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- Nelson, G., et al.
(författare)
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QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy
- 2021
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Ingår i: Journal of Microscopy. - : Wiley. - 0022-2720 .- 1365-2818. ; 284:1, s. 56-73
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Tidskriftsartikel (refereegranskat)abstract
- A modern day light microscope has evolved from a tool devoted to making primarily empirical observations to what is now a sophisticated , quantitative device that is an integral part of both physical and life science research. Nowadays, microscopes are found in nearly every experimental laboratory. However, despite their prevalent use in capturing and quantifying scientific phenomena, neither a thorough understanding of the principles underlying quantitative imaging techniques nor appropriate knowledge of how to calibrate, operate and maintain microscopes can be taken for granted. This is clearly demonstrated by the well-documented and widespread difficulties that are routinely encountered in evaluating acquired data and reproducing scientific experiments. Indeed, studies have shown that more than 70% of researchers have tried and failed to repeat another scientist's experiments, while more than half have even failed to reproduce their own experiments. One factor behind the reproducibility crisis of experiments published in scientific journals is the frequent underreporting of imaging methods caused by a lack of awareness and/or a lack of knowledge of the applied technique. Whereas quality control procedures for some methods used in biomedical research, such as genomics (e.g. DNA sequencing, RNA-seq) or cytometry, have been introduced (e.g. ENCODE), this issue has not been tackled for optical microscopy instrumentation and images. Although many calibration standards and protocols have been published, there is a lack of awareness and agreement on common standards and guidelines for quality assessment and reproducibility. In April 2020, the QUality Assessment and REProducibility for instruments and images in Light Microscopy (QUAREP-LiMi) initiative was formed. This initiative comprises imaging scientists from academia and industry who share a common interest in achieving a better understanding of the performance and limitations of microscopes and improved quality control (QC) in light microscopy. The ultimate goal of the QUAREP-LiMi initiative is to establish a set of common QC standards, guidelines, metadata models and tools, including detailed protocols, with the ultimate aim of improving reproducible advances in scientific research. This White Paper (1) summarizes the major obstacles identified in the field that motivated the launch of the QUAREP-LiMi initiative; (2) identifies the urgent need to address these obstacles in a grassroots manner, through a community of stakeholders including, researchers, imaging scientists, bioimage analysts, bioimage informatics developers, corporate partners, funding agencies, standards organizations, scientific publishers and observers of such; (3) outlines the current actions of the QUAREP-LiMi initiative and (4) proposes future steps that can be taken to improve the dissemination and acceptance of the proposed guidelines to manage QC. To summarize, the principal goal of the QUAREP-LiMi initiative is to improve the overall quality and reproducibility of light microscope image data by introducing broadly accepted standard practices and accurately captured image data metrics.
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| 2. |
- Gruber, T, et al.
(författare)
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Geodetic SAR for Height System Unification and Sea Level Research - Observation Concept and Results in the Baltic Sea
- 2021
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Konferensbidrag (refereegranskat)abstract
- Traditionally, sea level is observed at tide gauge stations, which usually also serve as height reference stations for national leveling networks and therefore define a height system of a country. Thus, sea level research across countries is closely linked to height system unification and needs to be regarded jointly. One of the main deficiencies to use tide gauge data for geodetic sea level research and height systems unification is that only a few stations are connected to permanent GNSS receivers next to the tide gauge in order to systematically observe vertical land motion. As a new observation technique, absolute positioning by SAR using active transponders on ground can fill this gap by systematically observing time series of geometric heights at tide gauge stations. By additionally knowing the tide gauge geoid heights in a global height reference frame, one can finally obtain absolute sea level heights at each tide gauge. With this information the impact of climate change on the sea level can be quantified in an absolute manner and height systems can be connected across the oceans. First results from applying this technique at selected tide gauges at the Baltic coasts are promising but also exhibit some problems related to the new technique. The paper presents the concept of using the new observation type in an integrated sea level observing system and provides results for a test network in the Baltic sea area by combining geometric and physical heights with tide gauge readings.
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| 3. |
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| 4. |
- Ivanov Öfverholm, I., et al.
