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  • 1.
    Ayoglu, Burcu
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Affinity Arrays for Profiling Proteins and Autoantibody Repertoires2014Doctoral thesis, comprehensive summary (Other academic)
  • 2.
    Bai, Yunpeng
    et al.
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Weibull, Emilie
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Jönsson, Håkan
    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.
    Interfacing picoliter droplet microfluidics with addressable microliter compartments using fluorescence activated cell sorting2014In: Sensors and actuators. B, Chemical, ISSN 0925-4005, E-ISSN 1873-3077, Vol. 194, p. 249-254Article in journal (Refereed)
    Abstract [en]

    Droplet microfluidic platforms have, while enabling high-throughput manipulations and the assaying of single cell scale compartments, been lacking interfacing to allow macro scale access to the output from droplet microfluidic operations. Here, we present a simple and high-throughput method for individually directing cell containing droplets to an addressable and macro scale accessible microwell slide for downstream analysis. Picoliter aqueous droplets containing low gelling point agarose and eGFP expressing Escherichia coli (E. coli) are created in a microfluidic device, solidified to agarose beads and transferred into an aqueous buffer. A Fluorescence activated cell sorter (FACS) is used to sort agarose beads containing cells into microwells in which the growth and expansion of cell colonies is monitored. We demonstrate fast sorting and high accuracy positioning of sorted 15 μm gelled droplet agarose beads into microwells (14 × 48) on a 25 mm × 75 mm microscope slide format using a FACS with a 100 μm nozzle and an xy-stage. The interfacing method presented here enables the products of high-throughput or single cell scale droplet microfluidics assays to be output to a wide range of microtiter plate formats familiar to biological researchers lowering the barriers for utilization of these microfluidic platforms.

  • 3. Bao, D.
    et al.
    Zou, Zhuo
    KTH, School of Information and Communication Technology (ICT), Industrial and Medical Electronics. KTH, School of Information and Communication Technology (ICT), Centres, VinnExcellence Center for Intelligence in Paper and Packaging, iPACK.
    Huan, Y.
    Zhai, Chuanying
    KTH, School of Information and Communication Technology (ICT), Industrial and Medical Electronics. KTH, School of Information and Communication Technology (ICT), Centres, VinnExcellence Center for Intelligence in Paper and Packaging, iPACK.
    Bagaian, T.
    Tenhunen, Hannu
    KTH, School of Information and Communication Technology (ICT), Industrial and Medical Electronics. KTH, School of Information and Communication Technology (ICT), Centres, VinnExcellence Center for Intelligence in Paper and Packaging, iPACK.
    Källbäck, B.
    Zheng, Lirong
    KTH, School of Information and Communication Technology (ICT), Industrial and Medical Electronics. KTH, School of Information and Communication Technology (ICT), Centres, VinnExcellence Center for Intelligence in Paper and Packaging, iPACK. State Key Laboratory of ASIC and System, Fudan University, Shanghai, China .
    A smart catheter system for minimally invasive brain monitoring2015In: Proceedings of the International Conference on Biomedical Electronics and Devices, SciTePress, 2015, p. 198-203Conference paper (Refereed)
    Abstract [en]

    This paper demonstrates a smart catheter system with intracranial pressure (ICP) and temperature sensing capability which is designed for real-time monitoring in traumatic brain injury (TBI) therapy. It uses a single flexible catheter with a 1 mm (3 Fr) diameter that integrates electrodes and sophisticated silicon chip on flexible substrates, enabling multimodality monitoring of physiological signals. A micro-electromechanical-system (MEMS) catheter pressure sensor is mounted on the distal end. It can be used for detecting both pressure and temperature by different switch configurations, which minimizes the size of catheter and reduces the cost. The interconnects (signalling conductors) are printed on a bio-compatible flexible substrate, and the sensor is interfaced with an embedded electronic system at the far-end. The electronic system consists of analog front end with analog-to-digital converter (ADC), a microcontroller, and data interface to the hospital infrastructure with a graphical user interface (GUI). The overall smart catheter system achieves a pressure sensing root mean square error (RMSE) of ±1.5 mmHg measured from 20 mmHg to 300 mmHg above 1 atm and a temperature sensing RMSE of ±0.08°C measured from 32°C to 42°C. The sampling rate can be up to 10S/s. The in vivo performance is demonstrated in laboratory animals.

  • 4.
    Bauer, Margit
    et al.
    Med Univ Graz, Dept Obstet & Gynecol, Graz, Austria..
    Mazza, Edoardo
    Swiss Fed Inst Technol, Dept Mech & Proc Engn, Zurich, Switzerland..
    Jabareen, Mahmood
    Swiss Fed Inst Technol, Dept Mech & Proc Engn, Zurich, Switzerland..
    Sultan, Leila
    Univ Zurich Hosp, Dept Obstet & Gynecol, CH-8091 Zurich, Switzerland..
    Bajka, Michael
    Univ Zurich Hosp, Dept Obstet & Gynecol, CH-8091 Zurich, Switzerland..
    Lang, Uwe
    Med Univ Graz, Dept Obstet & Gynecol, Graz, Austria..
    Zimmermann, Roland
    Univ Zurich Hosp, Dept Obstet & Gynecol, CH-8091 Zurich, Switzerland..
    Holzapfel, Gerhard A.
    KTH, School of Electrical Engineering (EES).
    In Vivo Biomechanical Testing of the Human Uterine Cervix in Pregnancy Using an Aspiration Device2009In: Reproductive Sciences, ISSN 1933-7191, E-ISSN 1933-7205, Vol. 16, no 3, p. 197A-197AArticle in journal (Other academic)
  • 5.
    Bjällmark, Anna
    KTH, School of Technology and Health (STH), Medical Engineering.
    New ultrasonographic approaches to monitoring cardiac and vascular function2009Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Atherosclerotic cardiovascular disease is the leading cause of death worldwide. To decrease mortality and morbidity in cardiovascular disease, the development of accurate, non-invasive methods for early diagnosis of atherosclerotic cardiac and vascular engagement is of considerable clinical interest. Cardiovascular ultrasound imaging is today the cornerstone in the routine evaluation of cardiovascular function and recent development has resulted in two new techniques, tissue velocity imaging (TVI) and speckle tracking, which allow objective quantification of cardiovascular function. TVI and speckle tracking are the basis for three new approaches to cardiac and vascular monitoring presented in this thesis: wave intensity wall analysis (WIWA), two-dimensional strain imaging in the common carotid artery, and the state diagram of the heart.

     

    WIWA uses longitudinal and radial strain rate as input for calculations of wave intensity in the arterial wall. In this thesis, WIWA was validated against a commercially available wave intensity system, showing that speckle tracking-derived strain variables can be useful in wave intensity analysis. WIWA was further tested in patients with end stage renal disease and documented high mortality in cardiovascular disease. The latter study evaluated the effects of a single session of hemodialysis using WIWA and TVI variables and showed improved systolic function after hemodialysis. The results also indicated that preload-adjusted early systolic wave intensity obtained by the WIWA system may contribute in the assessment of left ventricular contractility in this patient category. Two-dimensional strain imaging in the common carotid artery is a new approach showing great potential to detect age-dependent differences in mechanical properties of the common carotid artery. Among the measured strain variables, global circumferential strain had the best discriminating performance and appeared to be superior to conventional measures of arterial stiffness such as elastic modulus and β stiffness index. The state diagram is a visualisation tool that provides a quantitative overview of the temporal interrelationship of mechanical events in the left and right ventricles. Case examples and a small clinical study showed that state diagrams clearly visualize cardiac function and can be useful in the detection of non ST-elevation myocardial infarction (NSTEMI).

     

    Even though WIWA, two-dimensional strain imaging in the common carotid artery and the state diagram show potential to be useful in the evaluation of cardiovascular function, there still remains a considerable amount of work to be done before they can be used in the daily clinical practice.

