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  • 1.
    Heyden, Anders
    et al.
    Lunds universitet.
    Laurendeau, DenisFelsberg, MichaelLinköping University, The Institute of Technology. Linköping University, Department of Electrical Engineering, Computer Vision.Borga, MagnusLinköping University, Department of Biomedical Engineering. Linköping University, Faculty of Science & Engineering.
    22nd International Conference on Pattern Recognition (ICPR)2014Conference proceedings (editor) (Other academic)
  • 2.
    Josefsson, Mattias
    Linköping University, Department of Electrical Engineering, Computer Vision. Linköping University, The Institute of Technology.
    3D camera with built-in velocity measurement2011Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    In today's industry 3D cameras are often used to inspect products. The camera produces both a 3D model and an intensity image by capturing a series of profiles of the object using laser triangulation. In many of these setups a physical encoder is attached to, for example, the conveyor belt that the product is travelling on. The encoder is used to get an accurate reading of the speed that the product has when it passes through the laser. Without this, the output image from the camera can be distorted due to a variation in velocity.

    In this master thesis a method for integrating the functionality of this physical encoder into the software of the camera is proposed. The object is scanned together with a pattern, with the help of this pattern the object can be restored to its original proportions.

  • 3.
    Sanjuan, Joseba
    Linköping University, Department of Computer and Information Science. Linköping University, The Institute of Technology.
    3G Energy-Efficient Packet Handling Kernel Module for Android2012Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    The use of mobile devices is increasing due to the constant development of more advanced and appealing applications and computing features. However, these new features are very power hungry leading to short battery lifetimes. Research shows that a major reason for fast battery depletion is the excessive and inefficient use of the wireless interfaces. This thesis studies how we can attempt to increase the battery lifetime of the devices without having to sacrifice the usage of these advanced features in some applications.

    The thesis focuses on adapting the traffic pattern characteristics of mobile communication using a widespread wireless communication technology like 3G. Traffic pattern adaptation is performed at packet level in kernel space in Android. The data transfers are scheduled with the knowledge of the energy consumption characteristics of 3G. The performed measurements indicate that our solution can provide energy savings ranging from 7% to 59%.

    This work confirms that 3G conscious scheduling of network traffic reduces energy consumption, and that, both applications and energy saving libraries are potential directions to be further studied.

  • 4.
    Johansson, Ted
    et al.
    Linköping University, Department of Electrical Engineering, Electronic Devices. Linköping University, The Institute of Technology.
    Bengtsson, Olof
    Lotfi, Sara
    Uppsala University, Sweden.
    Vestling, Lars
    Uppsala University, Sweden.
    Norström, Hans
    Uppsala University, Sweden.
    Olsson, Jörgen
    Uppsala University, Sweden.
    Nyström, Christian
    A +32.8 dBm LDMOS power amplifier for WLAN in 65 nm CMOS technology2013Conference paper (Refereed)
    Abstract [en]

    Postlingually acquired hearing impairment (HI) is associated with changes in the representation of sound in semantic long-term memory. An indication of this is the lower performance on visual rhyme judgment tasks in conditions where phonological and orthographic cues mismatch, requiring high reliance on phonological representations. In this study, event-related potentials (ERPs) were used for the first time to investigate the neural correlates of phonological processing in visual rhyme judgments in participants with acquired HI and normal hearing (NH). Rhyme task word pairs rhymed or not and had matching or mismatching orthography. In addition, the inter-stimulus interval (ISI) was manipulated to be either long (800 ms) or short (50 ms). Long ISIs allow for engagement of explicit, top-down processes, while short ISIs limit the involvement of such mechanisms. We hypothesized lower behavioral performance and N400 and N2 deviations in HI in the mismatching rhyme judgment conditions, particularly in short ISI. However, the results showed a different pattern. As expected, behavioral performance in the mismatch conditions was lower in HI than in NH in short ISI, but ERPs did not differ across groups. In contrast, HI performed on a par with NH in long ISI. Further, HI, but not NH, showed an amplified N2-like response in the non-rhyming, orthographically mismatching condition in long ISI. This was also the rhyme condition in which participants in both groups benefited the most from the possibility to engage top-down processes afforded with the longer ISI. Taken together, these results indicate an early ERP signature of HI in this challenging phonological task, likely reflecting use of a compensatory strategy. This strategy is suggested to involve increased reliance on explicit mechanisms such as articulatory recoding and grapheme-to-phoneme conversion.

  • 5.
    Lindström, Tom
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, The Institute of Technology.
    Grear, Daniel A.
    Colorado State University, USA .
    Buhnerkempe, Michael
    Colorado State University, USA .
    Webb, Colleen T.
    Colorado State University, USA .
    Miller, Ryan S.
    US Anim and Plant Health Inspect Serv, CO USA .
    Portacci, Katie
    US Anim and Plant Health Inspect Serv, CO USA .
    Wennergren, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, The Institute of Technology.
    A Bayesian Approach for Modeling Cattle Movements in the United States: Scaling up a Partially Observed Network2013In: PLoS ONE, ISSN 1932-6203, Vol. 8, no 1Article in journal (Refereed)
    Abstract [en]

    Networks are rarely completely observed and prediction of unobserved edges is an important problem, especially in disease spread modeling where networks are used to represent the pattern of contacts. We focus on a partially observed cattle movement network in the U.S. and present a method for scaling up to a full network based on Bayesian inference, with the aim of informing epidemic disease spread models in the United States. The observed network is a 10% state stratified sample of Interstate Certificates of Veterinary Inspection that are required for interstate movement; describing approximately 20,000 movements from 47 of the contiguous states, with origins and destinations aggregated at the county level. We address how to scale up the 10% sample and predict unobserved intrastate movements based on observed movement distances. Edge prediction based on a distance kernel is not straightforward because the probability of movement does not always decline monotonically with distance due to underlying industry infrastructure. Hence, we propose a spatially explicit model where the probability of movement depends on distance, number of premises per county and historical imports of animals. Our model performs well in recapturing overall metrics of the observed network at the node level (U.S. counties), including degree centrality and betweenness; and performs better compared to randomized networks. Kernel generated movement networks also recapture observed global network metrics, including network size, transitivity, reciprocity, and assortativity better than randomized networks. In addition, predicted movements are similar to observed when aggregated at the state level (a broader geographic level relevant for policy) and are concentrated around states where key infrastructures, such as feedlots, are common. We conclude that the method generally performs well in predicting both coarse geographical patterns and network structure and is a promising method to generate full networks that incorporate the uncertainty of sampled and unobserved contacts.

  • 6.
    Jayachandra Pandiyan, Muneeswaran
    Linköping University, Department of Physics, Chemistry and Biology, Molecular genetics.
    A bioinformatics approach to investigate the function of non specific lipid transfer proteins in Arabidopsis thaliana2010Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    Plant non specific lipid transfer proteins (nsLTPs) enhance in vitro transfer of phospholipids between membranes. Our analysis exploited the large amount of Arabidopsis transcriptome data in public databases to learn more about the function of nsLTPs. The analysis revealed that some nsLTPs are expressed only in roots, some are seed specific, and others are specific for tissues above ground whereas certain nsLTPs show a more general expression pattern. Only few nsLTPs showed a strong up or downregulation after that the Arabidopsis plant had suffered from biotic or abiotic stresses. However, salt, high osmosis and UV-B radiation caused upregulation of some nsLTP genes. Further, when the coexpression pattern of the A.thaliana nsLTPs were investigated, we found that there were several modules of nsLTP genes that showed strong coexpression indicating an involvement in related biological processes. Our finding reveals that the nsLTPs gene was significantly correlated with lipase and peroxidase activity. Hence we concluded that the nsLTPs may play a role in seed germination, signalling and ligning biosynthesis.

  • 7.
    Saifullah, Mohammad
    et al.
    Linköping University, Department of Computer and Information Science. Linköping University, The Institute of Technology.
    Balkenius, Christian
    Lund University Cognitive Science, Sweden.
    Jönsson, Arne
    Linköping University, Department of Computer and Information Science, Human-Centered systems. Linköping University, Faculty of Arts and Sciences.
    A biologically based model for recognition of 2-D occluded patterns2014In: Cognitive Processing, ISSN 1612-4782, Vol. 15, no 1, 13-28 p.Article in journal (Refereed)
    Abstract [en]

    In this work, we present a biologically inspired model for recognition of occluded patterns. The general architecture of the model is based on the two visual information processing pathways of the human visual system, i.e. the ventral and the dorsal pathways. The proposed hierarchically structured model consists of three parallel processing channels. The main channel learns invariant representations of the input patterns and is responsible for pattern recognition task. But, it is limited to process one pattern at a time. The direct channel represents the biologically based direct connection from the lower to the higher processing level in the human visual cortex. It computes rapid top-down pattern-specific cues to modulate processing in the other two channels. The spatial channel mimics the dorsal pathway of the visual cortex. It generates a combined saliency map of the input patterns and, later, segments the part of the map representing the occluded pattern. This segmentation process is based on our hypothesis that the dorsal pathway, in addition to encoding spatial properties, encodes the shape representations of the patterns as well. The lateral interaction between the main and the spatial channels at appropriate processing levels and top-down, pattern-specific modulation of the these two channels by the direct channel strengthen the locations and features representing the occluded pattern. Consequently, occluded patterns become focus of attention in the ventral channel and also the pattern selected for further processing along this channel for final recognition.

