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| 2. |
- Andersson, Erik, et al.
(author)
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Ambio fit for the 2020s
- 2022
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In: Ambio. - : Springer Nature. - 0044-7447 .- 1654-7209. ; 51:5, s. 1091-1093
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Journal article (peer-reviewed)
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| 3. |
- Anistratov, Pavel, 1990, et al.
(author)
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Dynamics-Based Optimal Motion Planning of Multiple Lane Changes using Segmentation
- 2022
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In: IFAC-PapersOnLine. - : Elsevier BV. - 2405-8963 .- 2405-8963. ; 55:24, s. 233-240
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Conference paper (peer-reviewed)abstract
- Avoidance maneuvers at normal driving speed or higher are demanding driving situations that force the vehicle to the limit of tire-road friction in critical situations. To study and develop control for these situations, dynamic optimization has been in growing use in research. One idea to handle such optimization computations effectively is to divide the total maneuver into a sequence of sub-maneuvers and to associate a segmented optimization problem to each sub-maneuver. Here, the alternating augmented Lagrangian method is adopted, which like many other optimization methods benefits strongly from a good initialization, and to that purpose a method with motion candidates is proposed to get an initially feasible motion. The two main contributions are, firstly, the method for computing an initially feasible motion that is found to use obstacle positions and progress of vehicle variables to its advantage, and secondly, the integration with a subsequent step with segmented optimization showing clear improvements in paths and trajectories. Overall, the combined method is able to handle driving scenarios at demanding speeds.
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| 4. |
- Antonelli, Alexandre, 1978, et al.
(author)
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Embracing heterogeneity: Coalescing the tree of life and the future of phylogenomics
- 2019
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In: PeerJ. - : PeerJ. - 2167-8359. ; 2019:2
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Journal article (peer-reviewed)abstract
- Building the Tree of Life (ToL) is a major challenge of modern biology, requiring advances in cyberinfrastructure, data collection, theory, and more. Here, we argue that phylogenomics stands to benefit by embracing the many heterogeneous genomic signals emerging from the first decade of large-scale phylogenetic analysis spawned by high-throughput sequencing (HTS). Such signals include those most commonly encountered in phylogenomic datasets, such as incomplete lineage sorting, but also those reticulate processes emerging with greater frequency, such as recombination and introgression. Here we focus specifically on how phylogenetic methods can accommodate the heterogeneity incurred by such population genetic processes; we do not discuss phylogenetic methods that ignore such processes, such as concatenation or supermatrix approaches or supertrees. We suggest that methods of data acquisition and the types of markers used in phylogenomics will remain restricted until a posteriori methods of marker choice are made possible with routine whole-genome sequencing of taxa of interest. We discuss limitations and potential extensions of a model supporting innovation in phylogenomics today, the multispecies coalescent model (MSC). Macroevolutionary models that use phylogenies, such as character mapping, often ignore the heterogeneity on which building phylogenies increasingly rely and suggest that assimilating such heterogeneity is an important goal moving forward. Finally, we argue that an integrative cyberinfrastructure linking all steps of the process of building the ToL, from specimen acquisition in the field to publication and tracking of phylogenomic data, as well as a culture that values contributors at each step, are essential for progress.
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| 6. |
- Benson, Mikael, 1954, et al.
(author)
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Connectivity can be used to identify key genes in DNA microarray data: a study based on gene expression in nasal polyps before and after treatment with glucocorticoids
- 2007
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In: Acta Oto-Laryngologica. - : Informa UK Limited. - 1651-2251 .- 0001-6489. ; 127:10, s. 1074-1079
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Journal article (peer-reviewed)abstract
- Conclusions. The presented analysis of nasal polyposis using connectivity based on the PubGene literature co-citation network demonstrates that this tool can be used to identify key genes in DNA microarray studies of human polygenic diseases. Objectives. DNA microarray studies of complex diseases may reveal differential expression of hundreds of genes. According to network theory and studies of yeast cells, genes that are connected with several other genes appear to have key regulatory roles. This study aimed to examine if this principle can be translated to DNA microarray studies of human disease, using nasal polyposis as a base for the analysis. Materials and methods. The connectivity of differentially expressed genes from a previously described microarray study of nasal polyposis before and after treatment with glucocorticoids was determined. This was done using the literature co-citation network PubGene. Results. In all, 166 genes were differentially expressed; 39 of these were previously defined as inflammatory and considered important for nasal polyposis. The connectivity of all differentially expressed genes was analysed using the PubGene literature co-citation network. Seventy-four of the 166 genes were connected to other genes. By contrast, the average number of connected genes among 100 sets of 166 randomly chosen genes was 31.5. A small number of the differentially expressed genes were highly connected, while most genes had few or no connections. This indicated a scale-free network. The most connected gene was interleukin-8, an inflammatory gene of known importance for nasal polyposis. Twenty-eight of the 74 connected genes were inflammatory (38%), compared with 11 of the 92 unconnected genes (12%), p < 0.0001. Since most evidence suggests that nasal polyps are inflammatory in their nature, this supports the hypothesis that connected genes have more disease relevance than unconnected genes.
