Computer Methods and Programs in BiomedicineThis is an RSS file. You can use it to subscribe to this data in your favourite RSS reader, such as GoogleReader, or to display this data on your own website or blog. Subscribe to this data using MyMedWorm.Subscribe to this data using GoogleReader.Subscribe to this data using Bloglines.Subscribe to this data using MyYahoo.

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Comments on “Viscoelastic studies of human subscapularis tendon: Relaxation test and a Wiechert model” by C. Machiraju, A.V. Phan, A.W. Pearsall, S. Madanagopal, Computer Methods and Programs in Biomedicine (2006)Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: Referring to the approach for determining the material parameters for a Wiechert model of the human subscapularis tendon proposed by Machiraju et al. [C. Machiraju, A.V. Phan, A.W. Pearsall, S. Madanagopal, Viscoelastic studies of a human subscapularis tendon: relaxation test and a Wiechert model, Computer Methods and Programs in Biomedicine (2006), doi:10.1016/j.cmpb.2006.05.004], some comments are made on the basis of the result of an alternative method that is capable of giving more reasonable values for the Wiechart model with the fitting discrepancies minimized by a multi-variable optimization strategy. (Sou...
Source: Computer Methods and Programs in Biomedicine - October 5, 2009 Category: Bioinformatics Authors: Z.W. Wang, C.Y. Tang Tags: Correspondence Source Type: journals

CYCLOPS: A mobile robotic platform for testing and validating image processing and autonomous navigation algorithms in support of artificial vision prosthesesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: While artificial vision prostheses are quickly becoming a reality, actual testing time with visual prosthesis carriers is at a premium. Moreover, it is helpful to have a more realistic functional approximation of a blind subject. Instead of a normal subject with a healthy retina looking at a low-resolution (pixelated) image on a computer monitor or head-mounted display, a more realistic approximation is achieved by employing a subject-independent mobile robotic platform that uses a pixelated view as its sole visual input for navigation purposes. We introduce CYCLOPS: an AWD, remote controllable, mobile robotic pl...
Source: Computer Methods and Programs in Biomedicine - October 5, 2009 Category: Bioinformatics Authors: Wolfgang Fink, Mark A. Tarbell Tags: Section II: Systems and Programs Source Type: journals

Model checking of healthcare domain modelsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: This paper shows the application of a type of formal software verification technique known as lightweight model checking to a domain model in healthcare informatics in general and public health surveillance systems in particular. One of the most complex use cases of such a system is checked using assertions to verify one important system property. This use case is one of the major justifications for the complexity of the domain model. Alloy Analyzer verification tool is utilized for this purpose. Such verification work is very effective in either uncovering design flaws or in providing guarantees on certain desir...
Source: Computer Methods and Programs in Biomedicine - October 5, 2009 Category: Bioinformatics Authors: Dibyendu Baksi Tags: Section II: Systems and Programs Source Type: journals

A framework using cluster-based hybrid network architecture for collaborative virtual surgeryEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: Research on collaborative virtual environments (CVEs) opens the opportunity for simulating the cooperative work in surgical operations. It is however a challenging task to implement a high performance collaborative surgical simulation system because of the difficulty in maintaining state consistency with minimum network latencies, especially when sophisticated deformable models and haptics are involved. In this paper, an integrated framework using cluster-based hybrid network architecture is proposed to support collaborative virtual surgery. Multicast transmission is employed to transmit updated information among...
Source: Computer Methods and Programs in Biomedicine - October 5, 2009 Category: Bioinformatics Authors: Jing Qin, Kup-Sze Choi, Wai-Sang Poon, Pheng-Ann Heng Tags: Section II: Systems and Programs Source Type: journals

Motion correction based on an appropriate system matrix for statistical reconstruction of respiratory-correlated PET acquisitionsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: Respiratory motion correction in positron emission tomography (PET) seeks to incorporate motion information into an image reconstruction algorithm by using the full counting statistics of an acquisition to generate a single, motion-free volume. Here, we present a motion-incorporated ordered subsets expectation maximization (MOSEM) reconstruction based on a device-dedicated tomographic projector in which each matrix element is calculated directly from the voxels’ Cartesian coordinates alone. The motion is corrected by updating this projector as a function of the respiratory level. The performance of the reconstr...
Source: Computer Methods and Programs in Biomedicine - October 5, 2009 Category: Bioinformatics Authors: Loïc Fin, Pascal Bailly, Joël Daouk, Marc-Etienne Meyer Tags: Section I. Methodology Source Type: journals