  • 8.
    Saifullah, Mohammad
    Linköping University, Department of Computer and Information Science. Linköping University, The Institute of Technology.
    A Biologically Inspired Model for Occluded Patterns2011In: Neural Information Processing: proceedings of the 18th International Conference on Neural Information Processing, ICONIP 2011,  Shanghai, China, November 2011., 2011, 88-96 p.Conference paper (Refereed)
    Abstract [en]

    In this paper a biologically-inspired model for partly occluded patterns is proposed. The model is based on the hypothesis that in human visual system occluding patterns play a key role in recognition as well as in reconstructing internal representation for a pattern’s occluding parts. The proposed model is realized with a bidirectional hierarchical neural network. In this network top-down cues, generated by direct connections from the lower to higher levels of hierarchy, interact with the bottom-up information, generated from the un-occluded parts, to recognize occluded patterns. Moreover, positional cues of the occluded as well as occluding patterns, that are computed separately but in the same network, modulate the top-down and bottom-up processing to reconstruct the occluded patterns. Simulation results support the presented hypothesis as well as effectiveness of the model in providing a solution to recognition of occluded patterns. The behavior of the model is in accordance to the known human behavior on the occluded patterns.

  • 9.
    Saifullah, Mohammad
    Linköping University, Department of Computer and Information Science. Linköping University, The Institute of Technology.
    A Biologically-Inspired Model for Recognition of Overlapped Patterns2011In: Proceedings International ICST Conference on Bio-Inspired Models of Network, Information and Computing Systems, 2011Conference paper (Refereed)
    Abstract [en]

    In this paper a biologically-inspired model for recognition of overlapped patterns is proposed. Information processing in the two visual information processing pathways, i.e., the dorsal and the ventral pathway, is modeled as a solution to the problem. We hypothesize that dorsal pathway, in addition to encoding the spatial information, learns the shape representation of the patterns and, later uses this knowledge as a top-down guidance signal to segment the bottom-up, image-based saliency map. This process of segmentation in the dorsal pathway is implemented as an interactive process, where interaction between bottom-up image information and top-down shape cues lead to incremental development of a segmented saliency map for one of the overlapped object at a time. This segmented map encodes spatial as well as shape information of the respective pattern in the input. The interaction of the dorsal channel with the ventral channel leads to modulation and selective processing of the respective pattern in the ventral pathway for final recognition. Simulation results support the presented hypothesis as well as effectiveness of the model in providing a solution to the recognition of overlapped patterns. The behavior of the model is in accordance to the known human behavior on the occluded patterns.

  • 10.
    Knutsson, Lena
    Linköping University, Department of Culture and Communication. Linköping University, Faculty of Arts and Sciences.
    A Blueprint for Women’s Fulfilment: A Reading of Three Novels in the Early Fiction of Margaret Drabble2008Independent thesis Advanced level (degree of Master (Two Years)), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    This essay will argue that Margaret Drabble has developed a pattern, that there is a blueprint for fulfilment in the life of the modern independent woman to be found inher early work. Three of Drabble's novels will be examined, moving from The Millstone(1965) and The Waterfall (1967), with their descriptions of two young heroines'pregnancies and lives with infant children, on to the more mature main character of TheRealms of Gold (1975). These three books form a chronology, both in regard to whenthey were written and, more importantly, to the different stages of a woman’s life thatthey represent. This will make it possible to see how Drabble perceives the demands ofsociety and different relationships influencing a woman's actions, her search foridentity, and the direction and fulfilment of her life. The pattern will be traced throughthree themes which are made visible in the novels in varying degrees. These are singlemotherhood and the role of the family, missing husbands and sexual fulfilment, andcareer and social interaction.The method is an analysis of the texts where the selected novels form the basis andstructure of the essay.

  • 11.
    Eklund, Anders
    et al.
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Andersson, Mats
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Ohlsson, Henrik
    Linköping University, Department of Electrical Engineering, Automatic Control. Linköping University, The Institute of Technology.
    Ynnerman, Anders
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    Knutsson, Hans
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    A Brain Computer Interface for Communication Using Real-Time fMRI2010In: Proceedings of the 20th International Conference on Pattern Recognition, Los Alamitos, CA, USA: IEEE Computer Society, 2010, 3665-3669 p.Conference paper (Refereed)
    Abstract [en]

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

  • 12.
    Fahlgren, Anna
    et al.
    Linköping University, Faculty of Health Sciences. Linköping University, Department of Neuroscience and Locomotion, Orthopaedics and Sports Medicine.
    Chubinskaya, S
    Messner, Karola
    Linköping University, Faculty of Health Sciences. Linköping University, Department of Neuroscience and Locomotion, Orthopaedics and Sports Medicine. Östergötlands Läns Landsting, Orthopaedic Centre, Department of Orthopaedics Linköping.
    Aspenberg, Per
    Linköping University, Faculty of Health Sciences. Linköping University, Department of Neuroscience and Locomotion, Orthopaedics and Sports Medicine. Östergötlands Läns Landsting, Orthopaedic Centre, Department of Orthopaedics Linköping.
    A capsular incision leads to a fast osteoarthritic response, but also elevated levels of activated osteogenic protein-1 in rabbit knee joint cartilage2006In: Scandinavian Journal of Medicine and Science in Sports, ISSN 0905-7188, Vol. 16, no 6, 456-462 p.Article in journal (Refereed)
    Abstract [en]

    We studied whether a small capsular incision alone, or combined with meniscectomy could induce early osteoarthritic changes in the rabbit knee. Thirty-one rabbits were operated on with a capsular incision in the left knee and meniscectomy in the right knee. Another 12 rabbits were used as controls. The rabbits were killed 3, 6 and 12 weeks after surgery. Osteoarthritic changes in the articular cartilage were evaluated by the modified Mankin score. The subchondral bone was evaluated by scintimetry (99mTc-HDP) and semiquantitative grading of histological changes. Osteogenic protein (OP-1) in its mature and pro-form was examined by immunohistochemistry. Both a capsular incision and meniscectomy induced articular cartilage fibrillation and increased bone metabolic activity during the initial weeks after surgery. Capsular incision led to lesser changes than meniscectomy. Mature OP-1 was elevated, and its pro-form reduced, in meniscectomized knees. A similar pattern was observed in knees with capsular incision. Already 3 weeks after surgery, the articular cartilage and subchondral bone showed typical signs of early osteoarthritis (OA), and a reparative response was suggested by increased intensity of OP-1 staining. As these signs were also found in knees with capsular incision only, it appears that trauma-related factors such as increased bleeding and inflammation are critical for the development of OA. Copyright © Blackwell Munksgaard 2006.

  • 13.
    Pham, Tuan D
    et al.
    Bioinformatics Applications Research Center; School of Information Technology, James Cook University, Townsville, QLD, Australia.
    Shim, Byung-Sub
    Bioinformatics Applications Research Center.
    A cepstral distortion measure for protein comparison and identification2005In: Machine Learning and Cybernetics, 2005. Proceedings of 2005 International Conference on, 2005, Vol. 9, 5609-5614 p.Conference paper (Refereed)
    Abstract [en]

    Protein sequence comparison is the most powerful tool for the identification of novel protein structure and function. This type of inference is commonly based on the similar sequence-similar structure-similar function paradigm, and derived by sequence similarity searching on databases of protein sequences. As entire genomes have been being determined at a rapid rate, computational methods for comparing protein sequences will be more essential for probing the complexity of molecular machines. In this paper we introduce a pattern-comparison algorithm, which is based on the mathematical concept of linear-predictive-coding based cepstral distortion measure, for comparison and identification of protein sequences. Experimental results on a real data set of functionally related and functionally non-related protein sequences have shown the effectiveness of the proposed approach on both accuracy and computational efficiency.

  • 14.
    Tran, Dat T
    et al.
    School of Information Sciences and Engineering University of CanberraC ACT 2601 AUSTRALIA.
    Pham, Tuan D
    Bioinformatics Applications Research Centre School of Information Technology James Cook University Townsville, Australia.
    A combined Markov and noise clustering modeling method for cell phase classification2006In: WSEAS Transactions on Biology and Biomedicine, ISSN 1109-9518, E-ISSN 2224-2902, Vol. 3, no 3, 161-166 p.Article in journal (Refereed)
    Abstract [en]

    This paper proposes a classification method of cell nuclei in different mitotic phases using a combined Markov and noise clustering modeling technique. The method was tested with the data set containing 379519 cells in 892 cell sequences for 5 phases extracted from real image sequences recorded at every fifteen minutes with a time-lapse fluorescence microscopy. Experimental results showed that the proposed method performed better than the k-means modeling method.

  • 15.
    Lindholm, Maria
    Linköping University, Department of Culture and Communication. Linköping University, Faculty of Arts and Sciences.
    A COMMUNITY TEXT PATTERN IN THE EUROPEAN COMMISSION PRESS RELEASE? A GENERIC AND GENETIC VIEW2008In: Pragmatics: Quarterly Publication of the International Pragmatics Association, ISSN 1018-2101, Vol. 18, no 1, 33-58 p.Article in journal (Refereed)
    Abstract [en]

    This contribution is concerned with press releases from the European Commission and national ministries. Political press releases may serve other purposes than those issued by business organisations, and they are also a fairly unexplored field in press release research, which this study sets out to remedy, The linguistic dimension of EU communication is also a neglected field of study, and this paper is aimed at introducing the linguistic dimension of the European Commission communication as a field of study worthy of closer examination.

    Within a genre-based analytical framework, the present paper aims at examining to what extent we can identify a unique community text pattern in European Commission press releases. I propose a macrostructural text analysis in which I compare a number of press releases issued by the European Commission with national equivalents from French and Swedish ministries. In particular, I will focus on three recurrent and characteristic text features of the European Commission press release, viz. the introduction, the quotation and the intertextual references. It is shown that the way they are designed in the European Commission press release is quite special and that this can be explained with reference to the communicative situation of the European Commission. In doing so, I will be drawing on ethnographic data that I gathered from fieldwork at the European Commission,

    It will be suggested that the results from this study can be extrapolated to the study of press releases in general. That is, press release research may benefit from the genre-based methodological approach chosen here, since, indeed, the press release is a situated practice whose understanding depends on a comprehensive study of the communicative situations it functions within.

