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  • 301.
    Balkanyi, Laszlo
    et al.
    European Centre for Disease Prevention and Control, Stockholm, Sweden.
    Schulz, Stefan
    Medizinische Universität Graz, Austria and Freiburg University Medical Center, Freiburg, Germany.
    Cornet, Ronald
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Bodenreider, Olivier
    National Library of Medicine, Bethsheda, USA.
    Medical concept representation: the years beyond 2000.2013In: Proceedings of Studies in Health Technology & Informatics, vol. 192, IOS Press, 2013, Vol. 192, p. 1011-1011Conference paper (Refereed)
    Abstract [en]

    This work aims at understanding the state of the art in the broad contextual research area of "medical concept representation". Our data support the general understanding that the focus of research has moved toward medical ontologies, which we interpret as a paradigm shift. Both the opinion of socially active groups of researchers and changes in bibliometric data since 1988 support this opinion. Socially active researchers mention the OBO foundry, SNOMED CT, and the UMLS as anchor activities.

  • 302.
    Balsiger, Fabian
    Linköping University, Department of Biomedical Engineering, Biomedical Instrumentation. Linköping University, The Institute of Technology.
    Brain Tumor Volume Calculation: Segmentation and Visualization Using MR Images2012Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Background: Glioblastomas are highly aggressive and malignant brain tumors which are difficult to resect totally. The surgical extent of resection constitutes a key role due to its direct influence on the patient’s survival time. To determine the resection extent, the tumor volume on pre-operative and post-operative magnetic resonance (MR) images should be calculated and compared.

    Materials and Methods: An active contour segmentation method was implemented to segment glioblastoma brain tumors on pre-operative T1-contrast enhanced MR images in axial, coronal and sagittal planes by self-developed software. The volume was rendered from the tumor  contours using Delaunay triangulation. Besides the segmentation and volume rendering, a graphical user interface was developed to facilitate the rendering, visualization and volume calculation of the brain tumor. The software was implemented in MATLAB (version 7.2). Two MR image data sets from glioblastoma patients were used and the repeatability and reproducibility of volume calculation was tested. Dimensions of the calculated tumor volume were then compared to the dimensions obtained in Amira® software.

    Results: The tumor volumes for data set 1 and data set 2 were 62.7 and 39.0 cm3, respectively. When tumor was segmented by different users (n=4), the volumes were 62.5 ± 0.3 and 42.6 ± 3.5 cm3. Segmentation errors were seen during the segmentation of data set 2. Mainly under- and over-segmentation due to hypointense MR signals caused by cerebrospinal fluid, or hyperintense MR signals caused by skull bone and weak tumor boundaries led to wrong segmentation results.

    Conclusion: Segmentation using active contours method is able to detect the brain tumor boundaries. The volume rendering and visualization allows the user to explore the tumor tissue and its surrounding interactively. Using the software, tumor volume is precisely calculated.

  • 303.
    Banaem, Hossein Y.
    et al.
    Tehran University of Medical Sciences, Iran.
    Ahmadian, Alireza
    Tehran University of Medical Sciences, Iran.
    Saberi, Hooshangh
    Tehran University of Medical Sciences, Iran.
    Daneshmehr, Alireza
    Univiversity of Tehran, Iran.
    Khodadad, Davood
    Tehran University of Medical Sciences, Iran.
    Brain tumor modeling: glioma growth and interaction with chemotherapy2011In: Proc. SPIE 8285, International Conference on Graphic and Image Processing (ICGIP 2011), SPIE - International Society for Optical Engineering, 2011, article id 82851MConference paper (Refereed)
    Abstract [en]

    In last decade increasingly mathematical models of tumor growths have been studied, particularly on solid tumors which growth mainly caused by cellular proliferation. In this paper we propose a modified model to simulate the growth of gliomas in different stages. Glioma growth is modeled by a reaction-advection-diffusion. We begin with a model of untreated gliomas and continue with models of polyclonal glioma following chemotherapy. From relatively simple assumptions involving homogeneous brain tissue bounded by a few gross anatomical landmarks (ventricles and skull) the models have been expanded to include heterogeneous brain tissue with different motilities of glioma cells in grey and white matter. Tumor growth is characterized by a dangerous change in the control mechanisms, which normally maintain a balance between the rate of proliferation and the rate of apoptosis (controlled cell death). Result shows that this model closes to clinical finding and can simulate brain tumor behavior properly.

  • 304.
    Banaem, Hossein Yousefi
    et al.
    Tehran University of Medical Science, Tehran, Iran.
    Ahmadian, Alireza
    Tehran University of Medical Science, Tehran, Iran.
    Saberi, Hooshangh
    Tehran University of Medical Science, Tehran, Iran.
    Daneshmehr, Alireza
    University of Tehran, Tehran, Iran.
    Khodadad, Davood
    Tehran University of Medical Science, Tehran, Iran.
    Brain tumor modeling: glioma growth and interaction with chemotherapy2011In: International Conference on Graphic and Image Processing (ICGIP) / [ed] Yi Xie & Yanjun Zheng, SPIE - International Society for Optical Engineering, 2011, Vol. 8285, article id 82851MConference paper (Refereed)
    Abstract [en]

    In last decade increasingly mathematical models of tumor growths have been studied, particularly on solid tumors which growth mainly caused by cellular proliferation. In this paper we propose a modified model to simulate the growth of gliomas in different stages. Glioma growth is modeled by a reaction-advection-diffusion. We begin with a model of untreated gliomas and continue with models of polyclonal glioma following chemotherapy. From relatively simple assumptions involving homogeneous brain tissue bounded by a few gross anatomical landmarks (ventricles and skull) the models have been expanded to include heterogeneous brain tissue with different motilities of glioma cells in grey and white matter. Tumor growth is characterized by a dangerous change in the control mechanisms, which normally maintain a balance between the rate of proliferation and the rate of apoptosis (controlled cell death). Result shows that this model closes to clinical finding and can simulate brain tumor behavior properly.

  • 305.
    Bang, Le Thi
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Applied Materials Sciences.
    Filho, Luimar
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Applied Materials Sciences.
    Engqvist, Håkan
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Applied Materials Sciences.
    Xia, Wei
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Applied Materials Sciences.
    Persson, Cecilia
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Applied Materials Sciences.
    Synthesis and assessment of metallic ion migration through a novel calcium carbonate coating for biomedical implants2019In: Journal of Biomedical Materials Research. Part B - Applied biomaterials, ISSN 1552-4973, E-ISSN 1552-4981Article in journal (Refereed)
  • 306.
    Baranowski, Jacek
    et al.
    Linköping Heart Centre, University Hospital, Linköping University.
    Ahn, Henrik
    Linköping Heart Centre, University Hospital, Linköping University.
    Freter, Wolfgang
    Linköping Heart Centre, University Hospital, Linköping University.
    Nielsen, Niels-Erik
    Linköping Heart Centre, University Hospital, Linköping University.
    Nylander, Eva
    Linköping Heart Centre, University Hospital, Linköping University.
    Janerot-Sjöberg, Birgitta
    Linköping Heart Centre, University Hospital, Linköping University.
    Sandborg, Michael
    Linköping Heart Centre, University Hospital, Linköping University.
    Wallby, Lars
    Linköping Heart Centre, University Hospital, Linköping University.
    Echo-guided presentation of the aortic valve minimises contrast exposure in transcatheter valve recipients2011In: Catheterization and cardiovascular interventions, ISSN 1522-1946, E-ISSN 1522-726X, Vol. 77, no 2, p. 272-275Article in journal (Refereed)
    Abstract [en]

    OBJECTIVES: We have developed a method using transthoracic echocardiography in establishing optimal visualization of the aortic root, to reduce the amount of contrast medium used in each patient.

    BACKGROUND: During transcatheter aortic valve implantation, it is necessary to obtain an optimal fluoroscopic projection for deployment of the valve showing the aortic ostium with the three cusps aligned in the beam direction. This may require repeat aortic root angiograms at this stage of the procedure with a high amount of contrast medium with a risk of detrimental influence on renal function.

    METHODS: We studied the conventional way and an echo guided way to optimize visualisation of the aortic root. Echocardiography was used initially allowing easier alignment of the image intensifier with the transducer's direction.

    RESULTS: Contrast volumes, radiation/fluoroscopy exposure times, and postoperative creatinine levels were significantly less in patients having the echo-guided orientation of the optimal fluoroscopic angles compared with patients treated with the conventional approach.