  • 6. Bora, Kangkana
    et al.
    Chowdhury, Manish
    KTH, School of Technology and Health (STH).
    Mahanta, Lipi B.
    Kundu, Malay Kumar
    Das, Anup Kumar
    Automated classification of Pap smear images to detect cervical dysplasia2017In: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 138, p. 31-47Article in journal (Refereed)
    Abstract [en]

    Background and objectives: The present study proposes an intelligent system for automatic categorization of Pap smear images to detect cervical dysplasia, which has been an open problem ongoing for last five decades. Methods: The classification technique is based on shape, texture and color features. It classifies the cervical dysplasia into two-level (normal and abnormal) and three-level (Negative for Intraepithelial Lesion or Malignancy, Low-grade Squamous Intraepithelial Lesion and High-grade Squamous Intraepithelial Lesion) classes reflecting the established Bethesda system of classification used for diagnosis of cancerous or precancerous lesion of cervix. The system is evaluated on two generated databases obtained from two diagnostic centers, one containing 1610 single cervical cells and the other 1320 complete smear level images. The main objective of this database generation is to categorize the images according to the Bethesda system of classification both of which require lots of training and expertise. The system is also trained and tested on the benchmark Herlev University database which is publicly available. In this contribution a new segmentation technique has also been proposed for extracting shape features. Ripplet Type I transform, Histogram first order statistics and Gray Level Co-occurrence Matrix have been used for color and texture features respectively. To improve classification results, ensemble method is used, which integrates the decision of three classifiers. Assessments are performed using 5 fold cross validation. Results: Extended experiments reveal that the proposed system can successfully classify Pap smear images performing significantly better when compared with other existing methods. Conclusion: This type of automated cancer classifier will be of particular help in early detection of cancer.

  • 7. Bose, Indranil
    et al.
    Ohlander, Anna
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Kutter, Christoph
    Russom, Aman
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    DNA Analysis on integrated all foil based microdevicesManuscript (preprint) (Other academic)
  • 8.
    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.

  • 9.
    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%.

  • 10.
    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.

  • 11.
    Dijkstra, Erik J.
    et al.
    KTH, School of Engineering Sciences (SCI), Mechanics, Biomechanics.
    Gutierrez-Farewik, Elena M.
    KTH, School of Engineering Sciences (SCI), Mechanics, Biomechanics. Karolinska Institutet, Stockholm, Sweden.
    Computation of ground reaction force using Zero Moment Point2015In: Journal of Biomechanics, ISSN 0021-9290, E-ISSN 1873-2380, Vol. 48, no 14, p. 3776-3781Article in journal (Refereed)
    Abstract [en]

    Motion analysis is a common clinical assessment and research tool that uses a camera system or motion sensors and force plates to collect kinematic and kinetic information of a subject performing an activity of interest. The use of force plates can be challenging and sometimes even impossible. Over the past decade, several computational methods have been developed that aim to preclude the use of force plates. Useful in particular for predictive simulations, where a new motion or change in control strategy inherently means different external contact loads. These methods, however, often depend on prior knowledge of common observed ground reaction force (GRF) patterns, are computationally expensive, or difficult to implement. In this study, we evaluated the use of the Zero Moment Point as a computationally inexpensive tool to obtain the GRFs for normal human gait. The method was applied on ten healthy subjects walking in a motion analysis laboratory and predicted GRFs are evaluated against the simultaneously measured force plate data. Apart from the antero-posterior forces, GRFs are well-predicted and errors fall within the error ranges from other published methods. Joint extension moments were underestimated at the ankle and hip but overestimated at the knee, attributable to the observed discrepancy in the predicted application points of the GRFs. The computationally inexpensive method evaluated in this study can reasonably well predict the GRFs for normal human gait without using prior knowledge of common gait kinetics.

  • 12. Downs, J.
    et al.
    Velupillai, Sumithra
    KTH, School of Electrical Engineering and Computer Science (EECS), Theoretical Computer Science, TCS.
    George, G.
    Holden, R.
    Kikoler, M.
    Dean, H.
    Fernandes, A.
    Dutta, R.
    Detection of Suicidality in Adolescents with Autism Spectrum Disorders: Developing a Natural Language Processing Approach for Use in Electronic Health Records2017In: Advances in Printing and Media Technology, ISSN 0892-2284, E-ISSN 1942-597X, Vol. 2017, p. 641-649Article in journal (Refereed)
    Abstract [en]

    Over 15% of young people with autism spectrum disorders (ASD) will contemplate or attempt suicide during adolescence. Yet, there is limited evidence concerning risk factors for suicidality in childhood ASD. Electronic health records (EHRs) can be used to create retrospective clinical cohort data for large samples of children with ASD. However systems to accurately extract suicidality-related concepts need to be developed so that putative models of suicide risk in ASD can be explored. We present a systematic approach to 1) adapt Natural Language Processing (NLP) solutions to screen with high sensitivity for reference to suicidal constructs in a large clinical ASD EHR corpus (230,465 documents), and 2) evaluate within a screened subset of 500 patients, the performance of an NLP classification tool for positive and negated suicidal mentions within clinical text. When evaluated, the NLP classification tool showed high system performance for positive suicidality with precision, recall, and F1 scores all > 0.85 at a document and patient level. The application therefore provides accurate output for epidemiological research into the factors contributing to the onset and recurrence of suicidality, and potential utility within clinical settings as an automated surveillance or risk prediction tool for specialist ASD services.

  • 13. Ericsson, Anders B.
    et al.
    Kronander, Håkan
    Söderqvist, Emil
    Vaage, Jarle
    Brodin, Lars-Åke
    Correlation between a Mid-ventricular Volume Segment and Global Left Ventricular Volume Measured by the Conductance Catheter2001In: Scandinavian Cardiovascular Journal, ISSN 1401-7431, E-ISSN 1651-2006, Vol. 35, no 2, p. 129-135Article in journal (Refereed)
    Abstract [en]

    Objectives-To investigate whether acute volume changes in single volume segments of the left ventricle can be correlated with global volume changes. If so, changes in global volume might be predicted from changes in segmental volumes.

    Design-Volume changes were recorded in six pigs in five intraventricular segments, from apex to heart base, using the conductance catheter (at baseline, after 60 min of apical ischaemia, during preload reduction and afterload increase). A computer algorithm was created to calculate the instantaneous absolute difference between the curve shape of global and normalized segmental volume as a percentage of global stroke volume.

    Results-For a mid-cardiac volume segment constituting 34 (14-39)% [median (range)] of global stroke volume, the mean difference over a cardiac cycle was 4 (1-8)% at baseline. Apical ischaemia resulted in apical dyskinesia, but did not influence the mid-cardiac segment.

    Conclusions-The volume curve from a segment at mid-cardiac level seems to be a good estimator of the global volume curve, thus giving a foundation for estimation of global volume changes from such a segment.

  • 14.
    Eriksson, Magnus G.
    KTH, School of Industrial Engineering and Management (ITM), Machine Design (Dept.).
    A virtual and haptic milling surgery simulator2006Report (Other academic)
  • 15.
    Eriksson, Magnus G.
    KTH, School of Technology and Health (STH).
    Haptic and visual simulation of material cutting process: a study focused on bone surgery and the use of simulators for education and training2006Licentiate thesis, comprehensive summary (Other scientific)
    Abstract [en]

    A prototype of a haptic and virtual reality simulator has been developed for simulation of the bone milling and material removal process occurring in several operations, e.g. temporal bone surgery or dental milling. The milling phase of an operation is difficult, safety critical and very time consuming. Reduction of operation time by only a few percent would in the long run save society large expenses. In order to reduce operation time and to provide surgeons with an invaluable practicing environment, this licentiate thesis discusses the introduction of a simulator system to be used in both surgeon curriculum and in close connection to the actual operations.

    The virtual reality and haptic feedback topics still constitute a young and unexplored area. It has only been active for about 10-15 years for medical applications. High risk training on real patients and the change from open surgery to endoscopic procedures have enforced the introduction of haptic and virtual reality simulators for training of surgeons. Increased computer power and the similarity to the successful aviation simulators also motivate to start using simulators for training of surgical skills.

    The research focus has been twofold: 1) To develop a well working VR-system for realistic graphical representation of the skull itself including the changes resulting from milling, and 2) to find an efficient algorithm for haptic feedback to mimic the milling procedure using the volumetric Computer Tomography (CT) data of the skull. The developed haptic algorithm has been verified and tested in the simulator. The visualization of the milling process is rendered at a graphical frame rate of 30 Hz and the haptic rendering loop is updated at 1000 Hz. Test results show that the real-time demands are fulfilled. The visual and haptic implementations have been the two major steps to reach the over all goal with this research project.

    A survey study is also included where the use of VR and haptic simulators in the surgical curriculum is investigated. The study starts with a historical perspective of the VR and haptic topics and is built up by answering different questions related to this topic and the implementation of simulators at the medical centres. The questions are of general concern for those developing surgical VR and haptic simulators.

    Suggested future work includes modelling, development and validation of the haptic forces occurring in the milling process and, based on this, implementation in the simulator system. Also, further development of the simulator should be done in close cooperation with surgeons in order to get appropriate feedback for further improvements of the functionality and performance of the simulator.

