| 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. |
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| 5. |
- Berglund, Leo, 1986-
(författare)
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Kritiskt tänkande som utbildningsmål : Från modernistisk filosofi till policy för högre utbildning
- 2021
-
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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| 6. |
- 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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| 7. |
- Borgström, Erik, et al.
(författare)
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Phasing of single DNA molecules by massively parallel barcoding
- 2015
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 6
-
Tidskriftsartikel (refereegranskat)abstract
- High-throughput sequencing platforms mainly produce short-read data, resulting in a loss of phasing information for many of the genetic variants analysed. For certain applications, it is vital to know which variant alleles are connected to each individual DNA molecule. Here we demonstrate a method for massively parallel barcoding and phasing of single DNA molecules. First, a primer library with millions of uniquely barcoded beads is generated. When compartmentalized with single DNA molecules, the beads can be used to amplify and tag any target sequences of interest, enabling coupling of the biological information from multiple loci. We apply the assay to bacterial 16S sequencing and up to 94% of the hypothesized phasing events are shown to originate from single molecules. The method enables use of widely available short-read-sequencing platforms to study long single molecules within a complex sample, without losing phase information.
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| 8. |
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| 9. |
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Den förnekade kunskapen. En introduktion till Robert Pfallers filosofi
- 2019
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Samlingsverk (redaktörskap) (övrigt vetenskapligt/konstnärligt)abstract
- Robert Pfaller är en österrikisk filosof och kulturteoretiker med intressen som sträcker sig från epistemologi och psykoanalys, via konst och populärkultur, till ideologikritik och politik. Han ägnar sig åt frågan om ”trons form” – det vill säga inte vad vi tror på, utan hur vi tror. Pfaller kan hjälpa oss förstå sambandet mellan två aktuella tendenser i det moderna samhället: å ena sidan den av nyliberalismen pådrivna nedmonteringen av välfärdssystemen, vilken förändrar vårt samhälle och våra livsvillkor i grunden till det sämre; å andra sidan den tilltagande moralismen inom det politiska området, som fäster sig vid sådant som rökning, plastpåsar, musik på hög volym, könsstereotyper och köttätande. Pfaller gör det möjligt att i båda dessa tendenser identifiera ett narcissistiskt ”ansvarstagande” som är mer upptaget av att framställa sig själv som moraliskt högtstående, än att bereda väg för ett gott liv. Det är denna fråga – om det goda livet, och om lyckan, som Pfaller vill ge plats i den politiska debatten och i den filosofiska diskussionen. Föreliggande volym är en introduktion till Pfallers filosofi med bidrag som visar dess relevans inom områden som psykoanalys, sociologi, teologi, pedagogik och socialt arbete.
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| 10. |
- Dodillet, Susanne, 1977, et al.
(författare)
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Constructing professionalism in teacher education. Analytical tools from a comparative study.
- 2019
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Ingår i: Education Inquiry. - : Informa UK Limited. - 2000-4508. ; 10:3, s. 208-225
-
Tidskriftsartikel (refereegranskat)abstract
- This article studies the meaning of professionalism in current attempts to professionalise teachers by means of education. The point of departure for our analysis is a small-scale survey among Swedish and German student teachers on their perception of the meaning of professionalism with regard to teachers’ work. The article presents two contrasting ideal types of professionalism identified in this data: the concept of science-based professionalism is characterised by an ambition to develop theories that can be translated into more or less direct prescriptions for the efficient exercise of the profession; the concept of pedagogic professionalism, in contrast, originates in basic mistrust of this ambition concerning teachers’ work and instead aims to develop a thorough understanding of the paradoxes and antinomies of education. The article outlines the theoretical foundations of these ideal types and shows how they can shed light on the aims of educational research in different contexts, as well as help explain the rationale behind structural differences in the design of teacher education programmes.
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| 11. |
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| 12. |
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| 13. |
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| 14. |
- Dodillet, Susanne, 1977, et al.
(författare)
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Förskolningen av barndomen
- 2017
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Ingår i: alba.nu. - 1403-5448. ; mars
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 15. |
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| 16. |
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| 17. |
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| 18. |
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| 19. |
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| 20. |
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| 21. |
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| 22. |
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| 23. |
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| 24. |
- Dodillet, Susanne, 1977, et al.
(författare)
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Var står universiteten i krisen?
- 2023
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Ingår i: GU-Journalen. - 1402-9626. ; :1
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Tidskriftsartikel (populärvet., debatt m.m.)
