| 1. |
- Moberg, Christina, et al.
(författare)
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De unga gör helt rätt när de stämmer staten
- 2022
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Ingår i: Aftonbladet. - 1103-9000.
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Tidskriftsartikel (populärvet., debatt m.m.)abstract
- 1 620 forskare och lärare i forskarvärlden: Vi ställer oss bakom Auroras klimatkrav
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| 2. |
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| 3. |
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| 4. |
- Adhikari, Subash, et al.
(författare)
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A high-stringency blueprint of the human proteome
- 2020
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 11:1
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Forskningsöversikt (refereegranskat)abstract
- The Human Proteome Organization (HUPO) launched the Human Proteome Project (HPP) in 2010, creating an international framework for global collaboration, data sharing, quality assurance and enhancing accurate annotation of the genome-encoded proteome. During the subsequent decade, the HPP established collaborations, developed guidelines and metrics, and undertook reanalysis of previously deposited community data, continuously increasing the coverage of the human proteome. On the occasion of the HPP’s tenth anniversary, we here report a 90.4% complete high-stringency human proteome blueprint. This knowledge is essential for discerning molecular processes in health and disease, as we demonstrate by highlighting potential roles the human proteome plays in our understanding, diagnosis and treatment of cancers, cardiovascular and infectious diseases.
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| 5. |
- Agarwal, Pankhuri, et al.
(författare)
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Introduction
- 2021
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Ingår i: The Politics and Ethics of Representation in Qualitative Research : Addressing Moments of Discomfort - Addressing Moments of Discomfort.
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Bokkapitel (refereegranskat)abstract
- This chapter introduces the volume by presenting the questions of politics and ethics of representation in qualitative research. It also shows how these are approached in the following chapters through analyses of moments of discomfort in our research practice. We situate our work in critical, feminist and engaged scholarship and discuss how creating representation in qualitative research is linked to the issues of accountability and solidarity. The introduction then offers an overview of the chapters, showing how different representational practices, both in the field and in writing, open up for important ethical and political dilemmas.
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| 6. |
- Agarwal, Pankhuri, et al.
(författare)
-
Introduction
- 2021. - 1
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Ingår i: The Politics and Ethics of Representation in Qualitative Research. - London : Routledge. - 9780367281014 - 9780429299674 - 9780367281038 ; , s. 1-8
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- In qualitative research, the research process is often filled with moments of discomfort. These discomforts can appear at any stage of the research: when choosing thesubject of research, during fieldwork, in the process of analysis and when presenting research findings to different audiences. In this edited volume, we take thesemoments of discomfort seriously and use them as sites of knowledge production forreflecting on the politics and ethics of the qualitative research process. By locatingour experiences in implementing nine different PhD projects carried out in different disciplines and research contexts in social sciences, we argue that these momentsof discomfort help us to gain important insights into the methodological, theoretical, ethical and political issues that are crucial for the fields we engage with. Drawingon feminist and other critical discussions (Mulinari and Sandell 1999, Gunaratnam2003, Back 2007, Gunaratnam and Hamilton 2017), we deal with questions such as:What does it mean to write about the lives of others? What are the ethical modesand conundrums of producing representations? In research projects that are locatedin the tradition of critical or engaged scholarship, how are ethics and politics of representation intertwined, and when are they distinct? How are politics of representation linked to the practice of solidarity in research? What are the im/possibilities ofhope and care in research?
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| 7. |
- Andrews, B., et al.
(författare)
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Imaging cell biology
- 2022
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Ingår i: Nature Cell Biology. - : Springer Nature. - 1465-7392 .- 1476-4679. ; 24:8, s. 1180-1185
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Tidskriftsartikel (refereegranskat)
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| 8. |
- Bagheri, Neda, et al.
(författare)
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Commentary The new era of quantitative cell imaging-challenges and opportunities
- 2022
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Ingår i: Molecular Cell. - : Elsevier BV. - 1097-2765 .- 1097-4164. ; 82:2, s. 241-247
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Tidskriftsartikel (refereegranskat)abstract
- Quantitative optical microscopy-an emerging, transformative approach to single-cell biology-has seen dramatic methodological advancements over the past few years. However, its impact has been hampered by challenges in the areas of data generation, management, and analysis. Here we outline these technical and cultural challenges and provide our perspective on the trajectory of this field, ushering in a new era of quantitative, data-driven microscopy. We also contrast it to the three decades of enormous advances in the field of genomics that have significantly enhanced the reproducibility and wider adoption of a plethora of genomic approaches.
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| 9. |
- Björkman, Ida, et al.