Object density-based image segmentation and its applications in biomedical image analysisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: In many applications of medical image analysis, the density of an object is the most important feature for isolating an area of interest (image segmentation). In this research, an object density-based image segmentation methodology is developed, which incorporates intensity-based, edge-based and texture-based segmentation techniques. The proposed method consists of three main stages: preprocessing, object segmentation and final segmentation. Image enhancement, noise reduction and layer-of-interest extraction are several subtasks of preprocessing. Object segmentation utilizes a marker-controlled watershed techniqu...
Source: Computer Methods and Programs in Biomedicine - October 5, 2009 Category: Bioinformatics Authors: Jinhua Yu, Jinglu Tan Tags: Section I. Methodology Source Type: journals

Feature-based registration of histopathology images with different stains: An application for computerized follicular lymphoma prognosisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This study proposes a method for the automatic non-rigid registration of histological section images with different stain types. This method is based on matching high level features that are representative of small anatomical structures. This choice of feature provides a rich matching environment, but also results in a high mismatch probability. Matching confidence is increased by establishing local groups of coherent features through geometric reasoning. The proposed method is validated on a set of FL images representing different disease stages. Statistical analysis demonstrates that given a proper feature set the accura...
Source: Computer Methods and Programs in Biomedicine - October 5, 2009 Category: Bioinformatics Authors: Lee Cooper, Olcay Sertel, Jun Kong, Gerard Lozanski, Kun Huang, Metin Gurcan Tags: Section I. Methodology Source Type: journals

Does noise reduction matter for curve fitting in growth curve models?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: In this paper, we discuss the efficiency of noise reduction for curve fitting in nonlinear growth curve models. We use singular spectrum analysis as a nonlinear–nonparametric denoising method. A set of longitudinal measurements is used in considering the performance of the method. We also use artificially generated data sets with and without noise for the purpose of validation of the results obtained in this study. The results show that noise reduction is important for curve fitting in growth curve models and also, that the singular spectrum analysis technique can be used as a powerful tool for noise reduction ...
Source: Computer Methods and Programs in Biomedicine - October 5, 2009 Category: Bioinformatics Authors: Hossein Hassani, Mohammad Zokaei, Dietrich von Rosen, Saeid Amiri, Mansoureh Ghodsi Tags: Section I. Methodology Source Type: journals

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Source: Computer Methods and Programs in Biomedicine - October 5, 2009 Category: Bioinformatics Source Type: journals

Constant false alarm rate detection of saccadic eye movements in electro-oculographyEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This article considers a saccade detection method that is based on the constant false alarm rate technique, in which the detection sensitivity is continuously adjusted on the basis of the observed signal in order to keep the number of false alarms constant. The method is computationally efficient, it can operate autonomously without user intervention, and it is capable of detecting saccades in a sequential fashion. Therefore, the method finds potential use in applications that require automated analysis of electro-oculographic signals. Because of the constant false alarm rate property, the method can also perform in situat...
Source: Computer Methods and Programs in Biomedicine - September 2, 2009 Category: Bioinformatics Authors: P.-H. Niemenlehto Tags: Section II. Systems and Programs Source Type: journals

Architecture, cost-model and customization of real-time monitoring systems based on mobile biological sensor data-streamsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: Innovation in the fields of wireless data communications, mobile devices and biosensor technology enables the development of new types of monitoring systems that provide people with assistance anywhere and at any time. In this paper we present an architecture useful to build those kind of systems that monitor data streams generated by biological sensors attached to mobile users. We pay special attention to three aspects related to the system efficiency: selection of the optimal granularity, that is, the selection of the size of the input data stream package that has to be acquired in order to start a new processi...
Source: Computer Methods and Programs in Biomedicine - September 2, 2009 Category: Bioinformatics Authors: Alfredo Goñi, Alfredo Burgos, Lacramioara Dranca, Jimena Rodríguez, Arantza Illarramendi, Jesús Bermúdez Tags: Section II. Systems and Programs Source Type: journals

Simultaneous multi-modality ROI delineation in clinical practiceEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: The delineation of tumors and their surrounding organs at risk is a critical step of the treatment planning for radiation therapy. Besides computer tomography (CT), other imaging modalities are used to improve the quality of the delineations, such as magnetic resonance imaging (MRI) and positron emission tomography (PET). A practical framework is presented for using multiple datasets from different modalities during the delineation phase. The system is based on two basic principles. First, all image datasets of all available modalities are displayed in their original form (in their own coordinate system, with the...
Source: Computer Methods and Programs in Biomedicine - September 2, 2009 Category: Bioinformatics Authors: Gijsbert H. Bol, Alexis N.T.J. Kotte, Uulke A. van der Heide, Jan J.W. Lagendijk Tags: Section II. Systems and Programs Source Type: journals

