| 1. |
- Frazier-Wood, Alexis C., et al.
(author)
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Genetic variants associated with subjective well-being, depressive symptoms, and neuroticism identified through genome-wide analyses
- 2016
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In: Nature Genetics. - : Nature Research (part of Springer Nature). - 1061-4036 .- 1546-1718. ; 48, s. 624-
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Journal article (peer-reviewed)abstract
- Very few genetic variants have been associated with depression and neuroticism, likely because of limitations on sample size in previous studies. Subjective well-being, a phenotype that is genetically correlated with both of these traits, has not yet been studied with genome-wide data. We conducted genome-wide association studies of three phenotypes: subjective well-being (n = 298,420), depressive symptoms (n = 161,460), and neuroticism (n = 170,911). We identify 3 variants associated with subjective well-being, 2 variants associated with depressive symptoms, and 11 variants associated with neuroticism, including 2 inversion polymorphisms. The two loci associated with depressive symptoms replicate in an independent depression sample. Joint analyses that exploit the high genetic correlations between the phenotypes (vertical bar(p) over cap vertical bar approximate to 0.8) strengthen the overall credibility of the findings and allow us to identify additional variants. Across our phenotypes, loci regulating expression in central nervous system and adrenal or pancreas tissues are strongly enriched for association.
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| 2. |
- Sandås, Kristofer, et al.
(author)
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Nanometa Live : a user-friendly application for real-time metagenomic data analysis and pathogen identification
- 2024
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In: Bioinformatics. - : Oxford University Press. - 1367-4803 .- 1367-4811. ; 40:3
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Journal article (peer-reviewed)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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| 3. |
- Abdellah, Tebani, et al.
(author)
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Integration of molecular profiles in a longitudinal wellness profiling cohort.
- 2020
-
In: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 11:1
-
Journal article (peer-reviewed)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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| 4. |
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| 5. |
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| 6. |
- Corman, Jessica R., et al.
(author)
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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
-
In: Limnology and Oceanography. - : John Wiley & Sons. - 0024-3590 .- 1939-5590. ; 68:12, s. 2617-2631
-
Journal article (peer-reviewed)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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| 7. |
- Eidemüller,, et al.
(author)
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Breast cancer risk among Swedish hemangioma patients and possible consequences of radiation-induced genomic instability.
- 2009
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In: Mutation research. - 0027-5107.
-
Journal article (peer-reviewed)abstract
- Breast cancer incidence among 17,158 female Swedish hemangioma patients was analyzed with empirical excess relative risk models and with a biologically-based model of carcinogenesis. The patients were treated in infancy mainly by external application of radium-226. The mean and median absorbed doses to the breast were 0.29 and 0.04Gy, and a total of 678 breast cancer cases have been observed. Both models agree very well in the risk estimates with an excess relative risk and excess absolute risk at the age of 50 years, about the mean age of breast cancer incidence, of 0.25Gy(-1)(95% CI 0.14; 0.37) and 30.7 [Formula: see text] (95% CI 16.9; 42.8), respectively. Models incorporating effects of radiation-induced genomic instability were developed and applied to the hemangioma cohort. The biologically-based description of the radiation risk was significantly improved with a model of genomic instability at an early stage of carcinogenesis.
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| 8. |
- Eidemüller, Markus, et al.
(author)
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Breast cancer risk after radiation treatment at infancy: potential consequences of radiation-induced genomic instability.
- 2011
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In: Radiation protection dosimetry. - : Oxford University Press (OUP). - 1742-3406 .- 0144-8420. ; 143:2-4, s. 375-9
-
Journal article (peer-reviewed)abstract
- Swedish hemangioma patients were treated in infancy mainly by external application of radium-226 starting from 1920. This work analysed the radiation risk among 17,158 women with a total of 678 breast cancer incidence cases with models of carcinogenesis and empirical excess relative risk models. Models incorporating effects of genomic instability were developed and applied to the hemangioma cohort. The description of the radiation risk was significantly improved with a model of genomic instability at an early stage of carcinogenesis.
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| 9. |
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| 10. |
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| 11. |
- Ek, Kristine, 1975, et al.
(author)
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A harmonized method for automatable life cycle sustainability performance assessment and comparison of civil engineering works design concepts
- 2020
-
In: IOP Conference Series: Earth and Environmental Science. - : IOP Publishing. - 1755-1307 .- 1755-1315. ; 588:5
-
Conference paper (peer-reviewed)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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| 12. |
- Flink, Axel, et al.
(author)
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Influence of Si on the Microstructure of Arc Evaporated (Ti,Si)N Thin Films : Evidence for Cubic Solid Solutions and their Thermal Stability
- 2005
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In: Surface and Coatings Technology. - : Elsevier BV. - 0257-8972. ; 200:5-6, s. 1535-1542
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Journal article (peer-reviewed)abstract
- Ti1−xSixN (0 ≤ x ≤ 0.14) thin solid films were deposited onto cemented carbide (WC-Co) substrates by arc evaporation. X-ray diffraction and transmission electron microscopy showed that all films were of NaCl-structure type phase. The as-deposited films exhibited a competitive columnar growth mode where the structure transits to a feather-like nanostructure with increasing Si content. Films with 0 ≤ x ≤ 0.01 had a 111 crystallographic preferred orientation which changed to an exclusive 200 texture for 0.05 ≤ x ≤ 0.14. X-ray photoelectron spectroscopy revealed the presence of Si–N bonding, but no amorphous Si3N4. Band structure calculations performed using a full potential linear muffin tin orbital method showed that for a given NaCl-structure Ti1−xSixN solid solution, a phase separation into cubic SiN and TiN is energetically favorable. The microstructure was maintained for the Ti0.86Si0.14N film annealed at 900 °C, while recrystallization in the cubic state took place at 1100 °C annealing during 2 h. The Si content influenced the film hardness close to linearly, by combination of solid-solution hardening in the cubic state and defect hardening. For x = 0 and x = 0.14, nanoindentation gave a hardness of 31.3 ± 1.3 GPa and 44.7 ± 1.9 GPa, respectively. The hardness was retained after annealing at 900 °C, while it decreased to below 30 GPa for 1100 °C following recrystallization and W and Co interdiffusion.
