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PubMedDate not supplied

Use of general purpose mechanical computer assisted engineering software in orthopaedic surgical planning: advantages and limitations.

Two surgical plans were developed for an appropriately complex reconstructive orthopaedic surgery case. One plan was developed with customary methods using two-dimensional (2D) radiographs. The second plan was developed with general purpose mechanical computer assisted engineering (MCAE) software using x-ray computed tomography (CT) data. The limitations of each method are identified. To create a surgical plan using three-dimensional (3D) medical datasets and MCAE software, five necessary steps were identified: (a) data reduction; (b) contour extraction; (c) 3D model creation; (d) extraction of mass properties; (e) model idealization. The principal limitation of general purpose MCAE software is the lack of pre-processing modules with which to address the unique requirements of medical image datasets.

Acetabulum↗

PubMed2006

Drug Guru: a computer software program for drug design using medicinal chemistry rules.

Drug Guru (drug generation using rules) is a new web-based computer software program for medicinal chemists that applies a set of transformations, that is, rules, to an input structure. The transformations correspond to medicinal chemistry design rules-of-thumb taken from the historical lore of drug discovery programs. The output of the program is a list of target analogs that can be evaluated for possible future synthesis. A discussion of the features of the program is followed by an example of the software applied to sildenafil (Viagra) in generating ideas for target analogs for phosphodiesterase inhibition. Comparison with other computer-assisted drug design software is given.

Chemistry, Organic↗

PubMed2006

A new software tool for 3D motion analyses of the musculo-skeletal system.

BACKGROUND: Many clinical and biomechanical research studies, particularly in orthopaedics, nowadays involve forms of movement analysis. Gait analysis, video-fluoroscopy of joint replacement, pre-operative planning, surgical navigation, and standard radiostereometry would require tools for easy access to three-dimensional graphical representations of rigid segment motion. Relevant data from this variety of sources need to be organised in structured forms. Registration, integration, and synchronisation of segment position data are additional necessities. With this aim, the present work exploits the features of a software tool recently developed within a EU-funded project ('Multimod') in a series of different research studies. METHODS: Standard and advanced gait analysis on a normal subject, in vivo fluoroscopy-based three-dimensional motion of a replaced knee joint, patellar and ligament tracking on a knee specimen by a surgical navigation system, stem-to-femur migration pattern on a patient operated on total hip replacement, were analysed with standard techniques and all represented by this innovative software tool. Segment pose data were eventually obtained from these different techniques, and were successfully imported and organised in a hierarchical tree within the tool. FINDINGS: Skeletal bony segments, prosthesis component models and ligament links were registered successfully to corresponding marker position data for effective three-dimensional animations. These were shown in various combinations, in different views, from different perspectives, according to possible specific research interests. INTERPRETATION: Bioengineering and medical professionals would be much facilitated in the interpretation of the motion analysis measurements necessary in their research fields, and would benefit therefore from this software tool.

Aged↗

PubMed2004

A computer software for simulating single-compartmental model of neurons.

In this paper, a new computer software package, Yalzer, is introduced for simulating single-compartmental model of neurons. Passive or excitable membranes with voltage-gated ion channels can be modeled, and current clamp and voltage clamp experiments can be simulated. In the Yalzer, first-order differential equations used to define the dynamics of the gate variables and the membrane potential are solved by two separate integration methods with variable time steps: forward Euler and exponential Euler methods. Outputs of the simulation are shown on a spreadsheet template for allowing flexible data manipulation and can be graphically displayed. The user can define the model in detail, and examine the excitability of the model and the dynamics of voltage-gated ion channels. The software package addresses to ones who want to run simple simulations of neurons without need to any programming language skills or expensive software. It can also be used for educational purposes.

Computer Simulation↗

PubMed2006

An integrative software package for gastrointestinal biomagnetic data acquisition and analysis using SQUID magnetometers.