  • 16.
    Karlsson, Laila
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Ecology . Linköping University, The Institute of Technology.
    Milberg, Per
    Linköping University, Department of Physics, Chemistry and Biology, Ecology . Linköping University, The Institute of Technology.
    A Comparative Study of Germination Ecology of Four Papaver Taxa2007In: Annals of Botany, ISSN 0305-7364, Vol. 99, no 5, 935-946 p.Article in journal (Refereed)
    Abstract [en]

    Background and Aims: Comparative studies of closely related taxa can increase understanding of adaptations and changes in seed dormancy and germination preferences in an evolutionary perspective. For such studies, a method to describe and compare the performance of taxa in a general way is needed. The germination ecology of four Papaver taxa was studied with the aim of describing and comparing their responses to different seasonal temperature regimes.

    Methods: Germination of Papaver argemone, P. rhoeas, P. dubium ssp. dubium and P. dubium ssp. lecoqii was investigated in three different artificial climates over 2.5 years. Seeds were collected in southern Sweden, and samples from different populations were used as replicates of taxa.

    Key Results: Despite substantial intra-taxa variation, there were clear taxon-specific responses. Most germination occurred in the warmest climate. In general, the warmer the climate the more germination occurred in autumn instead of spring. Papaver argemone, phylogenetically most distant from the others, was, in contrast to the other taxa, restricted to germinating only at lower temperatures.

    Conclusions: Seed dormancy and germination may be described by dormancy pattern, germination preferences and dormancy strength. The general dormancy pattern was a common feature for these taxa and therefore probably an evolutionary conservative character. Germination preferences varied between taxa, resulting in different temperature optima and intervals for germination, and dormancy strength was to some extent taxon-specific, but highly variable. The dormancy pattern explained how the taxa can perform as winter annuals in warmer climates, but mainly as summer annuals in colder climates. Hence, there is no need to interpret the within-taxon temporal differences in seedling emergence as local adaptations. In the field, an entire seed cohort will not germinate during a single season. Instead, emergence will be distributed over several seasons, regardless of local climate, weather and soil cultivation methods.

  • 17.
    Pernestål, Anna
    et al.
    Linköping University, Department of Electrical Engineering, Vehicular Systems. Linköping University, The Institute of Technology.
    Wettig, Hannes
    Complex Systems Computations Group, Department of Computer Science, Helsinki Institute for Information Technology, Finland.
    Silander, Tomi
    Complex Systems Computations Group, Department of Computer Science, Helsinki Institute for Information Technology, Finland.
    Nyberg, Mattias
    Linköping University, Department of Electrical Engineering, Vehicular Systems. Linköping University, The Institute of Technology.
    Myllymäki, Petri
    Complex Systems Computations Group, Department of Computer Science, Helsinki Institute for Information Technology, Finland.
    A Comparison of Baysian Approaches to Learning in Fault Isolation2009In: Pattern Recognition Letters, ISSN 0167-8655Article in journal (Other academic)
    Abstract [en]

    Fault isolation is the task of localizing faults in a process, given observations from it. To do this, a model describing the relations between faults and observations is needed.

    In this paper we focus on learning such models both from training data and from prior knowledge. There are several challenges in learning for fault isolation.

    The number of data and the available computing resources are often limited. Furthermore, there may be previously unobserved fault patterns.

    To meet these challenges we take on a Bayesian approach.

    We compare five different approaches to learning for fault isolation, and evaluate their performance on a real application, namely the diagnosis of an automotive engine.

  • 18.
    Nyasulu, Jonas
    Linköping University, Department of Computer and Information Science.
    A Comparison of Vistrails and Taverna, and Workflow Interoperability2009Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    In silico experiments in the field of bioinformatics generate large amounts of data since most of the tasks are done in an exploratory fashion. Workflows are one of the many tools used by scientists to model complex tasks.The interoperability of data generated from these tools plays an important role in improving the efficiency of such tools and also in verifying results from other experiments.We aim to compare workflow systems by integrating bioinformatics data in Vistrails and Taverna. We also look at how the two systems use the open provenance model that has been developed to bring provenance interoperability. We developed web services to perform similar functions of some workflows in Vistrails. With the services we were able to perform most of the tasks we planned using both systems. Differences in how lists of items are processed in the two systems results in differences in how workflows are composed in the two systems. In Taverna there is implicit iteration and Vistrails requires the use of additional modules to perform iteration.There are also differences in the execution times of workflows using web services, with workflows in Taverna taking longer than their counterparts in Vistrails. There are some similarities in the execution pattern of workflows if same workflow is invokedmultiple times, with the first invocation taking longer time than the subsequent ones.

  • 19. Sparring Björkstén, Karin
    et al.
    Ekberg, Stefan
    Linköping University, Faculty of Health Sciences. Linköping University, Department of Medicine and Care, Radiation Physics. Östergötlands Läns Landsting, Centre of Surgery and Oncology, Department of Radiation Physics.
    Säfström, Pia
    Linköping University, Faculty of Health Sciences. Linköping University, Department of Medicine and Care, Medical Radiology. Östergötlands Läns Landsting, Centre for Medical Imaging, Department of Radiology UHL.
    Dige, N
    Granerus, Göran
    Linköping University, Faculty of Health Sciences. Linköping University, Department of Medicine and Care, Clinical Physiology. Östergötlands Läns Landsting, Heart Centre, Department of Clinical Physiology.
    A computerized human reference brain for rCBF/SPET technetium-99m exametazime (HMPAO) investigation of elderly2004In: Clinical Physiology and Functional Imaging, ISSN 1475-0961, Vol. 24, no 4, 196-204 p.Article in journal (Refereed)
    Abstract [en]

    Using the bull's eye approach, a reference brain from the single photon emission tomography (SPET) images of 10 subjects aged 62-81 years with excellent mental and physical health was constructed. SPET images were acquired twice, 1 week apart, using a single detector rotating gamma camera collecting 64 planar images over a 360° orbit. The centre of each transaxial slice was first defined with an automatic edge detecting algorithm applied to an anterior-posterior and a side profile of the brain. Each slice was divided into 40 sectors. Maximum counts/pixel in each sector was picked. The 40 maximum count values from one transaxial slice were allowed to form a horizontal row in a new parametric image on the x-axis and slice number from the vertex to the basal parts of the brain on the y-axis. This new image was scaled to a 64 × 16 pixel matrix by interpolation, which meant a normalization of all studies to the same size. The parametric image in each subject was scaled with regard to intensity by a factor calculated by a normalization procedure using the least squares analysis. Mean and SD for each pixel were calculated, thereby constructing a 'mean parametric image', and a 'SD parametric image'. These two images are meant to be used as the reference brain for evaluation of patient studies. This method can be used for objective measurements of diffuse brain changes and for pattern recognition in larger groups of patients. Statistical multifactorial analysis of parameters used for acquisition and data processing is possible. © 2004 Blackwell Publishing Ltd.

  • 20.
    Ohlsson, Henrik
    et al.
    Linköping University, Department of Electrical Engineering, Automatic Control. Linköping University, The Institute of Technology.
    Ljung, Lennart
    Linköping University, Department of Electrical Engineering, Automatic Control. Linköping University, The Institute of Technology.
    A Convex Approach to Subspace Clustering2011In: Proceedings of the 50th IEEE Conference on Decision and Control, 2011, 1467-1472 p.Conference paper (Refereed)
    Abstract [en]

    The identification of multiple affine subspaces from a set of data is of interest in fields such as system identification, data compression, image processing and signal processing and in the literature referred to as subspace clustering. If the origin of each sample would be known, the problem would be trivially solved by applying principal component analysis to samples originated from the same subspace. Now, not knowing what samples that originates from what subspace, the problem becomes considerably more difficult. We present a novel convex formulation for subspace clustering. The proposed method takes the shape of a least-squares problem with sum-of-norms regularization over optimization parameter differences, a generalization of the ℓ1-regularization. The regularization constant is used to trade off fit and the identified number of affine subspaces.

  • 21.
    Liu, Yang
    et al.
    Department of Information Technology, Vaasa University of Applied Sciences, Vaasa, Finland / School of Electrical and Electronic Engineering, Hubei University of Technology, Wuhan, China.
    Vo, Thanh Vinh
    Department of Information Technology, Vaasa University of Applied Sciences, Vaasa, Finland.
    A Fast Machine Vision for Automated Packaging2012In: Electrical, Information Engineering and Mechatronics 2011: Proceedings of the 2011 International Conference on Electrical, Information Engineering and Mechatronics (EIEM 2011) / [ed] Wang, Xudong; Wang, Fuzhong; Zhong, Shaobo, Springer, 2012, 719-726 p.Chapter in book (Other academic)
    Abstract [en]

    This paper introduces a fast, simple, cheap but accurate and reliable vision system designed for the automated packaging robot application, which is to replace manual product packaging. The objective is to develop a vision system and algorithm for such application and achieve pattern tracking in nearly real-time with a normal entry-level computer. This paper describes in detail the implementation of the proposed vision system including image processing and pattern recognition. The application uses only a simple gray scale image of product as sample pattern to track the product in the scene at real-time speed, which has come near to replace human eyes. The proposed machine vision has been implemented and equipped on a real ABB robot arm with other related hardware/software to achieve automated packaging. The performance has been evaluated as a success in both timing and precision. Its stability and reliability are also proved under laboratory testing environment.

