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  • 1.
    Adolfsson, Karin
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Visual Evaluation of 3D Image Enhancement2006Independent thesis Basic level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Technologies in image acquisition have developed and often provide image volumes in more than two dimensions. Computer tomography and magnet resonance imaging provide image volumes in three spatial dimensions. The image enhancement methods have developed as well and in this thesis work 3D image enhancement with filter networks is evaluated.

    The aims of this work are; to find a method which makes the initial parameter settings in the 3D image enhancement processing easier, to compare 2D and 3D processed image volumes visualized with different visualization techniques and to give an illustration of the benefits with 3D image enhancement processing visualized using these techniques.

    The results of this work are;

    1. a parameter setting tool that makes the initial parameter setting much easier and

    2. an evaluation of 3D image enhancement with filter networks that shows a significant enhanced image quality in 3D processed image volumes with a high noise level compared to the 2D processed volumes. These results are shown in slices, MIP and volume rendering. The differences are even more pronounced if the volume is presented in a different projection than the volume is 2D processed in.

  • 2.
    Ahlström, Christer
    Linköping University, Department of Biomedical Engineering, Physiological Measurements. Linköping University, The Institute of Technology.
    Processing of the Phonocardiographic Signal: methods for the intelligent stethoscope2006Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    Phonocardiographic signals contain bioacoustic information reflecting the operation of the heart. Normally there are two heart sounds, and additional sounds indicate disease. If a third heart sound is present it could be a sign of heart failure whereas a murmur indicates defective valves or an orifice in the septal wall. The primary aim of this thesis is to use signal processing tools to improve the diagnostic value of this information. More specifically, three different methods have been developed:

    • A nonlinear change detection method has been applied to automatically detect heart sounds. The first and the second heart sounds can be found using recurrence times of the first kind while the third heart sound can be found using recurrence times of the second kind. Most third heart sound occurrences were detected (98 %), but the amount of false extra detections was rather high (7 % of the heart cycles).

    • Heart sounds obscure the interpretation of lung sounds. A new method based on nonlinear prediction has been developed to remove this undesired disturbance. High similarity was obtained when comparing actual lung sounds with lung sounds after removal of heart sounds.

    • Analysis methods such as Shannon energy, wavelets and recurrence quantification analysis were used to extract information from the phonocardiographic signal. The most prominent features, determined by a feature selection method, were used to create a new feature set for heart murmur classification. The classification result was 86 % when separating patients with aortic stenosis, mitral insufficiency and physiological murmurs.

    The derived methods give reasonable results, and they all provide a step forward in the quest for an intelligent stethoscope, a universal phonocardiography tool able to enhance auscultation by improving sound quality, emphasizing abnormal events in the heart cycle and distinguishing different heart murmurs.

    List of papers
    1. Heart sound cancellation from lung sound recordings using recurrence time statistics and nonlinear prediction
    Open this publication in new window or tab >>Heart sound cancellation from lung sound recordings using recurrence time statistics and nonlinear prediction
    2005 (English)In: IEEE Signal Processing Letters, ISSN 1070-9908, E-ISSN 1558-2361, Vol. 12, no 12, p. 812-815Article in journal (Refereed) Published
    Abstract [en]

    Heart sounds (HS) obscure the interpretation of lung sounds (LS). This letter presents a new method to detect and remove this undesired disturbance. The HS detection algorithm is based on a recurrence time statistic that is sensitive to changes in a reconstructed state space. Signal segments that are found to contain HS are removed, and the arising missing parts are replaced with predicted LS using a nonlinear prediction scheme. The prediction operates in the reconstructed state space and uses an iterated integrated nearest trajectory algorithm. The HS detection algorithm detects HS with an error rate of 4% false positives and 8% false negatives. The spectral difference between the reconstructed LS signal and an LS signal with removed HS was 0.34/spl plusmn/0.25, 0.50/spl plusmn/0.33, 0.46/spl plusmn/0.35, and 0.94/spl plusmn/0.64 dB/Hz in the frequency bands 20-40, 40-70, 70-150, and 150-300 Hz, respectively. The cross-correlation index was found to be 99.7%, indicating excellent similarity between actual LS and predicted LS. Listening tests performed by a skilled physician showed high-quality auditory results.

    Place, publisher, year, edition, pages
    Institutionen för medicinsk teknik, 2005
    Keyword
    Bioacoustics, heart sound (HS), lung sound (LS), nonlinear prediction, recurrence time statistics
    National Category
    Engineering and Technology
    Identifiers
    urn:nbn:se:liu:diva-11857 (URN)10.1109/LSP.2005.859528 (DOI)
    Note
    Original publication: Ahlstrom, C., Liljefeldt, O., Hult, P. and Ask, P., Heart sound cancellation from lung sound recordings using recurrence time statistics and nonlinear prediction, 2005, IEEE Signal Processing Letters, (12), 12, 812-815. http://dx.doi.org/10.1109/LSP.2005.859528. Copyright: IEEE, http://ieeexplore.ieee.org/xpl/RecentIssue.jsp?punumber=97Available from: 2008-05-20 Created: 2008-05-20 Last updated: 2017-12-13
    2. Detection of the 3rd Heart Sound using Recurrence Time Statistics
    Open this publication in new window or tab >>Detection of the 3rd Heart Sound using Recurrence Time Statistics
    2006 (English)In: Proc. 31st IEEE Int. Conf. on Acoustics, Speech and Signal Processing, Toulouse, France, 2006, 2006, p. 1040-1043Conference paper, Published paper (Other academic)
    Abstract [en]

    The 3rd heart sound (S3) is normally heard during auscultation of younger individuals, but it is also common in many patients with heart failure. Compared to the 1st and 2nd heart sounds, S3 has low amplitude and low frequency content, making it hard to detect (both manually for the physician and automatically by a detection algorithm). We present an algorithm based on a recurrence time statistic which is sensitive to changes in a reconstructed state space, particularly for detection of transitions with very low energy. Heart sound signals from ten children were used in this study. Most S3 occurrences were detected (98 %), but the amount of false extra detections was rather high (7% of the heart cycles). In conclusion, the method seems capable of detecting S3 with high accuracy and robustness.

    Series
    IEEE International Conference on Acoustics, Speech and Signal Processing. Proceedings, ISSN 1520-6149
    Keyword
    acoustic, signal detection, bioacoustics, signal reconstruction, statistics, heart sound, auscultation, heart failure, reconstructed state space, recurrence time statistics
    National Category
    Medical and Health Sciences
    Identifiers
    urn:nbn:se:liu:diva-14058 (URN)
    Available from: 2006-10-09 Created: 2006-10-09 Last updated: 2009-04-21
    3. Feature Extraction for Systolic Heart Murmur Classification
    Open this publication in new window or tab >>Feature Extraction for Systolic Heart Murmur Classification
    Show others...
    2006 (English)In: Annals of Biomedical Engineering, ISSN 0090-6964, E-ISSN 1573-9686, Vol. 34, no 11, p. 1666-1677Article in journal (Refereed) Published
    Abstract [en]

    Heart murmurs are often the first signs of pathological changes of the heart valves, and they are usually found during auscultation in the primary health care. Distinguishing a pathological murmur from a physiological murmur is however difficult, why an “intelligent stethoscope” with decision support abilities would be of great value. Phonocardiographic signals were acquired from 36 patients with aortic valve stenosis, mitral insufficiency or physiological murmurs, and the data were analyzed with the aim to find a suitable feature subset for automatic classification of heart murmurs. Techniques such as Shannon energy, wavelets, fractal dimensions and recurrence quantification analysis were used to extract 207 features. 157 of these features have not previously been used in heart murmur classification. A multi-domain subset consisting of 14, both old and new, features was derived using Pudil’s sequential floating forward selection (SFFS) method. This subset was compared with several single domain feature sets. Using neural network classification, the selected multi-domain subset gave the best results; 86% correct classifications compared to 68% for the first runner-up. In conclusion, the derived feature set was superior to the comparative sets, and seems rather robust to noisy data.

    Keyword
    Auscultation, Bioacoustics, Feature selection, Heart sounds, Valvular disease
    National Category
    Engineering and Technology
    Identifiers
    urn:nbn:se:liu:diva-13044 (URN)10.1007/s10439-006-9187-4 (DOI)
    Available from: 2008-03-20 Created: 2008-03-20 Last updated: 2017-12-13
  • 3.
    Andersson, Christoffer R.
    et al.
    Örebro University, Sweden.
    Bergquist, Jonas
    Uppsala University, Sweden.
    Theodorsson, Elvar
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology and Molecular Medicine. Linköping University, Faculty of Medicine and Health Sciences. Region Östergötland, Center for Diagnostics, Department of Clinical Chemistry.
    Ström, Jakob
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology and Molecular Medicine. Linköping University, Faculty of Medicine and Health Sciences. Örebro University, Sweden.
    Comparisons between commercial salivary testosterone enzyme-linked immunosorbent assay kits2017In: Scandinavian Journal of Clinical and Laboratory Investigation, ISSN 0036-5513, E-ISSN 1502-7686, Vol. 77, no 8, p. 582-586Article in journal (Refereed)
    Abstract [en]

    Introduction: Measuring testosterone concentrations is of interest both in clinical situations and for research, the latter expanding rapidly during recent years. An increased demand for convenient methods has prompted a number of companies to develop enzyme-linked immunosorbent assay (ELISA) kits to measure testosterone concentrations in saliva. However, the inter-comparability of kits from different manufacturers have yet to be determined. Aim of study: The aim of this study was to compare commercially available ELISA kits from four different manufacturers (Salimetrics, IBL, DRG and Demeditec). Methods: Saliva was collected from 50 participants (25 men and 25 women). Each sample was analysed by the four ELISA kits. Results: The correlations between the ELISA kits from Demeditec, DRG and Salimetrics were moderate to high with r-values amp;gt;.77; however, proportional errors between the methods calls for caution. The ELISA kit from IBL malfunctioned and no results from this kit was obtained. Conclusions: Results from studies using the ELISA kits from Demeditec, DRG and Salimetrics are generally comparable; however, translation using the formulae presented in the current study could increase the accuracy of these comparisons.

  • 4.
    Antonsson, Johan
    et al.
    Linköping University, Department of Biomedical Engineering, Biomedical Instrumentation. Linköping University, The Institute of Technology.
    Eriksson, Ola
    Linköping University, Department of Biomedical Engineering, Biomedical Instrumentation. Linköping University, The Institute of Technology.
    Lundberg, Peter
    Linköping University, Department of Medical and Health Sciences, Radiation Physics. Linköping University, Faculty of Health Sciences.
    Wårdell, Karin
    Linköping University, Department of Biomedical Engineering, Biomedical Instrumentation. Linköping University, The Institute of Technology.
    Optical measurements during experimental stereotactic radiofrequency lesioning2006In: Stereotactic and Functional Neurosurgery, ISSN 1011-6125, E-ISSN 1423-0372, Vol. 84, no 2-3, p. 118-124Article in journal (Refereed)
    Abstract [en]

    The aim of this study was to evaluate in vivo a laser Doppler measurement system in porcine brain tissue during thermal lesioning. A 2-mm monopolar radiofrequency lesioning electrode was equipped with optical fibers in order to monitor the lesioning procedure. Laser Doppler and backscattered light intensity signals were measured along the electrode trajectory and during bilateral lesioning in the central gray (70, 80 and 90°C, n = 14). The time course of the coagulation process could be followed by optical recordings. Two separate groups of tissue were identified from the intensity signals. The changes in the perfusion levels in both groups displayed significant changes (p < 0.05, n = 48) at all temperature settings, while backscattered light intensity was significant for only one group at the different temperatures (p < 0.05, n = 39). These results indicate that optical measurements correlate with lesion development in vivo. The study also indicates that it is possible to follow the lesioning process intra-operatively.

  • 5.
    Ask, Per
    et al.
    Linköping University, Department of Biomedical Engineering, Physiological Measurements. Linköping University, The Institute of Technology.
    Edwall, G
    Tibbling, Lita
    Combined pH and pressure measurement device for oesophageal investigations.1981In: Medical and Biological Engineering and Computing, ISSN 0140-0118, E-ISSN 1741-0444, Vol. 19, no 4, p. 443-446Article in journal (Refereed)
    Abstract [en]

    A combined pH- and pressure-measurement device for oesophageal investigations has been designed using monocrystalline antimony pH electrodes and perfused polyvinyl catheters. The combined device facilitates pressure measurements simultaneously with pH recording, both distal and proximal to the pH electrode. The device is easier to pass through the nose to the oesophagus than the conventional glass pH electrode. pH and pressure measurements in the oesophagus are therefore simplified and valuable information about the function of the region of the lower oesophageal sphincter is added owing to the simultaneous recording of the two parameters.

  • 6.
    Ask, Per
    et al.
    Linköping University, Department of Biomedical Engineering, Physiological Measurements. Linköping University, The Institute of Technology.
    Sökjer, H.
    Tibbling, Lita
    Linköping University, Department of Neuroscience and Locomotion, Oto-Rhiono-Laryngology and Head & Neck Surgery. Linköping University, Faculty of Health Sciences.
    Mechanisms affecting lower oesophageal sphincter opening and oesophageal retention: A combined X-ray and manometry study1978In: Scandinavian Journal of Gastroenterology, ISSN 0036-5521, E-ISSN 1502-7708, Vol. 13, no 7, p. 857-861Article in journal (Refereed)
    Abstract [en]

    Using simultaneous manometry and cineradiography, oesophageal evacuation was studied while contrast medium was infused via a catheter. The distal half of the oesophagus could be filled with contrast medium without triggering peristalsis. The hydrostatic pressure necessary to open the lower oesophageal sphincter (LES) was of approximately the same magnitude as the pressure gradient between oesophagus and LES. No significant relaxation of the LES could be observed at the initiation of swallowing. The LES may be looked upon not only as a sphincter preventing reflux but also as a gate which must be forced open by food.