Interactive toothbrushing education by a smart toothbrush system via 3D visualizationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: The very first step for keeping good dental hygiene is to employ the correct toothbrushing style. Due to the possible occurrence of periodontal disease at an early age, it is critical to begin correct toothbrushing patterns as early as possible. With this aim, we proposed a novel toothbrush monitoring and training system to interactively educate on toothbrushing behavior in terms of the correct brushing motion and grip axis orientation. Our intelligent toothbrush monitoring system first senses a user's brushing pattern by analyzing the waveforms acquired from a built-in accelerometer and magnetic sensor. To disce...
Source: Computer Methods and Programs in Biomedicine - September 2, 2009 Category: Bioinformatics Authors: Kyeong-Seop Kim, Tae-Ho Yoon, Jeong-Whan Lee, Dong-Jun Kim Tags: Section II. Systems and Programs Source Type: journals

A multidimensional segmentation evaluation for medical image dataEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: Evaluation of segmentation methods is a crucial aspect in image processing, especially in the medical imaging field, where small differences between segmented regions in the anatomy can be of paramount importance. Usually, segmentation evaluation is based on a measure that depends on the number of segmented voxels inside and outside of some reference regions that are called gold standards. Although some other measures have been also used, in this work we propose a set of new similarity measures, based on different features, such as the location and intensity values of the misclassified voxels, and the connectivit...
Source: Computer Methods and Programs in Biomedicine - September 2, 2009 Category: Bioinformatics Authors: Rubén Cárdenes, Rodrigo de Luis-García, Meritxell Bach-Cuadra Tags: Section I. Methodology Source Type: journals

Motorized CPM/CAM physiotherapy device with sliding-mode Fuzzy Neural Network control loopEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: Continuous passive motion (CPM) and controllable active motion (CAM) physiotherapy devices promote rehabilitation of damaged joints. This paper presents a computerized CPM/CAM system that obviates the need for mechanical resistance devices such as springs. The system is controlled by a computer which performs sliding-mode Fuzzy Neural Network (FNN) calculations online. CAM-type resistance force is generated by the active performance of an electric motor which is controlled so as to oppose the motion of the patient's leg. A force sensor under the patient's foot on the device pedal provides data for feedback in a s...
Source: Computer Methods and Programs in Biomedicine - September 2, 2009 Category: Bioinformatics Authors: Hung-Jung Ho, Tien-Chi Chen Tags: Section I. Methodology Source Type: journals

Detection of blood vessels in ophthalmoscope images using MF/ant (matched filter/ant colony) algorithmEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: Blood vessels in ophthalmoscope images play an important role in diagnosis of some serious pathologies on retinal images. Hence, accurate extraction of vessels is becoming a main topic of this research area. Matched filter (MF) implementation for blood vessel detection is one of the methods giving more accurate results. Using this filter alone might not recover all the vessels (especially the capillaries). In this paper, a novel approach (MF/ant algorithm) is proposed to overcome the deficiency of the MF. The proposed method is a hybrid model of matched filter and ant colony algorithm. In this work, the accuracy ...
Source: Computer Methods and Programs in Biomedicine - September 2, 2009 Category: Bioinformatics Authors: Muhammed Gökhan Cinsdikici, Doğan Aydın Tags: Section I. Methodology Source Type: journals

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(Source: Computer Methods and Programs in Biomedicine)
Source: Computer Methods and Programs in Biomedicine - September 2, 2009 Category: Bioinformatics Source Type: journals

Interactive segmentation framework of the Medical Imaging Interaction ToolkitEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: Interactive methods are indispensable for real world applications of segmentation in medicine, at least to allow for convenient and fast verification and correction of automated techniques. Besides traditional interactive tasks such as adding or removing parts of a segmentation, adjustment of contours or the placement of seed points, the relatively recent Graph Cut and Random Walker segmentation methods demonstrate an interest in advanced interactive strategies for segmentation. Though the value of toolkits and extensible applications is generally accepted for the development of new segmentation algorithms, the t...
Source: Computer Methods and Programs in Biomedicine - July 25, 2009 Category: Bioinformatics Authors: D. Maleike, M. Nolden, H.-P. Meinzer, I. Wolf Tags: Section II. Systems and Programs Source Type: journals

SURVSOFT—Software for nonparametric survival analysisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: Long-term observed and relative survival are important outcome measures of cancer patient care reported routinely by many cancer registries, but no commercial statistical software exists for estimating relative survival or performing period survival analysis. The programs publicly available focus only on certain methods, require specific input data formats and often are macros or functions which require underlying software packages. Here we introduce SURVSOFT, a comprehensive, user-friendly Windows program with graphical user interface. It can handle different input data formats and incorporates a variety of nonp...
Source: Computer Methods and Programs in Biomedicine - July 25, 2009 Category: Bioinformatics Authors: Karla Geiss, Martin Meyer, Martin Radespiel-Tröger, Olaf Gefeller Tags: Section II. Systems and Programs Source Type: journals

