| 1. |
- Abu-Rmileh, Amjad, et al.
(författare)
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Wiener sliding-mode control for artificial pancreas : A new nonlinear approach to glucose regulation
- 2012
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Ingår i: Computer Methods and Programs in Biomedicine. - : Elsevier. - 0169-2607 .- 1872-7565. ; 107:2, s. 327-340
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Tidskriftsartikel (refereegranskat)abstract
- Type 1 diabetic patients need insulin therapy to keep their blood glucose close to normal. In this paper an attempt is made to show how nonlinear control-oriented model may be used to improve the performance of closed-loop control of blood glucose in diabetic patients. The nonlinear Wiener model is used as a novel modeling approach to be applied to the glucose control problem. The identified Wiener model is used in the design of a robust nonlinear sliding mode control strategy. Two configurations of the nonlinear controller are tested and compared to a controller designed with a linear model. The controllers are designed in a Smith predictor structure to reduce the effect of system time delay. To improve the meal compensation features, the controllers are provided with a simple feedforward controller to inject an insulin bolus at meal time. Different simulation scenarios have been used to evaluate the proposed controllers. The obtained results show that the new approach out-performs the linear control scheme, and regulates the glucose level within safe limits in the presence of measurement and modeling errors, meal uncertainty and patient variations.
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| 2. |
- Amiri, Saeid, et al.
(författare)
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On the efficiency of bootstrap method into the analysis contingency table
- 2011
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Ingår i: Computer Methods and Programs in Biomedicine. - : Elsevier BV. - 0169-2607 .- 1872-7565. ; 104:2, s. 182-187
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Tidskriftsartikel (refereegranskat)abstract
- The bootstrap method is a computer intensive statistical method that is widely used in performing nonparametric inference. Categorica ldata analysis,inparticular the analysis of contingency tables, is commonly used in applied field. This work considers nonparametric bootstrap tests for the analysis of contingency tables. There are only a few research papers which exploit this field. The p-values of tests in contingency tables are discrete and should be uniformly distributed under the null hypothesis. The results of this article show that corresponding bootstrap versions work better than the standard tests. Properties of the proposed tests are illustrated and discussed using Monte Carlo simulations. This article concludes with an analytical example that examines the performance of the proposed tests and the confidence interval of the association coefficient.
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| 3. |
- Bauwens, Maite, et al.
(författare)
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On Climate Reconstruction Using Bivalve Shells : Three Methods To Interpret the Chemical Signature of a Shell
- 2011
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Ingår i: Computer Methods and Programs in Biomedicine. - : Elsevier. - 0169-2607 .- 1872-7565. ; 104:2, s. 104-111
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Tidskriftsartikel (refereegranskat)abstract
- To improve our understanding of the climate process and to assess the human impact on current global warming, past climate reconstruction is essential. The chemical composition of a bivalve shell is strongly coupled to environmental variations and therefore ancient shells are potential climate archives. The nonlinear nature of the relation between environmental condition (e.g. the seawater temperature) and proxy composition makes it hard to predict the former from the latter, however. In this paper we compare the ability of three nonlinear system identification methods to reconstruct the ambient temperature from the chemical composition of a shell. The comparison shows that nonlinear multi-proxy approaches are potentially useful tools for climate reconstructions and that manifold based methods result in smoother and more precise temperature reconstruction.
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| 4. |
- Eklund, Anders, et al.
