data and fully explore patient level characteristics and outcomes. STROKOG could potentially transform our understanding of VCD and have a worldwide impact on promoting better vascular cognitive outcomes. © 2016 The Authors
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| 8. |
- Duffy, J. M. N., et al.
(författare)
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Top 10 priorities for future infertility research: an international consensus development study
- 2020
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Ingår i: Human Reproduction. - : Oxford University Press (OUP). - 0268-1161 .- 1460-2350. ; 35:12, s. 2715-2724
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Tidskriftsartikel (refereegranskat)abstract
- STUDY QUESTION: Can the priorities for future research in infertility be identified? SUMMARY ANSWER: The top 10 research priorities for the four areas of male infertility, female and unexplained infertility, medically assisted reproduction and ethics, access and organization of care for people with fertility problems were identified. WHAT IS KNOWN ALREADY: Many fundamental questions regarding the prevention, management and consequences of infertility remain unanswered. This is a barrier to improving the care received by those people with fertility problems. STUDY DESIGN, SIZE, DURATION: Potential research questions were collated from an initial international survey, a systematic review of clinical practice guidelines and Cochrane systematic reviews. A rationalized list of confirmed research uncertainties was prioritized in an interim international survey. Prioritized research uncertainties were discussed during a consensus development meeting. Using a formal consensus development method, the modified nominal group technique, diverse stakeholders identified the top 10 research priorities for each of the categories male infertility, female and unexplained infertility, medically assisted reproduction and ethics, access and organization of care. PARTICIPANTS/MATERIALS, SETTING, METHODS: Healthcare professionals, people with fertility problems and others (healthcare funders, healthcare providers, healthcare regulators, research funding bodies and researchers) were brought together in an open and transparent process using formal consensus methods advocated by the James Lind Alliance. MAIN RESULTS AND THE ROLE OF CHANCE: The initial survey was completed by 388 participants from 40 countries, and 423 potential research questions were submitted. Fourteen clinical practice guidelines and 162 Cochrane systematic reviews identified a further 236 potential research questions. A rationalized list of 231 confirmed research uncertainties was entered into an interim prioritization survey completed by 317 respondents from 43 countries. The top 10 research priorities for each of the four categories male infertility, female and unexplained infertility (including age-related infertility, ovarian cysts, uterine cavity abnormalities and tubal factor infertility), medically assisted reproduction (including ovarian stimulation, IUI and IVF) and ethics, access and organization of care were identified during a consensus development meeting involving 41 participants from I I countries. These research priorities were diverse and seek answers to questions regarding prevention, treatment and the longer-term impact of infertility. They highlight the importance of pursuing research which has often been overlooked, including addressing the emotional and psychological impact of infertility, improving access to fertility treatment, particularly in lower resource settings and securing appropriate regulation. Addressing these priorities will require diverse research methodologies, including laboratory-based science, qualitative and quantitative research and population science. LIMITATIONS, REASONS FOR CAUTION: We used consensus development methods, which have inherent limitations, including the representativeness of the participant sample, methodological decisions informed by professional judgment and arbitrary consensus definitions. WIDER IMPLICATIONS OF THE FINDINGS: We anticipate that identified research priorities, developed to specifically highlight the most pressing clinical needs as perceived by healthcare professionals, people with fertility problems and others, will help research funding organizations and researchers to develop their future research agenda.
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- Duffy, J. M. N., et al.