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| 25. |
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| 26. |
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| 27. |
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| 28. |
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| 29. |
- Ewels, Philip, et al.
(författare)
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MultiQC : summarize analysis results for multiple tools and samples in a single report
- 2016
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Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 32:19, s. 3047-3048
-
Tidskriftsartikel (refereegranskat)abstract
- Motivation: Fast and accurate quality control is essential for studies involving next-generation sequencing data. Whilst numerous tools exist to quantify QC metrics, there is no common approach to flexibly integrate these across tools and large sample sets. Assessing analysis results across an entire project can be time consuming and error prone; batch effects and outlier samples can easily be missed in the early stages of analysis.Results: We present MultiQC, a tool to create a single report visualising output from multiple tools across many samples, enabling global trends and biases to be quickly identified. MultiQC can plot data from many common bioinformatics tools and is built to allow easy extension and customization.
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| 30. |
- Grunewald, Johan, et al.
(författare)
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T-cell receptor-HLA-DRB1 associations suggest specific antigens in pulmonary sarcoidosis
- 2016
-
Ingår i: European Respiratory Journal. - : European Respiratory Society (ERS). - 0903-1936 .- 1399-3003. ; 47:3, s. 898-909
-
Tidskriftsartikel (refereegranskat)abstract
- In pulmonary sarcoidosis, CD4(+) T-cells expressing T-cell receptor V alpha 2.3 accumulate in the lungs of HLA-DRB1*03(+) patients. To investigate T-cell receptor-HLA-DRB1*03 interactions underlying recognition of hitherto unknown antigens, we performed detailed analyses of T-cell receptor expression on bronchoalveolar lavage fluid CD4(+) T-cells from sarcoidosis patients. Pulmonary sarcoidosis patients (n=43) underwent bronchoscopy with bronchoalveolar lavage. T-cell receptor alpha and beta chains of CD4(+) T-cells were analysed by flow cytometry, DNA-sequenced, and three-dimensional molecular models of T-cell receptor-HLA-DRB1*03 complexes generated. Simultaneous expression of V alpha 2.3 with the V beta 22 chain was identified in the lungs of all HLA-DRB1*03(+) patients. Accumulated V alpha 2.3/V beta 22-expressing T-cells were highly clonal, with identical or near-identical V alpha 2.3 chain sequences and inter-patient similarities in V beta 22 chain amino acid distribution. Molecular modelling revealed specific T-cell receptor-HLA-DRB1*03-peptide interactions, with a previously identified, sarcoidosis-associated vimentin peptide, (Vim)(429-443) DSLPLVDTHSKRTLL, matching both the HLA peptide-binding cleft and distinct T-cell receptor features perfectly. We demonstrate, for the first time, the accumulation of large clonal populations of specific V alpha 2.3/V beta 22 T-cell receptor-expressing CD4(+) T-cells in the lungs of HLA-DRB1*03(+) sarcoidosis patients. Several distinct contact points between V alpha 2.3/V beta 22 receptors and HLA-DRB1*03 molecules suggest presentation of prototypic vimentin-derived peptides.
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| 31. |
- Halskov, Gerd, et al.
(författare)
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Homologier
- 2008
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Ingår i: At sætte spor på en vandring fra Aquinas til Bourdieu- æresbog til Staf Callewaert. - 9788799205028 ; , s. 273-293
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Bokkapitel (övrigt vetenskapligt/konstnärligt)
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| 32. |
- Halskov, Gerd, et al.
