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  • 201.
    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.

  • 202.
    Cakici, Baki
    et al.
    KTH, School of Information and Communication Technology (ICT), Communication: Services and Infrastucture, Software and Computer Systems, SCS.
    Hebing, Kenneth
    Swedish Institute for Infectious Control (SMI), Solna, Sweden.
    Grünewald, Maria
    Swedish Institute for Infectious Control (SMI), Solna, Sweden.
    Saretok, Paul
    Swedish Institute for Infectious Control (SMI), Solna, Sweden.
    Hulth, Anette
    Swedish Institute for Infectious Control (SMI), Solna, Sweden.
    CASE: a framework for computer supported outbreak detection2010In: BMC Medical Informatics and Decision Making, ISSN 1472-6947, E-ISSN 1472-6947, Vol. 10, p. 14-Article in journal (Refereed)
    Abstract [en]

    Background: In computer supported outbreak detection, a statistical method is applied to a collection of cases to detect any excess cases for a particular disease. Whether a detected aberration is a true outbreak is decided by a human expert. We present a technical framework designed and implemented at the Swedish Institute for Infectious Disease Control for computer supported outbreak detection, where a database of case reports for a large number of infectious diseases can be processed using one or more statistical methods selected by the user. Results: Based on case information, such as diagnosis and date, different statistical algorithms for detecting outbreaks can be applied, both on the disease level and the subtype level. The parameter settings for the algorithms can be configured independently for different diagnoses using the provided graphical interface. Input generators and output parsers are also provided for all supported algorithms. If an outbreak signal is detected, an email notification is sent to the persons listed as receivers for that particular disease. Conclusions: The framework is available as open source software, licensed under GNU General Public License Version 3. By making the code open source, we wish to encourage others to contribute to the future development of computer supported outbreak detection systems, and in particular to the development of the CASE framework.

  • 203.
    Camacho, Emely
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Optimization of Lentivirus Production for Cancer Therapy2011Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Vectors based on lentivirus backbones have revolutionized our ability to transfer genesinto many cell types. Lentiviral vectors integrate into the chromatin of target cells and do not transfer any viral genes causing vector replication. Both of these features arecommonly used in gene therapy and have been used clinically in individuals sufferingfrom cancer, infections and genetic diseases. It has been discovered that T-cells can be genetically modified to be used as effective weapons against cancer: therefore virus mustbe produced to deliver the gene of interest into the T-cells. In this project, lentiviralvectors have been produced to transfer the gene coding for a chimeric antigen receptor(CAR) which is directed to CD19 on B-cells. The vectors will, hence, be used to generateCD19 retargeted T-cells in purpose to kill CD19 cells such as B-cell lymphoma andleukemia. We have evaluated two production protocols to determine a feasible method toculture these vectors. We have also stimulate T-cells with two different antibodies (anti-CD3 and anti-CD28) and transduced T-cells. Our results demonstrate that theconcentration of virus was higher after prolonged incubation in 4˚C, which can not beexplained. The stimulation demonstrated that bound anti-CD3 was the best stimulator,and moreover the FACS-analysis showed that addition of anti-CD28 gave a highertransduction level. In conclusion, the viral vectors may be kept in 4˚C for two days beforeconcentrating the virus, and bound anti-CD3 is a better choice than soluble anti-CD3 forstimulation of T-cells.

  • 204.
    Campillay, Amaya
    Karlstad University.
    Laktatdehydrogenas som ny point-of-care test för nyfödda barn: En precisionsanalys2013Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
  • 205.
    Cao, Minlu
    Karlstad University, Faculty of Health, Science and Technology (starting 2013), Department of Health Sciences.
    Role of PPAR-γ in Human Neuroblastoma (SH-SY5Y) Cell Differentiation: Effects on cell number and gene expression2014Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
  • 206.
    Carlie, Katarina
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Spädbarns tarmflora & probiotikas effekt vid kolik: Kan skillnader i spädbarns tarmflora förklara kolik och är probiotika en effektiv behandling vid kolik?2015Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    One out of five infants suffer from colic during the first three months of life. Otherwise healthy infants suffer from severe crying and are unable to be comforted during at least three consecutive hours per day for more than three days a week. Although colic is a common problem for both babies and parents, there is currently no effective treatment. The etiology is unclear, but smoking and  prepartum maternal mental illness, allergies to foods and an undeveloped gastrointestinal system in infants are believed to be contributing factors. This study reviews eight articles that examine the differences in intestinal flora between infants with and without colic, to see if the differences can explain colic and probiotic effect in colicky infants. Reviewed studies show that the prevalence of Proteobacteria, coliforms and Escherichia coli is higher in infants with colic. Unlike infants without colic, colicky infants exhibit a minor bacterial diversity, reduced colonization of Bacteroidetes and the beneficial bacterial genus of Lactobacillus and Bifidobacterium. Breastfed colicky infants treated with the probiotic bacterial strain, Lactobacillus reuteri DSM 17938, obtained, in two out of three studies, a positive effect on colic symtoms without any side effects, where the crying time was reduced to less than half. Results vary geographically and evidence for a probiotic effect on bottle-fed infants with colic is still inadequate. It remains unclear whether an altered intestinal flora can cause colic or is a result of colic as the intestinal flora is very complex and more studies are needed in this area.

  • 207.
    Carls, Stefan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Women's and Children's Health.
    Optimization of pyrosequencing method for copy number analysis of CYP2D62017Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    CYP2D6, a member of the cytochrome P450 enzyme system, has a central role in drug metabolism, it metabolizes 25 % of clinically used drugs. The gene that codes for the enzyme displays a high degree of polymorphism, which effects enzyme functions to various degrees. Aside from smaller mutations like SNPs, alleles may also feature duplications or deletion of the whole gene. Due to the clinical relevance of these mutations, a simple and precise method for genotyping is needed. In this study, a method based on pyrosequencing for copy number analysis was evaluated, wherein the copy number was determined by relative quantification to a reference gene CYP2D8P. During evaluation of the method, several adjustments were tried for optimization, including adjustments of annealing temperature and primer concentration. The results showed a difficulty in distinguishing between copy numbers using the method, as well as a high coefficient of variation. Therefore, further optimization is required before the method could be implemented into clinical practice.