(författare)
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fMRI Analysis on the GPU - Possibilities and Challenges
- 2012
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Ingår i: Computer Methods and Programs in Biomedicine. - : Elsevier. - 0169-2607 .- 1872-7565. ; 105:2, s. 145-161
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Tidskriftsartikel (refereegranskat)abstract
- Functional magnetic resonance imaging (fMRI) makes it possible to non-invasively measure brain activity with high spatial resolution.There are however a number of issues that have to be addressed. One is the large amount of spatio-temporal data that needsto be processed. In addition to the statistical analysis itself, several preprocessing steps, such as slice timing correction and motioncompensation, are normally applied. The high computational power of modern graphic cards has already successfully been used forMRI and fMRI. Going beyond the first published demonstration of GPU-based analysis of fMRI data, all the preprocessing stepsand two statistical approaches, the general linear model (GLM) and canonical correlation analysis (CCA), have been implementedon a GPU. For an fMRI dataset of typical size (80 volumes with 64 x 64 x 22 voxels), all the preprocessing takes about 0.5 s on theGPU, compared to 5 s with an optimized CPU implementation and 120 s with the commonly used statistical parametric mapping(SPM) software. A random permutation test with 10 000 permutations, with smoothing in each permutation, takes about 50 s ifthree GPUs are used, compared to 0.5 - 2.5 h with an optimized CPU implementation. The presented work will save time forresearchers and clinicians in their daily work and enables the use of more advanced analysis, such as non-parametric statistics, bothfor conventional fMRI and for real-time fMRI.
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| 5. |
- Gabrielsson, Johan, et al.
(författare)
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Maxsim2-Real-time interactive simulations for computer-assisted teaching of pharmacokinetics and pharmacodynamics.
- 2014
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Ingår i: Computer methods and programs in biomedicine. - : Elsevier BV. - 1872-7565 .- 0169-2607. ; 113, s. 815-829
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Tidskriftsartikel (refereegranskat)abstract
- We developed a computer program for use in undergraduate and graduate courses in pharmacology, pharmacokinetics and pharmacodynamics. This program can also be used in environmental and toxicological studies and preclinical simulation, to facilitate communication between modeling pharmacokineticists and project leaders or other decision-makers in the pharmaceutical industry. The program simulates the drug delivery and transport by means of (I) a six-compartment physiological pharmacokinetic flow model, (II) a system of traditional compartment models, or (III) a target-mediated drug disposition system. The program also can be used to simulate instantaneous equilibria between concentration and pharmacodynamic response, or as temporal delays between concentration and response. The latter is done by means of turnover models (indirect response models). Drug absorption, distribution, and elimination are represented by differential equations, which are described by organ and tissue volumes or other volumes of distribution, blood flows, clearance terms, and tissue-to-blood partition coefficients. The user can control and adjust these parameters by means of a slider in real time. By interactively changing the parameter values and simultaneously displaying the resulting concentration-time and/or response-time profiles, users can understand the major mechanisms that govern the disposition or the pharmacological response of the drug in the organism in real time. Schedule dependence is typically seen in clinical practice with a non-linear concentration-response relationship, and is difficult to communicate except via simulations. Here, we sought to illustrate the potential advantages of this approach in teaching pharmacology, pharmacokinetics, and pharmacodynamics to undergraduate pharmacy-, veterinary-, and medical students or to project teams in drug discovery/development.
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| 6. |
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| 7. |
- Liuhanen, Sasu, et al.
(författare)
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Indirect measurement of the vascular endothelial glycocalyx layer thickness in human submucosal capillaries with a plug-in for ImageJ
- 2013
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Ingår i: Computer Methods and Programs in Biomedicine. - : Elsevier BV. - 0169-2607 .- 1872-7565. ; 110:1, s. 38-47
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND:The thickness of vascular endothelial glycocalyx layer can be measured indirectly during a spontaneous leukocyte passage from oral submucosal capillaries in humans. The subsequent differences in red blood cell (RBC) column widths, before a spontaneous white blood cell passage (pre-WBC) and after a spontaneous WBC passage (post-WBC) can be used in off-line analysis to measure glycocalyx thickness: [pre-WBC width-post-WBC width]/2. We created and validated a semi-automatic plug-in for ImageJ to measure the endothelial glycocalyx layer thickness.METHODS:Video clips presenting human sublingual microvasculature were created with a side-stream dark field imaging device. Spontaneous leukocyte passages in capillaries were analyzed from video clips with ImageJ. The capillary glycocalyx layer thickness was measured by the indirect approach with two manual and two semi-automatic methods.RESULTS: There were no statistically significant differences between glycocalyx layer thicknesses measured with different methods, even though small inter-method differences in RBC column thicknesses could be detected. Inter-rater differences were systematically smaller with both semi-automatic methods. Intra-rater coefficient of variation [CV] (95% CI) was largest when measurements were made completely manually [9.2% (8.4-10.0)], but improved significantly with automatic image enhancement prior to manual measurement [7.2% (6.4-8.0)]. CV could be improved further when using semi-automatic analysis with an in-frame median filter radius of 1 pixel [5.8% (5.0-6.6)], or a median filter radius of 2 pixels [4.3% (3.5-5.1)].CONCLUSIONS: Semi-automatic analysis of glycocalyx decreased the intra-rater CV and the inter-rater differences compared to the manual method. On average, each of the four methods yielded equal results for the glycocalyx thickness. Being the only feasible bed side method in most clinical scenarios, indirect measurement of glycocalyx thickness with orthogonal polarization spectral imaging or side-stream dark field imaging device and our plug-in can advance the study of glycocalyx layer pathology in man.
