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  • 251.
    Liu, Wei
    et al.
    University of Newcastle, Australia.
    Williams, Mary-Anne
    University of Newcastle, Australia.
    A Framework for Multi-Agent Belief Revision, Part II: A Layered Model and Shared Knowledge Structure2000Report (Other academic)
    Abstract [en]

    In this paper, a framework of a belief revision agent in a multi-agent environment is presented. In the agent knowledge kernel, by separating domain knowledge from social knowledge, various level of belief revision capabilities has been modularized into multiple interactive layers. A vertical 4-layer 2-pass architecture is adopted for the BR engine. Therefore, the framework can model various levels of belief revision, including Single Belief Revision, BR using information from Multiple Sources and Multi-Agent Belief Revision. In order to achieve multi-agent belief revision in a heterogenous society, a Shared Knowledge Structure(SKS) is proposed, which allows the sharing of knowledge as well as protecting private knowledge. Using graded knowledge in the SKS, the process of multi-agent belief revision is implemented using knowledge migration, which is the procedure that reshapes the knowledge structure triggered by the new information.

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  • 252.
    Klein, Richard
    et al.
    Linköping University, The Tema Institute, Department of Water and Environmental Studies. Linköping University, The Tema Institute, Centre for Climate Science and Policy Research . Linköping University, Faculty of Arts and Sciences. Stockholm Environment Institute, Sweden.
    Juhola, Sirkku
    University of Helsinki, Finland; Aalto University, Finland .
    A framework for Nordic actor-oriented climate adaptation research2014In: Environmental Science and Policy, ISSN 1462-9011, E-ISSN 1873-6416, Vol. 40, p. 101-115Article in journal (Refereed)
    Abstract [en]

    The past ten years have seen a substantial increase in research on climate change adaptation, but a large gap remains between adaptation research and action. Adaptation researchers have either failed to demonstrate the relevance of their findings to practitioners and policymakers, or stakeholders have based their views and decisions on other kinds of information. In addition, in sectors such as agriculture, forestry, nature conservation, urban planning, water management and energy supply, adaptation has been studied separately from mitigation, which contradicts the reality of many practitioners. This paper identifies five bottlenecks to the use of adaptation research in adaptation practice and policy. These bottlenecks have gone unnoticed because the traditional framing of adaptation does not adequately consider the notion of agency, often rendering stakeholder interactions ineffective. Knowledge and use of actor-oriented theory when analysing and discussing adaptation needs and options could serve to find ways to overcome the bottlenecks and narrow the gap between research and action. The paper presents a novel framework for actor-oriented adaptation research that is being conducted within the Nordic Centre of Excellence for Strategic Adaptation Research (NORD-STAR). It frames climate adaptation as addressing both the impacts of climate change and the consequences of climate policy. Two methodological approaches - modelling and visualisation, and policy analysis - are applied to three thematic issues: land-use change, energy transitions, and insurance and finance.

  • 253.
    Kuiper, Erik
    et al.
    Saab Aeronautical, Linkoping, Sweden .
    Nadjm-Tehrani, Simin
    Linköping University, Department of Computer and Information Science, Software and Systems. Linköping University, The Institute of Technology.
    Yuan, Di
    Linköping University, Department of Science and Technology, Communications and Transport Systems. Linköping University, The Institute of Technology.
    A framework for performance analysis of geographic delay-tolerant routing2012In: EURASIP Journal on Wireless Communications and Networking, ISSN 1687-1472, E-ISSN 1687-1499, no 184Article in journal (Refereed)
    Abstract [en]

    A major tool used for evaluating routing protocols in ad hoc and delay-tolerant networks is simulation. Whereas the results from simulations give good insights, they are limited to the specific scenario set-up that is used. If the scenario changes, new and often time-consuming simulations have to be run. Moreover, the simulation time in packet-level simulators with fairly realistic physical layer implementation, such as ns-2, generally grows rapidly in the number of nodes. This practically limits the number of nodes in a simulation, even if the limit can be extended by the use of simulation federations. Larger scenarios can also be facilitated by the use of more abstraction in the physical layer; abstractions that may impact the validity of the results. In this article, we present the forward-wait framework--a mathematical model describing the packet movements for opportunistic geographic delay-tolerant routing protocols. By describing packet movements as a sequence of alternating forwarding and waiting phases, the framework can accurately predict the routing performance. Key input parameters to the framework are random variables describing the forwarding and waiting phases. We show how the properties of the random variables can be derived, both via abstract modeling and small scale ns-2 simulation data. The model is then used to demonstrate the prediction capabilities of the framework in providing results that are close to the (much slower) packet-level simulations.

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  • 254.
    Dastgeer, Usman
    et al.
    Linköping University, Department of Computer and Information Science, Software and Systems. Linköping University, The Institute of Technology.
    Kessler, Christoph
    Linköping University, Department of Computer and Information Science, Software and Systems. Linköping University, The Institute of Technology.
    A Framework for Performance-aware Composition of Applications for GPU-based Systems2013Conference paper (Refereed)
    Abstract [en]

    User-level components of applications can be made performance-aware by annotating them with performance model and other metadata. We present a component model and a composition framework for the performance-aware composition of applications for modern GPU-based systems from such components, which may expose multiple implementation variants. The framework targets the composition problem in an integrated manner, with particular focus on global performance-aware composition across multiple invocations. We demonstrate several key features of our framework relating to performance-aware composition including implementation selection, both with performance characteristics being known (or learned) beforehand as well as cases when they are learned at runtime. We also demonstrate hybrid execution capabilities of our framework on real applications. Furthermore, as an important step towards global composition, we present a bulk composition technique that can make better composition decisions by considering information about upcoming calls along with data flow information extracted from the source program by static analysis, thus improving over the traditional greedy performance-aware policy that only considers the current call for optimization.

  • 255.
    Kessler, Christoph
    et al.
    Linköping University, Department of Computer and Information Science, PELAB - Programming Environment Laboratory. Linköping University, The Institute of Technology.
    Löwe, Welf
    MSI Växjö universitet, Sweden.
    A Framework for Performance-Aware Composition of Explicitly Parallel Components2008In: Parallel Computing: Architectures, Algorithms and Applications, IOS Press, 2008, p. 227-234Conference paper (Refereed)
    Abstract [en]

    We describe the principles of a novel framework for performance-aware composition of explicitly parallel software components with implementation variants. Automatic composition results in a table-driven implementation that, for each parallel call of a performance-aware component, looks up the expected best implementation variant, processor allocation and schedule given the current problem and processor group sizes. The dispatch tables are computed off-line at component deployment time by interleaved dynamic programming algorithm from time-prediction metacode provided by the component supplier.

  • 256.
    Wzorek, Mariusz
    et al.
    Linköping University, Department of Computer and Information Science, Artificial Intelligence and Integrated Computer Systems. Linköping University, Faculty of Science & Engineering.
    Berger, Cyrille
    Linköping University, Department of Computer and Information Science, Artificial Intelligence and Integrated Computer Systems. Linköping University, Faculty of Science & Engineering.
    Doherty, Patrick
    Linköping University, Department of Computer and Information Science, Artificial Intelligence and Integrated Computer Systems. Linköping University, Faculty of Science & Engineering.
    A Framework for Safe Navigation of Unmanned Aerial Vehicles in Unknown Environments2017In: 2017 25TH INTERNATIONAL CONFERENCE ON SYSTEMS ENGINEERING (ICSENG), IEEE , 2017, p. 11-20Conference paper (Refereed)
    Abstract [en]

    This paper presents a software framework which combines reactive collision avoidance control approach with path planning techniques for the purpose of safe navigation of multiple Unmanned Aerial Vehicles (UAVs) operating in unknown environments. The system proposed leverages advantages of using a fast local sense-and-react type control which guarantees real-time execution with computationally demanding path planning algorithms which generate globally optimal plans. A number of probabilistic path planning algorithms based on Probabilistic Roadmaps and Rapidly-Exploring Random Trees have been integrated. Additionally, the system uses a reactive controller based on Optimal Reciprocal Collision Avoidance (ORCA) for path execution and fast sense-and-avoid behavior. During the mission execution a 3D map representation of the environment is build incrementally and used for path planning. A prototype implementation on a small scale quad-rotor platform has been developed. The UAV used in the experiments was equipped with a structured-light depth sensor to obtain information about the environment in form of occupancy grid map. The system has been tested in a number of simulated missions as well as in real flights and the results of the evaluations are presented.

  • 257.
    Schön, Thomas
    et al.
    Linköping University, Department of Electrical Engineering, Automatic Control. Linköping University, The Institute of Technology.
    Karlsson, Rickard
    Linköping University, Department of Electrical Engineering, Automatic Control. Linköping University, The Institute of Technology.
    Törnqvist, David
    Linköping University, Department of Electrical Engineering, Automatic Control. Linköping University, The Institute of Technology.
    Gustafsson, Fredrik
    Linköping University, Department of Electrical Engineering, Automatic Control. Linköping University, The Institute of Technology.
    A Framework for Simultaneous Localization and Mapping Utilizing Model Structure2007In: Proceedings of the 10th International Conference on Information Fusion, 2007, p. 1-8Conference paper (Refereed)
    Abstract [en]

    This contribution aims at unifying two recent trends in applied particle filtering (PF). The first trend is the major impact in simultaneous localization and mapping (SLAM) applications, utilizing the FastSLAM algorithm. The second one is the implications of the marginalized particle filter (MPF) or the Rao-Blackwellized particle filter (RBPF) in positioning and tracking applications. An algorithm is introduced, which merges FastSLAM and MPF, and the result is an MPF algorithm for SLAM applications, where state vectors of higher dimensions can be used. Results using experimental data from a 3D SLAM development environment, fusing measurements from inertial sensors (accelerometer and gyro) and vision are presented.

  • 258.
    Dutta, Rahul Kumar
    Linköping University, Department of Computer and Information Science. Linköping University, Faculty of Science & Engineering.
    A Framework for Software Security Testing and Evaluation2015Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Security in automotive industry is a thought of concern these days. As more smart electronic devices are getting connected to each other, the dependency on these devices are urging us to connect them with moving objects such as cars, buses, trucks etc. As such, safety and security issues related to automotive objects are becoming more relevant in the realm of internet connected devices and objects. In this thesis, we emphasize on certain factors that introduces security vulnerabilities in the implementation phase of Software Development Life Cycle (SDLC). Input invalidation is one of them that we address in our work. We implement a security evaluation framework that allows us to improve security in automotive software by identifying and removing software security vulnerabilities that arise due to input invalidation reasons during SDLC. We propose to use this framework in the implementation and testing phase so that the critical deficiencies of software in security by design issues could be easily addressed and mitigated.

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  • 259.
    Taxén, Lars
    Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    A Framework for the Coordination of Complex Systems’ Development2003Doctoral thesis, monograph (Other academic)
    Abstract [en]

    This study is about the coordination of complex systems’ development. A Framework has been designed and deployed by the author in the development practice of Ericsson, a major supplier of telecommunication systems on the global market. The main purpose of the study is to investigate the impacts on coordination from the Framework. The development projects are very large and subject to turbulent market conditions. Moreover, they have many participants (often several thousand), have tight time constraints and are distributed to many design centres all over the world. In these projects, coordination of the development is of crucial importance. The Framework is grounded in a tentative theory called the Activity Domain Theory, which in turn is based on the praxis philosophy. In this theory the interaction between the individual and her environment is mediated by signs. Coordination is conceived as a particular activity domain which provides coordination to the development projects. The coordination domain is gradually constructed by the actors in this domain by iteratively refining a conceptual model, a process model, a transition model, a stabilizing core and information system support. In this process individual knowledge, shared meaning and organizational artefacts evolve in a dialectical manner. The Framework has been introduced in the Ericsson development practice over a period of more than ten years. Between 1999 and 2002 approximately 140 main projects and sub-projects at Ericsson have been impacted by the Framework. These projects were distributed to more than 20 different development units around the world and were carried out in a fiercely turbulent environment. The findings indicate that the Framework has had a profound impact on the coordination of the development of the most complex nodes in the 3rd generation of mobile systems. The knowledge contributions include an account for the history of the Framework at Ericsson and an identification of elements which contribute to successful outcomes of development projects.