    CONCLUSION: We present a user-friendly echo-guided method to facilitate fluoroscopy adjustment during transcatheter aortic valve implantation. In our series, the amounts of contrast medium and radiation have been significantly reduced, with a concomitant reduction in detrimental effects on renal function in the early postoperative phase.

  • 307.
    Barba, Albert
    et al.
    Univ Politecn Cataluna, Dept Mat Sci & Met Engn, Biomat Biomech & Tissue Engn Grp, Ave Eduard Maristany 10-14, Barcelona 08019, Spain;Univ Politecn Cataluna, Barcelona Res Ctr Multiscale Sci & Engn, Ave Eduard Maristany 10-14, Barcelona 08019, Spain.
    Diez-Escudero, Anna
    Univ Politecn Cataluna, Dept Mat Sci & Met Engn, Biomat Biomech & Tissue Engn Grp, Ave Eduard Maristany 10-14, Barcelona 08019, Spain;Univ Politecn Cataluna, Barcelona Res Ctr Multiscale Sci & Engn, Ave Eduard Maristany 10-14, Barcelona 08019, Spain.
    Espanol, Montserrat
    Univ Politecn Cataluna, Dept Mat Sci & Met Engn, Biomat Biomech & Tissue Engn Grp, Ave Eduard Maristany 10-14, Barcelona 08019, Spain;Univ Politecn Cataluna, Barcelona Res Ctr Multiscale Sci & Engn, Ave Eduard Maristany 10-14, Barcelona 08019, Spain.
    Bonany, Mar
    Univ Politecn Cataluna, Dept Mat Sci & Met Engn, Biomat Biomech & Tissue Engn Grp, Ave Eduard Maristany 10-14, Barcelona 08019, Spain;Univ Politecn Cataluna, Barcelona Res Ctr Multiscale Sci & Engn, Ave Eduard Maristany 10-14, Barcelona 08019, Spain.
    Maria Sadowska, Joanna
    Univ Politecn Cataluna, Dept Mat Sci & Met Engn, Biomat Biomech & Tissue Engn Grp, Ave Eduard Maristany 10-14, Barcelona 08019, Spain;Univ Politecn Cataluna, Barcelona Res Ctr Multiscale Sci & Engn, Ave Eduard Maristany 10-14, Barcelona 08019, Spain.
    Guillem-Marti, Jordi
    Univ Politecn Cataluna, Dept Mat Sci & Met Engn, Biomat Biomech & Tissue Engn Grp, Ave Eduard Maristany 10-14, Barcelona 08019, Spain;Univ Politecn Cataluna, Barcelona Res Ctr Multiscale Sci & Engn, Ave Eduard Maristany 10-14, Barcelona 08019, Spain.
    Öhman-Mägi, Caroline
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Applied Materials Sciences.
    Persson, Cecilia
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Applied Materials Sciences.
    Manzanares, Maria-Cristina
    Univ Barcelona, Dept Pathol & Expt Therapeut, Human Anat & Embryol Unit, Barcelona 08907, Spain.
    Franch, Jordi
    Univ Autonoma Barcelona, Sch Vet, Small Anim Surg Dept, Bone Healing Grp, E-08193 Barcelona, Spain.
    Ginebra, Maria-Pau
    Univ Politecn Cataluna, Dept Mat Sci & Met Engn, Biomat Biomech & Tissue Engn Grp, Ave Eduard Maristany 10-14, Barcelona 08019, Spain;Univ Politecn Cataluna, Barcelona Res Ctr Multiscale Sci & Engn, Ave Eduard Maristany 10-14, Barcelona 08019, Spain;Barcelona Inst Technol BIST, Inst Bioengn Catalonia IBEC, Barcelona 08028, Spain.
    Impact of Biomimicry in the Design of Osteoinductive Bone Substitutes: Nanoscale Matters2019In: ACS Applied Materials and Interfaces, ISSN 1944-8244, E-ISSN 1944-8252, Vol. 11, no 9, p. 8818-8830Article in journal (Refereed)
    Abstract [en]

    Bone apatite consists of carbonated calcium-deficient hydroxyapatite (CDHA) nanocrystals. Biomimetic routes allow fabricating synthetic bone grafts that mimic biological apatite. In this work, we explored the role of two distinctive features of biomimetic apatites, namely, nanocrystal morphology (plate vs needle-like crystals) and carbonate content, on the bone regeneration potential of CDHA scaffolds in an in vivo canine model. Both ectopic bone formation and scaffold degradation were drastically affected by the nanocrystal morphology after intramuscular implantation. Fine-CDHA foams with needle-like nanocrystals, comparable in size to bone mineral, showed a markedly higher osteoinductive potential and a superior degradation than chemically identical coarse-CDHA foams with larger plate-shaped crystals. These findings correlated well with the superior bone-healing capacity showed by the fine-CDHA scaffolds when implanted intraosseously. Moreover, carbonate doping of CDHA, which resulted in small plate-shaped nanocrystals, accelerated both the intrinsic osteoinduction and the bone healing capacity, and significantly increased the cell-mediated resorption. These results suggest that tuning the chemical composition and the nanostructural features may allow the material to enter the physiological bone remodeling cycle, promoting a tight synchronization between scaffold degradation and bone formation.

  • 308.
    Barba, Albert
    et al.
    Biomaterials, Biomechanics and Tissue Engineering Group, Department of Materials Science and Metallurgical Engineering, Universitat Politecnica de Catalunya.
    Diez-Escudero, Anna
    Biomaterials, Biomechanics and Tissue Engineering Group, Department of Materials Science and Metallurgical Engineering, Universitat Politecnica de Catalunya.
    Maazouz, Yassine
    Biomaterials, Biomechanics and Tissue Engineering Group, Department of Materials Science and Metallurgical Engineering, Universitat Politecnica de Catalunya.
    Rappe, Katrin
    Bone Healing Group, Small Animal Surgery Department, Veterinary School, Universitat Autonoma de Barcelona.
    Espanol, Montserrat
    Barcelona Research Center in Multiscale Science and Engineering, Universitat Politecnica de Catalunya.
    Montufar, Edgar B
    Barcelona Research Center in Multiscale Science and Engineering, Universitat Politecnica de Catalunya.
    Bonany, Mar
    Barcelona Research Center in Multiscale Science and Engineering, Universitat Politecnica de Catalunya.
    Sadowska, Joanna M
    Barcelona Research Center in Multiscale Science and Engineering, Universitat Politecnica de Catalunya.
    Guillem-Marti, Jordi
    Barcelona Research Center in Multiscale Science and Engineering, Universitat Politecnica de Catalunya.
    Öhman, Caroline
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Applied Materials Sciences.
    Persson, Cecilia
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Applied Materials Sciences.
    Manzanares, Maria-Cristina
    Human Anatomy and Embryology Unit, Department of Pathology and Experimental Therapeutics, Universitat de Barcelona.
    Franch, Jordi
    Bone Healing Group, Small Animal Surgery Department, Veterinary School, Universitat Autonoma de Barcelona.
    Ginebra, Maria-Pau
    Biomaterials, Biomechanics and Tissue Engineering Group, Department of Materials Science and Metallurgical Engineering, Universitat Politecnica de Catalunya.
    Osteoinduction by Foamed and 3D-Printed Calcium Phosphate Scaffolds: Effect of Nanostructure and Pore Architecture2017In: ACS Applied Materials and Interfaces, ISSN 1944-8244, E-ISSN 1944-8252, Vol. 9, no 48, p. 41722-41736Article in journal (Refereed)
    Abstract [en]

    Some biomaterials are osteoinductive, that is, they are able to trigger the osteogenic process by inducing the differentiation of mesenchymal stem cells to the osteogenic lineage. Although the underlying mechanism is still unclear, microporosity and specific surface area (SSA) have been identified as critical factors in material-associated osteoinduction. However, only sintered ceramics, which have a limited range of porosities and SSA, have been analyzed so far. In this work, we were able to extend these ranges to the nanoscale, through the foaming and 3D-printing of biomimetic calcium phosphates, thereby obtaining scaffolds with controlled micro- and nanoporosity and with tailored macropore architectures. Calcium-deficient hydroxyapatite (CDHA) scaffolds were evaluated after 6 and 12 weeks in an ectopic-implantation canine model and compared with two sintered ceramics, biphasic calcium phosphate and β-tricalcium phosphate. Only foams with spherical, concave macropores and not 3Dprinted scaffolds with convex, prismatic macropores induced significant ectopic bone formation. Among them, biomimetic nanostructured CDHA produced the highest incidence of ectopic bone and accelerated bone formation when compared with conventional microstructured sintered calcium phosphates with the same macropore architecture. Moreover, they exhibited different bone formation patterns; in CDHA foams, the new ectopic bone progressively replaced the scaffold, whereas in sintered biphasic calcium phosphate scaffolds, bone was deposited on the surface of the material, progressively filling the pore space. In conclusion, this study demonstrates that the high reactivity of nanostructured biomimetic CDHA combined with a spherical, concave macroporosity allows the pushing of the osteoinduction potential beyond the limits of microstructured calcium phosphate ceramics.