  • 22.
    Nordberg, Klas
    et al.
    Linköping University, The Institute of Technology. Linköping University, Department of Electrical Engineering, Computer Vision.
    Doherty, Patrick
    Linköping University, The Institute of Technology. Linköping University, Department of Computer and Information Science, KPLAB - Knowledge Processing Lab.
    Forssén, Per-Erik
    Linköping University, The Institute of Technology. Linköping University, Department of Electrical Engineering, Computer Vision.
    Wiklund, Johan
    Linköping University, The Institute of Technology. Linköping University, Department of Electrical Engineering, Computer Vision.
    Andersson, Per
    A flexible runtime system for image processing in a distributed computational environment for an unmanned aerial vehicle2006In: International Journal of Pattern Recognition and Artificial Intelligence, ISSN 0218-0014, Vol. 20, no 5, 763-780 p.Article in journal (Refereed)
    Abstract [en]

    A runtime system for implementation of image processing operations is presented. It is designed for working in a flexible and distributed environment related to the software architecture of a newly developed UAV system. The software architecture can be characterized at a coarse scale as a layered system, with a deliberative layer at the top, a reactive layer in the middle, and a processing layer at the bottom. At a finer scale each of the three levels is decomposed into sets of modules which communicate using CORBA, allowing system development and deployment on the UAV to be made in a highly flexible way. Image processing takes place in a dedicated module located in the process layer, and is the main focus of the paper. This module has been designed as a runtime system for data flow graphs, allowing various processing operations to be created online and on demand by the higher levels of the system. The runtime system is implemented in Java, which allows development and deployment to be made on a wide range of hardware/software configurations. Optimizations for particular hardware platforms have been made using Java's native interface.

  • 23.
    Rantanen, V.-V.
    et al.
    Department of Mathematics, University of Turku, FIN-20014, Turku, Finland, Department of Biochemistry and Pharmacy, Åbo Akademi University, Tykistökatu 6 BioCity 3A, FIN-20521, Turku, Finland.
    Denessiouk, K.A.
    Department of Biochemistry and Pharmacy, Åbo Akademi University, Tykistökatu 6 BioCity 3A, FIN-20521, Turku, Finland.
    Gyllenberg, M.
    Department of Mathematics, University of Turku, FIN-20014, Turku, Finland.
    Koski, Timo
    Linköping University, The Institute of Technology. Linköping University, Department of Mathematics, Mathematical Statistics .
    Johnson, M.S.
    Department of Biochemistry and Pharmacy, Åbo Akademi University, Tykistökatu 6 BioCity 3A, FIN-20521, Turku, Finland.
    A fragment library based on Gaussian mixtures predicting favorable molecular interactions2001In: Journal of Molecular Biology, ISSN 0022-2836, Vol. 313, no 1, 197-214 p.Article in journal (Refereed)
    Abstract [en]

    Here, a protein atom-ligand fragment interaction library is described. The library is based on experimentally solved structures of protein-ligand and protein-protein complexes deposited in the Protein Data Bank (PDB) and it is able to characterize binding sites given a ligand structure suitable for a protein. A set of 30 ligand fragment types were defined to include three or more atoms in order to unambiguously define a frame of reference for interactions of ligand atoms with their receptor proteins. Interactions between ligand fragments and 24 classes of protein target atoms plus a water oxygen atom were collected and segregated according to type. The spatial distributions of individual fragment - target atom pairs were visually inspected in order to obtain rough-grained constraints on the interaction volumes. Data fulfilling these constraints were given as input to an iterative expectation-maximization algorithm that produces as output maximum likelihood estimates of the parameters of the finite Gaussian mixture models. Concepts of statistical pattern recognition and the resulting mixture model densities are used (i) to predict the detailed interactions between Chlorella virus DNA ligase and the adenine ring of its ligand and (ii) to evaluate the "error" in prediction for both the training and validation sets of protein-ligand interaction found in the PDB. These analyses demonstrate that this approach can successfully narrow down the possibilities for both the interacting protein atom type and its location relative to a ligand fragment. © 2001 Academic Press.

  • 24.
    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.

  • 25.
    Viksten, Fredrik
    et al.
    Linköping University, Department of Electrical Engineering, Computer Vision. Linköping University, The Institute of Technology.
    Nordberg, Klas
    Linköping University, Department of Electrical Engineering, Computer Vision. Linköping University, The Institute of Technology.
    A Geometry-Based Local Descriptor for Range Data2007In: Proceedings of the 9th Biennial Conference of the Australian Pattern Recognition Society on Digital Image Computing Techniques and Applications: Rome, Italy, ACM , 2007, 210-217 p.Conference paper (Refereed)
    Abstract [en]

    We present a novel local descriptor for range data that can describe one or more planes or lines in a local region. It is possible to recover the geometry of the described local region and extract the size, position and orientation of each local plane or line-like structure from the descriptor. This gives the descriptor a property that other popular local descriptors for range data, such as spin images or point signatures, does not have. The estimation of the descriptor is dependant on estimation of surface normals but does not depend on the specific normal estimation method used. It is shown that is possible to extract how many planar surface regions the descriptor represents and that this could be used as a point-of-interest detector.

  • 26.
    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, Vol. 11, no 7, 635-U109 p.Article 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.

  • 27.
    Wirén, Anna
    et al.
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology.
    Jensen, Per
    Linköping University, Department of Physics, Chemistry and Biology, Zoology. Linköping University, The Institute of Technology.
    A Growth QTL on Chicken Chromosome 1 Affects Emotionality and Sociality2011In: Behavior Genetics, ISSN 0001-8244, E-ISSN 1573-3297, Vol. 41, no 2, 303-311 p.Article in journal (Refereed)
    Abstract [en]

    Domestication of animals, regardless of species, is often accompanied by simultaneous changes in several physiological and behavioral traits (e.g. growth rate and fearfulness). In this study we compared the social behavior and emotional reactivity, as measured in a battery of behavioral tests, of two groups of chickens selected from a common genetic background, an advanced intercross line between the ancestral red junglefowl ("RJF") and the domesticated White Leghorn layer ("WL"). The birds were selected for homozygosity for alternative alleles at one locus (a microsatellite marker), centrally positioned in a previously identified pleiotropic growth QTL on chromosome 1, closely linked to one major candidate gene (AVPR1a) for certain aspects of social behavior. Birds homozygous for the WL allele ("WL genotype") had a modified pattern of social and emotional reactions than birds homozygous for the RJF allele ("RJF genotype"), shown by different scores in a principal components analysis. These results suggest that the growth QTL affects a number of domestication related behavioral traits, and may have been a primary target of selection during domestication. The QTL contains a multitude of genes, several of which have been linked to social behavior (for example the vasotocin receptor AVPR1a targeted in this experiment). Future studies aimed at making a higher resolution genotypic characterization of the QTL should give more information about which of these genes may be considered the strongest candidates for bringing about the behavioral changes associated with animal domestication.

  • 28.
    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.

  • 29.
    Jeppsson-Grassman, Eva
    et al.
    Linköping University, Department of Social and Welfare Studies, NISAL - National Institute for the Study of Ageing and Later Life. Linköping University, Faculty of Arts and Sciences.
    Taghizadeh Larsson, Annika
    Linköping University, Department of Social and Welfare Studies, NISAL - National Institute for the Study of Ageing and Later Life. Linköping University, Faculty of Arts and Sciences.
    “A home away from home”: The role of the Church of Sweden Abroad for Swedish migrants2013In: New Religiosity in Migration, 2013, 38-41 p.Conference paper (Refereed)
    Abstract [en]

    According to some studies, Sweden is one of the most secularized countries in the world. with low church attendance. For most Swedes, their contact with the church is limited to traditional rites. How are we then to understand that quite a few Swedes seem to act much like immigrant groups from less secularized nations, by turning to the ethnic church and to religious practices while moving – fully or part time – to foreign countries?

    The aim of the presentation is to discuss this question, based on results from a project in which the role of the Church of Sweden   Abroad has been explored. The Church of Sweden has a long traditions of creating parishes abroad, mainly in the larger European cities and in connection with harbors, as Seaman`s Churches. Since some decades, however, the Church has started to follow the streams of tourists and elderly migrants and parishes have been established, mainly in Southern Europe and, lately in Asian countries.

    The presentation will be based on a project consisting of three studies: 1) A qualitative case study, 2) A mapping of the web sites of all 45 parishes, and 3) An internet-based survey of all parishes. An interesting pattern turned out to be  that many church visitors who initially seemed to be attracted by the (Swedish) “home away from home”  that the parish offered through e.g. “Swedish coffee”, eventually began to participate regularly in the church services, even in Holy Communion.

     

     

  • 30.
    Hallgren, Mattias
    et al.
    Linköping University, Department of Management and Engineering, Production Economics. Linköping University, The Institute of Technology.
    Olhager, Jan
    Linköping University, Department of Management and Engineering, Production Economics. Linköping University, The Institute of Technology.
    Schroeder, Roger G.
    University of Minnesota, USA .
    A hybrid model of competitive capabilities2011In: International Journal of Operations & Production Management, ISSN 0144-3577, Vol. 31, no 5, 511-526 p.Article in journal (Refereed)
    Abstract [en]

    Purpose – The purpose of this paper is to present and test a new model for competitive capabilities.Traditionally, a cumulative model has been viewed as having one sequence of building competitivecapabilities in a firm in support of market needs, including quality, delivery, cost efficiency andflexibility. Although appealing as a conceptual model, empirical testing has not been able to fullysupport the cumulative model. This paper acknowledges the need for a hybrid approach to managingcapability progression. It brings together the literature on trade-offs, cumulative capabilities, andorder winners and qualifiers.Design/methodology/approach – A new hybrid approach for modelling competitive capabilities istested empirically using data from the high performance manufacturing (HPM) study, round 3,including three industries and seven countries – a total of 211 plants.Findings – The hybrid model shows significantly better fit with the data from the sample than thecumulative models suggested by previous literature. Empirical support is found for the traditionalperception that a high level of quality is a prerequisite for a high level of delivery performance.However, cost efficiency and flexibility do not exhibit a cumulative pattern. Instead, the results showthat they are developed in parallel. The findings suggest that a balance between cost efficiency andflexibility is built upon high levels of quality and delivery performance.Research limitations/implications – Since we limit the empirical investigation to three industriesand seven countries, it would be interesting to extend the testing of this model to more industries andcountries. This research shows that combining perspectives and insights from different researchstreams – in this case, trade-off theory and the concepts of cumulative capabilities, and order winnersand qualifiers – can be fruitful.Practical implications – The results of this paper provides managers with guidelines concerningthe configuration of competitive capabilities. First, a qualifying level of quality needs to be attained,followed by a qualifying level of delivery. Then, a balance between potential order winners, i.e. costefficiency and flexibility, needs to be attained.Originality/value – This paper presents a new approach to modelling competitive capabilities thatsynthesises previous research streams and perspectives from cumulative capabilities, contestingcapabilities (trade-offs), and order winners and qualifiers.

