| 1. |
- Sandås, Kristofer, et al.
(författare)
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Nanometa Live : a user-friendly application for real-time metagenomic data analysis and pathogen identification
- 2024
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Ingår i: Bioinformatics. - : Oxford University Press. - 1367-4803 .- 1367-4811. ; 40:3
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Tidskriftsartikel (refereegranskat)abstract
- Summary: Nanometa Live presents a user-friendly interface designed for real-time metagenomic data analysis and pathogen identification utilizing Oxford Nanopore Technologies’ MinION and Flongle flow cells. It offers an efficient workflow and graphical interface for the visualization and interpretation of metagenomic data as it is being generated. Key features include automated BLAST validation, streamlined handling of custom Kraken2 databases, and a simplified graphical user interface for enhanced user experience. Nanometa Live is particularly notable for its capability to run without constant internet or server access once installed, setting it apart from similar tools. It provides a comprehensive view of taxonomic composition and facilitates the detection of user-defined pathogens or other species of interest, catering to both researchers and clinicians.Availability and implementation: Nanometa Live has been implemented as a local web application using the Dash framework with Snakemake handling the data processing. The source code is freely accessible on the GitHub repository at https://github.com/FOIBioinformatics/nanometa_live and it is easily installable using Bioconda. It includes containerization support via Docker and Singularity, ensuring ease of use, reproducibility, and portability.
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| 2. |
- Abdellah, Tebani, et al.
(författare)
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Integration of molecular profiles in a longitudinal wellness profiling cohort.
- 2020
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Ingår i: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- An important aspect of precision medicine is to probe the stability in molecular profiles among healthy individuals over time. Here, we sample a longitudinal wellness cohort with 100 healthy individuals and analyze blood molecular profiles including proteomics, transcriptomics, lipidomics, metabolomics, autoantibodies andimmune cell profiling, complementedwith gut microbiota composition and routine clinical chemistry. Overall, our results show high variation between individuals across different molecular readouts, while the intra-individual baseline variation is low. The analyses show that each individual has a unique and stable plasma protein profile throughout the study period and that many individuals also show distinct profiles with regards to the other omics datasets, with strong underlying connections between the blood proteome and the clinical chemistry parameters. In conclusion, the results support an individual-based definition of health and show that comprehensive omics profiling in a longitudinal manner is a path forward for precision medicine.
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| 3. |
- Corman, Jessica R., et al.
(författare)
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Response of lake metabolism to catchment inputs inferred using high-frequency lake and stream data from across the northern hemisphere
- 2023
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Ingår i: Limnology and Oceanography. - : John Wiley & Sons. - 0024-3590 .- 1939-5590. ; 68:12, s. 2617-2631
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Tidskriftsartikel (refereegranskat)abstract
- In lakes, the rates of gross primary production (GPP), ecosystem respiration (R), and net ecosystem production (NEP) are often controlled by resource availability. Herein, we explore how catchment vs. within lake predictors of metabolism compare using data from 16 lakes spanning 39°N to 64°N, a range of inflowing streams, and trophic status. For each lake, we combined stream loads of dissolved organic carbon (DOC), total nitrogen (TN), and total phosphorus (TP) with lake DOC, TN, and TP concentrations and high frequency in situ monitoring of dissolved oxygen. We found that stream load stoichiometry indicated lake stoichiometry for C : N and C : P (r2 = 0.74 and r2 = 0.84, respectively), but not for N : P (r2 = 0.04). As we found a strong positive correlation between TN and TP, we only used TP in our statistical models. For the catchment model, GPP and R were best predicted by DOC load, TP load, and load N : P (R2 = 0.85 and R2 = 0.82, respectively). For the lake model, GPP and R were best predicted by TP concentrations (R2 = 0.86 and R2 = 0.67, respectively). The inclusion of N : P in the catchment model, but not the lake model, suggests that both N and P regulate metabolism and that organisms may be responding more strongly to catchment inputs than lake resources. Our models predicted NEP poorly, though it is unclear why. Overall, our work stresses the importance of characterizing lake catchment loads to predict metabolic rates, a result that may be particularly important in catchments experiencing changing hydrologic regimes related to global environmental change.
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| 4. |
- Ek, Kristine, 1975, et al.