(författare)
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Homologier
- 2008. - 1. udgave
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Ingår i: At sætte spor på en vandring fra Aquinas til Bourdieu. - : Hexis. - 9788799205028 ; , s. 273-293
-
Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- I denne lille artikel, vil vi bidrage med at ære Staf Callewaerts virke og de ’spor’ han har sat ved at sætte fokus på en delproblematik af OMOM-projektet (Petersen, Lundin, Halskov, 2007), nemlig: Bourdieus måde at forstå og betragte samfundet på, som et system af relationer mellem positioner. I denne måde at forstå et samfund på indtager hvert individ en vis position. Denne position har et specifikt forhold til andre positioner, som således andre individer indtager. Eller vi kan opstille det endnu mere generelt og sige, at systemet af positioner, Bourdieu kalder det for det sociale felt, indtages af de individer, som befinder sig inden for dette felt (Lundin, Petersen, 2005, 2007). Hvad karakteriserer da en vis position kan man spørge? De begreber, som Bourdieu anvender, kan kontrasteres mod et ræsonnement, hvor begrebet ’social oprindelse’ almindeligvis indebærer en kategorisering af oprindelse i tre store grupper. I de forskningstraditioner, der anvender denne form for kategorisering, studerer man sammenhæng mellem social oprindelse og for eksempel uddannelsesresultat, erhvervsposition eller indkomst. Man mener da, at den sociale oprindelse påvirker individernes uddannelsesbane og karriere, hvor en politisk målsætning på forskellig vis kunne være at mindske de negative effekter af fx lav social oprindelse. Bourdieu mener imidlertid, at en sådan måde at fremstille sagen på, er en forenkling og forsimpling. De tre kategorier, der anvendes for at klassificere ’social oprindelse’, er nemlig alt for grove, og man kan ikke, ifølge Bourdieu, sige, at denne oprindelse sui generis har nogen påvirkning på de uddannelsesbaner eller den erhvervskarriere den enkelte får. Og grunden er enkel: den klassificering, at tilhøre en bestemt social gruppe, eksisterer kun med de fælles træk, fordi nogle forskere i sociologi har defineret det på den måde! Mens det, som de facto former individerne under hele deres liv, er en myriade af vidt forskellige små mekanismer.
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| 33. |
- Hugerth, Luisa W., et al.
(författare)
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DegePrime, a Program for Degenerate Primer Design for Broad-Taxonomic-Range PCR in Microbial Ecology Studies
- 2014
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Ingår i: Applied and Environmental Microbiology. - 0099-2240 .- 1098-5336. ; 80:16, s. 5116-5123
-
Tidskriftsartikel (refereegranskat)abstract
- The taxonomic composition of a microbial community can be deduced by analyzing its rRNA gene content by, e. g., high-throughput DNA sequencing or DNA chips. Such methods typically are based on PCR amplification of rRNA gene sequences using broad-taxonomic-range PCR primers. In these analyses, the use of optimal primers is crucial for achieving an unbiased representation of community composition. Here, we present the computer program DegePrime that, for each position of a multiple sequence alignment, finds a degenerate oligomer of as high coverage as possible and outputs its coverage among taxonomic divisions. We show that our novel heuristic, which we call weighted randomized combination, performs better than previously described algorithms for solving the maximum coverage degenerate primer design problem. We previously used DegePrime to design a broad-taxonomic-range primer pair that targets the bacterial V3-V4 region (341F-805R) (D. P. Herlemann, M. Labrenz, K. Jurgens, S. Bertilsson, J. J. Waniek, and A. F. Andersson, ISME J. 5:1571-1579, 2011, http://dx.doi.org/10.1038/ismej.2011.41), and here we use the program to significantly increase the coverage of a primer pair (515F-806R) widely used for Illumina-based surveys of bacterial and archaeal diversity. By comparison with shotgun metagenomics, we show that the primers give an accurate representation of microbial diversity in natural samples.
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| 34. |
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| 35. |
- Lundgren, Ewa, et al.
(författare)
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Primary hyperparathyroidism revisited in menopausal women with serum calcium in upper normal range at population-based screening 8 years ago
- 2002
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Ingår i: World Journal of Surgery. - : Springer Science and Business Media LLC. - 0364-2313 .- 1432-2323. ; 26:8, s. 931-936
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Tidskriftsartikel (refereegranskat)abstract
- Abstract. Population-based screening showed 2.1% prevalence of primaryhyperparathyroidism (pHPT) in postmenopausal women. Individualswith total serum (s)-calcium levels of 2.55 mmol/L or more at screeningwere diagnosed with pHPT when subsequent analysis supported inappropriatelyelevated intact parathormone (PTH) levels in relation to evennormal s-calcium levels. The arbitrary diagnostic criteria were validatedby parathyroidectomy. Herein we reinvestigated biochemical signs ofpHPT in women not diagnosed with pHPT due to s-calcium 2.50 to 2.54mmol/L (group A, n 160) at screening or due to appropriate PTH levelson two occasions after screening (group B, n 70). Altogether, 99 womenin group A and 47 in group B underwent reinvestigation 8.8 years afterscreening when they were 65 to 84 years old. The s-calcium levels averaged2.56 mmol/L and had increased in group A (mean 0.04 mmol/L) anddecreased in group B (mean 0.05 mmol/L). A total of 48 and 18 females(48%, 38%), respectively, met the previously validated criteria of pHPT.Altogether 21% of them were hypercalcemic (range 2.60 –3.12 mmol/L).Subgroup analysis showed that PTH had not increased with time (n 47)and that atherogenic blood lipids, but not glucose levels, were similar inpHPT patients and matched controls (n 37). Assuming the existence ofpHPT already at screening, the prevalence of pHPT could be adjusted to3.4%. Even the most liberal diagnostic criteria utilized at pHPT screeningseemed to underdiagnose the disease by inefficient cutoff limits for scalciumand PTH. Because one-fifth of the women with pHPT progressedto hypercalcemia, long-term follow-up is advocated for those with scalciumin the upper normal range.