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| 13. |
- Flink, Axel, et al.
(author)
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The location and effects of Si in (Ti1-xSix)N-y thin films
- 2009
-
In: JOURNAL OF MATERIALS RESEARCH. - : Springer Science and Business Media LLC. - 0884-2914 .- 2044-5326. ; 24:8, s. 2483-2498
-
Journal article (peer-reviewed)abstract
- (Ti1-xSix)N-y (0 andlt;= x andlt;= 0.20; 0.99 andlt;= y(x) andlt;= 1.13) thin films deposited by arc evaporation have been investigated by analytical transmission electron microscopy, x-ray diffraction, x-ray photoelectron spectroscopy, and nanoindentation. Films with x andlt;= 0.09 are single-phase cubic (Ti,Si)N solid solutions with a dense columnar microstructure. Films with x andgt; 0.09 haven a featherlike microstructure consisting of cubic TiN:Si nanocrystallite bundles separated by metastable SiNz with coherent-to-semicoherent interfaces and a dislocation density of as much as 10(14) cm(-2) is present. The films exhibit retained composition and hardness between 31 and 42 GPa in annealing experiments to 1000 degrees C due to segregation of SiN, to the grain boundaries. During annealing at 1100-1200 degrees C, this tissue phase thickens and transforms to amorphous SiNz. At the same time, Si and N diffuse out of the films via the grain boundaries and TiN recrystallize.
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| 14. |
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| 15. |
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| 16. |
- Glise Sandblad, Katarina, 1982, et al.
(author)
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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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In: Clinical and applied thrombosis/hemostasis : official journal of the International Academy of Clinical and Applied Thrombosis/Hemostasis. - : SAGE Publications. - 1938-2723. ; 29
-
Journal article (peer-reviewed)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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| 17. |
- Gösta, Alexander, et al.
(author)
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Data-Informed Urban Design: An Overview of the Use of Data and Digital Tools in Urban Planning and Design
- 2020
-
In: Built Environment. - : Alexandrine Press. - 0263-7960. ; 46:4, s. 620-636
-
Journal article (peer-reviewed)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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| 18. |
- Hasselqvist-Ax, Ingela, et al.
(author)
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Early cardiopulmonary resuscitation in out-of-hospital cardiac arrest.
- 2015
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In: The New England journal of medicine. - 1533-4406 .- 0028-4793. ; 372:24, s. 2307-15
-
Journal article (peer-reviewed)abstract
- Three million people in Sweden are trained in cardiopulmonary resuscitation (CPR). Whether this training increases the frequency of bystander CPR or the survival rate among persons who have out-of-hospital cardiac arrests has been questioned.
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| 19. |
- Hirlekar, Geir, et al.
(author)
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Analysis of data for comorbidity and survival in out-of-hospital cardiac arrest.
- 2018
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In: Data in Brief. - : Elsevier BV. - 2352-3409. ; 21, s. 1541-1551
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Journal article (peer-reviewed)abstract
- The data presented in this article is supplementary to the research article titled "Comorbidity and survival in out-of-hospital cardiac arrest" (Hirlekar et al., 2018). The data contains information of how Charlson Comorbidity Index (CCI) is calculated and coded from ICD-10 codes. Multivariable logistic regression was used in the analysis of association between comorbidity and return of spontaneous circulation. We present baseline characteristics of patients found in VF/VT. All patients with non-missing data on all baseline variables are analyzed separately. We compare the baseline characteristics of patients with and without complete data set. Analysis of when comorbidity was identified in relation to outcome is also shown.
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| 20. |
- Hirlekar, Geir, et al.
(author)
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Comorbidity and bystander cardiopulmonary resuscitation in out-of-hospital cardiac arrest.
- 2020
-
In: Heart. - : BMJ. - 1355-6037 .- 1468-201X. ; 106:14, s. 1087-1093
-
Journal article (peer-reviewed)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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| 21. |
- Hirlekar, Geir, et al.
(author)
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Comorbidity and survival in out-of-hospital cardiac arrest.
- 2018
-
In: Resuscitation. - : Elsevier BV. - 0300-9572 .- 1873-1570. ; 133, s. 118-123
-
Journal article (peer-reviewed)abstract
- BACKGROUND: Patients suffering out-of-hospital cardiac arrest (OHCA) have a poor prognosis but survival among subgroups differs greatly. Previous studies have shown conflicting results on whether patient comorbidity affects outcome. The aim of this national study was to investigate the effect of comorbidity on outcome after OHCA in Sweden.METHODS: We included all patients with bystander-witnessed OHCA from 2011 to 2015 in the national Swedish Registry of Cardiopulmonary Resuscitation. In order to assess comorbidity, the database was merged with the comprehensive National Patient Registry, which includes all out-patient and in-patient care in Sweden. The Charlson comorbidity index (CCI) and the specific comorbidity conditions constituting the CCI was used to identify whether comorbidity was associated with outcome.RESULTS: A total of 12,012 patients were included in the study. Of these, 1598 patients survived to 30 days (13%). The most common comorbidities were a history of congestive heart failure (29%), myocardial infarction (24%), and diabetes without complications (23%). Renal disease (odds ratio [OR] 0.53; 95% CI 0.53‒0.72), diabetes with complications (OR 0.65; 95% CI 0.49‒0.84), diabetes without complications (OR 0.63; 95% CI 0.52‒0.75), congestive heart failure (OR 0.84; 95% CI 0.71‒0.99), and metastatic carcinoma (OR 0.61; 95% CI 0.40‒0.93) were significantly associated with a reduced chance of 30-day survival when adjusted for demographic characteristics and also resuscitation-associated factors such as shockable initial rhythm, bystander cardiopulmonary resuscitation (CPR), and place of arrest. With increasing comorbidity, the chance of 30-day survival decreased: adjusted OR was 0.82 (59% CI 0.68-0.99) for CCI 3-4, 0.62 (95% CI 0.47-0.83) for CCI 5-6, and 0.51 (95% CI 0.36-0.72) for CCI > 6, respectively, all in relation to those with CCI 0-2. Additionally, increasing morbidity was associated with reduced odds of return of spontaneous circulation (ROSC) and ROSC at hospital admission.CONCLUSION: This large national study showed that increasing comorbidity decreased the chance of survival to 30 days in OHCA. This association remained after covariate adjustment.