  • 16.
    Eriksson, Magnus G.
    et al.
    KTH, School of Industrial Engineering and Management (ITM), Machine Design (Dept.), Mechatronics.
    Dixon, Mark R.
    SenseGraphics.
    Wikander, Jan
    KTH, School of Industrial Engineering and Management (ITM), Machine Design (Dept.), Mechatronics.
    A haptic VR milling surgery simulator - using high-resolution CT-data2006In: Studies in Health Technology and Informatics, ISSN 0926-9630, E-ISSN 1879-8365, Vol. 119, p. 138-143Article in journal (Refereed)
    Abstract [en]

    A haptic virtual reality milling simulator using high resolution volumetric data is presented in this paper. We discuss the graphical rendering performed from an iso-surface generated using marching cubes with a hierarchical storage method to optimize for fast dynamic changes to the data during the milling process. We also present a stable proxy-based haptic algorithm used to maintain a tip position on the surface avoiding haptic fall-through.

  • 17.
    Eriksson, Magnus G.
    et al.
    KTH, School of Industrial Engineering and Management (ITM), Machine Design (Dept.).
    Wikander, Jan
    KTH, School of Industrial Engineering and Management (ITM), Machine Design (Dept.).
    von Holst, Hans
    KTH, School of Technology and Health (STH), Neuronic Engineering.
    The use of virtual reality and haptic simulators for training and education of surgical skills2006In: Simulation in Healthcare: journal of the society for simulation in healthcare, ISSN 1559-2332Article in journal (Other academic)
  • 18.
    Etcheverry, Sebastian
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Laser Physics. RISE Acreo AB, Sweden.
    Russom, Aman
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Laurell, Fredrik
    KTH, School of Engineering Sciences (SCI), Applied Physics, Laser Physics.
    Margulis, Walter
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Fluidic trapping and optical detection of microparticles with a functional optical fiberIn: Optics Express, ISSN 1094-4087, E-ISSN 1094-4087Article in journal (Other academic)
    Abstract [en]

    A fiber probe is presented that traps single micro-sized particles and allows detection of their optical properties. The trapping mechanism used is based on fluid suction with a micro-structured optical fiber that has five holes along its cladding. Proof-of-principle experiments with a diluted solution of fluorescently labeled particles are performed. The fiber probe presented here may find various applications in life-science and environmental monitoring.  

  • 19.
    Etehad Tavakol, Mahnaz
    et al.
    Isfahan University of Medical Sciences, Iran.
    Fatemi, Alimohammad
    Isfahan University of Medical Sciences, Iran.
    Karbalaie, Abdolamir
    KTH, School of Technology and Health (STH), Health Systems Engineering.
    Emrani, Zahra
    Isfahan University of Medical Sciences, Iran.
    Erlandsson, Björn-Erik
    KTH, School of Technology and Health (STH), Health Systems Engineering, Systems Safety and Management.
    Nailfold Capillaroscopy in Rheumatic Diseases: Which Parameters Should Be Evaluated?2015In: BioMed Research International, ISSN 2314-6133, E-ISSN 2314-6141, Vol. 2015, article id 974530Article in journal (Refereed)
    Abstract [en]

    Video nailfold capillaroscopy (NFC), considered as an extension of the widefield technique, allows a more accurate measuring andstoring of capillary data and a better defining, analyzing, and quantifying of capillary abnormalities. Capillaroscopic study is oftenperformed on the patients suspected of having microcirculation problems such as Raynaud’s phenomenon as the main indicationfor nailfold capillaroscopy. Capillaroscopic findings based on microcirculation studies can provide useful information in the fieldsof pathophysiology, differential diagnosis, and monitoring therapy. Nailfold capillaroscopy provides a vital assessment in clinicalpractices and research; for example, its reputation in the early diagnosis of systemic sclerosis is well established and it is also usedas a classification criterion in this regard. This review focuses on the manner of performing video nailfold capillaroscopy and on acommon approach for measuring capillary dimensions in fingers and toes.

  • 20.
    Faridi, Muhammad Asim
    et al.
    KTH.
    Shahzad, Adnan Faqui
    KTH.
    Russom, Aman
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Wiklund, Martin
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
    Milliliter scale acoustophoresis based bioparticle processing platform2018In: ASME 2018 16th International Conference on Nanochannels, Microchannels, and Minichannels, ICNMM 2018, ASME Press, 2018Conference paper (Refereed)
    Abstract [en]

    Bioparticles such as mammalian cells and bacteria can be manipulated directly or indirectly for multiple applications such as sample preparation for diagnostic applications mainly up-concentration, enrichment & separation as well as immunoassay development. There are various active and passive microfluidic particle manipulation techniques where Acoustophoresis is a powerful technique showing high cell viability. The use of disposable glass capillaries for acoustophoresis, instead of cleanroom fabricated glass-silicon chip can potentially bring down the cost factor substantially, aiding the realization of this technique for real-world diagnostic devices. Unlike available chips and capillary-based microfluidic devices, we report milliliter-scale platform able to accommodate 1ml of a sample for acoustophoresis based processing on a market available glass capillary. Although it is presented as a generic platform but as a demonstration we have shown that polystyrene suspending medium sample can be processed with trapping efficiency of 87% and the up-concentration factor of 10 times in a flow through manner i.e., at 35µl/min. For stationary volume accommodation, this platform practically offers 50 times more sample handling capacity than most of the microfluidic setups. Furthermore, we have also shown that with diluted blood (0.6%) in a flow-through manner, 82% of the white blood cells (WBCs) per ml could be kept trapped. This milliliter platform could potentially be utilized for assisting in sample preparation, plasma separation as well as a flow-through immunoassay assay development for clinical diagnostic applications.

  • 21. Fornell, Anna
    et al.
    Nilsson, Johan
    Jonsson, Linus
    Periyannan Rajeswari, Prem Kumar
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Jönsson, Håkan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Tenje, Maria
    Particle enrichment in two-phase microfluidic systems using acoustophoresis2016In: Acoustofluidics 2016, Kongens Lyngby, Denmark, September 22-23 2016, 2016Conference paper (Refereed)
  • 22.
    FOROUGHI ASL, HASSAN
    KTH, School of Computer Science and Communication (CSC).
    Inherited Risk Enrichment Analysis ofgene sets using Genome-wide AssociationStudies for Coronary Artery Disease2013Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Genome-wide association studies (GWAS) has been in the heartof medical research for the last 5 years. These studies seek forcommon variants in the genome that are linked to risk for commoncomplex diseases (CCDs). Although GWAS has defined a numberof interesting genetic loci for a range of CCDs, the current GWASanalysis has limitation such as investigating the DNA variantsone-by-one focusing on the most significant DNA variants. As aconsequence, most risk variants for CCDs are, in my belief, stillhidden in the GWAS data. Herein, I use a method of GWASanalysis that considers risk-enrichment for groups of functionallyassociated genes defined by for example gene networks, believedto play a role in CCDs.In this method, a set of expression SNP (single nucleotidepolymorphism) was selected from genes which are known to berelated to coronary artery disease (CAD) in a way that a singleeSNP was chosen for each gene. Then using the data availablefrom the International HapMap Project and a GWAS data available,it is possible to find SNPs which are in strong linkage withthe initial set, which we call it expanded set. Depending on theassociation of the initial set to the CAD, expanded set can showan enrichment score greater or smaller compared to the null distributionset of SNPs with same properties of the expanded set.In conclusions, CCDs are not a consequence of isolated geneticvariants/genes in isolated pathways but instead sets of geneticvariants/genes acting in conjunction, cause CAD. Genetic riskenrichment analysis is a fairly simple and straightforward methodto determine to what extent a group of functionally associatedgenetic variants/genes are enriched for a given CCD. In addition,this analysis can perhaps help to decipher some of the 90-85% ofrisk variation in populations that remains unaccounted.

  • 23.
    Fredenberg, Erik
    et al.
    KTH, School of Engineering Sciences (SCI), Physics, Medical Imaging.
    Cederström, Björn
    KTH, School of Engineering Sciences (SCI), Physics, Medical Imaging.
    Lundqvist, Mats
    Ribbing, Carolina
    Åslund, Magnus
    Diekmann, Felix
    Nishikawa, Robert
    Danielsson, Mats
    KTH, School of Engineering Sciences (SCI), Physics, Medical Imaging.
    Contrast-enhanced dual-energy subtraction imaging using electronic spectrum-splitting and multi-prism x-ray lenses2008In: Medical Imaging 2008 - Physics of Medical Imaging: PTS 1-3 / [ed] Hsieh, J; Samei, E, 2008, Vol. 6913, p. 91310-91310Conference paper (Refereed)
    Abstract [en]

    Dual-energy subtraction imaging (DES) is a method to improve the detectability of contrast agents over a lumpy background. Two images, acquired at x-ray energies above and below an absorption edge of the agent material, are logarithmically subtracted, resulting in suppression of the signal from the tissue background and a relative enhancement of the signal from the agent. Although promising, DES is still not widely used in clinical practice. One reason may be the need for two distinctly separated x-ray spectra that are still close to the absorption edge, realized through dual exposures which may introduce motion unsharpness. In this study, electronic spectrum-splitting with a silicon-strip detector is theoretically and experimentally investigated for a mammography model with iodinated contrast agent. Comparisons are made to absorption imaging and a near-ideal detector using a signal-to-noise ratio that includes both statistical and structural noise. Similar to previous studies, heavy absorption filtration was needed to narrow the spectra at the expense of a large reduction in x-ray flux. Therefore, potential improvements using a chromatic multi-prism x-ray lens (MPL) for filtering were evaluated theoretically. The MPL offers a narrow tunable spectrum, and we show that the image quality can be improved compared to conventional filtering methods.