  • 31. Brenne, Anne-Tove
    et al.
    Hejna Romstad, Lene
    Gimsing, Peter
    Juliusson, Gunnar
    Linköping University, Faculty of Health Sciences. Linköping University, Department of Biomedicine and Surgery, Oncology. Östergötlands Läns Landsting, Centre of Surgery and Oncology, Department of Haematology UHL.
    Turesson, Ingemar
    Romundstad, Pål
    Borset, Magne
    Sundan, Anders
    Waage, Anders
    A low serum level of soluble tumor necrosis factor receptor p55 predicts response to thalidomide in advanced multiple myeloma2004In: Haematologica, ISSN 0390-6078, Vol. 89, no 5, 552-556 p.Article in journal (Refereed)
    Abstract [en]

    Background and Objectives. Thalidomide modulates the production of tumor necrosis factor (TNF-α). Soluble TNF receptors, TNFR p55 and TNFR p75, modify TNF-α activity. In this study, we explored the relation between soluble TNF receptors and outcome in patients with advanced multiple myeloma treated with thalidomide. Design and Methods. The levels of soluble TNF receptor p55 and p75 were assessed in serum from 34 myeloma patients with relapsed or refractory disease before starting thalidomide treatment. Serial measurements were performed for 16 patients in serum collected during treatment. Results. The pre-treatment serum level of soluble TNFR p55 in thalidomide responders was significantly lower than that in non-responders (median 1.75 ng/mL (range 1.19-2.84) vs. 2.79 ng/mL (1.36-5.51), p=0.004). The levels of p55 declined significantly during treatment. The levels of p75 showed the same pattern as p55, but the differences were not significant. The median survival of myeloma patients with pre-treatment levels of p55 < 2.79 ng/mL was 404 days, the median survival of patients with pre-treatment levels ≥ 2.79 ng/mL was shorter (65 days, log-rank test p=0.02). Interpretation and Conclusions. We conclude that soluble TNFR p55 is an adverse prognostic factor in myeloma patients with relapsed or refractory disease treated with thalidomide. Patients with a low pre-treatment level of this receptor have a better response rate and a longer overall survival.

  • 32.
    Virojanadara, Chariya
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Semiconductor Materials. Linköping University, The Institute of Technology.
    Zakharov, A A
    Lund University.
    Watcharinyanon, Somsakul
    Linköping University, Department of Physics, Chemistry and Biology, Semiconductor Materials. Linköping University, The Institute of Technology.
    Yakimova, Rositsa
    Linköping University, Department of Physics, Chemistry and Biology, Semiconductor Materials. Linköping University, The Institute of Technology.
    Johansson, Leif I
    Linköping University, Department of Physics, Chemistry and Biology, Semiconductor Materials. Linköping University, The Institute of Technology.
    A low-energy electron microscopy and x-ray photo-emission electron microscopy study of Li intercalated into graphene on SiC(0001)2010In: NEW JOURNAL OF PHYSICS, ISSN 1367-2630, Vol. 12, no 125015Article in journal (Refereed)
    Abstract [en]

    The effects induced by the deposition of Li on 1 and 0 ML graphene grown on SiC(0001) and after subsequent heating were investigated using low-energy electron microscopy (LEEM) and x-ray photo-emission electron microscopy (XPEEM). For 1 ML samples, the collected photoelectron angular distribution patterns showed the presence of single pi-cones at the six equivalent K-points in the Brillouin zone before Li deposition but the presence of two pi-cones (pi-bands) after Li deposition and after heating to a few hundred degrees C. For 0 ML samples, no pi-band could be detected close to the Fermi level before deposition, but distinct pi-cones at the K-points were clearly resolved after Li deposition and after heating. Thus Li intercalation was revealed in both cases, transforming the carbon buffer layer (0 ML) to graphene. On 1 ML samples, but not on 0 ML, a (root 3 x root 3) R30 degrees diffraction pattern was observed immediately after Li deposition. This pattern vanished upon heating and then wrinkles/cracks appeared on the surface. Intercalation of Li was thus found to deteriorate the quality of the graphene layer, especially for 1 ML samples. These wrinkles/cracks did not disappear even after heating at temperatures andgt;= 500 degrees C, when no Li atoms remained on the substrate.

  • 33.
    Buckwalter, Claes
    Linköping University, Department of Science and Technology, Digital Media. Linköping University, The Institute of Technology.
    A Messaging-Based Integration Architecture for Print Production Workflow Systems2006In: Proceedings of Printing Technology SPb’06, 2006, 13-17 p.Conference paper (Refereed)
    Abstract [en]

    A print production workflow consists of a number of systems

    specialized at executing specific tasks. In order to realize an

    efficient workflow it is not enough to simply assemble all the

    required systems, the systems must also communicate with each

    other and exchange information. The printing industry has used

    several approaches for integrating systems. A common

    approach has been to use so-called “hot folders” to exchange

    content files, such as PDF documents, between systems.

    Another approach, which focuses on the exchange of production

    and configuration data, is the XML-based Job Definition

    Format (JDF) and its messaging protocol Job Messaging

    Format (JMF).

     

    The need to integrate heterogeneous systems is nothing unique

    to the printing industry. The experience and knowledge in this

    area has been documented in several pattern languages. By

    applying a combination of several such pattern languages, this

    paper presents a hypothetical integration architecture that

    enables a system to communicate with other systems using JMF

    messaging.

  • 34.
    Klenkar, Goran
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics . Linköping University, The Institute of Technology.
    Liedberg, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics . Linköping University, The Institute of Technology.
    A Microarray Chip for Label-Free Detection of Narcotics2008In: Analytical and Bioanalytical Chemistry, ISSN 1618-2642, Vol. 391, no 5, 1679-1688 p.Article in journal (Refereed)
    Abstract [en]

    A protein array chip for label-free optical detection of low molecular weight compounds has been developed. As a proof of principle, the chip is proven capable of rapidly (approximately 1 min) determining hits from aqueous cocktails composed of four common narcotics, cocaine, ecstasy, heroin, and amphetamine, using imaging surface plasmon resonance (SPR) as the detection principle. The chip is produced by injecting a mixture of antibodies and letting them self-sort and bind to narcotic analog coupled proteins already present in a predefined pattern on the supporting substrate. An indirect detection method, where antibodies are displaced from the surface upon recognition of their corresponding narcotics, is used to obtain the optical contrast and thus a detectable SPR and/or ellipsometric signal. Two types of readouts are possible from the present setup: intensity SPR images and SPR/ellipsometric sensorgrams. Positive hits were routinely obtained for analyte concentrations of 50 pg/μL and the limit of detection, without any parameter optimizations, seems to fall in the range 0.5 pg/μL (1.4 nM) for heroin, 2.5 pg/μL (8.2 nM) for cocaine, and 5 pg/μL for the other two narcotics (26 nM for ecstasy and 37 nM for amphetamine). With improved readout possibilities (sampling frequency), signal evaluation algorithms, and antibody–antigen design strategies, we believe this limit can be further improved. The chip is shown to work for many measurement cycles with excellent reproducibility. Moreover, with a more advanced fluidic system, excess injected antibodies could be collected and reused for many cycles, which could make the running costs of the system very low. The chip is in no way limited to detection of narcotics. Other low molecular weight compounds could easily be detected on the same chip. For example, trinitrotoluene detection has already been demonstrated using our chip. Possible areas of application for the system are therefore envisaged in airport and underground transport security, customs, drug interdiction, forensics, and as warning alerts on military equipment and personnel.

  • 35.
    Ganghoffer, J.F.
    et al.
    ICSI, 15, Rue Jean Starcky, BP 2478, 68057 Mulhouse Cedex, France.
    Simonsson, Kjell
    Linköping University, Department of Management and Engineering, Solid Mechanics. Linköping University, Faculty of Science & Engineering.
    A micromechanical model of the martensitic transformation1998In: Mechanics of Materials, ISSN 0167-6636, Vol. 27, no 3, 125-144 p.Article in journal (Refereed)
    Abstract [en]

    A micromechanical model of the martensitic transformation at the grain scale has been established, considering the more specific case of ferrous alloys. The transformation proceeds through the formation of successive variants of the product phase within a unit cell representative of a grain; interactions between neighbouring grains are simulated by the choice of periodic boundary conditions. From a thermodynamical analysis, a selection rule for the order and orientation of the forming martensitic variants has been established, based on internal stresses anisotropy. These concepts have been implemented into a two-dimensional finite element simulation of the transformation, considering an elastoplastic behaviour of both parent and product phases. Morphological and crystallographical features of the transformation are considered: one variant consists of a thin layer of elements within the mesh that can form with four possible discrete orientations. Simulation results show the development of the plate pattern as a combination of the influence of both external load and internal stresses built during the progress of the transformation. These are related to global evolutions of transformation plasticity vs. transformation progress. Comparison with experiments show a similar form of the evolutions of the total strain; however, the model overestimates the strain levels. The possible reasons for this discrepancy are discussed.

