| 1. |
- Andersson, Christian H., et al.
(författare)
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Mathematical understanding of training data and AI : a lesson plan for critical thinking and ethical perspectives
- 2024
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Ingår i: Proceedings / Actes CIEAEM 74. - Palermo, Italy. ; , s. 681-685
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Konferensbidrag (refereegranskat)abstract
- AI and machine learning are increasingly being applied to solve complex societal issues. One approach is to train algorithms on training data that describes human behavior. This is not without potential problems though. For example, historical human behavior may contain biases, and then algorithms may reproduce social injustices. This workshop contained lesson elements from a study where pre-service mathematics teachers conducted lessons to first conceptually teach how mathematical modelling based on machine learning works, and then to broaden the scope to consider critical thinking in relation to ethics and democratic values. The participants were invited to test and discuss the lesson elements.
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| 2. |
- Andersson, Mattias, et al.
(författare)
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Editor's Choice – Structured Computed Tomography Analysis can Identify the Majority of Patients at Risk of Post-Endovascular Aortic Repair Rupture
- 2022
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Ingår i: European Journal of Vascular and Endovascular Surgery. - : Elsevier BV. - 1078-5884 .- 1532-2165. ; 64, s. 166-174
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Tidskriftsartikel (refereegranskat)abstract
- Objective: The main objective was to report mechanisms and precursors for post-endovascular aneurysm repair (EVAR) rupture. The second was to apply a structured protocol to explore whether these factors were identifiable on follow up computed tomography (CT) prior to rupture. The third objective was to study the incidence, treatment, and outcome of post-EVAR rupture. Methods: This was a multicentre, retrospective study of patients treated with standard EVAR at five Swedish hospitals from 2008 to 2018. Patients were identified from the Swedvasc registry. Medical records were reviewed up to 2020. Index EVAR and follow up data were recorded. The primary endpoint was post-EVAR rupture. CT at follow up and at post-EVAR rupture were studied, using a structured protocol, to determine rupture mechanisms and identifiable precursors. Results: In 1 805 patients treated by EVAR, 45 post-EVAR ruptures occurred in 43 patients. The cumulative incidence was 2.5% over a mean follow up of 5.2 years. The incidence rate was 4.5/1 000 person years. Median time to post-EVAR rupture was 4.1 years. A further six cases of post-EVAR rupture in five patients found outside the main cohort were included in the analysis of rupture mechanisms only. The rupture mechanism was type IA in 20 of 51 cases (39%), IB in 20 of 51 (39%) and IIIA/B in 11 of 51 (22%). One of these had type IA + IB combined. One patient had an aortoduodenal fistula without another mechanism being identified. Precursors had been noted on CT follow up prior to post-EVAR rupture in 16 of 51 (31%). Retrospectively, using the structured protocol, precursors could be identified in 43 of 51 (84%). In 17 of 27 (63%) cases missed on follow up but retrospectively identifiable, the mechanisms were type IB/III. Overall, the 30 day mortality rate after post-EVAR rupture was 47% (n = 24/51) and the post-operative mortality rate was 21% (n = 7/33). Conclusions: Most precursors of post-EVAR rupture are underdiagnosed but identifiable before rupture using a structured follow up CT protocol. Precursors of type IB and III failures caused the majority of post-EVAR ruptures.
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| 3. |
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| 4. |
- Ansari, Daniel, et al.
(författare)
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Safety of pancreatic resection in the elderly : a retrospective analysis of 556 patients
- 2016
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Ingår i: Annals of Gastroenterology. - : Hellenic Society of Gastroenterology. - 1108-7471 .- 1792-7463. ; 29:2, s. 5-221
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: The safety of pancreatic resection for elderly patients is still controversial. We examined the postoperative morbidity and mortality in patients aged 75 years or more undergoing pancreatic resection.METHODS: Patients undergoing pancreatic resection were studied retrospectively and the outcomes were compared between patients aged <75 and ≥75 years.RESULTS: Of the 556 patients enrolled, 78 (14%) were ≥75 years old. Elderly patients had significantly more co-morbidities, especially cardiovascular pathology (P=0.005). Also, elderly patients had significantly lower body mass index prior to surgery (P=0.005). There were no significant differences in terms of surgical procedures and tumor types between age groups. The incidence of postoperative pancreatic fistula grade A was significantly lower in the elderly group (P=0.022), but no significant differences were noted in the overall morbidity or the incidence of postpancreatectomy hemorrhage, delayed gastric emptying, bile leakage, cardiac complications, pulmonary complications or septic complications. The 30-day mortality rate was similar between groups (0.8% vs. 1.3%; P=0.532).CONCLUSION: Pancreatic resection is a safe option for selected elderly patients. Our study confirms that age alone should not preclude potentially curative surgical therapy.
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| 5. |
- Bergvall, Hillevi, et al.
(författare)
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Development of competence in cognitive behavioural therapy and the role of metacognition among clinical psychology and psychotherapy students
- 2023
-
Ingår i: Behavioural and Cognitive Psychotherapy. - : CAMBRIDGE UNIV PRESS. - 1352-4658 .- 1469-1833. ; 51:3
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Tidskriftsartikel (refereegranskat)abstract
- Background:There is a paucity of research on therapist competence development following extensive training in cognitive behavioural therapy (CBT). In addition, metacognitive ability (the knowledge and regulation of ones cognitive processes) has been associated with learning in various domains but its role in learning CBT is unknown. Aims:To investigate to what extent psychology and psychotherapy students acquired competence in CBT following extensive training, and the role of metacognition. Method:CBT competence and metacognitive activity were assessed in 73 psychology and psychotherapy students before and after 1.5 years of CBT training, using role-plays with a standardised patient. Results:Using linear mixed modelling, we found large improvements of CBT competence from pre- to post-assessment. At post-assessment, 72% performed above the competence threshold (36 points on the Cognitive Therapy Scale-Revised). Higher competence was correlated with lower accuracy in self-assessment, a measure of metacognitive ability. The more competent therapists tended to under-estimate their performance, while less competent therapists made more accurate self-assessments. Metacognitive activity did not predict CBT competence development. Participant characteristics (e.g. age, clinical experience) did not moderate competence development. Conclusions:Competence improved over time and most students performed over the threshold post-assessment. The more competent therapists tended to under-rate their competence. In contrast to what has been found in other learning domains, metacognitive ability was not associated with competence development in our study. Hence, metacognition and competence may be unrelated in CBT or perhaps other methods are required to measure metacognition.
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| 6. |
- Boge, Lukas, 1987, et al.
(författare)
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Cubosomes for topical delivery of the antimicrobial peptide LL-37
- 2019
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Ingår i: European Journal of Pharmaceutics and Biopharmaceutics. - : Elsevier BV. - 1873-3441 .- 0939-6411. ; 134, s. 60-67
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Tidskriftsartikel (refereegranskat)abstract
- In this study, the use of cubosomes for topical delivery of the antimicrobial peptide (AMP) LL-37 was investigated. Topical delivery of AMPs is of great interest for treatment of skin infections caused by bacteria, such as Staphylococcus aureus. AMP containing cubosomes were produced by three different preparation protocols and compared: (i) pre-loading, where LL-37 was incorporated into a liquid crystalline gel, which thereafter was dispersed into nanoparticles, (ii) post-loading, where LL-37 was let to adsorb onto pre-formed cubosomes, and (iii) hydrotrope-loading, where LL-37 was incorporated during the spontaneously formed cubosomes in an ethanol/glycerol monooleate mixture. Particle size and size distribution were analyzed using dynamic light scattering (DLS), liquid crystalline structure by small angle x-ray scattering (SAXS) and release of LL-37 by a fluorescamine assay. Proteolytic protection of LL-37 as well as bactericidal effect after enzyme exposure was investigated. The skin irritation potential of cubosomes was examined by an in vitro epidermis model. Finally, the bacterial killing property of the cubosomes was examined by an ex vivo pig skin wound infection model with Staphylococcus aureus. Data showed that a high loading of LL-37 induced formation of vesicles in case of cubosomes prepared by sonication (pre-loading). No release of LL-37 was observed from the cubosomes, indicating strong association of the peptide to the particles. Proteolysis studies showed that LL-37 was fully protected against enzymatic attacks while associated with the cubosomes, also denoting strong association of the peptide to the particles. As a consequence, bactericidal effect after enzyme exposure remained, compared to pure LL-37 which was subjected to proteolysis. No skin irritation potential of the cubosomes was found, thus enabling for topical administration. The ex vivo wound infection model showed that LL-37 in pre-loaded cubosomes killed bacteria most efficient.
