| 1. |
- Aspholm-Hurtig, Marina, et al.
(author)
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Functional adaptation of BabA, the H. pylori ABO blood group antigen binding adhesin.
- 2004
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In: Science (New York, N.Y.). - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 305:5683, s. 519-22
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Journal article (peer-reviewed)abstract
- Adherence by Helicobacter pylori increases the risk of gastric disease. Here, we report that more than 95% of strains that bind fucosylated blood group antigen bind A, B, and O antigens (generalists), whereas 60% of adherent South American Amerindian strains bind blood group O antigens best (specialists). This specialization coincides with the unique predominance of blood group O in these Amerindians. Strains differed about 1500-fold in binding affinities, and diversifying selection was evident in babA sequences. We propose that cycles of selection for increased and decreased bacterial adherence contribute to babA diversity and that these cycles have led to gradual replacement of generalist binding by specialist binding in blood group O-dominant human populations.
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| 2. |
- Brink, Suzanne, et al.
(author)
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Curriculum agility at faculty, department, program and course level
- 2022
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In: 50th annual conference of the European society for engineering education. - 9788412322262 ; , s. 1872-1877
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Conference paper (peer-reviewed)abstract
- This short paper describes the first prototyping of a self-evaluation process of Curriculum Agility at a Faculty of Technology in Sweden. The process comprises guided, semi-structured, individual interviews at different organisational levels within the faculty, a joint narrative based on those interviews, prioritizing development strategies per level, and jointly mapping them on importance and implementation time. The self-evaluation is part of and based on the research on the principles of Curriculum Agility. The results show the interplay in timely curriculum change for futureproof engineering education between the teaching staff, the systems and the people who control the systems. The self-evaluation brings together the different perspectives and perceptions within the faculty and gives insight in how those affect the willingness towards and occurrence of curriculum development. This work in progress indicates how doing such a qualitative self-evaluation paves the road for transparent strategic dialogues on a holistic level about what to give attention and organize differently.
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| 3. |
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| 4. |
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| 5. |
- Daleke-Schermerhorn, Maria H., et al.
(author)
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Decoration of Outer Membrane Vesicles with Multiple Antigens by Using an Autotransporter Approach
- 2014
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In: Applied and Environmental Microbiology. - 0099-2240 .- 1098-5336. ; 80:18, s. 5854-5865
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Journal article (peer-reviewed)abstract
- Outer membrane vesicles (OMVs) are spherical nanoparticles that naturally shed from Gram-negative bacteria. They are rich in immunostimulatory proteins and lipopolysaccharide but do not replicate, which increases their safety profile and renders them attractive vaccine vectors. By packaging foreign polypeptides in OMVs, specific immune responses can be raised toward heterologous antigens in the context of an intrinsic adjuvant. Antigens exposed at the vesicle surface have been suggested to elicit protection superior to that from antigens concealed inside OMVs, but hitherto robust methods for targeting heterologous proteins to the OMV surface have been lacking. We have exploited our previously developed hemoglobin protease (Hbp) autotransporter platform for display of heterologous polypeptides at the OMV surface. One, two, or three of the Mycobacterium tuberculosis antigens ESAT6, Ag85B, and Rv2660c were targeted to the surface of Escherichia coli OMVs upon fusion to Hbp. Furthermore, a hypervesiculating Delta tolR Delta tolA derivative of attenuated Salmonella enterica serovar Typhimurium SL3261 was generated, enabling efficient release and purification of OMVs decorated with multiple heterologous antigens, exemplified by the M. tuberculosis antigens and epitopes from Chlamydia trachomatis major outer membrane protein (MOMP). Also, we showed that delivery of Salmonella OMVs displaying Ag85B to antigen-presenting cells in vitro results in processing and presentation of an epitope that is functionally recognized by Ag85B-specific T cell hybridomas. In conclusion, the Hbp platform mediates efficient display of (multiple) heterologous antigens, individually or combined within one molecule, at the surface of OMVs. Detection of antigen-specific immune responses upon vesicle-mediated delivery demonstrated the potential of our system for vaccine development.
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| 6. |
- Gamero, Anna, et al.
(author)
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Tracking Progress Toward EU Biodiversity Strategy Targets : EU Policy Effects in Preserving its Common Farmland Birds
- 2017
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In: Conservation Letters. - : Wiley. - 1755-263X. ; 10:4, s. 395-402
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Journal article (peer-reviewed)abstract
- Maximizing the area under biodiversity-related conservation measures is a main target of the European Union (EU) Biodiversity Strategy to 2020. We analyzed whether agrienvironmental schemes (AES) within EU common agricultural policy, special protected areas for birds (SPAs), and Annex I designation within EU Birds Directive had an effect on bird population changes using monitoring data from 39 farmland bird species from 1981 to 2012 at EU scale. Populations of resident and short-distance migrants were larger with increasing SPAs and AES coverage, while Annex I species had higher population growth rates with increasing SPAs, indicating that SPAs may contribute to the protection of mainly target species and species spending most of their life cycle in the EU. Because farmland birds are in decline and the negative relationship of agricultural intensification with their population growth rates was evident during the implementation of AES and SPAs, EU policies seem to generally attenuate the declines of farmland bird populations, but not to reverse them.