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| 22. |
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| 23. |
- Hörling, Anders, et al.
(author)
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Thermal stability of arc evaporated high aluminum-content Ti1−xAlxN thin films
- 2002
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In: Journal of Vacuum Science & Technology. A. Vacuum, Surfaces, and Films. - : American Vacuum Society. - 0734-2101 .- 1520-8559. ; 20:5, s. 1815-1823
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Journal article (peer-reviewed)abstract
- The thermal stability of Ti1−xAlxN films deposited by arc evaporation from Ti–Al cathodes with 67 and 75 at. % aluminum, respectively, has been investigated. The microstructure of as-deposited and isothermally annealed samples were studied using scanning electron microscopy, transmission electron microscopy, and x-ray diffraction. The chemical composition and elemental distribution were determined by energy dispersive x ray (EDX), Rutherford backscattering spectrometry, and EDX mapping. Transmission electron micrographs revealed a dense and columnar microstructure in the as-deposited condition. Films deposited from the 67 at. % cathodes were of cubic NaCl-structure phase, whereas films deposited from the 75 at. % cathodes exhibited nanocrystallites of wurzite-structure hexagonal-phase AlN in a cubic (c)-(Ti,Al)N matrix. Both films were stable during annealing at 900 °C/120 min with respect to phase composition and grain size. Annealing at 1100 °C of films deposited from the 67 at. % cathodes resulted in phase separation of c-TiN and h-AlN, via spinodal decomposition of c-TiN and c-AlN. (Ti,Al)N films undergo extensive stress relaxation and defect annihilation at relatively high temperatures, and aspects of these microstructural transformations are discussed.
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| 24. |
- Irigoyen, S, et al.
(author)
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The Sink-Specific Plastidic Phosphate Transporter PHT4;2 Influences Starch Accumulation and Leaf Size in Arabidopsis.
- 2011
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In: Plant Physiology. - : Oxford University Press (OUP). - 0032-0889 .- 1532-2548. ; 157:4, s. 1765-1777
-
Journal article (peer-reviewed)abstract
- Nonphotosynthetic plastids are important sites for the biosynthesis of starch, fatty acids, and amino acids. The uptake and subsequent use of cytosolic ATP to fuel these and other anabolic processes would lead to the accumulation of inorganic phosphate (Pi) if not balanced by a Pi export activity. However, the identity of the transporter(s) responsible for Pi export is unclear. The plastid-localized Pi transporter PHT4;2 of Arabidopsis (Arabidopsis thaliana) is expressed in multiple sink organs but is nearly restricted to roots during vegetative growth. We identified and used pht4;2 null mutants to confirm that PHT4;2 contributes to Pi transport in isolated root plastids. Starch accumulation was limited in pht4;2 roots, which is consistent with the inhibition of starch synthesis by excess Pi as a result of a defect in Pi export. Reduced starch accumulation in leaves and altered expression patterns for starch synthesis genes and other plastid transporter genes suggest metabolic adaptation to the defect in roots. Moreover, pht4;2 rosettes, but not roots, were significantly larger than those of the wild type, with 40% greater leaf area and twice the biomass when plants were grown with a short (8-h) photoperiod. Increased cell proliferation accounted for the larger leaf size and biomass, as no changes were detected in mature cell size, specific leaf area, or relative photosynthetic electron transport activity. These data suggest novel signaling between roots and leaves that contributes to the regulation of leaf size.
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| 25. |
- Johansson, Emil, et al.
(author)
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Hierarchical Clustering and Trajectory Analyses Reveal Viremia-Independent B-Cell Perturbations in HIV-2 Infection
- 2022
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In: Cells. - : MDPI. - 2073-4409. ; 11:19
-
Journal article (peer-reviewed)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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| 26. |
- Jonsson, Jacob, et al.
(author)
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Angle-dependent light scattering in materials with controlled diffuse solar optical properties
- 2004
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In: Solar Energy Materials and Solar Cells. - : Elsevier BV. - 0927-0248 .- 1879-3398. ; 84:1-4, s. 427-439
-
Journal article (peer-reviewed)abstract
- Light scattering plays a prominent role in a wide range of energy-efficient materials and solar applications. Some examples are materials for daylighting, diffusely reflecting sunscreens, foils for radiative cooling and nanocrystalline solar cells. Measurements of the angular profile of light scattering are very useful for obtaining a detailed characterization of the light scattering mechanisms. We review recent theoretical results on the forward and backward light scattering profiles. Forward scattering is of major importance for novel pigmented polymeric daylighting materials. Measurements of scattering profiles are in good agreement with Mie theory. Backscattering profiles from highly diffusely reflecting paints containing titanium oxide-based pigments have also been measured. It seems that scattering from the paint surface dominates at low pigment volume fractions. Results for paints with high pigment volume fractions are interpreted in terms of coherent backscattering effects from the pigment particles.
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| 27. |
- Karlsson, Ingemar, et al.
(author)
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Combining augmented reality and simulation-based optimization for decision support in manufacturing
- 2017
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In: Proceedings of the 2017 Winter Simulation Conference. - : Institute of Electrical and Electronics Engineers (IEEE). - 9781538634288 - 9781538634295 - 9781538634301 ; , s. 3988-3999
-
Conference paper (peer-reviewed)abstract
- Although the idea of using Augmented Reality and simulation within manufacturing is not a new one, the improvement of hardware enhances the emergence of new areas. For manufacturing organizations, simulation is an important tool used to analyze and understand their manufacturing systems; however, simulation models can be complex. Nonetheless, using Augmented Reality to display the simulation results and analysis can increase the understanding of the model and the modeled system. This paper introduces a decision support system, IDSS-AR, which uses simulation and Augmented Reality to show a simulation model in 3D. The decision support system uses Microsoft HoloLens, which is a head-worn hardware for Augmented Reality. A prototype of IDSS-AR has been evaluated with a simulation model depicting a real manufacturing system on which a bottleneck detection method has been applied. The bottleneck information is shown on the simulation model, increasing the possibility of realizing interactions between the bottlenecks.