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| 36. |
- Lundin, Margareta, 1967, et al.
(författare)
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A set of indicators for the assessment of temporal variations in the sustainability of sanitary systems
- 1998
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Ingår i: Water Science and Technology. ; 39:5, s. 235-242
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Tidskriftsartikel (refereegranskat)abstract
- The sustainability of an urban water system was studied by application of a set of indicators that focuses on environmental issues and the efficiency and performance of the technical system. Temporal variations of indicators reflecting freshwater resources, drinking water, wastewater and by-products, were investigated for the water and wastewater system in Goteborg. Extended time series of precise data were available for quantitative indicators such as water consumption, energy use and discharge loadings. Qualitative indicators such as drinking water quality, sewage sludge quality and ecosystem status were more difficult to assess, a situation complicated by variations in criteria set in different countries. Although large urban water systems are often considered unsustainable, the set of indicators demonstrate that the water and wastewater system in Goteborg has moved towards a more sustainable status; recycling of nutrients to agriculture remains, though, a major concern.
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| 37. |
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| 38. |
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| 39. |
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| 40. |
- Lundin, Margareta, 1967, et al.
(författare)
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Life Cycle Assessment of Wastewater Systems - Influence of System Boundaries and Scale on Calculated Environmental Loads
- 2000
-
Ingår i: Environmental Science & Technology. ; 34, s. 180-186
-
Tidskriftsartikel (refereegranskat)abstract
- Life cycle assessment (LCA) methodology was used to compare the environmental loads from wastewater systems with different technical solutions. This study compared proposed conventional wastewater systems, both large and small scale, with separation systems: one in which urine is handled separately and one in which black water is treated in a liquid composting process. The study showed that large economies of scale, in environmental terms, could be gained both for the operation and for the construction phase. The separation systems outperformed the conventional systems by showing lower emissions to water and more efficient recycling of nutrients to agriculture, especially of nitrogen but also of phosphorus. This implies that the use of separation systems could significantly reduce the need for, and hence the production of, mineral fertilizers and thus reduce the overall use of energy and phosphate minerals. The combination of large-scale wastewater treatment and urine separation was found to be especially advantageous in these respects. It is concluded that some of the most important environmental advantages of separation systems emerge only when models of wastewater systems are expanded to also include potential effects on the production of fertilizers.
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| 41. |
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| 42. |
- Lundin, Sverker, et al.
(författare)
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Endonuclease specificity and sequence dependence of Type IIS restriction enzymes
- 2015
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Ingår i: PLOS ONE. - : Public Library of Science. - 1932-6203. ; 10:1
-
Tidskriftsartikel (refereegranskat)abstract
- Restriction enzymes that recognize specific sequences but cleave unknown sequence outside the recognition site are extensively utilized tools in molecular biology. Despite this, systematic functional categorization of cleavage performance has largely been lacking. We established a simple and automatable model system to assay cleavage distance variation (termed slippage) and the sequence dependence thereof. We coupled this to massively parallel sequencing in order to provide sensitive and accurate measurement. With this system 14 enzymes were assayed (AcuI, BbvI, BpmI, BpuEI, BseRI, BsgI, Eco57I, Eco57MI, EcoP15I, FauI, FokI, GsuI, MmeI and SmuI). We report significant variation of slippage ranging from 1-54%, variations in sequence context dependence, as well as variation between isoschizomers. We believe this largely overlooked property of enzymes with shifted cleavage would benefit from further large scale classification and engineering efforts seeking to improve performance. The gained insights of in-vitro performance may also aid the in-vivo understanding of these enzymes.
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| 43. |
- Lundin, Sverker, 1975, et al.
(författare)
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Formella meriter är inte allt
- 2015
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Ingår i: Dagens Nyheter. - 1101-2447. ; :11 november
-
Tidskriftsartikel (populärvet., debatt m.m.)