  • 208.
    Carlsson, Lars
    Örebro University, Department of Clinical Medicine.
    Impedanskardiografi med Physio flow kontra ”Fick´s direkt” för beräkning av hjärtminutvolym på elitskidåkare under stakning.2007Independent thesis Basic level (professional degree), 10 credits / 15 HE creditsStudent thesis
    Abstract [sv]

    Trots tidigare oenighet bland forskare är den allmänna uppfattningen idag att det är hjärtminutvolymen (HMV) som är den enskilt största begränsande faktorn för maximalt syreupptag under arbete. Fortfarande råder dock osäkerhet bland arbetsfysiologer huruvida slagvolymen (SV) planar ut, minskar eller stiger vid maximalt arbete. En av de största utmaningarna inom arbetsfysiologin är utvecklandet av en tillförlitlig, billig och enkel non-invasiv utrustning i syfte att kunna mäta dessa parametrar. Detta har lett fram till metoden impedanskardiografi som baseras på motståndet av elektriska signaler som skickas genom thorax. Tidigare studier har visat på hög validitet mellan den impedanskardiografiska utrustningen Physio flowTM och den invasiva metoden ”Fick´s direkt” i vila och under cykelarbete på otränade. I detta arbete har ett första försök på elitskidåkare (n = 6) gjorts i syfte att jämföra metoderna under stakning, dessutom jämfördes resultaten av slagvolymen från impedansutrustningen mellan submaximalt och maximalt arbete. Resultatet visade att inte heller denna studie med säkerhet kunde skilja metoderna åt, vare sig under submaximalt arbete (p = 0,43) eller vid maximalt arbete (p = 0,17). Det ska dock poängteras att Fick´s beräkningsmetod modifierats i syfte att undvika katetrar genom hjärtat under maximal stakning, vilket kan ha påverkat resultatet. En intressant observation gällande SV gjordes mellan submaximal och maximal stakning. Här noterades en ökning från 150,1 till 175,5 ml (p = 0,01) vilket motsäger Åstrands klassiska ”platåteori” från 1964.

  • 209.
    Carlsson, Paula
    Karlstad University, Faculty of Health, Science and Technology (starting 2013), Department of Health Sciences.
    Påverkan på tillväxt och apoptos hos KCL22 i närvaro av Imatinib och Montelukast, separat samt kombinerat2015Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
  • 210.
    Casas Garcia, Belén
    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).
    Towards Personalized Models of the Cardiovascular System Using 4D Flow MRI2018Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Current diagnostic tools for assessing cardiovascular disease mostly focus on measuring a given biomarker at a specific spatial location where an abnormality is suspected. However, as a result of the dynamic and complex nature of the cardiovascular system, the analysis of isolated biomarkers is generally not sufficient to characterize the pathological mechanisms behind a disease. Model-based approaches that integrate the mechanisms through which different components interact, and present possibilities for system-level analyses, give us a better picture of a patient’s overall health status.

    One of the main goals of cardiovascular modelling is the development of personalized models based on clinical measurements. Recent years have seen remarkable advances in medical imaging and the use of personalized models is slowly becoming a reality. Modern imaging techniques can provide an unprecedented amount of anatomical and functional information about the heart and vessels. In this context, three-dimensional, three-directional, cine phase-contrast (PC) magnetic resonance imaging (MRI), commonly referred to as 4D Flow MRI, arises as a powerful tool for creating personalized models. 4D Flow MRI enables the measurement of time-resolved velocity information with volumetric coverage. Besides providing a rich dataset within a single acquisition, the technique permits retrospective analysis of the data at any location within the acquired volume.

    This thesis focuses on improving subject-specific assessment of cardiovascular function through model-based analysis of 4D Flow MRI data. By using computational models, we aimed to provide mechanistic explanations of the underlying physiological processes, derive novel or improved hemodynamic markers, and estimate quantities that typically require invasive measurements. Paper I presents an evaluation of current markers of stenosis severity using advanced models to simulate flow through a stenosis. Paper II presents a framework to personalize a reduced-order, mechanistic model of the cardiovascular system using exclusively non-invasive measurements, including 4D Flow MRI data. The modelling approach can unravel a number of clinically relevant parameters from the input data, including those representing the contraction and relaxation patterns of the left ventricle, and provide estimations of the pressure-volume loop. In Paper III, this framework is applied to study cardiovascular function at rest and during stress conditions, and the capability of the model to infer load-independent measures of heart function based on the imaging data is demonstrated. Paper IV focuses on evaluating the reliability of the model parameters as a step towards translation of the model to the clinic.

  • 211.
    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.

  • 212.
    Cedergren, Linda
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Expression of recombinant protein including an His-tag to facilitate purification for diagnosis of CCHF and Lassa Viruses2006Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Abstract

    Crimean-Congo Hemorrhagic Fever virus (CCHF) and Lassa virus are giving sources illness to humans. In addition to zoonotic transmission, CCHF and Lassa virus can spread from person to person. After a short incubation period, CCHF and Lassa virus infections are characterized by a sudden onset of high fever, chills, headache and cough just like flu. Even some people are vomiting and have diarrhoea. After a few days of illness hemorrhagic manifestations occur. Treatment options for CCHF and Lassa viruses are limited, and there is no vaccine available for use in humans. The purpose of the present study was to produce recombinant nucleocapsid protein of Lassavirus and CCHF virus including an aminoterminal His-tag by a Semliki Forest Virus Replicon (pSFV 4.2). The recombinant proteins are planned to be used in future development of diagnostic methods.

  • 213.
    Cederholm, Åsa
    Karlstad University, Faculty of Health, Science and Technology (starting 2013), Department of Health Sciences.
    Samband mellan trombocytvariabler: Finns det hos friska individer2015Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
  • 214.
    Celander, Daniel
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Förekomst av bakterier efter användning av nytt ytdesinfektionsmedel med kvardröjande effekt på en klinisk vårdavdelning2011Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    In Sweden approximately 10 % of patients receiving health care are afflicted with health care associated infections. To minimize the risks involved for patients and personnel, a great deal of attention is directed towards matters of hygiene, with the purpose of decreasing occurrence of infectious microorganisms. Improved hygiene is also considered to be a major part of the effort to limit the spread of antibiotic resistant bacteria.

    The purpose of this study was to examine if a surface disinfectant with a persistent effect could lead to a significant reduction in the occurrence of bacteria in a health care environment compared to the currently routinely used disinfectant. Samples were collected from 14 hand-touch surfaces in patient isolation rooms cleaned with either of the two desinfectants at a hospital ward. Simultaneously the presence of Staphylococcus aureus, enterococci, coliform bacteria and Pseudomonas aeruginosa was examined. Bacteria were cultured and identified using conventional microbiological laboratory methods.

    A significant difference between the different disinfectants could not be demonstrated, nor ruled out. Further, more extensive, studies are required to evaluate if a statistically significant reduction can be achieved with the new disinfectant. S. aureus was found in 106 out of 297 samples (36 %), and a correlation could be seen between the total count of bacteria and the number of S. aureus in individual samples. Enterococci were found in 72 out of 297 samples (24 %), of which 52 were identified as Enterococcus faecalis, 18 E. faecium and two samples containing both species. No correlation between the total count of bacteria and the number of enterococci could be seen. Coliform bacteria and P. aeruginosa were only found on one occasion respectively. 