  • 309.
    Barba, Albert
    et al.
    Biomaterials, Biomechanics and Tissue Engineering Group, Department of Materials Science and Metallurgical Engineering, Universitat Politècnica de Catalunya.
    Maazouz, Yassine
    Biomaterials, Biomechanics and Tissue Engineering Group, Department of Materials Science and Metallurgical Engineering, Universitat Politècnica de Catalunya.
    Diez-Escudero, Anna
    Biomaterials, Biomechanics and Tissue Engineering Group, Department of Materials Science and Metallurgical Engineering, Universitat Politècnica de Catalunya.
    Rappe, Katrin
    Bone Healing Group, Small Animal Surgery Department, Veterinary School, Universitat Autònoma de Barcelona.
    Espanol, Montserrat
    Biomaterials, Biomechanics and Tissue Engineering Group, Department of Materials Science and Metallurgical Engineering, Universitat Politècnica de Catalunya.
    Montufar, Edgar
    Biomaterials, Biomechanics and Tissue Engineering Group, Department of Materials Science and Metallurgical Engineering, Universitat Politècnica de Catalunya.
    Öhman, Caroline
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Applied Materials Sciences.
    Persson, Cecilia
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Applied Materials Sciences.
    Fontecha, Pedro
    Bone Healing Group, Small Animal Surgery Department, Veterinary School, Universitat Autònoma de Barcelona.
    Manzanares, Maria-Cristina
    Human Anatomy and Embryology Unit, Department of Pathology and Experimental Therapeutics, Universitat de Barcelona.
    Franch, Jordi
    Bone Healing Group, Small Animal Surgery Department, Veterinary School, Universitat Autònoma de Barcelona.
    Ginebra, Maria-Pau
    Biomaterials, Biomechanics and Tissue Engineering Group, Department of Materials Science and Metallurgical Engineering, Universitat Politècnica de Catalunya.
    Osteogenesis by foamed and 3D-printed nanostructured calcium phosphate scaffolds: Effect of pore architecture2018In: Acta Biomaterialia, ISSN 1742-7061, E-ISSN 1878-7568, Vol. 79, p. 135-147Article in journal (Refereed)
    Abstract [en]

    There is an urgent need of synthetic bone grafts with enhanced osteogenic capacity. This can be achieved by combining biomaterials with exogenous growth factors, which however can have numerous undesired side effects, but also by tuning the intrinsic biomaterial properties. In a previous study, we showed the synergistic effect of nanostructure and pore architecture of biomimetic calcium deficient hydroxyapatite (CDHA) scaffolds in enhancing osteoinduction, i.e. fostering the differentiation of mesenchymal stem cells to bone forming cells. This was demonstrated by assessing bone formation after implanting the scaffolds intramuscularly. The present study goes one step forward, since it analyzes the effect of the geometrical features of the same CDHA scaffolds, obtained either by 3D-printing or by foaming, on the osteogenic potential and resorption behaviour in a bony environment. After 6 and 12 weeks of intraosseous implantation, both bone formation and material degradation had been drastically affected by the macropore architecture of the scaffolds. Whereas nanostructured CDHA was shown to be highly osteoconductive both in the robocast and foamed scaffolds, a superior osteogenic capacity was observed in the foamed scaffolds, which was associated with their higher intrinsic osteoinductive potential. Moreover, they showed a significantly higher cell-mediated degradation than the robocast constructs, with a simultaneous and progressive replacement of the scaffold by new bone. In conclusion, these results demonstrate that the control of macropore architecture is a crucial parameter in the design of synthetic bone grafts, which allows fostering both material degradation and new bone formation. Statement of Significance 3D-printing technologies open new perspectives for the design of patient-specific bone grafts, since they allow customizing the external shape together with the internal architecture of implants. In this respect, it is important to design the appropriate pore geometry to maximize the bone healing capacity of these implants. The present study analyses the effect of pore architecture of nanostructured hydroxyapatite scaffolds, obtained either by 3D-printing or foaming, on the osteogenic potential and scaffold resorption in an in vivo model. While nanostructured hydroxyapatite showed excellent osteoconductive properties irrespective of pore geometry, we demonstrated that the spherical, concave macropores of foamed scaffolds significantly promoted both material resorption and bone regeneration compared to the 3D-printed scaffolds with orthogonal-patterned struts and therefore prismatic, convex macropores.

  • 310.
    Barba, Albert
    et al.
    Biomaterials, Biomechanics and Tissue Engineering Group, Department of Materials Science and Metallurgical Engineering, Universitat Politecnica de Catalunya.
    Rappe, Katrin
    Bone Healing Group, Small Animal Surgery Department, Veterinary School, Universitat Autonoma de Barcelona.
    Fontecha, P
    Bone Healing Group, Small Animal Surgery Department, Veterinary School, Universitat Autonoma de Barcelona.
    Diez-Escudero, Anna
    Biomaterials, Biomechanics and Tissue Engineering Group, Department of Materials Science and Metallurgical Engineering, Universitat Politecnica de Catalunya.
    Maazouz, Yassine
    Biomaterials, Biomechanics and Tissue Engineering Group, Department of Materials Science and Metallurgical Engineering, Universitat Politecnica de Catalunya.
    Espanol, Montserrat
    Biomaterials, Biomechanics and Tissue Engineering Group, Department of Materials Science and Metallurgical Engineering, Universitat Politecnica de Catalunya.
    Öhman Mägi, Caroline
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Applied Materials Sciences.
    Persson, Cecilia
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Applied Materials Sciences.
    Manzanares, Maria-Cristina
    Human Anatomy and Embryology Unit, Department of Pathology and Experimental Therapeutics, Universitat de Barcelona.
    Franch, Jordi
    Bone Healing Group, Small Animal Surgery Department, Veterinary School, Universitat Autonoma de Barcelona.
    Ginebra, Maria-Pau
    Biomaterials, Biomechanics and Tissue Engineering Group, Department of Materials Science and Metallurgical Engineering, Universitat Politecnica de Catalunya.
    Nanostructured Calcium Phosphate Scaffolds Trigger Osteoinduction and Osteogenesis2017Conference paper (Refereed)
  • 311.
    Bardolet Pettersson, Susana
    Linköping University, Department of Biomedical Engineering, Division of Biomedical Engineering.
    Managing imbalanced training data by sequential segmentation in machine learning2019Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Imbalanced training data is a common problem in machine learning applications. Thisproblem refers to datasets in which the foreground pixels are significantly fewer thanthe background pixels. By training a machine learning model with imbalanced data, theresult is typically a model that classifies all pixels as the background class. A result thatindicates no presence of a specific condition when it is actually present is particularlyundesired in medical imaging applications. This project proposes a sequential system oftwo fully convolutional neural networks to tackle the problem. Semantic segmentation oflung nodules in thoracic computed tomography images has been performed to evaluate theperformance of the system. The imbalanced data problem is present in the training datasetused in this project, where the average percentage of pixels belonging to the foregroundclass is 0.0038 %. The sequential system achieved a sensitivity of 83.1 % representing anincrease of 34 % compared to the single system. The system only missed 16.83% of thenodules but had a Dice score of 21.6 % due to the detection of multiple false positives. Thismethod shows considerable potential to be a solution to the imbalanced data problem withcontinued development.