An implementation of the Expectation-Maximisation (EM) algorithm for population pharmacokinetic–pharmacodynamic modelling in ACSLXTREMEEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: An implementation of the Expectation-Maximisation (EM) algorithm in ACSLXTREME (AEGIS Technologies) for the analyses of population pharmacokinetic–pharmacodynamic (PKPD) data is demonstrated. The parameter estimation results are compared with those from NONMEM (Globomax) using the first order conditional estimate method. The estimates are comparable and it is concluded that the EM algorithm is a useful technique in population pharmacokinetic–pharmacodynamic modelling. The implementation also demonstrates the ease with which parameter estimation algorithms for population data can be implemented in simulation s...
Source: Computer Methods and Programs in Biomedicine - July 25, 2009 Category: Bioinformatics Authors: James W.T. Yates Tags: Section II. Systems and Programs Source Type: journals

Simulation program for power and sample size determination in logistic analysis of single nucleotide polymorphisms when the response variable is subject to misclassificationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: The main objective of this study was to develop a simulation program to determine the sample size for a clinical study to confirm a genetic-disease association observed in a retrospective exploratory study. The effect of misclassification of a binary response variable on the power is also investigated. A general expression for the magnitude of the decrease in statistical power due to misclassification is obtained based on the Pitman asymptotic relative efficiency. The simulation program presents an estimate of the exact power when misclassification exists. Running the program several times under different setting...
Source: Computer Methods and Programs in Biomedicine - July 25, 2009 Category: Bioinformatics Authors: Tomomi Yamada, Naoko Kinukawa, Tsuyoshi Nakamura, Yoshiaki Nose Tags: Section II. Systems and Programs Source Type: journals

Prostate cancer biomarker discovery using high performance mass spectral serum profilingEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study, we search for potential biomarkers using our feature selection method, the Extended Markov Blanket (EMB). From the new marker selection algorithm, a panel of 26 peaks achieved an accuracy of 80.7%, a sensitivity of 83.5%, a specificity of 74.4%, a positive predictive value (PPV) of 87.9%, and a negative predictive value (NPV) of 68.2%. On the other hand, when PSA alone was used (with a cutoff of 4.0ng/ml), a sensitivity of 66.7%, a specificity of 53.6%, a PPV of 73.5%, and a NPV of 45.4% were obtained. (Source: Computer Methods and Programs in Biomedicine)
Source: Computer Methods and Programs in Biomedicine - July 25, 2009 Category: Bioinformatics Authors: Jung Hun Oh, Yair Lotan, Prem Gurnani, Kevin P. Rosenblatt, Jean Gao Tags: Section I. Methodology Source Type: journals

A computer-aided system for malignancy risk assessment of nodules in thyroid US images based on boundary featuresEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: In this paper, a novel computer-based approach is proposed for malignancy risk assessment of thyroid nodules in ultrasound images. The proposed approach is based on boundary features and is motivated by the correlation which has been addressed in medical literature between nodule boundary irregularity and malignancy risk. In addition, local echogenicity variance is utilized so as to incorporate information associated with local echogenicity distribution within nodule boundary neighborhood. Such information is valuable for the discrimination of high-risk nodules with blurred boundaries from medium-risk nodules wit...
Source: Computer Methods and Programs in Biomedicine - July 25, 2009 Category: Bioinformatics Authors: Michalis Savelonas, Dimitris Maroulis, Manolis Sangriotis Tags: Section I. Methodology Source Type: journals

New Doppler-based imaging method in echocardiography with applications in blood/tissue segmentationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: A parametric model for the ultrasound signals from blood and tissue is developed and a new imaging method, knowledge-based imaging, is defined. This method utilizes the likelihood ratio function to classify blood and tissue signals. The method separates blood and tissue signals by the difference in movement patterns in addition to the difference in powers. The prior information about the levels of expected system white noise and clutter noise are utilized to enhance the image quality. The implementation of knowledge-based imaging is outlined, and some knowledge-based images with different parameter settings are v...
Source: Computer Methods and Programs in Biomedicine - July 25, 2009 Category: Bioinformatics Authors: Sigve Hovda, Håvard Rue, Bjørn Olstad Tags: Section I. Methodology Source Type: journals