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| 28. |
- Karlsson, Jacob
(author)
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Capnodynamic determination of effective pulmonary blood flow and end expiratory lung volume : studies in children and paediatric animal models
- 2019
-
Doctoral thesis (other academic/artistic)abstract
- Dynamic capnography is a haemodynamic and respiratory monitoring technique enabling continuous cardiac output (Effective Pulmonary Blood Flow, COEPBF) and end expiratory lung volume (Effective Lung Volume, ELV) assessment in mechanically ventilated subjects. The method utilizes variations in exhaled CO2, implemented via periods of deliberate changes in the respiratory pattern. The method has been validated against high precision reference methods in animal experiments. Data from these studies have pointed to a potential use also in children, a patient group suffering from the lack of reliable and easy accessible cardiac output/functional residual capacity (CO/FRC) monitoring methods. We have validated dynamic capnography in a series of paediatric clinical studies and experimental models. COEPBF was tested for agreement of absolute values and ability to detect change against suprasternal Doppler, COSSD, in anaesthetized children and against transpulmonary flow probe, COTS, in a porcine model mimicking the clinical study. COEPBF was also tested for the same qualities, against COTS and CO2 Fick (COFick) in a model of hypoxia induced pulmonary hypertension in piglets. The respiratory parameter ELV was examined for consistency against helium wash out in a paediatric rabbit model of CO2-induced pneumoperitoneum. In addition to this, the same protocol was used to determine the PEEP level associated with most favorable conditions for preservation of lung homogeneity and CO2 clearance. COEPBF showed good agreement and trending ability when compared to COTS and COFick in the experimental setting. In the clinical study, COEPBF performed in the expected way. The reference method COSSD exhibited operator dependent qualities and appeared less reliable than COEPBF. Absolute values and changes in FRC could be monitored adequately by ELV, provided the application an adequate PEEP. The adequate PEEP level was also associated with optimal preservation lung homogeneity and CO2 removal, thus suggesting the use higher level of PEEP during laparoscopy. Dynamic capnography appears to be a reliable and accurate method for continuous CO and FRC monitoring and is a promising concept for future studies.
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| 29. |
- Karlsson, Linda, et al.
(author)
-
Cerebrospinal fluid reference proteins increase accuracy and interpretability of biomarkers for brain diseases.
- 2024
-
In: Nature Communications. - 2041-1723. ; 15:1
-
Journal article (peer-reviewed)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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| 30. |
- Karlsson, Lars O, 1975, et al.
(author)
-
Opioid receptor agonist Eribis peptide 94 reduces infarct size in different porcine models for myocardial ischaemia and reperfusion
- 2011
-
In: European Journal of Pharmacology. - : Elsevier BV. - 0014-2999 .- 1879-0712. ; 651:1-3, s. 146-151
-
Journal article (peer-reviewed)abstract
- Eribis peptide 94 (EP 94) is a novel enkephalin analog, thought to interact with the and delta-opioid receptors. The purpose of the present study was to examine the cardioprotective potential of EP 94 in two clinically relevant porcine models of myocardial ischaemia and reperfusion, and to investigate if such an effect is associated with an increased expression of endothelial nitric oxide synthase (eNOS). Forty-one anesthetized pigs underwent 40 min of coronary occlusion followed by 4 h of reperfusion. In Protocol I, balloon occlusion of the left anterior descending artery was performed with concurrent intravenous administration of (A) vehicle (n = 7), (B) EP 94 (1 ug/kg) after 5, 12, 19 and 26 min of ischaemia (n = 4) or (C) EP 94 (1 ug/kg) after 26, 33, 40 min of ischaemia (n = 6). In Protocol II, open-chest pigs were administered (D) vehicle (n = 6) or (E) 0.2 ug/kg/min of EP 94 (n = 6) through an intracoronary infusion into the jeopardized myocardium, started after 30 min of ischaemia and maintained for 15 min. The hearts were stained and the protein content of eNOS measured. EP 94 reduces infarct size when administered both early and late during ischaemia compared with vehicle (infarct size group A 61.6 +/- 2%, group B 50.2 +/- 3% and group C 49.2 +/- 2%, respectively, P < 0.05), as well as when infused intracoronary (infarct size group D 82.2 +/- 3.9% and group E 61.2 +/- 2.5% respectively, P < 0.01). Phosphorylated eNOS Ser(I177) in relation to total eNOS was significantly increased in the group administered EP 94. indicating activation of nitric oxide production.
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| 31. |
- Karlsson, Max, et al.
(author)
-
A single-cell type transcriptomics map of human tissues
- 2021
-
In: Science Advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 7:31
-
Journal article (peer-reviewed)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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| 32. |
- Karlsson, Simon, et al.