(författare)
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Person-centred care on the move : An interview study with programme directors in Swedish higher education
- 2022
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Ingår i: BMC Medical Education. - : Springer Science and Business Media LLC. - 1472-6920. ; 22:1
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: There is an increasing trend towards person-centred care (PCC) worldwide, suggesting that PCC should be mastered by future health care professionals. This study aims to explore programme directors' views on facilitators and barriers to implementing PCC in four of the largest national study programmes in Sweden training future health care professionals.METHODS: A qualitative design was applied and interviews were conducted with 19 programme directors of Swedish national study programmes in medicine, nursing, occupational therapy and physiotherapy. The interviews were analysed using qualitative content analysis. Themes were sorted according to the Consolidated Framework for Implementation Research (CFIR) in an abductive approach. COREQ guidelines were applied.RESULTS: The overarching theme, as interpreted from the programme directors' experiences, was 'Person-centred care is on the move at different paces.' The theme relates to the domains identified by the CFIR as outer setting, innovation, inner setting and process. PCC was understood as something familiar but yet new, and the higher education institutions were in a state of understanding and adapting PCC to their own contexts. The movement in the outer setting consists of numerous stakeholders advocating for increased patient influence, which has stirred a movement in the inner setting where the higher educational institutions are trying to accommodate these new demands. Different meanings and values are ascribed to PCC, and the concept is thus also 'on the move', being adapted to traditions at each educational setting.CONCLUSION: Implementation of PCC in Swedish higher education is ongoing but fragmented and driven by individuals with a specific interest. There is uncertainty and ambiguity around the meaning and value of PCC and how to implement it. More knowledge is needed about the core of PCC as a subject for teaching and learning and also didactic strategies suitable to support students in becoming person-centred practitioners.
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| 10. |
- Björner, Emma, et al.
(författare)
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Chinese tourism consumption vis-à-vis tourism development strategies in the Arctic
- 2021. - 1
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Ingår i: Asian Mobilities Consumption in a Changing Arctic. - : Routledge. - 9781003039518 ; , s. 29-42
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Bokkapitel (refereegranskat)abstract
- The current national Arctic strategies of Sweden, Norway, and Finland consider tourism as a key industry and point out its significance for sustainable development in the region. Concurrently, China’s Arctic Policy talks about China being the source of tourists to the Arctic. Additionally, the tourism industry’s own strategies recognise that the Asian market shows strong growth in the number of travellers over the last decade. Further, there is great potential in the longer term. This chapter addresses how tourism development and destination branding is portrayed in policy and strategy documents dealing with the Arctic and how that corresponds with Chinese tourism consumption in the case of the Swedish Arctic. The findings show that, at all levels, tourism development and destination branding as portrayed in policies and strategies s increasingly tied to all three pillars of sustainability, even though economic and environmental aspects still dominate. Furthermore, relevant Chinese consumption patterns are elaborated upon. These patterns indicate that Chinese tourists are both similar to and different from Western travellers and have certain traits, partly influenced by cultural and Confucian values. Policies and strategy documents should be aligned with this notion in order to facilitate sustainable tourism development in the Arctic.
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| 11. |
- Burnum-Johnson, Kristin E., et al.
(författare)
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New Views of Old Proteins : Clarifying the Enigmatic Proteome
- 2022
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Ingår i: Molecular & Cellular Proteomics. - : Elsevier BV. - 1535-9476 .- 1535-9484. ; 21:7
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Tidskriftsartikel (refereegranskat)abstract
- All human diseases involve proteins, yet our current tools to characterize and quantify them are limited. To better elucidate proteins across space, time, and molecular composition, we provide a >10 years of projection for technologies to meet the challenges that protein biology presents. With a broad perspective, we discuss grand opportunities to transition the science of proteomics into a more propulsive enterprise. Extrapolating recent trends, we describe a next generation of approaches to define, quantify, and visualize the multiple dimensions of the proteome, thereby transforming our understanding and interactions with human disease in the coming decade.
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| 12. |
- Bäckström, Anna, et al.
(författare)
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A Sample Preparation Protocol for High Throughput Immunofluorescence of Suspension Cells on an Adherent Surface
- 2020
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Ingår i: Journal of Histochemistry and Cytochemistry. - : SAGE Publications. - 0022-1554 .- 1551-5044. ; 68:7, s. 473-489
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Tidskriftsartikel (refereegranskat)abstract
- Imaging is a powerful approach for studying protein expression and has the advantage over other methodologies in providing spatial informationin situat single cell level. Using immunofluorescence and confocal microscopy, detailed information of subcellular distribution of proteins can be obtained. While adherent cells of different tissue origin are relatively easy to prepare for imaging applications, non-adherent cells from hematopoietic origin, present a challenge due to their poor attachment to surfaces and subsequent loss of a substantial fraction of the cells. Still, these cell types represent an important part of the human proteome and express genes that are not expressed in adherent cell types. In the era of cell mapping efforts, overcoming the challenge with suspension cells for imaging applications would enable systematic profiling of hematopoietic cells. In this work, we successfully established an immunofluorescence protocol for preparation of suspension cell lines, peripheral blood mononucleated cells (PBMC) and human platelets on an adherent surface. The protocol is based on a multi-well plate format with automated sample preparation, allowing for robust high throughput imaging applications. In combination with confocal microscopy, the protocol enables systematic exploration of protein localization to all major subcellular structures.
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| 13. |
- Chang, Yun Chien, et al.