  • 24.
    Fredenberg, Erik
    et al.
    KTH, School of Engineering Sciences (SCI), Physics, Medical Imaging.
    Cederström, Björn
    KTH, School of Engineering Sciences (SCI), Physics, Medical Imaging.
    Åslund, Magnus
    Nillius, Peter
    KTH, School of Engineering Sciences (SCI), Physics, Medical Imaging.
    Lundqvist, Mats
    Danielsson, Mats
    KTH, School of Engineering Sciences (SCI), Physics, Medical Imaging.
    Imaging with multi-prism x-ray lenses2008In: Medical Imaging 2008 - Physics of Medical Imaging: PTS 1-3 / [ed] Hsieh, J; Samei, E, 2008, Vol. 6913, p. 91308-91308Conference paper (Refereed)
    Abstract [en]

    The multi-prism lens (MPL) is a refractive x-ray lens consisting of two rows of prisms facing each other at an angle. Rays entering the lens at the periphery will encounter a larger number of prisms than will central ones, hence experiencing a greater refraction. The focusing effect of the MPL can be used to gather radiation from a large aperture onto a smaller detector, and accordingly to make better use of the available x-ray flux in medical x-ray imaging. Potential advantages of a better photon economy include shorter acquisition times, a reduced tube loading, or an improved resolution. Since the focusing effect is one-dimensional it matches the design of scanning systems. In this study we present the first images acquired with an MPL instead of the pre-breast slit collimator in a scanning mammography system. According to the measurements, the MPL is able to increase the flux 32% at equal resolution compared to the slit collimator, or to improve the resolution 2.4 mm(-1) at equal flux. If used with a custom-made absorption filter in a clinical set-up, the gain of flux of the MPL is expected to be at least 45%, and the corresponding improvement in resolution to be 3 mm(-1).

  • 25.
    Gasser, Thomas Christian
    et al.
    KTH, School of Engineering Sciences (SCI), Solid Mechanics (Dept.), Biomechanics.
    Auer, M.
    Biasetti, Jacopo
    KTH, School of Engineering Sciences (SCI), Solid Mechanics (Dept.), Biomechanics.
    Structural and Hemodynamical analysis of Aortic Aneurysms from Computerized Tomography Angiography data2010In: WORLD CONGRESS ON MEDICAL PHYSICS AND BIOMEDICAL ENGINEERING, VOL 25, PT 4: IMAGE PROCESSING, BIOSIGNAL PROCESSING, MODELLING AND SIMULATION, BIOMECHANICS, 2010, p. 1584-1587Conference paper (Refereed)
    Abstract [en]

    Evaluating rupture risk of Abdominal Aortic Aneurysms is critically important in reducing related mortality without unnecessarily increasing the rate of elective repair. According to the current clinical practice aneurysm rupture risk is (mainly) estimated from its maximum diameter and/or expansion rate; an approach motivated from statistics but known to fail often in individuals. In particular, the role of the Intraluminal Thrombus is unclear and further research is required to investigate and understand its multiple impacts on aneurysm disease. Biomechanical simulations might be helpful to explore this question, however, model development is time consuming and operator-variability limits their reliability. In this study we propose an automatic procedure to develop hemodynamic and structural models of healthy and diseased abdominal aortas, where Deformable Models segment Computerized Tomography Angiography data. In total 29 numerical models of the health and diseased abdominal aorta have been developed to investigate aneurysm's rupture risk and hemodynamic consequences of aneurismal dilations. The derived results underline the suitability of biomechanical simulations to enrich diagnostic information and to uncover mechanisms of aneurysm pathology.

  • 26. Gharehbaghi, A.
    et al.
    Ask, P.
    Nylander, E.
    Janerot-Sjoberg, Birgitta
    KTH, School of Technology and Health (STH). Karolinska Institutet.
    Ekman, I.
    Lindén, M.
    Babic, A.
    A hybrid model for diagnosing sever aortic stenosis in asymptomatic patients using phonocardiogram2015In: IFMBE Proceedings, Springer, 2015, p. 1006-1009Conference paper (Refereed)
    Abstract [en]

    This study presents a screening algorithm for severe aortic stenosis (AS), based on a processing method for phonocardiographic (PCG) signal. The processing method employs a hybrid model, constituted of a hidden Markov model and support vector machine. The method benefits from a preprocessing phase for an enhanced learning. The performance of the method is statistically evaluated using PCG signals recorded from 50 individuals who were referred to the echocardiography lab at Linköping University hospital. All the individuals were diagnosed as having a degree of AS, from mild to severe, according to the echocardiographic measurements. The patient group consists of 26 individuals with severe AS, and the rest of the 24 patients comprise the control group. Performance of the method is statistically evaluated using repeated random sub sampling. Results showed a 95% confidence interval of (80.5%-82.8%) /(77.8%- 80.8%) for the accuracy/sensitivity, exhibiting an acceptable performance to be used as decision support system in the primary healthcare center.

  • 27.
    Govind, Satish C.
    KTH, School of Technology and Health (STH), Medical Engineering.
    Myocardial Effects of Type 2 Diabetes, Co-morbidities, and Changing Loading Conditions: a Clinical Study by Tissue Velocity Echocardiography2007Doctoral thesis, comprehensive summary (Other scientific)
    Abstract [en]

    Ever since the validation of the tissue velocity echocardiography (TVE) technique more than a decade ago the modality has been used rather successfully in various clinical situations, at rest as well as during stress echocardiography. Hitherto, dobutamine stress echocardiography has been the hallmark of all forms of stress procedures, now with TVE, quantification of the longitudinal motions of the left ventricle shows far superiority, with improved sensitivity and specificity in the functional diagnosis of coronary artery disease. Morever there has been continued interest in this technique for even assessing subclinical myocardial systolic and diastolic function in clinical scenarios like diabetes, hypertension and chronic kidney disease.

    The aim of the present study was to evaluate left ventricular myocardial functions by applying TVE in human subjects having type 2 diabetes with or without co-morbidities and during changing loading conditions. The effects of changing loading conditions were analyzed during hemodialysis and following oral administration of an AT1 receptor blocker. The studied subjects included individuals with diabetes as well as those with associated hypertension, coronary artery disease, microalbuminuria and end-stage renal disease. All patients with type 2 diabetes and co-morbidities underwent TVE enhanced dobutamine stress echocardiography while load dependant left ventricular functions were analyzed at rest. There were 270 subjects in the study of type 2 diabetes and associated cardiovascular diseases and 101 subjects in the study of changing loading conditions.

    Patients with type 2 diabetes revealed subclinical left ventricular dysfunction characterized by reduced functional reserve. This influence becomes quantitatively more pronounced in the presence of coexistent coronary artery disease and hypertension. The coexistence of type 2 diabetes and hypertension appears to have additive negative effect on both systolic and diastolic left ventricular function, even in the absence of coronary artery disease. The presence of microalbuminuria in type 2 diabetes patients does not worsen diminished myocardial functional reserve. A single session of hemodialysis improves left ventricular function in patients with end-stage renal disease only in the absence of type 2 diabetes and co-morbidities, while a single dose of an AT1 receptor blocker valsartan results in reduction of afterload and, subsequently, in improvement of left ventricular function. TVE appears to be a sensitive tool for objective assessment of left ventricular function and can be successfully applied for the clinical evaluation of the effect of type 2 diabetes and co-morbidities on myocardial performance.