  • 215.
    Chabo, Maria
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Physiology.
    Ventilation heterogeneity, assessed by nitrogen washout, in relation to Chronic obstructive pulmonary disease symptoms2018Independent thesis Advanced level (professional degree), 10 credits / 15 HE creditsStudent thesis
  • 216.
    Chahrour, Yasmin
    et al.
    Jönköping University, School of Health and Welfare, HHJ, Dep. of Natural Science and Biomedicine.
    Ishak, Helen
    Jönköping University, School of Health and Welfare, HHJ, Dep. of Natural Science and Biomedicine.
    Fyllnadsnivåers påverkan, tidsförlängning innan analys och blodprovers stabilitet2018Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Background: Ionized calcium concentrations decrease when samples are exposed to air. Due to pre-analytical factors, the 4 hour time limit for analysis of standard bicarbonate, can sometimes be exceeded. There is limited documentation about additional analyses on post-analytic decapped serum samples stored at room temperature. Aim: The aim was to examine how lower sample volumes affect the concentration of ionized calcium, if the time limit for analysis of standard bicarbonate on whole blood can be prolonged and how long decapped serum samples can be stored at room temperature for eventual additional analyses. Methods: The concentration of ionized calcium was analyzed on serum samples filled with 1 mL and 2 mL and were compared to maximally filled samples. Refrigerated whole blood samples were analyzed for standard bicarbonate after 4-7 hours. Ten biochemical analytes were measured in decapped serum samples after 2-8 hours of storage at room temperature. The mean percentage deviation was compared to an analytical and biological imprecision limit to determine analyte stability. Results and conclusions: Ionized calcium concentrations in lower sample volumes were reliable. The stability of standard bicarbonate could not be determined, therefore a longer possible time limit could not be recommended. The biochemical analytes were stable for 8 hours.

  • 217.
    Chaillou, Thomas
    et al.
    Karolinska Institutet, Stockholm, Sweden.
    Cheng, Arthur J.
    Karolinska Institutet, Stockholm, Sweden.
    Integrative biology is needed to understand exercise adaptions from the whole body to the cellular level2016In: Journal of applied physiology, ISSN 8750-7587, E-ISSN 1522-1601, Vol. 121, no 2, p. 598-599Article in journal (Refereed)
  • 218.
    Chang, Keke
    et al.
    Department of Electrical Engineering, Henan Agricultural University, Zhengzhou, China.
    Chen, Ruipeng
    Department of Electrical Engineering, Henan Agricultural University, Zhengzhou, China.
    Wang, Shun
    Department of Electrical Engineering, Henan Agricultural University, Zhengzhou, China.
    Li, Jianwei
    Department of Electrical Engineering, Henan Agricultural University, Zhengzhou, China.
    Hu, Xinran
    School of Human Nutrition and Dietetics, McGill University, Canada..
    Liang, Hao
    University of Gävle, Faculty of Engineering and Sustainable Development, Department of Electronics, Mathematics and Natural Sciences.
    Cao, Baiqiong
    Department of Electrical Engineering, Henan Agricultural University, Zhengzhou, China.
    Sun, Xiaohui
    Department of Electrical Engineering, Henan Agricultural University, Zhengzhou, China.
    Ma, Liuzheng
    Department of Electrical Engineering, Henan Agricultural University, Zhengzhou, China.
    Zhu, Juanhua
    Department of Electrical Engineering, Henan Agricultural University, Zhengzhou, China.
    Jiang, Min
    College of life sciences, Henan Agricultural University, Zhengzhou, China.
    Hu, Jiandong
    Department of Electrical Engineering, Henan Agricultural University, Zhengzhou, China; State key laboratory of wheat and maize crop science, Zhengzhou, China.
    Considerations on Circuit Design and Data Acquisition of a Portable Surface Plasmon Resonance Biosensing System2015In: Sensors, ISSN 1424-8220, E-ISSN 1424-8220, Vol. 15, no 8, p. 20511-20523Article in journal (Refereed)
    Abstract [en]

    The aim of this study was to develop a circuit for an inexpensive portable biosensing system based on surface plasmon resonance spectroscopy. This portable biosensing system designed for field use is characterized by a special structure which consists of a microfluidic cell incorporating a right angle prism functionalized with a biomolecular identification membrane, a laser line generator and a data acquisition circuit board. The data structure, data memory capacity and a line charge-coupled device (CCD) array with a driving circuit for collecting the photoelectric signals are intensively focused on and the high performance analog-to-digital (A/D) converter is comprehensively evaluated. The interface circuit and the photoelectric signal amplifier circuit are first studied to obtain the weak signals from the line CCD array in this experiment. Quantitative measurements for validating the sensitivity of the biosensing system were implemented using ethanol solutions of various concentrations indicated by volume fractions of 5%, 8%, 15%, 20%, 25%, and 30%, respectively, without a biomembrane immobilized on the surface of the SPR sensor. The experiments demonstrated that it is possible to detect a change in the refractive index of an ethanol solution with a sensitivity of 4.99838 × 10(5) ΔRU/RI in terms of the changes in delta response unit with refractive index using this SPR biosensing system, whereby the theoretical limit of detection of 3.3537 × 10(-5) refractive index unit (RIU) and a high linearity at the correlation coefficient of 0.98065. The results obtained from a series of tests confirmed the practicality of this cost-effective portable SPR biosensing system.

  • 219.
    Chen, Gunilla
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Women's and Children's Health.
    Changes in adipose tissue mRNA expression due to perinatal exposure to bisphenol A in rats2014Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Bisphenol A (BPA) is an estrogen receptor binding chemical, widely used in the plastics industry, and as such commonly encountered from plastic containers etc. Even at very low doses, BPA is believed to induce obesity and to have various endocrine disruptive effects. The purpose of this study was to determine possible gene expression changes in gonadal and inguinal adipose tissue from rats perinatally exposed to BPA. The method used was quantitative real-time PCR, and genes found to be up-regulated were PLZF, adiponectin, RXRa and Tcf21, while down-regulated genes were PPARγ, Tmem26, EsR1, Resistin, LPL, Chemerin, Serpina6, TFAM and Ahr. This is so far largely unsupported by other studies, and more research is needed.

  • 220.
    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.