Robust real time eye tracking for computer interface for disabled peopleEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: Gaze is a natural input for a Human Computer Interface (HCI) for disabled people, who have of course an acute need for a communication system. An efficient eye tracking procedure is presented providing a non-invasive method for real time detection of a subject eyes in a sequence of frames captured by low cost equipment. The procedure can be easily adapted to any subject and is adequately insensitive to changing of the illumination. The eye identification is performed on a piece-wise constant approximation of the frames. It is based on a discrete level set formulation of the variational approach to the optimal seg...
Source: Computer Methods and Programs in Biomedicine - July 25, 2009 Category: Bioinformatics Authors: Alberto De Santis, Daniela Iacoviello Tags: Section I. Methodology Source Type: journals

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(Source: Computer Methods and Programs in Biomedicine)
Source: Computer Methods and Programs in Biomedicine - July 25, 2009 Category: Bioinformatics Source Type: journals

Semi-automated evaluation tool for retinal vasculopathyEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: The ocular fundus is the only area of human body where vascular system is visible using relatively simple instrumentation. Furthermore, there is medical suggestive evidence of a direct relationship between certain measures of vascular characteristics in the ocular fundus (arteriolar and venular calibers and focal arteriolar narrowing) and cardiovascular diseases. In order to establish such relationship on sound statistical basis a method must be provided to measure the needed values in an easy, yet precise and repeatable way. This paper presents a system to assist physicians in signaling and storing the data asso...
Source: Computer Methods and Programs in Biomedicine - July 5, 2009 Category: Bioinformatics Authors: X. Benavent, L. Martínez-Costa, G. Ayala, J. Domingo, P. Marco Tags: Section. III: Experiences with Methods, Systems and Programs Source Type: journals

A prediction model for blood–brain barrier permeation and analysis on its parameter biologicallyEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The objective of this paper is to build a reliable model based on the artificial neural network (ANN) for predicting the blood–brain barrier (BBB) permeability and reveal the effects of the molecular descriptor on the BBB permeability. Eight descriptors including high-affinity P-gp substrate probability and plasma protein binding ratio are selected to develop the model. The three layers feedforward neural network (8-5-1) is employed for the prediction of logBB. By analyzing the experimental results, polar surface area (PSA) seems to be the most important factor for BBB permeability. Different from traditional view, the A...
Source: Computer Methods and Programs in Biomedicine - July 5, 2009 Category: Bioinformatics Authors: Yan Chen, Qing-Jun Zhu, Jian Pan, Yi Yang, Xiao-Pei Wu Tags: Section. III: Experiences with Methods, Systems and Programs Source Type: journals

Discrimination of myocardial infarction stages by subjective feature extractionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: Lots of studies on myocardial infarction (MI) computer assisted diagnosis are based on certain important ECG components which only account for local information. 12-Lead ECG signals which were regarded as hyper-dimensional time-series data were utilized to extract features from global information in this study. Existing feature extraction techniques for classification attempt to classify all the classes included. However sometimes it is more important to better recognize certain specific classes rather than to discriminate all the classes. A feature extraction method based on subjective-classification was propose...
Source: Computer Methods and Programs in Biomedicine - July 5, 2009 Category: Bioinformatics Authors: Dingfei Ge, Lihui Sun, Jiayin Zhou, Yuquan Shao Tags: Section. II: Systems and Programs Source Type: journals

A wearable real-time image processor for a vision prosthesisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: Rapid progress in recent years has made implantable retinal prostheses a promising therapeutic option in the near future for patients with macular degeneration or retinitis pigmentosa. Yet little work on devices that encode visual images into electrical stimuli have been reported to date. This paper presents a wearable image processor for use as the external module of a vision prosthesis. It is based on a dual-core microprocessor architecture and runs the Linux operating system. A set of image-processing algorithms executes on the digital signal processor of the device, which may be controlled remotely via a stan...
Source: Computer Methods and Programs in Biomedicine - July 5, 2009 Category: Bioinformatics Authors: D. Tsai, J.W. Morley, G.J. Suaning, N.H. Lovell Tags: Section. II: Systems and Programs Source Type: journals

Feature selection and syndrome prediction for liver cirrhosis in traditional Chinese medicineEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: Traditional Chinese medicine (TCM) treatment is one of the safe and effective methods for liver cirrhosis. In the process of its treatment, a very important step, syndrome prediction is generally performed by physicians at present, which actually hinders the application prospects of TCM. Based on the data mining algorithm, a novel method called TCMSP (traditional Chinese medicine syndrome prediction) is proposed, which consists of two phases. In the first phase, based on an improved information gain method in multi-view, the critical features are filtered from the original features. In the second phase, the class...
Source: Computer Methods and Programs in Biomedicine - July 5, 2009 Category: Bioinformatics Authors: Yan Wang, Lizhuang Ma, Ping Liu Tags: Section. II: Systems and Programs Source Type: journals

