| 11. |
- Augustinsson, Annelie, et al.
(författare)
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Variations in the Referral Pattern for Genetic Counseling of Patients with Early-Onset Breast Cancer : A Population-Based Study in Southern Sweden
- 2020
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Ingår i: Public Health Genomics. - : S. Karger AG. - 1662-8063 .- 1662-4246. ; 23:3-4, s. 100-109
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Tidskriftsartikel (refereegranskat)abstract
- Swedish national breast cancer guidelines recommend that all women diagnosed with breast cancer (BC) at the age of 35 years or younger should be referred to their regional oncogenetic clinic for genetic counseling and testing, regardless of family history of cancer. The main objective of this study was to evaluate whether place of residence at BC diagnosis and treating hospital were associated with the fact that not all BC patients diagnosed at ≤35 years in the southern part of Sweden have attended genetic counseling and testing. Between 2000 and 2013, 279 women in the South Swedish Health Care Region were diagnosed with BC at ≤35 years. Information regarding place of residence at BC diagnosis, treating hospital, time of registration and first meeting at the Oncogenetic Clinic in Lund, and genetic testing was collected. With a follow-up period until August 2018, 64% were registered at the clinic (60% underwent genetic testing) and 36% were not. BC patients from 2 counties and from rural settings with a population of <10,000 inhabitants were significantly less likely to be registered at the clinic. Our results suggest that place of residence at BC diagnosis and treating hospital were associated with the probability of referral for genetic counseling and testing for women diagnosed with BC at ≤35 years in the South Swedish Health Care Region. We propose, as a generalizable finding, that further educational and outreach activities within the health care system and the community may be needed to ensure that all women diagnosed with early-onset BC receive proper genetic counseling.
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| 12. |
- Axelsson, Arvid, et al.
(författare)
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Tree species classification using Sentinel-2 imagery and Bayesian inference
- 2021
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Ingår i: International Journal of Applied Earth Observation and Geoinformation. - : Elsevier BV. - 1569-8432 .- 0303-2434. ; 100
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Tidskriftsartikel (refereegranskat)abstract
- The increased temporal frequency of optical satellite data acquisitions provides a data stream that has the potential to improve land cover mapping, including mapping of tree species. However, for large area operational mapping, partial cloud cover and different image extents can pose challenges. Therefore, methods are needed to assimilate new images in a straightforward way without requiring a total spatial coverage for each new image. This study shows that Bayesian inference applied sequentially has the potential to solve this problem. To test Bayesian inference for tree species classification in the boreo-nemoral zone of southern Sweden, field data from the study area of Remningstorp (58°27′18.35″ N, 13°39′8.03″ E) were used. By updating class likelihood with an increasing number of combined Sentinel-2 images, a higher and more stable cross-validated overall accuracy was achieved. Based on a Mahalanobis distance, 23 images were automatically chosen from the period of 2016 to 2018 (from 142 images total). An overall accuracy of 87% (a Cohen’s kappa of 78.5%) was obtained for four tree species classes: Betula spp., Picea abies, Pinus sylvestris, and Quercus robur. This application of Bayesian inference in a boreo-nemoral forest suggests that it is a practical way to provide a high and stable classification accuracy. The method could be applied where data are not always complete for all areas. Furthermore, the method requires less reference data than if all images were used for classification simultaneously.
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| 13. |
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| 14. |
- Bergström, Lena, et al.
(författare)
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Integration methods for Marine Strategy Framework Directive’s biodiversity assessments
- 2021
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- This report reviews the integration methods for MSFD biodiversity assessments under Descriptor 1 for species that are not covered by the Habitats Directive and are not commercial fish assessed under Descriptor 3 and used in Descriptor 1 assessments. It was carried out by experts from the MSFD Biodiversity expert network, which is coordinated by the JRC. It constitutes a knowledge base to support MSFD Article 8 assessments by evaluating the methods to integrate assessments of species at different levels: i) criteria to species, ii) species to species group, and iii) species groups/species to ecosystem component. Real data and realistic estimates were used to provide a robust evaluation of the main MSFD integration approaches, i.e. one out all out, proportional method, averages, weighted averages, and conditional rules. Results show that integration methods have advantages and disadvantages depending on the level of integration, the species group (including threatened species), and the available indicators for primary and secondary criteria. Therefore, different scenarios are proposed and evaluated from criteria to ecosystem components, for fish and bird species groups. To conclude, a common integration approach is feasible, when it is based on the commonly agreed ecological impact of each D1 criterion to the species groups, and can be used in all regions.