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| 7. |
- Boge, Lukas, et al.
(författare)
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Cubosomes for topical delivery of the antimicrobial peptide LL-37
- 2019
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Ingår i: European journal of pharmaceutics and biopharmaceutics. - : Elsevier BV. - 0939-6411 .- 1873-3441. ; 134, s. 60-67
-
Tidskriftsartikel (refereegranskat)abstract
- In this study, the use of cubosomes for topical delivery of the antimicrobial peptide (AMP) LL-37 was investigated. Topical delivery of AMPs is of great interest for treatment of skin infections caused by bacteria, such as Staphylococcus aureus. AMP containing cubosomes were produced by three different preparation protocols and compared: (i) pre-loading, where LL-37 was incorporated into a liquid crystalline gel, which thereafter was dispersed into nanoparticles, (ii) post-loading, where LL-37 was let to adsorb onto pre-formed cubosomes, and (iii) hydrotrope-loading, where LL-37 was incorporated during the spontaneously formed cubosomes in an ethanol/glycerol monooleate mixture. Particle size and size distribution were analyzed using dynamic light scattering (DLS), liquid crystalline structure by small angle x-ray scattering (SAXS) and release of LL-37 by a fluorescamine assay. Proteolytic protection of LL-37 as well as bactericidal effect after enzyme exposure was investigated. The skin irritation potential of cubosomes was examined by an in vitro epidermis model. Finally, the bacterial killing property of the cubosomes was examined by an ex vivo pig skin wound infection model with Staphylococcus aureus. Data showed that a high loading of LL-37 induced formation of vesicles in case of cubosomes prepared by sonication (pre-loading). No release of LL-37 was observed from the cubosomes, indicating strong association of the peptide to the particles. Proteolysis studies showed that LL-37 was fully protected against enzymatic attacks while associated with the cubosomes, also denoting strong association of the peptide to the particles. As a consequence, bactericidal effect after enzyme exposure remained, compared to pure LL-37 which was subjected to proteolysis. No skin irritation potential of the cubosomes was found, thus enabling for topical administration. The ex vivo wound infection model showed that LL-37 in pre-loaded cubosomes killed bacteria most efficient.
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| 8. |
- Dillner, Lena, et al.
(författare)
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Randomized healthservices study of human papillomavirus-based management of low-grade cytological abnormalities.
- 2011
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Ingår i: International Journal of Cancer. - : Wiley. - 0020-7136 .- 1097-0215. ; okt, s. 151-159
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Tidskriftsartikel (refereegranskat)abstract
- Human Papillomavirus (HPV)-based management of women with borderline (ASCUS) or mildly abnormal (CINI) cervical cytology has been extensively studied in the research setting. We wished to assess safety and healthcare resource use of a real-life healthcare policy using HPV triaging.All 15 outpatient clinics involved in the organized population-based screening program in Stockholm, Sweden screening program were randomized to either continue with prior policy (colposcopy of all women with ASCUS/CINI) or to implement a policy with HPV triaging and colposcopy only of HPV-positive women. The trial enrolled the 3319 women that were diagnosed with ASCUS (n=1335) or CINI (n=1984) in Stockholm during 17(th) March 2003 to 16(th) January 2006. Detection of high-grade cervical lesions (CINII+) and health care cost consumption was studied by registry linkages.The proportion of histopathology-verified CINII+ was similar for the 2 policies (395/1752 women (22.5%; 95% Confidence interval (CI): 20,6-24,6%) had CINII+ diagnosed with HPV triaging policy, 318/1567 women (20.3%; 95%CI: 18,3-22,4%)) had CINII+ with colposcopy policy). 64% of women with ASCUS and 77% of women with CINI were HPV-positive. HPV-positivity was age-dependent, with 81% of women below 35 years of age and 44% of women above 45 years of age testing HPV-positive. HPV triaging was cost-effective only above 35 years of age.In conclusion, a real-life randomised healthservices study of HPV triaging of women with ASCUS/CINI demonstrated similar detection of CINII+ as colposcopy of all women.
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| 9. |
- Gråsjö, Johan, et al.
(författare)
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Electronic structure of water molecules confined in a micelle lattice
- 2009
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 113:24, s. 8201-8205
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Tidskriftsartikel (refereegranskat)abstract
- Oxygen K absorption and emission spectra of water molecules confined in dodecyltrimethyl ammonium chloride micelle structures are presented. The local electronic structure of the water molecules is found to be dramatically different from the electronic structure of water molecules in the gas-phase as well as in liquid water. Hybridization with states of the ions in the surrounding ions is directly observed, and evidence for stabilization of the water molecules relative to molecules in bulk water is found.
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| 10. |
- Gråsjö, Johan, et al.
(författare)
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Local Electronic Structure of Functional Groups in Glycine As Anion, Zwitterion, and Cation in Aqueous Solution
- 2009
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 113:49, s. 16002-16006
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Tidskriftsartikel (refereegranskat)abstract
- Nitrogen and oxygen K emission spectra of glycine in the form of anions, zwitterions, and cations in aqueous solution are presented. It is shown that protonation has a dramatic influence on the local electronic structure and that the functional groups give a distinct spectral fingerprint.
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| 11. |
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| 12. |
- Hildebrandt, Franziska, 1994-, et al.
(författare)
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Spatial Transcriptomics to define transcriptional patterns of zonation and structural components in the mouse liver
- 2021
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 12:1
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Tidskriftsartikel (refereegranskat)abstract
- Reconstruction of heterogeneity through single cell transcriptional profiling has greatly advanced our understanding of the spatial liver transcriptome in recent years. However, global transcriptional differences across lobular units remain elusive in physical space. Here, we apply Spatial Transcriptomics to perform transcriptomic analysis across sectioned liver tissue. We confirm that the heterogeneity in this complex tissue is predominantly determined by lobular zonation. By introducing novel computational approaches, we enable transcriptional gradient measurements between tissue structures, including several lobules in a variety of orientations. Further, our data suggests the presence of previously transcriptionally uncharacterized structures within liver tissue, contributing to the overall spatial heterogeneity of the organ. This study demonstrates how comprehensive spatial transcriptomic technologies can be used to delineate extensive spatial gene expression patterns in the liver, indicating its future impact for studies of liver function, development and regeneration as well as its potential in pre-clinical and clinical pathology. Global transcriptional differences across lobular units in the liver remain unknown. Here the authors perform spatial transcriptomics of liver tissue to delineate transcriptional differences in physical space, confirm lobular zonation along transcriptional gradients and suggest the presence of previously uncharacterized structures within liver tissue.
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| 13. |
- Landberg, Göran, 1963, et al.