  • 7.
    Ask, Per
    et al.
    Linköping University, Department of Biomedical Engineering. Linköping University, The Institute of Technology.
    Tibbling, Lita
    Linköping University, Department of Neuroscience and Locomotion.
    Clinical evaluation of different fluid-filled systems for oesophageal manometry1979In: Scandinavian Journal of Gastroenterology, ISSN 0036-5521, E-ISSN 1502-7708, Vol. 14, no 1, p. 1-5Article in journal (Refereed)
    Abstract [en]

    In a clinical study of oesophageal manometry with fluid-filled catheters, both a non-perfused system and a perfused system with a syringe pump have been compared to a system with a low-compliance perfusion pump, which served as a reference. Significantly lower values of motility amplitudes, motility derivatives, and partly of LES pressures, and a time delay of up to 0.5 sec of the amplitude maximum were obtained with the non-perfused system and the system with a syringe pump in comparison to the low-compliance system. Since the oesophageal function can be erroneously evaluated by use of a non-perfused system or a perfused system with a syringe pump, such systems cannot be recommended for clinical use.

  • 8.
    Ask, Per
    et al.
    Linköping University, Department of Biomedical Engineering, Physiological Measurements. Linköping University, The Institute of Technology.
    Tibbling, Lita
    Linköping University, Department of Neuroscience and Locomotion, Oto-Rhiono-Laryngology and Head & Neck Surgery. Linköping University, Faculty of Health Sciences.
    Öberg, P.Å.
    Linköping University, Department of Biomedical Engineering. Linköping University, The Institute of Technology.
    Bandbreddskrav hos oesophagusmanometriska system.1978Conference paper (Refereed)
  • 9.
    Ask, Per
    et al.
    Linköping University, Department of Biomedical Engineering, Physiological Measurements. Linköping University, The Institute of Technology.
    Öberg, P. Åke
    Linköping University, Department of Biomedical Engineering. Linköping University, The Institute of Technology.
    Tibbling, Lita
    Linköping University, Department of Neuroscience and Locomotion, Oto-Rhiono-Laryngology and Head & Neck Surgery. Linköping University, Faculty of Health Sciences.
    Static and dynamic characteristics of fluid-filled esophageal manometry systems1977In: American Journal of Physiology, ISSN 0002-9513, Vol. 233, no 5, p. E389-E396Article in journal (Refereed)
    Abstract [en]

    Esophageal manometric systems with water-filled catheters have been characterized by the use of model experiments. The examined parameters have been: catheter dimension, catheter compliance, catheter resistance, pump type, pump compliance, and perfusion flow. Accurate static pressure measurements have been obtained for perfused systems independently of the investigated parameters. The dynamic characteristics vary with catheter diameter and perfusion flow. For catheters with low diameter, a narrow bandwidth is obtained for the investigated perfusion flows. The results have been expressed in terms of an electric model of the measurement system. Perfusion pumps with low compliance are recommended to improve the dynamic properties of the measurement system.

  • 10.
    Ask, Per
    et al.
    Linköping University, Department of Biomedical Engineering. Linköping University, The Institute of Technology.
    Öberg, Åke
    Linköping University, Department of Biomedical Engineering.
    Ödman, S.
    Linköping University, Department of Biomedical Engineering. Linköping University, The Institute of Technology.
    Tenland, T.
    Linköping University, Department of Biomedical Engineering. Linköping University, The Institute of Technology.
    Skogh, M.
    Linköping University, Department of Biomedical Engineering. Linköping University, The Institute of Technology.
    ECG Electrodes: A Study of Electrical and Mechanical Long-term Properties1979In: Acta Anaesthesiologica Scandinavica, ISSN 0001-5172, E-ISSN 1399-6576, Vol. 23, no 2, p. 189-206Article in journal (Refereed)
    Abstract [en]

    The long-term properties of commercially available ECG-electrodes were studied by investigating the parameters: polarization potential, electrical impedance, adhesion, and skin reactions during a period of 7 days. As expected, the most stable polarization potentials were obtained for Ag/AgCl electrodes. Certain simple disposable electrodes showed large polarization potential variations. The most stable electrode impedance was obtained for disposable electrodes with stable adhesion and equipped with an electrode cup or similar. Unchanged adhesion and mechanical properties during the test period were shown by the disposable electrodes with a large self-adhesive collar.

  • 11.
    Boiso, Samuel
    et al.
    Swedish National Forensic Centre, Linköping, Sweden.
    Dalin, Erik
    Swedish National Forensic Centre, Linköping, Sweden.
    Seidlitz, Heidi
    Swedish National Forensic Centre, Linköping, Sweden.
    Sidstedt, Maja
    Swedish National Forensic Centre, Linköping, Sweden / Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden.
    Trygg, Elias
    Swedish National Forensic Centre, Linköping, Sweden.
    Hedman, Johannes
    Swedish National Forensic Centre, Linköping, Sweden / Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden.
    Ansell, Ricky
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering. Swedish National Forensic Centre, Linköping, Sweden.
    RapidHIT for the purpose of stain analyses – An interrupted implementation2017In: Forensic Science International: Genetics Supplement Series, ISSN 1875-1768, E-ISSN 1875-175X, Vol. 6, no Supplement C, p. e589-e590Article in journal (Refereed)
    Abstract [en]

    Rapid DNA instruments have in recent years been developed, enabling analysis of forensic samples with a minimum of human intervention. Initially intended for fast handling of reference samples, such as samples from suspects in booking suites, attention shifted to include crime scene samples. The aim of this study was to determine whether or not the RapidHIT System (IntegenX) is fit for crime scene samples. The first runs gave very poor results, which was found to be due to an incorrect firmware setting leading to no or just minute amounts of amplicons being injected for electrophoresis. After solving this problem, 28 full runs (seven samples each) applying NGM SElect Express were performed comprising various amounts of blood on cotton swabs. Six of the runs failed completely, four due to cartridge leakage and in two runs the PCR mix was not injected. For 155 samples with 1–5ÎŒL blood (volumes for which complete DNA profiles are expected), 119 samples (77%) gave complete DNA profiles. Among the most serious failures were incorrect allele calling and leakage of DNA extract or PCR product. Other general issues were failure to export results, anode motor breakdown and broken capillary array. Due to the encountered problems with software, hardware and cartridges, together with the low success rate, it was decided not to continue towards implementation of the RapidHIT System in casework.

  • 12.
    Borga, Magnus
    et al.
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Friman, Ola
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Lundberg, Peter
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Medical and Health Sciences, Radiology. Linköping University, Faculty of Health Sciences.
    Knutsson, Hans
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Blind Source Separation of Functional MRI Data2002Conference paper (Other academic)
  • 13.
    Braian, Clara
    et al.
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology and Molecular Medicine. Linköping University, Faculty of Medicine and Health Sciences.
    Svensson, Mattias
    Karolinska Institute, Sweden.
    Brighenti, Susanna
    Karolinska Institute, Sweden.
    Lerm, Maria
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology and Molecular Medicine. Linköping University, Faculty of Medicine and Health Sciences.
    Parasa, Venkata R.
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology and Molecular Medicine. Linköping University, Faculty of Medicine and Health Sciences. Karolinska Institute, Sweden.
    A 3D Human Lung Tissue Model for Functional Studies on Mycobacterium tuberculosis Infection2015In: Journal of Visualized Experiments, ISSN 1940-087X, E-ISSN 1940-087X, no 104, p. 1-9, article id e53084Article in journal (Refereed)
    Abstract [en]

    Tuberculosis (TB) still holds a major threat to the health of people worldwide, and there is a need for cost-efficient but reliable models to help us understand the disease mechanisms and advance the discoveries of new treatment options. In vitro cell cultures of monolayers or co-cultures lack the three-dimensional (3D) environment and tissue responses. Herein, we describe an innovative in vitro model of a human lung tissue, which holds promise to be an effective tool for studying the complex events that occur during infection with Mycobacterium tuberculosis (M. tuberculosis). The 3D tissue model consists of tissue-specific epithelial cells and fibroblasts, which are cultured in a matrix of collagen on top of a porous membrane. Upon air exposure, the epithelial cells stratify and secrete mucus at the apical side. By introducing human primary macrophages infected with M. tuberculosis to the tissue model, we have shown that immune cells migrate into the infected-tissue and form early stages of TB granuloma. These structures recapitulate the distinct feature of human TB, the granuloma, which is fundamentally different or not commonly observed in widely used experimental animal models. This organotypic culture method enables the 3D visualization and robust quantitative analysis that provides pivotal information on spatial and temporal features of host cell-pathogen interactions. Taken together, the lung tissue model provides a physiologically relevant tissue micro-environment for studies on TB. Thus, the lung tissue model has potential implications for both basic mechanistic and applied studies. Importantly, the model allows addition or manipulation of individual cell types, which thereby widens its use for modelling a variety of infectious diseases that affect the lungs.

  • 14.
    Brodin, Henrik
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    CCASENSE: Canonical Correlation Analysis for Estimation of Sensitivity Maps for Fast MRI2006Independent thesis Basic level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Magnetic Resonance Imaging is an established technology for both imaging and functional studies in clinical and research environments. The field is still very research intense. Two major research areas are acquisition time and signal quality. The last decade has provided tools for more efficient possibilities of trading these factors against each other through parallel imaging. In this thesis one parallel imaging method, Sensitivity Encoding for fast MRI (SENSE) is examined. An alternative solution CCASENSE is developed. CCASENSE reduces the acquisition time by estimating the sensitivity maps required for SENSE to work instead of running a reference scan. The estimation process is done by Blind Source Separation through Canonical Correlation Analysis. It is shown that CCASENSE appears to estimate the sensitivity maps better than ICASENSE which is a similar algorithm.

  • 15.
    Brun, Anders
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Manifold learning and representations for image analysis and visualization2006Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    We present a novel method for manifold learning, i.e. identification of the low-dimensional manifold-like structure present in a set of data points in a possibly high-dimensional space. The main idea is derived from the concept of Riemannian normal coordinates. This coordinate system is in a way a generalization of Cartesian coordinates in Euclidean space. We translate this idea to a cloud of data points in order to perform dimension reduction. Our implementation currently uses Dijkstra's algorithm for shortest paths in graphs and some basic concepts from differential geometry. We expect this approach to open up new possibilities for analysis of e.g. shape in medical imaging and signal processing of manifold-valued signals, where the coordinate system is “learned” from experimental high-dimensional data rather than defined analytically using e.g. models based on Lie-groups.

    We propose a novel post processing method for visualization of fiber traces from DT-MRI data. Using a recently proposed non-linear dimensionality reduction technique, Laplacian eigenmaps (Belkin and Niyogi, 2002), we create a mapping from a set of fiber traces to a low dimensional Euclidean space. Laplacian eigenmaps constructs this mapping so that similar traces are mapped to similar points, given a custom made pairwise similarity measure for fiber traces. We demonstrate that when the low-dimensional space is the RGB color space, this can be used to visualize fiber traces in a way which enhances the perception of fiber bundles and connectivity in the human brain.

  • 16.
    Brun, Anders
    et al.
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Knutsson, Hans
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Tensor Glyph Warping - Visualizing Metric Tensor Fields using Riemannian Exponential Maps2009In: Visualization and Processing of Tensor Fields: Advances and Perspectives / [ed] Laidlaw, David H.; Weickert, Joachim, Springer Berlin/Heidelberg, 2009, p. 139-160Chapter in book (Refereed)
    Abstract [en]

    The Riemannian exponential map, and its inverse the Riemannian logarithm map, can be used to visualize metric tensor fields. In this chapter we first derive the well-known metric sphere glyph from the geodesic equations, where the tensor field to be visualized is regarded as the metric of a manifold. These glyphs capture the appearance of the tensors relative to the coordinate system of the human observer. We then introduce two new concepts for metric tensor field visualization: geodesic spheres and geodesically warped glyphs. These additions make it possible not only to visualize tensor anisotropy, but also the curvature and change in tensorshape in a local neighborhood. The framework is based on the exp maps, which can be computed by solving a second order Ordinary Differential Equation (ODE) or by manipulating the geodesic distance function. The latter can be found by solving the eikonal equation, a non-linear Partial Differential Equation (PDE), or it can be derived analytically for some manifolds. To avoid heavy calculations, we also include first and second order Taylor approximations to exp and log. In our experiments, these are shown to be sufficiently accurate to produce glyphs that visually characterize anisotropy, curvature and shape-derivatives in smooth tensor fields. 

  • 17.
    Bzdula, Jessica
    Linköping University, Faculty of Health Sciences.
    Den preanalytiska fasen – Hur viktigt är det att blanda serumrören?2014Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Background: Approximately 2/3 of all pre-analytical errors occur in the pre-analytical phase, where mixing of sample tubes directly after sampling is one of the factors. The purpose of the study was to compare the analytical results for the glucose, lactate dehydrogenase and potassium in serum from mixed tubes with unmixed tubes. The study's aim was also to investigate the durability of these three analytes at room temperature (25 °C) for seven days.

