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PubMed1998

A PC-based workstation for processing and analysis of MRI data.

The present work demonstrates that a low cost, flexible and user-friendly workstation for the MRI laboratory can be implemented by using a personal computer and public-domain software. The workstation is based on a Pentium personal computer, operating under the Linux operative system, and uses the software Khoros (Khoral Research, Albuquerque, NM). This software is a general purpose package for handling signals and we here report its suitability for MR images analysis. Khoros allows to create workspaces where different procedures (also written by the users) can be combined for implementing more complex procedures. We created workspaces for obtaining 2D and 3D images from time domain data which also allow for apodization and zero-filling. The time required for a 3D-FFT (matrix size 128x128x128) is about 12 min with the presently used microprocessor. We have also created workspaces for calculating apparent diffusion coefficient maps and for segmentation of MR images. Our results demonstrate that a personal computer equipped with public-domain software can represent a powerful tool to fulfil the MRI laboratory common needs.

Animals↗
PubMed2000

Hippocampal and cerebellar volumetry in serially acquired MRI volume scans.

In this work, we describe methodologies for serial volumetric measurements of hippocampi and cerebella. Serial scans were co-registered and intensity matched prior to the volumetric measurements. Manual drawing was used to define the boundaries of the hippocampi. For the cerebellar volumetric measurements, the brain was automatically segmented from the co-registered scans; manual drawing was used to define the boundary between the cerebellum and the cerebrum and brainstem. The operator was blinded to the nature of the subject (patient or normal control) and the chronological order of the scans. The coefficient of reliability of hippocampal volume measurements in a group of 20 controls was 0.078 cm(3) (3.1% of the mean baseline volume); for the cerebellum, the value was 3.8 cm(3) (3.0% of the mean baseline volume). We conclude that the methods presented are valid and that the software provides a useful integrated tool for the quantitative analysis of structural changes in serially acquired volume MRI data in prospective, blinded studies.

Adult↗
PubMed2006

Deblurring visual evoked potentials using commercially available software.

Visual evoked potentials are useful clinical tools to study visual pathways of the brain. Although the temporal resolution is unsurpassed by other brain imaging technologies, the spatial resolution is diminished or blurred by the low conductance of the electrical signals through the skull. Methods have been proposed to improve the spatial resolution by downwardly projecting the electrical signals measured on the scalp to the surface of the cerebral cortex through the inverse solution of the equations governing static current flow. We describe the adaptation and combination of commercially available engineering software programs to solve this inverse problem and report the results of a sample run of the system. Before deblurring, the visual evoked potentials appeared to be diffusely localized over the posterior scalp. After deblurring, the visual evoked potentials were only found at the electrodes closest to the visual cortex, as would be predicted by our current knowledge of neuroanatomy.

Brain↗
PubMedDate not supplied

EMGLAB: objective outcome measures in neurophysiological testing.

The aim of this work was to objectively measure and quantify the results of various neurophysiological tests and indirectly provide objective outcome measures for neurological therapy and rehabilitation. We have studied the silence of Electromyographic (EMG) activity after evoking motor potentials with magnetic cortical stimulation. Since different criteria were previously used to determine the level where the silence of muscle activity ends, an objective computer aided method was developed. This analysis was further developed to include objective testing of surface EMG, long latency reflexes, reciprocal inhibition of the H-reflex, H-reflex recovery curve and decrement testing. Responses were recorded at different sampling frequencies, depending on the application, time window, filter settings, etc. The developed software proved to be a fast and objective tool, able to standardize the determination of different neurophysiological tests, and as such a valuable tool facilitating multi-center studies and diminishing human bias. The software reduced the study time with each patient. Until date we have used the software with the Medtronic, Medelec and BTS EMG instruments.

Diagnosis, Computer-Assisted↗
PubMed2004

Vector NTI, a balanced all-in-one sequence analysis suite.

Vector NTI is a well-balanced desktop application integrated for molecular sequence analysis and biological data management. It has a centralised database and five application modules: Vector NTI, AlignX, BioAnnotator, ContigExpress and GenomBench. In this review, the features and functions available in this software are examined. These include database management, primer design, virtual cloning, alignments, sequence assembly, 3D molecular viewer and internet tools. Some problems encountered when using this software are also discussed. It is hoped that this review will introduce this software to more molecular biologists so they can make better-informed decisions when choosing computational tools to facilitate their everyday laboratory work. This tool can save time and enhance analysis but it requires some learning on the user's part and there are some issues that need to be addressed by the developer.

Algorithms↗
PubMed1999

SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model.