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| 7. |
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| 8. |
- Grünwald, Jan, et al.
(author)
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Ecological traits predict population trends of urban birds in Europe
- 2024
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In: Ecological Indicators. - 1470-160X. ; 160
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Journal article (peer-reviewed)abstract
- The population dynamics of urban animals has been so far remarkably understudied. At the same time, urban species’ population trends can provide important information on the consequences of environmental changes in cities. We modelled long-term population trends of 93 bird species breeding in urban areas in 16 European countries as a function of species’ traits, characterising variability in their urbanization and ecology. We found that: (i) earlier colonisers have more negative population trends than recent colonisers; (ii) more urbanized open habitat species had more positive population trends than less urbanized open habitat species; (iii) highly urbanized birds breeding above the ground had more negative trends than highly urbanized ground breeders. These patterns can be explained by several processes occurring in cities as well as outside city borders. Namely, (i) pre-industrial colonisers might struggle to persist in rapidly changing urban areas, limiting their foraging and breeding opportunities of the birds. (ii) Open habitats are under pressure of intensive agricultural exploitation in rural areas, which may negatively affect populations of less urbanized birds. In contrast, urban areas do not experience such pressure keeping the trends of urbanized open habitat species more positive. (iii) Differences in population trends between highly urbanized ground and above-ground breeders suggest that the latter may lose their breeding opportunities in modern buildings that do not provide suitable breeding sites. Our results indicate that even once successful, city dwellers may not keep pace with changes in urban areas, but these areas may also provide suitable habitats for biodiversity.
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| 9. |
- Illini, Oliver, et al.
(author)
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Real-world experience with capmatinib in MET exon 14-mutated non-small cell lung cancer (RECAP) : a retrospective analysis from an early access program
- 2022
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In: Therapeutic Advances in Medical Oncology. - : Sage Publications. - 1758-8340 .- 1758-8359. ; 14
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Journal article (peer-reviewed)abstract
- Background: Patients with non-small cell lung cancer (NSCLC) presenting with mesenchymal-epithelial transition (MET) exon 14 skipping mutation have an unfavorable prognosis with standard treatments. Capmatinib is a selective MET inhibitor, which showed promising efficacy in this patient population in early trials. Methods: We performed a retrospective, international, multicenter efficacy and safety analysis in patients with NSCLC treated with capmatinib in an early access program between March 2019 and December 2021. Results: Data from 81 patients with advanced MET exon 14 mutated NSCLC treated with capmatinib in first- or later-line therapy were analyzed. Median age was 77 years (range, 48-91), 56% were women, 86% had stage IV disease, and 27% had brain metastases. For all patients, the objective response rate (ORR) to capmatinib was 58% (95% CI, 47-69), whereas it was 68% (95% CI, 50-82) in treatment-naive and 50% (95% CI, 35-65) in pretreated patients. The median progression-free survival was 9.5 months (95% CI, 4.7-14.3), whereas it was 10.6 months (95% CI, 5.5-15.7) in first-line and 9.1 months (95% CI, 3.1-15.1) in pretreated patients. After a median follow-up of 11.0 months, the median overall survival was 18.2 months (95% CI, 13.2-23.1). In patients with measurable brain metastases (n = 11), the intracranial ORR was 46% (95% CI, 17-77). Capmatinib showed a manageable safety profile. Grade > 3 treatment-related adverse events included peripheral edema (13%), elevated creatinine (4%), and elevated liver enzymes (3%). Conclusion: In patients with MET exon 14 skipping mutation, capmatinib showed durable systemic and intracranial efficacy and a manageable safety profile. This analysis confirms previously reported phase II data in a real-world setting.
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| 10. |
- Nygren, Thomas, 1972-, et al.
(author)
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Digitala primärkällor i historieundervisningen : en utmaning för elevers historiska tänkande och historiska empati
- 2014
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In: Nordidactica. - Karlstad : CSD Karlstad. - 2000-9879. ; :2, s. 208-245
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Journal article (peer-reviewed)abstract
- In this study, 110 Swedish upper secondary students use a historical database designed for research. We analyze how they perceive the use of this digital tool in teaching and if they are able to use historical thinking and historical empathy in their historical writing and presentations. Using case-study methodology including questionnaires, observations, interviews and text analysis we find this to be a complex task for students. Our results highlight technological problems and problems in contextualizing historical evidence. However, students show interest in using primary sources and ability to use historical thinking and historical empathy, especially older students in more advanced courses when they have time to reflect upon the historical material.
