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PubMed2004

Assignment validation software suite for the evaluation and presentation of protein resonance assignment data.

We present a set of utilities and graphical user interface (GUI) tools for evaluating the quality of protein resonance assignments. The Assignment Validation Software (AVS) suite, together with new GUI features in the AutoAssign software package, provides a set of reports and graphs for validating protein resonance assignment data before its use in structure analysis and/or submission to the BioMagResBank (BMRB). Input includes a listing of resonance assignments and a summary of sequential connectivity data (i.e. triple resonance, NOE, or other data) used in deriving the assignments. These tools are useful for evaluating the accuracy of protein resonance assignments determined by either automated or manual methods.

Amino Acid Sequence↗

PubMed2006

Software for generating psychological experiments.

This review compares four software packages for generating and running psychological computer experiments. It aims to inform researchers' decisions about which software to choose for their lab. Four widely used general purpose commercial packages available for the Windows platform are considered: DirectRT, E-Prime, Inquisit, and SuperLab. An overview of each package is given, and the implementation of two test experiments is described. Packages are evaluated with regard to the amount of complexity reduction they provide for the task of programming an experiment and the variety of experimental designs they can accommodate.

Humans↗

PubMed1998

Expertise in professional software design: a process study.

Forty professional software designers participated in a study in which they worked on a software design task and reported strategies for accomplishing that task. High performers were identified by a peer-nomination method and performance on a design. Verbal protocol analysis based on a comparison of 12 high and 12 moderate performers indicated that high performers structured their design process by local planning and showed more feedback processing, whereas moderate performers were more engaged in analyzing requirements and verbalizing task-irrelevant cognitions. High performers more often described problem comprehension and cooperation with colleagues as useful strategies. High and moderate performers did not differ with respect to length of experience. None of the differences between the two performance groups could be explained by length of experience.

Achievement↗

PubMed2005

PIXImus DXA with different software needs individual calibration to accurately predict fat mass.

OBJECTIVE: To validate GE PIXImus2 DXA fat mass (FM) estimates by chemical analysis, to compare previously published correction equations with an equation from our machine, and to determine intermachine variation. RESEARCH METHODS AND PROCEDURES: C57BL/6J (n = 16) and Aston (n = 14) mice (including ob/ob), Siberian hamsters (Phodopus sungorus) (n = 15), and bank voles (Clethrionomys glareolus) (n = 37) were DXA scanned postmortem, dried, then fat extracted using a Soxhlet apparatus. We compared extracted FM with DXA-predicted FM corrected using an equation designed using wild-type animals from split-sample validation and multiple regression and two previously published equations. Sixteen animals were scanned on both a GE PIXImus2 DXA in France and a second machine in the United Kingdom. RESULTS: DXA underestimated FM of obese C57BL/6J by 1.4 +/- 0.19 grams but overestimated FM for wild-type C57BL/6J (2.0 +/- 0.11 grams), bank voles (1.1 +/- 0.09 grams), and hamsters (1.1 +/- 0.13 grams). DXA-predicted FM corrected using our equation accurately predicted extracted FM (accuracy 0.02 grams), but the other equations did not (accuracy, -1.3 and -1.8 grams; paired Student's t test, p < 0.001). Two similar DXA instruments gave the same FM for obese mutant but not lean wild-type animals. DISCUSSION: DXA using the same software could use the same correction equation to accurately predict FM for obese mutant but not lean wild-type animals. PIXImus machines purchased with new software need validating to accurately predict FM.

Absorptiometry, Photon↗

PubMed2004

HistoCheck: rating of HLA class I and II mismatches by an internet-based software tool.

HLA polymorphism is a major barrier for hematopoietic stem cell and solid organ transplantation. To estimate the allogeneic potential between HLA-mismatched stem cell donor/recipient pairs, we recently proposed a matching score (dissimilarity index) that is based on the structural data of HLA class I molecules, and on the functional similarity of amino acids (AA). This first approach revealed new features about presumptive subtype allogenicities within the HLA-A*23 and A*24 groups. We have now developed an internet-based software tool ("HistoCheck") that is capable to assess the allogenicity (matching score) between any pair of clinically relevant HLA class I, and also class II, alleles. Newly described HLA sequences will be regularly integrated into the database according to the nomenclature for factors of the HLA system updates. The software is intended to be a first step for estimating the allogenicity of HLA mismatches in peculiar clinical settings, as long as there are no reliable in vitro or clinical studies available. The algorithm can later be modified according to functional data, for example, peptide-binding specificities. With the extension of the sequence similarity concept to all clinically relevant HLA class I and II loci, HistoCheck may contribute to prevent HLA mismatching being a matter of chance.