(författare)
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Decrypting lysine deacetylase inhibitor action and protein modifications by dose-resolved proteomics
- 2024
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Ingår i: Cell Reports. - : Elsevier BV. - 2211-1247. ; 43:6
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Tidskriftsartikel (refereegranskat)abstract
- Lysine deacetylase inhibitors (KDACis) are approved drugs for cutaneous T cell lymphoma (CTCL), peripheral T cell lymphoma (PTCL), and multiple myeloma, but many aspects of their cellular mechanism of action (MoA) and substantial toxicity are not well understood. To shed more light on how KDACis elicit cellular responses, we systematically measured dose-dependent changes in acetylation, phosphorylation, and protein expression in response to 21 clinical and pre-clinical KDACis. The resulting 862,000 dose-response curves revealed, for instance, limited cellular specificity of histone deacetylase (HDAC) 1, 2, 3, and 6 inhibitors; strong cross-talk between acetylation and phosphorylation pathways; localization of most drug-responsive acetylation sites to intrinsically disordered regions (IDRs); an underappreciated role of acetylation in protein structure; and a shift in EP300 protein abundance between the cytoplasm and the nucleus. This comprehensive dataset serves as a resource for the investigation of the molecular mechanisms underlying KDACi action in cells and can be interactively explored online in ProteomicsDB.
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| 14. |
- Coppo, Rosanna, et al.
(författare)
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Is there long-term value of pathology scoring in immunoglobulin A nephropathy? : A validation study of the Oxford Classification for IgA Nephropathy (VALIGA) update
- 2020
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Ingår i: Nephrology, Dialysis and Transplantation. - : Oxford University Press (OUP). - 0931-0509 .- 1460-2385. ; 35:6, s. 1002-1009
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Tidskriftsartikel (refereegranskat)abstract
- Background: It is unknown whether renal pathology lesions in immunoglobulin A nephropathy (IgAN) correlate with renal outcomes over decades of follow-up.Methods: In 1130 patients of the original Validation Study of the Oxford Classification for IgA Nephropathy (VALIGA) cohort, we studied the relationship between the MEST score (mesangial hypercellularity, M; endocapillary hypercellularity, E; segmental glomerulosclerosis, S; tubular atrophy/interstitial fibrosis, T), crescents (C) and other histological lesions with both a combined renal endpoint [50% estimated glomerular filtration rate (eGFR) loss or kidney failure] and the rate of eGFR decline over a follow-up period extending to 35 years [median 7 years (interquartile range 4.1-10.8)].Results: In this extended analysis, M1, S1 and T1-T2 lesions as well as the whole MEST score were independently related with the combined endpoint (P < 0.01), and there was no effect modification by age for these associations, suggesting that they may be valid in children and in adults as well. Only T lesions were associated with the rate of eGFR loss in the whole cohort, whereas C showed this association only in patients not treated with immunosuppression. In separate prognostic analyses, the whole set of pathology lesions provided a gain in discrimination power over the clinical variables alone, which was similar at 5 years (+2.0%) and for the whole follow-up (+1.8%). A similar benefit was observed for risk reclassification analyses (+2.7% and +2.4%).Conclusion: Long-term follow-up analyses of the VALIGA cohort showed that the independent relationship between kidney biopsy findings and the risk of progression towards kidney failure in IgAN remains unchanged across all age groups and decades after the renal biopsy.
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| 15. |
- Danielsson, Benjamin, et al.
(författare)
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Classifying Implant-Bearing Patients via their Medical Histories : a Pre-Study on Swedish EMRs with Semi-Supervised GAN-BERT
- 2022
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Ingår i: 2022 Language Resources and Evaluation Conference, LREC 2022. - : European Language Resources Association (ELRA). - 9791095546726 ; , s. 5428-5435
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Konferensbidrag (refereegranskat)abstract
- In this paper, we compare the performance of two BERT-based text classifiers whose task is to classify patients (more precisely, their medical histories) as having or not having implant(s) in their body. One classifier is a fully-supervised BERT classifier. The other one is a semi-supervised GAN-BERT classifier. Both models are compared against a fully-supervised SVM classifier. Since fully-supervised classification is expensive in terms of data annotation, with the experiments presented in this paper, we investigate whether we can achieve a competitive performance with a semi-supervised classifier based only on a small amount of annotated data. Results are promising and show that the semi-supervised classifier has a competitive performance when compared with the fully-supervised classifier. © licensed under CC-BY-NC-4.0.
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| 16. |
- Danielsson, Bengt, et al.
(författare)
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Classifying Implant-Bearing Patients via their Medical Histories: a Pre-Study on Swedish EMRs with Semi-Supervised GAN-BERT
- 2022
-
Ingår i: LREC 2022: THIRTEEN INTERNATIONAL CONFERENCE ON LANGUAGE RESOURCES AND EVALUATION. - : EUROPEAN LANGUAGE RESOURCES ASSOC-ELRA. - 9791095546726 ; , s. 5428-5435
-
Konferensbidrag (refereegranskat)abstract
- In this paper, we compare the performance of two BERT-based text classifiers whose task is to classify patients (more precisely, their medical histories) as having or not having implant(s) in their body. One classifier is a fully-supervised BERT classifier. The other one is a semi-supervised GAN-BERT classifier. Both models are compared against a fully-supervised SVM classifier. Since fully-supervised classification is expensive in terms of data annotation, with the experiments presented in this paper, we investigate whether we can achieve a competitive performance with a semi-supervised classifier based only on a small amount of annotated data. Results are promising and show that the semi-supervised classifier has a competitive performance when compared with the fully-supervised classifier.
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| 17. |
- Danielsson, Frida, et al.
(författare)
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Spatial Characterization of the Human Centrosome Proteome Opens Up New Horizons for a Small but Versatile Organelle
- 2020
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Ingår i: Proteomics. - : Wiley-VCH Verlag. - 1615-9853 .- 1615-9861.