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| 11. |
- Nygren, Thomas, 1972-, et al.
(author)
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Treading old paths in new ways : upper secondary students using a digital tool of the professional historian
- 2013
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In: Education Sciences. - Basel : MDPI. - 2227-7102. ; 3, s. 50-73
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Journal article (peer-reviewed)abstract
- This article presents problems and possibilities associated with incorporating into history teaching a digital demographic database made for professional historians. We detect and discuss the outcome of how students in Swedish upper secondary schools respond to a teaching approach involving digitized registers comprising 19th century individuals and populations. Even though our results demonstrate that students experience the use of this digital database as messy, stressful, complicated, even meaningless and frustrating, they also perceive working with it as most interesting. We discuss this twofold outcome, its reasons and lessons to learn from it. When technology is functioning and the task is specialized and sufficiently guided by the teacher, which is not always the case, our results propose that digital databases can stimulate young people’s interest and historical thinking. Knowledge construction based upon historical thinking is evident in the students’ examination papers in which they present and debate their findings. These papers indicate that students can use a digital database and write history based upon empirical evidence, source criticism and historical empathy, just as professional historians do.
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| 12. |
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| 13. |
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| 14. |
- O'Reilly, Enya, et al.
(author)
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An assessment of relative habitat use as a metric for species’ habitat association and degree of specialization
- 2022
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In: Ecological Indicators. - : Elsevier BV. - 1470-160X. ; 135
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Journal article (peer-reviewed)abstract
- In order to understand species’ sensitivity to habitat change, we must correctly determine if a species is associated with a habitat or not, and if it is associated, its degree of specialization for that habitat. However, definitions of species’ habitat association and specialization are often static, categorical classifications that coarsely define species as either habitat specialists or generalists and can fail to account for potential temporal or spatial differences in association or specialization. In contrast, quantitative metrics can provide a more nuanced assessment, defining species’ habitat associations and specialization along a continuous scale and accommodate for temporal or spatial variation, but these approaches are less widely used. Here we explore relative habitat use (RHU) as a metric for quantifying species’ association with and degree of specialization for different habitat types. RHU determines the extent of a species’ association with a given habitat by comparing its abundance in that habitat relative to its mean abundance across all other habitats. Using monitoring data for breeding birds across Europe from 1998 to 2017; we calculate RHU scores for 246 species for five habitat types and compared them to the literature-based classifications of their association with and specialization for each of these habitats. We also explored the temporal variation in species’ RHU scores for each habitat and assessed how this varied according to association and degree of specialization. In general, species’ RHU and literature-derived classifications were well aligned, as RHU scores for a given habitat increased in line with reported association and specialization. In addition, temporal variation in RHU scores were influenced by association and degree of specialization, with lower scores for those associated with, and those more specialized to, a given habitat. As a continuous metric, RHU allows a detailed assessment of species’ association with and degree of specialization for different habitats that can be tailored to specific temporal and/or spatial requirements. It has the potential to be a valuable tool for identifying indicator species and in supporting the design, implementation and monitoring of conservation management actions.
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| 15. |
- Sandberg, Karin, 1981-
(author)
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Möte med det förflutna : digitaliserade primärkällor i historieundervisningen
- 2014
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Licentiate thesis (other academic/artistic)abstract
- In recent years, the Swedish educational system has undergone considerable change. A new curriculum and swift digitization via the implementation of the "one-to-one" system have increased the call for new teaching methods in schools. Previous research indicates that working with primary sources can enhance students’ historical thinking and historical empathy. The present licentiate dissertation aims to investigate Swedish upper secondary school students’ use of critical thinking and historical empathy when utilizing digitized primary sources, such as the parish registers stored in the Demographic Data Base at Umeå University. Five classes in grades 1-3, comprising 110 students, in the ages 16 to 19, and three teachers participated in the study. The students were assigned with compiling a report based on the digitised primary source material and presenting their findings in a written paper or oral presentation. The study was evaluated through (1) interviews with students and teachers, (2) classroom observation of the students while working with the material, (3) questionnaires on the students´ view of history, and (4) the completed assignments. The study shows that all the students achieved some result based on the information found in the digitised primary sources. While they applied historical empathy and historical thinking, it was mixed with presentism. The majority did not make use of corroboration, but those who did displayed more examples of historical thinking and historical empathy, primarily evident in grades 2 and 3 and in the free discussions held after the presentations. The students’ perception of primary sources shifted as a result of this exercise: Their preference for using primary sources had increased, although their trust in primary sources had simultaneously decreased. Teachers and students alike were generally satisfied with the assignment but argued that the database needed improvement in order to enhance its usefulness. Over the course of the assignment, students frequently expressed that the individuals in the digitized material came to life for them, generating feelings of empathy. The study’s contribution to history didactics is twofold. First, it clearly demonstrates how upper secondary students can make use of historical thinking and historical empathy when studying digitised parish records, even though they have difficulty contextualizing their results. Secondly, it provides insight into how Swedish students learn history and the kind of history that interests them. The results are predominantly in agreement with those from previous studies but this study is pioneering in basing its findings on primary sources that are digitised.