  • 221.
    Cheng, Xiaogang
    et al.
    KTH, School of Electrical Engineering and Computer Science (EECS). Nanjing Univ Posts & Telecommun, Coll Telecommun & Informat Engn, Nanjing 210003, Jiangsu, Peoples R China.;Umea Univ, Dept Appl Phys & Elect, S-90187 Umea, Sweden.
    Yang, Bin
    Umea Univ, Dept Appl Phys & Elect, S-90187 Umea, Sweden.;Xian Univ Architecture & Technol, Sch Environm & Municipal Engn, Xian 710055, Shaanxi, Peoples R China..
    Liu, Guoqing
    Nanjing Tech Univ, Sch Phys & Math Sci, Nanjing 211800, Jiangsu, Peoples R China..
    Olofsson, Thomas
    Umea Univ, Dept Appl Phys & Elect, S-90187 Umea, Sweden..
    Li, Haibo
    KTH, School of Electrical Engineering and Computer Science (EECS). Nanjing Univ Posts & Telecommun, Coll Telecommun & Informat Engn, Nanjing 210003, Jiangsu, Peoples R China..
    A Total Bounded Variation Approach to Low Visibility Estimation on Expressways2018In: Sensors, ISSN 1424-8220, E-ISSN 1424-8220, Vol. 18, no 2, article id 392Article in journal (Refereed)
    Abstract [en]

    Low visibility on expressways caused by heavy fog and haze is a main reason for traffic accidents. Real-time estimation of atmospheric visibility is an effective way to reduce traffic accident rates. With the development of computer technology, estimating atmospheric visibility via computer vision becomes a research focus. However, the estimation accuracy should be enhanced since fog and haze are complex and time-varying. In this paper, a total bounded variation (TBV) approach to estimate low visibility (less than 300 m) is introduced. Surveillance images of fog and haze are processed as blurred images (pse udo-blurred images), while the surveillance images at selected road points on sunny days are handled as clear images, when considering fog and haze as noise superimposed on the clear images. By combining image spectrum and TBV, the features of foggy and hazy images can be extracted. The extraction results are compared with features of images on sunny days. Firstly, the low visibility surveillance images can be filtered out according to spectrum features of foggy and hazy images. For foggy and hazy images with visibility less than 300 m, the high-frequency coefficient ratio of Fourier (discrete cosine) transform is less than 20%, while the low-frequency coefficient ratio is between 100% and 120%. Secondly, the relationship between TBV and real visibility is established based on machine learning and piecewise stationary time series analysis. The established piecewise function can be used for visibility estimation. Finally, the visibility estimation approach proposed is validated based on real surveillance video data. The validation results are compared with the results of image contrast model. Besides, the big video data are collected from the Tongqi expressway, Jiangsu, China. A total of 1,782,000 frames were used and the relative errors of the approach proposed are less than 10%.

  • 222.
    Chinnasamy, Thiruppathiraja
    et al.
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Segerink, Loes I.
    Nystrand, Mats
    Gantelius, Jesper
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Andersson Svahn, Helene
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    A lateral flow paper microarray for rapid allergy point of care diagnostics2014In: The Analyst, ISSN 0003-2654, E-ISSN 1364-5528, Vol. 139, no 10, p. 2348-2354Article in journal (Refereed)
    Abstract [en]

    There is a growing need for multiplexed specific IgE tests that can accurately evaluate patient sensitization profiles. However, currently available commercial tests are either single/low-plexed or require sophisticated instrumentation at considerable cost per assay. Here, we present a novel convenient lateral flow microarray-based device that employs a novel dual labelled gold nanoparticle-strategy for rapid and sensitive detection of a panel of 15 specific IgE responses in 35 clinical serum samples. Each gold nanoparticle was conjugated to an optimized ratio of HRP and anti-IgE, allowing significant enzymatic amplification to improve the sensitivity of the assay as compared to commercially available detection reagents. The mean inter-assay variability of the developed LFM assay was 12% CV, and analysis of a cohort of clinical samples (n = 35) revealed good general agreement with ImmunoCAP, yet with a varying performance among allergens (AUC = [0.54-0.88], threshold 1 kU). Due to the rapid and simple procedure, inexpensive materials and read-out by means of a consumer flatbed scanner, the presented assay may provide an interesting low-cost alternative to existing multiplexed methods when thresholds > 1 kU are acceptable.

  • 223.
    Chitheer, Athir
    Umeå University, Faculty of Medicine, Department of Clinical Microbiology, Biomedical Laboratory Science. Umeå University, Faculty of Medicine, Department of Clinical Microbiology, Virology.
    Generation of a Chimeric HAdV-5/56 Virus2018Independent thesis Basic level (professional degree), 10 credits / 15 HE creditsStudent thesis
  • 224.
    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.

  • 225.
    Chow, Joyce A
    et al.
    RISE Interactive Institute.
    Törnros, Martin E
    Interaktiva Rum Sverige.
    Waltersson, Marie
    Linköping University.
    Richard, Helen
    Linköping University Hospital.
    Kusoffsky, Madeleine
    RISE Interactive Institute.
    Lundström, Claes F
    Linköping University.
    Kurti, Arianit
    RISE Interactive Institute.
    A design study investigating augmented reality and photograph annotation in a digitalized grossing workstation2017In: Journal of Pathology Informatics, ISSN 2229-5089, E-ISSN 2153-3539, Vol. 8, article id 31Article in journal (Refereed)
    Abstract [en]

    Context: Within digital pathology, digitalization of the grossing procedure has been relatively underexplored in comparison to digitalization of pathology slides. Aims: Our investigation focuses on the interaction design of an augmented reality gross pathology workstation and refining the interface so that information and visualizations are easily recorded and displayed in a thoughtful view. Settings and Design: The work in this project occurred in two phases: the first phase focused on implementation of an augmented reality grossing workstation prototype while the second phase focused on the implementation of an incremental prototype in parallel with a deeper design study. Subjects and Methods: Our research institute focused on an experimental and “designerly” approach to create a digital gross pathology prototype as opposed to focusing on developing a system for immediate clinical deployment. Statistical Analysis Used: Evaluation has not been limited to user tests and interviews, but rather key insights were uncovered through design methods such as “rapid ethnography” and “conversation with materials”. Results: We developed an augmented reality enhanced digital grossing station prototype to assist pathology technicians in capturing data during examination. The prototype uses a magnetically tracked scalpel to annotate planned cuts and dimensions onto photographs taken of the work surface. This article focuses on the use of qualitative design methods to evaluate and refine the prototype. Our aims were to build on the strengths of the prototype's technology, improve the ergonomics of the digital/physical workstation by considering numerous alternative design directions, and to consider the effects of digitalization on personnel and the pathology diagnostics information flow from a wider perspective. A proposed interface design allows the pathology technician to place images in relation to its orientation, annotate directly on the image, and create linked information. Conclusions: The augmented reality magnetically tracked scalpel reduces tool switching though limitations in today's augmented reality technology fall short of creating an ideal immersive workflow by requiring the use of a monitor. While this technology catches up, we recommend focusing efforts on enabling the easy creation of layered, complex reports, linking, and viewing information across systems. Reflecting upon our results, we argue for digitalization to focus not only on how to record increasing amounts of data but also how these data can be accessed in a more thoughtful way that draws upon the expertise and creativity of pathology professionals using the systems.

