| 1. |
- Ameur, Adam, et al.
(författare)
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SweGen : a whole-genome data resource of genetic variability in a cross-section of the Swedish population
- 2017
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Ingår i: European Journal of Human Genetics. - : NATURE PUBLISHING GROUP. - 1018-4813 .- 1476-5438. ; 25:11, s. 1253-1260
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Tidskriftsartikel (refereegranskat)abstract
- Here we describe the SweGen data set, a comprehensive map of genetic variation in the Swedish population. These data represent a basic resource for clinical genetics laboratories as well as for sequencing-based association studies by providing information on genetic variant frequencies in a cohort that is well matched to national patient cohorts. To select samples for this study, we first examined the genetic structure of the Swedish population using high-density SNP-array data from a nation-wide cohort of over 10 000 Swedish-born individuals included in the Swedish Twin Registry. A total of 1000 individuals, reflecting a cross-section of the population and capturing the main genetic structure, were selected for whole-genome sequencing. Analysis pipelines were developed for automated alignment, variant calling and quality control of the sequencing data. This resulted in a genome-wide collection of aggregated variant frequencies in the Swedish population that we have made available to the scientific community through the website https://swefreq.nbis.se. A total of 29.2 million single-nucleotide variants and 3.8 million indels were detected in the 1000 samples, with 9.9 million of these variants not present in current databases. Each sample contributed with an average of 7199 individual-specific variants. In addition, an average of 8645 larger structural variants (SVs) were detected per individual, and we demonstrate that the population frequencies of these SVs can be used for efficient filtering analyses. Finally, our results show that the genetic diversity within Sweden is substantial compared with the diversity among continental European populations, underscoring the relevance of establishing a local reference data set.
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| 2. |
- Jemt, Anders, 1985-, et al.
(författare)
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Evaluation of methods for whole genome and transcriptome sequencing from nanograms of FFPE samples
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The most widely used method for the preservation of clinical tissue specimens is formalin fixation and paraffin embedding (FFPE). Simultaneous analysis of RNA and DNA from samples preserved using this method have long proved problematic, primarily due to lack of material. Here, we describe an attempt to build a complete analysis package for RNA and DNA extracted from single tissue sections. The workflow includes quality control of the extracted material, library preparation and data analysis. We extract DNA with varying integrity from FFPE sections and subject them to whole genome sequencing using two library preparation methods, Illumina TruSeq Nano using the Illumina NeoPrep and Rubicon Genomics ThruPlex. We are able to obtain some usable data, albeit with high duplication rates, demonstrating both the possibilities and challenges of sequencing damaged DNA. Two different approaches to transcriptome sequencing are assessed, the TruSeq RNA Access library preparation kit from Illumina and the SMARTer Stranded Total RNA-Seq Kit - Pico Input from Clonetech. The sequence capture approach of the TruSeq kit is shown to be more robust to low integrity RNA compared to the SMARTer kit. However, the SMARTer kit needs much less starting material and is able to yield data about all transcripts, not just protein coding mRNA.
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| 3. |
- Akan, Pelin, et al.
(författare)
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Comprehensive analysis of the genome transcriptome and proteome landscapes of three tumor cell lines
- 2012
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Ingår i: Genome Medicine. - : Springer Science and Business Media LLC. - 1756-994X. ; 4, s. 86-
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Tidskriftsartikel (refereegranskat)abstract
- We here present a comparative genome, transcriptome and functional network analysis of three human cancer cell lines (A431, U251MG and U2OS), and investigate their relation to protein expression. Gene copy numbers significantly influenced corresponding transcript levels; their effect on protein levels was less pronounced. We focused on genes with altered mRNA and/or protein levels to identify those active in tumor maintenance. We provide comprehensive information for the three genomes and demonstrate the advantage of integrative analysis for identifying tumor-related genes amidst numerous background mutations by relating genomic variation to expression/protein abundance data and use gene networks to reveal implicated pathways.