(författare)
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Standardizing definitions and reporting guidelines for the infertility core outcome set: an international consensus development study
- 2020
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Ingår i: Human Reproduction. - : Oxford University Press (OUP). - 0268-1161 .- 1460-2350. ; 35:12, s. 2735-2745
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Tidskriftsartikel (refereegranskat)abstract
- STUDY QUESTION: Can consensus definitions for the core outcome set for infertility be identified in order to recommend a standardized approach to reporting? SUMMARY ANSWER: Consensus definitions for individual core outcomes, contextual statements and a standardized reporting table have been developed. WHAT IS KNOWN ALREADY: Different definitions exist for individual core outcomes for infertility. This variation increases the opportunities for researchers to engage with selective outcome reporting, which undermines secondary research and compromises clinical practice guideline development. STUDY DESIGN, SIZE, DURATION: Potential definitions were identified by a systematic review of definition development initiatives and clinical practice guidelines and by reviewing Cochrane Gynaecology and Fertility Group guidelines. These definitions were discussed in a face-to-face consensus development meeting, which agreed consensus definitions. A standardized approach to reporting was also developed as part of the process. PARTICIPANTS/MATERIALS, SETTING, METHODS: Healthcare professionals, researchers and people with fertility problems were brought together in an open and transparent process using formal consensus development methods. MAIN RESULTS AND THE ROLE OF CHANCE: Forty-four potential definitions were inventoried across four definition development initiatives, including the Harbin Consensus Conference Workshop Group and International Committee for Monitoring Assisted Reproductive Technologies, 12 clinical practice guidelines and Cochrane Gynaecology and Fertility Group guidelines. Twenty-seven participants, from 11 countries, contributed to the consensus development meeting. Consensus definitions were successfully developed for all core outcomes. Specific recommendations were made to improve reporting. LIMITATIONS, REASONS FOR CAUTION: We used consensus development methods, which have inherent limitations. There was limited representation from low- and middle-income countries. WIDER IMPLICATIONS OF THE FINDINGS: A minimum data set should assist researchers in populating protocols, case report forms and other data collection tools. The generic reporting table should provide clear guidance to researchers and improve the reporting of their results within journal publications and conference presentations. Research funding bodies, the Standard Protocol Items: Recommendations for Interventional Trials statement, and over 80 specialty journals have committed to implementing this core outcome set.
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| 12. |
- Green, Richard E., et al.
(författare)
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Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs
- 2014
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 346:6215, s. 1335-
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Tidskriftsartikel (refereegranskat)abstract
- To provide context for the diversification of archosaurs-the group that includes crocodilians, dinosaurs, and birds-we generated draft genomes of three crocodilians: Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater crocodile), and Gavialis gangeticus (the Indian gharial). We observed an exceptionally slow rate of genome evolution within crocodilians at all levels, including nucleotide substitutions, indels, transposable element content and movement, gene family evolution, and chromosomal synteny. When placed within the context of related taxa including birds and turtles, this suggests that the common ancestor of all of these taxa also exhibited slow genome evolution and that the comparatively rapid evolution is derived in birds. The data also provided the opportunity to analyze heterozygosity in crocodilians, which indicates a likely reduction in population size for all three taxa through the Pleistocene. Finally, these data combined with newly published bird genomes allowed us to reconstruct the partial genome of the common ancestor of archosaurs, thereby providing a tool to investigate the genetic starting material of crocodilians, birds, and dinosaurs.
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| 13. |
- Kuderna, Lukas F. K., et al.
(författare)
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Identification of constrained sequence elements across 239 primate genomes
- 2024
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Ingår i: Nature. - : Springer Nature. - 0028-0836 .- 1476-4687. ; 625:7996, s. 735-742
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Tidskriftsartikel (refereegranskat)abstract
- Noncoding DNA is central to our understanding of human gene regulation and complex diseases1,2, and measuring the evolutionary sequence constraint can establish the functional relevance of putative regulatory elements in the human genome3,4,5,6,7,8,9. Identifying the genomic elements that have become constrained specifically in primates has been hampered by the faster evolution of noncoding DNA compared to protein-coding DNA10, the relatively short timescales separating primate species11, and the previously limited availability of whole-genome sequences12. Here we construct a whole-genome alignment of 239 species, representing nearly half of all extant species in the primate order. Using this resource, we identified human regulatory elements that are under selective constraint across primates and other mammals at a 5% false discovery rate. We detected 111,318 DNase I hypersensitivity sites and 267,410 transcription factor binding sites that are constrained specifically in primates but not across other placental mammals and validate their cis-regulatory effects on gene expression. These regulatory elements are enriched for human genetic variants that affect gene expression and complex traits and diseases. Our results highlight the important role of recent evolution in regulatory sequence elements differentiating primates, including humans, from other placental mammals.
