| 1. |
- Kulmala, M., et al.
(author)
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General overview: European Integrated project on Aerosol Cloud Climate and Air Quality interactions (EUCAARI) - integrating aerosol research from nano to global scales
- 2011
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In: Atmospheric Chemistry And Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 11:24, s. 13061-13143
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Journal article (peer-reviewed)abstract
- In this paper we describe and summarize the main achievements of the European Aerosol Cloud Climate and Air Quality Interactions project (EUCAARI). EUCAARI started on 1 January 2007 and ended on 31 December 2010 leaving a rich legacy including: (a) a comprehensive database with a year of observations of the physical, chemical and optical properties of aerosol particles over Europe, (b) comprehensive aerosol measurements in four developing countries, (c) a database of airborne measurements of aerosols and clouds over Europe during May 2008, (d) comprehensive modeling tools to study aerosol processes fron nano to global scale and their effects on climate and air quality. In addition a new Pan-European aerosol emissions inventory was developed and evaluated, a new cluster spectrometer was built and tested in the field and several new aerosol parameterizations and computations modules for chemical transport and global climate models were developed and evaluated. These achievements and related studies have substantially improved our understanding and reduced the uncertainties of aerosol radiative forcing and air quality-climate interactions. The EUCAARI results can be utilized in European and global environmental policy to assess the aerosol impacts and the corresponding abatement strategies.
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| 2. |
- Lappalainen, H. K., et al.
(author)
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Overview: Recent advances in the understanding of the northern Eurasian environments and of the urban air quality in China - a Pan-Eurasian Experiment (PEEX) programme perspective
- 2022
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In: Atmospheric Chemistry and Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 22:7, s. 4413-4469
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Journal article (peer-reviewed)abstract
- The Pan-Eurasian Experiment (PEEX) Science Plan, released in 2015, addressed a need for a holistic system understanding and outlined the most urgent research needs for the rapidly changing Arctic-boreal region. Air quality in China, together with the long-range transport of atmospheric pollutants, was also indicated as one of the most crucial topics of the research agenda. These two geographical regions, the northern Eurasian Arctic-boreal region and China, especially the megacities in China, were identified as a "PEEX region". It is also important to recognize that the PEEX geographical region is an area where science-based policy actions would have significant impacts on the global climate. This paper summarizes results obtained during the last 5 years in the northern Eurasian region, together with recent observations of the air quality in the urban environments in China, in the context of the PEEX programme. The main regions of interest are the Russian Arctic, northern Eurasian boreal forests (Siberia) and peatlands, and the megacities in China. We frame our analysis against research themes introduced in the PEEX Science Plan in 2015. We summarize recent progress towards an enhanced holistic understanding of the land-atmosphere-ocean systems feedbacks. We conclude that although the scientific knowledge in these regions has increased, the new results are in many cases insufficient, and there are still gaps in our understanding of large-scale climate-Earth surface interactions and feedbacks. This arises from limitations in research infrastructures, especially the lack of coordinated, continuous and comprehensive in situ observations of the study region as well as integrative data analyses, hindering a comprehensive system analysis. The fast-changing environment and ecosystem changes driven by climate change, socio-economic activities like the China Silk Road Initiative, and the global trends like urbanization further complicate such analyses. We recognize new topics with an increasing importance in the near future, especially "the enhancing biological sequestration capacity of greenhouse gases into forests and soils to mitigate climate change" and the "socio-economic development to tackle air quality issues".
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| 3. |
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| 4. |
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| 5. |
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| 6. |
- '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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| 7. |
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| 8. |
- Boy, M., et al.