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  • 260.
    Flodström, Raquel
    Linköping University, Department of Management and Engineering. Linköping University, The Institute of Technology.
    A Framework for the Strategic Management of Information Technology2006Licentiate thesis, monograph (Other academic)
    Abstract [en]

    Strategy and IT research has been extensively discussed during the past 40 years. Two scientific disciplines Management Science (MS) and Management Information Science (MIS) investigate the importance of IT as a competitive factor. However, although much research is available in both disciplines, it is still difficult to explain how to manage IT to enable competitive advantages. One reason is that MS research focuses on strategies and competitive environments but avoids the analysis of IT. Another reason is that MIS research focuses on IT as a competitive factor but avoids the analysis of the competitive environment. Consequently, there is a gap of knowledge in the understanding of the strategic management of information technology (SMIT).

    The strategic analysis of IT as a competitive factor is important for achieving the competitive advantages of IT. This thesis explores factors related to strategy and IT that should be considered for the strategic analysis of IT as a competitive factor, and proposes a framework for SMIT. The research is conducted by means of a qualitative analysis of theoretical data from the disciplines of MS and MIS. Data is explored to find factors related to SMIT.

    The results of the analysis show that the strategic management of information technology is a continuous process of evaluation, change, and alignment between factors such as competitive environment, competitive strategies (business and IT strategies), competitive outcome, and competitive factors (IT). Therefore, the understanding of the relationships between these factors is essential in order to achieve the competitive advantages of using IT.

    This thesis contributes to strategic management research by clarifying the relationships between strategic management, competitive environment, and IT as competitive factor into a holistic framework for strategic analysis. The framework proposed is valuable not only for business managers and for IT managers, but also for academics. The framework is designed to understand the relationship between competitive elements during the process of strategic analysis prior to the formulation of competitive strategies. Moreover, it can also be used as a communication tool between managers, in order to achieve alignment among company strategies. To academics, this thesis presents the state-of-the-art related to strategic management research; it can also be a valuable reference for strategic managers, as well as researchers interested in the strategic management of IT.

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  • 261.
    Yi, Yangpeiqi
    et al.
    Department of Materials, University of Manchester.
    Yu, Chuang
    Department of Computer Science, University of Manchester.
    Zhai, Heng
    Department of Materials, University of Manchester.
    Jin, Lu
    Department of Materials, University of Manchester.
    Cheng, Dongxu
    Department of Mechanical, Aerospace and Civil Engineering, University of Manchester.
    Lu, Yifeng
    College of Architecture, Hunan University.
    Chen, Zhongda
    Department of Materials, University of Manchester.
    Xu, Lulu
    Department of Materials, University of Manchester.
    Li, Jiashen
    Department of Materials, University of Manchester.
    Song, Qinwen
    School of Textile Science and Engineering, Xi’an Polytechnic University.
    Yue, Pengfei
    School of Textile Science and Engineering, Xi’an Polytechnic University.
    Liu, Zekun
    Department of Materials, University of Manchester.
    Li, Yi
    Department of Materials, University of Manchester and School of Textile Science and Engineering, Xi’an Polytechnic University.
    A free-standing humidity sensor with high sensing reliability for environmental and wearable detection2022In: Nano Energy, ISSN 2211-2855, E-ISSN 2211-3282, Vol. 103, p. 107780-107780, article id 107780Article in journal (Refereed)
    Abstract [en]

    Humidity measurement has been of extreme importance in both conventional environment monitoring and emerging digital health management. State-of-the-art flexible humidity sensors with combined structures, however, lack sensing reliability when they subject to high humidity with condensation and/or liquid water invasion. Here, we report a free-standing humidity sensor by creating a stable open porous graphite structure and controlling the number of oxygen-related groups at the molecular level. The sensor indicates high sensing reliability against water liquid wetting and machine washing as well as many mechanical deformations. We demonstrate the sensor has wide potential applications in challenge environmental monitoring and wearable body area sensing networks. Particularly, the concept of the humidity sensing strategy is applicative to not only cellulose-based materials such as cotton and linen, but also protein-based materials such as silk, paving a new route for producing high-performance and cost-effective humidity sensors.

  • 262.
    Karlsson, Daniel
    et al.
    Linköping University, The Institute of Technology. Linköping University, Department of Computer and Information Science, ESLAB - Embedded Systems Laboratory.
    Eles, Petru Ion
    Linköping University, The Institute of Technology. Linköping University, Department of Computer and Information Science, ESLAB - Embedded Systems Laboratory.
    Peng, Zebo
    Linköping University, The Institute of Technology. Linköping University, Department of Computer and Information Science, ESLAB - Embedded Systems Laboratory.
    A Front End to a Java Based Environment for the Design of Embedded Systems2001In: 4th IEEE DDECS Workshop,2001, 2001, p. 71-78Conference paper (Refereed)
    Abstract [en]

    During the design of embedded systems, at a certain point, the specification has to be transformed into an internal design representation. From that representation it should be possible to further perform system partitioning, mapping and scheduling. This report provides a framework to specify a system in Java and a way to automatically translate that specification into an internal design representation. That design representation is the Conditional Process Graph which captures both the data and the control flow at process level.

  • 263.
    Harris, L. F.
    et al.
    Dublin Institute Technology, Ireland.
    Rainey, P.
    Queens University of Belfast, North Ireland.
    Lindahl, Tomas
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology and Molecular Medicine. Linköping University, Faculty of Medicine and Health Sciences. Region Östergötland, Center for Diagnostics, Department of Clinical Chemistry.
    Killard, A. J.
    University of West England, England.
    A fully integrated microfluidic device for point of care monitoring of antithrombotics2016In: Analytical Methods, ISSN 1759-9660, E-ISSN 1759-9679, Vol. 8, no 35, p. 6500-6505Article in journal (Refereed)
    Abstract [en]

    The simplicity and efficiency of point of care diagnostics have revolutionised patient care. Current methods for measuring hypercoagulability often require trained technicians, large blood volumes, and result in long turnaround times. Standard testing for hypercoagulable disorders is performed in the central laboratory using automated coagulation analysers. However the trend is moving towards the development and implementation of point of care testing, as a result of the ever increasing number of patients on antithrombotic therapy. We present a novel microfluidic device and assay for monitoring the effect of two anticoagulants, unfractionated heparin (UFH) and low molecular weight heparin (LMWH). The assay is based on the anti-Xa assay principle but uses fluorescence detection. Our device is a disposable laminate microfluidic strip, fabricated from the cyclic polyolefin (COP), Zeonor (R), which is extremely suitable for application to fluorescent device platforms. We present data on the execution of the anti-Xa assay in this microfluidic format, demonstrating that the assay can be used to measure both UFH and LMWH in human plasma samples from 0 to 1 U mL(-1), with a rapid result obtained within 30-60 seconds.

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  • 264.
    Kindberg, Elin
    et al.
    Linköping University, Department of Clinical and Experimental Medicine, Molecular Virology. Linköping University, Faculty of Health Sciences.
    Vene, Sirkka
    Swedish Institute Infectious Disease Control.
    Mickiene, Aukse
    Kaunas University of Medicine.
    Lundkvist, Ake
    Swedish Institute Infectious Disease Control.
    Lindquist, Lars
    Karolinska University.
    Svensson, Lennart
    Linköping University, Department of Clinical and Experimental Medicine, Molecular Virology. Linköping University, Faculty of Health Sciences.
    A Functional Toll-Like Receptor 3 Gene (TLR3) May Be a Risk Factor for Tick-borne Encephalitis Virus (TBEV) Infection2011In: JOURNAL OF INFECTIOUS DISEASES, ISSN 0022-1899, Vol. 203, no 4, p. 523-528Article in journal (Refereed)
    Abstract [en]

    Background. Tick-borne encephalitis virus (TBEV) infections may be asymptomatic or cause severe symptoms in the central nervous system. A mutation in the chemokine receptor 5 gene has been associated with increased risk of TBE but explains only a limited number of cases. Investigations of further risk factors are needed. Method. To investigate the importance of the innate immune response, we analyzed 128 TBE patients, 77 patients with aseptic meningoencephalitis (AME) and 135 healthy controls, for 3mutations: 2 in the Toll-like receptor 3 (TLR3) gene and 1 in the 2-5-oligoadenylate synthetase (OAS1) gene. Results. Although no association was found between the mutation in the OAS1 gene and TBE, the genotype distribution ofrs3775291, a mutation in TLR3, differed significantly between TBE patients and controls; 61%, 32%, and 7% of the TBE patients were carriers of the wild-type, heterozygous, and mutant genotype of rs3775291, respectively. The corresponding percentages among healthy controls (n = 126) were 52%, 29%, and 19% (P = .02), and among AME patients (n = 75) were 47%, 32%, and 21% (P = .009). Additionally, the wild-type rs3775291 allele was more common among TBE patients than among healthy controls (allele frequency, .768 vs .663; P = .01). Conclusion. A functional TLR3 is a risk factor for TBEV infection.

  • 265.
    Lööw, Andreas
    Linköping University, Department of Computer and Information Science, Software and Systems. Linköping University, The Institute of Technology.
    A Functional-Level Simulator for the Configurable (Many-Core) PRAM-Like REPLICA Architecture2012Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    This master's thesis discusses the design and implementation of a simulator for the REPLICA architecture, a many-core PRAM-like machine. REPLICA provides a programming model that seemingly cannot be provided by mainstream hardware without significant slowdown compared to traditional models. This also implies that it is difficult to simulate REPLICA's programming model on mainstream hardware. Simulator design decisions are described and the resulting simulator is evaluated and compared to existing simulators, where we see that the simulator presented in this thesis is the fastest of them. As seen from the discussion focus in the thesis, most efforts were directed towards simulator execution speed rather than user-facing features.

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  • 266.
    Nordgren, Johan
    et al.
    Linköping University, Department of Clinical and Experimental Medicine, Medical Microbiology . Linköping University, Faculty of Health Sciences.
    Kindberg, Elin
    Linköping University, Department of Clinical and Experimental Medicine, Molecular Virology . Linköping University, Faculty of Health Sciences.
    Lindgren, Per-Eric
    Linköping University, Department of Clinical and Experimental Medicine, Medical Microbiology . Linköping University, Faculty of Health Sciences.
    Matussek, Andreas
    Department of Clinical Microbiology, Division of Laboratory Medicine, County Hospital Ryhov, Jönköping, Sweden/Department of Clinical Microbiology, Capio Diagnostik AB, Capio St Görans Hospital, Stockholm, Sweden.
    Svensson, Lennart
    Linköping University, Department of Clinical and Experimental Medicine, Molecular Virology . Linköping University, Faculty of Health Sciences.
    A FUT2 nonsense mutation (G428A) and Lewis-independent norovirus GI.3 outbreak2009Article in journal (Other academic)
    Abstract [en]

    Background: Norovirus (NoV) is recognized as the commonest cause of acute gastroenteritis among adults. Previous studies have shown that histo-blood group antigens (HBGAs) and secretor status are associated with susceptibility to symptomatic NoV infection, with non-secretors being almost completely resistant to disease. Here we report on a food-borne GI.3 NoV outbreak affecting 33/83 (40%) individuals.

    Methods: Secretor status and HBGA expression in saliva were determined with pyrosequencing and ELISA. Virus characterization was performed by sequencing the N/S region and the complete capsid gene.

    Results: A novel observation was that homozygous carriers of the nonsense FUT2 G428A allele were more susceptible to symptomatic infection than secretors (odds ratio [OR] 1.41 vs 0.71). Consistent with this observation was that Lewis a positive b negative (Lea+b-) individuals showed the highest susceptibility (OR 2.42) compared with other Lewis phenotypes. Blood group B was associated with partial protection (OR 0.27). The capsid gene of the outbreak strain exhibits high amino acid homology with the Kashiwa645 GI.3 strain, previously shown to recognize non-secretor saliva.

    Conclusion: We describe for the first time a NoV outbreak with Lea+b- individuals homozygous for the G428A nonsense mutation in the FUT2 gene being more susceptible for disease than secretor-positive individuals.