In this paper we present SFCHECK, a stand-alone software package that features a unified set of procedures for evaluating the structure-factor data obtained from X-ray diffraction experiments and for assessing the agreement of the atomic coordinates with these data. The evaluation is performed completely automatically, and produces a concise PostScript pictorial output similar to that of PROCHECK [Laskowski, MacArthur, Moss & Thornton (1993). J. Appl. Cryst. 26, 283-291], greatly facilitating visual inspection of the results. The required inputs are the structure-factor amplitudes and the atomic coordinates. Having those, the program summarizes relevant information on the deposited structure factors and evaluates their quality using criteria such as data completeness, structure-factor uncertainty and the optical resolution computed from the Patterson origin peak. The dependence of various parameters on the nominal resolution (d spacing) is also given. To evaluate the global agreement of the atomic model with the experimental data, the program recomputes the R factor, the correlation coefficient between observed and calculated structure-factor amplitudes and Rfree (when appropriate). In addition, it gives several estimates of the average error in the atomic coordinates. The local agreement between the model and the electron-density map is evaluated on a per-residue basis, considering separately the macromolecule backbone and side-chain atoms, as well as solvent atoms and heterogroups. Among the criteria are the normalized average atomic displacement, the local density correlation coefficient and the polymer chain connectivity. The possibility of computing these criteria using the omit-map procedure is also provided. The described software should be a valuable tool in monitoring the refinement procedure and in assessing structures deposited in databases.

Amino Acid Sequence↗
PubMed1997

[Orthopedic treatment of scoliosis: new technique using impression by optic procedure].

The authors present a new procedure for acquiring the whole external trunk shape. The construction of braces starts with corrected a positive mold using computer-assisted design software connected to a digital tooling machine. The computer-assisted design and construction of braces enable the determination, measurement, and modification of a three-dimensional image of the trunk, which allows the positive to be corrected. The outer-trunk can be re-balanced, derotated or rectified in the sagittal or frontal plane and the inner modeling of the spine and chest can be rectified. Moreover, in the case of scoliosis or kyphosis, the software produces automatic correction. This rapid (acquisition time < 2 seconds), non invasive, safe and painless procedure can also be used to detect and follow mild spinal deformities.

Adolescent↗
PubMed2006

Contrast-driven approach to intracranial segmentation using a combination of T2- and T1-weighted 3D MRI data sets.

PURPOSE: To develop a strategy for structural brain imaging when using FSL software for segmentation and subsequent volumetry. MATERIALS AND METHODS: Three-dimensional (3D) structural MRI of 1-mm isotropic resolution was performed on a 3-Tesla clinical imaging system. Prescribed signal evolution of a multiple spin-echo (SE) sequence with variable refocusing flip angle for T2 weighting, and a modified driven equilibrium Fourier transform (MDEFT) sequence were used for T1 weighting. Postprocessing included rigid-body coregistration, brain extraction, and segmentation using the tools of the FSL 3.2 software package. RESULTS: T2 weighting provided reliable delineation of the subarachnoidal space, while T1 weighting provided better segmentation of gray matter (GM) and white matter (WM). The combination of T1-weighted (T1-w) and T2-w data allowed the identification of a T2-hypointense class of "nonbrain" (NB) representing larger vessels and structures of connective tissue, as well as partial volume of bone and air-filled cavities. CONCLUSION: Brain extraction on T2-w data and subsequent segmentation of the combined T1- and T2-w intensity distribution into four classes are recommended.

Adult↗
PubMed2003

[Vocalab: a new software for voice evaluation and therapy].

When handling vocal pathologies, speech therapists need tools to visualise voice and speech, in order to correlate personal auditory analysis with accurate data. Vocalab2 is a spectral analysis tool designed for speech therapists, developed in partnership with INSA Toulouse, France. Vocalab is a simple and user-friendly tool with important features to be used during evaluation and therapy. The software is based on a set of phoniatric data and sophisticated real-time signal analysis (Fourier transform, fundamental detection). One of the key tools of Vocalab2 is the real-time spectrum for visualising, differentiating and comparing every cord approximation and speech movement. Animations are proposed for illustrating most phonemes, and videos related to folding cords in the case of pathologic and normal sound production are also proposed. An extensive test has been conducted during 18 month, with important feedback that has considerably improved the tool. The satisfaction ratio is around 8/10.

Acoustics↗
PubMed2006

CIVA: an expertise platform for simulation and processing NDT data.

Ultrasonic modeling and simulation are more and more widely used by the different actors of industrial NDT. The applications are numerous and show a great variety: help for diagnosis, data reconstruction, performance demonstration, probe design and inspection parameters settling, virtual testing etc. The CEA (the French Atomic Energy Commission) is strongly involved in this evolution with the development of the CIVA expertise platform which gathers in the same software advanced processing and modeling tools. In the aim of fulfilling requirements of an intensive use the choice has been made to mainly adopt semi-analytical approximated methods. The wave propagation modeling is based on an integral formulation of the radiated field and applies the so-called pencil method. The modeling of beam-defect interaction and echoes formation mechanisms apply approximated theories such as Kirchhoff approximation or GTD. Over the years and with successive versions of the software, this approach is enriched by adaptations and improvements of the existing models or by new models, in order to extend the field of applicability of the simulation.