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Tidskriftsartikel (refereegranskat)abstract
- After a century of research, the human centrosome continues to fascinate. Based on immunofluorescence and confocal microscopy, an extensive inventory of the protein components of the human centrosome, and the centriolar satellites, with the important contribution of over 300 novel proteins localizing to these compartments is presented. A network of candidate centrosome proteins involved in ubiquitination, including six interaction partners of the Kelch-like protein 21, and an additional network of protein phosphatases, together supporting the suggested role of the centrosome as an interactive hub for cell signaling, is identified. Analysis of multi-localization across cellular organelles analyzed within the Human Protein Atlas (HPA) project shows how multi-localizing proteins are particularly overrepresented in centriolar satellites, supporting the dynamic nature and wide range of functions for this compartment. In summary, the spatial dissection of the human centrosome and centriolar satellites described here provides a comprehensive knowledgebase for further exploration of their proteomes.
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| 18. |
- Dou, Diana R., et al.
(författare)
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Xist ribonucleoproteins promote female sex-biased autoimmunity
- 2024
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Ingår i: Cell. - : Elsevier BV. - 0092-8674 .- 1097-4172. ; 187:3, s. 16-733
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Tidskriftsartikel (refereegranskat)abstract
- Autoimmune diseases disproportionately affect females more than males. The XX sex chromosome complement is strongly associated with susceptibility to autoimmunity. Xist long non-coding RNA (lncRNA) is expressed only in females to randomly inactivate one of the two X chromosomes to achieve gene dosage compensation. Here, we show that the Xist ribonucleoprotein (RNP) complex comprising numerous autoantigenic components is an important driver of sex-biased autoimmunity. Inducible transgenic expression of a non-silencing form of Xist in male mice introduced Xist RNP complexes and sufficed to produce autoantibodies. Male SJL/J mice expressing transgenic Xist developed more severe multi-organ pathology in a pristane-induced lupus model than wild-type males. Xist expression in males reprogrammed T and B cell populations and chromatin states to more resemble wild-type females. Human patients with autoimmune diseases displayed significant autoantibodies to multiple components of XIST RNP. Thus, a sex-specific lncRNA scaffolds ubiquitous RNP components to drive sex-biased immunity.
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| 19. |
- Elsrud, Torun, et al.
(författare)
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Asylarkivet
- 2022
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Detta arkiv innehåller en tematiserad sammanställning av forskningsdata som samlats in i intervjuer med personer som har egna erfarenheter av asylprocessen i Sverige, personer som har erfarenheter av asylkontexten genom sina yrken och personer ur civilsamhället som har engagerat sig på frivillig basis för att stödja människor i asylprocess. Materialet är hämtat från projektet Insamling av forskningsdata för granskning av lagstiftning, lagtillämpning och rättssäkerhet för människor som sökte asyl i Sverige under perioden 2015-2017. Det är ett 1-årigt så kallat akutprojekt finansierat av Formas (Forskningsrådet för miljö, areella näringar och samhällsbyggande). Akutprojekt av detta slag syftar till att samla in data och att sammanställa denna som underlag för senare vetenskaplig forskning.
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| 20. |
- Elsrud, Torun, et al.
(författare)
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Transversal sanctuary enactments in Sweden : challenges, opportunities and implications
- 2023
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Ingår i: Journal of ethnic and migration studies. - : Taylor & Francis Group. - 1369-183X .- 1469-9451. ; 49:14, s. 3629-3648
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Tidskriftsartikel (refereegranskat)abstract
- This article contributes to scholarly discussions about sanctuary enactments. We analyse transversal sanctuary enactments, i.e. when migrants in search of protection are provided with basic welfare and an opportunity to remain, in contestation of the state's migration politics. The study draws on empirical data collected through a transdisciplinary research initiative in Sweden, the Asylum Commission. The analysis is based on interviews with 90 people, asylum seekers and people voluntarily or professionally involved in support work. The article explores bottom-up transversal processes paralleled and intertwined with a growing institutional disenchantment. By analysing practices and challenges in sanctuary enactments and their implications for individuals and institutions, we argue that such disenchantment may have broader societal implications in terms of fundamental changes in relationships between public institutions and civil society actors. Furthermore, our study points to the importance of seeing beyond the city as sites for sanctuary enactments and acknowledging sanctuary enactments initiated in Sweden's rural areas.