  • 267.
    Sandstrom, KJM
    et al.
    Natl Institute Working Life, SE-90713 Umea, Sweden; Cranfield University, Cranfield Biotechnol Centre, Silsoe MK45 4DT, Beds, England; .
    Sunesson, AL
    Natl Institute Working Life, SE-90713 Umea, Sweden; Cranfield University, Cranfield Biotechnol Centre, Silsoe MK45 4DT, Beds, England; .
    Levin, JO
    Natl Institute Working Life, SE-90713 Umea, Sweden; Cranfield University, Cranfield Biotechnol Centre, Silsoe MK45 4DT, Beds, England; .
    Turner, APF
    Cranfield University, UK.
    A gas-phase biosensor for environmental monitoring of formic acid: laboratory and field validation2003In: Journal of Environmental Monitoring, ISSN 1464-0325, E-ISSN 1464-0333, Vol. 5, no 3, p. 477-482Article in journal (Refereed)
    Abstract [en]

    In order to encourage more exposure measurements to be performed, a formic acid gas-phase biosensor has been developed for this purpose. In the present paper, an enzyme based biosensor has been validated with respect to analyte selectivity and on-site use. To ensure that the sampler developed measures the compound of interest the biosensor was exposed to three near structural homologues to formic acid, i.e. acetic acid, methanol and formaldehyde. These vapours were generated with and without formic acid and the only compound that was found to have an effect on the performance of the biosensor, albeit a small one, was acetic acid. The field test was performed in a factory using formic acid-containing glue for glulam products. In parallel to the measurements with the biosensor a well defined reference method was used for sampling and analysing formic acid. It was found that the biosensor worked satisfactorily in this environment when used in a stationary position. It was also shown that the biosensor could determine formic acid vapour concentrations down to 0.03 mg m(-3).

  • 268.
    Sederholm Lawesson, Sofia
    et al.
    Linköping University, Department of Medical and Health Sciences, Cardiology. Linköping University, Faculty of Health Sciences. Östergötlands Läns Landsting, Heart and Medicine Center, Department of Cardiology in Linköping.
    Alfredsson, Joakim
    Linköping University, Department of Medical and Health Sciences, Cardiology. Linköping University, Faculty of Health Sciences. Östergötlands Läns Landsting, Heart and Medicine Center, Department of Cardiology in Linköping.
    Fredrikson, Mats
    Linköping University, Department of Clinical and Experimental Medicine, Occupational and Environmental Medicine. Linköping University, Faculty of Health Sciences.
    Swahn, Eva
    Linköping University, Department of Medical and Health Sciences, Cardiology. Linköping University, Faculty of Health Sciences. Östergötlands Läns Landsting, Heart and Medicine Center, Department of Cardiology in Linköping.
    A gender perspective on short- and long term mortality in ST-elevation myocardial infarction: a report from the SWEDEHEART register2013In: International Journal of Cardiology, ISSN 0167-5273, E-ISSN 1874-1754, Vol. 18, no 2, p. 1041-1047Article in journal (Refereed)
    Abstract [en]

    Background: Previous studies of patients admitted for ST-elevation myocardial infarction [STEMI] have indicated that women have a higher risk of early mortality than do men. These studies have presented limited information on gender related differences in the short term and almost no information on the long term. Methods and results: We analysed a prospective, consecutively included STEMI population consisting of 54,146 patients (35% women). This population consists of almost all patients hospitalised in Sweden between January 1, 1995 and December 31, 2006 as recorded in the SWEDEHEART register (formerly RIKS-HIA). Follow-up time ranged from one to 13 years (mean 4.6). Women had a lower probability of being given reperfusion therapy, odds ratio [OR] 0.83 (95% confidence interval [CI] 0.79-0.88). During the time these STEMI patients were in the hospital, 13% of the women and 7% of men died, multivariable adjusted OR 1.21 (95% CI 1.11-1.32). During the follow up period, 46% of the women died as compared with 32% of the men. There was, however, no gender difference in age-adjusted risk of long term mortality (hazard ratio [HR] 0.98, 95% CI 0.95-1.01) whereas the multivariable adjusted risk was lower in women (HR 0.92, 95% CI 0.89-0.96). The long term risk of re-infarction was the same in men and women (HR 0.98, 95% CI 0.93-1.03) whereas men in the youngest group had a higher risk than women in that age group (HR 0.82, 95% CI 0.72-0.94). Conclusion: In STEMI, women had a higher risk of in-hospital mortality but the long-term risk of death was higher in men. More studies are needed in the primary percutaneous coronary intervention (pPCI) era that are designed to determine why women fare worse than men after STEMI during the first phase when they are in hospital

  • 269.
    Liljedahl, Helena
    et al.
    Lund Univ, Sweden.
    Karlsson, Anna
    Lund Univ, Sweden.
    Oskarsdottir, Gudrun N.
    Lund Univ, Sweden; Skane Univ Hosp, Sweden.
    Salomonsson, Annette
    Lund Univ, Sweden.
    Brunnstrom, Hans
    Lund Univ, Sweden; Lab Med Reg Skane, Sweden.
    Erlingsdottir, Gigja
    Landspitali Univ Hosp, Iceland; Skane Univ Hosp, Sweden.
    Jonsson, Mats
    Lund Univ, Sweden.
    Isaksson, Sofi
    Lund Univ, Sweden.
    Arbajian, Elsa
    Lund Univ, Sweden.
    Ortiz-Villalon, Cristian
    Karolinska Univ Hosp, Sweden.
    Hussein, Aziz
    Sahlgrens Univ Hosp, Sweden.
    Bergman, Bengt
    Sahlgrens Univ Hosp, Sweden.
    Vikström, Anders
    Region Östergötland, Center for Surgery, Orthopaedics and Cancer Treatment, Department of Respiratory Medicine.
    Nastaran, Nastaran
    Linköping University, Department of Clinical and Experimental Medicine, Divison of Neurobiology. Linköping University, Faculty of Medicine and Health Sciences. Region Östergötland, Center for Diagnostics, Clinical pathology.
    Branden, Eva
    Karolinska Inst, Sweden; Karolinska Univ Hosp Solna, Sweden; Uppsala Univ Reg Gavleborg, Sweden.
    Koyi, Hirsh
    Karolinska Inst, Sweden; Karolinska Univ Hosp Solna, Sweden; Uppsala Univ Reg Gavleborg, Sweden.
    de Petris, Luigi
    Karolinska Univ Hosp, Sweden; Karolinska Inst, Sweden.
    Patthey, Annika
    Umea Univ, Sweden.
    Behndig, Annelie F.
    Umea Univ, Sweden.
    Johansson, Mikael
    Umea Univ, Sweden.
    Planck, Maria
    Lund Univ, Sweden; Skane Univ Hosp, Sweden.
    Staaf, Johan
    Lund Univ, Sweden.
    A gene expression-based single sample predictor of lung adenocarcinoma molecular subtype and prognosis2021In: International Journal of Cancer, ISSN 0020-7136, E-ISSN 1097-0215, Vol. 148, no 1, p. 238-251Article in journal (Refereed)
    Abstract [en]

    Disease recurrence in surgically treated lung adenocarcinoma (AC) remains high. New approaches for risk stratification beyond tumor stage are needed. Gene expression-based AC subtypes such as the Cancer Genome Atlas Network (TCGA) terminal-respiratory unit (TRU), proximal-inflammatory (PI) and proximal-proliferative (PP) subtypes have been associated with prognosis, but show methodological limitations for robust clinical use. We aimed to derive a platform independent single sample predictor (SSP) for molecular subtype assignment and risk stratification that could function in a clinical setting. Two-class (TRU/nonTRU=SSP2) and three-class (TRU/PP/PI=SSP3) SSPs using the AIMS algorithm were trained in 1655 ACs (n = 9659 genes) from public repositories vs TCGA centroid subtypes. Validation and survival analysis were performed in 977 patients using overall survival (OS) and distant metastasis-free survival (DMFS) as endpoints. In the validation cohort, SSP2 and SSP3 showed accuracies of 0.85 and 0.81, respectively. SSPs captured relevant biology previously associated with the TCGA subtypes and were associated with prognosis. In survival analysis, OS and DMFS for cases discordantly classified between TCGA and SSP2 favored the SSP2 classification. In resected Stage I patients, SSP2 identified TRU-cases with better OS (hazard ratio [HR] = 0.30; 95% confidence interval [CI] = 0.18-0.49) and DMFS (TRU HR = 0.52; 95% CI = 0.33-0.83) independent of age, Stage IA/IB and gender. SSP2 was transformed into a NanoString nCounter assay and tested in 44 Stage I patients using RNA from formalin-fixed tissue, providing prognostic stratification (relapse-free interval, HR = 3.2; 95% CI = 1.2-8.8). In conclusion, gene expression-based SSPs can provide molecular subtype and independent prognostic information in early-stage lung ACs. SSPs may overcome critical limitations in the applicability of gene signatures in lung cancer.

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  • 270.
    Bernardi, R. E.
    et al.
    Heidelberg University, Germany.
    Zohsel, K.
    Heidelberg University, Germany.
    Hirth, N.
    Heidelberg University, Germany.
    Treutlein, J.
    Heidelberg University, Germany.
    Heilig, Markus
    Linköping University, Department of Clinical and Experimental Medicine, Division of Neuro and Inflammation Science. Linköping University, Faculty of Medicine and Health Sciences. Linköping University, Center for Social and Affective Neuroscience (CSAN). Region Östergötland, Local Health Care Services in Central Östergötland, Department of Psychiatry.
    Laucht, M.
    Heidelberg University, Germany.
    Spanagel, R.
    Heidelberg University, Germany.
    Sommer, W. H.
    Heidelberg University, Germany.
    A gene-by-sex interaction for nicotine reward: evidence from humanized mice and epidemiology2016In: Translational Psychiatry, E-ISSN 2158-3188, Vol. 6, no e861Article in journal (Refereed)
    Abstract [en]

    It has been proposed that vulnerability to nicotine addiction is moderated by variation at the mu-opioid receptor locus (OPRM1), but results from human studies vary and prospective studies based on genotype are lacking. We have developed a humanized mouse model of the most common functional OPRM1 polymorphism rs1799971_A4G (A118G). Here we use this model system together with a cohort of German youth to examine the role of the OPRM1 A118G variation on nicotine reward. Nicotine reinforcement was examined in the humanized mouse model using i.v. self-administration. Male (n = 17) and female (n = 26) mice homozygous either for the major human A allele (AA) or the minor G allele (GG) underwent eight daily 2 h sessions of nicotine self-administration. Furthermore, male (n = 104) and female (n = 118) subjects homozygous for the A allele or carrying the G allele from the Mannheim Study of Children at Risk were evaluated for pleasurable and unpleasant experiences during their initial smoking experience. A significant sex-by-genotype effect was observed for nicotine self-administration. Male 118GG mice demonstrated higher nicotine intake than male 118AA mice, suggesting increased nicotine reinforcement. In contrast, there was no genotype effect in female mice. Human male G allele carriers reported increased pleasurable effects from their first smoking experience, as compared to male homozygous A, female G and female homozygous A allele carriers. The 118G allele appears to confer greater sensitivity to nicotine reinforcement in males, but not females.

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  • 271.
    Pettersson, Mikael
    et al.
    Linköping University, Department of Computer and Information Science. Linköping University, The Institute of Technology.
    Fritzson, Peter
    Linköping University, Department of Computer and Information Science, PELAB - Programming Environment Laboratory. Linköping University, The Institute of Technology.
    A General and Practical Approach to Concrete Syntax Objects within ML1992Conference paper (Refereed)
    Abstract [en]

    The ML programming language has been an important tool and framework for research in language design and implementation. As the language and its implementations have matured, the range of applications has increased greatly. New applications, combined with new ideas in design and implementation, have stimulated a large number of significant activities in research and software development. This workshop, like the previous workshops in Princeton, Edinburgh, and Pittsburgh, provides a forum for these activities, with a special emphasis on applications of the language.

