| 1. |
- 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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| 2. |
- 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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| 3. |
- 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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| 4. |
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| 5. |
- 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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| 6. |
- Björnsson, Bergthor, et al.
(author)
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Digital twins to personalize medicine
- 2020
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In: Genome Medicine. - : Springer Science and Business Media LLC. - 1756-994X. ; 12:1
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Research review (peer-reviewed)abstract
- Personalized medicine requires the integration and processing of vast amounts of data. Here, we propose a solution to this challenge that is based on constructing Digital Twins. These are high-resolution models of individual patients that are computationally treated with thousands of drugs to find the drug that is optimal for the patient.
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| 7. |
- Djerf, Pauline, et al.
(author)
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Validation of the paracetamol absorption test for measuring gastric tube emptying in esophagectomized patients versus gold standard scintigraphy
- 2015
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In: Scandinavian Journal of Gastroenterology. - : TAYLOR and FRANCIS LTD. - 0036-5521 .- 1502-7708. ; 50:11, s. 1339-1347
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Journal article (peer-reviewed)abstract
- Objective. Scintigraphy is the gold standard for objective measurement of delayed gastric tube emptying after esophagectomy. The aim of this pilot study is to validate, by reference to scintigraphy, the paracetamol absorption test for measuring gastric tube emptying in esophagectomized patients. Material and methods. The paracetamol absorption test and scintigraphy were performed simultaneously in 13 patients who had undergone an esophagectomy with gastric tube reconstruction. Emptying was calculated for both methods and compared. Post-esophagectomy symptoms and quality of life (QoL) were assessed by European Organization on Research and Treatment of Cancer questionnaires. Results. Mean time to 50% emptying was 17 min measured with the paracetamol absorption test and 23 min with scintigraphy. For time to 25% emptying, Bland-Altman calculation gave a bias of 1.6 min and 95% limits of agreement (LoA) of -6.3 to 9.5 min. For time to 50% emptying, there was one outlier resulting in a bias of -6.33 min and 95% LoA of -36.4 to 23.8 min. For time to 75% emptying, bias was -11.6 min and 95% LoA of -38.5 to 15.4 min. Post-esophagectomy symptoms were similar to those reported previously, and QoL was comparable to the general Swedish population. Conclusions. There was reasonably close correlation between the paracetamol absorption test and scintigraphy for time to 25% and 50% emptying, except for one outlier. For time to 75% emptying the methods were in less accordance. The results indicate that the paracetamol absorption test may be a useful screening tool for identifying delayed gastric tube emptying in this patient group.
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| 8. |
- Elf, Mikael, 1959, et al.
(author)
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Young carers as co-designers of a web-based support system - the views of two publics
- 2012
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In: Informatics for Health and Social Care. - : Informa UK Limited. - 1753-8157 .- 1753-8165. ; 37:4, s. 203-216
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Journal article (peer-reviewed)abstract
- Aim: The aim of the study was to reveal young carers’ views of design of a web-based support system (WBSS) directed to them and the differences between their views and the views of project representatives (PRs), in a participatory design process. Methods: Eight young people, 17–24 years, were involved in either a work or a test group. The work group participated in video-recorded design meetings with representatives of the project. Content analysis and Dewey’s concept of public were applied on the data. The test group worked from their homes and data were collected via test forms and used as supplemental data. Results: Four themes were revealed, constituting key parts in the design of the WBSS: Communicating the message, Ideational working principles, User interaction and User interface. Furthermore, decisive differences between the views of participants and PRs were found. Conclusion: The four key parts should be considered in a WBSS directed to young carers. The study also suggests that early user involvement and critical reflection in the design process itself may be crucial to discern differences in perspective between designers and users.
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| 9. |
- Fagman, Erika, et al.
(author)
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High-quality annotations for deep learning enabled plaque analysis in SCAPIS cardiac computed tomography angiography
- 2023
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In: Heliyon. - : Elsevier BV. - 2405-8440. ; 9:5
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Journal article (peer-reviewed)abstract
- Background: Plaque analysis with coronary computed tomography angiography (CCTA) is a promising tool to identify high risk of future coronary events. The analysis process is time-consuming, and requires highly trained readers. Deep learning models have proved to excel at similar tasks, however, training these models requires large sets of expert-annotated training data. The aims of this study were to generate a large, high-quality annotated CCTA dataset derived from Swedish CArdioPulmonary BioImage Study (SCAPIS), report the reproducibility of the annotation core lab and describe the plaque characteristics and their association with established risk factors.Methods and results: The coronary artery tree was manually segmented using semi-automatic software by four primary and one senior secondary reader. A randomly selected sample of 469 subjects, all with coronary plaques and stratified for cardiovascular risk using the Systematic Coronary Risk Evaluation (SCORE), were analyzed. The reproducibility study (n = 78) showed an agreement for plaque detection of 0.91 (0.84-0.97). The mean percentage difference for plaque volumes was-0.6% the mean absolute percentage difference 19.4% (CV 13.7%, ICC 0.94). There was a positive correlation between SCORE and total plaque volume (rho = 0.30, p < 0.001) and total low attenuation plaque volume (rho = 0.29, p < 0.001).Conclusions: We have generated a CCTA dataset with high-quality plaque annotations showing good reproducibility and an expected correlation between plaque features and cardiovascular risk. The stratified data sampling has enriched high-risk plaques making the data well suited as training, validation and test data for a fully automatic analysis tool based on deep learning.
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| 10. |
- Fritzsche, Michael, et al.
(author)
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A Highly UV-transparent Fused Silica Biochip for Sensitive Hepatotoxicity Testing by Autofluorescence
- 2014
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In: Biochip Journal. - : Springer Science and Business Media LLC. - 2092-7843 .- 1976-0280. ; 8:2, s. 115-121
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Journal article (peer-reviewed)abstract
- Fabrication and application of a non-fluorescent and UV-transparent microfluidic biochip in fused silica that allows sensitive autofluorescence detection are described. The biochip is particularly useful in cell-based assays where the most informative autofluorescence signals from the cells reside in the ultraviolet spectral range and where plastic labware materials commonly used in cell culture work severely disturb such measurements. In this study the fused silica biochip was used for measuring intrinsic autofluorescence from liver cells in order to assess hepatotoxic effects of drugs. The assessment assay was carried out with the human liver cell line HepG2 under perfusion conditions in the microfluidics of the biochip. The autofluorescence from the.liver cells exposed to quinidine was readily recorded without background disturbance and correlated well with reference toxicity data.
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