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| 21. |
- Gnann, Christian, 1994-
(författare)
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Finding order in chaos : Dissecting single-cell heterogeneity in space and time
- 2024
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The cell is the smallest unit of life and contains DNA, RNA, proteins and a variety of other macromolecules. In recent years, technological advances in the field of single cell biology have revealed a staggering amount of phenotypic heterogeneity between cells in a population, which were previously considered homogenous. Previous work has largely been focused on studies of RNA. As proteins however are the ultimate effectors of genetic information, this thesis aims to provide a protein-centered view on cellular heterogeneity, particularly focusing on cell cycle and cellular metabolism.Most of my work has been performed within the framework of the Human Protein Atlas project. In the context of this project, we mapped the spatial distribution of more than 13.000 human proteins with subcellular resolution and found that around a quarter of all human proteins exhibit protein expression heterogeneity.In Paper I, we hypothesized that a majority of the observed cellular heterogeneity can be explained by differences in cell cycle progression. Therefore, we generated a map of proteomic and transcriptomic heterogeneity at subcellular resolution, which we precisely aligned to the cell cycle position of individual cells. This approach allowed us to identify hundreds of previously unknown cell cycle-related proteins. With sustained proliferative signaling representing a hallmark of cancer, novel cell-cycle proteins could serve as potential new drug targets against cancer. We further show that a large part of cell cycle dependent proteome variability is not established by transcriptomic cycling. This suggests that post-translational modifications are a major contributor to the regulation of cell cycle dependent protein level changes. Therefore, in Paper II, we carried out a deep phosphoproteome mass spectrometry profiling of the same cellular model as in Paper I and identified almost 5,000 cell cycle dependent phosphosites on over 2,000 proteins. The unprecedented scale of our phosphoproteomic data allows us to link cell cycle dependent protein expression dynamics to phosphorylation events. Furthermore, we identify a large set of proteins with stable expression levels and fluctuating phosphorylation patterns along cell cycle progression that likely alters protein function.Despite identifying hundreds of novel cell cycle dependent proteins in paper I, we observed that the majority of heterogeneously expressed proteins display variable expression independent of cell cycle progression, among them a large number of metabolic enzymes. Thus, we sought to describe the extent of subcellular metabolic complexity in human cells and tissues in Paper III. While we confirm metabolic compartmentalization in our dataset, we show that around 50% of metabolic enzymes localize to multiple cellular compartments. By integrating public protein-protein interaction data with our subcellular location information, we identify several enzymes with novel compartment-specific functions. Additionally, we observe a strongly elevated number of heterogeneously expressed enzymes compared to the background of the human proteome that is largely independent of cell cycle progression. We show that this heterogeneity can be manifested in the lineage of a single cell and is conserved in situ. To conclude, we suggest that the extensive metabolic heterogeneity can establish functional metabolic states in a population of human cells.Finally, in Paper IV, we assessed the heterogeneity of the mitochondrial proteome as they are metabolic powerhouses containing an elevated number of cell cycle independent variably expressed proteins. In this study, we correlated the variable expression of over 400 mitochondrial proteins to the expression of rate limiting enzymes in important mitochondrial pathways; such as the TCA cycle and ROS metabolism. We show that enzymes in the same pathways often correlate in their expression, indicating that their expression variability may contribute to the establishment of metabolic states.Altogether, the thesis illuminates the spatiotemporal complexity of the human proteome established by protein multilocalization and expression heterogeneity as fundamental non-genetic means of functional cell regulation.
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| 22. |
- Gnann, Christian, et al.
(författare)
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Illuminating Non-genetic Cellular Heterogeneity with Imaging-Based Spatial Proteomics
- 2021
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Ingår i: Trends in cancer. - : Elsevier BV. - 2405-8025 .- 2405-8033. ; 7:4, s. 278-282
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Cellular heterogeneity is an important biological phenomenon observed across space and time in human tissues. Imaging-based spatial proteomic technologies can provide fruitful new readouts of phenotypic states for individual cells at subcellular resolution, which may help unravel the roles of non-genetic cellular heterogeneity in tumorigenesis and drug resistance.
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| 23. |
- Gómez-de-Mariscal, E., et al.
(författare)
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DeepImageJ : A user-friendly environment to run deep learning models in ImageJ
- 2021
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Ingår i: Nature Methods. - : Springer Nature. - 1548-7091 .- 1548-7105. ; 18:10, s. 1192-1195
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Tidskriftsartikel (refereegranskat)abstract
- DeepImageJ is a user-friendly solution that enables the generic use of pre-trained deep learning models for biomedical image analysis in ImageJ. The deepImageJ environment gives access to the largest bioimage repository of pre-trained deep learning models (BioImage Model Zoo). Hence, nonexperts can easily perform common image processing tasks in life-science research with deep learning-based tools including pixel and object classification, instance segmentation, denoising or virtual staining. DeepImageJ is compatible with existing state of the art solutions and it is equipped with utility tools for developers to include new models. Very recently, several training frameworks have adopted the deepImageJ format to deploy their work in one of the most used softwares in the field (ImageJ). Beyond its direct use, we expect deepImageJ to contribute to the broader dissemination and reuse of deep learning models in life sciences applications and bioimage informatics.
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| 24. |
- Hickey, J. W., et al.
(författare)
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Spatial mapping of protein composition and tissue organization : a primer for multiplexed antibody-based imaging
- 2022
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Ingår i: Nature Methods. - : Nature Research. - 1548-7091 .- 1548-7105. ; 19:3, s. 284-295
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Tidskriftsartikel (refereegranskat)abstract
- Tissues and organs are composed of distinct cell types that must operate in concert to perform physiological functions. Efforts to create high-dimensional biomarker catalogs of these cells have been largely based on single-cell sequencing approaches, which lack the spatial context required to understand critical cellular communication and correlated structural organization. To probe in situ biology with sufficient depth, several multiplexed protein imaging methods have been recently developed. Though these technologies differ in strategy and mode of immunolabeling and detection tags, they commonly utilize antibodies directed against protein biomarkers to provide detailed spatial and functional maps of complex tissues. As these promising antibody-based multiplexing approaches become more widely adopted, new frameworks and considerations are critical for training future users, generating molecular tools, validating antibody panels, and harmonizing datasets. In this Perspective, we provide essential resources, key considerations for obtaining robust and reproducible imaging data, and specialized knowledge from domain experts and technology developers.