  • 312. Barrefelt, Åsa
    et al.
    Paradossi, Gaio
    Asem, Heba
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Functional Materials, FNM.
    Margheritelli, Silvia
    Saghafian, Maryam
    Oddo, Letizia
    Muhammed, Mamoun
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Functional Materials, FNM.
    Aspelin, Peter
    Hassan, Moustapha
    Brismar, Torkel B.
    DYNAMIC MR IMAGING, BIODISTRIBUTION AND PHARMACOKINETICS OF POLYMER SHELLED MICROBUBBLES CONTAINING SPION2014In: NANO, ISSN 1793-2920, Vol. 9, no 6, p. 1450069-Article in journal (Refereed)
    Abstract [en]

    Magnetic Resonance Imaging (MRI) is a noninvasive diagnostic method that provides information on morphological and physiological changes of the internal organs over time. Imaging and measurements can be repeated on the same subject, thereby reducing inter-individual variability effects and hence the number of subjects required. A potential MRI contrast agent consisting of microbubbles embedded with superparamagnetic iron oxide nanoparticles (SPION) in the shell (SPION MBs) was injected intravenously into rats to determine their biodistribution and pharmacokinetics using MR imaging. Agarose phantoms containing SPION MBs were scanned using 3 T MRI to construct a standard curve. Rats were injected with SPION MBs, free SPION or plain MBs and scanned dynamically at 3 T using a clinical MR scanner. The relaxation rate (R2*) was studied over time as a measure of the iron oxide concentrations to enable calculation of the pharmacokinetic parameters. The kinetics of SPION MBs in the liver was fitted to a one-compartment model. Furthermore, the biological fate of SPION MBs was examined via a histological survey of tissue samples using Perls' Prussian blue staining and immunohistochemistry (IHC). 1.2 h after injection of SPION MBs, T2* of the liver had decreased to its minimum. The elimination half-life of SPION MBs was 598.2 +/- 97.3 h, while the half-life for SPION was 222.6 +/- 26.4 h. Moreover, our study showed that SPION MBs were taken up by the macrophages in the lungs, spleen and liver. MBs labeled with SPION can be used for MR imaging. Moreover, MRI is a reliable and noninvasive tool that can be utilized in pharmacokinetic investigations of future contrast agents using SPION MBs and SPION in the rat.

  • 313.
    Bartholomay, S.
    et al.
    Germany.
    Marten, D.
    Germany.
    Martinez, Mariano Sanchez
    KTH.
    Alber, J.
    Germany.
    Pechlivanoglou, G.
    Germany.
    Nayeri, C. N.
    Germany.
    Paschereit, C. O.
    Germany.
    Klein, A. C.
    Germany.
    Lutz, T.
    Kramer, E.
    Cross-talk compensation for blade root flap-and edgewise moments on an experimental research wind turbine and comparison to numerical results2018In: Proceedings of the ASME Turbo Expo, ASME Press, 2018Conference paper (Refereed)
    Abstract [en]

    In the current paper a method to correct cross-talk effects for strain-gauge measurements is presented. Themethod is demonstrated on an experimental horizontal axiswind turbine. The procedure takes cross-moments (flapwise on edgewise moments and vice versa) as well as axialacceleration into account. The results from the experimental setup are compared to numerical URANS calculationsand the medium-fidelity code Qblade for a baseline caseand two yawed inflow situations.

  • 314.
    Barthélemy, Aude
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH).
    Exploratory Study on Lower Limb Amputee Patients : Use of IMUs to Monitor the Gait Quality During the Rehabilitation Period2019Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Specific rehabilitation is a key period for a lower-limb amputee patient. While learning how to walk with a prosthesis, the patient needs to avoid any gait compensations that may lead to future comorbidities. To reach a gait pattern close to the one of a healthy person, objective data may be of great help to complement the experience of the clinician team. By using 6 IMUs located on the feet, shanks and thighs accompanied by 3 accelerometers on the pelvis, sternum and head, data could be recorded during walking exercises of 7 rehabilitation sessions of a patient. To compute the absolute symmetry index of the stance phase duration and the stride duration all over the instrumented sessions, the gait events defining the transitions between gait phases were determined thanks to several algorithms. By first comparing the error obtained in the calculation of the stance phase duration with all tested algorithms as compared to the data from pressure insoles considered as a reference system, the algorithm developed by Trojaniello and collaborators [1] was found to be the most adapted to this situation. Using this algorithm on the data from all sessions highlighted the possibility to detect changes in the symmetry of stance phase duration and stride duration, that are relative to the gait quality. This means that IMUs seem to be able to monitor the progress of a patient during his rehabilitation. Hence, IMUs have proven themselves to be a system of great interest in the analysis of the gait pattern of a lower-limb amputee patient in rehabilitation, by allowing for an embedded measurement of much more parameters than the pressure insoles, whose calibration constituted a real limitation. 

  • 315.
    Barua, Shaibal
    et al.
    Mälardalen University, School of Innovation, Design and Engineering, Embedded Systems.
    Ahmed, Mobyen Uddin
    Mälardalen University, School of Innovation, Design and Engineering, Embedded Systems.
    Begum, Shahina
    Mälardalen University, School of Innovation, Design and Engineering, Embedded Systems.
    Distributed Multivariate Physiological Signal Analytics for Driver´s Mental State Monitoring2018In: Lecture Notes of the Institute for Computer Sciences, Social-Informatics and Telecommunications Engineering, LNICST, Volume 225, 2018, p. 26-33Conference paper (Refereed)
    Abstract [en]

    This paper presents a distributed data analytics approach for drivers’ mental state monitoring using multivariate physiological signals. Driver’s mental states such as cognitive distraction, sleepiness, stress, etc. can be fatal contributing factors and to prevent car crashes these factors need to be understood. Here, a cloud-based approach with heterogeneous sensor sources that generates extremely large data sets of physiological signals need to be handled and analyzed in a big data scenario. In the proposed physiological big data analytics approach, for driver state monitoring, heterogeneous data coming from multiple sources i.e., multivariate physiological signals are used, processed and analyzed to aware impaired vehicle drivers. Here, in a distributed big data environment, multi-agent case-based reasoning facilitates parallel case similarity matching and handles data that are coming from single and multiple physiological signal sources.

  • 316.
    Bassan, Gioia
    KTH, School of Technology and Health (STH).
    Dual-Probe Shear Wave Elastography in a Transversely Isotropic Phantom2015Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Shear Wave Elastography (SWE) is an ultrasound based technique which is able to measure tissue stiffness through the speed of induced shear waves. Tissue stiffness is often related to pathological conditions and detecting mechanical changes can help the recognition of potential diseases. The clinical use of SWE is limited to isotropic tissue due to the difficulty in assessing a theoretical model for more complex tissue and this project therefore aimed to evaluate the possibility of obtaining a full mechanical characterization of a transversely isotropic (TI) phantom with dual-probe SWE. A TI hydrogel phantom was developed and mechanical tests were performed to verify its anisotropy and determine the elastic moduli in both the perpendicular and longitudinal directions. Shear moduli were estimated using conventional and dual-probe SWE comparing the results to theoretical pure-transverse (PT) and quasi-transverse (QT) wave propagation modes. Both mechanical and SWE tests showed that the phantoms were transversely isotropic ET/EL=0.81. Moreover, multiple wave propagation modes calculated with dual-probe SWE showed a good agreement with the theoretical curves and indicated the possibility of measuring all the elasticity constants needed to fully characterize an incompressible, TI tissue with dual-probe SWE.

  • 317. Bassan, Gioia
    et al.
    Larsson, David
    KTH, Medicinsk bildteknik.
    Nordenfur, Tim
    KTH, Medicinsk bildteknik.
    Bjällmark, Anna
    KTH, Medicinsk bildteknik.
    Larsson, Matilda
    KTH, Medicinsk bildteknik.
    Acquisition of multiple mode shear wave propagation in transversely isotropic medium using dualprobe setup2015Conference paper (Refereed)
  • 318. Bassan, Gioia
    et al.
    Larsson, David
    KTH, School of Technology and Health (STH), Medical Engineering, Medical Imaging.
    Nordenfur, Tim
    KTH, School of Technology and Health (STH), Medical Engineering, Medical Imaging.
    Bjällmark, Anna
    KTH, School of Technology and Health (STH), Medical Engineering, Medical Imaging.
    Larsson, Matilda
    KTH, School of Technology and Health (STH), Medical Engineering, Medical Imaging.
    Acquisition of multiple mode shear wave propagation in transversely isotropic medium using dualprobe setup2015Conference paper (Refereed)
  • 319.
    Bastuck, Manuel
    et al.
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, Faculty of Science & Engineering. Saarland University, Germany.
    Baur, T.
    Lab Measurement Technology, Germany.
    Schutze, A.
    Lab Measurement Technology, Germany.
    Fusing Cyclic Sensor Data with Different Cycle Length2016In: 2016 IEEE INTERNATIONAL CONFERENCE ON MULTISENSOR FUSION AND INTEGRATION FOR INTELLIGENT SYSTEMS (MFI), IEEE , 2016, p. 72-77Conference paper (Refereed)
    Abstract [en]

    Cyclic modulation of sensor parameters can improve sensitivity and selectivity of gas sensors. If the modulated parameter influences the sens environment, several readings can be gained, eventually resulting in a multi-dimensional response which can be analyzed with, e.g., principal component analysis. In certain cases, e.g. temperature modulated gas sensors with different thermal time constants, the length of the used cycles, and, thus, the temporal resolution of the sensors can differ. As a consequence, different sensors can produce datasets with an unequal number of observations which, nevertheless, cover the same interval of time. In this work, we explore three different strategies which enable combination of those datasets in order to retain the maximum amount of information from two sensors when used in parallel. Simulated data show that simple combination of a short cycle with the last complete long cycle can improve correct classification rate by 15 percent points while maintaining the better temporal resolution. On the other hand, performance can be further increased at the expense of temporal resolution by adding either several of the short cycles, or their mean, to a long cycle, effectively reducing noise. The proposed combination strategies and their dependence on preprocessing are validated with a real dataset of two gas sensors. Overall, and taking into account differences in data performance for simulated and real data is observed.