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| 4. |
- Andersson, Pontus, 1971, et al.
(författare)
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Radiative lifetimes of metastable states of negative ions
- 2006
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Ingår i: Physical Review A. Atomic, Molecular, and Optical Physics. - 1050-2947 .- 1094-1622 .- 2469-9926 .- 2469-9934. ; 73, s. 032705-
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Tidskriftsartikel (refereegranskat)abstract
- We present a technique for measuring the radiative lifetimes of metastable states of negative ions that involves the use of a heavy-ion storage ring. The method has been applied to investigate the radiative decay of the np(3) P-2(1/2) levels of Te-(n=5) and Se-(n=4) and the 3p(3) D-2 state of Si- for which the J=3/2 and 5/2 levels were unresolved. All of these states are metastable and decay primarily by emission of E2 and M1 radiation. Multi Configuration Dirac-Hartree-Fock calculations of rates for the transitions in Te- and Se- yielded lifetimes of 0.45 s and 4.7 s, respectively. The measured values agree well with these predicted values. In the case of the D-2 state of Si-, however, our measurement was only able to set a lower limit on the lifetime. The upper limit of the lifetime that can be measured with our apparatus is set by how long the ions can be stored in the ring, a limit determined by the rate of collisional detachment. Our lower limit of 1 min for the lifetime of the D-2 state is consistent with both the calculated lifetimes of 162 s for the D-2(3/2) level and 27.3 h for the D-2(5/2) level reported by O'Malley and Beck and 14.5 h and 12.5 h, respectively, from our Breit-Pauli calculations.
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| 5. |
- Baltar, Federico, et al.
(författare)
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Prokaryotic Responses to Ammonium and Organic Carbon Reveal Alternative CO2 Fixation Pathways and Importance of Alkaline Phosphatase in the Mesopelagic North Atlantic
- 2016
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Ingår i: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- To decipher the response of mesopelagic prokaryotic communities to input of nutrients, we tracked changes in prokaryotic abundance, extracellular enzymatic activities, heterotrophic production, dark dissolved inorganic carbon (DIC) fixation, community composition (16S rRNA sequencing) and community gene expression (metatranscriptomics) in 3 microcosm experiments with water from the mesopelagic North Atlantic. Responses in 3 different treatments amended with thiosulfate, ammonium or organic matter (i.e., pyruvate plus acetate) were compared to unamended controls. The strongest stimulation was found in the organic matter enrichments, where all measured rates increased >10-fold. Strikingly, in the organic matter treatment, the dark DIC fixation rates-assumed to be related to autotrophic metabolisms-were equally stimulated as all the other heterotrophic-related parameters. This increase in DIC fixation rates was paralleled by an up-regulation of genes involved in DIC assimilation via anaplerotic pathways. Alkaline phosphatase was the metabolic rate most strongly stimulated and its activity seemed to be related to cross-activation by nonpartner histidine kinases, and/or the activation of genes involved in the regulation of elemental balance during catabolic processes. These findings suggest that episodic events such as strong sedimentation of organic matter into the mesopelagic might trigger rapid increases of originally rare members of the prokaryotic community, enhancing heterotrophic and autotrophic carbon uptake rates, ultimately affecting carbon cycling. Our experiments highlight a number of fairly unstudied microbial processes of potential importance in mesopelagic waters that require future attention.
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| 6. |
- Becanovic, Vlatko, et al.
(författare)
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HUGIN: a small satellite trying to be intelligent
- 1999
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Ingår i: Proc. SPIE. ; 3728, s. 98-
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Konferensbidrag (refereegranskat)abstract
- Micro and nano-satellites are important tools to explore and test new ideas and various new devices for space missions without spending extreme amounts of money. The actual launch cost per kilogram payload on a micro or nano-satellite can be as high or even higher than ordinary satellites but the turn around time and quick responses are extremely important. The HUGIN project is a nano-satellite (less than 10 kg) explicitly designed to test magnetic coils and adaptive artificial neural network (ANN) algorithms for attitude control purposes. A small PC video camera is also included and if the control function is successful then also tests of adaptive image processing using other ANN and biologically inspired methods will be performed.