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| 16. |
- Schlegel, Susan, et al.
(author)
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Bacterial-based membrane protein production
- 2014
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In: Biochimica et Biophysica Acta. Molecular Cell Research. - : Elsevier BV. - 0167-4889 .- 1879-2596. ; 1843:8, s. 1739-1749
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Research review (peer-reviewed)abstract
- Escherichia coli is by far the most widely used bacterial host for the production of membrane proteins. Usually, different strains, culture conditions and production regimes are screened for to design the optimal production process. However, these E. coli-based screening approaches often do not result in satisfactory membrane protein production yields. Recently, it has been shown that (i) E. coli strains with strongly improved membrane protein production characteristics can be engineered or selected for, (ii) many membrane proteins can be efficiently produced in E. coli-based cell-free systems, (iii) bacteria other than E. coli can be used for the efficient production of membrane proteins, and, (iv) membrane protein variants that retain functionality but are produced at higher yields than the wild-type protein can be engineered or selected for. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey.
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| 17. |
- Soultan, Alaaeldin, et al.
(author)
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The future distribution of wetland birds breeding in Europe validated against observed changes in distribution
- 2022
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In: Environmental Research Letters. - : IOP Publishing. - 1748-9318 .- 1748-9326. ; 17:2
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Journal article (peer-reviewed)abstract
- Wetland bird species have been declining in population size worldwide as climate warming and land-use change affect their suitable habitats. We used species distribution models (SDMs) to predict changes in range dynamics for 64 non-passerine wetland birds breeding in Europe, including range size, position of centroid, and margins. We fitted the SDMs with data collected for the first European Breeding Bird Atlas and climate and land-use data to predict distributional changes over a century (the 1970s-2070s). The predicted annual changes were then compared to observed annual changes in range size and range centroid over a time period of 30 years using data from the second European Breeding Bird Atlas. Our models successfully predicted ca. 75% of the 64 bird species to contract their breeding range in the future, while the remaining species (mostly southerly breeding species) were predicted to expand their breeding ranges northward. The northern margins of southerly species and southern margins of northerly species, both, predicted to shift northward. Predicted changes in range size and shifts in range centroids were broadly positively associated with the observed changes, although some species deviated markedly from the predictions. The predicted average shift in core distributions was ca. 5 km yr-1 towards the north (5% northeast, 45% north, and 40% northwest), compared to a slower observed average shift of ca. 3.9 km yr-1. Predicted changes in range centroids were generally larger than observed changes, which suggests that bird distribution changes may lag behind environmental changes leading to 'climate debt'. We suggest that predictions of SDMs should be viewed as qualitative rather than quantitative outcomes, indicating that care should be taken concerning single species. Still, our results highlight the urgent need for management actions such as wetland creation and restoration to improve wetland birds' resilience to the expected environmental changes in the future.
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| 18. |
- Åberg, Anna, et al.
(author)
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Helicobacter pylori adapts to chronic infection and gastric disease via ph-responsive baba-mediated adherence
- 2017
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In: Cell Host and Microbe. - : Elsevier BV. - 1931-3128 .- 1934-6069. ; 21:3, s. 376-389
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Journal article (peer-reviewed)abstract
- The BabA adhesin mediates high-affinity binding of Helicobacter pylori to the ABO blood group antigen-glycosylated gastric mucosa. Here we show that BabA is acid responsive-binding is reduced at low pH and restored by acid neutralization. Acid responsiveness differs among strains; often correlates with different intragastric regions and evolves during chronic infection and disease progression; and depends on pH sensor sequences in BabA and on pH reversible formation of high-affinity binding BabA multimers. We propose that BabA's extraordinary reversible acid responsiveness enables tight mucosal bacterial adherence while also allowing an effective escape from epithelial cells and mucus that are shed into the acidic bactericidal lumen and that bio-selection and changes in BabA binding properties through mutation and recombination with babA-related genes are selected by differences among individuals and by changes in gastric acidity over time. These processes generate diverse H. pylori subpopulations, in which BabA's adaptive evolution contributes to H. pylori persistence and overt gastric disease.
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