| 1. |
- Fenstermacher, M.E., et al.
(author)
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DIII-D research advancing the physics basis for optimizing the tokamak approach to fusion energy
- 2022
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In: Nuclear Fusion. - : IOP Publishing. - 0029-5515 .- 1741-4326. ; 62:4
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Journal article (peer-reviewed)abstract
- DIII-D physics research addresses critical challenges for the operation of ITER and the next generation of fusion energy devices. This is done through a focus on innovations to provide solutions for high performance long pulse operation, coupled with fundamental plasma physics understanding and model validation, to drive scenario development by integrating high performance core and boundary plasmas. Substantial increases in off-axis current drive efficiency from an innovative top launch system for EC power, and in pressure broadening for Alfven eigenmode control from a co-/counter-I p steerable off-axis neutral beam, all improve the prospects for optimization of future long pulse/steady state high performance tokamak operation. Fundamental studies into the modes that drive the evolution of the pedestal pressure profile and electron vs ion heat flux validate predictive models of pedestal recovery after ELMs. Understanding the physics mechanisms of ELM control and density pumpout by 3D magnetic perturbation fields leads to confident predictions for ITER and future devices. Validated modeling of high-Z shattered pellet injection for disruption mitigation, runaway electron dissipation, and techniques for disruption prediction and avoidance including machine learning, give confidence in handling disruptivity for future devices. For the non-nuclear phase of ITER, two actuators are identified to lower the L-H threshold power in hydrogen plasmas. With this physics understanding and suite of capabilities, a high poloidal beta optimized-core scenario with an internal transport barrier that projects nearly to Q = 10 in ITER at ∼8 MA was coupled to a detached divertor, and a near super H-mode optimized-pedestal scenario with co-I p beam injection was coupled to a radiative divertor. The hybrid core scenario was achieved directly, without the need for anomalous current diffusion, using off-axis current drive actuators. Also, a controller to assess proximity to stability limits and regulate β N in the ITER baseline scenario, based on plasma response to probing 3D fields, was demonstrated. Finally, innovative tokamak operation using a negative triangularity shape showed many attractive features for future pilot plant operation.
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| 2. |
- Gray, E., et al.
(author)
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A multi-center study of neurofilament assay reliability and inter-laboratory variability
- 2020
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In: Amyotrophic Lateral Sclerosis and Frontotemporal Degeneration. - : Informa UK Limited. - 2167-8421 .- 2167-9223. ; 21:5-6, s. 452-458
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Journal article (peer-reviewed)abstract
- Objectives: Significantly elevated levels of neurofilament light chain (NfL) and phosphorylated neurofilament heavy chain (pNfH) have been described in the blood and cerebrospinal fluid (CSF) of amyotrophic lateral sclerosis (ALS) patients. The aim of this study was to evaluate the analytical performance of different neurofilament assays in a round robin with 10 centers across Europe/U.S.Methods: Serum, plasma and CSF samples from a group of five ALS and five neurological control patients were distributed across 10 international specialist neurochemical laboratories for analysis by a range of commercial and in-house neurofilament assays. The performance of all assays was evaluated for their ability to differentiate between the groups. The inter-assay coefficient of variation was calculated where appropriate from sample measurements performed across multiple laboratories using the same assay.Results:All assays could differentiate ALS patients from controls in CSF. Inter-assay coefficient of variation of analytical platforms performed across multiple laboratories varied between 6.5% and 41.9%.Conclusions:This study is encouraging for the growing momentum toward integration of neurofilament measurement into the specialized ALS clinic. It demonstrates the importance of 'round robin' studies necessary to ensure the analytical quality required for translation to the routine clinical setting. A standardized neurofilament probe is needed which can be used as international benchmark for analytical performance in ALS.
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| 3. |
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| 4. |
- Miller, A. M., et al.
