| 1. |
- Grüning, Björn, et al.
(författare)
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Bioconda: A sustainable and comprehensive software distribution for the life sciences
- 2017
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- We present Bioconda (https://bioconda.github.io), a distribution of bioinformatics software for the lightweight, multi-platform and language-agnostic package manager Conda. Currently, Bioconda offers a collection of over 3000 software packages, which is continuously maintained, updated, and extended by a growing global community of more than 200 contributors. Bioconda improves analysis reproducibility by allowing users to define isolated environments with defined software versions, all of which are easily installed and managed without administrative privileges.
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| 6. |
- Hjalmarson, Emil, et al.
(författare)
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Design space exploration and trade-offs in analog amplifier design
- 2003
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Ingår i: Integrated Circuit and System Design. Power and Timing Modeling, Optimization and Simulation. - Berlin, Heidelberg : Springer Berlin/Heidelberg. - 3540200746 - 9783540200741 - 9783540397625 ; , s. 338-347
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Konferensbidrag (refereegranskat)abstract
- In this paper, we discuss an optimization-based approach for design space exploration to find limitations and possible trade-offs between performance metrics in analog circuits. The exploration guides the designer when making design decisions. For the design space exploration, which is expensive in terms of computation time, we use an optimization-based device sizing tool that runs concurrent optimization tasks on a network of workstations. The tool enables efficient and accurate exploration of the available design space. As a design example, we investigate three operational transconductance amplifiers, OTAs, implemented in a standard 0.35-mum CMOS process. This example shows that large savings in terms of chip area and power consumption can be made by selecting the most suitable circuit.
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| 10. |
- Hägglund, Emil
(författare)
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Evolution of biological systems linked to complex cell architectures in Planctomycetota
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The eukaryotic cells have a nucleus and membrane-enclosed organelles for functions such as energy production, whereas the prokaryotic cells have a cell wall but no intracellular membrane-bound structures. Species of the Planctomycetota phylum are classified as bacteria but have diverse and complex cell architectures. For example, members of the Gemmataceae have highly invaginated cytoplasmic membranes, the anammox bacteria have a membrane-bound organelle for energy production, and one species, “Candidatus Uabimicrobium amorphum”, can form digestive vacuoles during phagocytotic-like engulfment of other cells.In this thesis, we have performed comparative genomics and evolutionary analyses of bacteria in the Planctomycetota to learn more about the evolution of cellular complexity. The thesis also presents a new workflow to facilitate the assembly of datasets for comparative and evolutionary analysis of prokaryotic species.Comparative analyses of several novel genomes in the Gemmatacea family showed that new protein families have evolved by massive paralogization and fusion of prokaryotic-like domains with eukaryotic-like domains. The analyses showed no strict boundary between prokaryotic and eukaryotic genomes regarding gene lengths, gene paralogy and protein domain composition patterns.Analysis of the “Candidatus Uabimicrobium amorphum” genome revealed an extreme expansion of genes for serine/threonine protein kinases, possibly related to the predatory lifestyle of this species. However, the associated domains differed from those of serine/threonine protein kinases in eukaryotes, suggesting that the expansion and diversification process has occurred independently in eukaryotes and Planctomycetota.Evolutionary studies of the enzymes in the anammox pathway showed that the central enzyme, hydrazine synthase, previously of unknown origin, has homologs in other bacteria, including other members of the Planctomycetota. However, the homologs lacked key residues involved in the formation of hydrazine, suggesting that the anammox reaction has only originated once. Other enzymes in this pathway have been acquired by horizontal gene transfer events followed by duplication and divergence. Further, by studying the evolution of the heme biosynthesis pathway in this phylum, we show that this pathway has been replaced in the anammox bacteria with a strictly anaerobic pathway following horizontal gene transfers from archaea and other bacteria.Thus, although members of the Planctomycetota share many traits with eukaryotes, such as the same types of protein domains and similarities in cellular structures, our analyses show that these features have independent origins and reflect convergent evolution. The results have implications for our understanding of the origin of cellular complexity.
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| 12. |
- Hägglund, Emil, et al.
