| 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. |
- Buckland, Philip I., et al.
(författare)
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Integrating human dimensions of Arctic palaeoenvironmental science : SEAD – the strategic environmental archaeology database
- 2011
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Ingår i: Journal of Archaeological Science. - : Elsevier. - 0305-4403 .- 1095-9238. ; 38:2, s. 345-351
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Tidskriftsartikel (refereegranskat)abstract
- Environmental change has a human dimension, and has had so for at least the last 10 000 years. The prehistoric impact of people on the Arctic landscape has occasionally left visible traces, such as house and field structures. More often than not, however, the only evidence available is at the microscopic or geochemical level, such as fossil insect and seed assemblages or changes in the physical and chemical properties of soils and sediments. These records are the subject of SEAD, a multidisciplinary database and software project currently underway at Umeå University, Sweden, which aims to create an online database and set of tools for investigating these traces, as part of an international research infrastructure for palaeoecology and environmental archaeology.
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| 3. |
- Brindefalk, Björn, et al.
(författare)
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A Phylometagenomic Exploration of Oceanic Alphaproteobacteria Reveals Mitochondrial Relatives Unrelated to the SAR11 Clade
- 2011
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 6:9, s. e24457-
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Tidskriftsartikel (refereegranskat)abstract
- Background: According to the endosymbiont hypothesis, the mitochondrial system for aerobic respiration was derived from an ancestral Alphaproteobacterium. Phylogenetic studies indicate that the mitochondrial ancestor is most closely related to the Rickettsiales. Recently, it was suggested that Candidatus Pelagibacter ubique, a member of the SAR11 clade that is highly abundant in the oceans, is a sister taxon to the mitochondrial-Rickettsiales clade. The availability of ocean metagenome data substantially increases the sampling of Alphaproteobacteria inhabiting the oxygen-containing waters of the oceans that likely resemble the originating environment of mitochondria. Methodology/Principal Findings: We present a phylogenetic study of the origin of mitochondria that incorporates metagenome data from the Global Ocean Sampling (GOS) expedition. We identify mitochondrially related sequences in the GOS dataset that represent a rare group of Alphaproteobacteria, designated OMAC (Oceanic Mitochondria Affiliated Clade) as the closest free-living relatives to mitochondria in the oceans. In addition, our analyses reject the hypothesis that the mitochondrial system for aerobic respiration is affiliated with that of the SAR11 clade. Conclusions/Significance: Our results allude to the existence of an alphaproteobacterial clade in the oxygen-rich surface waters of the oceans that represents the closest free-living relative to mitochondria identified thus far. In addition, our findings underscore the importance of expanding the taxonomic diversity in phylogenetic analyses beyond that represented by cultivated bacteria to study the origin of mitochondria.
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| 4. |
- Brindefalk, Björn, 1977-, et al.
(författare)
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Lost and Found at Sea: a Phylomentagenomic Exploration of Mitochondrial Affiliations with Oceanic Bacteria.