Journal Article↗
PubMed2005

Object-oriented implementation for the dual surface minimisation algorithm.

The automatic surface extraction from volumetric images is important for the medical image analysis. The delineation task is challenging especially with functional imaging where images are noisy and the content of image depends on the study. We have earlier developed a new dual surface minimisation (DSM) algorithm for the optimisation of deformable surfaces and applied it successfully to fully automatic surface extraction from positron emission tomography images. We present a fast object-oriented implementation for the DSM algorithm with a conventional command line interface. The DSM software is a freely available tool for the Internet community at http://www.cs.uta.fi/research/software/. The implementation of the DSM algorithm provides new opportunities to extend experiments, to develop and to study new applications with noisy volumetric images emerging from medical or other applications.

Algorithms↗
PubMed1999

Peptide and protein identification by matrix-assisted laser desorption ionization (MALDI) and MALDI-post-source decay time-of-flight mass spectrometry.

The potential of matrix-assisted laser desorption ionization (MALDI) and MALDI-post-source decay (PSD) time-of-flight mass spectrometry for the characterization of peptides and proteins is discussed. Recent instrumental developments provide for levels of sensitivity and accuracy that make these techniques major analytical tools for proteome analysis. New software developments employing protein database searches have greatly enhanced the fields of application of MALDI-PSD. Peptides and proteins can be easily identified even if only a partial sequence information is determined. Derivatization procedures have been optimized for MALDI-PSD to increase the structural information and to obtain a complete peptide sequence even in critical cases. They are fast, simple and can be performed on target. MALDI-PSD is also a very powerful tool to characterize or elucidate post-translational or chemically induced modifications. In association with database searches, proteins issued from electrophoretic gels can be identified after specific enzymatic cleavages and peptide mapping.

Amino Acid Sequence↗
PubMed1996

Real world data--retrieval and validation of consultation data from four general practices.

OBJECTIVE: We aimed to retrieve data on consultations from general practice databases and to develop and use appropriate methods of validation for these data. METHOD: MIQUEST software was used to retrieve the data from four practices. The data were validated by comparing them with figures generated by practice-based searches, measuring the uptake of recording of consultations over time, and comparing records of consultations in the case notes with those on the practice computers. RESULTS: The required data were retrieved from general practice databases, but the path to success was difficult, and typified by uncertainty and unpredictability. The recording of consultations on the computers of four practices was more complete than the recording in the paper case records. There was a time period in the early months of computer use when the recording of consultations was less complete. There were differences in the completeness of recording consultations between practices, doctors, and patients. CONCLUSIONS: This study confirms the potential of general practice databases for research, demonstrates how MIQUEST software can be a useful tool in retrieving data from general practice databases, and indicates how the completeness of data recording permitted further analysis for the purposes of our study.

Data Collection↗
PubMed2006

Therapeutic modulation of DMD splicing by blocking exonic splicing enhancer sites with antisense oligonucleotides.

Antisense oligonucleotides (AONs) can be used to correct the disrupted reading frame of Duchenne muscular dystophy patients (DMD). We have a collection of 121 AONs, of which 79 are effective in inducing the specific skipping of 38 out of the 79 different DMD exons. All AONs are located within exons and were hypothesized to act by steric hindrance of serine-arginine rich (SR) protein binding to exonic splicing enhancer (ESE) sites. Indeed, retrospective in silico analysis of effective versus ineffective AONs revealed that the efficacy of AONs is correlated to the presence of putative ESE sites (as predicted by the ESEfinder and RESCUE-ESE software). ESE predicting software programs are thus valuable tools for the optimization of exon-internal antisense target sequences.

Dystrophin↗
PubMed2004

Measurement of body surface area in atopic dermatitis using specific PC software (ScoradCard).

