| 1. |
- Andersson, Christian, et al.
(författare)
-
Derivative-free Parameter Optimization of Functional Mock-up Units
- 2012
-
Ingår i: [Host publication title missing].
-
Konferensbidrag (refereegranskat)abstract
- Representing a physical system with a mathematical model requires knowledge not only about the physical laws governing the dynamics but also about the parameter values of the system. The parameters can sometimes be measured or calculated, however some of them are often difficult or impossible to obtain in these ways. Finding accurate parameter values is crucial for the accuracy of the mathematical model. Estimating the parameters using optimization algorithms which attempt to minimize the error between the response from the mathematical model and the physical system is a common approach for improving the accuracy of the model. Optimization algorithms usually requires information about the derivatives which may not always be available or not be appropriate for estimation which forces the use of derivative-free optimization algorithms. In this paper, we present an implementation of derivative-free optimization algorithms for parameter estimation in the JModelica.org platform. The implementation allows the underlying dynamic system to be represented as a Functional Mock-up Unit (FMU), thus enables parameter estimation of models designed in modeling tools following the standardized interface, the Functional Mock-up Interface (FMI), such as Dymola.
|
|
| 2. |
- Berglundh, Sofia, et al.
(författare)
-
C-reactive protein, bone loss, fracture, and mortality in elderly women: a longitudinal study in the OPRA cohort.
- 2015
-
Ingår i: Osteoporosis International. - : Springer Science and Business Media LLC. - 1433-2965 .- 0937-941X. ; 26:2, s. 727-735
-
Tidskriftsartikel (refereegranskat)abstract
- This longitudinal study investigates the association between C-reactive protein (CRP), osteoporosis, fractures, and mortality in 1044 elderly women. CRP was not an indicator for low bone mineral density (BMD), bone loss, or fracture in elderly women; however, women with elevated CRP levels over a prolonged period lost more bone over the 10-year follow-up, although fracture risk was not increased.
|
|
| 3. |
|
|
| 4. |
- Lagerholm, Sofia, et al.
(författare)
-
Genetic loci for bone architecture determined by three-dimensional CT in crosses with the diabetic GK rat.
- 2010
-
Ingår i: Bone. - : Elsevier BV. - 1873-2763 .- 8756-3282. ; 47, s. 1039-1047
-
Tidskriftsartikel (refereegranskat)abstract
- The F344 rat carries alleles contributing to bone fragility while the GK rat spontaneously develops type-2 diabetes. These characteristics make F344xGK crosses well suited for the identification of genes related to bone size and allow for future investigation on the association with type-2 diabetes. The aim of this study was to identify quantitative trait loci (QTLs) for bone size phenotypes measured by a new application of three-dimensional computed tomography (3DCT) and to investigate the effects of sex- and reciprocal cross. Tibia from male and female GK and F344 rats, representing the parental, F1 and F2 generations, were examined with 3DCT and analyzed for: total and cortical volumetric BMD, straight and curved length, peri- and endosteal area at mid-shaft. F2 progeny (108 male and 98 female) were genotyped with 192 genome-wide microsatellite markers (average distance 10cM). Sex- and reciprocal cross-separated QTL analyses were performed for the identification of QTLs linked to 3DCT phenotypes and true interactions were confirmed by likelihood ratio analysis in all F2 animals. Several genome-wide significant QTLs were found in the sex- and reciprocal cross-separated progeny on chromosomes (chr) 1, 3, 4, 9, 10, 14, and 17. Overlapping QTLs for both males and females in the (GKxF344)F2 progeny were located on chr 1 (39-67cM). This region confirms previously reported pQCT QTLs and overlaps loci for fasting glucose. Sex separated linkage analysis confirmed a male specific QTL on chr 9 (67-82cM) for endosteal area at the fibula site. Analyses separating the F2 population both by sex and reciprocal cross identified cross specific QTLs on chr 14 (males) and chr 3 and 4 (females). Two loci, chr 4 and 6, are unique to 3DCT and separate from pQCT generated loci. The 3DCT method was highly reproducible and provided high precision measurements of bone size in the rat enabling identification of new sex- and cross-specific loci. The QTLs on chr 1 indicate potential genetic association between bone-related phenotypes and traits affecting type-2 diabetes. The results illustrate the complexity of the genetic architecture of bone size phenotypes and demonstrate the importance of complementary methods for bone analysis.
|
|
| 5. |
- Lagerholm, Sofia, et al.
(författare)
-
Genetic Regulation of Bone Traits Is Influenced by Sex and Reciprocal Cross in F-2 Progeny From GK and F344 Rats
- 2009
-
Ingår i: Journal of Bone and Mineral Research. - 1523-4681. ; 24:6, s. 1066-1074
-
Tidskriftsartikel (refereegranskat)abstract
- A genome-wide linkage analysis to identify quantitative trait loci (QTLs) for bone phenotypes was performed in an F-2 intercross of inbred spontaneously type 2 diabetic GK and normoglycemic F344 rats (108 males and 98 females). The aim of the study was to locate genome regions with candidate genes affecting trabecular and cortical bone and to investigate the effects of sex and reciprocal cross. pQCT was used to determine tibia] bone phenotypes in the F2 rats, comprising reciprocal crosses with divergent mitochondrial (mt) DNA. Sex and reciprocal cross-separated QTL analyses were performed followed by assessment of specific interactions. Four genome-wide significant QTLs linked to either cortical vBMD, tibia length, body length, or metaphyseal area were identified in males on chromosomes (chr) 1, 8, and 15. In females, three significant QTLs linked to cortical BMC or metaphyseal total vBMD were identified on chr 1 and 2. Several additional suggestive loci for trabecular and cortical traits were detected in both males and females. Four female-specific QTLs on chr 2, 3, 5, and 10 and four reciprocal cross-specific QTLs on chr 1, 10, and 18 were identified, suggesting that both sex and mt genotype influence the expression of bone phenotypes. J Bone Miner Res 2009;24:1066-1074. Published online on December 29, 2008; doi: 10.1359/JBMR.081252
|
|
| 6. |
- Lagerholm, Sofia, et al.