HipMatch: An object-oriented cross-platform program for accurate determination of cup orientation using 2D–3D registration of single standard X-ray radiograph and a CT volumeEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: The widely used procedure of evaluation of cup orientation following total hip arthroplasty using single standard anteroposterior (AP) radiograph is known inaccurate, largely due to the wide variability in individual pelvic orientation relative to X-ray plate. 2D–3D image registration methods have been introduced for an accurate determination of the post-operative cup alignment with respect to an anatomical reference extracted from the CT data. Although encouraging results have been reported, their extensive usage in clinical routine is still limited. This may be explained by their requirement of a CAD model of...
Source: Computer Methods and Programs in Biomedicine - July 5, 2009 Category: Bioinformatics Authors: Guoyan Zheng, Xuan Zhang, Simon D. Steppacher, Stephen B. Murphy, Klaus A. Siebenrock, Moritz Tannast Tags: Section. II: Systems and Programs Source Type: journals

An interactive multiblock approach to meshing the spineEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: Finite element (FE) analysis is a useful tool to study spine biomechanics as a complement to laboratory-driven experimental studies. Although individualized models have the potential to yield clinically relevant results, the demands associated with modeling the geometric complexity of the spine often limit its utility. Existing spine FE models share similar characteristics and are often based on similar assumptions, but vary in geometric fidelity due to the mesh generation techniques that were used. Using existing multiblock techniques, we propose mesh generation methods that ease the effort and reduce the time r...
Source: Computer Methods and Programs in Biomedicine - July 5, 2009 Category: Bioinformatics Authors: Nicole A. Kallemeyn, Srinivas C. Tadepalli, Kiran H. Shivanna, Nicole M. Grosland Tags: Section I. Methodology Source Type: journals

Generic screen representations for future-proof systems, is it possible? There is more to a GUI than meets the eyeEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The approach leads to a flexible GUI that can adapt not only to information structures that had not been predefined within the receiving system, but also to novel ways of displaying the information. We also found that, ideally, the openEHR Archetype Definition Language should receive minor adjustments to allow for generic binding. (Source: Computer Methods and Programs in Biomedicine)
Source: Computer Methods and Programs in Biomedicine - July 5, 2009 Category: Bioinformatics Authors: Helma van der Linden, Tony Austin, Jan Talmon Tags: Section I. Methodology Source Type: journals

Determining physiological cross-sectional area of extensor carpi radialis longus and brevis as a whole and by regions using 3D computer muscle models created from digitized fiber bundle dataEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: Architectural parameters and physiological cross-sectional area (PCSA) are important determinants of muscle function. Extensor carpi radialis longus (ECRL) and brevis (ECRB) are used in muscle transfers; however, their regional architectural differences have not been investigated. The aim of this study is to develop computational algorithms to quantify and compare architectural parameters (fiber bundle length, pennation angle, and volume) and PCSA of ECRL and ECRB. Fiber bundles distributed throughout the volume of ECRL (75±20) and ECRB (110±30) were digitized in eight formalin embalmed cadaveric specimens. The...
Source: Computer Methods and Programs in Biomedicine - July 5, 2009 Category: Bioinformatics Authors: Kajeandra Ravichandiran, Mayoorendra Ravichandiran, Michele L. Oliver, Karan S. Singh, Nancy H. McKee, Anne M.R. Agur Tags: Section I. Methodology Source Type: journals

EEG under anesthesia—Feature extraction with TESPAREmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: We investigated the problem of automatic depth of anesthesia (DOA) estimation from electroencephalogram (EEG) recordings. We employed Time Encoded Signal Processing And Recognition (TESPAR), a time-domain signal processing technique, in combination with multi-layer perceptrons to identify DOA levels. The presented system learns to discriminate between five DOA classes assessed by human experts whose judgements were based on EEG mid-latency auditory evoked potentials (MLAEPs) and clinical observations. We found that our system closely mimicked the behavior of the human expert, thus proving the utility of the metho...
Source: Computer Methods and Programs in Biomedicine - July 5, 2009 Category: Bioinformatics Authors: Vasile V. Moca, Bertram Scheller, Raul C. Mureşan, Michael Daunderer, Gordon Pipa Tags: Section I. Methodology Source Type: journals

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(Source: Computer Methods and Programs in Biomedicine)
Source: Computer Methods and Programs in Biomedicine - July 5, 2009 Category: Bioinformatics Source Type: journals