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| 25. |
- Jain, Yashvardhan, et al.
(författare)
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Segmenting functional tissue units across human organs using community-driven development of generalizable machine learning algorithms
- 2023
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 14:1
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Tidskriftsartikel (refereegranskat)abstract
- The development of a reference atlas of the healthy human body requires automated image segmentation of major anatomical structures across multiple organs based on spatial bioimages generated from various sources with differences in sample preparation. We present the setup and results of the Hacking the Human Body machine learning algorithm development competition hosted by the Human Biomolecular Atlas (HuBMAP) and the Human Protein Atlas (HPA) teams on the Kaggle platform. We create a dataset containing 880 histology images with 12,901 segmented structures, engaging 1175 teams from 78 countries in community-driven, open-science development of machine learning models. Tissue variations in the dataset pose a major challenge to the teams which they overcome by using color normalization techniques and combining vision transformers with convolutional models. The best model will be productized in the HuBMAP portal to process tissue image datasets at scale in support of Human Reference Atlas construction.
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| 26. |
- Johnson, Graham T., et al.
(författare)
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Building the next generation of virtual cells to understand cellular biology
- 2023
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Ingår i: Biophysical Journal. - : Elsevier BV. - 0006-3495 .- 1542-0086. ; 122:18, s. 3560-3569
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Tidskriftsartikel (refereegranskat)abstract
- Cell science has made significant progress by focusing on understanding individual cellular processes through reductionist approaches. However, the sheer volume of knowledge collected presents challenges in integrating this information across different scales of space and time to comprehend cellular behaviors, as well as making the data and methods more accessible for the community to tackle complex biological questions. This perspective proposes the creation of next-generation virtual cells, which are dynamic 3D models that integrate information from diverse sources, including simulations, biophysical models, image-based models, and evidence-based knowledge graphs. These virtual cells would provide statistically accurate and holistic views of real cells, bridging the gap between theoretical concepts and experimental data, and facilitating productive new collaborations among researchers across related fields.
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| 27. |
- Jonnergård, Annie, 1986, et al.
(författare)
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Person-centred care in the context of higher education - a discourse analysis based on interviews with programme directors
- 2024
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Ingår i: BMC MEDICAL EDUCATION. - 1472-6920. ; 24:1
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundAs person centred care (PCC) is being implemented globally, higher educational institutions (HEI) have begun to play a crucial part in enabling this transition. In Sweden, however, the delivery of PCC is inconsistently implemented in medicine, nursing, occupational therapy, and physiotherapy study programmes. This inconsistency is partly the result of a lack of a national strategy across HEI. Program directors are responsible for the PCC content of their programs, so their views influence how PCC is taught. Using interviews with programme directors in higher education, we aim to deepen the understanding of the preconditions needed to implement PCC by exploring discourses and identifying subject positions of how PCC is taught and learned.MethodsWe performed a discourse analysis based on interviews with program directors in the above-mentioned national study programmes. A discourse can be seen as a struggle over identity. The subject position - i.e., discourses designate positions for persons to occupy as subjects - guided our analysis and identification of the subject positions of the teacher and the student in teaching and learning PCC.ResultsThis study unfolded in two main antagonistic aspects with respect to teaching and learning PCC, resulting in four subject positions for the teacher and four corresponding subject positions for the students. First, the teacher and student were given a subject position as change agents towards a more egalitarian healthcare and were assigned a subject position to cope with a practical reality they could not change. Second, the teacher and student were assigned a subject position that embodied profession-specific identities, navigating and valuing these boundaries. Simultaneously, both teachers and students assumed a subject position that required interprofessional interaction and co-creation for teaching and learning PCC.ConclusionThis study demonstrates the discursive tension surrounding the implementation of PCC in HEI, and the findings can serve as a basis for creating future relevant and high-quality learning activities. The process of negotiating diverse and co-existing perspectives as well as building interprofessional trust when incorporating PCC into higher education is essential and requires further exploration.
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| 28. |
- Jonson, Emma, 1981, et al.
(författare)
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Exploring the competition between variable renewable electricity and a carbon-neutral baseload technology
- 2020
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Ingår i: Energy Systems. - : Springer Science and Business Media LLC. - 1868-3975 .- 1868-3967. ; 11:1, s. 21-44
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Tidskriftsartikel (refereegranskat)abstract
- In this paper we explore the competition between variable renewable energy sources (VRE) and a carbon-neutral baseload technology in the transition to a low-carbon power system. We study a stylized system subject to a gradually increasing carbon tax using an agent-based model where agents are power companies investing in new capacity. The agents make predictions of the profitability of different investment options. Five electricity generating technologies are available in the model: coal, gas, wind, solar PV and a more expensive carbon-neutral baseload technology. We compare the output from our model with a corresponding optimization model. We present two main findings: (1) installed capacity of VRE initially increases with a carbon tax. However, once the carbon tax has reached a certain level the installed capacity of VRE starts to decline due to competition with the stylized carbon-neutral baseload technology. (2) With limited foresight we find that the model underinvests (first 25 years) in wind and then overinvests in wind compared to the optimal solution. The reasons for these dynamic phenomena are explained and an extensive sensitivity analysis is carried out.