  • 272.
    Kling, Daniel
    et al.
    Norwegian Institute Public Heatlh, Norway; Norwegian University of Life Science, Norway.
    Tillmar, Andreas
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology and Molecular Medicine. Linköping University, Faculty of Medicine and Health Sciences. National Board Forens Med, Department Forens Genet and Forens Toxicol, Linkoping, Sweden.
    Egeland, Thore
    Norwegian University of Life Science, Norway; Norwegian Institute Public Heatlh, Norway.
    Mostad, Petter
    Norwegian University of Life Science, Norway; University of Gothenburg, Sweden.
    A general model for likelihood computations of genetic marker data accounting for linkage, linkage disequilibrium, and mutations2015In: International journal of legal medicine, ISSN 0937-9827, E-ISSN 1437-1596, Vol. 129, no 5, p. 943-954Article in journal (Refereed)
    Abstract [en]

    Several applications necessitate an unbiased determination of relatedness, be it in linkage or association studies or in a forensic setting. An appropriate model to compute the joint probability of some genetic data for a set of persons given some hypothesis about the pedigree structure is then required. The increasing number of markers available through high-density SNP microarray typing and NGS technologies intensifies the demand, where using a large number of markers may lead to biased results due to strong dependencies between closely located loci, both within pedigrees (linkage) and in the population (allelic association or linkage disequilibrium (LD)). We present a new general model, based on a Markov chain for inheritance patterns and another Markov chain for founder allele patterns, the latter allowing us to account for LD. We also demonstrate a specific implementation for X chromosomal markers that allows for computation of likelihoods based on hypotheses of alleged relationships and genetic marker data. The algorithm can simultaneously account for linkage, LD, and mutations. We demonstrate its feasibility using simulated examples. The algorithm is implemented in the software FamLinkX, providing a user-friendly GUI for Windows systems (FamLinkX, as well as further usage instructions, is freely available at www.famlink.se). Our software provides the necessary means to solve cases where no previous implementation exists. In addition, the software has the possibility to perform simulations in order to further study the impact of linkage and LD on computed likelihoods for an arbitrary set of markers.

  • 273.
    Sheshadri, Krishnamurthy
    et al.
    Connexios Life Sciences, Bangalore, India.
    Fritzson, Peter
    Linköping University, Department of Computer and Information Science, PELAB - Programming Environment Laboratory. Linköping University, The Institute of Technology.
    A general symbolic PDE solver generator: Beyond explicit schemes2003In: Scientific Programming, ISSN 1058-9244, E-ISSN 1875-919X, Vol. 11, no 3, p. 225-235Article in journal (Refereed)
    Abstract [en]

    This paper presents an extension of our Mathematica- and MathCode-based symbolic-numeric framework for solving a variety of partial differential equation (PDE) problems. The main features of our earlier work, which implemented explicit finite-difference schemes, include the ability to handle (1) arbitrary number of dependent variables, (2) arbitrary dimensionality, and (3) arbitrary geometry, as well as (4) developing finite-difference schemes to any desired order of approximation. In the present paper, extensions of this framework to implicit schemes and the method of lines are discussed. While C++ code is generated, using the MathCode system for the implicit method, Modelica code is generated for the method of lines. The latter provides a preliminary PDE support for the Modelica language. Examples illustrating the various aspects of the solver generator are presented.

  • 274.
    Sheshadri, Krishnamurthy
    et al.
    Connexios Life Sciences, Bangalore, India.
    Fritzson, Peter
    Linköping University, Department of Computer and Information Science, PELAB - Programming Environment Laboratory. Linköping University, The Institute of Technology.
    A General Symbolic PDE-Solver Generator: Explicit Schemes2003In: Scientific Programming, ISSN 1058-9244, E-ISSN 1875-919X, Vol. 11, no 1, p. 39-55Article in journal (Refereed)
    Abstract [en]

    A symbolic solver generator to deal with a system of partial differential equations (PDEs) in functions of an arbitrary number of variables is presented; it can also handle arbitrary domains (geometries) of the independent variables. Given a system of PDEs, the solver generates a set of explicit finite-difference methods to any specified order, and a Fourier stability criterion for each method. For a method that is stable, an iteration function is generated symbolically using the PDE and its initial and boundary conditions. This iteration function is dynamically generated for every PDE problem, and its evaluation provides a solution to the PDE problem. A C++/Fortran 90 code for the iteration function is generated using the MathCode system, which results in a performance gain of the order of a thousand over Mathematica, the language that has been used to code the solver generator. Examples of stability criteria are presented that agree with known criteria; examples that demonstrate the generality of the solver and the speed enhancement of the generated C++ and Fortran 90 codes are also presented.

  • 275.
    Bruhn, Sören
    et al.
    Linköping University, Department of Clinical and Experimental Medicine, Division of Clinical Sciences. Linköping University, Faculty of Health Sciences.
    Fang, Yu
    Guiyang Medical Coll, Peoples R China University of Gothenburg, Sweden .
    Barrenäs, Fredrik
    Linköping University, Department of Clinical and Experimental Medicine, Division of Clinical Sciences. Linköping University, Faculty of Health Sciences.
    Gustafsson, Mika
    Linköping University, Department of Clinical and Experimental Medicine, Division of Clinical Sciences. Linköping University, Faculty of Health Sciences.
    Zhang, Huan
    Linköping University, Department of Clinical and Experimental Medicine, Division of Clinical Sciences. Linköping University, Faculty of Health Sciences.
    Konstantinell, Aelita
    Linköping University, Department of Clinical and Experimental Medicine, Division of Clinical Sciences. Linköping University, Faculty of Health Sciences.
    Kronke, Andrea
    Cenix BioScience GmbH, Germany .
    Sonnichsen, Birte
    Cenix BioScience GmbH, Germany .
    Bresnick, Anne
    Albert Einstein Coll Med, NY 10461 USA .
    Dulyaninova, Natalya
    Albert Einstein Coll Med, NY 10461 USA .
    Wang, Hui
    Linköping University, Department of Clinical and Experimental Medicine, Division of Clinical Sciences. Linköping University, Faculty of Health Sciences.
    Zhao, Yelin
    Linköping University, Department of Clinical and Experimental Medicine, Division of Clinical Sciences. Linköping University, Faculty of Health Sciences.
    Klingelhofer, Jorg
    University of Copenhagen, Denmark .
    Ambartsumian, Noona
    University of Copenhagen, Denmark .
    Beck, Mette K.
    Technical University of Denmark, Denmark .
    Nestor, Colm
    Linköping University, Department of Clinical and Experimental Medicine, Division of Clinical Sciences. Linköping University, Faculty of Health Sciences.
    Bona, Elsa
    Boras Hospital, Sweden .
    Xiang, Zou
    University of Gothenburg, Sweden .
    Benson, Mikael
    Linköping University, Department of Clinical and Experimental Medicine, Division of Clinical Sciences. Linköping University, Faculty of Health Sciences. Östergötlands Läns Landsting, Heart and Medicine Center, Allergy Center. Östergötlands Läns Landsting, Center of Paediatrics and Gynaecology and Obstetrics, Department of Paediatrics in Linköping.
    A Generally Applicable Translational Strategy Identifies S100A4 as a Candidate Gene in Allergy2014In: Science Translational Medicine, ISSN 1946-6234, E-ISSN 1946-6242, Vol. 6, no 218Article in journal (Refereed)
    Abstract [en]

    The identification of diagnostic markers and therapeutic candidate genes in common diseases is complicated by the involvement of thousands of genes. We hypothesized that genes co-regulated with a key gene in allergy, IL13, would form a module that could help to identify candidate genes. We identified a T helper 2 (T(H)2) cell module by small interfering RNA-mediated knockdown of 25 putative IL13-regulating transcription factors followed by expression profiling. The module contained candidate genes whose diagnostic potential was supported by clinical studies. Functional studies of human TH2 cells as well as mouse models of allergy showed that deletion of one of the genes, S100A4, resulted in decreased signs of allergy including TH2 cell activation, humoral immunity, and infiltration of effector cells. Specifically, dendritic cells required S100A4 for activating T cells. Treatment with an anti-S100A4 antibody resulted in decreased signs of allergy in the mouse model as well as in allergen-challenged T cells from allergic patients. This strategy, which may be generally applicable to complex diseases, identified and validated an important diagnostic and therapeutic candidate gene in allergy.

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  • 276.
    Chen, W.
    et al.
    Department of Informatics, Clausthal University of Technology, Germany.
    Huhn, M.
    Department of Informatics, Clausthal University of Technology, Germany.
    Fritzson, Peter
    Linköping University, Department of Computer and Information Science.
    A generic FMU interface for modelica2011In: Proceedings of the 4th International Workshop on Equation-Based Object-Oriented Modeling Languages and Tools, EOOLT 2011, 2011, p. 19-24Conference paper (Refereed)
    Abstract [en]

    This paper discusses technical issues and implementation of a generic interface to import a Functional Mock-up Unit (FMU) into Modelica simulators, specifically the Open- Modelica environment. Whereas other approaches for importing the FMUs rely on functionality specific to the simulator environment, this approach tries to provide a generic Modelica interface for embedding an FMU to be imported into a Modelica model. In this way any FMU conforming to the Functional Mock-up Interface (FMI) for Model Exchange v1.0 Specification for model exchange from MODELISAR can be imported into any Modelica simulator. When importing an FMU into a model, the resulting Modelica model can be used just like any pure Modelica models. Hence, a better reusability and interoperability for both sides, namely the external models provided via FMI and the Modelica environment, are achieved.

  • 277.
    Lind Jonsson, Oskar
    Linköping University, Department of Electrical Engineering, Vehicular Systems. Fordonssystem LiU.
    A GENeric Internal Combustion Engine model: LiU-Genie2021Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    As the demand for control in modern vehicles grows, models are needed to develop a better understanding of processes and engine behavior. The thesis contributes with a generic extended MVEM with SI and CI as well as VVA compatibility and modeling structure using MATLAB/Simulink environment. 

    The model contains the engine components air filter, compressor with bypass valve, intercooler, throttle, intake manifold, cylinder, exhaust manifold, EGR, turbine with a wastegate, and exhaust system, keeping track of pressures, mass flows, temperatures, and oxygen concentrations. 

    This thesis presents models, parametrization, and signals that needed to be measured to make it possible to parametrize other engines with the same method. A 6-cylinder 12.7 liter Scania diesel engine and a 4-cylinder 2 liter Volvo petrol engine are used to validate the model. The model shows agreement with measured data for pressure, mass flow, temperature, and oxygen concentration on several operational points. That shows the model can handle most engines with just small adjustments. The component-based model structure also enables the possibility to change and adjust the models used by, for example using the extended ellipse model for compressor efficiency or implement a double Vibe function for combustion calculations.

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  • 278.
    Schminder, Jörg
    et al.
    Linköping University, Department of Management and Engineering, Applied Thermodynamics and Fluid Mechanics. Linköping University, Faculty of Science & Engineering.
    Gårdhagen, Roland
    Linköping University, Department of Management and Engineering, Applied Thermodynamics and Fluid Mechanics. Linköping University, Faculty of Science & Engineering.
    A generic simulation model for prediction of thermal conditions and human performance in cockpits2018In: Building and Environment, ISSN 0360-1323, E-ISSN 1873-684X, Vol. 143, p. 120-129Article in journal (Refereed)
    Abstract [en]

    This paper presents a computational approach to predict the thermal environment in a cockpit during on-ground and in-flight aircraft operation. A method was developed to model cockpit air temperature, which serves as input to black-globe and wet-bulb temperature computation. Subsequently the simulated temperatures are used to compute common heat stress indices such as Wet Bulb Globe Temperature (WBGT), Fighter Index of Thermal Stress (FITS), or Predicted Mean Vote (PMV). To demonstrate the manifold information made available by the computed heat stress indices, WBGT e.g. is set in relation to different types of occupational exposure limits demonstrating not only the possibility to predict physiological constraints but mental performance too. The generic cockpit model and thermal comfort computations were validated against experimental data gained from on ground temperature measurements inside an aircraft cockpit, which underwent a sudden large temperature change. The results exemplify how thermal comfort and possible physical as well as mental degradation of aircrews can be assessed quickly using the presented model.

