| 1. |
- Albrecht, Mario, et al.
(author)
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On Open Problems in Biological Network Visualization
- 2009
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In: Graph Drawing. - Berlin Heidelberg New York : Springer. - 9783642118043 ; , s. 256-267
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Book chapter (peer-reviewed)abstract
- Much of the data generated and analyzed in the life sciences can be interpreted and represented by networks or graphs. Network analysis and visualization methods help in investigating them, and many universal as well as special-purpose tools and libraries are available for this task. However, the two fields of graph drawing and network biology are still largely disconnected. Hence, visualization of biological networks does typically not apply state-of-the-art graph drawing techniques, and graph drawing tools do not respect the drawing conventions of the life science community.In this paper, we analyze some of the major problems arising in biological network visualization.We characterize these problems and formulate a series of open graph drawing problems. These use cases illustrate the need for efficient algorithms to present, explore, evaluate, and compare biological network data. For each use case, problems are discussed and possible solutions suggested.
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| 2. |
- Backer, Vibeke, et al.
(author)
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Clinical characteristics of the BREATHE cohort–a real-life study on patients with asthma and COPD
- 2020
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In: European clinical respiratory journal. - : Informa UK Limited. - 2001-8525. ; 7:1
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Journal article (peer-reviewed)abstract
- Background: The BREATHE study is a cross-sectional study of real-life patients with asthma and/or COPD in Denmark and Sweden aiming to increase the knowledge across severities and combinations of obstructive airway disease. Design: Patients with suspicion of asthma and/or COPD and healthy controls were invited to participate in the study and had a standard evaluation performed consisting of questionnaires, physical examination, FeNO and lung function, mannitol provocation test, allergy test, and collection of sputum and blood samples. A subgroup of patients and healthy controls had a bronchoscopy performed with a collection of airway samples. Results: The study population consisted of 1403 patients with obstructive airway disease (859 with asthma, 271 with COPD, 126 with concurrent asthma and COPD, 147 with other), and 89 healthy controls (smokers and non-smokers). Of patients with asthma, 54% had moderate-to-severe disease and 46% had mild disease. In patients with COPD, 82% had groups A and B, whereas 18% had groups C and D classified disease. Patients with asthma more frequently had childhood asthma, atopic dermatitis, and allergic rhinitis, compared to patients with COPD, asthma + COPD and Other, whereas FeNO levels were higher in patients with asthma and asthma + COPD compared to COPD and Other (18 ppb and 16 ppb vs 12.5 ppb and 14 ppb, p < 0.001). Patients with asthma, asthma + COPD and Other had higher sputum eosinophilia (1.5%, 1.5%, 1.2% vs 0.75%, respectively, p < 0.001) but lower sputum neutrophilia (39.3, 43.5%, 40.8% vs 66.8%, p < 0.001) compared to patients with COPD. Conclusions: The BREATHE study provides a unique database and biobank with clinical information and samples from 1403 real-life patients with asthma, COPD, and overlap representing different severities of the diseases. This research platform is highly relevant for disease phenotype- and biomarker studies aiming to describe a broad spectrum of obstructive airway diseases.
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| 3. |
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| 4. |
- Feldhahn, Niklas, et al.
(author)
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Activation-induced cytidine deaminase acts as a mutator in BCR-ABL1-transformed acute lymphoblastic leukemia cells
- 2007
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In: Journal of Experimental Medicine. - : Rockefeller University Press. - 0022-1007 .- 1540-9538. ; 204:5, s. 1157-1166
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Journal article (peer-reviewed)abstract
- The Philadelphia chromosome (Ph) encoding the oncogenic BCR-ABL1 kinase defines a subset of acute lymphoblastic leukemia (ALL) with a particularly unfavorable prognosis. ALL cells are derived from B cell precursors in most cases and typically carry rearranged immunoglobulin heavy chain (IGH) variable (V) region genes devoid of somatic mutations. Somatic hypermutation is restricted to mature germinal center B cells and depends on activation-induced cytidine deaminase (AID). Studying AID expression in 108 cases of ALL, we detected AID mRNA in 24 of 28 Ph(+) ALLs as compared with 6 of 80 Ph(-) ALLs. Forced expression of BCR-ABL1 in Ph(-) ALL cells and inhibition of the BCR-ABL1 kinase showed that aberrant expression of AID depends on BCR-ABL1 kinase activity. Consistent with aberrant AID expression in Ph(+) ALL, IGH V region genes and BCL6 were mutated in many Ph(+) but unmutated in most Ph(-) cases. In addition, AID introduced DNA single-strand breaks within the tumor suppressor gene CDKN2B in Ph(+) ALL cells, which was sensitive to BCR-ABL1 kinase inhibition and silencing of AID expression by RNA interference. These findings identify AID as a BCR-ABL1-induced mutator in Ph(+) ALL cells, which may be relevant with respect to the particularly unfavorable prognosis of this leukemia subset.
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| 5. |
- Feyer, Stefan P., et al.
(author)
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2D, 2.5D, or 3D? : An Exploratory Study on Multilayer Network Visualisations in Virtual Reality
- 2024
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In: IEEE Transactions on Visualization and Computer Graphics. - : IEEE. - 1077-2626 .- 1941-0506. ; 30:1, s. 469-479
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Journal article (peer-reviewed)abstract
- Relational information between different types of entities is often modelled by a multilayer network (MLN) - a network with subnetworks represented by layers. The layers of an MLN can be arranged in different ways in a visual representation, however, the impact of the arrangement on the readability of the network is an open question. Therefore, we studied this impact for several commonly occurring tasks related to MLN analysis. Additionally, layer arrangements with a dimensionality beyond 2D, which are common in this scenario, motivate the use of stereoscopic displays. We ran a human subject study utilising a Virtual Reality headset to evaluate 2D, 2.5D, and 3D layer arrangements. The study employs six analysis tasks that cover the spectrum of an MLN task taxonomy, from path finding and pattern identification to comparisons between and across layers. We found no clear overall winner. However, we explore the task-to-arrangement space and derive empirical-based recommendations on the effective use of 2D, 2.5D, and 3D layer arrangements for MLNs.