  • 36.
    Nordberg, Klas
    Linköping University, Department of Electrical Engineering, Computer Vision. Linköping University, The Institute of Technology.
    A minimal parameterization of the trifocal tensor2009In: IEEE Computer Science Conference on Computer Vision and Pattern Recognition (CVPR), 2009, 1224-1230 p.Conference paper (Refereed)
    Abstract [en]

    The paper describes a minimal set of 18 parameters that can representany trifocal tensor consistent with the internal constraints.  9parameters describe three orthogonal matrices and 9 parameters describe10 elements of a sparse tensor T' with 17 elements in well-defined positions equal to zero.  Any valid trifocal tensor isthen given as some specific T' transformed by the orthogonalmatrices in the respective image domain.  The paper also describes asimple approach for estimating the three orthogonal matrices in thecase of a general 3 x 3 x 3 tensor, i.e., when the internalconstraints are not satisfied.  This can be used to accomplish a leastsquares approximation of a general tensor to a tensor that satisfies the internal constraints.  This type of constraint enforcement, inturn, can be used to obtain an improved estimate of the trifocal tensorbased on the normalized linear algorithm, with the constraintenforcement as a final step.  This makes the algorithm more similar tothe corresponding algorithm for estimation of the fundamental matrix. An experiment on synthetic data shows that the constraint enforcementof the trifocal tensor produces a significantly better result thanwithout enforcement, expressed by the positions of the epipoles, giventhat the constraint enforcement is made in normalized image coordinates.

  • 37.
    Viljanen, Johan
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Organic Chemistry. Linköping University, The Institute of Technology.
    Larsson, Jenny
    Linköping University, Department of Clinical and Experimental Medicine, Medical Microbiology. Linköping University, Faculty of Health Sciences.
    Larsson (Kaiser), Andréas
    Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics. Linköping University, The Institute of Technology.
    Broo, Kerstin S.
    Linköping University, Department of Physics, Chemistry and Biology, Organic Chemistry. Linköping University, The Institute of Technology.
    A Multipurpose Receptor Composed of Promiscuous Proteins. Analyte Detection through Pattern Recognition2007In: Bioconjugate Chemistry, ISSN 1043-1802, Vol. 18, no 6, 1935-1945 p.Article in journal (Refereed)
    Abstract [en]

    A multipurpose receptor akin to the “electronic nose” was composed of coumarin-labeled mutants of human glutathione transferase A1. We have previously constructed a kit for site-specific modification of a lysine residue (A216K) using a thiol ester of glutathione (GSC-Coubio) as a modifying reagent. In the present investigation, we scrambled the hydrophobic binding site (H-site) of the protein scaffold through mutations at position M208 via random mutagenesis and isolated a representative library of 11 A216K/M208X mutants. All of the double mutants could be site-specifically labeled to form the K216Cou conjugates. The labeled proteins responded to the addition of different analytes with signature changes in their fluorescence spectra resulting in a matrix of 96 data points per analyte. Ligands as diverse as n-valeric acid, fumaric acid monoethyl ester, lithocholic acid, 1-chloro-2,4-dinitrobenzene (CDNB), glutathione (GSH), S-methyl-GSH, S-hexyl-GSH, and GS-DNB all gave rise to signals that potentially can be interpreted through pattern recognition. The measured Kd values range from low micromolar to low millimolar. The cysteine residue C112 was used to anchor the coumarin-labeled protein to a PEG-based hydrogel chip in order to develop surface-based biosensing systems. We have thus initiated the development of a multipurpose, artificial receptor composed of an array of promiscuous proteins where detection of the analyte occurs through pattern recognition of fluorescence signals. In this system, many relatively poor binders each contribute to detailed readout in a truly egalitarian fashion.

  • 38.
    Koschorrek, Philipp
    et al.
    Linköping University, Department of Electrical Engineering, Computer Vision. Linköping University, The Institute of Technology.
    Piccini, Tommaso
    Linköping University, Department of Electrical Engineering, Computer Vision. Linköping University, The Institute of Technology.
    Öberg, Per
    Linköping University, Department of Electrical Engineering, Computer Vision. Linköping University, Department of Electrical Engineering, Vehicular Systems. Linköping University, The Institute of Technology.
    Felsberg, Michael
    Linköping University, Department of Electrical Engineering, Computer Vision. Linköping University, The Institute of Technology.
    Nielsen, Lars
    Linköping University, Department of Electrical Engineering, Vehicular Systems. Linköping University, The Institute of Technology.
    Mester, Rudolf
    Linköping University, Department of Electrical Engineering, Computer Vision. Linköping University, The Institute of Technology. University of Frankfurt, Germany.
    A multi-sensor traffic scene dataset with omnidirectional video2013In: 2013 IEEE CONFERENCE ON COMPUTER VISION AND PATTERN RECOGNITION WORKSHOPS (CVPRW), IEEE conference proceedings, 2013, 727-734 p.Conference paper (Refereed)
    Abstract [en]

    The development of vehicles that perceive their environment, in particular those using computer vision, indispensably requires large databases of sensor recordings obtained from real cars driven in realistic traffic situations. These datasets should be time shaped for enabling synchronization of sensor data from different sources. Furthermore, full surround environment perception requires high frame rates of synchronized omnidirectional video data to prevent information loss at any speeds.

    This paper describes an experimental setup and software environment for recording such synchronized multi-sensor data streams and storing them in a new open source format. The dataset consists of sequences recorded in various environments from a car equipped with an omnidirectional multi-camera, height sensors, an IMU, a velocity sensor, and a GPS. The software environment for reading these data sets will be provided to the public, together with a collection of long multi-sensor and multi-camera data streams stored in the developed format.

  • 39.
    Johansson, Anders
    Linköping University, The Institute of Technology. Linköping University, Department of Biomedical Engineering, Physiological Measurements.
    A neural network for photoplethysmographic respiratory rate monitoring2001In: Proceedings of SPIE, the International Society for Optical Engineering, ISSN 0277-786X, Vol. 4434, 109-118 p.Conference paper (Other academic)
    Abstract [en]

    The photoplethysmographic signal (PPG) includes respiratory components seen as frequency modulation of the heart rate (respiratory sinus arrhythmia, RSA), amplitude modulation of the cardiac pulse, and respiratory induced intensity variations (RIIV) in the PPG baseline. The aim of this study was to evaluate the accuracy of these components in determining respiratory rate, and to combine the components in a neural network for improved accuracy. The primary goal is to design a PPG ventilation monitoring system. PPG signals were recorded from 15 healthy subjects. From these signals, the systolic waveform, diastolic waveform, respiratory sinus arrhythmia, pulse amplitude and RIIV were extracted. By using simple algorithms, the rates of false positive and false negative detection of breaths were calculated for each of the five components in a separate analysis. Furthermore, a simple neural network (NN) was tried out in a combined pattern recognition approach. In the separate analysis, the error rates (sum of false positives and false negatives) ranged from 9.7% (pulse amplitude) to 14.5% (systolic waveform). The corresponding value of the NN analysis was 9.5-9.6%.

  • 40.
    Hol, Jeroen
    et al.
    Linköping University, Department of Electrical Engineering, Automatic Control. Linköping University, The Institute of Technology.
    Schön, Thomas
    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 New Algorithm for Calibrating a Combined Camera and IMU Sensor Unit2008Report (Other academic)
    Abstract [en]

    This paper is concerned with the problem of estimating the relative translation and orientation between an inertial measurement unit and a camera which are rigidly connected. The key is to realise that this problem is in fact an instance of a standard problem within the area of system identification, referred to as a gray-box problem. We propose a new algorithm for estimating the relative translation and orientation, which does not require any additional hardware, except a piece of paper with a checkerboard pattern on it. Furthermore, covariance expressions are provided for all involved estimates. The experimental results shows that the method works well in practice.

  • 41.
    Hol, Jeroen
    et al.
    Linköping University, Department of Electrical Engineering, Automatic Control. Linköping University, The Institute of Technology.
    Schön, Thomas
    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 New Algorithm for Calibrating a Combined Camera and IMU Sensor Unit2008In: Proceedings of the 10th International Conference on Control, Automation, Robotics and Vision, 2008, 1857-1862 p.Conference paper (Refereed)
    Abstract [en]

    This paper is concerned with the problem of estimating the relative translation and orientation between an inertial measurement unit and a camera which are rigidly connected. The key is to realise that this problem is in fact an instance of a standard problem within the area of system identification, referred to as a gray-box problem. We propose a new algorithm for estimating the relative translation and orientation, which does not require any additional hardware, except a piece of paper with a checkerboard pattern on it. Furthermore, covariance expressions are provided for all involved estimates. The experimental results shows that the method works well in practice. 

  • 42.
    Pham, Tuan D
    et al.
    ADFA School of Information Technology and Electrical Engineering The University of New South Wales Canberra, Australia.
    Eisenblätter, Uwe
    ADFA School of Information Technology and Electrical Engineering The University of New South Wales Canberra, ACT 2600, Australia.
    A New Spatial Approach to Image Restoration2008In: Image Processing Theory, Tools and Applications, 2008. IPTA 2008. First Workshops on, 2008, 1-8 p.Conference paper (Refereed)
    Abstract [en]

    Study in restoring images from their degraded states has been an important research topic in image processing and has potential applications in complex pattern recognition. We propose in this paper a new adaptive image restoration method using the concept of random-function realizations in geostatistics. This conceptual framework allows us to derive the model means and variances in the context of spatial statistics. Experimental results demonstrate the superior performance of the proposed approach to other image restoration algorithms.