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  • 279.
    Benito-Sipos, Jonathan
    et al.
    University Autonoma of Madrid.
    Estacio-Gomez, Alicia
    University Autonoma of Madrid.
    Moris-Sanz, Marta
    University Autonoma of Madrid.
    Baumgardt, Magnus
    Linköping University, Faculty of Health Sciences. Linköping University, Department of Clinical and Experimental Medicine, Developmental Biology, IKE.
    Thor, Stefan
    Linköping University, Faculty of Health Sciences. Linköping University, Department of Clinical and Experimental Medicine, Developmental Biology, IKE.
    J Diaz-Benjumea, Fernando
    University Autonoma of Madrid.
    A genetic cascade involving klumpfuss, nab and castor specifies the abdominal leucokinergic neurons in the Drosophila CNS2010In: DEVELOPMENT, ISSN 0950-1991, Vol. 137, no 19, p. 3327-3336Article in journal (Refereed)
    Abstract [en]

    Identification of the genetic mechanisms underlying the specification of large numbers of different neuronal cell fates from limited numbers of progenitor cells is at the forefront of developmental neurobiology. In Drosophila, the identities of the different neuronal progenitor cells, the neuroblasts, are specified by a combination of spatial cues. These cues are integrated with temporal competence transitions within each neuroblast to give rise to a specific repertoire of cell types within each lineage. However, the nature of this integration is poorly understood. To begin addressing this issue, we analyze the specification of a small set of peptidergic cells: the abdominal leucokinergic neurons. We identify the progenitors of these neurons, the temporal window in which they are specified and the influence of the Notch signaling pathway on their specification. We also show that the products of the genes klumpfuss, nab and castor play important roles in their specification via a genetic cascade.

  • 280.
    Benito-Sipos, Jonathan
    et al.
    Centro de Biología Molecular-Severo Ochoa, Universidad Autónoma de Madrid-C.S.I.C., Madrid, Spain.
    Estacio-Gómez, Alicia
    Centro de Biología Molecular-Severo Ochoa, Universidad Autónoma de Madrid-C.S.I.C., Madrid, Spain.
    Moris-Sanz, Marta
    Centro de Biología Molecular-Severo Ochoa, Universidad Autónoma de Madrid-C.S.I.C., Madrid, Spain.
    Baumgardt, Magnus
    Linköping University, Department of Clinical and Experimental Medicine, Developmental Biology, IKE. Linköping University, Faculty of Health Sciences.
    Thor, Stefan
    Linköping University, Department of Clinical and Experimental Medicine, Developmental Biology, IKE. Linköping University, Faculty of Health Sciences.
    Díaz-Benjumea, Fernando J.
    Centro de Biología Molecular-Severo Ochoa, Universidad Autónoma de Madrid-C.S.I.C., Madrid, Spain.
    A genetic cascade involving the genes klumfuss, nab and castor specifies the abdominal leucokinergic neurons in the Drosophila CNSManuscript (preprint) (Other academic)
    Abstract [en]

    The genetic mechanisms underlying the specification of a large number of different cell fates starting from a limited group of progenitor cells are a major focus of investigations of central nervous system development. In Drosophila the identities of the different neuronal progenitor cells, the neuroblasts, are specified by a combination of spatial and temporal factors. But how each neuroblast gives rise to a specific repertoire of cell types via a precise programme is poorly understood. In this report we analyse the specification of a small set of peptidergic cells, the abdominal leucokinergic neurons. We identify the progenitors of these neurons, the temporal window in which they are specified, and the influence of the Notch signalling pathway on their specification. We also show that the products of the genes klumfuss, nab and castor play important roles in their specification via a genetic cascade.

  • 281.
    Ulvklo, Carina
    et al.
    Linköping University, Department of Clinical and Experimental Medicine, Developmental Biology. Linköping University, Faculty of Health Sciences.
    Bivik, Caroline
    Linköping University, Department of Clinical and Experimental Medicine, Developmental Biology. Linköping University, Faculty of Health Sciences.
    Fransson, Fredrik
    Linköping University, Department of Clinical and Experimental Medicine, Developmental Biology. Linköping University, Faculty of Health Sciences.
    Thor, Stefan
    Linköping University, Department of Clinical and Experimental Medicine, Developmental Biology. Linköping University, Faculty of Health Sciences.
    A genetic screen for genes controlling Ap neuron specificationManuscript (preprint) (Other academic)
    Abstract [en]

    A central theme in developmental biology pertains to how the diversity of different cell types is generated. In addition, it is important to understand how the numbers of each cell type are regulated. In the developing Drosophila ventral nerve cord, only six neurons, the Ap4 neurons, express the neuropeptide gene FMRFamide (FMRFa). This is the result of proper lineage development and a cascade of regulatory information leading to final cell specification. In addition to these cascades, FMRFa expression is critically dependent upon a retrogarade TGFβ/BMP signal from the axonal target. Its restricted expression pattern and the wealth of information regarding its gene regulation, makes FMRFa a useful marker for understanding cell specification, as well as axon path finding and retrograde signaling. To identify novel genes acting at any level of neuronal development, including pattern formation, stem cell competence, cell cycle control, cell specification, axon transport and retrograde signaling, we have conducted a single cell resolution, forward genetic screen utilizing an FMRFa-EGFP reporter as our read-out. A total of 9,781 EMS-mutated chromosomes were screened for perturbations in FMRFa-EGFP expression, and 611 mutants were identified. Complementation tests showed that many of the previously known regulators had been isolated, which confirmed the validity of the screen. However, in addition to these known genes, the majority of mutants represent novel genes with previously undefined functions in neural development.

  • 282.
    Bivik, Caroline
    et al.
    Linköping University, Department of Clinical and Experimental Medicine, Developmental Biology. Linköping University, Faculty of Health Sciences.
    Ulvklo, Carina
    Linköping University, Department of Clinical and Experimental Medicine, Developmental Biology. Linköping University, Faculty of Health Sciences.
    Lundin, Erika
    Linköping University, Department of Clinical and Experimental Medicine. Linköping University, Faculty of Health Sciences.
    Nilsson, Patrik
    Linköping University, Department of Clinical and Experimental Medicine. Linköping University, Faculty of Health Sciences.
    Angel, Anna
    Linköping University, Department of Clinical and Experimental Medicine, Developmental Biology. Linköping University, Faculty of Health Sciences.
    Thor, Stefan
    Linköping University, Department of Clinical and Experimental Medicine, Developmental Biology. Linköping University, Faculty of Health Sciences.
    A genetic screen for genes controlling Apterous neuron identity and FMRFamide expression2010In: Journal of neurogenetics, ISSN 0167-7063, E-ISSN 1563-5260, Vol. 24, no Suppl. 1, p. 70-71Article in journal (Other academic)
    Abstract [en]

    n/a

  • 283.
    Ulvklo, Carina
    et al.
    Linköping University, Department of Clinical and Experimental Medicine, Developmental Biology, IKE. Linköping University, Faculty of Health Sciences.
    Nilsson, Patrik
    Linköping University, Department of Clinical and Experimental Medicine. Linköping University, Faculty of Health Sciences.
    Angel, Anna
    Linköping University, Department of Clinical and Experimental Medicine, Developmental Biology, IKE. Linköping University, Faculty of Health Sciences.
    Thor, Stefan
    Linköping University, Department of Clinical and Experimental Medicine, Developmental Biology, IKE. Linköping University, Faculty of Health Sciences.
    A genetic screen for genes controlling Tv neuron identity and FMRFamide expression2009In: in MECHANISMS OF DEVELOPMENT, vol 126, 2009, Vol. 126, p. S165-S165Conference paper (Refereed)
    Abstract [en]

    n/a

  • 284.
    Huyghe, Jeroen R
    et al.
    University of Antwerp.
    Fransen, Erik
    University of Antwerp.
    Hannula, Samuli
    University of Oulu.
    Van Laer, Lut
    University of Antwerp.
    Van Eyken, Els
    University of Antwerp.
    Mäki-Torkko, Elina
    Linköping University, Department of Clinical and Experimental Medicine, Technical Audiology. Linköping University, Faculty of Health Sciences.
    Aikio, Pekka
    University of Oulu.
    Sorri, Martti
    University of Oulu.
    Huentelman, Matthew J
    Translat Genom Research Institute, Phoenix.
    Van Camp, Guy
    University of Antwerp.
    A genome-wide analysis of population structure in the Finnish Saami with implications for genetic association studies2011In: EUROPEAN JOURNAL OF HUMAN GENETICS, ISSN 1018-4813, Vol. 19, no 3, p. 347-352Article in journal (Refereed)
    Abstract [en]

    The understanding of patterns of genetic variation within and among human populations is a prerequisite for successful genetic association mapping studies of complex diseases and traits. Some populations are more favorable for association mapping studies than others. The Saami from northern Scandinavia and the Kola Peninsula represent a population isolate that, among European populations, has been less extensively sampled, despite some early interest for association mapping studies. In this paper, we report the results of a first genome-wide SNP-based study of genetic population structure in the Finnish Saami. Using data from the HapMap and the human genome diversity project (HGDP-CEPH) and recently developed statistical methods, we studied individual genetic ancestry. We quantified genetic differentiation between the Saami population and the HGDP-CEPH populations by calculating pair-wise F-ST statistics and by characterizing identity-by-state sharing for pair-wise population comparisons. This study affirms an east Asian contribution to the predominantly European-derived Saami gene pool. Using model-based individual ancestry analysis, the median estimated percentage of the genome with east Asian ancestry was 6% (first and third quartiles: 5 and 8%, respectively). We found that genetic similarity between population pairs roughly correlated with geographic distance. Among the European HGDP-CEPH populations, F-ST was smallest for the comparison with the Russians (F-ST=0.0098), and estimates for the other population comparisons ranged from 0.0129 to 0.0263. Our analysis also revealed fine-scale substructure within the Finnish Saami and warns against the confounding effects of both hidden population structure and undocumented relatedness in genetic association studies of isolated populations.

  • 285.
    Kharazmi, Mohammad
    et al.
    Uppsala Univ, Sweden.
    Michaelsson, Karl
    Uppsala Univ, Sweden.
    Schilcher, Jörg
    Linköping University, Department of Clinical and Experimental Medicine, Division of Surgery, Orthopedics and Oncology. Linköping University, Faculty of Medicine and Health Sciences. Region Östergötland, Center for Surgery, Orthopaedics and Cancer Treatment, Department of Orthopaedics in Linköping.
    Eriksson, Niclas
    Uppsala Univ, Sweden.
    Melhus, Hakan
    Uppsala Univ, Sweden.
    Wadelius, Mia
    Uppsala Univ, Sweden.
    Hallberg, Par
    Uppsala Univ, Sweden.
    A Genome-Wide Association Study of Bisphosphonate-Associated Atypical Femoral Fracture2019In: Calcified Tissue International, ISSN 0171-967X, E-ISSN 1432-0827, Vol. 105, no 1, p. 51-67Article in journal (Refereed)
    Abstract [en]

    Atypical femoral fracture is a well-documented adverse reaction to bisphosphonates. It is strongly related to duration of bisphosphonate use, and the risk declines rapidly after drug withdrawal. The mechanism behind bisphosphonate-associated atypical femoral fracture is unclear, but a genetic predisposition has been suggested. With the aim to identify common genetic variants that could be used for preemptive genetic testing, we performed a genome-wide association study. Cases were recruited mainly through reports of adverse drug reactions sent to the Swedish Medical Products Agency on a nation-wide basis. We compared atypical femoral fracture cases (n=51) with population-based controls (n=4891), and to reduce the possibility of confounding by indication, we also compared with bisphosphonate-treated controls without a current diagnosis of cancer (n=324). The total number of single-nucleotide polymorphisms after imputation was 7,585,874. A genome-wide significance threshold of pamp;lt;5x10(-8) was used to correct for multiple testing. In addition, we performed candidate gene analyses for a panel of 29 genes previously implicated in atypical femoral fractures (significance threshold of pamp;lt;5.7x10(-6)). Compared with population controls, bisphosphonate-associated atypical femoral fracture was associated with four isolated, uncommon single-nucleotide polymorphisms. When cases were compared with bisphosphonate-treated controls, no statistically significant genome-wide association remained. We conclude that the detected associations were either false positives or related to the underlying disease, i.e., treatment indication. Furthermore, there was no significant association with single-nucleotide polymorphisms in the 29 candidate genes. In conclusion, this study found no evidence of a common genetic predisposition for bisphosphonate-associated atypical femoral fracture. Further studies of larger sample size to identify possible weakly associated genetic traits, as well as whole exome or whole-genome sequencing studies to identify possible rare genetic variation conferring a risk are warranted.