(author)
-
An evaluation and shortening of the Cooking and Food Provisioning Action Scale (CAFPAS) using item response theory
- 2023
-
In: Food Quality and Preference. - : Elsevier Ltd. - 0950-3293 .- 1873-6343. ; 108
-
Journal article (peer-reviewed)abstract
- The Cooking and Food Provisioning Action Scale (CAFPAS) is a 28-item validated tool for measuring food agency, a latent construct representing an individual's ability to make and achieve food-preparation and -provisioning goals. Here, key measurement parameters (targeting, threshold ordering, item fit, unidimensionality, differential item functioning, local dependency, and person reliability) of the CAFPAS are evaluated using a specific case of item response theory, Rasch analysis, on data from a development sample (N = 1853; 910 from Sweden; 943 from the US). Winsteps (v.5.1.7) is used for this analysis. The similarity of the Swedish version of the CAFPAS to the original is also assessed. Based on an iterative assessment of the measurement properties with different combinations of items in the development sample, ways to shorten the CAFPAS without jeopardizing construct validity or person reliability are examined. After removing items that do not fit the Rasch model, or that appear redundant in relation to other items, an 11-item version (CAFPAS-short) is suggested and tested using further Rasch analysis on both the development sample and an additional US-based validation sample (N = 1457). Scores of cooking confidence and attitudes are then modelled with measures from the CAFPAS and CAFPAS-short using frequentist and Bayesian analysis. Results suggest that the CAFPAS-short performs similarly to the full-length version, and potential future improvements to the CAFPAS are discussed. This study represents a successful application of item response theory to investigate and shorten a psychometric scale, reducing cognitive load on participants in studies using the CAFPAS whilst minimizing loss of data reliability. © 2023 The Author(s)
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| 33. |
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| 34. |
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| 35. |
- Larsen, P, et al.
(author)
-
Parallelizing more loops with compiler guided refactoring
- 2012
-
In: Proceedings of the International Conference on Parallel Processing. 41st International Conference on Parallel Processing, ICPP 2012, Pittsburgh, PA, 10 - 13 September 2012. - 0190-3918. - 9780769547961 ; , s. 410-419
-
Conference paper (peer-reviewed)abstract
- The performance of many parallel applications relies not on instruction-level parallelism but on loop-level parallelism. Unfortunately, automatic parallelization of loops is a fragile process, many different obstacles affect or prevent it in practice. To address this predicament we developed an interactive compilation feedback system that guides programmers in iteratively modifying their application source code. This helps leverage the compiler's ability to generate loop-parallel code. We employ our system to modify two sequential benchmarks dealing with image processing and edge detection, resulting in scalable parallelized code that runs up to 8.3 times faster on an eight-core Intel Xeon 5570 system and up to 12.5 times faster on a quad-core IBM POWER6 system. Benchmark performance varies significantly between the systems. This suggests that semi-automatic parallelization should be combined with target-specific optimizations. Furthermore, comparing the first benchmark to manually-parallelized, hand-optimized pthreads and OpenMP versions, we find that code generated using our approach typically outperforms the pthreads code (within 93-339%). It also performs competitively against the OpenMP code (within 75-111%). The second benchmark outperforms manually-parallelized and optimized OpenMP code (within 109-242%).
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| 36. |
- Lewin, Harris A., et al.
(author)
-
The Earth BioGenome Project 2020 : Starting the clock
- 2022
-
In: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences (PNAS). - 0027-8424 .- 1091-6490. ; 119:4
-
Journal article (other academic/artistic)
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| 37. |
- Libungan, Berglind, et al.
(author)
-
Out-of-hospital cardiac arrest in the elderly : A large-scale population-based study.
- 2015
-
In: Resuscitation. - : Elsevier BV. - 0300-9572 .- 1873-1570. ; 94
-
Journal article (peer-reviewed)abstract
- BACKGROUND: There is little information on elderly people who suffer from out-of-hospital cardiac arrest (OHCA).AIM: To determine 30-day mortality and neurological outcome in elderly patients with OHCA.METHODS: OHCA patients ≥ 70 years of age who were registered in the Swedish Cardiopulmonary Resuscitation Register between 1990 and 2013 were included and divided into three age categories (70-79, 80-89, and ≥ 90 years). Multiple logistic regression analyses were performed to identify independent predictors of 30-day survival.RESULTS: Altogether, 36,605 cases were included in the study. Thirty-day survival was 6.7% in patients aged 70-79 years, 4.4% in patients aged 80-89 years, and 2.4% in those over 90 years. For patients with witnessed OHCA of cardiac aetiology found in a shockable rhythm, survival was higher: 20%, 15%, and 11%, respectively. In 30-day survivors, the distribution according to the cerebral performance categories (CPC) score at discharge from hospital was similar in the three age groups. In multivariate analysis, in patients over 70 years of age, the following factors were associated with increased chance of 30-day survival: younger age, OHCA outside the home, witnessed OHCA, CPR before arrival of EMS, shockable first-recorded rhythm, and short emergency response time.CONCLUSIONS: Advanced age is an independent predictor of mortality in OHCA patients over 70 years of age. However, even in patients above 90 years of age, defined subsets with a survival rate of more than 10% exist. In survivors, the neurological outcome remains similar regardless of age.
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| 38. |
- Ludewig, Kristin, et al.
(author)
-
Phenology and morphology of the invasive legume Lupinus polyphyllus along a latitudinal gradient in Europe
- 2022
-
In: NeoBiota. - : Pensoft Publishers. - 1619-0033 .- 1314-2488. ; 78
-
Journal article (peer-reviewed)abstract
- Plant phenology, i. e. the timing of life cycle events, is related to individual fitness and species distributionranges. Temperature is one of the most important drivers of plant phenology together with day length.The adaptation of their phenology may be important for the success of invasive plant species. The presentstudy aims at understanding how the performance and the phenology of the invasive legume Lupinuspolyphyllus vary with latitude. We sampled data across a >2000 km latitudinal gradient from Centralto Northern Europe. We quantified variation in phenology of flowering and fruiting of L. polyphyllususing >1600 digital photos of inflorescences from 220 individual plants observed weekly at 22 sites. Theday of the year at which different phenological phases were reached, increased 1.3–1.8 days per degreelatitude, whereas the growing degree days (gdd) required for these phenological phases decreased 5–16 gddper degree latitude. However, this difference disappeared, when the day length of each day included inthe calculation of gdd was considered. The day of the year of the earliest and the latest climatic zone toreach any of the three studied phenological phases differed by 23–30 days and temperature requirementsto reach these stages differed between 62 and 236 gdd. Probably, the invasion of this species will furtherincrease in the northern part of Europe over the next decades due to climate warming. For invasive speciescontrol, our results suggest that in countries with a large latitudinal extent, the mowing date should shiftby ca. one week per 500 km at sites with similar elevations.