(author)
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Interactions between the atmosphere, cryosphere, and ecosystems at northern high latitudes
- 2019
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In: Atmospheric Chemistry and Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 19:3, s. 2015-2061
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Journal article (peer-reviewed)abstract
- The Nordic Centre of Excellence CRAICC (Cryosphere-Atmosphere Interactions in a Changing Arctic Climate), funded by NordForsk in the years 2011-2016, is the largest joint Nordic research and innovation initiative to date, aiming to strengthen research and innovation regarding climate change issues in the Nordic region. CRAICC gathered more than 100 scientists from all Nordic countries in a virtual centre with the objectives of identifying and quantifying the major processes controlling Arctic warming and related feedback mechanisms, outlining strategies to mitigate Arctic warming, and developing Nordic Earth system modelling with a focus on short-lived climate forcers (SLCFs), including natural and anthropogenic aerosols. The outcome of CRAICC is reflected in more than 150 peer-reviewed scientific publications, most of which are in the CRAICC special issue of the journal Atmospheric Chemistry and Physics. This paper presents an overview of the main scientific topics investigated in the centre and provides the reader with a state-of-the-art comprehensive summary of what has been achieved in CRAICC with links to the particular publications for further detail. Faced with a vast amount of scientific discovery, we do not claim to completely summarize the results from CRAICC within this paper, but rather concentrate here on the main results which are related to feedback loops in climate change-cryosphere interactions that affect Arctic amplification.
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| 11. |
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| 12. |
- Kukkola, J, et al.
(author)
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Novel printed nanostructured gas sensors
- 2011
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In: Procedia Engineering. - : Elsevier. - 1877-7058. ; 25, s. 896-899
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Journal article (peer-reviewed)abstract
- There is a need for low-cost mass-production circuits on various substrates, possibly performing some simple functions as switches, antennas, displays, and sensors. Also in the field of gas sensors widely used in several applications there is a need for such novel fabrication technologies and materials. In this paper, we present three gas sensor structures fabricated using novel printing techniques. Inkjet and gravure printing techniques were used for fabrication of resistive WO3 nanoparticle gas sensors for detection of NO, and inkjet printing was utilized for fabrication of solid electrolyte (mixture of H3PW12O40 and PVC) in a nanostructured Metal-Electrolyte-Insulator- Semiconductor (MEIS) transistor for detection of H2. The sensor structures were found to be sensitive for detection of NO below 10 ppm, and H2 below 100 ppm concentrations in synthetic air, respectively.
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| 13. |
- Kulmala, M., et al.
(author)
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Introduction : The Pan-Eurasian Experiment (PEEX) - multidisciplinary, multiscale and multicomponent research and capacity-building initiative
- 2015
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In: Atmospheric Chemistry And Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 15:22, s. 13085-13096
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Journal article (peer-reviewed)abstract
- The Pan-Eurasian Experiment (PEEX) is a multidisciplinary, multiscale and multicomponent research, research infrastructure and capacity-building program. PEEX has originated from a bottom-up approach by the science communities and is aiming at resolving the major uncertainties in Earth system science and global sustainability issues concerning the Arctic and boreal pan-Eurasian regions, as well as China. The vision of PEEX is to solve interlinked, global grand challenges influencing human well-being and societies in northern Eurasia and China. Such challenges include climate change; air quality; biodiversity loss; urbanization; chemicalization; food and freshwater availability; energy production; and use of natural resources by mining, industry, energy production and transport sectors. Our approach is integrative and supra-disciplinary, recognizing the important role of the Arctic and boreal ecosystems in the Earth system. The PEEX vision includes establishing and maintaining long-term, coherent and coordinated research activities as well as continuous, comprehensive research and educational infrastructure and related capacity-building across the PEEX domain. In this paper we present the PEEX structure and summarize its motivation, objectives and future outlook.
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| 14. |
- 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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| 15. |
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| 16. |
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| 17. |
- Bastuck, Manuel, et al.
(author)
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Exploring the selectivity of WO3 with iridium catalyst in an ethanol/naphthalene mixture using multivariate statistics
- 2016
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In: Thin Solid Films. - : ELSEVIER SCIENCE SA. - 0040-6090 .- 1879-2731. ; 618, s. 263-270
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Journal article (peer-reviewed)abstract
- Temperature cycled operation and multivariate statistics have been used to compare the selectivity of two gate (i.e. sensitive) materials for gas-sensitive, silicon carbide based field effect transistors towards naphthalene and ethanol in different mixtures of the two substances. Both gates have a silicon dioxide (SiO2) insulation layer and a porous iridium (Ir) electrode. One of it has also a dense tungsten trioxide (WO3) interlayer between Ir and SiO2. Both static and transient characteristics play an important role and can contribute to improve the sensitivity and selectivity of the gas sensor. The Ir/SiO2 is strongly influenced by changes in ethanol concentration, and is, thus, able to quantify ethanol in a range between 0 and 5 ppm with a precision of 500 ppb, independently of the naphthalene concentrations applied in this investigation. On the other hand, this sensitivity to ethanol reduces its selectivity towards naphthalene, whereas Ir/WO3/SiO2 shows an almost binary response to ethanol. Hence, the latter has a better selectivity towards naphthalene and can quantify legally relevant concentrations down to 5 ppb with a precision of 2.5 ppb, independently of a changing ethanol background between 0 and 5 ppm. (C) 2016 Elsevier B.V. All rights reserved.