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  • 286.
    Neely, G Gregory
    et al.
    Austrian Academy of Science.
    Hess, Andreas
    University of Erlangen Nurnberg.
    Costigan, Michael
    Harvard University.
    Keene, Alex C
    NYU.
    Goulas, Spyros
    Austrian Academy of Science.
    Langeslag, Michiel
    Innsbruck Medical University.
    Griffin, Robert S
    Massachusetts General Hospital.
    Belfer, Inna
    University of Pittsburgh.
    Dai, Feng
    University of Pittsburgh.
    Smith, Shad B
    University N Carolina.
    Diatchenko, Luda
    University N Carolina.
    Gupta, Vaijayanti
    Strand Life Science Pvt Ltd.
    Xia, Cui-Ping
    Austrian Academy Science.
    Amann, Sabina
    Austrian Academy of Science.
    Kreitz, Silke
    University of Erlangen Nurnberg.
    Heindl-Erdmann, Cornelia
    University of Erlangen Nurnberg.
    Wolz, Susanne
    University of Erlangen Nurnberg.
    Ly, Cindy V
    Strand Life Science Pvt Ltd.
    Sarangi, Rinku
    Strand Life Science Pvt Ltd.
    Dan, Debasis
    Strand Life Science Pvt Ltd.
    Novatchkova, Maria
    Austrian Academy of Science.
    Rosenzweig, Mark
    Brandeis University.
    Gibson, Dustin G
    University N Carolina.
    Truong, Darwin
    Austrian Academy of Science.
    Schramek, Daniel
    Austrian Academy of Science.
    Zoranovic, Tamara
    Austrian Academy of Science.
    Cronin, Shane J F
    Austrian Academy of Science.
    Angjeli, Belinda
    Austrian Academy of Science.
    Brune, Kay
    University of Erlangen Nurnberg.
    Dietzl, Georg
    Stanford University.
    Maixner, William
    University N Carolina.
    Meixner, Arabella
    Austrian Academy of Science.
    Thomas, Winston
    Deltagen Inc.
    Pospisilik, J Andrew
    Max Planck Institute.
    Alenius, Mattias
    Linköping University, Faculty of Health Sciences. Linköping University, Department of Clinical and Experimental Medicine, Developmental Biology, IKE.
    Kress, Michaela
    Innsbruck Medical University.
    Subramaniam, Sai
    Strand Life Science Pvt Ltd.
    Garrity, Paul A
    Brandeis University.
    Bellen, Hugo J
    Baylor College of Medicine.
    Woolf, Clifford J
    Harvard University.
    Penninger, Josef M
    Austrian Academy of Science.
    A Genome-wide Drosophila Screen for Heat Nociception Identifies alpha 2 delta 3 as an Evolutionarily Conserved Pain Gene2010In: CELL, ISSN 0092-8674, Vol. 143, no 4, p. 628-638Article in journal (Refereed)
    Abstract [en]

    Worldwide, acute, and chronic pain affects 20% of the adult population and represents an enormous financial and emotional burden. Using genome-wide neuronal-specific RNAi knockdown in Drosophila, we report a global screen for an innate behavior and identify hundreds of genes implicated in heat nociception, including the alpha 2 delta family calcium channel subunit straightjacket (stj). Mice mutant for the stj ortholog CACNA2D3 (alpha 2 delta 3) also exhibit impaired behavioral heat pain sensitivity. In addition, in humans, alpha 2 delta 3 SNP variants associate with reduced sensitivity to acute noxious heat and chronic back pain. Functional imaging in alpha 2 delta 3 mutant mice revealed impaired transmission of thermal pain-evoked signals from the thalamus to higher-order pain centers. Intriguingly, in alpha 2 delta 3 mutant mice, thermal pain and tactile stimulation triggered strong cross-activation, or synesthesia, of brain regions involved in vision, olfaction, and hearing.

  • 287.
    Hmani-Aifa, Mounira
    et al.
    Centre for Biotechnology, Tunisia.
    Ben Salem, Salma
    Centre for Biotechnology, Tunisia.
    Benzina, Zeineb
    CHU Habib Bourguiba, Tunisia.
    Bouassida, Walid
    CHU Habib Bourguiba, Tunisia.
    Messaoud, Riadh
    CHU Habib Bourguiba, Tunisia.
    Turki, Khalil
    CHU Habib Fattouma, Tunisia.
    Khairallah, Moncef
    CHU Habib Bourguiba, Tunisia.
    Rebai, Ahmed
    CHU Habib Fattouma, Tunisia.
    Fakhfekh, Faiza
    Faculty of Medicine, Lab Genet Mol Humaine, Tunisia.
    Söderkvist, Peter
    Linköping University, Department of Clinical and Experimental Medicine, Cell Biology. Linköping University, Faculty of Health Sciences.
    Ayadi, Hammadi
    Centre for Biotechnology, Tunisia.
    A genome-wide linkage scan in Tunisian families identifies a novel locus for non-syndromic posterior microphthalmia to chromosome 2q37.12009In: HUMAN GENETICS, ISSN 0340-6717, Vol. 126, no 4, p. 575-587Article in journal (Refereed)
    Abstract [en]

    Posterior microphthalmia (PM) is a relatively rare autosomal recessive condition with normal anterior segment and small posterior segment resulting in high hyperopia and retinal folding. It is an uncommon subtype of microphthalmia that has been mostly reported to coexist with several other ophthalmic conditions and to occur in sporadic cases. The membrane-type frizzled-related protein (MFRP) is the only gene so far reported implicated in autosomal recessive, non-syndromic and syndromic forms of PM. Here, we performed a clinical and genetic analysis using six consanguineous families ascertained from different regions of Tunisia and affected with non-syndromic PM that segregates as an autosomal recessive trait. To identify the disease-causing defect in these families, we first analysed MFRP gene, then some candidate genes (CHX10, OPA1, MITF, SOX2, CRYBB1-3 and CRYBA4) and loci (MCOP1, NNO1 and NNO2) previously implicated in different forms of microphthalmia. After exclusion of these genes and loci, we performed a genome-wide scan using a high density single nucleotide polymorphism (SNP) array 50 K in a large consanguineous pedigree. SNP genotyping revealed eight homozygous candidate regions on chromosomes 1, 2, 3, 6, 15, 17 and 21. Linkage analysis with additional microsatellite markers only retained the 2q37.1 region with a maximum LOD score of 8.85 obtained for D2S2344 at theta = 0.00. Further investigations are compatible for linkage of four more families to this region with a refined critical interval of 2.35 Mb. The screening of five candidate genes SAG, PDE6D, CHRND, CHRNG and IRK13 did not reveal any disease-causing mutation.

  • 288. Enström, Camilla
    et al.
    Osman, Abdimajid
    Linköping University, Faculty of Health Sciences. Linköping University, Department of Clinical and Experimental Medicine, Clinical Chemistry. Östergötlands Läns Landsting, Centre for Laboratory Medicine, Department of Clinical Chemistry.
    Lindahl, Tomas
    Linköping University, Faculty of Health Sciences. Linköping University, Department of Clinical and Experimental Medicine, Clinical Chemistry. Östergötlands Läns Landsting, Centre for Laboratory Medicine, Department of Clinical Chemistry.
    A genotyping method for VKORC1 1173C>T by Pyrosequencing® technology2008In: Scandinavian Journal of Clinical and Laboratory Investigation, ISSN 0036-5513, E-ISSN 1502-7686, Vol. 68, no 5, p. 427-430Article in journal (Refereed)
    Abstract [en]

    Vitamin K epoxide reductase complex subunit 1 (VKORC1) is the site of inhibition by warfarin and other anti-vitamin K drugs during oral anticoagulant therapy. The SNP rs9934438 in intron 1 of VKORC1 (c.173+1000C>T or 1173C>T) discriminating the VKORC1*2 haplotype is associated with low warfarin dose requirement and unstable prothrombin time - international normalized ratio. To genotype this SNP, we have developed a rapid method using Pyrosequencing® technology. The proposed method takes a post-PCR sample preparation of less than 1 h and a DNA sequencing time of less than 15 min to genotype 96 samples. The current method was compared with a dHPLC method that we reported previously. Genotype frequencies at VKORC1 1173C>T for our Swedish population were 38 % wild-type, 40 % heterozygote and 22 % homozygote. The frequency of the T-allele was 0.42, which exactly matches the frequency previously reported for Germans. The current method can be used to determine whether patients initiating warfarin therapy are carriers of SNP 1173 C>T that is strongly associated with low warfarin dose requirement. © 2008 Informa UK Ltd (Informa Healthcare, Taylor & Francis AS).

  • 289.
    Bendtsen, Marcus
    Linköping University, Department of Medical and Health Sciences, Division of Community Medicine. Linköping University, Faculty of Medicine and Health Sciences.
    A Gentle Introduction to the Comparison Between Null Hypothesis Testing and Bayesian Analysis: Reanalysis of Two Randomized Controlled Trials2018In: Journal of Medical Internet Research, E-ISSN 1438-8871, Vol. 20, no 10, article id e10873Article in journal (Refereed)
    Abstract [en]

    The debate on the use and misuse of P values has risen and fallen throughout their almost century-long existence in scientific discovery. Over the past few years, the debate has again received front-page attention, particularly through the public reminder by the American Statistical Association on how P values should be used and interpreted. At the core of the issue lies a fault in the way that scientific evidence is dichotomized and research is subsequently reported, and this fault is exacerbated by researchers giving license to statistical models to do scientific inference. This paper highlights a different approach to handling the evidence collected during a randomized controlled trial, one that does not dichotomize, but rather reports the evidence collected. Through the use of a coin flipping experiment and reanalysis of real-world data, the traditional approach of testing null hypothesis significance is contrasted with a Bayesian approach. This paper is meant to be understood by those who rely on statistical models to draw conclusions from data, but are not statisticians and may therefore not be able to grasp the debate that is primarily led by statisticians.

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  • 290.
    Abu Syeed, Kazi
    Linköping University, Department of Computer and Information Science. Linköping University, The Institute of Technology.
    A GIS based Site Suitability Analysis for Shrimp Cultivation in the Coastal Region of Bangladesh2007Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Bangladesh geographically comprised one of the largest delta landscapes of the world. Almost 6.7% of country’stotal area (147570 sqkm.) is covered byrivers and inland water bodies. These water bodies being rich in fishproduction meet the majority of the demand of protein. Bangladesh produces world's fourth largest quantity of fishand it is collected from the inland water bodies. Though shrimps were easily available in the inland water bodies forhundreds of years but shrimp culture as an export-oriented activity is a phenomenon of recent past. Bangladeshearned US$ 2.9 million by exporting shrimp in 1972-73 which was 1 % of the country's total exports. It increased to US$ 33 million in 1980 and to US$ 90.0 million in 1985. But until the mid-1980’s shrimp culture was principallydependent on open-water catches of shrimp it means that time shrimps were not cultivated in a proper planned way.But the culture of shrimp totally for export purpose started after the mid 1980’s. Since then the professional cultivation of shrimp had a very positive and effective impact on the economy of Bangladesh. Exports of shrimpfrom Bangladesh increased from US$ 91 million in FY (Fiscal Year) 1986 to US$ 280 million in FY1997. Duringthe corresponding period, the quantity of shrimp exports increased from 17.2 thousand tonnes to 25.2 thousandtonnes. As most of the shrimp farms have been developed without considering the sustainability of the environmentand some other factors like water pH & salinity, soil pH & salinity, soil texture etc. the farmers are getting lessreturn but affecting the environment most. Geographical Information System (GIS) can give an easier but effectivesolution here through selecting the best suitable sites for shrimp cultivation. Moreover GIS can solve thetransportation problem of this perishable product from the production area to the harbor or airport through transport route selection. This cansave a lot of money and time and consequently make the shrimp cultivation moreeconomic.

