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  • 51. Su, Fan-Chi
    et al.
    Mavroidis, Panayiotis
    Stockholms universitet, Naturvetenskapliga fakulteten, Medicinsk strålningsfysik (tills m KI).
    Shi, Chengyu
    Ferreira, Brigida Costa
    Papanikolaou, Niko
    A graphic user interface toolkit for specification, report and comparison of dose-response relations and treatment plans using the biologically effective uniform dose2010Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 100, nr 1, s. 69-78Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A toolkit (BEUDcal) has been developed for evaluating the effectiveness and for predicting the outcome of treatment plans by calculating the biologically effective uniform dose (BEUD) and complication-free tumor control probability. The input for the BEUDcal is the differential dose-volume histograms of organs exported from the treatment planning system. A clinical database is built for the dose-response parameters of different tumors and normal tissues. Dose-response probabilities of all the examined organs are illustrated together with the corresponding BEUDs and the P+ values. Furthermore, BEUDcal is able to generate a report that simultaneously presents the radiobiological evaluation together with the physical dose indices, showing the complementary relation between the physical and radiobiological treatment plan analysis performed by BEUDcal. Comparisons between treatment plans for helical tomotherapy and multileaf collimator-based intensity modulated radiotherapy of a lung patient were demonstrated to show the versatility of BEUDcal in the assessment and report of dose-response relations.

  • 52.
    Tammi, Martti
    et al.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för genetik och patologi.
    Arner, Erik
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för genetik och patologi.
    Andersson, Björn
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för genetik och patologi.
    TRAP: Tandem Repeat Assembly Program produces improved shotgun assemblies of repetitive sequences2003Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 70, nr 1, s. 47-59Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The software commonly used for assembly of shotgun sequence data has several limitations. One such limitation becomes obvious when repetitive sequences are encountered. Shotgun assembly is a difficult task, even for non-repetitive regions, but the use of quality assessments of the data and efficient matching algorithms have made it possible to assemble most sequences efficiently. In the case of highly repetitive sequences, however, these algorithms fail to distinguish between sequencing errors and single base differences in regions containing nearly identical repeats. None of the currently available fragment assembly programs are able to correctly assemble highly similar repetitive data, and we, therefore, present a novel shotgun assembly program, Tandem Repeat Assembly Program (TRAP). The main feature of this program is the ability to separate long repetitive regions from each other by distinguishing single base substitutions as well as insertions/deletions from sequencing errors. This is accomplished by using a novel multiple-alignment based analysis method. Since repeats are a common complication in most sequencing projects, this software should be of use for the whole sequencing community.

  • 53.
    Thurfjell, Lennart
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datoriserad bildanalys.
    Bohm, Christian
    Bengtsson, Ewert
    CBA—an atlas-based software tool used to facilitate the interpretation of neuroimaging data1995Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 47, nr 1, s. 51-71Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    CBA, a software tool used to improve quantification and evaluation of neuroimaging data has been developed. It uses a detailed 3-dimensional brain atlas that can be adapted to fit the brain of an individual patient represented by a series of displayed ima

  • 54.
    Verikas, Antanas
    et al.
    Högskolan i Halmstad, Sektionen för Informationsvetenskap, Data– och Elektroteknik (IDE), Halmstad Embedded and Intelligent Systems Research (EIS).
    Gelzinis, Adas
    Department of Applied Electronics, Kaunas University of Technology, Studentu 50, LT-51368 Kaunas, Lithuania.
    Valincius, Donatas
    Department of Applied Electronics, Kaunas University of Technology, Studentu 50, LT-51368 Kaunas, Lithuania.
    Bacauskiene, Marija
    Department of Applied Electronics, Kaunas University of Technology, Studentu 50, LT-51368 Kaunas, Lithuania.
    Uloza, Virgilijus
    Department of Otolaryngology, Kaunas University of Medicine, LT-50009 Kaunas, Lithuania.
    Multiple feature sets based categorization of laryngeal images2007Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 85, nr 3, s. 257-266Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    This paper is concerned with an automated analysis of laryngeal images aiming to categorize the images into three decision classes, namely healthy, nodular, and diffuse. The problem is treated as an image analysis and classification task. Aiming to obtain a comprehensive description of laryngeal images, multiple feature sets exploiting information on image colour, texture, geometry, image intensity gradient direction, and frequency content are extracted. A separate support vector machine (SVM) is used to categorize features of each type into the decision classes. The final image categorization is then obtained based on the decisions provided by a committee of support vector machines. Bearing in mind a high similarity of the decision classes, the correct classification rate of over 94% obtained when testing the system on 785 laryngeal images recorded at the Department of Otolaryngology, Kaunas University of Medicine is rather promising.

  • 55.
    Wallin, Johan E.
    et al.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för farmaceutisk biovetenskap.
    Friberg, Lena E.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för farmaceutisk biovetenskap.
    Karlsson, Mats O.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för farmaceutisk biovetenskap.
    A tool for neutrophil guided dose adaptation in chemotherapy2009Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 93, nr 3, s. 283-291Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Chemotherapy dosing in anticancer treatment is a balancing act between achieving concentrations that are effective towards the malignancy and that result in acceptable side-effects. Neutropenia is one major side-effect of many antitumor agents, and is related to an increased risk of infection. A model capable of describing the time-course of myelosuppression from administered drug could be used in individual dose selection. In this paper we describe the transfer of a previously developed semi-mechanistic model for myelosuppression from NONMEM to a dosing tool in MS Excel, with etoposide as an example. The tool proved capable to solve a differential equation system describing the pharmacokinetics and pharmacodynamics, with estimation performance comparable to NONMEM. In the dosing tool the user provides neutrophil measures from a previous treatment course and request for the dose that results in a desired nadir in the upcoming course through a Bayesian estimation procedure.