The study of bioelectric and biomagnetic activity in the human gastrointestinal (GI) tract is of great interest in clinical research due to the proven possibility to detect pathological conditions thereof from electric and magnetic field recordings. The magnetogastrogram (MGG) and magnetoenterogram (MENG) can be recorded using superconducting quantum interference device (SQUID) magnetometers, which are the most sensitive magnetic flux-to-voltage converters currently available. To address the urgent need for powerful acquisition and analysis software tools faced by many researchers and clinicians in this important area of investigation, an integrative and modular computer program was developed for the acquisition, processing and analysis of GI SQUID signals. In addition to a robust hardware implementation for efficient data acquisition, a number of signal processing and analysis modules were developed to serve in a variety of both clinical procedures and scientific investigations. Implemented software features include data processing and visualization, waterfall plots of signal frequency spectra as well as spatial maps of GI signal frequencies. Moreover, a software tool providing powerful 3D visualizations of GI signals was created using realistic models of the human torso and internal organs.

Gastrointestinal Diseases↗

PubMed2006

A modular and evolutive component oriented software architecture for patient modeling.

This paper deals with the design aspect of a software aiming at modeling the anatomical and pathological structures of patients from medical images, for diagnosis purposes. In terms of functionalities, it allows to combine image processing algorithms, and to visualize and manipulate 3D models and images. The proposed software uses specific extensible and reusable components and a system managing their combination, thanks to a formal XML-based description of their interfaces. This architecture facilitates the dynamic integration of new functionalities, in particular in terms of image processing algorithms. We describe the structural and behavioral aspects of the proposed reusable component-based architecture. We also discuss the potential of this work for developing other softwares in the field of computer aided surgery.

Computer Simulation↗

PubMed2006

Multi-slice computer tomography of left ventricular function with automated analysis software in comparison with conventional ventriculography.

PURPOSE: To evaluate the accuracy of left ventricular volumetric and functional parameters from multi-slice computed tomography using automated analysis software, and to correlate results with those of invasive left ventriculography. MATERIALS AND METHODS: In 145 consecutive patients (mean age, 61 years+/-12) known or suspected to have coronary artery disease, a 16-channel multi-slice computed tomography (Philips Mx8000 IDT 16) was performed using a standard technique. Using short-axis secondary multi-slice computed tomography reformations, we determined end-diastolic and end-systolic left ventricular volumes and ejection fraction with a commercially available analysis software capable of automated contour detection. Conventional left ventriculography was performed according to standard techniques within the following 24 h. Bland-Altman analysis was performed to calculate the limits of agreement and systematic errors between multi-slice computed tomography and conventional left ventriculography. RESULTS: As determined by computer tomography, mean end-systolic (53+/-29 mL) left ventricular volumes had an acceptable correlation with conventional ventriculography (67+/-50 mL; r=0.74; p<0.001) and mean end-diastolic (119+/-33 mL) left ventricular volumes a poor correlation with conventional ventriculography measurements (154+/-69 mL; r=0.41). Left ventricular ejection fraction (57%+/-14 versus 55%+/-14 for conventional ventriculography; r=0.79) showed a very good correlation (p<0.001). Bland-Altman analysis showed acceptable limits of agreement (+/-9.2% for ejection fraction) without systematic errors. CONCLUSION: The use of a multi-slice computed tomography with an automatic calculation software has a good correlation with conventional ventriculography findings and could accurately assess left ventricular function, but should not be used for ventricular volumes, because of biased estimations.

Cineradiography↗

PubMed2006

A software tool to aid long-term care budget planning at local authority level.