  • 28.
    Gyllensten, Illapha Cuba
    et al.
    KTH, School of Computer Science and Communication (CSC).
    Bonomi, Alberto G.
    Identifying Types of Physical Activity With a Single Accelerometer: Evaluating Laboratory-trained Algorithms in Daily Life2011In: IEEE Transactions on Biomedical Engineering, ISSN 0018-9294, E-ISSN 1558-2531, Vol. 58, no 9, p. 2656-2663Article in journal (Refereed)
    Abstract [en]

    Accurate identification of physical activity types has been achieved in laboratory conditions using single-site accelerometers and classification algorithms. This methodology is then applied to free-living subjects to determine activity behavior. This study is aimed at analyzing the reproducibility of the accuracy of laboratory-trained classification algorithms in free-living subjects during daily life. A support vector machine (SVM), a feed-forward neural network (NN), and a decision tree (DT) were trained with data collected by a waist-mounted accelerometer during a laboratory trial. The reproducibility of the classification performance was tested on data collected in daily life using a multiple-site accelerometer augmented with an activity diary for 20 healthy subjects (age: 30 +/- 9; BMI: 23.0 +/- 2.6 kg/m(2)). Leave-one-subject-out cross validation of the training data showed accuracies of 95.1 +/- 4.3%, 91.4 +/- 6.7%, and 92.2 +/- 6.6% for the SVM, NN, and DT, respectively. All algorithms showed a significantly decreased accuracy in daily life as compared to the reference truth represented by the IDEEA and diary classifications (75.6 +/- 10.4%, 74.8 +/- 9.7%, and 72.2 +/- 10.3%; p<0.05). In conclusion, cross validation of training data overestimates the accuracy of the classification algorithms in daily life.

  • 29.
    Hansson, Sven Ove
    KTH, Superseded Departments, History of Science and Technology.
    The ethics of biobanks2004In: Cambridge Quarterly of Healthcare Ethics, ISSN 0963-1801, E-ISSN 1469-2147, Vol. 13, no 4, p. 319-326Article in journal (Refereed)
  • 30.
    Hauser, Janosch
    et al.
    KTH, School of Electrical Engineering and Computer Science (EECS), Micro and Nanosystems.
    Lenk, Gabriel
    KTH, School of Electrical Engineering and Computer Science (EECS), Micro and Nanosystems.
    Ullah, Shahid
    Karolinska Univ Hosp, Clin Pharmacol, S-11486 Stockholm, Sweden..
    Beck, Olof
    Karolinska Univ Hosp, Clin Pharmacol, S-11486 Stockholm, Sweden..
    Stemme, Göran
    KTH, School of Electrical Engineering and Computer Science (EECS), Micro and Nanosystems.
    Roxhed, Niclas
    KTH, School of Electrical Engineering and Computer Science (EECS), Micro and Nanosystems.
    An Autonomous Microfluidic Device for Generating Volume-Defined Dried Plasma Spots2019In: Analytical Chemistry, ISSN 0003-2700, E-ISSN 1520-6882, Vol. 91, no 11, p. 7125-7130Article in journal (Refereed)
    Abstract [en]

    Obtaining plasma from a blood sample and preparing it for subsequent analysis is currently a laborious process involving experienced health-care professionals and centrifugation. We circumvent this by utilizing capillary forces and microfluidic engineering to develop an autonomous plasma sampling device that filters and stores an exact amount of plasma as a dried plasma spot (DPS) from a whole blood sample in less than 6 min. We tested 24 prototype devices with whole blood from 10 volunteers, various input volumes (40-80 mu L), and different hematocrit levels (39-45%). The resulting mean plasma volume, assessed gravimetrically, was 11.6 mu L with a relative standard deviation similar to manual pipetting (3.0% vs 1.4%). LC-MS/MS analysis of caffeine concentrations in the generated DPS (12 duplicates) showed a strong correlation (R-2 = 0.99) to, but no equivalence with, concentrations prepared from corresponding plasma obtained by centrifugation. The presented autonomous DPS device may enable patient-centric plasma sampling through minimally invasive finger-pricking and allow generatation of volume-defined DPS for quantitative blood analysis.

  • 31. Hernandez, Fidel
    et al.
    Wu, Lyndia C.
    Yip, Michael C.
    Laksari, Kaveh
    Hoffman, Andrew R.
    Lopez, Jaime R.
    Grant, Gerald A.
    Kleiven, Svein
    KTH, School of Technology and Health (STH), Medical Engineering, Neuronic Engineering.
    Camarillo, David B.
    Six Degree-of-Freedom Measurements of Human Mild Traumatic Brain Injury2015In: Annals of Biomedical Engineering, ISSN 0090-6964, E-ISSN 1573-9686, Vol. 43, no 8, p. 1918-1934Article in journal (Refereed)
    Abstract [en]

    This preliminary study investigated whether direct measurement of head rotation improves prediction of mild traumatic brain injury (mTBI). Although many studies have implicated rotation as a primary cause of mTBI, regulatory safety standards use 3 degree-of-freedom (3DOF) translation-only kinematic criteria to predict injury. Direct 6DOF measurements of human head rotation (3DOF) and translation (3DOF) have not been previously available to examine whether additional DOFs improve injury prediction. We measured head impacts in American football, boxing, and mixed martial arts using 6DOF instrumented mouthguards, and predicted clinician-diagnosed injury using 12 existing kinematic criteria and 6 existing brain finite element (FE) criteria. Among 513 measured impacts were the first two 6DOF measurements of clinically diagnosed mTBI. For this dataset, 6DOF criteria were the most predictive of injury, more than 3DOF translation-only and 3DOF rotation-only criteria. Peak principal strain in the corpus callosum, a 6DOF FE criteria, was the strongest predictor, followed by two criteria that included rotation measurements, peak rotational acceleration magnitude and Head Impact Power (HIP). These results suggest head rotation measurements may improve injury prediction. However, more 6DOF data is needed to confirm this evaluation of existing injury criteria, and to develop new criteria that considers directional sensitivity to injury.

  • 32.
    Hertz, Hans M.
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
    Hemberg, O.
    Otendal, M.
    Tuohimaa, T.
    Hansson, B. A. M.
    Electron-Impact Liquid-Metal-Jet Hard x-Ray Sources2014In: Comprehensive Biomedical Physics, Elsevier, 2014, Vol. 8, p. 91-109Chapter in book (Other academic)
    Abstract [en]

    The power and brightness of electron-impact microfocus x-ray sources have long been limited by thermal damage in the target. This is a major constraint for a wide range of biomedical applications, from imaging to diffraction. Here, we describe the development of an x-ray microfocus source based on a new target concept, the liquid-metal jet (LMJ). The regenerative nature of this target allows for significantly higher e-beam power density than on conventional targets, resulting in this source showing promise for >. 100. × higher brightness than state-of-the-art sources. We first discuss the basic physics of the two important subsystems of the source, LMJ in vacuum and focused electron-beam systems, and then describe the properties of several versions of the source, from early prototypes to the first LMJ sources now reaching the market. Finally, we review some early applications of the source for biomedical imaging and diffraction.

  • 33.
    Hjelm, Barbara
    et al.
    KTH, School of Biotechnology (BIO), Proteomics (closed 20130101).
    Brennan, Donal J
    Zendehrokh, Nooreldin
    Eberhard, Jakob
    Nodin, Björn
    Gaber, Alexander
    Pontén, Fredrik
    Johannesson, Henrik
    Smaragdi, Kristina
    Frantz, Christian
    Hober, Sophia
    KTH, School of Biotechnology (BIO), Proteomics (closed 20130101).
    Johnson, Louis B
    Påhlman, Sven
    Jirström, Karin
    Uhlén, Mathias
    KTH, School of Biotechnology (BIO), Proteomics (closed 20130101). KTH, Centres, Science for Life Laboratory, SciLifeLab.
    High nuclear RBM3 expression is associated with an improved prognosis in colorectal cancer2011In: Proteomics. Clinical applications, ISSN 1862-8354, Vol. 5, no 11-12, p. 624-35Article in journal (Refereed)
    Abstract [en]

    Purpose: In this study, we investigated the prognostic impact of human RBM3 expression in colorectal cancer using tissue microarray-based immunohistochemical analysis. Experimental design: One polyclonal antibody and four monoclonal anti-RBM3 antibodies were generated and epitope mapped using two different methods. Bacterial display revealed five distinct epitopes for the polyclonal antibody, while the four mouse monoclonal antibodies were found to bind to three of the five epitopes. A peptide suspension bead array assay confirmed the five epitopes of the polyclonal antibody, while only one of the monoclonal antibodies could be mapped using this approach. Antibody specificity was confirmed by Western blotting and immunohistochemistry, including siRNA-mediated knock-down. Two of the antibodies (polyclonal and monoclonal) were subsequently used to analyze RBM3 expression in tumor samples from two independent colorectal cancer cohorts, one consecutive cohort (n=270) and one prospectively collected cohort of patients with cancer of the sigmoid colon (n=305). RBM3-expression was detected, with high correlation between both antibodies (R=0.81, p<0.001). Results: In both cohorts, tumors with high nuclear RBM3 staining had significantly prolonged the overall survival. This was also confirmed in multivariate analysis, adjusted for established prognostic factors. Conclusion and clinical relevance: These data demonstrate that high tumor-specific nuclear expression of RBM3 is an independent predictor of good prognosis in colorectal cancer.