    Method: 100 mixed and 100 unmixed serum tubes with gel, from 100 patients, were analyzed on Architect ci2800. Assay results were statistically compared with the paired t-test. All the serum tubes were stored at room temperature for seven days and the three analytes were analyzed daily. The results of the analysis were compared statistically by ANOVA.

    Results: No statistical significant difference (p > 0,05) was found for glucose and potassium between the unmixed and mixed tubes. Lactate dehydrogenase showed a small but statistical significant difference (p < 0,05) between the unmixed and mixed tubes. The differences in durability between day 1, day 2 and day 7 of the glucose, lactate dehydrogenase and potassium was found to be statistic significant (p < 0,05).

    Conclusion: This study indicates that it is not necessary to mix the serum tubes immediately after the blood sampling, however it is important to mix other types of tubes, such as citrate tube. Therefore it is good to create a routine while you are mixing all the tubes. Glucose is the most stable analyte in room temperature for seven days while the potassium is the least stable.

  • 18.
    Börjesson, Emma
    Linköping University, Department of Medical and Health Sciences. Linköping University, Faculty of Medicine and Health Sciences.
    Analys av 25-hydroxyvitamin D i primärvården2015Independent thesis Basic level (degree of Bachelor), 180 HE creditsStudent thesis
    Abstract [en]

    Background: The interest of vitamin D has increased in the last years. That is because there is so many possible positive effects of vitamin D and also because many individuals has vitamin D deficiency. Modern man spends much time indoors which leads to lower levels of vitamin D. People who have emigrated from a sunny climate to a Nordic climate often gets a deficiency due to a more pigmented skin which requires a larger amount of UVB to get an adequate synthesis of vitamin D.

    Aim: The aim with this study is to compare and evaluate how similar the instrument mini VIDAS measures 25(OH)D total against the current existing method cobas e 602. A discussion about if 25(OH)D total has a place in primary health care is included in the study.

    Method: The comparison was based on 39 samples. The samples was analyzed on cobas e 602 and mini VIDAS. A precision test was performed. External controls from DEQAS was also included in the study. The results have been presented with simple linear regression analysis, mean value, SD and CV.

    Results: The comparison between cobas e 602 and mini VIDAS gave a coefficient of determination of 81,34 %. mini VIDAS was closest to the external controls target values.

    Conclusion: There is no obvious conclusions about if mini VIDAS fulfills the requirement to be introduced to primary health care. The coefficient of determination of 81,34 % should be at least 95 %. However is mini VIDAS closer to the external controls target values then cobas e 602. There is factors that implies that 25(OH)D total has a place in primary health care with regards to demand, use and because many individuals has vitamin D deficiency. The instrument is also user-friendly to a primary health care laboratory.

  • 19.
    Caesar, Jenny
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Segmentation of the Brain from MR Images2005Independent thesis Basic level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    KTH, Division of Neuronic Engineering, have a finite element model of the head. However, this model does not contain detailed modeling of the brain. This thesis project consists of finding a method to extract brain tissues from T1-weighted MR images of the head. The method should be automatic to be suitable for patient individual modeling.

    A summary of the most common segmentation methods is presented and one of the methods is implemented. The implemented method is based on the assumption that the probability density function (pdf) of an MR image can be described by parametric models. The intensity distribution of each tissue class is modeled as a Gaussian distribution. Thus, the total pdf is a sum of Gaussians. However, the voxel values are also influenced by intensity inhomogeneities, which affect the pdf. The implemented method is based on the expectation-maximization algorithm and it corrects for intensity inhomogeneities. The result from the algorithm is a classification of the voxels. The brain is extracted from the classified voxels using morphological operations.

  • 20.
    Casas Garcia, Belén
    et al.
    Linköping University, Department of Medical and Health Sciences, Division of Cardiovascular Medicine. Linköping University, Faculty of Medicine and Health Sciences. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Lantz, Jonas
    Linköping University, Department of Medical and Health Sciences, Division of Cardiovascular Medicine. Linköping University, Faculty of Medicine and Health Sciences. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Viola, Frederica
    Linköping University, Department of Medical and Health Sciences, Division of Cardiovascular Medicine. Linköping University, Faculty of Medicine and Health Sciences.
    Cedersund, Gunnar
    Linköping University, Department of Biomedical Engineering, Division of Biomedical Engineering. Linköping University, Faculty of Science & Engineering.
    Bolger, Ann F.
    Linköping University, Department of Medical and Health Sciences, Division of Cardiovascular Medicine. Linköping University, Faculty of Medicine and Health Sciences. Region Östergötland, Heart and Medicine Center, Department of Clinical Physiology in Linköping. University of Calif San Francisco, CA USA.
    Carlhäll, Carljohan
    Linköping University, Department of Medical and Health Sciences, Division of Cardiovascular Medicine. Linköping University, Faculty of Medicine and Health Sciences. Region Östergötland, Heart and Medicine Center, Department of Clinical Physiology in Linköping. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Karlsson, Matts
    Linköping University, Department of Management and Engineering, Applied Thermodynamics and Fluid Mechanics. Linköping University, Faculty of Science & Engineering. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Ebbers, Tino
    Linköping University, Department of Medical and Health Sciences, Division of Cardiovascular Medicine. Linköping University, Faculty of Medicine and Health Sciences. Region Östergötland, Heart and Medicine Center, Department of Clinical Physiology in Linköping. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Bridging the gap between measurements and modelling: a cardiovascular functional avatar2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 6214Article in journal (Refereed)
    Abstract [en]

    Lumped parameter models of the cardiovascular system have the potential to assist researchers and clinicians to better understand cardiovascular function. The value of such models increases when they are subject specific. However, most approaches to personalize lumped parameter models have thus far required invasive measurements or fall short of being subject specific due to a lack of the necessary clinical data. Here, we propose an approach to personalize parameters in a model of the heart and the systemic circulation using exclusively non-invasive measurements. The personalized model is created using flow data from four-dimensional magnetic resonance imaging and cuff pressure measurements in the brachial artery. We term this personalized model the cardiovascular avatar. In our proof-of-concept study, we evaluated the capability of the avatar to reproduce pressures and flows in a group of eight healthy subjects. Both quantitatively and qualitatively, the model-based results agreed well with the pressure and flow measurements obtained in vivo for each subject. This non-invasive and personalized approach can synthesize medical data into clinically relevant indicators of cardiovascular function, and estimate hemodynamic variables that cannot be assessed directly from clinical measurements.

  • 21.
    Chen, Rong
    et al.
    Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
    Enberg, G.
    Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden.
    Klein, Gunnar O.
    Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden + Department of Medicine, Karolinska Institutet, Stockholm, Sweden.
    Julius - a template based supplementary electronic health record system2007In: BMC Medical Informatics and Decision Making, ISSN 1472-6947, E-ISSN 1472-6947, Vol. 7, no 10Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: EHR systems are widely used in hospitals and primary care centres but it is usually difficult to share information and to collect patient data for clinical research. This is partly due to the different proprietary information models and inconsistent data quality. Our objective was to provide a more flexible solution enabling the clinicians to define which data to be recorded and shared for both routine documentation and clinical studies. The data should be possible to reuse through a common set of variable definitions providing a consistent nomenclature and validation of data. Another objective was that the templates used for the data entry and presentation should be possible to use in combination with the existing EHR systems.

    METHODS: We have designed and developed a template based system (called Julius) that was integrated with existing EHR systems. The system is driven by the medical domain knowledge defined by clinicians in the form of templates and variable definitions stored in a common data repository. The system architecture consists of three layers. The presentation layer is purely web-based, which facilitates integration with existing EHR products. The domain layer consists of the template design system, a variable/clinical concept definition system, the transformation and validation logic all implemented in Java. The data source layer utilizes an object relational mapping tool and a relational database.

    RESULTS: The Julius system has been implemented, tested and deployed to three health care units in Stockholm, Sweden. The initial responses from the pilot users were positive. The template system facilitates patient data collection in many ways. The experience of using the template system suggests that enabling the clinicians to be in control of the system, is a good way to add supplementary functionality to the present EHR systems.

    CONCLUSION: The approach of the template system in combination with various local EHR systems can facilitate the sharing and reuse of validated clinical information from different health care units. However, future system developments for these purposes should consider using the openEHR/CEN models with shareable archetypes.

  • 22.
    Cholujová, Dana
    et al.
    Laboratory of Molecular Oncology, Cancer Research Institute, Slovak Academy of Sciences, Vlárska 7, Bratislava, Slovakia.
    Jakubíková, Jana
    Laboratory of Tumor Immunology, Cancer Research Institute, Slovak Academy of Sciences, Vlárska 7, Bratislava, Slovakia.
    Kubeš, Miroslav
    Institute of Virology, Slovak Academy of Sciences, Dubravska cesta 9, Bratislava, Slovakia.
    Arendacká, Barbora
    Institute of Measurement Science, Slovak Academy of Sciences, Dubravska cesta 9, Bratislava, Slovakia.
    Sapák, Michal
    Institute of Immunology, Medical Faculty of Comenius University, Sasinkova 4, Bratislava, Slovakia.
    Ihnatko, Robert
    Institute of Virology, Slovak Academy of Sciences, Dubravska cesta 9, Bratislava, Slovakia.
    Sedlák, Ján
    Laboratory of Tumor Immunology, Cancer Research Institute, Slovak Academy of Sciences, Vlárska 7, Bratislava, Slovakia.
    Comparative study of four fluorescent probes for evaluation of natural killer cell cytotoxicity assays2008In: Immunobiology, ISSN 0171-2985, E-ISSN 1878-3279, Vol. 213, no 8, p. 629-640Article in journal (Refereed)
    Abstract [en]

    Cytotoxicity is one of the major defence mechanisms against both virus-infected and tumor cells. Radioactive 51chromium (51Cr) release assay is a “gold standard” for assessment of natural killer (NK) cytolytic activity in vitro. Several disadvantages of this assay led us to design alternative tools based on flow cytometry analysis. Four different fluorescent dyes, calcein acetoxymethyl ester (CAM), carboxyfluorescein succinimidyl ester (CFSE), Vybrant DiO (DiO) and MitoTracker Green (MTG) were tested for labeling of NK target K-562 cells. Target staining stability, spontaneous release of fluorochromes and subsequent accumulation in bystander unstained cells were measured using fluorimetry and flow cytometry. Healthy donor peripheral blood mononuclear cells and affinity column purified NK cells were used as effectors coincubated with target K-562 cells at different E:T ratios for 3h and 90min, respectively. Fluorescent probe 7-amino-actinomycin D was used for live and dead cell discrimination. Bland–Altman statistical method was applied to measure true agreement for all CAM–51Cr, CFSE–51Cr, DiO–51Cr and MTG–51Cr pairs analyzed. Based on the data, none of the four proposed methods can be stated equivalent to the standard 51Cr release assay. Considering linear relationships between data obtained with four fluorochromes and 51Cr release assay as well as linear regression analysis with R2=0.9393 value for CAM–51Cr pair, we found the CAM assay to be the most closely related to the 51Cr assay.

  • 23.
    Cros, Olivier
    Linköping University, Department of Biomedical Engineering. Linköping University, Faculty of Science & Engineering.
    Structural properties of the mastoid using image analysis and visualization2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The mastoid, located in the temporal bone, houses an air cell system whose cells have a variation in size that can go far below current conventional clinical CT scanner resolution. Therefore, the mastoid air cell system is only partially represented in a CT scan. Where the conventional clinical CT scanner lacks level of minute details, micro-CT scanning provides an overwhelming amount of ne details. The temporal bone being one of the most complex in the human body, visualization of micro-CT scanning of this boneawakens the curiosity of the experimenter, especially with the correct visualization settings.

    This thesis first presents a statistical analysis determining the surface area to volume ratio of the mastoid air cell system of human temporal bone, from micro-CT scanning using methods previously applied for conventional clinical CT scans. The study compared current results with previous studies, with successive downsampling the data down to a resolution found in conventional clinical CT scanning. The results from the statistical analysis showed that all the small mastoid air cells, that cannot be detected in conventional clinical CT scans, do heavily contribute to the estimation of the surface area, and in consequence to the estimation of the surface area to volume ratio by a factor of about 2.6. Such a result further strengthens the idea of the mastoid to play an active role in pressure regulation and gas exchange.

    Discovery of micro-channels through specific use of a non-traditional transfer function was then reported, where a qualitative and a quantitative pre-analysis were performed and reported. To gain more knowledge about these micro-channels, a local structure tensor analysis was applied where structures are described in terms of planar, tubular, or isotropic structures. The results from this structural tensor analysis suggest these microchannels to potentially be part of a more complex framework, which hypothetically would provide a separate blood supply for the mucosa lining the mastoid air cell system.

    The knowledge gained from analysing the micro-channels as locally providing blood to the mucosa, led to the consideration of how inflammation of the mucosa could impact the pneumatization of the mastoid air cell system. Though very primitive, a 3D shape analysis of the mastoid air cell system was carried out. The mastoid air cell system was first represented in a compact form through a medial axis, from which medial balls could be used. The medial balls, representative of how large the mastoid air cells can be locally, were used in two complementary clustering methods, one based on the size diameter of the medial balls and one based on their location within the mastoid air cell system. From both quantitative and qualitative statistics, it was possible to map the clusters based on pre-defined regions already described in the literature, which opened the door for new hypotheses concerning the effect of mucosal inflammation on the mastoid pneumatization.