  • 43.
    Li, Cai
    et al.
    University of Skovde, Sweden.
    Lowe, Robert
    University of Skovde, Sweden.
    Ziemke, Tom
    Linköping University, Department of Computer and Information Science, Human-Centered systems. Linköping University, The Institute of Technology. University of Skovde, Sweden.
    A novel approach to locomotion learning: Actor-Critic architecture using central pattern generators and dynamic motor primitives2014In: Frontiers in Neurorobotics, ISSN 1662-5218, Vol. 8Article in journal (Refereed)
    Abstract [en]

    In this article, we propose an architecture of a bio-inspired controller that addresses the problem of learning different locomotion gaits for different robot morphologies. The modeling objective is split into two: baseline motion modeling and dynamics adaptation. Baseline motion modeling aims to achieve fundamental functions of a certain type of locomotion and dynamics adaptation provides a "reshaping" function for adapting the baseline motion to desired motion. Based on this assumption, a three-layer architecture is developed using central pattern generators (CPGs, a bio-inspired locomotor center for the baseline motion) and dynamic motor primitives (DMPs, a model with universal "reshaping" functions). In this article, we use this architecture with the actor-critic algorithms for finding a good "reshaping" function. In order to demonstrate the learning power of the actor-critic based architecture, we tested it on two experiments: (1) learning to crawl on a humanoid and, (2) learning to gallop on a puppy robot. Two types of actor-critic algorithms (policy search and policy gradient) are compared in order to evaluate the advantages and disadvantages of different actor-critic based learning algorithms for different morphologies. Finally, based on the analysis of the experimental results, a generic view/architecture for locomotion learning is discussed in the conclusion.

  • 44.
    Vitiazeva, Varvara
    et al.
    Karolinska Institute, Sweden .
    Li, Jianjun
    National Research Council Canada, Canada .
    Hood, Derek W.
    MRC Harwell, England .
    Moxon, Richard E.
    University of Oxford Nuffield, England .
    Schweda, Elke
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, The Institute of Technology.
    A novel branching pattern in the lipopolysaccharide expressed by non-typeable Haemophilus influenzae strain 12322013In: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 378, 114-122 p.Article in journal (Refereed)
    Abstract [en]

    We report the novel branching pattern in lipopolysaccharide (LPS) expressed by non-typeable Haemophilus influenzae (NTHi) strain 1232. The strain expressed the beta-D-Glcp-(1 -andgt; 4)-[alpha-D-Galp-(1 -andgt; 4)-beta-D-Galp-(1 -andgt; 7)]-D-alpha-D-Hepp-(1 -andgt; 6)-beta-D-Glcp chain linked to the proximal heptose (HepI) of the conserved triheptosyl inner-core moiety of NTHi LPS: L-alpha-D-HepIIIp-(1 -andgt; 2)-[PEtn -andgt; 6]-L-alpha-D-HepIIp-(1 -andgt; 3)-L-alpha-D-HepIp-(1 -andgt; 5)-[PPEtn -andgt; 4]-alpha-Kdop-(2 -andgt; 6)-lipid A. The structure has been elucidated using NMR spectroscopy, electrospray ionization mass spectrometry (ESI-MS) and capillary electrophoresis coupled to electrospray ionization tandem mass spectrometry (CE-ESI-MSn) on O-deacylated LPS and core oligosaccharide (OS) materials, as well as HPLC-ESI-MSo on permethylated, dephosphorylated OS. It was also found that a tetrasaccharide unit bearing sialic acid [alpha-Neu5Ac-(2 -andgt; 3)-beta-D-Galp-(1 -andgt; 4)-beta-D-GlcNAcp-(1 -andgt; 3)-beta-D-Galp-(1 -andgt;] could substitute O-4 of the beta-D-Glcp linked to HepI. In addition, the distal heptose (HepIII) was substituted by PCho -andgt; 6-beta-D-Galp-(1 -andgt; at the O-2 position.

  • 45.
    Lindgren, David
    et al.
    Linköping University, Department of Electrical Engineering, Automatic Control. Linköping University, The Institute of Technology.
    Spångéus, Per
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology.
    A Novel Feature Extraction Algorithm for Asymmetric Classification2002Report (Other academic)
    Abstract [en]

    A linear feature extraction technique for asymmetric distributions is introduced, the asymmetric class projection (ACP). By emph {asymmetric classification} is understood discrimination among distributions with different covariance matrices. Two distributions with unequal covariance matrices do not in general have a symmetry plane, a fact that makes the analysis more difficult compared to the symmetric case. The ACP is similar to linear discriminant analysis (LDA) in the respect that both aim at extracting discriminating features (linear combinations or projections) from many variables. However, the drawback of the well known LDA is the assumption of symmetric classes with separated centroids. The ACP, incontrast, works on (two) possibly concentric distributions with unequal covariance matrices. The ACP is tested on data from anarray of semiconductor gas sensors with the purpose of distinguish bad grain from good.

  • 46.
    Lindgren, David
    et al.
    Linköping University, Department of Electrical Engineering, Automatic Control. Linköping University, The Institute of Technology.
    Spångeus, Per
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology.
    A Novel Feature Extraction Algorithm for Asymmetric Classification2004In: IEEE Sensors Journal, ISSN 1530-437X, E-ISSN 1558-1748, Vol. 4, 643-650 p.Article in journal (Refereed)
    Abstract [en]

    A linear feature extraction technique for asymmetric distributions is introduced, the asymmetric class projection (ACP). By emph {asymmetric classification} is understood discrimination among distributions with different covariance matrices. Two distributions with unequal covariance matrices do not in general have a symmetry plane, a fact that makes the analysis more difficult compared to the symmetric case. The ACP is similar to linear discriminant analysis (LDA) in the respect that both aim at extracting discriminating features (linear combinations or projections) from many variables. However, the drawback of the well known LDA is the assumption of symmetric classes with separated centroids. The ACP, incontrast, works on (two) possibly concentric distributions with unequal covariance matrices. The ACP is tested on data from anarray of semiconductor gas sensors with the purpose of distinguish bad grain from good.

  • 47.
    Lindgren, David
    et al.
    Linköping University, Department of Electrical Engineering, Automatic Control. Linköping University, The Institute of Technology.
    Spångéus, Per
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology.
    A Novel Feature Extraction Algorithm for Asymmetric Classification II2003Report (Other academic)
    Abstract [en]

    A linear feature extraction technique for asymmetric distributions is introduced, the asymmetric class projection (ACP). By asymmetric classification is understood discrimination among distributions with different covariance matrices. Two distributions with unequal covariance matrices do not in general have a symmetry plane, a fact that makes the analysis more difficult compared to the symmetric case. The ACP is similar to linear discriminant analysis (LDA) in the respect that both aim at extracting discriminating features (linear combinations or projections) from many variables. However, the drawback of the well known LDA is the assumption of symmetric classes with separated centroids. The ACP, incontrast, works on (two) possibly concentric distributions with unequal covariance matrices. The ACP is tested on data from anarray of semiconductor gas sensors with the purpose of distinguish bad grain from good.

  • 48.
    Viljanen, Johan
    Linköping University, Department of Physics, Chemistry and Biology, Organic Chemistry . Linköping University, The Institute of Technology.
    A Novel Route for Construction of Multipurpose Receptors through Chemical Modification of Glutathione Transferases2008Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis describes how the human Alpha class glutathione transferase (GST) A1-1 can be reprogrammed either to function as a multipurpose biosensor for detection of small molecule analytes, or as a handle providing for more efficient protein purification.

    A novel, user-friendly, and efficient method for site-specific introduction of functional groups into the active site of hGST A1-1 is the platform for these achievements. The designed thioester reagents are glutathione-based and they are able to label one single nucleophile (Y9) and leave the other 50 nucleophiles (in hGST A1-1) intact. The modification reaction was tested with five classes of GSTs (Alpha, Mu, Pi, Theta and Omega) and was found to be specific for the Alpha class isoenzymes. The reaction was further refined to target a single lysine residue, K216 in the hGST A1-1 mutant A216K, providing a stable amide bond between the protein and the labeling group. To further improve the labeling process, biotinylated reagents that could deliver the acyl group to Y9 (wt hGST A1-1) or K216 in the lysine mutant, while attached to streptavidin-coated agarose beads, were designed and synthesized.

    A focused library of eleven A216K/M208X mutants was made via random mutagenesis to provide an array of proteins with altered micro-environments in the hydrophobic binding site, where M208 is situated. Through the invented route for site-specific labeling, a fluorescent probe (coumarin) was introduced on K216 in all double mutants, with the purpose of developing a protein-based biosensor, akin to the olfactory system. The array of coumarin-labeled proteins responded differently to the addition of different analytes, and the responses were analyzed through pattern recognition of the fluorescence signals. The labeled proteins could also be site-specifically immobilized on a PEG-based biosensor chip via the single C112 on the surface of the protein, enabling development of surface-based biosensing systems.

    Also, a refined system for efficient detection and purification of GST-fusion proteins is presented. Through a screening process involving A216K and all produced A216K/M208X mutants, two candidates (A216K and A216K/M208F) were singled out as scaffolds for the next generation of fusion proteins. In addition to the features present in commercially available GST fusion constructs, the new mutants can be site-specifically labeled with a fluorophore in bacterial lysates providing quick and sensitive monitoring of expression and purification. Furthermore, the proteins could be labeled with a unique aldehyde moiety providing for a novel protein purification scheme.