(author)
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Multicenter immunoassay validation of cerebrospinal fluid neurofilament light: a biomarker for neurodegeneration
- 2016
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In: Bioanalysis. - : Future Science Ltd. - 1757-6180 .- 1757-6199. ; 8:21, s. 2243-2254
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Journal article (peer-reviewed)abstract
- Aim: Neurofilament light (NfL) chain, a putative cerebrospinal fluid biomarker, can support neurodegenerative disease diagnosis and indicate disease severity and prognosis. Universal validation protocols when used to measure biomarkers can reduce pre and analytical laboratory variation, thus increasing end-user confidence in the consistency of validation data across sites. Methodology: Here, a commercially available NfL ELISA (UmanDiagnostics, Ume dagger, Sweden) was validated in a multicentered setting using comprehensive newly developed standard operating procedures. Results: The data showed good assay sensitivity and intra and interassay precision. Interlaboratory precision was, however, suboptimal. Conclusion: The UmanDiagnostics assay is suitable for the quantification of NfL in human cerebrospinal fluid. However, sources of interlaboratory variation in the data require further investigation.
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| 5. |
- Altmae, S, et al.
(author)
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Meta-signature of human endometrial receptivity: a meta-analysis and validation study of transcriptomic biomarkers
- 2017
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In: Scientific reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 7:1, s. 10077-
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Journal article (peer-reviewed)abstract
- Previous transcriptome studies of the human endometrium have revealed hundreds of simultaneously up- and down-regulated genes that are involved in endometrial receptivity. However, the overlap between the studies is relatively small, and we are still searching for potential diagnostic biomarkers. Here we perform a meta-analysis of endometrial-receptivity associated genes on 164 endometrial samples (76 from ‘pre-receptive’ and 88 from mid-secretory, ‘receptive’ phase endometria) using a robust rank aggregation (RRA) method, followed by enrichment analysis, and regulatory microRNA prediction. We identify a meta-signature of endometrial receptivity involving 57 mRNA genes as putative receptivity markers, where 39 of these we confirm experimentally using RNA-sequencing method in two separate datasets. The meta-signature genes highlight the importance of immune responses, the complement cascade pathway and the involvement of exosomes in mid-secretory endometrial functions. Bioinformatic prediction identifies 348 microRNAs that could regulate 30 endometrial-receptivity associated genes, and we confirm experimentally the decreased expression of 19 microRNAs with 11 corresponding up-regulated meta-signature genes in our validation experiments. The 57 identified meta-signature genes and involved pathways, together with their regulatory microRNAs could serve as promising and sought-after biomarkers of endometrial receptivity, fertility and infertility.
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| 6. |
- Aid, T., et al.
(author)
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Saccharification of lignocellulosic biomasses via ionic liquid pretreatment
- 2016
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In: Industrial crops and products (Print). - : Elsevier. - 0926-6690 .- 1872-633X. ; 92, s. 336-341
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Journal article (peer-reviewed)abstract
- The current work focuses on the pretreatment efficiency of ILs combined with heat for woody biomass consisting of spruce, birch and pine as well as winter wheat straw. The latter was investigated as a comparison and with the aim to enhance its digestibility during enzymatic hydrolysis whereby the influence of IL-treatment to cellulose resistance for hydrolysis was investigated. Considering the wood species, the most common and industrially important wood species in Northern Europe were chosen in the present work and the goal was to obtain fermentable sugars and their degradation product, i.e. 5-hydroxymethylfurfural (5-HMF), which is known valuable platform chemical. Further, the differences in the yields of IL-obtainable carbohydrates between these species were studied. The highest sugar yields were obtained to glucose in the case of spruce and arabinose in the case of pine sapwood, 12.07 and 7.72 mmol/L, respectively. The highest 5-HMF yield was obtained for spruce heartwood (9.18 mmol/L) with longer treatment time, such as 100h. However, regarding woody biomass, the present work was focused more on the study and analysis of the IL-containing liquid part, wood hydrolysate, after IL-treatment aiming to answer the analysis challenges related to this fraction.
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| 7. |
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| 8. |
- Hyvärinena, S., et al.