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| 8. |
- Malm, Patrik, et al.
(författare)
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Debris removal in Pap-smear images
- 2013
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Ingår i: Computer Methods and Programs in Biomedicine. - : Elsevier BV. - 0169-2607 .- 1872-7565. ; 111:1, s. 128-138
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Tidskriftsartikel (refereegranskat)abstract
- Since its introduction in the 1940s the Pap-smear test has helped reduce the incidence of cervical cancer dramatically in countries where regular screening is standard. The automation of this procedure is an open problem that has been ongoing for over fifty years without reaching satisfactory results. Existing systems are discouragingly expensive and yet they are only able to make a correct distinction between normal and abnormal samples in a fraction of cases. Therefore, they are limited to acting as support for the cytotechnicians as they perform their manual screening. The main reason for the current limitations is that the automated systems struggle to overcome the complexity of the cell structures. Samples are covered in artefacts such as blood cells, overlapping and folded cells, and bacteria, that hamper the segmentation processes and generate large number of suspicious objects. The classifiers designed to differentiate between normal cells and pre-cancerous cells produce unpredictable results when classifying artefacts. In this paper, we propose a sequential classification scheme focused on removing unwanted objects, debris, from an initial segmentation result, intended to be run before the actual normal/abnormal classifier. The method has been evaluated using three separate datasets obtained from cervical samples prepared using both the standard Pap-smear approach as well as the more recent liquid based cytology sample preparation technique. We show success in removing more than 99% of the debris without loosing more than around one percent of the epithelial cells detected by the segmentation process.
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| 9. |
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| 10. |
- Memedi, Mevludin, 1983-, et al.
(författare)
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A web application for follow-up of results from a mobile device test battery for Parkinson’s disease patients
- 2011
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Ingår i: Computer Methods and Programs in Biomedicine. - Amsterdam : Elsevier BV. - 0169-2607 .- 1872-7565. ; 104:2, s. 219-226
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Tidskriftsartikel (refereegranskat)abstract
- A test battery consisting of self-assessments and motor tests for patients with Parkinson’s disease (PD) was constructed and implemented on a hand computer with touch screen in a telemedicine setting. In this work, a Web-based system was developed to deliver decision support information to treating clinical staff for assessing PD symptoms in their patients. Test results from the hand unit are transferred to a central server and processed into scores for different symptom dimensions and an “overall test score” reflecting the overall condition of the patient during a test period. The IBM Computer System Usability Questionnaire was administered to assess the users’ satisfaction with the system. Results showed that a majority of users who completed the evaluation were quite satisfied with the usability although a sizeable minority were not. Response times were tested by simulating up to 100 users accessing the web application at the same time. The average page completion times were in the range of 0.5 seconds indicating fast response. The system was able to summarize the test-battery data and present them in a useful manner. Its main contribution is a novel way to easily access symptom information from the home environment of patients.
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| 11. |
- Nyberg, Joakim, et al.