  • 34.
    Holden, Richard J.
    KTH, School of Technology and Health (STH), Ergonomics.
    Physicians' beliefs about using EMR and CPOE: In pursuit of a contextualized understanding of health IT use behavior2010In: International Journal of Medical Informatics, ISSN 1386-5056, E-ISSN 1872-8243, Vol. 79, no 2, p. 71-80Article in journal (Refereed)
    Abstract [en]

    Purpose: To identify and describe physicians' beliefs about use of electronic medical records (EMR) and computerized provider order entry (CPOE) for inpatient and outpatient care, to build an understanding of what factors shape information technology (IT) use behavior in the unique context of health care delivery. Methods: Semi-structured qualitative research interviews were carried out, following the beliefs elicitation approach. Twenty physicians from two large Midwest US hospitals participated. Physicians were asked questions to elicit beliefs and experiences pertaining to their use of EMR and CPOE. Questions were based on a broad set of behavior-shaping beliefs and the methods commonly used to elicit those beliefs. Results: Qualitative analysis revealed numerous themes related to the perceived emotional and instrumental outcomes of EMR and CPOE use; perceived external and personal normative pressure to use those systems; perceived volitional control over use behavior; perceived facilitators and barriers to system use; and perceptions about the systems and how they were implemented. EMR and CPOE were commonly believed to both improve and worsen the ease and quality of personal performance, productivity and efficiency, and patient outcomes. Physicians felt encouraged by employers and others to use the systems but also had personal role-related and moral concerns about doing so. Perceived facilitators and barriers were numerous and had their sources in all aspects of the work system. Conclusion: Given the breadth and detail of elicited beliefs, numerous design and policy implications can be identified. Additionally, the findings are a first step toward developing a theory of health IT acceptance and use contextualized to the unique setting of health care.

  • 35.
    Häggmark, Anna
    et al.
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Mikus, Maria
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Mohsenchian, Atefeh
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Hong, Mun-Gwan
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Forsström, Björn
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Gajewska, Beata
    Baranczyk-Kuzma, Anna
    Uhlén, Mathias
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Schwenk, Jochen M.
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Kuzma-Kozakiewicz, Magdalena
    Nilsson, Peter
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Plasma profiling revelas three proteins associated to amyotrophic lateral sclerosis2014In: Annals of Clinical and Translational Neurology, ISSN 2328-9503, Vol. 1, no 8, p. 544-553Article in journal (Refereed)
    Abstract [en]

    OBJECTIVE: Amyotrophic lateral sclerosis (ALS) is the most common adult motor neuron disease leading to muscular paralysis and death within 3-5 years from onset. Currently, there are no reliable and sensitive markers able to substantially shorten the diagnosis delay. The objective of the study was to analyze a large number of proteins in plasma from patients with various clinical phenotypes of ALS in search for novel proteins or protein profiles that could serve as potential indicators of disease.

    METHODS: Affinity proteomics in the form of antibody suspension bead arrays were applied to profile plasma samples from 367 ALS patients and 101 controls. The plasma protein content was directly labeled and protein profiles obtained using 352 antibodies from the Human Protein Atlas targeting 278 proteins. A focused bead array was then built to further profile eight selected protein targets in all available samples.

    RESULTS: Disease-associated significant differences were observed and replicated for profiles from antibodies targeting the proteins: neurofilament medium polypeptide (NEFM), solute carrier family 25 (SLC25A20), and regulator of G-protein signaling 18 (RGS18).

    INTERPRETATION: Upon further validation in several independent cohorts with inclusion of a broad range of other neurological disorders as controls, the alterations of these three protein profiles in plasma could potentially provide new molecular markers of disease that contribute to the quest of understanding ALS pathology.

  • 36.
    Häggmark, Anna
    et al.
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Zandian, Arash
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Forsström, Björn
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Uhlén, Mathias
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Schwenk, Jochen M.
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Nilsson, Peter
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Autoantibody targets in vaccine-associated narcolepsyManuscript (preprint) (Other academic)
  • 37. Jiang, Mingzhe
    et al.
    Gia, Tuan Nguyen
    Anzanpour, Arman
    Rahmani, Amir
    KTH, School of Information and Communication Technology (ICT), Industrial and Medical Electronics.
    Westerlund, Tomi
    Salantera, Sanna
    Liljeberg, Pasi
    Tenhunen, Hannu
    KTH, School of Information and Communication Technology (ICT), Industrial and Medical Electronics.
    IoT-based Remote Facial Expression Monitoring System with sEMG Signal2016In: 2016 IEEE SENSORS APPLICATIONS SYMPOSIUM (SAS 2016) PROCEEDINGS, IEEE, 2016, p. 211-216Conference paper (Refereed)
    Abstract [en]

    Biopotentials including Electrocardiography (ECG), Electromyography (EMG) and Electroencephalography (EEG) measure the activity of heart, muscles and brain, respectively. They can be used for noninvasive diagnostic applications, assistance in rehabilitation medicine and human-computer interaction. The concept of Internet of Things (IoT) can bring added value to applications with biopotential signals in healthcare and human-computer interaction by integrating multiple technologies such as sensors, wireless communication and data science. In this work, we present a wireless biopotentials remote monitoring and processing system. A prototype with the case study of facial expression recognition using four channel facial sEMG signals is implemented. A multivariate Gaussian classifier is trained offline from one person's surface EMG (sEMG) signals with four facial expressions: neutral, smile, frown and wrinkle nose. The presented IoT application system is implemented on the basis of an eight channel biopotential measurement device, Wi-Fi module as well as signal processing and classification provided as a Cloud service. In the system, the real-time sEMG data stream is filtered, feature extracted and classified within each data segment and the processed data is visualized in a browser remotely together with the classification result.

  • 38.
    Johansson, Sebastian
    et al.
    Stockholms Universitet.
    Juhos, Szilveszter
    Stockholms Universitet.
    Redin, David
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Ahmadian, Afshin
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Käller, Max
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Comprehensive haplotyping of the HLA gene family using nanopore sequencingManuscript (preprint) (Other academic)
    Abstract [en]

    The HLA gene family is the most polymorphic loci in the human genome; it encodes for the major histocompatibility complexes (MHC) which mediates the immune response in terms of cellular interactions with antigens. Compatibility between HLA alleles is thus of great medical interest for recipients of allogeneic transplantations. Traditional serological techniques to evaluate compatibility are now being replaced by more accurate DNA sequencing-based methods. However, short read sequencing data typically result in collapsed sequences representing a mixture of variants from native haplotypes. In addition, most previous studies have been limited to a few highly polymorphic exons of various HLA genes. Here we present haplotype-resolved full-length sequencing of the six most clinically relevant MHC Class I and Class II genes, to characterize the haplotypes of eight reference individuals, using a single MinION flow cell. The results show that full-length sequencing of single molecules enables haplotypes to be resolved to the highest degree of accuracy (four-field resolution). In this study, a majority of the alleles were classified with four-field resolution and could be verified through previously published genotyping studies. These results support the notion that nanopore sequencing could be a viable solution for highly accurate clinical evaluation of histocompatibility.

  • 39.
    Johansson, Staffan B.
    et al.
    KTH, School of Electrical Engineering (EES), Micro and Nanosystems.
    Eklund, Anders
    Malm, Jan
    Stemme, Göran
    KTH, School of Electrical Engineering (EES), Micro and Nanosystems.
    Roxhed, Niclas
    KTH, School of Electrical Engineering (EES), Micro and Nanosystems.
    A MEMS-based passive hydrocephalus shunt for body position controlled intracranial pressure regulation2014In: Biomedical microdevices (Print), ISSN 1387-2176, E-ISSN 1572-8781, Vol. 16, no 4, p. 529-536Article in journal (Refereed)
    Abstract [en]

    This paper reports a novel micro electro mechanical system (MEMS) valve with posture controlled flow characteristics for improved treatment of hydrocephalus, a disease that is characterized by elevated pressure in the cerebrospinal fluid (CSF) that surrounds the brain and spinal cord. In contrast to conventional differential pressure CSF valves, the CSF valve presented here features a third port which utilizes hydrostatic pressure from a pressure compensating catheter to adapt CSF drainage to optimized levels irrespective of body position. Prototypes have been fabricated using standard MEMS manufacturing processes and the experimental evaluation successfully showed that the flow rate was adjustable with a varying hydrostatic pressure on the third port. Measured data showed that flow rate was at near ideal values at laying body position and that the flow rate can be adjusted to optimal values at standing body position by selecting an appropriate length of the pressure compensating catheter. This is the first pressure balanced CSF valve intended for body position controlled CSF pressure regulation.