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| 29. |
- King, Matthew R., et al.
(författare)
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Macromolecular condensation organizes nucleolar sub-phases to set up a pH gradient
- 2024
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Ingår i: Cell. - : Elsevier BV. - 0092-8674 .- 1097-4172. ; 187:8, s. 24-1889
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Tidskriftsartikel (refereegranskat)abstract
- Nucleoli are multicomponent condensates defined by coexisting sub-phases. We identified distinct intrinsically disordered regions (IDRs), including acidic (D/E) tracts and K-blocks interspersed by E-rich regions, as defining features of nucleolar proteins. We show that the localization preferences of nucleolar proteins are determined by their IDRs and the types of RNA or DNA binding domains they encompass. In vitro reconstitutions and studies in cells showed how condensation, which combines binding and complex coacervation of nucleolar components, contributes to nucleolar organization. D/E tracts of nucleolar proteins contribute to lowering the pH of co-condensates formed with nucleolar RNAs in vitro. In cells, this sets up a pH gradient between nucleoli and the nucleoplasm. By contrast, juxta-nucleolar bodies, which have different macromolecular compositions, featuring protein IDRs with very different charge profiles, have pH values that are equivalent to or higher than the nucleoplasm. Our findings show that distinct compositional specificities generate distinct physicochemical properties for condensates.
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| 30. |
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| 33. |
- Le, Trang, et al.
(författare)
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Analysis of the Human Protein Atlas Weakly Supervised Single-Cell Classification competition
- 2022
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Ingår i: Nature Methods. - : Springer Nature. - 1548-7091 .- 1548-7105. ; 19:10, s. 1221-1229
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Tidskriftsartikel (refereegranskat)abstract
- While spatial proteomics by fluorescence imaging has quickly become an essential discovery tool for researchers, fast and scalable methods to classify and embed single-cell protein distributions in such images are lacking. Here, we present the design and analysis of the results from the competition Human Protein Atlas – Single-Cell Classification hosted on the Kaggle platform. This represents a crowd-sourced competition to develop machine learning models trained on limited annotations to label single-cell protein patterns in fluorescent images. The particular challenges of this competition include class imbalance, weak labels and multi-label classification, prompting competitors to apply a wide range of approaches in their solutions. The winning models serve as the first subcellular omics tools that can annotate single-cell locations, extract single-cell features and capture cellular dynamics.
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| 34. |
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| 35. |
- Lundberg, Anna, Professor, 1972-, et al.
(författare)
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Rättsosäkerheten och nämndepersonerna
- 2021
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Ingår i: Artikel 14. - 1104-1846. ; , s. 18-21:4, s. 18-21
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Tidskriftsartikel (populärvet., debatt m.m.)
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| 36. |
- Lundberg, Erik, 1978, et al.
(författare)
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Communicating inclusiveness through major sporting events: development and application of a framework
- 2024
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Ingår i: SCANDINAVIAN JOURNAL OF HOSPITALITY AND TOURISM. - : Taylor & Francis. - 1502-2250 .- 1502-2269.
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Tidskriftsartikel (refereegranskat)abstract
- Major sporting events (MSEs) have been used by governments to improve the image of cities and nations, and to attract tourists. In the wake of criticism of how global MSEs handle human-rights issues, governments are pressured to rethink how these events are organised and branded. Developing and employing an analytical framework based on inclusive place branding and pathways to progressive human-rights outcomes, this study explores how and to whom inclusiveness is communicated in five Olympic Games candidate files. A quantitative content analysis is performed using keywords related to inclusiveness and three characteristics of inclusiveness are analysed qualitatively: democratic representation, inclusive participation, and committed transformation. The findings show that three of the candidate files predominantly belong to the traditional place branding paradigm through their focus on external stakeholders, while two have adopted a more inclusive place branding strategy and put emphasis on internal stakeholders. The analytical framework introduced in this study can be useful for both researchers and practitioners - such as prospective hosts of MSEs and other events - as a conceptual tool to analyse and develop inclusiveness in major events.
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| 37. |
- Lundberg, Emma, 1984, et al.
(författare)
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Deconstructing spiritual care: Discursive underpinnings within palliative care research
- 2024
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Ingår i: Nursing Inquiry. - 1320-7881. ; 31:3
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Tidskriftsartikel (refereegranskat)abstract
- Religion and spirituality are integral to the philosophy of palliative care, shaping its approach to spiritual care. This article aims to examine the discourses within palliative care research to illuminate prevailing assumptions regarding spiritual care. Eighteen original articles were analyzed to examine how spiritual care is understood within palliative care. The analysis, informed by Foucault, aimed to identify recurring discourses. The finding reveals that, in palliative care research, spirituality is viewed as enigmatic yet inherently human and natural, assuming that every individual has a spiritual dimension. The analysis points to healthcare professionals being expected to hold certain qualities to put spiritual care into practice. The analysis also reveals that in the analyzed articles, the concept of spiritual care is rooted in a Christian context, with the belief that all individuals possess inherent spirituality or religiosity, a concept often associated with Christian theology. The included articles often utilize theological terms and emphasize a monotheistic viewpoint. Spirituality is articulated as a complex, distinct concept, challenging clear definitions and professional responsibilities. Further, a moral formation of healthcare professionals is described, interpelling and ascribing qualities that healthcare professionals need to provide spiritual care.