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| 6. |
- Happe, Anne-Kathrin, et al.
(author)
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Predatory arthropods in apple orchards across Europe : Responses to agricultural management, adjacent habitat, landscape composition and country
- 2019
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In: Agriculture, Ecosystems & Environment. - : Elsevier BV. - 0167-8809 .- 1873-2305. ; 273, s. 141-150
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Journal article (peer-reviewed)abstract
- Local agri-environmental schemes, including hedgerows, flowering strips, organic management, and a landscape rich in semi-natural habitat patches, are assumed to enhance the presence of beneficial arthropods and their contribution to biological control in fruit crops. We studied the influence of local factors (orchard management and adjacent habitats) and of landscape composition on the abundance and community composition of predatory arthropods in apple orchards in three European countries. To elucidate how local and landscape factors influence natural enemy effectiveness in apple production systems, we calculated community energy use as a proxy for the communities' predation potential based on biomass and metabolic rates of predatory arthropods. Predator communities were assessed by standardised beating samples taken from apple trees in 86 orchards in Germany, Spain and Sweden. Orchard management included integrated production (IP; i.e. the reduced and targeted application of synthetic agrochemicals), and organic management practices in all three countries. Predator communities differed between management types and countries. Several groups, including beetles (Coleoptera), predatory bugs (Heteroptera), flies (Diptera) and spiders (Araneae) benefited from organic management depending on country. Woody habitat and IP supported harvestmen (Opiliones). In both IP and organic orchards we detected aversive influences of a high-quality surrounding landscape on some predator groups: for example, high covers of woody habitat reduced earwig abundances in German orchards but enhanced their abundance in Sweden, and high natural plant species richness tended to reduce predatory bug abundance in Sweden and IP orchards in Spain. We conclude that predatory arthropod communities and influences of local and landscape factors are strongly shaped by orchard management, and that the influence of management differs between countries. Our results indicate that organic management improves the living conditions for effective predator communities.
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| 7. |
- Jax, Elinor, et al.
(author)
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Health monitoring in birds using bio-loggers and whole blood transcriptomics
- 2021
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In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 11:1
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Journal article (peer-reviewed)abstract
- Monitoring and early detection of emerging infectious diseases in wild animals is of crucial global importance, yet reliable ways to measure immune status and responses are lacking for animals in the wild. Here we assess the usefulness of bio-loggers for detecting disease outbreaks in free-living birds and confirm detailed responses using leukocyte composition and large-scale transcriptomics. We simulated natural infections by viral and bacterial pathogens in captive mallards (Anas platyrhynchos), an important natural vector for avian influenza virus. We show that body temperature, heart rate and leukocyte composition change reliably during an acute phase immune response. Using genome-wide gene expression profiling of whole blood across time points we confirm that immunostimulants activate pathogen-specific gene regulatory networks. By reporting immune response related changes in physiological and behavioural traits that can be studied in free-ranging populations, we provide baseline information with importance to the global monitoring of zoonotic diseases.
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| 8. |
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| 9. |
- Kotlarek, Joseph, et al.
(author)
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A Study of Mental Maps in Immersive Network Visualization
- 2020
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In: 2020 IEEE Pacific Visualization Symposium (PacificVis). - : IEEE. - 9781728156972 - 9781728156989 ; , s. 1-10
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Conference paper (peer-reviewed)abstract
- The visualization of a network influences the quality of the mental map that the viewer develops to understand the network. In this study, we investigate the effects of a 3D immersive visualization environment compared to a traditional 2D desktop environment on the comprehension of a networks structure. We compare the two visualization environments using three tasks—interpreting network structure, memorizing a set of nodes, and identifying the structural changes—commonly used for evaluating the quality of a mental map in network visualization. The results show that participants were able to interpret network structure more accurately when viewing the network in an immersive environment, particularly for larger networks. However, we found that 2D visualizations performed better than immersive visualization for tasks that required spatial memory.
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| 10. |
- Li, Shunyi, et al.
(author)
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Intrinsic energy band alignment of functional oxides
- 2014
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In: Physica Status Solidi - Rapid Research Letetrs. - : Wiley. - 1862-6254 .- 1862-6270. ; 8:6, s. 571-576
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Journal article (peer-reviewed)abstract
- The energy band alignment at interfaces between different materials is a key factor, which determines the function of electronic devices. While the energy band alignment of conventional semiconductors is quite well understood, systematic experimental studies on oxides are still missing. This work presents an extensive study on the intrinsic energy band alignment of a wide range of functional oxides using photoelectron spectroscopy with in-situ sample preparation. The studied materials have particular technological importance in diverse fields as solar cells, piezotronics, multiferroics, photoelectrochemistry and oxide electronics. Particular efforts have been made to verify the validity of transitivity, in order to confirm the intrinsic nature of the obtained band alignment and to understand the underlying principles. Valence band offsets up to 1.6 eV are observed. The large variation of valence band maximum energy can be explained by the different orbital contributions to the density of states in the valence band. The framework provided by this work enables the general understanding and prediction of energy band alignment at oxide interfaces, and furthermore the tailoring of energy level matching for charge transfer in functional oxides. (C) 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
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