(författare)
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A harmonized method for automatable life cycle sustainability performance assessment and comparison of civil engineering works design concepts
- 2020
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Ingår i: IOP Conference Series: Earth and Environmental Science. - : IOP Publishing. - 1755-1307 .- 1755-1315. ; 588:5
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Konferensbidrag (refereegranskat)abstract
- The life cycle sustainability performance of civil engineering works is increasingly important. The possibility to influence the sustainability of a project design is larger in the conceptual stage than in later stages. Better-informed decisions regarding design choices’ impact on sustainability can be made by comparing conceptual project designs based on an assessment of their life cycle sustainability performance. It is essential that concepts are assessed in a harmonized way and compared impartially. Current standards provide the general framework for the assessment of sustainability performance, but do not give detailed guidance on calculation of sustainability indicators and their aggregation. Since design in automated systems is becoming increasingly common, there is a growing need for machine-readable data and automatable assessment methods. Assessment methods which can be applied using open-access data is important to achieve fair competition. This paper aims to provide a method for life cycle sustainability performance assessment and comparison of civil engineering works design concepts, possible to apply using open-access Environmental Product Declarations (EPDs) and life cycle assessment (LCA) data. The purpose is to enable fair and automatable sustainability assessments of design concepts, to facilitate impartial comparisons of such assessments as a basis for choosing sustainable designs. A literature review of relevant standards and scientific papers on sustainability assessment of construction and civil engineering works was performed. A harmonized, fair and automatable method for life cycle sustainability assessment and comparison of civil engineering works design concepts, well-suited for optimization purposes, is presented. However, the aim currently limits categories and indicators possible to include. The proposed method includes guidance on the calculation of environmental, social and economic indicators, based on LCA, life cycle costing (LCC) and external costs, and aggregation using normalisation and weighting factors of the Product Environmental Footprint (PEF). The proposed method allows for an impartial comparison of the sustainability of design concepts, resulting in better-informed decisions.
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| 5. |
- Glise Sandblad, Katarina, 1982, et al.
(författare)
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Prevalence of Cancer in Patients with Venous Thromboembolism: A Retrospective Nationwide Case-Control Study in Sweden.
- 2023
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Ingår i: Clinical and applied thrombosis/hemostasis : official journal of the International Academy of Clinical and Applied Thrombosis/Hemostasis. - : SAGE Publications. - 1938-2723. ; 29
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Tidskriftsartikel (refereegranskat)abstract
- Cancer is a risk factor for venous thromboembolism (VTE). We aimed to define sex-specific risk of preceding cancer in patients with a first-time VTE by conducting a nationwide Swedish registry-based study including 298172 patients with VTE and 1185079 matched controls. This included 44685 patients with a diagnosis of cancer at/or within 1 year before a VTE diagnosis. Female patients with VTE had a higher multivariable adjusted odds ratios of preceding cancer than male patients with VTE (5.5 [99% confidence interval 5.4-5.7] vs 3.9 [3.8-4.0]). The highest risk of cancer in patients with VTE were found for pancreatic cancer (women: 19.6 [15.8-24.4]; men: 17.2 [13.7-21.6]) and brain cancer (women: 17.4 [12.9-23.4]; men: 17.5 [13.8-22.2]). Weak associations were seen between VTE and bladder/urothelial cancer (women: 1.31 [1.12-1.53]; men: 1.34 [1.23-1.47]), prostate cancer (men: 2.17 [2.07-2.27]), malignant melanoma (women: 2.51 [2.07-3.05]; men: 2.67 [2.23-3.18]), and kidney cancer (women: 3.20 [2.49-4.11]; men: 3.33 [2.79-4.07]). In conclusion, associations with VTE were weak for bladder/urothelial cancer and kidney cancer, and strong for pancreatic, brain, and biliary cancers.
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| 6. |
- Gösta, Alexander, et al.
(författare)
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Data-Informed Urban Design: An Overview of the Use of Data and Digital Tools in Urban Planning and Design
- 2020
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Ingår i: Built Environment. - : Alexandrine Press. - 0263-7960. ; 46:4, s. 620-636
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Tidskriftsartikel (refereegranskat)abstract
- This article aims to map how different digital tools can be useful for architects and how they might affect their work processes. Researchers and professionals were interviewed to investigate what they found valuable to measure, which methods they used within their analyses, as well as the opportunities and risks they see for the future of the field with regards to digital tools. As part of the survey, a workshop was held with architects and project managers examining the possibilities of connecting existing methods and tools to the sustainability certification system, City Lab Action Guide, and through that, to achieve a more ambitious set of sustainability goals for the projects. Findings from the study indicate that there are risks associated with giving data an increasingly important role in the design work. A working model never provides the full truth but is inherently limited by its constraints. It is important to acknowledge that all angles and aspects of a problem can never be represented in a model. Another possible risk identified lies in the quality of, and access to, data. In a scenario where data plays an increasingly important role, it is not only the quality of the datasets that is of utmost importance, but it is equally important that the urban planners who request the analyses ask the questions first, and then collect the necessary data, instead of vice versa.
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| 7. |
- Hirlekar, Geir, et al.
(författare)
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Comorbidity and bystander cardiopulmonary resuscitation in out-of-hospital cardiac arrest.