SNPit: A federated data integration system for the purpose of functional SNP annotationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: Genome wide association studies can potentially identify the genetic causes behind the majority of human diseases. With the advent of more advanced genotyping techniques, there is now an explosion of data gathered on single nucleotide polymorphisms (SNPs). The need exists for an integrated system that can provide up-to-date functional annotation information on SNPs. We have developed the SNP Integration Tool (SNPit) system to address this need. Built upon a federated data integration system, SNPit provides current information on a comprehensive list of SNP data sources. Additional logical inference analysis was i...
Source: Computer Methods and Programs in Biomedicine - May 4, 2009 Category: Bioinformatics Authors: Terry H. Shen, Christopher S. Carlson, Peter Tarczy-Hornoch Tags: Section II: Systems and Programs Source Type: journals

A minimal model of lung mechanics and model-based markers for optimizing ventilator treatment in ARDS patientsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: A majority of patients admitted to the Intensive Care Unit (ICU) require some form of respiratory support. In the case of Acute Respiratory Distress Syndrome (ARDS), the patient often requires full intervention from a mechanical ventilator. ARDS is also associated with mortality rate as high as 70%. Despite many recent studies on ventilator treatment of the disease, there are no well established methods to determine the optimal Positive End-Expiratory Pressure (PEEP) or other critical ventilator settings for individual patients. A model of fundamental lung mechanics is developed based on capturing the recruitment...
Source: Computer Methods and Programs in Biomedicine - May 4, 2009 Category: Bioinformatics Authors: Ashwath Sundaresan, Toshinori Yuta, Christopher E. Hann, J. Geoffrey Chase, Geoffrey M. Shaw Tags: Section II: Systems and Programs Source Type: journals

HANOIPC3: A computer program to evaluate executive functionsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This article describes a computer program (HANOIPC3) based on the Tower of Hanoi game that, by analyzing a series of parameters during execution, allows a fast and accurate evaluation of data related to certain executive functions, especially planning, organizing and problem-solving. This computerized version has only one level of difficulty based on the use of 3 disks, but it stipulates an additional rule: only one disk may be moved at a time, and only to an adjacent peg (i.e., no peg can be skipped over). In the original version – without this stipulation – the minimum number of movements required to complete the tas...
Source: Computer Methods and Programs in Biomedicine - May 4, 2009 Category: Bioinformatics Authors: M.A. Guevara, L. Rizo, M. Ruiz-Díaz, M. Hernández-González Tags: Section II: Systems and Programs Source Type: journals

STAMPS: Software Tool for Automated MRI Post-processing on a supercomputerEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: This paper describes a Software Tool for Automated MRI Post-processing (STAMP) of multiple types of brain MRIs on a workstation and for parallel processing on a supercomputer (STAMPS). This software tool enables the automation of nonlinear registration for a large image set and for multiple MR image types. The tool uses standard brain MRI post-processing tools (such as SPM, FSL, and HAMMER) for multiple MR image types in a pipeline fashion. It also contains novel MRI post-processing features. The STAMP image outputs can be used to perform brain analysis using Statistical Parametric Mapping (SPM) or single-/multi-...
Source: Computer Methods and Programs in Biomedicine - May 4, 2009 Category: Bioinformatics Authors: Don C. Bigler, Yaman Aksu, David J. Miller, Qing X. Yang Tags: Section II: Systems and Programs Source Type: journals

A statistical metadata model for clinical trials’ data managementEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: We introduce a statistical, process-oriented metadata model to describe the process of medical research data collection, management, results analysis and dissemination. Our approach explicitly provides a structure for pieces of information used in Clinical Study Data Management Systems, enabling a more active role for any associated metadata. Using the object-oriented paradigm, we describe the classes of our model that participate during the design of a clinical trial and the subsequent collection and management of the relevant data. The advantage of our approach is that we focus on presenting the structural inte...
Source: Computer Methods and Programs in Biomedicine - May 4, 2009 Category: Bioinformatics Authors: Maria Vardaki, Haralambos Papageorgiou, Fragkiskos Pentaris Tags: Section I. Methodology Source Type: journals

Multiple correspondence analysis in predictive logistic modelling: Application to a living-donor kidney transplantation dataEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: This work deals with the use of multiple correspondence analysis (MCA) and a weighted Euclidean distance (the tolerance distance) as an exploratory tool in developing predictive logistic models. The method was applied to a living-donor kidney transplant data set with 109 cases and 13 predictors. This approach, followed by backward and forward selection procedures, yielded two models, one with four and another with two predictors. These models were compared to two other models, ordinarily built by backward and forward stepwise selection, which yielded, respectively, five and two predictors. After internal validati...
Source: Computer Methods and Programs in Biomedicine - May 4, 2009 Category: Bioinformatics Authors: Renan Moritz Varnier R. Almeida, Antonio Fernando C. Infantosi, José Hermógenes R. Suassuna, João Carlos G.D. Costa Tags: Section I. Methodology Source Type: journals