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| 18. |
- Bergman, TH, et al.
(author)
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Acceptance and Commitment Therapy Group Intervention for Parents of Children with Disabilities (Navigator ACT): An Open Feasibility Trial
- 2023
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In: Journal of autism and developmental disorders. - : Springer Science and Business Media LLC. - 1573-3432 .- 0162-3257. ; 53:5, s. 1834-1849
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Journal article (peer-reviewed)abstract
- Parents of children with autism spectrum disorder and other disabilities report high levels of distress, but systematically evaluated interventions are few. This study aimed to evaluate the feasibility of a novel, manualized Acceptance and Commitment Therapy group intervention (Navigator ACT) in a sample of 94 parents of children with disabilities. Feasibility was measured by treatment completion, credibility, and satisfaction, and preliminary outcomes by using self-rating scales administered at the baseline, post-intervention, and follow-up. The results imply the intervention is feasible in the context of Swedish outpatient habilitation services. A preliminary analysis of the outcome measures suggests that parents experienced significant improvements in well-being. The results indicate that the treatment is feasible and should be evaluated in a randomized controlled trial.
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| 19. |
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| 20. |
- Glinos, Dafni A., et al.
(author)
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Transcriptome variation in human tissues revealed by long-read sequencing
- 2022
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In: Nature. - : Springer Nature. - 0028-0836 .- 1476-4687. ; 608:7922, s. 353-359
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Journal article (peer-reviewed)abstract
- Regulation of transcript structure generates transcript diversity and plays an important role in human disease(1-7). The advent oflong-read sequencing technologies offers the opportunity to study the role of genetic variation in transcript structure(8-)(16). In this Article, we present a large human long-read RNA-seq dataset using the Oxford Nanopore Technologies platform from 88 samples from Genotype-Tissue Expression (GTEx) tissues and cell lines, complementing the GTEx resource. We identified just over 70,000 novel transcripts for annotated genes, and validated the protein expression of 10% of novel transcripts. We developed a new computational package, LORALS, to analyse the genetic effects of rare and common variants on the transcriptome by allele-specific analysis of long reads. We characterized allele-specific expression and transcript structure events, providing new insights into the specific transcript alterations caused by common and rare genetic variants and highlighting the resolution gained from long-read data. We were able to perturb the transcript structure upon knockdown of PTBP1, an RNA binding protein that mediates splicing, thereby finding genetic regulatory effects that are modified by the cellular environment. Finally, we used this dataset to enhance variant interpretation and study rare variants leading to aberrant splicing patterns.
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| 21. |
- Greger, Liliana, et al.
(author)
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Tandem RNA chimeras contribute to transcriptome diversity in human population and are associated with intronic genetic variants.
- 2014
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In: PloS one. - : Public Library of Science (PLoS). - 1932-6203. ; 9:8, s. e104567-
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Journal article (peer-reviewed)abstract
- Chimeric RNAs originating from two or more different genes are known to exist not only in cancer, but also in normal tissues, where they can play a role in human evolution. However, the exact mechanism of their formation is unknown. Here, we use RNA sequencing data from 462 healthy individuals representing 5 human populations to systematically identify and in depth characterize 81 RNA tandem chimeric transcripts, 13 of which are novel. We observe that 6 out of these 81 chimeras have been regarded as cancer-specific. Moreover, we show that a prevalence of long introns at the fusion breakpoint is associated with the chimeric transcripts formation. We also find that tandem RNA chimeras have lower abundances as compared to their partner genes. Finally, by combining our results with genomic data from the same individuals we uncover intronic genetic variants associated with the chimeric RNA formation. Taken together our findings provide an important insight into the chimeric transcripts formation and open new avenues of research into the role of intronic genetic variants in post-transcriptional processing events.