(författare)
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PopED : An extended, parallelized, nonlinear mixed effects models optimal design tool
- 2012
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Ingår i: Computer Methods and Programs in Biomedicine. - : Elsevier BV. - 0169-2607 .- 1872-7565. ; 108:2, s. 789-805
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Tidskriftsartikel (refereegranskat)abstract
- Several developments have facilitated the practical application and increased the general use of optimal design for nonlinear mixed effects models. These developments include new methodology for utilizing advanced pharmacometric models, faster optimization algorithms and user friendly software tools. In this paper we present the extension of theoptimal design software PopED, which incorporates many of these recent advances into aneasily useable enhanced GUI. Furthermore, we present new solutions to problems related to the design of experiments such as: faster and more robust FIM calculations and optimizations, optimizing over cost/utility functions and diagnostic tools and plots to evaluate designperformance. Examples for; (i) Group size optimization and efficiency translation, (ii) Cost/constraint optimization, (iii) Optimizations with different FIM approximations and (iv) optimization with parallel computing demonstrate the new features in PopED and underline the potential use of this tool when designing experiments.
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| 12. |
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| 13. |
- Pham, Tuan D
(författare)
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Supervised restoration of degraded medical images using multiple-point geostatistics
- 2012
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Ingår i: Computer Methods and Programs in Biomedicine. - : Elsevier. - 0169-2607 .- 1872-7565. ; 106:3, s. 201-209
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Tidskriftsartikel (refereegranskat)abstract
- Reducing noise in medical images has been an important issue of research and development for medical diagnosis, patient treatment, and validation of biomedical hypotheses. Noise inherently exists in medical and biological images due to the acquisition and transmission in any imaging devices. Being different from image enhancement, the purpose of image restoration is the process of removing noise from a degraded image in order to recover as much as possible its original version. This paper presents a statistically supervised approach for medical image restoration using the concept of multiple-point geostatistics. Experimental results have shown the effectiveness of the proposed technique which has potential as a new methodology for medical and biological image processing.
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| 14. |
- Sarve, Hamid, et al.
(författare)
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Extracting 3D information on bone remodeling in the proximity of titanium implants in SRμCT image volumes.
- 2011
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Ingår i: Computer methods and programs in biomedicine. - : Elsevier BV. - 1872-7565 .- 0169-2607. ; 102:1, s. 25-34
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Tidskriftsartikel (refereegranskat)abstract
- Bone-implant integration is measured in several ways. Traditionally and routinely, 2D histological sections of samples, containing bone and the biomaterial, are stained and analyzed using a light microscope. Such histological section provides detailed cellular information about the bone regeneration in the proximity of the implant. However, this information reflects the integration in only a very small fraction, a 10 μm thick slice, of the sample. In this study, we show that feature values quantified on 2D sections are highly dependent on the orientation and the placement of the section, suggesting that a 3D analysis of the whole sample is of importance for a more complete judgment of the bone structure in the proximity of the implant. We propose features describing the 3D data by extending the features traditionally used for 2D-analysis. We present a method for extracting these features from 3D image data and we measure them on five 3D SRμCT image volumes. We also simulate cuts through the image volume positioned at all possible section positions. These simulations show that the measurement variations due to the orientation of the section around the center line of the implant are about 30%.
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| 15. |
- Sepehri, Amir A., et al.
(författare)
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A novel method for pediatric heart sound segmentation without using the ECG
- 2010
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Ingår i: Computer Methods and Programs in Biomedicine. - : Elsevier BV. - 0169-2607 .- 1872-7565. ; 99:1, s. 43-48
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Tidskriftsartikel (refereegranskat)abstract
- In this paper, we propose a novel method for pediatric heart sounds segmentation by paying special attention to the physiological effects of respiration on pediatric heart sounds. The segmentation is accomplished in three steps. First, the envelope of a heart sounds signal is obtained with emphasis on the first heart sound (Si) and the second heart sound (S(2)) by using short time spectral energy and autoregressive (AR) parameters of the signal. Then, the basic heart sounds are extracted taking into account the repetitive and spectral characteristics of Si and S2 sounds by using a Multi-Layer Perceptron (MLP) neural network classifier. In the final step, by considering the diastolic and systolic intervals variations due to the effect of a child's respiration, a complete and precise heart sounds end-pointing and segmentation is achieved.
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| 16. |
- Sjöberg, Carl, et al.