  • 40.
    Jonas, Hansson
    et al.
    KTH, School of Electrical Engineering (EES), Micro and Nanosystems.
    Yasuga, Hiroki
    KTH, School of Electrical Engineering (EES), Micro and Nanosystems.
    Haraldsson, Tommy
    KTH, School of Electrical Engineering (EES), Micro and Nanosystems.
    van der Wijngaart, Wouter
    KTH, School of Electrical Engineering (EES), Micro and Nanosystems.
    Synthetic microfluidic paper: high surface area and high porosity polymer micropillar arrays2016In: Lab on a Chip, ISSN 1473-0197, E-ISSN 1473-0189, Vol. 16, no 2, p. 298-304Article in journal (Refereed)
    Abstract [en]

    We introduce Synthetic Microfluidic Paper, a novel porous material for microfluidic applications that consists of an OSTE polymer that is photostructured in a well-controlled geometry of slanted and interlocked micropillars. We demonstrate the distinct benefits of Synthetic Microfluidic Paper over other porous microfluidic materials, such as nitrocellulose, traditional paper and straight micropillar arrays: in contrast to straight micropillar arrays, the geometry of Synthetic Microfluidic Paper was miniaturized without suffering capillary collapse during manufacturing and fluidic operation, resulting in a six-fold increased internal surface area and a three-fold increased porous fraction. Compared to commercial nitrocellulose materials for capillary assays, Synthetic Microfluidic Paper shows a wider range of capillary pumping speed and four times lower device-to-device variation. Compared to the surfaces of the other porous microfluidic materials that are modified by adsorption, Synthetic Microfluidic Paper contains free thiol groups and has been shown to be suitable for covalent surface chemistry, demonstrated here for increasing the material hydrophilicity. These results illustrate the potential of Synthetic Microfluidic Paper as a porous microfluidic material with improved performance characteristics, especially for bioassay applications such as diagnostic tests.

  • 41.
    Jönsson, Håkan
    et al.
    KTH, School of Biotechnology (BIO), Nano Biotechnology (closed 20130101).
    Samuels, Michael L.
    Brouzes, Eric R.
    Medkova, Martina
    Uhlén, Mathias
    KTH, School of Biotechnology (BIO), Proteomics (closed 20130101).
    Link, Darren R.
    Andersson-Svahn, Helene
    KTH, School of Biotechnology (BIO), Nano Biotechnology (closed 20130101).
    Detection and Analysis of Low-Abundance Cell-Surface Biomarkers Using Enzymatic Amplification in Microfluidic Droplets2009In: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 48, no 14, p. 2518-2521Article in journal (Refereed)
    Abstract [en]

    Finding the few: Cell-surface proteins are useful disease biomarkers, but current high-throughput methods are limited to detecting cells expressing more than several hundred proteins. Enzymatic amplification in microfluidic droplets (see picture) is a high-throughput method for detection and analysis of cell-surface biomarkers expressed at very low levels on individual human cells. Droplet optical labels allow concurrent analysis of several samples.

  • 42. Kane, Bridget
    et al.
    Groth, Kristina
    KTH, School of Computer Science and Communication (CSC), Media Technology and Interaction Design, MID. Karolinska University Hospital, Sweden.
    Multidisciplinary Work Practices: A Comparison of Three Major European Hospitals2014Conference paper (Refereed)
    Abstract [en]

    This paper reviews the practices of multidisciplinary teamwork (MDT) for cancer care in three large teaching hospitals in separate jurisdictions. Ethnographic observations provide the main source of data, which are verified though interviews, and in some cases by surveys and analysis of video recordings. We demonstrate how MDT practices develop among different groups, and in different jurisdictions. Common practices are identified and differences explained. Work practice analysis is an integral part of our research, and this study provides insights into medical teamwork and decision-making.

  • 43. Katona, Borbala
    et al.
    Ibrahim, Ahmed
    Sundberg, Mårten
    Williams, Cecilia
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Antibody Validation Strategy for Nuclear Receptors.2019In: Methods in Molecular Biology, ISSN 1064-3745, E-ISSN 1940-6029, Vol. 1966, p. 79-99Article in journal (Refereed)
    Abstract [en]

    Antibodies are invaluable biological tools that we can use to detect the presence, location, or alteration of nuclear receptors. However, antibodies frequently cross-react with other proteins and their performance can vary from batch to batch, from application to application and from lab to lab. When each lot of antibody is not thoroughly validated for each assay, each sample type, and each lab and user, antibody-based assays can lead to flawed interpretations and reproducibility problems. In this chapter, we describe a scheme for thorough antibody validation, suitable for nuclear receptors. The method is based on using highly characterized positive and negative controls assembled into a validation tissue microarray (TMA). Through correlation of immunohistochemical staining (IHC) and mRNA levels over multiple tissues, use of current public databases, and assessment of binding to intended and nonintended targets using western blotting (WB), immunoprecipitation (IP), and mass spectrometry (MS), we describe a path for thoroughly validation of antibodies.

  • 44.
    Kazemzadeh, Amin
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Lapins, Noa
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Banerjee, Indradumna
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Akhtar, Ahmad Saleem
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Russom, Aman
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Mobile-LabDisc for Point-of-Care DiagnosticsManuscript (preprint) (Other academic)
    Abstract [en]

    At resource limited settings, point of care devices require a very low-cost, robust and easy to use platform that is preferably capable of automating and multiplexing intricate bioassays. We report on a mobile lab-disc platform that is specifically designed to meet the needs at resource- limited settings. It uses a smartphone as an electrical power source and a disposable, rigid and portable casing made of cardboard that securely accommodate the entire lab-disc system rotor, lightning and wiring and other accessories. The mobile lab-disc is light, less-expensive and functional at places where the electrical power infrastructure is not available. We show that the electrical energy stored in most mobile phones can be used for spinning a lab-Disc at up to 5500 rpm, a speed sufficient for most of the required functional steps in a bioassay including ELISA. We develop individual components of the mobile lab-disc system by experimentally conducting colorimetric assays using HRP and sandwich immunoassay. Finally, the full potential of the mobile lab-disc for integrating and multiplexing bioassays is demonstrated by measuring the hematocrit level in whole blood. The mobile phone-operated process integrates sample preparation i.e., blood-plasma separation, imaging and image analysis. The total cost of our prototype system for the tests, excluding the phone is ~$5, assuming that a lab-disc unit is worth $1.

  • 45.
    Kothapalli, Satya V.V.N.
    et al.
    KTH, School of Technology and Health (STH), Medical Engineering, Medical Imaging.
    Wiklund, Martin
    KTH, School of Engineering Sciences (SCI), Applied Physics, Cell Physics.
    Janerot Sjöberg, Birgitta
    KTH, School of Technology and Health (STH), Medical Engineering, Medical Imaging. Karolinska Institutet, Sweden; Karolinska University Hospital, Sweden .
    Paradossi, Gaio
    Diapartimento di Chimica, Università di Roma Tor Vergata.
    Brodin, Lars-Åke
    KTH, School of Technology and Health (STH), Medical Engineering, Medical Imaging.
    Grishenkov, Dmitry
    KTH, School of Technology and Health (STH), Medical Engineering, Medical Imaging. Karolinska Institutet, Sweden; Karolinska University Hospital, Sweden .
    Investigation of Polymer-Shelled Microbubble Motions in AcoustophoresisManuscript (preprint) (Other academic)
    Abstract [en]

    The objective of this paper is to explore the trajectory motion of microsize (typically smaller than a redblood cell) encapsulated polymer-shelled gas bubbles propelled by radiation force in an acousticstanding-wave field and to compare the corresponding movements of solid polymer microbeads. Theexperimental setup consists of a microfluidic chip coupled to a piezoelectric crystal (PZT) with aresonance frequency of about 2.8 MHz. The microfluidic channel consists of a rectangular chamberwith a width, w, corresponding to one wavelength of the ultrasound standing wave. It creates one fullwave ultrasound of a standing-wave pattern with two pressure nodes at4w and43w and threeantinodes at 0,2w , and w. The peak-to-peak amplitude of the electrical potential over the PZT wasvaried between 1 and 10 volts. From Gor’kov’s potential equation, the acoustic contrast factor, Φ, forthe polymer-shelled microbubbles was calculated to about -60.7. Experimental results demonstratethat the polymer-shelled microbubbles are translated and accumulated at the pressure antinode planes.This trajectory motion of polymer-shelled microbubbles toward the pressure antinode plane is similarto what has been described for other acoustic contrast particles with a negative Φ. First, primaryradiation forces dragged the polymer-shelled microbubbles into proximity with each other at thepressure antinode planes. Then, secondary radiation forces caused them to aggregate at different spotsalong the channel. The relocation time for polymer-shelled microbubbles was 40 times shorter thanthat for polymer microbeads, and in contrast to polymer microbeads, the polymer-shelledmicrobubbles were actuated even at driving voltages (proportional to radiation forces) as low as 1 volt.In short, the polymer-shelled microbubbles demonstrate the behavior attributed to the negativeacoustic contrast factor particles and thus can be trapped at the antinode plane and thereby seperatedfrom solid particles, such as cells. This phenomenon could be utilized in exploring future applications,such as bioassay, bioaffinity, and cell interaction studies in vitro in a well-controlled environment.