  • 226.
    Christiansson, Lisa
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Clinical Immunology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Mustjoki, Satu
    University of Helsinki.
    Loskog, Angelica S I
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Clinical Immunology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Mangsbo, Sara
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Clinical Immunology.
    A Comparison of Multiplex Platforms for Absolute and Relative Protein QuantificationManuscript (preprint) (Other academic)
  • 227.
    Christoffersson, Jonas
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biotechnology. Linköping University, Faculty of Science & Engineering.
    Meier, Florian
    Boehringer Ingelheim Pharma GmbH and Co. KG, Nonclinical Drug Safety Germany, D-88397 Biberach an der Riss, Germany.
    Kempf, Henning
    Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany.
    Schwanke, Kristin
    Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany.
    Coffee, Michelle
    Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany.
    Beilmann, Mario
    Boehringer Ingelheim Pharma GmbH and Co. KG, Nonclinical Drug Safety Germany, D-88397 Biberach an der Riss, Germany.
    Zweigerdt, Robert
    Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany.
    Mandenius, Carl-Fredrik
    Linköping University, Department of Physics, Chemistry and Biology, Biotechnology. Linköping University, Faculty of Science & Engineering.
    A Cardiac Cell Outgrowth Assay for Evaluating Drug Compounds Using a Cardiac Spheroid-on-a-Chip Device2018In: Bioengineering, E-ISSN 2306-5354, Vol. 5, no 2, p. 1-13, article id 36Article in journal (Refereed)
    Abstract [en]

    Three-dimensional (3D) models with cells arranged in clusters or spheroids have emerged as valuable tools to improve physiological relevance in drug screening. One of the challenges with cells cultured in 3D, especially for high-throughput applications, is to quickly and non-invasively assess the cellular state in vitro. In this article, we show that the number of cells growing out from human induced pluripotent stem cell (hiPSC)-derived cardiac spheroids can be quantified to serve as an indicator of a drug’s effect on spheroids captured in a microfluidic device. Combining this spheroid-on-a-chip with confocal high content imaging reveals easily accessible, quantitative outgrowth data. We found that effects on outgrowing cell numbers correlate to the concentrations of relevant pharmacological compounds and could thus serve as a practical readout to monitor drug effects. Here, we demonstrate the potential of this semi-high-throughput “cardiac cell outgrowth assay” with six compounds at three concentrations applied to spheroids for 48 h. The image-based readout complements end-point assays or may be used as a non-invasive assay for quality control during long-term culture.

  • 228.
    Claesson, Cim
    University of Skövde, School of Life Sciences.
    Is Multiplex Ligation-dependent Probe Amplification a good method for screening formalin fixed paraffin embedded neuroblastoma tumors?2011Independent thesis Basic level (degree of Bachelor), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Neuroblastoma is one of the most enigmatic solid tumors for scientists and pediatric oncologists. Neuroblastoma is primary a childhood form of cancer, consisting of neuroectodermal cells that originate from the neural crest and is destined for the  adrenal medulla and sympathetic nervous system. The Neuroblastoma group at The University of Gothenburg received formalin-fixed paraffin-embedded  tumor samples from Vietnam and this project was to examine if the quality of the DNA from, is good enough to run comparative genome hybridization array experiment  on by using a cheaper technique Multiplex  Ligation-dependent Probe Amplification   technique. Multiplex Ligation-dependent Probe Amplification (MRC Holland) is a multiplex PCR method that can detect abnormalities such as deletions and amplifications. By using probes consisting of one short synthetic arm with a PCR primer sequence Y at the 3´end, and one long probe with a stuffer sequence, and a PCR primer sequence X at the 5´end that can hybridize and ligate. If these probes ligate it is possible to amplify them by PCR just using specific primers for the X and Y sequences. The resulting amplification products can then be analyzed bycapillary electrophoresis. These patient that the DNA was derived from had all stage 4  neuroblastoma, and that is why they all present many aberrations. Among the fascinating data from this experiment, there are many patients with both 11q  deletions and has an extreme amplification of MYCN. In Sweden only a few cases has been discovered. In this material even though all patients are stage 4 patients, 16 have this combination.   

  • 229.
    Claesson, Terese
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Women's and Children's Health.
    Optimization of immunofluorence-based methods to detect anti-nuclear antibodies2015Independent thesis Basic level (professional degree), 10 credits / 15 HE creditsStudent thesis
  • 230.
    Claesson, Thomas
    Umeå University, Faculty of Medicine, Department of Clinical Microbiology, Biomedical Laboratory Science.
    Bärextrakts effekt på trombocytfunktion: Nyuppsatt metod med helblodsaggregometri2013Independent thesis Basic level (professional degree), 10 credits / 15 HE creditsStudent thesis
  • 231.
    Classon, Lisa
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Atypiskt terminalt komplementkomplex: Kvantifiering av in vivo-nivåer av atypiskt terminalt komplementkomplex under normala och patofysiologiska betingelser2018Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    The late steps of complement activation involves a cleavage of complement protein C5, to C5a and C5b, which initiates the formation of terminal complement complex (TCC). The final complex is referred to as the membrane-attack-complex (MAC) which forms cytotoxic pores in, inter alia, gram-negative bacteria. The formation of MAC can be inhibited by endogenous regulators and the TCC is then released as a soluble complex, sC5b-9, in plasma. In the degree project, another type of TCC was studied, which in previous studies had shown to form independently of C3 and C5 convertases when serum was acidified to pH <7.0 in vitro. The purpose of the study was to investigate whether this atypical TCC (aTCC) was formed in piglets, which in a model of meconium aspiration syndrome (MAS), received a reduced systemic pH in vivo. The purpose was also to establish an ELISA for analyzing aTCC. Sandwich ELISA, with monoclonal anti-C5a / C5a (desArg) (clone T13/9) as a capture antibody and monoclonal anti-C9 (clone aE11) as a detection antibody, was used to analyse aTCC in plasma samples from 18 MAS piglets, and in control samples consisting of pig serum acidified to pH 6.8 and 6.4 in vitro. The amount of aTCC in the control samples increased when the pH was lowered, but the content of aTCC in the plasma samples decreased over the course of the MAS study. When the relative change in aTCC was related to the final pH of the MAS pigs, a significant relationship could be seen (p = 0.02) which showed that a major change in the aTCC coincided with a lower final pH. aTCC were generally higher in plasma samples compared with control samples, which could be due to differences in plasma vs serum for aTCC or that the samples came from pigs of different age and weight. Lack of pig-specific standard and negative control as well as low signal to noise ratio contribute to sources of error for the analysis and this requires continued optimization.