    List of papers
    1. Programmed Delivery of Novel Functional Groups to the Alpha Class Glutathione Transferases
    Open this publication in new window or tab >>Programmed Delivery of Novel Functional Groups to the Alpha Class Glutathione Transferases
    2003 (English)In: Biochemistry, ISSN 0006-2960, Vol. 42, no 34, 10260-10268 p.Article in journal (Refereed) Published
    Abstract [en]

    Here we describe a new route to site- and class-specific protein modification that will allow us to create novel functional proteins with artificial chemical groups. Glutathione transferases from the alpha but not the mu, pi, omega, or theta classes can be rapidly and site-specifically acylated with thioesters of glutathione (GS-thioesters) that are similar to compounds that have been demonstrated to occur in vivo. The human isoforms A1-1, A2-2, A3-3, and A4-4 from the alpha class all react with the reagent at a conserved tyrosine residue (Y9) that is crucial in catalysis of detoxication reactions. The yield of modified protein is virtually quantitative in less than 30 min under optimized conditions. The acylated product is stable for more than 24 h at pH 7 and 25 °C. The modification is reversible in the presence of excess glutathione, but the labeled protein can be protected by adding S-methylglutathione. The stability of the ester with respect to added glutathione depends on the acyl moiety. The reaction can also take place in Escherichia coli lysates doped with alpha class glutathione transferases. A control substance that lacks the peptidyl backbone required for binding to the glutathione transferases acylates surface-exposed lysines. There is some acyl group specificity since one out of the three different GS-thioesters that we tried was not able to acylate Y9.

    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:liu:diva-13363 (URN)10.1021/bi0343525 (DOI)
    Available from: 2005-09-23 Created: 2005-09-23 Last updated: 2017-10-27
    2. Combinatorial Chemical Reengineering of the Alpha Class Glutathione Transferases
    Open this publication in new window or tab >>Combinatorial Chemical Reengineering of the Alpha Class Glutathione Transferases
    2004 (English)In: Bioconjugate Chemistry, ISSN 1043-1802, Vol. 15, no 4, 718-727 p.Article in journal (Refereed) Published
    Abstract [en]

    Previously, we discovered that human glutathione transferases (hGSTs) from the alpha class can be rapidly and quantitatively modified on a single tyrosine residue (Y9) using thioesters of glutathione (GS-thioesters) as acylating reagents. The current work was aimed at exploring the potential of this site-directed acylation using a combinatorial approach, and for this purpose a panel of 17 GS-thioesters were synthesized in parallel and used in screening experiments with the isoforms hGSTs A1-1, A2-2, A3-3, and A4-4. Through analytical HPLC and MALDI-MS experiments, we found that between 70 and 80% of the reagents are accepted and this is thus a very versatile reaction. The range of ligands that can be used to covalently reprogram these proteins is now expanded to include functionalities such as fluorescent groups, a photochemical probe, and an aldehyde as a handle for further chemical derivatization. This site-specific modification reaction thus allows us to create novel functional proteins with a great variety of artificial chemical groups in order to, for example, specifically tag GSTs in biological samples or create novel enzymatic function using appropriate GS-thioesters.

    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:liu:diva-13196 (URN)10.1021/bc034192+ (DOI)
    Available from: 2008-04-28 Created: 2008-04-28 Last updated: 2009-06-08
    3. Surface-Assisted Delivery of Fluorescent Groups to hGST A1-1 and a Lysine Mutant
    Open this publication in new window or tab >>Surface-Assisted Delivery of Fluorescent Groups to hGST A1-1 and a Lysine Mutant
    2006 (English)In: Bioconjugate Chemistry, ISSN 1043-1802, Vol. 17, no 2, 429-437 p.Article in journal (Refereed) Published
    Abstract [en]

    Human glutathione transferase (hGST) A1-1 and a lysine mutant (A216K) can both be rapidly and site-specifically acylated on Y9 and K216, respectively, using a range of thiolesters of glutathione (GS-thiolesters) as modifying reagents. The present investigation was aimed at developing a method with which to deliver a fluorescent acyl group from a solid support under conditions compatible with standard protein purification schemes. A number of fluorescent GS-thiolesters with modified peptide backbones were therefore prepared and tested for reactivity toward hGST A1-1 and the A216K mutant. Substitutions at the α-NH2 part of the glutathione backbone were not tolerated by the proteins. However, two fluorescent reagents that carry a biotin moiety at the C-terminal part of glutathione were found through MALDI-MS experiments to react in solution with Y9 of the wild-type protein and one reagent with K216 of A216K. The reaction can take place in the presence of glutathione and even in a crude E. coli lysate of cells expressing A216K. Delivery of the fluorescent group to Y9 or K216 was possible using NeutrAvidin (NA) beads that had been preincubated with biotinylated reagent. Alternatively, excess reagent can be removed by a brief incubation with NA beads. We have thus now developed a system for protein labeling with easy removal of excess and used up low-molecular weight reagent. This strategy can conceivably be utilized in future protein purification and labeling experiments.

    Keyword
    human GST A1-1, site-specific covalent modification, tyrosine 9, alanine 216, lysine 216, pre-programmed, solid support delivery, biotin, streptavidin
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:liu:diva-13197 (URN)10.1021/bc0502762 (DOI)
    Available from: 2008-04-28 Created: 2008-04-28 Last updated: 2009-06-08
    4. A Multipurpose Receptor Composed of Promiscuous Proteins. Analyte Detection through Pattern Recognition
    Open this publication in new window or tab >>A Multipurpose Receptor Composed of Promiscuous Proteins. Analyte Detection through Pattern Recognition
    2007 (English)In: Bioconjugate Chemistry, ISSN 1043-1802, Vol. 18, no 6, 1935-1945 p.Article in journal (Refereed) Published
    Abstract [en]

    A multipurpose receptor akin to the “electronic nose” was composed of coumarin-labeled mutants of human glutathione transferase A1. We have previously constructed a kit for site-specific modification of a lysine residue (A216K) using a thiol ester of glutathione (GSC-Coubio) as a modifying reagent. In the present investigation, we scrambled the hydrophobic binding site (H-site) of the protein scaffold through mutations at position M208 via random mutagenesis and isolated a representative library of 11 A216K/M208X mutants. All of the double mutants could be site-specifically labeled to form the K216Cou conjugates. The labeled proteins responded to the addition of different analytes with signature changes in their fluorescence spectra resulting in a matrix of 96 data points per analyte. Ligands as diverse as n-valeric acid, fumaric acid monoethyl ester, lithocholic acid, 1-chloro-2,4-dinitrobenzene (CDNB), glutathione (GSH), S-methyl-GSH, S-hexyl-GSH, and GS-DNB all gave rise to signals that potentially can be interpreted through pattern recognition. The measured Kd values range from low micromolar to low millimolar. The cysteine residue C112 was used to anchor the coumarin-labeled protein to a PEG-based hydrogel chip in order to develop surface-based biosensing systems. We have thus initiated the development of a multipurpose, artificial receptor composed of an array of promiscuous proteins where detection of the analyte occurs through pattern recognition of fluorescence signals. In this system, many relatively poor binders each contribute to detailed readout in a truly egalitarian fashion.

    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:liu:diva-13198 (URN)10.1021/bc700247x (DOI)
    Available from: 2008-04-28 Created: 2008-04-28 Last updated: 2015-10-13
    5. Orthogonal Protein Purification - Expanding the Repertoire of GST Fusion Systems
    Open this publication in new window or tab >>Orthogonal Protein Purification - Expanding the Repertoire of GST Fusion Systems
    2008 (English)In: Protein Expression & Purification, ISSN 1046-5928, Vol. 57, no 1, 17-26 p.Article in journal (Refereed) Published
    Abstract [en]

    We have previously developed a labeling scheme that can be used to site-specifically link human glutathione transferases (hGSTs) from the alpha class to chemical entities such as fluorophores and aldehydes. The reagents are in-house synthesized derivatives of glutathione (GS-derivatives). We have focused on a lysine mutant of hGST A1:A216K. In this study, we wanted to utilize these findings and improve on protein purification schemes that are using GSTs as fusion partners. We have used random mutagenesis to scramble the hydrophobic binding site of A216K through mutations at position M208 and isolated a library of 11 A216K/M208X mutants. All mutants were easily expressed and purified and retained all or parts of the catalytic properties of the parent GST. The mutants were stable over several days at room temperature. The A216K/M208X mutants could be site-specifically labeled using our designed fluorescent reagents. Furthermore, reaction with an aldehyde-containing reagent termed GS-Al results in site-specific introduction of an orthogonal handle for subsequent conjugation with aldehyde-reactive probes. Labeling with coumarin results in a fluorescent protein-conjugate that can bind glutathione (GSH) derivatives for subsequent affinity purification. The Kd for S-hexyl-GSH of coumarin-labeled A216K was measured to be 2.5 μM. The candidate proteins A216K and A216K/M208F could be purified in high yield in a one-step procedure through affinity chromatography (Glutathione Sepharose™ 4B). The proteins can readily be perceived as improved GST fusion partners.

    Keyword
    Human GST A1-1 mutants; Site-specific covalent modification; Lysine 216; Methionine 208; Protein purification; Fusion partner
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:liu:diva-13199 (URN)10.1016/j.pep.2007.09.011 (DOI)
    Available from: 2008-04-28 Created: 2008-04-28 Last updated: 2009-05-18
  • 49.
    Merkel, Magnus
    et al.
    Linköping University, The Institute of Technology. Linköping University, Department of Computer and Information Science, NLPLAB - Natural Language Processing Laboratory.
    Lange, Andreas
    A pattern extraction workbench combining multiple linguistic levels2004In: Conference on Language Resouces and Evaluation LREC,2004, Paris: ELDA , 2004Conference paper (Refereed)
  • 50.
    Gharehbaghi, Arash
    et al.
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, Faculty of Science & Engineering.
    Ask, Per
    Linköping University, Department of Biomedical Engineering, Physiological Measurements. Linköping University, Faculty of Science & Engineering.
    Babic, Ankica
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, Faculty of Science & Engineering. Department of Information Science and Media Studies, University of Bergen, Norway.
    A pattern recognition framework for detecting dynamic changes on cyclic time series2015In: Pattern Recognition, ISSN 0031-3203, E-ISSN 1873-5142, Vol. 48, no 3, 696-708 p.Article in journal (Refereed)
    Abstract [en]

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

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