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| 15. |
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| 16. |
- Betancourt, Lazaro Hiram, et al.
(författare)
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The human melanoma proteome atlas-Defining the molecular pathology
- 2021
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Ingår i: Clinical and Translational Medicine. - : Wiley. - 2001-1326. ; 11:7, s. 1-20
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Tidskriftsartikel (refereegranskat)abstract
- The MM500 study is an initiative to map the protein levels in malignant melanoma tumor samples, focused on in-depth histopathology coupled to proteome characterization. The protein levels and localization were determined for a broad spectrum of diverse, surgically isolated melanoma tumors originating from multiple body locations. More than 15,500 proteoforms were identified by mass spectrometry, from which chromosomal and subcellular localization was annotated within both primary and metastatic melanoma. The data generated by global proteomic experiments covered 72% of the proteins identified in the recently reported high stringency blueprint of the human proteome. This study contributes to the NIH Cancer Moonshot initiative combining detailed histopathological presentation with the molecular characterization for 505 melanoma tumor samples, localized in 26 organs from 232 patients.
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| 17. |
- Burden, Håkan, et al.
(författare)
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Proposed EU Regulations’ Impact on Data Utilisation– A Multi-Case Study within Public Transport
- 2023
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Motivation: In a broad sense data sharing onboard public transport vehicles is governed by two different business models – interoperable and free of charge access for some data versus data that is restricted to specific uses by commercial contracts and existing legislation. Under the Digital Decade the EU has proposed new legislation with the ambition to promote a single digital market. The question then arises – how will the upcoming regulations affect existing business models for data utilisation?Method: We have investigated two different cases where existing technology meets upcoming EU legislation. The questions have been framed through dialogue with actors in the industry, to cover topics and questions that are both concrete and current. Using the policy lab methodology, we have investigated the possibility to re-use surveillance film from public transport vehicles for passenger counting. The analysis compares GDPR and the Swedish camera surveillance act with the proposed AI Act, to see what new possibilities or obstacles arise. We have also explored the changes that the Data Act may impose on different actors’ access to data derived from the batteries installed in an electric bus.Results: The AI Act will not change the business models within the eco-system but facilitate access to more personal data (including personal data where GDPR otherwise would be a barrier), useful for training automated passenger counting. Those responsible for placing the system on the market will still need to ensure that they are compliant with GDPR in terms of processing personal data. In terms of the Data Act the outcome is more disruptive as the owner and user of a vehicle is entitled to all data representing their usage, free of charge, and this will impair existing business models for data access. It is also possible for multiple actors to be users, for instance if the vehicle is owned by a public transport authority and leased by an operator.Discussion: Our analysis shows that while the impact of the Data Act can resonate with the ambitions behind the regulation in terms of making more data interoperable and available free of charge, it can also have the opposite effect. The latter is specifically the case where altruistic data sharing already is in place and the Data Act imposes standard contracts for and role-based restrictions towards utilisation. Both the AI Act and the Data Act are complex and often difficult to assess. In relation to the Data Act, the recitals were helpful for interpreting the application of articles and definitions. For understanding the relationship between the AI Act and GDPR we combined the legal analysis with prototyping the impacts and relied on sharing insights with other actors. This highlights the need for multiple ways of performing the data collection and analysis as well as the suitability of policy labs as a research method
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| 18. |
- Burden, Håkan, et al.