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| 39. |
- Ludewig, Kristin, et al.
(author)
-
Phenology of Lupinus polyphyllus from Central to Northern Europe
- 2022
-
Other publicationabstract
- Plant phenology, i. e. the timing of life cycle events, is related to individual fitness and species distribution ranges. Among the environmental factors, phenology is mostly driven by temperature and day length. Rapid adaptation of their phenology may also be important for the success of invasive plant species. Our main aim was to understand how the performance, timing, and temperature dependence of the phenology of the invasive legume Lupinus polyphyllus varies with latitude. L. polyphyllus is one of the most frequent invasive species in Europe, and the gained information may help to make management more effective by adjustments to latitude and phenology.Methods:We quantified variation in phenology across a >2000 km latitudinal gradient from Central to Northern Europe. We sampled data of flowering and fruiting of L. polyphyllus using >1600 digital photos of inflorescences from 220 individual plants observed weekly at 22 locations. We calculated the accumulated growing degree days for each observation date at each site from the temperature data of the meteorological stations, which are listed in the metadata of the dataset.
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| 40. |
- Lundgren, Sebastian, et al.
(author)
-
The clinical importance of tumour-infiltrating macrophages and dendritic cells in periampullary adenocarcinoma differs by morphological subtype
- 2017
-
In: Journal of Translational Medicine. - : Springer Science and Business Media LLC. - 1479-5876. ; 15:1
-
Journal article (peer-reviewed)abstract
- Background: Dendritic cells (DC) and tumour-associated macrophages (TAM) are essential in linking the innate and adaptive immune response against tumour cells and tumour progression. These cells are also potential target for immunotherapy as well as providing a handle to investigate immune status in the tumour microenvironment. The aim of the present study was to examine their impact on prognosis and chemotherapy response in periampullary adenocarcinoma, including pancreatic cancer, with particular reference to morphological subtype. Methods: The density of tolerogenic immature CD1a+ dendritic cells (DC), and MARCO+, CD68+ and CD163+ tissue-associated macrophages (TAM) was analysed by immunohistochemistry in tissue micro arrays with tumours from 175 consecutive cases of periampullary adenocarcinoma who had undergone pancreaticoduodenectomy, 110 with pancreatobiliary type (PB-type) and 65 with intestinal type (I-type) morphology. Kaplan-Meier and Cox regression analyses were applied to determine the impact of immune cell infiltration on 5-year overall survival (OS). Results: High density of CD1a+ DCs was an independent prognostic factor for a reduced OS in PB-type but not in I-type tumours (adjusted HR = 2.35; 95% CI 1.13-4.87). High density of CD68+ and CD163+ TAM was significantly associated with poor OS in the whole cohort, however only in unadjusted analysis (HR = 1.67; 95% CI 1.06-2.63, and HR = 1.84; 95% CI 1.09-3.09, respectively) and not in strata according to morphological subtype. High density of MARCO+ macrophages was significantly associated with poor prognosis in I-type but not in PB-type tumours (HR = 2.14 95% CI 1.03-4.44), and this association was only evident in patients treated with adjuvant chemotherapy. The prognostic value of the other investigated immune cells did not differ significantly in strata according to adjuvant chemotherapy. Conclusions: The results from this study demonstrate that high infiltration of tolerogenic immature DCs independently predicts a shorter survival in patients with PB-type periampullary adenocarcinoma, and that high density of the MARCO+ subtype of TAMs predicts a shorter survival in patients with I-type tumours. These results emphasise the importance of taking morphological subtype into account in biomarker studies related to periampullary cancer, and indicate that therapies targeting dendritic cells may be of value in the treatment of PB-type tumours, which are associated with the worst prognosis.
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| 41. |
- Mayrhofer, Paul H., et al.
(author)
-
Self-organized nanostructures in the Ti-Al-N system
- 2003
-
In: Applied Physics Letters. - : AIP Publishing. - 0003-6951 .- 1077-3118. ; 83:10, s. 2049-2051
-
Journal article (peer-reviewed)abstract
- The phenomenon of age hardening could be evidenced in thin film applications. A model system, Ti1-xAlxN was chosen as such coatings are known for their excellent wear resistance enabling improved machining processes like high-speed and dry cutting. Here, we show unambiguously that metastable Ti1-xAlxN coatings initially undergo spinodal decomposition into coherent cubic-phase nanometer-size domains, causing an increase in hardness at elevated temperatures. These intermediate metastable domains transform into their stable phases TiN and AlN during further thermal treatment. Activation energies for the processes indicate defect-assisted segregation of Ti and Al. The findings are corroborated by ab initio calculations. A long-standing discussion on the thermal stability of this important class of ceramics is thus resolved.
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| 42. |
- Megquier, Kate, et al.
(author)
-
BarkBase : Epigenomic Annotation of Canine Genomes
- 2019
-
In: Genes. - : MDPI. - 2073-4425. ; 10:6
-
Journal article (peer-reviewed)abstract
- Dogs are an unparalleled natural model for investigating the genetics of health and disease, particularly for complex diseases like cancer. Comprehensive genomic annotation of regulatory elements active in healthy canine tissues is crucial both for identifying candidate causal variants and for designing functional studies needed to translate genetic associations into disease insight. Currently, canine geneticists rely primarily on annotations of the human or mouse genome that have been remapped to dog, an approach that misses dog-specific features. Here, we describe BarkBase, a canine epigenomic resource available at barkbase.org. BarkBase hosts data for 27 adult tissue types, with biological replicates, and for one sample of up to five tissues sampled at each of four carefully staged embryonic time points. RNA sequencing is complemented with whole genome sequencing and with assay for transposase-accessible chromatin using sequencing (ATAC-seq), which identifies open chromatin regions. By including replicates, we can more confidently discern tissue-specific transcripts and assess differential gene expression between tissues and timepoints. By offering data in easy-to-use file formats, through a visual browser modeled on similar genomic resources for human, BarkBase introduces a powerful new resource to support comparative studies in dogs and humans.