(författare)
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Characterization of cell-free breast cancer patient-derived scaffolds using liquid chromatography-mass spectrometry/mass spectrometry data and RNA sequencing data
- 2020
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Ingår i: Data in Brief. - : Elsevier BV. - 2352-3409. ; 31
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Tidskriftsartikel (refereegranskat)abstract
- Patient-derived scaffolds (PDSs) generated from primary breast cancer tumors can be used to model the tumor microenvironment in vitro . Patient-derived scaffolds are generated by repeated detergent washing, removing all cells. Here, we analyzed the protein composition of 15 decellularized PDSs using liquid chromatography-mass spectrometry/mass spectrometry. One hundred forty-three proteins were detected and their relative abundance was calculated using a reference sample generated from all PDSs. We performed heatmap analysis of all the detected proteins to display their expression patterns across different PDSs together with pathway enrichment analysis to reveal which processes that were connected to PDS protein composition. This protein dataset together with clinical information is useful to investigators studying the microenvironment of breast cancers. Further, after repopulating PDSs with either MCF7 or MDA-MB-231 cells, we quantified their gene expression profiles using RNA sequencing. These data were also compared to cells cultured in conventional 2D conditions, as well as to cells cultured as xenografts in immune-deficient mice. We investigated the overlap of genes regulated between these different culture conditions and performed pathway enrichment analysis of genes regulated by both PDS and xenograft cultures compared to 2D in both cell lines to describe common processes associated with both culture conditions. Apart from our described analyses of these systems, these data are useful when comparing different experimental model systems. Downstream data analyses and interpretations can be found in the research article "Patient-derived scaffolds uncover breast cancer promoting properties of the microenvironment" [1] . (C) 2020 The Authors. Published by Elsevier Inc.
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| 14. |
- Landberg, Göran, et al.
(författare)
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Patient-derived scaffolds uncover breast cancer promoting properties of the microenvironment
- 2020
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Ingår i: Biomaterials. - : Elsevier Ltd. - 0142-9612 .- 1878-5905. ; 235
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Tidskriftsartikel (refereegranskat)abstract
- Tumor cells interact with the microenvironment that specifically supports and promotes tumor development. Key components in the tumor environment have been linked to various aggressive cancer features and can further influence the presence of subpopulations of cancer cells with specific functions, including cancer stem cells and migratory cells. To model and further understand the influence of specific microenvironments we have developed an experimental platform using cell-free patient-derived scaffolds (PDSs) from primary breast cancers infiltrated with standardized breast cancer cell lines. This PDS culture system induced a series of orchestrated changes in differentiation, epithelial-mesenchymal transition, stemness and proliferation of the cancer cell population, where an increased cancer stem cell pool was confirmed using functional assays. Furthermore, global gene expression profiling showed that PDS cultures were similar to xenograft cultures. Mass spectrometry analyses of cell-free PDSs identified subgroups based on their protein composition that were linked to clinical properties, including tumor grade. Finally, we observed that an induction of epithelial-mesenchymal transition-related genes in cancer cells growing on the PDSs were significantly associated with clinical disease recurrences in breast cancer patients. Patient-derived scaffolds thus mimics in vivo-like growth conditions and uncovers unique information about the malignancy-inducing properties of tumor microenvironment. © 2019 The Authors
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| 15. |
- Lundgren, Marcus, et al.
(författare)
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Optical study on combustion transition from HCCI to PPC with gasoline compression ignition in a HD engine
- 2016. - April
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Ingår i: SAE 2016 World Congress and Exhibition. - 400 Commonwealth Drive, Warrendale, PA, United States : SAE International. ; 2016-April
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Konferensbidrag (refereegranskat)abstract
- The partially premixed combustion (PPC) concept has shown high efficiency with low soot emissions. However, the in-cylinder phenomena are still to be explained and evaluated for further progress in the research. This work studies the start of combustion process during a transition from homogenous charge compression ignition (HCCI) to PPC. The process is visualized using a heavy-duty, non-swirling engine modified for optical access. High speed video was used to capture the natural luminosity of the combustion. The fuel used was PRF87. Single and double injection strategies were used at a load kept to the moderate level of 7.5 bar IMEPg. Single injections were swept from early HCCI to retarded PPC conditions whilst running a cycle to cycle temperature sweep, to capture the effect of injection timing and temperature differences simultaneously. Results show that retarded injections show less cycle-to-cycle variation due to temperature variations. Advanced in-bowl injections show a stochastic behavior in the location of the first combustion, due to large variations in local fuel rich zones. For the double injection case the main injection cools the bulk temperature and hence delays the start of combustion before igniting in the fuel rich zones.
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| 16. |
- Nordanstig, Joakim, et al.
(författare)
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Mortality with Paclitaxel-Coated Devices in Peripheral Artery Disease.
- 2020
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Ingår i: The New England journal of medicine. - : Massachusetts Medical Society. - 1533-4406 .- 0028-4793. ; 383, s. 2538-46
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Tidskriftsartikel (refereegranskat)abstract
- The results of a recent meta-analysis aroused concern about an increased risk of death associated with the use of paclitaxel-coated angioplasty balloons and stents in lower-limb endovascular interventions for symptomatic peripheral artery disease.We conducted an unplanned interim analysis of data from a multicenter, randomized, open-label, registry-based clinical trial. At the time of the analysis, 2289 patients had been randomly assigned to treatment with drug-coated devices (the drug-coated-device group, 1149 patients) or treatment with uncoated devices (the uncoated-device group, 1140 patients). Randomization was stratified according to disease severity on the basis of whether patients had chronic limb-threatening ischemia (1480 patients) or intermittent claudication (809 patients). The single end point for this interim analysis was all-cause mortality.No patients were lost to follow-up. Paclitaxel was used as the coating agent for all the drug-coated devices. During a mean follow-up of 2.49 years, 574 patients died, including 293 patients (25.5%) in the drug-coated-device group and 281 patients (24.6%) in the uncoated-device group (hazard ratio, 1.06; 95% confidence interval, 0.92 to 1.22). At 1 year, all-cause mortality was 10.2% (117 patients) in the drug-coated-device group and 9.9% (113 patients) in the uncoated-device group. During the entire follow-up period, there was no significant difference in the incidence of death between the treatment groups among patients with chronic limb-threatening ischemia (33.4% [249 patients] in the drug-coated-device group and 33.1% [243 patients] in the uncoated-device group) or among those with intermittent claudication (10.9% [44 patients] and 9.4% [38 patients], respectively).In this randomized trial in which patients with peripheral artery disease received treatment with paclitaxel-coated or uncoated endovascular devices, the results of an unplanned interim analysis of all-cause mortality did not show a difference between the groups in the incidence of death during 1 to 4 years of follow-up. (Funded by the Swedish Research Council and others; ClinicalTrials.gov number, NCT02051088.).
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| 17. |
- Thollander, Patrik, 1976-, et al.
(författare)
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Energinyckeltal och växthusgasutsläpp baserade på industrins energianvändande processer
- 2021
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Rapport (refereegranskat)abstract
- Svensk industri bör strategiskt arbeta mot ökad energi- och resurseffektivitet på en global marknad med knappare resurser. I detta sammanhang spelar beslutsunderlag och nyckeltal en central roll för att nå ökad effektivitet. Även för tillsynsmyndigheter är rättvisande nyckeltal avseende slutenergianvändning av mycket stor vikt för att kunna bedriva ett rättvist förebyggande och proaktivt arbete med svenska företag. De nyckeltal som finns på internationell och nationell nivå är baserade på tillförd energi och ofta relaterade till en ekonomisk output, till exempel förädlingsvärde. Det saknas emellertid nyckeltal kring slutenergianvändningen inom svensk industri fördelat på energibärare såsom el och olja och fördelat på slutenergiprocesser såsom ugnar, tryckluftskompressorer, etc. De siffror som ibland anges är baserade på grova uppskattningar. Projektets mål har därför varit att generera ett processträd avseende flera av de största, till slutenergianvändning räknat, svenska industribranscherna avseende hur slutenergianvändningen är fördelad på processnivå och olika energibärare, samt att allokera växthusgasutsläpp på dessa olika processer. Resultaten indikerar att nyckeltal baserade på energianvändning och indirekta växthusgasutsläpp på processnivå kan bidra till bättre kunskap om i vilka industriella energianvändande processer den största potentialen för energieffektivisering och minskning av växthusgasutsläpp finns. För att upprätthålla kunskap om var den största potentialen för förbättring finns krävs att energidata regelbundet samlas in efter en standardiserad kategorisering av energianvändande processer. Även om projektet har avgränsats till svensk industri kan resultatet vara till nytta också för andra medlemsstater inom EU liksom globalt.
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| 18. |
- Uhlén, Mathias, et al.