OBJECTIVE: Local authorities face real challenges when it comes to annual budget planning for funding the system of long-term care. Uncertainty about the long-term cost of caring for current residents in the system, in addition to unknown future admissions, have made the tasks of local authority budget managers very complex and demanding. In this paper, we present a software implementation of a novel forecasting framework developed by the authors to provide useful information to local authority budget planners involved in long-term care. METHODS: The tool is built upon a forecasting framework, which combines unit costs of care with an estimated underlying survival model for publicly funded residents in long-term care, to provide forecasts of the cost of maintaining the group of elderly people who are currently in long-term care (referred to as known commitments) for a period of time. A prototype version of the software tool, which was created and tested in collaboration with an English borough, allows user interaction via a friendly graphical interface that guides through a set of screens of options in a familiar wizard fashion. RESULTS AND DISCUSSION: Feedback from care planners and managers show that the tool helps them gain better understanding of the patterns of length-of-stay of residents under their care, and provides quantitative inputs into their decision making on budget planning for long-term care. The development of the software tool brings advanced modelling techniques out of research papers into the hands of decision makers in the public sector and contributes to improving the delivery of long-term care.

Activities of Daily Living↗

PubMed2005

A software solution for the control of visual behavioral experimentation.

Psychophysical and neurophysiological research requires precise control of experimental devices for the purpose of delivering stimuli and monitoring behavioral and neural responses. This has previously been accomplished by complex, often proprietary, programmable systems, interfacing with a limited range of hardware. We have developed a software solution entirely within the Matlab environment that can achieve high-speed control of experimental and behavioral variables. We make this Wake-Forest Visual Experimentation (WaVE) software freely available under the GNU public license, and demonstrate how to customize it to individual laboratory needs. WaVE takes advantage of existing Matlab libraries and toolboxes to present visual stimuli, collect experimental data, update behavioral variables, and communicate with other computers. Although we have developed it for use in a Windows-based Personal Computer, the portability of the Matlab code makes possible its customization for use in a variety of other systems. We present simulation results showing sub-millisecond sampling rate and updating precision, running on single-processor, desktop PCs. The WaVE software offers a simple, flexible and powerful solution that compares favorably with many of its costly alternatives.

Animals↗

PubMed2007

Measurements of DNA damage on silver stained comets using free Internet software.

Silver stain offers the possibility to stain comets permanently, but up to now it was impossible to measure the majority of the comet parameters, because the distinction between head and tail was not recognised by software. Here, we report a silver staining protocol that allows the measurement of comet parameters using the free Internet software CASP. We validated the silver stain protocol by comparing the behaviour of the parameter '% DNA in tail' in silver and fluorescent stained comets. The range of % DNA in tail for different visual categories of damage in silver stained comets was similar to that reported with fluorescence staining. The range was for category 0 (no damage), <1%; category 1 (low damage), 1-25%; category 2 (medium damage), >25-45%; category 3 (high damage), >45-70%; category 4 (very high damage), >70%. The mean of % DNA in tail in silver stained comets was also similar to that reported with fluorescence staining. The mean was for category 0, 0.4+/-0.34%; category 1, 12+/-7%; category 2, 37+/-4%; category 3, 57+/-5% and category 4, 83+/-6%. Others comet parameters such as tail length, tail moment and Olive tail moment can be also measured. The silver staining protocol reported here opens new opportunities for those working in the assay without fluorescent microscope as the measurement of comet parameters using free Internet software and conventional microscope becomes possible.

Comet Assay↗

PubMed2005

Development of computer-generated phantoms for FMRI software evaluation.

Functional magnetic resonance imaging (FMRI) is a major tool for the evaluation of brain function and architecture. It is widely used by physicians, neuroscientists, psychologists and others. In order to process the data collected using FMRI, it is necessary to use post-acquisition processing software that employs motion correction and statistical modeling capabilities. These types of programs permit the user to extract the information about areas of brain activations that have occurred during a study. How well a particular motion-correction technique works and what effect it has on statistical processing are difficult to evaluate, since the level of activation present is not known a priori. This paper provides a description of the construction of a software phantom for use with FMRI post-acquisition processing tools with the properties that it is based on real subject data, has known locations and levels of activation, has known amounts of rigid body motion and noise added, and can be used to evaluate a processing system as if it were a real data set. Versions of the software phantom are available for downloading at the website: .

Humans↗

PubMed2004

The LONI Debabeler: a mediator for neuroimaging software.