Algorithms↗

PubMed1991

Mass spectrometry software for biochemical analysis in electrospray and fast atom bombardment modes.

New mass spectrometry techniques, such as electrospray ionization (ESI), allow the study of large biomolecules and peptide mixtures. The data produced are complex and interpretation can be a long and tedious process. A new suite of data-processing software is described which allows many of these operations to be carried out in a rapid, automated way. Software is described for the deconvolution of the spectra of multiply charged ions, for both pure compounds and mixtures. The rapid peptide mapping of protein digests from h.p.l.c.-m.s. data and peptide sequence confirmation from multiple-stage (MS)-m.s. data using tandem quadrupole m.s. are also described. In addition preliminary results are presented on first principle sequencing of unknown peptides from MS-m.s. experiments.

Amino Acid Sequence↗

PubMed2003

Semi-automated software for the three-dimensional delineation of complex vascular networks.

The understanding of tumour angiogenesis is of great importance in cancer research, as is the tumour response to vascular-targeted drugs. This paper presents software aimed at aiding these investigations and other situations where linear or dendritic structures are to be delineated from three-dimensional (3D) data sets. This software application was written to analyse the data from 3D data sets by allowing the manual and semi-automated tracking and delineation of the vascular tree, including the measurement of vessel diameter. A new algorithm, CHARM, based on a compact Hough transform and the formation of a radial map, has been used to locate vessel centres and measure diameters automatically. The robustness of this algorithm to image smoothing and noise has been investigated.

Blood Vessels↗

PubMed1996

Can software be used to predict antigenic regions in Plasmodium falciparum peptides?

We compared the antigenicity of p126 Plasmodium falciparum peptides with predicted antigenic regions identified using the methods described by Garnier et al. (1978) and Chou & Fasman (1974). For this purpose nine different P. falciparum peptides were synthesized in accordance with the deduced amino acid sequence of the p126 gene, and their reactivity was tested using an enzyme linked immunosorbent assay against sera from individuals with a natural malaria infection. Both predictive methods gave similar antigenic-index scores, however, a comparison of these predictive results with data obtained by ELISA showed that the probability of a correct prediction was only around 45% for both cases. Thus, in our view computer software could not be used in isolation for screening purposes, and other parameters must also be taken into account when using such software to assess antigenicity.

Animals↗

PubMed2001

Comparative evaluation of three commercial software packages for analysis of DNA polymorphism patterns.

OBJECTIVE: In the present study we have compared three commercial software packages, GelCompar, Molecular Analyst Fingerprinting, and BioImage, to determine if the results generated by the programs were comparable and correlated adequately with visual interpretation of electrophoretic gels, in the analysis of several well characterized incidents of infections. METHODS: Infections caused by Pseudomonas aeruginosa, Candida dubliniensis, C. albicans, and serotypes of Salmonella were characterized by restriction endonuclease analysis, macrorestriction analysis of genomic DNA with pulsed-field gel electrophoresis, and random amplified polymorphic DNA. The genotypes were visually detected based on band presence or absence in the different gels. The similarity values of DNA profiles were computed using Dice coefficient and were presented in dendrograms by UPGMA. The concordance or agreement between the number of genotypes obtained and their clustering, using the computerized programs, was determined. RESULTS: In general, agreement in number of genotypes obtained visually and by using the commercial DNA analysis software was achieved, but discrepancies were also denoted between the systems. The concordance between the visual and the computerized analysis ranged from 72% to 100%. CONCLUSION: In our experience, although the programs evaluated in the present study performed acceptably well, such programs may be used as an aid in the analysis of complex banding patterns, and they do not provide an indisputably correct analysis in genotype definition.

Animals↗

PubMed2006

Software tools that facilitate kinetic modelling with large data sets: an example using growth modelling in sugarcane.