(författare)
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A human protein atlas for normal and cancer tissues based on antibody proteomics
- 2005
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Ingår i: Molecular & Cellular Proteomics. - 1535-9476 .- 1535-9484. ; 4:12, s. 1920-1932
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Tidskriftsartikel (refereegranskat)abstract
- Antibody-based proteomics provides a powerful approach for the functional study of the human proteome involving the systematic generation of protein-specific affinity reagents. We used this strategy to construct a comprehensive, antibody-based protein atlas for expression and localization profiles in 48 normal human tissues and 20 different cancers. Here we report a new publicly available database containing, in the first version, similar to 400,000 high resolution images corresponding to more than 700 antibodies toward human proteins. Each image has been annotated by a certified pathologist to provide a knowledge base for functional studies and to allow queries about protein profiles in normal and disease tissues. Our results suggest it should be possible to extend this analysis to the majority of all human proteins thus providing a valuable tool for medical and biological research.
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| 19. |
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| 20. |
- Wallén-Mackenzie, Åsa, et al.
(författare)
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Restricted cortical and amygdaloid removal of vesicular glutamate transporter 2 in preadolescent mice impacts dopaminergic activity and neuronal circuitry of higher brain function.
- 2009
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Ingår i: The Journal of neuroscience : the official journal of the Society for Neuroscience. - 1529-2401 .- 0270-6474. ; 29:7, s. 2238-51
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Tidskriftsartikel (refereegranskat)abstract
- A major challenge in neuroscience is to resolve the connection between gene functionality, neuronal circuits, and behavior. Most, if not all, neuronal circuits of the adult brain contain a glutamatergic component, the nature of which has been difficult to assess because of the vast cellular abundance of glutamate. In this study, we wanted to determine the role of a restricted subpopulation of glutamatergic neurons within the forebrain, the Vglut2-expressing neurons, in neuronal circuitry of higher brain function. Vglut2 expression was selectively deleted in the cortex, hippocampus, and amygdala of preadolescent mice, which resulted in increased locomotor activity, altered social dominance and risk assessment, decreased sensorimotor gating, and impaired long-term spatial memory. Presynaptic VGLUT2-positive terminals were lost in the cortex, striatum, nucleus accumbens, and hippocampus, and a downstream effect on dopamine binding site availability in the striatum was evident. A connection between the induced late-onset, chronic reduction of glutamatergic neurotransmission and dopamine signaling within the circuitry was further substantiated by a partial attenuation of the deficits in sensorimotor gating by the dopamine-stabilizing antipsychotic drug aripiprazole and an increased sensitivity to amphetamine. Somewhat surprisingly, given the restricted expression of Vglut2 in regions responsible for higher brain function, our analyses show that VGLUT2-mediated neurotransmission is required for certain aspects of cognitive, emotional, and social behavior. The present study provides support for the existence of a neurocircuitry that connects changes in VGLUT2-mediated neurotransmission to alterations in the dopaminergic system with schizophrenia-like behavioral deficits as a major outcome.
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| 21. |
- Abad, Manuel David, et al.
(författare)
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Identification of Ternary Phases in TiBC/a-C Nanocomposite Thin Films : Influence on the Electrical and Optical Properties
- 2011
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Ingår i: Plasma Processes and Polymers. - : Wiley. - 1612-8850 .- 1612-8869. ; 8:7, s. 579-588
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Tidskriftsartikel (refereegranskat)abstract
- The local structure of TiBC and amorphous carbon (a-C) nanocomposite films (TiBC/a-C) was correlated with their optical and electrical properties. TiBC/a-C films with increasing C content were deposited by magnetron co-sputtering from TiC:TiB(2) (60: 40) and graphite targets. Chemical composition is determined by electron energy-loss spectroscopy. Grazing incidence X-ray diffraction reveals that the microstructure of the films is amorphous with small nanocrystallites emerging by increasing the C content that could be attributed to the formation of ternary (TiB(x)C(y)) or mixed binary (TiB(2) and TiC) phases. Further information was then obtained by studying the chemical bonding by measuring the near-edge fine structure (NES) by electron energy-loss (B K-, C K-, and Ti L-edges) and X-ray absorption (B K-and Ti L-edges) spectroscopies. The NES analysis indicates the formation of a nanocrystalline ternary TiB(x)C(y) compound concomitant with the segregation of an a-C phase as the carbon content is increased. The optical properties were studied by spectroscopic ellipsometry and the electrical resistivity was measured by the Van der Pauw method between 20 and 300 K. The films continuously lose their metallic character in terms of optical constants and resistivity with increasing carbon content. Theoretical fitting of the electrical properties using the grain-boundary scattering model supported the formation of a nanocomposite structure based on a ternary TiB(x)C(y) phase embedded in a matrix of a-C. The electron transport properties are mainly limited by the high density of point defects, grain size, and transmission probability.
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| 22. |
- Abboud, Amina, et al.
(författare)
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Årsbok 2018 : Socialhögskolan, Lunds universitet
- 2019
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Socialhögskolans årsbok ger en liten inblick i vad vi gör och vi hoppas att den bidrar till att presentera utsnitt från vår verksamhet på ett trevligt och samlat sätt. Årsboken som är Socialhögskolans tredje uppmärksammar inte bara det som skett på Socialhögskolan under 2018. Den uppmärksammar även att 2018 var året då svensk äldreomsorg fyllde 100 år. Årsbokens gästredaktör Per Gunnar Edebalk inleder därför bokens forskningsavsnitt med att i år skriva om just hundraåringens historia. Det är inledningen på ett avsnitt där flera forskare vid Socialhögskolan bjuder på bidrag som lyfter fram aspekter av äldreomsorg och åldrande.Håkan Jönson och Tove Harnett resonerar om de begrepp som omgärdar äldreomsorgens möten och organisering sett i ett socialt arbetets perspektiv. De två har även skrivit en artikel om huruvida behov ska ses annorlunda mellan grupper bara för att man passerat en viss ålder.Däremellan presenteras en text av Erika Werner som låter oss möta frågor kring en sviken generation, här genom ett möte med Agnes, som hamnade mitt i skarven när pensionssystemet reformerades. Elisabeth Carlstedt presenterar en text om hur äldreomsorgens särskilda boenden arbetar i relation till Socialtjänstlagens direktiv om meningsfullhet och värdighet, och hur svårt det är. Lars Harrysson presenterar därefter ett avsnitt om två forskningsprojekt som han och Erika Werner gjort där fokus har legat dels på pensioner för personer i ekonomiskt utsatta grupper, speciellt med migrantbakgrund, dels om hur tro och äldreomsorg samspelar, eller inte. Äldreomsorgsavsnittet avslutas sedan med en intervju som Patrik Hekkala gjort med Peter Andersson som startade kursen socialt arbete med äldre och med Tove Harnett som tagit över och fortsatt utvecklingsarbetet till dags datum.Årsboken avslutas sedan med fyra texter. En av Amina Abboud, snart färdig socionom, som skriver om sina erfarenheter av och i uppsatsskrivandet. Sedan en där vi får möta Carina Olsson som arbetat hos oss länge, men som faktiskt arbetat vid universitetet i 40 år 2018. Emelie Dahlström, Joakim Grina och Jan Abrahamsson ger sedan en bakgrundsteckning till en hos Socialhögskolan verksam social accelerator, SoPact. Som avrundning finner du sedan lite mer information om vår verksamhet här vid Socialhögskolan.
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| 23. |
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| 24. |
- Agåker, Marcus, et al.
(författare)
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Spectroscopy in the vacuum-ultraviolet
- 2011
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Ingår i: Nature Photonics. - : Springer Science and Business Media LLC. - 1749-4885 .- 1749-4893. ; 5:5, s. 248-248
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Tidskriftsartikel (refereegranskat)
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| 25. |
- Ahlberg, Erik, et al.
(författare)
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"Vi klimatforskare stödjer Greta och skolungdomarna"
- 2019
-
Ingår i: Dagens nyheter (DN debatt). - 1101-2447.