(författare)
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TADA : Taxonomy-Aware Dataset Aggregator
- 2023
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Ingår i: Bioinformatics. - : Oxford University Press. - 1367-4803 .- 1367-4811. ; 39:12
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Tidskriftsartikel (refereegranskat)abstract
- The profusion of sequenced genomes across the bacterial and archeal domains offers unprecedented possibilities for phylogenetic and comparative genomic analyses. In general, phylogenetic reconstruction is improved by the use of more data. However, including all available data is (i) not computationally tractable, and (ii) prone to biases, as the abundance of genomes is very unequally distributed over the biological diversity. Thus, in most cases, subsampling taxa to build a phylogeny is necessary. Currently, though, there is no available software to perform that handily. Here we present TADA, a taxonomic-aware dataset selection workflow that allows sampling across user-defined portions of the prokaryotic diversity with variable granularity, while setting constraints on genome quality and balance between branches.
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| 20. |
- Mahajan, Mayank, et al.
(författare)
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Paralogization and New Protein Architectures in Planctomycetes Bacteria with Complex Cell Structures
- 2020
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Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 37:4, s. 1020-1040
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Tidskriftsartikel (refereegranskat)abstract
- Bacteria of the phylum Planctomycetes have a unique cell plan with an elaborate intracellular membrane system, thereby resembling eukaryotic cells. The origin and evolution of these remarkable features is debated. To study the evolutionary genomics of bacteria with complex cell architectures, we have re-sequenced the 9.2 Mb genome of the model organism Gemmata obscuriglobus and sequenced the 10 Mb genome of Gemmata massiliana Soil9, the 7.9 Mb genome of Cjuql4 and the 6.7 Mb genome of Tuwongella immobilis, all of which belong to the family Gemmataceae. A gene flux analysis of the Planctomycetes revealed a massive emergence of novel protein families at multiple nodes within the Gemmataceae. The expanded protein families have unique multi-domain architectures composed of domains that are characteristic of prokaryotes, such as the sigma factor domain of extracytoplasmic sigma factors, and domains that have proliferated in eukaryotes, such as the WD40, LRR, TPR and Ser/Thr kinase domains. Proteins with identifiable domains in the Gemmataceae have longer lengths and linkers than proteins in most other bacteria, and the analyses suggest that these traits were ancestrally present in the Planctomycetales. A broad comparison of protein length distribution profiles revealed an overlap between the longest proteins in prokaryotes and the shortest proteins in eukaryotes. We conclude that the many similarities between proteins in the Planctomycetales and the eukaryotes are due to convergent evolution and that there is no strict boundary between prokaryotes and eukaryotes with regard to features such as gene paralogy, protein length and protein domain composition patterns.
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| 21. |
- Odelgard, Anna, et al.
(författare)
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Phylogeny and Expansion of Serine/Threonine Kinases in Phagocytotic Bacteria in the Phylum Planctomycetota
- 2024
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Ingår i: Genome Biology and Evolution. - : Oxford University Press. - 1759-6653. ; 16:4
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Tidskriftsartikel (refereegranskat)abstract
- The recently isolated bacterium "Candidatus Uabimicrobium amorphum" is the only known prokaryote that can engulf other bacterial cells. Its proteome contains a high fraction of proteins involved in signal transduction systems, which is a feature normally associated with multicellularity in eukaryotes. Here, we present a protein-based phylogeny which shows that "Ca. Uabimicrobium amorphum" represents an early diverging lineage that clusters with the Saltatorellus clade within the phylum Planctomycetota. A gene flux analysis indicated a gain of 126 protein families for signal transduction functions in "Ca. Uabimicrobium amorphum", of which 66 families contained eukaryotic-like Serine/Threonine kinases with Pkinase domains. In total, we predicted 525 functional Serine/Threonine kinases in "Ca. Uabimicrobium amorphum", which represent 8% of the proteome and is the highest fraction of Serine/Threonine kinases in a bacterial proteome. The majority of Serine/Threonine kinases in this species are membrane proteins and 30% contain long, tandem arrays of WD40 or TPR domains. The pKinase domain was predicted to be located in the cytoplasm, while the WD40 and TPR domains were predicted to be located in the periplasm. Such domain combinations were also identified in the Serine/Threonine kinases of other species in the Planctomycetota, although in much lower abundances. A phylogenetic analysis of the Serine/Threonine kinases in the Planctomycetota inferred from the Pkinase domain alone provided support for lineage-specific expansions of the Serine/Threonine kinases in "Ca. Uabimicrobium amorphum". The results imply that expansions of eukaryotic-like signal transduction systems are not restricted to multicellular organisms, but have occurred in parallel in prokaryotes with predatory lifestyles and phagocytotic-like behaviors.
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| 22. |
- Sundström, Emil, et al.