  • 320.
    Basu, Alex
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Celma, Gunta
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Strömme, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Ferraz, Natalia
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    In Vitro and in Vivo Evaluation of the Wound Healing Properties of Nanofibrillated Cellulose Hydrogels2018In: ACS Applied Bio MaterialsArticle in journal (Refereed)
    Abstract [en]

    Current trends in wound care research move toward the development of wound healing dressings designed to treat different types of wounds (e.g., burns and chronic wounds) and toward tailoring treatments for different stages of the wound healing process. In this context, the development of advanced nanotherapeutic materials is highlighted as a promising strategy to efficiently control specific phases of the wound healing process. Here, Ca2+-cross-linked wood-derived nanofibrillated cellulose (NFC) hydrogels are evaluated as wound healing dressings. In vitro biocompatibility assays were performed to study the interaction of the NFC hydrogels with cellular processes that are tightly related to wound healing. Moreover, an in vivo dermo-epidermic full thickness wound healing model in rat was used to uncover the wound healing ability of the Ca2+-cross-linked NFC hydrogels. The in vitro experiments showed that the NFC hydrogels were able to support fibroblast and keratinocyte proliferation. A potential effect of the hydrogels on triggering keratinocyte differentiation was furthermore proposed. In vivo, the NFC hydrogels stimulated healing without causing any adverse local tissue effects, potentially owing to their moisture-donating properties and the herein discussed aiding effect of the Ca2+-cross-linker on epidermal generation. Thus, this work extensively demonstrates the wound healing ability of NFC hydrogels and presents an important milestone in the research on NFC toward advanced wound healing applications.

  • 321.
    Batool, Nazre
    KTH, School of Technology and Health (STH).
    Detection and Spatial Analysis of Hepatic Steatosis in Histopathology Images using Sparse Linear Models2016In: 2016 SIXTH INTERNATIONAL CONFERENCE ON IMAGE PROCESSING THEORY, TOOLS AND APPLICATIONS (IPTA), IEEE, 2016Conference paper (Refereed)
    Abstract [en]

    Hepatic steatosis is a defining feature of nonalcoholic fatty liver disease, emerging with the increasing incidence of obesity and metabolic syndrome. The research in image-based analysis of hepatic steatosis mostly focuses on the quantification of fat in biopsy images. This work furthers the image-based analysis of hepatic steatosis by exploring the spatial characteristics of fat globules in whole slide biopsy images after performing fat detection. An algorithm based on morphological filtering and sparse linear models is presented for fat detection. Then the spatial properties of detected fat globules in relation to the hepatic anatomical structures of central veins and portal tracts are explored. The test dataset consists of 38 high resolution images from 21 patients. The experimental results provide an insight into the size distributions of fat globules and their location with respect to the anatomical structures.

  • 322.
    Batool, Nazre
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Biomedical Engineering and Health Systems, Medical Imaging.
    Chowdhury, Manish
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Biomedical Engineering and Health Systems, Medical Imaging.
    Smedby, Örjan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Biomedical Engineering and Health Systems, Medical Imaging.
    Moreno, Rodrigo
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Biomedical Engineering and Health Systems, Medical Imaging.
    Estimation of trabecular bone thickness in gray scale: a validation study2017In: International Journal of Computer Assisted Radiology and Surgery, Vol. 12, no Supplement 1Article in journal (Refereed)
  • 323. Bauer, Margit
    et al.
    Mazza, Edoardo
    Jabareen, Mahmood
    Sultan, Leila
    Bajka, Michael
    Lang, Uwe
    Zimmermann, Roland
    Holzapfel, Gerhard A.
    KTH, School of Engineering Sciences (SCI), Solid Mechanics (Dept.), Solid Mechanics (Div.).
    Assessment of the in vivo biomechanical properties of the human uterine cervix in pregnancy using the aspiration test A feasibility study2009In: European Journal of Obstetrics, Gynecology, and Reproductive Biology, ISSN 0301-2115, E-ISSN 1872-7654, Vol. 144, p. S77-S81Article in journal (Refereed)
    Abstract [en]

    Objective: To date no diagnostic tool is yet available to objectively assess the in vivo biomechanical properties of the uterine cervix during gestation. Methods: We show the first clinical application of an aspiration device to assess the in vivo biomechanical properties of the cervix in pregnancy with the aim to describe the physiological biomechanical changes throughout gestation in order to eventually detect pregnant women at risk for cervical insufficiency (CI). Results: Out of 15 aspiration measurements, 12 produced valid results. The stiffness values were in the range between 0.013 and 0.068 bar/mm. The results showed a good reproducibility of the aspiration test. In our previous test series on non-pregnant cervices our repetitive measurements showed a standard deviation of > 20% compared to <+/- 10% to our data on pregnant cervices. Stiffness values are decreasing with gestational age which indicates a progressive softening of cervical tissue towards the end of pregnancy. Three pregnant women had two subsequent measurements within a time interval of four weeks. Decreasing stiffness values in the range of 20% were recorded. Discussion: This preliminary study on the clinical practicability of aspiration tests showed promising results in terms of reproducibility (reliability) and clinical use (feasibility). Ongoing studies will provide further insights on its usefulness in clinical practice and in the detection of substantial changes of the cervix in pregnancy indicative for threatened preterm birth or cervical insufficiency.

  • 324.
    Baumann, Michael
    KTH, School of Technology and Health (STH).
    Performance of a Micro-CT System: Characterisation of Hamamatsu X-ray source L10951-04 and flat panel C7942CA-222014Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    This master thesis evaluated the performance of a micro-CT system consisting of Hamamatsu microfocus X-ray source L10951-04 and CMOS flat panel C7942CA-22. The X-ray source and flat panel have been characterised in terms of dark current, image noise and beam profile. Additionally, the micro-CT system’s spatial resolution, detector lag and detector X-ray response have been measured. Guidance for full image correction and methods for characterisation and performance test of the X-ray source and detector is presented.

    A spatial resolution of 7 lp/mm at 10 % MTF was measured. A detector lag of 0.3 % was observed after ten minutes of radiation exposure. The performance of the micro-CT system was found to be sufficient for high resolution X-ray imaging. However, the detector lag effect is strong enough to reduce image quality during subsequent image acquisition and must either be avoided or corrected for.

  • 325.
    Baumann, Michael
    et al.
    KTH, School of Technology and Health (STH).
    Damberg, Emmy
    KTH, School of Technology and Health (STH).
    Preoperativ värmning för att minska risken för hypotermi vid stor bukkirurgi: en pilotstudie2012Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
  • 326.
    Baumgarten, Matthias
    et al.
    University of Ulster.
    Guldenring, Daniel
    University of Ulster.
    Nugent, Chris
    University of Ulster.
    Hallberg, Josef
    Luleå University of Technology, Department of Computer Science, Electrical and Space Engineering, Signals and Systems.
    Embedding self-awareness into objects of daily life: the smart kettle2010In: 6th International Conference on Intelligent Environments: IE 2010 : Kuala Lumpur; 19 July 2010 - 21 July 2010, Los Alamitos, Calif, 2010, p. 34-39Conference paper (Refereed)
    Abstract [en]

    Intelligent Environments on varying scales and for different purposes are slowly becoming a reality. In the near future, global smart world infrastructures will become a commodity that will support various activities of daily life at different degrees of realism. Such infrastructures have the potential to offer dedicated, context- and situation-aware information and services by simultaneously providing the next-generation of data collection, execution and service provisioning layers. One key aspect of this vision is the correct monitoring and understanding of how people interact with their environment; how they can actually benefit from the added intelligence; and finally how future services can be improved or better personalized to enhance human environment interaction as a whole. This level of intelligence is of particular relevance in the health and social care domain where person-centric services can be deployed to assist or even enable a person in performing activities of daily living. This paper discusses the concept of embedded self-aware profiles for smart devices that can be used to gain a deeper contextual understanding of their use and also discusses the emergence of a general model of Ambient Intelligence that is based on the collective existence and behavior of such smart devices. Although generic in principle, the proposed concepts have been exemplified by a distinct use case, namely a smart kettle.