A solution to manage cumbersome data sets associated with large modelling projects is described. A kinetic model of sucrose accumulation in sugarcane is used to predict changes in sucrose metabolism with sugarcane internode maturity. This results in large amounts of output data to be analysed. Growth is simulated by reassigning maximal activity values, specific to each internode of the sugarcane plant, to parameter attributes of a model object. From a programming perspective, only one model definition file is required for the simulation software used; however, the amount of input data increases with each extra interrnode that is modelled, and likewise the amount of output data that is generated also increases. To store, manipulate and analyse these data, the modelling was performed from within a spreadsheet. This was made possible by the scripting language Python and the modelling software PySCeS through an embedded Python interpreter available in the Gnumeric spreadsheet program.

Algorithms↗

PubMed2001

[A software tool for automatic image-based ventilation analysis using dynamic chest CT-scanning in healthy and in ARDS lungs].

PURPOSE: Density measurements in dynamic CT image series of the lungs allow one to quantify ventilated, hyperinflated, and atelectatic pulmonary compartments with high temporal resolution. Fast automatic segmentation of lung parenchyma and a subsequent evaluation of it's respective density values are a prerequisite for any clinical application of this technique. MATERIAL AND METHODS: For automatic lung segmentation in thoracic CT scans, an algorithm was developed which uses (a) different density masks, and (b) anatomic knowledge to differentiate heart, diaphragm and chest wall from ventilated and atelectatic lung parenchyma. With Animal Care Committee approval, the automated technique was tested in 8 anaesthetized ventilated pigs undergoing dynamic CT before and after induction of lavage-ARDS. Images were acquired in one supradiaphragmatic, cross-sectional slice (temporal resolution of 100 ms; slice thickness of 1 mm, high resolution reconstruction algorithm). In 120 CT images the total pixel number and the calculated MLD from the automatically segmentated lung were compared to the values obtained from an interactive lung segmentation. RESULTS: The software tool was able to read all image series (DICOM standard). Automatic and interactive segmentation were in high agreement (R(2) = 0.99 for the total number of pixels and the MLD). Originally, the most frequent error was misclassification of atelectasis as extrapulmonary solid tissue. CONCLUSION: An automatic software tool is presented for lung segmentation in healthy lungs and in ARDS. Aerated lung and atelectasis were identified with high accuracy. This post-processing tool allows for a quantitative, CT based assessment of ventilation and recruitment processes in the lung. Thus, it may help to optimize ventilation patterns in patients with ARDS.

Animals↗

PubMed2004

[Manual endothelial cell enumeration for transplanted corneas in comparison to software controlled, automatic enumeration].

BACKGROUND: The evaluation of the endothelial cells is the most important criterion for assessing human donor corneas. The number, morphology and the vitality of the endothelial cells are decisive for the transparency of a cornea. The study has the following aim: to verify whether there is any difference between the manual and the automatic count of the cells by means of the NAVIS(R) system. MATERIAL AND METHODS: Both methods were performed on 57 corneas of 35 patients. A photo was taken for the manual count by a microscope at 40-fold enlargement and was printed for further analysis. A grid was applied to this photo and the number of the endothelial cells was projected by a multiplicator to one square millimeter. For the automatic evaluation a picture was made with 20-fold microscopic enlargement; the examiner chose an area to be analysed. There the count of the cells was controlled by software and directly projected to one square millimetre. This was followed by a manual correction. The measurement data were statistically evaluated. RESULTS: No statistically significant difference was found between the manual and automatic counts. CONCLUSION: The manual count of the endothelial cells can be replaced by software-controlled automatic analysis and count.

Algorithms↗

PubMed1995

[A new software for handling surgical data in strabology].

BACKGROUND: Numerous measurements and data are the hallmark of strabismology. Handling these data is greatly facilitated by the use of computers. An adequate software should also allow surgical results analysis and quality control. Standardisation of data is mandatory. METHODOLOGY: We developed such an application based on a commercially available database (4th Dimension, ACI Paris). It uses 5 relational files. RESULTS: This software is userfriendly and can be used by anyone. No special code is necessary to enter data and these values are automatically verified. Patient's data, diagnosis, type of surgery and angle measurements (pre- and post surgery) can be entered, usually by an orthoptist, right after examination. CONCLUSION: Numerisation of strabologic surgical data can be easily realised with the help of a programmable database, but rigorous terminology is mandatory. Indeed the use of a strict terminology is helpful in teaching hospitals.

Computer Graphics↗

PubMed2002

'Ten golden rules' for designing software in medical education: results from a formative evaluation of DIALOG.