(författare)
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Reference Implementation of the PID Controller
- 2024
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Ingår i: IFAC Proceedings Volumes (IFAC-PapersOnline). - 2405-8963.
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Tidskriftsartikel (refereegranskat)abstract
- The PID controller is the by far most frequently employed type of controller. As you read, billions of digitally implemented PID controllers are running, shaping the dynamic behavior of anything from the fan speed in your laptop to safety-critical components in nuclear power plants. Given the abundance of commissioned PID controllers, it is surprisingly hard to find a single source that provides a well-documented, and motivated reference implementation of the PID controller in text-based code. This work provides one. We use the incremental (velocity) form, motivated by its intrinsic integrator anti-windup and bumpless transfer behavior. In addition, we discuss our implementation in terms of measurement filtering, setpoint handling, and runtime environment, among other implementation aspects. Our reference implementation is a living “document”, and a link to a GitHub repository hosting the latest version is provided.
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| 23. |
- Ögmundsdóttir Michelsen, Halldóra, et al.
(författare)
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The effect of audit and feedback and implementation support on guideline adherence and patient outcomes in cardiac rehabilitation : a study protocol for an open-label cluster-randomized effectiveness-implementation hybrid trial
- 2024
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Ingår i: Implementation Science. - : BioMed Central (BMC). - 1748-5908. ; 19:1
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundProviding secondary prevention through structured and comprehensive cardiac rehabilitation programmes to patients after a myocardial infarction (MI) reduces mortality and morbidity and improves health-related quality of life. Cardiac rehabilitation has the highest recommendation in current guidelines. While treatment target attainment rates at Swedish cardiac rehabilitation centres is among the highest in Europe, there are considerable differences in service delivery and variations in patient-level outcomes between centres. In this trial, we aim to study whether centre-level guideline adherence and patient-level outcomes across Swedish cardiac rehabilitation centres can be improved through a) regular audit and feedback of cardiac rehabilitation structure and processes through a national quality registry and b) supporting cardiac rehabilitation centres in implementing guidelines on secondary prevention. Furthermore, we aim to evaluate the implementation process and costs.MethodsThe study is an open-label cluster-randomized effectiveness-implementation hybrid trial including all 78 cardiac rehabilitation centres (attending to approximately 10 000 MI patients/year) that report to the SWEDEHEART registry. The centres will be randomized 1:1:1 to three clusters: 1) reporting cardiac rehabilitation structure and process variables to SWEDEHEART every six months (audit intervention) and being offered implementation support to implement guidelines on secondary prevention (implementation support intervention); 2) audit intervention only; or 3) no intervention offered. Baseline cardiac rehabilitation structure and process variables will be collected. The primary outcome is an adherence score measuring centre-level adherence to secondary prevention guidelines. Secondary outcomes include patient-level secondary prevention risk factor goal attainment at one-year after MI and major adverse coronary outcomes for up to five-years post-MI. Implementation outcomes include barriers and facilitators to guideline adherence evaluated using semi-structured focus-group interviews and relevant questionnaires, as well as costs and cost-effectiveness assessed by a comparative health economic evaluation.DiscussionOptimizing cardiac rehabilitation centres’ delivery of services to meet standards set in guidelines may lead to improvement in cardiovascular risk factors, including lifestyle factors, and ultimately a decrease in morbidity and mortality after MI.
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| 24. |
- Öhrman, Caroline, et al.
(författare)
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Reorganized Genomic Taxonomy of Francisellaceae Enables Design of Robust Environmental PCR Assays for Detection of Francisella tularensis
- 2021
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Ingår i: Microorganisms. - : MDPI. - 2076-2607. ; 9:1
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Tidskriftsartikel (refereegranskat)abstract
- In recent years, an increasing diversity of species has been recognized within the family Francisellaceae. Unfortunately, novel isolates are sometimes misnamed in initial publications or multiple sources propose different nomenclature for genetically highly similar isolates. Thus, unstructured and occasionally incorrect information can lead to confusion in the scientific community. Historically, detection of Francisella tularensis in environmental samples has been challenging due to the considerable and unknown genetic diversity within the family, which can result in false positive results. We have assembled a comprehensive collection of genome sequences representing most known Francisellaceae species/strains and restructured them according to a taxonomy that is based on phylogenetic structure. From this structured dataset, we identified a small number of genomic regions unique to F. tularensis that are putatively suitable for specific detection of this pathogen in environmental samples. We designed and validated specific PCR assays based on these genetic regions that can be used for the detection of F. tularensis in environmental samples, such as water and air filters.
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