(författare)
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Självkörande landsbygd
- 2021
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Hur skulle autonoma fordon kunna användas inom kollektivtrafiken på landsbygden? Genom intervjuer, workshops och en RFI (request for information, ett första steg mot upphandling) har vi undersökt frågan utifrån fyra konkreta områden i Sverige – Lund, Gotland, Eskilstuna och Skellefteå. Med en definition av landsbygd baserad på individens mobilitet har vi sett att Sveriges landsbygd rymmer mindre orter på väg att avfolkas där äldre, barn och de utan körkort hade kunnat få bättre tillgång till samhällelig service med autonoma fordon. Vi har också sett att flera av landets nya arbetsplatser kommer befinna sig på landsbygden och därmed skapa ett mobilitetsbehov från staden till landet. För att kunna realisera de identifierade möjligheterna finns ett behov av att framföra fordonen i högre hastigheter samt att de ska kunna hantera mer komplexa trafiksituationer än vad dagens piloter i städerna visat. På landsbygden finns alltså ett utrymme för nya fordon att visa upp sig. Samtidigt ser vi hur man inte ska förvänta sig att investeringarna i autonoma fordon kommer betala sig på en linje, snarare behöver man lyfta blicken och se systemeffekten när stomlinjetrafiken blir mer attraktiv då bussarna går raka vägen istället för via mindre samhällen. Vi har inte sett några belägg på att den digitala infrastrukturen behöver utvecklas för att möjliggöra försök med autonoma fordon på någon av de undersökta rutterna. Dagens 4G-täckning är fullgod och fordonen borde ha tillgång till tillräckligt bra positioneringsdata för att bedriva verksamheten. Däremot ställs flera frågor om hur ersättningstrafiken organiseras när fordonen inte klarar av vädret, vem som står för säkrare hållplatser och hur chaufförens övriga ansvar realiseras när fordonet är förarlöst.
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| 19. |
- Cabrita, Rita, et al.
(författare)
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Tertiary lymphoid structures improve immunotherapy and survival in melanoma
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 577:7791, s. 561-565
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Tidskriftsartikel (refereegranskat)abstract
- Checkpoint blockade therapies that reactivate tumour-associated T cells can induce durable tumour control and result in the long-term survival of patients with advanced cancers1. Current predictive biomarkers for therapy response include high levels of intratumour immunological activity, a high tumour mutational burden and specific characteristics of the gut microbiota2,3. Although the role of T cells in antitumour responses has thoroughly been studied, other immune cells remain insufficiently explored. Here we use clinical samples of metastatic melanomas to investigate the role of B cells in antitumour responses, and find that the co-occurrence of tumour-associated CD8+ T cells and CD20+ B cells is associated with improved survival, independently of other clinical variables. Immunofluorescence staining of CXCR5 and CXCL13 in combination with CD20 reveals the formation of tertiary lymphoid structures in these CD8+CD20+ tumours. We derived a gene signature associated with tertiary lymphoid structures, which predicted clinical outcomes in cohorts of patients treated with immune checkpoint blockade. Furthermore, B-cell-rich tumours were accompanied by increased levels of TCF7+ naive and/or memory T cells. This was corroborated by digital spatial-profiling data, in which T cells in tumours without tertiary lymphoid structures had a dysfunctional molecular phenotype. Our results indicate that tertiary lymphoid structures have a key role in the immune microenvironment in melanoma, by conferring distinct T cell phenotypes. Therapeutic strategies to induce the formation of tertiary lymphoid structures should be explored to improve responses to cancer immunotherapy.
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| 20. |
- Cabrita, Rita, et al.
(författare)
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Tertiary lymphoid structures improve immunotherapy and survival in melanoma.
- 2020
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Ingår i: Nature. - : Nature Publishing Group. - 1476-4687 .- 0028-0836. ; 577:7791, s. 561-565
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Tidskriftsartikel (refereegranskat)abstract
- Checkpoint blockade therapies that reactivate tumour-associated T cells can induce durable tumour control and result in the long-term survival of patients with advanced cancers1. Current predictive biomarkers for therapy response include high levels of intratumour immunological activity, a high tumour mutational burden and specific characteristics of the gut microbiota2,3. Although the role of T cells in antitumour responses has thoroughly been studied, other immune cells remain insufficiently explored. Here we use clinical samples of metastatic melanomas to investigate the role of B cells in antitumour responses, and find that the co-occurrence of tumour-associated CD8+ T cells and CD20+ B cells is associated with improved survival, independently of other clinical variables. Immunofluorescence staining of CXCR5 and CXCL13 in combination with CD20 reveals the formation of tertiary lymphoid structures in these CD8+CD20+ tumours. We derived a gene signature associated with tertiary lymphoid structures, which predicted clinical outcomes in cohorts of patients treated with immune checkpoint blockade. Furthermore, B-cell-rich tumours were accompanied by increased levels of TCF7+ naive and/or memory T cells. This was corroborated by digital spatial-profiling data, in which T cells in tumours without tertiary lymphoid structures had a dysfunctional molecular phenotype. Our results indicate that tertiary lymphoid structures have a key role in the immune microenvironment in melanoma, by conferring distinct T cell phenotypes. Therapeutic strategies to induce the formation of tertiary lymphoid structures should be explored to improve responses to cancer immunotherapy.
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