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| 43. |
- Meyer-Jacob, Carsten, 1984-
(author)
-
Infrared spectroscopy as a tool to reconstruct past lake-ecosystem changes : Method development and application in lake-sediment studies
- 2015
-
Doctoral thesis (other academic/artistic)abstract
- Natural archives such as lake sediments allow us to assess contemporary ecosystem responses to climate and environmental changes in a long-term context beyond the few decades to at most few centuries covered by monitoring or historical data. To achieve a comprehensive view of the changes preserved in sediment records, multi-proxy studies – ideally in high resolution – are necessary. However, this combination of including a range of analyses and high resolution constrains the amount of material available for analyses and increases the analytical costs. Infrared spectroscopic methods are a cost-efficient alternative to conventional methods because they offer a) a simple sample pre-treatment, b) a rapid measurement time, c) the non- or minimal consumption of sample material, and d) the potential to extract quantitative and qualitative information about organic and inorganic sediment components from a single measurement.The main objective of this doctoral thesis was twofold. The first part was to further explore the potential of Fourier transform infrared (FTIR) and visible-near infrared (VNIR) spectroscopy in paleolimnological studies as a) an alternative tool to conventional methods for quantifying biogenic silica (bSi) – a common proxy of paleoproductivity in lakes – in sediments and b) as a tool to infer past lake-water total organic carbon (TOC) levels from sediments. In a methodological study, I developed an independent application of FTIR spectroscopy and PLS modeling for determining bSi in sediments by using synthetic sediment mixtures with known bSi content. In contrast to previous models, this model is independent from conventional wet-chemical techniques, which had thus far been used as the calibration reference, and their inherent measurement uncertainties. The second part of the research was to apply these techniques as part of three multi-proxy studies aiming to a) improve our understanding of long-term element cycling in boreal and arctic landscapes in response to climatic and environmental changes, and b) to assess ongoing changes, particularly in lake-water TOC, on a centennial to millennial time scale.In the first applied study, high-resolution FTIR measurements of the 318-m long sediment record of Lake El’gygytgyn provided a detailed insight into long-term climate variability in the Siberian Arctic over the past 3.6 million years. Highest bSi accumulation occurred during the warm middle Pliocene (3.6-3.3 Ma), followed by a gradual but variable decline, which reflects the first onset of glacial periods and then the finally full establishment of glacial–interglacial cycles during the Quaternary. The second applied study investigated the sediment record of Torneträsk in subarctic northern Sweden also in relation to climate change, but only over the recent post-glacial period (~10 ka). By comparing responses to past climatic and environmental forcings that were recorded in this large-lake system with those recorded in small lakes from its catchment, I determined the significance and magnitude of larger-scale changes across the study region. Three different types of response were identified over the Holocene: i) a gradual response to the early landscape development following deglaciation (~10000-5300 cal yr BP); ii) an abrupt but delayed response following climate cooling during the late Holocene, which occurred c. 1300 cal yr BP – about 1000-2000 years later than in smaller lakes from the area; and iii) an immediate response to the ongoing climate change during the past century. The rapid, recent response in a previously rather insensitive lake-ecosystem emphasizes the unprecedented scale of ongoing climate change in northern Fennoscandia. In the third applied study, VNIR-inferred lake-water TOC concentrations from lakes across central Sweden showed that the ongoing, observed increase in surface water TOC in this region was in fact preceded by a long-term decline beginning already AD 1450-1600. These dynamics coincided with early human land use activities in the form of widespread summer forest grazing and farming that ceased over the past century. The results of this study show the strong impact of past human activities on past as well as ongoing TOC levels in surface waters, which has thus far been underestimated. The research in this thesis demonstrates that infrared spectroscopic methods can be an essential component in high-resolution, multi-proxy studies of past environmental and climate changes.
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| 44. |
- Mulder, Jacob, et al.
(author)
-
New Reference Materials, Analytical Procedures and Data Reduction Strategies for Sr Isotope Measurements in Geological Materials by LA‐MC‐ICP‐MS
- 2023
-
In: Geostandards and Geoanalytical Research. - : Wiley. - 1639-4488 .- 1751-908X. ; 47:2, s. 311-336
-
Journal article (peer-reviewed)abstract
- Laser ablation multi-collector mass spectrometry (LA-MC-ICP-MS) has emerged as the technique of choice for in situ measurements of Sr isotopes in geological minerals. However, the method poses analytical challenges and there is no widely adopted standardised approach to collecting these data or correcting the numerous potential isobaric inferences. Here, we outline practical analytical procedures and data reduction strategies to help establish a consistent framework for collecting and correcting Sr isotope measurements in geological materials by LA-MC-ICP-MS. We characterise a new set of plagioclase reference materials, which are available for distribution to the community, and present a new data reduction scheme for the Iolite software package to correct isobaric interferences for different materials and analytical conditions. Our tests show that a combination of Kr-baseline subtraction, Rb-peak-stripping using βRb derived from a bracketing glass reference material, and a CaCa or CaAr correction for plagioclase and CaCa or CaAr + REE2+ correction for rock glasses, yields the most accurate and precise 87Sr/86Sr measurements for these materials. Using the analytical and correction procedures outlined herein, spot analyses using a beam diameter of 100 μm or rastering with a 50–65 μm diameter beam can readily achieve < 100 ppm 2SE repeatability ("internal") precision for 87Sr/86Sr measurements for materials with < 1000 μg g-1 Sr.
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| 45. |
- Nilsson, Åsa, et al.
(author)
-
Visualisering av råvaruflöden och hållbarhet för framtida svenskt skogsbruk : Från skog till produkt
- 2022
-
Reports (peer-reviewed)abstract
- Rapporten, som är framtagen inom Mistra Digital Forest, visar hur visualiseringsverktyget BioMapp kan användas för att analysera påverkan på olika aspekter av hållbarhet från tänkbara alternativa användningar av skogsråvara längs hela värdekedjan, från skog till produkt.BioMapp kan förse beslutsfattare med de underlag de behöver för att fatta faktabaserade beslut, för ökad hållbarhet inom svensk skoglig sektor. Rapporten visar exempel på den typ av resultat som kan genereras med BioMapp.