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Tidskriftsartikel (populärvet., debatt m.m.)abstract
- DN DEBATT 15/3. Sedan industrialiseringens början har vi använt omkring fyra femtedelar av den mängd fossilt kol som får förbrännas för att vi ska klara Parisavtalet. Vi har bara en femtedel kvar och det är bråttom att kraftigt reducera utsläppen. Det har Greta Thunberg och de strejkande ungdomarna förstått. Därför stödjer vi deras krav, skriver 270 klimatforskare.
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| 26. |
- Aivaz Ihari, Mahia, et al.
(författare)
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Long-term functional consequences of cranial nerve injuries after carotid endarterectomy.
- 2022
-
Ingår i: The Journal of cardiovascular surgery. - 1827-191X. ; 63:6, s. 695-699
-
Tidskriftsartikel (refereegranskat)abstract
- The aim of the study was to investigate long-term patient consequences of cranial nerve injury (CNI) caused by carotid endarterectomy (CEA) in patients with identified CNI at the 30-day follow-up.Consecutive patients operated for symptomatic carotid artery stenosis 2015-2019 with a documented CNI at the 30-day follow-up after CEA were recruited to this cross-sectional survey. Telephone interviews were conducted >1 year after CEA utilizing survey instruments developed to uncover CNI symptoms. Patients graded their symptoms on a 4-point scale: 1) no symptoms; 2) mild symptoms; 3) moderate symptoms; and 4) severe symptoms.Altogether, 477 patients underwent CEA, of which 82 were diagnosed with CNI; 70/82 patients remained alive at the time for the survey and 68 patients completed the interview. The mean follow-up time was 3.7 years. Severe persistent CNI symptoms were reported in 2/68 (2.9%), moderate symptoms in 1/68 (1.5%) and mild symptoms in 14/68 (21%) whereas 51/68 patients (75%) reported no residual symptoms. When extrapolating these findings to all patients, approximately 4.4% reported persistent symptoms at the long-term follow-up and only 0.8% reported moderate or severe symptoms.The long-term consequences of CNI following CEA are benign in most patients, with a high rate of symptom resolution and a very low rate of persistent clinically significant symptoms.
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| 27. |
- Ambjörnsson, Joakim, et al.
(författare)
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Prehospital suspicion and identification of adult septic patients : Experiences of a screening tool
- 2016
-
Ingår i: 2nd Global Conference on Emergency Nursing and Trauma Care, Melia Sitges, September 22-24, 2016.
-
Konferensbidrag (refereegranskat)abstract
- Introduction: Sepsis is life threatening and requires urgent healthcare to reduce suffering and death. Therefore it is important that septic patients are identified early to enable treatment. Aim: To investigate to what extent EMS personnel identified patients with sepsis using the “BAS 90-30-90” model, and to describe assessments and medical procedures that were undertaken by the personnel.Methods: This was a retrospective study where 185 EMS medical records were reviewed. The inclusion was based on patients who were later diagnosed with sepsis in the hospital. Results: A physician assessed the patients in 74 of the EMS cases, which lead to exclusion of these records in regard to the EMS personnel’s ability to identify sepsis. The personnel documented suspicion of severe sepsis in eight (n=8) of the remaining 111 records (7.2%). The proportion of patients ˃65 years of age was 73% (n=135) of which 37% (n=50) were over 80 years old. Thirty-nine percent (39%, n=72) were females. The personnel documented blood pressure in 91% (n=168), respiratory rate in 76% (n=140), saturation in 100% (n=185), temperature in 76% (n=141), and heart rate in 94% (n=174) of the records. Systolic blood pressure <90 mmHg was documented in 14,2% (n=24), respiratory rate ˃30 in 36% (n=50), saturation <90 in 49% (n=91), temperature >38°C in 37.6% (n=53), and heart rate ˃90 in 70% (n=121) of the records. Documented medical procedures and treatments were intravenous lines (70%, n=130), intravenous fluids (10%, n=19) and administration of oxygen (72%, n=133).Conclusion: The EMS personnel identified only a few septic patients with the help of the BAS 90-30-90 model when all three criteria would be met for severe sepsis. Either advanced age (>65 years), fever (>38°C) or tachypnea (˃20 breaths/min) appeared to increase the personnel’s suspicion of sepsis. Oxygen, but not intravenous fluids, was given in an adequate way.
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| 28. |
- Anderberg, Rozita H, 1976, et al.
(författare)
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Treatment with RNase alleviates brain injury but not neuroinflammation in neonatal hypoxia/ischemia
- 2024
-
Ingår i: JOURNAL OF NEUROSCIENCE RESEARCH. - 0360-4012 .- 1097-4547. ; 102:4
-
Tidskriftsartikel (refereegranskat)abstract
- There is a need for new treatments to reduce brain injuries derived from neonatal hypoxia/ischemia. The only viable option used in the clinic today in infants born at term is therapeutic hypothermia, which has a limited efficacy. Treatments with exogenous RNase have shown great promise in a range of different adult animal models including stroke, ischemia/reperfusion injury, or experimental heart transplantation, often by conferring vascular protective and anti-inflammatory effects. However, any neuroprotective function of RNase treatment in the neonate remains unknown. Using a well-established model of neonatal hypoxic/ischemic brain injury, we evaluated the influence of RNase treatment on RNase activity, gray and white matter tissue loss, blood-brain barrier function, as well as levels and expression of inflammatory cytokines in the brain up to 6 h after the injury using multiplex immunoassay and RT-PCR. Intraperitoneal treatment with RNase increased RNase activity in both plasma and cerebropinal fluids. The RNase treatment resulted in a reduction of brain tissue loss but did not affect the blood-brain barrier function and had only a minor modulatory effect on the inflammatory response. It is concluded that RNase treatment may be promising as a neuroprotective regimen, whereas the mechanistic effects of this treatment appear to be different in the neonate compared to the adult and need further investigation.
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| 29. |
- Anders, Andre, et al.
(författare)
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High quality ZnO:Al transparent conducting oxide films synthesized by pulsed filtered cathodic arc deposition
- 2010
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Ingår i: Thin Solid Films. - : Elsevier BV. - 0040-6090 .- 1879-2731. ; 518:12, s. 3313-3319
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Tidskriftsartikel (refereegranskat)abstract
- Aluminum-doped zinc oxide, ZnO:Al or AZO, is a well-known n-type transparent conducting oxide with great potential in a number of applications currently dominated by indium tin oxide. In this study, the optical and electrical properties of AZO thin films deposited on glass and silicon by pulsed filtered cathodic arc deposition are systematically studied. In contrast to magnetron sputtering, this technique does not produce energetic negative ions, and therefore ion damage can be minimized. The quality of the AZO films strongly depends on growth temperature while only marginal improvements are obtained with post-deposition annealing. The best films, grown at a temperature of about 200 degrees C, have resistivities in the low to mid 10(-4) Omega cm range with a transmittance better than 85% in the visible part of the spectrum. It is remarkable that relatively good films of small thickness (60 nm) can be fabricated using this method.
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| 30. |
- Anderson, Johan, et al.
(författare)
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Experimental and Numerical Characterization of an Electrically Propelled Vehicles Battery Casing Including Battery Module
- 2014
-
Ingår i: Journal of Thermal Science and Engineering Applications. - : ASME International. - 1948-5085 .- 1948-5093. ; 6:4
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Tidskriftsartikel (refereegranskat)abstract
- This paper demonstrates the possibility to predict a battery system's performance in a fire resistance test according to the new amendment of United Nations Regulation No. 100 "Uniform Provisions Concerning the Approval of Vehicles with Regard to Specific Requirements for the Electric Power Train" (R100) based on careful measurements of the physical properties of the casing material, as well as modeling of the battery modules and computer simulations. The methodology of the work consists of estimating the heat transfer coefficients by using a gasoline pool fire model in the computational fluid dynamics (CFD) software FIRE DYNAMICS SIMULATOR (FDS), followed by finite-element (FE) calculations of the temperatures in the battery.