  • 56.
    Westin, Jerker
    et al.
    Högskolan Dalarna, Akademin Industri och samhälle, Datateknik.
    Dougherty, Mark
    Högskolan Dalarna, Akademin Industri och samhälle, Datateknik.
    Nyholm, Dag
    Groth, Torgny
    A home environment test battery for status assessment in patients with advanced Parkinson's disease2010Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 98, nr 1, s. 27-35Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A test battery for assessing patient state in advanced Parkinson's disease, consisting of self-assessments and motor tests, was constructed and implemented on a hand computer with touch screen in a telemedicine setting. The aim of this work was to construct an assessment device, applicable during motor fluctuations in the patient's home environment. Selection of self-assessment questions was based on questions from an e-diary, previously used in a clinical trial. Both un-cued and cued tapping tests and spiral drawing tests were designed for capturing upper limb stiffnes, slowness and involuntary movements. The patient interface gave an audible signal at scheduled response times and was locked otherwise. Data messages in an XML-format were sent from the hand unit to a central server for storage, processing and presentation. In tapping tests, speed and accuracy were calculated and in spiral tests, standard deviation of frequency filtered radial drawing velocity was calculated. An overall test score, combining repeated assessments of the different test items during a test period, was defined based on principal component analysis and linear regression. An evaluation with two pilot patients before and after receiving new types of treatments was performed. Compliance and usability was assessed in a clinical trial (65 patients with advanced Parkinson's disease) and correlations between different test items and internal consistency were investigated. The test battery could detect treatment effect in the two pilot patients, both in self-assessments, tapping tests' results and spiral scores. It had good patient compliance and acceptable usability according to nine nurses. Correlation analysis showed that tapping results provided different information as compared to diary responses. Internal consistency of the test battery was good and learning effects in the tapping tests were small. (C) 2009 Elsevier Ireland Ltd. All rights reserved.

  • 57.
    Westin, Jerker
    et al.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinska vetenskaper, Biomedicinsk informatik och teknik.
    Dougherty, Mark
    Dalarna University.
    Nyholm, Dag
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för neurovetenskap, Neurologi.
    Groth, Torgny
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinska vetenskaper, Biomedicinsk informatik och teknik.
    A home environment test battery for status assessment in patients with advanced Parkinson's disease2010Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 98, nr 1, s. 27-35Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A test battery for assessing patient state in advanced Parkinson's disease, consisting of self-assessments and motor tests, was constructed and implemented on a hand computer with touch screen in a telemedicine setting. The aim of this work was to construct an assessment device, applicable during motor fluctuations in the patient's home environment. Selection of self-assessment questions was based on questions from an e-diary, previously used in a clinical trial. Both un-cued and cued tapping tests and spiral drawing tests were designed for capturing upper limb stiffnes, slowness and involuntary movements. The patient interface gave an audible signal at scheduled response times and was locked otherwise. Data messages in an XML-format were sent from the hand unit to a central server for storage, processing and presentation. In tapping tests, speed and accuracy were calculated and in spiral tests, standard deviation of frequency filtered radial drawing velocity was calculated. An overall test score, combining repeated assessments of the different test items during a test period, was defined based on principal component analysis and linear regression. An evaluation with two pilot patients before and after receiving new types of treatments was performed. Compliance and usability was assessed in a clinical trial (65 patients with advanced Parkinson's disease) and correlations between different test items and internal consistency were investigated. The test battery could detect treatment effect in the two pilot patients, both in self-assessments, tapping tests' results and spiral scores. It had good patient compliance and acceptable usability according to nine nurses. Correlation analysis showed that tapping results provided different information as compared to diary responses. Internal consistency of the test battery was good and learning effects in the tapping tests were small.

  • 58.
    Wigertz, Ove
    Linköpings universitet, Tekniska högskolan. Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik.
    Clinical decision support - how, when and for whom1995Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 48, s. 15-20Artikkel i tidsskrift (Fagfellevurdert)
  • 59.
    Xiao-Ming, Gao
    et al.
    Linköpings universitet, Tekniska högskolan. Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik.
    Johansson, Bo
    IMT .
    Shahsavar, Nosrat
    Linköpings universitet, Tekniska högskolan. Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik.
    Arkad, Kristina
    Linköpings universitet, Tekniska högskolan. Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik.
    Åhlfeldt, Hans
    Linköpings universitet, Tekniska högskolan. Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik.
    Wigertz, Ove
    Linköpings universitet, Tekniska högskolan. Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik.
    Pre-compiling medical logic modules into C++ in building medical decision support systems1993Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 41, s. 107-119Artikkel i tidsskrift (Fagfellevurdert)
  • 60.
    Åhlfeldt, Hans
    et al.
    Linköpings universitet, Tekniska högskolan. Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik.
    Shahsavar, Nosrat
    Linköpings universitet, Tekniska högskolan. Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik.
    Xiao-Ming, Gao
    Linköpings universitet, Tekniska högskolan. Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik.
    Arkad, Kristina
    Linköpings universitet, Tekniska högskolan. Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik.
    Johansson, Bo
    Linköpings universitet, Tekniska högskolan. Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik.
    Wigertz, Ove
    Linköpings universitet, Tekniska högskolan. Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik.
    Data driven medical decision support based on Arden Syntax within the HELIOS environment1994Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 45, nr suppl, s. S97-S106Artikkel i tidsskrift (Fagfellevurdert)
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