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| 46. |
- Olsson, Lina, et al.
(author)
-
FINAL REPORT DENCITY UDI PHASE 2
- 2018
-
Reports (other academic/artistic)abstract
- The DenCity Project is a collaboration project between 21 organisations that develops innovative solutions for sustainable passenger, freight and waste transport in dense urban areas, with high demands on transport efficiency, attractiveness, accessibility and sustainability.
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| 47. |
- Petersson, Alexandra, et al.
(author)
-
Branching copy number evolution and parallel immune profiles across the regional tumor space of resected pancreatic cancer
- 2022
-
In: Molecular Cancer Research. - 1557-3125. ; 20:5, s. 749-761
-
Journal article (peer-reviewed)abstract
- Pancreatic ductal adenocarcinoma (PDAC) remains a highly lethal disease. The only option for curative treatment is resection of the tumor followed by standard adjuvant chemotherapy. Yet, early relapse due to chemoresistance is almost inevitable. Herein, we delineated the genetic intratumor heterogeneity in resected PDAC, with the aim to identify evolutionary patterns that may be associated with overall survival (OS) following treatment with curative intent. Potential relationships with the adjacent immune microenvironment were also examined. The genetic and immune landscapes of the regional tumor space were analyzed in nine patients with resected PDAC. Targeted deep sequencing and genome wide SNP array were followed by clonal deconvolution and phylogenetic analysis. A mathematical complexity score was developed to calculate the network extent of each phylogeny. Spatial variation in abundancy and tumor nest infiltration of immune cells was analyzed by double immunohistochemical staining. Copy number heterogeneity was denoted as the major contributing factor to the branching architectures of the produced phylogenetic trees. Increased tree complexity was significantly inversely associated with OS, and larger regional maximum aberrations (higher treetops) were associated with increased PD-L1 expression on tumor cells. Contrastingly, a FREM1 gene amplification, found in one patient, coincided with a particularly vigorous immune response. Findings from this limited case series suggest that complex evolutionary patterns may be associated with a shorter survival in surgically treated PDAC patients. Some hypothesis-generating associations with the surrounding immune microenvironment were also detected.Implications: Evolutionary copy number patterns may be associated with survival in patients with resected PDAC.
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| 48. |
- Polyzoi, Maria, et al.
(author)
-
Cost-Effectiveness Analysis of Adjuvant Olaparib Versus Watch and Wait in the Treatment of Germline BRCA1/2-Mutated, High-Risk, HER2-Negative Early Breast Cancer in Sweden
- 2024
-
In: PHARMACOECONOMICS-OPEN. - 2509-4262 .- 2509-4254. ; 8:2, s. 277-289
-
Journal article (peer-reviewed)abstract
- Introduction This study evaluated the cost effectiveness of adjuvant olaparib versus watch and wait (WaW) in patients with germline breast cancer susceptibility gene 1/2 (gBRCA1/2)-mutated, high-risk, human epidermal growth factor receptor 2 (HER2)-negative early breast cancer (eBC), previously treated with neoadjuvant or adjuvant chemotherapy, from a Swedish healthcare perspective.Methods A five-state (invasive disease-free survival [IDFS], non-metastatic breast cancer [non-mBC], early-onset mBC, late-onset mBC, death) semi-Markov state transition model with a lifetime horizon was developed. Transition probabilities were informed by data from the Phase III OlympiA trial, supplemented with data from additional studies in BRCA-mutated, HER2-negative mBC. Health state utilities were derived via mapping of OlympiA data and supplemented by literature estimates. Treatment, adverse events and other medical costs were extracted from publicly available Swedish sources. Incremental cost per life-year (LY) and quality-adjusted life-year (QALY) gained were estimated. Costs and outcomes were discounted at 3% annually. One-way deterministic and probabilistic sensitivity analyses (PSA) were conducted.Results Over a lifetime horizon, adjuvant olaparib was associated with an additional 1.50 LYs and 1.22 QALYs, and incremental cost of 471,156 Swedish krona (SEK) versus WaW (discounted). The resulting ICER was 385,183SEK per QALY gained for olaparib versus WaW. ICERs remained below 1,000,000SEK across a range of scenarios, and were consistent across subgroups (hormone receptor [HR]-positive/HER2-negative and triple-negative breast cancer [TNBC]). In PSA, the probability of olaparib being cost effective at 1,000,000SEK per QALY was 99.8%.Conclusions At list price, adjuvant olaparib is a cost-effective alternative to WaW in patients with gBRCA1/2-mutated, high-risk, HER2-negative eBC in Sweden.
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| 49. |
- Rangaiah, Pramod K. B., et al.
(author)
-
Design of constant width branch line directional coupler for the microwave sensing application
- 2020
-
In: 14th European Conference on Antennas and Propagation (EuCAP). - 9788831299008 - 9781728137124
-
Conference paper (peer-reviewed)abstract
- This paper investigates the design of directional branch-line coupler using constant width multiple sections of series and open microstrip line stubs. This device is operating at the center frequency of 2.45 GHz. The designed coupler is having good performance for the frequency band 2-3 GHz. The proposed design is compared with a typical branch line coupler and shows the improved performance. The design is simulated and fabricated on the Fibreglass-resin laminate (FR4) substrate of height 1.5 mm. The results of simulated and experimented circuits are discussed and analyzed. The circuit is measured using Combination Analyzer N9918A Field Fox Handheld Microwave Analyzer. The proposed topology is easy to design and fabricate with a planar microstrip line technology. The designed coupler shows the good results at 2.45GHz i.e. S 11 = -61.26 dB, S 21 = -45 dB, S 31 = -2dB and S 41 = -4.5dB. The main target of this work is to design a coupler to differentiate between transmitted and reflected signals in the split ring resonator (SRR) sensor for Bone Density Measurement Analysis (BDAS) system.
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| 50. |
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