  • 232.
    Clausson, Carl-Magnus
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Molecular tools.
    Making Visible the Proximity Between Proteins2014Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Genomic DNA is the template of life - the entity which is characterized by a self-sustaining anatomical development, regulated signaling processes, the ability to reproduce and to respond to stimuli. Through what is classically known as the central dogma, the genome is transcribed into mRNA, which in turn is translated into proteins. The proteins take part in most, if not all, cellular processes, and it is by unraveling these processes that we can begin to understand life and disease-causing mechanisms.

    In vitro and in vivo assays are two levels at which protein communication may be studied, and which permit manipulation and control over the proteins under investigation. But in order to retrieve a representation of the processes as close to reality as possible, in situ analysis may instead be applied as a complement to the other two levels of study. In situ PLA offers the ability to survey protein activity in tissue samples and primary cell lines, at a single cell level, detecting single targets in their natural unperturbed environment.  

    In this thesis new developments of the in situ PLA are described, along with a new technique offering in situ enzyme-free detection of proximity between biomolecules.

    The dynamic range of in situ PLA has now been increased by several orders of magnitude to cover analogous ranges of protein expression; the output signals have been modified to offer a greater signal-to-noise ratio and to limit false-positive-rates while also extending the dynamic range further; simultaneous detection of multiple protein complexes is now possible; proximity-HCR is presented as a robust and inexpensive enzyme-free assay for protein complex detection.

    The thesis also covers descriptions on how the techniques may be simultaneously applied, also together with other techniques, for the multiple data-point acquisition required by the emerging realm of systems biology. A future perspective is presented for how much more information may be simultaneously acquired from tissue samples to describe biomolecular interactions in a new manner. This will allow new types of biomarkers and drugs to be discovered, and a new holistic understanding of life.

  • 233.
    Cocha, Laura Romina
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Metodutveckling för prövning av lektiners påverkan på patogena svampar2015Independent thesis Basic level (professional degree), 180 HE creditsStudent thesis
  • 234. Cornes, Michael
    et al.
    van Dongen-Lases, Edmée
    Grankvist, Kjell
    Umeå University, Faculty of Medicine, Department of Medical Biosciences, Clinical chemistry.
    Ibarz, Mercedes
    Kristensen, Gunn
    Lippi, Giuseppe
    Nybo, Mads
    Simundic, Ana-Maria
    Order of blood draw: Opinion Paper by the European Federation for Clinical Chemistry and Laboratory Medicine (EFLM) Working Group for the Preanalytical Phase (WG-PRE)2017In: Clinical Chemistry and Laboratory Medicine, ISSN 1434-6621, E-ISSN 1437-4331, Vol. 55, no 1, p. 27-31Article in journal (Refereed)
    Abstract [en]

    It has been well reported over recent years that most errors within the total testing process occur in the pre-analytical phase (46%-68.2%), an area that is usually outside of the direct control of the laboratory and which includes sample collection (phlebotomy). National and international (WHO, CLSI) guidelines recommend that the order of draw of blood during phlebotomy should be blood culture/sterile tubes, then plain tubes/gel tubes, then tubes containing additives. This prevents contamination of sample tubes with additives from previous tubes that could cause erroneous results. There have been a number of studies recently looking at whether order of draw remains a problem with modern phlebotomy techniques and materials, or it is an outdated practice followed simply because of historical reasons. In the following article, the European Federation of Clinical Chemistry and Laboratory Medicine Working Group for the Preanalytical Phase (EFLM WG-PRE) provides an overview and summary of the literature with regards to order of draw in venous blood collection. Given the evidence presented in this article, the EFLM WG-PRE herein concludes that a significant frequency of sample contamination does occur if order of draw is not followed during blood collection and when performing venipuncture under less than ideal circumstances, thus putting patient safety at risk. Moreover, given that order of draw is not difficult to follow and knowing that ideal phlebotomy conditions and protocols are not always followed or possible, EFLM WG-PRE supports the continued recommendation of ensuring a correct order of draw for venous blood collection.

  • 235.
    Cornet, Ronald
    et al.
    Linköping University, Department of Biomedical Engineering, Division of Biomedical Engineering. Linköping University, Faculty of Science & Engineering. Univ Amsterdam, Netherlands.
    Hill, Carly
    Univ Amsterdam, Netherlands.
    de Keizer, Nicolette
    Univ Amsterdam, Netherlands.
    Comparison of Three English-to-Dutch Machine Translations of SNOMED CT Procedures2017In: MEDINFO 2017: PRECISION HEALTHCARE THROUGH INFORMATICS, IOS PRESS , 2017, Vol. 245, p. 848-852Conference paper (Refereed)
    Abstract [en]

    Dutch interface terminologies are needed to use SNOMED CT in the Netherlands. Machine translation may support in their creation. The aim of our study is to compare different machine translations of procedures in SNOMED CT. Procedures were translated using Google Translate, Matecat, and Thot. Google Translate and Matecat are tools with large but general translation memories. The translation memory of Thot was trained and tuned with various configurations of a Dutch translation of parts of SNOMED CT, a medical dictionary and parts of the UMLS Metathesaurus. The configuration with the highest BLEU score, representing closeness to human translation, was selected. Similarity was determined between Thot translations and those by Google and Matecat. The validity of translations was assessed through random samples. Google and Matecat translated similarly in 85.4% of the cases and generally better than Thot. Whereas the quality of translations was considered acceptable, machine translations alone are yet insufficient.