    Last but not least, discovery of other structures, previously unreported in the literature, were also visually observed and briefly discussed in this thesis. Further analysis of these unknown structures is needed.

    List of papers
    1. Determination of the mastoid surface area and volume based on micro-CT scanning of human temporal bone: Geometrical parameters dependence on scanning resolutions
    Open this publication in new window or tab >>Determination of the mastoid surface area and volume based on micro-CT scanning of human temporal bone: Geometrical parameters dependence on scanning resolutions
    Show others...
    2016 (English)In: Hearing Research, ISSN 0378-5955, E-ISSN 1878-5891, Vol. 340, p. 127-134Article in journal (Other academic) Published
    Abstract [en]

    The mastoid air cell system (MACS) with its large complex of interconnected air cells reflects an enhanced surface area (SA) relative to its volume (V), which may indicate that the MACS is adapted to gas exchange and has a potential role in middle ear pressure regulation. Thus, these geometric parameters of the MACS have been studied by high resolution clinical CT scanning. However, the resolution of these scans is limited to a voxel size of around 0.6 mm in all dimensions, and so, the geometrical parameters are also limited. Small air cells may appear below the resolution and cannot be detected. Such air cells may contribute to a much higher SA than the V, and thus, also the SA/V ratio. More accurate parameters are important for analysis of the function of the MACS including physiological modeling.

    Our aim was to determine the SA, V, and SA/V ratio in MACS in human temporal bones at highest resolution by using micro-CT-scanning. Further, the influence of the resolution on these parameters was investigated by downsampling the data. Eight normally aerated temporal bones were scanned at the highest possible resolution (30-60 μm). The SA was determined using a triangular mesh fitted onto the segmented MACS. The V was determined by summing all the voxels containing air. Downsampling of the original data was applied four times by a factor of 2.

    The mean SA was 194 cm2, the mean V was 9 cm3, and the mean SA/V amounted to 22 cm-1. Decreasing the resolution resulted in a non-linear decrement of SA and SA/V, whereas V was mainly independent of the resolution.

    The current study found significantly higher SA and SA/V compared with previous studies using clinical CT scanning at lower resolutions. These findings indicate a separate role of the MACS compared with the tympanum, and the results are important for a more accurate modeling of the middle ear physiology.

    Keyword
    Mastoid air cells; medical imaging; micro-CT; surface area; volume
    National Category
    Radiology, Nuclear Medicine and Medical Imaging
    Identifiers
    urn:nbn:se:liu:diva-122176 (URN)10.1016/j.heares.2015.12.005 (DOI)000386417900016 ()
    Available from: 2015-10-23 Created: 2015-10-23 Last updated: 2017-12-01Bibliographically approved
    2. Micro-channels in the mastoid anatomy. Indications of a separate blood supply of the air cell system mucosa by micro-CT scanning
    Open this publication in new window or tab >>Micro-channels in the mastoid anatomy. Indications of a separate blood supply of the air cell system mucosa by micro-CT scanning
    Show others...
    2013 (English)In: Hearing Research, ISSN 0378-5955, E-ISSN 1878-5891, Vol. 301, p. 60-65Article in journal (Refereed) Published
    Abstract [en]

    The mastoid air cell system has traditionally been considered to have a passive role in gas exchange and pressure regulation of the middle ear possibly with some acoustic function. However, more evidence has focused on the mucosa of the mastoid, which may play a more active role in regulation of middle ear pressure.

    In this study we have applied micro-CT scanning on a series of three human temporal bones. This approach greatly enhances the resolution (40–60 μm), so that we have discovered anatomical details, which has not been reported earlier. Thus, qualitative analysis using volume rendering has demonstrated notable micro-channels connecting the surface of the compact bone directly to the mastoid air cells as well as forming a network of connections between the air cells. Quantitative analysis on 2D slices was employed to determine the average diameter of these micro-channels (158 μm; range = 40–440 μm) as well as their density at a localized area (average = 75 cm−2; range = 64–97 cm−2).

    These channels are hypothesized to contain a separate vascular supply for the mastoid mucosa. However, future studies of the histological structure of the micro-channels are warranted to confirm the hypothesis. Studies on the mastoid mucosa and its blood supply may improve our knowledge of its physiological properties, which may have important implications for our understanding of the pressure regulation of the middle ear.

    Place, publisher, year, edition, pages
    Elsevier, 2013
    Keyword
    mastoid, micro CT, middle ear
    National Category
    Otorhinolaryngology Radiology, Nuclear Medicine and Medical Imaging Medical Image Processing
    Identifiers
    urn:nbn:se:liu:diva-92813 (URN)10.1016/j.heares.2013.03.002 (DOI)000320478100009 ()23518400 (PubMedID)
    Available from: 2013-05-22 Created: 2013-05-22 Last updated: 2017-12-06Bibliographically approved
    3. Structural Analysis of Micro-channels in Human Temporal Bone
    Open this publication in new window or tab >>Structural Analysis of Micro-channels in Human Temporal Bone
    2015 (English)In: IEEE 12th International Symposium on Biomedical Imaging (ISBI), 2015 IEEE 12th International Symposium on, Institute of Electrical and Electronics Engineers (IEEE), 2015, p. 9-12Conference paper, Published paper (Refereed)
    Abstract [en]

    Recently, numerous micro-channels have been discovered in the human temporal bone by micro-CT-scanning. Preliminary structure of these channels has suggested they contain a new separate blood supply for the mucosa of the mastoid air cells, which may have important functional implications. This paper proposes a structural analysis of the microchannels to corroborate this role. A local structure tensor is first estimated. The eigenvalues obtained from the estimated local structure tensor were then used to build probability maps representing planar, tubular, and isotropic tensor types. Each tensor type was assigned a respective RGB color and the full structure tensor was rendered along with the original data. Such structural analysis provides new and relevant information about the micro-channels but also their connections to mastoid air cells. Before carrying a future statistical analysis, a more accurate representation of the micro-channels in terms of local structure tensor analysis using adaptive filtering is needed.

    Place, publisher, year, edition, pages
    Institute of Electrical and Electronics Engineers (IEEE), 2015
    Series
    IEEE International Symposium on Biomedical Imaging, ISSN 1945-7928
    Keyword
    Human temporal bone, mastoid, microchannels, quadrature filters, structure tensor, visualization
    National Category
    Radiology, Nuclear Medicine and Medical Imaging
    Identifiers
    urn:nbn:se:liu:diva-122177 (URN)10.1109/ISBI.2015.7163804 (DOI)000380546000003 ()978-1-4799-2374-8 (ISBN)
    Conference
    IEEE 12th International Symposium on Biomedical Imaging (ISBI), 2015 IEEE 12th International Symposium on, 16-19 April, New York, USA
    Available from: 2015-10-23 Created: 2015-10-23 Last updated: 2017-05-10Bibliographically approved
    4. Enhancement of micro-channels within the human mastoid bone based on local structure tensor analysis
    Open this publication in new window or tab >>Enhancement of micro-channels within the human mastoid bone based on local structure tensor analysis
    2016 (English)In: Image Proceessing Theory, Tools and Apllications, IEEE, 2016Conference paper, Published paper (Refereed)
    Abstract [en]

    Numerous micro-channels have recently been discovered in the human temporal bone by x-ray micro-CT-scanning. After a preliminary study suggesting that these micro-channels form a separate blood supply for the mucosa of the mastoid air cells, a structural analysis of the micro-channels using a local structure tensor was carried out. Despite the high-resolution of the micro-CT scan, presence of noise within the air cells along with missing information in some micro-channels suggested the need of image enhancement. This paper proposes an adaptive enhancement of the micro-channels based on a local structure analysis while minimizing the impact of noise on the overall data. Comparison with an anisotropic diffusion PDE based scheme was also performed.

    Place, publisher, year, edition, pages
    IEEE, 2016
    Series
    International Conference on Image Processing Theory Tools and Applications (IPTA), E-ISSN 2154-512X
    Keyword
    Micro-channels, Structure tensor analysis, Image enhancement, Adaptive filtering, Human temporal bone, Mastoid bone
    National Category
    Medical Engineering
    Identifiers
    urn:nbn:se:liu:diva-134434 (URN)10.1109/IPTA.2016.7821019 (DOI)000393589800071 ()9781467389105 (ISBN)9781467389112 (ISBN)
    Conference
    6th International Conference on Image Processing Theory Tools and Applications (IPTA), Oulu, Finland, 12-15 December 2016
    Note

    Funding agencies: Obel Family Foundation (Denmark)

    Available from: 2017-02-13 Created: 2017-02-13 Last updated: 2017-06-21
  • 24.
    Dahlqvist Leinhard, Olof
    et al.
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Medical and Health Sciences. Linköping University, Faculty of Health Sciences.
    Johansson, Andreas
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Rydell, Joakim
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Kihlberg, Johan
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Faculty of Health Sciences. Linköping University, Department of Medical and Health Sciences. Östergötlands Läns Landsting, Center for Diagnostics, Department of Radiology in Linköping.
    Smedby, Örjan
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Medical and Health Sciences, Radiology. Linköping University, Faculty of Health Sciences. Östergötlands Läns Landsting, Centre for Medical Imaging, Department of Radiology in Linköping.
    Nyström, Fredrik H.
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Medical and Health Sciences. Linköping University, Faculty of Health Sciences.
    Lundberg, Peter
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Medical and Health Sciences, Radiology. Linköping University, Faculty of Health Sciences. Östergötlands Läns Landsting, Centre for Medical Imaging, Department of Radiology in Linköping.
    Borga, Magnus
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Quantification of abdominal fat accumulation during hyperalimentation using MRI2009In: Proceedings of the ISMRM Annual Meeting (ISMRM'09), 2009, Berkeley, CA, USA: International Society for Magnetic Resonance in Medicine , 2009, p. 206-Conference paper (Other academic)
    Abstract [en]

    There is an increasing demand for imaging methods that can be used for automatic, accurate and quantitative determination of the amounts of abdominal fat. Such methods are important as they will allow the evaluation of some of the risk factors underlying the ’metabolic syndrome’. The metabolic syndrome is becoming common in large parts of the world, and it appears that a dominant risk factor for developing this syndrome is abdominal obesity. Subjects that are afflicted with the metabolic syndrome are exposed to a high risk for developing a large range of diseases such as type 2 diabetes, cardiac failure, and stroke. The aim of this work

  • 25.
    D'Arcy, Padraig
    et al.
    Department of Oncology and Pathology, Karolinska Institute, SE-171 76 Stockholm, Sweden.
    Wang, Xin
    Linköping University, Department of Medical and Health Sciences, Division of Drug Research. Linköping University, Faculty of Health Sciences. Department of Oncology and Pathology, Karolinska Institute, SE-171 76 Stockholm, Sweden.
    Linder, Stig
    Linköping University, Department of Medical and Health Sciences, Division of Drug Research. Linköping University, Faculty of Health Sciences. Department of Oncology and Pathology, Karolinska Institute, SE-171 76 Stockholm, Sweden.
    Deubiquitinase inhibition as a cancer therapeutic strategy2015In: Pharmacology and Therapeutics, ISSN 0163-7258, E-ISSN 1879-016X, Vol. 147, p. 32-54Article, review/survey (Refereed)
    Abstract [en]

    The ubiquitin proteasome system (UPS) is the main system for controlled protein degradation and a key regulator of fundamental cellular processes. The dependency of cancer cells on a functioning UPS has made this an attractive target for development of drugs that show selectivity for tumor cells. Deubiquitinases (DUBs, ubiquitin isopeptidases) are components of the UPS that catalyze the removal of ubiquitin moieties from target proteins or polyubiquitin chains, resulting in altered signaling or changes in protein stability. A number of DUBs regulate processes associated with cell proliferation and apoptosis, and as such represent candidate targets for cancer therapeutics. The majority of DUBs are cysteine proteases and are likely to be more "druggable" than E3 ligases. Cysteine residues in the active sites of DUBs are expected to be reactive to various electrophiles. Various compounds containing α,β-unsaturated ketones have indeed been demonstrated to inhibit cellular DUB activity. Inhibition of proteasomal cysteine DUB enzymes (i.e. USP14 and UCHL5) can be predicted to be particularly cytotoxic to cancer cells as it leads to blocking of proteasome function and accumulation of proteasomal substrates. We here provide an overall review of DUBs relevant to cancer and of various small molecules which have been demonstrated to inhibit DUB activity.

  • 26.
    Dyverfeldt, Petter
    Linköping University, Center for Medical Image Science and Visualization, CMIV. Linköping University, Department of Medicine and Health Sciences, Clinical Physiology . Linköping University, Faculty of Health Sciences. Linköping University, Department of Management and Engineering, Applied Thermodynamics and Fluid Mechanics . Linköping University, The Institute of Technology.
    Extending MRI to the Quantification of Turbulence Intensity2010Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    In cardiovascular medicine, the assessment of blood flow is fundamental to the understanding and detection of disease. Many pharmaceutical, interventional, and surgical treatments impact the flow. The primary purpose of the cardiovascular system is to drive, control and maintain blood flow to all parts of the body. In the normal cardiovascular system, fluid transport is maintained at high efficiency and the blood flow is essentially laminar. Disturbed and turbulent blood flow, on the other hand, appears to be present in many cardiovascular diseases and may contribute to their initiation and progression. Despite strong indications of an important interrelationship between flow and cardiovascular disease, medical imaging has lacked a non-invasive tool for the in vivo assessment of disturbed and turbulent flow. As a result, the extent and role of turbulence in the blood flow of humans have not yet been fully investigated.