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  • 291.
    Hinkel, Jochen
    et al.
    Global Climate Forum (GCF), Germany .
    Nicholls, Robert J.
    University of Southampton, England .
    Tol, Richard S. J.
    University of Sussex, England Vrije University of Amsterdam, Netherlands .
    Wang, Zheng B.
    Delft University of Technology, Netherlands Deltares, Netherlands .
    Hamilton, Jacqueline M.
    University of Hamburg, Germany .
    Boot, Gerben
    Deltares, Netherlands .
    Vafeidis, Athanasios T.
    University of Kiel, Germany .
    McFadden, Loraine
    Middlesex University, England .
    Ganopolski, Andrey
    Potsdam Institute Climate Impact Research PIK, Germany .
    Klein, Richard
    Linköping University, Department of Thematic Studies, Department of Water and Environmental Studies. Linköping University, Faculty of Arts and Sciences. Linköping University, Department of Thematic Studies, Centre for Climate Science and Policy Research. Stockholm Environment Institute, Stockholm, Sweden.
    A global analysis of erosion of sandy beaches and sea-level rise: An application of DIVA2013In: Global and Planetary Change, ISSN 0921-8181, E-ISSN 1872-6364, Vol. 111, p. 150-158Article in journal (Refereed)
    Abstract [en]

    This paper presents a first assessment of the global effects of climate-induced sea-level rise on the erosion of sandy beaches, and its consequent impacts in the form of land loss and forced migration of people. We consider direct erosion on open sandy coasts and indirect erosion near selected tidal inlets and estuaries, using six global mean sea-level scenarios (in the range of 0.2-0.8 m) and six SRES socio-economic development scenarios for the 21st century. Impacts are assessed both without and with adaptation in the form of shore and beach nourishment, based on cost-benefit analysis that includes the benefits of maintaining sandy beaches for tourism. Without nourishment, global land loss would amount to about 6000-17,000 km(2) during the 21st century, leading to 1.6-5.3 million people being forced to migrate and migration costs of US$ 300-1000 billion (not discounted). Optimal beach and shore nourishment would cost about US$ 65-220 billion (not discounted) during the 21st century and would reduce land loss by 8-14%, forced migration by 56-68% and the cost of forced migration by 77-84% (not discounted). The global share of erodible coast that is nourished increases from about 4% in 2000 to 18-33% in 2100, with beach nourishment being 3-4 times more frequent than shore nourishment, reflecting the importance of tourism benefits. In absolute terms, with or without nourishment, large counties with long shorelines appear to have the largest costs, but in relative terms, small island states appear most impacted by erosion. Considerable uncertainty remains due to the limited availability of basic coastal geomorphological data and models on a global scale. Future work should also further explore the effects of beach tourism, including considering sub-national distributions of beach tourists.

  • 292. Order onlineBuy this publication >>
    Johansson, Gustaf
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    A Global Linear Optimization Framework for Adaptive Filtering and Image Registration2015Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    Digital medical atlases can contain anatomical information which is valuable for medical doctors in diagnosing and treating illnesses. The increased availability of such atlases has created an interest for computer algorithms which are capable of integrating such atlas information into patient specific dataprocessing. The field of medical image registration aim at calculating how to match one medical image to another. Here the atlas information could give important hints of which kinds of motion are plausible in different locations of the anatomy. Being able to incorporate such atlas specific information could potentially improve the matching of images and plausibility of image registration - ultimately providing a more correct information on which to base health care diagnosis and treatment decisions.

    In this licentiate thesis a generic signal processing framework is derived : Global Linear Optimization (GLO). The power of the GLO framework is first demonstrated quantitatively in a very high performing image denoiser. Important proofs of concepts are then made deriving and implementing three important capabilities regarding adaptive filtering of vector fields in medica limage registration:

    1. Global regularization with local anisotropic certainty metric.
    2. Allowing sliding motion along organ and tissue boundaries.
    3. Enforcing an incompressible motion in specific areas or volumes.

    In the three publications included in this thesis, the GLO framework is shown to be able to incorporate one each of these capabilities. In the third and final paper a demonstration is made how to integrate more and more of the capabilities above into the same GLO to perform adaptive processing on relevant clinical data. It is shown how each added capability improves the result of the image registration. In the end of the thesis there is a discussion which highlights the advantage of the contributions made as compared to previous methods in the scientific literature.

    List of papers
    1. Globally Optimal Displacement Fields Using Local Tensor Metric
    Open this publication in new window or tab >>Globally Optimal Displacement Fields Using Local Tensor Metric
    2012 (English)In: Image Processing (ICIP), 2012 19th IEEE International Conference on, 2012, p. 2957-2960Conference paper, Poster (with or without abstract) (Other academic)
    Abstract [en]

    In this paper, we propose a novel algorithm for regularizing displacement fields in image registration. The method uses the local structure tensor and gradients of the displacement field to impose a local metric, which is then used optimizing a global cost function. The method allows for linear operators, such as tensors and differential operators modeling the underlying physical anatomy of the human body in medical images. The algorithm is tested using output from the Morphon image registration algorithm on MRI data as well as synthetic test data and the result is compared to the initial displacement field. The results clearly demonstrate the power of the method and the unique features brought forth through the global optimization approach.

    Keywords
    Image Processing, Image Registration, Regularization, Optimization, Tensor
    National Category
    Medical Image Processing Signal Processing
    Identifiers
    urn:nbn:se:liu:diva-81947 (URN)10.1109/ICIP.2012.6467520 (DOI)978-1-4673-2534-9 (ISBN)
    Conference
    2012 IEEE International Conference on Image Processing, September 30 - October 3, 2012, Orlando, Florida, USA
    Projects
    Dynamic Context Atlases for Image Denoising and Patient Safety
    Funder
    Swedish Research Council, 2011-5176Swedish Research Council, 2007-4786
    Available from: 2012-09-26 Created: 2012-09-26 Last updated: 2015-04-17Bibliographically approved
    2. Motion Field Regularization for Sliding Objects using Global Linear Optimization
    Open this publication in new window or tab >>Motion Field Regularization for Sliding Objects using Global Linear Optimization
    2015 (English)Conference paper, Published paper (Refereed)
    Abstract [en]

    In image registration it is often necessary to employ regularization in one form or another to be able to find a plausible displacement field. In medical applications, it is useful to define different constraints for different areas of the data. For instance to measure if organs have moved as expected after a finished treatment. One common problem is how to find plausible motion vectors far away from known motion. This paper introduces a new method to build and solve a Global Linear Optimizations (GLO) problem with a novel set of terms which enable specification of border areas to allow a sliding motion. The GLO approach is important especially because it allows simultaneous incorporation of several different constraints using information from medical atlases such as localization and properties of organs. The power and validity of the method is demonstrated using two simple, but relevant 2D test images. Conceptual comparisons with previous methods are also made to highlight the contributions made in this paper. The discussion explains important future work and experiments as well as exciting future improvements to the GLO framework.

    Place, publisher, year, edition, pages
    SciTePress, 2015
    Keywords
    Image Registration, Missing Data, Medical Image Processing, Global Linear Optimization
    National Category
    Radiology, Nuclear Medicine and Medical Imaging
    Identifiers
    urn:nbn:se:liu:diva-112210 (URN)10.5220/0005281403180323 (DOI)978-989-758-077-2 (ISBN)
    Conference
    The 4th International Conference on Pattern Recognition Applications and Methods, Januari 10-12, Lisbon, Portugal
    Projects
    Dynamic Context Atlases for Image Denoising and Patient SafetyGlobal Linear Optimization
    Funder
    Swedish Research Council, 2011-5176Linnaeus research environment CADICS
    Available from: 2014-11-18 Created: 2014-11-18 Last updated: 2020-07-10Bibliographically approved
    3. Regularization in Medical Image Registration using Global Linear Optimization
    Open this publication in new window or tab >>Regularization in Medical Image Registration using Global Linear Optimization
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Common problems in image registration include having large parts of the images contain noisy, uncertain, missing or impossible motion. Regularization is the field that aims to overcome these problems. In this article, we propose a novel framework : Global Linear Optimization (GLO) which we demonstrate has the capabilities to simultaneously and globally regularize with respect to : (1) anisotropic certainty of prior motion field, (2) sliding of organ boundaries and (3) incompressibility of organ interiors. The power of the presented framework consists of being able to spatially adapt which subsets of the data each constraint should affect and then solve a large sparse linear equations system which automatically propagates a solution over the data set through an overlapping localized metric. We demonstrate the validity of the methods and the power of the GLO framework on relevant test cases and on medical data from the DIR-lab.

    Keywords
    Keywords—Image Registration, Medical Image Analysis, Regularization, Adaptive Filtering, Medical Atlases, Global Methods, Optimization, Global Linear Optimization, Structure Tensor, Anisotropic Filtering, Partial Differential Equations
    National Category
    Medical Image Processing Other Computer and Information Science
    Identifiers
    urn:nbn:se:liu:diva-117140 (URN)
    Available from: 2015-04-17 Created: 2015-04-17 Last updated: 2018-01-11Bibliographically approved
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  • 293.
    C. Lin, Yin
    et al.
    University of California San Diego.
    Jhunjhunwala, Suchit
    University of California San Diego.
    Benner, Christopher
    University of California San Diego.
    Heinz, Sven
    University of California San Diego.
    Welinder, Eva
    University of California San Diego.
    Mansson, Robert
    University of California San Diego.
    Sigvardsson, Mikael
    Linköping University, Department of Clinical and Experimental Medicine, Experimental Hematology . Linköping University, Faculty of Health Sciences.
    Hagman, James
    National Jewish Health, Denver.
    A. Espinoza, Celso
    University of California San Diego.
    Dutkowski, Janusz
    University of California San Diego.
    Ideker, Trey
    University of California San Diego.
    Glass, Christopher K.
    University of California San Diego.
    Murre, Cornelis
    University of California San Diego.
    A global network of transcription factors, involving E2A, EBF1 and Foxo1, that orchestrates B cell fate2010In: Nature Immunology, ISSN 1529-2908, E-ISSN 1529-2916, Vol. 11, no 7, p. 635-U109Article in journal (Refereed)
    Abstract [en]

    It is now established that the transcription factors E2A, EBF1 and Foxo1 have critical roles in B cell development. Here we show that E2A and EBF1 bound regulatory elements present in the Foxo1 locus. E2A and EBF1, as well as E2A and Foxo1, in turn, were wired together by a vast spectrum of cis-regulatory sequences. These associations were dynamic during developmental progression. Occupancy by the E2A isoform E47 directly resulted in greater abundance, as well as a pattern of monomethylation of histone H3 at lysine 4 (H3K4) across putative enhancer regions. Finally, we divided the pro-B cell epigenome into clusters of loci with occupancy by E2A, EBF and Foxo1. From this analysis we constructed a global network consisting of transcriptional regulators, signaling and survival factors that we propose orchestrates B cell fate.

  • 294.
    Lundqvist, Jan Olof
    Linköping University, Faculty of Arts and Sciences. Linköping University, The Tema Institute, Department of Water and Environmental Studies.
    A global perspective on water and the environment2000In: Physics and chemistry of the earth. Part B: Hydrology, oceans and atmosphere, ISSN 1464-1909, E-ISSN 1873-4677, Vol. 25, no 3, p. 259-264Conference paper (Other academic)
    Abstract [en]

    At the turn to a new millennium, it is titillating to try to foresee what issues that are likely to be significant when we enter into the next century. Many of the water issues that we have been pre-occupied with in the past will, no doubt, continue to be important. But in addition, we should be prepared for new dimensions in what is now called the 'impending water crisis'. A pro-active behaviour that would make it possible to avoid a new generation of problems is warranted as a complement to the need to re-act to and take care of old problems. As will be argued below, connections between water quantity and quality and between water and the environment have been overlooked in the past. (C) 2000 Elsevier Science Ltd. All rights reserved.