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| 44. |
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| 45. |
- Lundin, Sverker, 1975
(författare)
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Hating school, loving mathematics: On the ideological function of critique and reform in mathematics education
- 2012
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Ingår i: Educational Studies in Mathematics. - : Springer Science and Business Media LLC. - 0013-1954 .- 1573-0816. ; 80:1-2, s. 73-85
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Tidskriftsartikel (refereegranskat)abstract
- Students’ engagement with fictions in the form of “word problems” plays an important role in classroom practice as well as in theories of mathematical learning. Drawing on the Dutch historian Johan Huizinga and the Austrian philosopher Robert Pfaller I show that this activity can be seen as a form of play or game, where it is pretended that mathematics is useful in real life in a way that it is not. With Pfaller I argue that play can take hold of the imagination of the players, infusing everyday life with meaning borrowed from the imagery of the play and that these effects are more powerful when the play is forced and takes an institutionalized form. I show that mathematics education does in fact have these characteristics, including sophisticated mechanisms for translating in-game performance (test scores) to real-life goods (grades and exams). A central theme of the article is the perceived discrepancy between mathematics education as it is, and how it supposedly could and should be in light of the properties of mathematics. The analysis implies that this gap actually is an effect of play and thus an inherent property of mathematics education itself.
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| 46. |
- Lundin, Sverker, et al.
(författare)
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Hierarchical molecular tagging to resolve long continuous sequences by massively parallel sequencing
- 2013
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 3, s. 1186-
-
Tidskriftsartikel (refereegranskat)abstract
- Here we demonstrate the use of short-read massive sequencing systems to in effect achieve longer read lengths through hierarchical molecular tagging. We show how indexed and PCR-amplified targeted libraries are degraded, sub-sampled and arrested at timed intervals to achieve pools of differing average length, each of which is indexed with a new tag. By this process, indices of sample origin, molecular origin, and degree of degradation is incorporated in order to achieve a nested hierarchical structure, later to be utilized in the data processing to order the reads over a longer distance than the sequencing system originally allows. With this protocol we show how continuous regions beyond 3000 bp can be decoded by an Illumina sequencing system, and we illustrate the potential applications by calling variants of the lambda genome, analysing TP53 in cancer cell lines, and targeting a variable canine mitochondrial region.
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| 47. |
- Lundin, Sverker, et al.
(författare)
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Increased Throughput by Parallelization of Library Preparation for Massive Sequencing
- 2010
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 5:3, s. e10029-
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Tidskriftsartikel (refereegranskat)abstract
- Background: Massively parallel sequencing systems continue to improve on data output, while leaving labor-intensive library preparations a potential bottleneck. Efforts are currently under way to relieve the crucial and time-consuming work to prepare DNA for high-throughput sequencing. Methodology/Principal Findings: In this study, we demonstrate an automated parallel library preparation protocol using generic carboxylic acid-coated superparamagnetic beads and polyethylene glycol precipitation as a reproducible and flexible method for DNA fragment length separation. With this approach the library preparation for DNA sequencing can easily be adjusted to a desired fragment length. The automated protocol, here demonstrated using the GS FLX Titanium instrument, was compared to the standard manual library preparation, showing higher yield, throughput and great reproducibility. In addition, 12 libraries were prepared and uniquely tagged in parallel, and the distribution of sequence reads between these indexed samples could be improved using quantitative PCR-assisted pooling. Conclusions/Significance: We present a novel automated procedure that makes it possible to prepare 36 indexed libraries per person and day, which can be increased to up to 96 libraries processed simultaneously. The yield, speed and robust performance of the protocol constitute a substantial improvement to present manual methods, without the need of extensive equipment investments. The described procedure enables a considerable efficiency increase for small to midsize sequencing centers.
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- Lundin, Sverker, 1975
(författare)
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Läs våra föregångares debatt i Skolmatematiskt arkiv
- 2012
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Ingår i: Nämnaren. - 0348-2723. ; :1, s. 3-11
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Ett historiskt perspektiv på undervisning kan ge oss en djupare förståelse för vår roll som lärare. De frågor som diskuteras idag, däribland lärobokens roll, förståelse kontra färdighet och den grundläggande räkneundervisningen, har lärare diskuterat under lång tid. Möjligheten att få insikt i våra föregångares diskussioner har ökat, då vi nu kan läsa texter från den svenska skolmatematikens historia på nätet. I Skolmatematiskt arkiv, förkortat SMA, ligger drygt 700 dokument från mitten av 1800-talet och framåt.
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