(författare)
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Overexpression of chromatin remodeling and tyrosine kinase genes in iAMP21-positive acute lymphoblastic leukemia
- 2020
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Ingår i: Leukemia and Lymphoma. - : Informa UK Limited. - 1042-8194 .- 1029-2403. ; 61:3, s. 604-613
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Tidskriftsartikel (refereegranskat)abstract
- Intrachromosomal amplification of chromosome 21 (iAMP21) is a cytogenetic subtype associated with relapse and poor prognosis in pediatric B-cell precursor acute lymphoblastic leukemia (BCP ALL). The biology behind the high relapse risk is unknown and the aim of this study was to further characterize the genomic and transcriptional landscape of iAMP21. Using DNA arrays and sequencing, we could identify rearrangements and aberrations characteristic for iAMP21. RNA sequencing revealed that only half of the genes in the minimal region of amplification (20/45) were differentially expressed in iAMP21. Among them were the top overexpressed genes (p < 0.001) in iAMP21 vs. BCP ALL without iAMP21 and three candidate genes could be identified, the tyrosine kinase gene DYRK1A and chromatin remodeling genes CHAF1B and SON. While overexpression of DYRK1A and CHAF1B is associated with poor prognosis in malignant diseases including myeloid leukemia, this is the first study to show significant correlation with iAMP21-positive ALL.
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| 6. |
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| 7. |
- Monfort-Pires, M., et al.
(författare)
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Serum short-chain fatty acids are associated with brown adipose tissue metabolism in humans
- 2023
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Ingår i: Diabetologia. - 1432-0428 .- 0012-186X. ; 66:SUPPL 1, s. S297-S298
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Short-chain fatty acids (SCFAs) result from the fermentation of dietary fibre in the colon and are shown to play an important role in energy metabolism. The relationship between circulating SCFA and brown adipose tissue (BAT) in humans remains to be clarified. We investigated the associations between circulating SCFA and BAT function in humans.
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| 8. |
- Anastasopoulou, Stavroula, et al.
(författare)
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Acute central nervous system toxicity during treatment of pediatric acute lymphoblastic leukemia : phenotypes, risk factors and genotypes
- 2020
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Ingår i: Haematologica. - : Ferrata Storti Foundation. - 0390-6078 .- 1592-8721. ; 107:10, s. 2318-2328
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Tidskriftsartikel (refereegranskat)abstract
- Central nervous system (CNS) toxicity is common at diagnosis and during treatment of pediatric acute lymphoblastic leukemia (ALL). We studied CNS toxicity in 1,464 children aged 1.0-17.9 years, diagnosed with ALL and treated according to the Nordic Society of Pediatric Hematology and Oncology ALL2008 protocol. Genome-wide association studies, and a candidate single-nucleotide polymorphism (SNP; n=19) study were performed in 1,166 patients. Findings were validated in an independent Australian cohort of children with ALL (n=797) in whom two phenotypes were evaluated: diverse CNS toxicities (n=103) and methotrexate-related CNS toxicity (n=48). In total, 135/1,464 (9.2%) patients experienced CNS toxicity for a cumulative incidence of 8.7% (95% confidence interval: 7.31-10.20) at 12 months from diagnosis. Patients aged >= 10 years had a higher risk of CNS toxicity than had younger patients (16.3% vs. 7.4%; P < 0.001). The most common CNS toxicities were posterior reversible encephalopathy syndrome (n=52, 43 with seizures), sinus venous thrombosis (n=28, 9 with seizures), and isolated seizures (n=16). The most significant SNP identified by the genome-wide association studies did not reach genomic significance (lowest P-value: 1.11x10(-6)), but several were annotated in genes regulating neuronal functions. In candidate SNP analysis, ATXN1 rs68082256, related to epilepsy, was associated with seizures in patients < 10 years (P=0.01). ATXN1 rs68082256 was validated in the Australian cohort with diverse CNS toxicities (P=0.04). The role of ATXN1 as well as the novel SNP in neurotoxicity in pediatric ALL should be further explored.
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| 9. |
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| 10. |
- Kotilainen, K., et al.
(författare)
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From energy consumers to prosumers-how do policies influence the transition?
- 2021
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Ingår i: Electrification. - : Elsevier. - 9780128221433 - 9780128221761 ; , s. 197-215
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- Active producer-consumers (prosumers) still number relatively few in most countries, excluding frontrunner countries such as Germany and the USA, where small-scale solar power generation by property-owners has made strong inroads. To unleash their potential for a transition to a more climate-neutral electric energy system, identifying the potential enablers and constraints for the proliferation of prosumption is crucial. Policy mixes have been identified as important enablers for industry transitions. We report a case comparing the similarities and differences among prosumer-related policies in five European countries: Finland, France, Germany, Italy, and Switzerland. We also introduce an empirical case study on how policies in these countries may influence consumer attitudes in favor of small-scale renewable energy production. We conclude the chapter by discussing the best practices and the mix of more precise policy instruments deployable for involving citizens in order to accelerate the electrification of the energy system.
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