- 2020
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Ingår i: Heart. - : BMJ. - 1355-6037 .- 1468-201X. ; 106:14, s. 1087-1093
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVE: Cardiopulmonary resuscitation (CPR) performed before the arrival of emergency medical services (EMS) is associated with increased survival after out-of-hospital cardiac arrest (OHCA). The aim of this study was to determine whether patients who receive bystander CPR have a different comorbidity compared with patients who do not, and to determine the association between bystander CPR and 30-day survival when adjusting for such a possible difference. METHODS: Patients with witnessed OHCA in the Swedish Registry for Cardiopulmonary Resuscitation between 2011 and 2015 were included, and merged with the National Patient Registry. The Charlson Comorbidity Index (CCI) was used to measure comorbidity. Multiple logistic regression was used to examine the effect of CCI on the association between bystander CPR and outcome. RESULTS: In total, 11 955 patients with OHCA were included, 71% of whom received bystander CPR. Patients who received bystander CPR had somewhat lower comorbidity (CCI) than those who did not (mean±SD: 2.2±2.3 vs 2.5±2.4; p<0.0001). However, this difference in comorbidity had no influence on the association between bystander CPR and 30-day survival in a multivariable model including other possible confounders (OR 2.34 (95% CI 2.01 to 2.74) without adjustment for CCI and OR 2.32 (95% CI 1.98 to 2.71) with adjustment for CCI). CONCLUSION: Patients who undergo CPR before the arrival of EMS have a somewhat lower degree of comorbidity than those who do not. Taking this difference into account, bystander CPR is still associated with a marked increase in 30-day survival after OHCA.
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| 8. |
- Johansson, Emil, et al.
(författare)
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Hierarchical Clustering and Trajectory Analyses Reveal Viremia-Independent B-Cell Perturbations in HIV-2 Infection
- 2022
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Ingår i: Cells. - : MDPI. - 2073-4409. ; 11:19
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Tidskriftsartikel (refereegranskat)abstract
- Time to AIDS in HIV-2 infection is approximately twice as long compared to in HIV-1 infection. Despite reduced viremia, HIV-2-infected individuals display signs of chronic immune activation. In HIV-1-infected individuals, B-cell hyperactivation is driven by continuous antigen exposure. However, the contribution of viremia to B-cell perturbations in HIV-2-infected individuals remains largely unexplored. Here, we used polychromatic flow cytometry, consensus hierarchical clustering and pseudotime trajectory inference to characterize B-cells in HIV-1- or HIV-2-infected and in HIV seronegative individuals. We observed increased frequencies of clusters containing hyperactivated T-bethighCD95highCD27int and proliferating T-bet+CD95highCD27+CD71+ memory B-cells in viremic HIV-1 (p < 0.001 and p < 0.001, respectively), viremic HIV-2 (p < 0.001 and p = 0.014, respectively) and in treatment-naïve aviremic HIV-2 (p = 0.004 and p = 0.020, respectively)-infected individuals, compared to seronegative individuals. In contrast, these expansions were not observed in successfully treated HIV-1-infected individuals. Finally, pseudotime trajectory inference showed that T-bet-expressing hyperactivated and proliferating memory B-cell populations were located at the terminal end of two trajectories, in both HIV-1 and HIV-2 infections. As the treatment-naïve aviremic HIV-2-infected individuals, but not the successfully ART-treated HIV-1-infected individuals, showed B-cell perturbations, our data suggest that aviremic HIV-2-infected individuals would also benefit from antiretroviral treatment.
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| 9. |
- Karlsson, Linda, et al.
(författare)
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Cerebrospinal fluid reference proteins increase accuracy and interpretability of biomarkers for brain diseases.
- 2024
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Ingår i: Nature Communications. - 2041-1723. ; 15:1
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Tidskriftsartikel (refereegranskat)abstract
- Cerebrospinal fluid (CSF) biomarkers reflect brain pathophysiology and are used extensively in translational research as well as in clinical practice for diagnosis of neurological diseases, e.g., Alzheimer's disease (AD). However, CSF biomarker concentrations may be influenced by non-disease related inter-individual variability. Here we use a data-driven approach to demonstrate the existence of inter-individual variability in mean standardized CSF protein levels. We show that these non-disease related differences cause many commonly reported CSF biomarkers to be highly correlated, thereby producing misleading results if not accounted for. To adjust for this inter-individual variability, we identified and evaluated high-performing reference proteins which improved the diagnostic accuracy of key CSF AD biomarkers. Our reference protein method attenuates the risk for false positive findings, and improves the sensitivity and specificity of CSF biomarkers, with broad implications for both research and clinical practice.
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| 10. |
- Karlsson, Max, et al.
(författare)
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A single-cell type transcriptomics map of human tissues
- 2021
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Ingår i: Science Advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 7:31
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Tidskriftsartikel (refereegranskat)abstract
- Advances in molecular profiling have opened up the possibility to map the expression of genes in cells, tissues, and organs in the human body. Here, we combined single-cell transcriptomics analysis with spatial antibody-based protein profiling to create a high-resolution single-cell type map of human tissues. An open access atlas has been launched to allow researchers to explore the expression of human protein-coding genes in 192 individual cell type clusters. An expression specificity classification was performed to determine the number of genes elevated in each cell type, allowing comparisons with bulk transcriptomics data. The analysis highlights distinct expression clusters corresponding to cell types sharing similar functions, both within the same organs and between organs.
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