    Magnetic resonance imaging (MRI) is a versatile tool for the non-invasive assessment of flow and has several important clinical and research applications, but might not yet have reached its full potential. Conventional MRI techniques for the assessment of flow are based on measurements of the mean velocity within an image voxel. The mean velocity corresponds to the first raw moment of the distribution of velocities within a voxel. An MRI framework for the quantification of any moment (mean, standard deviation, skew, etc.) of arbitrary velocity distributions is presented in this thesis.

    Disturbed and turbulent flows are characterized by velocity fluctuations that are superimposed on the mean velocity. The intensity of these velocity fluctuations can be quantified by their standard deviation, which is a commonly used measure of turbulence intensity. This thesis focuses on the development of a novel MRI method for the quantification of turbulence intensity. This method is mathematically derived and experimentally validated. Limitations and sources of error are investigated and guidelines for adequate application of MRI measurements of turbulence intensity are outlined. Furthermore, the method is adapted to the quantification of turbulence intensity in the pulsatile blood flow of humans and applied to a wide range of cardiovascular diseases. In these applications, elevated turbulence intensity was consistently detected in regions where highly disturbed flow was anticipated, and the effects of potential sources of errors were small.

    Diseased heart valves are often replaced with prosthetic heart valves, which, in spite of improved benefits and durability, continue to fall short of matching native flow patterns. In an in vitro setting, MRI was used to visualize and quantify turbulence intensity in the flow downstream from four common designs of prosthetic heart valves. Marked differences in the extent and degree of turbulence intensity were detected between the different valves.

    Mitral valve regurgitation is a common valve lesion associated with progressive left atrial and left ventricular remodelling, which may often require surgical correction to avoid irreversible ventricular dysfunction. The spatiotemporal dynamics of flow disturbances in mitral regurgitation were assessed based on measurements of flow patterns and turbulence intensity in a group of patients with significant regurgitation arising from similar valve lesions. Peak turbulence intensity occurred at the same time in all patients and the total turbulence intensity in the left atrium appeared closely related to the severity of regurgitation.

    MRI quantification of turbulence intensity has the potential to become a valuable tool in investigating the extent, timing and role of disturbed blood flow in the human cardiovascular system, as well as in the assessment of the effects of different therapeutic options in patients with vascular or valvular disorders.

    List of papers
    1. Quantification of intravoxel velocity standard deviation and turbulence intensity by generalizing phase-contrast MRI
    Open this publication in new window or tab >>Quantification of intravoxel velocity standard deviation and turbulence intensity by generalizing phase-contrast MRI
    2006 (English)In: Magnetic Resonance in Medicine, ISSN 0740-3194, E-ISSN 1522-2594, Vol. 56, no 4, p. 850-858Article in journal (Refereed) Published
    Abstract [en]

    Turbulent flow, characterized by velocity fluctuations, is a contributing factor to the pathogenesis of several cardiovascular diseases. A clinical noninvasive tool for assessing turbulence is lacking, however. It is well known that the occurrence of multiple spin velocities within a voxel during the influence of a magnetic gradient moment causes signal loss in phase-contrast magnetic resonance imaging (PC-MRI). In this paper a mathematical derivation of an expression for computing the standard deviation (SD) of the blood flow velocity distribution within a voxel is presented. The SD is obtained from the magnitude of PC-MRI signals acquired with different first gradient moments. By exploiting the relation between the SD and turbulence intensity (TI), this method allows for quantitative studies of turbulence. For validation, the TI in an in vitro flow phantom was quantified, and the results compared favorably with previously published laser Doppler anemometry (LDA) results. This method has the potential to become an important tool for the noninvasive assessment of turbulence in the arterial tree.

    Keyword
    phase-contrast magnetic resonance imaging, turbulent flow, intravoxel velocity distribution, turbulence intensity, atherosclerosis
    National Category
    Medical and Health Sciences Physiology Fluid Mechanics and Acoustics Medical Laboratory and Measurements Technologies
    Identifiers
    urn:nbn:se:liu:diva-37249 (URN)10.1002/mrm.21022 (DOI)000240897000017 ()34073 (Local ID)34073 (Archive number)34073 (OAI)
    Available from: 2009-10-10 Created: 2009-10-10 Last updated: 2018-01-13
    2. On MRI turbulence quantification
    Open this publication in new window or tab >>On MRI turbulence quantification
    Show others...
    2009 (English)In: Magnetic Resonance Imaging, ISSN 0730-725X, E-ISSN 1873-5894, Vol. 27, no 7, p. 913-922Article in journal (Refereed) Published
    Abstract [en]

    Turbulent flow, characterized by velocity fluctuations, accompanies many forms of cardiovascular disease and may contribute to their progression and hemodynamic consequences. Several studies have investigated the effects of turbulence on the magnetic resonance imaging (MRI) signal. Quantitative MRI turbulence measurements have recently been shown to have great potential for application both in human cardiovascular flow and in engineering flow. In this article, potential pitfalls and sources of error in MRI turbulence measurements are theoretically and numerically investigated. Data acquisition strategies suitable for turbulence quantification are outlined. The results show that the sensitivity of MRI turbulence measurements to intravoxel mean velocity variations is negligible, but that noise may degrade the estimates if the turbulence encoding parameter is set improperly. Different approaches for utilizing a given amount of scan time were shown to influence the dynamic range and the uncertainty in the turbulence estimates due to noise. The findings reported in this work may be valuable for both in vitro and in vivo studies employing MRI methods for turbulence quantification.

    Keyword
    Turbulence quantification, Turbulent flow, Phase-contrast magnetic resonance imaging, Constriction, Numerical flow phantom
    National Category
    Medical and Health Sciences
    Identifiers
    urn:nbn:se:liu:diva-20746 (URN)10.1016/j.mri.2009.05.004 (DOI)000269613000004 ()
    Note

    Original Publication: Petter Dyverfeldt, Roland Gårdhagen, Andreas Sigfridsson, Matts Karlsson and Tino Ebbers, On MRI turbulence quantification, 2009, MAGNETIC RESONANCE IMAGING, (27), 7, 913-922. http://dx.doi.org/10.1016/j.mri.2009.05.004 Copyright: Elsevier Science B.V., Amsterdam. http://www.elsevier.com/

    Available from: 2009-09-18 Created: 2009-09-18 Last updated: 2017-12-13
    3. Assessment of fluctuating velocities in disturbed cardiovascular blood flow: in vivo feasibility of generalized phase-contrast MRI
    Open this publication in new window or tab >>Assessment of fluctuating velocities in disturbed cardiovascular blood flow: in vivo feasibility of generalized phase-contrast MRI
    Show others...
    2008 (English)In: Journal of Magnetic Resonance Imaging, ISSN 1053-1807, E-ISSN 1522-2586, Vol. 28, no 3, p. 655-663Article in journal (Refereed) Published
    Abstract [en]

    Purpose

    To evaluate the feasibility of generalized phase-contrast magnetic resonance imaging (PC-MRI) for the noninvasive assessment of fluctuating velocities in cardiovascular blood flow.

    Materials and Methods

    Multidimensional PC-MRI was used in a generalized manner to map mean flow velocities and intravoxel velocity standard deviation (IVSD) values in one healthy aorta and in three patients with different cardiovascular diseases. The acquired data were used to assess the kinetic energy of both the mean (MKE) and the fluctuating (TKE) velocity field.

    Results

    In all of the subjects, both mean and fluctuating flow data were successfully acquired. The highest TKE values in the patients were found at sites characterized by abnormal flow conditions. No regional increase in TKE was found in the normal aorta.

    Conclusion

    PC-MRI IVSD mapping is able to detect flow abnormalities in a variety of human cardiovascular conditions and shows promise for the quantitative assessment of turbulence. This approach may assist in clarifying the role of disturbed hemodynamics in cardiovascular diseases.

    National Category
    Medical and Health Sciences
    Identifiers
    urn:nbn:se:liu:diva-43135 (URN)10.1002/jmri.21475 (DOI)000259106900013 ()71980 (Local ID)71980 (Archive number)71980 (OAI)
    Available from: 2009-10-10 Created: 2009-10-10 Last updated: 2017-12-13
    4. In Vitro Assessment of Flow Patterns and Turbulence Intensity in Prosthetic Heart Valves Using Generalized Phase-Contrast Magnetic Resonance Imaging
    Open this publication in new window or tab >>In Vitro Assessment of Flow Patterns and Turbulence Intensity in Prosthetic Heart Valves Using Generalized Phase-Contrast Magnetic Resonance Imaging
    Show others...
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Purpose: To assess in vitro the three-dimensional mean velocity field and the extent and degree of turbulenceintensity in different prosthetic heart valves using a generalization of phase-contrast magnetic resonance imaging(PC-MRI).

    Material and Methods: Four 27 mm aortic valves (Björk-Shiley Monostrut tilting-disc, St. Jude MedicalStandard bileaflet, Medtronic Mosaic stented and Freestyle stentless porcine valve) were tested under steadyinflow conditions in a Plexiglas phantom. Three-dimensional PC-MRI data were acquired to measure the meanvelocity field and the turbulent kinetic energy (TKE), a direction-independent measure of turbulence intensity.

    Results: Velocity and turbulence intensity estimates could be obtained up and downstream of the valves, exceptwhere metallic structure in the valves caused signal void. Distinct differences in the location, extent and peakvalues of velocity and turbulence intensity were observed between the valves tested. The maximum values ofTKE varied between the different valves: tilting disc, 100 J/m3; bileaflet, 115 J/m3; stented, 200 J/m3; stentless,145 J/m3.

    Conclusion: The turbulence intensity downstream from a prosthetic heart valve is dependent on the specificvalve design. Generalized PC-MRI can be used to quantify velocity and turbulence intensity downstream fromprosthetic heart valves, which may allow assessment of these aspects of prosthetic valvular function inpostoperative patients.

    Keyword
    Turbulence intensity, prosthetic heart valves, phase-contrast magnetic resonance imaging
    National Category
    Medical and Health Sciences
    Identifiers
    urn:nbn:se:liu:diva-53189 (URN)
    Available from: 2010-01-19 Created: 2010-01-19 Last updated: 2013-09-03Bibliographically approved
    5. Hemodynamic aspects of mitral regurgitation assessed by generalized phase-contrast MRI
    Open this publication in new window or tab >>Hemodynamic aspects of mitral regurgitation assessed by generalized phase-contrast MRI
    Show others...
    2011 (English)In: Journal of Magnetic Resonance Imaging, ISSN 1053-1807, E-ISSN 1522-2586, Vol. 33, no 3, p. 582-588Article in journal (Refereed) Published
    Abstract [en]

    Purpose: Mitral regurgitation creates a high velocity jet into the left atrium (LA), contributing both volume andpressure; we hypothesized that the severity of regurgitation would be reflected in the degree of LA flowdistortion.

    Material and Methods: Three-dimensional cine PC-MRI was applied to determine LA flow patterns andturbulent kinetic energy (TKE) in seven subjects (five patients with posterior mitral leaflet prolapse, two normalsubjects). In addition, the regurgitant volume and the time-velocity profiles in the pulmonary veins weremeasured.

    Results: The LA flow in the mitral regurgitation patients was highly disturbed with elevated values of TKE.Peak TKE occurred consistently at late systole. The total LA TKE was closely related to the regurgitant volume.LA flow patterns were characterized by a pronounced vortex in proximity to the regurgitant jet. In some patients,pronounced discordances were observed between individual pulmonary venous inflows, but these could not berelated to the direction of the flow jet or parameters describing global LA hemodynamics.

    Conclusion: PC-MRI permits investigations of atrial and pulmonary vein flow patterns and TKE in significantmitral regurgitation, reflecting the impact of the highly disturbed blood flow that accompanies this importantvalve disease.