Brain image analysis often involves processing neuroimaging data with different software packages. Using different software packages together requires exchanging files between them; the output files of one package are used as input files to the next package in the processing sequence. File exchanges become problematic when different packages use different file formats or different conventions within the same file format. Although comprehensive medical image file formats have been developed, no one format exists that satisfies the needs of analyses that involve multiple processing algorithms. The LONI Debabeler acts as a mediator between neuroimaging software packages by automatically using an appropriate file translation to convert files between each pair of linked packages. These translations are built and edited using the Debabeler graphical interface and compensate for package-dependent variations that result in intrapackage incompatibilities. The Debabeler gives neuroimaging processing environments a configurable automaton for file translation and provides users a flexible application for developing robust solutions to translation problems.

Animals↗

PubMed2006

A systematic review of computer-based softwares for educating patients with coronary heart disease.

OBJECTIVE: To evaluate the use of computer-based softwares for educating patients with coronary heart disease. METHODS: A systematic electronic search for randomised controlled trials and comparison studies published from 1999 to the end of 2005 using the MEDLINE (1999-2005), EMBASE (1999-2005) and CINAHL (1999-2005) was carried out. Articles including the reference lists in the following journals were hand-searched: Patient Education and Counselling and Patient Counselling and Health Education. RESULTS: A total of 487 articles were identified. Based on a review of abstracts, five studies fulfilled the inclusion criteria of the review. A scoring sheet was used to assess the papers' quality. All studies reported significantly increased knowledge in patients using the educational software when compared to standard education. The difference in knowledge between the intervention and control groups remained high even at 6 months follow up. Furthermore, patients reported high satisfaction with the educational programs. CONCLUSION: Despite there only being five studies that met the inclusion criteria, this review supports the successful use of computer software to increase knowledge in patients with coronary heart disease. The reviewed articles reveal that computer-based education has an important role in increasing patients' knowledge about their condition. PRACTICAL IMPLICATIONS: It is commonly reported that patients want more information about their illness. This study shows that computer-based education can be a useful, acceptable to patients and effective way to deliver education about coronary heart disease.

Adult↗

PubMed2006

Development of a novel CASA system based on open source software for characterization of zebrafish sperm motility parameters.

Although computer-assisted sperm analysis (CASA) outperforms manual techniques, many investigators rely on non-automated analysis due to the high cost of commercial options. In this study, we have written and validated a free CASA software primarily for analysis of fish sperm. This software is a plugin for the free National Institutes of Health software ImageJ and is available with documentation at . That it is open source makes possible external validation, should improve quality control and enhance the comparative value of data obtained among laboratories. In addition, we have improved upon the traditional velocity straight line (VSL) algorithm, eliminating inaccurate characterization of highly curved fish sperm paths. Using this system, the motion of zebrafish (Danio rerio) sperm was characterized relative to time post-activation and the impact of acquisition conditions upon data analysis determined. There were decreases in velocity and path straightness (STR), but not linearity (LIN), relative to time. From 30 to 300 frames/s, frame rate significantly affected curvilinear velocity (VCL) and STR measurements. Sperm density in the field of view did not affect any measured parameter. There was significant inter-male variation for VCL, VSL, velocity average path (VAP), percent motility, path character (STR, LIN), and duration of motility. Furthermore, relative sperm output (a measure reflecting both semen volume and concentration) was positively correlated to percent motility. For all motion parameters measured (except duration), the average CV was < or =10%, comparable to values obtained using commercial systems.

Algorithms↗

PubMed2005

In silico screening of chemicals for bacterial mutagenicity using electrotopological E-state indices and MDL QSAR software.