(författare)
-
Identification of Candidate Gene Regions in the Rat by Co-Localization of QTLs for Bone Density, Size, Structure and Strength.
- 2011
-
Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 6:7
-
Tidskriftsartikel (refereegranskat)abstract
- Susceptibility to osteoporotic fracture is influenced by genetic factors that can be dissected by whole-genome linkage analysis in experimental animal crosses. The aim of this study was to characterize quantitative trait loci (QTLs) for biomechanical and two-dimensional dual-energy X-ray absorptiometry (DXA) phenotypes in reciprocal F2 crosses between diabetic GK and normo-glycemic F344 rat strains and to identify possible co-localization with previously reported QTLs for bone size and structure. The biomechanical measurements of rat tibia included ultimate force, stiffness and work to failure while DXA was used to characterize tibial area, bone mineral content (BMC) and areal bone mineral density (aBMD). F2 progeny (108 males, 98 females) were genotyped with 192 genome-wide markers followed by sex- and reciprocal cross-separated whole-genome QTL analyses. Significant QTLs were identified on chromosome 8 (tibial area; logarithm of odds (LOD) = 4.7 and BMC; LOD = 4.1) in males and on chromosome 1 (stiffness; LOD = 5.5) in females. No QTLs showed significant sex-specific interactions. In contrast, significant cross-specific interactions were identified on chromosome 2 (aBMD; LOD = 4.7) and chromosome 6 (BMC; LOD = 4.8) for males carrying F344mtDNA, and on chromosome 15 (ultimate force; LOD = 3.9) for males carrying GKmtDNA, confirming the effect of reciprocal cross on osteoporosis-related phenotypes. By combining identified QTLs for biomechanical-, size- and qualitative phenotypes (pQCT and 3D CT) from the same population, overlapping regions were detected on chromosomes 1, 3, 4, 6, 8 and 10. These are strong candidate regions in the search for genetic risk factors for osteoporosis.
|
|
| 7. |
|
|
| 8. |
- Martin, Tina, et al.
(författare)
-
Examining biofilm growth and metabolism of Escherichia coli at laboratory scale using geoelectrical methods
- 2023
-
Ingår i: Vatten: tidskrift för vattenvård /Journal of Water Management and research. - 0042-2886. ; :1-2, s. 71-90
-
Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- To link geophysical field data to specific biological phenomena, controlled laboratory experiments are needed for the understanding of the response of geophysical parameters to changes in biological conditions. In this study, suspensions of bacteria were mixed with sand to create a biofilm growing on a surface and these mixtures were monitored using the geoelectrical spectral induced polarization method (SIP). The beginning growth of the biofilm was confirmed by scanning electron microscopy and the amount of bacteria in liquid and sand estimated using culture and DNA based methods (i.e. qPCR, quantitative polymerase chain reaction). While changes in SIP signal could not be clearly related to microbial activity, fluctuations in the phase shift were concomitant with the detection of two unidentified metabolites in the liquid extracted from the sand. These metabolites were only detected when the biofilm was produced under oxygen limiting conditions. Even though the experimental design was not optimal for the SIP measurements, the results support the idea that these measurements are not measuring cell mass but are influenced by the presence of smaller charged molecules that may be produced as microbial metabolites. As microbial metabolites would change in the field during bioremediation, this method could be applied for this type of monitoring.
|
|
| 9. |
- Nivorlis, Aristeidis, et al.
(författare)
-
Multidisciplinary monitoring of an in-situ remediation test of chlorinated solvents
- 2024
-
Ingår i: Science of the Total Environment. - 0048-9697. ; 922
-
Tidskriftsartikel (refereegranskat)abstract
- Pollutions on and within the underground poses risks for groundwater contamination and is a widespread global problem. Common remediation methods based on digging and removal can be expensive and have limitations, while in-situ remediation is an attractive alternative. However, there is a need to develop tools to monitor the effectiveness both in terms of the successful injection of remediation fluids but also the effectiveness of the treatment, i.e., degree of degradation/removal of the pollutants and possible metabolites. This paper presents a methodology for monitoring the changes following an in-situ remediation treatment of a site contaminated with chlorinated solvents. The methodology consists of two different methods, where Direct Current resistivity and time-domain Induced Polarization (DCIP) was used to acquire daily data and geochemical analyses on water samples were collected approximately every three months. The geophysical results provide insights on how the injected fluids are spreading and assist in acquiring a better understanding of the geological and hydrogeological system. On the other hand, the geochemical sampling enhances our knowledge about the hydrochemistry of the system and the concentration of the pollutants. Our research highlights the challenges of monitoring in-situ bioremediation experiments in complex environments and in cases where pollutants are situated in low hydraulic conductivity formations. The joint interpretation of the data shows the importance of an interdisciplinary approach to understand complex systems.
|
|
| 10. |
|
|