  • 236.
    Croce, Daniel
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Women's and Children's Health, Obstetrics and Gynaecology.
    Investigation of Syndecan-1 Ectodomain Isolated from Chinese Hamster Ovary (CHO) Cell Culture Medium2015Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Syndecan-1 is a cell surface proteoglycan which participates in cell adhesion, differentiation, motility, morphogenesis and intracellular signaling. The two glycosaminoglycans heparan sulfate and chondroitin sulfate are covalently attached to the ectodomain of syndecan-1 via a tetra saccharide linkage sequence. However, the ectodomain can be modified having only one or neither of the glycosaminglycans attached. The glycosaminoglycans are capable of binding ligands such as fibroblast growth factors (FGFs) and support activation of receptors. The ectodomain is proteolytically cleaved from the cell surface by metalloproteinases in a process known as shedding. Shedding turns the ectodomain into a soluble effector which can stimulate other cells in the surroundings by delivering growth factors and also translocate into cells through endocytosis. In this study the aim was to find out if a modified ectodomain, which only contains chondroitin sulfate, could support intracellular signaling in the absence of heparan sulfate. The aim was also to find out whether a modified ectodomain could translocate into the cell. The methods used were cell culturing, isolation and purification of syndecan-1 ectodomain, cell signaling and immunohistochemistry. It was found that modified shed syndecan-1 ectodomain was able to support intracellular signaling almost to the same degree as wild type syndecan-1 ectodomain. This may suggest that heparan sulfate does not have to be present on the ectodomain to support intracellular signaling, although the signal is slightly higher when present. When trying to detect translocation of the ectodomain the results were too uncertain and further research is required.

  • 237.
    Cronskär, Marie
    et al.
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Quality Technology and Management, Mechanical Engineering and Mathematics.
    Bäckström, Mikael
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Quality Technology and Management, Mechanical Engineering and Mathematics.
    Modeling of fractured clavicles and reconstruction plates using CAD, finite element analysis and real musculoskeletal forces input2013In: WIT Transactions on Biomedicine and Health, WIT Press, 2013, p. 235-243Conference paper (Refereed)
    Abstract [en]

    This study focuses on the treatment options for clavicle fractures, more specifically the cases with a need for internal fixation: non-unions and some complex fractures. Enhancing the understanding of the loading of the bone and fixation device enables treatment options to be improved. The aim of the study was to develop a method for the realistic simulation of stresses and displacements in the bone and fixation device and to use this method to make comparisons between a conventional reconstruction plate and a customized plate, designed from patient-specific computed tomography (CT) data. In an earlier study, a finite element (FE) mesh of the clavicle geometry was created from CT data, subjected to muscle forces and other boundary conditions from a multibody musculoskeletal model and imported into the FE solver. In this study, a solid 3D model of the same clavicle geometry was created and the mesh was replaced by the solid model to make the FE-model more suitable for the comparison of different plates. An LCP Reco-Plate 3.5 straight, 6 holes (by Synthes) was compared with a customized plate which was designed to follow the anatomy of the bone. The LCP-Reco plate has tapered reconstruction segments throughout the plate to allow for the plate reshaping during surgery. The customized plate was designed without such segments and with a lower width than the LCP plate. The two different plates showed stresses and displacements of similar magnitudes. The customized plate had a more even stress distribution while the LCP plate had higher stress concentrations in the middle of the plate and on the edges of the tapered reconstruction segments. To the authors' best knowledge, this is the first FE model of a clavicle bone with plate and it may, upon further development, serve as a useful instrument for improved clavicle fixation.

  • 238.
    Cronskär, Marie
    et al.
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Engineering and Sustainable Development.
    Rännar, Lars-Erik
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Engineering and Sustainable Development.
    Bäckström, Mikael
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Engineering and Sustainable Development.
    Implementation of digital design and solid free-form fabrication for customization of implants in trauma orthopaedics2012In: Journal of medical and biological engineering, ISSN 1609-0985, Vol. 32, no 2, p. 91-96Article in journal (Refereed)
    Abstract [en]

    Bone plates for the fixation of complex fractures in proximity to joints often have to be reshaped to follow the bone contour. Good adhesion of the screws in areas where the bone is osteoporotic is also a challenge. One possible solution to these issues is to tailor-make plates by creating a digital three-dimensional model of the fracture from a computed tomography (CT) scan, digitally reducing the fracture, designing a plate, and finally manufacturing it directly from the digital model with solid free-form fabrication (SFF) technology. This study designs a custom plate for a distal tibia fracture, and investigates and refines the procedure from the CT scan to the final implant, with the aim of making it usable in trauma orthopaedics. The bone plate is manufactured using electron beam melting (EBM) technology. The challenges of bone plate design using digitalization and SFF are discussed. The virtual models created by the engineer while digitally reducing the fracture and modeling the plate are valuable for the physician while planning the surgery. A combination of surgery planning and digital plate design improves the surgeon's preparations and ensures correspondence between the plan and the designed implant. The proposed procedure, with the approximate required time in brackets, includes the separation of bone in the DICOM file (60 min), the reduction of fracture (5-30 min), revision (30 min), modelling of the plate (30-120 min), confirmation (30 min), manufacturing with SFF (10 h), post-processing (60 min), and finally cleaning and sterilization (90 min). The whole procedure requires about three working days.

  • 239.
    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.

  • 240.
    Curiche, Natalia
    Umeå University, Faculty of Medicine, Department of Clinical Microbiology, Biomedical Laboratory Science.
    Visualization of Propionibacterium acnes in Patients Diagnosed with Acne Vulgaris. - Propionibacterium acnes Detected with Immuno­fluorescence and Fluorescence in situ Hybridization.2011Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
  • 241.
    Dadarman, Mina
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Möjlig mekanism bakom antiinflammatorisk polymer, polyvinylalkoholkarbazat: Studier av apoptos och viabilitet i cellkultur2018Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
  • 242.
    Dagsberg, Jacob
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Förekomst av aviärt influensavirus bland vilda fåglar provtagna vid Ottenby fågelstation under 2017: Detektion och fylogenetisk analys av neuraminidas subtyp 6-virus2018Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Avian influenza virus (AIV) is divided into subtypes based on two glycoproteins on its surface. Among birds there are 16 subtypes of hemagglutinin (H) and 9 subtypes of neuraminidase (N). Some H subtypes can mutate into highly pathogenic viruses and cause deadly infections. One such highly pathogenic virus was reported in northern Europe in 2017. Spread amongst highly pathogenic H5 is well mapped out. Reverse transcription followed by amplification in real time is used to detect neuraminidase in AIV, based on synthesis of complementary DNA, which gets amplified and detected using fluorescent probe. Sanger sequencing of neuraminidase coding gene segments is used to verify the results from RT-qPCR screening and analysing phylogenetic relationship. To contribute with knowledge about neuraminidase subtype 6, RT-qPCR analysis was used on 282 AIV positive samples from wild birds, sampled at Ottenby bird station in 2017. Gene segments coding for hemaglutinin and neuraminidase among viruses in N6 positive samples was sequenced to validate the N6-RT-qPCR analyses, determine H subtype and to analyse phylogenetic relationship among N6-sequences. The RT-qPCR resulted in 37 N6 positive samples where 26 of these was confirmed as N6 with traditional PCR and sequencing. AIV from the analyses occurred in subtype constellations of: 14 H1N6, 3 H3N6, 8 H4N6 and 1 H5N6. Three samples failed to give H subtype, three different samples gave no N6 sequence. Detected H5N6 was low pathogenic. The phylogenetic analysis showed that AIV N6 sequences from Ottenby, in tandem with sequences from GenBank, formed four genotypes. N6 sequences from two viruses sequenced in this study, associated with subtypes H3N6 and H1N6 formed genotype two, together with four H5N6, possibly high pathogenic viruses from Japan.