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| 31. |
- Andersson, Anders, et al.
(författare)
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A transcriptional timetable of autumn senescence
- 2004
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Ingår i: Genome Biology. - : Springer Science and Business Media LLC. - 1465-6906 .- 1474-760X. ; 5:4, s. R24-
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Tidskriftsartikel (refereegranskat)abstract
- Background We have developed genomic tools to allow the genus Populus (aspens and cottonwoods) to be exploited as a full-featured model for investigating fundamental aspects of tree biology. We have undertaken large-scale expressed sequence tag (EST) sequencing programs and created Populus microarrays with significant gene coverage. One of the important aspects of plant biology that cannot be studied in annual plants is the gene activity involved in the induction of autumn leaf senescence. Results On the basis of 36,354 Populus ESTs, obtained from seven cDNA libraries, we have created a DNA microarray consisting of 13,490 clones, spotted in duplicate. Of these clones, 12,376 (92%) were confirmed by resequencing and all sequences were annotated and functionally classified. Here we have used the microarray to study transcript abundance in leaves of a free-growing aspen tree (Populus tremula) in northern Sweden during natural autumn senescence. Of the 13,490 spotted clones, 3,792 represented genes with significant expression in all leaf samples from the seven studied dates. Conclusions We observed a major shift in gene expression, coinciding with massive chlorophyll degradation, that reflected a shift from photosynthetic competence to energy generation by mitochondrial respiration, oxidation of fatty acids and nutrient mobilization. Autumn senescence had much in common with senescence in annual plants; for example many proteases were induced. We also found evidence for increased transcriptional activity before the appearance of visible signs of senescence, presumably preparing the leaf for degradation of its components.
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| 32. |
- Andersson, Alexander, 1991, et al.
(författare)
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CEO Compensation and Just Pay Theories
- 2022
-
Ingår i: Poff, D.C. & Michalos, A.C. (eds.), Encyclopedia of Business and Professional Ethics. - Cham : Springer. - 9783319235141 ; , s. 1-5
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Bokkapitel (refereegranskat)
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| 33. |
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| 34. |
- Andersson, Alma, 1995-
(författare)
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Computational methods for analysis of spatial transcriptomics data : An exploration of the spatial gene expression landscape
- 2022
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Transcriptomics techniques, whether in the form of bulk, single cell/nuclei, or spatial methods have fueled a substantial expansion of our knowledge about the biological systems within and around us. In addition, the rate of innovation has accelerated over the last decade, resulting in a multitude of technological advances and new methods for generation of transcriptomics data. In 2009, isolating and characterizing the transcriptome of a single cell was seen as a major achievement, ten years later, in 2019, studies surveying a hundred thousand cells were commonplace. The field of spatial transcriptomics went through an equally transformative phase; from struggling with simultaneous characterization of a few targets, to seamlessly provide spatially resolved maps of the full transcriptome. Inevitably, we’re approaching an inflection point where the generation of data is no longer the bottleneck, but rather its analysis. Alas, with standardized commercial products, high-quality spatial transcriptomics data can now be generated en masse. Hence, questions about data analysis have started to replace those of data generation. The work in this thesis seeks to address some of these emerging questions; the five articles it encompasses presents new methods for analysis of spatial transcriptomics data and examples of their application. Furthermore, it contains an introduction to current experimental and computational spatial transcriptomics techniques, as well as a section about data modeling. In Article I, a probabilistic model for integration of single cell/nuclei and spatial transcriptomics data is presented. In short, the method allows for mixed signals – present in certain spatial transcriptomics platforms – to be decomposed into contributions from biologically relevant cell types or states derived from single cell/nuclei data. The model was implemented in code as a software, stereoscope, which is open source and publicly available. The same policy of open source and high transparency holds true for all software or code associated with this thesis. The stereoscope method has been used in several studies, one example being Article II, where we examined the spatial transcriptomics landscape of HER2-positive breast cancer patients. By integrating single cell and spatial transcriptomics data, several intriguing co-localization signals emerged. These signals allowed us to identify a signature for tertiary lymphoid structures and evidence of a trifold interaction involving: type I interferon signals, a T-cell subset, and a macrophage subset. However, the work also included other forms of explorative data analysis, such as unsupervised expression-based clustering. The clusters from this analysis, once annotated, exhibited high concordance with annotations provided by a pathologist and the tissue morphology. Taken together, this makes a compelling case for the use of spatial transcriptomics in the age of “digital pathology.” Finally, we also derived “core signatures” from the expression-based clusters, representing common expression profiles shared across the patients.In Article III, we present a computational method, sepal, designed to identify genes with distinct spatial patterns, often referred to as “spatially variable genes.” The method uses Fick’s second law to simulate diffusion of transcripts in the tissue, measuring the time until convergence (a spatially uniform and homogeneous state). It then ranks the genes by their “diffusion time.” The assumption being that genes exhibiting strong spatial patterns will take longer time to converge compared to genes with no pattern, thus relating the diffusion time to the degree of spatial structure. Article IV constitutes a study of the mouse liver using spatial transcriptomics. As before, we employed stereoscope for the purpose of single cell integration, but realized more tailored computational tools – towards the specific tissue – were required to address certain questions. Thus, we developed two computational methods, one devoted to vein type identity prediction, the other enabling a change of data representation. In essence, to predict the vein identities, we first assembled spatially weighted composite expression profiles from – to the vein – neighboring observations. Then, a logistic classifier was trained using the composite profiles. Once the model was trained, it could be used to assign vein type identities to ambiguous or unannotated veins. In the second method, the two-dimensional spatial data was recast into a more informative one-dimensional representation by treating gene expression as a function of an observation’s distance to its nearest vein structure.The final work, Article V, expands the idea of recasting data into a more informative or helpful representation. More precisely, we present a method, eggplant, that allows the user to transfer spatial transcriptomics data from multiple sources to a common coordinate framework (CCF). Transfer of information to a CCF means spatial signals can be compared across conditions and time points, unlocking a plethora of valuable downstream analyses. For example, we perform spatiotemporal modeling of a synthetic system, and introduce the concept of “spatial arithmetics” to study local expression differences. With a growing corpus of spatial trancsriptomics data and ambitious international efforts like the Human Cell Atlas, we deem these sort of methods essential to leverage the data’s full potential.
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| 35. |
- Andersson, Axel, et al.
(författare)
-
End-to-end Multiple Instance Learning with Gradient Accumulation
- 2022
-
Ingår i: 2022 IEEE International Conference on Big Data (Big Data). - : Institute of Electrical and Electronics Engineers (IEEE). - 9781665480451 - 9781665480468 ; , s. 2742-2746
-
Konferensbidrag (refereegranskat)abstract
- Being able to learn on weakly labeled data and provide interpretability are two of the main reasons why attention-based deep multiple instance learning (ABMIL) methods have become particularly popular for classification of histopathological images. Such image data usually come in the form of gigapixel-sized whole-slide-images (WSI) that are cropped into smaller patches (instances). However, the sheer volume of the data poses a practical big data challenge: All the instances from one WSI cannot fit the GPU memory of conventional deep-learning models. Existing solutions compromise training by relying on pre-trained models, strategic selection of instances, sub-sampling, or self-supervised pre-training. We propose a training strategy based on gradient accumulation that enables direct end-to-end training of ABMIL models without being limited by GPU memory. We conduct experiments on both QMNIST and Imagenette to investigate the performance and training time and compare with the conventional memory-expensive baseline as well as a recent sampled-based approach. This memory-efficient approach, although slower, reaches performance indistinguishable from the memory-expensive baseline.
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| 36. |
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| 37. |
- Andersson, Alexander, 1991, et al.
(författare)
-
Moralising Economic Desert
- 2019
-
Ingår i: Business Ethics after the Global Financial Crisis: Lessons from the Crash, ed. by Cristopher Cowton, James Dempsey, and Tom Sorell. - New York : Routledge. - 9781138330504 ; , s. 165-184
-
Bokkapitel (refereegranskat)
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| 38. |
- Andersson, Alma, et al.