Symmetric inverse consistent nonlinear registration driven by mutual informationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: A nonlinear viscoelastic image registration algorithm based on the demons paradigm and incorporating inverse consistent constraint (ICC) is implemented. An inverse consistent and symmetric cost function using mutual information (MI) as a similarity measure is employed. The cost function also includes regularization of transformation and inverse consistent error (ICE). The uncertainties in balancing various terms in the cost function are avoided by alternatively minimizing the similarity measure, the regularization of the transformation, and the ICE terms. The diffeomorphism of registration for preventing folding ...
Source: Computer Methods and Programs in Biomedicine - May 4, 2009 Category: Bioinformatics Authors: Guozhi Tao, Renjie He, Sushmita Datta, Ponnada A. Narayana Tags: Section I. Methodology Source Type: journals

An event-driven distributed processing architecture for image-guided cardiac ablation therapyEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We describe our prototype image-guidance system and demonstrate its functionality by emulating a cardiac ablation procedure with a patient-specific phantom. The proposed architecture, designed to be modular, flexible, and intuitive, is a key step towards our goal of developing a complete system for visualization and targeting in image-guided cardiac ablation procedures. (Source: Computer Methods and Programs in Biomedicine)
Source: Computer Methods and Programs in Biomedicine - May 4, 2009 Category: Bioinformatics Authors: M.E. Rettmann, D.R. Holmes, B.M. Cameron, R.A. Robb Tags: Section I. Methodology Source Type: journals

Editorial BoardEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
(Source: Computer Methods and Programs in Biomedicine)
Source: Computer Methods and Programs in Biomedicine - May 4, 2009 Category: Bioinformatics Source Type: journals

A SAS macro for a clustered permutation testEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We describe a flexible and efficient SAS macro that implements the 2-sample clustered permutation test. We discuss the theory and applications behind this test as well as details of the SAS code. (Source: Computer Methods and Programs in Biomedicine)
Source: Computer Methods and Programs in Biomedicine - April 24, 2009 Category: Bioinformatics Authors: Margaret R. Stedman, David R. Gagnon, Robert A. Lew, Daniel H. Solomon, Elena Losina, M. Alan Brookhart Tags: Section II. Systems and Programs Source Type: journals

A comparative study of individual and ensemble majority vote cDNA microarray image segmentation schemes, originating from a spot-adjustable based restoration frameworkEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: The aim of this study was to comparatively evaluate the performances of various segmentation algorithms, in conjunction with a noise reduction step, for gene expression levels intensity extraction in cDNA microarray images. Different segmentation algorithms, based on histogram and unsupervised classification methods, which have never been previously employed in microarray image analysis, were employed either individually or in ensemble majority vote structures for separating spot-images from background pixels. The performances of segmentation algorithms or ensemble structures were evaluated by assessing the valid...
Source: Computer Methods and Programs in Biomedicine - April 24, 2009 Category: Bioinformatics Authors: Antonis Daskalakis, Dimitris Glotsos, Spiros Kostopoulos, Dionisis Cavouras, George Nikiforidis Tags: Section II. Systems and Programs Source Type: journals

Interactive image analysis programs for quantifying injury-induced axonal beading and microtubule disruptionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: Focal axonal beading and focal disruption of microtubule structure are characteristic to traumatic axonal injury. We have recently reproduced these morphological and structural changes in our in vitro model system [D. Kilinc, G. Gallo, K.A. Barbee, Mechanically induced membrane poration causes axonal beading and localized cytoskeletal damage, Exp. Neurol. 212 (2008) 422–430]. In order to measure bead formation objectively, an observer-independent quantification of beading was necessary. In addition, a quantitative measure for the extent of co-localization of axonal beads and microtubule disruptions was required...
Source: Computer Methods and Programs in Biomedicine - April 24, 2009 Category: Bioinformatics Authors: Devrim Kilinc, Gianluca Gallo, Kenneth A. Barbee Tags: Section II. Systems and Programs Source Type: journals

Support Vectors Machine-based identification of heart valve diseases using heart soundsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: Taking into account that heart auscultation remains the dominant method for heart examination in the small health centers of the rural areas and generally in primary healthcare set-ups, the enhancement of this technique would aid significantly in the diagnosis of heart diseases. In this context, the present paper initially surveys the research that has been conducted concerning the exploitation of heart sound signals for automated and semi-automated detection of pathological heart conditions. Then it proposes an automated diagnosis system for the identification of heart valve diseases based on the Support Vector ...
Source: Computer Methods and Programs in Biomedicine - April 24, 2009 Category: Bioinformatics Authors: Ilias Maglogiannis, Euripidis Loukis, Elias Zafiropoulos, Antonis Stasis Tags: Section II. Systems and Programs Source Type: journals