  • 295.
    Kastbom, Lisa
    et al.
    Linköping University, Department of Medical and Health Sciences, Division of Community Medicine. Linköping University, Faculty of Medicine and Health Sciences. Region Östergötland, Primary Care Center, Primary Health Care Center Ljungsbro.
    Milberg, Anna
    Linköping University, Department of Social and Welfare Studies, Division of Nursing Science. Linköping University, Faculty of Medicine and Health Sciences. Region Östergötland, Local Health Care Services in East Östergötland, Department of Advanced Home Care in Norrköping. Region Östergötland, Local Health Care Services in East Östergötland, Center of Palliative Care.
    Karlsson, Marit
    Linköping University, Department of Clinical and Experimental Medicine, Division of Neuro and Inflammation Science. Linköping University, Faculty of Medicine and Health Sciences. Region Östergötland, Local Health Care Services in Central Östergötland, Department of Advanced Home Care in Linköping.
    A good death from the perspective of palliative cancer patients2017In: Supportive Care in Cancer, ISSN 0941-4355, E-ISSN 1433-7339, Vol. 25, no 3, p. 933-939Article in journal (Refereed)
    Abstract [en]

    Although previous research has indicated some recurrent themes and similarities between what patients from different cultures regard as a good death, the concept is complex and there is lack of studies from the Nordic countries. The aim of this study was to explore the perception of a good death in dying cancer patients in Sweden. Interviews were conducted with 66 adult patients with cancer in the palliative phase who were recruited from home care and hospital care. Interviews were analysed using qualitative content analysis. Participants viewed death as a process. A good death was associated with living with the prospect of imminent death, preparing for death and dying comfortably, e.g., dying quickly, with independence, with minimised suffering and with social relations intact. Some were comforted by their belief that death is predetermined. Others felt uneasy as they considered death an end to existence. Past experiences of the death of others influenced participants views of a good death. Healthcare staff caring for palliative patients should consider asking them to describe what they consider a good death in order to identify goals for care. Exploring patients personal experience of death and dying can help address their fears as death approaches.

  • 296.
    Lindhagen, Alva
    Linköping University, Department of Computer and Information Science.
    A guide to novel instructors in Emergo Train System®2022Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Swedish law states that county councils and municipalities need to prepare for crisis and receive training in crisis management. As crises are infrequent events, training must be conducted on potential scenarios. Scenarios can be simulated using the Emergo Train System (ETS). ETS is a low fidelity educational simulation-tool that tests and educates care personnel in crisis management. The tool is communicative, cooperative and challenges participants in handling sufficient resources during a crisis or major incident. Planning, facilitation, and evaluation is done by an ETS-instructor. To become an ETS-instructor one must take a three-day course at an ETS-faculty. Previous research proposed that novel Senior instructors need additional support in managing exercises. To explore this further this project’s aim is to explore and deepen current knowledge about ETS-instructors, their work, and design a manual for novel instructors. Information about instructor work was gathered through semi-structured interviews. Seven interviews were conducted with novel and experienced instructors. During interviews the participants were asked about their work process and actors involved in conducting exercises. Additionally, the interviewer and the participants constructed a journey map and an actor’s map together. The gathered data was analysed through reflexive thematic analysis (TA) described by Braun and Clarke (2022) and the seven actor’s maps and journey maps were merged into summarised maps. Five themes were gathered from the thematic analysis: Roles, Realism, Defining purpose and goals, Learning, and Planning and acting. The theme Roles included Other instructors, Participants, Exercise leaders, Colleagues, and Evaluator which were defined as more involved in managing an exercise than other roles. Instructors gather information about participants to increase realism, such as participant profession, workplace, and geographical surroundings. Purpose and goal should be clear and contemplated thoroughly together with customer. The instructors adjust their exercises to suit participant level of knowledge and the instructors recommend prioritising feedback given to the participants and to always give positive feedback at the end of the exercise. It is beneficial for learning to create a safe learning environment, where the participants feel they can act, make mistakes, and self-reflect. The instructor plan realistic and purposeful injects in an action schedule along with their scenario planning. Injects can also be improvised to aid participants or to keep them within the frames of the scenario. The instructors act as different pre-planned roles that are required in the scenario, but that the participants cannot take themselves. The study discusses contradictions in the results about how different terms should be defined and how the results were incorporated into the manual. Contributions of this study are the mapping of actors and the instructor’s work process as earlier visualisation of the ETS-instructors work process has been made. The greatest contributions were (1) the support of defining goals, purpose, and indicators (2) the immense considerations during scenario planning regarding realism, and (3) the proficient conduct of managing complex situations during exercise. 

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    Lindhagen, A. A guide to novel instructors in Emergo Train System®
  • 297.
    Sabe, Emelie
    Linköping University, Department of Science and Technology.
    A Haptic Guidance System for Stroke Rehabilitation2007Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Stroke is the third largest cause of death in Sweden. In 2005, 30.000 people in Sweden suffered from a stroke. The consequences of a stroke varies, but the most common disability among stroke survivors is abnormal reaching movements, which is the primer reason for limitations in activities of everyday living. Rehabilitation is essential in order to get back to everyday life.

    Physical assistance (or guidance) is used in rehabilitation by physiotherapists and occupational therapists to help a patient through a dicult movement for example. Today, this guidance is limited to be performed by medical personnel. With the technology of virtual environments (VE) and haptics – force feedback from a computer – there is a possibility to create guidance which does not need medical personnel. This should be used as a complement to the traditional therapy.

    The intention of this work is to create an invisible guidance eld, which should guide a patient's hand to a desired movement pattern, i.e. aid the patient to perform a task in a virtual environment with haptics. This guidance is added to an already existing assessment tool, which is a part of the Curictus AB rehabilitation system. The guiding system is implemented using SenseGraphics AB's H3D API.

    To create the feeling of guidance and a guidance eld, the Volume Haptics Toolkit, developed by Dr. Karljohan Lundin Palmerius at Linköping University, was used. The basic idea of the algorithm is to calculate an orientation vector, for every position, in which direction the guidance should guide the patient. The guidance, which is generated via a haptic device, is adaptive to the patient's movements and always guides the patient towards the target in a smooth trajectory.

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  • 298.
    Zheng, Xin
    et al.
    Linköping University, Department of Computer and Information Science, Software and Systems. Linköping University, Faculty of Science & Engineering. Guangdong Univ Technol, Peoples R China.
    Liang, Shouzhi
    Guangdong Univ Technol, Peoples R China.
    Xiong, Xiaoming
    Guangdong Univ Technol, Peoples R China.
    A hardware/software partitioning method based on graph convolution network2021In: Design automation for embedded systems, ISSN 0929-5585, E-ISSN 1572-8080, Vol. 25, no 4, p. 325-351Article in journal (Refereed)
    Abstract [en]

    Hardware/software (HW/SW) partitioning is the crucial step in HW/SW co-design, which can significantly reduce the time-to-market and improves the performance of an embedded system. Due to that the majority of previous works have large exploration time and generate often low-quality solutions for large scale systems, we propose a fast HW/SW partitioning approach based on graph convolution network (GCN) to address this problem. To the best of our knowledge, it is a new partitioning method based on GCN which is a gradient-based optimization approach. It can aggressively speed up the partitioning process. To quantify the quality of solutions, the scheduling is integrated into the partitioning process. The experiment results show that not only does our proposed method outperform existing metaheuristics approaches in terms of the efficiency (e.g., 18x faster than Kernighan-Lin algorithm for the task graphs with 1000 nodes), but it also improves the quality of HW/SW partitioning (e.g., more than 10% acceleration ratio (AR) improvement for the 1000 nodes graphs).

  • 299.
    Nyman, Elin
    et al.
    Linköping University, Department of Clinical and Experimental Medicine, Cell Biology. Linköping University, Faculty of Health Sciences.
    Brännmark, Cecilia
    Linköping University, Department of Clinical and Experimental Medicine, Cell Biology. Linköping University, Faculty of Health Sciences.
    Palmér, Robert
    Linköping University, Department of Clinical and Experimental Medicine, Cell Biology. Linköping University, Faculty of Health Sciences.
    Brugård, Jan
    MathCore Engn.
    Nyström, Fredrik
    Linköping University, Department of Medical and Health Sciences, Internal Medicine. Linköping University, Faculty of Health Sciences. Östergötlands Läns Landsting, Heart and Medicine Centre, Department of Endocrinology and Gastroenterology UHL.
    Strålfors, Peter
    Linköping University, Department of Clinical and Experimental Medicine, Cell Biology. Linköping University, Faculty of Health Sciences.
    Cedersund, Gunnar
    Linköping University, Department of Clinical and Experimental Medicine, Cell Biology. Linköping University, Faculty of Health Sciences.
    A Hierarchical Whole-body Modeling Approach Elucidates the Link between in Vitro Insulin Signaling and in Vivo Glucose Homeostasis2011In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 286, no 29, p. 26028-26041Article in journal (Refereed)
    Abstract [en]

    Type 2 diabetes is a metabolic disease that profoundly affects energy homeostasis. The disease involves failure at several levels and subsystems and is characterized by insulin resistance in target cells and tissues (i.e. by impaired intracellular insulin signaling). We have previously used an iterative experimental-theoretical approach to unravel the early insulin signaling events in primary human adipocytes. That study, like most insulin signaling studies, is based on in vitro experimental examination of cells, and the in vivo relevance of such studies for human beings has not been systematically examined. Herein, we develop a hierarchical model of the adipose tissue, which links intracellular insulin control of glucose transport in human primary adipocytes with whole-body glucose homeostasis. An iterative approach between experiments and minimal modeling allowed us to conclude that it is not possible to scale up the experimentally determined glucose uptake by the isolated adipocytes to match the glucose uptake profile of the adipose tissue in vivo. However, a model that additionally includes insulin effects on blood flow in the adipose tissue and GLUT4 translocation due to cell handling can explain all data, but neither of these additions is sufficient independently. We also extend the minimal model to include hierarchical dynamic links to more detailed models (both to our own models and to those by others), which act as submodules that can be turned on or off. The resulting multilevel hierarchical model can merge detailed results on different subsystems into a coherent understanding of whole-body glucose homeostasis. This hierarchical modeling can potentially create bridges between other experimental model systems and the in vivo human situation and offers a framework for systematic evaluation of the physiological relevance of in vitro obtained molecular/cellular experimental data.

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  • 300.
    Samuelsson, Ulf
    et al.
    Linköping University, Department of Clinical and Experimental Medicine, Division of Clinical Sciences. Linköping University, Faculty of Health Sciences. Östergötlands Läns Landsting, Center of Paediatrics and Gynaecology and Obstetrics, Department of Paediatrics in Linköping.
    Steineck, Isabelle
    Herning Hospital, Denmark .
    Gubbjornsdottir, Soffia
    University of Gothenburg, Sweden .
    A high mean-HbA1c value 3-15 months after diagnosis of type 1 diabetes in childhood is related to metabolic control, macroalbuminuria, and retinopathy in early adulthood - a pilot study using two nation-wide population based quality registries2014In: Pediatric Diabetes, ISSN 1399-543X, E-ISSN 1399-5448, Vol. 15, no 3, p. 229-235Article in journal (Refereed)
    Abstract [en]

    BackgroundIntensive treatment of patients with type 1 diabetes delays the onset of long-term complications. ObjectivesOn the basis of the information from two nation-wide quality registers, we investigated to which extent HbA1c values 3-15months after diagnosis in childhood are related to metabolic control, albuminuria, and retinopathy in early adulthood. MethodsIn Sweden, physicians register all children and adolescents with type 1 diabetes mellitus in the Swedish Pediatric Quality Registry. After 18yr of age, people with diabetes are followed by the Swedish National Diabetes Register. We identified 1543 children and adolescents with a mean age of 13.9yr at diagnosis and a mean duration of type 1 diabetes mellitus of 7.1yr. ResultsChildren and adolescents with poor metabolic control (mean HbA1c 70mmol/mol (8.6 %)) adjacent to diagnosis had a significantly higher mean HbA1c value years later as adults than did patients with a good metabolic control [less than50mmol/mol (6.7%) (pless than0.001)]. The patients in the high group were also less physically active and smoked more as adults. The proportion of females was higher in the poor metabolic group. Patients with a high mean HbA1c 3-15months after diagnosis had significantly more often macroalbuminuria and retinopathy in early adulthood. ConclusionsMetabolic control adjacent to the diagnosis of type 1 diabetes in childhood or adolescence can predict metabolic control in early adulthood. It is therefore very important that pediatric diabetes teams identify key factors for successful early metabolic control. Actively using quality registries may be one such factor.

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