(författare)
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sepal : identifying transcript profiles with spatial patterns by diffusion-based modeling
- 2021
-
Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811 .- 1460-2059. ; 37:17, s. 2644-2650
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Tidskriftsartikel (refereegranskat)abstract
- Motivation: Collection of spatial signals in large numbers has become a routine task in multiple omics-fields, but parsing of these rich datasets still pose certain challenges. In whole or near-full transcriptome spatial techniques, spurious expression profiles are intermixed with those exhibiting an organized structure. To distinguish profiles with spatial patterns from the background noise, a metric that enables quantification of spatial structure is desirable. Current methods designed for similar purposes tend to be built around a framework of statistical hypothesis testing, hence we were compelled to explore a fundamentally different strategy. Results: We propose an unexplored approach to analyze spatial transcriptomics data, simulating diffusion of individual transcripts to extract genes with spatial patterns. The method performed as expected when presented with synthetic data. When applied to real data, it identified genes with distinct spatial profiles, involved in key biological processes or characteristic for certain cell types. Compared to existing methods, ours seemed to be less informed by the genes' expression levels and showed better time performance when run with multiple cores.
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| 39. |
- Andersson, Alma, et al.
(författare)
-
Single-cell and spatial transcriptomics enables probabilistic inference of cell type topography
- 2020
-
Ingår i: Communications Biology. - : Nature Research. - 2399-3642. ; 3:1
-
Tidskriftsartikel (refereegranskat)abstract
- The field of spatial transcriptomics is rapidly expanding, and with it the repertoire of available technologies. However, several of the transcriptome-wide spatial assays do not operate on a single cell level, but rather produce data comprised of contributions from a – potentially heterogeneous – mixture of cells. Still, these techniques are attractive to use when examining complex tissue specimens with diverse cell populations, where complete expression profiles are required to properly capture their richness. Motivated by an interest to put gene expression into context and delineate the spatial arrangement of cell types within a tissue, we here present a model-based probabilistic method that uses single cell data to deconvolve the cell mixtures in spatial data. To illustrate the capacity of our method, we use data from different experimental platforms and spatially map cell types from the mouse brain and developmental heart, which arrange as expected.
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| 40. |
- Andersson, Alma, et al.
(författare)
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Spatial deconvolution of HER2-positive breast cancer delineates tumor-associated cell type interactions
- 2021
-
Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 12:1
-
Tidskriftsartikel (refereegranskat)abstract
- In the past decades, transcriptomic studies have revolutionized cancer treatment and diagnosis. However, tumor sequencing strategies typically result in loss of spatial information, critical to understand cell interactions and their functional relevance. To address this, we investigate spatial gene expression in HER2-positive breast tumors using Spatial Transcriptomics technology. We show that expression-based clustering enables data-driven tumor annotation and assessment of intra- and interpatient heterogeneity; from which we discover shared gene signatures for immune and tumor processes. By integration with single cell data, we spatially map tumor-associated cell types to find tertiary lymphoid-like structures, and a type I interferon response overlapping with regions of T-cell and macrophage subset colocalization. We construct a predictive model to infer presence of tertiary lymphoid-like structures, applicable across tissue types and technical platforms. Taken together, we combine different data modalities to define a high resolution map of cellular interactions in tumors and provide tools generalizing across tissues and diseases. While transcriptomics have enhanced our understanding for cancer, spatial transcriptomics enable the characterisation of cellular interactions. Here, the authors integrate single cell data with spatial information for HER2 + tumours and develop tools for the prediction of interactions between tumour-infiltrating cells.
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| 41. |
- Andersson, Alma, et al.
(författare)
-
Spatial Deconvolution of HER2-positive Breast Tumors Reveals Novel Intercellular Relationships
- 2020
-
Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- In the past decades, transcriptomic studies have revolutionized cancer treatment and diagnosis. However, tumor sequencing strategies typically result in loss of spatial information, critical to understand cell interactions and their functional relevance. To address this, we investigate spatial gene expression in HER2-positive breast tumors using Spatial Transcriptomics technology. We show that expression-based clustering enables data-driven tumor annotation and assessment of intra-and interpatient heterogeneity; from which we discover shared gene signatures for immune and tumor processes. We integrate and spatially map tumor-associated types from single cell data to find: segregated epithelial cells, interactions between B and T-cells and myeloid cells, co-localization of macrophage and T-cell subsets. A model is constructed to infer presence of tertiary lymphoid structures, applicable across tissue types and technical platforms. Taken together, we combine different data modalities to define novel interactions between tumor-infiltrating cells in breast cancer and provide tools generalizing across tissues and diseases.
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| 42. |
- Andersson, B, et al.
(författare)
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Being a hospice volunteer
- 2005
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Ingår i: Palliative Medicine. - 0269-2163 .- 1477-030X. ; 19, s. 602-609
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Tidskriftsartikel (refereegranskat)
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| 43. |
- Andersson, Birgit, et al.
(författare)
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Being a hospice volunteer
- 2005
-
Ingår i: Palliative Medicine. - : SAGE Publications. - 0269-2163 .- 1477-030X. ; 19, s. 602-609
-
Tidskriftsartikel (refereegranskat)abstract
- The aim of this study was to obtain an understanding of what it means to be a hospice volunteer in a country without a tradition of hospice or palliative volunteer care services. Ten volunteers from three different hospices in Sweden were interviewed. Their narratives were interpreted with a phenomenological hermeneutic method. Three themes were disclosed: motives for becoming involved in hospices, encountering the hospice and encountering the patient. The interpretations disclose a need for the volunteer to be affirmed as a caring person and received in fellowship at the hospice. Positive encounters with a hospice are closely related to personal growth. Volunteers feel rejected if their need for meaning and for belonging to the hospice is not satisfied. This shows that hospices need to set goals in terms of volunteer support, particularly regarding existential issues following the encounter with the hospice and the patient. PMID: 16450877 [PubMed - indexed for MEDLINE]
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| 44. |
- Andersson, Camilla, et al.
(författare)
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Achievements and experiences from science–policy interaction in the field of air pollution : Synthesising 20 years of research and outreach,thinking about future needs
- 2021
-
Rapport (övrigt vetenskapligt/konstnärligt)abstract
- For 20 years, the Swedish Environmental Protection Agency together with the MISTRA research foundation have funded five air pollution research programmes with focus on producing knowledge that supports policy and emission control in national and international arenas. The research has been multidisciplinary and has included research on emissions, atmospheric transport and transformation processes, human health effects, ecosystem effects, and emission control strategies. Research has also been conducted on the interaction between air pollution and climate change.Over these years, the link between the research programmes and the development of emission control strategies and policies in Sweden, the EU, and the UNECE Air Convention has been of high importance. This report presents how the research programmes have created societal benefits through support for the development of air pollution policies and emission control measures. The report also identifies future research needs to ensure continued progress towards even better air quality for future generations.
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| 45. |
- Andersson, Camilla, 1979-
(författare)
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Air Pollution Dependency on Climate Variability and Source Region : Past, Current and Future Air Pollution Scenarios over Europe
- 2009
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The main objectives of this thesis were to investigate the dependency of European air pollution on climate variability and emission source region. Calculations with a chemistry transport model (CTM) were conducted to investigate the influence of climate variability. The CTM was forced by both simulated past (a re-analysis spanning 1958-2001) and future (a climate simulation spanning 1961-2100) meteorology keeping anthropogenic emissions constant. To investigate the influence of emission source region emissions were varied in western, eastern and northern Europe in seven-year (1997-2003) simulations. The main conclusions in this thesis are § There is variability in air pollution due to climate variability on time scales from year to year to decades and long-term trends. Hence, what is measured now will not be valid in a decade, or even next year. § Interannual variability in air pollution due to climate variability is greater than interannual variability in anthropogenic emissions. § The extreme conditions in 2003, resulting in elevated surface O3 concentrations, could be an indication on what we can expect in the future. § The trend in surface O3 over the past due to climate change is similar to the projected trend due to future climate change: increasing in south-western and central Europe and decreasing in north-eastern Europe. § Changes in isoprene emissions and dry deposition dependency on soil moisture are of importance for changes in surface O3 in central and southern Europe. It is vital to include these processes, especially the latter in climate change effect studies of surface O3. § This work indicates that it is of greater importance for health benefits of the European population to reduce primary PM emissions than precursors of secondary inorganic aerosol under the assumption of higher relative risk for primary PM. This is especially the case in western Europe.