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| 22. |
- Gustafsson, G, et al.
(author)
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The electric field and wave experiment for the Cluster mission
- 1997
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In: Space Science Reviews. - 0038-6308 .- 1572-9672. ; 79, s. 137-156
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Journal article (peer-reviewed)abstract
- The electric-field and wave experiment (EFW) on Cluster is designed to measure the electric-field and density fluctuations with sampling rates up to 36 000 samples s(-1). Langmuir probe sweeps can also be made to determine the electron density and temperature. The instrument has several important capabilities. These include (1) measurements of quasi-static electric fields of amplitudes lip to 700 mV m(-1) with high amplitude and time resolution, (2) measurements over short periods of time of up to five simualtaneous waveforms (two electric signals and three magnetic signals from the seach coil magnetometer sensors) of a bandwidth of 4 kHz with high time resolution, (3) measurements of density fluctuations in four points with high time resolution. Among the more interesting scientific objectives of the experiment are studies of nonlinear wave phenomena that result in acceleration of plasma as well as large- and small-scale interferometric measurements. By using four spacecraft for large-scale differential measurements and several Langmuir probes on one spacecraft for small-scale interferometry, it will be possible to study motion and shape of plasma structures on a wide range of spatial and temporal scales. This paper describes the primary scientific objectives of the EFW experiment and the technical capabilities of the instrument.
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| 23. |
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| 24. |
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| 25. |
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| 26. |
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| 27. |
- Lappalainen, T, et al.
(author)
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Migration waves to the Baltic Sea region
- 2008
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In: Annals of Human Genetics. - Oxford : Blackwell Publishing. - 0003-4800 .- 1469-1809. ; 72, s. 337-348
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Journal article (peer-reviewed)abstract
- In this study, the population history of the Baltic Sea region, known to be affected by a variety of migrations and genetic barriers, was analyzed using both mitochondrial DNA and Y-chromosomal data. Over 1200 samples from Finland, Sweden, Karelia, Estonia, Setoland, Latvia and Lithuania were genotyped for 18 Y-chromosomal biallelic polymorphisms and 9 STRs, in addition to analyzing 17 coding region polymorphisms and the HVS1 region from the mtDNA. It was shown that the populations surrounding the Baltic Sea are genetically similar, which suggests that it has been an important route not only for cultural transmission but also for population migration. However, many of the migrations affecting the area from Central Europe, the Volga-Ural region and from Slavic populations have had a quantitatively different impact on the populations, and, furthermore, the effects of genetic drift have increased the differences between populations especially in the north. The possible explanations for the high frequencies of several haplogroups with an origin in the Iberian refugia (H1, U5b, I1a) are also discussed.
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| 28. |
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| 29. |
- Lim, Elaine T, et al.
(author)
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Distribution and Medical Impact of Loss-of-Function Variants in the Finnish Founder Population.
- 2014
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In: PLoS Genetics. - : Public Library of Science (PLoS). - 1553-7404. ; 10:7
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Journal article (peer-reviewed)abstract
- Exome sequencing studies in complex diseases are challenged by the allelic heterogeneity, large number and modest effect sizes of associated variants on disease risk and the presence of large numbers of neutral variants, even in phenotypically relevant genes. Isolated populations with recent bottlenecks offer advantages for studying rare variants in complex diseases as they have deleterious variants that are present at higher frequencies as well as a substantial reduction in rare neutral variation. To explore the potential of the Finnish founder population for studying low-frequency (0.5-5%) variants in complex diseases, we compared exome sequence data on 3,000 Finns to the same number of non-Finnish Europeans and discovered that, despite having fewer variable sites overall, the average Finn has more low-frequency loss-of-function variants and complete gene knockouts. We then used several well-characterized Finnish population cohorts to study the phenotypic effects of 83 enriched loss-of-function variants across 60 phenotypes in 36,262 Finns. Using a deep set of quantitative traits collected on these cohorts, we show 5 associations (p<5×10-8) including splice variants in LPA that lowered plasma lipoprotein(a) levels (P = 1.5×10-117). Through accessing the national medical records of these participants, we evaluate the LPA finding via Mendelian randomization and confirm that these splice variants confer protection from cardiovascular disease (OR = 0.84, P = 3×10-4), demonstrating for the first time the correlation between very low levels of LPA in humans with potential therapeutic implications for cardiovascular diseases. More generally, this study articulates substantial advantages for studying the role of rare variation in complex phenotypes in founder populations like the Finns and by combining a unique population genetic history with data from large population cohorts and centralized research access to National Health Registers.