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| 14. |
- Hickey, C. A., et al.
(författare)
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Colitogenic Bacteroides thetaiotaomicron Antigens Access Host Immune Cells in a Sulfatase-Dependent Manner via Outer Membrane Vesicles
- 2015
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Ingår i: Cell Host & Microbe. - : Elsevier BV. - 1931-3128. ; 17:5, s. 672-680
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Tidskriftsartikel (refereegranskat)abstract
- Microbes interact with the host immune system via several potential mechanisms. One essential step for each mechanismis themethod by which intestinal microbes or their antigens access specific host immune cells. Using genetically susceptible mice (dnKO) that develop spontaneous, fulminant colitis, triggered by Bacteroides thetaiotaomicron (B. theta), we investigated the mechanism of intestinal microbial access under conditions that stimulate colonic inflammation. B. theta antigens localized to host immune cells through outer membrane vesicles (OMVs) that harbor bacterial sulfatase activity. We deleted the anaerobic sulfatase maturating enzyme (anSME) from B. theta, which is required for post-translational activation of all B. theta sulfatase enzymes. This bacterial mutant strain did not stimulate colitis in dnKO mice. Lastly, access of B. theta OMVs to host immune cells was sulfatase dependent. These data demonstrate that bacterial OMVs and associated enzymes promote inflammatoryimmune stimulation in genetically susceptible hosts.
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- Corcoran, Padraic, et al.
(författare)
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Quantifying functional heterothallism in the pseudohomothallic ascomycete Neurospora tetrasperma
- 2012
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Ingår i: Fungal Biology. - : Elsevier BV. - 1878-6146 .- 1878-6162. ; 116:9, s. 962-975
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Tidskriftsartikel (refereegranskat)abstract
- Neurospora tetrasperma is a pseudohomothallic filamentous ascomycete that has evolved from heterothallic ancestors. Throughout its life cycle, it is predominantly heterokaryotic for mating type, and thereby self-fertile. However, studies of N. tetrasperma have revealed the occasional production of self-sterile asexual and sexual spores of a single-mating type, indicating that it can be functionally heterothallic. Here, we report the extensive sampling and isolation of natural, heterokaryotic, strains of N. tetrasperma from the United Kingdom (UK): 99 strains were collected from Surrey, England, and four from Edinburgh, Scotland. We verified by phylogenetic analyses that these strains belong to N. tetrasperma. We isolated cultures from single germinated asexual spores (conidia) from 17 of these newly sampled UK strains from Surrey, and 16 previously sampled strains of N. tetrasperma from New Zealand (NZ). Our results show that the N. tetrasperrna strains from the UK population produced a significantly greater proportion of self-sterile, homokaryotic conidia than the NZ population: the proportion of homokaryotic conidia was 42.6 % (133/312 spores) and 15.3 % (59/386) from the UK and the NZ populations, respectively. Although homokaryons recovered from several strains show a bias for one of the mating types, the total ratio of mat A to mat a mating type in homokaryons (UK: 72/61, NZ 28/31) did not deviate significantly from the expected 1:1 ratio for either of these populations. These results indicate that different populations exhibit differences in their life cycle characteristics, and that a higher degree of outcrossing might be expected from the UK population. This study points to the importance of studying multiple strains and populations when investigating life history traits of an organism with a complex life cycle, as previously undetected differences between populations may be revealed.
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| 18. |
- Hickey, C. D., et al.