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| 7. |
- Benson, Mikael, 1954, et al.
(author)
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Gene profiling reveals increased expression of uteroglobin and other anti-inflammatory genes in glucocorticoid-treated nasal polyps.
- 2004
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In: Journal of Allergy and Clinical Immunology. - : Elsevier BV. - 0091-6749 .- 1097-6825. ; 113:6, s. 1137-43
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Journal article (peer-reviewed)abstract
- BACKGROUND: Treatment with local glucocorticoids (GCs) decreases symptoms and the size of nasal polyps. This might depend on the downregulation of proinflammatory genes, as well as the upregulation of anti-inflammatory genes. OBJECTIVE: We sought to identify GC-regulated anti-inflammatory genes in nasal polyps. METHODS: Affymetrix DNA microarrays were used to analyze the expression of 22,283 genes in 4 nasal polyps before and after local treatment with fluticasone (400 microg/d). Expression of uteroglobin and mammaglobin B was analyzed with real-time PCR in 6 nasal polyps and in nasal biopsy specimens from 6 healthy control subjects. RESULTS: Two hundred three genes had changed in expression in treated polyps, and 139 had known functions: 54 genes were downregulated, and 85 were upregulated. Genes associated with inflammation constituted the largest single functional group. These genes affected key steps in inflammation (eg, immunoglobulin production; antigen processing and presentation; and the chemoattraction and activation of granulocytes, T cells, and B cells). Several proinflammatory genes were downregulated. In contrast, some anti-inflammatory genes were upregulated. The gene that increased most in terms of expression was uteroglobin. This was confirmed with real-time PCR. By contrast, expression of uteroglobin was lower in untreated polyps than in healthy nasal mucosa. Immunohistochemical investigation showed staining of uteroglobin in the epithelium and in seromucous glands in control subjects and in nasal polyps. CONCLUSION: Upregulation of anti-inflammatory genes, such as uteroglobin, might contribute to the effects of local treatment with GCs in nasal polyps.
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| 9. |
- Bergek, Anna, et al.
(author)
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Analyzing the functional dynamics of technological innovation systems : A scheme of analysis
- 2008
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In: Research Policy. - : Elsevier BV. - 0048-7333 .- 1873-7625. ; 37:3, s. 407-429
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Journal article (peer-reviewed)abstract
- Various researchers and policy analysts have made empirical studies of innovation systems in order to understand their current structure and trace their dynamics. However, policy makers often experience difficulties in extracting practical guidelines from studies of this kind. In this paper, we operationalize our previous work on a functional approach to analyzing innovation system dynamics into a practical scheme of analysis for policy makers. The scheme is based on previous literature and our own experience in developing and applying functional thinking. It can be used by policy makers not only to identify the key policy issues but also to set policy goals. © 2007 Elsevier B.V. All rights reserved.
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| 10. |
- Berndes, Göran, 1966, et al.
(author)
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Multifunctional biomass production systems - an overview with presentation of specific applications in India and Sweden
- 2008
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In: Biofuels, Bioproducts and Biorefining. - : Wiley. - 1932-104X .- 1932-1031. ; 2:1, s. 16-25
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Journal article (peer-reviewed)abstract
- This perspective discusses multi-functional biomass production systems, which are located, designed, integrated and managed so as to provide specific environmental services, in addition to biomass supply. Besides discussing the general concept and outlining a range of different possible applications, we present in somewhat more detail specific applications of such systems for the cases of Sweden and India. The overall conclusion is that the environmental benefits from a large-scale establishment of multi-functional biomass production systems could be substantial. Given that suitable mechanisms to put a premium on the provided environmental services can be identified and implemented, additional revenues can be linked to biomass production systems and this could enhance the socioeconomic attractiveness and significantly improve the competitiveness of the produced biomass on the market. The provision of additional environmental services also contributes to local sustainable development, which is in many cases a prerequisite for local support for the production systems.
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