  • 327.
    Bayat, Narges
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Lopes, Viviana R.
    Schoelermann, Julia
    Dahl Jensen, Lasse
    Cristobal, Susana
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Vascular toxicity of ultra-small TiO2 nanoparticles and single walled carbon nanotubes in vitro and in vivo2015In: Biomaterials, ISSN 0142-9612, E-ISSN 1878-5905, Vol. 63, p. 1-13Article in journal (Refereed)
    Abstract [en]

    Ultra-small nanoparticles (USNPs) at 1-3 nm are a subset of nanoparticles (NPs) that exhibit intermediate physicochemical properties between molecular dispersions and larger NPs. Despite interest in their utilization in applications such as theranostics, limited data about their toxicity exist. Here the effect of TiO2-USNPs on endothelial cells in vitro, and zebrafish embryos in vivo, was studied and compared to larger TiO2-NPs (30 nm) and to single walled carbon nanotubes (SWCNTs). In vitro exposure showed that TiO2-USNPs were neither cytotoxic, nor had oxidative ability, nevertheless were genotoxic. In vivo experiment in early developing zebrafish embryos in water at high concentrations of TiO2-USNPs caused mortality possibly by acidifying the water and caused malformations in the form of pericardial edema when injected. Myo1C involved in glomerular development of zebrafish embryos was upregulated in embryos exposed to TiO2-USNPs. They also exhibited anti-angiogenic effects both in vitro and in vivo plus decreased nitric oxide concentration. The larger TiO2-NPs were genotoxic but not cytotoxic. SWCNTs were cytotoxic in vitro and had the highest oxidative ability. Neither of these NPs had significant effects in vivo. To our knowledge this is the first study evaluating the effects of TiO2-USNPs on vascular toxicity in vitro and in vivo and this strategy could unravel USNPs potential applications.

  • 328.
    Bayisa, Fekadu
    et al.
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Kuljus, Kristi
    Institute of Mathematics and Statistics, University of Tartu, Tartu, Estonia.
    Johansson, Adam
    Umeå University, Faculty of Medicine, Department of Radiation Sciences.
    Bolin, David
    Department of Mathematical Sciences, Chalmers and University of Gothenburg, Gothenburg, Sweden.
    Yu, Jun
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Prediction of CT images from MR images with hidden Markov and random field models2016In: Proceedings of the 8th International Workshop on Spatio-Temporal Modelling / [ed] A. Iftimi, J. Mateu and F. Montes, 2016, p. 163-163Conference paper (Other academic)
  • 329.
    Bayisa, Fekadu
    et al.
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Liu, Xijia
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Garpebring, Anders
    Umeå University, Faculty of Medicine, Department of Radiation Sciences.
    Yu, Jun
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Statistical learning in computed tomography image estimation2018In: Medical physics (Lancaster), ISSN 0094-2405, Vol. 45, no 12, p. 5450-5460Article in journal (Refereed)
    Abstract [en]

    Purpose: There is increasing interest in computed tomography (CT) image estimations from magneticresonance (MR) images. The estimated CT images can be utilized for attenuation correction, patientpositioning, and dose planning in diagnostic and radiotherapy workflows. This study aims to introducea novel statistical learning approach for improving CT estimation from MR images and to compare theperformance of our method with the existing model-based CT image estimation methods.

    Methods: The statistical learning approach proposed here consists of two stages. At the trainingstage, prior knowledge about tissue types from CT images was used together with a Gaussian mixturemodel (GMM) to explore CT image estimations from MR images. Since the prior knowledge is notavailable at the prediction stage, a classifier based on RUSBoost algorithm was trained to estimatethe tissue types from MR images. For a new patient, the trained classifier and GMMs were used topredict CT image from MR images. The classifier and GMMs were validated by using voxel-leveltenfold cross-validation and patient-level leave-one-out cross-validation, respectively.

    Results: The proposed approach has outperformance in CT estimation quality in comparison withthe existing model-based methods, especially on bone tissues. Our method improved CT image estimationby 5% and 23% on the whole brain and bone tissues, respectively.

    Conclusions: Evaluation of our method shows that it is a promising method to generate CTimage substitutes for the implementation of fully MR-based radiotherapy and PET/MRI applications

  • 330.
    Bayisa, Fekadu
    et al.
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Yu, Jun
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Model-based Estimation of Computed Tomography Images2017Conference paper (Other academic)
  • 331.
    Bayisa, Fekadu
    et al.
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Yu, Jun
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Model-based Estimation of Computed Tomography Images2017Manuscript (preprint) (Other academic)
    Abstract [en]

    There is a growing interest to get a fully MR based radiotherapy. The most important development needed is to obtain improved bone tissue estimation. Existing model-based methods have performed poorly on bone tissues. This paper aims to obtainimproved estimation of bone tissues. Skew-Gaussian mixture model (SGMM) isproposed to further investigate CT image estimation from MR images. The estimation quality of the proposed model is evaluated using leave-one-out cross-validation method on real data. In comparison with the existing model-based approaches, the approach utilized in this paper outperforms in estimation of bone tissues, especiallyon dense bone tissues.

  • 332.
    Bayisa, Fekadu
    et al.
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Zhou, Zhiyong
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Cronie, Ottmar
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Yu, Jun
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Adaptive algorithm for sparse signal recovery2019In: Digital signal processing (Print), ISSN 1051-2004, E-ISSN 1095-4333, Vol. 87, p. 16p. 10-18Article in journal (Refereed)
    Abstract [en]

    The development of compressive sensing in recent years has given much attention to sparse signal recovery. In sparse signal recovery, spike and slab priors are playing a key role in inducing sparsity. The use of such priors, however, results in non-convex and mixed integer programming problems. Most of the existing algorithms to solve non-convex and mixed integer programming problems involve either simplifying assumptions, relaxations or high computational expenses. In this paper, we propose a new adaptive alternating direction method of multipliers (AADMM) algorithm to directly solve the suggested non-convex and mixed integer programming problem. The algorithm is based on the one-to-one mapping property of the support and non-zero element of the signal. At each step of the algorithm, we update the support by either adding an index to it or removing an index from it and use the alternating direction method of multipliers to recover the signal corresponding to the updated support. Moreover, as opposed to the competing “adaptive sparsity matching pursuit” and “alternating direction method of multipliers” methods our algorithm can solve non-convex problems directly. Experiments on synthetic data and real-world images demonstrated that the proposed AADMM algorithm provides superior performance and is computationally cheaper than the recently developed iterative convex refinement (ICR) and adaptive matching pursuit (AMP) algorithms.

  • 333.
    Begum, Shahina
    et al.
    Mälardalen University, School of Innovation, Design and Engineering, Embedded Systems.
    Barua, Shaibal
    Mälardalen University, School of Innovation, Design and Engineering, Embedded Systems.
    Ahmed, Mobyen Uddin
    Mälardalen University, School of Innovation, Design and Engineering, Embedded Systems.
    Funk, Peter
    Mälardalen University, School of Innovation, Design and Engineering, Embedded Systems.
    A Fusion Based System for Physiological Sensor Signal Classification2014In: Medicinteknikdagarna 2014 MTD10, 2014Conference paper (Refereed)
    Abstract [en]

    Today, usage of physiological sensor signals is essential in medical applications for diagnoses and classification of diseases. Clinicians often rely on information collected from several physiological sensor signals to diagnose a patient. However, sensor signals are mostly non-stationary and noisy, and single sensor signal could easily be contaminated by uncertain noises and interferences that could cause miscalculation of measurements and reduce clinical usefulness. Therefore, an apparent choice is to use multiple sensor signals that could provide more robust and reliable decision. Therefore, a physiological signal classification approach is presented based on sensor signal fusion and case-based reasoning. To classify Stressed and Relaxed individuals from physiological signals, data level and decision level fusion are performed and case-based reasoning is applied as classification algorithm. Five physiological sensor signals i.e., Heart Rate (HR), Finger Temperature (FT), Respiration Rate (RR), Carbon dioxide (CO2) and Oxygen Saturation (SpO2) are collected during the data collection phase. Here, data level fusion is performed using Multivariate Multiscale Entropy (MMSE) and extracted features are then used to build a case- library. Decision level fusion is performed on the features extracted using traditional time and frequency domain analysis. Case-Based Reasoning (CBR) is applied for the classification of the signals. The experimental result shows that the proposed system could classify Stressed or Relaxed individual 87.5% accurately compare to an expert in the domain. So, it shows promising result in the psychophysiological domain and could be possible to adapt this approach to other relevant healthcare systems.