    Place, publisher, year, edition, pages
    John Wiley and Sons, 2011
    Keyword
    Hemodynamics, mitral valve insufficiency, turbulent flow, phase-contrast magnetic resonance imaging, pulmonary veins, blood flow velocity
    National Category
    Medical and Health Sciences
    Identifiers
    urn:nbn:se:liu:diva-53190 (URN)10.1002/jmri.22407 (DOI)000287951100009 ()
    Available from: 2010-01-19 Created: 2010-01-19 Last updated: 2017-12-12
  • 27.
    Dyverfeldt, Petter
    et al.
    Linköping University, Center for Medical Image Science and Visualization, CMIV. Linköping University, The Institute of Technology. Linköping University, Department of Medicine and Health Sciences, Clinical Physiology . Östergötlands Läns Landsting, Heart Centre, Department of Clinical Physiology.
    Escobar Kvitting, John Peder
    Linköping University, Center for Medical Image Science and Visualization, CMIV. Linköping University, The Institute of Technology. Linköping University, Department of Medicine and Health Sciences, Physiology . Östergötlands Läns Landsting, Heart Centre, Department of Thoracic and Vascular Surgery.
    Boano, G.
    Östergötlands Läns Landsting.
    Carlhäll, Carljohan
    Linköping University, Center for Medical Image Science and Visualization, CMIV. Linköping University, The Institute of Technology. Linköping University, Department of Medicine and Health Sciences, Clinical Physiology . Östergötlands Läns Landsting, Heart Centre, Department of Clinical Physiology.
    Sigfridsson, Andreas
    Linköping University, Center for Medical Image Science and Visualization, CMIV. Linköping University, The Institute of Technology. Linköping University, Department of Medicine and Health Sciences, Clinical Physiology . Östergötlands Läns Landsting, Heart Centre, Department of Clinical Physiology.
    Hermansson, Ulf
    Linköping University, Department of Medicine and Health Sciences, Thoracic Surgery. Linköping University, Faculty of Health Sciences. Östergötlands Läns Landsting, Heart Centre, Department of Thoracic and Vascular Surgery.
    Bolger, A.F.
    University of California, San Fransisco, San Franisco, California, United States.
    Engvall, Jan
    Linköping University, Center for Medical Image Science and Visualization, CMIV. Linköping University, The Institute of Technology. Linköping University, Department of Medicine and Health Sciences, Clinical Physiology . Östergötlands Läns Landsting, Heart Centre, Department of Clinical Physiology.
    Ebbers, Tino
    Linköping University, Center for Medical Image Science and Visualization, CMIV. Linköping University, The Institute of Technology. Linköping University, Department of Medicine and Health Sciences, Clinical Physiology . Östergötlands Läns Landsting, Heart Centre, Department of Clinical Physiology.
    Turbulence Mapping Extends the Utility of Phase-Contrast MRI in Mitral Valve Regurgitation2009In: Proc. Intl. Soc. Mag. Reson. Med., 2009, p. 3939-Conference paper (Refereed)
  • 28.
    Dyverfeldt, Petter
    et al.
    Linköping University, Center for Medical Image Science and Visualization, CMIV. Linköping University, Department of Medicine and Health Sciences, Clinical Physiology . Linköping University, Faculty of Health Sciences. Östergötlands Läns Landsting, Heart Centre, Department of Clinical Physiology.
    Escobar Kvitting, John-Peder
    Linköping University, Center for Medical Image Science and Visualization, CMIV. Linköping University, Department of Medicine and Health Sciences, Physiology . Linköping University, Faculty of Health Sciences. Östergötlands Läns Landsting, Heart Centre, Department of Thoracic and Vascular Surgery.
    Sigfridsson, Andreas
    Linköping University, Center for Medical Image Science and Visualization, CMIV. Linköping University, Department of Medicine and Health Sciences, Clinical Physiology . Linköping University, Faculty of Health Sciences. Östergötlands Läns Landsting, Heart Centre, Department of Clinical Physiology.
    Franzén, Stefan
    Linköping University, Department of Medicine and Health Sciences, Thoracic Surgery. Linköping University, Faculty of Health Sciences. Östergötlands Läns Landsting, Heart Centre, Department of Thoracic and Vascular Surgery.
    Bolger, Ann F.
    University of California San Fransisco, San Fransisco, California, United States.
    Ebbers, Tino
    Linköping University, Center for Medical Image Science and Visualization, CMIV. Linköping University, Department of Medicine and Health Sciences, Clinical Physiology . Linköping University, Faculty of Health Sciences. Östergötlands Läns Landsting, Heart Centre, Department of Clinical Physiology.
    In-Vitro Turbulence Mapping in Prosthetic Heart Valves using Generalized Phase-Contrast MRI2009In: Proc. Intl. Soc. Mag. Reson. Med., 2009, p. 3941-Conference paper (Refereed)
  • 29.
    Dyverfeldt, Petter
    et al.
    Linköping University, Center for Medical Image Science and Visualization, CMIV. Linköping University, The Institute of Technology. Linköping University, Department of Medicine and Health Sciences, Clinical Physiology . Östergötlands Läns Landsting, Heart Centre, Department of Clinical Physiology.
    Gårdhagen, Roland
    Linköping University, Department of Management and Engineering, Applied Thermodynamics and Fluid Mechanics . Linköping University, Center for Medical Image Science and Visualization, CMIV. Linköping University, The Institute of Technology.
    Sigfridsson, Andreas
    Linköping University, Center for Medical Image Science and Visualization, CMIV. Linköping University, The Institute of Technology. Linköping University, Department of Medicine and Health Sciences, Clinical Physiology . Östergötlands Läns Landsting, Heart Centre, Department of Clinical Physiology.
    Karlsson, Matts
    Linköping University, Department of Management and Engineering, Applied Thermodynamics and Fluid Mechanics . Linköping University, Center for Medical Image Science and Visualization, CMIV. Linköping University, The Institute of Technology.
    Ebbers, Tinno
    Linköping University, Center for Medical Image Science and Visualization, CMIV. Linköping University, The Institute of Technology. Linköping University, Department of Medicine and Health Sciences, Clinical Physiology . Östergötlands Läns Landsting, Heart Centre, Department of Clinical Physiology.
    MRI Turbulence Quantification2009In: Proc. Intl. Soc. Mag. Reson. Med., 2009, p. 1858-Conference paper (Refereed)
  • 30.
    Dyverfeldt, Petter
    et al.
    Linköping University, Department of Medicine and Health Sciences, Clinical Physiology . Linköping University, Faculty of Health Sciences. Östergötlands Läns Landsting, Heart Centre, Department of Clinical Physiology.
    Sigfridsson, Andreas
    Linköping University, Center for Medical Image Science and Visualization, CMIV. Linköping University, Department of Medicine and Health Sciences, Clinical Physiology . Linköping University, Faculty of Health Sciences. Östergötlands Läns Landsting, Heart Centre, Department of Clinical Physiology.
    Escobar Kvitting, John-Peder
    Linköping University, Center for Medical Image Science and Visualization, CMIV. Linköping University, Department of Medicine and Health Sciences, Physiology . Linköping University, Faculty of Health Sciences. Östergötlands Läns Landsting, Heart Centre, Department of Thoracic and Vascular Surgery.
    Ebbers, Tino
    Linköping University, Department of Medicine and Health Sciences, Clinical Physiology . Linköping University, Faculty of Health Sciences. Östergötlands Läns Landsting, Heart Centre, Department of Clinical Physiology.
    Quantification of Turbulance Intensity by Generalizing Phase-Contrast MRI2006Conference paper (Refereed)
  • 31.
    Ebbers, Tino
    Linköping University, Center for Medical Image Science and Visualization, CMIV. Linköping University, Department of Medical and Health Sciences, Physiology. Linköping University, Department of Management and Engineering, Applied Thermodynamics and Fluid Mechanics. Linköping University, The Institute of Technology. Östergötlands Läns Landsting, Heart and Medicine Centre, Department of Clinical Physiology UHL.
    Flow Imaging: Cardiac Applications of 3D Cine Phase-Contrast MRI2011In: Current Cardiovascular Imaging Reports, ISSN 1941-9074, Vol. 4, no 2, p. 127-133Article, review/survey (Refereed)
    Abstract [en]

    Global and regional blood flow dynamics are of pivotal importance to cardiac function. Fluid mechanical forces can affect hemolysis and platelet aggregation, as well as myocardial remodeling. In recent years, assessment of blood flow patterns based on time-resolved, three-dimensional, three-directional phase-contrast MRI (3D cine PC MRI) has become possible and rapidly gained popularity. Initially, this technique was mainly known for its intuitive and appealing visualizations of the cardiovascular blood flow. Most recently, the technique has begun to go beyond compelling images toward comprehensive and quantitative assessment of blood flow. In this article, cardiac applications of 3D cine PC MRI data are discussed, starting with a review of the acquisition and analysis techniques, and including descriptions of promising applications of cardiac 3D cine PC MRI for the clinical evaluation of myocardial, valvular, and vascular disorders.

  • 32.
    Ebbers, Tino
    et al.
    Linköping University, Department of Medicine and Health Sciences, Clinical Physiology . Linköping University, Faculty of Health Sciences. Östergötlands Läns Landsting, Heart Centre, Department of Clinical Physiology.
    Dyverfeldt, Petter
    Linköping University, Department of Medicine and Health Sciences, Clinical Physiology . Linköping University, Faculty of Health Sciences. Östergötlands Läns Landsting, Heart Centre, Department of Clinical Physiology.
    Sigfridsson, Andreas
    Linköping University, Center for Medical Image Science and Visualization, CMIV. Linköping University, Department of Medicine and Health Sciences, Clinical Physiology . Linköping University, Faculty of Health Sciences. Östergötlands Läns Landsting, Heart Centre, Department of Clinical Physiology.
    Escobar Kvitting, John-Peder
    Linköping University, Department of Medicine and Health Sciences, Clinical Physiology . Linköping University, Faculty of Health Sciences.
    Quantification of Mean and Fluctuating Flow2006Conference paper (Refereed)
  • 33.
    Ebbers, Tino
    et al.
    Linköping University, Center for Medical Image Science and Visualization, CMIV. Linköping University, Department of Medicine and Health Sciences, Clinical Physiology . Linköping University, Faculty of Health Sciences. Östergötlands Läns Landsting, Heart Centre, Department of Clinical Physiology.
    Haraldsson, Henrik
    Linköping University, Center for Medical Image Science and Visualization, CMIV. Linköping University, Department of Medicine and Health Sciences, Clinical Physiology . Linköping University, Faculty of Health Sciences. Östergötlands Läns Landsting, Heart Centre, Department of Clinical Physiology.
    Dyverfeldt, Petter
    Linköping University, Center for Medical Image Science and Visualization, CMIV. Linköping University, Department of Medicine and Health Sciences, Clinical Physiology . Linköping University, Faculty of Health Sciences. Östergötlands Läns Landsting, Heart Centre, Department of Clinical Physiology.
    Sigfridsson, Andreas
    Linköping University, Center for Medical Image Science and Visualization, CMIV. Linköping University, Department of Medicine and Health Sciences, Clinical Physiology . Linköping University, Faculty of Health Sciences. Östergötlands Läns Landsting, Heart Centre, Department of Clinical Physiology.
    Warntjes, Marcel Jan Bertus
    Linköping University, Center for Medical Image Science and Visualization, CMIV. Linköping University, Department of Medicine and Health Sciences, Clinical Physiology . Linköping University, Faculty of Health Sciences. Östergötlands Läns Landsting, Heart Centre, Department of Clinical Physiology.
    Wigström, Lars
    Linköping University, Center for Medical Image Science and Visualization, CMIV. Linköping University, Department of Medicine and Health Sciences, Clinical Physiology . Linköping University, Faculty of Health Sciences.
    Higher order weighted least-squares phase offset correction for improved accuracy in phase-contrast MRI2008Conference paper (Refereed)
    Abstract [en]

    Phase-contrast magnetic resonance imaging has the ability to accurately measure blood flow and myocardial velocities in the human body. Unwanted spatially varying phase offsets are, however, always present and may deteriorate the measurements significantly. Some of these phase offsets can be estimated based on the pulse sequence (1), but effects caused by eddy currents are more difficult to predict. A linear fit of the phase values is often estimated from either a number of manually defined areas containing stationary tissue or by semi-automatic detection of stationary tissue using the

  • 34.
    Einarsson, Henrik
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Implementation and Performance Analysis of Filternets2006Independent thesis Basic level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Today Image acquisition equipment produces huge amounts of data that needs to be processed. Often the data describes signals with a dimensionality higher then 2, as with ordinary images. This introduce a problem when it comes to process this high dimensional data since ordinary signal processing tools are no longer suitable. New faster and more efficient tools need to be developed to fully exploit the advantages with e. g. a 3D CT-scan.

    One such tool is filternets, a layered networklike structure, which the signal propagates through. A filternet has three fundamental advantages which will decrease the filtering time. The network structure allows complex filter to be decomposed into simpler ones, intermediate result may be reused and filters may be implemented with very few nonzero coefficients (sparse filters).

    The aim of this study has been to create an implementation for filternets and optimize it with respect to execution time. Specially the possibility to use filternets that approximates a harmonic filterset for estimating orientation in 3D signals is investigated.

    Tests show that this method is up to about 30 times faster than a full filterset consisting of dense filters. They also show a slightly larger error in the estimated orientation compared with the dense filters, this error should however not limit the usability of the method.

  • 35.
    Eklund, Anders
    et al.
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Andersson, Mats
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Ohlsson, Henrik
    Linköping University, Department of Electrical Engineering, Automatic Control. Linköping University, The Institute of Technology.
    Ynnerman, Anders
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    Knutsson, Hans
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    A Brain Computer Interface for Communication Using Real-Time fMRI2010In: Proceedings of the 20th International Conference on Pattern Recognition, Los Alamitos, CA, USA: IEEE Computer Society, 2010, p. 3665-3669Conference paper (Refereed)
    Abstract [en]

    We present the first step towards a brain computer interface (BCI) for communication using real-time functional magnetic resonance imaging (fMRI). The subject in the MR scanner sees a virtual keyboard and steers a cursor to select different letters that can be combined to create words. The cursor is moved to the left by activating the left hand, to the right by activating the right hand, down by activating the left toes and up by activating the right toes. To select a letter, the subject simply rests for a number of seconds. We can thus communicate with the subject in the scanner by for example showing questions that the subject can answer. Similar BCI for communication have been made with electroencephalography (EEG). The subject then focuses on a letter while different rows and columns of the virtual keyboard are flashing and the system tries to detect if the correct letter is flashing or not. In our setup we instead classify the brain activity. Our system is neither limited to a communication interface, but can be used for any interface where five degrees of freedom is necessary.