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| 7. |
- Berglund, Leo, 1986-
(författare)
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Kritiskt tänkande som utbildningsmål : Från modernistisk filosofi till policy för högre utbildning
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The goal of critical thinking in higher education is paradoxical, since it implies a form of education that both directs the student towards a pre-defined goal, and commands the student to be autonomous. This paradox is studied in four contexts, as to investigate what pedagogical contradictions the goal of critical thinking generates, and how they transform pedagogical thinking. 1) In the 1930s, European logical positivists cooperated with American pragmatists to "unify science". For Dewey, the realisation of this ideal depended on individuals adopting a "scientific attitude", which could be cultivated in schools and universities. Dewey’s position influenced a pedagogical discourse of critical thinking as the spirit of rational and democratic citizenship. 2) In the 1980s, the Critical Thinking Movement (CTM) addressed the issue on how to make logical thinking applicable in everyday life. Understanding critical thinking as individuals’ problem-solving skills, the CTM essentially inverted the collectivist political orientation of Dewey and the neo-positivists. 3) In the Swedish 1968 governmental investigation of higher education (U 68), a sociologically informed conception of critical thinking, that involved the student in the project of social planning, was promoted. However, educational experts perceived critical thinking as a vague goal, which could not be operationalised. In the 1990s, critical thinking reappeared as part of the doctrine of learning, but only as a generic term used to signify advanced cognitive operations in relation to different subject matters. 4) In contemporary courses in critical thinking held at Swedish universities, radically diverse conceptions are being taught. An analysis of three courses identified three subjectivities "called" by the arrangements and bodies of literature in the courses: the critical thinker as reason, intellect, and moral consciousness. Each of the subjectivities, however, comprises inconsistencies and contradictions, since they are all to be both produced by and autonomous from the orders that the educational institution represents. The dissertation is concluded by a discussion on critical thinking as both a goal and a by-product of education.
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| 8. |
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| 9. |
- Borgström, Erik, et al.
(författare)
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Large Scale Library Generation for High Throughput Sequencing Authors and Affiliations
- 2011
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 6:4, s. e19119-
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Tidskriftsartikel (refereegranskat)abstract
- Background: Large efforts have recently been made to automatethe sample preparation protocols for massively parallel sequencing in order to match the increasing instrument throughput. Still, the size selection through agarose gel electrophoresis separation is a labor-intensive bottleneck of these protocols. Methodology/Principal Findings: In this study a method for automatic library preparation and size selection on a liquid handling robot is presented. The method utilizes selective precipitation of certain sizes of DNA molecules on to paramagnetic beads for cleanup and selection after standard enzymatic reactions. Conclusions/Significance: The method is used to generate libraries for de novo and re-sequencing on the Illumina HiSeq 2000 instrument with a throughput of 12 samples per instrument in approximately 4 hours. The resulting output data show quality scores and pass filter rates comparable to manually prepared samples. The sample size distribution can be adjusted for each application, and are suitable for all high throughput DNA processing protocols seeking to control size intervals.
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| 10. |
- Brodin, Gert, et al.
(författare)
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Nonlinear quantum electrodynamics in vacuum and plasmas
- 2010
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Ingår i: New frontiers in advanced plasma physics. - : American Institute of Physics (AIP). - 9780735408623 ; , s. 24-34
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Konferensbidrag (refereegranskat)abstract
- We consider high field physics due to quantum electrodynamics, in particular those that can be studied in the next generation of laser facilities. Effective field theories based on the Euler-Heisenberg Lagrangian are briefly reviewed, and examples involving plasma- and vacuum physics are given.
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