  • 334.
    Begum, Shahina
    et al.
    Mälardalen University, School of Innovation, Design and Engineering, Embedded Systems.
    Kerstis, Birgitta
    Mälardalen University, School of Health, Care and Social Welfare, Health and Welfare.
    Barua, Shaibal
    Mälardalen University, School of Innovation, Design and Engineering, Embedded Systems.
    Westerlund, Hanna
    Camanio Care AB, Sweden.
    Hjortsberg, Cecilia
    Västerås stad, Sweden.
    Food4You: A Personalized System for Adaptive Mealtime Situations for Elderly2017In: Medicinteknikdagarna 2017 MTD 2017, 2017Conference paper (Refereed)
  • 335.
    Begum, Shahina
    et al.
    Mälardalen University, Department of Computer Science and Electronics. Dalarna University, Borlänge, Sweden .
    Westin, Jerker
    Dalarna University, Borlänge, Sweden .
    Funk, Peter
    Mälardalen University, Department of Computer Science and Electronics.
    Dougherty, Mark
    Dalarna University, Borlänge, Sweden .
    Induction of an Adaptive Neuro-Fuzzy Inference System for Investigating Fluctuation in Parkinson´s Disease: The 23rd Annual Workshop of the Swedish Artificial Intelligence Society Umeå, May 10-12, 20062006In: Proceedings of SAIS 2006, 2006, p. 67-72Conference paper (Refereed)
    Abstract [en]

    This paper presents a methodology to formulate natural language rules for an adaptive neuro-fuzzy system based on discovered knowledge, supported by prior knowledge and statistical modeling. These rules could be improved using statistical methods and neural nets. This gives clinicians a valuable tool to explore the importance of different variables and their relations in a disease and could aid treatment selection. A prototype using the proposed methodology has been used to induce an Adaptive Neuro Fuzzy Inference Model that has been used to "discover" relationships between fluctuation, treatment and disease severity in Parkinson. Preliminary results from this project are promising and show that Neuro-fuzzy techniques in combination with statistical methods may offer medical research and medical applications a useful combination of methods.

  • 336.
    Behjat, Hamid
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Statistical Parametric Mapping of fMRI data using Spectral Graph Wavelets2012Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    In typical statistical parametric mapping (SPM) of fMRI data, the functional data are pre-smoothed using a Gaussian kernel to reduce noise at the cost of losing spatial specificity. Wavelet approaches have been incorporated in such analysis by enabling an efficient representation of the underlying brain activity through spatial transformation of the original, un-smoothed data; a successful framework is the wavelet-based statistical parametric mapping (WSPM) which enables integrated wavelet processing and spatial statistical testing. However, in using the conventional wavelets, the functional data are considered to lie on a regular Euclidean space, which is far from reality, since the underlying signal lies within the complex, non rectangular domain of the cerebral cortex. Thus, using wavelets that function on more complex domains such as a graph holds promise. The aim of the current project has been to integrate a recently developed spectral graph wavelet transform as an advanced transformation for fMRI brain data into the WSPM framework. We introduce the design of suitable weighted and un-weighted graphs which are defined based on the convoluted structure of the cerebral cortex. An optimal design of spatially localized spectral graph wavelet frames suitable for the designed large scale graphs is introduced. We have evaluated the proposed graph approach for fMRI analysis on both simulated as well as real data. The results show a superior performance in detecting fine structured, spatially localized activation maps compared to the use of conventional wavelets, as well as normal SPM. The approach is implemented in an SPM compatible manner, and is included as an extension to the WSPM toolbox for SPM.

  • 337.
    Behm, Pascal
    Linköping University, Department of Biomedical Engineering, Biomedical Instrumentation. Linköping University, The Institute of Technology. Institute for Medical ans Analytical Technologies, University of Northwestern Switzerland.
    Experimental set-up for near infrared fluorescence measurements during surgery2013Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    In case a tumour grows in a tissue close to the lymphatic system, biopsies of the first draining lymph nodes connected to the tumour, also known as sentinel lymph nodes, allow determining if the cancer has already metastasized. Lymph node mapping is used in oncology surgery to find the patients lymph nodes connected to the tumour. The fluorescence marker indocyanine green (ICG) has shown successful results to trace the lymph nodes and arise to replace the currently used radioactive tracers. Because the ICG fluorescence is in the near infrared region and not visible to the human eye, imaging systems are used to visualise the fluorescence. A preliminary spectroscopy measurement system was developed at the Department of Biomedical Engineering, Linköping University. The aim of this thesis was to develop a combined spectroscopy and imaging set-up for simultaneous recordings of ICG fluorescence and suggest further developments.

    The combined system consisted of a fibre-optical based spectroscopy system together with a camera imaging system. An optical phantom that mimicked breast tissue (μs = 4.66 mm-1) was developed for the measurements. Phantoms with different ICG concentrations of 6.45 μM, 64.5 μM and 645 μM simulated different concentrations of fluorescence dye in the lymph system. The set-up and the settings of the devices were adjusted to enable simultaneous measurements with both systems. The phantoms were solidified with agar to measure the fluorescence decay (photobleaching) of ICG. To simulate a lymph node deep in the tissue, a tube containing pure ICG was covered with different layer thicknesses of breast tissue-like phantom.

    Measurements at the same time with both systems were possible when the probe was positioned in an 80 degree angle with 5 mm distance relative to the phantom surface and the camera in 10 cm distance with a 30 degree angle. To visualise the ICG fluorescence emission with the excitation light (4 mW) and an integration time of 600 ms was necessary for the camera. Higher laser power caused saturation in the spectrometer. The spectroscopy measurements and camera images showed maximum fluorescence intensity at an optimal ICG concentration (10-16 μM) in the phantom. Also the photobleaching measurements showed to be dependent on the ICG concentration and associated with the optimal concentration. ICG concentrations equal and lower than the optimal concentration decayed with exposure to the excitation light. The fluorescence intensity of higher concentrations initially increased and decayed after reaching a maximum intensity when exposed to the excitation light. The detection depth in the simulated tissue was limited to 0.3 mm for spectroscopy. A detection depth of 2 mm was achieved with the camera while using the maximum excitation power of 50 mW and integration time of 700 ms.

    Simultaneous measurements were possible with the set-up on the same phantom. An optimal concentration of ICG was found for the developed phantom. The ICG fluorescence intensity was concentration dependent and showed a relatively slow photobleaching. The fibre-optical based spectroscopy system was able to measure low ICG emissions. Subtracting the background spectrum of surrounding tissue might increase the detection of weak ICG signals in depth. High excitation power and an increased integration time were needed to record ICG fluorescence emission with the camera. The obtained results allowed suggestions for the further improvement of set-up and its intraoperative use.