  • 36.
    Eriksson-Bylund, Nina
    et al.
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Ressner, Marcus
    Linköping University, Department of Biomedical Engineering, Physiological Measurements. Linköping University, The Institute of Technology.
    Knutsson, Hans
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Reverberation Reduction Using 3D Wiener Filtering2003Conference paper (Other academic)
    Abstract [en]

    One of the most common artifacts in ultrasound imaging is reverberations. These are multiple reflection echoes that register as coming from a deeper region than the depth of the interface that are causing them, and result in ghost echoes in the ultrasound image. A method to reduce these unwanted artifacts using a three dimensional (2D + time) Wiener filter has been developed. Two sequences of iq-data, the least processed signal possible to retrieve from the ultrasound system (Vingmed System Five), have been used to test the method: One sequence on a tissue-mimicking agar gel phantom in which bars of glass simulating ribs give rise to reverberations, and one sequence on an open-chest pig with a strong reverberation from a water-filled rubber glove used as a medium between the heart and the transducer. The procedure works as follows: In a graphic interface the operator is shown the image sequence. In one of the frames two areas must be marked out; One area which contains a typical reverberation artifact, and one area which will represent an artifact free signal. After creating the three dimensional Wiener filter post-processing of the sequence is performed. The developed method significantly reduced the magnitude of the reverberation artifact in the tested sequences.

  • 37.
    Escobar Kvitting, John-Peder
    et al.
    Linköping University, Department of Medicine and Health Sciences, Clinical Physiology . Linköping University, Faculty of Health Sciences. Linköping University, Center for Medical Image Science and Visualization, CMIV. Linköping University, Department of Medicine and Health Sciences, Clinical Physiology . Linköping University, Faculty of Health Sciences.
    Sigfridsson, Andreas
    Linköping University, Center for Medical Image Science and Visualization, CMIV. Linköping University, Department of Medicine and Health Sciences, Clinical Physiology . Linköping University, Faculty of Health Sciences. Östergötlands Läns Landsting, Heart Centre, Department of Clinical Physiology.
    Wigström, Lars
    Linköping University, Center for Medical Image Science and Visualization, CMIV. Linköping University, Department of Medicine and Health Sciences, Clinical Physiology . Linköping University, Faculty of Health Sciences.
    Bolger, A.F.
    University of California, San Fransisco, San Fransisco, USA.
    Karlsson, Matts
    Linköping University, Center for Medical Image Science and Visualization, CMIV. Linköping University, Department of Biomedical Engineering, Biomedical Modelling and Simulation. Linköping University, The Institute of Technology.
    Virtual makers for noninvasive assessment of myocardial dynamics2005Conference paper (Refereed)
    Abstract [en]

       

     

     

     

     

     

     

     

     

     

     

     

     

      

     

  • 38.
    Forsberg, Daniel
    et al.
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Andersson, Mats
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Knutsson, Hans
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Adaptive Anisotropic Regularization of Deformation Fields for Non-Rigid Registration2010Conference paper (Other academic)
    Abstract [en]

    Image registration is a crucial task in many applications and applied in a variety of different areas. In addition to the primary task of image alignment, the deformation field is valuable when studying structural/volumetric changes in the brain. In most applications a regularizing term is added to achieve a smoothly varying deformation field. This can sometimes cause conflicts in situations of local complex deformations. In this paper we present a new regularizer, which aims at handling local complex deformations while maintaining an overall smooth deformation field. It is based on an adaptive anisotropic regularizer and its usefulness is demonstrated by two examples, one synthetic and one with real MRI data from a pre- and post-op situation with normal pressure hydrocephalus.

  • 39.
    Forsberg, Daniel
    et al.
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Andersson, Mats
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Knutsson, Hans
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Adaptive anisotropic regularization of deformation fields for non-rigid registration using the Morphon framework2010In: IEEE International Conference on Acoustics, Speech, and Signal Processing, IEEE , 2010, p. 473-476Conference paper (Refereed)
    Abstract [en]

    Image registration is a crucial task in many applications and applied in a variety of different areas. In addition to the primary task of image alignment, the deformation field is valuable when studying structural/volumetric changes in the brain. In most applications a regularizing term is added to achieve a smoothly varying deformation field. This can sometimes cause conflicts in situations of local complex deformations. In this paper we present a new regularizer, which aims at handling local complex deformations while maintaining an overall smooth deformation field. It is based on an adaptive anisotropic regularizer and its usefulness is demonstrated by two examples, one synthetic and one with real MRI data from a pre- and post-op situation with normal pressure hydrocephalus.

  • 40.
    Forsberg, Daniel
    et al.
    Linköping University, Department of Biomedical Engineering. Linköping University, The Institute of Technology.
    Andersson, Mats
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Knutsson, Hans
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Classification of multivariate medical datasets using deformable models - A work in progress2009Conference paper (Other academic)
    Abstract [en]

    This paper presents an overview of the project “Classification of multivariate medical datasets using deformable models” and the current work within the project. The project is a joint venture between the Department of Biomedical Engineering (Linköping University), the Center for Medical Image Science and Visualization (Linköping University) and Sectra Imtec AB (Linköping) and focuses on extending a deformable model approach, named the Morphon, to 3D and to utilize multi-variate data with multiple priors. Recent work in the project includes evaluating different methods for estimating the displacement field and automatic scale control.

  • 41.
    Forsgren, Mikael
    Linköping University, Department of Medical and Health Sciences, Division of Radiological Sciences. Linköping University, Faculty of Medicine and Health Sciences. Region Östergötland, Center for Surgery, Orthopaedics and Cancer Treatment, Department of Radiation Physics. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    The Non-Invasive Liver Biopsy: Determining Hepatic Function in Diffuse and Focal LiverDisease2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The liver is one of the largest organs within the human body and it handles many vital tasks such as nutrient processing, toxin removal, and synthesis of important proteins. The number of people suffering from chronic liver disease is on the rise, likely due to the present ‘western’ lifestyle. As disease develops in the liver there are pathophysiological manifestations within the liver parenchyma that are both common and important to monitor. These manifestations include inflammation, fatty infiltration (steatosis), excessive scar tissue formation (fibrosis and cirrhosis), and iron loading. Importantly, as the disease progresses there is concurrent loss of liver function. Furthermore, postoperative liver function insufficiency is an important concern when planning surgical treatment of the liver, because it is associated with both morbidity and mortality. Liver function can also be hampered due to drug-induced injuries, an important aspect to consider in drug-development.

    Currently, an invasive liver needle biopsy is required to determine the aetiology and to stage or grade the pathophysiological manifestations. There are important limitations with the biopsy, which include, risk of serious complications, mortality, morbidity, inter- and intra-observer variability, sampling error, and sampling variability. Cleary, it would be beneficial to be able investigate the pathophysiological manifestations accurately, non-invasively, and on regional level.

    Current available laboratory liver function blood panels are typically insufficient and often only indicate damage at a late stage. Thus, it would be beneficial to have access to biomarkers that are both sensitive and responds to early changes in liver function in both clinical settings and for the pharmaceutical industry and regulatory agencies.

    The main aim of this thesis was to develop and evaluate methods that can be used for a ‘non-invasive liver biopsy’ using magnetic resonance (MR). We also aimed to develop sensitive methods for measure liver function based on gadoxetate-enhanced MR imaging (MRI).

    The presented work is primarily based on a prospective study on c. 100 patients suffering from chronic liver disease of varying aetiologies recruited due to elevated liver enzyme levels, without clear signs of decompensated cirrhosis. Our results show that the commonly used liver fat cut-off for diagnosing steatosis should be lowered from 5% to 3% when using MR proton-density fat fraction (PDFF). We also show that MR elastography (MRE) is superior in staging fibrosis.

    Finally we presented a framework for quantifying liver function based on gadoxetate-enhanced MRI. The method is based on clinical images and a clinical approved contrast agent (gadoxetate). The framework consists of; state-of the-art image reconstruction and correction methods, a mathematical model, and a precise model parametrization method. The model was developed and validated on healthy subjects. Thereafter the model was found applicable on the chronic liver disease cohort as well as validated using gadoxetate levels in biopsy samples and blood samples. The liver function parameters correlated with clinical markers for liver function and liver fibrosis (used as a surrogate marker for liver function).

    In summary, it should be possible to perform a non-invasive liver biopsy using: MRI-PDFF for liver fat and iron loading, MRE for liver fibrosis and possibly also inflammation, and measure liver function using the presented framework for analysing gadoxetate-enhanced MRI. With the exception of an MREtransducer no additional hardware is required on the MR scanner. The liver function method is likely to be useful both in a clinical setting and in pharmaceutical trials.

    List of papers
    1. Separation of advanced from mild hepatic fibrosis by quantification of the hepatobiliary uptake of Gd-EOB-DTPA
    Open this publication in new window or tab >>Separation of advanced from mild hepatic fibrosis by quantification of the hepatobiliary uptake of Gd-EOB-DTPA
    Show others...
    2013 (English)In: European Radiology, ISSN 0938-7994, E-ISSN 1432-1084, Vol. 23, no 1, p. 174-181Article in journal (Refereed) Published
    Abstract [en]

    Objectives

    To apply dynamic contrast-enhanced (DCE) MRI on patients presenting with elevated liver enzymes without clinical signs of hepatic decompensation in order to quantitatively compare the hepatocyte-specific uptake of Gd-EOB-DTPA with histopathological fibrosis stage.

    Methods

    A total of 38 patients were prospectively examined using 1.5-T MRI. Data were acquired from regions of interest in the liver and spleen by using time series of single-breath-hold symmetrically sampled two-point Dixon 3D images (non-enhanced, arterial and venous portal phase; 3, 10, 20 and 30 min) following a bolus injection of Gd-EOB-DTPA (0.025 mmol/kg). The signal intensity (SI) values were reconstructed using a phase-sensitive technique and normalised using multiscale adaptive normalising averaging (MANA). Liver-to-spleen contrast ratios (LSC_N) and the contrast uptake rate (KHep) were calculated. Liver biopsy was performed and classified according to the Batts and Ludwig system.

    Results

    Area under the receiver-operating characteristic curve (AUROC) values of 0.71, 0.80 and 0.78, respectively, were found for KHep, LSC_N10 and LSC_N20 with regard to severe versus mild fibrosis. Significant group differences were found for KHep (borderline), LSC_N10 and LSC_N20.

    Conclusions

    Liver fibrosis stage strongly influences the hepatocyte-specific uptake of Gd-EOB-DTPA. Potentially the normalisation technique and KHep will reduce patient and system bias, yielding a robust approach to non-invasive liver function determination.

    Place, publisher, year, edition, pages
    Springer, 2013
    Keyword
    Quantification, Gd-EOB-DTPA, Dynamic contrast-enhanced MRI, Pharmacokinetics, Liver
    National Category
    Medical and Health Sciences
    Identifiers
    urn:nbn:se:liu:diva-87242 (URN)10.1007/s00330-012-2583-2 (DOI)000312324500022 ()
    Projects
    NILB
    Note

    Funding Agencies|Swedish Research Council|VR/M 2007-2884|Medical Research Council of South-east Sweden|FORSS 12621|Linkoping University, Linkoping University Hospital Research Foundations||County Council of Ostergotland||

    Available from: 2013-01-14 Created: 2013-01-14 Last updated: 2017-12-06
    2. Physiologically Realistic and Validated Mathematical Liver Model Revels Hepatobiliary Transfer Rates for Gd-EOB-DTPA Using Human DCE-MRI Data
    Open this publication in new window or tab >>Physiologically Realistic and Validated Mathematical Liver Model Revels Hepatobiliary Transfer Rates for Gd-EOB-DTPA Using Human DCE-MRI Data
    Show others...
    2014 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 9, no 4, p. 0095700-Article in journal (Refereed) Published
    Abstract [en]

    Objectives: Diffuse liver disease (DLD), such as non-alcoholic fatty liver disease (NASH) and cirrhosis, is a rapidly growing problem throughout the Westernized world. Magnetic resonance imaging (MRI), based on uptake of the hepatocyte-specific contrast agent (CA) Gd-EOB-DTPA, is a promising non-invasive approach for diagnosing DLD. However, to fully utilize the potential of such dynamic measurements for clinical or research purposes, more advanced methods for data analysis are required. Methods: A mathematical model that can be used for such data-analysis was developed. Data was obtained from healthy human subjects using a clinical protocol with high spatial resolution. The model is based on ordinary differential equations and goes beyond local diffusion modeling, taking into account the complete system accessible to the CA. Results: The presented model can describe the data accurately, which was confirmed using chi-square statistics. Furthermore, the model is minimal and identifiable, meaning that all parameters were determined with small degree of uncertainty. The model was also validated using independent data. Conclusions: We have developed a novel approach for determining previously undescribed physiological hepatic parameters in humans, associated with CA transport across the liver. The method has a potential for assessing regional liver function in clinical examinations of patients that are suffering of DLD and compromised hepatic function.