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| 38. |
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| 39. |
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| 40. |
- Lundberg, Emma, 1984, et al.
(författare)
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Place of death among foreign-born individuals: a national population-based register study.
- 2023
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Ingår i: Palliative care and social practice. - 2632-3524. ; 17
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Tidskriftsartikel (refereegranskat)abstract
- Relatively little is known about where foreign-born individuals die in Sweden and how birth region might influence place of death. Thus, there is a need for population-based studies investigating place of death and associated factors among foreign-born individuals.The aim of this study was to identify variations in place of death among foreign-born individuals residing in Sweden and to compare place of death between the foreign- and domestic-born population. We also examine the association between place of death, underlying cause of death and sociodemographic characteristics among the foreign-born population.A population-based register study.All deceased individuals ⩾18years of age in Sweden with a registered place of death between 2012 and 2019 (n=682,697). Among these, 78,466 individuals were foreign-born. Univariable multinomial logistic regression modelling and multivariable multinomial logistic regression analyses were performed.Overall, hospital was the most common place of death among the foreign-born population. However, there were variations in place of death related to region of birth. Compared to domestic-born, a higher proportion of foreign-born individuals dies at home, the majority of whom were born on the African continent.Region of birth is one of the several factors associated with place of death among foreign-born individuals. Further research is needed to explore both preferences and barriers to place of death among foreign-born individuals.
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| 41. |
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| 44. |
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| 45. |
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| 46. |
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| 47. |
- Lundin, Emma
(creator_code:cre_t)
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Maktquiz
- 2023
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Annan publikation (populärvet., debatt m.m.)
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| 48. |
- Mahdessian, Diana, et al.
(författare)
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Spatiotemporal dissection of the cell cycle with single-cell proteogenomics
- 2021
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Ingår i: Nature. - : Springer Nature. - 0028-0836 .- 1476-4687. ; 590:7847
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Tidskriftsartikel (refereegranskat)abstract
- Spatial and temporal variations among individual human cell proteomes are comprehensively mapped across the cell cycle using proteomic imaging and transcriptomics. The cell cycle, over which cells grow and divide, is a fundamental process of life. Its dysregulation has devastating consequences, including cancer(1-3). The cell cycle is driven by precise regulation of proteins in time and space, which creates variability between individual proliferating cells. To our knowledge, no systematic investigations of such cell-to-cell proteomic variability exist. Here we present a comprehensive, spatiotemporal map of human proteomic heterogeneity by integrating proteomics at subcellular resolution with single-cell transcriptomics and precise temporal measurements of individual cells in the cell cycle. We show that around one-fifth of the human proteome displays cell-to-cell variability, identify hundreds of proteins with previously unknown associations with mitosis and the cell cycle, and provide evidence that several of these proteins have oncogenic functions. Our results show that cell cycle progression explains less than half of all cell-to-cell variability, and that most cycling proteins are regulated post-translationally, rather than by transcriptomic cycling. These proteins are disproportionately phosphorylated by kinases that regulate cell fate, whereas non-cycling proteins that vary between cells are more likely to be modified by kinases that regulate metabolism. This spatially resolved proteomic map of the cell cycle is integrated into the Human Protein Atlas and will serve as a resource for accelerating molecular studies of the human cell cycle and cell proliferation.
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| 49. |
- Melani, Rafael D., et al.
(författare)
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The Blood Proteoform Atlas : A reference map of proteoforms in human hematopoietic cells
- 2022
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 375:6579, s. 411-
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Tidskriftsartikel (refereegranskat)abstract
- Human biology is tightly linked to proteins, yet most measurements do not precisely determine alternatively spliced sequences or posttranslational modifications. Here, we present the primary structures of similar to 30,000 unique proteoforms, nearly 10 times more than in previous studies, expressed from 1690 human genes across 21 cell types and plasma from human blood and bone marrow. The results, compiled in the Blood Proteoform Atlas (BPA), indicate that proteoforms better describe protein-level biology and are more specific indicators of differentiation than their corresponding proteins, which are more broadly expressed across cell types. We demonstrate the potential for clinical application, by interrogating the BPA in the context of liver transplantation and identifying cell and proteoform signatures that distinguish normal graft function from acute rejection and other causes of graft dysfunction.
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| 50. |
- Moffitt, J. R., et al.
(författare)
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The emerging landscape of spatial profiling technologies
- 2022
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Ingår i: Nature reviews genetics. - : Springer Nature. - 1471-0056 .- 1471-0064. ; 23:12, s. 741-759
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Tidskriftsartikel (refereegranskat)abstract
- Improved scale, multiplexing and resolution are establishing spatial nucleic acid and protein profiling methods as a major pillar for cellular atlas building of complex samples, from tissues to full organisms. Emerging methods yield omics measurements at resolutions covering the nano- to microscale, enabling the charting of cellular heterogeneity, complex tissue architectures and dynamic changes during development and disease. We present an overview of the developing landscape of in situ spatial genome, transcriptome and proteome technologies, exemplify their impact on cell biology and translational research, and discuss current challenges for their community-wide adoption. Among many transformative applications, we envision that spatial methods will map entire organs and enable next-generation pathology.
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