(författare)
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Influence of buttermilk powder or buttermilk addition on phospholipid content, chemical and bio-chemical composition and bacterial viability in Cheddar style-cheese
- 2017
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Ingår i: Food Research International. - : Elsevier BV. - 0963-9969 .- 1873-7145. ; 102, s. 748-758
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Tidskriftsartikel (refereegranskat)abstract
- The effect of buttermilk powder addition post-curd formation or buttermilk addition to cheese milk on total and individual phospholipid content, chemical composition, enzyme activity, microbial populations and microstructure within Cheddar-style cheese was investigated. Buttermilk or buttermilk powder addition resulted in significant increases in total phospholipid content and their distribution throughout the cheese matrix. Addition of 10% buttermilk powder resulted in higher phospholipid content, moisture, pH and salt in moisture levels, and lower fat, fat in dry matter, L. helveticus and non-starter bacteria levels in cheeses. Buttermilk powder inclusion resulted in lower pH 4.6/Soluble Nitrogen (SN) levels and significantly lower free amino acid levels in 10% buttermilk powder cheeses. Buttermilk addition provided a more porous cheese microstructure with greater fat globule coalescence and increased free fat pools, while also increasing moisture and decreasing protein, fat and pH levels. Addition of buttermilk in liquid or powdered form offers potential for new cheeses with associated health benefits. © 2017 Elsevier Ltd
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| 19. |
- Hickey, J. W., et al.
(författare)
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Spatial mapping of protein composition and tissue organization : a primer for multiplexed antibody-based imaging
- 2022
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Ingår i: Nature Methods. - : Nature Research. - 1548-7091 .- 1548-7105. ; 19:3, s. 284-295
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Tidskriftsartikel (refereegranskat)abstract
- Tissues and organs are composed of distinct cell types that must operate in concert to perform physiological functions. Efforts to create high-dimensional biomarker catalogs of these cells have been largely based on single-cell sequencing approaches, which lack the spatial context required to understand critical cellular communication and correlated structural organization. To probe in situ biology with sufficient depth, several multiplexed protein imaging methods have been recently developed. Though these technologies differ in strategy and mode of immunolabeling and detection tags, they commonly utilize antibodies directed against protein biomarkers to provide detailed spatial and functional maps of complex tissues. As these promising antibody-based multiplexing approaches become more widely adopted, new frameworks and considerations are critical for training future users, generating molecular tools, validating antibody panels, and harmonizing datasets. In this Perspective, we provide essential resources, key considerations for obtaining robust and reproducible imaging data, and specialized knowledge from domain experts and technology developers.
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| 20. |
- Muir, Duncan D., et al.
(författare)
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Experimental constraints on dacite pre-eruptive magma storage conditions beneath Uturuncu Volcano
- 2014
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Ingår i: Journal of Petrology. - : Oxford University Press (OUP). - 0022-3530 .- 1460-2415. ; 55:4, s. 749-767
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Tidskriftsartikel (refereegranskat)abstract
- Cerro Uturuncu is a long-dormant, compositionally monotonous, effusive dacitic volcano in the Altiplano–Puna Volcanic Complex (APVC) of SW Bolivia. The volcano recently gained attention following the discovery of an ∼70 km diameter Interferometric Synthetic Aperture Radar (InSAR) anomaly roughly centred on its edifice. Uturuncu dacites, erupted over the past ∼1 Myr, invariably have a phase assemblage of plagioclase–orthopyroxene–biotite–ilmenite–magnetite–apatite–zircon and rhyolite glass. To better constrain storage conditions of the dacite magmas and to help understand their relationship with the observed deformation, petrological experiments were performed in cold-seal hydrothermal vessels. Volatile-saturated (PH2O = PTOTAL and PH2O + PCO2 = PTOTAL) phase equilibria experiments were run between 50 and 250 MPa and 760 and 900°C at fO2 ∼ Ni–NiO. Two synthetic starting compositions were investigated based on a typical Uturuncu dacite whole-rock and its rhyolitic groundmass glass. Pre-eruptive magma storage conditions have been estimated by comparing results from the experiments with natural phase assemblages, modes, and mineral and glass compositions. H2O-saturated experiments constrain storage pressures to 100 ± 50 MPa, equivalent to 1·9–5·7 km below surface. In the dacite, natural phase assemblages are reproduced at 870°C, 100 MPa with both orthopyroxene and biotite stabilized concurrently. Natural glass chemistries are most closely replicated at 50 MPa at 870°C, reflecting the role of decompression crystallization prior to eruption. In H2O-saturated rhyolite experiments the natural phase assemblage is most closely replicated at 870°C, 50 MPa. Isothermal, mixed volatile dacite experiments at 870°C further constrain storage pressures to 110 ± 10 MPa. Assuming that there has been no dramatic change in the eruptive behaviour of Uturuncu in the last 270 kyr, pre-eruptive storage of dacite magmas at ∼100 MPa precludes their role in producing the large diameter deformation anomaly. If deformation is a result of magmatic intrusion, then intrusion of less evolved magmas into deeper, mid-crustal storage regions is a more probable explanation. Intrusion within the Altiplano–Puna Magma Body (APMB), the extent of which is roughly coincident with the APVC, is most likely. It is proposed that dacite magmas form from andesitic parents, via fractionation and/or assimilation, within the APMB. Dacites then rise buoyantly to shallow storage levels where they stall and crystallize prior to eruption. Microlites form during subsequent ascent from the storage region to the surface.