    Place, publisher, year, edition, pages
    Public Library of Science, 2014
    National Category
    Medical and Health Sciences
    Identifiers
    urn:nbn:se:liu:diva-106962 (URN)10.1371/journal.pone.0095700 (DOI)000335226500139 ()
    Available from: 2014-06-04 Created: 2014-06-02 Last updated: 2017-12-05
    3. Using a 3% Proton Density Fat Fraction as a Cut-off Value Increases Sensitivity of Detection of Hepatic Steatosis, Based on Results from Histopathology Analysis
    Open this publication in new window or tab >>Using a 3% Proton Density Fat Fraction as a Cut-off Value Increases Sensitivity of Detection of Hepatic Steatosis, Based on Results from Histopathology Analysis
    Show others...
    2017 (English)In: Gastroenterology, ISSN 0016-5085, E-ISSN 1528-0012, Vol. 153, no 1, p. 53-+Article in journal (Refereed) Published
    Abstract [en]

    It is possible to estimate hepatic triglyceride content by calculating the proton density fat fraction (PDFF), using proton magnetic resonance spectroscopy (less thansuperscriptgreater than1less than/superscriptgreater thanH-MRS), instead of collecting and analyzing liver biopsies to detect steatosis. However, the current PDFF cut-off value (5%) used to define steatosis by magnetic resonance was derived from studies that did not use histopathology as the reference standard. We performed a prospective study to determine the accuracy of less thansuperscriptgreater than1less than/superscriptgreater thanH-MRS PDFF in measurement of steatosis using histopathology analysis as the standard. We collected clinical, serologic, less thansuperscriptgreater than1less than/superscriptgreater thanH-MRS PDFF, and liver biopsy data from 94 adult patients with increased levels of liver enzymes (6 months or more) referred to the Department of Gastroenterology and Hepatology at Linköping University Hospital in Sweden from 2007 through 2014. Steatosis was graded using the conventional histopathology method and fat content was quantified in biopsy samples using stereological point counts (SPCs). We correlated less thansuperscriptgreater than1less than/superscriptgreater thanH-MRS PDFF findings with SPCs (r = 0.92; P less than.001). less thansuperscriptgreater than1less than/superscriptgreater thanH-MRS PDFF results correlated with histopathology results (ρ = 0.87; P less than.001), and SPCs correlated with histopathology results (ρ = 0.88; P less than.001). All 25 subjects with PDFF values of 5.0% or more had steatosis based on histopathology findings (100% specificity for PDFF). However, of 69 subjects with PDFF values below 5.0% (negative result), 22 were determined to have steatosis based on histopathology findings (53% sensitivity for PDFF). Reducing the PDFF cut-off value to 3.0% identified patients with steatosis with 100% specificity and 79% sensitivity; a PDFF cut-off value of 2.0% identified patients with steatosis with 94% specificity and 87% sensitivity. These findings might be used to improve non-invasive detection of steatosis.

    Place, publisher, year, edition, pages
    Elsevier, 2017
    National Category
    Gastroenterology and Hepatology
    Identifiers
    urn:nbn:se:liu:diva-136544 (URN)10.1053/j.gastro.2017.03.005 (DOI)000403918300022 ()
    Note

    Funding agencies: Swedish Research Council/Medicine and Health [VR/M 2007-2884, VR/M 2012-3199]; Swedish Research Council/Natural and Engineering Sciences [VR/NT 2014-6157]; Swedish Innovation Agency VINNOVA [2013-01314]; Region Ostergotland (ALF)

    Available from: 2017-04-19 Created: 2017-04-19 Last updated: 2018-04-18Bibliographically approved
  • 42.
    Forss, Mattias
    et al.
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Hjalmarsson, Johan
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Utveckling av en arketypeditor: Ett verktyg för modellering av struktur i elektroniska patientjournaler2006Independent thesis Basic level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Present-day electronic health record systems have limited possibilities to structure and store patient information in a similarly manner. This causes problems with exchanging patient record data between different systems and it gives rise to problems with, among other things, research and patient information availability. Lack of availability will in turn decrease the possibility of giving good care irrespective of where the patient is located.

    Within the openEHR project an idea with so called archetypes has been introduced as a uniform way to structure exchangeable patient record data in order to meet future requirements on electronic health records and systems. Archetypes are formal models of clinical information entities, for example blood pressure. They are constructed from constraints, structure and terms which may have bindings to medical terminology systems. Furthermore, medical knowledge in the archetypes is separated from the patient record systems.

    The purpose of the thesis has been to develop a tool, a so called archetype editor, that can be used to create and edit archetypes. In addition, the possibilities of implementing a connection to medical terminology systems should be explored. The development has followed an iterative process with focus on stability and usability. Another task has also been to find out the purpose with an archetype editor.

    The result is a platform-independent and stable tool, developed according to usability principles with a connection to the terminology system Unified Medical Language System (UMLS). An archetype editor’s purpose in a wider perspective is to solve shortcomings in medical information systems of today, which are brought up in this thesis. Although the openEHR project is new, there are many technically applicable ideas but also problems because of insufficient practical testing and application.

  • 43.
    Fredriksson, Ingemar
    et al.
    Linköping University, Department of Biomedical Engineering, Biomedical Instrumentation. Linköping University, The Institute of Technology.
    Larsson, Marcus
    Linköping University, Department of Biomedical Engineering. Linköping University, Department of Biomedical Engineering, Biomedical Instrumentation.
    Nyström, Fredrik
    Linköping University, Department of Medicine and Health Sciences. Linköping University, Department of Medicine and Health Sciences, Cardiology .
    Länne, Toste
    Linköping University, Department of Medicine and Health Sciences. Linköping University, Department of Medicine and Health Sciences, Cardiology .
    Östgren, Carl Johan
    Linköping University, Department of Medicine and Health Sciences, General Practice. Linköping University, Faculty of Health Sciences. Östergötlands Läns Landsting, Local Health Care Services in the West of Östergötland, West County Primary Health Care.
    Strömberg, Tomas
    Linköping University, Department of Biomedical Engineering, Biomedical Instrumentation. Linköping University, The Institute of Technology.
    Microcirculatory changes in type 2 diabetes assessed with velocity resolved quantitative laser Doppler flowmetryManuscript (preprint) (Other academic)
    Abstract [en]

    The response to local heating (44oC for 20 min) was evaluated in 28 type 2 diabetes patients (DM) and 29 non-diabetes controls (ND). Microcirculatory perfusion was assessed using conventional and quantitative Laser Doppler flowmetry (cLDF and qLDF), respectively. The qLDF estimates perfusion in a physiological relevant unit (g RBC / 100 g tissue × mm/s) in a fixed output volume, separated into three velocity regions, v < 1 mm/s, 1 - 10 mm/s, and v > 10 mm/s. Perfusion in cLDF is given in arbitrary units with unknown velocity distribution and measurement volume.

    A significantly lower response in DM than in ND was found after heat provocation both for the initial peak and the plateau response, while no significant differences were found at baseline. The qLDF showed increased perfusion for the velocity regions 1-10 mm/s and above 10 mm/s, while no significant increase was found for v < 1 mm/s. In conclusion, we found a lowered LDF response to local heating in DM. The new qLDF method showed that the increased blood flow occurs in vessels with a velocity above 1 mm/s. Baseline qLDF-data indicated that a redistribution of flow to higher velocity regions was associated with longer DM duration and for DM a negative correlation between perfusion and BMI.

  • 44.
    Freiberger, Manuel
    Linköping University, Department of Biomedical Engineering.
    A time domain optical coherence tomograph for laboratory investigations on phantoms and human skin2005Independent thesis Basic level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Optical coherence tomography is an imaging modality with an outstanding resolution. During the project, a time domain OCT system based on a Michelson fibre interferometer was implemented and put into operation. A super-luminescent diode with a centre wavelength of 1295nm and a bandwidth of 45nm was selected as light source and a linear variable delay line as reference. Basic tests were made on phantoms constructed of filter foils and on gel-like agar slices with optical properties similar to human tissue. It was shown that the achievable resolution was at least 36um and can be increased. The system can easily be enhanced to create two-dimensional images.

  • 45.
    Friman, O.
    et al.
    MeVis Research, Bremen, Germany.
    Dahlqvist Leinhard, Olof
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Medical and Health Sciences, Radiation Physics. Linköping University, Faculty of Health Sciences.
    Lundberg, Peter
    Linköping University, Department of Medical and Health Sciences. Linköping University, Faculty of Health Sciences. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Borga, Magnus
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    A General Method for Correction of Intensity Inhomogenity in Two Point Dixon Imaging2009In: Proc. Intl. Soc. Mag. Reson. Med., 2009, p. 4637-Conference paper (Refereed)
  • 46.
    Friman, Ola
    et al.
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Borga, Magnus
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Lundberg, Peter
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Medical and Health Sciences, Radiology. Linköping University, Faculty of Health Sciences.
    Knutsson, Hans
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Imaging Brain Function2002Conference paper (Other academic)
  • 47.
    Friman, Ola
    et al.
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Borga, Magnus
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Lundberg, Peter
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Medical and Health Sciences, Radiology. Linköping University, Faculty of Health Sciences.
    Tylén, U.
    Göteborgs universitet.
    Knutsson, Hans
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Emphysema Detection in CT Images2002Conference paper (Other academic)
    Abstract [en]

    This paper describes a fully automatic approach for detecting emphysema in CT im ages of the lungs. The method combines an image processing step, where potential emphysematous area s are extracted, and a neural network step trained to rec

  • 48.
    Gbaguidi, Bénédicte
    et al.
    Free University of Brussels, Belgium .
    Hakizimana, Pierre
    Free University of Brussels, Belgium .
    Vandenbussche, G
    Free University of Brussels, Belgium .
    Ruysschaert, Jean-Marie
    Free University of Brussels, Belgium .
    Conformational changes in a bacterial multidrug transporter are phosphatidylethanolamine-dependent2007In: Cellular and Molecular Life Sciences (CMLS), ISSN 1420-682X, E-ISSN 1420-9071, Vol. 64, no 12, p. 1571-1582Article in journal (Refereed)
    Abstract [en]

    LmrP is an electrogenic H(+)/drug antiporter that extrudes a broad spectrum of antibiotics. Five carboxylic residues are implicated in drug binding (Asp142 and Glu327) and proton motive force-mediated restructuring (Asp68, Asp128 and Asp235). ATR-FTIR (Attenuated Total Reflection - Fourier Transform Infrared) and tryptophan quenching experiments revealed that phosphatidylethanolamine (PE) is required to generate the structural intermediates induced by ionization of carboxylic residues. Surprisingly, no ionization-induced conformational changes were detectable in the absence of PE, suggesting either that carboxylic acid residues do not ionize or that ionization does not lead to any conformational change. The mean pKa of carboxylic residues evaluated by ATR-FTIR spectroscopy was 6.5 for LmrP reconstituted in PE liposomes, whereas the pKa calculated in the absence of PE was 4.6. Considering that 16 of the 19 carboxylic residues are located in the extramembrane loops, the pKa values obtained in the absence and in the presence of PE suggest that the interaction of the loop acid residues with the membrane interface depends on the lipid composition.

  • 49.
    Gharehbaghi, Arash
    et al.
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, Faculty of Science & Engineering.
    Ask, Per
    Linköping University, Department of Biomedical Engineering, Physiological Measurements. Linköping University, Faculty of Science & Engineering.
    Babic, Ankica
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, Faculty of Science & Engineering. Department of Information Science and Media Studies, University of Bergen, Norway.
    A pattern recognition framework for detecting dynamic changes on cyclic time series2015In: Pattern Recognition, ISSN 0031-3203, E-ISSN 1873-5142, Vol. 48, no 3, p. 696-708Article in journal (Refereed)
    Abstract [en]

    This paper proposes a framework for binary classification of the time series with cyclic characteristics. The framework presents an iterative algorithm for learning the cyclic characteristics by introducing the discriminative frequency bands (DFBs) using the discriminant analysis along with k-means clustering method. The DFBs are employed by a hybrid model for learning dynamic characteristics of the time series within the cycles, using statistical and structural machine learning techniques. The framework offers a systematic procedure for finding the optimal design parameters associated with the hybrid model. The proposed  model is optimized to detect the changes of the heart sound recordings (HSRs) related to aortic stenosis. Experimental results show that the proposed framework provides efficient tools for classification of the HSRs based on the heart murmurs. It is also evidenced that the hybrid model, proposed by the framework, substantially improves the classification performance when it comes to detection of the heart disease.

  • 50.
    Gharehbaghi, Arash
    et al.
    Linköping University, Department of Biomedical Engineering. Linköping University, The Institute of Technology.
    Ask, Per
    Linköping University, Department of Biomedical Engineering. Linköping University, The Institute of Technology.
    Lindèn, Maria
    Mälardalen University, Sweden.
    Babic, Ankica
    Linköping University, Department of Biomedical Engineering. Linköping University, The Institute of Technology. Univeristy of Bergen, Norway.
    A Novel Model for Screening Aortic Stenosis Using Phonocardiogram2015In: 16th Nordic-Baltic Conference on Biomedical Engineering / [ed] Henrik Mindedal and Mikael Persson, Springer Science Business Media , 2015, p. 48-51Conference paper (Refereed)
    Abstract [en]

    This study presents an algorithm for screening aortic stenosis, based on heart sound signal processing. It benefits from an artificial intelligent-based (AI-based) model using a multi-layer perceptron neural network. The AI-based model learns disease related murmurs using non-stationary features of the murmurs. Performance of the model is statistically evaluated using two different databases, one of children and the other of elderly volunteers with normal heart condition and aortic stenosis. Results showed a 95% confidence interval of the high accuracy/sensitivity (84.1%-86.0%)/(86.0%-88.4%) thus exhibiting a superior performance to a cardiologist who relies on the conventional auscultation. The study suggests including the heart sound signal in the clinical decision making due to its potential to improve the screening accuracy.

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