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Background According to the endosymbiont hypothesis, the mitochondrial system for aerobic respiration was derived from a free-living bacterium related to present-day alpha-proteobacteria. Recent studies have identified two lineages as the closest mitochondrial relatives among bacteria with sequenced genomes; the Rickettsiales, a lineage comprising obligate intracellular pathogens, and Pelagibacter ubique, a member of the SAR11 clade that is highly abundant in the upper surface waters of the global oceans. Principal Findings Here, we present a phylogenetic study incorporating metagenomic data of mitochondrial genes for aerobic respiration that includes sequence data from the Global Ocean Sampling (GOS) Expedition, thereby increasing the sampling of alpha-proteobacterial sequences available for analysis greatly. Phylogenetic analysis of these expanded datasets including oceanic sequences that had been pruned down in numbers but still maintained the full genetic diversity present failed to show an increased support for a specific mitochondrial affiliation to any alpha-proteobacterial group, although concatenated datasets of different genes gave good support for conflicting mitochondrial placement. We utilized a jack-knifing method to randomly sample sequences from the GOS dataset and examined how the inclusion of such sequences influenced the support for mitochondrial affiliation in trees inferred from proteins in aerobic respiration. No evidence of an increased support for a specific mitochondrial placement in the alpha-proteobacterial tree in the jack-knifing analysis was obtained. A systematic search for sequences affiliated with mitochondria in the GOS dataset suggests the existence of previously unidentified clades of deeply diverging alpha-proteobacteria, with an unclear affiliation. Conclusions/Significance Our findings have several important implications. First, they support an early divergence of the mitochondrial ancestor from the alpha-proteobacterial lineage, possibly pre-dating the radiation of alpha-proteobacterial species with sequenced genomes. Second, they reject the hypothesis that the system for aerobic respiration in mitochondria is affiliated with the SAR11 clade. Third, they indicate horizontal transfer of genes for respiratory chain proteins in bacteria adapted to the upper surface waters of the oceans. Fourth, they show the presence of oceanic sequences for respiratory chain proteins that diverge as deeply as mitochondria in the alpha-proteobacterial phylogeny, possibly indicating a previously unidentified alpha-proteobacterial group at a basal position of the alpha-proteobacterial tree, underscoring the importance of expanding studies on mitochondrial origins beyond those of cultivated and intracellular bacteria. Finally, our study outlines a new methodology, phylometagenomics, which provides guidance on how to incorporate metagenome data into a phylogenetic framework for inferences of early evolutionary events.
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| 5. |
- Brindefalk, Björn, et al.
(författare)
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Origin and evolution of the mitochondrial aminoacyl-tRNA synthetases
- 2007
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Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 24:3, s. 743-756
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Tidskriftsartikel (refereegranskat)abstract
- Many theories favor a fusion of 2 prokaryotic genomes for the origin of the Eukaryotes, but there are disagreements on the origin, timing, and cellular structures of the cells involved. Equally controversial is the source of the nuclear genes for mitochondrial proteins, although the α-proteobacterial contribution to the mitochondrial genome is well established. Phylogenetic inferences show that the nuclearly encoded mitochondrial aminoacyl-tRNA synthetases (aaRSs) occupy a position in the tree that is not close to any of the currently sequenced α-proteobacterial genomes, despite cohesive and remarkably well-resolved α-proteobacterial clades in 12 of the 20 trees. Two or more α-proteobacterial clusters were observed in 8 cases, indicative of differential loss of paralogous genes or horizontal gene transfer. Replacement and retargeting events within the nuclear genomes of the Eukaryotes was indicated in 10 trees, 4 of which also show split α-proteobacterial groups. A majority of the mitochondrial aaRSs originate from within the bacterial domain, but none specifically from the α-Proteobacteria. For some aaRS, the endosymbiotic origin may have been erased by ongoing gene replacements on the bacterial as well as the eukaryotic side. For others that accurately resolve the α-proteobacterial divergence patterns, the lack of affiliation with mitochondria is more surprising. We hypothesize that the ancestral eukaryotic gene pool hosted primordial "bacterial-like" genes, to which a limited set of α-proteobacterial genes, mostly coding for components of the respiratory chain complexes, were added and selectively maintained.
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| 6. |
- Fritzson, Dag, et al.
(författare)
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Object-Oriented Mathematical Modelling – Applied to Machine Elements
- 1994
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Ingår i: Computers & structures. - : Elsevier. - 0045-7949 .- 1879-2243. ; 51:3, s. 241-253
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Tidskriftsartikel (refereegranskat)abstract
- Machine element analysis has a goal of describing function and other aspects of machine elements in a theoretical form. This paper shows how ideas from object-oriented modelling can be applied to machine element analysis. The models thus obtained are both easier to understand, better structured, and allow a higher degree of re-use than conventional models. An object-oriented model description is natural and suitable for machine element analysis. As a realistic example an equational model of rolling bearings is presented. The structure of the model is general, and applies to many types of rolling bearings. The model and one solution require approximately 200 + 200 equations. The model is extensible, e.g. simple submodels of detailed properties can be made more complex without altering the overall structure. The example model has been implemented in a language of our own design, ObjectMath (Object-oriented Mathematical language for scientific computing). Using ObjectMath, it is possible to model classes of equation objects, to support multiple and single inheritance of equations, to support composition of equations, and to solve systems of equations. Algebraic transformations can conveniently be done since ObjectMath models are translated into the Mathematica computer algebra language. When necessary, equations can be transformed to C++ code for efficient numerical solution. The re-use of equations through inheritance reduced the size of the model by a factor of two, compared to a direct representation of the model in the Mathematica computer algebra language.