  • 243.
    Dahlberg, Ida
    Umeå University, Faculty of Medicine, Department of Clinical Microbiology, Biomedical Laboratory Science.
    Förekomsten av Propionibacterium acnes är låg hos patienter med Rosacea: En studie av sambandet mellan Propionibacterium acnes och Rosacea med immunofluorescens2011Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
  • 244.
    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

  • 245. Dahlström, Märta
    et al.
    Forsström, Daniel
    Johannesson, Malin
    Huque-Andersson, Yasmin
    Björk, Marie
    Silfverplatz, Erik
    Sanin, Andrei
    Schaal, Wesley
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences.
    Pelcman, Benjamin
    Forsell, Pontus K A
    Development of a fluorescent intensity assay amenable for high-throughput screening for determining 15-lipoxygenase activity.2010In: Journal of Biomolecular Screening, ISSN 1087-0571, E-ISSN 1552-454X, Vol. 15, no 6, p. 671-9Article in journal (Refereed)
    Abstract [en]

    15-Lipoxygenase-1 catalyzes the introduction of molecular oxygen into polyunsaturated fatty acids to form a lipid hydroperoxide. The authors have developed an assay for the detection of lipid hydroperoxides formed by human 15-lipoxygenase (15-LO) in enzyme or cellular assays using either a 96-well or a 384-well format. The assays described take advantage of the ability of lipid hydroperoxides to oxidize nonfluorescent diphenyl-1-pyrenylphosphine (DPPP) to a fluorescent phosphine oxide. Oxidation of DPPP yields a fluorescent compound, which is not sensitive to temperature and is stable for more than 2 h. The assay is sensitive toward inhibition and robust with a Z' value of 0.79 and 0.4 in a 96- and 384-well format, respectively, and thus amenable for high-throughput screening. The utility of DPPP as a marker for 15-lipoxygenase activity was demonstrated with both enzyme- and cell-based assays for the identification of hits and to determine potency by IC(50) determinations.

  • 246.
    Dahmani, Younes
    Umeå University, Faculty of Medicine, Department of Clinical Microbiology, Biomedical Laboratory Science.
    Uttryck av Nfr2 och dess kliniska roll i klarcellig njurcancer2012Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
  • 247.
    Dakhil, Aseel
    Kristianstad University, School of Education and Environment.
    HLA-typning: Jämförelse mellan mastermix med tillsatt eller inkluderat Ampli Taq DNA polymerase2016Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Transplantation is based on a satisfactory matching of the patient and donor genes for Human Leukocyte Antigen (HLA), which increases the chance of a successful transplantation. HLA gives individual cell surface markers. The Major Histocompatibility Complex (MHC) region, encoding HLA in humans, is the most polymorphic in the human genome. The genes are located on chromosome six and consists of 200 genes. Those genes encode protein products essential for the acquired immune system. MHC molecule’s role is to represent foreign substance for B- and T-lymphocytes. MHC is an important system as it contributes to the activation of the immune system to combat viruses, bacteria, parasites and cancer cells. HLA-typing is determined through certain antigens in the HLA system. The classical transplantation antigens are HLA-A, -B, -C, -DR, -DQ and -DP. By amplifying the DNA with sequence specific primers in the Polymerase Chain Reaction (PCR), the amplicons can be detected and alleles present in the patient genome can be determined. The purpose of this study was to compare occurrence of non-specific DNA binding using master mix where Ampli Taq DNA polymerase is added and master mix with polymerase included in the PCR. Samples from 16 patients were tested with both master mix- solutions. The analyses were performed with primer plates for HLA-A, HLA-B and HLA-DRP1. The results showed that the master mix with Taq polymerase included should be applied, because it gave clearer specific band, better image quality and gave weaker and approximately 30% fewer non- specific DNA binding compared to the master mix with added Taq polymerase.

  • 248.
    Dalsätt, Johan
    Umeå University, Faculty of Medicine, Department of Clinical Microbiology, Biomedical Laboratory Science. Umeå University, Faculty of Medicine, Department of Medical Biosciences, Pathology.
    Utvärdering av olika RNA-preparationsmetoder samt karakterisering av KLK7-uttryck i prostatacancer-relaterade cellinjer och tumörer2015Independent thesis Basic level (professional degree), 10 credits / 15 HE creditsStudent thesis
  • 249.
    Dammström, Magdalena
    Örebro University, School of Health and Medical Sciences, Örebro University, Sweden.
    Användning av Small interfering RNA med syftet att minska uttrycket av insulin like growth factor-1 receptor hos melanomceller2012Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
  • 250.
    Danielsson, Micaela
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Bindningsmönster av aviärt influensa A-virus till mag-tarmkanalen hos andfåglar2018Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Influenza A virus is a major human disease, with recurrent seasonal outbreaks that cause up to 500,000 deaths worldwide every year. The natural reservoir and home to most subtypes of the virus is wild water birds. To get a better understanding of how so many different viruses can infect wild birds, the binding pattern of the virus to the host can be studied with the virus histochemistry technique. The purpose of this work was to investigate the binding pattern of avian influenza virus, subtype H4, H9, H13 and H16, to gastrointestinal tract tissues from different species of ducks to see which cells and in what quantity these viruses bind to. The techniques that have been used are propagation of the virus by culturing embryonated chicken eggs, sucrose gradient purification, formalin inactivation and then fluorescein isothiocyanate (FITC) labeling. The titre of the virus was measured by hemagglutination assay, showing the result that the titre after harvesting eggs for H4 was: 256 HAU/100 μl, H9: 512 HAU/100 μl, H13: 384 HAU/100 μl and for H16: 768 HAU/100 μl. FITC-labeled virus titer was measured to H4: 15 360 HAU/100 μl, H9: 30 720 HAU/100 μl, H13: 163 840 HAU/100 μl and H16: 81 920 HAU/100 μl. Virus histochemistry was not performed and therefore the result of the binding pattern is still unknown and the question of this work unanswered with in the time limit of this thesis. What is expected from the result, however, is that subtype H4 and H9, common to found in birds ducks, will bind to epithelial cells in the gastrointestinal tract of ducks while subtype H16 and H13, which have only been found in isolate from ducks in a few cases, are not expected bind to the gastrointestinal tract of ducks to the same extent.

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