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| 46. |
- Andersson, Camilla, 1979-, et al.
(författare)
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Inter-annual variations of ozone and nitrogen dioxide over Europe during 1958-2003 simulated with a regional CTM
- 2007
-
Ingår i: Water, Air and Soil Pollution. - Netherlands : Springer. - 0049-6979 .- 1573-2932 .- 1567-7230 .- 1573-2940. ; 7, s. 15-23
-
Tidskriftsartikel (refereegranskat)abstract
- Abstract Inter-annual variability of surface ozone(O3) and nitrogen dioxide (NO2) over Europe hasbeen studied over the period 1958-2003 using athree-dimensional Chemistry-Transport Model coupledto meteorological data from the ERA40 data setproduced at the European Centre of Medium-rangeWeather Forecasts (ECMWF). Emissions and boundaryconditions were kept at present levels throughoutthe simulation period. It was found that the annualmean NO2 concentration varies between ±50% andthe summer mean O3 concentration varies between-10 and +20 percent (%) compared to the 46-yearaverage over the model domain. There is alsovariation in ozone and NO2 over longer time scales.The last 22 years display high concentrations ofozone in central and south-western Europe and lowconcentrations in north-eastern Europe. The first22 years display very high concentrations of NO2over the North Sea. There is indication of trends inozone and nitrogen dioxide but this has to beinvestigated further. Such information is one factorthat should be taken into account when consideringfuture control strategies.
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| 47. |
- Andersson, Camilla, 1979-, et al.
(författare)
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Interannual variation and trends in air pollution over Europe due to climate variability during 1958–2001 simulated with a regional CTM coupled to the ERA40 reanalysis
- 2007
-
Ingår i: Tellus. Series B, Chemical and physical meteorology. - Stockholm : Tellus. - 0280-6509 .- 1600-0889. ; 59, s. 77-98
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Tidskriftsartikel (refereegranskat)abstract
- A three-dimensional Chemistry Transport Model was used to study the meteorologically induced interannual variability and trends in deposition of sulphur and nitrogen as well as concentrations of surface ozone (O3), nitrogen dioxide (NO2) and particulate matter (PM) and its constituents over Europe during 1958–2001. The model was coupled to the meteorological reanalysis ERA40, produced at the European Centre for Medium-range Weather Forecasts. Emissions and boundary conditions of chemical compounds and PM were kept constant at present levels. The average European interannual variation, due to meteorological variability, ranges from 3% for O3, 5%for NO2, 9% for PM, 6–9% for dry deposition, to about 20% for wet deposition of sulphur and nitrogen. For the period 1979–2001 the trend in ozone, due to climate variability is increasing in central and southwestern Europe and decreasing in northeastern Europe, the trend in NO2 is approximately opposite. The trend in PM is positive in eastern Europe. There are negative trends in wet deposition in southwestern and central Europe and positive trends in dry deposition overall. A bias in ERA40 precipitation could be partly responsible for the trends. The variation and trends need to be considered when interpreting measurements and designing measurement campaigns.
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| 48. |
- Andersson, Dan I., et al.
(författare)
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Evolution of New Functions De Novo and from Preexisting Genes
- 2015
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Ingår i: Cold Spring Harbor Perspectives in Biology. - : Cold Spring Harbor Laboratory. - 1943-0264. ; 7:6
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Forskningsöversikt (refereegranskat)abstract
- How the enormous structural and functional diversity of new genes and proteins was generated (estimated to be 10^10-€“10^12 different proteins in all organisms on earth [Choi I-G, Kim S-H. 2006. Evolution of protein structural classes and protein sequence families. Proc Natl Acad Sci 103: 14056–14061] is a central biological question that has a long and rich history. Extensive work during the last 80 years have shown that new genes that play important roles in lineage-specific phenotypes and adaptation can originate through a multitude of different mechanisms, including duplication, lateral gene transfer, gene fusion/fission, and de novo origination. In this review, we focus on two main processes as generators of new functions: evolution of new genes by duplication and divergence of pre-existing genes and de novo gene origination in which a whole protein-coding gene evolves from a noncoding sequence.
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| 49. |
- Andersson, E. Axel, et al.
(författare)
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Circulating tight-junction proteins are potential biomarkers for blood-brain barrier function in a model of neonatal hypoxic/ischemic brain injury
- 2021
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Ingår i: Fluids and Barriers of the CNS. - : Springer Science and Business Media LLC. - 2045-8118. ; 18:1
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Tidskriftsartikel (refereegranskat)abstract
- Background Neonatal encephalopathy often leads to lifelong disabilities with limited treatments currently available. The brain vasculature is an important factor in many neonatal neurological disorders but there is a lack of diagnostic tools to evaluate the brain vascular dysfunction of neonates in the clinical setting. Measurement of blood-brain barrier tight-junction (TJ) proteins have shown promise as biomarkers for brain injury in the adult. Here we tested the biomarker potential of tight-junctions in the context of neonatal brain injury. Methods The levels of TJ-proteins (occluding, claudin-5, and zonula occludens protein 1) in both blood plasma and cerebrospinal fluid (CSF) as well as blood-brain barrier function via C-14-sucrose (342 Da) and Evans blue extravasation were measured in a hypoxia/ischemia brain-injury model in neonatal rats. Results Time-dependent changes of occludin and claudin-5 levels could be measured in blood and CSF after hypoxia/ischemia with males generally having higher levels than females. The levels of claudin-5 in CSF correlated with the severity of the brain injury at 24 h post- hypoxia/ischemia. Simultaneously, we detected early increase in blood-brain barrier-permeability at 6 and 24 h after hypoxia/ischemia. Conclusions Levels of circulating claudin-5 and occludin are increased after hypoxic/ischemic brain injuries and blood-brain barrier-impairment and have promise as early biomarkers for cerebral vascular dysfunction and as a tool for risk assessment of neonatal brain injuries.
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| 50. |
- Andersson, E. Axel, et al.
(författare)
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Function and Biomarkers of the Blood-Brain Barrier in a Neonatal Germinal Matrix Haemorrhage Model
- 2021
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Ingår i: Cells. - : MDPI AG. - 2073-4409. ; 10:7
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Tidskriftsartikel (refereegranskat)abstract
- Germinal matrix haemorrhage (GMH), caused by rupturing blood vessels in the germinal matrix, is a prevalent driver of preterm brain injuries and death. Our group recently developed a model simulating GMH using intrastriatal injections of collagenase in 5-day-old rats, which corresponds to the brain development of human preterm infants. This study aimed to define changes to the blood-brain barrier (BBB) and to evaluate BBB proteins as biomarkers in this GMH model. Regional BBB functions were investigated using blood to brain C-14-sucrose uptake as well as using biotinylated BBB tracers. Blood plasma and cerebrospinal fluids were collected at various times after GMH and analysed with ELISA for OCLN and CLDN5. The immunoreactivity of BBB proteins was assessed in brain sections. Tracer experiments showed that GMH produced a defined region surrounding the hematoma where many vessels lost their integrity. This region expanded for at least 6 h following GMH, thereafter resolution of both hematoma and re-establishment of BBB function occurred. The sucrose experiment indicated that regions somewhat more distant to the hematoma also exhibited BBB dysfunction; however, BBB function was normalised within 5 days of GMH. This shows that GMH leads to a temporal dysfunction in the BBB that may be important in pathological processes as well as in connection to therapeutic interventions. We detected an increase of tight-junction proteins in both CSF and plasma after GMH making them potential biomarkers for GMH.
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