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| 31. |
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| 32. |
- Santillán Martínez, G., et al.
(author)
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Automatic Generation of a High-Fidelity Dynamic Thermal-hydraulic Process Simulation Model from a 3D Plant Model
- 2018
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In: IEEE Access. - : Institute of Electrical and Electronics Engineers (IEEE). - 2169-3536. ; 6, s. 45217-45232
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Journal article (peer-reviewed)abstract
- Dynamic thermal-hydraulic simulation models have been extensively used by process industry for decision support in sectors such as power generation, mineral processing, pulp and paper, and oil and gas. Ever-growing competitiveness in the process industry forces experts to rely even more on dynamic simulation results to take decisions across the process plant lifecycle. However, time-consuming development of simulation models increases model generation costs, limiting their use in a wider number of applications. Detailed 3D plant models, developed during early plant engineering for process design, could potentially be used as a source of information to enable rapid development of high-fidelity simulation models. This paper presents a method for automatic generation of a thermal-hydraulic process simulation model from a 3D plant model. Process structure, dimensioning and component connection information included in the 3D plant model is extracted from the machine-readable export of the 3D design tool and used to automatically generate and configure a dynamic thermal-hydraulic simulation model. In particular, information about the piping dimensions and elevations is retrieved from the 3D plant model and used to calculate head loss coefficients of the pipelines and to configure the piping network model. This step, not considered in previous studies, is crucial for obtaining high-fidelity industrial process models. The proposed method is tested using a laboratory process and the results of the automatically generated model are compared with experimental data from the physical system as well as with a simulation model developed using design data utilized by existing methods on the state-of-the-art. Results show that the proposed method is able to generate high-fidelity models which are able to accurately predict the targeted system, even during operational transients.
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| 33. |
- Torbert, R. B., et al.
(author)
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The FIELDS Instrument Suite on MMS : Scientific Objectives, Measurements, and Data Products
- 2016
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In: Space Science Reviews. - : Springer Science+Business Media B.V.. - 0038-6308 .- 1572-9672. ; 199:1-4, s. 105-135
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Research review (peer-reviewed)abstract
- The FIELDS instrumentation suite on the Magnetospheric Multiscale (MMS) mission provides comprehensive measurements of the full vector magnetic and electric fields in the reconnection regions investigated by MMS, including the dayside magnetopause and the night-side magnetotail acceleration regions out to 25 Re. Six sensors on each of the four MMS spacecraft provide overlapping measurements of these fields with sensitive cross-calibrations both before and after launch. The FIELDS magnetic sensors consist of redundant flux-gate magnetometers (AFG and DFG) over the frequency range from DC to 64 Hz, a search coil magnetometer (SCM) providing AC measurements over the full whistler mode spectrum expected to be seen on MMS, and an Electron Drift Instrument (EDI) that calibrates offsets for the magnetometers. The FIELDS three-axis electric field measurements are provided by two sets of biased double-probe sensors (SDP and ADP) operating in a highly symmetric spacecraft environment to reduce significantly electrostatic errors. These sensors are complemented with the EDI electric measurements that are free from all local spacecraft perturbations. Cross-calibrated vector electric field measurements are thus produced from DC to 100 kHz, well beyond the upper hybrid resonance whose frequency provides an accurate determination of the local electron density. Due to its very large geometric factor, EDI also provides very high time resolution (similar to 1 ms) ambient electron flux measurements at a few selected energies near 1 keV. This paper provides an overview of the FIELDS suite, its science objectives and measurement requirements, and its performance as verified in calibration and cross-calibration procedures that result in anticipated errors less than 0.1 nT in B and 0.5 mV/m in E. Summaries of data products that result from FIELDS are also described, as well as algorithms for cross-calibration. Details of the design and performance characteristics of AFG/DFG, SCM, ADP, SDP, and EDI are provided in five companion papers.
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