Evaluation of educational material has become very important in a climate where there is increasing concern with assessing and maintaining quality. DIALOG (acronym for Distance Interactive Learning in Obstetrics and Gynaecology) is an electronic program on CD-ROM for continuing education. A formative evaluation of DIALOG was carried out to determine whether DIALOG was achieving its educational objectives. The results of the evaluation helped to suggest '10 golden rules' for designing software for the purpose of CPD for medical practitioners. These 'rules' should help in designing future software in medical education. They highlight the importance of content, presentation, design, use of hypermedia and multimedia and reduced cost in order to facilitate appropriate use of such programmes.

CD-ROM↗

PubMed1987

Stereotactic software for the GE 8800 CT scanner.

A computer software program (Seapit) was developed for precise determination of intracranial targets identified by stereotactic computed tomography (CT). This program was added to the software of a GE 8800 CT scanner to perform the following operations: millimetre precise calculation and display of the rectilinear coordinates of a target identified on axial CT images; preplotting of phantom target trajectories on the CT images or electronic radiographs; calculation of probe angles required to achieve various trajectories; display of a coordinate scale on each CT image to allow direct target determination without mathematical calculations; calculation of the intercommissural plane for functional neurosurgery. In a series of 100 patients undergoing stereotactic surgery, the Seapit program proved to be a superior and accurate method of target coordinate calculation. Preview display on the CT images of 'phantom' probes significantly enhanced the safety of stereotactic intervention.

Biopsy↗

PubMedDate not supplied

Hardware-software co-design of portable functional gastrointestinal stimulator system.

In the recent years, functional electrical stimulation has been applied to restore impaired motility in the gastrointestinal tract. Unlike other methods of electrical stimulation of the gut, microprocessor-controlled, sequential electrical stimulation has been shown to induce peristalsis and enhance emptying in acute canine gastric and colonic models. This study aims at completing the development of a portable microprocessor-based functional stimulator system consisting of a microelectronic stimulator, patient-specific computer-based real-time software and a programming interfacing device. The ultimate goals of the design are to ensure that (1) the portable stimulator can be efficiently utilized in chronic animal experiments; and (2) the device can be further miniaturized into an implantable version. The designed portable stimulator generates four channel sequential bipolar rectangular pulse trains with programmable parameters within the stimulation requirements obtained from a previously developed computer model. Real-time simulation of colonic peristalsis and a case-specific stimulation model were implemented using patient-specific computer-based software. A chronic canine case study confirmed the feasibility of this microprocessor-controlled stimulation method for future clinical applications in humans.

Algorithms↗

PubMed2006

Application of automated mass spectrometry deconvolution and identification software for pesticide analysis in surface waters.

A new approach to surface water analysis has been investigated in order to enhance the detection of different organic contaminants in Nathan Creek, British Columbia. Water samples from Nathan Creek were prepared by liquid/liquid extraction using dichloromethane (DCM) as an extraction solvent and analyzed by gas chromatography mass spectrometry method in scan mode (GC-MS scan). To increase sensitivity for pesticides detection, acquired scan data were further analyzed by Automated Mass Spectrometry Deconvolution and Identification Software (AMDIS) incorporated into the Agilent Deconvolution Reporting Software (DRS), which also includes mass spectral libraries for 567 pesticides. Extracts were reanalyzed by gas chromatography mass spectrometry single ion monitoring (GC-MS-SIM) to confirm and quantitate detected pesticides. Pesticides: atrazine, dimethoate, diazinone, metalaxyl, myclobutanil, napropamide, oxadiazon, propazine and simazine were detected at three sampling sites on the mainstream of the Nathan Creek. Results of the study are further discussed in terms of detectivity and identification level for each pesticide found. The proposed approach of monitoring pesticides in surface waters enables their detection and identification at trace levels.

Automation↗

PubMed1993

Brief communication: dietary habits of first-year medical students as determined by computer software analysis of three-day food records.

Nutrition training for medical students has long been a low priority for most medical schools. Given the growing body of knowledge linking health promotion to proper dietary habits, there is a need to increase the quantity and quality of nutrition training for medical students. In the present study, first-year medical students recorded food intake for 3 days and analyzed their diets for nutrient contents with a computer software program. Use of the interactive software created a personalized approach to increasing nutrition knowledge as the students became aware of their own dietary habits. Female students had a low consumption of kilocalories, dietary fiber, calcium, iron, zinc, potassium, and polyunsaturated fat. Male students exceeded current recommended intakes for fat, saturated fat, cholesterol, and sodium.

Diet Records↗