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| 7. |
- Fritzson, Peter, et al.
(författare)
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High-level mathematical modeling and programming in Scientific Computing
- 1995
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Ingår i: IEEE Software. - : IEEE. - 0740-7459 .- 1937-4194. ; 12:4, s. 77-87
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Tidskriftsartikel (refereegranskat)abstract
- Scientific computing and advanced mechanical analysis demand high-level support for modeling and solving complex equations. To meet this need, the authors designed ObjectMath and applied it to real problems in machine-element analysis
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| 8. |
- Fritzson, Peter, et al.
(författare)
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Industrial Application of Object-Oriented Mathematical Modeling and Computer Algebra in Mechanical Analysis
- 1992
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Konferensbidrag (refereegranskat)abstract
- The past ten to fifteen years has seen active research in the area of automatically generating the code generator part of compilers from formal specifications. However, less work has been done on evaluating and applying these systems in an industrial setting. This paper attempts to fill this gap.Three systems for automatic generation of code generators are evaluated in this paper: CGSS, BEG and TWIG. CGSS is an older Graham-Glanville style system based on pattern matching through parsing, whereas BEG and TWIG are more recent systems based on tree pattern matching combined with dynamic programming. An industrial-strength code generator previously implemented for a special-purpose language using the CGSS system is described and compared in some detail to our new implementation based on the BEG system. Several problems of integrating local and global register allocation within automatically generated code generators are described, and some solutions proposed. We finally conclude that current technology of automatically generating code generators is viable in an industrial setting. However, further research needs to be done on the problem of properly integrating register allocation with instruction selection, when both are generated from declarative specifications.
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| 9. |
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| 10. |
- Fråne, Anna, et al.
(författare)
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Framtida avfallsmängder och avfallsbehandlingskapacitet
- 2017
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- SMED har på uppdrag av Naturvårdsverket uppskattat hur stor mängd avfall som förväntas uppkomma fram till 2030 baserat på prognos från Konjunkturinstitutet för 2035. SMED har även satt de förväntade avfallsmängderna i relation till befintlig och planerad avfallsbehandlingskapacitet i Sverige för samma period, och bedömt huruvida behandlingskapaciteten är tillräcklig för att ta hand om de avfallsmängder som förväntas uppkomma. Hur avfall kommer att behandlas i framtiden beror dels på vilka styrmedel som sätts in både nationellt och på EU-nivå, dels på hur marknaderna för avfall och för sekundära råvaror utvecklas.Storleksordningen på den sammanlagda deponikapaciteten i Sverige är svårbedömd. SMED uppskattar dock att återstående kapacitetet väl överstiger de avfallsmängder som deponeras idag och att det finns en återstående kapacitet som räcker längre än till 2030.SMED bedömer att kapaciteten för att använda avfall som bränsle fram till 2030 är tillräcklig för att täcka det svenska behovet förutsatt att befintlig kapacitet behålls. Idag byggs kapaciteten ut. Rötningskapaciteten kommer sannolikt, precis som idag, vara beroende av ekonomiska styrmedel för att nå lönsamhet. Idag sker dock en utbyggnad av rötningskapacitet, vilket är ett tecken på att branschen tror på en långsiktig lönsamhet.Marknadsförhållanden gör att materialåtervinning av svenskt aluminiumskrot, järn- och stålskrot samt returpapper sker både i Sverige och utomlands samtidigt som råvarorna både importeras och exporteras till och från Sverige. Handeln innebär en flexibilitet och att materialåtervinningen inte är beroende av att behandlingskapaciteten finns i just Sverige. Om mer avfall uppkommer i Sverige skulle det potentiellt kunna ersätta importerade mängder. Sverige har för tillfället inte tillräcklig kapacitet för att producera sekundär plastråvara av insamlade plastförpackningarna, export till Tyskland förekommer redan idag. Materialåtervinningskapaciteten för glasförpackningar kommer sannolikt fortsätta finnas i Sverige.
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