Quantitative structure-activity relationship (QSAR) software offers a rapid, cost effective means of prioritizing the mutagenic potential of chemicals. MDL QSAR models were developed using atom-type E-state indices and non-parametric discriminant analysis. Models were developed for Salmonella typhimurium gene mutation, combining results from strains TA97, TA98, TA100, TA1535, TA1536, TA1537, and TA1538 (n=3228), and Escherichia coli gene mutation tests WP2, WP100, and polA (n=472). Composite microbial mutation models (n=3338) were developed combining all Salmonella, E. coli, and the Bacillus subtilis rec spot test study results. The datasets contained 74% non-pharmaceuticals and 26% pharmaceuticals. Salmonella and microbial mutagenesis external validation studies included a total of 1444 and 1485 compounds, respectively. The average specificity, sensitivity, positive predictivity, concordance, and coverage of Salmonella models was 76, 81, 73, 78, and 98%, respectively, with similar performance for the microbial mutagenesis models. MDL QSAR and discriminant analysis provides rapid and highly automated mutagenicity screening software with good specificity, sensitivity, and coverage that is simpler and requires less user intervention than other similar software. MDL QSAR modules for microbial mutagenicity can provide efficient and cost effective large scale screening of compounds for mutagenic potential for the chemical and pharmaceutical industry.

Algorithms↗

PubMed1998

Evaluation of the finite element software ABAQUS for biomechanical modelling of biphasic tissues.

The biphasic cartilage model proposed by Mow et al. (1980) has proven successful to capture the essential mechanical features of articular cartilage. In order to analyse the joint contact mechanics in real, anatomical joints, the cartilage model needs to be implemented into a suitable finite element code to approximate the irregular surface geometries of such joints. However, systematic and extensive evaluation of the capacity of commercial software for modelling the contact mechanics with biphasic cartilage layers has not been made. This research was aimed at evaluating the commercial finite element software ABAQUS for analysing biphasic soft tissues. The solutions obtained using ABAQUS were compared with those obtained using other finite element models and analytical solutions for three numerical tests: an unconfined indentation test, a test with the contact of a spherical cartilage surface with a rigid plate, and an axi-symmetric joint contact test. It was concluded that the biphasic cartilage model can be implemented into the commercial finite element software ABAQUS to analyse practical joint contact problems with biphasic articular cartilage layers.

Animals↗

PubMed1998

Software assessment under consideration of validation aspects: PPS and PMS systems.

Due to safety aspects, business risks and regulations of the FDA [FDA, 1983, Guide to Inspection of Computerized Systems in Drug Processing. USA] and the EU [EU-Leitfaden einer Guten Herstellpraxis for Arzneimittel, 1989, III/2244/87 Rev. 3. Jan. 1989], computer based systems used in the pharmaceutical production have to be validated. In this paper we assessed which modules of production planning and control (PPS) and production management systems (PMS) have to be validated using a risk analysis procedure. It could be shown that the necessity of the validation concerns, above all, the modules of production management systems. Furthermore, a software supplier questionnaire was developed according to the V-model of Royce [National Computing Centre, 1989. STARTS Publications, UK.]. The software supplier questionnaire was applied on four software products, which are mostly used in the pharmaceutical industry. Although these were developed according to a life cycle concept they fulfil the validation requirements, measured with the developed questionnaire, to a different degree. Especially the key element of the risk analysis was differently interpreted.

Computer Systems↗

PubMed2002

Seafood Spoilage Predictor--development and distribution of a product specific application software.

To allow shelf-life prediction of a range of products, the Seafood Spoilage Predictor (SSP) software has been developed to include both kinetic models for growth of specific spoilage microorganisms and empirical relative rates of spoilage models. SSP can read and evaluate temperature profile data of different formats and in this way the software is a flexible device for electronic time-temperature integration. Predicted values of microbial growth and of remaining product shelf life can be exported from SSP as graphs and tables in ASCII, HTML and eXtensible Mark-up Language (XML) formats and this allows SSP to be used in combination with other programmes. More than 300 people have downloaded SSP and distribution of this software from the internet has been efficient in stimulating the application of predictive microbiology and of mathematical seafood shelf-life models within industry, research, seafood inspection and teaching.

Animals↗