(författare)
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Multi-atlas based segmentation using probabilistic label fusion with adaptive weighting of image similarity measures
- 2013
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Ingår i: Computer Methods and Programs in Biomedicine. - : Elsevier BV. - 0169-2607 .- 1872-7565. ; 110:3, s. 308-319
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Tidskriftsartikel (refereegranskat)abstract
- Label fusion multi-atlas approaches for image segmentation can give better segmentation results than single atlas methods. We present a multi-atlas label fusion strategy based on probabilistic weighting of distance maps. Relationships between image similarities and segmentation similarities are estimated in a learning phase and used to derive fusion weights that are proportional to the probability for each atlas to improve the segmentation result. The method was tested using a leave-one-out strategy on a database of 21 pre-segmented prostate patients for different image registrations combined with different image similarity scorings. The probabilistic weighting yields results that are equal or better compared to both fusion with equal weights and results using the STAPLE algorithm. Results from the experiments demonstrate that label fusion by weighted distance maps is feasible, and that probabilistic weighted fusion improves segmentation quality more the stronger the individual atlas segmentation quality depends on the corresponding registered image similarity. The regions used for evaluation of the image similarity measures were found to be more important than the choice of similarity measure.
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| 17. |
- Stathakis, Sotirios, et al.
(författare)
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gamma(+) index : A new evaluation parameter for quantitative quality assurance
- 2014
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Ingår i: Computer Methods and Programs in Biomedicine. - : Elsevier BV. - 0169-2607 .- 1872-7565. ; 114:1
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: The accuracy dose delivery and the evaluation of differences between calculated and delivered dose distributions, has been studied by several groups. The aim of this investigation is to extend the gamma index by including radiobiological information and to propose a new index that we will here forth refer to as the gamma plus (gamma(+)). Further more, to validate the robustness of this new index in performing a quality control analysis of an IMRT treatment plan using pure radiobiological measures such as the biologically effective uniform dose ((D) over bar) and complication-free tumor control probability (P+). Material and methods: A new quality assurance index, the (gamma(+)), is proposed based on the theoretical concept of gamma index presented by Low et al. (1998). In this study, the dose difference, including the radiobiological dose information (biological effective dose, BED) is used instead of just the physical dose difference when performing the gamma(+) calculation. An in-house software was developed to compare different dose distributions based on the gamma(+) concept. A test pattern for a two-dimensional dose comparison was built using the in-house software platform. The gamma(+) index was tested using planar dose distributions (exported from the treatment planning system) and delivered (film) dose distributions acquired in a solid water phantom using a test pattern and a theoretical clinical case. Furthermore, a lung cancer case for a patient treated with IMRT was also selected for the analysis. The respective planar dose distributions from the treatment plan and the film were compared based on the gamma(+) index and were evaluated using the radiobiological measures of P+ and (D) over bar. Results: The results for the test pattern analysis indicate that the gamma(+) index distributions differ from those of the gamma index since the former considers radiobiological parameters that may affect treatment outcome. For the theoretical clinical case, it is observed that the gamma(+) index varies for different treatment parameters (e.g. dose per fraction). The dose area histogram (DAH) from the plan and film dose distributions are associated with P+ values of 50.8% and 49.0%, for a (D) over bar to the target of 54.0 Gy and 53.3 Gy, respectively. Conclusion: The gamma(+) index shows advantageous properties in the quantitative evaluation of dose delivery and quality control of IMRT treatments because it includes information about the expected responses and radiobiological doses of the individual tissues.
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| 18. |
- Su, Fan-Chi, et al.
(författare)
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A graphic user interface toolkit for specification, report and comparison of dose-response relations and treatment plans using the biologically effective uniform dose
- 2010
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Ingår i: Computer Methods and Programs in Biomedicine. - : Elsevier BV. - 0169-2607 .- 1872-7565. ; 100:1, s. 69-78
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 19. |
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| 20. |
- Westin, Jerker, 1971-, et al.
(författare)
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A home environment test battery for status assessment in patients with advanced Parkinson's disease
- 2010
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Ingår i: Computer Methods and Programs in Biomedicine. - : Elsevier BV. - 0169-2607 .- 1872-7565. ; 98:1, s. 27-35
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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