  • 338. Beillas, P.
    et al.
    Petit, P.
    Kleiven, Svein
    KTH, School of Technology and Health (STH), Medical Engineering, Neuronic Engineering.
    Kirscht, S.
    Chawla, A.
    Jolivet, E.
    Faure, F.
    Praxl, N.
    Bhaskar, A.
    Specifications of a software framework to position and personalise human body models2015In: 2015 IRCOBI Conference Proceedings - International Research Council on the Biomechanics of Injury, International Research Council on the Biomechanics of Injury , 2015, p. 594-595Conference paper (Refereed)
  • 339. Beillas, Philippe
    et al.
    Lafon, Yoann
    Frechede, Bertrand
    Janak, Tomas
    Dupeux, Thomas
    Mear, Matthieu
    Kleiven, Svein
    Giordano, Chiara
    Alvarez, Victor
    Li, Xiaogai
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Biomedical Engineering and Health Systems, Neuronic Engineering.
    Chawla, Anoop
    Chhabra, A
    Paruchuri, S an Singh, S
    Kaushik, D
    Mukherjee, S
    Kumar, S
    Devane, K
    Mishra, K
    Machina, G
    Jolivet, Erwan
    Lemaire, Thomas
    Faure, François
    Gilles, Benjamin
    Vimont, Ulysse
    Lecomte, Christophe
    D3. 8 Final version of the personalization and positioning software tool with documentation. PIPER EU Project2017Report (Refereed)
  • 340.
    Bekkouche, Bo
    KTH, School of Technology and Health (STH), Medical Engineering.
    Functional Implications from Changes in Volume and Periaxonal Space of C-fibers2012Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
  • 341. Belfrage, Sara
    Without informed consent2013In: Moral, Ethical, and Social Dilemmas in the Age of Technology: Theories and Practice, IGI Global, 2013, p. 291-305Chapter in book (Other academic)
    Abstract [en]

    The requirement of always obtaining participants' informed consent in research with human subjects cannot always be met, for a variety of reasons. This paper describes and categorises research situations where informed consent is unobtainable. Some of these kinds of situations, common in biomedicine and psychology, have been previously discussed, whereas others, for example, those more prevalent in infrastructure research, introduce new perspectives. The advancement of new technology may lead to an increase in research of these kinds. The paper also provides a review of methods intended to compensate for lack of consent, and their applicability and usefulness for the different categories of situations are discussed. The aim of this is to provide insights into one important aspect of the question of permitting research without informed consent, namely, how well that which informed consent is meant to safeguard can be achieved by other means.

  • 342. Bendazzoli, Simone
    et al.
    Brusini, Irene
    Damberg, Peter
    Smedby, Örjan
    Andersson, Leif
    Wang, Chunliang
    Automatic rat brain segmentation from MRI using statistical shape models and random forest2019In: Medical Imaging 2019: Image Processing, 2019, Vol. 10949Conference paper (Refereed)
  • 343.
    Bendazzoli, Simone
    et al.
    KTH Royal Inst Technol, Dept Biomed Engn & Hlth Syst, Halsovagen 11, S-14157 Huddinge, Sweden.
    Brusini, Irene
    KTH Royal Inst Technol, Dept Biomed Engn & Hlth Syst, Halsovagen 11, S-14157 Huddinge, Sweden;Karolinska Inst, Dept Neurobiol Care Sci & Soc, Alfred Nobels Alle 23,D3, S-14152 Huddinge, Sweden.
    Damberg, Peter
    Karolinska Inst, Dept Clin Neurosci, Tomtebodavagen 18A P1 5, S-17177 Stockholm, Sweden.
    Smedby, Örjan
    KTH Royal Inst Technol, Dept Biomed Engn & Hlth Syst, Halsovagen 11, S-14157 Huddinge, Sweden.
    Andersson, Leif
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Wang, Chunliang
    KTH Royal Inst Technol, Dept Biomed Engn & Hlth Syst, Halsovagen 11, S-14157 Huddinge, Sweden.
    Automatic rat brain segmentation from MRI using statistical shape models and random forest2019In: MEDICAL IMAGING 2019: IMAGE PROCESSING / [ed] Angelini, ED Landman, BA, SPIE-INT SOC OPTICAL ENGINEERING , 2019, article id 109492OConference paper (Refereed)
    Abstract [en]

    In MRI neuroimaging, the shimming procedure is used before image acquisition to correct for inhomogeneity of the static magnetic field within the brain. To correctly adjust the field, the brain's location and edges must first be identified from quickly-acquired low resolution data. This process is currently carried out manually by an operator, which can be time-consuming and not always accurate. In this work, we implement a quick and automatic technique for brain segmentation to be potentially used during the shimming. Our method is based on two main steps. First, a random forest classifier is used to get a preliminary segmentation from an input MRI image. Subsequently, a statistical shape model of the brain, which was previously generated from ground-truth segmentations, is fitted to the output of the classifier to obtain a model-based segmentation mask. In this way, a-priori knowledge on the brain's shape is included in the segmentation pipeline. The proposed methodology was tested on low resolution images of rat brains and further validated on rabbit brain images of higher resolution. Our results suggest that the present method is promising for the desired purpose in terms of time efficiency, segmentation accuracy and repeatability. Moreover, the use of shape modeling was shown to be particularly useful when handling low-resolution data, which could lead to erroneous classifications when using only machine learning-based methods.

  • 344. Bendazzoli, Simone
    et al.
    Brusini, Irene
    Damberg, Peter
    Smedby, Örjan
    Wang, Chunliang
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Biomedical Engineering and Health Systems, Medical Imaging.
    Wang, Chunliang
    Automatic rat brain segmentation from MRI using statistical shape models and random forest2019Conference paper (Refereed)
  • 345.
    Bengtsson, Ewert
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Quantitative and automated microscopy: Where do we stand after 80 years of research?2014In: Proc. 11th International Symposium on Biomedical Imaging, Piscataway, NJ: IEEE Press, 2014, p. 274-277Conference paper (Refereed)
  • 346.
    Bengtsson, Ewert
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Centre for Image Analysis.
    Dahlqvist, Bengt
    Eriksson, Olle
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Centre for Image Analysis.
    Jarkrans, Torsten
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Centre for Image Analysis.
    Nordin, Bo
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Centre for Image Analysis.
    Stenkvist, Björn
    Cervical Pre-screening Using Computerized Image Analysis1983In: Proceedings of the 3rd Scandinavian Conference on Image Analysis, Köpenhamn, 1983, p. 404-411Conference paper (Refereed)
  • 347.
    Bengtsson, Ewert
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Centre for Image Analysis.
    Dahlqvist, Bengt
    Eriksson, Olle
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Centre for Image Analysis.
    Jarkrans, Torsten
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Centre for Image Analysis.
    Nordin, Bo
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Centre for Image Analysis.
    Stenkvist, Björn
    Studie av reproducerbarheten av mikroskopiska cellbilder med TV-kamera1982Report (Other academic)
  • 348.
    Bengtsson, Ewert
    et al.
    Uppsala University, Sweden.
    Danielsen, Havard
    Oslo University Hospital, Norway.
    Treanor, Darren
    Linköping University, Department of Clinical and Experimental Medicine, Division of Neuro and Inflammation Science. Linköping University, Faculty of Medicine and Health Sciences. University of Leeds, England; Leeds Teaching Hospital NHS Trust, England.
    Gurcan, Metin N.
    Ohio State University, OH 43210 USA.
    MacAulay, Calum
    British Columbia Cancer Research Centre, Canada.
    Molnar, Bela
    Semmelweis University, Hungary.
    Computer-aided diagnostics in digital pathology2017In: Cytometry Part A, ISSN 1552-4922, E-ISSN 1552-4930, Vol. 91, no 6, p. 551-554Article in journal (Other academic)
    Abstract [en]

    n/a

  • 349.
    Bengtsson, Ewert
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Malm, Patrik
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Screening for Cervical Cancer Using Automated Analysis of PAP-Smears2014In: Computational & Mathematical Methods in Medicine, ISSN 1748-670X, E-ISSN 1748-6718, Vol. 2014, p. 842037:1-12Article, review/survey (Refereed)
    Abstract [en]

    Cervical cancer is one of the most deadly and common forms of cancer among women if no action is taken to prevent it, yet it is preventable through a simple screening test, the so-called PAP-smear. This is the most effective cancer prevention measure developed so far. But the visual examination of the smears is time consuming and expensive and there have been numerous attempts at automating the analysis ever since the test was introduced more than 60 years ago. The first commercial systems for automated analysis of the cell samples appeared around the turn of the millennium but they have had limited impact on the screening costs. In this paper we examine the key issues that need to be addressed when an automated analysis system is developed and discuss how these challenges have been met over the years. The lessons learned may be useful in the efforts to create a cost-effective screening system that could make affordable screening for cervical cancer available for all women globally, thus preventing most of the quarter million annual unnecessary deaths still caused by this disease.

  • 350.
    Bengtsson, Ewert
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Ranefall, Petter
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Image analysis in digital pathology: Combining automated assessment of Ki67 staining quality with calculation of Ki67 cell proliferation index2019In: Cytometry Part A, ISSN 1552-4922, E-ISSN 1552-4930, Vol. 95, no 7, p. 714-716Article in journal (Other academic)
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