In skin diseases, evaluation of involved surface area is a crucial factor in grading the degree of severity. We examined the reliability of body surface area assessment and relative inter-observer and intra-observer variability using new software (ScoraCard), specifically designed to evaluate automatically the extension of the involved area in the SCORAD index. Twenty pediatricians, untrained in the evaluation of skin disease, estimated the percentage of surface area involved in photo-tests of two children with artificial well-delimited lesions, at first by sight and then through software. As "gold standard" the exact amount of pixels was counted for the whole body surface of the children, for the different body zones and for the painted artificial lesions, expressed as percentage of the respective zone. For photo 1, gold standard was 38.06% and median percentage was 43.44% (95% CI 40.7-46.21) by sight (p = 0.002) and 37.99% (95% CI 36.04-39.94) by ScoradCard (p = 0.79). For photo 2, gold standard was 27.84%, median percentage was 30.44% (95% CI 28.25-32.63) by sight (p = 0.047) and 27.8% (95% CI 26.55-29.04) by ScoradCard (p = 0.79). The level of agreement (kappa statistic), cumulative for the two photo tests, was 0.38 (fair agreement) by sight method and 0.67 (good agreement) by ScoradCard. Among the 10 pediatricians who repeated the computer aided evaluation 3 months apart, the intra-observer variability was not significantly different: the median percentage was 31.5% (95% CI 27.0-49.4) at time 0 and 29.0% (95% CI 26.7-47.2) 3 months later (p = 0.76). This new software could be a useful tool in evaluating skin lesions extension, minimizing inter- and intra-observer variability, which is an important goal in multi-centre studies.

Adolescent↗
PubMed1997

Approaches for certification of electronic prescription software.

The proper management of drug treatment is essential, since adverse drug reactions are common reasons of hospitalisations. Expenditure on drug therapy has also been growing faster than any other aspect of health care in many countries. Savings and quality improvements in drug treatment could be achieved with computerised prescribing. In this paper, the architecture of an electronic prescription system is described in the light of software certification and registration. An electronic prescription system is an example of a system supporting shared care and therefore it should be person based, integrated, secure and confidential and data should be shared among health care institutions. The system architecture shares the idea of a virtual patient record and a smart card will be used as a key to prescription data located on the network. The certification and registration of medical software is a difficult and costly procedure. Ensuring the quality of software can be based on; certification of development process, voluntary evaluation, and post-market surveillance. Voluntary evaluation practice would be a precious tool for both the customers and software developers, and it would also be an invaluable source of information in terms of developing new software.

Certification↗
PubMed2002

Sepsis gene expression profiling: murine splenic compared with hepatic responses determined by using complementary DNA microarrays.

OBJECTIVE: DNA microarrays allow genome-wide assessment of changes in relative messenger RNA abundance and thus can be used to monitor changes in gene expression. The aim of this series of experiments was to gain experience in sepsis gene expression profiling in a well-accepted model of murine polymicrobial abdominal sepsis and begin characterizing (in the parlance of genomics) the sepsis "transcriptome." DESIGN: Prospective animal study. SETTING: University-based animal research facility.SUBJECTS C57BL/6 mice. INTERVENTIONS: After induction of general anesthesia, cecal ligation and puncture were performed to induce peritonitis and polymicrobial sepsis. The control group had sham laparotomy only. Three samples of spleen and liver were collected from septic and sham animals at 24 hrs after laparotomy. Changes in expression were measured for 588 annotated mouse genes by using a commercially available complementary DNA microarray kit. MEASUREMENTS AND MAIN RESULTS: Broad-scale gene expression profiles were characterized for septic liver and spleen and compared with sham controls. The analytical tools used included commercially available software packages and a novel analysis program. Very little overlap was observed in the septic gene expression profiles of these two organs. Most of the genes identified have previously been linked to regulation of the inflammatory response; importantly, however, some have not. In addition, hierarchical cluster analysis showed that cecal ligation and puncture at 24 hrs induced coordinate expression of genes that alter cell signaling and survival pathways in spleen, consistent with previously published reports of sepsis-induced splenocyte apoptosis. The current limitations of microarray analysis as reflected in these studies are also discussed. CONCLUSIONS: Microarray technology provides a powerful new tool for rapidly analyzing tissue-specific changes in gene expression induced by sepsis in animal models. To our knowledge, these data constitute the first report on the use of microarrays to determine the sepsis transcriptome.

Animals↗
PubMed1991

Computer-assisted compounding of neonatal/pediatric parenteral nutrition solutions.

A computer software package was developed to perform the calculations involved in compounding neonatal/pediatric parenteral nutrition (PN) solutions. A 16-bit micro-computer was used to develop and evaluate the software. The program requires a minimum of user input and is menu-driven. It performs the calculations, prints appropriate labels, a preparation card and a summary of the nutritional content of the solution. Error check routines and a check for calcium-phosphate compatibility are imbedded in the program. The effect of the package on PN compounding was evaluated using a computer model. The evaluation indicated the computer-assisted system was more efficient than a manual system and the possibility of computational error was reduced. The increase in efficiency with the computer-assisted system was between 12-15% compared to a manual system. Computer modeling appeared to be a useful tool in both evaluating the software package and determining the effect it would have on work flow.

Canada↗