  • 46.
    Langer, Krzysztof
    et al.
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Jönsson, Håkan
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Rapid production and recovery of cell spheroids by automated droplet microfluidics2019Manuscript (preprint) (Other academic)
    Abstract [en]

    Droplet microfluidics enables high throughput cell processing, analysis and screening by miniaturizing the reaction vessels to nano- or pico-liter water-in oil droplets, but like many other microfluidic formats, droplet microfluidics have not been interfaced with or automated by laboratory robotics. Here we demonstrate automation of droplet microfluidics based on an inexpensive liquid handling robot for the automated production of human scaffold-free cell spheroids, using pipette actuation and interfacing the pipetting tip with a droplet generating microfluidic chip. In this chip we produce highly mono-disperse 290μm droplets with diameter CV of 1.7%. By encapsulating cells in these droplets, we produce cell spheroids in droplets and recover them to standard formats at a throughput of 85000 spheroids per microfluidic circuit per hour. The viability of the cells in spheroids remains high after recovery only decreased by 4% starting from 96% after 16 hours incubation in nanoliter droplets. Scaffold-free cell spheroids and 3D tissue constructs recapitulate many aspects of functional human tissue more accurately than 2D or single cell cultures, but assembly methods for spheroids, e.g. hanging drop micro-plates, has had limited throughput. The increased throughput and decreased cost of our method enables spheroid production at the scale needed for lead discovery drug screening and approaches the cost where these micro tissues could be used as building blocks for organ scale regenerative medicine.

  • 47. Li, F.
    et al.
    Zhu, H.
    Wu, S.
    Gao, Q.
    Hu, Z.
    Xu, J.
    Xu, G.
    He, Sailing
    KTH, School of Electrical Engineering (EES), Electromagnetic Engineering. South China Normal University (SCNU).
    Effect of frequent degree of deceiving on the prefrontal cortical response to deception: A functional near-infrared spectroscopy (fNIRS) study2015Conference paper (Refereed)
    Abstract [en]

    Functional near-infrared spectroscopy (fNIRS) is an emerging brain-imaging technique which has been used to various areas. Previous studies have indicated that frequent deceiving would make deceiving easier. In this study, fNIRS was used to explore the effect of frequent degree of deceiving on the prefrontal cortical response to deception. Self-related questions were used in the experiment. The results showed different patterns of neural activation between non-frequent deceiving and frequent deceiving. In Channel 11 (in the left prefrontal cortex), non-frequent deceiving led to a greater neural activation than telling the truth, while this pattern did not appear in frequent deceiving. Our finding suggested that fNIRS has ability to detect deception under different situations.

  • 48.
    Lindroos, Robert
    KTH, School of Computer Science and Communication (CSC).
    A simplied Medium SpinyNeuron-model with retained intrinsic characteristics and plateau properties2013Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    This master thesis studies how a morphological reduction aects theperformance of a biophysically detailed model of a medium spiny neuron. Themorphological reduction is done using a MATLAB toolbox developed forautomatic 3-dimensional morphological reduction. Two versions of the toolboxare developed in which dierent criteria are used during the merge. Theevaluation of the two toolboxes shows that keeping the absolute distance to thesoma of the branching points and the surface area of the dendrites gives a moreaccurate result than if these criteria are not used. These criteria are implementedin Toolbox 2. In total 8 models with dierent maximal compartment length arethen constructed using Toolbox 2. The number of compartments in the resultingmodels range from 1/2 to 1/10 of the compartments in the original model. Furtherthe performance of the reduced models are evaluated against the original model.The results of this evaluation shows that an increasing compartment length givesa decrease in consistency with the response of the original model. However theresponse of all models are largely similar to the original model.

  • 49.
    Lundin, Sverker
    KTH, School of Biotechnology (BIO), Gene Technology.
    Methods to Prepare DNA for Efficient Massive Sequencing2012Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Massive sequencing has transformed the field of genome biology due to the continuous introduction and evolution of new methods. In recent years, the technologies available to read through genomes have undergone an unprecedented rate of development in terms of cost-reduction. Generating sequence data has essentially ceased to be a bottleneck for analyzing genomes instead to be replaced by limitations in sample preparation and data analysis. In this work, new strategies are presented to increase both the throughput of library generation prior to sequencing, and the informational content of libraries to aid post-sequencing data processing. The protocols developed aim to enable new possibilities for genome research concerning project scale and sequence complexity.

    The first two papers that underpin this thesis deal with scaling library production by means of automation. Automated library preparation is first described for the 454 sequencing system based on a generic solid-phase polyethylene-glycol precipitation protocol for automated DNA handling. This was one of the first descriptions of automated sample handling for producing next generation sequencing libraries, and substantially improved sample throughput. Building on these results, the use of a double precipitation strategy to replace the manual agarose gel excision step for Illumina sequencing is presented. This protocol considerably improved the scalability of library construction for Illumina sequencing. The third and fourth papers present advanced strategies for library tagging in order to multiplex the information available in each library. First, a dual tagging strategy for massive sequencing is described in which two sets of tags are added to a library to trace back the origins of up to 4992 amplicons using 122 tags. The tagging strategy takes advantage of the previously automated pipeline and was used for the simultaneous sequencing of 3700 amplicons. Following that, an enzymatic protocol was developed to degrade long range PCR-amplicons and forming triple-tagged libraries containing information of sample origin, clonal origin and local positioning for the short-read sequences. Through tagging, this protocol makes it possible to analyze a longer continuous sequence region than would be possible based on the read length of the sequencing system alone. The fifth study investigates commonly used enzymes for constructing libraries for massive sequencing. We analyze restriction enzymes capable of digesting unknown sequences located some distance from their recognition sequence. Some of these enzymes have previously been extensively used for massive nucleic acid analysis. In this first high throughput study of such enzymes, we investigated their restriction specificity in terms of the distance from the recognition site and their sequence dependence. The phenomenon of slippage is characterized and shown to vary significantly between enzymes. The results obtained should favor future protocol development and enzymatic understanding.

    Through these papers, this work aspire to aid the development of methods for massive sequencing in terms of scale, quality and knowledge; thereby contributing to the general applicability of the new paradigm of sequencing instruments.

  • 50.
    Maksuti, Elira
    et al.
    KTH, School of Technology and Health (STH), Medical Engineering, Medical Imaging.
    Bjällmark, Anna
    KTH, School of Technology and Health (STH), Medical Engineering, Medical Imaging. Karolinska Institute, Sweden .
    Broomé, Michael
    KTH, School of Technology and Health (STH), Medical Engineering, Medical Imaging. Karolinska Institute, Sweden .
    Modelling the heart with the atrioventricular plane as a piston unit2015In: Medical Engineering and Physics, ISSN 1350-4533, E-ISSN 1873-4030, Vol. 37, no 1, p. 87-92Article in journal (Refereed)
    Abstract [en]

    Medical imaging and clinical studies have proven that the heart pumps by means of minor outer volume changes and back-and-forth longitudinal movements in the atrioventricular (AV) region. The magnitude of AV-plane displacement has also shown to be a reliable index for diagnosis of heart failure. Despite this, AV-plane displacement is usually omitted from cardiovascular modelling. We present a lumped-parameter cardiac model in which the heart is described as a displacement pump with the AV plane functioning as a piston unit (AV piston). This unit is constructed of different upper and lower areas analogous with the difference in the atrial and ventricular cross-sections. The model output reproduces normal physiology, with a left ventricular pressure in the range of 8-130 mmHg, an atrial pressure of approximatly 9 mmHg, and an arterial pressure change between 75 mmHg and 130 mmHg. In addition, the model reproduces the direction of the main systolic and diastolic movements of the AV piston with realistic velocity magnitude (similar to 10 cm/s). Moreover, changes in the simulated systolic ventricular-contraction force influence diastolic filling, emphasizing the coupling between cardiac systolic and diastolic functions. The agreement between the simulation and normal physiology highlights the importance of myocardial longitudinal movements and of atrioventricular interactions in cardiac pumping.

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