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| 21. |
- Ring, Lena, et al.
(författare)
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Individual quality of life : can it be accounted for by psychological or subjective well-being?
- 2007
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Ingår i: Social Indicators Research. - : Springer Science and Business Media LLC. - 0303-8300 .- 1573-0921. ; 82:3, s. 443-461
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Tidskriftsartikel (refereegranskat)abstract
- There is ongoing discussion in the scientific literature about the need for a more theoretical foundation to underpin quality of life (QoL) measurement. This paper applied Keyes et al.'s [J. Pers. Soc. Psychol. 82 (2002) 1007] model of well-being as a framework to assess whether respondents (n = 136 students) focus on elements of subjective well-being (SWB), such as satisfaction and happiness, or on elements of psychological well-being (PWB), such as meaning and personal growth, when making individual QoL (IQoL) judgments using the Schedue of the Evaluation of Individual Quality of Life (SEIQoL). The Keyes et al.'s model was confirmed and explained 41% of the variance in SEIQoL scores. Both SWB and PWB were correlated with the SEIQoL Index Score and SWB was found to be an important mediating variable in the relationship between PWB and SEIQoL. When analyzing different well-being combinations, respondents with high SWB/high PWB had significantly higher SEIQoL scores than did those with low SWB/low PWB. Respondents with high PWB/high SWB had higher SEIQoL scores than did those with high PWB/low SWB. Longitudinal studies in different patient groups are needed to explore the dynamic relationship between IQoL and well-being. Further investigation of the relationship between PWB and SWB with other instruments purporting to measure QoL would contribute to an enhanced understanding of the underlying nature of QoL.
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| 22. |
- Wagenaar-Bos, Ineke G. A., et al.
(författare)
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Functional C1-inhibitor diagnostics in hereditary angioedema: Assay evaluation and recommendations
- 2008
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Ingår i: Journal of Immunological Methods. - : Elsevier BV. - 1872-7905 .- 0022-1759. ; 338:1-2, s. 14-20
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Tidskriftsartikel (refereegranskat)abstract
- Hereditary angioedema (HAE) is an autosomal dominant disease characterized by recurrent episodes of potentially life-threatening angioedema. The most widespread underlying genetic deficiency is a heterozygous deficiency of the serine protease inhibitor Cl esterase inhibitor (C1-Inh). In addition to low C4 levels, the most important laboratory parameter for correct diagnosis of HAE or angioedema due to acquired C1-Inh deficiency is reduced C1-Inh function (fC1-Inh). No direct recommendations about the assays for fC1-Inh or sample handling conditions are available, although this would prove especially useful when a laboratory first starts to offer assays on fC1-Inh for HAE diagnosis. In the present study we evaluated the performance of fC1-Inh assays in the 15 different laboratories that are specialised in HAE diagnostics and assessed inter-laboratory variation with each laboratory using their own assays and standards. A double-blind survey was conducted using plasma/serum samples from healthy donors and HAE patients and the uniformity of HAE diagnosis was evaluated. It can be concluded that the diagnosis of fC1-Inh deficiency was made correctly inmost cases in this survey. We can recommend the chromogenic assay for the determination of fC1-Inh, while the complex ELISA needs further investigation. (C) 2008 Elsevier B.V. All rights reserved.
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