(author)
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Sugars and sugar derivatives in ionic liquid media obtained from lignocellulosic biomass : comparison of capillary electrophoresis and chromatographic analysis
- 2014
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In: Catalysis Today. - : Elsevier. - 0920-5861 .- 1873-4308. ; 223, s. 18-24
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Journal article (peer-reviewed)abstract
- Processing of woody lignocellulosic biomass, under heating in combination with ionic liquids (ILs) was studied in order to obtain simple (fermentable) sugars. Due to the new environmental challenges, finding greener ways to produce platform chemicals and/or bio-fuels has become a popular research area. Various industrial, pilot or laboratory scale technologies for the depolymerization or fractionation of lignocellulosic polysaccharides to monomers are known. One of the new, interesting, methods is to utilize ILs in biomass pre-treatment procedures with an aim to bypass other pre-treatment methods. Furthermore, in order even to initiate studies whether ILs can contribute to catalytic depolymerization, there has to be a robust way to analyze the IL-treated lignocellulosics. This is a major issue since woody samples that contain any salts such as ILs can indeed be quite challenging from the analytic point of view. The applied capillary electrophoresis was found to be an excellent analytical method providing substantial improvements compared to the earlier used chromatographic methods.In this work it was demonstrated that application of ILs, at elevated temperatures, contributes to hydrolysis and depolymerization of lignocellulose. The effect is time and temperature dependent: in harsh conditions sugars degrade but too low processing temperatures or short treatment times result in no meaningful effect. The formation of the degradation products of the monosaccharides is a good indicator of the harshness of the applied chemical conditions. Evidently, furfural and 5-(hydroxymethyl)furfural formed in rather short treatment times.
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| 11. |
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| 12. |
- Krjutskov, K, et al.
(author)
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Globin mRNA reduction for whole-blood transcriptome sequencing
- 2016
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In: Scientific reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 6, s. 31584-
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Journal article (peer-reviewed)abstract
- The transcriptome analysis of whole-blood RNA by sequencing holds promise for the identification and tracking of biomarkers; however, the high globin mRNA (gmRNA) content of erythrocytes hampers whole-blood and buffy coat analyses. We introduce a novel gmRNA locking assay (GlobinLock, GL) as a robust and simple gmRNA reduction tool to preserve RNA quality, save time and cost. GL consists of a pair of gmRNA-specific oligonucleotides in RNA initial denaturation buffer that is effective immediately after RNA denaturation and adds only ten minutes of incubation to the whole cDNA synthesis procedure when compared to non-blood RNA analysis. We show that GL is fully effective not only for human samples but also for mouse and rat and so far incompletely studied cow, dog and zebrafish.
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| 13. |
- Petzold, Axel, et al.
(author)
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Neurofilament ELISA validation
- 2010
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In: JOURNAL OF IMMUNOLOGICAL METHODS. - 0022-1759. ; 352:1-2, s. 23-31
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Journal article (peer-reviewed)
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| 14. |
- Petzold, Axel, et al.
(author)
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Neurofilament ELISA validation
- 2010
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In: JIM - Journal of Immunological Methods. - : Elsevier BV. - 0022-1759 .- 1872-7905. ; 352:1-2, s. 23-31
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Journal article (peer-reviewed)abstract
- BACKGROUND: Neurofilament proteins (Nf) are highly specific biomarkers for neuronal death and axonal degeneration. As these markers become more widely used, an inter-laboratory validation study is required to identify assay criteria for high quality performance. METHODS: The UmanDiagnostics NF-light (R)enzyme-linked immunoabsorbent assays (ELISA) for the neurofilament light chain (NfL, 68kDa) was used to test the intra-assay and inter-laboratory coefficient of variation (CV) between 35 laboratories worldwide on 15 cerebrospinal fluid (CSF) samples. Critical factors, such as sample transport and storage, analytical delays, reaction temperature and time, the laboratories' accuracy and preparation of standards were documented and used for the statistical analyses. RESULTS: The intra-laboratory CV averaged 3.3% and the inter-laboratory CV 59%. The results from the test laboratories correlated with those from the reference laboratory (R=0.60, p<0.0001). Correcting for critical factors improved the strength of the correlation. Differences in the accuracy of standard preparation were identified as the most critical factor. Correcting for the error introduced by variation in the protein standards improved the correlation to R=0.98, p<0.0001 with an averaged inter-laboratory CV of 14%. The corrected overall inter-rater agreement was subtantial (0.6) according to Fleiss' multi-rater kappa and Gwet's AC1 statistics. CONCLUSION: This multi-center validation study identified the lack of preparation of accurate and consistent protein standards as the main reason for a poor inter-laboratory CV. This issue is also relevant to other protein biomarkers based on this type of assay and will need to be solved in order to achieve an acceptable level of analytical accuracy. The raw data of this study is available online.
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| 17. |
- Teder, H, et al.
(author)
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TAC-seq: targeted DNA and RNA sequencing for precise biomarker molecule counting
- 2018
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In: NPJ genomic medicine. - : Springer Science and Business Media LLC. - 2056-7944. ; 3, s. 34-
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Journal article (peer-reviewed)abstract
- Targeted next-generation sequencing (NGS) methods have become essential in medical research and diagnostics. In addition to NGS sensitivity and high-throughput capacity, precise biomolecule counting based on unique molecular identifier (UMI) has potential to increase biomolecule detection accuracy. Although UMIs are widely used in basic research its introduction to clinical assays is still in progress. Here, we present a robust and cost-effective TAC-seq (Targeted Allele Counting by sequencing) method that uses UMIs to estimate the original molecule counts of mRNAs, microRNAs, and cell-free DNA. We applied TAC-seq in three different clinical applications and compared the results with standard NGS. RNA samples extracted from human endometrial biopsies were analyzed using previously described 57 mRNA-based receptivity biomarkers and 49 selected microRNAs at different expression levels. Cell-free DNA aneuploidy testing was based on cell line (47,XX, +21) genomic DNA. TAC-seq mRNA profiling showed identical clustering results to transcriptome RNA sequencing, and microRNA detection demonstrated significant reduction in amplification bias, allowing to determine minor expression changes between different samples that remained undetermined by standard NGS. The mimicking experiment for cell-free DNA fetal aneuploidy analysis showed that TAC-seq can be applied to count highly fragmented DNA, detecting significant (p = 7.6 × 10−4) excess of chromosome 21 molecules at 10% fetal fraction level. Based on three proof-of-principle applications we demonstrate that TAC-seq is an accurate and highly potential biomarker profiling method for advanced medical research and diagnostics.
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| 18. |
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| 19. |
- Andreasson, Ulf, 1968, et al.
(author)
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A Practical Guide to Immunoassay Method Validation.
- 2015
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In: Frontiers in neurology. - : Frontiers Media SA. - 1664-2295. ; 6
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Journal article (peer-reviewed)abstract
- Biochemical markers have a central position in the diagnosis and management of patients in clinical medicine, and also in clinical research and drug development, also for brain disorders, such as Alzheimer's disease. The enzyme-linked immunosorbent assay (ELISA) is frequently used for measurement of low-abundance biomarkers. However, the quality of ELISA methods varies, which may introduce both systematic and random errors. This urges the need for more rigorous control of assay performance, regardless of its use in a research setting, in clinical routine, or drug development. The aim of a method validation is to present objective evidence that a method fulfills the requirements for its intended use. Although much has been published on which parameters to investigate in a method validation, less is available on a detailed level on how to perform the corresponding experiments. To remedy this, standard operating procedures (SOPs) with step-by-step instructions for a number of different validation parameters is included in the present work together with a validation report template, which allow for a well-ordered presentation of the results. Even though the SOPs were developed with the intended use for immunochemical methods and to be used for multicenter evaluations, most of them are generic and can be used for other technologies as well.
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